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sjplimp 2011-03-26 23:02:38 +00:00
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LAMMPS (27 Mar 2011)
# Big colloid particles and small LJ particles
units lj
atom_style atomic
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 processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
mass 1 9
mass 2 1
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 = 2.20285 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 0.032912604 2.0516927 0.4026689 6790.5438
21000 2.0347446 0.019902556 2.0523864 0.4007124 6532.5107
22000 2.0264802 0.027247056 2.0514756 0.41874743 6310.6473
23000 2.0284647 0.030679317 2.0568901 0.4253006 6110.0448
24000 1.9937762 0.06381727 2.0553781 0.49092603 5923.5093
25000 2.0353922 0.027248288 2.0603789 0.45091442 5737.0476
26000 2.0237478 0.037618141 2.0591174 0.53619978 5562.6505
27000 2.0242618 0.033821875 2.0558345 0.4959782 5460.2661
28000 2.0482322 0.01320251 2.0591589 0.44939498 5345.4687
29000 2.0287333 0.03621241 2.0626916 0.55562251 5180.2806
30000 2.0040988 0.059211727 2.0610838 0.61808251 5068.541
31000 2.0042212 0.061798172 2.0637924 0.64370526 4957.2604
32000 2.0245435 0.035546139 2.0578402 0.59067342 4872.1932
33000 1.9919557 0.078345663 2.0680881 0.68910022 4765.4334
34000 2.0262779 0.047027618 2.0710541 0.65966618 4657.8074
35000 1.9912139 0.080509163 2.0695106 0.69023472 4598.459
36000 2.0190325 0.053614947 2.0704041 0.67782728 4531.4932
37000 2.0131766 0.063296775 2.0742365 0.74369947 4450.7232
38000 2.0192742 0.059523787 2.0765544 0.72790998 4369.6931
39000 2.0259464 0.057405211 2.0811006 0.76212505 4290.5877
40000 2.0257778 0.050559606 2.0740865 0.75709818 4241.812
41000 2.0210186 0.056870746 2.0756437 0.76054223 4186.8833
42000 1.9726145 0.10828461 2.0787073 0.96623593 4130.8878
43000 2.0163335 0.068098169 2.0821913 0.7724108 4088.3897
44000 1.9702837 0.11909487 2.0871894 0.978469 4023.8067
45000 2.003942 0.090213491 2.0919289 0.92974367 3981.7386
46000 2.0200434 0.069364002 2.0871629 0.8297056 3926.0172
47000 2.041283 0.050439502 2.0894544 0.84552678 3880.6095
48000 2.0172704 0.082594045 2.097623 0.97243304 3823.5355
49000 2.0208893 0.082783178 2.101427 0.97976434 3742.0596
50000 1.9739277 0.11636826 2.0881027 1.0449823 3710.4102
Loop time of 14.2309 on 1 procs for 50000 steps with 900 atoms
Pair time (%) = 7.41369 (52.0957)
Neigh time (%) = 1.58633 (11.1471)
Comm time (%) = 0.34565 (2.42887)
Outpt time (%) = 0.344466 (2.42055)
Other time (%) = 4.54078 (31.9079)
Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 585 ave 585 max 585 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6048 ave 6048 max 6048 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6048
Ave neighs/atom = 6.72
Neighbor list builds = 3124
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# Big colloid particles and small LJ particles
units lj
atom_style atomic
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 processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
mass 1 9
mass 2 1
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 = 2.10785 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 2.0027128 0.050847835 2.0513354 0.39430768 7044.3881
20000 2.0325646 0.021042471 2.0513486 0.35372598 6769.9838
21000 2.0124313 0.042181593 2.0523768 0.4063794 6509.7544
22000 2.0156252 0.041583224 2.0549689 0.49055441 6281.6377
23000 2.0075157 0.050694007 2.0559791 0.45052595 6080.274
24000 2.0154057 0.036452118 2.0496185 0.48202632 5968.6572
25000 2.0327476 0.029856988 2.060346 0.45561293 5789.7049
26000 1.9897031 0.073921207 2.0614135 0.60112592 5586.2292
27000 2.0440727 0.021849226 2.0636507 0.4825674 5413.6275
28000 2.0045554 0.055337087 2.0576652 0.5591706 5298.2659
29000 2.027287 0.038894068 2.0639286 0.56087137 5177.1542
30000 2.0205914 0.043248372 2.0615947 0.53487433 5070.7318
31000 2.0184388 0.050748054 2.0669441 0.57538446 4976.0508
32000 2.0204751 0.051328968 2.0695591 0.64728677 4878.005
33000 2.0111467 0.060162066 2.0690742 0.62331567 4778.195
34000 2.0284013 0.037363433 2.0635109 0.59724203 4697.3593
35000 1.9845749 0.089467073 2.0718369 0.80254883 4596.7715
36000 2.0062209 0.06902456 2.0730164 0.7322564 4510.2606
37000 2.0232674 0.050125477 2.0711448 0.67066837 4442.9312
38000 2.0347246 0.038024633 2.0704884 0.64951947 4386.1564
39000 2.036067 0.047110384 2.0809151 0.69569962 4289.3392
40000 2.0172137 0.061776712 2.0767491 0.83452283 4219.7458
41000 2.0169547 0.064700391 2.079414 0.89024009 4172.0666
42000 1.9900577 0.089235744 2.0770823 0.85956089 4130.4701
43000 2.0171326 0.075093255 2.0899846 0.86806073 4054.2948
44000 2.0245424 0.062474807 2.0847677 0.87695757 3994.1455
45000 1.9781553 0.10428775 2.0802451 1.0152832 3960.5022
46000 2.0360719 0.056999986 2.0908095 0.78346649 3913.7871
47000 2.0117075 0.078216122 2.0876884 0.95590478 3872.147
48000 1.9995682 0.090946084 2.0882926 0.94568469 3834.7404
49000 1.9904732 0.10585353 2.0941151 0.97553505 3797.357
50000 2.0135224 0.080467977 2.0917532 0.94694354 3769.7374
Loop time of 6.07169 on 4 procs for 50000 steps with 900 atoms
Pair time (%) = 1.86265 (30.6775)
Neigh time (%) = 0.397185 (6.54159)
Comm time (%) = 1.58736 (26.1436)
Outpt time (%) = 0.248944 (4.10007)
Other time (%) = 1.97556 (32.5373)
Nlocal: 225 ave 237 max 201 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Nghost: 316.25 ave 350 max 291 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 1511.25 ave 1653 max 1354 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 6045
Ave neighs/atom = 6.71667
Neighbor list builds = 3136
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# 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 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 = 2.80471 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
1 10.099643 -3.5063151 -3.5076155 -3.5076155 0 27.512983 3023.4645 14.46 14.46 14.46 0
2 10.098572 -3.5063151 -3.5076153 -3.5076153 0 27.563765 3023.4645 14.46 14.46 14.46 0
3 10.096788 -3.5063151 -3.5076151 -3.5076151 0 27.64839 3023.4645 14.46 14.46 14.46 0
4 10.094291 -3.5063151 -3.5076148 -3.5076148 0 27.766843 3023.4645 14.46 14.46 14.46 0
5 10.09108 -3.5063151 -3.5076144 -3.5076144 0 27.919101 3023.4645 14.46 14.46 14.46 0
6 10.087158 -3.5063151 -3.5076139 -3.5076139 0 28.105138 3023.4645 14.46 14.46 14.46 0
7 10.082524 -3.5063151 -3.5076133 -3.5076133 0 28.324919 3023.4645 14.46 14.46 14.46 0
8 10.077179 -3.5063151 -3.5076126 -3.5076126 0 28.578403 3023.4645 14.46 14.46 14.46 0
9 10.071123 -3.5063151 -3.5076118 -3.5076118 0 28.865545 3023.4645 14.46 14.46 14.46 0
10 10.06436 -3.5063151 -3.5076109 -3.5076109 0 29.186292 3023.4645 14.46 14.46 14.46 0
Loop time of 0.802534 on 1 procs for 10 steps with 256 atoms
Pair time (%) = 0.80151 (99.8723)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000503063 (0.0626843)
Outpt time (%) = 0.000286579 (0.0357093)
Other time (%) = 0.000234842 (0.0292626)
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 (27 Mar 2011)
# 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 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 = 2.29838 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
1 10.099638 -3.5063151 -3.5076155 -3.5076155 0 27.513531 3023.4645 14.46 14.46 14.46 0
2 10.098553 -3.5063151 -3.5076153 -3.5076153 0 27.565957 3023.4645 14.46 14.46 14.46 0
3 10.096744 -3.5063151 -3.5076151 -3.5076151 0 27.653322 3023.4645 14.46 14.46 14.46 0
4 10.094212 -3.5063151 -3.5076148 -3.5076148 0 27.775611 3023.4645 14.46 14.46 14.46 0
5 10.090958 -3.5063151 -3.5076144 -3.5076144 0 27.932801 3023.4645 14.46 14.46 14.46 0
6 10.086981 -3.5063151 -3.5076139 -3.5076139 0 28.124863 3023.4645 14.46 14.46 14.46 0
7 10.082283 -3.5063151 -3.5076132 -3.5076132 0 28.351761 3023.4645 14.46 14.46 14.46 0
8 10.076864 -3.5063151 -3.5076125 -3.5076125 0 28.613454 3023.4645 14.46 14.46 14.46 0
9 10.070725 -3.5063151 -3.5076118 -3.5076118 0 28.909893 3023.4645 14.46 14.46 14.46 0
10 10.063868 -3.5063151 -3.5076109 -3.5076109 0 29.241022 3023.4645 14.46 14.46 14.46 0
Loop time of 0.202334 on 4 procs for 10 steps with 256 atoms
Pair time (%) = 0.197941 (97.8289)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0038377 (1.89672)
Outpt time (%) = 0.000359058 (0.177458)
Other time (%) = 0.000196099 (0.0969187)
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 (27 Mar 2011)
# 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 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 = 5.54555 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.72421193 -1.4484239 25.62 25.62 25.62 16816.568
1 0.99888668 -3.8382371 -3.8383662 -0.98185761 -2.8565085 0.72421093 -1.4484219 25.62 25.62 25.62 16816.568
2 0.99630957 -3.8382376 -3.8383663 -0.98186477 -2.8565015 0.7242097 -1.4484194 25.62 25.62 25.62 16816.568
Loop time of 2.50572 on 1 procs for 2 steps with 1296 atoms
Pair time (%) = 0.309569 (12.3545)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000235319 (0.00939126)
Outpt time (%) = 0.000140905 (0.00562334)
Other time (%) = 2.19578 (87.6305)
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
Memory usage per processor = 6.84256 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 0.99630957 -3.845015 -3.8451437 -0.97307269 -2.872071 0.7242097 -1.4484194 25.62 25.62 25.62 16816.568
3 0.99630957 -3.8450358 -3.8451645 -0.96977625 -2.8753882 0.7242097 -1.4484194 25.59438 25.594381 25.59438 16766.17
4 0.99630957 -3.8450358 -3.8451645 -0.96977625 -2.8753882 0.7242097 -1.4484194 25.59438 25.594381 25.59438 16766.17
Loop time of 2.3633 on 1 procs for 2 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.8451437267 -3.84516448476 -3.84516448476
Force two-norm initial, final = 14.0243 26.0587
Force max component initial, final = 8.07088 15.0312
Final line search alpha, max atom move = 1.62423e-08 2.44141e-07
Iterations, force evaluations = 2 14
Pair time (%) = 2.35645 (99.7102)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00155354 (0.0657359)
Outpt time (%) = 6.8903e-05 (0.00291554)
Other time (%) = 0.00522709 (0.221178)
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
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 5.7222 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
4 0.99630957 -3.8450358 -3.8451645 -0.96977625 -2.8753882 0.72227767 -1.4445553 25.59438 25.594381 25.59438 16766.17
5 0.99306642 -3.8417608 -3.8418891 -0.98316073 -2.8587283 0.7222782 -1.4445564 25.59438 25.594381 25.59438 16766.17
Loop time of 1.11878 on 1 procs for 1 steps with 1296 atoms
Pair time (%) = 0.159516 (14.258)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000136137 (0.0121683)
Outpt time (%) = 8.70228e-05 (0.00777836)
Other time (%) = 0.959042 (85.722)
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
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
run 10
Memory usage per processor = 5.98075 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
5 25.59438 25.594381 25.59438 0 0 0 -23857347 -23854274 -23856348 -44222.028 -67044.325 -59938.384
6 25.594636 25.594381 25.59438 0 0 0 -23857347 -23854274 -23856348 -44222.028 -67044.325 -59938.384
7 25.594892 25.594381 25.59438 0 0 0 -23528290 -23833303 -23835377 -44220.96 -67042.938 -59932.976
8 25.595148 25.594381 25.59438 0 0 0 -23199233 -23812337 -23814412 -44219.892 -67041.552 -59927.569
9 25.595404 25.594381 25.59438 0 0 0 -22870176 -23791377 -23793451 -44218.824 -67040.166 -59922.162
10 25.59566 25.594381 25.59438 0 0 0 -22541119 -23770422 -23772497 -44217.757 -67038.78 -59916.756
11 25.595916 25.594381 25.59438 0 0 0 -22212062 -23749473 -23751547 -44216.69 -67037.395 -59911.349
12 25.596172 25.594381 25.59438 0 0 0 -21883006 -23728529 -23730604 -44215.624 -67036.01 -59905.943
13 25.596428 25.594381 25.59438 0 0 0 -21553950 -23707591 -23709665 -44214.559 -67034.624 -59900.537
14 25.596684 25.594381 25.59438 0 0 0 -21224894 -23686658 -23688732 -44213.493 -67033.238 -59895.132
15 25.59694 25.594381 25.59438 0 0 0 -20895838 -23665731 -23667805 -44212.427 -67031.853 -59889.727
Loop time of 1.73011 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.72171 (99.5144)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0015142 (0.0875201)
Outpt time (%) = 0.00608492 (0.351706)
Other time (%) = 0.000802755 (0.046399)
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
## 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 = 6.49784 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
15 25.59694 25.594381 25.59438 0 0 0 -20566782 -23644809 -23646883 -44211.362 -67030.467 -59884.323
16 25.59694 25.594381 25.594636 0 0 0 -20566782 -23644809 -23646883 -44211.362 -67030.467 -59884.323
17 25.59694 25.594381 25.594892 0 0 0 -20545864 -23623833 -23317879 -44205.686 -67029.08 -59883.21
18 25.59694 25.594381 25.595148 0 0 0 -20524951 -23602862 -22988874 -44200.011 -67027.694 -59882.097
19 25.59694 25.594381 25.595404 0 0 0 -20504043 -23581897 -22659870 -44194.336 -67026.307 -59880.984
20 25.59694 25.594381 25.59566 0 0 0 -20483141 -23560937 -22330866 -44188.661 -67024.921 -59879.872
21 25.59694 25.594381 25.595916 0 0 0 -20462244 -23539983 -22001862 -44182.986 -67023.535 -59878.76
22 25.59694 25.594381 25.596172 0 0 0 -20441353 -23519034 -21672859 -44177.311 -67022.148 -59877.647
23 25.59694 25.594381 25.596428 0 0 0 -20420468 -23498091 -21343855 -44171.636 -67020.762 -59876.536
24 25.59694 25.594381 25.596683 0 0 0 -20399588 -23477153 -21014852 -44165.962 -67019.375 -59875.424
25 25.59694 25.594381 25.596939 0 0 0 -20378713 -23456221 -20685849 -44160.287 -67017.989 -59874.312
Loop time of 1.72041 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.71271 (99.5523)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00122261 (0.0710651)
Outpt time (%) = 0.00582957 (0.338848)
Other time (%) = 0.000650644 (0.0378192)
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
## 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 = 7.01493 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
25 25.59694 25.594381 25.596939 0 0 0 -20357844 -23435294 -20356846 -44154.613 -67016.603 -59873.2
26 25.59694 25.594381 25.596939 0 0 5.1193879e-07 -20357844 -23435294 -20356846 -44154.613 -67016.603 -59873.2
27 25.59694 25.594381 25.596939 0 0 1.0238776e-06 -20357844 -23435294 -20356846 -44154.607 -67016.597 -59608.802
28 25.59694 25.594381 25.596939 0 0 1.5358164e-06 -20357844 -23435294 -20356846 -44154.601 -67016.592 -59344.404
29 25.59694 25.594381 25.596939 0 0 2.0477552e-06 -20357844 -23435294 -20356846 -44154.595 -67016.586 -59080.005
30 25.59694 25.594381 25.596939 0 0 2.5596939e-06 -20357844 -23435294 -20356846 -44154.589 -67016.58 -58815.607
31 25.59694 25.594381 25.596939 0 0 3.0716327e-06 -20357844 -23435294 -20356845 -44154.583 -67016.575 -58551.209
32 25.59694 25.594381 25.596939 0 0 3.5835715e-06 -20357844 -23435294 -20356845 -44154.577 -67016.569 -58286.811
33 25.59694 25.594381 25.596939 0 0 4.0955103e-06 -20357844 -23435294 -20356845 -44154.571 -67016.563 -58022.413
34 25.59694 25.594381 25.596939 0 0 4.6074491e-06 -20357844 -23435294 -20356845 -44154.565 -67016.558 -57758.014
35 25.59694 25.594381 25.596939 0 0 5.1193879e-06 -20357844 -23435294 -20356845 -44154.559 -67016.552 -57493.616
Loop time of 1.71669 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.70907 (99.5561)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00118637 (0.0691079)
Outpt time (%) = 0.00573516 (0.334082)
Other time (%) = 0.000698328 (0.0406787)
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
## 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 = 7.53202 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
35 25.59694 25.594381 25.596939 0 0 5.1193879e-06 -20357844 -23435294 -20356845 -44154.553 -67016.546 -57229.218
36 25.59694 25.594381 25.596939 5.1188761e-07 0 5.1193879e-06 -20357844 -23435294 -20356845 -44154.553 -67016.546 -57229.218
37 25.59694 25.594381 25.596939 1.0237752e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -43890.216 -67016.542 -57229.211
38 25.59694 25.594381 25.596939 1.5356628e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -43625.88 -67016.537 -57229.203
39 25.59694 25.594381 25.596939 2.0475505e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -43361.543 -67016.533 -57229.196
40 25.59694 25.594381 25.596939 2.5594381e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -43097.206 -67016.528 -57229.189
41 25.59694 25.594381 25.596939 3.0713257e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -42832.87 -67016.523 -57229.181
42 25.59694 25.594381 25.596939 3.5832133e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -42568.533 -67016.519 -57229.174
43 25.59694 25.594381 25.596939 4.0951009e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -42304.196 -67016.514 -57229.167
44 25.59694 25.594381 25.596939 4.6069885e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -42039.86 -67016.51 -57229.159
45 25.59694 25.594381 25.596939 5.1188761e-06 0 5.1193879e-06 -20357844 -23435294 -20356845 -41775.523 -67016.505 -57229.152
Loop time of 1.7178 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 1.71014 (99.5539)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00127482 (0.0742126)
Outpt time (%) = 0.00568557 (0.33098)
Other time (%) = 0.000703096 (0.0409301)
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

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examples/comb/log.comb.Cu2O.elastic.28Mar11.linux.4 Normal file
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LAMMPS (27 Mar 2011)
# 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 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 = 2.98849 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.7250204 -1.4500408 25.62 25.62 25.62 16816.568
1 0.99832063 -3.8339963 -3.8341252 -0.98121146 -2.8529137 0.72501959 -1.4500392 25.62 25.62 25.62 16816.568
2 0.99477315 -3.8339968 -3.8341253 -0.98121736 -2.8529079 0.72501849 -1.450037 25.62 25.62 25.62 16816.568
Loop time of 0.649422 on 4 procs for 2 steps with 1296 atoms
Pair time (%) = 0.0756464 (11.6483)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00136131 (0.209619)
Outpt time (%) = 0.000139356 (0.0214584)
Other time (%) = 0.572275 (88.1207)
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
Memory usage per processor = 4.17364 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 0.99477315 -3.8448334 -3.8449619 -0.96671781 -2.8782441 0.72501849 -1.450037 25.62 25.62 25.62 16816.568
3 0.99477315 -3.8448541 -3.8449826 -0.96342109 -2.8815615 0.72501849 -1.450037 25.594519 25.594381 25.59438 16766.261
4 0.99477315 -3.8448541 -3.8449826 -0.96342109 -2.8815615 0.72501849 -1.450037 25.594519 25.594381 25.59438 16766.261
Loop time of 0.600445 on 4 procs for 2 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.8449619337 -3.84498261759 -3.84498261759
Force two-norm initial, final = 13.89 26.1585
Force max component initial, final = 7.99462 15.1024
Final line search alpha, max atom move = 1.61657e-08 2.44141e-07
Iterations, force evaluations = 2 14
Pair time (%) = 0.58064 (96.7016)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0166085 (2.76603)
Outpt time (%) = 5.75781e-05 (0.00958924)
Other time (%) = 0.00313872 (0.522733)
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: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 3.14651 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
4 0.99477315 -3.8448541 -3.8449826 -0.96342109 -2.8815615 0.7219669 -1.4439338 25.594519 25.594381 25.59438 16766.261
5 0.99149942 -3.839274 -3.839402 -0.9840769 -2.8553251 0.72196775 -1.4439355 25.594519 25.594381 25.59438 16766.261
Loop time of 0.308691 on 4 procs for 1 steps with 1296 atoms
Pair time (%) = 0.038758 (12.5556)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00141472 (0.458295)
Outpt time (%) = 7.1466e-05 (0.0231513)
Other time (%) = 0.268447 (86.963)
Nlocal: 324 ave 333 max 320 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 4943 ave 4947 max 4934 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 208350 max 200056 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
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
run 10
Memory usage per processor = 3.38354 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
5 25.594519 25.594381 25.59438 0 0 0 -23724673 -23883860 -23885828 -18837.532 -68466.96 -61872.751
6 25.594775 25.594381 25.59438 0 0 0 -23724673 -23883860 -23885828 -18837.532 -68466.96 -61872.751
7 25.595031 25.594381 25.59438 0 0 0 -23395545 -23862932 -23864900 -18836.656 -68465.521 -61867.388
8 25.595287 25.594381 25.59438 0 0 0 -23066417 -23842010 -23843978 -18835.782 -68464.082 -61862.025
9 25.595543 25.594381 25.59438 0 0 0 -22737289 -23821093 -23823061 -18834.907 -68462.645 -61856.662
10 25.595799 25.594381 25.59438 0 0 0 -22408162 -23800182 -23802150 -18834.033 -68461.207 -61851.299
11 25.596055 25.594381 25.59438 0 0 0 -22079034 -23779276 -23781244 -18833.16 -68459.769 -61845.937
12 25.596311 25.594381 25.59438 0 0 0 -21749907 -23758375 -23760343 -18832.287 -68458.331 -61840.575
13 25.596567 25.594381 25.59438 0 0 0 -21420780 -23737480 -23739449 -18831.414 -68456.893 -61835.213
14 25.596822 25.594381 25.59438 0 0 0 -21091653 -23716591 -23718559 -18830.541 -68455.455 -61829.852
15 25.597078 25.594381 25.59438 0 0 0 -20762526 -23695707 -23697675 -18829.669 -68454.017 -61824.492
Loop time of 0.438967 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.415694 (94.6982)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0144061 (3.28183)
Outpt time (%) = 0.00844461 (1.92375)
Other time (%) = 0.000422597 (0.0962708)
Nlocal: 324 ave 333 max 319 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 4943 ave 4948 max 4934 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 208350 max 199418 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
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 = 3.8576 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
15 25.597078 25.594381 25.59438 0 0 0 -20433400 -23674828 -23676797 -18828.796 -68452.579 -61819.131
16 25.597078 25.594381 25.594636 0 0 0 -20433400 -23674828 -23676797 -18828.796 -68452.579 -61819.131
17 25.597078 25.594381 25.594892 0 0 0 -20412525 -23653892 -23347726 -18823.344 -68451.141 -61818.018
18 25.597078 25.594381 25.595148 0 0 0 -20391655 -23632962 -23018656 -18817.892 -68449.702 -61816.905
19 25.597078 25.594381 25.595404 0 0 0 -20370791 -23612037 -22689585 -18812.441 -68448.264 -61815.793
20 25.597078 25.594381 25.59566 0 0 0 -20349932 -23591118 -22360515 -18806.99 -68446.826 -61814.68
21 25.597078 25.594381 25.595916 0 0 0 -20329079 -23570204 -22031445 -18801.538 -68445.388 -61813.567
22 25.597078 25.594381 25.596172 0 0 0 -20308231 -23549295 -21702375 -18796.087 -68443.95 -61812.455
23 25.597078 25.594381 25.596428 0 0 0 -20287389 -23528392 -21373306 -18790.636 -68442.512 -61811.343
24 25.597078 25.594381 25.596683 0 0 0 -20266552 -23507494 -21044236 -18785.185 -68441.074 -61810.231
25 25.597078 25.594381 25.596939 0 0 0 -20245721 -23486602 -20715167 -18779.734 -68439.636 -61809.119
Loop time of 0.438571 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.415724 (94.7906)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0140231 (3.19746)
Outpt time (%) = 0.00841451 (1.91862)
Other time (%) = 0.000409245 (0.0933134)
Nlocal: 324 ave 333 max 319 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 4943 ave 4948 max 4934 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 208350 max 199418 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
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 = 4.33166 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
25 25.597078 25.594381 25.596939 0 0 0 -20224895 -23465716 -20386098 -18774.283 -68438.199 -61808.007
26 25.597078 25.594381 25.596939 0 0 5.1193879e-07 -20224895 -23465716 -20386098 -18774.283 -68438.199 -61808.007
27 25.597078 25.594381 25.596939 0 0 1.0238776e-06 -20224895 -23465716 -20386098 -18774.277 -68438.194 -61543.649
28 25.597078 25.594381 25.596939 0 0 1.5358164e-06 -20224895 -23465716 -20386098 -18774.271 -68438.189 -61279.291
29 25.597078 25.594381 25.596939 0 0 2.0477552e-06 -20224895 -23465716 -20386098 -18774.264 -68438.185 -61014.933
30 25.597078 25.594381 25.596939 0 0 2.5596939e-06 -20224895 -23465716 -20386098 -18774.258 -68438.18 -60750.575
31 25.597078 25.594381 25.596939 0 0 3.0716327e-06 -20224895 -23465716 -20386098 -18774.252 -68438.175 -60486.217
32 25.597078 25.594381 25.596939 0 0 3.5835715e-06 -20224895 -23465716 -20386098 -18774.245 -68438.171 -60221.859
33 25.597078 25.594381 25.596939 0 0 4.0955103e-06 -20224895 -23465716 -20386098 -18774.239 -68438.166 -59957.501
34 25.597078 25.594381 25.596939 0 0 4.6074491e-06 -20224895 -23465716 -20386098 -18774.233 -68438.161 -59693.142
35 25.597078 25.594381 25.596939 0 0 5.1193879e-06 -20224895 -23465716 -20386098 -18774.227 -68438.157 -59428.784
Loop time of 0.438326 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.415411 (94.772)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0141624 (3.23101)
Outpt time (%) = 0.00836039 (1.90734)
Other time (%) = 0.000393033 (0.0896667)
Nlocal: 324 ave 333 max 319 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 4943 ave 4948 max 4934 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 208350 max 199418 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
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 = 4.80572 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
35 25.597078 25.594381 25.596939 0 0 5.1193879e-06 -20224895 -23465716 -20386098 -18774.22 -68438.152 -59164.426
36 25.597078 25.594381 25.596939 5.1188762e-07 0 5.1193879e-06 -20224895 -23465716 -20386098 -18774.22 -68438.152 -59164.426
37 25.597078 25.594381 25.596939 1.0237752e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -18509.926 -68438.147 -59164.419
38 25.597078 25.594381 25.596939 1.5356628e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -18245.633 -68438.143 -59164.411
39 25.597078 25.594381 25.596939 2.0475505e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -17981.339 -68438.138 -59164.403
40 25.597078 25.594381 25.596939 2.5594381e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -17717.045 -68438.134 -59164.396
41 25.597078 25.594381 25.596939 3.0713257e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -17452.751 -68438.129 -59164.388
42 25.597078 25.594381 25.596939 3.5832133e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -17188.458 -68438.124 -59164.38
43 25.597078 25.594381 25.596939 4.0951009e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -16924.164 -68438.12 -59164.373
44 25.597078 25.594381 25.596939 4.6069885e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -16659.87 -68438.115 -59164.365
45 25.597078 25.594381 25.596939 5.1188762e-06 0 5.1193879e-06 -20224895 -23465716 -20386098 -16395.577 -68438.111 -59164.357
Loop time of 0.438004 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.415312 (94.8193)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0140703 (3.21238)
Outpt time (%) = 0.00822508 (1.87786)
Other time (%) = 0.000396073 (0.0904268)
Nlocal: 324 ave 333 max 319 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 4943 ave 4948 max 4934 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 208350 max 199418 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# 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 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 = 3.18525 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
1 10.097843 -4.6284152 -4.6297179 -4.6297179 0 1140.8131 10246.592 21.72 21.72 21.72 0
2 10.091376 -4.6284152 -4.6297171 -4.6297171 0 1140.8972 10246.592 21.72 21.72 21.72 0
3 10.080606 -4.6284152 -4.6297157 -4.6297157 0 1141.0373 10246.592 21.72 21.72 21.72 0
4 10.065546 -4.6284152 -4.6297137 -4.6297137 0 1141.233 10246.592 21.72 21.72 21.72 0
5 10.046214 -4.6284152 -4.6297113 -4.6297113 0 1141.4842 10246.592 21.72 21.72 21.72 0
6 10.022634 -4.6284152 -4.6297082 -4.6297082 0 1141.7906 10246.592 21.72 21.72 21.72 0
7 9.9948348 -4.6284152 -4.6297046 -4.6297046 0 1142.1515 10246.592 21.72 21.72 21.72 0
8 9.9628496 -4.6284152 -4.6297005 -4.6297005 0 1142.5666 10246.592 21.72 21.72 21.72 0
9 9.9267173 -4.6284152 -4.6296958 -4.6296958 0 1143.0353 10246.592 21.72 21.72 21.72 0
10 9.8864817 -4.6284152 -4.6296906 -4.6296906 0 1143.5568 10246.592 21.72 21.72 21.72 0
Loop time of 0.449238 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.447972 (99.7182)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000600338 (0.133635)
Outpt time (%) = 0.000299215 (0.0666051)
Other time (%) = 0.000366449 (0.0815713)
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 (27 Mar 2011)
# 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 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 = 2.33625 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
1 10.097841 -4.6284152 -4.6297179 -4.6297179 0 1140.8134 10246.592 21.72 21.72 21.72 0
2 10.091367 -4.6284152 -4.6297171 -4.6297171 0 1140.8983 10246.592 21.72 21.72 21.72 0
3 10.080586 -4.6284152 -4.6297157 -4.6297157 0 1141.0397 10246.592 21.72 21.72 21.72 0
4 10.065511 -4.6284152 -4.6297137 -4.6297137 0 1141.2373 10246.592 21.72 21.72 21.72 0
5 10.046161 -4.6284152 -4.6297112 -4.6297112 0 1141.4909 10246.592 21.72 21.72 21.72 0
6 10.02256 -4.6284152 -4.6297082 -4.6297082 0 1141.8001 10246.592 21.72 21.72 21.72 0
7 9.9947353 -4.6284152 -4.6297046 -4.6297046 0 1142.1645 10246.592 21.72 21.72 21.72 0
8 9.9627224 -4.6284152 -4.6297005 -4.6297005 0 1142.5835 10246.592 21.72 21.72 21.72 0
9 9.9265602 -4.6284152 -4.6296958 -4.6296958 0 1143.0565 10246.592 21.72 21.72 21.72 0
10 9.8862927 -4.6284152 -4.6296906 -4.6296906 0 1143.5829 10246.592 21.72 21.72 21.72 0
Loop time of 0.118667 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.112987 (95.2134)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00507617 (4.27764)
Outpt time (%) = 0.000378549 (0.319)
Other time (%) = 0.000225365 (0.189913)
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 (27 Mar 2011)
# 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 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
Memory usage per processor = 3.87189 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295963 -4.6297253 -4.6297253 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.768104 on 1 procs for 3 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550036 -4.62972550036
Force two-norm initial, final = 5.86582 0.235602
Force max component initial, final = 3.38663 0.136025
Final line search alpha, max atom move = 0.000114869 1.5625e-05
Iterations, force evaluations = 3 16
Pair time (%) = 0.763957 (99.46)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0010047 (0.130802)
Outpt time (%) = 7.00951e-05 (0.00912572)
Other time (%) = 0.00307274 (0.400042)
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
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move
Memory usage per processor = 2.88007 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.0448351 on 1 procs for 1 steps with 512 atoms
Pair time (%) = 0.0447428 (99.7942)
Neigh time (%) = 0 (0)
Comm time (%) = 5.81741e-05 (0.129751)
Outpt time (%) = 1.5974e-05 (0.0356284)
Other time (%) = 1.81198e-05 (0.0404144)
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
### 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
run 10
Memory usage per processor = 3.33784 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 21.728073 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 1.9450404e-06 2.4752556e-06 -1.6071587e-06
5 21.728291 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 1.8110987e-06 2.6015226e-06 -1.1358357e-06
6 21.728508 21.728073 21.728073 0 0 0 364177.1 295296.39 295296.39 -4.4966424e-06 1.848553e-07 -2.2958737e-06
7 21.728725 21.728073 21.728073 0 0 0 510377.09 372612.85 372612.85 2.4287963e-06 2.6615821e-06 -1.9832618e-06
8 21.728942 21.728073 21.728073 0 0 0 656576.36 449925.76 449925.76 2.4447348e-06 2.4469323e-06 -8.4990897e-07
9 21.72916 21.728073 21.728073 0 0 0 802774.92 527235.13 527235.13 4.0363922e-06 -5.9982754e-06 -2.3201799e-06
10 21.729377 21.728073 21.728073 0 0 0 948972.76 604540.97 604540.97 2.8253812e-06 2.5964234e-06 -8.931554e-07
11 21.729594 21.728073 21.728073 0 0 0 1095169.9 681843.26 681843.26 2.3933505e-06 2.283704e-06 -3.9266049e-07
12 21.729811 21.728073 21.728073 0 0 0 1241366.3 759142.02 759142.02 2.2037259e-06 2.6987214e-06 3.737462e-07
13 21.730029 21.728073 21.728073 0 0 0 1387562 836437.23 836437.23 2.6802555e-06 2.9969439e-06 1.7521287e-07
14 21.730246 21.728073 21.728073 0 0 0 1533757 913728.91 913728.91 4.4634386e-06 -4.2738918e-06 3.2367003e-07
Loop time of 0.48314 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.479521 (99.2508)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000623703 (0.129094)
Outpt time (%) = 0.0027349 (0.566067)
Other time (%) = 0.000261068 (0.0540357)
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
## 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 = 3.7956 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 21.730246 21.728073 21.728073 0 0 0 1679951.2 991017.05 991017.05 1.3848713e-06 1.8198295e-06 -3.1488289e-06
15 21.730246 21.728073 21.728291 0 0 0 1679951.2 991017.05 991017.05 1.4477769e-06 2.1276907e-06 -2.7563351e-06
16 21.730246 21.728073 21.728508 0 0 0 1757243.6 1068312.4 1137190.1 2.1162843e-06 -3.0681281e-06 -1.8698946e-06
17 21.730246 21.728073 21.728725 0 0 0 1834532.4 1145604.2 1283362.4 1.5226892e-06 3.1081802e-06 -2.6821714e-06
18 21.730246 21.728073 21.728942 0 0 0 1911817.6 1222892.5 1429534 -7.5700513e-07 1.7188656e-06 4.1051196e-06
19 21.730246 21.728073 21.72916 0 0 0 1989099.3 1300177.3 1575704.9 -1.4391091e-06 2.0797417e-06 3.9123487e-06
20 21.730246 21.728073 21.729377 0 0 0 2066377.5 1377458.5 1721875.1 -1.5213551e-06 1.9181068e-06 -2.1773741e-06
21 21.730246 21.728073 21.729594 0 0 0 2143652.1 1454736.2 1868044.5 -1.4238005e-06 1.7984361e-06 -2.0333083e-06
22 21.730246 21.728073 21.729811 0 0 0 2220923.2 1532010.3 2014213.3 4.4088785e-06 2.5805071e-06 -2.1480169e-06
23 21.730246 21.728073 21.730029 0 0 0 2298190.7 1609280.9 2160381.3 -9.3407459e-07 2.1740278e-06 -1.3082692e-06
24 21.730246 21.728073 21.730246 0 0 0 2375454.8 1686547.9 2306548.6 -1.7972725e-06 2.108669e-06 -1.6910019e-06
Loop time of 0.48289 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.479337 (99.2643)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000632048 (0.130889)
Outpt time (%) = 0.0026505 (0.548883)
Other time (%) = 0.00026989 (0.0558906)
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
## 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 = 4.25336 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 21.730246 21.728073 21.730246 0 0 0 2452715.2 1763811.4 2452715.2 -1.7548117e-06 3.6087566e-06 -3.6198628e-06
25 21.730246 21.728073 21.730246 0 0 4.3460492e-07 2452715.2 1763811.4 2452715.2 -1.7167978e-06 3.4304272e-06 -2.9804569e-06
26 21.730246 21.728073 21.730246 0 0 8.6920984e-07 2452715.2 1763811.4 2452715.2 -1.8729445e-06 4.5840765e-06 243.65136
27 21.730246 21.728073 21.730246 0 0 1.3038148e-06 2452715.2 1763811.4 2452715.2 -1.2316967e-06 2.6286266e-06 487.30276
28 21.730246 21.728073 21.730246 0 0 1.7384197e-06 2452715.2 1763811.4 2452715.2 -1.3251453e-06 2.7225014e-06 730.95419
29 21.730246 21.728073 21.730246 0 0 2.1730246e-06 2452715.2 1763811.4 2452715.2 -8.5464495e-07 -6.3592996e-07 974.60551
30 21.730246 21.728073 21.730246 0 0 2.6076295e-06 2452715.2 1763811.4 2452715.2 -1.7272259e-06 2.0497545e-06 1218.2569
31 21.730246 21.728073 21.730246 0 0 3.0422344e-06 2452715.2 1763811.4 2452715.2 -4.6626464e-07 2.1955509e-06 1461.9083
32 21.730246 21.728073 21.730246 0 0 3.4768394e-06 2452715.2 1763811.4 2452715.2 -1.1296433e-06 2.2397275e-06 1705.5598
33 21.730246 21.728073 21.730246 0 0 3.9114443e-06 2452715.2 1763811.4 2452715.2 -1.388603e-06 1.2425658e-06 1949.2111
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -1.1793341e-06 1.7092936e-06 2192.8625
Loop time of 0.483123 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.479436 (99.2368)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000645638 (0.133638)
Outpt time (%) = 0.00276113 (0.571516)
Other time (%) = 0.00028038 (0.058035)
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
## 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 = 4.71113 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -1.7294679e-06 4.8293026e-06 2436.5139
35 21.730246 21.728073 21.730246 4.3456146e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -1.4630595e-06 4.5052213e-06 2436.5139
36 21.730246 21.728073 21.730246 8.6912293e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 243.63758 -0.00012576585 2436.5139
37 21.730246 21.728073 21.730246 1.3036844e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 487.27522 -0.00025542614 2436.5139
38 21.730246 21.728073 21.730246 1.7382459e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 730.91286 -0.00038565598 2436.5139
39 21.730246 21.728073 21.730246 2.1728073e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 974.55045 -0.00051669611 2436.5138
40 21.730246 21.728073 21.730246 2.6073688e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1218.188 -0.00064706412 2436.5139
41 21.730246 21.728073 21.730246 3.0419303e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1461.8257 -0.0007779958 2436.5139
42 21.730246 21.728073 21.730246 3.4764917e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1705.4633 -0.00090716273 2436.5138
43 21.730246 21.728073 21.730246 3.9110532e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1949.1009 -0.001038008 2436.5138
44 21.730246 21.728073 21.730246 4.3456146e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2192.7385 -0.0011663311 2436.5138
Loop time of 0.484576 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.480966 (99.255)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000598431 (0.123496)
Outpt time (%) = 0.00274968 (0.567441)
Other time (%) = 0.000261784 (0.0540232)
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

273
examples/comb/log.comb.Si.elastic.28Mar11.linux.4 Normal file
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LAMMPS (27 Mar 2011)
# 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 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
Memory usage per processor = 3.02671 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295963 -4.6297253 -4.6297253 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.250542 on 4 procs for 3 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550036 -4.62972550036
Force two-norm initial, final = 5.86582 0.235602
Force max component initial, final = 3.38663 0.136025
Final line search alpha, max atom move = 0.000114869 1.5625e-05
Iterations, force evaluations = 3 16
Pair time (%) = 0.191762 (76.5388)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0565124 (22.556)
Outpt time (%) = 5.87702e-05 (0.0234572)
Other time (%) = 0.00220919 (0.881761)
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: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move
Memory usage per processor = 2.03489 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.0146563 on 4 procs for 1 steps with 512 atoms
Pair time (%) = 0.01146 (78.1916)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00314051 (21.4277)
Outpt time (%) = 3.39746e-05 (0.231809)
Other time (%) = 2.18153e-05 (0.148846)
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: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
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
run 10
Memory usage per processor = 2.49265 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 21.728073 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 -5.331517e-06 3.0239293e-06 -4.7684649e-06
5 21.728291 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 -4.2797025e-06 2.0730342e-06 -3.2414474e-06
6 21.728508 21.728073 21.728073 0 0 0 364177.1 295296.39 295296.39 6.7462199e-07 1.6210516e-06 -2.8184106e-06
7 21.728725 21.728073 21.728073 0 0 0 510377.09 372612.85 372612.85 -3.9337607e-06 2.4599063e-06 -4.2531358e-06
8 21.728942 21.728073 21.728073 0 0 0 656576.36 449925.76 449925.76 -3.6805931e-06 3.0030584e-06 -2.6648247e-06
9 21.72916 21.728073 21.728073 0 0 0 802774.92 527235.13 527235.13 1.0867248e-05 -8.1694237e-06 -1.7161938e-06
10 21.729377 21.728073 21.728073 0 0 0 948972.76 604540.97 604540.97 -3.2850644e-06 1.3204575e-06 -1.5057612e-06
11 21.729594 21.728073 21.728073 0 0 0 1095169.9 681843.26 681843.26 -3.6006336e-06 2.4158409e-06 -2.7959314e-06
12 21.729811 21.728073 21.728073 0 0 0 1241366.3 759142.02 759142.02 -3.3313125e-06 1.4697892e-06 -2.7046099e-06
13 21.730029 21.728073 21.728073 0 0 0 1387562 836437.23 836437.23 -4.1963855e-06 1.8017491e-06 -2.3957259e-06
14 21.730246 21.728073 21.728073 0 0 0 1533757 913728.91 913728.91 8.2405636e-06 -9.2080568e-06 -2.6979061e-06
Loop time of 0.162016 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.123017 (75.9293)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0340899 (21.0411)
Outpt time (%) = 0.00473952 (2.92535)
Other time (%) = 0.000169039 (0.104335)
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: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
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 = 2.95041 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 21.730246 21.728073 21.728073 0 0 0 1679951.2 991017.05 991017.05 -4.8604756e-06 3.7251477e-06 -2.9550019e-06
15 21.730246 21.728073 21.728291 0 0 0 1679951.2 991017.05 991017.05 -3.8939866e-06 2.9223391e-06 -2.2819697e-06
16 21.730246 21.728073 21.728508 0 0 0 1757243.6 1068312.4 1137190.1 -3.6671782e-06 -3.9050298e-06 -2.216407e-06
17 21.730246 21.728073 21.728725 0 0 0 1834532.4 1145604.2 1283362.4 -3.9258267e-06 2.221206e-06 -2.1819285e-06
18 21.730246 21.728073 21.728942 0 0 0 1911817.6 1222892.5 1429534 -3.1570557e-06 8.2160424e-07 4.7018758e-06
19 21.730246 21.728073 21.72916 0 0 0 1989099.3 1300177.3 1575704.9 -3.572314e-06 1.2809206e-06 4.3456208e-06
20 21.730246 21.728073 21.729377 0 0 0 2066377.5 1377458.5 1721875.1 -2.6839761e-06 1.8703615e-06 -2.1448559e-06
21 21.730246 21.728073 21.729594 0 0 0 2143652.1 1454736.2 1868044.5 -2.7199703e-06 1.6784208e-06 -2.426873e-06
22 21.730246 21.728073 21.729811 0 0 0 2220923.2 1532010.3 2014213.3 -2.5654468e-06 2.0648963e-06 -1.6998995e-06
23 21.730246 21.728073 21.730029 0 0 0 2298190.7 1609280.9 2160381.3 -3.3044419e-06 2.6103683e-06 -2.5246759e-06
24 21.730246 21.728073 21.730246 0 0 0 2375454.8 1686547.9 2306548.6 -3.5025824e-06 1.2024729e-06 -1.5524318e-06
Loop time of 0.161845 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.122915 (75.946)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0340765 (21.055)
Outpt time (%) = 0.00468802 (2.89661)
Other time (%) = 0.000165582 (0.102309)
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: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
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 = 3.40818 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 21.730246 21.728073 21.730246 0 0 0 2452715.2 1763811.4 2452715.2 -2.4048644e-06 3.3513607e-06 -2.8722185e-06
25 21.730246 21.728073 21.730246 0 0 4.3460492e-07 2452715.2 1763811.4 2452715.2 -2.481322e-06 3.6480379e-06 -3.1092437e-06
26 21.730246 21.728073 21.730246 0 0 8.6920984e-07 2452715.2 1763811.4 2452715.2 -3.0751506e-06 5.8376744e-06 243.65136
27 21.730246 21.728073 21.730246 0 0 1.3038148e-06 2452715.2 1763811.4 2452715.2 -2.7247323e-06 2.3340173e-06 487.30277
28 21.730246 21.728073 21.730246 0 0 1.7384197e-06 2452715.2 1763811.4 2452715.2 -2.8719517e-06 4.5249397e-06 730.95419
29 21.730246 21.728073 21.730246 0 0 2.1730246e-06 2452715.2 1763811.4 2452715.2 -2.6310243e-06 -6.3464035e-07 974.60551
30 21.730246 21.728073 21.730246 0 0 2.6076295e-06 2452715.2 1763811.4 2452715.2 -2.5635976e-06 3.5771871e-06 1218.2569
31 21.730246 21.728073 21.730246 0 0 3.0422344e-06 2452715.2 1763811.4 2452715.2 -3.2260573e-06 2.5233788e-06 1461.9083
32 21.730246 21.728073 21.730246 0 0 3.4768394e-06 2452715.2 1763811.4 2452715.2 -3.0611909e-06 3.1329051e-06 1705.5598
33 21.730246 21.728073 21.730246 0 0 3.9114443e-06 2452715.2 1763811.4 2452715.2 -2.6095826e-06 1.3805022e-06 1949.2111
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -2.8236839e-06 1.8352159e-06 2192.8625
Loop time of 0.161851 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.122992 (75.9912)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0339996 (21.0068)
Outpt time (%) = 0.00469309 (2.89964)
Other time (%) = 0.000165641 (0.102342)
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: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
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 = 3.86594 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -2.4937771e-06 4.8352356e-06 2436.5139
35 21.730246 21.728073 21.730246 4.3456146e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 -2.6268441e-06 5.4186954e-06 2436.5139
36 21.730246 21.728073 21.730246 8.6912293e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 243.63758 -0.00012459169 2436.5139
37 21.730246 21.728073 21.730246 1.3036844e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 487.27522 -0.00025416174 2436.5139
38 21.730246 21.728073 21.730246 1.7382459e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 730.91286 -0.00038484627 2436.5139
39 21.730246 21.728073 21.730246 2.1728073e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 974.55045 -0.00051633193 2436.5138
40 21.730246 21.728073 21.730246 2.6073688e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1218.188 -0.00064696028 2436.5138
41 21.730246 21.728073 21.730246 3.0419303e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1461.8257 -0.00077648633 2436.5139
42 21.730246 21.728073 21.730246 3.4764917e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1705.4633 -0.00090632398 2436.5138
43 21.730246 21.728073 21.730246 3.9110532e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1949.1009 -0.0010366567 2436.5138
44 21.730246 21.728073 21.730246 4.3456146e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2192.7385 -0.0011656542 2436.5138
Loop time of 0.150393 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.123172 (81.9005)
Neigh time (%) = 0 (0)
Comm time (%) = 0.022368 (14.8731)
Outpt time (%) = 0.0046854 (3.11545)
Other time (%) = 0.000166953 (0.111011)
Nlocal: 128 ave 152 max 112 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 3073 ave 3089 max 3049 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 63232 max 46592 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# 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 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
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 12.7818 on 1 procs for 5000 steps with 8141 atoms
Pair time (%) = 10.9406 (85.5951)
Neigh time (%) = 0.403301 (3.15527)
Comm time (%) = 0.00951362 (0.0744309)
Outpt time (%) = 0.125842 (0.984542)
Other time (%) = 1.30255 (10.1906)
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 (27 Mar 2011)
# 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 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
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 3.4854 on 4 procs for 5000 steps with 8141 atoms
Pair time (%) = 2.6865 (77.0788)
Neigh time (%) = 0.106176 (3.04632)
Comm time (%) = 0.220427 (6.3243)
Outpt time (%) = 0.102362 (2.93688)
Other time (%) = 0.36993 (10.6137)
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 (27 Mar 2011)
# Point dipoles in a 2d box
units lj
atom_style 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 processor grid
create_atoms 1 box
Created 200 atoms
mass 1 1.0
shape 1 1 1 1
dipole 1 0.75
set group all dipole/random 98934
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 = 3.0531 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 -2.8019061 0.19532181 -2.3829095 0.18067142
2000 0.39019935 -2.791487 0.22407032 -2.4032386 -0.40913692
2500 0.40240606 -2.8139309 0.24275491 -2.4135369 -0.33839305
3000 0.41889117 -2.8310674 0.24638389 -2.4142707 -0.071480473
3500 0.41664896 -2.7505011 0.17937876 -2.3359354 -0.34413079
4000 0.4399873 -2.8093287 0.22438034 -2.3715414 -0.16626012
4500 0.43361189 -2.8162656 0.24187231 -2.3848217 0.13489299
5000 0.39259055 -2.7471068 0.21065822 -2.3564792 -0.15485345
5500 0.42121291 -2.7676815 0.21145234 -2.3485747 -0.085961294
6000 0.46934915 -2.8576035 0.26500223 -2.3906011 -0.21441119
6500 0.41344307 -2.7863091 0.2478621 -2.3749333 -0.12807499
7000 0.45597995 -2.7959254 0.22846639 -2.3422254 -0.47086714
7500 0.39910433 -2.7779885 0.25742031 -2.3808797 -0.19465195
8000 0.46690622 -2.7777549 0.19323901 -2.3131832 -0.063292514
8500 0.45022765 -2.814943 0.25463601 -2.3669665 0.15612777
9000 0.47294866 -2.7986322 0.2117454 -2.3280483 0.21776933
9500 0.50062288 -2.8318393 0.22438459 -2.3337195 -0.20077418
10000 0.48531399 -2.8185842 0.23564567 -2.3356968 -0.1417187
Loop time of 1.86084 on 1 procs for 10000 steps with 200 atoms
Pair time (%) = 1.50143 (80.6853)
Neigh time (%) = 0.0485067 (2.60671)
Comm time (%) = 0.0729742 (3.92157)
Outpt time (%) = 0.0331767 (1.78288)
Other time (%) = 0.204759 (11.0035)
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 150 ave 150 max 150 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 = 683
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# Point dipoles in a 2d box
units lj
atom_style 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 processor grid
create_atoms 1 box
Created 200 atoms
mass 1 1.0
shape 1 1 1 1
dipole 1 0.75
set group all dipole/random 98934
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 = 3.05241 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 0.18067142
2000 0.39019888 -2.7914865 0.22407033 -2.4032386 -0.40913106
2500 0.4023511 -2.81393 0.24280405 -2.4135906 -0.33881491
3000 0.38615692 -2.818646 0.26460202 -2.4344198 -0.0079725577
3500 0.42122454 -2.8127945 0.23501007 -2.3936761 -0.12887917
4000 0.44161593 -2.8007801 0.20799836 -2.3613722 -0.079523244
4500 0.4231261 -2.7826844 0.22673018 -2.361674 -0.55083706
5000 0.4440514 -2.799822 0.22995936 -2.3579908 -0.28425958
5500 0.45033043 -2.7886448 0.21727591 -2.340566 0.0059789839
6000 0.45676909 -2.8007108 0.23936573 -2.3462256 0.12294031
6500 0.52050628 -2.8509712 0.2362808 -2.3330675 -0.22427307
7000 0.41855625 -2.8254088 0.31121935 -2.4089453 -0.48809423
7500 0.36025589 -2.7101495 0.25308278 -2.3516949 -0.29426489
8000 0.44494177 -2.7665688 0.23326231 -2.3238517 -0.57748114
8500 0.4336595 -2.7378567 0.2235799 -2.3063655 0.030370416
9000 0.41942743 -2.6901214 0.19875084 -2.2727911 0.18043421
9500 0.42853326 -2.7396334 0.23748738 -2.3132428 -0.01076467
10000 0.46672835 -2.7582561 0.22673928 -2.2938614 -0.16751321
Loop time of 0.861498 on 4 procs for 10000 steps with 200 atoms
Pair time (%) = 0.374077 (43.4217)
Neigh time (%) = 0.0131148 (1.52232)
Comm time (%) = 0.346431 (40.2127)
Outpt time (%) = 0.0234395 (2.72078)
Other time (%) = 0.104435 (12.1225)
Nlocal: 50 ave 56 max 41 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 87.5 ave 91 max 85 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 411.25 ave 502 max 304 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 1645
Ave neighs/atom = 8.225
Neighbor list builds = 686
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# 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 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 1.97708 on 1 procs for 100 steps with 2000 atoms
Pair time (%) = 1.76707 (89.3779)
Neigh time (%) = 0.176 (8.90203)
Comm time (%) = 0.00904274 (0.457379)
Outpt time (%) = 0.000144005 (0.00728372)
Other time (%) = 0.0248206 (1.25542)
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 (27 Mar 2011)
# 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 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 0.527222 on 4 procs for 100 steps with 2000 atoms
Pair time (%) = 0.448031 (84.9795)
Neigh time (%) = 0.0419526 (7.9573)
Comm time (%) = 0.0275348 (5.22263)
Outpt time (%) = 0.000249505 (0.0473245)
Other time (%) = 0.00945419 (1.79321)
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

