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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1839 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2008-05-16 21:57:36 +00:00
parent fc90ae381b
commit 07ed5774a3
91 changed files with 4776 additions and 5424 deletions
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LAMMPS (21 May 2008)
# 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 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0
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 = 1.84805 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.7223559 0.00098929183 1.7214314 0.015437595 101049.21
2000 1.9986757 0.00075885378 1.9972138 0.018605636 99044.305
3000 2.117844 0.0022972154 2.1177881 0.0290761 68969.85
4000 2.0898816 0.0057833635 2.0933428 0.047715809 41724.713
5000 2.0439342 4.9494163e-05 2.0417126 0.068595136 27281.204
6000 2.0064511 0.0044083308 2.0086301 0.099885102 20425.198
7000 2.0093135 0.00030033275 2.0073813 0.1121452 16950.524
8000 1.9916421 0.007621323 1.9970505 0.13964337 14953.142
9000 1.9903947 0.01453264 2.0027158 0.15594249 13489.913
10000 1.9988985 0.0052414174 2.0019189 0.17202156 12266.498
11000 2.00691 0.01129961 2.0159797 0.1963436 11187.939
12000 2.023487 0.002118289 2.023357 0.19929988 10338.246
13000 1.9848513 0.023120894 2.0057668 0.27040057 9647.688
14000 2.0010828 0.016195647 2.0150551 0.23608408 9076.0171
15000 1.9851734 0.02269988 2.0056676 0.30152394 8550.0935
16000 1.9911017 0.024538799 2.0134282 0.29719998 8065.2116
17000 2.0092834 0.013074179 2.020125 0.33224922 7611.4535
18000 2.0039464 0.015002702 2.0167225 0.34918313 7266.7936
19000 2.0019869 0.030678635 2.0304411 0.35155001 6969.7731
20000 2.0248332 0.023656323 2.0462397 0.35430625 6665.3958
21000 2.0260129 0.011469083 2.0352308 0.37670894 6451.5167
22000 1.9932271 0.02944517 2.0204576 0.44088832 6286.6382
23000 1.9979731 0.022604615 2.0183578 0.40240249 6093.5172
24000 2.0256254 0.014021814 2.0373965 0.43187961 5869.4093
25000 1.9843937 0.046591133 2.0287799 0.44796375 5709.9348
26000 2.0101586 0.017301084 2.0252262 0.51214936 5534.8985
27000 1.9887979 0.042607087 2.0291953 0.5364801 5383.6677
28000 2.0273894 0.010574688 2.0357114 0.53575221 5277.3504
29000 2.0114853 0.026487843 2.0357382 0.5019495 5183.9253
30000 1.9850719 0.036881749 2.019748 0.6029796 5083.5559
31000 1.9896683 0.035584301 2.0230419 0.63219014 4941.787
32000 1.9931863 0.045315686 2.0362874 0.59040131 4851.7745
33000 1.9857406 0.047506524 2.0310408 0.67712512 4778.4773
34000 1.9868172 0.057482705 2.0420923 0.71724066 4683.1331
35000 2.0166361 0.039653294 2.0540487 0.65881549 4607.7207
36000 1.9947118 0.057664381 2.0501599 0.73270964 4500.9296
37000 2.0026862 0.056070861 2.0565318 0.75439865 4419.1699
38000 2.0029796 0.058127694 2.0588818 0.75965407 4349.8826
39000 2.0123422 0.051811215 2.0619175 0.73967495 4280.3846
40000 1.979341 0.064620417 2.0417622 0.91817043 4210.1251
41000 1.9987965 0.048789657 2.0453653 0.77100684 4156.1718
42000 1.9941581 0.053682864 2.0456253 0.81849452 4093.031
43000 2.0170196 0.047788852 2.0625674 0.80410205 4049.9079
44000 2.0256856 0.039232233 2.062667 0.75599759 4004.6084
45000 1.9948188 0.046497265 2.0390996 0.94849943 3947.7148
46000 1.985315 0.080755658 2.0638648 0.88383148 3925.0434
47000 2.0102018 0.055513279 2.0634815 0.89218971 3877.3667
48000 1.9836965 0.073263577 2.054756 1.0335461 3819.6995
49000 2.016596 0.049424893 2.0637802 0.89744695 3789.3397
50000 2.0091046 0.054246496 2.0611188 0.97651208 3721.2095
Loop time of 14.0034 on 1 procs for 50000 steps with 900 atoms
Pair time (%) = 8.39301 (59.9356)
Neigh time (%) = 1.62176 (11.5812)
Comm time (%) = 0.390372 (2.7877)
Outpt time (%) = 0.311517 (2.22459)
Other time (%) = 3.28672 (23.4709)
Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 574 ave 574 max 574 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6018 ave 6018 max 6018 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6018
Ave neighs/atom = 6.68667
Neighbor list builds = 2802
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0
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 = 1.72729 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.7223559 0.00098929183 1.7214314 0.015437595 101049.21
2000 1.9986757 0.00075885378 1.9972138 0.018605636 99044.305
3000 2.117844 0.0022972154 2.1177881 0.0290761 68969.85
4000 2.0898816 0.0057833635 2.0933428 0.047715809 41724.713
5000 2.0439342 4.9493696e-05 2.0417126 0.068595137 27281.204
6000 2.0064128 0.0044188137 2.0086023 0.099926529 20425.195
7000 2.009238 0.00046917886 2.0074747 0.11213609 16950.59
8000 1.9949838 0.0052143802 1.9979815 0.1425616 14958.04
9000 2.0011383 0.0069562003 2.005871 0.14834553 13504.001
10000 1.979696 0.02095102 1.9984473 0.19710313 12322.476
11000 1.9924355 0.020996961 2.0112186 0.19380381 11317.61
12000 2.0174806 0.0045044349 2.0197434 0.19561004 10406.802
13000 2.0141962 0.012098292 2.0240564 0.23000265 9574.4324
14000 2.0117821 0.011995258 2.0215421 0.24369426 8941.3844
15000 2.0145336 0.0075091224 2.0198044 0.27014029 8427.7465
16000 1.9951071 0.016297672 2.009188 0.29810761 8032.5886
17000 1.9873425 0.017851879 2.0029862 0.37277713 7672.305
18000 2.0113338 0.011550523 2.0206495 0.31040003 7349.9335
19000 2.0042474 0.021677746 2.0236982 0.34923741 7038.9595
20000 2.0132671 0.01770125 2.0287314 0.34219638 6788.2687
21000 1.9990052 0.025514077 2.0222981 0.41034791 6511.8494
22000 1.9920265 0.034234411 2.0240476 0.447435 6265.757
23000 1.9785405 0.033612536 2.0099547 0.48855923 6083.2627
24000 2.0072694 0.020012143 2.0250513 0.42997092 5921.4392
25000 1.9999409 0.025903294 2.023622 0.48047026 5734.6208
26000 1.9957819 0.025572875 2.0191372 0.51207606 5567.496
27000 2.0045855 0.021594009 2.0239522 0.55039179 5429.0002
28000 2.0095018 0.031277686 2.0385467 0.53154624 5292.7192
29000 1.9973043 0.031158435 2.0262435 0.66732668 5135.6507
30000 2.0052408 0.043659151 2.0466719 0.54053464 5006.0454
31000 2.0054687 0.028869471 2.0321099 0.6486529 4917.9379
32000 2.0014648 0.039097706 2.0383386 0.63590098 4830.9602
33000 2.0109706 0.027207161 2.0359434 0.62127582 4737.6015
34000 1.9926472 0.053463886 2.043897 0.70086128 4628.5249
35000 2.0042786 0.043819947 2.0458716 0.70552776 4561.5216
36000 2.0055993 0.032340095 2.035711 0.7089785 4483.1738
37000 1.9884127 0.059230504 2.0454339 0.81716796 4421.5811
38000 2.0051674 0.045925715 2.0488651 0.7107607 4384.2193
39000 1.985589 0.050501548 2.0338844 0.85566246 4298.1153
40000 1.9893789 0.06330525 2.0504737 0.80004664 4229.6943
41000 2.0113301 0.036227311 2.0453226 0.87163382 4148.2176
42000 1.9889787 0.05762879 2.0443975 0.76189797 4150.7988
43000 2.0165757 0.042412435 2.0567475 0.7515161 4110.7711
44000 2.0115095 0.047339399 2.0566139 0.80198372 4004.5573
45000 2.0097681 0.061366139 2.0689011 0.84636277 3915.4567
46000 1.9952706 0.065316805 2.0583704 0.84815375 3888.9886
47000 2.0295555 0.04141762 2.0687181 0.85366092 3877.8183
48000 2.0043454 0.064491592 2.0666099 0.93867902 3831.6649
49000 1.995415 0.078541445 2.0717394 0.86534452 3757.6528
50000 2.0184848 0.052970859 2.0692129 1.1246952 3732.4184
Loop time of 30.607 on 4 procs for 50000 steps with 900 atoms
Pair time (%) = 2.29298 (7.49168)
Neigh time (%) = 0.420455 (1.37372)
Comm time (%) = 15.7757 (51.5429)
Outpt time (%) = 0.357466 (1.16792)
Other time (%) = 11.7603 (38.4238)
Nlocal: 225 ave 243 max 213 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Nghost: 321.5 ave 334 max 315 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Neighs: 1507.5 ave 1590 max 1436 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 6030
Ave neighs/atom = 6.7
Neighbor list builds = 2800
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0
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 = 1.84805 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4375978 0.014375923 90000
1000 1.7223464 0.00099729506 1.7204731 0.015431199 101039.13
2000 1.9986619 0.00075906115 1.9960899 0.018607661 99018.745
3000 2.1174664 0.0023215952 2.1162589 0.029169081 68947.872
4000 2.0922515 0.0027117962 2.0914762 0.048247413 41709.954
5000 2.0457094 -0.0017934808 2.0405064 0.069440615 27252.713
6000 2.0094249 -0.0030357548 2.0030401 0.095318346 20437.896
7000 1.9791016 0.015378539 1.9911816 0.12201039 16963.981
8000 2.0037567 0.00087754405 2.0012947 0.13624715 14904.297
9000 1.9954986 0.0074776387 1.9996504 0.15437139 13466.422
10000 2.0017119 0.0090860936 2.0074618 0.15967653 12285.361
11000 1.9965885 0.020076864 2.0133378 0.20431975 11226.299
12000 1.9893265 0.029138936 2.0151499 0.22508119 10359.215
13000 2.0096277 0.0055549561 2.0118333 0.23118708 9650.1073
14000 1.9874756 0.025360954 2.009524 0.25223651 9022.125
15000 1.9818513 0.036888053 2.0154362 0.3116855 8475.2794
16000 1.9928816 0.018897335 2.0084574 0.30081232 8067.2389
17000 1.9990591 0.025240285 2.0209676 0.30592349 7632.1957
18000 2.0101337 0.01582473 2.0226082 0.35986446 7250.9935
19000 2.0091976 0.019233907 2.0250828 0.33919836 6974.9737
20000 2.0064131 0.017623877 2.020693 0.35420372 6745.1629
21000 1.9971779 0.023499432 2.0173487 0.40913112 6504.8686
22000 1.9899433 0.036716791 2.0233435 0.46792355 6249.486
23000 2.0165042 0.030701843 2.0438452 0.43797608 6047.9924
24000 2.0162136 0.034428645 2.0472819 0.45591758 5884.7421
25000 2.0127204 0.035477231 2.0448431 0.5131322 5698.5164
26000 2.0187252 0.017160139 2.0325208 0.43758584 5558.1903
27000 1.9830248 0.049563853 2.0292837 0.56069898 5409.6546
28000 2.0189391 0.019264404 2.0348386 0.48027834 5284.0336
29000 1.9713776 0.050692614 2.0187846 0.61025529 5173.3555
30000 1.9819168 0.039816462 2.0184301 0.63355537 5059.7477
31000 1.9957876 0.045223147 2.0376844 0.60945681 4940.036
32000 2.0208255 0.028176971 2.0456344 0.62584685 4820.4303
33000 2.0103751 0.039181534 2.046206 0.69487302 4753.2781
34000 1.9959594 0.061461733 2.0540945 0.611319 4671.1011
35000 1.9843152 0.063438307 2.0444463 0.67227839 4580.8853
36000 2.0187362 0.029117024 2.0444886 0.67437268 4451.5952
37000 1.9767721 0.064543976 2.0380214 0.75641695 4386.7451
38000 2.0054158 0.038665525 2.040739 0.75284861 4340.2087
39000 2.0190605 0.028863116 2.0445585 0.72515667 4322.6267
40000 1.99241 0.056203851 2.0452932 0.77541878 4240.6248
41000 1.9794314 0.06647082 2.0426031 0.91929985 4161.9926
42000 2.0137404 0.050868342 2.0612525 0.76319297 4112.588
43000 2.0251176 0.041454389 2.0631968 0.8153631 4098.5268
44000 1.9931653 0.058795109 2.0486384 0.83341834 4025.7567
45000 1.992498 0.059944502 2.0491217 0.9195581 3949.158
46000 1.950407 0.087564106 2.0347204 1.0730912 3904.5945
47000 1.9829495 0.079781556 2.0594262 0.99133843 3840.5951
48000 2.0085408 0.051200913 2.0563942 0.91558928 3817.7264
49000 1.9929984 0.063176682 2.0528534 0.97184545 3811.188
50000 1.9924895 0.066841874 2.0560106 1.0256436 3768.1172
Loop time of 14.0171 on 1 procs for 50000 steps with 900 atoms
Pair time (%) = 8.39109 (59.8632)
Neigh time (%) = 1.62785 (11.6133)
Comm time (%) = 0.380158 (2.7121)
Outpt time (%) = 0.311819 (2.22456)
Other time (%) = 3.3062 (23.5868)
Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 506 ave 506 max 506 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6031 ave 6031 max 6031 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6031
Ave neighs/atom = 6.70111
Neighbor list builds = 2778
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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 2.0 2.0 1.0 xyz 0.0 1.0 10.0 drag 1.0
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 = 1.72729 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4375978 0.014375923 90000
1000 1.7223464 0.00099729506 1.7204731 0.015431199 101039.13
2000 1.9986619 0.00075906115 1.9960899 0.018607661 99018.745
3000 2.1174664 0.0023215952 2.1162589 0.029169081 68947.872
4000 2.0922515 0.0027117962 2.0914762 0.048247413 41709.954
5000 2.0457094 -0.0017934811 2.0405064 0.069440615 27252.713
6000 2.0094247 -0.0030357089 2.00304 0.095318361 20437.896
7000 1.9787517 0.015727213 1.991181 0.12210082 16963.98
8000 1.9983 0.0017433401 1.9967129 0.14165341 14903.677
9000 1.9927888 0.013406349 2.0028739 0.17008104 13468.549
10000 1.99929 0.011927067 2.0078849 0.18343491 12299.949
11000 2.0150846 0.00018121827 2.0119074 0.18478179 11314.797
12000 2.0039613 0.0083020972 2.0089234 0.22215222 10404.632
13000 2.0089431 0.00048942212 2.0060843 0.2159184 9598.2333
14000 1.9642202 0.03348398 1.9944305 0.29178119 8913.182
15000 1.9865717 0.028923917 2.0121846 0.29202685 8385.9226
16000 1.9824603 0.021603392 2.0007596 0.35043111 7979.2443
17000 2.0212495 0.0013151574 2.0191959 0.29445176 7613.1843
18000 2.00735 0.016693347 2.0206977 0.35537739 7292.1647
19000 1.9996379 0.025020058 2.0213252 0.35594894 6980.3692
20000 1.99304 0.035528694 2.025247 0.39068018 6690.3555
21000 1.9996323 0.017458241 2.0137578 0.39735127 6497.3837
22000 1.9949617 0.028866687 2.0205034 0.40527844 6223.7318
23000 2.0109325 0.017646321 2.0252272 0.4171507 5971.5878
24000 2.0065992 0.020958573 2.0242135 0.44285242 5811.3038
25000 2.0162034 0.013608049 2.0264511 0.44820753 5670.6039
26000 2.0155947 0.021613098 2.0338484 0.50646486 5560.9474
27000 1.9867282 0.061035788 2.0444527 0.52834033 5416.229
28000 2.0182277 0.027696843 2.0425608 0.50068529 5248.3423
29000 1.9969804 0.025362049 2.0190142 0.62372967 5114.3052
30000 1.9919721 0.031513314 2.0201654 0.58566807 5040.2167
31000 1.9717581 0.065297706 2.0337695 0.58587707 4925.982
32000 2.0031236 0.027941441 2.0277265 0.63718249 4800.1641
33000 2.009939 0.035745131 2.0423342 0.5565546 4716.8179
34000 2.0133737 0.032514079 2.0425322 0.59840543 4661.2112
35000 1.9946613 0.050844465 2.0421813 0.75006325 4544.451
36000 2.013397 0.0397056 2.0497469 0.65849841 4483.7497
37000 2.0006181 0.037963997 2.0352477 0.77598608 4414.6609
38000 1.9575408 0.06996425 2.0242425 0.86318741 4362.8063
39000 1.9858721 0.064218347 2.0467806 0.72824697 4313.8724
40000 2.0033244 0.046949963 2.0469355 0.71735138 4210.7464
41000 1.9841673 0.05811834 2.0389787 0.77792196 4140.5996
42000 2.0176912 0.035140169 2.0494686 0.72179939 4106.7454
43000 1.9910197 0.055696348 2.0433977 0.78813392 4042.2245
44000 1.9684218 0.090017002 2.0551581 0.89775094 3964.1659
45000 1.9934298 0.063845821 2.0539532 0.87564355 3943.1864
46000 2.0098408 0.043671419 2.0501625 0.9380022 3914.699
47000 2.0085323 0.055757448 2.0609422 0.83280289 3838.9374
48000 1.9935643 0.064908847 2.0551505 0.9287581 3822.0687
49000 2.0102242 0.045686005 2.0525598 0.92639038 3796.1209
50000 1.9866234 0.069280947 2.0525933 0.98907678 3713.7478
Loop time of 36.2457 on 4 procs for 50000 steps with 900 atoms
Pair time (%) = 2.46031 (6.78788)
Neigh time (%) = 0.449679 (1.24064)
Comm time (%) = 19.0279 (52.4971)
Outpt time (%) = 0.376391 (1.03844)
Other time (%) = 13.9313 (38.4359)
Nlocal: 225 ave 253 max 182 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 297.5 ave 310 max 275 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 1518.5 ave 1657 max 1246 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 6074
Ave neighs/atom = 6.74889
Neighbor list builds = 2768
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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
neigh_modify exclude type 2 3
dump 1 all atom 500 dump.crack
run 5000
Memory usage per processor = 1.98601 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 12.8237 on 1 procs for 5000 steps with 8141 atoms
Pair time (%) = 11.0154 (85.8987)
Neigh time (%) = 0.39023 (3.04304)
Comm time (%) = 0.00849199 (0.066221)
Outpt time (%) = 0.114103 (0.889782)
Other time (%) = 1.29548 (10.1022)
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 (21 May 2008)
# 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
neigh_modify exclude type 2 3
dump 1 all atom 500 dump.crack
run 5000
Memory usage per processor = 1.7559 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 5.55919 on 4 procs for 5000 steps with 8141 atoms
Pair time (%) = 2.79903 (50.3495)
Neigh time (%) = 0.104656 (1.88258)
Comm time (%) = 1.8012 (32.4004)
Outpt time (%) = 0.109615 (1.97177)
Other time (%) = 0.744692 (13.3957)
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 (22 Jan 2008)
# 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
neigh_modify exclude type 2 3
dump 1 all atom 500 dump.crack
run 5000
Memory usage per processor = 1.98601 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.065655433 -3.2595015 0 -3.1987293 -0.036254085 8602.1883
200 0.060090071 -3.2531939 0 -3.1975731 -0.23134429 8635.3999
400 0.060537254 -3.2509976 0 -3.1949629 -0.4307124 8675.8282
600 0.060833381 -3.2466952 0 -3.1903864 -0.60309195 8713.3311
800 0.061681012 -3.2413218 0 -3.1842284 -0.74857006 8752.7925
1000 0.062387584 -3.2349276 0 -3.1771802 -0.87459498 8789.6707
1200 0.063713197 -3.2276097 0 -3.1686353 -0.98058579 8825.4383
1400 0.065408625 -3.2196611 0 -3.1591173 -1.0699564 8863.0337
1600 0.067583821 -3.2110381 0 -3.1484809 -1.1460853 8897.2148
1800 0.069328584 -3.2018539 0 -3.1376817 -1.2025675 8929.5481
2000 0.071019398 -3.192111 0 -3.1263738 -1.243493 8960.5103
2200 0.072997487 -3.1818704 0 -3.1143022 -1.2706215 9000.9304
2400 0.075005457 -3.1712316 0 -3.1018048 -1.2835823 9031.5099
2600 0.076848328 -3.1601006 0 -3.088968 -1.279733 9068.6358
2800 0.078676694 -3.148775 0 -3.07595 -1.2664473 9100.4495
3000 0.080718743 -3.137326 0 -3.0626108 -1.2445399 9131.0428
3200 0.083100049 -3.1260245 0 -3.0491051 -1.2150134 9165.484
3400 0.085430328 -3.1146626 0 -3.0355863 -1.1843864 9203.385
3600 0.087402049 -3.1029496 0 -3.0220482 -1.1438487 9230.2535
3800 0.089013695 -3.0908222 0 -3.0084291 -1.100499 9255.4996
4000 0.089818767 -3.079408 0 -2.9962696 -1.0632516 9278.2794
4200 0.085852921 -3.0668561 0 -2.9873886 -1.0383666 9305.2639
4400 0.086203112 -3.0559681 0 -2.9761765 -1.0292349 9325.4147
4600 0.086772028 -3.0437629 0 -2.9634447 -1.0212674 9358.4354
4800 0.088200815 -3.0328504 0 -2.9512097 -1.027596 9392.0468
5000 0.08942145 -3.0228831 0 -2.9401125 -1.0219214 9432.5895
Loop time of 12.9137 on 1 procs for 5000 steps with 8141 atoms
Pair time (%) = 11.1063 (86.0039)
Neigh time (%) = 0.387242 (2.99868)
Comm time (%) = 0.0083847 (0.0649286)
Outpt time (%) = 0.112896 (0.874232)
Other time (%) = 1.2989 (10.0583)
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 (22 Jan 2008)
# 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
neigh_modify exclude type 2 3
dump 1 all atom 500 dump.crack
run 5000
Memory usage per processor = 1.7559 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.065997177 -3.2595015 0 -3.1984129 -0.035954718 8602.1883
200 0.060038948 -3.253189 0 -3.1976155 -0.22766954 8635.1229
400 0.060546481 -3.2510709 0 -3.1950277 -0.42828826 8674.4108
600 0.060580716 -3.2468162 0 -3.1907413 -0.60041431 8714.1872
800 0.060806514 -3.241348 0 -3.185064 -0.74528707 8753.0176
1000 0.06181595 -3.2349944 0 -3.1777762 -0.8716433 8793.5158
1200 0.063175404 -3.2277554 0 -3.1692788 -0.98049057 8819.7019
1400 0.065129472 -3.2198034 0 -3.159518 -1.0694359 8855.3817
1600 0.067258319 -3.2111274 0 -3.1488716 -1.1445455 8889.1999
1800 0.069393919 -3.2019692 0 -3.1377365 -1.1995445 8930.2901
2000 0.07128093 -3.1921624 0 -3.1261831 -1.2400341 8965.5702
2200 0.073248099 -3.1818812 0 -3.114081 -1.2653291 8994.1741
2400 0.075068232 -3.1711705 0 -3.1016856 -1.2777213 9035.0033
2600 0.076794061 -3.160066 0 -3.0889837 -1.2759869 9070.0027
2800 0.07876477 -3.1487145 0 -3.075808 -1.2642785 9102.721
3000 0.080596945 -3.1372363 0 -3.0626339 -1.2393574 9139.2753
3200 0.082282083 -3.1254232 0 -3.049261 -1.2059897 9165.9158
3400 0.084294646 -3.1136555 0 -3.0356304 -1.1676855 9201.297
3600 0.086725204 -3.102118 0 -3.0218431 -1.1268035 9229.7361
3800 0.089269145 -3.090924 0 -3.0082944 -1.0904239 9261.5209
4000 0.091383162 -3.0795096 0 -2.9949232 -1.0585032 9293.4417
4200 0.092671959 -3.0678751 0 -2.9820957 -1.0394459 9327.7894
4400 0.09056253 -3.0560492 0 -2.9722224 -1.0327842 9358.5052
4600 0.088770595 -3.0446045 0 -2.9624363 -1.0281074 9387.8048
4800 0.089473674 -3.0337454 0 -2.9509265 -1.023674 9423.1942
5000 0.089916902 -3.023759 0 -2.9405298 -1.0178836 9448.3239
Loop time of 5.86098 on 4 procs for 5000 steps with 8141 atoms
Pair time (%) = 2.87086 (48.9826)
Neigh time (%) = 0.104604 (1.78475)
Comm time (%) = 1.96126 (33.4629)
Outpt time (%) = 0.111139 (1.89626)
Other time (%) = 0.813119 (13.8734)
Nlocal: 2035.25 ave 2064 max 2015 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 198.25 ave 249 max 150 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 17849.5 ave 18249 max 17601 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 71398
Ave neighs/atom = 8.77018
Neighbor list builds = 106
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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 tag type x y z mux muy muz
run 10000
Memory usage per processor = 2.56176 Mbytes
Step Temp E_pair erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.34147461 -2.7418258 0.19338547 -2.4020585 -0.8249727
1000 0.40747968 -2.8229537 0.21834492 -2.4175114 -0.38840717
1500 0.46154716 -2.8375913 0.18215373 -2.3783518 -0.53206048
2000 0.4260216 -2.8138111 0.19511361 -2.3899196 0.25105158
2500 0.46433558 -2.8605248 0.20450084 -2.3985109 -0.10749413
3000 0.37036684 -2.7740526 0.22758113 -2.4055376 0.14916017
3500 0.40204495 -2.7807076 0.21535453 -2.3806729 0.11443486
4000 0.48414345 -2.8671661 0.22749713 -2.3854433 0.018686085
4500 0.47100691 -2.824163 0.20797533 -2.3555111 -0.28502945
5000 0.44520193 -2.8032518 0.21804415 -2.3602759 0.45640206
5500 0.43822519 -2.8303277 0.26920423 -2.3942937 -0.38492346
6000 0.42622278 -2.7949298 0.23879498 -2.3708381 -0.10124264
6500 0.4806966 -2.8484234 0.24787183 -2.3701303 -0.12613324
7000 0.4538584 -2.7937993 0.22316547 -2.3422102 -0.30300725
7500 0.41925032 -2.76312 0.22603976 -2.3459659 -0.36661933
8000 0.4445679 -2.8027613 0.24552024 -2.3604162 0.045204393
8500 0.41376651 -2.7621404 0.23914419 -2.3504427 0.1157167
9000 0.43955192 -2.7181551 0.19988038 -2.280801 -0.40091142
9500 0.48346196 -2.7777386 0.22316491 -2.296694 -0.097144544
10000 0.49780786 -2.7547088 0.2022762 -2.25939 0.077725534
Loop time of 1.81301 on 1 procs for 10000 steps with 200 atoms
Pair time (%) = 1.45147 (80.0584)
Neigh time (%) = 0.0490155 (2.70354)
Comm time (%) = 0.0771546 (4.25561)
Outpt time (%) = 0.0313296 (1.72804)
Other time (%) = 0.204043 (11.2544)
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 147 ave 147 max 147 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1657 ave 1657 max 1657 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1657
Ave neighs/atom = 8.285
Neighbor list builds = 693
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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 tag type x y z mux muy muz
run 10000
Memory usage per processor = 2.55191 Mbytes
Step Temp E_pair erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.34147461 -2.7418258 0.19338547 -2.4020585 -0.8249727
1000 0.40747968 -2.8229537 0.21834492 -2.4175114 -0.38840717
1500 0.46154713 -2.8375913 0.18215384 -2.3783519 -0.53206031
2000 0.42597513 -2.8139804 0.19520391 -2.3901351 0.25133976
2500 0.40224412 -2.8042036 0.20729219 -2.4039707 -0.13768351
3000 0.44950081 -2.8607567 0.2163603 -2.4135034 -0.37718214
3500 0.42561192 -2.8200273 0.20127716 -2.3965435 -0.2446625
4000 0.38695908 -2.7984855 0.23451044 -2.4134612 -0.085904856
4500 0.39315776 -2.7972983 0.24188008 -2.4061063 -0.1483928
5000 0.43431963 -2.7938176 0.1924971 -2.3616696 0.16044322
5500 0.53852608 -2.8823448 0.19537417 -2.3465113 0.14220621
6000 0.50125727 -2.8270371 0.18662068 -2.3282861 -0.12637044
6500 0.42401402 -2.7997548 0.24141194 -2.3778609 -0.016170475
7000 0.40501108 -2.7515392 0.22505849 -2.3485531 -0.2059805
7500 0.48308411 -2.8009045 0.19665048 -2.3202358 0.10495345
8000 0.48408101 -2.8505581 0.24762262 -2.3688975 -0.092482458
8500 0.40591248 -2.7151281 0.20375135 -2.3112452 -0.43234161
9000 0.44299739 -2.7437233 0.20190578 -2.3029409 0.17321304
9500 0.44248616 -2.7891931 0.26840058 -2.3489194 -0.34093083
10000 0.46831122 -2.7619603 0.21675378 -2.2959906 0.06991871
Loop time of 4.52779 on 4 procs for 10000 steps with 200 atoms
Pair time (%) = 0.408237 (9.01626)
Neigh time (%) = 0.0151789 (0.335238)
Comm time (%) = 3.24156 (71.5926)
Outpt time (%) = 0.0510209 (1.12684)
Other time (%) = 0.811791 (17.9291)
Nlocal: 50 ave 53 max 45 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 88.75 ave 92 max 84 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 411.5 ave 439 max 344 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Total # of neighbors = 1646
Ave neighs/atom = 8.23
Neighbor list builds = 690
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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/dipole
fix 2 all enforce2d
timestep 0.005
thermo_style dipole
thermo 500
dump 1 all custom 200 dump.dipole tag type x y z mux muy muz
run 10000
Memory usage per processor = 2.56176 Mbytes
Step Temp E_pair RotKEdip TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.34233475 -2.7418258 0.24173184 -2.4020585 -0.8249727
1000 0.40850608 -2.8229537 0.27293115 -2.4175114 -0.38840717
1500 0.46270975 -2.8375913 0.22769216 -2.3783518 -0.53206048
2000 0.4270947 -2.8138111 0.24389202 -2.3899196 0.25105158
2500 0.46550519 -2.8605248 0.25562605 -2.3985109 -0.10749413
3000 0.37129975 -2.7740526 0.28447642 -2.4055376 0.14916017
3500 0.40305766 -2.7807076 0.26919316 -2.3806729 0.11443486
4000 0.48536295 -2.8671661 0.28437141 -2.3854433 0.018686085
4500 0.47219333 -2.824163 0.25996916 -2.3555111 -0.28502945
5000 0.44632334 -2.8032518 0.27255518 -2.3602759 0.45640206
5500 0.43932904 -2.8303277 0.33650528 -2.3942937 -0.38492346
6000 0.42729639 -2.7949298 0.29849372 -2.3708381 -0.10124264
6500 0.48190742 -2.8484234 0.30983979 -2.3701303 -0.12613324
7000 0.45500162 -2.7937993 0.27895684 -2.3422102 -0.30300725
7500 0.42030636 -2.76312 0.2825497 -2.3459659 -0.36661933
8000 0.44568772 -2.8027613 0.3069003 -2.3604162 0.045204393
8500 0.41480874 -2.7621404 0.29893023 -2.3504427 0.1157167
9000 0.44065911 -2.7181551 0.24985047 -2.280801 -0.40091142
9500 0.48467975 -2.7777386 0.27895614 -2.296694 -0.097144544
10000 0.49906178 -2.7547088 0.25284525 -2.25939 0.077725534
Loop time of 1.88938 on 1 procs for 10000 steps with 200 atoms
Pair time (%) = 1.46976 (77.7907)
Neigh time (%) = 0.0489957 (2.59322)
Comm time (%) = 0.0787163 (4.16625)
Outpt time (%) = 0.0311885 (1.65073)
Other time (%) = 0.260716 (13.7991)
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 147 ave 147 max 147 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1657 ave 1657 max 1657 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1657
Ave neighs/atom = 8.285
Neighbor list builds = 693
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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/dipole
fix 2 all enforce2d
timestep 0.005
thermo_style dipole
thermo 500
dump 1 all custom 200 dump.dipole tag type x y z mux muy muz
run 10000
Memory usage per processor = 2.55191 Mbytes
Step Temp E_pair RotKEdip TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.34233475 -2.7418258 0.24173184 -2.4020585 -0.8249727
1000 0.40850608 -2.8229537 0.27293115 -2.4175114 -0.38840717
1500 0.46270972 -2.8375913 0.2276923 -2.3783519 -0.53206031
2000 0.42704811 -2.8139804 0.24400489 -2.3901351 0.25133976
2500 0.40325733 -2.8042036 0.25911523 -2.4039707 -0.13768351
3000 0.45063306 -2.8607567 0.27045037 -2.4135034 -0.37718214
3500 0.42668399 -2.8200273 0.25159644 -2.3965435 -0.2446625
4000 0.38793379 -2.7984855 0.29313805 -2.4134612 -0.085904856
4500 0.39414808 -2.7972983 0.3023501 -2.4061063 -0.1483928
5000 0.43541363 -2.7938176 0.24062138 -2.3616696 0.16044322
5500 0.53988257 -2.8823448 0.24421771 -2.3465113 0.14220621
6000 0.50251988 -2.8270371 0.23327585 -2.3282861 -0.12637044
6500 0.42508207 -2.7997548 0.30176493 -2.3778609 -0.016170475
7000 0.40603126 -2.7515392 0.28132311 -2.3485531 -0.2059805
7500 0.48430095 -2.8009045 0.2458131 -2.3202358 0.10495345
8000 0.48530036 -2.8505581 0.30952827 -2.3688975 -0.092482458
8500 0.40693493 -2.7151281 0.25468919 -2.3112452 -0.43234161
9000 0.44411326 -2.7437233 0.25238223 -2.3029409 0.17321304
9500 0.44360073 -2.7891931 0.33550072 -2.3489194 -0.34093083
10000 0.46949085 -2.7619603 0.27094222 -2.2959906 0.06991871
Loop time of 4.8123 on 4 procs for 10000 steps with 200 atoms
Pair time (%) = 0.457601 (9.50898)
Neigh time (%) = 0.0173309 (0.360137)
Comm time (%) = 3.3977 (70.6044)
Outpt time (%) = 0.0532327 (1.10618)
Other time (%) = 0.886439 (18.4203)
Nlocal: 50 ave 53 max 45 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 88.75 ave 92 max 84 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 411.5 ave 439 max 344 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Total # of neighbors = 1646
Ave neighs/atom = 8.23
Neighbor list builds = 690
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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
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 tag type x y z quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.resquared # tag type x y z quatw quati quatj quatk
fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
fix 2 all enforce2d
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 2.5914 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7442957 0 1.8380516 0.035762064 20558.675
200 2.2770743 0 2.399467 0.046545738 20620.294
300 1.8572884 0 1.9571177 0.042405959 18460.78
400 2.1710835 -0.00050891124 2.2872701 0.06679187 13689.462
500 1.9873905 -0.043659593 2.0341938 0.099193852 8475.4542
600 2.0886735 -0.24318018 1.8272333 0.2239289 4674.8623
700 2.2603303 -0.73326624 1.481118 0.57180409 2507.1015
800 1.8732232 -1.6161321 0.22091752 1.3050105 1420.4282
900 2.1404535 -3.0146811 -0.84038856 3.3565533 922.07286
1000 1.5928029 -4.5754252 -2.9697801 2.5495232 743.19039
1100 1.8380048 -4.8820036 -3.0604389 2.2950612 708.01399
1200 2.0550725 -4.5701129 -2.4719895 1.4665076 753.52887
1300 2.0004882 -4.075851 -2.0317412 0.35616813 842.13637
1400 2.1055439 -3.7337832 -1.6632225 0.58520115 925.55921
1500 1.9237101 -3.5796185 -1.638185 0.25036967 1006.9876
1600 2.1423718 -3.4821215 -1.3475831 0.62921366 1061.9476
1700 1.8831547 -3.3012167 -1.452471 0.55662052 1120.1928
1800 2.0778263 -3.0986863 -1.0206119 1.0072124 1165.8323
1900 1.8691514 -3.1095986 -1.2252585 0.8080875 1190.9616
2000 1.9636929 -3.1701486 -1.2453089 1.1030872 1176.9149
Loop time of 1.2504 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.93252 (74.5778)
Neigh time (%) = 0.0132384 (1.05874)
Comm time (%) = 0.0220492 (1.76337)
Outpt time (%) = 0.0338867 (2.71007)
Other time (%) = 0.248705 (19.89)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 235 ave 235 max 235 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2893 ave 2893 max 2893 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2893
Ave neighs/atom = 7.2325
Neighbor list builds = 113
Dangerous builds = 67
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.5919 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9636929 -3.1701486 -1.2453089 1.1030872 1176.9149
2100 1.9786552 -3.1838438 -1.1881672 0.49856381 1176.9149
2200 1.9734868 -3.180021 -1.1802031 0.79402856 1176.9149
2300 1.9986019 -3.2105474 -1.2230998 0.74682866 1176.9149
2400 2.0588205 -3.2718878 -1.1680024 0.65794795 1176.9149
2500 2.0355464 -3.2470841 -1.2102204 0.72578641 1176.9149
2600 2.0540796 -3.2674115 -1.1840972 0.60223605 1176.9149
2700 2.0456166 -3.2583563 -1.177938 0.5998038 1176.9149
2800 2.0424993 -3.2552445 -1.1893022 0.70082467 1176.9149
2900 1.9846451 -3.1943095 -1.2115539 0.66453466 1176.9149
3000 1.9581081 -3.1653173 -1.1986913 0.50999007 1176.9149
3100 1.9857943 -3.1963058 -1.256007 0.37827202 1176.9149
3200 2.0076052 -3.2177296 -1.2236764 0.483867 1176.9149
3300 1.9802529 -3.1914149 -1.2047975 0.5938853 1176.9149
3400 2.0450405 -3.2607288 -1.2259986 0.28609172 1176.9149
3500 1.9999875 -3.2132498 -1.1854255 0.62924224 1176.9149
3600 2.0631028 -3.2811837 -1.1722628 0.5970612 1176.9149
3700 1.9794507 -3.1924321 -1.202882 0.82058842 1176.9149
3800 2.0379967 -3.2512273 -1.1964393 0.40334248 1176.9149
3900 2.1120245 -3.3297924 -1.2091066 0.51931911 1176.9149
4000 2.0733971 -3.2925123 -1.2307427 0.56552238 1176.9149
Loop time of 1.4074 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.14031 (81.0225)
Neigh time (%) = 0.00835967 (0.593981)
Comm time (%) = 0.0250871 (1.78252)
Outpt time (%) = 0.033994 (2.41538)
Other time (%) = 0.199648 (14.1856)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 224 ave 224 max 224 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2985 ave 2985 max 2985 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2985
Ave neighs/atom = 7.4625
Neighbor list builds = 48
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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
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 tag type x y z quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.resquared # tag type x y z quatw quati quatj quatk
fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
fix 2 all enforce2d
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 2.55985 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7442957 0 1.8380516 0.035762064 20558.675
200 2.2770743 0 2.399467 0.046545738 20620.294
300 1.8572884 0 1.9571177 0.042405959 18460.78
400 2.1710835 -0.00050891124 2.2872701 0.06679187 13689.462
500 1.9873905 -0.043659593 2.0341938 0.099193852 8475.4542
600 2.0886735 -0.24318018 1.8272333 0.2239289 4674.8623
700 2.2603303 -0.73326624 1.481118 0.57180409 2507.1015
800 1.8732232 -1.6161321 0.22091752 1.3050105 1420.4282
900 2.1404535 -3.0146811 -0.84038856 3.3565533 922.07286
1000 1.5928029 -4.5754252 -2.9697801 2.5495232 743.19039
1100 1.8380048 -4.8820036 -3.0604389 2.2950612 708.01399
1200 2.0550725 -4.5701129 -2.4719895 1.4665076 753.52887
1300 2.0004882 -4.075851 -2.0317412 0.35616813 842.13637
1400 2.1055439 -3.7337832 -1.6632225 0.58520115 925.55921
1500 1.9237101 -3.5796185 -1.638185 0.25036967 1006.9876
1600 2.1423718 -3.4821215 -1.3475831 0.62921366 1061.9476
1700 1.8831547 -3.3012167 -1.452471 0.55662052 1120.1928
1800 2.0778263 -3.0986863 -1.0206119 1.0072124 1165.8323
1900 1.8691514 -3.1095986 -1.2252585 0.80808749 1190.9616
2000 1.9636929 -3.1701486 -1.2453089 1.1030871 1176.9149
Loop time of 1.41726 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.254874 (17.9836)
Neigh time (%) = 0.00383508 (0.270599)
Comm time (%) = 0.669287 (47.2241)
Outpt time (%) = 0.0560044 (3.9516)
Other time (%) = 0.433258 (30.5701)
Nlocal: 100 ave 114 max 80 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 141.75 ave 153 max 131 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 723.25 ave 903 max 497 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 2893
Ave neighs/atom = 7.2325
Neighbor list builds = 113
Dangerous builds = 67
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.56129 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9636929 -3.1701486 -1.2453089 1.1030871 1176.9149
2100 1.9786552 -3.1838438 -1.1881672 0.49856382 1176.9149
2200 1.9734867 -3.1800209 -1.1802031 0.79402882 1176.9149
2300 1.9986018 -3.2105474 -1.2230998 0.74682898 1176.9149
2400 2.0588206 -3.2718879 -1.1680027 0.65794654 1176.9149
2500 2.0355453 -3.2470829 -1.2102212 0.72578578 1176.9149
2600 2.0540797 -3.2674115 -1.1840971 0.60223907 1176.9149
2700 2.0456165 -3.2583562 -1.1779378 0.59979597 1176.9149
2800 2.0425097 -3.2552542 -1.189297 0.70076228 1176.9149
2900 1.9846096 -3.1942735 -1.2115473 0.6646236 1176.9149
3000 1.9581313 -3.1653426 -1.1986472 0.51000292 1176.9149
3100 1.9853906 -3.1960037 -1.256084 0.37948337 1176.9149
3200 2.0079056 -3.2180488 -1.2235777 0.48228921 1176.9149
3300 1.9790253 -3.1899998 -1.2044075 0.59676043 1176.9149
3400 2.0479977 -3.2638333 -1.2261703 0.27621482 1176.9149
3500 2.0066637 -3.2203747 -1.1864954 0.62437852 1176.9149
3600 2.0689199 -3.2865465 -1.1668082 0.58048934 1176.9149
3700 1.9862678 -3.1988748 -1.207327 0.8353193 1176.9149
3800 2.0401189 -3.2549146 -1.214896 0.34234416 1176.9149
3900 2.0378699 -3.2539328 -1.1893919 0.66653795 1176.9149
4000 2.0609507 -3.2820151 -1.2128386 0.64471907 1176.9149
Loop time of 1.22293 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.311134 (25.4416)
Neigh time (%) = 0.00231725 (0.189483)
Comm time (%) = 0.670141 (54.7979)
Outpt time (%) = 0.0586291 (4.79414)
Other time (%) = 0.180711 (14.7769)
Nlocal: 100 ave 121 max 70 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 143 ave 155 max 129 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Neighs: 750.5 ave 1001 max 418 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 3002
Ave neighs/atom = 7.505
Neighbor list builds = 47
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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
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 # tag type x y z quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.resquared tag type x y z quatw quati quatj quatk
fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
fix 2 all enforce2d
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 2.5914 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7442957 0 1.8380516 0.035762064 20558.675
200 2.2770743 0 2.399467 0.046545738 20620.294
300 1.8572884 0 1.9571177 0.042405959 18460.78
400 2.1709476 -2.7650868e-05 2.2876084 0.066840176 13689.499
500 1.9974207 0.016918546 2.0563673 0.11517079 8482.9842
600 2.0623605 0.078682156 2.0822655 0.2882877 4776.2504
700 2.110577 0.19687352 2.3261907 0.85200625 2756.4677
800 1.7458278 0.29268299 1.9788694 1.629108 1832.8121
900 1.7925286 0.2406461 2.0272778 1.7295734 1516.7707
1000 1.8280565 0.16642416 1.9844287 1.431503 1517.365
1100 2.1579097 0.10561885 2.2607523 0.98798133 1744.9685
1200 1.7966192 0.057740166 1.8308675 0.54361557 2182.8329
1300 2.2982919 0.036420252 2.3349773 0.45727558 2731.1191
1400 1.766633 0.038034214 1.7891558 0.32935291 3230.8068
1500 2.3052769 0.08089522 2.3763972 0.45778471 3432.038
1600 1.8587716 0.067481187 1.9188742 0.39446029 3276.3409
1700 2.1802595 0.13974472 2.3397684 0.70931895 2829.789
1800 1.9313351 0.14233089 2.0646735 0.83838184 2321.0971
1900 2.0664832 0.16461014 2.1858936 1.1676882 1900.719
2000 1.9340159 0.16879369 2.1186931 1.3526231 1658.4096
Loop time of 2.3213 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.99781 (86.0641)
Neigh time (%) = 0.014091 (0.60703)
Comm time (%) = 0.0165789 (0.714207)
Outpt time (%) = 0.034477 (1.48524)
Other time (%) = 0.258347 (11.1294)
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: 1894 ave 1894 max 1894 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1894
Ave neighs/atom = 4.735
Neighbor list builds = 152
Dangerous builds = 77
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.5919 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9340159 0.16879369 2.1186931 1.3526231 1658.4096
2100 1.9499859 0.15215993 2.1113673 1.1823056 1658.4096
2200 1.947135 0.15513968 2.1194838 1.2327003 1658.4096
2300 1.9248051 0.17868446 2.099053 1.3075669 1658.4096
2400 1.9130129 0.1909732 2.1178764 1.360918 1658.4096
2500 1.923006 0.18047305 2.0814946 1.300819 1658.4096
2600 1.9861146 0.11411525 2.0953259 1.0398086 1658.4096
2700 1.9100096 0.19413009 2.0711987 1.3442038 1658.4096
2800 1.9229156 0.18068077 2.0604436 1.3326936 1658.4096
2900 1.9390668 0.16374522 2.084979 1.2648628 1658.4096
3000 1.8823323 0.22349207 2.0853271 1.5182108 1658.4096
3100 1.904216 0.2002807 2.0777595 1.3868716 1658.4096
3200 1.9189112 0.18492983 2.069413 1.3303671 1658.4096
3300 1.8823024 0.22351455 2.0549801 1.5696985 1658.4096
3400 1.9062113 0.19834529 2.0909042 1.452763 1658.4096
3500 1.9502985 0.15175121 2.0880307 1.2382766 1658.4096
3600 1.9785887 0.12200393 2.1051591 1.0976058 1658.4096
3700 1.8929677 0.21215454 2.0740511 1.4270618 1658.4096
3800 1.9312361 0.17174214 2.0694738 1.30501 1658.4096
3900 1.9552683 0.14654684 2.0903398 1.2082694 1658.4096
4000 1.9147075 0.18935225 2.1044998 1.3672816 1658.4096
Loop time of 4.08604 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 3.80795 (93.1941)
Neigh time (%) = 0.00631857 (0.154638)
Comm time (%) = 0.0228438 (0.55907)
Outpt time (%) = 0.0349987 (0.856542)
Other time (%) = 0.213933 (5.23569)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 205 ave 205 max 205 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1885 ave 1885 max 1885 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1885
Ave neighs/atom = 4.7125
Neighbor list builds = 46
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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
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 # tag type x y z quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.resquared tag type x y z quatw quati quatj quatk
fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
fix 2 all enforce2d
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 2.55985 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7442957 0 1.8380516 0.035762064 20558.675
200 2.2770743 0 2.399467 0.046545738 20620.294
300 1.8572884 0 1.9571177 0.042405959 18460.78
400 2.1709476 -2.7650868e-05 2.2876084 0.066840176 13689.499
500 1.9974207 0.016918546 2.0563673 0.11517079 8482.9842
600 2.0623605 0.078682156 2.0822655 0.2882877 4776.2504
700 2.110577 0.19687352 2.3261907 0.85200625 2756.4677
800 1.7458278 0.29268299 1.9788694 1.629108 1832.8121
900 1.7925286 0.2406461 2.0272778 1.7295734 1516.7707
1000 1.8280565 0.16642416 1.9844287 1.431503 1517.365
1100 2.1579097 0.10561885 2.2607523 0.98798133 1744.9685
1200 1.7966192 0.057740166 1.8308675 0.54361557 2182.8329
1300 2.2982919 0.036420252 2.3349773 0.45727558 2731.1191
1400 1.766633 0.038034214 1.7891558 0.32935291 3230.8068
1500 2.3052769 0.08089522 2.3763972 0.45778471 3432.038
1600 1.8587716 0.067481187 1.9188742 0.39446029 3276.3409
1700 2.1802595 0.13974472 2.3397684 0.70931895 2829.789
1800 1.9313351 0.14233089 2.0646735 0.83838184 2321.0971
1900 2.0664832 0.16461014 2.1858936 1.1676882 1900.719
2000 1.9340159 0.16879369 2.1186931 1.3526231 1658.4096
Loop time of 1.55915 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.516469 (33.1252)
Neigh time (%) = 0.00421089 (0.270077)
Comm time (%) = 0.611745 (39.2359)
Outpt time (%) = 0.0517598 (3.31975)
Other time (%) = 0.37496 (24.0491)
Nlocal: 100 ave 109 max 96 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 115.75 ave 120 max 108 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 473.5 ave 500 max 456 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 1894
Ave neighs/atom = 4.735
Neighbor list builds = 152
Dangerous builds = 77
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.56081 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9340159 0.16879369 2.1186931 1.3526231 1658.4096
2100 1.9499859 0.15215993 2.1113673 1.1823056 1658.4096
2200 1.947135 0.15513969 2.1194838 1.2327003 1658.4096
2300 1.9248051 0.17868446 2.099053 1.3075669 1658.4096
2400 1.9130129 0.1909732 2.1178764 1.360918 1658.4096
2500 1.923006 0.18047305 2.0814946 1.300819 1658.4096
2600 1.9861146 0.11411525 2.0953259 1.0398086 1658.4096
2700 1.9100096 0.1941301 2.0711987 1.3442038 1658.4096
2800 1.9229156 0.1806807 2.0604436 1.3326933 1658.4096
2900 1.9390667 0.16374526 2.0849791 1.264863 1658.4096
3000 1.8823324 0.22349199 2.0853271 1.5182104 1658.4096
3100 1.904216 0.20028063 2.0777596 1.3868713 1658.4096
3200 1.9189114 0.18492962 2.069413 1.3303662 1658.4096
3300 1.8823026 0.22351436 2.0549801 1.569697 1658.4096
3400 1.9062107 0.1983459 2.0909008 1.4527662 1658.4096
3500 1.9503014 0.15174814 2.0880308 1.2382499 1658.4096
3600 1.9785903 0.12200228 2.1051589 1.0976001 1658.4096
3700 1.8929681 0.21215409 2.0740513 1.4270612 1658.4096
3800 1.9312505 0.17172697 2.0694714 1.3049156 1658.4096
3900 1.9552504 0.14656576 2.0903398 1.2083612 1658.4096
4000 1.9147153 0.18934405 2.1044888 1.3672132 1658.4096
Loop time of 1.85192 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.984376 (53.1543)
Neigh time (%) = 0.00186694 (0.100811)
Comm time (%) = 0.630368 (34.0385)
Outpt time (%) = 0.0533838 (2.88262)
Other time (%) = 0.181929 (9.82376)
Nlocal: 100 ave 104 max 95 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 117 ave 121 max 110 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 471.25 ave 509 max 428 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 1885
Ave neighs/atom = 4.7125
Neighbor list builds = 46
Dangerous builds = 0

147
examples/ellipse/log.gayberne.22Jan08.linux.1
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LAMMPS (22 Jan 2008)
# 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
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.gayberne tag type x y z quatw quati quatj quatk
#dump 1 all custom 100 dump.resquared # tag type x y z quatw quati quatj quatk
fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
fix 2 all enforce2d
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 2.5914 Mbytes
Step rot E_pair TotEng Press Volume
0 2.1564825 0 2.391 0.04782 20000
100 1.838411 0 2.0383382 0.039613219 20582.404
200 2.1840926 0 2.4216127 0.046586295 20792.49
300 1.9277991 0 2.1374472 0.045558261 18766.715
400 2.1320898 -0.00053003398 2.3634243 0.067260787 14046.57
500 2.0125529 -0.044948035 2.1687617 0.10245426 8750.3467
600 2.0786425 -0.23406014 1.9442479 0.22613511 4851.3617
700 2.2133435 -0.69014988 1.5954372 0.54309778 2612.3736
800 1.9098353 -1.4850103 0.51347537 1.3704181 1483.4256
900 2.1260352 -2.8142501 -0.59067406 3.1656374 962.6457
1000 1.6045695 -4.3144152 -2.6174061 2.546312 768.15096
1100 1.8583682 -4.7215526 -2.7550345 2.2351608 721.1814
1200 2.0033979 -4.4224318 -2.3394492 1.497766 762.68534
1300 1.9444498 -3.9403965 -1.8821931 0.71183994 853.44376
1400 2.0389741 -3.5330024 -1.3903083 0.56027235 953.42519
1500 1.9557022 -3.3648518 -1.315844 0.5652338 1045.7045
1600 2.0224945 -3.2441781 -1.0982354 0.54437381 1120.6403
1700 2.0299156 -3.0845458 -0.92406001 0.48408419 1184.9462
1800 2.0251982 -2.9795387 -0.83247158 0.52149705 1215.081
1900 2.0206629 -3.159343 -1.0374344 0.72829367 1196.1151
2000 1.9665091 -3.2421939 -1.2158182 0.66817261 1162.3788
Loop time of 1.24429 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.909927 (73.1284)
Neigh time (%) = 0.0135996 (1.09297)
Comm time (%) = 0.0220442 (1.77163)
Outpt time (%) = 0.0341184 (2.74201)
Other time (%) = 0.264597 (21.2649)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 241 ave 241 max 241 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2899 ave 2899 max 2899 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2899
Ave neighs/atom = 7.2475
Neighbor list builds = 116
Dangerous builds = 66
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.5924 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9665091 -3.2421939 -1.2158182 0.66817261 1162.3788
2100 1.8708937 -3.1339765 -1.2087845 0.65485928 1162.3788
2200 1.9126691 -3.1751558 -1.1398886 0.64965308 1162.3788
2300 1.8486671 -3.106799 -1.1627689 0.7992831 1162.3788
2400 1.9064396 -3.1727593 -1.1529333 0.65253656 1162.3788
2500 1.9271407 -3.196764 -1.170919 0.69672634 1162.3788
2600 1.9128576 -3.1780462 -1.1737268 0.49259816 1162.3788
2700 1.8577605 -3.1183107 -1.1469431 0.69798298 1162.3788
2800 1.8968015 -3.1635109 -1.1706025 0.72238772 1162.3788
2900 1.9243377 -3.1936655 -1.2164049 0.71602441 1162.3788
3000 1.9744936 -3.2522509 -1.1675852 0.973599 1162.3788
3100 1.9958325 -3.2744643 -1.1947121 0.74284674 1162.3788
3200 1.970421 -3.2446567 -1.1999887 0.82553849 1162.3788
3300 2.0258625 -3.3090808 -1.1388773 0.92883543 1162.3788
3400 1.8890826 -3.1558929 -1.1949006 0.79651332 1162.3788
3500 1.995457 -3.2762027 -1.1679919 0.56633624 1162.3788
3600 1.931652 -3.2051941 -1.1993639 0.64332962 1162.3788
3700 1.9274391 -3.1996536 -1.1892997 0.30677766 1162.3788
3800 1.9107307 -3.1825901 -1.2150398 0.76019944 1162.3788
3900 2.0003232 -3.2826031 -1.2144381 0.69551187 1162.3788
4000 1.9971268 -3.2783688 -1.2104061 0.67606395 1162.3788
Loop time of 1.41674 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.12906 (79.6942)
Neigh time (%) = 0.00786209 (0.554944)
Comm time (%) = 0.0250032 (1.76484)
Outpt time (%) = 0.0342295 (2.41608)
Other time (%) = 0.220585 (15.5699)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 240 ave 240 max 240 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2941 ave 2941 max 2941 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2941
Ave neighs/atom = 7.3525
Neighbor list builds = 46
Dangerous builds = 0