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LAMMPS (27 Mar 2011)
# 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 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 group all quat/random 18238
400 settings made for quat/random
mass 1 1.0
mass 2 1.5
shape 1 1 1 1
shape 2 3 1 1
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
dump 1 all custom 100 dump.ellipse.gayberne id type x y z quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z quatw quati quatj quatk
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 = 3.06749 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 1.28801 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.936182 (72.6843)
Neigh time (%) = 0.0181944 (1.4126)
Comm time (%) = 0.0219097 (1.70105)
Outpt time (%) = 0.0356205 (2.76554)
Other time (%) = 0.276105 (21.4365)
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 = 3.0695 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 0.33981977 1187.4615
2200 1.9674878 -3.1385619 -1.1467435 1.1720134 1187.4615
2300 2.0160349 -3.191283 -1.1652127 0.98222378 1187.4615
2400 2.1323063 -3.3152815 -1.1669961 0.7609986 1187.4615
2500 2.0866911 -3.269205 -1.1766061 0.67971558 1187.4615
2600 2.0982823 -3.277443 -1.1869915 0.90454873 1187.4615
2700 2.0482785 -3.2229463 -1.1928887 0.69425526 1187.4615
2800 1.9676368 -3.1400446 -1.1685879 0.75779083 1187.4615
2900 2.0421383 -3.2182299 -1.1866946 0.7937753 1187.4615
3000 2.1073889 -3.2869759 -1.2013081 0.18890292 1187.4615
3100 2.0467451 -3.2228328 -1.1821281 0.70497485 1187.4615
3200 2.1166717 -3.2985096 -1.1590407 0.51905745 1187.4615
3300 2.1526773 -3.3388713 -1.1806099 0.4510048 1187.4615
3400 2.0962387 -3.2790768 -1.1607666 0.7517609 1187.4615
3500 2.0602553 -3.2409952 -1.1416561 0.79266623 1187.4615
3600 2.0251393 -3.2024628 -1.1698576 0.51604302 1187.4615
3700 2.0147428 -3.1885349 -1.1821832 0.26661154 1187.4615
3800 1.9640896 -3.1344959 -1.1907397 0.52870297 1187.4615
3900 2.042533 -3.2187558 -1.1810341 0.71118836 1187.4615
4000 2.0882357 -3.2628943 -1.18488 0.69781619 1187.4615
Loop time of 1.42811 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.16699 (81.7159)
Neigh time (%) = 0.00850844 (0.595783)
Comm time (%) = 0.0236228 (1.65413)
Outpt time (%) = 0.0354347 (2.48123)
Other time (%) = 0.193552 (13.553)
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: 2912 ave 2912 max 2912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2912
Ave neighs/atom = 7.28
Neighbor list builds = 47
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# 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 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 group all quat/random 18238
400 settings made for quat/random
mass 1 1.0
mass 2 1.5
shape 1 1 1 1
shape 2 3 1 1
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
dump 1 all custom 100 dump.ellipse.gayberne id type x y z quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z quatw quati quatj quatk
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 = 3.05653 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 0.471032 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.233772 (49.6298)
Neigh time (%) = 0.0046134 (0.979424)
Comm time (%) = 0.0967541 (20.5409)
Outpt time (%) = 0.0360661 (7.65683)
Other time (%) = 0.0998262 (21.1931)
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 = 3.05737 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 0.33981977 1187.4615
2200 1.9674878 -3.1385618 -1.1467435 1.1720135 1187.4615
2300 2.0160348 -3.1912829 -1.1652126 0.98222401 1187.4615
2400 2.1323062 -3.3152814 -1.1669962 0.7609989 1187.4615
2500 2.0866913 -3.2692051 -1.1766059 0.67971628 1187.4615
2600 2.0982825 -3.2774432 -1.1869919 0.90454622 1187.4615
2700 2.0482776 -3.2229453 -1.192888 0.69426696 1187.4615
2800 1.9676403 -3.1400511 -1.1685935 0.75777885 1187.4615
2900 2.0421568 -3.2182511 -1.1867014 0.79371143 1187.4615
3000 2.1074324 -3.2870215 -1.201353 0.18881974 1187.4615
3100 2.0468246 -3.2229216 -1.1821138 0.70504941 1187.4615
3200 2.1169492 -3.2986856 -1.1589351 0.51871921 1187.4615
3300 2.1536413 -3.3397682 -1.180639 0.44887653 1187.4615
3400 2.0978165 -3.280631 -1.1610415 0.75128792 1187.4615
3500 2.0587882 -3.2398235 -1.1433609 0.80394373 1187.4615
3600 2.0255166 -3.2025649 -1.1720208 0.54192507 1187.4615
3700 2.0154027 -3.1893307 -1.1657023 0.28402513 1187.4615
3800 1.9277814 -3.0960105 -1.1854881 0.77670745 1187.4615
3900 2.0112013 -3.1831546 -1.1850665 0.67676688 1187.4615
4000 2.0284348 -3.2011574 -1.1772834 0.41947147 1187.4615
Loop time of 0.539757 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.289897 (53.7087)
Neigh time (%) = 0.00209838 (0.388764)
Comm time (%) = 0.148968 (27.599)
Outpt time (%) = 0.0367653 (6.81144)
Other time (%) = 0.0620289 (11.492)
Nlocal: 100 ave 119 max 68 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 137.25 ave 151 max 128 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 735.25 ave 965 max 403 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 2941
Ave neighs/atom = 7.3525
Neighbor list builds = 46
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# 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 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 group all quat/random 18238
400 settings made for quat/random
mass 1 1.0
mass 2 1.5
shape 1 1 1 1
shape 2 3 1 1
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
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.resquared id type x y z quatw quati quatj quatk
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 = 3.06749 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 2.35265 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.99574 (84.8295)
Neigh time (%) = 0.0173743 (0.738497)
Comm time (%) = 0.0161958 (0.688404)
Outpt time (%) = 0.0359209 (1.52682)
Other time (%) = 0.287418 (12.2168)
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 = 3.0695 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 1.3384026 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 0.19775138 2.0931298 1.4157493 1657.9242
3100 1.9114597 0.19296345 2.1126573 1.4113468 1657.9242
3200 1.9427389 0.15998512 2.0865326 1.3075164 1657.9242
3300 1.9111615 0.19317464 2.1216596 1.4309791 1657.9242
3400 1.9538373 0.14833011 2.1210138 1.2276235 1657.9242
3500 1.9244333 0.17929245 2.0825151 1.3186853 1657.9242
3600 1.9511827 0.151075 2.1197983 1.2271865 1657.9242
3700 1.9369709 0.16601302 2.0970219 1.281288 1657.9242
3800 1.9418076 0.16093985 2.1231367 1.2354776 1657.9242
3900 1.9450409 0.1576083 2.139479 1.239228 1657.9242
4000 1.935011 0.16819134 2.1142338 1.2676432 1657.9242
Loop time of 4.09014 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 3.82004 (93.3962)
Neigh time (%) = 0.00708961 (0.173334)
Comm time (%) = 0.0222418 (0.543791)
Outpt time (%) = 0.0359786 (0.879641)
Other time (%) = 0.204794 (5.00702)
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

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LAMMPS (27 Mar 2011)
# 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 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 group all quat/random 18238
400 settings made for quat/random
mass 1 1.0
mass 2 1.5
shape 1 1 1 1
shape 2 3 1 1
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
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.resquared id type x y z quatw quati quatj quatk
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 = 3.05653 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 0.739788 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.503251 (68.0264)
Neigh time (%) = 0.00446272 (0.603243)
Comm time (%) = 0.0924973 (12.5032)
Outpt time (%) = 0.0361266 (4.88337)
Other time (%) = 0.10345 (13.9837)
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 = 3.05737 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 1.9450942 0.15744768 2.0838764 1.2106283 1657.9242
2700 1.9229729 0.18066635 2.1170012 1.3384024 1657.9242
2800 1.9512215 0.15099707 2.0988078 1.2134332 1657.9242
2900 1.9211262 0.18279164 2.0994516 1.3620722 1657.9242
3000 1.9067872 0.19775145 2.0931298 1.4157496 1657.9242
3100 1.9114596 0.19296351 2.1126573 1.4113471 1657.9242
3200 1.9427387 0.15998532 2.0865326 1.3075175 1657.9242
3300 1.9111617 0.19317443 2.1216596 1.4309782 1657.9242
3400 1.9538372 0.14833016 2.1210136 1.227624 1657.9242
3500 1.9244336 0.17929216 2.0825143 1.3186829 1657.9242
3600 1.9511833 0.15107439 2.1197975 1.2271826 1657.9242
3700 1.936968 0.16601605 2.0970224 1.281307 1657.9242
3800 1.9418139 0.16093313 2.1231352 1.2354467 1657.9242
3900 1.9450405 0.15760875 2.1394706 1.2392359 1657.9242
4000 1.9350206 0.16818121 2.1142436 1.2676066 1657.9242
Loop time of 1.18441 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.955088 (80.6381)
Neigh time (%) = 0.00181705 (0.153414)
Comm time (%) = 0.131738 (11.1227)
Outpt time (%) = 0.03601 (3.04033)
Other time (%) = 0.0597591 (5.04546)
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 (27 Mar 2011)
# 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 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
# Poisseuille 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
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 0.586487 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.211832 (36.1187)
Neigh time (%) = 0.0697327 (11.8899)
Comm time (%) = 0.0170028 (2.8991)
Outpt time (%) = 0.128883 (21.9754)
Other time (%) = 0.159037 (27.1169)
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 (27 Mar 2011)
# 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 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
# Poisseuille 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
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 0.41448 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.0529404 (12.7727)
Neigh time (%) = 0.0177063 (4.27193)
Comm time (%) = 0.159481 (38.4773)
Outpt time (%) = 0.0909385 (21.9404)
Other time (%) = 0.0934139 (22.5376)
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 (27 Mar 2011)
# 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 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
# Poisseuille 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
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 0.765119 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.230286 (30.0981)
Neigh time (%) = 0.0396361 (5.18039)
Comm time (%) = 0.0152719 (1.99602)
Outpt time (%) = 0.258458 (33.7801)
Other time (%) = 0.221467 (28.9454)
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 (27 Mar 2011)
# 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 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
# Poisseuille 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
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 0.623361 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.0576158 (9.24276)
Neigh time (%) = 0.0104457 (1.6757)
Comm time (%) = 0.179585 (28.8092)
Outpt time (%) = 0.173133 (27.7741)
Other time (%) = 0.202582 (32.4983)
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 (27 Mar 2011)
# 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 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
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 10.6353 on 1 procs for 20000 steps with 1724 atoms
Pair time (%) = 8.85169 (83.2295)
Neigh time (%) = 0.454272 (4.27137)
Comm time (%) = 0.0700171 (0.658347)
Outpt time (%) = 0.106286 (0.999372)
Other time (%) = 1.15302 (10.8415)
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 (27 Mar 2011)
# 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 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
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 3.65225 on 4 procs for 20000 steps with 1724 atoms
Pair time (%) = 2.22406 (60.8956)
Neigh time (%) = 0.111846 (3.06239)
Comm time (%) = 0.684649 (18.7459)
Outpt time (%) = 0.240481 (6.58446)
Other time (%) = 0.391215 (10.7116)
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 (27 Mar 2011)
# 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 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
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 4.48839 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 3.32296 (74.0347)
Neigh time (%) = 0.0993707 (2.21395)
Comm time (%) = 0.0551386 (1.22847)
Outpt time (%) = 0.0783148 (1.74483)
Other time (%) = 0.932601 (20.7781)
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 4.02696 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 3.30979 (82.1908)
Neigh time (%) = 0.0998025 (2.47836)
Comm time (%) = 0.0567474 (1.40919)
Outpt time (%) = 0.078594 (1.95169)
Other time (%) = 0.482025 (11.97)
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

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LAMMPS (27 Mar 2011)
# 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 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
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 2.15339 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 0.834652 (38.76)
Neigh time (%) = 0.0253125 (1.17548)
Comm time (%) = 0.6108 (28.3646)
Outpt time (%) = 0.207858 (9.6526)
Other time (%) = 0.474765 (22.0474)
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 1.76434 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 0.824768 (46.7466)
Neigh time (%) = 0.0261157 (1.4802)
Comm time (%) = 0.6177 (35.0103)
Outpt time (%) = 0.0596796 (3.38255)
Other time (%) = 0.236074 (13.3803)
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

404
examples/indent/log.indent.min.28Mar11.linux.1 Normal file
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LAMMPS (27 Mar 2011)
# 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 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
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 0.0884922 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 (%) = 0.0747404 (84.4599)
Neigh time (%) = 0.000659704 (0.745495)
Comm time (%) = 0.000694275 (0.784561)
Outpt time (%) = 0.00545716 (6.16683)
Other time (%) = 0.0069406 (7.84318)
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
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 0.0995409 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 (%) = 0.0757627 (76.1121)
Neigh time (%) = 0.00378561 (3.80307)
Comm time (%) = 0.000819445 (0.823224)
Outpt time (%) = 0.00627327 (6.3022)
Other time (%) = 0.0128999 (12.9594)
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
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 0.107578 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 (%) = 0.0807207 (75.0345)
Neigh time (%) = 0.00420499 (3.90878)
Comm time (%) = 0.000867605 (0.806489)
Outpt time (%) = 0.00791669 (7.35902)
Other time (%) = 0.0138681 (12.8912)
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
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 0.0679569 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 (%) = 0.0498948 (73.4212)
Neigh time (%) = 0.0028069 (4.13041)
Comm time (%) = 0.000552416 (0.812891)
Outpt time (%) = 0.00547743 (8.06015)
Other time (%) = 0.00922537 (13.5753)
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
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 0.176604 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 (%) = 0.131893 (74.683)
Neigh time (%) = 0.00583577 (3.30444)
Comm time (%) = 0.00148368 (0.840116)
Outpt time (%) = 0.0149209 (8.44882)
Other time (%) = 0.0224705 (12.7236)
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
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 0.170806 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 (%) = 0.13136 (76.906)
Neigh time (%) = 0.0067091 (3.92791)
Comm time (%) = 0.00150347 (0.88022)
Outpt time (%) = 0.010102 (5.91433)
Other time (%) = 0.0211313 (12.3715)
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
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 0.239795 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 (%) = 0.182819 (76.2399)
Neigh time (%) = 0.00830817 (3.4647)
Comm time (%) = 0.00199533 (0.832096)
Outpt time (%) = 0.0170641 (7.11612)
Other time (%) = 0.029608 (12.3472)
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.28Mar11.linux.4 Normal file
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LAMMPS (27 Mar 2011)
# 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 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
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 0.0379065 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 (%) = 0.0186192 (49.1188)
Neigh time (%) = 0.000171363 (0.452068)
Comm time (%) = 0.00722551 (19.0614)
Outpt time (%) = 0.00571096 (15.0659)
Other time (%) = 0.00617945 (16.3018)
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
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 0.0430946 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 (%) = 0.0184599 (42.8358)
Neigh time (%) = 0.000846982 (1.9654)
Comm time (%) = 0.00861949 (20.0013)
Outpt time (%) = 0.00648999 (15.0599)
Other time (%) = 0.00867826 (20.1377)
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
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 0.0572262 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 (%) = 0.024202 (42.2918)
Neigh time (%) = 0.00122923 (2.14801)
Comm time (%) = 0.0118026 (20.6245)
Outpt time (%) = 0.00885069 (15.4661)
Other time (%) = 0.0111417 (19.4696)
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
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 0.062937 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 (%) = 0.0241739 (38.4096)
Neigh time (%) = 0.0016433 (2.61102)
Comm time (%) = 0.0132205 (21.006)
Outpt time (%) = 0.0120705 (19.1787)
Other time (%) = 0.0118288 (18.7947)
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
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 0.0711412 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 (%) = 0.0263076 (36.9794)
Neigh time (%) = 0.00178152 (2.50421)
Comm time (%) = 0.0165319 (23.2382)
Outpt time (%) = 0.0136525 (19.1907)
Other time (%) = 0.0128677 (18.0875)
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
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 0.0300033 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 (%) = 0.0115876 (38.6211)
Neigh time (%) = 0.000545442 (1.81794)
Comm time (%) = 0.00724971 (24.163)
Outpt time (%) = 0.00480968 (16.0305)
Other time (%) = 0.00581086 (19.3674)
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
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 0.0232177 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 (%) = 0.00926459 (39.9032)
Neigh time (%) = 0.000253439 (1.09158)
Comm time (%) = 0.00583363 (25.1258)
Outpt time (%) = 0.00319672 (13.7685)
Other time (%) = 0.00466931 (20.111)
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 (27 Mar 2011)
# 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 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 0.129397 on 1 procs for 100 steps with 128 atoms
Pair time (%) = 0.122473 (94.6495)
Neigh time (%) = 0.00316429 (2.44541)
Comm time (%) = 0.000795126 (0.614486)
Outpt time (%) = 0.0022583 (1.74525)
Other time (%) = 0.000705719 (0.545391)
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 (27 Mar 2011)
# 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 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 0.073782 on 4 procs for 100 steps with 128 atoms
Pair time (%) = 0.0618048 (83.7668)
Neigh time (%) = 0.000865817 (1.17348)
Comm time (%) = 0.00796497 (10.7953)
Outpt time (%) = 0.00274181 (3.7161)
Other time (%) = 0.000404596 (0.548367)
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 (27 Mar 2011)
# 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 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
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 2.5416 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 2.50755 (98.6603)
Neigh time (%) = 0.0220699 (0.868349)
Comm time (%) = 0.00254846 (0.10027)
Outpt time (%) = 0.000214577 (0.00844259)
Other time (%) = 0.00921631 (0.362619)
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
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 309.15673 -8081.8589 0 -8045.0276 10527.674 20988.916
1300 304.48416 -8064.5597 0 -8028.2851 10066.832 21118.364
1400 300 -8046.7607 0 -8011.0202 10976.597 21230.714
1500 300 -8041.3545 0 -8005.6141 11944.043 21366.268
1600 309.60362 -8035.2271 0 -7998.3426 11344.441 21522.036
1700 300 -8029.1688 0 -7993.4283 11303.125 21627.406
1800 300 -8034.2214 0 -7998.4809 9637.4925 21728.966
1900 307.8766 -8037.1068 0 -8000.428 6165.8684 21849.865
2000 307.93939 -8029.9415 0 -7993.2552 3171.4159 22004.863
2100 300 -8032.6008 0 -7996.8604 1295.9263 22098.991
2200 300 -8042.3739 0 -8006.6334 1615.3416 22223.554
2300 309.98225 -8040.4009 0 -8003.4713 3571.2277 22340.79
2400 295.53749 -8036.0363 0 -8000.8275 5496.7006 22470.237
2500 300 -8038.9034 0 -8003.163 6990.6617 22588.694
2600 300 -8039.3156 0 -8003.5751 8774.3909 22712.036
2700 300 -8041.8829 0 -8006.1425 8212.4486 22830.493
2800 300 -8041.7538 0 -8006.0133 7007.2322 22956.277
2900 308.45087 -8041.8224 0 -8005.0752 6596.7027 23078.397
3000 304.66557 -8039.5734 0 -8003.2772 3648.991 23201.739
Loop time of 80.2078 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 78.7984 (98.2427)
Neigh time (%) = 0.961029 (1.19817)
Comm time (%) = 0.0793548 (0.0989364)
Outpt time (%) = 0.0915716 (0.114168)
Other time (%) = 0.277497 (0.345972)
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: 23414 ave 23414 max 23414 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 46828 ave 46828 max 46828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46828
Ave neighs/atom = 24.4916
Neighbor list builds = 225
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# 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 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
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 0.680185 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.660636 (97.1258)
Neigh time (%) = 0.00543064 (0.798406)
Comm time (%) = 0.0110168 (1.61968)
Outpt time (%) = 0.000174105 (0.0255967)
Other time (%) = 0.00292808 (0.430482)
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
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 12498.159 21361.383
1600 300 -8032.3339 0 -7996.5935 13558.654 21487.167
1700 300 -8021.6093 0 -7985.8689 13720.959 21608.067
1800 300 -8013.5338 0 -7977.7933 10671.997 21727.745
1900 300 -8014.5801 0 -7978.8397 6968.6165 21849.865
2000 300 -8026.6564 0 -7990.916 3269.5142 21974.428
2100 300 -8033.104 0 -7997.3635 1537.6968 22102.655
2200 306.76458 -8028.5483 0 -7992.002 3816.212 22221.112
2300 300 -8028.9662 0 -7993.2258 3429.3646 22348.117
2400 300 -8035.5372 0 -7999.7968 2897.9007 22464.131
2500 300 -8039.4612 0 -8003.7208 1164.0875 22581.367
2600 303.83211 -8036.4648 0 -8000.2678 2956.6036 22710.815
2700 300 -8037.9929 0 -8002.2524 3272.0339 22824.387
2800 308.111 -8042.3302 0 -8005.6235 1981.3196 22951.392
2900 300 -8039.5639 0 -8003.8235 2710.0878 23079.619
3000 300 -8038.5652 0 -8002.8248 1297.2939 23190.748
Loop time of 21.7748 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 20.9228 (96.087)
Neigh time (%) = 0.237493 (1.09068)
Comm time (%) = 0.435934 (2.00201)
Outpt time (%) = 0.0909243 (0.417566)
Other time (%) = 0.0876888 (0.402707)
Nlocal: 478 ave 510 max 445 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 786 ave 821 max 750 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 5752.25 ave 6082 max 5380 min
Histogram: 1 0 0 0 1 0 0 1 0 1
FullNghs: 11504.5 ave 12167 max 10785 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 46018
Ave neighs/atom = 24.068
Neighbor list builds = 224
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# 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 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 1.26498 on 1 procs for 250 steps with 4000 atoms
Pair time (%) = 1.06745 (84.3844)
Neigh time (%) = 0.114981 (9.0895)
Comm time (%) = 0.0207102 (1.63719)
Outpt time (%) = 0.0310349 (2.45339)
Other time (%) = 0.0308092 (2.43554)
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 (27 Mar 2011)
# 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 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 0.404644 on 4 procs for 250 steps with 4000 atoms
Pair time (%) = 0.270148 (66.7619)
Neigh time (%) = 0.0298547 (7.37801)
Comm time (%) = 0.0646951 (15.9881)
Outpt time (%) = 0.0312538 (7.72378)
Other time (%) = 0.00869256 (2.1482)
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 (27 Mar 2011)
# 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 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 1.0+elapsed*(20.0-1.0)/1000
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 0.296398 on 1 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.200801 (67.747)
Bond time (%) = 0.0198426 (6.69459)
Neigh time (%) = 0.0258448 (8.71963)
Comm time (%) = 0.00579762 (1.95603)
Outpt time (%) = 0.000420332 (0.141813)
Other time (%) = 0.0436919 (14.741)
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 = 2.47141 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727752 0.05861303 -1.4645372 1.9980559
2000 0.46587559 -2.0010695 0.060132019 -1.4754502 1.6451314
3000 0.45 -2.0239533 0.060188604 -1.5141397 1.3362681
4000 0.44834861 -2.017092 0.075251306 -1.4938657 1.3591114
5000 0.46547677 -2.0295012 0.06522447 -1.4991878 1.4829383
6000 0.45112324 -2.0400767 0.057098347 -1.532231 1.3518067
7000 0.44247078 -2.0322979 0.061094323 -1.5291015 1.3509414
8000 0.44140196 -2.0331192 0.05744003 -1.5346451 1.3707189
9000 0.45834759 -2.0515773 0.064928813 -1.5286828 1.145884
10000 0.44422962 -2.0520572 0.064728062 -1.5434697 1.0352924
11000 0.44657877 -2.0576388 0.060199889 -1.5512323 1.0720569
12000 0.45932682 -2.0703871 0.063351227 -1.5480918 1.0967735
13000 0.44237042 -2.0576326 0.068901547 -1.5467293 1.1195422
14000 0.46121453 -2.0665558 0.055978332 -1.5497473 1.1175972
15000 0.45747219 -2.0779313 0.060680029 -1.5601603 0.99866486
16000 0.45429178 -2.0845936 0.056184721 -1.5744956 0.91128707
17000 0.45003817 -2.0771509 0.06367887 -1.5638089 1.0122036
18000 0.43888179 -2.0846743 0.06944096 -1.5767173 0.971981
19000 0.44335805 -2.0612088 0.058067557 -1.5601527 0.99290954
20000 0.4506188 -2.1018273 0.05802854 -1.5935555 0.76679566
21000 0.45936109 -2.0845223 0.065767359 -1.5597766 0.91857679
22000 0.45828878 -2.0702734 0.063718131 -1.5486484 1.0969511
23000 0.44804616 -2.0818323 0.067842002 -1.5663175 0.89004476
24000 0.45413437 -2.0920704 0.054952858 -1.5833616 0.80823231
25000 0.45091841 -2.0934074 0.058857672 -1.5840071 0.97464475
26000 0.45883711 -2.1026861 0.065370285 -1.5788611 0.84967846
27000 0.43566393 -2.0958727 0.063741443 -1.5968303 0.81983036
28000 0.44046192 -2.0986493 0.055330217 -1.6032243 0.90370082
29000 0.44029391 -2.1000906 0.061396091 -1.5987675 0.79211615
30000 0.4371858 -2.0881128 0.05257556 -1.5987158 0.75023874
31000 0.46815272 -2.1054823 0.06284246 -1.5748772 0.87763011
32000 0.437177 -2.0852561 0.062964736 -1.5854787 1.0251783
33000 0.45710857 -2.1060149 0.067344455 -1.5819428 0.75532522
34000 0.4579388 -2.0999311 0.056482819 -1.5858911 0.69171145
35000 0.45761944 -2.0965841 0.060166016 -1.57918 0.74063424
36000 0.45029618 -2.0865974 0.051546598 -1.5851299 0.85273679
37000 0.45396896 -2.109932 0.058733613 -1.5976078 0.58197256
38000 0.44507197 -2.1117681 0.061283206 -1.6057838 0.64866585
39000 0.45121883 -2.100855 0.062691498 -1.5873207 0.75821877
40000 0.4427874 -2.1036896 0.054300413 -1.6069708 0.8444976
41000 0.43711084 -2.1034438 0.057613878 -1.6090834 0.68362843
42000 0.45397342 -2.1247332 0.065573339 -1.6055648 0.6910664
43000 0.46822343 -2.1242114 0.050835039 -1.6055432 0.65559737
44000 0.45 -2.1041756 0.068284127 -1.5862665 0.65389608
45000 0.44692359 -2.1187515 0.065054942 -1.6071454 0.73631867
46000 0.45 -2.1312623 0.053036678 -1.6286007 0.61134132
47000 0.45 -2.1058191 0.059512612 -1.5966815 0.68403253
48000 0.45 -2.1089791 0.061279964 -1.5980742 0.55935538
49000 0.44985379 -2.1086199 0.06208867 -1.5970524 0.73999748
50000 0.45655588 -2.1056744 0.055013138 -1.5944858 0.81660096
51000 0.45156245 -2.1008465 0.063727798 -1.5859326 0.82015936
52000 0.44546442 -2.1135816 0.058084069 -1.6104043 0.65777603
53000 0.46298329 -2.1386912 0.0609544 -1.6151393 0.57284818
54000 0.45060418 -2.1256349 0.056545594 -1.6188607 0.67817929
55000 0.44259009 -2.1078309 0.057601584 -1.608008 0.6154451
56000 0.4422812 -2.1129054 0.058954254 -1.6120385 0.71532785
57000 0.45359829 -2.1296397 0.063847735 -1.6125716 0.55207492
58000 0.46008134 -2.1414051 0.057599187 -1.6241079 0.44207558
59000 0.45426598 -2.1129681 0.05234106 -1.6067396 0.69726167
60000 0.43676084 -2.1377437 0.063677824 -1.637669 0.59828188
Loop time of 24.2876 on 1 procs for 60000 steps with 1200 atoms
Pair time (%) = 17.1009 (70.41)
Bond time (%) = 1.19335 (4.91343)
Neigh time (%) = 2.72018 (11.1999)
Comm time (%) = 0.500614 (2.0612)
Outpt time (%) = 0.22157 (0.912279)
Other time (%) = 2.55096 (10.5032)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 406 ave 406 max 406 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9908 ave 9908 max 9908 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9908
Ave neighs/atom = 8.25667
Ave special neighs/atom = 0.5
Neighbor list builds = 4886
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# 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 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 1.0+elapsed*(20.0-1.0)/1000
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 0.100452 on 4 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.0498564 (49.6318)
Bond time (%) = 0.0050841 (5.0612)
Neigh time (%) = 0.00650609 (6.47678)
Comm time (%) = 0.0233545 (23.2493)
Outpt time (%) = 0.000514746 (0.512427)
Other time (%) = 0.0151367 (15.0685)
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 -1.9727835 0.05861666 -1.4645418 1.9980702
2000 0.46517822 -1.9780359 0.067948374 -1.445297 1.6965722
3000 0.44442239 -2.0071128 0.06120835 -1.5018524 1.5222883
4000 0.456308 -2.0153434 0.068213403 -1.4912023 1.3436315
5000 0.45229687 -2.0329915 0.065645602 -1.5154259 1.3436126
6000 0.46701618 -2.0356824 0.058021883 -1.5110335 1.2118104
7000 0.45362932 -2.0410707 0.052825913 -1.5349935 1.2114606
8000 0.45330066 -2.0560304 0.064359835 -1.5387477 1.1605865
9000 0.44442449 -2.0424175 0.058181773 -1.5401815 1.3190707
10000 0.46232512 -2.0463389 0.057161043 -1.527238 1.2070304
11000 0.44942662 -2.0701128 0.061226132 -1.5598346 1.1178151
12000 0.45601961 -2.0723253 0.059483024 -1.5572027 1.0316073
13000 0.45362657 -2.0630142 0.060128442 -1.5496372 0.9455288
14000 0.43808761 -2.0810282 0.059128884 -1.5841768 0.81637225
15000 0.45358991 -2.0708073 0.059724848 -1.5578706 0.97357454
16000 0.44935223 -2.0692994 0.051726351 -1.5685953 1.0546408
17000 0.45483699 -2.0843859 0.064229583 -1.5656983 1.0315804
18000 0.45321723 -2.0971259 0.062856742 -1.5814296 0.8064773
19000 0.44605522 -2.0879682 0.053946638 -1.5883381 0.90406663
20000 0.43883059 -2.0866775 0.065276391 -1.5829362 0.85370633
21000 0.45545364 -2.101552 0.062142765 -1.5843352 0.81845553
22000 0.45522151 -2.0828807 0.067256218 -1.5607823 0.9706995
23000 0.4650054 -2.0787018 0.059805932 -1.554278 1.0704161
24000 0.46474788 -2.0971913 0.059949964 -1.5728808 0.84000607
25000 0.45575402 -2.092695 0.054822549 -1.5824982 0.84453305
26000 0.44899326 -2.0874465 0.064886311 -1.5739411 0.89968195
27000 0.45053157 -2.0799405 0.054863749 -1.5749207 0.90453322
28000 0.45323794 -2.0874733 0.06139382 -1.5732192 0.81255445
29000 0.45236043 -2.0802746 0.062148229 -1.5661429 0.9286698
30000 0.45228211 -2.0817408 0.057599616 -1.5722359 0.8828485
31000 0.46130206 -2.0996882 0.064059349 -1.5747112 0.72706411
32000 0.44534262 -2.1045296 0.060633126 -1.5989249 0.74293421
33000 0.45221806 -2.0870053 0.056047653 -1.5791165 0.76379253
34000 0.44398407 -2.1079801 0.066002834 -1.5983632 0.82114412
35000 0.45218038 -2.1020507 0.057932117 -1.5923151 0.60323129
36000 0.45 -2.0862438 0.06294955 -1.5736692 0.89405641
37000 0.46461064 -2.1168858 0.059082275 -1.5935801 0.66402939
38000 0.44611243 -2.1172658 0.064007093 -1.607518 0.60584348
39000 0.44502953 -2.1179471 0.055025825 -1.6182626 0.7442726
40000 0.4430766 -2.1093867 0.059208508 -1.6074708 0.72223244
41000 0.45769603 -2.1169038 0.061091289 -1.5984979 0.67027735
42000 0.44670519 -2.1172363 0.054443831 -1.6164595 0.63471914
43000 0.45577636 -2.1166993 0.063751464 -1.5975513 0.69416588
44000 0.45428732 -2.1087584 0.05642599 -1.5984236 0.68383294
45000 0.45738702 -2.1030486 0.052726869 -1.5933159 0.7233588
46000 0.45998025 -2.1142799 0.056695699 -1.5979873 0.58743722
47000 0.45197287 -2.1014927 0.060987432 -1.588909 0.72101434
48000 0.43822132 -2.1054338 0.068738038 -1.5988397 0.70635431
49000 0.44953933 -2.097976 0.053783258 -1.5950281 0.83327442
50000 0.43830319 -2.0898516 0.048393286 -1.6035203 0.77052441
51000 0.43608504 -2.0999577 0.060852704 -1.6033833 0.73608027
52000 0.4424344 -2.1028022 0.064831031 -1.5959055 0.76043239
53000 0.44681552 -2.0834716 0.056812197 -1.5802163 0.93109587
54000 0.44529438 -2.1224654 0.062327333 -1.6152148 0.72285005
55000 0.44057465 -2.1137836 0.061999177 -1.611577 0.67756677
56000 0.44316786 -2.1034592 0.055369897 -1.6052907 0.67310676
57000 0.45412509 -2.1243503 0.063043641 -1.60756 0.57719521
58000 0.43932103 -2.103872 0.061324794 -1.6035923 0.78396172
59000 0.44641652 -2.107381 0.054942721 -1.6063938 0.64141771
60000 0.45448663 -2.1393061 0.069265122 -1.6159331 0.66414458
Loop time of 8.08898 on 4 procs for 60000 steps with 1200 atoms
Pair time (%) = 4.24161 (52.4369)
Bond time (%) = 0.305831 (3.78083)
Neigh time (%) = 0.685794 (8.47812)
Comm time (%) = 1.87783 (23.2147)
Outpt time (%) = 0.18264 (2.25789)
Other time (%) = 0.795272 (9.83154)
Nlocal: 300 ave 317 max 286 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 217.25 ave 235 max 203 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 2408.75 ave 2478 max 2355 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 9635
Ave neighs/atom = 8.02917
Ave special neighs/atom = 0.5
Neighbor list builds = 4884
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# 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 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 0.348465 on 1 procs for 1000 steps with 800 atoms
Pair time (%) = 0.231879 (66.5429)
Neigh time (%) = 0.0653319 (18.7485)
Comm time (%) = 0.0083065 (2.38374)
Outpt time (%) = 0.0123622 (3.54763)
Other time (%) = 0.0305855 (8.77722)
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 0.546157 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 (%) = 0.452761 (82.8993)
Neigh time (%) = 0.0265779 (4.86636)
Comm time (%) = 0.00702667 (1.28657)
Outpt time (%) = 0.017199 (3.1491)
Other time (%) = 0.0425928 (7.79863)
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 (27 Mar 2011)
# 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 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 0.127753 on 4 procs for 1000 steps with 800 atoms
Pair time (%) = 0.057333 (44.8778)
Neigh time (%) = 0.016416 (12.8498)
Comm time (%) = 0.0303358 (23.7456)
Outpt time (%) = 0.0127025 (9.94295)
Other time (%) = 0.0109662 (8.58386)
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 0.209153 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 (%) = 0.123585 (59.0883)
Neigh time (%) = 0.00630492 (3.0145)
Comm time (%) = 0.0376325 (17.9928)
Outpt time (%) = 0.0141935 (6.78618)
Other time (%) = 0.0274371 (13.1182)
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 (27 Mar 2011)
# 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 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 6.19878 on 1 procs for 100 steps with 23328 atoms
Pair time (%) = 5.89596 (95.115)
Neigh time (%) = 0.0967462 (1.56073)
Comm time (%) = 0.052855 (0.852669)
Outpt time (%) = 0.0015583 (0.0251389)
Other time (%) = 0.151652 (2.44648)
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 7.99099 on 1 procs for 100 steps with 23328 atoms
Pair time (%) = 5.95126 (74.4747)
Neigh time (%) = 0.19278 (2.41247)
Comm time (%) = 0.0422211 (0.528359)
Outpt time (%) = 0.0197036 (0.246573)
Other time (%) = 1.78502 (22.3379)
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 (27 Mar 2011)
# 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 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 1.58084 on 4 procs for 100 steps with 23328 atoms
Pair time (%) = 1.40697 (89.0013)
Neigh time (%) = 0.023333 (1.47599)
Comm time (%) = 0.106886 (6.76136)
Outpt time (%) = 0.0017578 (0.111194)
Other time (%) = 0.0418939 (2.65011)
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 2.02493 on 4 procs for 100 steps with 23328 atoms
Pair time (%) = 1.42248 (70.2482)
Neigh time (%) = 0.0467892 (2.31066)
Comm time (%) = 0.107583 (5.31292)
Outpt time (%) = 0.00649673 (0.320837)
Other time (%) = 0.441585 (21.8074)
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 (27 Mar 2011)
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 (27 Mar 2011)
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 (27 Mar 2011)
# 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 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 1.73364 on 1 procs for 50000 steps with 160 atoms
Pair time (%) = 0.319555 (18.4325)
Neigh time (%) = 0.202125 (11.659)
Comm time (%) = 0.0959871 (5.53673)
Outpt time (%) = 0.0306251 (1.76652)
Other time (%) = 1.08535 (62.6052)
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 (27 Mar 2011)
# 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 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 1.40921 on 4 procs for 50000 steps with 160 atoms
Pair time (%) = 0.0880941 (6.25131)
Neigh time (%) = 0.0557205 (3.95402)
Comm time (%) = 0.611955 (43.4254)
Outpt time (%) = 0.0255623 (1.81394)
Other time (%) = 0.627878 (44.5553)
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 (27 Mar 2011)
# 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 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
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 3.50378 on 1 procs for 25000 steps with 769 atoms
Pair time (%) = 0.838852 (23.9413)
Neigh time (%) = 0.201731 (5.75751)
Comm time (%) = 0.0474997 (1.35567)
Outpt time (%) = 0.516879 (14.752)
Other time (%) = 1.89882 (54.1935)
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 (27 Mar 2011)
# 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 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
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 1.66526 on 4 procs for 25000 steps with 769 atoms
Pair time (%) = 0.206591 (12.4059)
Neigh time (%) = 0.0515214 (3.0939)
Comm time (%) = 0.399153 (23.9694)
Outpt time (%) = 0.211481 (12.6996)
Other time (%) = 0.796512 (47.8311)
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 (27 Mar 2011)
# 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 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
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 = 1.7148 (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 = 3.4440 (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 = 5.2162 (sec) ----------------
TotEng = -5287.2845 KinEng = 1098.6039 Temp = 273.0740
PotEng = -6385.8884 E_bond = 17.4924 E_angle = 32.8593
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
E_coul = 26716.7990 E_long = -33906.8220 Press = -333.1912
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50836e-07
8 1.08 6.58288e-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 = 6.9555 (sec) ----------------
TotEng = -5308.4531 KinEng = 1100.5081 Temp = 273.5473
PotEng = -6408.9612 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8150 E_impro = 2.6054 E_vdwl = 686.3253
E_coul = 26735.6523 E_long = -33901.9341 Press = -1470.4125
---------------- Step 250 ----- CPU = 8.7399 (sec) ----------------
TotEng = -5294.1792 KinEng = 1071.1639 Temp = 266.2534
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 = 26713.3849 E_long = -33908.2636 Press = -188.7523
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78179e-06
6 0.997001 3.49519e-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 7.67605e-06
31 104.52 0.000806296
---------------- Step 300 ----- CPU = 10.5266 (sec) ----------------
TotEng = -5251.4367 KinEng = 1123.6271 Temp = 279.2938
PotEng = -6375.0637 E_bond = 14.2250 E_angle = 38.4733
E_dihed = 18.1306 E_impro = 2.3699 E_vdwl = 715.4580
E_coul = 26744.9478 E_long = -33908.6682 Press = -469.4705
Loop time of 10.5266 on 1 procs for 300 steps with 2004 atoms
Pair time (%) = 8.0904 (76.8567)
Bond time (%) = 0.0330784 (0.314237)
Kspce time (%) = 1.24323 (11.8104)
Neigh time (%) = 0.953025 (9.05349)
Comm time (%) = 0.0600786 (0.570731)
Outpt time (%) = 0.0094595 (0.0898628)
Other time (%) = 0.137332 (1.30462)
FFT time (% of Kspce) = 0.136628 (10.9898)
FFT Gflps 3d (1d only) = 1.2041 1.8243
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 (27 Mar 2011)
# 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 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
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 = 0.5035 (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 = 1.0089 (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 = 1.5261 (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 = 26716.7990 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 = 2.0277 (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 = 2.5482 (sec) ----------------
TotEng = -5294.1793 KinEng = 1071.1639 Temp = 266.2534
PotEng = -6365.3432 E_bond = 14.2022 E_angle = 39.1951
E_dihed = 19.4554 E_impro = 3.1386 E_vdwl = 753.5442
E_coul = 26713.3849 E_long = -33908.2636 Press = -188.7520
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78179e-06
6 0.997001 3.49518e-06
8 1.08 2.09281e-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 0.000806295
---------------- Step 300 ----- CPU = 3.0773 (sec) ----------------
TotEng = -5251.4367 KinEng = 1123.6267 Temp = 279.2938
PotEng = -6375.0634 E_bond = 14.2250 E_angle = 38.4733
E_dihed = 18.1306 E_impro = 2.3699 E_vdwl = 715.4580
E_coul = 26744.9481 E_long = -33908.6682 Press = -469.4697
Loop time of 3.07745 on 4 procs for 300 steps with 2004 atoms
Pair time (%) = 1.94511 (63.2051)
Bond time (%) = 0.00942487 (0.306256)
Kspce time (%) = 0.515528 (16.7518)
Neigh time (%) = 0.224395 (7.29158)
Comm time (%) = 0.221778 (7.20655)
Outpt time (%) = 0.00817496 (0.26564)
Other time (%) = 0.153044 (4.97309)
FFT time (% of Kspce) = 0.0852013 (16.527)
FFT Gflps 3d (1d only) = 1.93089 6.56039
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 (27 Mar 2011)
# 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 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 = 24.3825 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 2407361.6 0 8.994088e+08 2.269543e+14 2.6348959e-06
900 1.2358395e+28 4532520.7 0 8.9673706e+08 1.8249059e+14 3.2593627e-06
1000 1.2341057e+28 3219947.1 0 8.9417281e+08 1.5276039e+14 3.8882369e-06
Loop time of 64.495 on 1 procs for 1000 steps with 3487 atoms
Pair time (%) = 63.2867 (98.1265)
Neigh time (%) = 0.822339 (1.27504)
Comm time (%) = 0.0034833 (0.00540088)
Outpt time (%) = 0.106164 (0.164607)
Other time (%) = 0.276313 (0.428426)
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: 567140 ave 567140 max 567140 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 (27 Mar 2011)
# 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 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 = 18.8838 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 2407361.5 0 8.994088e+08 2.269543e+14 2.6348959e-06
900 1.2358395e+28 4532519.9 0 8.9673706e+08 1.8249059e+14 3.2593627e-06
1000 1.2341057e+28 3219971.4 0 8.9417285e+08 1.5276039e+14 3.8882369e-06
Loop time of 17.7788 on 4 procs for 1000 steps with 3487 atoms
Pair time (%) = 15.3638 (86.4159)
Neigh time (%) = 0.200702 (1.12888)
Comm time (%) = 2.03985 (11.4734)
Outpt time (%) = 0.0963216 (0.541777)
Other time (%) = 0.0782183 (0.439951)
Nlocal: 871.75 ave 923 max 823 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 1343.25 ave 1392 max 1292 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 141785 ave 171378 max 115621 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 (27 Mar 2011)
# Pour granular particles into chute container, then induce flow
atom_style granular
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 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 = 9.53798 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 62.604955 6600
9000 1206 1243.5289 52.989305 6600
10000 1608 1403.0711 56.9465 6600
11000 1608 1225.8111 52.938639 6600
12000 1608 1180.1935 40.544973 6600
13000 2010 1328.8958 49.216222 6600
14000 2010 1178.4104 44.431482 6600
15000 2010 998.18775 45.388975 6600
16000 2412 1050.7228 44.704814 6600
17000 2412 1025.5915 40.030825 6600
18000 2412 919.51551 36.650545 6600
19000 2814 1006.5829 41.592546 6600
20000 2814 964.34863 40.248622 6600
21000 2814 755.00069 47.423444 6600
22000 2814 516.03089 37.374261 6600
23000 3000 412.07349 38.529474 6600
24000 3000 352.98971 25.413823 6600
25000 3000 224.4892 26.293648 6600
Loop time of 16.2706 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 9.93414 (61.0559)
Neigh time (%) = 1.52613 (9.37968)
Comm time (%) = 0.33667 (2.06919)
Outpt time (%) = 0.0725436 (0.445858)
Other time (%) = 4.40109 (27.0494)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 675 ave 675 max 675 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13593 ave 13593 max 13593 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13593
Ave neighs/atom = 4.531
Neighbor list builds = 1154
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Memory usage per processor = 10.3382 Mbytes
Step Atoms KinEng 1 Volume
25000 3000 224.4892 26.293648 6600
26000 3000 109.35155 19.099437 6600
27000 3000 106.58675 12.27262 6600
28000 3000 183.89427 10.880842 6600
29000 3000 292.94648 11.873629 6600
30000 3000 464.71914 16.448049 6600
31000 3000 686.57043 21.625578 6600
32000 3000 928.71115 29.23142 6600
33000 3000 1306.1411 35.231678 6600
34000 3000 1749.5669 40.390136 6600
35000 3000 2276.5984 52.718937 6600
36000 3000 2903.9133 59.451797 6600
37000 3000 3546.0796 61.447694 6600
38000 3000 4236.2302 80.403853 6600
39000 3000 5094.5896 91.929565 6600
40000 3000 5945.8279 104.35396 6600
41000 3000 6966.1795 111.16923 6600
42000 3000 8070.0072 125.57778 6600
43000 3000 9283.327 145.20852 6600
44000 3000 10603.168 165.13356 6600
45000 3000 11844.495 162.80115 6600
46000 3000 13223.004 179.54672 6600
47000 3000 14640.883 189.5725 6600
48000 3000 16191.178 222.62089 6600
49000 3000 17788.584 221.35968 6600
50000 3000 19393.123 255.33084 6600
Loop time of 31.9877 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 21.7568 (68.0161)
Neigh time (%) = 2.29067 (7.1611)
Comm time (%) = 0.723586 (2.26207)
Outpt time (%) = 0.118071 (0.369114)
Other time (%) = 7.09858 (22.1916)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 763 ave 763 max 763 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14168 ave 14168 max 14168 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14168
Ave neighs/atom = 4.72267
Neighbor list builds = 807
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# Pour granular particles into chute container, then induce flow
atom_style granular
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 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 = 9.4131 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 1403.019 62.696462 6600
9000 1206 1246.5766 52.235655 6600
10000 1608 1384.2206 51.017669 6600
11000 1608 1247.6415 50.760042 6600
12000 1608 1195.7464 41.478899 6600
13000 2010 1319.9158 53.65564 6600
14000 2010 1195.3567 44.039046 6600
15000 2010 978.10764 39.976633 6600
16000 2412 1050.2028 45.306777 6600
17000 2412 1042.2556 39.814723 6600
18000 2412 894.58742 40.161025 6600
19000 2814 1009.3277 35.382235 6600
20000 2814 959.77476 43.212143 6600
21000 2814 757.47849 39.534175 6600
22000 2814 516.06689 40.398841 6600
23000 3000 425.8695 34.108574 6600
24000 3000 364.2896 21.08092 6600
25000 3000 233.88996 22.425122 6600
Loop time of 5.35857 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 2.58517 (48.2436)
Neigh time (%) = 0.38742 (7.22992)
Comm time (%) = 0.998725 (18.6379)
Outpt time (%) = 0.0733539 (1.36891)
Other time (%) = 1.3139 (24.5197)
Nlocal: 750 ave 756 max 739 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 393.25 ave 396 max 391 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 3579.5 ave 3599 max 3555 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 14318
Ave neighs/atom = 4.77267
Neighbor list builds = 1152
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Memory usage per processor = 10.193 Mbytes
Step Atoms KinEng 1 Volume
25000 3000 233.88996 22.425122 6600
26000 3000 94.802134 17.549122 6600
27000 3000 84.658562 11.506407 6600
28000 3000 149.0234 10.886705 6600
29000 3000 243.83101 12.132532 6600
30000 3000 381.15166 15.317159 6600
31000 3000 587.71932 21.367984 6600
32000 3000 826.0934 26.605551 6600
33000 3000 1140.3342 31.96551 6600
34000 3000 1505.7889 37.710536 6600
35000 3000 1960.1845 45.237554 6600
36000 3000 2472.9089 53.069981 6600
37000 3000 3112.7739 62.581623 6600
38000 3000 3734.7804 67.445495 6600
39000 3000 4500.8872 84.18578 6600
40000 3000 5355.3316 93.151633 6600
41000 3000 6255.1324 108.97752 6600
42000 3000 7324.1987 117.58036 6600
43000 3000 8367.5898 121.51706 6600
44000 3000 9496.1313 142.43277 6600
45000 3000 10606.37 154.24175 6600
46000 3000 11882.466 176.47919 6600
47000 3000 13234.56 183.71094 6600
48000 3000 14627.514 184.71949 6600
49000 3000 16011.412 206.20932 6600
50000 3000 17388.366 220.15287 6600
Loop time of 10.2705 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 5.70912 (55.5874)
Neigh time (%) = 0.565246 (5.50358)
Comm time (%) = 1.71767 (16.7243)
Outpt time (%) = 0.119911 (1.16752)
Other time (%) = 2.15857 (21.0172)
Nlocal: 750 ave 763 max 736 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost: 398.5 ave 403 max 392 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 3670 ave 3803 max 3551 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 14680
Ave neighs/atom = 4.89333
Neighbor list builds = 784
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# Pour 2d granular particles into container
dimension 2
atom_style granular
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 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 = 9.65629 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 111.88801 5000
10000 896 1655.1664 91.582952 5000
11000 896 1550.2423 70.438544 5000
12000 896 1488.1978 65.021653 5000
13000 1000 1482.2858 69.55715 5000
14000 1000 1355.7496 55.162745 5000
15000 1000 1137.9735 56.730082 5000
16000 1000 778.31206 50.833407 5000
17000 1000 460.23433 41.153574 5000
18000 1000 332.84841 29.77631 5000
19000 1000 145.02651 27.327555 5000
20000 1000 41.913445 19.800906 5000
21000 1000 20.443051 12.249147 5000
22000 1000 15.845191 9.3147926 5000
23000 1000 13.747307 6.6221816 5000
24000 1000 12.729284 4.9740484 5000
25000 1000 9.7364787 3.6669868 5000
Loop time of 5.29054 on 1 procs for 25000 steps with 1000 atoms
Pair time (%) = 2.4216 (45.7723)
Neigh time (%) = 0.442273 (8.35969)
Comm time (%) = 0.0201485 (0.38084)
Outpt time (%) = 0.124567 (2.35452)
Other time (%) = 2.28195 (43.1327)
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: 2371 ave 2371 max 2371 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2371
Ave neighs/atom = 2.371
Neighbor list builds = 2038
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# Pour 2d granular particles into container
dimension 2
atom_style granular
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)
2 by 2 by 1 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 = 9.62945 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 111.88801 5000
10000 896 1655.1664 91.582951 5000
11000 896 1550.2472 70.43916 5000
12000 896 1486.6001 65.153062 5000
13000 1000 1476.4232 71.426666 5000
14000 1000 1349.7768 53.749226 5000
15000 1000 1107.954 60.40274 5000
16000 1000 774.48863 54.712077 5000
17000 1000 441.06089 41.934396 5000
18000 1000 325.90138 28.773792 5000
19000 1000 150.83424 30.229981 5000
20000 1000 34.992857 16.39147 5000
21000 1000 22.700146 10.795777 5000
22000 1000 17.092041 8.5901648 5000
23000 1000 12.187351 6.5022377 5000
24000 1000 9.5515285 4.4264435 5000
25000 1000 8.5321058 4.1425938 5000
Loop time of 2.89865 on 4 procs for 25000 steps with 1000 atoms
Pair time (%) = 0.607728 (20.9659)
Neigh time (%) = 0.112781 (3.89081)
Comm time (%) = 0.193524 (6.67636)
Outpt time (%) = 0.103656 (3.57601)
Other time (%) = 1.88096 (64.8909)
Nlocal: 250 ave 503 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5.25 ave 11 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 598.5 ave 1221 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 2394
Ave neighs/atom = 2.394
Neighbor list builds = 2033
Dangerous builds = 0