147
examples/ellipse/log.gayberne.22Jan08.linux.4
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LAMMPS (22 Jan 2008)
# 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
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.gayberne tag type x y z quatw quati quatj quatk
#dump 1 all custom 100 dump.resquared # tag type x y z quatw quati quatj quatk
fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
fix 2 all enforce2d
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 2.55985 Mbytes
Step rot E_pair TotEng Press Volume
0 2.1564825 0 2.391 0.04782 20000
100 1.838411 0 2.0383382 0.039613219 20582.404
200 2.1840926 0 2.4216127 0.046586295 20792.49
300 1.9277991 0 2.1374472 0.045558261 18766.715
400 2.1320898 -0.00053003398 2.3634243 0.067260787 14046.57
500 2.0125529 -0.044948035 2.1687617 0.10245426 8750.3467
600 2.0786425 -0.23406014 1.9442479 0.22613511 4851.3617
700 2.2133435 -0.69014988 1.5954372 0.54309778 2612.3736
800 1.9098353 -1.4850103 0.51347537 1.3704181 1483.4256
900 2.1260352 -2.8142501 -0.59067406 3.1656374 962.6457
1000 1.6045695 -4.3144152 -2.6174061 2.546312 768.15096
1100 1.8583682 -4.7215526 -2.7550345 2.2351608 721.1814
1200 2.0033979 -4.4224318 -2.3394492 1.497766 762.68534
1300 1.9444498 -3.9403965 -1.8821931 0.71183994 853.44376
1400 2.0389741 -3.5330024 -1.3903083 0.56027235 953.42519
1500 1.9557022 -3.3648518 -1.315844 0.5652338 1045.7045
1600 2.0224945 -3.2441781 -1.0982355 0.54437381 1120.6403
1700 2.0299156 -3.0845458 -0.92406001 0.48408419 1184.9462
1800 2.0251982 -2.9795387 -0.83247158 0.52149705 1215.081
1900 2.0206629 -3.159343 -1.0374344 0.72829366 1196.1151
2000 1.9665091 -3.2421939 -1.2158181 0.66817261 1162.3788
Loop time of 1.46444 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.262376 (17.9165)
Neigh time (%) = 0.00438559 (0.299471)
Comm time (%) = 0.695195 (47.4716)
Outpt time (%) = 0.0550858 (3.76155)
Other time (%) = 0.447401 (30.5509)
Nlocal: 100 ave 114 max 89 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Nghost: 143.75 ave 150 max 134 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 724.75 ave 888 max 603 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 2899
Ave neighs/atom = 7.2475
Neighbor list builds = 116
Dangerous builds = 66
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.56108 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9665091 -3.2421939 -1.2158181 0.66817261 1162.3788
2100 1.8708938 -3.1339766 -1.2087845 0.65485904 1162.3788
2200 1.9126692 -3.1751559 -1.1398886 0.64965265 1162.3788
2300 1.8486668 -3.1067986 -1.1627689 0.79928388 1162.3788
2400 1.9064384 -3.172758 -1.1529331 0.65253881 1162.3788
2500 1.9271407 -3.1967644 -1.170919 0.69672795 1162.3788
2600 1.9128672 -3.1780573 -1.173728 0.49255026 1162.3788
2700 1.8577651 -3.118316 -1.1469407 0.69794398 1162.3788
2800 1.896808 -3.1635198 -1.1706185 0.72233802 1162.3788
2900 1.9244369 -3.1937775 -1.2164447 0.71557304 1162.3788
3000 1.9743523 -3.2520956 -1.1675977 0.97482809 1162.3788
3100 1.996246 -3.2749273 -1.194868 0.74170535 1162.3788
3200 1.9705094 -3.2447603 -1.1997475 0.8278483 1162.3788
3300 2.0273054 -3.3108123 -1.1389432 0.92136684 1162.3788
3400 1.8906596 -3.1579072 -1.1949426 0.76619179 1162.3788
3500 1.9983053 -3.2795554 -1.1695681 0.60352395 1162.3788
3600 1.9635271 -3.2409899 -1.2167445 0.4863415 1162.3788
3700 1.9144359 -3.1843815 -1.2155475 0.42825617 1162.3788
3800 1.9125088 -3.1825738 -1.2078829 0.58850208 1162.3788
3900 1.9607643 -3.2375105 -1.2043099 0.50399343 1162.3788
4000 1.9199974 -3.1924774 -1.1937016 1.0992901 1162.3788
Loop time of 1.30653 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.327121 (25.0374)
Neigh time (%) = 0.00245857 (0.188176)
Comm time (%) = 0.719629 (55.0794)
Outpt time (%) = 0.0561987 (4.30137)
Other time (%) = 0.201123 (15.3937)
Nlocal: 100 ave 112 max 86 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 152.5 ave 161 max 131 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 740.5 ave 888 max 623 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 2962
Ave neighs/atom = 7.405
Neighbor list builds = 46
Dangerous builds = 0

147
examples/ellipse/log.resquared.22Jan08.linux.1
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@ -1,147 +0,0 @@
LAMMPS (22 Jan 2008)
# 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
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.gayberne # tag type x y z quatw quati quatj quatk
dump 1 all custom 100 dump.resquared tag type x y z quatw quati quatj quatk
fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
fix 2 all enforce2d
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 2.5914 Mbytes
Step rot E_pair TotEng Press Volume
0 2.1564825 0 2.391 0.04782 20000
100 1.838411 0 2.0383382 0.039613219 20582.404
200 2.1840926 0 2.4216127 0.046586295 20792.49
300 1.9277991 0 2.1374472 0.045558261 18766.715
400 2.1319531 -2.8942919e-05 2.363774 0.067309702 14046.61
500 2.0159993 0.025003198 2.192142 0.12365516 8758.5309
600 2.0502951 0.082711121 2.1869989 0.2914997 4953.8346
700 2.1346857 0.19349894 2.4259271 0.83641851 2850.8843
800 1.7500542 0.31713085 2.1311843 1.7957167 1886.6112
900 1.7954476 0.2020433 2.0534119 1.5200892 1555.0105
1000 1.9617502 0.11559302 2.1882642 1.2192863 1547.216
1100 2.029642 0.11732822 2.28763 1.0329822 1776.5022
1200 1.932547 0.055745664 2.0771327 0.56592224 2220.4328
1300 2.1273555 0.022049267 2.2406619 0.39671812 2776.2006
1400 1.9348031 0.041576451 2.0680195 0.34763372 3284.7889
1500 2.145937 0.05819306 2.2958826 0.39414678 3503.5721
1600 1.925752 0.13306059 2.1690861 0.54488654 3303.1224
1700 2.1312499 0.14010948 2.3616269 0.69736084 2818.368
1800 1.9625036 0.1767238 2.2308375 0.96298372 2310.965
1900 1.9411448 0.23022702 2.301414 1.3620231 1895.482
2000 1.989287 0.23799274 2.3113674 1.6330055 1665.9849
Loop time of 2.25316 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.93077 (85.6918)
Neigh time (%) = 0.0138793 (0.615992)
Comm time (%) = 0.0163372 (0.725077)
Outpt time (%) = 0.0341411 (1.51525)
Other time (%) = 0.258029 (11.4518)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 208 ave 208 max 208 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1896 ave 1896 max 1896 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1896
Ave neighs/atom = 4.74
Neighbor list builds = 152
Dangerous builds = 77
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.5924 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.989287 0.23799274 2.3113674 1.6330055 1665.9849
2100 2.0653748 0.15379429 2.3138055 1.2692328 1665.9849
2200 2.0296751 0.19333047 2.3431266 1.4194185 1665.9849
2300 2.031445 0.19134884 2.3346008 1.4455022 1665.9849
2400 2.0416873 0.17998527 2.3055585 1.3819478 1665.9849
2500 1.9732771 0.25585123 2.3498283 1.7058898 1665.9849
2600 2.0186547 0.2054707 2.2994266 1.5413429 1665.9849
2700 2.0300352 0.19285781 2.2682949 1.384344 1665.9849
2800 2.0258032 0.1974685 2.3003298 1.4218564 1665.9849
2900 2.0506397 0.16996513 2.3131175 1.3967849 1665.9849
3000 1.9768248 0.251823 2.3267822 1.6698709 1665.9849
3100 2.0005064 0.22563045 2.2868834 1.540767 1665.9849
3200 2.0309162 0.19193638 2.3082578 1.4597896 1665.9849
3300 2.0483286 0.17251967 2.3200717 1.3676295 1665.9849
3400 2.0019218 0.22424333 2.3467104 1.6024582 1665.9849
3500 2.0060182 0.21959616 2.3235298 1.582482 1665.9849
3600 2.0000757 0.22586393 2.3411772 1.5632004 1665.9849
3700 2.0293619 0.1936261 2.3426439 1.4262837 1665.9849
3800 2.0256136 0.19784063 2.3112499 1.5090404 1665.9849
3900 2.0554399 0.16475477 2.3129868 1.281966 1665.9849
4000 2.0845029 0.13253315 2.3282445 1.2142775 1665.9849
Loop time of 4.02238 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 3.74757 (93.1678)
Neigh time (%) = 0.00655437 (0.162947)
Comm time (%) = 0.0214994 (0.534494)
Outpt time (%) = 0.0341754 (0.849631)
Other time (%) = 0.212587 (5.2851)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 206 ave 206 max 206 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1869 ave 1869 max 1869 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1869
Ave neighs/atom = 4.6725
Neighbor list builds = 50
Dangerous builds = 0

147
examples/ellipse/log.resquared.22Jan08.linux.4
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LAMMPS (22 Jan 2008)
# 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
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.gayberne # tag type x y z quatw quati quatj quatk
dump 1 all custom 100 dump.resquared tag type x y z quatw quati quatj quatk
fix 1 all npt/asphere 2.0 2.0 0.1 xyz 0.0 1.0 1.0
fix 2 all enforce2d
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 2.55985 Mbytes
Step rot E_pair TotEng Press Volume
0 2.1564825 0 2.391 0.04782 20000
100 1.838411 0 2.0383382 0.039613219 20582.404
200 2.1840926 0 2.4216127 0.046586295 20792.49
300 1.9277991 0 2.1374472 0.045558261 18766.715
400 2.1319531 -2.8942919e-05 2.363774 0.067309702 14046.61
500 2.0159993 0.025003198 2.192142 0.12365516 8758.5309
600 2.0502951 0.082711121 2.1869989 0.2914997 4953.8346
700 2.1346857 0.19349894 2.4259271 0.83641851 2850.8843
800 1.7500542 0.31713085 2.1311843 1.7957167 1886.6112
900 1.7954476 0.2020433 2.0534119 1.5200892 1555.0105
1000 1.9617502 0.11559302 2.1882642 1.2192863 1547.216
1100 2.029642 0.11732822 2.28763 1.0329822 1776.5022
1200 1.932547 0.055745664 2.0771327 0.56592224 2220.4328
1300 2.1273555 0.022049267 2.2406619 0.39671812 2776.2006
1400 1.9348031 0.041576451 2.0680195 0.34763372 3284.7889
1500 2.145937 0.05819306 2.2958826 0.39414678 3503.5721
1600 1.925752 0.13306059 2.1690861 0.54488654 3303.1224
1700 2.1312499 0.14010948 2.3616269 0.69736084 2818.368
1800 1.9625036 0.1767238 2.2308375 0.96298372 2310.965
1900 1.9411448 0.23022702 2.301414 1.3620231 1895.482
2000 1.989287 0.23799274 2.3113674 1.6330055 1665.9849
Loop time of 1.70624 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.53287 (31.2306)
Neigh time (%) = 0.00461602 (0.270537)
Comm time (%) = 0.702465 (41.1703)
Outpt time (%) = 0.0564025 (3.30566)
Other time (%) = 0.40989 (24.0229)
Nlocal: 100 ave 103 max 98 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 118.25 ave 121 max 114 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 474 ave 509 max 460 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 1896
Ave neighs/atom = 4.74
Neighbor list builds = 152
Dangerous builds = 77
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 2.56054 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.989287 0.23799274 2.3113674 1.6330055 1665.9849
2100 2.0653748 0.15379429 2.3138055 1.2692328 1665.9849
2200 2.0296751 0.19333047 2.3431266 1.4194185 1665.9849
2300 2.031445 0.19134884 2.3346008 1.4455022 1665.9849
2400 2.0416873 0.17998527 2.3055585 1.3819478 1665.9849
2500 1.9732771 0.25585123 2.3498283 1.7058898 1665.9849
2600 2.0186547 0.2054707 2.2994266 1.5413428 1665.9849
2700 2.0300352 0.19285781 2.2682949 1.384344 1665.9849
2800 2.0258032 0.19746848 2.3003298 1.4218563 1665.9849
2900 2.0506396 0.16996525 2.3131178 1.3967855 1665.9849
3000 1.9768248 0.25182299 2.3267824 1.6698709 1665.9849
3100 2.0005068 0.22563005 2.286884 1.5407669 1665.9849
3200 2.0309161 0.19193653 2.3082598 1.4597915 1665.9849
3300 2.0483373 0.1725101 2.3200665 1.3675732 1665.9849
3400 2.0019136 0.22425249 2.3467007 1.6025191 1665.9849
3500 2.0060157 0.21959893 2.3235339 1.5824949 1665.9849
3600 2.0000689 0.22587176 2.3411757 1.5633105 1665.9849
3700 2.0292856 0.19371118 2.342629 1.4266405 1665.9849
3800 2.0255614 0.19789877 2.3112561 1.5093285 1665.9849
3900 2.0554045 0.16479373 2.3130089 1.2821629 1665.9849
4000 2.0844571 0.13258442 2.3284091 1.2146999 1665.9849
Loop time of 1.94966 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 1.01464 (52.0418)
Neigh time (%) = 0.00212574 (0.109032)
Comm time (%) = 0.695318 (35.6636)
Outpt time (%) = 0.0557072 (2.85728)
Other time (%) = 0.181869 (9.32825)
Nlocal: 100 ave 108 max 90 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 122.25 ave 128 max 114 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 467.25 ave 524 max 403 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 1869
Ave neighs/atom = 4.6725
Neighbor list builds = 50
Dangerous builds = 0

2
examples/flow/in.flow.couette
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@ -50,7 +50,7 @@ velocity upper set 3.0 0.0 0.0
fix 3 boundary setforce 0.0 0.0 0.0
fix 4 all enforce2d
# Poiseuille flow
# Poisseuille flow
#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0

2
examples/flow/in.flow.poiss
View File

@ -50,7 +50,7 @@ fix_modify 2 temp mobile
#fix 3 boundary setforce 0.0 0.0 0.0
#fix 4 all enforce2d
# Poiseuille flow
# Poisseuille flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0