732
examples/prd/log.prd.0.28Mar11.linux.4 Normal file
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LAMMPS (27 Mar 2011)
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
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 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 1000
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
110 846.80459 -2134.8152 0 -2078.9916 11904.208
120 1130.5577 -2151.6282 0 -2077.0988 9631.0553
130 1011.5223 -2141.5579 0 -2074.8757 9674.727
140 828.13015 -2127.6781 0 -2073.0856 10663.754
150 1213.6842 -2151.0205 0 -2071.0112 9358.162
160 1118.1701 -2142.223 0 -2068.5102 9705.042
170 815.94964 -2120.3781 0 -2066.5885 11111.781
180 1149.9499 -2140.3762 0 -2064.5684 10362.874
190 1265.3227 -2145.3133 0 -2061.8998 10208.885
200 967.96035 -2123.4032 0 -2059.5927 11429.676
210 1154.8198 -2133.5775 0 -2057.4487 10697.231
220 1309.6664 -2141.0968 0 -2054.7601 10123.484
230 1123.114 -2126.2814 0 -2052.2427 11010.813
240 1262.1761 -2133.0492 0 -2049.8432 10358.728
250 1387.1979 -2138.5224 0 -2047.0746 9224.1203
260 1099.3995 -2117.0127 0 -2044.5373 9902.009
270 1119.6867 -2116.1281 0 -2042.3154 9925.7178
280 1412.0178 -2132.6875 0 -2039.6036 8270.5884
290 1321.0773 -2123.8202 0 -2036.7313 8809.0223
300 1216.0708 -2114.3828 0 -2034.2162 9035.0512
310 1359.9122 -2121.2409 0 -2031.5918 7895.5635
320 1322.8642 -2116.0313 0 -2028.8245 8661.9299
330 1272.4262 -2110.1033 0 -2026.2215 10341.489
340 1451.8803 -2119.1983 0 -2023.4865 10343.627
350 1488.8525 -2118.6967 0 -2020.5476 10786.017
360 1330.5957 -2105.5746 0 -2017.8582 11501.105
370 1452.1996 -2110.9637 0 -2015.2308 11534.951
380 1598.8893 -2117.7127 0 -2012.3096 12209.282
390 1593.9074 -2114.5133 0 -2009.4386 13050.071
400 1580.9099 -2110.9274 0 -2006.7096 12007.149
410 1499.3026 -2102.9454 0 -2004.1074 10088.553
420 1368.9435 -2091.8877 0 -2001.6433 8465.3083
430 1297.2041 -2084.7532 0 -1999.2381 7269.5758
440 1450.1063 -2092.2353 0 -1996.6405 7033.8027
450 1534.8081 -2094.9394 0 -1993.7608 9081.5997
460 1556.639 -2093.5424 0 -1990.9246 12400.015
470 1803.1464 -2106.8774 0 -1988.0092 14192.515
480 1865.4976 -2108.05 0 -1985.0714 16740.251
490 1809.642 -2101.8102 0 -1982.5137 17670.617
500 1875.0318 -2103.7815 0 -1980.1744 15726.048
510 1835.5401 -2099.0223 0 -1978.0186 13590.87
520 1592.2743 -2081.0889 0 -1976.1219 12889.185
530 1621.098 -2081.1646 0 -1974.2975 12097.358
540 1787.4042 -2090.0335 0 -1972.203 11006.55
550 1629.769 -2077.5584 0 -1970.1196 11828.612
560 1633.9967 -2075.8478 0 -1968.1303 13013.747
570 1867.8884 -2089.0683 0 -1965.9321 12589.17
580 1897.3799 -2088.7925 0 -1963.7122 12142.767
590 1675.1213 -2072.2289 0 -1961.8004 12668.905
600 1852.5707 -2082.1073 0 -1959.9809 11872.082
610 1895.1634 -2083.0113 0 -1958.0771 12732.408
620 1759.7637 -2072.4168 0 -1956.4085 14720.014
630 1867.9005 -2077.9673 0 -1954.8303 15446.507
640 1882.4501 -2077.3643 0 -1953.2682 16189.673
650 1830.0215 -2072.5142 0 -1951.8743 15952.621
660 1989.6605 -2081.7336 0 -1950.5699 14441.731
670 2019.3348 -2082.5674 0 -1949.4475 13093.568
680 1806.7881 -2067.7448 0 -1948.6365 13695.415
690 1860.9944 -2070.6335 0 -1947.9518 13711.769
700 2035.4273 -2081.5085 0 -1947.3277 13969.607
710 1924.1115 -2073.7877 0 -1946.9451 14669.272
720 1925.0897 -2073.7075 0 -1946.8005 14665.913
730 1979.7127 -2077.3504 0 -1946.8425 14625.754
740 1932.6041 -2074.5197 0 -1947.1173 15051.1
750 1873.6645 -2071.0745 0 -1947.5575 14804.579
760 1916.3833 -2074.4703 0 -1948.1372 13868.322
770 1893.2199 -2073.6709 0 -1948.8647 14320.209
780 1868.0258 -2072.8444 0 -1949.6991 13913.255
790 1903.3142 -2076.1305 0 -1950.6589 13542.781
800 1852.3079 -2073.8193 0 -1951.7102 13663.021
810 1874.015 -2076.3795 0 -1952.8394 12583.329
820 1897.7242 -2079.181 0 -1954.0779 12629.436
830 1810.9511 -2074.7734 0 -1955.3907 13791.194
840 1751.9411 -2072.1105 0 -1956.6178 14705.479
850 1904.2872 -2083.4009 0 -1957.8652 14745.454
860 1916.5803 -2085.6068 0 -1959.2607 14829.039
870 1838.661 -2081.9371 0 -1960.7276 14932.396
880 1847.5879 -2084.017 0 -1962.219 14581.23
890 1850.4293 -2085.7191 0 -1963.7338 13109.312
900 1822.6233 -2085.4213 0 -1965.2691 13769.397
910 1786.0307 -2084.4806 0 -1966.7407 13450.462
920 1823.0469 -2088.3777 0 -1968.1976 12242.2
930 1731.0515 -2083.7104 0 -1969.5949 11686.755
940 1635.923 -2078.6209 0 -1970.7765 11861.596
950 1731.8445 -2085.9611 0 -1971.7933 11269.332
960 1735.3582 -2087.1207 0 -1972.7212 11587.883
970 1672.4435 -2083.7706 0 -1973.5187 12217.898
980 1703.4917 -2086.4744 0 -1974.1757 12431.952
990 1733.7211 -2089.007 0 -1974.7155 12829.553
1000 1764.9513 -2091.5262 0 -1975.1759 13614.2
Loop time of 3.87373 on 1 procs for 1000 steps with 511 atoms
Pair time (%) = 3.78581 (97.7302)
Neigh time (%) = 0.043046 (1.11123)
Comm time (%) = 0.0138795 (0.358299)
Outpt time (%) = 0.00143099 (0.0369408)
Other time (%) = 0.0295713 (0.76338)
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: 13440 ave 13440 max 13440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13440
Ave neighs/atom = 26.3014
Neighbor list builds = 44
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
Memory usage per processor = 3.73877 Mbytes
Step Temp PotEng pe Press press
1000 1764.9513 -2091.5262 -2091.5262 13614.2 -13614.2
1010 1764.9513 -2212.5976 -2212.5976 8682.8748 -8682.8748
1018 1764.9513 -2213.2997 -2213.2997 8735.7723 -8735.7723
Loop time of 0.0829201 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1000 1764.9513 -2091.5262 -2091.5262 13614.2 -13614.2
1010 1757.2735 -2089.1317 -2089.1317 13651.785 -13651.785
1020 1753.3209 -2086.4297 -2086.4297 14480.022 -14480.022
1030 1823.2413 -2088.3273 -2088.3273 14763.358 -14763.358
1040 1747.4815 -2085.2135 -2085.2135 14107.148 -14107.148
1050 1865.3945 -2089.8927 -2089.8927 13443.954 -13443.954
1060 1749.5134 -2086.9237 -2086.9237 12463.908 -12463.908
1070 1818.3433 -2088.489 -2088.489 11702.598 -11702.598
1080 1774.4835 -2087.1583 -2087.1583 11968.636 -11968.636
1090 1791.8684 -2086.9717 -2086.9717 12476.027 -12476.027
1100 1776.7994 -2085.7785 -2085.7785 12557.411 -12557.411
Loop time of 0.402554 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1000 1776.7994 -2085.7785 -2085.7785 12557.411 -12557.411
1010 1781.5983 -2086.4116 -2086.4116 12411.379 -12411.379
1020 1766.8628 -2085.7302 -2085.7302 12437.454 -12437.454
1030 1724.3526 -2083.1516 -2083.1516 12967.409 -12967.409
1040 1813.5458 -2089.2031 -2089.2031 12731.996 -12731.996
1050 1823.2025 -2090.0138 -2090.0138 13073.37 -13073.37
1060 1744.3078 -2084.9931 -2084.9931 13907.188 -13907.188
1070 1762.0451 -2086.2933 -2086.2933 13637.485 -13637.485
1080 1812.7166 -2089.7323 -2089.7323 12912.923 -12912.923
1090 1759.0885 -2086.2747 -2086.2747 12825.799 -12825.799
1100 1747.6057 -2085.5621 -2085.5621 12412.448 -12412.448
Loop time of 0.402513 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1100 1747.6057 -2085.5621 -2085.5621 12412.448 -12412.448
1117 1747.6057 -2213.2559 -2213.2559 8609.8758 -8609.8758
Loop time of 0.0778799 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1100 1747.6057 -2085.5621 -2085.5621 12412.448 -12412.448
1110 1758.5768 -2086.2635 -2086.2635 11888.153 -11888.153
1120 1734.4951 -2084.5929 -2084.5929 11320.95 -11320.95
1130 1711.6046 -2082.9218 -2082.9218 10834.46 -10834.46
1140 1700.5918 -2081.9216 -2081.9216 10862.964 -10862.964
1150 1728.5246 -2083.3718 -2083.3718 11768.766 -11768.766
1160 1748.6602 -2084.2015 -2084.2015 12214.411 -12214.411
1170 1780.4912 -2085.7329 -2085.7329 13228.339 -13228.339
1180 1828.0881 -2088.2684 -2088.2684 14154.284 -14154.284
1190 1828.6577 -2087.7149 -2087.7149 14621.558 -14621.558
1200 1889.7698 -2091.2099 -2091.2099 14799.493 -14799.493
Loop time of 0.402273 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1200 1889.7698 -2091.2099 -2091.2099 14799.493 -14799.493
1217 1889.7698 -2213.2775 -2213.2775 9590.9432 -9590.9432
Loop time of 0.0774601 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1200 1889.7698 -2091.2099 -2091.2099 14799.493 -14799.493
1210 1817.0061 -2091.8637 -2091.8637 14115.007 -14115.007
1220 1769.2701 -2089.3809 -2089.3809 13154.1 -13154.1
1230 1791.8173 -2088.3806 -2088.3806 12662.593 -12662.593
1240 1775.1839 -2086.2759 -2086.2759 12186.686 -12186.686
1250 1876.826 -2090.8664 -2090.8664 12548.202 -12548.202
1260 1731.6933 -2085.9256 -2085.9256 12359.402 -12359.402
1270 1774.9438 -2083.8086 -2083.8086 12563.909 -12563.909
1280 1848.0675 -2086.5149 -2086.5149 12558.975 -12558.975
1290 1818.1154 -2087.2768 -2087.2768 11723.226 -11723.226
1300 1747.08 -2083.3509 -2083.3509 11535.663 -11535.663
Loop time of 0.403034 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1200 1747.08 -2083.3509 -2083.3509 11535.663 -11535.663
1210 1752.9691 -2083.2609 -2083.2609 11834.866 -11834.866
1220 1823.3212 -2087.3629 -2087.3629 12499.403 -12499.403
1230 1774.9776 -2083.6328 -2083.6328 12533.22 -12533.22
1240 1725.7016 -2079.8262 -2079.8262 12633.851 -12633.851
1250 1802.8471 -2084.2886 -2084.2886 11908.609 -11908.609
1260 1765.2569 -2081.1366 -2081.1366 11995.465 -11995.465
1270 1772.7085 -2080.9417 -2080.9417 13011.132 -13011.132
1280 1879.131 -2087.2376 -2087.2376 13701.265 -13701.265
1290 1829.1775 -2083.2706 -2083.2706 13627.162 -13627.162
1300 1827.4168 -2082.5603 -2082.5603 13177.852 -13177.852
Loop time of 0.404705 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1300 1827.4168 -2082.5603 -2082.5603 13177.852 -13177.852
1319 1827.4168 -2213.3119 -2213.3119 9167.0378 -9167.0378
Loop time of 0.0734391 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1300 1827.4168 -2087.163 -2087.163 13112.67 -13112.67
1310 1796.3845 -2084.5418 -2084.5418 12877.075 -12877.075
1320 1804.7815 -2084.5307 -2084.5307 12329.177 -12329.177
1330 1760.2395 -2081.0245 -2081.0245 11376.822 -11376.822
1340 1707.4542 -2076.9345 -2076.9345 9898.7628 -9898.7628
1350 1788.1812 -2081.5651 -2081.5651 9675.5562 -9675.5562
1360 1761.7393 -2079.0647 -2079.0647 9312.9566 -9312.9566
1370 1669.2576 -2072.1836 -2072.1836 11208.069 -11208.069
1380 1803.1435 -2080.1133 -2080.1133 12095.508 -12095.508
1390 1915.98 -2086.5826 -2086.5826 13264.932 -13264.932
1400 1823.7614 -2079.6473 -2079.6473 14329.499 -14329.499
Loop time of 0.4068 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1400 1823.7614 -2079.6473 -2079.6473 14329.499 -14329.499
1418 1823.7614 -2213.3012 -2213.3012 9138.9829 -9138.9829
Loop time of 0.0820811 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1400 1823.7614 -2079.6473 -2079.6473 14329.499 -14329.499
1410 1836.7633 -2083.9051 -2083.9051 14250.169 -14250.169
1420 1785.8049 -2082.2333 -2082.2333 14417.759 -14417.759
1430 1877.1603 -2086.5842 -2086.5842 14013.962 -14013.962
1440 1793.9809 -2085.4935 -2085.4935 12849.985 -12849.985
1450 1794.6106 -2084.4385 -2084.4385 13285.03 -13285.03
1460 1808.7748 -2084.319 -2084.319 13418.461 -13418.461
1470 1862.4196 -2087.7471 -2087.7471 13825.267 -13825.267
1480 1724.2503 -2082.0886 -2082.0886 13650.767 -13650.767
1490 1818.9616 -2082.618 -2082.618 14249.096 -14249.096
1500 1877.1401 -2086.9965 -2086.9965 13415.256 -13415.256
Loop time of 0.405397 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1400 1877.1401 -2086.9965 -2086.9965 13415.256 -13415.256
1410 1853.9818 -2084.822 -2084.822 13372.402 -13372.402
1420 1743.8168 -2076.9932 -2076.9932 13208 -13208
1430 1770.557 -2078.1674 -2078.1674 12799.186 -12799.186
1440 1857.6278 -2083.2642 -2083.2642 12283.874 -12283.874
1450 1823.6185 -2080.4181 -2080.4181 12111.743 -12111.743
1460 1769.7941 -2076.305 -2076.305 12296.853 -12296.853
1470 1869.2545 -2082.3071 -2082.3071 12401.939 -12401.939
1480 1771.1947 -2075.2969 -2075.2969 12829.718 -12829.718
1490 1817.4941 -2077.8337 -2077.8337 13290.882 -13290.882
1500 1943.883 -2085.652 -2085.652 13794.905 -13794.905
Loop time of 0.404942 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1500 1943.883 -2085.652 -2085.652 13794.905 -13794.905
1520 1943.883 -2213.3255 -2213.3255 9966.5151 -9966.5151
Loop time of 0.0861681 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1500 1943.883 -2085.652 -2085.652 13794.905 -13794.905
1510 1902.6049 -2082.5706 -2082.5706 13914.49 -13914.49
1520 1810.6671 -2076.2814 -2076.2814 13894.184 -13894.184
1530 1921.2021 -2083.42 -2083.42 13415.642 -13415.642
1540 1848.6946 -2078.6011 -2078.6011 12924.458 -12924.458
1550 1722.4625 -2070.2819 -2070.2819 13294.077 -13294.077
1560 1873.7756 -2080.2487 -2080.2487 12297.132 -12297.132
1570 1856.4219 -2079.1242 -2079.1242 12113.992 -12113.992
1580 1834.7147 -2077.8144 -2077.8144 12689.368 -12689.368
1590 1804.9482 -2075.9995 -2075.9995 13294.751 -13294.751
1600 1856.5909 -2079.5913 -2079.5913 13103.6 -13103.6
Loop time of 0.405926 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1600 1856.5909 -2079.5913 -2079.5913 13103.6 -13103.6
1619 1856.5909 -2213.2905 -2213.2905 9362.9644 -9362.9644
Loop time of 0.092042 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1600 1856.5909 -2079.5913 -2079.5913 13103.6 -13103.6
1610 1872.5062 -2080.8936 -2080.8936 12857.235 -12857.235
1620 1894.1291 -2082.6822 -2082.6822 14225.45 -14225.45
1630 1905.1025 -2083.9149 -2083.9149 15128.568 -15128.568
1640 1843.7493 -2080.4943 -2080.4943 14687.965 -14687.965
1650 1847.0973 -2081.4043 -2081.4043 14022.852 -14022.852
1660 1911.7961 -2086.4601 -2086.4601 13335.97 -13335.97
1670 1816.5545 -2081.0829 -2081.0829 13288.229 -13288.229
1680 1691.8634 -2073.6944 -2073.6944 13739.446 -13739.446
1690 1820.9023 -2082.9567 -2082.9567 13286.961 -13286.961
1700 1830.8516 -2084.3979 -2084.3979 12591.506 -12591.506
Loop time of 0.407682 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1700 1830.8516 -2084.3979 -2084.3979 12591.506 -12591.506
1718 1830.8516 -2213.2889 -2213.2889 9188.2547 -9188.2547
Loop time of 0.080869 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1700 1830.8516 -2087.6647 -2087.6647 12647.034 -12647.034
1710 1781.7291 -2085.2355 -2085.2355 13342.158 -13342.158
1720 1753.6485 -2084.15 -2084.15 12521.031 -12521.031
1730 1789.4412 -2087.2263 -2087.2263 12016.078 -12016.078
1740 1777.2163 -2087.1133 -2087.1133 11759.495 -11759.495
1750 1728.4234 -2084.5329 -2084.5329 12153.344 -12153.344
1760 1759.0263 -2087.1012 -2087.1012 12283.283 -12283.283
1770 1794.1876 -2089.9477 -2089.9477 12397.928 -12397.928
1780 1684.6744 -2083.1766 -2083.1766 13026.967 -13026.967
1790 1787.6124 -2090.3399 -2090.3399 12227.435 -12227.435
1800 1785.4311 -2090.5309 -2090.5309 12127.971 -12127.971
Loop time of 0.403539 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1800 1785.4311 -2090.5309 -2090.5309 12127.971 -12127.971
1818 1785.4311 -2213.2979 -2213.2979 8874.1326 -8874.1326
Loop time of 0.0777798 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1800 1785.4311 -2086.3241 -2086.3241 14237.597 -14237.597
1810 1918.507 -2095.523 -2095.523 13666.937 -13666.937
1820 1724.6412 -2083.2182 -2083.2182 14011.6 -14011.6
1830 1798.6383 -2088.5457 -2088.5457 13059.581 -13059.581
1840 1818.6155 -2090.3328 -2090.3328 11731.7 -11731.7
1850 1527.4515 -2071.4928 -2071.4928 11697.062 -11697.062
1860 1647.2859 -2079.5226 -2079.5226 11334.81 -11334.81
1870 1823.0832 -2091.0629 -2091.0629 11366.978 -11366.978
1880 1667.7445 -2080.7094 -2080.7094 13478.364 -13478.364
1890 1736.1891 -2085.0097 -2085.0097 14321.25 -14321.25
1900 2002.185 -2102.2695 -2102.2695 13972.239 -13972.239
Loop time of 0.404675 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
1900 2002.185 -2102.2695 -2102.2695 13972.239 -13972.239
1915 2002.185 -2213.2292 -2213.2292 10360.023 -10360.023
Loop time of 0.0607271 on 1 procs for 15 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1900 2002.185 -2102.2695 -2102.2695 13972.239 -13972.239
1910 1788.8275 -2084.0536 -2084.0536 12265.481 -12265.481
1920 1787.8258 -2083.0286 -2083.0286 12116.717 -12116.717
1930 1737.9359 -2078.6988 -2078.6988 11353.359 -11353.359
1940 1784.2854 -2077.3907 -2077.3907 11984.047 -11984.047
1950 1762.2976 -2074.6032 -2074.6032 11533.666 -11533.666
1960 1843.1628 -2077.1232 -2077.1232 11898.025 -11898.025
1970 1876.6206 -2081.8932 -2081.8932 11427.224 -11427.224
1980 1733.4297 -2077.2501 -2077.2501 11450.967 -11450.967
1990 1833.6341 -2079.1971 -2079.1971 11725.605 -11725.605
2000 1709.1932 -2072.9342 -2072.9342 10821.172 -10821.172
Loop time of 0.408754 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
1900 1709.1932 -2072.9342 -2072.9342 10821.172 -10821.172
1910 1806.446 -2078.9958 -2078.9958 10817.607 -10817.607
1920 1903.1662 -2084.9998 -2084.9998 11187.52 -11187.52
1930 1815.466 -2078.929 -2078.929 12306.709 -12306.709
1940 1846.9897 -2080.7847 -2080.7847 12435.927 -12435.927
1950 1849.6235 -2080.7759 -2080.7759 13228.482 -13228.482
1960 1835.9275 -2079.747 -2079.747 14091.162 -14091.162
1970 1928.3128 -2085.7926 -2085.7926 13599.09 -13599.09
1980 1894.2673 -2083.6543 -2083.6543 12405.33 -12405.33
1990 1742.6618 -2073.8472 -2073.8472 12518.714 -12518.714
2000 1849.9788 -2081.1175 -2081.1175 12525.185 -12525.185
Loop time of 0.409867 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
2000 1849.9788 -2081.1175 -2081.1175 12525.185 -12525.185
2018 1849.9788 -2213.3121 -2213.3121 9316.5096 -9316.5096
Loop time of 0.081013 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2000 1849.9788 -2081.1175 -2081.1175 12525.185 -12525.185
2010 1879.9916 -2083.3422 -2083.3422 12343.403 -12343.403
2020 1763.0383 -2075.9488 -2075.9488 12909.373 -12909.373
2030 1812.0591 -2079.4896 -2079.4896 12980.784 -12980.784
2040 1915.5724 -2086.684 -2086.684 12792.194 -12792.194
2050 1813.8598 -2080.4575 -2080.4575 13629.345 -13629.345
2060 1786.939 -2079.1974 -2079.1974 13775.147 -13775.147
2070 1840.8911 -2083.2839 -2083.2839 13067.981 -13067.981
2080 1820.7692 -2082.5412 -2082.5412 11627.112 -11627.112
2090 1768.3414 -2079.6773 -2079.6773 11394.217 -11394.217
2100 1809.2469 -2082.9637 -2082.9637 11569.174 -11569.174
Loop time of 0.410635 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
2100 1809.2469 -2082.9637 -2082.9637 11569.174 -11569.174
2118 1809.2469 -2213.267 -2213.267 9042.6736 -9042.6736
Loop time of 0.0747659 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2100 1809.2469 -2082.9637 -2082.9637 11569.174 -11569.174
2110 1778.8009 -2081.5436 -2081.5436 12115.814 -12115.814
2120 1753.2121 -2080.4046 -2080.4046 11687.8 -11687.8
2130 1816.5924 -2085.1105 -2085.1105 12184.268 -12184.268
2140 1803.7233 -2084.8061 -2084.8061 12645.687 -12645.687
2150 1739.7511 -2081.1103 -2081.1103 12897.726 -12897.726
2160 1799.2515 -2085.5158 -2085.5158 12342.394 -12342.394
2170 1809.5854 -2086.6867 -2086.6867 12079.69 -12079.69
2180 1732.9309 -2082.1018 -2082.1018 12739.154 -12739.154
2190 1784.3142 -2085.9061 -2085.9061 12725.543 -12725.543
2200 1851.3105 -2090.747 -2090.747 13131.566 -13131.566
Loop time of 0.406492 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
2200 1851.3105 -2090.747 -2090.747 13131.566 -13131.566
2216 1851.3105 -2213.2546 -2213.2546 9356.824 -9356.824
Loop time of 0.065825 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2200 1851.3105 -2090.747 -2090.747 13131.566 -13131.566
2210 1728.4848 -2086.4483 -2086.4483 12763.127 -12763.127
2220 1869.2268 -2091.4617 -2091.4617 12345.509 -12345.509
2230 1748.5328 -2088.5167 -2088.5167 12331.154 -12331.154
2240 1828.4798 -2090.877 -2090.877 11944.504 -11944.504
2250 1671.249 -2082.8299 -2082.8299 11981.936 -11981.936
2260 1803.8541 -2083.5098 -2083.5098 11825.621 -11825.621
2270 1783.8565 -2082.87 -2082.87 12321.579 -12321.579
2280 1802.6142 -2083.478 -2083.478 12892.956 -12892.956
2290 1873.6274 -2088.8319 -2088.8319 12640.162 -12640.162
2300 1748.1477 -2085.9312 -2085.9312 12182.08 -12182.08
Loop time of 0.406777 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2200 1748.1477 -2085.9312 -2085.9312 12182.08 -12182.08
2210 1737.1223 -2085.6717 -2085.6717 12674.818 -12674.818
2220 1780.721 -2088.9818 -2088.9818 12059.005 -12059.005
2230 1683.4804 -2082.9481 -2082.9481 11521.791 -11521.791
2240 1683.4871 -2083.2141 -2083.2141 11645.317 -11645.317
2250 1766.0609 -2088.8134 -2088.8134 11873.583 -11873.583
2260 1760.5802 -2088.5494 -2088.5494 12045.37 -12045.37
2270 1750.6376 -2087.9506 -2087.9506 12278.48 -12278.48
2280 1764.7771 -2088.883 -2088.883 12338.109 -12338.109
2290 1775.2688 -2089.5286 -2089.5286 12711.119 -12711.119
2300 1744.4431 -2087.3965 -2087.3965 12137.524 -12137.524
Loop time of 0.408874 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
2300 1744.4431 -2087.3965 -2087.3965 12137.524 -12137.524
2318 1744.4431 -2213.2926 -2213.2926 8591.6382 -8591.6382
Loop time of 0.082566 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2300 1744.4431 -2088.3257 -2088.3257 12585.86 -12585.86
2310 1671.1466 -2083.2878 -2083.2878 13129.826 -13129.826
2320 1823.166 -2092.9509 -2092.9509 12802.838 -12802.838
2330 1864.4223 -2095.2301 -2095.2301 13029.361 -13029.361
2340 1735.1868 -2086.2632 -2086.2632 12646.158 -12646.158
2350 1761.5574 -2087.4854 -2087.4854 11133.801 -11133.801
2360 1635.2722 -2078.4643 -2078.4643 11199.557 -11199.557
2370 1602.7307 -2075.3996 -2075.3996 11325.477 -11325.477
2380 1792.2259 -2086.6129 -2086.6129 11066.178 -11066.178
2390 1779.6059 -2084.255 -2084.255 12155.297 -12155.297
2400 1807.024 -2084.5506 -2084.5506 13930.07 -13930.07
Loop time of 0.405474 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
2400 1807.024 -2084.5506 -2084.5506 13930.07 -13930.07
2416 1807.024 -2213.2643 -2213.2643 9025.9846 -9025.9846
Loop time of 0.0604129 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2400 1807.024 -2084.5506 -2084.5506 13930.07 -13930.07
2410 1789.2623 -2081.0159 -2081.0159 13216.137 -13216.137
2420 1868.1832 -2084.1484 -2084.1484 13674.14 -13674.14
2430 1815.8238 -2084.0504 -2084.0504 13193.686 -13193.686
2440 1761.6489 -2080.5612 -2080.5612 12620.462 -12620.462
2450 1942.764 -2089.1534 -2089.1534 12560.444 -12560.444
2460 1761.4968 -2085.9894 -2085.9894 12044.253 -12044.253
2470 1832.5793 -2087.6087 -2087.6087 13042.599 -13042.599
2480 1719.2467 -2081.8214 -2081.8214 12359.123 -12359.123
2490 1854.8455 -2084.9927 -2084.9927 13001.039 -13001.039
2500 1754.8221 -2081.6196 -2081.6196 13354.565 -13354.565
Loop time of 0.39944 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2400 1754.8221 -2081.6196 -2081.6196 13354.565 -13354.565
2410 1847.5489 -2087.3573 -2087.3573 13279.43 -13279.43
2420 1857.0687 -2087.6534 -2087.6534 13007.397 -13007.397
2430 1829.3543 -2085.5876 -2085.5876 13129.892 -13129.892
2440 1857.1726 -2087.2604 -2087.2604 13005.421 -13005.421
2450 1732.2638 -2078.9022 -2078.9022 12655.025 -12655.025
2460 1672.8241 -2074.8001 -2074.8001 12792.342 -12792.342
2470 1813.545 -2083.7757 -2083.7757 12397.761 -12397.761
2480 1843.7288 -2085.4348 -2085.4348 12918.842 -12918.842
2490 1753.2569 -2079.1765 -2079.1765 13719.969 -13719.969
2500 1814.6389 -2082.9091 -2082.9091 13082.817 -13082.817
Loop time of 0.403145 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
2500 1814.6389 -2082.9091 -2082.9091 13082.817 -13082.817
2517 1814.6389 -2213.2724 -2213.2724 9077.1094 -9077.1094
Loop time of 0.0749681 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2500 1814.6389 -2085.5282 -2085.5282 13473.748 -13473.748
2510 1830.6878 -2086.254 -2086.254 13514.766 -13514.766
2520 1820.4168 -2085.2604 -2085.2604 13774.977 -13774.977
2530 1819.7357 -2084.9269 -2084.9269 13791.306 -13791.306
2540 1822.2331 -2084.8254 -2084.8254 13511.1 -13511.1
2550 1737.9592 -2078.9962 -2078.9962 13035.17 -13035.17
2560 1747.9559 -2079.3214 -2079.3214 12366.667 -12366.667
2570 1814.8736 -2083.3028 -2083.3028 12567.454 -12567.454
2580 1812.6737 -2082.6848 -2082.6848 13509.323 -13509.323
2590 1824.1355 -2082.9605 -2082.9605 13579.715 -13579.715
2600 1808.8179 -2081.4431 -2081.4431 13783.499 -13783.499
Loop time of 0.409016 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
2600 1808.8179 -2081.4431 -2081.4431 13783.499 -13783.499
2617 1808.8179 -2213.2777 -2213.2777 9035.0068 -9035.0068
Loop time of 0.0756919 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2600 1808.8179 -2081.4431 -2081.4431 13783.499 -13783.499
2610 1778.9399 -2080.2036 -2080.2036 13525.725 -13525.725
2620 1769.8298 -2077.5881 -2077.5881 12710.991 -12710.991
2630 1909.9948 -2084.1402 -2084.1402 13185.774 -13185.774
2640 1812.6099 -2084.2544 -2084.2544 12323.026 -12323.026
2650 1847.6152 -2086.6168 -2086.6168 12401.635 -12401.635
2660 1774.4533 -2084.097 -2084.097 12007.426 -12007.426
2670 1880.7444 -2088.4628 -2088.4628 12742.628 -12742.628
2680 1789.6064 -2086.7865 -2086.7865 12405.705 -12405.705
2690 1805.4657 -2086.0746 -2086.0746 13046.691 -13046.691
2700 1715.9361 -2079.3921 -2079.3921 13550.296 -13550.296
Loop time of 0.404266 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2600 1715.9361 -2079.3921 -2079.3921 13550.296 -13550.296
2610 1769.8826 -2081.7109 -2081.7109 13346.338 -13346.338
2620 1917.8144 -2090.1178 -2090.1178 13745.69 -13745.69
2630 1800.6371 -2081.1476 -2081.1476 15416.227 -15416.227
2640 1826.9321 -2081.8258 -2081.8258 14684.23 -14684.23
2650 1835.7532 -2081.4253 -2081.4253 13979.269 -13979.269
2660 1816.4976 -2079.3394 -2079.3394 14076.099 -14076.099
2670 1854.8835 -2081.1776 -2081.1776 15215.906 -15215.906
2680 1930.4826 -2085.6342 -2085.6342 15410.549 -15410.549
2690 1807.3276 -2077.1822 -2077.1822 15495.416 -15495.416
2700 1765.2476 -2074.1571 -2074.1571 14895.899 -14895.899
Loop time of 0.406336 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
2700 1765.2476 -2074.1571 -2074.1571 14895.899 -14895.899
2717 1765.2476 -2213.3086 -2213.3086 8736.1326 -8736.1326
Loop time of 0.0730708 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2700 1765.2476 -2074.1571 -2074.1571 14895.899 -14895.899
2710 1932.7218 -2084.997 -2084.997 13902.489 -13902.489
2720 1822.4199 -2077.6323 -2077.6323 14483.587 -14483.587
2730 1800.5942 -2076.1722 -2076.1722 14278.621 -14278.621
2740 1918.5585 -2083.9722 -2083.9722 13671.108 -13671.108
2750 1810.9326 -2076.9785 -2076.9785 14527.675 -14527.675
2760 1827.8625 -2078.2331 -2078.2331 14562.523 -14562.523
2770 1936.0711 -2085.565 -2085.565 14897.342 -14897.342
2780 1875.7442 -2081.9066 -2081.9066 15317.97 -15317.97
2790 1807.583 -2077.789 -2077.789 15199.853 -15199.853
2800 1918.0402 -2085.4868 -2085.4868 13912.669 -13912.669
Loop time of 0.404737 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
2800 1918.0402 -2085.4868 -2085.4868 13912.669 -13912.669
2816 1918.0402 -2213.2806 -2213.2806 9786.7754 -9786.7754
Loop time of 0.0667641 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2800 1918.0402 -2085.4868 -2085.4868 13912.669 -13912.669
2810 1884.6142 -2083.8092 -2083.8092 13921.428 -13921.428
2820 1715.3054 -2073.1756 -2073.1756 14773.37 -14773.37
2830 1798.7229 -2079.1189 -2079.1189 14194.791 -14194.791
2840 1861.2736 -2083.6681 -2083.6681 13581.117 -13581.117
2850 1788.1708 -2079.2967 -2079.2967 14366.864 -14366.864
2860 1802.9411 -2080.6891 -2080.6891 15197.867 -15197.867
2870 1897.2584 -2087.3478 -2087.3478 14694.389 -14694.389
2880 1837.217 -2083.9084 -2083.9084 15138.466 -15138.466
2890 1746.8234 -2078.4519 -2078.4519 16095.128 -16095.128
2900 1840.4892 -2085.0945 -2085.0945 15441.757 -15441.757
Loop time of 0.408428 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
2900 1840.4892 -2085.0945 -2085.0945 15441.757 -15441.757
2918 1840.4892 -2213.2962 -2213.2962 9251.7041 -9251.7041
Loop time of 0.074095 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
2900 1840.4892 -2085.0945 -2085.0945 15441.757 -15441.757
2910 1845.6426 -2085.9186 -2085.9186 14719.474 -14719.474
2920 1788.0277 -2082.6226 -2082.6226 15135.698 -15135.698
2930 1813.3681 -2084.7672 -2084.7672 15223.094 -15223.094
2940 1854.5573 -2087.976 -2087.976 14902.44 -14902.44
2950 1793.0896 -2084.4254 -2084.4254 15276.721 -15276.721
2960 1801.5081 -2085.4707 -2085.4707 14369.243 -14369.243
2970 1737.2525 -2081.6733 -2081.6733 13137.903 -13137.903
2980 1667.5915 -2077.4002 -2077.4002 13540.818 -13540.818
2990 1731.5672 -2081.7775 -2081.7775 14579.571 -14579.571
3000 1848.771 -2089.5988 -2089.5988 14254.75 -14254.75
Loop time of 0.40837 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.34912 Mbytes
Step Temp PotEng pe Press press
3000 1848.771 -2089.5988 -2089.5988 14254.75 -14254.75
3017 1848.771 -2213.2902 -2213.2902 9311.2757 -9311.2757
Loop time of 0.074677 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.66248 Mbytes
Step Temp PotEng pe Press press
3000 1848.771 -2080.3808 -2080.3808 14030.45 -14030.45
Loop time of 13.0574 on 1 procs for 17 steps with 511 atoms
PRD stats:
Dephase time (%) = 2.83022 (21.6753)
Dynamics time (%) = 8.12443 (62.221)
Quench time (%) = 1.5123 (11.5819)
Other time (%) = 0.297621 (2.27933)
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: 13428 ave 13428 max 13428 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13428
Ave neighs/atom = 26.2779
Neighbor list builds = 95
Dangerous builds = 0