122
examples/flow/log.flow.couette.21May08.linux.1 Normal file
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@ -0,0 +1,122 @@
LAMMPS (21 May 2008)
# 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
dump 1 all atom 50 dump.flow
run 10000
Memory usage per processor = 1.68525 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 -0.40814277 0 0.30376199 2.9235162 571.43371
2500 1.1929962 -0.38734818 0 0.4619515 2.8343165 571.43371
3000 1 -0.44746792 0 0.26443684 2.6627188 571.43371
3500 1.010095 -0.40989137 0 0.30920005 2.5630541 571.43371
4000 1 -0.41152442 0 0.30038034 2.6280421 571.43371
4500 1.0014311 -0.38736161 0 0.32556193 2.4644773 571.43371
5000 1 -0.39407987 0 0.31782489 2.4614403 571.43371
5500 1.1069931 -0.45231944 0 0.3357542 2.4643506 571.43371
6000 1 -0.45436915 0 0.25753561 2.5746902 571.43371
6500 1.0330238 -0.38921069 0 0.34620389 2.7826579 571.43371
7000 1 -0.44431846 0 0.2675863 2.5673807 571.43371
7500 1.0140984 -0.46901787 0 0.25292361 2.3961693 571.43371
8000 1 -0.45965057 0 0.2522542 2.1341657 571.43371
8500 0.99284806 -0.43949501 0 0.26731825 2.3634229 571.43371
9000 1 -0.46508823 0 0.24681654 2.3230725 571.43371
9500 1.1114345 -0.4020811 0 0.3891544 2.559154 571.43371
10000 1.0176833 -0.42582303 0 0.29867054 2.5282372 571.43371
Loop time of 0.582808 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.215462 (36.9697)
Neigh time (%) = 0.0678575 (11.6432)
Comm time (%) = 0.0175343 (3.00858)
Outpt time (%) = 0.122674 (21.0489)
Other time (%) = 0.15928 (27.3297)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 52 ave 52 max 52 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 957 ave 957 max 957 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 957
Ave neighs/atom = 2.27857
Neighbor list builds = 994
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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
dump 1 all atom 50 dump.flow
run 10000
Memory usage per processor = 1.67714 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 -0.41052951 0 0.30137525 2.8657415 571.43371
2500 1.1228466 -0.37043294 0 0.42892693 2.9450302 571.43371
3000 1 -0.37926849 0 0.33263627 2.5756937 571.43371
3500 1.0426371 -0.46446342 0 0.27779493 2.6309178 571.43371
4000 1 -0.43996746 0 0.2719373 2.7108953 571.43371
4500 0.97471021 -0.43234275 0 0.26155809 2.4118441 571.43371
5000 1 -0.38709789 0 0.32480687 2.6100243 571.43371
5500 1.0551901 -0.42334943 0 0.32784545 2.4333785 571.43371
6000 1 -0.45014484 0 0.26175993 2.5188073 571.43371
6500 1.0439428 -0.46442749 0 0.27876034 2.2352899 571.43371
7000 1 -0.42616126 0 0.2857435 2.4560563 571.43371
7500 1.0680429 -0.41282904 0 0.34751579 2.5532595 571.43371
8000 1 -0.44461273 0 0.26729203 2.1838508 571.43371
8500 1.0212571 -0.43065547 0 0.29638229 2.2193889 571.43371
9000 1 -0.43364252 0 0.27826224 2.4244927 571.43371
9500 1.1269004 -0.48721451 0 0.31503125 2.3601218 571.43371
10000 1 -0.50814904 0 0.20375572 2.3234126 571.43371
Loop time of 3.99854 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.064626 (1.61624)
Neigh time (%) = 0.0206351 (0.516066)
Comm time (%) = 3.09756 (77.4671)
Outpt time (%) = 0.163689 (4.0937)
Other time (%) = 0.652038 (16.3069)
Nlocal: 105 ave 116 max 93 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 40.25 ave 43 max 36 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 238.75 ave 307 max 175 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 955
Ave neighs/atom = 2.27381
Neighbor list builds = 967
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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
dump 1 all atom 50 dump.flow
run 10000
Memory usage per processor = 1.68525 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71071429 0.5223703 571.43371
500 1.0604224 -0.31549525 0 0.4381621 3.006258 571.43371
1000 1 -0.34356865 0 0.36714563 2.9191962 571.43371
1500 1.1738082 -0.382026 0 0.45221625 2.8125373 571.43371
2000 1 -0.42682429 0 0.28389 2.7423533 571.43371
2500 1.0249762 -0.41630229 0 0.31216293 2.8311931 571.43371
3000 1 -0.415763 0 0.29495128 2.6837339 571.43371
3500 1.1483583 -0.44275044 0 0.37340417 2.5003955 571.43371
4000 1 -0.45903245 0 0.25168184 2.5138215 571.43371
4500 1.044392 -0.37885141 0 0.3634129 2.7980973 571.43371
5000 1 -0.45198477 0 0.25872952 2.3725427 571.43371
5500 1.1128857 -0.45615742 0 0.33478637 2.5476457 571.43371
6000 1 -0.44232084 0 0.26839344 2.6421628 571.43371
6500 1.1004439 -0.44788873 0 0.33421246 2.4753882 571.43371
7000 1 -0.44594794 0 0.26476635 2.1411957 571.43371
7500 0.96700164 -0.4037758 0 0.28348608 2.500408 571.43371
8000 1 -0.44011344 0 0.27060085 2.3472773 571.43371
8500 1.0317945 -0.42782829 0 0.30548278 2.6086809 571.43371
9000 1 -0.42662876 0 0.28408553 2.5753183 571.43371
9500 1.0439722 -0.43196226 0 0.3100037 2.4421759 571.43371
10000 1 -0.42551472 0 0.28519957 2.4293664 571.43371
Loop time of 0.571892 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.211723 (37.0215)
Neigh time (%) = 0.0664635 (11.6217)
Comm time (%) = 0.0170681 (2.98451)
Outpt time (%) = 0.118025 (20.6376)
Other time (%) = 0.158613 (27.7347)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 47 ave 47 max 47 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 958 ave 958 max 958 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 958
Ave neighs/atom = 2.28095
Neighbor list builds = 986
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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
dump 1 all atom 50 dump.flow
run 10000
Memory usage per processor = 1.67714 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71071429 0.5223703 571.43371
500 1.0967867 -0.3465085 0 0.43299345 3.2514265 571.43371
1000 1 -0.36129869 0 0.3494156 3.1353617 571.43371
1500 1.1299217 -0.37859354 0 0.42445794 2.9270341 571.43371
2000 1 -0.34287506 0 0.36783923 3.0258649 571.43371
2500 1.0916596 -0.3872134 0 0.38864469 2.8426168 571.43371
3000 1 -0.42816199 0 0.2825523 2.7129793 571.43371
3500 0.94744822 -0.47483071 0 0.19853427 2.7259788 571.43371
4000 1 -0.3684736 0 0.34224069 2.6328623 571.43371
4500 0.99502131 -0.37808208 0 0.32909378 2.5909215 571.43371
5000 1 -0.41230276 0 0.29841152 2.9229369 571.43371
5500 1.0560855 -0.48401682 0 0.26655822 2.472482 571.43371
6000 1 -0.4068915 0 0.30382279 2.3428133 571.43371
6500 1.0437572 -0.41914338 0 0.32266981 2.6151758 571.43371
7000 1 -0.42595992 0 0.28475437 2.3109881 571.43371
7500 1.0600587 -0.336143 0 0.41725588 2.3511832 571.43371
8000 1 -0.40369591 0 0.30701838 2.6195769 571.43371
8500 1.0750756 -0.43763885 0 0.32643275 2.2469938 571.43371
9000 1 -0.44198063 0 0.26873366 2.5250617 571.43371
9500 1.0263815 -0.43395816 0 0.29550586 2.5922753 571.43371
10000 1 -0.47197889 0 0.23873539 2.4144186 571.43371
Loop time of 4.11115 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.0713452 (1.73541)
Neigh time (%) = 0.0230771 (0.561329)
Comm time (%) = 3.20043 (77.8475)
Outpt time (%) = 0.163546 (3.9781)
Other time (%) = 0.652753 (15.8776)
Nlocal: 105 ave 116 max 95 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 41.75 ave 46 max 39 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 237.5 ave 301 max 178 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 950
Ave neighs/atom = 2.2619
Neighbor list builds = 973
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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
dump 1 all atom 25 dump.flow
run 10000
Memory usage per processor = 1.68525 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 1.2404529 -0.63017441 0 0.25290988 1.7684925 535.11692
4000 1 -0.71550459 0 -0.0035998233 2.2080667 516.62241
4500 1.2252925 -0.76523375 0 0.10705778 2.6150526 503.09392
5000 1 -0.79183795 0 -0.079933193 3.0396463 499.00782
5500 1.2154662 -0.76641284 0 0.098883321 2.5749248 501.79835
6000 1 -0.64579024 0 0.066114526 2.1632023 511.927
6500 1.2040094 -0.67569325 0 0.18144675 1.988296 515.52367
7000 1 -0.67495483 0 0.036949936 1.8145292 515.56679
7500 1.224424 -0.70211643 0 0.16955688 1.9563915 513.39341
8000 1 -0.68750419 0 0.024400573 2.2133264 508.15889
8500 1.1991285 -0.81030024 0 0.04336508 2.5391079 501.58914
9000 1 -0.79950245 0 -0.087597685 2.5700917 498.68874
9500 1.2060053 -0.68460543 0 0.17395548 2.4774286 501.9809
10000 1 -0.7187822 0 -0.0068774412 2.1346851 507.66533
Loop time of 0.73335 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.235934 (32.1721)
Neigh time (%) = 0.0389028 (5.3048)
Comm time (%) = 0.0151122 (2.0607)
Outpt time (%) = 0.239849 (32.7059)
Other time (%) = 0.203552 (27.7565)
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: 1126 ave 1126 max 1126 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1126
Ave neighs/atom = 2.68095
Neighbor list builds = 560
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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
dump 1 all atom 25 dump.flow
run 10000
Memory usage per processor = 1.67714 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 0.44989865 1.4547395 570.04942
3000 1 -0.49143404 0 0.22047072 1.5348968 554.87718
3500 1.2444907 -0.59761795 0 0.28834088 1.8757604 536.90691
4000 1 -0.70134359 0 0.010561171 2.1398674 521.35908
4500 1.2204821 -0.74251795 0 0.1263491 2.7628995 507.52799
5000 1 -0.77812124 0 -0.066216477 2.9593453 500.99765
5500 1.2036047 -0.76286922 0 0.093982666 2.6929974 506.25167
6000 1 -0.77204718 0 -0.060142418 2.4240012 509.91665
6500 1.2142987 -0.71937137 0 0.14509369 2.2503511 517.34969
7000 1 -0.65416249 0 0.057742269 2.147319 518.76914
7500 1.2280812 -0.68399882 0 0.19027806 2.0299907 517.0026
8000 1 -0.71589339 0 -0.0039886296 2.2415408 513.76983
8500 1.2274811 -0.70229467 0 0.17155497 2.1849604 512.25569
9000 1 -0.75920668 0 -0.047301917 2.4592389 508.74337
9500 1.2470681 -0.69158384 0 0.1962099 2.1530665 508.86868
10000 1 -0.74646656 0 -0.034561799 2.3332271 509.78267
Loop time of 4.49466 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.0739097 (1.64439)
Neigh time (%) = 0.0121227 (0.269713)
Comm time (%) = 2.82285 (62.8044)
Outpt time (%) = 0.281245 (6.25731)
Other time (%) = 1.30454 (29.0242)
Nlocal: 105 ave 107 max 103 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 44.75 ave 49 max 41 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 278 ave 296 max 259 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 1112
Ave neighs/atom = 2.64762
Neighbor list builds = 565
Dangerous builds = 0

122
examples/flow/log.flow.poiss.22Jan08.linux.1
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LAMMPS (22 Jan 2008)
# 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
dump 1 all atom 25 dump.flow
run 10000
Memory usage per processor = 1.68525 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71071429 0.5223703 571.43371
500 1.1036177 -0.37435595 0 0.4100009 2.5048411 575.42182
1000 1 -0.40278179 0 0.30793249 1.9811241 584.83497
1500 1.2346487 -0.41204291 0 0.46543956 1.5657713 586.36408
2000 1 -0.40773469 0 0.3029796 1.46174 583.54346
2500 1.2225527 -0.43831252 0 0.43057314 1.4819315 570.69513
3000 1 -0.49535278 0 0.21536151 1.5237868 553.26289
3500 1.2493782 -0.5997175 0 0.28823343 1.6851599 536.49066
4000 1 -0.67585271 0 0.034861579 2.0031708 518.19517
4500 1.1920623 -0.75096037 0 0.096255336 2.9347272 502.79894
5000 1 -0.82965482 0 -0.11894053 3.1069174 498.40593
5500 1.1922661 -0.78951149 0 0.057849031 3.0213496 502.16585
6000 1 -0.7308371 0 -0.020122809 2.394881 511.15935
6500 1.2295832 -0.71069261 0 0.16318977 1.971859 519.77333
7000 1 -0.64017925 0 0.070535035 2.0286235 520.82147
7500 1.2330112 -0.64928351 0 0.22703517 1.899572 518.70836
8000 1 -0.62643742 0 0.084276866 1.8527516 514.8535
8500 1.2117799 -0.71296056 0 0.14826876 2.280841 506.58294
9000 1 -0.72064639 0 -0.0099321068 2.2778589 504.4823
9500 1.2309735 -0.77916374 0 0.095706684 2.3907829 498.66444
10000 1 -0.7626132 0 -0.051898912 2.4826365 501.23793
Loop time of 0.716502 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.234028 (32.6626)
Neigh time (%) = 0.0383184 (5.34798)
Comm time (%) = 0.0147507 (2.05871)
Outpt time (%) = 0.235236 (32.8312)
Other time (%) = 0.194169 (27.0996)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 48 ave 48 max 48 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1144 ave 1144 max 1144 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1144
Ave neighs/atom = 2.72381
Neighbor list builds = 560
Dangerous builds = 0

122
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LAMMPS (22 Jan 2008)
# 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
dump 1 all atom 25 dump.flow
run 10000
Memory usage per processor = 1.67714 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71071429 0.5223703 571.43371
500 1.0778761 -0.35048279 0 0.41557918 2.7734524 574.92238
1000 1 -0.38740705 0 0.32330724 2.1851606 585.40362
1500 1.2052679 -0.37768559 0 0.47891551 1.5598219 585.77368
2000 1 -0.38060118 0 0.33011311 1.4422178 578.14206
2500 1.2211447 -0.39689947 0 0.47098548 1.5039485 566.96926
3000 1 -0.46632695 0 0.24438733 1.5055761 554.63863
3500 1.2338306 -0.57219064 0 0.30471041 1.750976 537.18508
4000 1 -0.70062676 0 0.01008753 2.2214089 518.64479
4500 1.2113785 -0.71432757 0 0.14661646 2.924362 503.68263
5000 1 -0.75295272 0 -0.042238438 3.0703778 500.62274
5500 1.2231978 -0.7326692 0 0.13667498 2.4722796 507.17803
6000 1 -0.69221877 0 0.018495519 2.1186078 514.07585
6500 1.2130182 -0.64829278 0 0.21381659 2.025108 517.78662
7000 1 -0.65011103 0 0.06060326 1.9907035 517.57821
7500 1.2244611 -0.68871579 0 0.1815262 2.1613555 512.52321
8000 1 -0.70033438 0 0.010379908 2.1994922 511.09769
8500 1.2325381 -0.73996991 0 0.13601255 2.2631942 507.50923
9000 1 -0.72281872 0 -0.012104437 2.4807895 504.20901
9500 1.2301783 -0.74960296 0 0.1247023 2.4156775 505.4057
10000 1 -0.76295913 0 -0.05224484 2.3054863 506.85774
Loop time of 5.06933 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.078612 (1.55074)
Neigh time (%) = 0.0138444 (0.2731)
Comm time (%) = 3.1048 (61.2466)
Outpt time (%) = 0.311994 (6.15453)
Other time (%) = 1.56009 (30.775)
Nlocal: 105 ave 106 max 104 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 44.5 ave 46 max 43 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 277.25 ave 292 max 254 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 1109
Ave neighs/atom = 2.64048
Neighbor list builds = 558
Dangerous builds = 0

66
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LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# 2d friction simulation
dimension 2
@ -98,43 +98,43 @@ dump 1 all atom 500 dump.friction
run 20000
Memory usage per processor = 1.73539 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1333672 0 -3.0921549 -1.1440307 2444.4558
1000 0.085622556 -3.0583969 0 -3.0231098 0.033995503 2444.4558
2000 0.085921887 -3.0572271 0 -3.0218167 -0.51378547 2444.4558
3000 0.10739474 -3.0650606 0 -3.0208008 -0.035547438 2444.4558
4000 0.089682132 -3.04809 0 -3.01113 -0.19064505 2444.4558
5000 0.10934102 -3.0485926 0 -3.0035307 0.1034494 2444.4558
6000 0.10817011 -3.0584907 0 -3.0139113 -0.31026241 2444.4558
7000 0.10519386 -3.0511555 0 -3.0078027 -0.23777457 2444.4558
8000 0.11660726 -3.0348032 0 -2.9867467 -0.40191693 2444.4558
9000 0.1 -3.0308538 0 -2.9896415 -0.30056676 2444.4558
10000 0.10422874 -3.0468394 0 -3.0038843 -0.41010239 2444.4558
11000 0.10907653 -3.0470568 0 -3.0021038 -0.39779677 2444.4558
12000 0.10518096 -3.0467458 0 -3.0033983 -0.28073637 2444.4558
13000 0.1052846 -3.0424889 0 -2.9990987 -0.39335018 2444.4558
14000 0.10942544 -3.0462295 0 -3.0011328 -0.31177088 2444.4558
15000 0.10696705 -3.0423514 0 -2.9982679 -0.39759929 2444.4558
16000 0.11637773 -3.0496752 0 -3.0017132 -0.19541362 2444.4558
17000 0.11090878 -3.0452336 0 -2.9995256 -0.41097653 2444.4558
18000 0.11274493 -3.0471847 0 -3.0007199 -0.31516775 2444.4558
19000 0.1058703 -3.0463493 0 -3.0027177 -0.28413841 2444.4558
20000 0.11224126 -3.0475136 0 -3.0012564 -0.24520009 2444.4558
Loop time of 10.8085 on 1 procs for 20000 steps with 1724 atoms
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 -0.32430283 2444.4558
8000 0.1 -3.0346457 0 -2.9934044 -0.38023276 2444.4558
9000 0.1 -3.0327792 0 -2.9915379 -0.43204961 2444.4558
10000 0.11908329 -3.0384756 0 -2.9893641 -0.34377218 2444.4558
11000 0.1 -3.0307666 0 -2.9895253 -0.46039249 2444.4558
12000 0.11748666 -3.0410033 0 -2.9925503 -0.21956005 2444.4558
13000 0.1 -3.0416003 0 -3.000359 -0.3651589 2444.4558
14000 0.11069381 -3.0439855 0 -2.998334 -0.28704457 2444.4558
15000 0.11218605 -3.0480708 0 -3.0018038 -0.32666261 2444.4558
16000 0.11189162 -3.0483127 0 -3.0021671 -0.23171462 2444.4558
17000 0.11423906 -3.0474938 0 -3.0003802 -0.34260897 2444.4558
18000 0.11548632 -3.047828 0 -3.0002 -0.31060102 2444.4558
19000 0.10034246 -3.0488263 0 -3.0074438 -0.2527683 2444.4558
20000 0.10505024 -3.0494404 0 -3.0061164 -0.31791192 2444.4558
Loop time of 10.9957 on 1 procs for 20000 steps with 1724 atoms
Pair time (%) = 9.04044 (83.642)
Neigh time (%) = 0.445875 (4.12523)
Comm time (%) = 0.0687661 (0.636223)
Outpt time (%) = 0.096189 (0.889939)
Other time (%) = 1.15723 (10.7067)
Pair time (%) = 9.05434 (82.344)
Neigh time (%) = 0.448596 (4.07973)
Comm time (%) = 0.0685506 (0.623428)
Outpt time (%) = 0.262556 (2.38779)
Other time (%) = 1.1617 (10.565)
Nlocal: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 142 ave 142 max 142 min
Nghost: 146 ave 146 max 146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14388 ave 14388 max 14388 min
Neighs: 14389 ave 14389 max 14389 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14388
Ave neighs/atom = 8.34571
Neighbor list builds = 736
Total # of neighbors = 14389
Ave neighs/atom = 8.34629
Neighbor list builds = 723
Dangerous builds = 0

140
examples/friction/log.friction.21May08.linux.4 Normal file
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LAMMPS (21 May 2008)
# 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
dump 1 all atom 500 dump.friction
run 20000
Memory usage per processor = 1.69136 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 -0.46354951 2444.4558
8000 0.11937916 -3.0305564 0 -2.9813229 -0.30779256 2444.4558
9000 0.11110731 -3.0274253 0 -2.9816032 -0.5245514 2444.4558
10000 0.11533593 -3.0167931 0 -2.969227 -0.3589085 2444.4558
11000 0.11347587 -3.0130738 0 -2.9662749 -0.47723571 2444.4558
12000 0.10688909 -3.0229092 0 -2.9788267 -0.31337183 2444.4558
13000 0.11881914 -3.0191983 0 -2.9701958 -0.43871352 2444.4558
14000 0.10970971 -3.0345115 0 -2.9892658 -0.26475254 2444.4558
15000 0.10683593 -3.030202 0 -2.9861414 -0.37883026 2444.4558
16000 0.11039182 -3.0315771 0 -2.9860501 -0.31830843 2444.4558
17000 0.11294566 -3.0314496 0 -2.9848693 -0.34449141 2444.4558
18000 0.11747267 -3.0330363 0 -2.984589 -0.21439976 2444.4558
19000 0.11287946 -3.0392425 0 -2.9926895 -0.38778831 2444.4558
20000 0.10942894 -3.0360473 0 -2.9909174 -0.3375786 2444.4558
Loop time of 9.87621 on 4 procs for 20000 steps with 1724 atoms
Pair time (%) = 2.4164 (24.4668)
Neigh time (%) = 0.115138 (1.16582)
Comm time (%) = 5.67421 (57.4533)
Outpt time (%) = 0.102493 (1.03777)
Other time (%) = 1.56798 (15.8763)
Nlocal: 431 ave 494 max 376 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 95 ave 124 max 75 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 3578.5 ave 4170 max 3130 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 14314
Ave neighs/atom = 8.30278
Neighbor list builds = 703
Dangerous builds = 0

140
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LAMMPS (22 Jan 2008)
# 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
dump 1 all atom 500 dump.friction
run 20000
Memory usage per processor = 1.69136 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1333672 0 -3.0921549 -1.1440307 2444.4558
1000 0.08936608 -3.060858 0 -3.0240282 0.015747058 2444.4558
2000 0.087353242 -3.0615115 0 -3.0255112 -0.49966222 2444.4558
3000 0.097185838 -3.0626106 0 -3.0225581 -0.084736345 2444.4558
4000 0.10514697 -3.0540883 0 -3.0107549 -0.34379432 2444.4558
5000 0.10965701 -3.0502726 0 -3.0050804 0.13242136 2444.4558
6000 0.1142368 -3.0461587 0 -2.9990791 -0.23407787 2444.4558
7000 0.1 -3.038824 0 -2.9976117 -0.3283908 2444.4558
8000 0.11116944 -3.0485104 0 -3.0026949 -0.42926135 2444.4558
9000 0.11429391 -3.0445555 0 -2.9974523 -0.39751757 2444.4558
10000 0.10617044 -3.050964 0 -3.0072087 -0.4320286 2444.4558
11000 0.10925063 -3.0492538 0 -3.0042291 -0.39877306 2444.4558
12000 0.11491574 -3.0511726 0 -3.0038132 -0.24990158 2444.4558
13000 0.10704872 -3.0467833 0 -3.0026661 -0.4272322 2444.4558
14000 0.10931685 -3.0488184 0 -3.0037664 -0.23385297 2444.4558
15000 0.103619 -3.0474073 0 -3.0047036 -0.39914954 2444.4558
16000 0.11669382 -3.0538214 0 -3.0057292 -0.29282079 2444.4558
17000 0.10983692 -3.0489199 0 -3.0036536 -0.30423885 2444.4558
18000 0.11157946 -3.0516854 0 -3.005701 -0.3165345 2444.4558
19000 0.11408792 -3.0522616 0 -3.0052433 -0.39019198 2444.4558
20000 0.10714842 -3.0629068 0 -3.0187485 -0.2392859 2444.4558
Loop time of 11.275 on 4 procs for 20000 steps with 1724 atoms
Pair time (%) = 2.6525 (23.5254)
Neigh time (%) = 0.125193 (1.11036)
Comm time (%) = 6.57651 (58.328)
Outpt time (%) = 0.108834 (0.965266)
Other time (%) = 1.81201 (16.071)
Nlocal: 431 ave 483 max 383 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nghost: 100 ave 118 max 84 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 3600.5 ave 4171 max 3180 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 14402
Ave neighs/atom = 8.35383
Neighbor list builds = 724
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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
# indenter
fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
fix 5 all enforce2d
# Run with indenter
timestep 0.003
thermo 1000
thermo_modify temp new
dump 1 all atom 250 dump.indent
run 30000
Memory usage per processor = 1.681 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 0.38108755 440.41873
11000 0.11198118 -3.0743549 0 -2.9786377 0.67596956 438.41816
12000 0.10823034 -3.0621355 0 -2.9696244 0.66497739 441.05346
13000 0.1194298 -3.0579575 0 -2.9558734 1.0886185 437.64369
14000 0.12310404 -3.051382 0 -2.9461573 0.8709418 445.45576
15000 0.11148459 -3.0402208 0 -2.944928 1.0042516 451.82353
16000 0.12322327 -3.041552 0 -2.9362254 0.75832747 456.81933
17000 0.12311088 -3.0300335 0 -2.924803 1.0485184 452.83217
18000 0.12062516 -3.0261639 0 -2.9230581 1.3986189 451.63458
19000 0.11958004 -3.0142969 0 -2.9120844 1.3964253 457.84108
20000 0.12231468 -3.0015738 0 -2.8970239 1.1240498 470.04449
21000 0.12075603 -3.0281424 0 -2.9249248 0.77047496 472.82097
22000 0.1140902 -3.0149866 0 -2.9174666 0.59890761 475.27346
23000 0.11660315 -3.022367 0 -2.9226991 0.86533578 474.33185
24000 0.11788061 -3.0130282 0 -2.9122684 1.0089196 468.47962
25000 0.11677694 -3.027 0 -2.9271835 0.95315571 470.28897
26000 0.12227277 -3.0174852 0 -2.9129711 1.0595574 469.3955
27000 0.11778994 -3.0019697 0 -2.9012873 1.2973295 472.846
28000 0.10834261 -2.9909288 0 -2.8983217 1.4598621 471.38654
29000 0.11506991 -2.9815688 0 -2.8832114 1.6220695 475.78184
30000 0.1137611 -2.9910145 0 -2.8937758 1.5390363 476.49487
Loop time of 4.35277 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 3.3632 (77.2656)
Neigh time (%) = 0.0964704 (2.2163)
Comm time (%) = 0.056159 (1.29019)
Outpt time (%) = 0.0744166 (1.70964)
Other time (%) = 0.762532 (17.5183)
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: 3704 ave 3704 max 3704 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3704
Ave neighs/atom = 8.81905
Neighbor list builds = 620
Dangerous builds = 0
# Run without indenter
unfix 4
run 30000
Memory usage per processor = 1.68109 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.1137611 -2.9910145 0 -2.8937758 1.5390363 476.49487
31000 0.11111993 -3.0361785 0 -2.9411974 -0.27734293 487.43496
32000 0.12226168 -3.0352443 0 -2.9307397 -0.65334794 484.5377
33000 0.12141332 -3.0559903 0 -2.9522108 0.2052495 480.86455
34000 0.11608515 -3.0513192 0 -2.952094 -0.40452569 486.60815
35000 0.12135397 -3.0431351 0 -2.9394063 -0.54073868 492.67492
36000 0.11867423 -3.0517805 0 -2.9503423 0.17502223 481.35439
37000 0.11592678 -3.0389976 0 -2.9399078 -0.45434566 489.41107
38000 0.12303667 -3.0448814 0 -2.9397144 -0.37442535 488.51063
39000 0.11824399 -3.0658885 0 -2.964818 -0.020875637 485.34869
40000 0.10891424 -3.0684735 0 -2.9753777 -0.40194667 490.36569
41000 0.11971963 -3.0777108 0 -2.975379 -0.31502752 485.70356
42000 0.12242279 -3.0800244 0 -2.975382 -0.29154762 485.64123
43000 0.11191041 -3.0710358 0 -2.9753791 -0.47381376 485.98823
44000 0.11663432 -3.0750759 0 -2.9753813 -0.16155045 483.58595
45000 0.11931527 -3.0773695 0 -2.9753833 -0.26683012 485.76005
46000 0.11602561 -3.0745521 0 -2.9753778 -0.43504309 488.91425
47000 0.11378336 -3.072636 0 -2.9753783 -0.065265912 485.31689
48000 0.11466706 -3.0733926 0 -2.9753796 -0.34617216 489.24951
49000 0.11892658 -3.0770335 0 -2.9753796 -0.34745886 486.45808
50000 0.11518751 -3.0738396 0 -2.9753817 -0.13713339 483.56692
51000 0.11924377 -3.0773057 0 -2.9753807 -0.46696512 487.41041
52000 0.12732939 -3.084182 0 -2.9753457 -0.31430325 483.886
53000 0.1184932 -3.0766623 0 -2.9753788 -0.22727456 485.05121
54000 0.10979213 -3.0692247 0 -2.9753786 -0.46578194 487.22102
55000 0.11813596 -3.0763601 0 -2.975382 -0.21269197 485.60016
56000 0.11927788 -3.0820716 0 -2.9801174 -0.39257652 488.29363
57000 0.11370876 -3.077309 0 -2.9801151 -0.42695354 487.36404
58000 0.10977322 -3.0750653 0 -2.9812353 -0.13698023 483.43933
59000 0.11837611 -3.0824237 0 -2.9812403 -0.42226934 488.24864
60000 0.12513787 -3.0760063 0 -2.9690432 -0.27843098 488.02101
Loop time of 4.04106 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 3.33419 (82.5078)
Neigh time (%) = 0.0975268 (2.4134)
Comm time (%) = 0.0565064 (1.39831)
Outpt time (%) = 0.0741966 (1.83607)
Other time (%) = 0.478639 (11.8444)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 106 ave 106 max 106 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3564 ave 3564 max 3564 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3564
Ave neighs/atom = 8.48571
Neighbor list builds = 632
Dangerous builds = 0