732
examples/prd/log.prd.1.28Mar11.linux.4 Normal file
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LAMMPS (27 Mar 2011)
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
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 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 1000
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
110 846.80459 -2134.8152 0 -2078.9916 11904.208
120 1130.5577 -2151.6282 0 -2077.0988 9631.0553
130 1011.5223 -2141.5579 0 -2074.8757 9674.727
140 828.13015 -2127.6781 0 -2073.0856 10663.754
150 1213.6842 -2151.0205 0 -2071.0112 9358.162
160 1118.1701 -2142.223 0 -2068.5102 9705.042
170 815.94964 -2120.3781 0 -2066.5885 11111.781
180 1149.9499 -2140.3762 0 -2064.5684 10362.874
190 1265.3227 -2145.3133 0 -2061.8998 10208.885
200 967.96035 -2123.4032 0 -2059.5927 11429.676
210 1154.8198 -2133.5775 0 -2057.4487 10697.231
220 1309.6664 -2141.0968 0 -2054.7601 10123.484
230 1123.114 -2126.2814 0 -2052.2427 11010.813
240 1262.1761 -2133.0492 0 -2049.8432 10358.728
250 1387.1979 -2138.5224 0 -2047.0746 9224.1203
260 1099.3995 -2117.0127 0 -2044.5373 9902.009
270 1119.6867 -2116.1281 0 -2042.3154 9925.7178
280 1412.0178 -2132.6875 0 -2039.6036 8270.5884
290 1321.0773 -2123.8202 0 -2036.7313 8809.0223
300 1216.0708 -2114.3828 0 -2034.2162 9035.0512
310 1359.9122 -2121.2409 0 -2031.5918 7895.5635
320 1322.8642 -2116.0313 0 -2028.8245 8661.9299
330 1272.4262 -2110.1033 0 -2026.2215 10341.489
340 1451.8803 -2119.1983 0 -2023.4865 10343.627
350 1488.8525 -2118.6967 0 -2020.5476 10786.017
360 1330.5957 -2105.5746 0 -2017.8582 11501.105
370 1452.1996 -2110.9637 0 -2015.2308 11534.951
380 1598.8893 -2117.7127 0 -2012.3096 12209.282
390 1593.9074 -2114.5133 0 -2009.4386 13050.071
400 1580.9099 -2110.9274 0 -2006.7096 12007.149
410 1499.3026 -2102.9454 0 -2004.1074 10088.553
420 1368.9435 -2091.8877 0 -2001.6433 8465.3083
430 1297.2041 -2084.7532 0 -1999.2381 7269.5758
440 1450.1063 -2092.2353 0 -1996.6405 7033.8027
450 1534.8081 -2094.9394 0 -1993.7608 9081.5997
460 1556.639 -2093.5424 0 -1990.9246 12400.015
470 1803.1464 -2106.8774 0 -1988.0092 14192.515
480 1865.4976 -2108.05 0 -1985.0714 16740.251
490 1809.642 -2101.8102 0 -1982.5137 17670.617
500 1875.0318 -2103.7815 0 -1980.1744 15726.048
510 1835.5401 -2099.0223 0 -1978.0186 13590.87
520 1592.2743 -2081.0889 0 -1976.1219 12889.185
530 1621.098 -2081.1646 0 -1974.2975 12097.358
540 1787.4042 -2090.0335 0 -1972.203 11006.55
550 1629.769 -2077.5584 0 -1970.1196 11828.612
560 1633.9967 -2075.8478 0 -1968.1303 13013.747
570 1867.8884 -2089.0683 0 -1965.9321 12589.17
580 1897.3799 -2088.7925 0 -1963.7122 12142.767
590 1675.1213 -2072.2289 0 -1961.8004 12668.905
600 1852.5707 -2082.1073 0 -1959.9809 11872.082
610 1895.1634 -2083.0113 0 -1958.0771 12732.408
620 1759.7637 -2072.4168 0 -1956.4085 14720.014
630 1867.9005 -2077.9673 0 -1954.8303 15446.507
640 1882.4501 -2077.3643 0 -1953.2682 16189.673
650 1830.0215 -2072.5142 0 -1951.8743 15952.621
660 1989.6605 -2081.7336 0 -1950.5699 14441.731
670 2019.3348 -2082.5674 0 -1949.4475 13093.568
680 1806.7881 -2067.7448 0 -1948.6365 13695.415
690 1860.9944 -2070.6335 0 -1947.9518 13711.769
700 2035.4273 -2081.5085 0 -1947.3277 13969.607
710 1924.1115 -2073.7877 0 -1946.9451 14669.272
720 1925.0897 -2073.7075 0 -1946.8005 14665.913
730 1979.7127 -2077.3504 0 -1946.8425 14625.754
740 1932.6041 -2074.5197 0 -1947.1173 15051.1
750 1873.6645 -2071.0745 0 -1947.5575 14804.579
760 1916.3833 -2074.4703 0 -1948.1372 13868.322
770 1893.2199 -2073.6709 0 -1948.8647 14320.209
780 1868.0258 -2072.8444 0 -1949.6991 13913.255
790 1903.3142 -2076.1305 0 -1950.6589 13542.781
800 1852.3079 -2073.8193 0 -1951.7102 13663.021
810 1874.015 -2076.3795 0 -1952.8394 12583.329
820 1897.7242 -2079.181 0 -1954.0779 12629.436
830 1810.9511 -2074.7734 0 -1955.3907 13791.194
840 1751.9411 -2072.1105 0 -1956.6178 14705.479
850 1904.2872 -2083.4009 0 -1957.8652 14745.454
860 1916.5803 -2085.6068 0 -1959.2607 14829.039
870 1838.661 -2081.9371 0 -1960.7276 14932.396
880 1847.5879 -2084.017 0 -1962.219 14581.23
890 1850.4293 -2085.7191 0 -1963.7338 13109.312
900 1822.6233 -2085.4213 0 -1965.2691 13769.397
910 1786.0307 -2084.4806 0 -1966.7407 13450.462
920 1823.0469 -2088.3777 0 -1968.1976 12242.2
930 1731.0515 -2083.7104 0 -1969.5949 11686.755
940 1635.923 -2078.6209 0 -1970.7765 11861.596
950 1731.8445 -2085.9611 0 -1971.7933 11269.332
960 1735.3582 -2087.1207 0 -1972.7212 11587.883
970 1672.4435 -2083.7706 0 -1973.5187 12217.898
980 1703.4917 -2086.4744 0 -1974.1757 12431.952
990 1733.7211 -2089.007 0 -1974.7155 12829.553
1000 1764.9513 -2091.5262 0 -1975.1759 13614.2
Loop time of 3.87675 on 1 procs for 1000 steps with 511 atoms
Pair time (%) = 3.78905 (97.7376)
Neigh time (%) = 0.0428236 (1.10462)
Comm time (%) = 0.0136051 (0.350941)
Outpt time (%) = 0.00150704 (0.0388739)
Other time (%) = 0.0297732 (0.767994)
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: 13440 ave 13440 max 13440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13440
Ave neighs/atom = 26.3014
Neighbor list builds = 44
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
Memory usage per processor = 3.73877 Mbytes
Step Temp PotEng pe Press press
1000 1764.9513 -2091.5262 -2091.5262 13614.2 -13614.2
1010 1764.9513 -2212.5976 -2212.5976 8682.8748 -8682.8748
1018 1764.9513 -2213.2997 -2213.2997 8735.7723 -8735.7723
Loop time of 0.0829408 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1000 1764.9513 -2091.5262 -2091.5262 13614.2 -13614.2
1010 1768.0231 -2089.8576 -2089.8576 14069.687 -14069.687
1020 1840.9705 -2093.0158 -2093.0158 13640.395 -13640.395
1030 1755.752 -2090.5439 -2090.5439 13280.689 -13280.689
1040 1826.8029 -2092.7589 -2092.7589 13181.779 -13181.779
1050 1776.3468 -2091.6533 -2091.6533 13954.866 -13954.866
1060 1773.3034 -2090.3356 -2090.3356 13916.088 -13916.088
1070 1795.8634 -2090.4918 -2090.4918 13926.917 -13926.917
1080 1795.808 -2090.644 -2090.644 14030.734 -14030.734
1090 1805.9489 -2091.4575 -2091.4575 14139.145 -14139.145
1100 1776.3872 -2090.3308 -2090.3308 13931.217 -13931.217
Loop time of 0.399661 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1000 1776.3872 -2090.3308 -2090.3308 13931.217 -13931.217
1010 1712.3527 -2086.4783 -2086.4783 13676.101 -13676.101
1020 1773.2651 -2090.7926 -2090.7926 11769.858 -11769.858
1030 1745.811 -2089.2242 -2089.2242 11082.566 -11082.566
1040 1685.4357 -2085.405 -2085.405 11445.939 -11445.939
1050 1707.5011 -2086.8974 -2086.8974 11100.371 -11100.371
1060 1724.8482 -2087.9616 -2087.9616 11269.4 -11269.4
1070 1692.6868 -2085.6478 -2085.6478 12051.435 -12051.435
1080 1719.7035 -2087.1262 -2087.1262 11754.86 -11754.86
1090 1717.3779 -2086.5464 -2086.5464 10848.031 -10848.031
1100 1695.2395 -2084.5596 -2084.5596 10561.497 -10561.497
Loop time of 0.406004 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1100 1695.2395 -2084.5596 -2084.5596 10561.497 -10561.497
1118 1695.2395 -2213.2819 -2213.2819 8253.375 -8253.375
Loop time of 0.0788689 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1100 1695.2395 -2085.5621 -2085.5621 12052.794 -12052.794
1110 1759.7112 -2089.1757 -2089.1757 11420.522 -11420.522
1120 1719.3433 -2085.7874 -2085.7874 12104.819 -12104.819
1130 1656.7898 -2080.863 -2080.863 11757.729 -11757.729
1140 1747.6443 -2085.9116 -2085.9116 11751.355 -11751.355
1150 1726.5994 -2083.4603 -2083.4603 11696.227 -11696.227
1160 1722.7632 -2082.097 -2082.097 11467.602 -11467.602
1170 1859.5796 -2089.9139 -2089.9139 11963.175 -11963.175
1180 1821.2672 -2086.1996 -2086.1996 13940.393 -13940.393
1190 1724.5395 -2078.7249 -2078.7249 15197.593 -15197.593
1200 1876.9955 -2087.6513 -2087.6513 14394.071 -14394.071
Loop time of 0.406977 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1200 1876.9955 -2087.6513 -2087.6513 14394.071 -14394.071
1216 1876.9955 -2213.3001 -2213.3001 9506.9447 -9506.9447
Loop time of 0.0700822 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1200 1876.9955 -2087.6513 -2087.6513 14394.071 -14394.071
1210 1748.5027 -2086.5985 -2086.5985 13477.545 -13477.545
1220 1873.206 -2090.297 -2090.297 13690.876 -13690.876
1230 1799.2263 -2089.1831 -2089.1831 12948.344 -12948.344
1240 1755.6743 -2085.2322 -2085.2322 12896.7 -12896.7
1250 1799.916 -2084.1788 -2084.1788 12267.266 -12267.266
1260 1853.4935 -2086.658 -2086.658 13132.756 -13132.756
1270 1707.9154 -2079.6013 -2079.6013 12541.979 -12541.979
1280 1865.0991 -2082.8694 -2082.8694 12628.918 -12628.918
1290 1792.7221 -2081.4252 -2081.4252 11681.254 -11681.254
1300 1774.5114 -2078.7833 -2078.7833 12833.515 -12833.515
Loop time of 0.402396 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1200 1774.5114 -2078.7833 -2078.7833 12833.515 -12833.515
1210 1880.2753 -2084.7794 -2084.7794 12098.962 -12098.962
1220 1818.22 -2079.765 -2079.765 11730.115 -11730.115
1230 1776.9489 -2076.1976 -2076.1976 12691.405 -12691.405
1240 1917.7053 -2084.6275 -2084.6275 12965.205 -12965.205
1250 1902.4756 -2082.8622 -2082.8622 12981.253 -12981.253
1260 1773.9381 -2073.7791 -2073.7791 13163.414 -13163.414
1270 1831.2137 -2076.9757 -2076.9757 12749.983 -12749.983
1280 1909.2985 -2081.5636 -2081.5636 12187.88 -12187.88
1290 1783.9267 -2072.8303 -2072.8303 12773.94 -12773.94
1300 1796.286 -2073.217 -2073.217 12103.505 -12103.505
Loop time of 0.407996 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1300 1796.286 -2073.217 -2073.217 12103.505 -12103.505
1316 1796.286 -2213.2427 -2213.2427 8948.5426 -8948.5426
Loop time of 0.0672061 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1300 1796.286 -2087.163 -2087.163 12898.861 -12898.861
1310 1822.9931 -2088.4635 -2088.4635 13268.024 -13268.024
1320 1786.9809 -2085.6534 -2085.6534 11674.271 -11674.271
1330 1790.1957 -2085.4338 -2085.4338 11382.56 -11382.56
1340 1726.7764 -2080.7832 -2080.7832 11763.011 -11763.011
1350 1765.8778 -2082.8376 -2082.8376 11233.94 -11233.94
1360 1774.2034 -2082.7941 -2082.7941 10282.68 -10282.68
1370 1666.6126 -2075.0672 -2075.0672 10548.535 -10548.535
1380 1680.5297 -2075.2375 -2075.2375 11659.582 -11659.582
1390 1793.4394 -2081.7681 -2081.7681 12448.884 -12448.884
1400 1905.2561 -2088.1648 -2088.1648 13379.381 -13379.381
Loop time of 0.406403 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1400 1905.2561 -2088.1648 -2088.1648 13379.381 -13379.381
1420 1905.2561 -2213.3144 -2213.3144 9698.8994 -9698.8994
Loop time of 0.095921 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1400 1905.2561 -2088.1648 -2088.1648 13379.381 -13379.381
1410 1774.4051 -2079.5711 -2079.5711 13488.205 -13488.205
1420 1829.4154 -2080.5978 -2080.5978 13751.25 -13751.25
1430 1851.2033 -2083.0872 -2083.0872 12498.845 -12498.845
1440 1755.8872 -2079.3406 -2079.3406 12452.402 -12452.402
1450 1804.3802 -2078.759 -2078.759 13993.109 -13993.109
1460 1884.3691 -2083.448 -2083.448 13170.851 -13170.851
1470 1839.897 -2085.2586 -2085.2586 13423.334 -13423.334
1480 1851.4486 -2087.8651 -2087.8651 13518.48 -13518.48
1490 1815.1706 -2088.1191 -2088.1191 13198.588 -13198.588
1500 1796.5751 -2087.1636 -2087.1636 13390.796 -13390.796
Loop time of 0.405801 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1400 1796.5751 -2087.1636 -2087.1636 13390.796 -13390.796
1410 1844.0954 -2089.5757 -2089.5757 12213.93 -12213.93
1420 1722.6248 -2080.8706 -2080.8706 11975.191 -11975.191
1430 1711.5694 -2079.4182 -2079.4182 12007.431 -12007.431
1440 1807.4864 -2084.8985 -2084.8985 11651.207 -11651.207
1450 1841.0046 -2086.2416 -2086.2416 11994.885 -11994.885
1460 1703.9208 -2076.3752 -2076.3752 12914.67 -12914.67
1470 1751.6279 -2078.6616 -2078.6616 12681.322 -12681.322
1480 1923.0387 -2088.9994 -2088.9994 12267.054 -12267.054
1490 1910.9354 -2087.3393 -2087.3393 12875.768 -12875.768
1500 1814.3345 -2080.2802 -2080.2802 13742.56 -13742.56
Loop time of 0.409854 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1500 1814.3345 -2080.2802 -2080.2802 13742.56 -13742.56
1520 1814.3345 -2213.2885 -2213.2885 9068.2013 -9068.2013
Loop time of 0.0951979 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1500 1814.3345 -2080.2802 -2080.2802 13742.56 -13742.56
1510 1861.5673 -2082.7836 -2082.7836 13474.394 -13474.394
1520 1809.7911 -2078.8033 -2078.8033 12818.516 -12818.516
1530 1755.2845 -2074.6788 -2074.6788 12301.065 -12301.065
1540 1845.1966 -2080.0437 -2080.0437 12087.827 -12087.827
1550 1860.4567 -2080.5052 -2080.5052 11942.542 -11942.542
1560 1801.4846 -2076.1483 -2076.1483 12428.07 -12428.07
1570 1816.1026 -2076.6626 -2076.6626 13366.05 -13366.05
1580 1889.0795 -2081.0577 -2081.0577 13579.026 -13579.026
1590 1816.7327 -2075.9316 -2075.9316 12993.355 -12993.355
1600 1881.7661 -2079.9497 -2079.9497 13154.519 -13154.519
Loop time of 0.41341 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1600 1881.7661 -2079.9497 -2079.9497 13154.519 -13154.519
1620 1881.7661 -2213.3208 -2213.3208 9538.9205 -9538.9205
Loop time of 0.0903962 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1600 1881.7661 -2079.9497 -2079.9497 13154.519 -13154.519
1610 1835.3737 -2076.6779 -2076.6779 12898.536 -12898.536
1620 1828.8122 -2076.0976 -2076.0976 12367.521 -12367.521
1630 1909.4557 -2081.3267 -2081.3267 12174.734 -12174.734
1640 1860.7602 -2078.1358 -2078.1358 12273.383 -12273.383
1650 1846.435 -2077.312 -2077.312 12169.973 -12169.973
1660 1893.7748 -2080.6316 -2080.6316 13083.049 -13083.049
1670 1910.9077 -2082.0981 -2082.0981 13382.159 -13382.159
1680 1825.8649 -2076.9434 -2076.9434 14129.966 -14129.966
1690 1824.78 -2077.3787 -2077.3787 13962.169 -13962.169
1700 1847.4368 -2079.4239 -2079.4239 13743.769 -13743.769
Loop time of 0.413006 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1700 1847.4368 -2079.4239 -2079.4239 13743.769 -13743.769
1719 1847.4368 -2213.3063 -2213.3063 9303.0343 -9303.0343
Loop time of 0.084692 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1700 1847.4368 -2087.6647 -2087.6647 12760.942 -12760.942
1710 1734.6814 -2080.7937 -2080.7937 12962.211 -12962.211
1720 1710.2016 -2079.6676 -2079.6676 12111.814 -12111.814
1730 1767.796 -2083.8521 -2083.8521 11760.429 -11760.429
1740 1830.6146 -2088.3603 -2088.3603 12100.287 -12100.287
1750 1818.6121 -2087.9665 -2087.9665 12487.462 -12487.462
1760 1800.3385 -2087.1855 -2087.1855 12277.436 -12277.436
1770 1794.2396 -2087.2142 -2087.2142 11879.932 -11879.932
1780 1758.3735 -2085.267 -2085.267 11711.265 -11711.265
1790 1690.8403 -2081.1557 -2081.1557 11307.898 -11307.898
1800 1705.9352 -2082.3754 -2082.3754 11796.945 -11796.945
Loop time of 0.404108 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1800 1705.9352 -2082.3754 -2082.3754 11796.945 -11796.945
1817 1705.9352 -2213.2953 -2213.2953 8328.1057 -8328.1057
Loop time of 0.074266 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1800 1705.9352 -2086.3241 -2086.3241 13691.613 -13691.613
1810 1838.3444 -2095.2285 -2095.2285 13740.51 -13740.51
1820 1659.2342 -2083.5493 -2083.5493 13816.697 -13816.697
1830 1764.203 -2090.5078 -2090.5078 11818.545 -11818.545
1840 1824.5859 -2094.4771 -2094.4771 11689.913 -11689.913
1850 1554.2092 -2076.5765 -2076.5765 13114.216 -13114.216
1860 1621.3196 -2080.7337 -2080.7337 12821.904 -12821.904
1870 1819.436 -2093.2901 -2093.2901 11422.922 -11422.922
1880 1647.8199 -2081.3802 -2081.3802 12649.571 -12649.571
1890 1708.729 -2084.7107 -2084.7107 13622.22 -13622.22
1900 2016.2792 -2104.1532 -2104.1532 14301.182 -14301.182
Loop time of 0.407473 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1900 2016.2792 -2104.1532 -2104.1532 14301.182 -14301.182
1918 2016.2792 -2213.3036 -2213.3036 10463.653 -10463.653
Loop time of 0.0821629 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1900 2016.2792 -2104.1532 -2104.1532 14301.182 -14301.182
1910 1774.0282 -2082.7355 -2082.7355 13427.246 -13427.246
1920 1907.071 -2089.0563 -2089.0563 13241.652 -13241.652
1930 1807.249 -2088.8683 -2088.8683 12954.733 -12954.733
1940 1759.8304 -2085.5703 -2085.5703 12719.331 -12719.331
1950 1879.4877 -2090.1659 -2090.1659 13108.619 -13108.619
1960 1732.6399 -2085.1217 -2085.1217 12090.042 -12090.042
1970 1805.7391 -2084.8602 -2084.8602 13047.636 -13047.636
1980 1762.2623 -2081.7323 -2081.7323 12136.361 -12136.361
1990 1888.198 -2086.8875 -2086.8875 13081.416 -13081.416
2000 1716.0072 -2080.7323 -2080.7323 12593.867 -12593.867
Loop time of 0.405347 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1900 1716.0072 -2080.7323 -2080.7323 12593.867 -12593.867
1910 1758.3173 -2082.8511 -2082.8511 12427.317 -12427.317
1920 1805.2325 -2085.1868 -2085.1868 12757.457 -12757.457
1930 1792.9618 -2083.619 -2083.619 13503.347 -13503.347
1940 1801.1953 -2083.4074 -2083.4074 14112.753 -14112.753
1950 1836.0788 -2084.96 -2084.96 14151.387 -14151.387
1960 1856.2673 -2085.5891 -2085.5891 14431.077 -14431.077
1970 1838.7353 -2083.8002 -2083.8002 14410.454 -14410.454
1980 1858.3026 -2084.5287 -2084.5287 13894.657 -13894.657
1990 1869.6109 -2084.7899 -2084.7899 13517.649 -13517.649
2000 1762.9686 -2077.3419 -2077.3419 13790.214 -13790.214
Loop time of 0.409344 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2000 1762.9686 -2077.3419 -2077.3419 13790.214 -13790.214
2018 1762.9686 -2213.2744 -2213.2744 8719.7774 -8719.7774
Loop time of 0.079597 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2000 1762.9686 -2077.3419 -2077.3419 13790.214 -13790.214
2010 1796.1726 -2079.1236 -2079.1236 12969.272 -12969.272
2020 1800.824 -2078.9819 -2078.9819 12656.681 -12656.681
2030 1811.9419 -2079.2717 -2079.2717 13576.195 -13576.195
2040 1863.0719 -2082.2086 -2082.2086 13853.312 -13853.312
2050 1835.4719 -2080.0147 -2080.0147 13560.299 -13560.299
2060 1799.3276 -2077.3053 -2077.3053 13140.862 -13140.862
2070 1832.1323 -2079.1555 -2079.1555 13428.16 -13428.16
2080 1835.2331 -2079.0662 -2079.0662 14276.717 -14276.717
2090 1853.312 -2080.0085 -2080.0085 15653.942 -15653.942
2100 1893.7057 -2082.4893 -2082.4893 16495.887 -16495.887
Loop time of 0.410765 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2100 1893.7057 -2082.4893 -2082.4893 16495.887 -16495.887
2120 1893.7057 -2213.31 -2213.31 9619.9705 -9619.9705
Loop time of 0.085947 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2100 1893.7057 -2082.9637 -2082.9637 12149.243 -12149.243
2110 1847.0322 -2079.8 -2079.8 12700.583 -12700.583
2120 1835.3859 -2079.0245 -2079.0245 13703.719 -13703.719
2130 1844.4758 -2079.6664 -2079.6664 13897.973 -13897.973
2140 1842.7138 -2079.6526 -2079.6526 13308.603 -13308.603
2150 1850.2994 -2080.32 -2080.32 11761.856 -11761.856
2160 1860.4543 -2081.2432 -2081.2432 10575.83 -10575.83
2170 1801.9382 -2077.7054 -2077.7054 11552.34 -11552.34
2180 1778.4832 -2076.5031 -2076.5031 12291.924 -12291.924
2190 1795.7049 -2077.9669 -2077.9669 12905.545 -12905.545
2200 1866.2313 -2082.9789 -2082.9789 13325.123 -13325.123
Loop time of 0.410584 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2200 1866.2313 -2082.9789 -2082.9789 13325.123 -13325.123
2218 1866.2313 -2213.2747 -2213.2747 9436.2647 -9436.2647
Loop time of 0.0767519 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2200 1866.2313 -2082.9789 -2082.9789 13325.123 -13325.123
2210 1729.0096 -2086.7073 -2086.7073 12711.066 -12711.066
2220 1783.5771 -2085.9921 -2085.9921 12412.287 -12412.287
2230 1773.7489 -2084.6394 -2084.6394 11920.082 -11920.082
2240 1806.9924 -2085.4997 -2085.4997 11931.524 -11931.524
2250 1778.4199 -2084.4813 -2084.4813 11718.165 -11718.165
2260 1741.7805 -2081.0247 -2081.0247 12896.049 -12896.049
2270 1802.0248 -2081.5405 -2081.5405 12806.844 -12806.844
2280 1761.0213 -2079.345 -2079.345 12392.424 -12392.424
2290 1874.7024 -2084.6806 -2084.6806 12967.892 -12967.892
2300 1773.016 -2083.3451 -2083.3451 12557.602 -12557.602
Loop time of 0.405068 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2200 1773.016 -2083.3451 -2083.3451 12557.602 -12557.602
2210 1754.3271 -2082.5393 -2082.5393 11845.323 -11845.323
2220 1735.7856 -2081.7019 -2081.7019 11197.024 -11197.024
2230 1745.7899 -2082.6878 -2082.6878 10290.088 -10290.088
2240 1783.4029 -2085.46 -2085.46 10398.174 -10398.174
2250 1746.2925 -2083.2856 -2083.2856 11606.704 -11606.704
2260 1674.989 -2078.787 -2078.787 11477.748 -11477.748
2270 1742.8803 -2083.3535 -2083.3535 11728.746 -11728.746
2280 1813.742 -2088.0471 -2088.0471 11766.749 -11766.749
2290 1761.9893 -2084.6481 -2084.6481 12135.212 -12135.212
2300 1755.15 -2084.1763 -2084.1763 12421.621 -12421.621
Loop time of 0.409006 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2300 1755.15 -2084.1763 -2084.1763 12421.621 -12421.621
2319 1755.15 -2213.3127 -2213.3127 8669.1055 -8669.1055
Loop time of 0.0860112 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2300 1755.15 -2088.3257 -2088.3257 12659.396 -12659.396
2310 1735.1121 -2086.8898 -2086.8898 14017.441 -14017.441
2320 1857.3817 -2094.7844 -2094.7844 12919.269 -12919.269
2330 1764.5002 -2088.4745 -2088.4745 12758.723 -12758.723
2340 1708.2044 -2084.5448 -2084.5448 11530.545 -11530.545
2350 1716.2798 -2084.719 -2084.719 10611.498 -10611.498
2360 1632.8877 -2078.6877 -2078.6877 10248.136 -10248.136
2370 1591.7472 -2075.1919 -2075.1919 9695.8831 -9695.8831
2380 1748.7695 -2084.4218 -2084.4218 9907.1273 -9907.1273
2390 1827.6168 -2088.2146 -2088.2146 12557.45 -12557.45
2400 1815.5439 -2085.9837 -2085.9837 14539.65 -14539.65
Loop time of 0.406806 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2400 1815.5439 -2085.9837 -2085.9837 14539.65 -14539.65
2417 1815.5439 -2213.2814 -2213.2814 9082.4404 -9082.4404
Loop time of 0.0755031 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2400 1815.5439 -2085.9837 -2085.9837 14539.65 -14539.65
2410 1915.7237 -2089.7427 -2089.7427 12770.389 -12770.389
2420 1741.0374 -2084.6412 -2084.6412 12546.024 -12546.024
2430 1816.3609 -2084.5695 -2084.5695 12524.307 -12524.307
2440 1850.7859 -2086.893 -2086.893 11932.085 -11932.085
2450 1732.0764 -2081.5387 -2081.5387 12544.68 -12544.68
2460 1886.2676 -2086.439 -2086.439 12818.408 -12818.408
2470 1721.8063 -2080.6343 -2080.6343 12242.28 -12242.28
2480 1829.9216 -2081.9868 -2081.9868 12875.094 -12875.094
2490 1798.9573 -2081.3591 -2081.3591 13283.118 -13283.118
2500 1877.6923 -2085.9938 -2085.9938 13717.146 -13717.146
Loop time of 0.402789 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2400 1877.6923 -2085.9938 -2085.9938 13717.146 -13717.146
2410 1805.3325 -2080.8416 -2080.8416 14579.288 -14579.288
2420 1801.1726 -2080.2605 -2080.2605 14645.78 -14645.78
2430 1865.9245 -2084.2472 -2084.2472 13799.716 -13799.716
2440 1878.9171 -2084.9185 -2084.9185 13701.347 -13701.347
2450 1790.8157 -2079.0088 -2079.0088 13198.167 -13198.167
2460 1801.8082 -2079.6593 -2079.6593 12804.796 -12804.796
2470 1797.2233 -2079.2783 -2079.2783 13932.587 -13932.587
2480 1769.52 -2077.3565 -2077.3565 13972.364 -13972.364
2490 1871.3543 -2083.9764 -2083.9764 13823.979 -13823.979
2500 1895.3668 -2085.5282 -2085.5282 14028.193 -14028.193
Loop time of 0.408902 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2500 1895.3668 -2085.5282 -2085.5282 14028.193 -14028.193
2518 1895.3668 -2213.3171 -2213.3171 9633.2742 -9633.2742
Loop time of 0.0795321 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2500 1895.3668 -2085.5282 -2085.5282 14028.193 -14028.193
2510 1869.8104 -2083.9504 -2083.9504 14491.442 -14491.442
2520 1803.0741 -2079.7291 -2079.7291 14019.189 -14019.189
2530 1823.1788 -2081.2743 -2081.2743 13635.326 -13635.326
2540 1800.2867 -2080.0035 -2080.0035 14010.572 -14010.572
2550 1828.9783 -2082.1575 -2082.1575 13714.394 -13714.394
2560 1881.6485 -2085.976 -2085.976 13058.642 -13058.642
2570 1772.4537 -2079.2027 -2079.2027 14080.862 -14080.862
2580 1805.2429 -2081.8195 -2081.8195 13640.15 -13640.15
2590 1869.3324 -2086.5742 -2086.5742 13047.134 -13047.134
2600 1796.867 -2082.4373 -2082.4373 13224.706 -13224.706
Loop time of 0.409968 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2600 1796.867 -2082.4373 -2082.4373 13224.706 -13224.706
2618 1796.867 -2213.2937 -2213.2937 8958.1498 -8958.1498
Loop time of 0.0716832 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2600 1796.867 -2082.4373 -2082.4373 13224.706 -13224.706
2610 1802.6643 -2083.342 -2083.342 11994.785 -11994.785
2620 1803.9207 -2084.414 -2084.414 11635.164 -11635.164
2630 1768.4732 -2083.216 -2083.216 11195.997 -11195.997
2640 1817.2134 -2085.3387 -2085.3387 11833.757 -11833.757
2650 1850.0509 -2089.7668 -2089.7668 11362.265 -11362.265
2660 1708.7921 -2084.9337 -2084.9337 10409.943 -10409.943
2670 1752.9645 -2083.0376 -2083.0376 10171.006 -10171.006
2680 1733.6815 -2079.8226 -2079.8226 11759.735 -11759.735
2690 1777.3162 -2079.4658 -2079.4658 11285.073 -11285.073
2700 1780.1943 -2079.2519 -2079.2519 12213.79 -12213.79
Loop time of 0.399546 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2600 1780.1943 -2079.2519 -2079.2519 12213.79 -12213.79
2610 1746.9585 -2078.0203 -2078.0203 13027.376 -13027.376
2620 1857.2789 -2086.1675 -2086.1675 13264.945 -13264.945
2630 1891.2521 -2089.2926 -2089.2926 12670.387 -12670.387
2640 1796.637 -2083.905 -2083.905 12478.573 -12478.573
2650 1741.2685 -2080.9505 -2080.9505 12317.517 -12317.517
2660 1805.5574 -2085.7371 -2085.7371 12106.005 -12106.005
2670 1771.8977 -2083.9694 -2083.9694 12962.924 -12962.924
2680 1711.4061 -2080.288 -2080.288 14121.523 -14121.523
2690 1858.0183 -2090.1762 -2090.1762 13291.477 -13291.477
2700 1838.5355 -2089.1089 -2089.1089 13702.529 -13702.529
Loop time of 0.405325 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2700 1838.5355 -2089.1089 -2089.1089 13702.529 -13702.529
2718 1838.5355 -2213.2859 -2213.2859 9238.9808 -9238.9808
Loop time of 0.0834019 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2700 1838.5355 -2089.1089 -2089.1089 13702.529 -13702.529
2710 1774.7686 -2085.128 -2085.128 13300.887 -13300.887
2720 1839.3884 -2089.5765 -2089.5765 13322.286 -13322.286
2730 1848.9734 -2090.4311 -2090.4311 12381.462 -12381.462
2740 1652.1266 -2077.6365 -2077.6365 11722.405 -11722.405
2750 1673.4321 -2079.0859 -2079.0859 10859.387 -10859.387
2760 1736.9228 -2083.1572 -2083.1572 10327.062 -10327.062
2770 1735.8621 -2082.8831 -2082.8831 11471.944 -11471.944
2780 1802.6631 -2087.0351 -2087.0351 11844.925 -11844.925
2790 1797.5979 -2086.437 -2086.437 12050.594 -12050.594
2800 1772.4707 -2084.5278 -2084.5278 12885.826 -12885.826
Loop time of 0.405378 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2800 1772.4707 -2084.5278 -2084.5278 12885.826 -12885.826
2817 1772.4707 -2213.2994 -2213.2994 8788.498 -8788.498
Loop time of 0.0710671 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2800 1772.4707 -2084.5278 -2084.5278 12885.826 -12885.826
2810 1788.0397 -2085.2771 -2085.2771 13123.426 -13123.426
2820 1831.2464 -2087.8518 -2087.8518 12673.574 -12673.574
2830 1743.4114 -2081.7896 -2081.7896 13066.36 -13066.36
2840 1755.5989 -2082.2867 -2082.2867 13031.535 -13031.535
2850 1871.213 -2089.5583 -2089.5583 13088.117 -13088.117
2860 1820.5044 -2085.8967 -2085.8967 14054.93 -14054.93
2870 1804.2018 -2084.5559 -2084.5559 14287.296 -14287.296
2880 1838.5761 -2086.5677 -2086.5677 13105.322 -13105.322
2890 1732.0926 -2079.2996 -2079.2996 12808.515 -12808.515
2900 1687.6862 -2076.0516 -2076.0516 11823.268 -11823.268
Loop time of 0.408826 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2900 1687.6862 -2076.0516 -2076.0516 11823.268 -11823.268
2917 1687.6862 -2213.258 -2213.258 8204.3947 -8204.3947
Loop time of 0.0732229 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2900 1687.6862 -2076.0516 -2076.0516 11823.268 -11823.268
2910 1810.0632 -2083.67 -2083.67 10723.225 -10723.225
2920 1748.9758 -2079.0976 -2079.0976 12060.108 -12060.108
2930 1751.5908 -2078.6657 -2078.6657 12791.425 -12791.425
2940 1838.7023 -2083.6783 -2083.6783 13260.13 -13260.13
2950 1883.1789 -2085.8378 -2085.8378 13268.034 -13268.034
2960 1821.7492 -2081.0324 -2081.0324 13707.928 -13707.928
2970 1899.0671 -2085.3931 -2085.3931 14048.633 -14048.633
2980 1923.3543 -2086.2737 -2086.2737 14581.955 -14581.955
2990 1793.3815 -2077.0772 -2077.0772 14609.194 -14609.194
3000 1853.0706 -2080.3808 -2080.3808 14059.98 -14059.98
Loop time of 0.407646 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
3000 1853.0706 -2080.3808 -2080.3808 14059.98 -14059.98
3019 1853.0706 -2213.315 -2213.315 9346.3242 -9346.3242
Loop time of 0.0833499 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
3000 1853.0706 -2080.3808 -2080.3808 14059.98 -14059.98
Loop time of 13.0575 on 1 procs for 19 steps with 511 atoms
PRD stats:
Dephase time (%) = 2.82061 (21.6015)
Dynamics time (%) = 8.16778 (62.5525)
Quench time (%) = 1.60486 (12.2907)
Other time (%) = 0.275477 (2.10973)
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: 13428 ave 13428 max 13428 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13428
Ave neighs/atom = 26.2779
Neighbor list builds = 97
Dangerous builds = 0

732
examples/prd/log.prd.2.28Mar11.linux.4 Normal file
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LAMMPS (27 Mar 2011)
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
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 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 1000
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
110 846.80459 -2134.8152 0 -2078.9916 11904.208
120 1130.5577 -2151.6282 0 -2077.0988 9631.0553
130 1011.5223 -2141.5579 0 -2074.8757 9674.727
140 828.13015 -2127.6781 0 -2073.0856 10663.754
150 1213.6842 -2151.0205 0 -2071.0112 9358.162
160 1118.1701 -2142.223 0 -2068.5102 9705.042
170 815.94964 -2120.3781 0 -2066.5885 11111.781
180 1149.9499 -2140.3762 0 -2064.5684 10362.874
190 1265.3227 -2145.3133 0 -2061.8998 10208.885
200 967.96035 -2123.4032 0 -2059.5927 11429.676
210 1154.8198 -2133.5775 0 -2057.4487 10697.231
220 1309.6664 -2141.0968 0 -2054.7601 10123.484
230 1123.114 -2126.2814 0 -2052.2427 11010.813
240 1262.1761 -2133.0492 0 -2049.8432 10358.728
250 1387.1979 -2138.5224 0 -2047.0746 9224.1203
260 1099.3995 -2117.0127 0 -2044.5373 9902.009
270 1119.6867 -2116.1281 0 -2042.3154 9925.7178
280 1412.0178 -2132.6875 0 -2039.6036 8270.5884
290 1321.0773 -2123.8202 0 -2036.7313 8809.0223
300 1216.0708 -2114.3828 0 -2034.2162 9035.0512
310 1359.9122 -2121.2409 0 -2031.5918 7895.5635
320 1322.8642 -2116.0313 0 -2028.8245 8661.9299
330 1272.4262 -2110.1033 0 -2026.2215 10341.489
340 1451.8803 -2119.1983 0 -2023.4865 10343.627
350 1488.8525 -2118.6967 0 -2020.5476 10786.017
360 1330.5957 -2105.5746 0 -2017.8582 11501.105
370 1452.1996 -2110.9637 0 -2015.2308 11534.951
380 1598.8893 -2117.7127 0 -2012.3096 12209.282
390 1593.9074 -2114.5133 0 -2009.4386 13050.071
400 1580.9099 -2110.9274 0 -2006.7096 12007.149
410 1499.3026 -2102.9454 0 -2004.1074 10088.553
420 1368.9435 -2091.8877 0 -2001.6433 8465.3083
430 1297.2041 -2084.7532 0 -1999.2381 7269.5758
440 1450.1063 -2092.2353 0 -1996.6405 7033.8027
450 1534.8081 -2094.9394 0 -1993.7608 9081.5997
460 1556.639 -2093.5424 0 -1990.9246 12400.015
470 1803.1464 -2106.8774 0 -1988.0092 14192.515
480 1865.4976 -2108.05 0 -1985.0714 16740.251
490 1809.642 -2101.8102 0 -1982.5137 17670.617
500 1875.0318 -2103.7815 0 -1980.1744 15726.048
510 1835.5401 -2099.0223 0 -1978.0186 13590.87
520 1592.2743 -2081.0889 0 -1976.1219 12889.185
530 1621.098 -2081.1646 0 -1974.2975 12097.358
540 1787.4042 -2090.0335 0 -1972.203 11006.55
550 1629.769 -2077.5584 0 -1970.1196 11828.612
560 1633.9967 -2075.8478 0 -1968.1303 13013.747
570 1867.8884 -2089.0683 0 -1965.9321 12589.17
580 1897.3799 -2088.7925 0 -1963.7122 12142.767
590 1675.1213 -2072.2289 0 -1961.8004 12668.905
600 1852.5707 -2082.1073 0 -1959.9809 11872.082
610 1895.1634 -2083.0113 0 -1958.0771 12732.408
620 1759.7637 -2072.4168 0 -1956.4085 14720.014
630 1867.9005 -2077.9673 0 -1954.8303 15446.507
640 1882.4501 -2077.3643 0 -1953.2682 16189.673
650 1830.0215 -2072.5142 0 -1951.8743 15952.621
660 1989.6605 -2081.7336 0 -1950.5699 14441.731
670 2019.3348 -2082.5674 0 -1949.4475 13093.568
680 1806.7881 -2067.7448 0 -1948.6365 13695.415
690 1860.9944 -2070.6335 0 -1947.9518 13711.769
700 2035.4273 -2081.5085 0 -1947.3277 13969.607
710 1924.1115 -2073.7877 0 -1946.9451 14669.272
720 1925.0897 -2073.7075 0 -1946.8005 14665.913
730 1979.7127 -2077.3504 0 -1946.8425 14625.754
740 1932.6041 -2074.5197 0 -1947.1173 15051.1
750 1873.6645 -2071.0745 0 -1947.5575 14804.579
760 1916.3833 -2074.4703 0 -1948.1372 13868.322
770 1893.2199 -2073.6709 0 -1948.8647 14320.209
780 1868.0258 -2072.8444 0 -1949.6991 13913.255
790 1903.3142 -2076.1305 0 -1950.6589 13542.781
800 1852.3079 -2073.8193 0 -1951.7102 13663.021
810 1874.015 -2076.3795 0 -1952.8394 12583.329
820 1897.7242 -2079.181 0 -1954.0779 12629.436
830 1810.9511 -2074.7734 0 -1955.3907 13791.194
840 1751.9411 -2072.1105 0 -1956.6178 14705.479
850 1904.2872 -2083.4009 0 -1957.8652 14745.454
860 1916.5803 -2085.6068 0 -1959.2607 14829.039
870 1838.661 -2081.9371 0 -1960.7276 14932.396
880 1847.5879 -2084.017 0 -1962.219 14581.23
890 1850.4293 -2085.7191 0 -1963.7338 13109.312
900 1822.6233 -2085.4213 0 -1965.2691 13769.397
910 1786.0307 -2084.4806 0 -1966.7407 13450.462
920 1823.0469 -2088.3777 0 -1968.1976 12242.2
930 1731.0515 -2083.7104 0 -1969.5949 11686.755
940 1635.923 -2078.6209 0 -1970.7765 11861.596
950 1731.8445 -2085.9611 0 -1971.7933 11269.332
960 1735.3582 -2087.1207 0 -1972.7212 11587.883
970 1672.4435 -2083.7706 0 -1973.5187 12217.898
980 1703.4917 -2086.4744 0 -1974.1757 12431.952
990 1733.7211 -2089.007 0 -1974.7155 12829.553
1000 1764.9513 -2091.5262 0 -1975.1759 13614.2
Loop time of 3.86951 on 1 procs for 1000 steps with 511 atoms
Pair time (%) = 3.78222 (97.7443)
Neigh time (%) = 0.0427818 (1.10561)
Comm time (%) = 0.0135326 (0.349725)
Outpt time (%) = 0.00138354 (0.035755)
Other time (%) = 0.0295873 (0.764627)
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: 13440 ave 13440 max 13440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13440
Ave neighs/atom = 26.3014
Neighbor list builds = 44
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
Memory usage per processor = 3.73877 Mbytes
Step Temp PotEng pe Press press
1000 1764.9513 -2091.5262 -2091.5262 13614.2 -13614.2
1010 1764.9513 -2212.5976 -2212.5976 8682.8748 -8682.8748
1018 1764.9513 -2213.2997 -2213.2997 8735.7723 -8735.7723
Loop time of 0.0829132 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1000 1764.9513 -2091.5262 -2091.5262 13614.2 -13614.2
1010 1819.2378 -2093.2474 -2093.2474 13531.715 -13531.715
1020 1813.3519 -2094.5984 -2094.5984 13263.815 -13263.815
1030 1860.9582 -2099.1408 -2099.1408 12526.032 -12526.032
1040 1719.5348 -2094.3594 -2094.3594 11973.442 -11973.442
1050 1747.6032 -2091.4086 -2091.4086 12303.295 -12303.295
1060 1712.9261 -2086.1105 -2086.1105 13343.858 -13343.858
1070 1803.4404 -2086.7641 -2086.7641 14986.719 -14986.719
1080 1781.4485 -2085.9398 -2085.9398 14338.369 -14338.369
1090 1820.0336 -2087.6573 -2087.6573 13616.057 -13616.057
1100 1715.8133 -2082.4654 -2082.4654 13193.661 -13193.661
Loop time of 0.40147 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1000 1715.8133 -2082.4654 -2082.4654 13193.661 -13193.661
1010 1739.9691 -2084.3249 -2084.3249 12648.268 -12648.268
1020 1785.2788 -2087.5099 -2087.5099 12368.814 -12368.814
1030 1753.9701 -2085.612 -2085.612 12945.536 -12945.536
1040 1726.867 -2083.9236 -2083.9236 13616.716 -13616.716
1050 1821.8225 -2090.2246 -2090.2246 13092.097 -13092.097
1060 1815.5365 -2089.8567 -2089.8567 13780.034 -13780.034
1070 1724.7099 -2083.9132 -2083.9132 13602.863 -13602.863
1080 1754.4888 -2085.8575 -2085.8575 13133.622 -13133.622
1090 1793.6045 -2088.3564 -2088.3564 13163.32 -13163.32
1100 1727.8922 -2083.9031 -2083.9031 13038.694 -13038.694
Loop time of 0.409442 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1100 1727.8922 -2083.9031 -2083.9031 13038.694 -13038.694
1118 1727.8922 -2213.2976 -2213.2976 8480.3214 -8480.3214
Loop time of 0.0825701 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1100 1727.8922 -2085.5621 -2085.5621 12277.055 -12277.055
1110 1756.6327 -2087.2841 -2087.2841 11368.553 -11368.553
1120 1701.1354 -2083.3707 -2083.3707 11164.561 -11164.561
1130 1649.8139 -2079.6229 -2079.6229 11450.441 -11450.441
1140 1699.8954 -2082.3909 -2082.3909 11535.348 -11535.348
1150 1765.3613 -2086.0313 -2086.0313 11925.995 -11925.995
1160 1732.4283 -2083.1024 -2083.1024 12804.169 -12804.169
1170 1770.4018 -2084.7946 -2084.7946 12978.113 -12978.113
1180 1832.0095 -2087.9893 -2087.9893 13155.054 -13155.054
1190 1775.2461 -2083.3846 -2083.3846 14138.08 -14138.08
1200 1912.8176 -2091.6206 -2091.6206 14075.801 -14075.801
Loop time of 0.404857 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1200 1912.8176 -2091.6206 -2091.6206 14075.801 -14075.801
1219 1912.8176 -2213.323 -2213.323 9753.9239 -9753.9239
Loop time of 0.08847 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1200 1912.8176 -2091.6206 -2091.6206 14075.801 -14075.801
1210 1791.1869 -2089.4314 -2089.4314 13473.919 -13473.919
1220 1778.9267 -2087.2615 -2087.2615 13739.455 -13739.455
1230 1865.1198 -2090.7879 -2090.7879 12588.104 -12588.104
1240 1759.0389 -2087.3561 -2087.3561 12335.042 -12335.042
1250 1870.6206 -2091.2848 -2091.2848 12895.105 -12895.105
1260 1862.5179 -2094.7315 -2094.7315 12098.522 -12098.522
1270 1669.1055 -2085.4484 -2085.4484 11424.528 -11424.528
1280 1820.863 -2086.0862 -2086.0862 12314.591 -12314.591
1290 1835.1062 -2087.6906 -2087.6906 11781.843 -11781.843
1300 1817.4069 -2088.158 -2088.158 11477.319 -11477.319
Loop time of 0.4023 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1200 1817.4069 -2088.158 -2088.158 11477.319 -11477.319
1210 1785.366 -2085.3845 -2085.3845 11333.481 -11333.481
1220 1735.7669 -2081.4513 -2081.4513 9901.2553 -9901.2553
1230 1682.6307 -2077.2188 -2077.2188 9626.947 -9626.947
1240 1728.0753 -2079.3709 -2079.3709 10498.108 -10498.108
1250 1815.6783 -2084.1815 -2084.1815 11957.739 -11957.739
1260 1812.1974 -2082.978 -2082.978 13040.779 -13040.779
1270 1793.5848 -2080.8035 -2080.8035 13075.548 -13075.548
1280 1858.6019 -2084.1626 -2084.1626 12031.094 -12031.094
1290 1873.3607 -2084.2555 -2084.2555 12440.634 -12440.634
1300 1855.6542 -2082.3133 -2082.3133 13072.26 -13072.26
Loop time of 0.406179 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1300 1855.6542 -2082.3133 -2082.3133 13072.26 -13072.26
1319 1855.6542 -2213.3073 -2213.3073 9358.0717 -9358.0717
Loop time of 0.0832541 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1300 1855.6542 -2087.163 -2087.163 13306.606 -13306.606
1310 1847.0104 -2085.9117 -2085.9117 13831.059 -13831.059
1320 1821.9089 -2083.6534 -2083.6534 13315.577 -13315.577
1330 1837.6483 -2084.1326 -2084.1326 12108.286 -12108.286
1340 1751.5492 -2077.923 -2077.923 11366.904 -11366.904
1350 1737.9508 -2076.4759 -2076.4759 10019.736 -10019.736
1360 1793.2086 -2079.484 -2079.484 9276.4821 -9276.4821
1370 1783.8893 -2078.2076 -2078.2076 10007.533 -10007.533
1380 1710.0898 -2072.6513 -2072.6513 11000.817 -11000.817
1390 1826.9639 -2079.6043 -2079.6043 11641.706 -11641.706
1400 1872.7191 -2081.8353 -2081.8353 13073.794 -13073.794
Loop time of 0.407173 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1400 1872.7191 -2081.8353 -2081.8353 13073.794 -13073.794
1419 1872.7191 -2213.2913 -2213.2913 9474.1695 -9474.1695
Loop time of 0.082969 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1400 1872.7191 -2081.8353 -2081.8353 13073.794 -13073.794
1410 1786.7702 -2081.1802 -2081.1802 13660.592 -13660.592
1420 1769.4554 -2078.4675 -2078.4675 13618.424 -13618.424
1430 1827.6814 -2079.5734 -2079.5734 13362.845 -13362.845
1440 1719.9736 -2073.5901 -2073.5901 13504.886 -13504.886
1450 1830.1696 -2074.8242 -2074.8242 14776.946 -14776.946
1460 1857.7603 -2077.899 -2077.899 13865.35 -13865.35
1470 1854.2545 -2080.7823 -2080.7823 12531.918 -12531.918
1480 1766.2046 -2077.8774 -2077.8774 12393.929 -12393.929
1490 1761.4143 -2074.6139 -2074.6139 13084.551 -13084.551
1500 1825.4626 -2075.5562 -2075.5562 13605.18 -13605.18
Loop time of 0.410289 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1400 1825.4626 -2075.5562 -2075.5562 13605.18 -13605.18
1410 1884.0819 -2078.701 -2078.701 13442.359 -13442.359
1420 1872.6531 -2077.3178 -2077.3178 13573.731 -13573.731
1430 1872.973 -2076.8189 -2076.8189 13508.422 -13508.422
1440 1878.5594 -2076.7714 -2076.7714 12908.412 -12908.412
1450 1850.5046 -2074.5967 -2074.5967 13159.712 -13159.712
1460 1914.1141 -2078.5628 -2078.5628 12407.852 -12407.852
1470 1857.2255 -2074.7062 -2074.7062 12005.587 -12005.587
1480 1779.7172 -2069.5645 -2069.5645 11735.8 -11735.8
1490 1835.6711 -2073.2281 -2073.2281 11433.734 -11433.734
1500 1886.5398 -2076.6018 -2076.6018 12767.753 -12767.753
Loop time of 0.407191 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1500 1886.5398 -2076.6018 -2076.6018 12767.753 -12767.753
1519 1886.5398 -2213.3157 -2213.3157 9574.6829 -9574.6829
Loop time of 0.085706 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1500 1886.5398 -2076.6018 -2076.6018 12767.753 -12767.753
1510 1837.4263 -2073.4744 -2073.4744 14084.489 -14084.489
1520 1881.6317 -2076.5682 -2076.5682 15206.984 -15206.984
1530 2014.91 -2085.7033 -2085.7033 16139.498 -16139.498
1540 1939.8504 -2081.3506 -2081.3506 16318.524 -16318.524
1550 1918.2957 -2080.7423 -2080.7423 14753.262 -14753.262
1560 1917.5479 -2081.6617 -2081.6617 13793.844 -13793.844
1570 1881.2015 -2080.3879 -2080.3879 12378.607 -12378.607
1580 1780.2825 -2074.8721 -2074.8721 11855.074 -11855.074
1590 1794.5197 -2076.8941 -2076.8941 12493.037 -12493.037
1600 1827.5395 -2080.1465 -2080.1465 12167.977 -12167.977
Loop time of 0.410306 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1600 1827.5395 -2080.1465 -2080.1465 12167.977 -12167.977
1618 1827.5395 -2213.2886 -2213.2886 9165.4928 -9165.4928
Loop time of 0.0679748 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1600 1827.5395 -2080.1465 -2080.1465 12167.977 -12167.977
1610 1776.5777 -2077.8381 -2077.8381 11792.617 -11792.617
1620 1808.7495 -2080.9613 -2080.9613 12166.045 -12166.045
1630 1873.6933 -2086.2878 -2086.2878 12862.254 -12862.254
1640 1789.9125 -2081.8308 -2081.8308 13181.26 -13181.26
1650 1766.9021 -2081.3252 -2081.3252 13554.202 -13554.202
1660 1826.7423 -2086.2422 -2086.2422 13076.865 -13076.865
1670 1818.0463 -2086.6711 -2086.6711 12349.806 -12349.806
1680 1707.4648 -2080.3046 -2080.3046 12320.035 -12320.035
1690 1766.1538 -2084.9966 -2084.9966 11616.707 -11616.707
1700 1794.7226 -2087.6647 -2087.6647 12398.897 -12398.897
Loop time of 0.403318 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1700 1794.7226 -2087.6647 -2087.6647 12398.897 -12398.897
1719 1794.7226 -2213.2878 -2213.2878 8932.017 -8932.017
Loop time of 0.0875909 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1700 1794.7226 -2087.6647 -2087.6647 12398.897 -12398.897
1710 1708.1668 -2082.6759 -2082.6759 13411.842 -13411.842
1720 1728.0552 -2084.5976 -2084.5976 11943.19 -11943.19
1730 1778.7136 -2088.4725 -2088.4725 11609.722 -11609.722
1740 1738.6395 -2086.3169 -2086.3169 12488.055 -12488.055
1750 1726.2202 -2085.9032 -2085.9032 13358.698 -13358.698
1760 1769.9502 -2089.116 -2089.116 13419.859 -13419.859
1770 1791.7387 -2090.8471 -2090.8471 13164.614 -13164.614
1780 1791.1611 -2091.0916 -2091.0916 13248.484 -13248.484
1790 1784.3829 -2090.9253 -2090.9253 13533.256 -13533.256
1800 1711.0215 -2086.3241 -2086.3241 13726.547 -13726.547
Loop time of 0.403541 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1800 1711.0215 -2086.3241 -2086.3241 13726.547 -13726.547
1817 1711.0215 -2213.2911 -2213.2911 8363.9684 -8363.9684
Loop time of 0.0716879 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1800 1711.0215 -2086.3241 -2086.3241 13726.547 -13726.547
1810 1723.9787 -2087.3167 -2087.3167 13692.211 -13692.211
1820 1817.3762 -2093.5379 -2093.5379 12798.158 -12798.158
1830 1817.1145 -2093.5962 -2093.5962 12513.323 -12513.323
1840 1674.7131 -2084.2672 -2084.2672 12636.802 -12636.802
1850 1665.0535 -2083.5668 -2083.5668 11935.487 -11935.487
1860 1747.01 -2088.7523 -2088.7523 11330.04 -11330.04
1870 1695.8643 -2085.0465 -2085.0465 11173.678 -11173.678
1880 1718.4846 -2086.1048 -2086.1048 11156.069 -11156.069
1890 1713.6873 -2085.2259 -2085.2259 11674.731 -11674.731
1900 1718.085 -2084.8514 -2084.8514 12035.048 -12035.048
Loop time of 0.405354 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1900 1718.085 -2084.8514 -2084.8514 12035.048 -12035.048
1918 1718.085 -2213.2988 -2213.2988 8414.4676 -8414.4676
Loop time of 0.0805008 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1900 1718.085 -2084.8514 -2084.8514 12035.048 -12035.048
1910 1793.2322 -2083.6327 -2083.6327 13288.48 -13288.48
1920 1727.7794 -2078.0914 -2078.0914 12888.134 -12888.134
1930 1912.2241 -2084.6701 -2084.6701 13474.49 -13474.49
1940 1832.9231 -2086.1226 -2086.1226 12319.217 -12319.217
1950 1822.842 -2086.9261 -2086.9261 13136.097 -13136.097
1960 1782.9637 -2085.1432 -2085.1432 12187.624 -12187.624
1970 1753.4226 -2081.4113 -2081.4113 13150.587 -13150.587
1980 1853.5974 -2084.2683 -2084.2683 12547.654 -12547.654
1990 1871.645 -2088.347 -2088.347 13969.401 -13969.401
2000 1800.9624 -2087.837 -2087.837 13177.288 -13177.288
Loop time of 0.404571 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1900 1800.9624 -2087.837 -2087.837 13177.288 -13177.288
1910 1710.5536 -2081.292 -2081.292 13401.971 -13401.971
1920 1670.0325 -2077.9688 -2077.9688 12625.54 -12625.54
1930 1719.2125 -2080.407 -2080.407 12379.815 -12379.815
1940 1833.2077 -2086.9988 -2086.9988 12258.809 -12258.809
1950 1840.7671 -2086.5719 -2086.5719 12677.905 -12677.905
1960 1802.8764 -2083.2325 -2083.2325 12902.499 -12902.499
1970 1813.8827 -2083.1592 -2083.1592 13386.118 -13386.118
1980 1831.3863 -2083.5345 -2083.5345 13491.623 -13491.623
1990 1847.0481 -2083.8451 -2083.8451 12706.426 -12706.426
2000 1872.4408 -2084.874 -2084.874 11429.205 -11429.205
Loop time of 0.409858 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2000 1872.4408 -2084.874 -2084.874 11429.205 -11429.205
2021 1872.4408 -2213.3226 -2213.3226 9475.104 -9475.104
Loop time of 0.0984049 on 1 procs for 21 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2000 1872.4408 -2084.874 -2084.874 11429.205 -11429.205
2010 1765.2948 -2077.2433 -2077.2433 12146.16 -12146.16
2020 1757.8432 -2076.1983 -2076.1983 12504.09 -12504.09
2030 1813.1051 -2079.2312 -2079.2312 11436.942 -11436.942
2040 1826.7944 -2079.521 -2079.521 11478.147 -11478.147
2050 1806.837 -2077.6208 -2077.6208 12373.568 -12373.568
2060 1849.089 -2079.856 -2079.856 13074.725 -13074.725
2070 1818.256 -2077.308 -2077.308 13032.274 -13032.274
2080 1771.8222 -2073.7601 -2073.7601 13645.475 -13645.475
2090 1909.9579 -2082.3796 -2082.3796 13751.485 -13751.485
2100 1975.4045 -2086.2999 -2086.2999 14179.349 -14179.349
Loop time of 0.409143 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2100 1975.4045 -2086.2999 -2086.2999 14179.349 -14179.349
2119 1975.4045 -2213.3085 -2213.3085 10184.77 -10184.77
Loop time of 0.07934 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2100 1975.4045 -2082.9637 -2082.9637 12710.356 -12710.356
2110 1868.4161 -2075.7329 -2075.7329 12966.332 -12966.332
2120 1798.1017 -2071.0269 -2071.0269 12328.302 -12328.302
2130 1848.2629 -2074.2884 -2074.2884 12341.548 -12341.548
2140 1862.7086 -2075.2436 -2075.2436 13004.344 -13004.344
2150 1862.3015 -2075.3023 -2075.3023 12790.451 -12790.451
2160 1903.324 -2078.2038 -2078.2038 11734.028 -11734.028
2170 1854.7871 -2075.3256 -2075.3256 11859.837 -11859.837
2180 1825.8707 -2073.8281 -2073.8281 13166.464 -13166.464
2190 1894.2186 -2078.8152 -2078.8152 13494.086 -13494.086
2200 1950.2952 -2083.1832 -2083.1832 12303.724 -12303.724
Loop time of 0.412743 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2200 1950.2952 -2083.1832 -2083.1832 12303.724 -12303.724
2222 1950.2952 -2213.3198 -2213.3198 10002.569 -10002.569
Loop time of 0.10001 on 1 procs for 22 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2200 1950.2952 -2083.1832 -2083.1832 12303.724 -12303.724
2210 1769.771 -2089.6643 -2089.6643 12302.911 -12302.911
2220 1770.8889 -2088.4834 -2088.4834 12656.727 -12656.727
2230 1813.6417 -2090.1493 -2090.1493 12982.815 -12982.815
2240 1692.7818 -2083.7862 -2083.7862 13008.705 -13008.705
2250 1827.7114 -2086.3237 -2086.3237 12916.999 -12916.999
2260 1691.4508 -2079.8213 -2079.8213 12850.565 -12850.565
2270 1798.6086 -2080.3442 -2080.3442 13878.31 -13878.31
2280 1794.1974 -2080.5532 -2080.5532 13988.43 -13988.43
2290 1730.8266 -2076.5209 -2076.5209 14913.737 -14913.737
2300 1833.1591 -2079.2373 -2079.2373 14690.562 -14690.562
Loop time of 0.408337 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2200 1833.1591 -2079.2373 -2079.2373 14690.562 -14690.562
2210 1853.3231 -2081.1489 -2081.1489 12693.533 -12693.533
2220 1825.1492 -2079.9344 -2079.9344 12869.745 -12869.745
2230 1807.4181 -2079.4417 -2079.4417 12015.847 -12015.847
2240 1760.6729 -2077.0282 -2077.0282 11049.918 -11049.918
2250 1745.0921 -2076.6006 -2076.6006 11852.562 -11852.562
2260 1845.1183 -2083.7716 -2083.7716 12522.198 -12522.198
2270 1848.7947 -2084.6456 -2084.6456 13780.446 -13780.446
2280 1771.56 -2080.214 -2080.214 15118.29 -15118.29
2290 1810.9084 -2083.4423 -2083.4423 13697.379 -13697.379
2300 1874.5715 -2088.3257 -2088.3257 13479.591 -13479.591
Loop time of 0.405848 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2300 1874.5715 -2088.3257 -2088.3257 13479.591 -13479.591
2318 1874.5715 -2213.2825 -2213.2825 9487.1289 -9487.1289
Loop time of 0.068012 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2300 1874.5715 -2088.3257 -2088.3257 13479.591 -13479.591
2310 1799.9066 -2084.1365 -2084.1365 13764.662 -13764.662
2320 1806.3902 -2085.2995 -2085.2995 13501.488 -13501.488
2330 1809.6795 -2086.2598 -2086.2598 13038.078 -13038.078
2340 1728.7746 -2081.6123 -2081.6123 12506.517 -12506.517
2350 1749.5618 -2083.5764 -2083.5764 11892.613 -11892.613
2360 1764.9524 -2085.1076 -2085.1076 11816.029 -11816.029
2370 1725.4759 -2082.9357 -2082.9357 12073.491 -12073.491
2380 1776.5011 -2086.6482 -2086.6482 12089.877 -12089.877
2390 1790.7081 -2087.8936 -2087.8936 12491.991 -12491.991
2400 1718.6191 -2083.3981 -2083.3981 12564.395 -12564.395
Loop time of 0.406805 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2400 1718.6191 -2083.3981 -2083.3981 12564.395 -12564.395
2417 1718.6191 -2213.2938 -2213.2938 8416.0699 -8416.0699
Loop time of 0.0702372 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2400 1718.6191 -2083.3981 -2083.3981 12564.395 -12564.395
2410 1783.1812 -2082.5143 -2082.5143 12488.592 -12488.592
2420 1740.6277 -2078.7813 -2078.7813 13656.427 -13656.427
2430 1843.4455 -2081.8167 -2081.8167 14136.267 -14136.267
2440 1784.5508 -2080.9749 -2080.9749 12677.88 -12677.88
2450 1772.8791 -2079.3362 -2079.3362 13511.342 -13511.342
2460 1808.4916 -2080.0209 -2080.0209 13578.29 -13578.29
2470 1806.8503 -2080.5826 -2080.5826 13865.598 -13865.598
2480 1773.5282 -2078.9234 -2078.9234 12934.632 -12934.632
2490 1831.8516 -2081.1045 -2081.1045 13293.179 -13293.179
2500 1761.2282 -2078.6184 -2078.6184 12685.303 -12685.303
Loop time of 0.40278 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2400 1761.2282 -2078.6184 -2078.6184 12685.303 -12685.303
2410 1865.9955 -2085.5849 -2085.5849 12418.549 -12418.549
2420 1858.6339 -2085.2406 -2085.2406 12294.6 -12294.6
2430 1758.9969 -2078.8937 -2078.8937 12480.947 -12480.947
2440 1840.6222 -2084.5641 -2084.5641 11944.258 -11944.258
2450 1818.6705 -2083.5453 -2083.5453 11142.112 -11142.112
2460 1653.6497 -2073.2015 -2073.2015 10876.683 -10876.683
2470 1712.3081 -2077.637 -2077.637 10812.088 -10812.088
2480 1821.2072 -2085.4884 -2085.4884 10444.81 -10444.81
2490 1722.8782 -2079.8162 -2079.8162 12584.047 -12584.047
2500 1749.4477 -2082.4239 -2082.4239 13138.948 -13138.948
Loop time of 0.407317 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2500 1749.4477 -2082.4239 -2082.4239 13138.948 -13138.948
2522 1749.4477 -2213.3181 -2213.3181 8629.9873 -8629.9873
Loop time of 0.091347 on 1 procs for 22 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2500 1749.4477 -2085.5282 -2085.5282 13026.011 -13026.011
2510 1847.5881 -2092.971 -2092.971 11626.051 -11626.051
2520 1756.1279 -2088.0134 -2088.0134 11851.217 -11851.217
2530 1632.9814 -2080.8808 -2080.8808 12087.856 -12087.856
2540 1673.5799 -2084.3724 -2084.3724 11214.772 -11214.772
2550 1691.2987 -2086.2212 -2086.2212 10888.491 -10888.491
2560 1652.2967 -2084.1605 -2084.1605 11411.934 -11411.934
2570 1743.6642 -2090.5705 -2090.5705 11308.438 -11308.438
2580 1718.418 -2089.1864 -2089.1864 12259.871 -12259.871
2590 1719.7172 -2089.4648 -2089.4648 13337.02 -13337.02
2600 1791.7534 -2094.3153 -2094.3153 13816.645 -13816.645
Loop time of 0.406918 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2600 1791.7534 -2094.3153 -2094.3153 13816.645 -13816.645
2616 1791.7534 -2213.2887 -2213.2887 8922.5524 -8922.5524
Loop time of 0.069011 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2600 1791.7534 -2094.3153 -2094.3153 13816.645 -13816.645
2610 1830.4835 -2084.3182 -2084.3182 12861.619 -12861.619
2620 1769.7016 -2082.3952 -2082.3952 12728.134 -12728.134
2630 1844.7689 -2085.411 -2085.411 13489.575 -13489.575
2640 1838.041 -2088.023 -2088.023 12178.747 -12178.747
2650 1773.4583 -2086.3884 -2086.3884 12294.504 -12294.504
2660 1802.1971 -2086.6509 -2086.6509 12616.41 -12616.41
2670 1750.3937 -2083.4939 -2083.4939 12473.23 -12473.23
2680 1773.9202 -2081.8494 -2081.8494 13591.569 -13591.569
2690 1823.2947 -2083.454 -2083.454 13427.02 -13427.02
2700 1752.2886 -2080.3613 -2080.3613 12790.155 -12790.155
Loop time of 0.401977 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2600 1752.2886 -2080.3613 -2080.3613 12790.155 -12790.155
2610 1747.3086 -2080.0268 -2080.0268 11842.898 -11842.898
2620 1756.8501 -2080.5841 -2080.5841 11650.923 -11650.923
2630 1747.7557 -2079.8425 -2079.8425 11330.938 -11330.938
2640 1755.4611 -2080.1294 -2080.1294 11951.432 -11951.432
2650 1796.0637 -2082.5176 -2082.5176 12140.389 -12140.389
2660 1773.9674 -2080.712 -2080.712 13347.273 -13347.273
2670 1862.117 -2086.1376 -2086.1376 14170.648 -14170.648
2680 1911.7101 -2089.049 -2089.049 14196.35 -14196.35
2690 1811.8014 -2082.1976 -2082.1976 14254.813 -14254.813
2700 1824.6227 -2082.814 -2082.814 14492.429 -14492.429
Loop time of 0.40459 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2700 1824.6227 -2082.814 -2082.814 14492.429 -14492.429
2717 1824.6227 -2213.2652 -2213.2652 9144.515 -9144.515
Loop time of 0.078146 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2700 1824.6227 -2082.814 -2082.814 14492.429 -14492.429
2710 1899.9842 -2087.5754 -2087.5754 14396.883 -14396.883
2720 1831.8355 -2082.9558 -2082.9558 14576.427 -14576.427
2730 1791.3788 -2080.2118 -2080.2118 14051.507 -14051.507
2740 1827.7221 -2082.5277 -2082.5277 13104.608 -13104.608
2750 1812.4592 -2081.4575 -2081.4575 12891.571 -12891.571
2760 1773.9654 -2078.8585 -2078.8585 13099.073 -13099.073
2770 1805.6317 -2080.8621 -2080.8621 12315.736 -12315.736
2780 1803.1617 -2080.6043 -2080.6043 11644.637 -11644.637
2790 1717.1009 -2074.8069 -2074.8069 11760.938 -11760.938
2800 1735.4119 -2075.7987 -2075.7987 12827.546 -12827.546
Loop time of 0.406149 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2800 1735.4119 -2075.7987 -2075.7987 12827.546 -12827.546
2819 1735.4119 -2213.3013 -2213.3013 8530.1318 -8530.1318
Loop time of 0.0863049 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2800 1735.4119 -2075.7987 -2075.7987 12827.546 -12827.546
2810 1802.2056 -2079.855 -2079.855 13919.562 -13919.562
2820 1940.1885 -2088.5707 -2088.5707 14470.417 -14470.417
2830 1933.0396 -2087.8198 -2087.8198 14840.734 -14840.734
2840 1844.1755 -2081.8479 -2081.8479 14604.061 -14604.061
2850 1837.3212 -2081.3583 -2081.3583 14352.808 -14352.808
2860 1826.4544 -2080.6436 -2080.6436 13623.339 -13623.339
2870 1838.1223 -2081.4645 -2081.4645 12763.961 -12763.961
2880 1790.3185 -2078.404 -2078.404 12533.594 -12533.594
2890 1791.5839 -2078.5836 -2078.5836 13205.719 -13205.719
2900 1837.4548 -2081.7215 -2081.7215 13683.351 -13683.351
Loop time of 0.405185 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2900 1837.4548 -2081.7215 -2081.7215 13683.351 -13683.351
2918 1837.4548 -2213.2997 -2213.2997 9235.1507 -9235.1507
Loop time of 0.0724921 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2900 1837.4548 -2081.7215 -2081.7215 13683.351 -13683.351
2910 1814.6656 -2080.3673 -2080.3673 14429.667 -14429.667
2920 1907.2868 -2086.7045 -2086.7045 14525.85 -14525.85
2930 1906.7527 -2087.0631 -2087.0631 14293.074 -14293.074
2940 1859.239 -2084.5047 -2084.5047 13134.716 -13134.716
2950 1790.1922 -2080.6548 -2080.6548 12058.463 -12058.463
2960 1692.7243 -2074.9055 -2074.9055 12611.244 -12611.244
2970 1787.0958 -2081.7786 -2081.7786 11928.751 -11928.751
2980 1787.3509 -2082.4521 -2082.4521 11435.785 -11435.785
2990 1725.6798 -2079.0412 -2079.0412 12294.304 -12294.304
3000 1709.8977 -2078.5866 -2078.5866 13352.743 -13352.743
Loop time of 0.404583 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
3000 1709.8977 -2078.5866 -2078.5866 13352.743 -13352.743
3021 1709.8977 -2213.306 -2213.306 8358.7077 -8358.7077
Loop time of 0.0929589 on 1 procs for 21 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
3000 1709.8977 -2080.3808 -2080.3808 13076.659 -13076.659
Loop time of 13.0575 on 1 procs for 21 steps with 511 atoms
PRD stats:
Dephase time (%) = 2.83172 (21.6866)
Dynamics time (%) = 8.1365 (62.3128)
Quench time (%) = 1.63699 (12.5368)
Other time (%) = 0.275642 (2.11098)
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: 13428 ave 13428 max 13428 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13428
Ave neighs/atom = 26.2779
Neighbor list builds = 92
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
Running on 4 partitions of processors
Step CPU Clock Event Correlated Coincident Replica
1000 0.000 0 0 0 0 0
1100 0.909 400 1 0 1 0
1300 2.326 900 2 0 1 3
1700 4.801 2200 3 0 1 2
1800 5.300 2300 4 1 1 2
2100 7.243 3200 5 0 1 0
2300 8.695 3700 6 0 1 2
2500 10.111 4200 7 0 1 1
3000 13.049 5900 8 0 2 1
Loop time of 13.0574 on 4 procs for 2000 steps with 511 atoms