169
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LAMMPS (21 May 2008)
# 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
# indenter
fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
fix 5 all enforce2d
# Run with indenter
timestep 0.003
thermo 1000
thermo_modify temp new
dump 1 all atom 250 dump.indent
run 30000
Memory usage per processor = 1.67582 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 0.65396033 442.56232
13000 0.11686417 -3.0600388 0 -2.9601477 1.0043055 438.41699
14000 0.12557378 -3.0570017 0 -2.949666 0.85725522 442.01753
15000 0.11934083 -3.0498848 0 -2.9478768 1.0394141 451.6596
16000 0.12576916 -3.0452181 0 -2.9377154 1.3482057 441.18585
17000 0.11546551 -3.0348365 0 -2.9361409 1.6321334 439.4002
18000 0.1214883 -3.0221153 0 -2.9182718 1.6092045 449.17018
19000 0.11883751 -3.0036774 0 -2.9020996 1.5203993 447.04217
20000 0.11165763 -3.0038239 0 -2.9083832 1.4080186 461.67014
21000 0.11347925 -2.9899447 0 -2.8929469 1.1346232 473.86859
22000 0.11913997 -3.0239282 0 -2.9220919 0.81021913 473.09495
23000 0.1148535 -3.0126427 0 -2.9144703 1.1401379 470.54689
24000 0.11671309 -3.016222 0 -2.9164601 0.84429095 472.7482
25000 0.11161515 -3.0207137 0 -2.9253093 1.0597826 467.28214
26000 0.11294692 -3.0085312 0 -2.9119885 1.0112464 469.64427
27000 0.12828831 -3.010401 0 -2.9007451 1.0769835 473.94697
28000 0.12123681 -3.0107629 0 -2.9071343 0.81020478 478.51729
29000 0.12528058 -3.01932 0 -2.912235 1.0826534 472.26351
30000 0.11527728 -3.0030382 0 -2.9045036 1.5931211 465.76942
Loop time of 12.2538 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 1.06251 (8.67087)
Neigh time (%) = 0.0298207 (0.243358)
Comm time (%) = 8.70494 (71.0387)
Outpt time (%) = 0.0981069 (0.800624)
Other time (%) = 2.35843 (19.2465)
Nlocal: 105 ave 112 max 97 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 95.5 ave 100 max 92 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 914.75 ave 1023 max 810 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3659
Ave neighs/atom = 8.7119
Neighbor list builds = 616
Dangerous builds = 0
# Run without indenter
unfix 4
run 30000
Memory usage per processor = 1.67614 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.11527728 -3.0030382 0 -2.9045036 1.5932587 465.72917
31000 0.11671309 -3.0142211 0 -2.9144592 -0.37706203 481.50962
32000 0.11671309 -3.0227063 0 -2.9229444 -0.58012876 480.95432
33000 0.10635055 -3.0482223 0 -2.9573179 0.45560579 464.47424
34000 0.11877148 -3.0703768 0 -2.9688555 -0.32968186 475.82732
35000 0.1157547 -3.0679911 0 -2.9690484 -0.55386822 490.09322
36000 0.12250126 -3.0847099 0 -2.9800005 0.16762425 482.76837
37000 0.11211273 -3.076227 0 -2.9803973 -0.56416688 485.40738
38000 0.12332877 -3.074982 0 -2.9695653 -0.35777769 490.47511
39000 0.11065377 -3.0755102 0 -2.9809275 0.014347118 478.2741
40000 0.10710169 -3.0724742 0 -2.9809278 -0.55516693 490.26814
41000 0.1088162 -3.0739373 0 -2.9809254 -0.069868958 482.39533
42000 0.12792219 -3.0902767 0 -2.9809336 -0.26461148 484.55637
43000 0.11058857 -3.0754557 0 -2.9809288 -0.64800221 488.40619
44000 0.11162461 -3.0763412 0 -2.9809287 0.075505051 482.91497
45000 0.11497594 -3.0792046 0 -2.9809275 -0.38338131 485.15347
46000 0.10637288 -3.0718511 0 -2.9809276 -0.47729139 489.49592
47000 0.11706089 -3.0809897 0 -2.9809305 0.0034214827 482.52084
48000 0.11104829 -3.075849 0 -2.9809292 -0.58552878 486.85862
49000 0.11245495 -3.0770533 0 -2.9809311 -0.32773345 487.81722
50000 0.11875403 -3.0824388 0 -2.9809324 -0.1284175 480.82151
51000 0.10815089 -3.0733705 0 -2.9809273 -0.59528979 488.33208
52000 0.11766627 -3.0713521 0 -2.9707755 -0.14820961 485.02169
53000 0.12125512 -3.0857543 0 -2.98211 -0.27980304 483.66006
54000 0.11567186 -3.0809806 0 -2.9821087 -0.51734052 487.77367
55000 0.11215173 -3.0779718 0 -2.9821088 -0.13169059 482.81031
56000 0.10952092 -3.0757199 0 -2.9821056 -0.35508967 485.28191
57000 0.12592796 -3.0770934 0 -2.969455 -0.39550089 487.7802
58000 0.11671309 -3.0836904 0 -2.9839285 -0.17868279 485.62136
59000 0.10785966 -3.0761158 0 -2.9839215 -0.36413012 486.36951
60000 0.12108723 -3.0736236 0 -2.9701228 -0.30955784 486.51342
Loop time of 11.802 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 0.984152 (8.33884)
Neigh time (%) = 0.0291511 (0.247001)
Comm time (%) = 8.40175 (71.1891)
Outpt time (%) = 0.100835 (0.854389)
Other time (%) = 2.28613 (19.3707)
Nlocal: 105 ave 119 max 89 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 88 ave 91 max 84 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 891.5 ave 1073 max 705 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3566
Ave neighs/atom = 8.49048
Neighbor list builds = 625
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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
# indenter
fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
fix 5 all enforce2d
# Run with indenter
timestep 0.003
thermo 1000
thermo_modify temp new
dump 1 all atom 250 dump.indent
run 30000
Memory usage per processor = 1.681 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.2 -3.1727576 0 -3.0020433 -1.4366826 444.44898
1000 0.11979027 -3.0878285 0 -2.9855789 -0.037115753 440.68307
2000 0.12095292 -3.0888211 0 -2.9855791 -0.39926994 444.26707
3000 0.1167364 -3.0841547 0 -2.9845118 -0.34877104 442.84444
4000 0.12249143 -3.1004175 0 -2.9958623 -0.051696807 438.73578
5000 0.10957873 -3.0886367 0 -2.9951034 -0.48968706 443.75021
6000 0.12346008 -3.0985964 0 -2.9932144 -0.061988469 442.24069
7000 0.10994736 -3.0850721 0 -2.9912241 -0.17265831 443.86094
8000 0.11557891 -3.086042 0 -2.9873871 0.19299422 440.53674
9000 0.12016755 -3.084536 0 -2.9819645 0.28219762 439.46924
10000 0.12659552 -3.0852403 0 -2.977182 0.34547052 440.85673
11000 0.12524777 -3.0736607 0 -2.9667528 0.65889968 439.12793
12000 0.11844672 -3.0571177 0 -2.9560149 0.65697119 441.00263
13000 0.12031568 -3.0583679 0 -2.9556699 1.0789051 437.17067
14000 0.1167364 -3.0548463 0 -2.9552034 0.92252944 441.75844
15000 0.1167364 -3.0549235 0 -2.9552806 1.104037 444.57625
16000 0.12471788 -3.052462 0 -2.9460064 1.3976876 440.83011
17000 0.12078165 -3.0356476 0 -2.9325518 1.6287355 437.90579
18000 0.11738015 -3.0294797 0 -2.9292874 1.685709 448.54282
19000 0.12273217 -3.0164912 0 -2.9117305 1.6952163 444.70626
20000 0.1254989 -3.0011836 0 -2.8940613 1.5120085 459.5423
21000 0.12037276 -2.9934283 0 -2.8906816 1.1633617 475.10793
22000 0.12303026 -3.0181561 0 -2.913141 0.80041224 476.32611
23000 0.12012255 -3.0180582 0 -2.915525 1.0242864 469.70124
24000 0.11834242 -3.011825 0 -2.9108113 0.91924231 471.07582
25000 0.11662147 -3.0266029 0 -2.9270581 1.2863229 465.94453
26000 0.10849743 -3.0122074 0 -2.9195971 1.0346219 471.89139
27000 0.11442546 -3.0195569 0 -2.9218866 0.95642369 472.17747
28000 0.12607822 -3.018653 0 -2.9110362 0.80288611 478.81533
29000 0.11485475 -3.0026613 0 -2.9046245 1.0162131 478.56821
30000 0.11957018 -3.007796 0 -2.9057344 1.1519595 473.32666
Loop time of 4.36496 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 3.38296 (77.5027)
Neigh time (%) = 0.0948896 (2.17389)
Comm time (%) = 0.055548 (1.27259)
Outpt time (%) = 0.071348 (1.63456)
Other time (%) = 0.760214 (17.4163)
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: 3663 ave 3663 max 3663 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3663
Ave neighs/atom = 8.72143
Neighbor list builds = 615
Dangerous builds = 0
# Run without indenter
unfix 4
run 30000
Memory usage per processor = 1.68117 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.11957018 -3.007796 0 -2.9057344 1.1538424 472.55425
31000 0.10960776 -3.0320499 0 -2.9384919 -0.1111492 475.04939
32000 0.11696413 -3.017537 0 -2.9176998 -0.46118163 479.36156
33000 0.11881079 -3.0604548 0 -2.9590413 0.089398143 475.85863
34000 0.11291474 -3.0762007 0 -2.9798199 -0.53925844 467.63944
35000 0.12091623 -3.07146 0 -2.9682494 -0.30643332 465.79963
36000 0.11443202 -3.0773212 0 -2.9796453 -0.16930354 468.00022
37000 0.10847358 -3.0722351 0 -2.9796452 -0.40417498 466.35112
38000 0.12257573 -3.0842762 0 -2.979649 -0.3539779 464.74783
39000 0.10919826 -3.0728543 0 -2.9796458 -0.10190087 462.71616
40000 0.11592052 -3.0785918 0 -2.9796454 -0.56392258 466.79575
41000 0.1187654 -3.0810202 0 -2.9796454 -0.24959896 464.94494
42000 0.11065271 -3.0740978 0 -2.9796478 -0.13938683 463.95585
43000 0.11213075 -3.0753593 0 -2.9796477 -0.57295952 467.53433
44000 0.11851463 -3.0808118 0 -2.9796511 -0.072822043 462.69799
45000 0.11513293 -3.0779198 0 -2.9796456 -0.38690299 464.92762
46000 0.11802643 -3.0727964 0 -2.9720524 -0.41876651 467.61475
47000 0.10968445 -3.0767131 0 -2.9830896 0.00035992413 462.33575
48000 0.10986927 -3.0768658 0 -2.9830845 -0.50973722 466.84125
49000 0.11716516 -3.0730443 0 -2.9730355 -0.25528257 465.09708
50000 0.114152 -3.0811614 0 -2.9837245 -0.25131852 463.16554
51000 0.11151236 -3.0789097 0 -2.983726 -0.49587211 466.97181
52000 0.12287592 -3.0773446 0 -2.9724612 -0.23319519 466.44897
53000 0.12184618 -3.076465 0 -2.9724606 -0.32085107 465.19617
54000 0.11183696 -3.067917 0 -2.9724562 -0.31965796 465.50492
55000 0.11759344 -3.0728319 0 -2.9724575 -0.25579782 466.03182
56000 0.11864906 -3.0737344 0 -2.9724589 -0.21452862 465.36224
57000 0.12056652 -3.0753734 0 -2.9724613 -0.38889467 465.52022
58000 0.12467619 -3.0788817 0 -2.9724617 -0.25977738 463.35348
59000 0.1143898 -3.0802997 0 -2.9826599 -0.36709007 463.95776
60000 0.11996036 -3.0850555 0 -2.9826607 -0.43924518 465.21821
Loop time of 4.03837 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 3.33861 (82.6721)
Neigh time (%) = 0.0961225 (2.38023)
Comm time (%) = 0.0559936 (1.38654)
Outpt time (%) = 0.071291 (1.76534)
Other time (%) = 0.476356 (11.7957)
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: 3565 ave 3565 max 3565 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3565
Ave neighs/atom = 8.4881
Neighbor list builds = 620
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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
# indenter
fix 4 all indent 1000.0 sphere 10 13 0 5.0 vel 0.0 -0.02 0.0
fix 5 all enforce2d
# Run with indenter
timestep 0.003
thermo 1000
thermo_modify temp new
dump 1 all atom 250 dump.indent
run 30000
Memory usage per processor = 1.67582 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.2 -3.1727576 0 -3.0020433 -1.4366826 444.44898
1000 0.11576832 -3.0966334 0 -2.9978168 -0.2046953 441.73683
2000 0.11528823 -3.0962223 0 -2.9978155 -0.38254021 442.23432
3000 0.11379051 -3.0840496 0 -2.9869213 -0.42664207 444.50384
4000 0.11595816 -3.085882 0 -2.9869034 -0.040632221 439.82253
5000 0.11272851 -3.0844605 0 -2.9882386 -0.48630294 445.8137
6000 0.12387775 -3.0900283 0 -2.9842898 0.0061789692 439.90649
7000 0.1113616 -3.0914902 0 -2.9964351 -0.10825389 441.94247
8000 0.1167364 -3.0879355 0 -2.9882926 0.17566419 441.73938
9000 0.11504768 -3.0918767 0 -2.9936753 0.29955458 440.3699
10000 0.11864876 -3.0776022 0 -2.976327 0.38844091 441.0787
11000 0.12749806 -3.0769801 0 -2.9681514 0.60370474 438.20684
12000 0.11068569 -3.0664256 0 -2.9719474 0.66212034 439.45966
13000 0.11341038 -3.0596733 0 -2.9628694 0.98257147 440.29995
14000 0.1176102 -3.058063 0 -2.9576743 1.0265509 439.75724
15000 0.12582685 -3.054119 0 -2.9467168 0.89411243 448.51929
16000 0.11716115 -3.0359807 0 -2.9359753 0.94392052 458.9918
17000 0.1183619 -3.0276207 0 -2.9265904 0.91928551 455.52056
18000 0.12271609 -3.017155 0 -2.9124081 1.2843751 467.90439
19000 0.11746036 -3.0102895 0 -2.9100287 1.3852631 472.51702
20000 0.12089249 -2.9967314 0 -2.893541 1.5300149 474.35237
21000 0.12575365 -2.9947646 0 -2.8874248 1.5751315 479.52718
22000 0.1167364 -2.9837589 0 -2.884116 1.2716662 486.91315
23000 0.12415934 -3.0113215 0 -2.9053426 1.0113981 485.76489
24000 0.12324594 -3.0224444 0 -2.9172451 1.1058302 484.29936
25000 0.12325265 -3.0115298 0 -2.9063249 0.95737324 492.3559
26000 0.1209802 -3.0094161 0 -2.9061509 0.72298537 503.98811
27000 0.12584652 -3.0019729 0 -2.8945539 1.1273224 494.9013
28000 0.1167364 -2.9910191 0 -2.8913762 1.2902722 496.61985
29000 0.1167364 -3.0029616 0 -2.9033188 0.89371934 502.82784
30000 0.1212253 -3.0101062 0 -2.9066317 0.66514457 508.68846
Loop time of 14.6334 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 1.07639 (7.3557)
Neigh time (%) = 0.0313419 (0.214181)
Comm time (%) = 10.5831 (72.3219)
Outpt time (%) = 0.117674 (0.804145)
Other time (%) = 2.82484 (19.3041)
Nlocal: 105 ave 123 max 86 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 95.75 ave 103 max 88 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 905.25 ave 1127 max 678 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3621
Ave neighs/atom = 8.62143
Neighbor list builds = 622
Dangerous builds = 0
# Run without indenter
unfix 4
run 30000
Memory usage per processor = 1.67641 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.1212253 -3.0101062 0 -2.9066317 0.66472805 509.0072
31000 0.10753955 -3.0244479 0 -2.9326552 0.014150137 507.50974
32000 0.11147629 -3.0158355 0 -2.9206825 -0.28843033 519.21836
33000 0.11978091 -3.0365035 0 -2.9342619 -0.068567574 508.39504
34000 0.12177378 -3.0706615 0 -2.9667189 -0.21120889 505.55013
35000 0.12309818 -3.0718302 0 -2.9667571 -0.38249432 511.72908
36000 0.10844583 -3.0593175 0 -2.9667512 -0.2638784 503.54833
37000 0.11777916 -3.0777872 0 -2.9772543 -0.21323143 506.08932
38000 0.11033046 -3.0714259 0 -2.977251 -0.39909252 507.81232
39000 0.11215445 -3.0729827 0 -2.9772508 -0.23485622 509.16831
40000 0.11255907 -3.0733302 0 -2.977253 -0.2578202 504.01334
41000 0.11432059 -3.0748349 0 -2.9772541 -0.45901053 510.3073
42000 0.11170702 -3.0726007 0 -2.9772508 -0.15551038 504.69646
43000 0.11223315 -3.0730128 0 -2.9772138 -0.26797241 510.09817
44000 0.11243348 -3.0732228 0 -2.9772528 -0.38149257 508.55354
45000 0.1131438 -3.0738274 0 -2.9772511 -0.13310154 504.34955
46000 0.10933879 -3.0705795 0 -2.977251 -0.35927728 506.78452
47000 0.11758866 -3.0776231 0 -2.9772528 -0.27765047 506.95034
48000 0.11761342 -3.0776456 0 -2.9772542 -0.21700914 503.52997
49000 0.11471014 -3.0751668 0 -2.9772535 -0.44906884 508.46902
50000 0.11788451 -3.0778781 0 -2.9772553 -0.11247392 504.06984
51000 0.11837104 -3.0782917 0 -2.9772536 -0.27620472 505.52699
52000 0.10745291 -3.0689667 0 -2.9772479 -0.31961002 506.98322
53000 0.11244133 -3.0732297 0 -2.977253 -0.12156293 504.93407
54000 0.11314629 -3.0738292 0 -2.9772508 -0.4429982 506.82187
55000 0.11648474 -3.0766799 0 -2.9772519 -0.316804 507.16995
56000 0.12597906 -3.0847878 0 -2.9772557 -0.27802324 507.19137
57000 0.11827315 -3.0671955 0 -2.9662409 -0.32983726 508.50022
58000 0.12508397 -3.0730087 0 -2.9662406 -0.24866953 505.02704
59000 0.12079689 -3.0693502 0 -2.9662414 -0.23782258 505.35377
60000 0.1183543 -3.0672642 0 -2.9662403 -0.39709624 507.80337
Loop time of 14.8577 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 1.05365 (7.09162)
Neigh time (%) = 0.0316316 (0.212898)
Comm time (%) = 10.8588 (73.0857)
Outpt time (%) = 0.117559 (0.791232)
Other time (%) = 2.796 (18.8186)
Nlocal: 105 ave 121 max 84 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 94.75 ave 104 max 87 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 889.75 ave 1087 max 662 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 3559
Ave neighs/atom = 8.47381
Neighbor list builds = 632
Dangerous builds = 0

55
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LAMMPS (21 May 2008)
# 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 1000 1000
ERROR: Illegal minimize command

55
examples/indent/log.indent.min.21May08.linux.4 Normal file
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@ -0,0 +1,55 @@
LAMMPS (21 May 2008)
# 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 1000 1000
ERROR: Illegal minimize command