732
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LAMMPS (27 Mar 2011)
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
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 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 1000
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
110 846.80459 -2134.8152 0 -2078.9916 11904.208
120 1130.5577 -2151.6282 0 -2077.0988 9631.0553
130 1011.5223 -2141.5579 0 -2074.8757 9674.727
140 828.13015 -2127.6781 0 -2073.0856 10663.754
150 1213.6842 -2151.0205 0 -2071.0112 9358.162
160 1118.1701 -2142.223 0 -2068.5102 9705.042
170 815.94964 -2120.3781 0 -2066.5885 11111.781
180 1149.9499 -2140.3762 0 -2064.5684 10362.874
190 1265.3227 -2145.3133 0 -2061.8998 10208.885
200 967.96035 -2123.4032 0 -2059.5927 11429.676
210 1154.8198 -2133.5775 0 -2057.4487 10697.231
220 1309.6664 -2141.0968 0 -2054.7601 10123.484
230 1123.114 -2126.2814 0 -2052.2427 11010.813
240 1262.1761 -2133.0492 0 -2049.8432 10358.728
250 1387.1979 -2138.5224 0 -2047.0746 9224.1203
260 1099.3995 -2117.0127 0 -2044.5373 9902.009
270 1119.6867 -2116.1281 0 -2042.3154 9925.7178
280 1412.0178 -2132.6875 0 -2039.6036 8270.5884
290 1321.0773 -2123.8202 0 -2036.7313 8809.0223
300 1216.0708 -2114.3828 0 -2034.2162 9035.0512
310 1359.9122 -2121.2409 0 -2031.5918 7895.5635
320 1322.8642 -2116.0313 0 -2028.8245 8661.9299
330 1272.4262 -2110.1033 0 -2026.2215 10341.489
340 1451.8803 -2119.1983 0 -2023.4865 10343.627
350 1488.8525 -2118.6967 0 -2020.5476 10786.017
360 1330.5957 -2105.5746 0 -2017.8582 11501.105
370 1452.1996 -2110.9637 0 -2015.2308 11534.951
380 1598.8893 -2117.7127 0 -2012.3096 12209.282
390 1593.9074 -2114.5133 0 -2009.4386 13050.071
400 1580.9099 -2110.9274 0 -2006.7096 12007.149
410 1499.3026 -2102.9454 0 -2004.1074 10088.553
420 1368.9435 -2091.8877 0 -2001.6433 8465.3083
430 1297.2041 -2084.7532 0 -1999.2381 7269.5758
440 1450.1063 -2092.2353 0 -1996.6405 7033.8027
450 1534.8081 -2094.9394 0 -1993.7608 9081.5997
460 1556.639 -2093.5424 0 -1990.9246 12400.015
470 1803.1464 -2106.8774 0 -1988.0092 14192.515
480 1865.4976 -2108.05 0 -1985.0714 16740.251
490 1809.642 -2101.8102 0 -1982.5137 17670.617
500 1875.0318 -2103.7815 0 -1980.1744 15726.048
510 1835.5401 -2099.0223 0 -1978.0186 13590.87
520 1592.2743 -2081.0889 0 -1976.1219 12889.185
530 1621.098 -2081.1646 0 -1974.2975 12097.358
540 1787.4042 -2090.0335 0 -1972.203 11006.55
550 1629.769 -2077.5584 0 -1970.1196 11828.612
560 1633.9967 -2075.8478 0 -1968.1303 13013.747
570 1867.8884 -2089.0683 0 -1965.9321 12589.17
580 1897.3799 -2088.7925 0 -1963.7122 12142.767
590 1675.1213 -2072.2289 0 -1961.8004 12668.905
600 1852.5707 -2082.1073 0 -1959.9809 11872.082
610 1895.1634 -2083.0113 0 -1958.0771 12732.408
620 1759.7637 -2072.4168 0 -1956.4085 14720.014
630 1867.9005 -2077.9673 0 -1954.8303 15446.507
640 1882.4501 -2077.3643 0 -1953.2682 16189.673
650 1830.0215 -2072.5142 0 -1951.8743 15952.621
660 1989.6605 -2081.7336 0 -1950.5699 14441.731
670 2019.3348 -2082.5674 0 -1949.4475 13093.568
680 1806.7881 -2067.7448 0 -1948.6365 13695.415
690 1860.9944 -2070.6335 0 -1947.9518 13711.769
700 2035.4273 -2081.5085 0 -1947.3277 13969.607
710 1924.1115 -2073.7877 0 -1946.9451 14669.272
720 1925.0897 -2073.7075 0 -1946.8005 14665.913
730 1979.7127 -2077.3504 0 -1946.8425 14625.754
740 1932.6041 -2074.5197 0 -1947.1173 15051.1
750 1873.6645 -2071.0745 0 -1947.5575 14804.579
760 1916.3833 -2074.4703 0 -1948.1372 13868.322
770 1893.2199 -2073.6709 0 -1948.8647 14320.209
780 1868.0258 -2072.8444 0 -1949.6991 13913.255
790 1903.3142 -2076.1305 0 -1950.6589 13542.781
800 1852.3079 -2073.8193 0 -1951.7102 13663.021
810 1874.015 -2076.3795 0 -1952.8394 12583.329
820 1897.7242 -2079.181 0 -1954.0779 12629.436
830 1810.9511 -2074.7734 0 -1955.3907 13791.194
840 1751.9411 -2072.1105 0 -1956.6178 14705.479
850 1904.2872 -2083.4009 0 -1957.8652 14745.454
860 1916.5803 -2085.6068 0 -1959.2607 14829.039
870 1838.661 -2081.9371 0 -1960.7276 14932.396
880 1847.5879 -2084.017 0 -1962.219 14581.23
890 1850.4293 -2085.7191 0 -1963.7338 13109.312
900 1822.6233 -2085.4213 0 -1965.2691 13769.397
910 1786.0307 -2084.4806 0 -1966.7407 13450.462
920 1823.0469 -2088.3777 0 -1968.1976 12242.2
930 1731.0515 -2083.7104 0 -1969.5949 11686.755
940 1635.923 -2078.6209 0 -1970.7765 11861.596
950 1731.8445 -2085.9611 0 -1971.7933 11269.332
960 1735.3582 -2087.1207 0 -1972.7212 11587.883
970 1672.4435 -2083.7706 0 -1973.5187 12217.898
980 1703.4917 -2086.4744 0 -1974.1757 12431.952
990 1733.7211 -2089.007 0 -1974.7155 12829.553
1000 1764.9513 -2091.5262 0 -1975.1759 13614.2
Loop time of 3.87072 on 1 procs for 1000 steps with 511 atoms
Pair time (%) = 3.78343 (97.745)
Neigh time (%) = 0.0427222 (1.10373)
Comm time (%) = 0.0135248 (0.349412)
Outpt time (%) = 0.00139475 (0.0360333)
Other time (%) = 0.0296438 (0.765847)
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: 13440 ave 13440 max 13440 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13440
Ave neighs/atom = 26.3014
Neighbor list builds = 44
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
Memory usage per processor = 3.73877 Mbytes
Step Temp PotEng pe Press press
1000 1764.9513 -2091.5262 -2091.5262 13614.2 -13614.2
1010 1764.9513 -2212.5976 -2212.5976 8682.8748 -8682.8748
1018 1764.9513 -2213.2997 -2213.2997 8735.7723 -8735.7723
Loop time of 0.0828302 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1000 1764.9513 -2091.5262 -2091.5262 13614.2 -13614.2
1010 1834.8521 -2094.3013 -2094.3013 12230.025 -12230.025
1020 1788.4153 -2094.0289 -2094.0289 11526.376 -11526.376
1030 1718.6535 -2089.1334 -2089.1334 11778.672 -11778.672
1040 1758.9268 -2086.8503 -2086.8503 12461.878 -12461.878
1050 1812.0032 -2088.0691 -2088.0691 11504.047 -11504.047
1060 1675.9043 -2080.2513 -2080.2513 11187.457 -11187.457
1070 1878.1639 -2085.7821 -2085.7821 11141.419 -11141.419
1080 1754.6906 -2083.1783 -2083.1783 11883.271 -11883.271
1090 1755.0825 -2080.5598 -2080.5598 12810.039 -12810.039
1100 1773.4324 -2079.1267 -2079.1267 12213.815 -12213.815
Loop time of 0.40258 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1000 1773.4324 -2079.1267 -2079.1267 12213.815 -12213.815
1010 1768.6075 -2079.0905 -2079.0905 12599.877 -12599.877
1020 1778.9872 -2080.0251 -2080.0251 11999.911 -11999.911
1030 1775.3752 -2079.999 -2079.999 11956.363 -11956.363
1040 1811.4825 -2082.5736 -2082.5736 13045.817 -13045.817
1050 1857.444 -2085.8297 -2085.8297 13368.842 -13368.842
1060 1807.8684 -2082.8382 -2082.8382 14221.151 -14221.151
1070 1770.9296 -2080.6812 -2080.6812 14764.483 -14764.483
1080 1866.0553 -2087.2498 -2087.2498 12934.836 -12934.836
1090 1788.0574 -2082.429 -2082.429 12145.714 -12145.714
1100 1796.7073 -2083.3393 -2083.3393 13219.949 -13219.949
Loop time of 0.409394 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1100 1796.7073 -2083.3393 -2083.3393 13219.949 -13219.949
1119 1796.7073 -2213.2857 -2213.2857 8950.2482 -8950.2482
Loop time of 0.0817189 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1100 1796.7073 -2085.5621 -2085.5621 12749.682 -12749.682
1110 1750.5827 -2082.8155 -2082.8155 11973.974 -11973.974
1120 1748.5509 -2082.9291 -2082.9291 10734.144 -10734.144
1130 1673.4261 -2078.1286 -2078.1286 10562.538 -10562.538
1140 1654.6136 -2076.8965 -2076.8965 11764.85 -11764.85
1150 1724.3547 -2081.3371 -2081.3371 11837.922 -11837.922
1160 1789.0551 -2085.3383 -2085.3383 11666.866 -11666.866
1170 1753.7677 -2082.7026 -2082.7026 12675.689 -12675.689
1180 1796.824 -2085.1982 -2085.1982 13903.742 -13903.742
1190 1872.0159 -2089.7921 -2089.7921 14584.813 -14584.813
1200 1916.4398 -2092.4391 -2092.4391 14959.949 -14959.949
Loop time of 0.408302 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1200 1916.4398 -2092.4391 -2092.4391 14959.949 -14959.949
1217 1916.4398 -2213.3155 -2213.3155 9778.489 -9778.489
Loop time of 0.078119 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1200 1916.4398 -2092.4391 -2092.4391 14959.949 -14959.949
1210 1675.7593 -2082.4079 -2082.4079 14585.22 -14585.22
1220 1845.2242 -2085.095 -2085.095 14281.38 -14281.38
1230 1779.4946 -2083.466 -2083.466 14423.928 -14423.928
1240 1861.3885 -2087.2255 -2087.2255 13713.134 -13713.134
1250 1872.7715 -2091.7812 -2091.7812 12764.426 -12764.426
1260 1825.2394 -2093.2555 -2093.2555 12369.817 -12369.817
1270 1839.9173 -2095.7337 -2095.7337 13020.922 -13020.922
1280 1799.7895 -2095.606 -2095.606 13163.659 -13163.659
1290 1715.9861 -2089.9263 -2089.9263 13140.033 -13140.033
1300 1795.312 -2089.4428 -2089.4428 13766.346 -13766.346
Loop time of 0.402283 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1200 1795.312 -2089.4428 -2089.4428 13766.346 -13766.346
1210 1768.9906 -2087.5243 -2087.5243 12982.75 -12982.75
1220 1705.7092 -2083.1216 -2083.1216 12557.139 -12557.139
1230 1724.1144 -2084.0042 -2084.0042 11625.882 -11625.882
1240 1784.4172 -2087.553 -2087.553 11642.759 -11642.759
1250 1739.4891 -2084.1093 -2084.1093 12660.681 -12660.681
1260 1741.2481 -2083.6821 -2083.6821 13501.897 -13501.897
1270 1898.2074 -2093.4307 -2093.4307 13680.577 -13680.577
1280 1814.3041 -2087.3387 -2087.3387 13984.674 -13984.674
1290 1728.5937 -2081.1956 -2081.1956 14152.533 -14152.533
1300 1827.4489 -2087.163 -2087.163 13112.89 -13112.89
Loop time of 0.408596 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1300 1827.4489 -2087.163 -2087.163 13112.89 -13112.89
1318 1827.4489 -2213.2636 -2213.2636 9162.3198 -9162.3198
Loop time of 0.0800829 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1300 1827.4489 -2087.163 -2087.163 13112.89 -13112.89
1310 1824.6764 -2086.4198 -2086.4198 12595.394 -12595.394
1320 1704.6794 -2077.9725 -2077.9725 12519.487 -12519.487
1330 1733.9238 -2079.3053 -2079.3053 10955.938 -10955.938
1340 1767.4849 -2080.8047 -2080.8047 10529.7 -10529.7
1350 1762.8843 -2079.7423 -2079.7423 11122.068 -11122.068
1360 1815.5163 -2082.4132 -2082.4132 12334.647 -12334.647
1370 1830.8674 -2082.619 -2082.619 13476.773 -13476.773
1380 1836.8237 -2082.253 -2082.253 14022.573 -14022.573
1390 1853.5334 -2082.6462 -2082.6462 14666.103 -14666.103
1400 1859.7676 -2082.4142 -2082.4142 15051.952 -15051.952
Loop time of 0.410802 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1400 1859.7676 -2082.4142 -2082.4142 15051.952 -15051.952
1418 1859.7676 -2213.2763 -2213.2763 9381.7315 -9381.7315
Loop time of 0.070435 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1400 1859.7676 -2082.4142 -2082.4142 15051.952 -15051.952
1410 1893.8876 -2088.047 -2088.047 14042.151 -14042.151
1420 1656.6444 -2078.0482 -2078.0482 13960.779 -13960.779
1430 1977.0382 -2089.1253 -2089.1253 14883.226 -14883.226
1440 1816.1299 -2089.7082 -2089.7082 12909.044 -12909.044
1450 1806.4515 -2089.692 -2089.692 11739.293 -11739.293
1460 1714.9443 -2083.6389 -2083.6389 11714.61 -11714.61
1470 1801.9111 -2083.2878 -2083.2878 11904.078 -11904.078
1480 1807.3084 -2083.283 -2083.283 11797.261 -11797.261
1490 1750.4004 -2079.5205 -2079.5205 12103.929 -12103.929
1500 1826.9416 -2080.7804 -2080.7804 13680.5 -13680.5
Loop time of 0.404239 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1400 1826.9416 -2080.7804 -2080.7804 13680.5 -13680.5
1410 1862.2011 -2082.6116 -2082.6116 13879.33 -13879.33
1420 1850.4127 -2081.4124 -2081.4124 13534.06 -13534.06
1430 1798.6982 -2077.6455 -2077.6455 13422.583 -13422.583
1440 1845.9989 -2080.4286 -2080.4286 13746.467 -13746.467
1450 1906.4945 -2084.1305 -2084.1305 14400.739 -14400.739
1460 1888.6219 -2082.7918 -2082.7918 14196.206 -14196.206
1470 1863.8249 -2081.1143 -2081.1143 14470.026 -14470.026
1480 1896.4747 -2083.342 -2083.342 14564.107 -14564.107
1490 1840.0294 -2079.7889 -2079.7889 15217.99 -15217.99
1500 1857.0723 -2081.1669 -2081.1669 14907.999 -14907.999
Loop time of 0.411172 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1500 1857.0723 -2081.1669 -2081.1669 14907.999 -14907.999
1520 1857.0723 -2213.2604 -2213.2604 9362.185 -9362.185
Loop time of 0.0970201 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1500 1857.0723 -2081.1669 -2081.1669 14907.999 -14907.999
1510 1862.6554 -2081.858 -2081.858 13573.264 -13573.264
1520 1832.9218 -2080.309 -2080.309 12402.702 -12402.702
1530 1785.3092 -2077.6036 -2077.6036 11814.149 -11814.149
1540 1825.9059 -2080.7261 -2080.7261 11770.252 -11770.252
1550 1795.8155 -2079.2124 -2079.2124 13174.86 -13174.86
1560 1744.7307 -2076.2845 -2076.2845 13250.941 -13250.941
1570 1794.5229 -2079.9675 -2079.9675 12122.881 -12122.881
1580 1797.9896 -2080.5822 -2080.5822 11926.482 -11926.482
1590 1775.9043 -2079.5023 -2079.5023 12677.412 -12677.412
1600 1832.3086 -2083.5913 -2083.5913 13977.106 -13977.106
Loop time of 0.408911 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1600 1832.3086 -2083.5913 -2083.5913 13977.106 -13977.106
1621 1832.3086 -2213.3137 -2213.3137 9196.559 -9196.559
Loop time of 0.0975041 on 1 procs for 21 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1600 1832.3086 -2083.5913 -2083.5913 13977.106 -13977.106
1610 1880.4604 -2087.2026 -2087.2026 15086.696 -15086.696
1620 1786.0535 -2081.4694 -2081.4694 14896.103 -14896.103
1630 1836.272 -2085.2962 -2085.2962 13775.173 -13775.173
1640 1892.5825 -2089.5967 -2089.5967 13148.608 -13148.608
1650 1771.3954 -2082.266 -2082.266 13180.554 -13180.554
1660 1722.0245 -2079.6093 -2079.6093 13182.384 -13182.384
1670 1827.7886 -2087.1366 -2087.1366 12746.428 -12746.428
1680 1789.6814 -2085.1909 -2085.1909 13160.817 -13160.817
1690 1721.5672 -2081.2173 -2081.2173 14170.727 -14170.727
1700 1844.2249 -2089.7859 -2089.7859 14599.737 -14599.737
Loop time of 0.406368 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1700 1844.2249 -2089.7859 -2089.7859 14599.737 -14599.737
1717 1844.2249 -2213.2611 -2213.2611 9275.9867 -9275.9867
Loop time of 0.080898 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1700 1844.2249 -2087.6647 -2087.6647 12738.882 -12738.882
1710 1814.5475 -2086.2123 -2086.2123 14107.726 -14107.726
1720 1773.1656 -2084.0002 -2084.0002 14449.417 -14449.417
1730 1834.0635 -2088.5249 -2088.5249 13597.224 -13597.224
1740 1865.1657 -2091.147 -2091.147 12703.147 -12703.147
1750 1773.8268 -2085.7417 -2085.7417 12346.629 -12346.629
1760 1749.9529 -2084.7483 -2084.7483 12323.265 -12323.265
1770 1763.6027 -2086.1766 -2086.1766 11974.478 -11974.478
1780 1724.2073 -2084.0301 -2084.0301 11865.223 -11865.223
1790 1797.6762 -2089.2757 -2089.2757 11445.896 -11445.896
1800 1779.8767 -2088.4809 -2088.4809 10285.887 -10285.887
Loop time of 0.407208 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1800 1779.8767 -2088.4809 -2088.4809 10285.887 -10285.887
1816 1779.8767 -2213.2303 -2213.2303 8829.5454 -8829.5454
Loop time of 0.0715559 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1800 1779.8767 -2086.3241 -2086.3241 14199.449 -14199.449
1810 1963.5412 -2098.9207 -2098.9207 13956.106 -13956.106
1820 1753.2743 -2085.643 -2085.643 15049.903 -15049.903
1830 1761.817 -2086.7699 -2086.7699 13908.44 -13908.44
1840 1821.9139 -2091.283 -2091.283 11939.624 -11939.624
1850 1609.9437 -2077.7938 -2077.7938 11999.742 -11999.742
1860 1576.119 -2075.8191 -2075.8191 11623.222 -11623.222
1870 1760.9032 -2088.0697 -2088.0697 10214.742 -10214.742
1880 1625.1319 -2079.027 -2079.027 11759.632 -11759.632
1890 1706.1163 -2084.1255 -2084.1255 13505.074 -13505.074
1900 2028.3849 -2105.0322 -2105.0322 13575.891 -13575.891
Loop time of 0.409337 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
1900 2028.3849 -2105.0322 -2105.0322 13575.891 -13575.891
1917 2028.3849 -2213.2753 -2213.2753 10540.806 -10540.806
Loop time of 0.0757649 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1900 2028.3849 -2105.0322 -2105.0322 13575.891 -13575.891
1910 1710.5601 -2078.3574 -2078.3574 12757.803 -12757.803
1920 1835.7195 -2080.3835 -2080.3835 13164.925 -13164.925
1930 1898.9488 -2086.6346 -2086.6346 12737.979 -12737.979
1940 1821.2008 -2087.8239 -2087.8239 11845.85 -11845.85
1950 1747.4523 -2084.1487 -2084.1487 10859.973 -10859.973
1960 1837.3402 -2086.3748 -2086.3748 11955.123 -11955.123
1970 1800.5442 -2086.1944 -2086.1944 11390.897 -11390.897
1980 1781.0658 -2084.7277 -2084.7277 11612.595 -11612.595
1990 1888.7735 -2090.3722 -2090.3722 12064.74 -12064.74
2000 1774.4774 -2088.5245 -2088.5245 11977.716 -11977.716
Loop time of 0.407705 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
1900 1774.4774 -2088.5245 -2088.5245 11977.716 -11977.716
1910 1745.4216 -2086.4038 -2086.4038 11788.462 -11788.462
1920 1750.1793 -2086.453 -2086.453 12053.602 -12053.602
1930 1744.5431 -2085.7408 -2085.7408 12066.016 -12066.016
1940 1741.0435 -2085.0883 -2085.0883 11478.678 -11478.678
1950 1794.5224 -2088.1241 -2088.1241 10863.736 -10863.736
1960 1758.7026 -2085.2218 -2085.2218 11203.404 -11203.404
1970 1768.7224 -2085.3092 -2085.3092 11657.077 -11657.077
1980 1811.3753 -2087.4961 -2087.4961 11091.279 -11091.279
1990 1747.8981 -2082.6727 -2082.6727 11548.445 -11548.445
2000 1755.9915 -2082.5343 -2082.5343 11333.481 -11333.481
Loop time of 0.407647 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2000 1755.9915 -2082.5343 -2082.5343 11333.481 -11333.481
2019 1755.9915 -2213.3066 -2213.3066 8674.2556 -8674.2556
Loop time of 0.089658 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2000 1755.9915 -2082.5343 -2082.5343 11333.481 -11333.481
2010 1761.1094 -2082.1317 -2082.1317 11084.246 -11084.246
2020 1744.6823 -2080.26 -2080.26 11524.056 -11524.056
2030 1808.8206 -2083.6502 -2083.6502 11971.904 -11971.904
2040 1829.9048 -2084.1883 -2084.1883 12142.306 -12142.306
2050 1836.4413 -2083.8244 -2083.8244 12001.056 -12001.056
2060 1781.8854 -2079.486 -2079.486 11768.476 -11768.476
2070 1794.7673 -2079.6173 -2079.6173 12166.543 -12166.543
2080 1873.1739 -2084.0683 -2084.0683 12126.602 -12126.602
2090 1821.6532 -2080.0204 -2080.0204 12255.663 -12255.663
2100 1802.2063 -2078.1614 -2078.1614 11727.78 -11727.78
Loop time of 0.409856 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2100 1802.2063 -2078.1614 -2078.1614 11727.78 -11727.78
2119 1802.2063 -2213.2929 -2213.2929 8991.4741 -8991.4741
Loop time of 0.0743029 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2100 1802.2063 -2082.9637 -2082.9637 11520.819 -11520.819
2110 1793.1593 -2081.8009 -2081.8009 11125.958 -11125.958
2120 1754.5303 -2078.6831 -2078.6831 11793.164 -11793.164
2130 1786.5596 -2080.1874 -2080.1874 11778.309 -11778.309
2140 1817.4038 -2081.5833 -2081.5833 12754.803 -12754.803
2150 1860.3499 -2083.7984 -2083.7984 13352.499 -13352.499
2160 1855.8568 -2082.9459 -2082.9459 13288.364 -13288.364
2170 1842.645 -2081.6082 -2081.6082 12420.723 -12420.723
2180 1798.1901 -2078.2551 -2078.2551 12701.879 -12701.879
2190 1850.2207 -2081.2903 -2081.2903 12735.397 -12735.397
2200 1855.7827 -2081.2935 -2081.2935 13374.582 -13374.582
Loop time of 0.40881 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2200 1855.7827 -2081.2935 -2081.2935 13374.582 -13374.582
2219 1855.7827 -2213.3068 -2213.3068 9361.4835 -9361.4835
Loop time of 0.0855231 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2200 1855.7827 -2081.2935 -2081.2935 13374.582 -13374.582
2210 1695.2731 -2082.804 -2082.804 12630.321 -12630.321
2220 1800.3325 -2082.439 -2082.439 12850.891 -12850.891
2230 1770.4518 -2080.0844 -2080.0844 12724.119 -12724.119
2240 1806.8299 -2080.0756 -2080.0756 12814.992 -12814.992
2250 1912.2973 -2087.0341 -2087.0341 13273.364 -13273.364
2260 1741.8142 -2082.7771 -2082.7771 11373.1 -11373.1
2270 1791.5148 -2081.7326 -2081.7326 11674.374 -11674.374
2280 1809.6684 -2081.8344 -2081.8344 12620.287 -12620.287
2290 1801.0314 -2081.3547 -2081.3547 12248.713 -12248.713
2300 1828.8191 -2082.6771 -2082.6771 12396.637 -12396.637
Loop time of 0.409151 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2200 1828.8191 -2082.6771 -2082.6771 12396.637 -12396.637
2210 1852.3889 -2083.6639 -2083.6639 13257.91 -13257.91
2220 1861.8897 -2083.7723 -2083.7723 13370.054 -13370.054
2230 1788.0538 -2078.4361 -2078.4361 13998.855 -13998.855
2240 1794.212 -2078.3662 -2078.3662 13775.655 -13775.655
2250 1866.778 -2082.65 -2082.65 13506.462 -13506.462
2260 1839.2432 -2080.3603 -2080.3603 13172.468 -13172.468
2270 1839.9435 -2079.9745 -2079.9745 14361.753 -14361.753
2280 1887.7781 -2082.7306 -2082.7306 14552.554 -14552.554
2290 1925.7098 -2084.9175 -2084.9175 14519.907 -14519.907
2300 1916.0079 -2084.1046 -2084.1046 14584.913 -14584.913
Loop time of 0.409067 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2300 1916.0079 -2084.1046 -2084.1046 14584.913 -14584.913
2319 1916.0079 -2213.2993 -2213.2993 9773.1171 -9773.1171
Loop time of 0.0894969 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2300 1916.0079 -2088.3257 -2088.3257 13764.179 -13764.179
2310 1814.5886 -2081.586 -2081.586 14763.224 -14763.224
2320 1875.0182 -2085.6036 -2085.6036 14365.334 -14365.334
2330 1859.2579 -2084.6751 -2084.6751 13654.954 -13654.954
2340 1774.0363 -2079.2509 -2079.2509 12594.742 -12594.742
2350 1753.4548 -2078.1016 -2078.1016 12122.001 -12122.001
2360 1688.1782 -2073.9515 -2073.9515 10903.365 -10903.365
2370 1699.8238 -2074.7632 -2074.7632 10769.884 -10769.884
2380 1806.129 -2081.7078 -2081.7078 11357.625 -11357.625
2390 1837.812 -2083.7012 -2083.7012 13519.308 -13519.308
2400 1826.2652 -2082.8658 -2082.8658 15180.439 -15180.439
Loop time of 0.411544 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2400 1826.2652 -2082.8658 -2082.8658 15180.439 -15180.439
2417 1826.2652 -2213.3092 -2213.3092 9155.6156 -9155.6156
Loop time of 0.0703421 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2400 1826.2652 -2082.8658 -2082.8658 15180.439 -15180.439
2410 1765.7942 -2081.0768 -2081.0768 12933.963 -12933.963
2420 1824.4274 -2082.5842 -2082.5842 13311.919 -13311.919
2430 1880.4116 -2087.8123 -2087.8123 12328.175 -12328.175
2440 1720.9864 -2082.5145 -2082.5145 12731.77 -12731.77
2450 1806.7242 -2082.7946 -2082.7946 12945.304 -12945.304
2460 1831.3683 -2084.6693 -2084.6693 13773.335 -13773.335
2470 1818.9364 -2085.7078 -2085.7078 13027.028 -13027.028
2480 1822.7531 -2086.9924 -2086.9924 12394.215 -12394.215
2490 1776.8696 -2085.2206 -2085.2206 12737.989 -12737.989
2500 1851.6152 -2088.3462 -2088.3462 12516.663 -12516.663
Loop time of 0.406191 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2400 1851.6152 -2088.3462 -2088.3462 12516.663 -12516.663
2410 1786.5123 -2083.7928 -2083.7928 12797.716 -12797.716
2420 1780.159 -2083.1059 -2083.1059 13333.963 -13333.963
2430 1765.7236 -2081.8298 -2081.8298 13096.054 -13096.054
2440 1746.165 -2080.1478 -2080.1478 12767.858 -12767.858
2450 1827.0178 -2084.9985 -2084.9985 12818.323 -12818.323
2460 1848.5558 -2085.9208 -2085.9208 12742.955 -12742.955
2470 1705.6862 -2076.0101 -2076.0101 13465.144 -13465.144
2480 1755.6215 -2078.7318 -2078.7318 12536.565 -12536.565
2490 1899.8246 -2087.5597 -2087.5597 12201.591 -12201.591
2500 1793.6778 -2079.9054 -2079.9054 13211.504 -13211.504
Loop time of 0.408345 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2500 1793.6778 -2079.9054 -2079.9054 13211.504 -13211.504
2519 1793.6778 -2213.2913 -2213.2913 8942.3029 -8942.3029
Loop time of 0.085089 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2500 1793.6778 -2085.5282 -2085.5282 13329.786 -13329.786
2510 1813.0407 -2086.1987 -2086.1987 13104.609 -13104.609
2520 1787.2892 -2083.8682 -2083.8682 13292.371 -13292.371
2530 1809.8629 -2084.7137 -2084.7137 12551.343 -12551.343
2540 1805.5762 -2083.7605 -2083.7605 13063.749 -13063.749
2550 1793.2104 -2082.2809 -2082.2809 12744.592 -12744.592
2560 1770.3168 -2080.0819 -2080.0819 11764.673 -11764.673
2570 1790.0827 -2080.6602 -2080.6602 11962.803 -11962.803
2580 1819.1303 -2081.8151 -2081.8151 12532.765 -12532.765
2590 1824.7175 -2081.4349 -2081.4349 13202.784 -13202.784
2600 1825.2987 -2080.7548 -2080.7548 14306.382 -14306.382
Loop time of 0.406173 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2600 1825.2987 -2080.7548 -2080.7548 14306.382 -14306.382
2618 1825.2987 -2213.3059 -2213.3059 9150.7731 -9150.7731
Loop time of 0.0768468 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2600 1825.2987 -2080.7548 -2080.7548 14306.382 -14306.382
2610 1784.9821 -2080.6813 -2080.6813 12985.059 -12985.059
2620 1843.7523 -2082.8626 -2082.8626 12889.055 -12889.055
2630 1800.4269 -2082.209 -2082.209 13818.476 -13818.476
2640 1839.5397 -2084.1465 -2084.1465 13399.821 -13399.821
2650 1821.0879 -2084.8907 -2084.8907 13328.045 -13328.045
2660 1789.0961 -2083.5551 -2083.5551 12582.728 -12582.728
2670 1783.3233 -2081.837 -2081.837 12501.936 -12501.936
2680 1951.4454 -2091.2365 -2091.2365 12332.666 -12332.666
2690 1713.8438 -2085.0703 -2085.0703 10952.772 -10952.772
2700 1754.4056 -2081.5244 -2081.5244 10044.432 -10044.432
Loop time of 0.403806 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2600 1754.4056 -2081.5244 -2081.5244 10044.432 -10044.432
2610 1751.1104 -2080.7397 -2080.7397 9944.2439 -9944.2439
2620 1793.1869 -2082.8983 -2082.8983 10283.032 -10283.032
2630 1753.7841 -2079.6747 -2079.6747 9864.1828 -9864.1828
2640 1634.5724 -2071.1529 -2071.1529 9893.7968 -9893.7968
2650 1767.151 -2079.1178 -2079.1178 10547.214 -10547.214
2660 1871.7471 -2085.1534 -2085.1534 12009.968 -12009.968
2670 1821.4368 -2081.0824 -2081.0824 14019.852 -14019.852
2680 1871.8392 -2083.7726 -2083.7726 14367.625 -14367.625
2690 1959.1372 -2089.0439 -2089.0439 12166.14 -12166.14
2700 1828.2882 -2080.1299 -2080.1299 12793.753 -12793.753
Loop time of 0.407702 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2700 1828.2882 -2080.1299 -2080.1299 12793.753 -12793.753
2721 1828.2882 -2213.3285 -2213.3285 9173.7894 -9173.7894
Loop time of 0.0986738 on 1 procs for 21 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2700 1828.2882 -2080.1299 -2080.1299 12793.753 -12793.753
2710 1816.4004 -2079.1813 -2079.1813 11823.058 -11823.058
2720 1877.706 -2083.108 -2083.108 10556.298 -10556.298
2730 1775.5997 -2076.3317 -2076.3317 11741.929 -11741.929
2740 1755.1843 -2074.9343 -2074.9343 12585.733 -12585.733
2750 1864.4172 -2082.0747 -2082.0747 11527.238 -11527.238
2760 1792.1277 -2077.2833 -2077.2833 11836.835 -11836.835
2770 1748.8951 -2074.4154 -2074.4154 11324.664 -11324.664
2780 1835.5108 -2080.0744 -2080.0744 10942.566 -10942.566
2790 1851.8779 -2081.1448 -2081.1448 11080.974 -11080.974
2800 1747.4946 -2074.2759 -2074.2759 12177.968 -12177.968
Loop time of 0.410337 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2800 1747.4946 -2074.2759 -2074.2759 12177.968 -12177.968
2818 1747.4946 -2213.2785 -2213.2785 8613.9615 -8613.9615
Loop time of 0.0771759 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2800 1747.4946 -2074.2759 -2074.2759 12177.968 -12177.968
2810 1863.2903 -2081.9222 -2081.9222 12267.805 -12267.805
2820 1914.2959 -2085.354 -2085.354 13681.201 -13681.201
2830 1858.6704 -2081.8678 -2081.8678 14955.854 -14955.854
2840 1919.1063 -2086.1193 -2086.1193 13785.748 -13785.748
2850 1961.8598 -2089.3537 -2089.3537 12806.759 -12806.759
2860 1791.6941 -2078.6502 -2078.6502 12300.141 -12300.141
2870 1706.8756 -2073.4991 -2073.4991 11049.969 -11049.969
2880 1761.9399 -2077.4437 -2077.4437 10260.512 -10260.512
2890 1746.8886 -2076.6825 -2076.6825 10092.346 -10092.346
2900 1672.4156 -2071.8929 -2071.8929 10600.89 -10600.89
Loop time of 0.406457 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
2900 1672.4156 -2071.8929 -2071.8929 10600.89 -10600.89
2917 1672.4156 -2213.2396 -2213.2396 8097.4138 -8097.4138
Loop time of 0.0706711 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
2900 1672.4156 -2071.8929 -2071.8929 10600.89 -10600.89
2910 1777.2823 -2078.8099 -2078.8099 11179.362 -11179.362
2920 1855.0223 -2083.8989 -2083.8989 11882.495 -11882.495
2930 1822.0838 -2081.7366 -2081.7366 13823.043 -13823.043
2940 1895.6335 -2086.6487 -2086.6487 14884.575 -14884.575
2950 1981.0864 -2092.5002 -2092.5002 14084.26 -14084.26
2960 1845.9932 -2083.9972 -2083.9972 12386.166 -12386.166
2970 1761.7427 -2078.8941 -2078.8941 11938.071 -11938.071
2980 1795.2713 -2081.5266 -2081.5266 11328.682 -11328.682
2990 1732.1529 -2077.755 -2077.755 11706.457 -11706.457
3000 1671.6507 -2074.0434 -2074.0434 11937.414 -11937.414
Loop time of 0.406952 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.27283 Mbytes
Step Temp PotEng pe Press press
3000 1671.6507 -2074.0434 -2074.0434 11937.414 -11937.414
3018 1671.6507 -2213.2792 -2213.2792 8092.9613 -8092.9613
Loop time of 0.0796878 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.58618 Mbytes
Step Temp PotEng pe Press press
3000 1671.6507 -2080.3808 -2080.3808 12813.976 -12813.976
Loop time of 13.0575 on 1 procs for 18 steps with 511 atoms
PRD stats:
Dephase time (%) = 2.83595 (21.7191)
Dynamics time (%) = 8.17298 (62.5925)
Quench time (%) = 1.63057 (12.4876)
Other time (%) = 0.276808 (2.11992)
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: 13428 ave 13428 max 13428 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13428
Ave neighs/atom = 26.2779
Neighbor list builds = 96
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# 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 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 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 = 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
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
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
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
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
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
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
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
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
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
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 0.487912 on 1 procs for 100 steps with 21 atoms
Pair time (%) = 0.484811 (99.3644)
Neigh time (%) = 0.00102997 (0.211097)
Comm time (%) = 0.000718117 (0.147182)
Outpt time (%) = 0.00103259 (0.211635)
Other time (%) = 0.000320435 (0.0656747)
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 (27 Mar 2011)
# 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 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 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 = 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
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
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
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
40 3.0282685 -2047.891 -2047.7104 30.336595 -3289.3528 -47.139173 38.279831 0 66.53636 0 -49.390316 0 -11.653427 -10.563935 1329.3595 -250.00754 0 176.0405
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
60 3.0218388 -2047.8023 -2047.6221 885.1484 -3292.0396 -45.863086 38.789338 0 65.025617 0 -49.476197 0 -12.121867 -10.716179 1332.8811 -253.48777 0 179.20626
70 3.797826 -2048.011 -2047.7846 -398.03857 -3284.608 -48.012567 38.532982 0 63.022244 0 -49.543287 0 -12.778329 -10.464772 1330.5391 -254.32484 0 179.62647
80 3.7467426 -2047.9462 -2047.7229 225.47933 -3288.7606 -46.997709 38.381051 0 63.608793 0 -49.422504 0 -11.700043 -10.431202 1332.0713 -252.49254 0 177.79726
90 2.6678279 -2047.73 -2047.571 -443.01212 -3285.3945 -48.014399 38.024282 0 64.621005 0 -49.342673 0 -12.417475 -10.291001 1329.5228 -249.44266 0 175.00454
100 2.767748 -2047.8632 -2047.6981 -203.18448 -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 0.379835 on 4 procs for 100 steps with 21 atoms
Pair time (%) = 0.260089 (68.4743)
Neigh time (%) = 0.000309467 (0.0814741)
Comm time (%) = 0.117555 (30.9489)
Outpt time (%) = 0.00158453 (0.417162)
Other time (%) = 0.000297129 (0.0782258)
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 (27 Mar 2011)
# 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 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 -6403.603 0 4322.6325
4 24.486471 -45005.44 -44977.485 361762.17 -65920.24 24.475564 608.40641 0 2039.9553 5.3711579 -423.11592 -3576.4623 -444.04851 -518.30012 25279.759 -6405.6643 0 4324.4241
5 38.17262 -45021.065 -44977.486 367944.35 -65936.199 33.013132 609.35384 0 2036.8556 5.3670795 -422.37437 -3581.9521 -443.93515 -518.52248 25278.899 -6408.1551 0 4326.5837
6 54.814793 -45040.072 -44977.492 375525.24 -65955.782 43.548646 610.50446 0 2033.0959 5.3622834 -421.45833 -3588.6378 -443.79722 -518.79674 25277.871 -6411.2602 0 4329.2785
7 74.361854 -45062.565 -44977.67 384488.11 -65979.036 56.14069 611.85396 0 2028.6932 5.3568834 -420.36227 -3596.6686 -443.63511 -519.12443 25276.688 -6414.9043 0 4332.4333
8 96.753115 -45088.134 -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 -6419.1781 0 4336.151
9 121.91206 -45116.369 -44977.188 406680.23 -66036.769 87.771045 615.12844 0 2018.7397 5.3448206 -417.60463 -3616.0503 -443.24033 -519.94764 25273.922 -6423.9824 0 4340.3188
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 -6429.3928 0 4345.02
11 180.18901 -45182.93 -44977.217 433126.48 -66109.859 128.51815 619.12702 0 2005.8371 5.3321158 -414.04636 -3639.6783 -442.75323 -521.00943 25270.759 -6435.3936 0 4350.2365
12 213.10176 -45220.695 -44977.407 447323.77 -66152.305 152.51815 621.3781 0 1998.6206 5.3259063 -411.94885 -3653.2385 -442.47944 -521.6355 25269.085 -6441.9987 0 4355.9833
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 4362.2746
14 285.77131 -45303.579 -44977.328 474776.65 -66249.179 208.15938 626.33277 0 1982.9202 5.3142108 -407.08274 -3682.8223 -441.87093 -523.08579 25265.687 -6457.0633 0 4369.1114
15 325.13312 -45348.554 -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 -6465.5342 0 4376.504
16 366.14805 -45395.422 -44977.409 493592.8 -66361.841 274.33138 631.79729 0 1966.107 5.3026576 -401.28492 -3716.0758 -441.19624 -524.7927 25262.409 -6474.6447 0 4384.466
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 -6484.3973 0 4392.998
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 -6494.7905 0 4402.1013
19 494.65084 -45542.336 -44977.618 473698.75 -66556.967 392.9281 640.57527 0 1941.6376 5.2731328 -390.79122 -3771.3986 -440.08124 -527.67642 25258.211 -6505.8237 0 4411.777
20 537.15237 -45590.95 -44977.71 445393.53 -66627.054 437.01837 643.53106 0 1934.773 5.253285 -386.81774 -3790.967 -439.68929 -528.63394 25257.103 -6517.4576 0 4421.9908
21 578.07544 -45637.77 -44977.81 403759.01 -66698.344 482.89589 646.43599 0 1929.1799 5.2239444 -382.61485 -3810.9481 -439.2906 -529.52762 25256.17 -6529.7434 0 4432.792
22 616.45505 -45681.683 -44977.907 349235.79 -66769.835 530.15195 649.24824 0 1925.2752 5.1819278 -378.19171 -3831.2452 -438.88741 -530.31106 25255.425 -6542.6381 0 4444.143
23 651.3754 -45721.629 -44977.987 284158.55 -66840.508 578.34297 651.92981 0 1923.441 5.1243532 -373.56052 -3851.7589 -438.48202 -530.9385 25254.87 -6556.0384 0 4455.9487
24 682.06338 -45756.048 -44977.37 211816.13 -66909.459 627.03832 654.45076 0 1923.9682 5.0492645 -368.73671 -3872.421 -437.32012 -531.38912 25254.506 -6570.0032 0 4468.2687
25 708.05182 -45785.744 -44977.396 138937.29 -66976.018 675.86582 656.79217 0 1927.0098 4.9561644 -363.73915 -3893.0659 -436.84675 -531.60529 25254.329 -6584.4413 0 4481.0194
Loop time of 8.51769 on 1 procs for 25 steps with 384 atoms
Pair time (%) = 8.43445 (99.0227)
Neigh time (%) = 0.0736611 (0.864802)
Comm time (%) = 0.00435424 (0.05112)
Outpt time (%) = 0.00265884 (0.0312156)
Other time (%) = 0.00256538 (0.0301183)
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 (27 Mar 2011)
# 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 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 -44977.461 -44977.461 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 4320.617
1 1.5362502 -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 -44993.222 -44977.469 356972.83 -65907.867 17.887012 607.66575 0 2042.3809 5.3744256 -423.68764 -3572.1806 -444.13698 -518.12843 25280.439 -6403.6018 0 4322.6343
4 24.486472 -45005.435 -44977.48 361762.2 -65920.24 24.475564 608.40641 0 2039.9553 5.3711579 -423.11592 -3576.4623 -444.04851 -518.30012 25279.759 -6405.6504 0 4324.4149
5 38.17262 -45021.065 -44977.485 367944.29 -65936.199 33.013132 609.35384 0 2036.8556 5.3670795 -422.37437 -3581.9521 -443.93515 -518.52248 25278.899 -6408.1788 0 4326.6082
6 54.814793 -45040.077 -44977.498 375525.32 -65955.782 43.548646 610.50446 0 2033.0959 5.3622834 -421.45833 -3588.6378 -443.79722 -518.79674 25277.871 -6411.2291 0 4329.2422
7 74.361855 -45062.564 -44977.668 384488.1 -65979.036 56.14069 611.85396 0 2028.6932 5.3568834 -420.36227 -3596.6686 -443.63511 -519.12443 25276.688 -6414.9069 0 4332.4373
8 96.753116 -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 -6419.1802 0 4336.1534
9 121.91207 -45116.368 -44977.187 406680.22 -66036.769 87.771046 615.12844 0 2018.7397 5.3448206 -417.60463 -3616.0503 -443.24033 -519.94764 25273.922 -6423.9915 0 4340.3289
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 -6429.3929 0 4345.02
11 180.18901 -45182.929 -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 -6435.3961 0 4350.2395
12 213.10176 -45220.694 -44977.407 447323.76 -66152.305 152.51815 621.3781 0 1998.6206 5.3259063 -411.94884 -3653.2385 -442.47944 -521.6355 25269.085 -6442.0014 0 4355.9864
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 -6449.2199 0 4362.2727
14 285.77131 -45303.579 -44977.328 474776.65 -66249.179 208.15938 626.33277 0 1982.9202 5.3142108 -407.08274 -3682.8223 -441.87093 -523.08579 25265.687 -6457.0638 0 4369.1122
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 -6465.5366 0 4376.507
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 -6474.6459 0 4384.4667
17 408.43184 -45443.753 -44977.466 495609.05 -66423.751 311.37652 634.67308 0 1957.6248 5.2956906 -398.02733 -3733.8675 -440.83661 -525.72714 25260.887 -6484.3961 0 4392.9961
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 4402.101
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 -6505.8236 0 4411.7772
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
21 578.07545 -45637.772 -44977.812 403758.92 -66698.343 482.89588 646.43599 0 1929.1799 5.2239444 -382.61485 -3810.9481 -439.2906 -529.52762 25256.17 -6529.7678 0 4432.8145
22 616.45506 -45681.684 -44977.908 349235.77 -66769.835 530.15195 649.24824 0 1925.2752 5.1819278 -378.19171 -3831.2452 -438.88741 -530.31106 25255.425 -6542.6396 0 4444.1437
23 651.3754 -45721.629 -44977.987 284158.54 -66840.508 578.34296 651.92981 0 1923.441 5.1243532 -373.56052 -3851.7589 -438.48202 -530.9385 25254.87 -6556.0397 0 4455.9499
24 682.06338 -45756.048 -44977.37 211816.12 -66909.459 627.0383 654.45076 0 1923.9682 5.0492644 -368.73671 -3872.421 -437.32012 -531.38912 25254.506 -6570.0032 0 4468.2687
25 708.05182 -45785.744 -44977.396 138937.27 -66976.018 675.8658 656.79217 0 1927.0098 4.9561644 -363.73915 -3893.0659 -436.84675 -531.60529 25254.329 -6584.4428 0 4481.0208
Loop time of 3.80064 on 4 procs for 25 steps with 384 atoms
Pair time (%) = 3.66354 (96.3927)
Neigh time (%) = 0.015378 (0.404616)
Comm time (%) = 0.115007 (3.026)
Outpt time (%) = 0.00477654 (0.125677)
Other time (%) = 0.00193667 (0.0509566)
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

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LAMMPS (27 Mar 2011)
# 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 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 1411.6048 -3290.6584 -45.555509 38.801279 0 64.431326 0 -49.368043 0 -12.014532 -10.833851 1332.1957 -252.57913 0 177.96199
10 3.6250736 -2047.8374 -2047.6213 -299.29829 -3286.7576 -47.570891 38.391844 0 64.071067 0 -49.560102 0 -12.514521 -10.341012 1331.2323 -253.18314 0 178.39472
20 3.4851571 -2047.9794 -2047.7716 475.17197 -3288.1123 -47.134466 38.410333 0 64.729744 0 -49.370824 0 -11.882234 -10.574848 1330.3468 -251.64146 0 177.24987
30 2.5132567 -2047.7703 -2047.6205 -340.58027 -3285.523 -48.991839 38.019629 0 66.457341 0 -49.559781 0 -13.100438 -9.9781313 1329.2274 -251.73025 0 177.40868
40 3.0231887 -2047.9594 -2047.7792 21.728411 -3289.2578 -47.147539 38.279854 0 66.537166 0 -49.390313 0 -11.6525 -10.56356 1329.2707 -250.10062 0 176.06519
50 1.9906598 -2047.738 -2047.6193 -714.50458 -3287.2232 -47.871166 38.207263 0 66.115847 0 -49.56157 0 -12.880112 -10.303605 1329.9751 -251.47558 0 177.279
60 3.0207109 -2047.8057 -2047.6256 877.2639 -3291.9702 -45.868802 38.789231 0 65.02199 0 -49.476446 0 -12.119869 -10.715776 1332.8195 -253.50063 0 179.21528
70 3.7979763 -2048.0143 -2047.7879 -407.82326 -3284.4648 -48.020744 38.534103 0 63.022018 0 -49.542838 0 -12.774295 -10.465479 1330.3966 -254.29918 0 179.60038
80 3.7164236 -2047.8611 -2047.6396 221.03512 -3288.6584 -46.999283 38.381573 0 63.615121 0 -49.422688 0 -11.69681 -10.432279 1331.9642 -252.4304 0 177.81787
90 2.6655277 -2047.8079 -2047.649 -449.31726 -3285.2633 -48.012893 38.024005 0 64.608023 0 -49.343114 0 -12.394096 -10.291743 1329.3837 -249.55674 0 175.0383
100 2.7731297 -2047.8848 -2047.7195 -235.96703 -3287.2628 -47.364058 38.017426 0 64.838565 0 -49.418531 0 -11.4724 -10.400455 1329.4667 -249.32512 0 175.03591
Loop time of 0.407478 on 1 procs for 100 steps with 21 atoms
Pair time (%) = 0.392693 (96.3715)
Neigh time (%) = 0.00102925 (0.252591)
Comm time (%) = 0.000811338 (0.199112)
Outpt time (%) = 0.00113606 (0.278804)
Other time (%) = 0.0118086 (2.89798)
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 (27 Mar 2011)
# 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 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 3.6250763 -2047.8374 -2047.6213 -299.29961 -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 3.4851601 -2047.9794 -2047.7716 475.177 -3288.1123 -47.134472 38.41033 0 64.729741 0 -49.370823 0 -11.882238 -10.574847 1330.3468 -251.63834 0 177.24676
30 2.5132495 -2047.7703 -2047.6205 -340.63105 -3285.5228 -48.991899 38.019618 0 66.457328 0 -49.559778 0 -13.100481 -9.978123 1329.2273 -251.73049 0 177.40891
40 3.023138 -2047.9594 -2047.7792 21.784283 -3289.2581 -47.147492 38.279854 0 66.537192 0 -49.390312 0 -11.652463 -10.563564 1329.2709 -250.09804 0 176.06263
50 1.9906916 -2047.738 -2047.6193 -714.56736 -3287.2232 -47.871142 38.207258 0 66.115853 0 -49.561569 0 -12.880106 -10.303609 1329.9751 -251.48521 0 177.28861
60 3.0206107 -2047.8057 -2047.6256 877.20269 -3291.9699 -45.868864 38.789238 0 65.021972 0 -49.47644 0 -12.119943 -10.715773 1332.8194 -253.49682 0 179.2115
70 3.7979962 -2048.0143 -2047.7879 -407.75626 -3284.4655 -48.020621 38.534097 0 63.022067 0 -49.542848 0 -12.774213 -10.465487 1330.397 -254.29981 0 179.601
80 3.7164021 -2047.8611 -2047.6396 221.00835 -3288.6585 -46.999348 38.381591 0 63.615194 0 -49.422685 0 -11.696925 -10.432272 1331.9643 -252.4348 0 177.82228
90 2.665471 -2047.8079 -2047.649 -449.13886 -3285.2639 -48.012876 38.024028 0 64.608075 0 -49.343141 0 -12.394068 -10.291728 1329.3842 -249.55681 0 175.03837
100 2.7731596 -2047.8849 -2047.7195 -235.89478 -3287.263 -47.364049 38.01747 0 64.838635 0 -49.418528 0 -11.4725 -10.400464 1329.4669 -249.33027 0 175.04104
Loop time of 0.334878 on 4 procs for 100 steps with 21 atoms
Pair time (%) = 0.197596 (59.0055)
Neigh time (%) = 0.00030601 (0.0913796)
Comm time (%) = 0.0738816 (22.0622)
Outpt time (%) = 0.00190711 (0.569494)
Other time (%) = 0.0611869 (18.2714)
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 (27 Mar 2011)
# 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 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 -6401.5056 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 4328.3358
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 -6414.1756 0 4331.1645
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 -6418.205 0 4334.4649
9 189.37675 -47623.461 -47407.259 313657.41 -66076.819 155.7255 612.33235 0 2025.8058 5.3434729 -406.71536 -6142.3156 -442.31046 -519.46452 25249.523 -6422.8092 0 4338.2435
10 231.43585 -47671.519 -47407.301 328587.17 -66121.512 192.23538 613.62172 0 2021.2961 5.3367337 -402.34181 -6175.5187 -441.8774 -519.85491 25242.583 -6427.9967 0 4342.5091
11 276.83946 -47723.386 -47407.332 344707.8 -66171.401 233.45314 615.03589 0 2016.4265 5.3299208 -397.42613 -6211.7372 -441.40653 -520.29759 25235.142 -6433.7664 0 4347.2608
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 -6440.1491 0 4352.5299
13 376.251 -47836.96 -47407.413 378838.09 -66287.031 330.7004 618.22869 0 2005.7662 5.3165582 -385.91779 -6292.4987 -440.38084 -521.35077 25219.034 -6447.1773 0 4358.3497
14 429.43119 -47897.722 -47407.462 395422.84 -66352.796 386.98376 620.00107 0 2000.0824 5.310092 -379.312 -6336.5797 -439.83211 -521.96502 25210.516 -6454.8651 0 4364.7349
15 484.29024 -47960.407 -47407.517 410219.58 -66423.764 448.4463 621.88466 0 1994.2638 5.3036142 -372.14102 -6382.7634 -439.26609 -522.63766 25201.793 -6463.2191 0 4371.6932
16 540.2724 -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 -6472.2439 0 4379.2305
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 -6481.9679 0 4387.3767
18 652.97945 -48153.246 -47407.772 426139.97 -66665.188 662.84851 628.11261 0 1977.327 5.2783594 -347.41486 -6530.7092 -437.51898 -524.94491 25175.22 -6492.3876 0 4396.1305
19 708.14773 -48216.32 -47407.863 414483.78 -66753.439 743.33762 630.33041 0 1972.545 5.2638935 -338.21442 -6581.929 -436.93886 -525.76007 25166.493 -6503.4824 0 4405.4739
20 761.31746 -48277.121 -47407.962 390656.82 -66844.203 827.47653 632.5816 0 1968.689 5.2429366 -328.6187 -6633.4776 -436.36881 -526.55296 25157.953 -6515.3219 0 4415.4797
21 811.48466 -48334.789 -47408.357 353426.75 -66936.342 914.52388 634.8376 0 1966.1348 5.2125915 -318.69323 -6685.2728 -435.81367 -527.28375 25149.662 -6527.9504 0 4426.1956
22 857.60828 -48386.919 -47407.831 302318.23 -67028.575 1003.62 637.06904 0 1965.2746 5.1697369 -308.51151 -6736.3658 -434.60389 -527.92872 25141.674 -6541.2235 0 4437.4824
23 898.73557 -48433.1 -47407.059 240278.93 -67119.589 1093.8368 639.2496 0 1966.4695 5.1115298 -298.15265 -6786.38 -433.44406 -528.43404 25134.029 -6555.0936 0 4449.2976
24 934.08594 -48471.379 -47404.979 169550.94 -67208.178 1184.2453 641.36027 0 1969.9934 5.0360099 -287.6986 -6835.3943 -430.80657 -528.78009 25126.757 -6569.585 0 4461.6712
25 963.21978 -48503.674 -47404.014 97838.921 -67293.361 1273.9734 643.39191 0 1976.3578 4.9426402 -277.2317 -6883.3292 -429.31805 -528.89112 25119.879 -6584.7234 0 4474.6354
Loop time of 6.66767 on 1 procs for 25 steps with 384 atoms
Pair time (%) = 5.98506 (89.7624)
Neigh time (%) = 0.0735049 (1.10241)
Comm time (%) = 0.00389314 (0.0583882)
Outpt time (%) = 0.00265288 (0.0397872)
Other time (%) = 0.602559 (9.03701)
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
examples/reax/log.reaxc.tatb.28Mar11.linux.4 Normal file
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LAMMPS (27 Mar 2011)
# 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 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 -6414.1756 0 4331.1645
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 -6418.205 0 4334.4649
9 189.37675 -47623.461 -47407.259 313657.41 -66076.819 155.7255 612.33235 0 2025.8058 5.3434729 -406.71536 -6142.3156 -442.31046 -519.46452 25249.523 -6422.8092 0 4338.2435
10 231.43585 -47671.519 -47407.301 328587.17 -66121.512 192.23538 613.62172 0 2021.2961 5.3367337 -402.34181 -6175.5187 -441.8774 -519.85491 25242.583 -6427.9967 0 4342.5091
11 276.83946 -47723.386 -47407.332 344707.8 -66171.401 233.45314 615.03589 0 2016.4265 5.3299208 -397.42613 -6211.7372 -441.40653 -520.29759 25235.142 -6433.7664 0 4347.2608
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 -6440.1491 0 4352.53
13 376.251 -47836.96 -47407.413 378838.09 -66287.031 330.7004 618.22869 0 2005.7662 5.3165582 -385.91779 -6292.4987 -440.38084 -521.35077 25219.034 -6447.1773 0 4358.3497
14 429.43119 -47897.722 -47407.462 395422.84 -66352.796 386.98376 620.00107 0 2000.0824 5.310092 -379.312 -6336.5797 -439.83211 -521.96502 25210.516 -6454.8649 0 4364.7347
15 484.29024 -47960.407 -47407.517 410219.58 -66423.764 448.4463 621.88466 0 1994.2638 5.3036142 -372.14102 -6382.7634 -439.26609 -522.63766 25201.793 -6463.2189 0 4371.693
16 540.2724 -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 -6472.2438 0 4379.2303
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 -6481.9679 0 4387.3767
18 652.97945 -48153.246 -47407.772 426139.97 -66665.188 662.84851 628.11261 0 1977.327 5.2783594 -347.41486 -6530.7092 -437.51898 -524.94491 25175.22 -6492.3878 0 4396.1308
19 708.14773 -48216.32 -47407.863 414483.79 -66753.439 743.33762 630.33041 0 1972.545 5.2638935 -338.21442 -6581.929 -436.93886 -525.76007 25166.493 -6503.4796 0 4405.4711
20 761.31746 -48277.121 -47407.962 390656.81 -66844.203 827.47653 632.5816 0 1968.689 5.2429366 -328.6187 -6633.4776 -436.36881 -526.55296 25157.953 -6515.324 0 4415.4817
21 811.48467 -48334.789 -47408.357 353426.71 -66936.342 914.52388 634.8376 0 1966.1348 5.2125915 -318.69323 -6685.2728 -435.81367 -527.28375 25149.662 -6527.9624 0 4426.2076
22 857.6083 -48386.919 -47407.831 302318.24 -67028.575 1003.62 637.06904 0 1965.2746 5.1697369 -308.51151 -6736.3658 -434.60389 -527.92872 25141.674 -6541.2161 0 4437.4749
23 898.73559 -48433.1 -47407.059 240278.97 -67119.589 1093.8368 639.2496 0 1966.4695 5.1115298 -298.15265 -6786.38 -433.44406 -528.43404 25134.029 -6555.0807 0 4449.2846
24 934.08595 -48471.379 -47404.979 169551.02 -67208.178 1184.2454 641.36027 0 1969.9934 5.0360099 -287.69859 -6835.3943 -430.80657 -528.78009 25126.757 -6569.5606 0 4461.647
25 963.21978 -48503.674 -47404.014 97838.939 -67293.361 1273.9734 643.39191 0 1976.3578 4.9426402 -277.2317 -6883.3292 -429.31805 -528.89112 25119.879 -6584.712 0 4474.6241
Loop time of 3.35783 on 4 procs for 25 steps with 384 atoms
Pair time (%) = 2.92392 (87.0778)
Neigh time (%) = 0.0153629 (0.457525)
Comm time (%) = 0.106456 (3.1704)
Outpt time (%) = 0.00500518 (0.14906)
Other time (%) = 0.30708 (9.14518)
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

306
examples/rigid/log.rigid.28Mar11.linux.1 Normal file
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LAMMPS (27 Mar 2011)
# 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 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 -7.9722862e-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 12.011621
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 -0.0053156161 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191524 0 5269.5092 12.011013
9700 16735.041 1.0589895 0 5269.4979 12.062708
9750 16738.013 0.13550073 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394973
9850 16738.489 -0.00067270555 0 5269.5237 11.395098
9900 16738.489 -0.00024984581 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 0.240772 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0153747 (6.38557)
Neigh time (%) = 0.0424147 (17.6161)
Comm time (%) = 0.0163877 (6.80631)
Outpt time (%) = 0.0295906 (12.2899)
Other time (%) = 0.137004 (56.9021)
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

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LAMMPS (27 Mar 2011)
# 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 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 -7.9722858e-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 12.011621
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 -0.0003765244 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 0.13550078 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394973
9850 16738.489 -0.00067270552 0 5269.5237 11.395098
9900 16738.489 -0.00024984578 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 0.374086 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.00579989 (1.55042)
Neigh time (%) = 0.0136012 (3.63585)
Comm time (%) = 0.171026 (45.7184)
Outpt time (%) = 0.0344212 (9.20142)
Other time (%) = 0.149238 (39.894)
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

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LAMMPS (27 Mar 2011)
# 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 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 5.53478 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.282449 (5.10317)
Neigh time (%) = 0.124412 (2.24782)
Comm time (%) = 0.0167849 (0.303262)
Outpt time (%) = 0.0310278 (0.560597)
Other time (%) = 5.08011 (91.7852)
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

306
examples/rigid/log.rigid.poems.28Mar11.linux.4 Normal file
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LAMMPS (27 Mar 2011)
# 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 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 6.27886 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0720805 (1.14799)
Neigh time (%) = 0.034766 (0.553699)
Comm time (%) = 0.425238 (6.77253)
Outpt time (%) = 0.666104 (10.6087)
Other time (%) = 5.08067 (80.9171)
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 (27 Mar 2011)
# 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 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
WARNING: More than one fix poems
WARNING: One or more atoms are time integrated more than once
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 5.96365 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.209019 (3.50489)
Neigh time (%) = 0.095875 (1.60766)
Comm time (%) = 0.0209796 (0.351792)
Outpt time (%) = 0.0316613 (0.530904)
Other time (%) = 5.60612 (94.0048)
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
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LAMMPS (27 Mar 2011)
# 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 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
WARNING: More than one fix poems
WARNING: One or more atoms are time integrated more than once
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 6.08953 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0539414 (0.885805)
Neigh time (%) = 0.0267847 (0.439848)
Comm time (%) = 0.356341 (5.8517)
Outpt time (%) = 0.039064 (0.641494)
Other time (%) = 5.6134 (92.1811)
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 (27 Mar 2011)
# 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 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
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 0.467525 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 0.442986 (94.7512)
Neigh time (%) = 0.0125439 (2.68305)
Comm time (%) = 0.00302339 (0.646679)
Outpt time (%) = 0.000116825 (0.024988)
Other time (%) = 0.00885534 (1.89409)
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
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 14.3984 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 13.285 (92.2668)
Neigh time (%) = 0.668192 (4.64072)
Comm time (%) = 0.0943213 (0.655079)
Outpt time (%) = 0.0897267 (0.623169)
Other time (%) = 0.261218 (1.81421)
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 (27 Mar 2011)
# 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 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
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 0.131948 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.117257 (88.8661)
Neigh time (%) = 0.00305372 (2.31434)
Comm time (%) = 0.00862199 (6.53437)
Outpt time (%) = 0.000149608 (0.113384)
Other time (%) = 0.00286567 (2.17182)
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
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 4.06506 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 3.46559 (85.2531)
Neigh time (%) = 0.166769 (4.10251)
Comm time (%) = 0.256573 (6.31166)
Outpt time (%) = 0.0899622 (2.21306)
Other time (%) = 0.0861639 (2.11962)
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 (27 Mar 2011)
# 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 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
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 0.401654 on 1 procs for 100 steps with 1708 atoms
Pair time (%) = 0.380565 (94.7494)
Neigh time (%) = 0.0104229 (2.59501)
Comm time (%) = 0.0026443 (0.658353)
Outpt time (%) = 0.000112057 (0.0278988)
Other time (%) = 0.00790977 (1.9693)
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
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 12.3268 on 1 procs for 3000 steps with 1708 atoms
Pair time (%) = 11.3831 (92.3445)
Neigh time (%) = 0.541932 (4.39636)
Comm time (%) = 0.0839798 (0.681277)
Outpt time (%) = 0.0798285 (0.6476)
Other time (%) = 0.237946 (1.93031)
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 (27 Mar 2011)
# 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 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
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 0.108857 on 4 procs for 100 steps with 1708 atoms
Pair time (%) = 0.0974257 (89.4988)
Neigh time (%) = 0.00321561 (2.95398)
Comm time (%) = 0.00554669 (5.09539)
Outpt time (%) = 0.000126958 (0.116628)
Other time (%) = 0.00254208 (2.33525)
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
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 3.40379 on 4 procs for 3000 steps with 1708 atoms
Pair time (%) = 2.92736 (86.0029)
Neigh time (%) = 0.133528 (3.92291)
Comm time (%) = 0.187747 (5.51583)
Outpt time (%) = 0.0808322 (2.37477)
Other time (%) = 0.0743239 (2.18356)
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

220
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LAMMPS (27 Mar 2011)
# 2d SRD test: big + small particles
units lj
atom_style colloid
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 processor grid
create_atoms 1 region box
Created 100 atoms
mass 1 1.0
mass 2 0.01
shape 1 1.0 1.0 1.0
shape 2 0.0 0.0 0.0
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 = 2.5952 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 0.0268159 on 1 procs for 1000 steps with 100 atoms
Pair time (%) = 0.0152068 (56.7082)
Neigh time (%) = 0.00354433 (13.2173)
Comm time (%) = 0.00297976 (11.1119)
Outpt time (%) = 1.4782e-05 (0.0551239)
Other time (%) = 0.00507021 (18.9075)
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
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 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
# 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 = 10.237 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 1.1854519 3969 0.0020564907 -0.8709642 0.30263317 0.89895867 7567 82 82 0 0 12996 3018 1.0025076 0
200 1.0912203 3969 0.00077322095 -0.96652094 0.11378719 0.53220883 7617 91 91 0 0 12996 3019 1.0315077 0
300 0.99609974 3969 -8.9958107e-05 -0.99937698 -0.013238235 0.30744437 7686 92 92 0 0 12996 3014 1.0224789 0
400 0.97378829 3969 -1.0310777e-06 -0.96420214 -0.00015173339 0.29401458 7517 104 104 0 0 12996 3015 1.0354258 0
500 1.0704853 3969 0.00045875378 -0.99227027 0.067510207 0.23723623 7507 90 90 0 0 12996 3013 1.0255432 0
600 0.98490603 3969 -0.00036594295 -1.0289091 -0.053852164 0.17457127 7475 84 84 0 0 12996 2994 1.0362491 0
700 1.1128816 3969 0.00061003578 -1.0119799 0.089772865 0.44497962 7680 97 97 0 0 12996 3017 1.0076201 0
800 0.96861977 3969 -0.00069285411 -1.060894 -0.10196041 0.3497781 7534 74 74 0 0 12996 3008 1.0271614 0
900 1.0407967 3969 0.00047726289 -0.9601547 0.070234006 0.70144271 7521 97 97 0 0 12996 2988 1.0115957 0
1000 1.0543264 3969 7.8805118e-05 -1.0321862 0.011596961 0.41617549 7499 82 82 0 0 12996 3022 1.0039293 0
1100 0.79276143 3969 -0.0014999076 -1.0055602 -0.22072641 0.38874703 7333 100 100 0 0 12996 3013 1.0389616 0
1200 1.084432 3969 0.00068593846 -0.97264494 0.1009427 0.60176004 7348 81 81 0 0 12996 2999 1.0009925 0
1300 1.0487612 3969 0.00032122262 -0.9910025 0.047271121 0.49732554 7551 94 94 0 0 12996 2988 1.0221747 0
1400 1.0098443 3969 4.0826801e-05 -0.99373776 0.006008072 0.51403259 7619 89 89 0 0 12996 3007 1.0344942 0
1500 1.218401 3969 0.00097129173 -1.0632817 0.14293529 0.38730792 7414 87 87 0 0 12996 3015 1.0519305 0
1600 1.1501145 3969 0.00047446251 -1.0687914 0.069821903 0.35607234 7383 80 80 0 0 12996 3014 1.0203142 0
1700 0.94258444 3969 -0.0007994931 -1.050812 -0.1176534 0.40572317 7597 92 92 0 0 12996 3002 1.0469204 0
1800 1.1205745 3969 0.00014712615 -1.0877177 0.021651085 0.37897578 7585 82 82 0 0 12996 2991 1.0389588 0
1900 0.95430392 3969 -0.0010155747 -1.0942129 -0.14945198 0.24556839 7703 85 85 0 0 12996 3001 1.0246638 0
2000 0.92246887 3969 -0.0011696335 -1.0853675 -0.17212327 0.23953568 7636 100 100 0 0 12996 3022 1.0204788 0
2100 0.91529221 3969 -0.0012601691 -1.0915858 -0.18544648 0.22735286 7481 80 80 0 0 12996 3026 1.0280942 0
2200 0.89505853 3969 -0.00064151149 -0.98051277 -0.094404831 0.51723842 7418 87 87 0 0 12996 3000 1.027661 0
2300 0.98485557 3969 -0.00075152689 -1.0856017 -0.1105947 0.24927644 7590 80 80 0 0 12996 2999 1.0258603 0
2400 0.91841201 3969 -0.0010505855 -1.0638321 -0.15460417 0.23326098 7587 103 103 0 0 12996 3001 1.0282876 0
2500 1.0358998 3969 6.5299645e-05 -1.0159313 0.0096094958 0.34899097 7452 93 93 0 0 12996 2975 1.0426326 0
2600 0.94743566 3969 -0.00053875484 -1.0172445 -0.079283162 0.22735975 7560 66 66 0 0 12996 2996 1.0211493 0
2700 0.87106832 3969 -0.0010996524 -1.0241825 -0.16182485 0.25604039 7329 83 83 0 0 12996 3005 1.0305366 0
2800 1.0803159 3969 0.00030634738 -1.0244307 0.045082081 0.45643311 7418 108 108 0 0 12996 3023 1.0340188 0
2900 1.1283591 3969 0.00084010869 -0.99344512 0.12363039 0.83746145 7308 91 91 0 0 12996 2981 1.0189882 0
3000 1.1876657 3969 0.0016273526 -0.93630787 0.23948121 0.97168782 7453 87 87 0 0 12996 2979 1.0166656 0
3100 1.0004566 3969 -0.00032761995 -1.0386645 -0.048212552 0.61341839 7470 87 87 0 0 12996 3031 1.017823 0
3200 1.2257669 3969 0.00099290366 -1.0673936 0.1461157 0.61730027 7545 86 86 0 1 12996 2963 1.0419479 0
3300 1.0483473 3969 -0.00031074739 -1.0835934 -0.045729586 0.52991291 7442 84 84 0 0 12996 3010 1.015561 0
3400 1.1060909 3969 0.00030818848 -1.049677 0.045353017 0.7068218 7459 87 87 0 0 12996 3002 1.0231151 0
3500 1.0538669 3969 -0.00036380882 -1.0968664 -0.053538106 0.45965228 7648 81 81 0 0 12996 3020 1.0228882 0
3600 0.9403379 3969 -0.00095052032 -1.0708131 -0.13987857 0.29232958 7731 104 104 0 0 12996 3015 1.0308016 0
3700 0.87576431 3969 -0.0013620431 -1.0674449 -0.20043826 0.20807819 7570 93 93 0 0 12996 2999 1.027521 0
3800 1.0214205 3969 -0.00025908571 -1.0493333 -0.038127053 0.35110253 7480 95 95 0 0 12996 3023 1.0189546 0
3900 1.0399628 3969 -0.0004657163 -1.098098 -0.068534811 0.14477785 7597 84 84 0 0 12996 3001 1.0391639 0
4000 0.96223871 3969 -0.00087553027 -1.0814594 -0.12884303 0.32672058 7506 91 91 0 0 12996 3026 1.0273983 0
4100 0.9978966 3969 -0.00014719261 -1.0095785 -0.021660865 0.54900472 7553 89 89 0 0 12996 3008 1.0214976 0
4200 0.99324797 3969 -0.00014342613 -1.0044221 -0.02110659 0.5121817 7423 77 77 0 0 12996 3008 1.0621727 0
4300 0.90689211 3969 -0.00089523015 -1.0295653 -0.13174207 0.41794731 7614 77 77 0 0 12996 3009 1.0361369 0
4400 0.94201541 3969 -0.00126231 -1.1183568 -0.18576154 0.16778284 7600 91 91 0 0 12996 3004 1.035561 0
4500 0.97003803 3969 -0.00090250856 -1.0931508 -0.13281316 0.37787471 7505 96 96 0 0 12996 2998 1.0335568 0
4600 0.96052354 3969 -0.00093721969 -1.0888396 -0.13792125 0.48917838 7532 72 72 0 0 12996 2999 1.0124728 0
4700 0.95086208 3969 -0.00076105324 -1.0533501 -0.11199659 0.60704145 7429 104 104 0 0 12996 2988 1.0095829 0
4800 0.94826516 3969 -0.0010878926 -1.0988768 -0.16009427 0.50867751 7351 93 93 0 0 12996 2968 1.0212405 0
4900 1.0540371 3969 -4.230244e-06 -1.0441192 -0.00062252271 0.6999864 7454 91 91 0 0 12996 2998 1.0019459 0
5000 0.94814157 3969 -0.0007896491 -1.0548649 -0.11620476 0.61244147 7362 76 76 0 0 12996 2976 1.0250728 0
Loop time of 5.43949 on 1 procs for 5000 steps with 14716 atoms
Pair time (%) = 0.0842001 (1.54794)
Neigh time (%) = 0.303599 (5.58138)
Comm time (%) = 0.0637748 (1.17244)
Outpt time (%) = 0.455503 (8.374)
Other time (%) = 4.53241 (83.3242)
Nlocal: 14716 ave 14716 max 14716 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 87 ave 87 max 87 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 480 ave 480 max 480 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 480
Ave neighs/atom = 0.0326176
Neighbor list builds = 250
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# 2d SRD test: big + small particles
units lj
atom_style colloid
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 processor grid
create_atoms 1 region box
Created 100 atoms
mass 1 1.0
mass 2 0.01
shape 1 1.0 1.0 1.0
shape 2 0.0 0.0 0.0
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 = 2.59465 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 0.0258421 on 4 procs for 1000 steps with 100 atoms
Pair time (%) = 0.00398111 (15.4056)
Neigh time (%) = 0.00100678 (3.8959)
Comm time (%) = 0.0163288 (63.1869)
Outpt time (%) = 4.4167e-05 (0.170911)
Other time (%) = 0.0044812 (17.3407)
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
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 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
# 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 = 5.44263 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 1.3582446 3969 0.0026789295 -0.95043087 0.39423126 0.73581726 7479 87 87 0 0 22500 2999 1.0285157 0
200 1.2572907 3969 0.0019616669 -0.95603884 0.28867891 0.62749376 7394 98 98 0 0 22500 2994 1.0253343 0
300 1.12798 3969 0.00057755533 -1.0317072 0.084993042 0.30262448 7311 88 88 0 0 22500 2997 1.022263 0
400 1.1466105 3969 0.00088785773 -1.0044873 0.13065714 0.40537124 7467 82 82 0 0 22500 2993 1.0139003 0
500 1.0151043 3969 -0.00021014381 -1.0358781 -0.030924763 0.19673928 7587 81 81 0 0 22500 2994 1.0145019 0
600 0.99210691 3969 -0.0002577968 -1.0201232 -0.037937377 0.2625174 7449 92 92 0 0 22500 2968 0.98574736 0
700 0.92572874 3969 -0.00067753277 -1.0161772 -0.099705722 0.19520999 7537 78 78 0 0 22500 2998 1.0064032 0
800 0.94627244 3969 -0.0003639106 -0.9903628 -0.053553084 0.22241336 7602 79 79 0 1 22500 3010 1.0134331 0
900 0.92523394 3969 -0.00080502966 -1.0344498 -0.11846816 0.18846804 7576 72 72 0 1 22500 3015 1.0136704 0
1000 1.0322972 3969 -0.00037569219 -1.0772611 -0.055286863 0.13263626 7601 88 88 0 0 22500 3000 1.0224061 0
1100 0.9726161 3969 -0.00041776377 -1.0243681 -0.061478117 0.3120931 7425 87 87 0 0 22500 2991 1.0216981 0
1200 0.9785542 3969 -0.00036217362 -1.0220661 -0.053297471 0.37956001 7634 94 94 0 0 22500 3022 1.0055215 0
1300 1.102684 3969 0.00056306573 -1.0087964 0.082860753 0.50039902 7380 94 94 0 0 22500 3011 1.0298198 0
1400 1.2416072 3969 0.0016380507 -0.98813558 0.24105553 0.6709785 7532 95 95 0 0 22500 3005 1.0272106 0
1500 1.1009579 3969 0.00041059416 -1.0295252 0.060423037 0.4271012 7443 86 86 0 0 22500 2990 1.0322439 0
1600 0.97932726 3969 -0.00044406974 -1.0348833 -0.065349303 0.23710215 7541 85 85 0 0 22500 3005 1.0504545 0
1700 1.07156 3969 0.0003309407 -1.0121432 0.048701233 0.32615222 7660 90 90 0 1 22500 3010 1.0192163 0
1800 0.94379054 3969 -0.00060529206 -1.0234274 -0.08907478 0.28437994 7706 92 92 0 0 22500 2983 1.0197247 0
1900 1.1935542 3969 0.001087796 -1.0215386 0.16008006 0.32082985 7633 102 102 0 0 22500 3026 1.0227294 0
2000 1.0794535 3969 0.00017035747 -1.0435892 0.025069805 0.12933714 7547 76 76 0 0 22500 3028 1.0339312 0
2100 1.11728 3969 0.001197717 -0.92985122 0.17625603 0.4877601 7424 88 88 0 0 22500 2986 1.0268223 0
2200 1.022726 3969 -0.00017383526 -1.0380804 -0.025581597 0.18522494 7414 92 92 0 0 22500 3004 1.0254694 0
2300 1.2289681 3969 0.0014918151 -0.99714295 0.21953551 0.56571933 7669 90 90 0 0 22500 3008 1.0265701 0
2400 1.0261081 3969 0.00016550325 -0.99149158 0.024355459 0.53332928 7499 83 83 0 0 22500 3019 1.0160353 0
2500 1.0155015 3969 -0.00056230464 -1.0880952 -0.082748751 0.22398562 7712 79 79 0 0 22500 3017 1.03801 0
2600 0.8756954 3969 -0.0014956069 -1.087032 -0.22009351 0.10400097 7542 85 85 0 0 22500 2985 1.024091 0
2700 0.97964461 3969 -0.00075911535 -1.0815596 -0.11171141 0.27927544 7449 86 86 0 0 22500 2993 1.0166909 0
2800 0.97102332 3969 -0.00081115436 -1.0806826 -0.11936948 0.36647698 7662 85 85 0 0 22500 3014 1.0148134 0
2900 1.1405082 3969 0.00078035444 -1.0142661 0.11483696 0.73653576 7451 82 82 0 0 22500 3007 1.0296379 0
3000 1.0460256 3969 -0.00031837206 -1.082417 -0.046851633 0.25310003 7494 83 83 0 0 22500 3013 1.043192 0
3100 1.128752 3969 0.00043203186 -1.0538867 0.063577808 0.37101933 7458 89 89 0 1 22500 2981 1.0082866 0
3200 1.0546223 3969 0.00023156986 -1.0099982 0.034077821 0.66191884 7451 92 92 0 0 22500 2988 1.0254862 0
3300 1.0859707 3969 -5.4375056e-05 -1.0831128 -0.0080018333 0.3552947 7441 74 74 0 0 22500 2978 1.0252244 0
3400 0.90831095 3969 -0.0011506108 -1.0685517 -0.16932389 0.26027658 7478 76 76 0 0 22500 2997 1.0306308 0
3500 1.0971397 3969 0.00047675241 -1.0160094 0.070158884 0.39394719 7510 87 87 0 0 22500 2999 1.0303505 0
3600 1.0758592 3969 5.1451605e-05 -1.057529 0.0075716182 0.23217468 7505 98 98 0 0 22500 3022 1.0133265 0
3700 0.99184036 3969 -0.00051911023 -1.0583142 -0.076392262 0.2659259 7566 104 104 0 0 22500 3006 1.0284719 0
3800 0.86950687 3969 -0.0014525295 -1.074566 -0.21375425 0.27380224 7552 80 80 0 0 22500 3013 1.0351337 0
3900 0.86286132 3969 -0.0010595017 -1.010149 -0.15591627 0.56043933 7547 104 104 0 0 22500 2992 1.0313609 0
4000 0.76083626 3969 -0.0014009914 -0.9593978 -0.2061699 0.64813923 7448 101 101 0 0 22500 3032 1.0109258 0
4100 1.0071575 3969 -0.00018734554 -1.0246557 -0.027569769 0.55964495 7489 76 76 0 0 22500 3016 1.0175384 0
4200 0.88374612 3969 -0.0010981928 -1.0365187 -0.16161005 0.41352036 7481 92 92 0 0 22500 2995 1.0123735 0
4300 0.98819505 3969 -0.00066821798 -1.0766481 -0.098334958 0.41489158 7557 79 79 0 0 22500 2998 1.0400745 0
4400 1.1772685 3969 0.0010725317 -1.007662 0.15783376 0.7912903 7522 76 76 0 0 22500 2991 1.0176624 0
4500 1.0836741 3969 0.00021867511 -1.0406572 0.032180229 0.58489302 7800 93 93 0 0 22500 2997 1.0023484 0
4600 1.0334731 3969 -0.00015378918 -1.04577 -0.022631616 0.53872329 7542 94 94 0 0 22500 2996 0.98823241 0
4700 1.2126127 3969 0.0011423373 -1.0323802 0.16810636 0.49583696 7387 81 81 0 0 22500 3001 1.0425378 0
4800 1.1593219 3969 0.0010239969 -0.99703726 0.15069139 0.37192735 7374 80 80 0 1 22500 2988 1.0278368 0
4900 0.87223689 3969 -0.00099601272 -1.0100878 -0.14657323 0.11585542 7448 89 89 0 0 22500 3000 1.0267238 0
5000 0.87426493 3969 -0.0010817587 -1.0247139 -0.15919161 0.15322481 7587 100 100 0 0 22500 2988 1.0030228 0
Loop time of 1.76678 on 4 procs for 5000 steps with 14716 atoms
Pair time (%) = 0.0225935 (1.27879)
Neigh time (%) = 0.0765792 (4.33439)
Comm time (%) = 0.132309 (7.48868)
Outpt time (%) = 0.371439 (21.0235)
Other time (%) = 1.16386 (65.8746)
Nlocal: 3679 ave 3872 max 3379 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 48.25 ave 51 max 45 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 118 ave 167 max 87 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 472
Ave neighs/atom = 0.0320739
Neighbor list builds = 250
Dangerous builds = 0

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LAMMPS (27 Mar 2011)
# 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 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 1 3969 0.99995309 85.26 0 0 0
200 1 3969 0.99995309 85.26 0 0 0
300 1 3969 0.99995309 85.26 0 0 0
400 1 3969 0.99995309 85.26 0 0 0
500 1 3969 0.99995309 85.26 0 0 0
600 1 3969 0.99995309 85.26 0 0 0
700 1 3969 0.99995309 85.26 0 0 0
800 1 3969 0.99995309 85.26 0 0 0
900 1 3969 0.99995309 85.26 0 0 0
1000 1 3969 0.99995309 85.26 0 0 0
1100 1 3969 0.99995309 85.26 0 0 0
1200 1 3969 0.99995309 85.26 0 0 0
1300 1 3969 0.99995309 85.26 0 0 0
1400 1 3969 0.99995309 85.26 0 0 0
1500 1 3969 0.99995309 85.26 0 0 0
1600 1 3969 0.99995309 85.26 0 0 0
1700 1 3969 0.99995309 85.26 0 0 0
1800 1 3969 0.99995309 85.26 0 0 0
1900 1 3969 0.99995309 85.26 0 0 0
2000 1 3969 0.99995309 85.26 0 0 0
2100 1 3969 0.99995309 85.26 0 0 0
2200 1 3969 0.99995309 85.26 0 0 0
2300 1 3969 0.99995309 85.26 0 0 0
2400 1 3969 0.99995309 85.26 0 0 0
2500 1 3969 0.99995309 85.26 0 0 0
2600 1 3969 0.99995309 85.26 0 0 0
2700 1 3969 0.99995309 85.26 0 0 0
2800 1 3969 0.99995309 85.26 0 0 0
2900 1 3969 0.99995309 85.26 0 0 0
3000 1 3969 0.99995309 85.26 0 0 0
3100 1 3969 0.99995309 85.26 0 0 0
3200 1 3969 0.99995309 85.26 0 0 0
3300 1 3969 0.99995309 85.26 0 0 0
3400 1 3969 0.99995309 85.26 0 0 0
3500 1 3969 0.99995309 85.26 0 0 0
3600 1 3969 0.99995309 85.26 0 0 0
3700 1 3969 0.99995309 85.26 0 0 0
3800 1 3969 0.99995309 85.26 0 0 0
3900 1 3969 0.99995309 85.26 0 0 0
4000 1 3969 0.99995309 85.26 0 0 0
4100 1 3969 0.99995309 85.26 0 0 0
4200 1 3969 0.99995309 85.26 0 0 0
4300 1 3969 0.99995309 85.26 0 0 0
4400 1 3969 0.99995309 85.26 0 0 0
4500 1 3969 0.99995309 85.26 0 0 0
4600 1 3969 0.99995309 85.26 0 0 0
4700 1 3969 0.99995309 85.26 0 0 0
4800 1 3969 0.99995309 85.26 0 0 0
4900 1 3969 0.99995309 85.26 0 0 0
5000 1 3969 0.99995309 85.26 0 0 0
Loop time of 10.5758 on 1 procs for 5000 steps with 21316 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 5.91816 (55.9592)
Comm time (%) = 0.92819 (8.77652)
Outpt time (%) = 0.661721 (6.25691)
Other time (%) = 3.06777 (29.0073)
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 (27 Mar 2011)
# 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 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 1 3969 0.99995309 85.26 0 0 0
200 1 3969 0.99995309 85.26 0 0 0
300 1 3969 0.99995309 85.26 0 0 0
400 1 3969 0.99995309 85.26 0 0 0
500 1 3969 0.99995309 85.26 0 0 0
600 1 3969 0.99995309 85.26 0 0 0
700 1 3969 0.99995309 85.26 0 0 0
800 1 3969 0.99995309 85.26 0 0 0
900 1 3969 0.99995309 85.26 0 0 0
1000 1 3969 0.99995309 85.26 0 0 0
1100 1 3969 0.99995309 85.26 0 0 0
1200 1 3969 0.99995309 85.26 0 0 0
1300 1 3969 0.99995309 85.26 0 0 0
1400 1 3969 0.99995309 85.26 0 0 0
1500 1 3969 0.99995309 85.26 0 0 0
1600 1 3969 0.99995309 85.26 0 0 0
1700 1 3969 0.99995309 85.26 0 0 0
1800 1 3969 0.99995309 85.26 0 0 0
1900 1 3969 0.99995309 85.26 0 0 0
2000 1 3969 0.99995309 85.26 0 0 0
2100 1 3969 0.99995309 85.26 0 0 0
2200 1 3969 0.99995309 85.26 0 0 0
2300 1 3969 0.99995309 85.26 0 0 0
2400 1 3969 0.99995309 85.26 0 0 0
2500 1 3969 0.99995309 85.26 0 0 0
2600 1 3969 0.99995309 85.26 0 0 0
2700 1 3969 0.99995309 85.26 0 0 0
2800 1 3969 0.99995309 85.26 0 0 0
2900 1 3969 0.99995309 85.26 0 0 0
3000 1 3969 0.99995309 85.26 0 0 0
3100 1 3969 0.99995309 85.26 0 0 0
3200 1 3969 0.99995309 85.26 0 0 0
3300 1 3969 0.99995309 85.26 0 0 0
3400 1 3969 0.99995309 85.26 0 0 0
3500 1 3969 0.99995309 85.26 0 0 0
3600 1 3969 0.99995309 85.26 0 0 0
3700 1 3969 0.99995309 85.26 0 0 0
3800 1 3969 0.99995309 85.26 0 0 0
3900 1 3969 0.99995309 85.26 0 0 0
4000 1 3969 0.99995309 85.26 0 0 0
4100 1 3969 0.99995309 85.26 0 0 0
4200 1 3969 0.99995309 85.26 0 0 0
4300 1 3969 0.99995309 85.26 0 0 0
4400 1 3969 0.99995309 85.26 0 0 0
4500 1 3969 0.99995309 85.26 0 0 0
4600 1 3969 0.99995309 85.26 0 0 0
4700 1 3969 0.99995309 85.26 0 0 0
4800 1 3969 0.99995309 85.26 0 0 0
4900 1 3969 0.99995309 85.26 0 0 0
5000 1 3969 0.99995309 85.26 0 0 0
Loop time of 3.44932 on 4 procs for 5000 steps with 21316 atoms
Pair time (%) = 0 (0)
Neigh time (%) = 1.42294 (41.2527)
Comm time (%) = 0.748812 (21.709)
Outpt time (%) = 0.539738 (15.6476)
Other time (%) = 0.737835 (21.3907)
Nlocal: 5329 ave 5381 max 5260 min
Histogram: 1 0 0 0 1 0 0 0 1 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

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LAMMPS (27 Mar 2011)
Running on 3 partitions of processors
Step CPU N M Status Barrier Margin t_lo delt_lo
1000 0.000 0 0 E 0.000 0.000 0.000 0.000
1150 1.543 0 0 DF 2.957 0.000 0.000 17626.816
1550 4.348 0 1 DF 0.510 0.049 0.000 1251.448
1950 7.461 0 2 D 2.971 0.610 0.000 114049.225
2350 10.432 0 3 D 0.510 0.867 0.000 3071.754
2800 13.868 0 4 D 2.971 1.156 0.000 216085.667
1550 13.868 1 1 E 0.510 0.000 1251.448 1251.448
1650 14.838 1 0 DF 0.510 0.000 1251.448 227.532
1750 15.811 1 1 D 0.510 0.461 1251.448 455.047
1850 16.807 1 2 D 0.510 0.692 1251.448 682.596
1950 17.784 1 3 D 0.510 0.923 1251.448 910.144
2050 18.781 1 4 D 0.510 1.154 1251.448 1137.675
1650 18.781 2 0 E 0.510 0.000 1478.980 227.532
1850 20.399 2 0 DF 0.510 0.000 1478.980 455.054
2050 22.028 2 1 D 0.510 0.549 1478.980 910.140
2250 23.656 2 2 D 0.510 0.823 1478.980 1365.169
2450 25.304 2 3 D 0.510 1.098 1478.980 1820.232
1850 25.304 3 0 E 0.510 0.000 1934.033 455.054
1950 26.326 3 0 DF 0.510 0.000 1934.033 227.541
2050 27.381 3 1 D 0.510 0.461 1934.033 455.092
2150 28.410 3 2 D 0.510 0.692 1934.033 682.654
2250 29.439 3 3 D 0.510 0.923 1934.033 910.147
2350 30.618 3 4 D 0.510 1.154 1934.033 1137.725
1950 30.618 4 0 E 0.510 0.000 2161.574 227.541
2100 32.278 4 0 DF 2.518 0.000 2161.574 8681.348
2250 33.632 4 1 DF 0.510 0.045 2161.574 682.611
2400 35.322 4 2 D 2.518 0.455 2161.574 26042.889
2550 36.694 4 3 D 0.510 0.607 2161.574 1365.321
2700 38.417 4 4 D 2.518 0.759 2161.574 43403.531
2850 39.797 4 5 D 0.510 0.911 2161.574 2047.918
3000 41.603 4 6 D 2.518 1.063 2161.574 60770.044
2250 41.603 5 1 E 0.510 0.000 2844.185 682.611
2450 43.345 5 0 DF 0.510 0.000 2844.185 455.071
2700 45.402 5 1 D 0.510 0.617 2844.185 1023.952
2950 47.493 5 2 D 0.510 0.960 2844.185 1592.756
Loop time of 47.7979 on 3 procs for 2000 steps with 511 atoms

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Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
1150 11.6554 6.62337 0.377272 0.761559 11.8694 5.1085 2.15591 2.72809 0 -2213.28 0.5 -2208.17 1 -2210.33
1170 11.6512 6.62037 0.377248 0.761453 11.8653 5.10773 2.15515 2.72809 0 -2213.28 0.5 -2208.17 1 -2210.33
1190 11.5433 6.54347 0.376636 0.758709 11.7601 5.08807 2.13555 2.7281 0 -2213.28 0.499996 -2208.19 1 -2210.33
1210 9.72273 5.2217 0.36548 0.70781 9.99449 4.75847 1.8071 2.72903 0 -2213.28 0.499949 -2208.52 1 -2210.33
1230 4.03625 1.89401 0.285681 0.33788 4.64048 3.01397 0.0693848 2.84058 0 -2213.29 0.503837 -2210.27 1 -2210.34
1250 2.91187 0.632304 0.149015 0.285227 0.285227 2.95113 0 4.16068 0 -2213.32 0.483278 -2212.44 1 -2210.37
1270 2.21864 0.412087 0.0735697 0.213012 0.213012 2.9596 0 5.43034 0 -2213.34 0.415854 -2210.57 1 -2210.38
1290 1.26025 0.240655 0.0851694 0.274204 0.274204 2.95838 0 4.65566 0 -2213.34 0.426179 -2212.71 1 -2210.38
1310 1.19063 0.562065 0.178273 1.12853 1.12853 2.97311 0 3.93499 0 -2213.34 0.442578 -2213.23 1 -2210.36
1330 0.895322 0.472645 0.0176755 0.895322 0.895322 2.96769 0 3.68571 0 -2213.34 0.470276 -2213.3 1 -2210.37
1350 0.335826 0.115869 0.00293675 0.223978 0.223978 2.95803 0 3.61669 0 -2213.34 0.479093 -2213.29 1 -2210.38
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
1350 0.335826 0.115869 0.00293675 0.223978 0.223978 2.95803 0 3.61669 0 -2213.34 0.479093 -2213.29 1 -2210.38
1370 0.335823 0.115843 0.00293641 0.223928 0.223928 2.95803 0 3.61669 0 -2213.34 0.479093 -2213.29 1 -2210.38
1390 0.335758 0.115176 0.00292783 0.222641 0.222641 2.95802 0 3.61669 0 -2213.34 0.479095 -2213.29 1 -2210.38
1410 0.334544 0.102935 0.0027735 0.199029 0.199029 2.9579 0 3.61655 0 -2213.34 0.479146 -2213.29 1 -2210.38
1430 0.315628 0.0285281 0.00192657 0.0510591 0.0510591 2.95743 0 3.61286 0 -2213.34 0.480234 -2213.29 1 -2210.38
1450 0.119947 0.0618074 0.00138469 0.119947 0.119947 2.95758 0 3.56152 0 -2213.34 0.49978 -2213.23 1 -2210.38
1470 0.0579776 0.029747 0.000739585 0.0579776 0.0579776 2.95744 0 3.56502 0 -2213.34 0.503437 -2213.22 1 -2210.38
1490 0.0278376 0.0143442 0.000335725 0.0278376 0.0278376 2.9574 0 3.571 0 -2213.34 0.501089 -2213.24 1 -2210.38
1510 0.00809973 0.00339832 0.000224324 0.00662292 0.00662292 2.95739 0 3.57185 0 -2213.34 0.500243 -2213.24 1 -2210.38
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
1550 0.997487 0.231841 0.377272 0.469509 0.99882 0.492541 0.448998 1.93124 0 -2213.28 0.5 -2212.79 1 -2213.24
1570 0.99736 0.231816 0.377248 0.469487 0.998693 0.492536 0.448994 1.93124 0 -2213.28 0.5 -2212.79 1 -2213.24
1590 0.994079 0.231185 0.376636 0.468915 0.995416 0.492412 0.448881 1.93121 0 -2213.28 0.499998 -2212.79 1 -2213.24
1610 0.933531 0.219448 0.365631 0.4586 0.93495 0.490188 0.446871 1.93068 0 -2213.28 0.499962 -2212.79 1 -2213.24
1630 0.375577 0.0561858 0.287182 0.375577 0.308748 0.474594 0.435012 1.92179 0 -2213.29 0.499365 -2212.81 1 -2213.25
1650 0.305843 0.0564951 0.146318 0.173362 0.305756 0.502736 0.494561 1.78494 0 -2213.33 0.504227 -2212.82 1 -2213.32
1670 0.0660515 0.0139069 0.0286019 0.0581794 0.0660189 0.510608 0.509844 1.73932 0 -2213.34 0.503366 -2212.83 1 -2213.34
1690 0.0938827 0.00850809 0.0658485 0.0871284 0.0939675 0.510236 0.510117 1.7431 0 -2213.34 0.498559 -2212.83 1 -2213.34
1710 0.015938 0.0015162 0.0106223 0.0153275 0.0159323 0.5101 0.510089 1.74154 0 -2213.34 0.500123 -2212.83 1 -2213.34
1716 0.00937149 0.00102351 0.00622571 0.00806101 0.00937371 0.510095 0.510091 1.74152 0 -2213.34 0.500405 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
1716 0.00937371 0.00102355 0.00622571 0.00806101 0.00937371 0.510095 0.510091 1.74152 0 -2213.34 0.500405 -2212.83 1 -2213.34
1717 0.00937371 0.00102355 0.00622571 0.00806101 0.00937371 0.510095 0.510091 1.74152 0 -2213.34 0.500405 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
1950 9.66579 5.33469 0.377272 0.420868 10.0934 3.90418 0.943966 2.04888 0 -2213.28 0.5 -2209.38 1 -2210.32
1970 9.66276 5.33259 0.377248 0.420812 10.0906 3.90365 0.943439 2.04888 0 -2213.28 0.5 -2209.38 1 -2210.32
1990 9.58501 5.27857 0.376636 0.419364 10.018 3.89012 0.929915 2.04885 0 -2213.28 0.500002 -2209.39 1 -2210.32
2010 8.24737 4.3339 0.365508 0.392952 8.78496 3.65982 0.699697 2.0491 0 -2213.28 0.500082 -2209.62 1 -2210.32
2030 2.90751 1.32314 0.285411 0.255973 0.255973 2.96135 0 2.151 0 -2213.29 0.509189 -2210.93 1 -2210.33
2050 1.8118 0.323286 0.191894 0.184345 0.184345 2.96791 0 2.47639 0 -2213.32 0.426354 -2212.42 1 -2210.35
2070 0.91671 0.235455 0.122249 0.130442 0.130442 2.96954 0 2.24338 0 -2213.33 0.419591 -2212.14 1 -2210.36
2090 0.396851 0.21211 0.0812484 0.0752039 0.0752039 2.97033 0 2.23813 0 -2213.33 0.478539 -2211.6 1 -2210.36
2110 0.179174 0.0738539 0.0513511 0.0489922 0.0489922 2.97062 0 2.23658 0 -2213.34 0.493184 -2211.44 1 -2210.36
2130 0.205743 0.112934 0.033966 0.0336078 0.0336078 2.97071 0 2.24428 0 -2213.34 0.497571 -2211.38 1 -2210.37
2150 0.127962 0.0713942 0.0163296 0.0176185 0.0176185 2.9707 0 2.24796 0 -2213.34 0.498358 -2211.34 1 -2210.37
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2150 0.127962 0.0713942 0.0163296 0.0176185 0.0176185 2.9707 0 2.24796 0 -2213.34 0.498358 -2211.34 1 -2210.37
2170 0.127931 0.0713768 0.0163295 0.0176184 0.0176184 2.9707 0 2.24796 0 -2213.34 0.498358 -2211.34 1 -2210.37
2190 0.127142 0.0709263 0.0163276 0.0176159 0.0176159 2.9707 0 2.24796 0 -2213.34 0.498359 -2211.34 1 -2210.37
2210 0.112633 0.0626267 0.0162914 0.0175702 0.0175702 2.9707 0 2.248 0 -2213.34 0.498367 -2211.34 1 -2210.37
2230 0.0489489 0.0243788 0.015609 0.0168856 0.0168856 2.97069 0 2.24866 0 -2213.34 0.498505 -2211.34 1 -2210.37
2250 0.0128754 0.00397205 0.00914949 0.0105864 0.0105864 2.97067 0 2.25308 0 -2213.34 0.49915 -2211.32 1 -2210.37
2263 0.00946178 0.00261171 0.00794995 0.00939525 0.00939525 2.97066 0 2.25378 0 -2213.34 0.499217 -2211.32 1 -2210.37
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2350 1.04323 0.23682 0.377272 0.528633 1.04504 0.499935 0.543083 1.80325 0 -2213.28 0.5 -2212.78 1 -2213.32
2370 1.0431 0.236795 0.377248 0.528564 1.0449 0.49993 0.543078 1.80325 0 -2213.28 0.5 -2212.78 1 -2213.32
2390 1.03964 0.236164 0.376636 0.52677 1.04145 0.499792 0.542961 1.80322 0 -2213.28 0.500003 -2212.78 1 -2213.32
2410 0.975729 0.224408 0.365622 0.493823 0.977684 0.497323 0.54084 1.80267 0 -2213.28 0.500052 -2212.78 1 -2213.32
2430 0.313898 0.0651164 0.286579 0.21056 0.31975 0.479891 0.523927 1.79411 0 -2213.29 0.500889 -2212.81 1 -2213.33
2450 0.368714 0.0658953 0.143978 0.147406 0.368888 0.504843 0.515405 1.74252 0 -2213.33 0.49593 -2212.82 1 -2213.34
2470 0.0774982 0.0147639 0.0415413 0.0480402 0.0811687 0.509946 0.510594 1.74615 0 -2213.34 0.492687 -2212.83 1 -2213.34
2490 0.0296877 0.00551982 0.0272649 0.0138884 0.0320966 0.509846 0.510355 1.74093 0 -2213.34 0.497743 -2212.83 1 -2213.34
2510 0.0222406 0.00287926 0.0222406 0.00802056 0.0205251 0.509891 0.510271 1.74079 0 -2213.34 0.498679 -2212.83 1 -2213.34
2527 0.00967123 0.00197849 0.00613088 0.00481446 0.010164 0.510098 0.510109 1.74091 0 -2213.34 0.50088 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2527 0.010164 0.00221896 0.00613088 0.00481446 0.010164 0.510098 0.510109 1.74091 0 -2213.34 0.50088 -2212.83 1 -2213.34
2547 0.0101634 0.00221894 0.00613027 0.00481407 0.0101634 0.510098 0.510109 1.74091 0 -2213.34 0.50088 -2212.83 1 -2213.34
2567 0.010149 0.0022186 0.00611473 0.00480409 0.010149 0.510098 0.510109 1.74091 0 -2213.34 0.50088 -2212.83 1 -2213.34
2584 0.00999437 0.00221473 0.00594804 0.00469678 0.00999437 0.510098 0.510109 1.74091 0 -2213.34 0.500875 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2800 11.0399 6.46908 0.377272 0.825083 11.3892 4.43199 1.43082 2.15148 0 -2213.28 0.5 -2208.85 1 -2210.28
2820 11.0359 6.46633 0.377248 0.825009 11.3854 4.4313 1.43014 2.15148 0 -2213.28 0.5 -2208.85 1 -2210.28
2840 10.9344 6.39578 0.376636 0.823086 11.2884 4.41366 1.41258 2.15145 0 -2213.28 0.500002 -2208.87 1 -2210.28
2860 9.20859 5.17667 0.365481 0.787236 9.65277 4.11769 1.11805 2.15179 0 -2213.28 0.500088 -2209.16 1 -2210.28
2880 3.20288 1.49713 0.285234 0.393643 0.393643 2.98421 0 2.26254 0 -2213.29 0.50896 -2210.65 1 -2210.3
2900 3.40331 1.53436 0.159731 0.294584 0.294584 2.97084 0 2.56277 0 -2213.32 0.408982 -2212.36 1 -2210.35
2920 1.19524 0.681719 0.121667 0.117788 0.117788 2.96965 0 2.39729 0 -2213.33 0.400443 -2212.36 1 -2210.36
2940 0.609388 0.284608 0.0615082 0.0601282 0.0601282 2.97048 0 2.27611 0 -2213.33 0.505136 -2211.21 1 -2210.36
2960 0.066563 0.0218099 0.0492357 0.0480547 0.0480547 2.97057 0 2.27859 0 -2213.34 0.50329 -2211.25 1 -2210.36
2980 0.0458954 0.0127066 0.0441669 0.0427633 0.0427633 2.9706 0 2.27959 0 -2213.34 0.502755 -2211.26 1 -2210.37
3000 0.0851206 0.0426169 0.0128535 0.0135736 0.0135736 2.97065 0 2.2672 0 -2213.34 0.498179 -2211.3 1 -2210.37
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
3000 0.0851206 0.0426169 0.0128535 0.0135736 0.0135736 2.97065 0 2.2672 0 -2213.34 0.498179 -2211.3 1 -2210.37
3020 0.0851005 0.042605 0.0128535 0.0135736 0.0135736 2.97065 0 2.2672 0 -2213.34 0.498179 -2211.3 1 -2210.37
3040 0.0845841 0.0422986 0.0128524 0.0135723 0.0135723 2.97065 0 2.2672 0 -2213.34 0.498179 -2211.3 1 -2210.37
3060 0.0751118 0.0366524 0.0128306 0.0135485 0.0135485 2.97065 0 2.26719 0 -2213.34 0.498188 -2211.3 1 -2210.37
3080 0.0377055 0.022783 0.0123463 0.0130421 0.0130421 2.97065 0 2.26701 0 -2213.34 0.49843 -2211.3 1 -2210.37
3100 0.0333719 0.0194216 0.0069713 0.00762863 0.00762863 2.97064 0 2.26555 0 -2213.34 0.500451 -2211.28 1 -2210.37
3105 0.00924307 0.00347619 0.00683845 0.00748907 0.00748907 2.97064 0 2.26545 0 -2213.34 0.50042 -2211.28 1 -2210.37
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
1650 1.04323 0.254204 0.469509 0.437271 1.04342 0.490208 0.543327 1.79104 0 -2213.24 0.5 -2212.75 1 -2213.29
1670 1.04311 0.254178 0.469487 0.437252 1.04329 0.490203 0.543322 1.79104 0 -2213.24 0.5 -2212.75 1 -2213.29
1690 1.03988 0.253523 0.468915 0.436762 1.04007 0.490077 0.543191 1.79102 0 -2213.24 0.499996 -2212.75 1 -2213.29
1710 0.980544 0.241339 0.458605 0.427805 0.980738 0.487814 0.54085 1.79071 0 -2213.24 0.499931 -2212.75 1 -2213.29
1730 0.392925 0.070632 0.375934 0.32886 0.393102 0.471903 0.523603 1.78673 0 -2213.25 0.498691 -2212.77 1 -2213.3
1750 0.315643 0.0548588 0.173453 0.139362 0.316436 0.502085 0.514484 1.75517 0 -2213.32 0.491871 -2212.82 1 -2213.33
1770 0.0836219 0.0149353 0.0611587 0.0714119 0.0842677 0.510189 0.509993 1.7481 0 -2213.34 0.499239 -2212.83 1 -2213.34
1790 0.0820862 0.0110115 0.0345932 0.0354318 0.0821162 0.510122 0.510179 1.74275 0 -2213.34 0.499823 -2212.83 1 -2213.34
1810 0.0132645 0.00114201 0.0132645 0.0102348 0.0128348 0.510035 0.510101 1.74254 0 -2213.34 0.499933 -2212.83 1 -2213.34
1824 0.00661539 0.000714038 0.00607802 0.00494911 0.00666292 0.510083 0.510096 1.74236 0 -2213.34 0.499931 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
1824 0.00666292 0.000699856 0.00607802 0.00494911 0.00666292 0.510083 0.510096 1.74236 0 -2213.34 0.499931 -2212.83 1 -2213.34
1825 0.00666292 0.000699856 0.00607802 0.00494911 0.00666292 0.510083 0.510096 1.74236 0 -2213.34 0.499931 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
1750 1.04284 0.261627 0.469509 0.485909 1.04532 0.49243 0.559283 1.73642 0 -2213.24 0.5 -2212.74 1 -2213.3
1770 1.04272 0.261601 0.469487 0.485854 1.04519 0.492425 0.559278 1.73642 0 -2213.24 0.5 -2212.74 1 -2213.3
1790 1.03942 0.260948 0.468915 0.484436 1.0419 0.492299 0.559155 1.73643 0 -2213.24 0.500001 -2212.74 1 -2213.3
1810 0.978646 0.248805 0.458598 0.458528 0.981277 0.49004 0.556922 1.73655 0 -2213.24 0.500025 -2212.75 1 -2213.3
1830 0.382002 0.0766396 0.375475 0.249481 0.387441 0.474704 0.538515 1.74043 0 -2213.25 0.500349 -2212.77 1 -2213.31
1850 0.332152 0.0602748 0.173138 0.113594 0.333604 0.502554 0.517733 1.74541 0 -2213.32 0.49102 -2212.81 1 -2213.33
1870 0.0883173 0.0154087 0.0634502 0.0603986 0.0909643 0.510136 0.510641 1.74059 0 -2213.34 0.493269 -2212.83 1 -2213.34
1890 0.0854635 0.00968635 0.0418161 0.0645812 0.0853611 0.510085 0.510227 1.74431 0 -2213.34 0.502231 -2212.83 1 -2213.34
1910 0.0158716 0.00165467 0.0158716 0.0113115 0.0156279 0.510017 0.510146 1.74172 0 -2213.34 0.500515 -2212.83 1 -2213.34
1929 0.00928034 0.000637617 0.00928034 0.00530168 0.00725899 0.510061 0.510114 1.74187 0 -2213.34 0.500047 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
1929 0.00928034 0.000637617 0.00928034 0.00530168 0.00725899 0.510061 0.510114 1.74187 0 -2213.34 0.500047 -2212.83 1 -2213.34
1930 0.00928034 0.000637617 0.00928034 0.00530168 0.00725899 0.510061 0.510114 1.74187 0 -2213.34 0.500047 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
1850 1.03888 0.258546 0.469509 0.34231 1.03913 0.495895 0.551699 1.77757 0 -2213.24 0.5 -2212.74 1 -2213.29
1870 1.03876 0.25852 0.469487 0.342283 1.039 0.49589 0.551694 1.77757 0 -2213.24 0.5 -2212.74 1 -2213.29
1890 1.03554 0.25786 0.468915 0.341573 1.03578 0.495765 0.551554 1.77756 0 -2213.24 0.499996 -2212.74 1 -2213.29
1910 0.976161 0.245586 0.458601 0.328746 0.976408 0.493526 0.549031 1.77731 0 -2213.24 0.499932 -2212.74 1 -2213.29
1930 0.388696 0.0721148 0.375688 0.23815 0.388876 0.477929 0.528255 1.77449 0 -2213.25 0.498708 -2212.77 1 -2213.3
1950 0.322139 0.0547331 0.17394 0.122024 0.323173 0.503617 0.513746 1.75128 0 -2213.32 0.492611 -2212.81 1 -2213.33
1970 0.0792069 0.0148936 0.0609789 0.0296465 0.0799153 0.510045 0.510968 1.74857 0 -2213.34 0.498945 -2212.83 1 -2213.34
1990 0.0717325 0.00922189 0.0353019 0.0333551 0.0717505 0.510086 0.510214 1.74291 0 -2213.34 0.499919 -2212.83 1 -2213.34
2010 0.0146049 0.00128062 0.0146049 0.0109095 0.0138486 0.510037 0.51011 1.74269 0 -2213.34 0.499985 -2212.83 1 -2213.34
2024 0.00730227 0.000749331 0.00671943 0.00537878 0.00732762 0.510084 0.510097 1.74226 0 -2213.34 0.499943 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2024 0.00732762 0.000749331 0.00671943 0.00537878 0.00732762 0.510084 0.510097 1.74226 0 -2213.34 0.499943 -2212.83 1 -2213.34
2025 0.00732762 0.000749331 0.00671943 0.00537878 0.00732762 0.510084 0.510097 1.74226 0 -2213.34 0.499943 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
1950 1.04658 0.272824 0.469509 0.501521 1.04685 0.535735 0.52145 1.72854 0 -2213.24 0.5 -2212.7 1 -2213.22
1970 1.04646 0.272798 0.469487 0.501492 1.04673 0.53573 0.521445 1.72854 0 -2213.24 0.5 -2212.7 1 -2213.22
1990 1.04341 0.272125 0.468915 0.500734 1.04368 0.535603 0.521323 1.72855 0 -2213.24 0.500005 -2212.7 1 -2213.22
2010 0.98738 0.25963 0.458607 0.487117 0.987669 0.533314 0.519115 1.72872 0 -2213.24 0.5001 -2212.7 1 -2213.22
2030 0.453268 0.0837992 0.376219 0.392432 0.453877 0.515452 0.502012 1.73336 0 -2213.25 0.501724 -2212.73 1 -2213.23
2050 0.317313 0.0492381 0.174992 0.194783 0.317325 0.511265 0.50793 1.74612 0 -2213.32 0.501603 -2212.81 1 -2213.31
2070 0.0794155 0.0136423 0.0560461 0.0372835 0.0792902 0.510298 0.510738 1.74044 0 -2213.34 0.498539 -2212.83 1 -2213.34
2090 0.0603955 0.00875978 0.0307324 0.0251612 0.0604301 0.510148 0.510161 1.74443 0 -2213.34 0.501497 -2212.83 1 -2213.34
2110 0.0134192 0.00108978 0.0134192 0.0121379 0.0134935 0.510092 0.510091 1.74198 0 -2213.34 0.500189 -2212.83 1 -2213.34
2124 0.00710228 0.000711432 0.00548597 0.00561915 0.00709725 0.510095 0.510094 1.74207 0 -2213.34 0.499852 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2124 0.00709725 0.000711227 0.00548597 0.00561915 0.00709725 0.510095 0.510094 1.74207 0 -2213.34 0.499852 -2212.83 1 -2213.34
2125 0.00709725 0.000711227 0.00548597 0.00561915 0.00709725 0.510095 0.510094 1.74207 0 -2213.34 0.499852 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2050 1.0445 0.255151 0.469509 0.444116 1.04494 0.489093 0.557769 1.78016 0 -2213.24 0.5 -2212.75 1 -2213.31
2070 1.04437 0.255126 0.469487 0.444059 1.04481 0.489088 0.557764 1.78016 0 -2213.24 0.5 -2212.75 1 -2213.31
2090 1.04107 0.254481 0.468915 0.442589 1.04151 0.488962 0.557634 1.78015 0 -2213.24 0.499996 -2212.75 1 -2213.31
2110 0.980321 0.242484 0.458597 0.415671 0.980779 0.486693 0.555286 1.7799 0 -2213.24 0.499922 -2212.75 1 -2213.31
2130 0.378293 0.0712051 0.375376 0.202584 0.378788 0.471274 0.535141 1.77699 0 -2213.25 0.498483 -2212.78 1 -2213.31
2150 0.331507 0.0578658 0.173556 0.13232 0.3327 0.501863 0.515313 1.75216 0 -2213.32 0.491098 -2212.82 1 -2213.33
2170 0.0730576 0.0143627 0.0586407 0.0185188 0.0739207 0.510181 0.511099 1.74861 0 -2213.34 0.49933 -2212.83 1 -2213.34
2190 0.0964106 0.00852229 0.0701176 0.0639029 0.0964171 0.510194 0.510292 1.74188 0 -2213.34 0.500303 -2212.83 1 -2213.34
2210 0.0156796 0.00150999 0.0117599 0.00904826 0.0156845 0.510093 0.510107 1.74203 0 -2213.34 0.500045 -2212.83 1 -2213.34
2216 0.00980696 0.000921796 0.00731057 0.00596568 0.00984731 0.510092 0.510099 1.74222 0 -2213.34 0.499971 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2216 0.00984731 0.000927893 0.00731057 0.00596568 0.00984731 0.510092 0.510099 1.74222 0 -2213.34 0.499971 -2212.83 1 -2213.34
2217 0.00984731 0.000927893 0.00731057 0.00596568 0.00984731 0.510092 0.510099 1.74222 0 -2213.34 0.499971 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
1850 0.981907 0.210156 0.437271 0.33614 0.981976 0.505479 0.501303 1.81301 0 -2213.29 0.5 -2212.78 1 -2213.29
1870 0.981783 0.210134 0.437252 0.336119 0.981852 0.505475 0.501298 1.81301 0 -2213.29 0.5 -2212.78 1 -2213.29
1890 0.978592 0.209555 0.436762 0.335588 0.978662 0.505362 0.501174 1.81299 0 -2213.29 0.499999 -2212.78 1 -2213.29
1910 0.919738 0.198795 0.427801 0.325992 0.919813 0.503353 0.498951 1.81277 0 -2213.29 0.499978 -2212.79 1 -2213.29
1930 0.327953 0.0558812 0.327953 0.257002 0.317156 0.490415 0.482494 1.81009 0 -2213.3 0.499645 -2212.81 1 -2213.29
1950 0.310691 0.0542981 0.141794 0.119776 0.310763 0.507763 0.504145 1.76178 0 -2213.33 0.5029 -2212.82 1 -2213.33
1970 0.0777893 0.0109954 0.0705257 0.0406362 0.0776658 0.509714 0.510614 1.74409 0 -2213.34 0.501699 -2212.83 1 -2213.34
1990 0.0369547 0.00452618 0.0297545 0.018503 0.0371449 0.509965 0.510031 1.74403 0 -2213.34 0.498928 -2212.83 1 -2213.34
2010 0.0305468 0.0028626 0.0172222 0.0129669 0.0306436 0.51004 0.510035 1.7419 0 -2213.34 0.499733 -2212.83 1 -2213.34
2020 0.00857419 0.000717184 0.00828505 0.00828103 0.00867555 0.51007 0.510056 1.74194 0 -2213.34 0.499873 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2020 0.00867555 0.000710864 0.00828505 0.00828103 0.00867555 0.51007 0.510056 1.74194 0 -2213.34 0.499873 -2212.83 1 -2213.34
2021 0.00867555 0.000710864 0.00828505 0.00828103 0.00867555 0.51007 0.510056 1.74194 0 -2213.34 0.499873 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2050 1.06816 0.23287 0.437271 0.689328 1.06817 0.533582 0.525644 1.74356 0 -2213.29 0.5 -2212.76 1 -2213.28
2070 1.06803 0.232844 0.437252 0.68926 1.06803 0.533576 0.525641 1.74356 0 -2213.29 0.5 -2212.76 1 -2213.28
2090 1.06462 0.232184 0.436762 0.687498 1.06463 0.533438 0.525544 1.74355 0 -2213.29 0.500001 -2212.76 1 -2213.28
2110 1.00183 0.219926 0.4278 0.654882 1.00184 0.530962 0.523809 1.74341 0 -2213.29 0.500027 -2212.76 1 -2213.28
2130 0.364028 0.0569251 0.327436 0.276671 0.364071 0.513543 0.510944 1.74296 0 -2213.3 0.500439 -2212.78 1 -2213.3
2150 0.336522 0.0521192 0.142419 0.243493 0.336573 0.513489 0.509791 1.7464 0 -2213.33 0.502275 -2212.82 1 -2213.33
2170 0.127261 0.0172089 0.0747287 0.0442807 0.127263 0.50992 0.511029 1.74436 0 -2213.34 0.499921 -2212.83 1 -2213.34
2190 0.073988 0.0103244 0.0524331 0.0255024 0.0739926 0.509878 0.510557 1.7438 0 -2213.34 0.499902 -2212.83 1 -2213.34
2210 0.0288354 0.00375284 0.0176777 0.00979293 0.0288466 0.510089 0.510124 1.74219 0 -2213.34 0.500035 -2212.83 1 -2213.34
2227 0.00937128 0.00083182 0.00937128 0.00700012 0.00886158 0.510092 0.510101 1.74205 0 -2213.34 0.500048 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2227 0.00937128 0.00085675 0.00937128 0.00700012 0.00886158 0.510092 0.510101 1.74205 0 -2213.34 0.500048 -2212.83 1 -2213.34
2228 0.00937128 0.00085675 0.00937128 0.00700012 0.00886158 0.510092 0.510101 1.74205 0 -2213.34 0.500048 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2250 1.04287 0.218919 0.437271 0.748959 1.04307 0.511728 0.479017 1.81624 0 -2213.29 0.5 -2212.78 1 -2213.26
2270 1.04275 0.218896 0.437252 0.748921 1.04294 0.511723 0.479014 1.81624 0 -2213.29 0.5 -2212.78 1 -2213.26
2290 1.03955 0.218315 0.436762 0.747947 1.03974 0.511592 0.478938 1.81622 0 -2213.29 0.500001 -2212.78 1 -2213.26
2310 0.980544 0.207525 0.427809 0.729822 0.98074 0.509254 0.477596 1.81586 0 -2213.29 0.50002 -2212.78 1 -2213.26
2330 0.461735 0.0615012 0.329122 0.461735 0.364978 0.492267 0.473499 1.81118 0 -2213.3 0.500313 -2212.81 1 -2213.28
2350 0.310395 0.0502434 0.147267 0.178366 0.31044 0.50813 0.503663 1.76363 0 -2213.33 0.50231 -2212.82 1 -2213.33
2370 0.0813051 0.0101348 0.0740651 0.0629995 0.0814367 0.509633 0.510567 1.74704 0 -2213.34 0.501225 -2212.83 1 -2213.34
2390 0.0410537 0.00446406 0.0321619 0.031961 0.0411064 0.509984 0.51002 1.74297 0 -2213.34 0.499673 -2212.83 1 -2213.34
2410 0.0350811 0.00326861 0.0184579 0.0169826 0.0351173 0.510052 0.510044 1.74189 0 -2213.34 0.499805 -2212.83 1 -2213.34
2420 0.00987454 0.00111504 0.00827041 0.00987454 0.00943558 0.510073 0.510058 1.74188 0 -2213.34 0.499913 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2420 0.00987454 0.00111504 0.00827041 0.00987454 0.00943558 0.510073 0.510058 1.74188 0 -2213.34 0.499913 -2212.83 1 -2213.34
2421 0.00987454 0.00111504 0.00827041 0.00987454 0.00943558 0.510073 0.510058 1.74188 0 -2213.34 0.499913 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2450 0.994296 0.202592 0.437271 0.222772 0.994737 0.512259 0.5502 1.73928 0 -2213.29 0.5 -2212.78 1 -2213.33
2470 0.994171 0.20257 0.437252 0.222759 0.994613 0.512254 0.550195 1.73928 0 -2213.29 0.5 -2212.78 1 -2213.33
2490 0.990966 0.202006 0.436762 0.222431 0.991408 0.512138 0.550058 1.73927 0 -2213.29 0.499999 -2212.78 1 -2213.33
2510 0.931835 0.191528 0.4278 0.216371 0.932296 0.510064 0.547599 1.73916 0 -2213.29 0.499984 -2212.78 1 -2213.33
2530 0.327583 0.0522569 0.327583 0.141092 0.326228 0.496393 0.527785 1.7389 0 -2213.3 0.499684 -2212.8 1 -2213.33
2550 0.328018 0.055305 0.144909 0.0744174 0.328349 0.509583 0.514932 1.7459 0 -2213.33 0.496259 -2212.82 1 -2213.34
2570 0.11779 0.0151659 0.0758845 0.0313355 0.11805 0.509664 0.51102 1.74654 0 -2213.34 0.497947 -2212.83 1 -2213.34
2590 0.0712323 0.00962094 0.0540428 0.0194492 0.0714806 0.509719 0.510585 1.74487 0 -2213.34 0.498723 -2212.83 1 -2213.34
2610 0.0300608 0.0037913 0.0182772 0.00569048 0.0300424 0.510067 0.51015 1.74157 0 -2213.34 0.500369 -2212.83 1 -2213.34
2627 0.00946336 0.00078524 0.00946336 0.00285014 0.00771619 0.510076 0.510118 1.74178 0 -2213.34 0.500147 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2627 0.00946336 0.00078524 0.00946336 0.00285014 0.00771619 0.510076 0.510118 1.74178 0 -2213.34 0.500147 -2212.83 1 -2213.34
2628 0.00946336 0.00078524 0.00946336 0.00285014 0.00771619 0.510076 0.510118 1.74178 0 -2213.34 0.500147 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
1950 0.997919 0.221204 0.33614 0.333397 0.998738 0.518465 0.540505 1.75275 0 -2213.29 0.5 -2212.77 1 -2213.31
1970 0.997795 0.221181 0.336119 0.333377 0.998615 0.51846 0.5405 1.75275 0 -2213.29 0.5 -2212.77 1 -2213.31
1990 0.994607 0.220571 0.335588 0.332855 0.995429 0.518332 0.540371 1.75275 0 -2213.29 0.500003 -2212.77 1 -2213.31
2010 0.935821 0.209238 0.325989 0.323372 0.936703 0.516022 0.538057 1.75269 0 -2213.29 0.500051 -2212.77 1 -2213.31
2030 0.348349 0.0576607 0.256932 0.240451 0.350796 0.498254 0.52012 1.75327 0 -2213.29 0.500922 -2212.79 1 -2213.31
2050 0.325858 0.0594428 0.121566 0.121106 0.325857 0.507736 0.51271 1.74437 0 -2213.33 0.49933 -2212.82 1 -2213.33
2070 0.0822712 0.0152207 0.0322371 0.0377336 0.0840189 0.511317 0.511303 1.74544 0 -2213.34 0.495622 -2212.83 1 -2213.34
2090 0.0267698 0.00373441 0.0125378 0.00975336 0.0268072 0.510208 0.510239 1.74664 0 -2213.34 0.500198 -2212.83 1 -2213.34
2110 0.0259636 0.00277018 0.0120379 0.0124437 0.0259851 0.510138 0.510155 1.74375 0 -2213.34 0.499888 -2212.83 1 -2213.34
2125 0.00966941 0.000778797 0.00454033 0.00513242 0.00966719 0.510107 0.510114 1.74328 0 -2213.34 0.500073 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2125 0.00966719 0.000852177 0.00454033 0.00513242 0.00966719 0.510107 0.510114 1.74328 0 -2213.34 0.500073 -2212.83 1 -2213.34
2126 0.00966719 0.000852177 0.00454033 0.00513242 0.00966719 0.510107 0.510114 1.74328 0 -2213.34 0.500073 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2050 1.0029 0.226947 0.33614 0.56781 1.00299 0.529868 0.523141 1.68202 0 -2213.29 0.5 -2212.76 1 -2213.28
2070 1.00278 0.226924 0.336119 0.567736 1.00287 0.529863 0.523137 1.68202 0 -2213.29 0.5 -2212.76 1 -2213.28
2090 0.99956 0.22634 0.335588 0.565841 0.999654 0.529733 0.523038 1.68204 0 -2213.29 0.499999 -2212.76 1 -2213.28
2110 0.940239 0.215468 0.325985 0.53125 0.94034 0.527397 0.521242 1.68236 0 -2213.29 0.499977 -2212.76 1 -2213.28
2130 0.352214 0.0621839 0.256843 0.290692 0.35263 0.509426 0.506624 1.69058 0 -2213.29 0.499469 -2212.78 1 -2213.29
2150 0.346483 0.0677538 0.126792 0.172126 0.347213 0.511196 0.511793 1.75095 0 -2213.33 0.493454 -2212.81 1 -2213.33
2170 0.0806858 0.0141501 0.0417583 0.0573244 0.0820847 0.511042 0.510767 1.75282 0 -2213.34 0.501133 -2212.83 1 -2213.34
2190 0.0780329 0.00817447 0.030645 0.0767452 0.0784496 0.510285 0.510238 1.74497 0 -2213.34 0.502213 -2212.83 1 -2213.34
2210 0.0188017 0.00191346 0.0131587 0.018631 0.0193436 0.510164 0.510183 1.7432 0 -2213.34 0.500727 -2212.83 1 -2213.34
2230 0.0250467 0.00196804 0.00823152 0.0250467 0.01857 0.510126 0.510129 1.74291 0 -2213.34 0.500079 -2212.83 1 -2213.34
2236 0.00951366 0.000827147 0.00771865 0.00735174 0.009567 0.510122 0.510132 1.74286 0 -2213.34 0.500074 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2236 0.009567 0.000935961 0.00771865 0.00735174 0.009567 0.510122 0.510132 1.74286 0 -2213.34 0.500074 -2212.83 1 -2213.34
2237 0.009567 0.000935961 0.00771865 0.00735174 0.009567 0.510122 0.510132 1.74286 0 -2213.34 0.500074 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2150 1.06394 0.242878 0.33614 0.745372 1.06394 0.532151 0.507541 1.73685 0 -2213.29 0.5 -2212.75 1 -2213.26
2170 1.0638 0.242852 0.336119 0.745266 1.0638 0.532146 0.507537 1.73685 0 -2213.29 0.5 -2212.75 1 -2213.26
2190 1.06023 0.242168 0.335588 0.742552 1.06023 0.531997 0.507453 1.73685 0 -2213.29 0.500003 -2212.75 1 -2213.26
2210 0.994362 0.229462 0.32598 0.692805 0.994362 0.529336 0.505937 1.73688 0 -2213.29 0.500053 -2212.76 1 -2213.26
2230 0.364883 0.0566757 0.256713 0.320454 0.36492 0.509481 0.493441 1.73939 0 -2213.29 0.500921 -2212.78 1 -2213.27
2250 0.373483 0.071274 0.132675 0.216457 0.37358 0.511027 0.506977 1.75424 0 -2213.33 0.499109 -2212.81 1 -2213.32
2270 0.0825645 0.0162987 0.0351032 0.0518506 0.0824026 0.511489 0.510813 1.75518 0 -2213.34 0.49849 -2212.83 1 -2213.34
2290 0.0489606 0.0065091 0.020071 0.0416946 0.0491796 0.510276 0.510172 1.74714 0 -2213.34 0.501942 -2212.83 1 -2213.34
2310 0.0266206 0.0031489 0.0108576 0.0256646 0.0267344 0.510184 0.51013 1.74459 0 -2213.34 0.500376 -2212.83 1 -2213.34
2330 0.0124618 0.00154357 0.00672691 0.0106036 0.0124415 0.510139 0.510119 1.74358 0 -2213.34 0.499793 -2212.83 1 -2213.34
2333 0.00990034 0.00107295 0.00636252 0.00781094 0.00988001 0.510137 0.510118 1.74359 0 -2213.34 0.499816 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2333 0.00988001 0.000993445 0.00636252 0.00781094 0.00988001 0.510137 0.510118 1.74359 0 -2213.34 0.499816 -2212.83 1 -2213.34
2334 0.00988001 0.000993445 0.00636252 0.00781094 0.00988001 0.510137 0.510118 1.74359 0 -2213.34 0.499816 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2250 0.996415 0.226541 0.33614 0.294715 0.998142 0.507062 0.541521 1.7556 0 -2213.29 0.5 -2212.78 1 -2213.32
2270 0.996288 0.226516 0.336119 0.294694 0.998016 0.507057 0.541516 1.7556 0 -2213.29 0.5 -2212.78 1 -2213.32
2290 0.993027 0.225873 0.335588 0.294144 0.99476 0.506929 0.541384 1.75559 0 -2213.29 0.500004 -2212.78 1 -2213.32
2310 0.932829 0.213927 0.325987 0.284121 0.934675 0.50463 0.539014 1.7554 0 -2213.29 0.500067 -2212.78 1 -2213.32
2330 0.317772 0.0558429 0.256826 0.194665 0.322529 0.487675 0.520672 1.75348 0 -2213.29 0.501174 -2212.8 1 -2213.32
2350 0.336471 0.058994 0.125201 0.0813743 0.337252 0.505663 0.5149 1.74235 0 -2213.33 0.494492 -2212.82 1 -2213.34
2370 0.0805508 0.0152189 0.0341883 0.0511 0.0823246 0.510855 0.510463 1.75083 0 -2213.34 0.492865 -2212.83 1 -2213.34
2390 0.0429446 0.00673353 0.0202532 0.0185029 0.0428344 0.510144 0.510179 1.74345 0 -2213.34 0.502622 -2212.83 1 -2213.34
2410 0.0184444 0.00219777 0.0101706 0.00892228 0.0184911 0.5101 0.510129 1.74292 0 -2213.34 0.500302 -2212.83 1 -2213.34
2421 0.00886009 0.00121876 0.00586664 0.00452904 0.00878744 0.510097 0.510113 1.7427 0 -2213.34 0.499429 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2421 0.00878744 0.00121876 0.00586664 0.00452904 0.00878744 0.510097 0.510113 1.7427 0 -2213.34 0.499429 -2212.83 1 -2213.34
2422 0.00878744 0.00121876 0.00586664 0.00452904 0.00878744 0.510097 0.510113 1.7427 0 -2213.34 0.499429 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2350 1.04273 0.240655 0.33614 0.508249 1.04401 0.527557 0.526184 1.76274 0 -2213.29 0.5 -2212.76 1 -2213.28
2370 1.0426 0.240629 0.336119 0.508207 1.04388 0.527551 0.526179 1.76274 0 -2213.29 0.5 -2212.76 1 -2213.28
2390 1.03932 0.239956 0.335588 0.5071 1.0406 0.52741 0.526059 1.76273 0 -2213.29 0.500007 -2212.76 1 -2213.28
2410 0.978793 0.227464 0.32599 0.486861 0.980188 0.524858 0.523892 1.76246 0 -2213.29 0.50013 -2212.76 1 -2213.29
2430 0.371763 0.0583308 0.256947 0.300972 0.37612 0.504695 0.507551 1.75915 0 -2213.29 0.502365 -2212.79 1 -2213.29
2450 0.338848 0.0691689 0.122243 0.180359 0.338853 0.5096 0.51009 1.74028 0 -2213.33 0.501023 -2212.82 1 -2213.33
2470 0.092183 0.0202091 0.0318257 0.0591619 0.0945665 0.511374 0.510966 1.75436 0 -2213.34 0.491425 -2212.83 1 -2213.34
2490 0.0963363 0.0144314 0.0440435 0.0324312 0.0971622 0.510364 0.510383 1.74148 0 -2213.34 0.503903 -2212.83 1 -2213.34
2510 0.0405848 0.0036363 0.0186432 0.0156764 0.0407552 0.510144 0.510144 1.74223 0 -2213.34 0.500904 -2212.83 1 -2213.34
2526 0.00967745 0.00195758 0.00385858 0.00407659 0.0101524 0.510119 0.510118 1.74224 0 -2213.34 0.500749 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2526 0.0101524 0.00221708 0.00385858 0.00407659 0.0101524 0.510119 0.510118 1.74224 0 -2213.34 0.500749 -2212.83 1 -2213.34
2546 0.0101522 0.00221703 0.0038585 0.00407655 0.0101522 0.510119 0.510118 1.74224 0 -2213.34 0.500749 -2212.83 1 -2213.34
2566 0.0101476 0.00221581 0.00385645 0.00407535 0.0101476 0.510119 0.510118 1.74224 0 -2213.34 0.500749 -2212.83 1 -2213.34
2586 0.010062 0.002193 0.00381945 0.0040536 0.010062 0.510119 0.510117 1.74224 0 -2213.34 0.500743 -2212.83 1 -2213.34
2590 0.00999691 0.00217513 0.00379201 0.00403716 0.00999691 0.510119 0.510117 1.74225 0 -2213.34 0.500738 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2100 10.2118 6.13448 0.333397 0.691048 10.5287 4.03029 1.49548 1.966 0 -2213.31 0.5 -2209.28 1 -2210.77
2120 10.2084 6.13211 0.333377 0.690971 10.5254 4.0297 1.4949 1.966 0 -2213.31 0.5 -2209.28 1 -2210.77
2140 10.1208 6.07103 0.332855 0.689009 10.4416 4.0146 1.47985 1.96601 0 -2213.31 0.499998 -2209.29 1 -2210.77
2160 8.62177 5.00813 0.323257 0.652414 9.01598 3.75933 1.22555 1.96694 0 -2213.31 0.500016 -2209.55 1 -2210.77
2180 2.95223 1.29528 0.236832 0.265951 0.265951 2.52594 0 2.08787 0 -2213.31 0.507924 -2210.88 1 -2210.79
2200 0.960646 0.349523 0.173565 0.203148 0.203148 2.52524 0 2.24095 0 -2213.32 0.505671 -2211.35 1 -2210.79
2220 0.405569 0.059463 0.103759 0.131658 0.131658 2.52247 0 2.23822 0 -2213.33 0.490478 -2211.49 1 -2210.81
2240 0.358252 0.105699 0.0522882 0.0680958 0.0680958 2.51896 0 2.23869 0 -2213.34 0.4963 -2211.42 1 -2210.82
2260 0.135058 0.0667444 0.0406034 0.0494972 0.0494972 2.51864 0 2.25231 0 -2213.34 0.499907 -2211.41 1 -2210.82
2280 0.119565 0.0661889 0.0256169 0.0313618 0.0313618 2.51823 0 2.25889 0 -2213.34 0.500182 -2211.41 1 -2210.82
2300 0.0842853 0.0464771 0.0212474 0.0260478 0.0260478 2.51814 0 2.26099 0 -2213.34 0.500128 -2211.41 1 -2210.82
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2300 0.0842853 0.0464771 0.0212474 0.0260478 0.0260478 2.51814 0 2.26099 0 -2213.34 0.500128 -2211.41 1 -2210.82
2320 0.0842666 0.0464656 0.0212473 0.0260477 0.0260477 2.51814 0 2.26099 0 -2213.34 0.500128 -2211.41 1 -2210.82
2340 0.0837842 0.04617 0.0212455 0.0260455 0.0260455 2.51814 0 2.26099 0 -2213.34 0.500128 -2211.41 1 -2210.82
2360 0.074964 0.0407291 0.0212113 0.026004 0.026004 2.51814 0 2.26102 0 -2213.34 0.500131 -2211.41 1 -2210.82
2380 0.0367864 0.0172307 0.0205054 0.025147 0.025147 2.51813 0 2.26154 0 -2213.34 0.500166 -2211.41 1 -2210.82
2400 0.0514076 0.0285844 0.0112449 0.013903 0.013903 2.518 0 2.26706 0 -2213.34 0.500245 -2211.41 1 -2210.82
2415 0.00956962 0.0017633 0.00710127 0.00887173 0.00887173 2.51796 0 2.26996 0 -2213.34 0.500288 -2211.42 1 -2210.82
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2250 1.02668 0.231587 0.333397 0.402399 1.02688 0.535566 0.523543 1.74202 0 -2213.31 0.5 -2212.77 1 -2213.3
2270 1.02655 0.231563 0.333377 0.402367 1.02675 0.53556 0.523538 1.74202 0 -2213.31 0.5 -2212.77 1 -2213.3
2290 1.02324 0.230939 0.332855 0.401554 1.02344 0.535423 0.523408 1.74201 0 -2213.31 0.499999 -2212.77 1 -2213.3
2310 0.962197 0.219348 0.323371 0.386758 0.962414 0.532957 0.521076 1.74185 0 -2213.31 0.499974 -2212.78 1 -2213.3
2330 0.347275 0.0608878 0.240338 0.268402 0.347942 0.514008 0.503436 1.74059 0 -2213.31 0.49951 -2212.8 1 -2213.3
2350 0.343751 0.0639803 0.121885 0.113218 0.344074 0.510887 0.511593 1.74046 0 -2213.33 0.496403 -2212.82 1 -2213.33
2370 0.0799157 0.0136883 0.0704584 0.0605622 0.0798817 0.510054 0.510156 1.74531 0 -2213.34 0.49861 -2212.83 1 -2213.34
2390 0.0325862 0.00467599 0.0301488 0.0250515 0.0325966 0.510002 0.510065 1.74339 0 -2213.34 0.501291 -2212.83 1 -2213.34
2410 0.0277898 0.00427192 0.0193737 0.0205939 0.0278062 0.510058 0.510069 1.74283 0 -2213.34 0.49996 -2212.83 1 -2213.34
2430 0.0115472 0.00143779 0.00458108 0.00554618 0.0115587 0.510099 0.510098 1.74269 0 -2213.34 0.499944 -2212.83 1 -2213.34
2431 0.00579851 0.000650075 0.00316633 0.00318128 0.00582033 0.510098 0.510097 1.74268 0 -2213.34 0.499946 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2431 0.00582033 0.000700972 0.00316633 0.00318128 0.00582033 0.510098 0.510097 1.74268 0 -2213.34 0.499946 -2212.83 1 -2213.34
2432 0.00582033 0.000700972 0.00316633 0.00318128 0.00582033 0.510098 0.510097 1.74268 0 -2213.34 0.499946 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2400 10.2235 6.14088 0.333397 0.560941 10.5304 4.06096 1.54124 1.96552 0 -2213.31 0.5 -2209.25 1 -2210.79
2420 10.2201 6.1385 0.333377 0.560887 10.5271 4.06037 1.54065 1.96552 0 -2213.31 0.5 -2209.25 1 -2210.79
2440 10.1323 6.07713 0.332855 0.559496 10.4429 4.04524 1.52554 1.96552 0 -2213.31 0.5 -2209.26 1 -2210.79
2460 8.62948 5.00926 0.323256 0.533609 9.01248 3.78943 1.27028 1.96637 0 -2213.31 0.500041 -2209.52 1 -2210.79
2480 2.97111 1.29084 0.236868 0.275829 0.275829 2.51426 0 2.08784 0 -2213.31 0.507861 -2210.86 1 -2210.8
2500 0.959443 0.351175 0.173619 0.172681 0.172681 2.51292 0 2.24331 0 -2213.32 0.50556 -2211.33 1 -2210.81
2520 0.38588 0.0603714 0.103802 0.0912192 0.0912192 2.51462 0 2.24375 0 -2213.33 0.491583 -2211.47 1 -2210.81
2540 0.288587 0.0726165 0.0538558 0.0609575 0.0609575 2.51719 0 2.24671 0 -2213.34 0.497432 -2211.41 1 -2210.82
2560 0.202676 0.106656 0.0382176 0.0309594 0.0309594 2.51749 0 2.26086 0 -2213.34 0.500857 -2211.41 1 -2210.82
2580 0.0429794 0.0221957 0.0299599 0.0238534 0.0238534 2.51766 0 2.26336 0 -2213.34 0.500746 -2211.41 1 -2210.82
2600 0.0322687 0.0175135 0.015823 0.0127789 0.0127789 2.51787 0 2.26631 0 -2213.34 0.499901 -2211.42 1 -2210.82
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2600 0.0322687 0.0175135 0.015823 0.0127789 0.0127789 2.51787 0 2.26631 0 -2213.34 0.499901 -2211.42 1 -2210.82
2620 0.0322623 0.0175093 0.0158229 0.0127789 0.0127789 2.51787 0 2.26631 0 -2213.34 0.499901 -2211.42 1 -2210.82
2640 0.0320965 0.0174025 0.0158216 0.0127778 0.0127778 2.51787 0 2.26631 0 -2213.34 0.499902 -2211.42 1 -2210.82
2660 0.0290885 0.0154397 0.0157959 0.0127563 0.0127563 2.51787 0 2.26634 0 -2213.34 0.499906 -2211.42 1 -2210.82
2680 0.0155258 0.00477329 0.0153023 0.0123506 0.0123506 2.51787 0 2.26679 0 -2213.34 0.499984 -2211.42 1 -2210.82
2700 0.0211868 0.0104682 0.00817366 0.00669815 0.00669815 2.51792 0 2.27114 0 -2213.34 0.500275 -2211.42 1 -2210.82
2705 0.00670979 0.00350172 0.00300281 0.00258959 0.00258959 2.51794 0 2.2734 0 -2213.34 0.500053 -2211.42 1 -2210.82
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2550 1.07249 0.264594 0.333397 0.740445 1.07301 0.55072 0.49949 1.74628 0 -2213.31 0.5 -2212.76 1 -2213.26
2570 1.07236 0.264567 0.333377 0.740341 1.07287 0.550714 0.499486 1.74628 0 -2213.31 0.5 -2212.76 1 -2213.26
2590 1.06883 0.263852 0.332855 0.737674 1.06935 0.550563 0.499399 1.74626 0 -2213.31 0.500002 -2212.76 1 -2213.26
2610 1.00377 0.250543 0.323364 0.688819 1.00431 0.547846 0.497813 1.74601 0 -2213.31 0.500031 -2212.76 1 -2213.26
2630 0.364976 0.0625081 0.239814 0.325576 0.366173 0.527038 0.484594 1.74336 0 -2213.31 0.500503 -2212.79 1 -2213.27
2650 0.382696 0.0730307 0.125706 0.244586 0.382887 0.515802 0.504716 1.74258 0 -2213.33 0.499732 -2212.82 1 -2213.32
2670 0.104285 0.0162542 0.0376625 0.0582349 0.106022 0.511355 0.510917 1.75709 0 -2213.34 0.50184 -2212.83 1 -2213.34
2690 0.0616293 0.00845784 0.0222288 0.05303 0.0634796 0.510718 0.510407 1.75285 0 -2213.34 0.502132 -2212.83 1 -2213.34
2710 0.0256004 0.00437569 0.00763474 0.0256004 0.0219846 0.510215 0.510159 1.74627 0 -2213.34 0.501154 -2212.83 1 -2213.34
2730 0.00960281 0.00140235 0.00304618 0.00745892 0.00973351 0.510142 0.510128 1.74469 0 -2213.34 0.500025 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2730 0.00973351 0.0016775 0.00304618 0.00745892 0.00973351 0.510142 0.510128 1.74469 0 -2213.34 0.500025 -2212.83 1 -2213.34
2731 0.00973351 0.0016775 0.00304618 0.00745892 0.00973351 0.510142 0.510128 1.74469 0 -2213.34 0.500025 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2700 10.4043 6.30602 0.333397 0.712523 10.6906 4.14369 1.62341 2.00092 0 -2213.31 0.5 -2209.16 1 -2210.79
2720 10.4008 6.30356 0.333377 0.712453 10.6872 4.14308 1.6228 2.00092 0 -2213.31 0.5 -2209.16 1 -2210.79
2740 10.3102 6.24014 0.332855 0.710664 10.6 4.1274 1.60719 2.00091 0 -2213.31 0.500002 -2209.18 1 -2210.79
2760 8.76124 5.13831 0.323254 0.677236 9.11961 3.8629 1.34375 2.00163 0 -2213.31 0.500076 -2209.45 1 -2210.79
2780 3.03032 1.32078 0.236853 0.270629 0.270629 2.50926 0 2.12106 0 -2213.31 0.508274 -2210.81 1 -2210.8
2800 0.959411 0.341284 0.173572 0.157402 0.157402 2.51044 0 2.2733 0 -2213.32 0.507033 -2211.3 1 -2210.81
2820 0.383219 0.0557002 0.103892 0.0832242 0.0832242 2.51371 0 2.26292 0 -2213.33 0.49384 -2211.46 1 -2210.81
2840 0.298418 0.0764882 0.0533911 0.0445197 0.0445197 2.51688 0 2.25172 0 -2213.34 0.497224 -2211.42 1 -2210.82
2860 0.102174 0.0499693 0.0410915 0.028773 0.028773 2.5172 0 2.26291 0 -2213.34 0.500215 -2211.41 1 -2210.82
2880 0.088089 0.0494011 0.0259378 0.0180907 0.0180907 2.51764 0 2.26622 0 -2213.34 0.500173 -2211.41 1 -2210.82
2900 0.024413 0.00815881 0.024413 0.0170138 0.0170138 2.51768 0 2.26655 0 -2213.34 0.500154 -2211.41 1 -2210.82
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2900 0.024413 0.00815881 0.024413 0.0170138 0.0170138 2.51768 0 2.26655 0 -2213.34 0.500154 -2211.41 1 -2210.82
2920 0.024413 0.00815732 0.024413 0.0170137 0.0170137 2.51768 0 2.26655 0 -2213.34 0.500154 -2211.41 1 -2210.82
2940 0.0244109 0.00811882 0.0244109 0.0170123 0.0170123 2.51768 0 2.26655 0 -2213.34 0.500154 -2211.41 1 -2210.82
2960 0.024372 0.00741607 0.024372 0.0169854 0.0169854 2.51768 0 2.26656 0 -2213.34 0.500153 -2211.41 1 -2210.82
2980 0.0236779 0.00193974 0.0236779 0.0165065 0.0165065 2.51769 0 2.26673 0 -2213.34 0.500151 -2211.41 1 -2210.82
3000 0.0125045 0.00465071 0.0125045 0.00879736 0.00879736 2.51787 0 2.27026 0 -2213.34 0.500225 -2211.42 1 -2210.82
3003 0.00734388 0.00280677 0.00696949 0.00497533 0.00497533 2.51792 0 2.27235 0 -2213.34 0.500255 -2211.42 1 -2210.82
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2850 1.02576 0.227789 0.333397 0.520132 1.02731 0.547543 0.502429 1.72979 0 -2213.31 0.5 -2212.76 1 -2213.26
2870 1.02564 0.227765 0.333377 0.5201 1.02719 0.547538 0.502424 1.72979 0 -2213.31 0.5 -2212.76 1 -2213.26
2890 1.02243 0.227154 0.332855 0.519286 1.02399 0.547401 0.502311 1.72979 0 -2213.31 0.499998 -2212.76 1 -2213.26
2910 0.963356 0.215807 0.323376 0.504337 0.964997 0.544937 0.500275 1.72976 0 -2213.31 0.499959 -2212.76 1 -2213.26
2930 0.36698 0.0621231 0.240717 0.339068 0.370777 0.525273 0.486264 1.73106 0 -2213.31 0.499259 -2212.79 1 -2213.27
2950 0.325241 0.0658099 0.120377 0.174695 0.325454 0.514627 0.506087 1.74593 0 -2213.33 0.498611 -2212.82 1 -2213.32
2970 0.0833702 0.0131246 0.0364962 0.0514897 0.0875782 0.511304 0.510779 1.75544 0 -2213.34 0.504295 -2212.83 1 -2213.34
2990 0.0672459 0.0101732 0.0292887 0.0479852 0.0672612 0.510291 0.51028 1.74401 0 -2213.34 0.499509 -2212.83 1 -2213.34
3010 0.0280737 0.00215786 0.0131924 0.0280737 0.0239316 0.510147 0.510129 1.74333 0 -2213.34 0.499514 -2212.83 1 -2213.34
3018 0.00859213 0.000860338 0.00413808 0.00492247 0.00861342 0.510123 0.510119 1.74332 0 -2213.34 0.499622 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
3018 0.00861342 0.000859006 0.00413808 0.00492247 0.00861342 0.510123 0.510119 1.74332 0 -2213.34 0.499622 -2212.83 1 -2213.34
3019 0.00861342 0.000859006 0.00413808 0.00492247 0.00861342 0.510123 0.510119 1.74332 0 -2213.34 0.499622 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
3000 9.69974 5.72119 0.333397 1.03445 10.0369 3.86161 1.31734 1.9417 0 -2213.31 0.5 -2209.45 1 -2210.76
3020 9.69666 5.71904 0.333377 1.0343 10.034 3.86108 1.31682 1.9417 0 -2213.31 0.5 -2209.45 1 -2210.76
3040 9.61772 5.66396 0.332855 1.03045 9.95898 3.84745 1.30333 1.9417 0 -2213.31 0.5 -2209.46 1 -2210.76
3060 8.2604 4.70104 0.323267 0.95884 8.67957 3.61585 1.07424 1.94241 0 -2213.31 0.500054 -2209.69 1 -2210.77
3080 2.82078 1.21278 0.237028 0.306129 0.306129 2.5258 0 2.0574 0 -2213.31 0.508181 -2210.96 1 -2210.79
3100 0.948828 0.346323 0.173671 0.193772 0.193772 2.52607 0 2.21131 0 -2213.32 0.505566 -2211.41 1 -2210.79
3120 0.407957 0.0602332 0.103631 0.140457 0.140457 2.52346 0 2.2191 0 -2213.33 0.488574 -2211.55 1 -2210.8
3140 0.364612 0.102646 0.0523422 0.108105 0.108105 2.51928 0 2.23191 0 -2213.34 0.494133 -2211.44 1 -2210.82
3160 0.137524 0.0697319 0.0405944 0.0516647 0.0516647 2.51879 0 2.2475 0 -2213.34 0.49884 -2211.42 1 -2210.82
3180 0.121252 0.0666785 0.0256245 0.0323847 0.0323847 2.51829 0 2.25652 0 -2213.34 0.499961 -2211.42 1 -2210.82
3200 0.0858341 0.047264 0.0212534 0.0268825 0.0268825 2.51818 0 2.25906 0 -2213.34 0.499925 -2211.42 1 -2210.82
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
3200 0.0858341 0.047264 0.0212534 0.0268825 0.0268825 2.51818 0 2.25906 0 -2213.34 0.499925 -2211.42 1 -2210.82
3220 0.0858151 0.0472524 0.0212533 0.0268824 0.0268824 2.51818 0 2.25906 0 -2213.34 0.499925 -2211.42 1 -2210.82
3240 0.085325 0.0469521 0.0212515 0.0268802 0.0268802 2.51818 0 2.25906 0 -2213.34 0.499925 -2211.42 1 -2210.82
3260 0.0763647 0.0414249 0.0212174 0.0268374 0.0268374 2.51818 0 2.25909 0 -2213.34 0.499928 -2211.42 1 -2210.82
3280 0.0373586 0.0171503 0.0205115 0.0259547 0.0259547 2.51817 0 2.25968 0 -2213.34 0.499969 -2211.42 1 -2210.82
3300 0.0525021 0.0291791 0.0112418 0.0143847 0.0143847 2.51801 0 2.26611 0 -2213.34 0.500148 -2211.42 1 -2210.82
3315 0.00985993 0.00176473 0.00709388 0.00921546 0.00921546 2.51797 0 2.2694 0 -2213.34 0.500243 -2211.42 1 -2210.82
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2450 0.993099 0.219189 0.402399 0.299711 0.9931 0.511368 0.52034 1.77348 0 -2213.3 0.5 -2212.78 1 -2213.3
2470 0.992973 0.219166 0.402367 0.299693 0.992974 0.511363 0.520335 1.77348 0 -2213.3 0.5 -2212.78 1 -2213.3
2490 0.989735 0.218564 0.401554 0.299221 0.989735 0.511243 0.520204 1.77347 0 -2213.3 0.499999 -2212.78 1 -2213.3
2510 0.929951 0.207364 0.386757 0.29067 0.929952 0.50909 0.51786 1.77329 0 -2213.3 0.499981 -2212.79 1 -2213.3
2530 0.311709 0.0591171 0.26832 0.219457 0.311721 0.49341 0.500071 1.77158 0 -2213.3 0.499654 -2212.81 1 -2213.31
2550 0.329861 0.0581088 0.116527 0.112332 0.329932 0.509482 0.507808 1.75105 0 -2213.33 0.501354 -2212.82 1 -2213.33
2570 0.0732633 0.0107973 0.0723075 0.0248689 0.0737526 0.509227 0.510943 1.75093 0 -2213.34 0.502102 -2212.83 1 -2213.34
2590 0.0537146 0.00771337 0.0204217 0.0153441 0.0537728 0.510146 0.510177 1.74063 0 -2213.34 0.498757 -2212.83 1 -2213.34
2610 0.0165171 0.0013944 0.00731874 0.00722755 0.0165147 0.510092 0.510095 1.74163 0 -2213.34 0.499642 -2212.83 1 -2213.34
2620 0.00850767 0.00125433 0.00334354 0.00416019 0.00855943 0.510094 0.510092 1.74235 0 -2213.34 0.500172 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2620 0.00855943 0.00125025 0.00334354 0.00416019 0.00855943 0.510094 0.510092 1.74235 0 -2213.34 0.500172 -2212.83 1 -2213.34
2621 0.00855943 0.00125025 0.00334354 0.00416019 0.00855943 0.510094 0.510092 1.74235 0 -2213.34 0.500172 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2700 1.06077 0.264354 0.402399 0.530036 1.06107 0.538798 0.471977 1.76907 0 -2213.3 0.5 -2212.76 1 -2213.23
2720 1.06064 0.264327 0.402367 0.530007 1.06094 0.538793 0.471973 1.76907 0 -2213.3 0.5 -2212.76 1 -2213.23
2740 1.05725 0.263625 0.401554 0.529264 1.05755 0.538653 0.47185 1.76905 0 -2213.3 0.500004 -2212.76 1 -2213.23
2760 0.994796 0.250596 0.386764 0.515813 0.99511 0.536133 0.469656 1.76872 0 -2213.3 0.500086 -2212.76 1 -2213.23
2780 0.404941 0.0701096 0.268704 0.404941 0.370314 0.516704 0.455927 1.76436 0 -2213.3 0.501563 -2212.78 1 -2213.24
2800 0.337868 0.0612732 0.107069 0.176834 0.33791 0.515031 0.499538 1.75826 0 -2213.33 0.504663 -2212.82 1 -2213.32
2820 0.0855987 0.0138592 0.0699199 0.0737132 0.0872703 0.51004 0.510006 1.76565 0 -2213.34 0.501259 -2212.83 1 -2213.34
2840 0.0807166 0.011249 0.0360377 0.0510637 0.0808097 0.510304 0.510123 1.74392 0 -2213.34 0.500983 -2212.83 1 -2213.34
2860 0.0153061 0.00168927 0.0106301 0.0153061 0.0154766 0.510175 0.510069 1.74465 0 -2213.34 0.500234 -2212.83 1 -2213.34
2874 0.00846157 0.000819038 0.00367139 0.0076394 0.00846576 0.510119 0.510095 1.74353 0 -2213.34 0.499829 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2874 0.00846576 0.000818597 0.00367139 0.0076394 0.00846576 0.510119 0.510095 1.74353 0 -2213.34 0.499829 -2212.83 1 -2213.34
2875 0.00846576 0.000818597 0.00367139 0.0076394 0.00846576 0.510119 0.510095 1.74353 0 -2213.34 0.499829 -2212.83 1 -2213.34
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
2950 1.01375 0.227712 0.402399 0.410783 1.01377 0.519697 0.490944 1.8246 0 -2213.3 0.5 -2212.78 1 -2213.27
2970 1.01362 0.227687 0.402367 0.410747 1.01364 0.519693 0.490939 1.8246 0 -2213.3 0.5 -2212.78 1 -2213.27
2990 1.0103 0.227052 0.401554 0.409841 1.01032 0.519567 0.490814 1.82458 0 -2213.3 0.500003 -2212.78 1 -2213.27
3010 0.949127 0.215248 0.386756 0.393552 0.949146 0.517305 0.48857 1.82413 0 -2213.3 0.500056 -2212.78 1 -2213.27
3030 0.326309 0.061663 0.268408 0.297216 0.326309 0.500699 0.472314 1.81726 0 -2213.3 0.501038 -2212.8 1 -2213.27
3050 0.332946 0.0600054 0.114537 0.162865 0.334055 0.510685 0.500574 1.75605 0 -2213.33 0.50719 -2212.82 1 -2213.32
3070 0.0722203 0.0108067 0.0711354 0.0293276 0.0731129 0.509283 0.510779 1.75008 0 -2213.34 0.501912 -2212.83 1 -2213.34
3090 0.060973 0.00929441 0.024278 0.0415372 0.0610094 0.510177 0.510156 1.74196 0 -2213.34 0.498623 -2212.83 1 -2213.34
3110 0.0251508 0.00200643 0.00825568 0.0251508 0.0201461 0.5101 0.510081 1.7422 0 -2213.34 0.49985 -2212.83 1 -2213.34
3117 0.0086436 0.000986795 0.00355547 0.0086436 0.00832142 0.510096 0.510086 1.74244 0 -2213.34 0.500287 -2212.83 1 -2213.34
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
3117 0.0086436 0.00115855 0.00355547 0.0086436 0.00832142 0.510096 0.510086 1.74244 0 -2213.34 0.500287 -2212.83 1 -2213.34
3118 0.0086436 0.00115855 0.00355547 0.0086436 0.00832142 0.510096 0.510086 1.74244 0 -2213.34 0.500287 -2212.83 1 -2213.34