382
examples/indent/log.indent.min.22Jan08.linux.1
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@ -1,382 +0,0 @@
LAMMPS (22 Jan 2008)
# 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 1000 1000
Memory usage per processor = 2.13877 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5980059 444.44898
10 0 -3.1820434 0 -3.1820434 -1.1317017 440.97368
20 0 -3.1892762 0 -3.1892762 -0.875018 437.63427
30 0 -3.1906231 0 -3.1906231 -0.77012131 437.63427
38 0 -3.1909329 0 -3.1909329 -0.6923326 437.63427
Loop time of 0.0332251 on 1 procs for 38 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -3.17276 -3.19093 -3.19093
Gradient 2-norm init/final= 6.74302 0.251767
Gradient inf-norm init/final= 1.46877 0.0232337
Iterations = 38
Force evaluations = 148
Pair time (%) = 0.0271435 (81.6958)
Neigh time (%) = 0.00029707 (0.894113)
Comm time (%) = 0.000262022 (0.788628)
Outpt time (%) = 0.00231719 (6.97422)
Other time (%) = 0.0032053 (9.64723)
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 = 2
Dangerous builds = 0
fix 4 all indent 5000.0 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 2.13877 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
38 0 -3.1909329 0 -2.1718641 -0.69556621 435.59976
40 0 -3.169091 0 -2.8877594 -0.46675955 435.59973
50 0 -3.1711852 0 -3.1696057 -0.33713462 435.60143
60 0 -3.1780204 0 -3.1769046 -0.33322968 435.79292
70 0 -3.1800811 0 -3.1793038 -0.26556467 435.79292
80 0 -3.1809088 0 -3.1801828 -0.19926217 435.79292
90 0 -3.1811924 0 -3.1805002 -0.14442628 434.68835
100 0 -3.1812635 0 -3.1805822 -0.12227185 434.68835
103 0 -3.1812545 0 -3.180591 -0.12009024 434.68835
Loop time of 0.0514102 on 1 procs for 65 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -2.17186 -3.18059 -3.18059
Gradient 2-norm init/final= 1621.12 0.469022
Gradient inf-norm init/final= 1193.11 0.272199
Iterations = 65
Force evaluations = 211
Pair time (%) = 0.0386546 (75.1885)
Neigh time (%) = 0.000748396 (1.45573)
Comm time (%) = 0.000388145 (0.754997)
Outpt time (%) = 0.0052855 (10.281)
Other time (%) = 0.00633359 (12.3197)
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: 3586 ave 3586 max 3586 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3586
Ave neighs/atom = 8.5381
Neighbor list builds = 5
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 2.13877 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
103 0 -3.1812545 0 -0.21951029 -0.1202861 433.98055
110 0 -2.9284097 0 -2.6466557 2.0617709 433.9793
120 0 -3.0511214 0 -3.0267128 1.4983726 433.97719
130 0 -3.0919408 0 -3.0831141 1.2624464 434.23068
140 0 -3.1001312 0 -3.0930458 1.209277 434.23068
150 0 -3.102631 0 -3.0950311 1.2237232 434.73394
160 0 -3.1037978 0 -3.09648 1.3260564 431.60915
170 0 -3.1041785 0 -3.0969724 1.3941622 431.60915
180 0 -3.1042622 0 -3.0971039 1.4149115 431.60915
186 0 -3.1042077 0 -3.0971259 1.4187834 431.60915
Loop time of 0.0678358 on 1 procs for 83 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -0.21951 -3.09712 -3.09713
Gradient 2-norm init/final= 1753.54 0.525185
Gradient inf-norm init/final= 923.56 0.20363
Iterations = 83
Force evaluations = 279
Pair time (%) = 0.0514042 (75.7774)
Neigh time (%) = 0.00167418 (2.46798)
Comm time (%) = 0.000550032 (0.810828)
Outpt time (%) = 0.00602508 (8.88185)
Other time (%) = 0.00818229 (12.0619)
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: 3642 ave 3642 max 3642 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3642
Ave neighs/atom = 8.67143
Neighbor list builds = 11
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 2.13877 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
186 0 -3.1042077 0 1.9876467 1.4209266 430.95816
190 0 -2.7684954 0 -1.1554028 4.1104961 430.51479
200 0 -2.7738026 0 -2.6431045 4.5613937 435.03877
210 0 -2.892911 0 -2.863976 3.765261 442.55285
220 0 -2.9428319 0 -2.9275563 3.3111711 447.69227
230 0 -2.9566576 0 -2.9427828 3.183237 451.95964
240 0 -2.9622154 0 -2.9537038 3.0997525 453.12625
250 0 -2.9685121 0 -2.9588966 3.0016498 455.11967
260 0 -2.9851957 0 -2.9793281 2.7575287 455.75205
270 0 -3.0137593 0 -3.0035449 2.449694 453.80579
280 0 -3.0182039 0 -3.0121893 2.3442266 454.59869
290 0 -3.0271401 0 -3.0194953 2.053625 459.16264
300 0 -3.0332671 0 -3.0255652 2.059571 459.16264
310 0 -3.0346445 0 -3.0270706 2.0755976 456.56027
320 0 -3.0355796 0 -3.0277669 2.0482597 456.56027
330 0 -3.0359691 0 -3.0280778 2.0154636 456.56027
340 0 -3.0358963 0 -3.0281771 1.9966785 456.56027
350 0 -3.0359324 0 -3.0282261 1.9824739 456.56027
Loop time of 0.141067 on 1 procs for 164 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = 1.98765 -3.02822 -3.02823
Gradient 2-norm init/final= 2323.65 0.605548
Gradient inf-norm init/final= 1037.31 0.149721
Iterations = 164
Force evaluations = 579
Pair time (%) = 0.107919 (76.5017)
Neigh time (%) = 0.00395179 (2.80135)
Comm time (%) = 0.00117111 (0.830181)
Outpt time (%) = 0.0119934 (8.50192)
Other time (%) = 0.016032 (11.3648)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 109 ave 109 max 109 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3789 ave 3789 max 3789 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3789
Ave neighs/atom = 9.02143
Neighbor list builds = 25
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 2.13877 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
350 0 -3.0359324 0 6.9766773 1.9786928 457.43272
360 0 -2.335093 0 -1.5707757 7.5510257 457.43998
370 0 -2.5599881 0 -2.4347598 6.4272916 457.91764
380 0 -2.7844216 0 -2.7584649 4.9001971 463.20184
390 0 -2.8656166 0 -2.8440742 4.2220788 464.98354
400 0 -2.9109956 0 -2.8923852 3.6096589 468.48088
410 0 -2.9467505 0 -2.9334194 3.210818 471.50863
420 0 -2.9744267 0 -2.9577148 3.1040552 470.74251
430 0 -2.9926456 0 -2.9736412 2.9546044 471.59618
440 0 -2.9975451 0 -2.9801205 2.8912377 471.28646
450 0 -2.9996109 0 -2.9820253 2.8472599 472.36332
460 0 -2.9987284 0 -2.9829306 2.8127874 472.36332
470 0 -2.9987247 0 -2.9846006 2.6439865 473.77264
480 0 -3.002881 0 -2.9903844 2.3001851 478.94935
490 0 -3.0065806 0 -2.9942666 2.1491834 481.91432
500 0 -3.0095236 0 -2.9964104 2.0319452 484.64425
510 0 -3.0114745 0 -2.9990245 1.9606412 485.51456
520 0 -3.0120857 0 -3.0020722 1.9278832 485.273
530 0 -3.0221073 0 -3.0141559 1.8289206 487.68636
540 0 -3.0307927 0 -3.0222342 1.7165806 489.75746
550 0 -3.0387697 0 -3.0286577 1.6073926 490.88326
560 0 -3.0423031 0 -3.0330395 1.586802 491.73724
570 0 -3.043509 0 -3.0343313 1.5673862 491.73724
580 0 -3.0440104 0 -3.0348575 1.558385 491.73724
590 0 -3.0439091 0 -3.0353446 1.5465643 490.86256
600 0 -3.0456641 0 -3.0369635 1.5266002 490.36123
610 0 -3.047406 0 -3.0381862 1.4944371 489.9176
620 0 -3.0502537 0 -3.0405998 1.4555164 491.15806
625 0 -3.0521001 0 -3.0423852 1.4492467 491.59747
Loop time of 0.242592 on 1 procs for 275 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = 6.97668 -3.04203 -3.04239
Gradient 2-norm init/final= 3559.61 9.34801
Gradient inf-norm init/final= 1438.88 3.86075
Iterations = 275
Force evaluations = 1002
Pair time (%) = 0.185928 (76.6423)
Neigh time (%) = 0.0070498 (2.90603)
Comm time (%) = 0.00214314 (0.883435)
Outpt time (%) = 0.0202661 (8.35396)
Other time (%) = 0.027205 (11.2143)
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: 3678 ave 3678 max 3678 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3678
Ave neighs/atom = 8.75714
Neighbor list builds = 44
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 2.13885 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
625 0 -3.0521001 0 -2.6498801 1.4488549 491.7304
630 0 -2.9718737 0 -2.9110758 2.2436261 491.72959
640 0 -2.9788109 0 -2.9552133 2.2865455 491.95942
650 0 -2.9876288 0 -2.9678188 2.2441267 492.6284
660 0 -2.9897692 0 -2.9724888 2.2915736 492.03371
670 0 -2.9919535 0 -2.9762524 2.3486047 491.26568
680 0 -2.9958204 0 -2.9792159 2.3471087 490.11049
690 0 -3.0003811 0 -2.9827328 2.2999787 490.21162
700 0 -3.0023138 0 -2.9853549 2.2675318 491.33245
710 0 -3.0027659 0 -2.9867895 2.2883282 491.33245
720 0 -3.0031834 0 -2.9875047 2.3106077 489.42967
730 0 -3.0036556 0 -2.9876211 2.3088756 489.42967
740 0 -3.0038433 0 -2.9876825 2.3055494 489.42967
743 0 -3.0038605 0 -2.9876906 2.3053223 489.42967
Loop time of 0.0952809 on 1 procs for 118 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -2.64988 -2.98769 -2.98769
Gradient 2-norm init/final= 391.935 0.735748
Gradient inf-norm init/final= 174.478 0.254377
Iterations = 118
Force evaluations = 392
Pair time (%) = 0.072511 (76.1023)
Neigh time (%) = 0.0017426 (1.82891)
Comm time (%) = 0.000789404 (0.828502)
Outpt time (%) = 0.00900126 (9.44707)
Other time (%) = 0.0112367 (11.7932)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 116 ave 116 max 116 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3810 ave 3810 max 3810 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3810
Ave neighs/atom = 9.07143
Neighbor list builds = 11
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 2.13885 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
743 0 -3.0038605 0 -2.4096618 2.3078479 488.89405
750 0 -2.8899993 0 -2.8291939 3.4288679 488.89459
760 0 -2.8929447 0 -2.8576475 3.4739485 489.19553
770 0 -2.8951789 0 -2.8655275 3.4824252 489.19553
780 0 -2.8954908 0 -2.8692017 3.5158206 489.53759
790 0 -2.8987436 0 -2.8799874 3.417111 498.10919
800 0 -2.9103982 0 -2.8925867 3.1813363 505.60533
810 0 -2.923822 0 -2.9049543 2.7634162 510.69079
820 0 -2.9690464 0 -2.959277 2.1615844 511.87122
830 0 -3.0137954 0 -3.0063127 1.9411075 511.76042
840 0 -3.0263936 0 -3.018511 1.8625841 511.33281
850 0 -3.0332313 0 -3.0246203 1.785449 510.58928
860 0 -3.0400639 0 -3.0311608 1.660562 511.39199
870 0 -3.0490546 0 -3.0399986 1.5037912 513.99632
880 0 -3.0640791 0 -3.0552023 1.3477777 514.73114
890 0 -3.0696238 0 -3.0605878 1.3338106 514.97796
900 0 -3.072344 0 -3.0631492 1.3146094 515.21041
910 0 -3.0725478 0 -3.0638124 1.3020946 515.21041
920 0 -3.0733416 0 -3.0644345 1.2853311 516.14828
930 0 -3.0748377 0 -3.0658391 1.3067919 516.24534
940 0 -3.0750618 0 -3.066135 1.3077775 516.24534
950 0 -3.075108 0 -3.066207 1.3119176 516.24534
953 0 -3.0751175 0 -3.0662144 1.3125012 516.24534
Loop time of 0.181291 on 1 procs for 210 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -2.40966 -3.06621 -3.06621
Gradient 2-norm init/final= 493.48 0.611378
Gradient inf-norm init/final= 186.721 0.300913
Iterations = 210
Force evaluations = 750
Pair time (%) = 0.13778 (75.9992)
Neigh time (%) = 0.00535512 (2.95388)
Comm time (%) = 0.00162768 (0.897829)
Outpt time (%) = 0.0157762 (8.70211)
Other time (%) = 0.0207524 (11.447)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 120 ave 120 max 120 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 = 34
Dangerous builds = 0

384
examples/indent/log.indent.min.22Jan08.linux.4
View File

@ -1,384 +0,0 @@
LAMMPS (22 Jan 2008)
# 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 1000 1000
Memory usage per processor = 2.13359 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5980059 444.44898
10 0 -3.1820434 0 -3.1820434 -1.1317017 440.97368
20 0 -3.1892762 0 -3.1892762 -0.875018 437.63427
30 0 -3.1906231 0 -3.1906231 -0.77012131 437.63427
38 0 -3.1909329 0 -3.1909329 -0.6923326 437.63427
Loop time of 0.116816 on 4 procs for 38 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -3.17276 -3.19093 -3.19093
Gradient 2-norm init/final= 6.74302 0.251767
Gradient inf-norm init/final= 1.46877 0.0232337
Iterations = 38
Force evaluations = 148
Pair time (%) = 0.00820065 (7.02014)
Neigh time (%) = 9.92417e-05 (0.0849556)
Comm time (%) = 0.052792 (45.1924)
Outpt time (%) = 0.00496787 (4.25273)
Other time (%) = 0.0507563 (43.4498)
Nlocal: 105 ave 110 max 100 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 84 ave 89 max 79 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 895 ave 900 max 890 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 2
Dangerous builds = 0
fix 4 all indent 5000.0 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 2.13359 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
38 0 -3.1909329 0 -2.1718641 -0.69556621 435.59976
40 0 -3.169091 0 -2.8877594 -0.46675955 435.59973
50 0 -3.1711852 0 -3.1696057 -0.33713462 435.60143
60 0 -3.1780204 0 -3.1769046 -0.33322968 435.79292
70 0 -3.1800811 0 -3.1793038 -0.26556467 435.79292
80 0 -3.1809088 0 -3.1801828 -0.19926217 435.79292
90 0 -3.1811924 0 -3.1805002 -0.14442628 434.68835
100 0 -3.1812635 0 -3.1805822 -0.12227185 434.68835
103 0 -3.1812545 0 -3.180591 -0.12009024 434.68835
Loop time of 0.196576 on 4 procs for 65 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -2.17186 -3.18059 -3.18059
Gradient 2-norm init/final= 1621.12 0.469022
Gradient inf-norm init/final= 1193.11 0.272199
Iterations = 65
Force evaluations = 211
Pair time (%) = 0.0115743 (5.88792)
Neigh time (%) = 0.000268996 (0.13684)
Comm time (%) = 0.0783743 (39.8696)
Outpt time (%) = 0.0115461 (5.87361)
Other time (%) = 0.0948128 (48.232)
Nlocal: 105 ave 112 max 100 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 87 ave 89 max 83 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 896.5 ave 1006 max 797 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 3586
Ave neighs/atom = 8.5381
Neighbor list builds = 5
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 2.13366 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
103 0 -3.1812545 0 -0.21951029 -0.1202861 433.98055
110 0 -2.9284097 0 -2.6466557 2.0617709 433.9793
120 0 -3.0511214 0 -3.0267128 1.4983726 433.97719
130 0 -3.0919408 0 -3.0831141 1.2624464 434.23068
140 0 -3.1001312 0 -3.0930458 1.209277 434.23068
150 0 -3.102631 0 -3.0950311 1.2237232 434.73394
160 0 -3.1037978 0 -3.09648 1.3260564 431.60915
170 0 -3.1041785 0 -3.0969724 1.3941622 431.60915
180 0 -3.1042622 0 -3.0971039 1.4149115 431.60915
186 0 -3.1042077 0 -3.0971259 1.4187834 431.60915
Loop time of 0.257513 on 4 procs for 83 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -0.21951 -3.09712 -3.09713
Gradient 2-norm init/final= 1753.54 0.525185
Gradient inf-norm init/final= 923.56 0.20363
Iterations = 83
Force evaluations = 279
Pair time (%) = 0.0152845 (5.93545)
Neigh time (%) = 0.0005458 (0.211951)
Comm time (%) = 0.105214 (40.8577)
Outpt time (%) = 0.0132536 (5.14678)
Other time (%) = 0.123215 (47.8481)
Nlocal: 105 ave 110 max 99 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 95 ave 96 max 93 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 910.5 ave 990 max 829 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3642
Ave neighs/atom = 8.67143
Neighbor list builds = 11
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 2.13366 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
186 0 -3.1042077 0 1.9876467 1.4209266 430.95816
190 0 -2.7684954 0 -1.1554028 4.1104961 430.51479
200 0 -2.7738026 0 -2.6431045 4.5613937 435.03877
210 0 -2.892911 0 -2.863976 3.765261 442.55285
220 0 -2.9428319 0 -2.9275563 3.3111711 447.69227
230 0 -2.9566576 0 -2.9427828 3.183237 451.95964
240 0 -2.9622154 0 -2.9537038 3.0997525 453.12625
250 0 -2.9685121 0 -2.9588966 3.0016498 455.11967
260 0 -2.9851957 0 -2.9793281 2.7575287 455.75205
270 0 -3.0137593 0 -3.0035449 2.449694 453.80579
280 0 -3.0182039 0 -3.0121893 2.3442266 454.59869
290 0 -3.0271401 0 -3.0194953 2.053625 459.16264
300 0 -3.0332671 0 -3.0255652 2.059571 459.16264
310 0 -3.0346445 0 -3.0270706 2.0755976 456.56027
320 0 -3.0355796 0 -3.0277669 2.0482597 456.56027
330 0 -3.0359691 0 -3.0280778 2.0154636 456.56027
340 0 -3.0358963 0 -3.0281771 1.9966785 456.56027
350 0 -3.0359324 0 -3.0282261 1.9824739 456.56027
Loop time of 0.532273 on 4 procs for 164 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = 1.98765 -3.02822 -3.02823
Gradient 2-norm init/final= 2323.65 0.605548
Gradient inf-norm init/final= 1037.31 0.149724
Iterations = 164
Force evaluations = 579
Pair time (%) = 0.0322834 (6.06519)
Neigh time (%) = 0.00126213 (0.23712)
Comm time (%) = 0.218928 (41.1307)
Outpt time (%) = 0.0269612 (5.0653)
Other time (%) = 0.252839 (47.5017)
Nlocal: 105 ave 110 max 100 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 97.5 ave 103 max 92 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 947.25 ave 1037 max 853 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3789
Ave neighs/atom = 9.02143
Neighbor list builds = 25
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 2.1337 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
350 0 -3.0359324 0 6.9766773 1.9786928 457.43272
360 0 -2.335093 0 -1.5707757 7.5510255 457.43998
370 0 -2.5599881 0 -2.4347597 6.4272915 457.91764
380 0 -2.7844215 0 -2.7584649 4.9001975 463.20184
390 0 -2.8656166 0 -2.8440742 4.2220787 464.98354
400 0 -2.9109956 0 -2.8923852 3.609659 468.48088
410 0 -2.9467505 0 -2.9334194 3.2108178 471.50864
420 0 -2.9744266 0 -2.9577148 3.1040552 470.74252
430 0 -2.9926466 0 -2.9736421 2.954598 471.59623
440 0 -2.9975379 0 -2.9801201 2.8913452 471.28684
450 0 -2.9996147 0 -2.9820225 2.8472573 472.36037
460 0 -2.9987772 0 -2.9829659 2.8129364 472.36037
470 0 -2.9988242 0 -2.984577 2.645832 473.75442
480 0 -3.0028611 0 -2.9903017 2.3005134 478.93214
490 0 -3.0065053 0 -2.994241 2.1434534 481.91632
500 0 -3.0101863 0 -2.997213 1.9981452 484.51804
510 0 -3.0141308 0 -3.0026782 1.8875017 486.09135
520 0 -3.016887 0 -3.0072286 1.8425613 486.25796
530 0 -3.0268257 0 -3.0179688 1.7806625 488.6896
540 0 -3.0327843 0 -3.0231488 1.7139694 488.6896
550 0 -3.0367114 0 -3.0272129 1.6635813 490.88644
560 0 -3.0416842 0 -3.0327314 1.6227923 491.57531
570 0 -3.0427518 0 -3.0338239 1.6110728 491.67857
580 0 -3.0441228 0 -3.0350202 1.5954365 490.32292
590 0 -3.0451747 0 -3.0365103 1.5821495 489.47103
600 0 -3.0459148 0 -3.0370886 1.5554566 489.47103
610 0 -3.0467598 0 -3.0376733 1.5248062 489.47103
620 0 -3.0478594 0 -3.0383087 1.4861327 491.72302
630 0 -3.049164 0 -3.0394832 1.4414188 492.07812
Loop time of 0.908247 on 4 procs for 280 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = 6.97668 -3.03933 -3.03948
Gradient 2-norm init/final= 3559.61 5.36456
Gradient inf-norm init/final= 1438.88 1.92793
Iterations = 280
Force evaluations = 1001
Pair time (%) = 0.0553258 (6.0915)
Neigh time (%) = 0.00230616 (0.253914)
Comm time (%) = 0.37568 (41.3632)
Outpt time (%) = 0.0444704 (4.89629)
Other time (%) = 0.430465 (47.3951)
Nlocal: 105 ave 121 max 91 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 92.5 ave 100 max 85 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 926.25 ave 1120 max 713 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 3705
Ave neighs/atom = 8.82143
Neighbor list builds = 45
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 2.13417 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
630 0 -3.049164 0 -2.6055395 1.4407137 492.31894
640 0 -2.9649975 0 -2.9343234 2.3582078 492.33219
650 0 -2.9752101 0 -2.9533487 2.332525 492.9171
660 0 -2.9831117 0 -2.9657992 2.3325621 491.8941
670 0 -2.9882854 0 -2.973258 2.3854087 491.08948
680 0 -2.9949851 0 -2.9787092 2.3588144 490.19902
690 0 -3.0018179 0 -2.9844849 2.3054542 489.23828
700 0 -3.0037328 0 -2.9866112 2.2732947 489.64495
710 0 -3.0036981 0 -2.9872548 2.2790001 489.64495
720 0 -3.0037586 0 -2.9874991 2.2976654 489.14253
730 0 -3.003966 0 -2.9876811 2.3010688 489.14253
740 0 -3.0042756 0 -2.9878462 2.3085029 489.14253
750 0 -3.0042803 0 -2.9882934 2.3139843 488.81187
760 0 -3.0045102 0 -2.9884423 2.311861 488.51868
770 0 -3.0045801 0 -2.9885408 2.3084529 488.51868
777 0 -3.0047746 0 -2.9886028 2.3027508 488.51868
Loop time of 0.455153 on 4 procs for 147 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -2.60554 -2.9886 -2.9886
Gradient 2-norm init/final= 417.28 0.769176
Gradient inf-norm init/final= 169.788 0.25824
Iterations = 147
Force evaluations = 497
Pair time (%) = 0.0273476 (6.00845)
Neigh time (%) = 0.00065726 (0.144404)
Comm time (%) = 0.185723 (40.8046)
Outpt time (%) = 0.0233747 (5.13558)
Other time (%) = 0.21805 (47.907)
Nlocal: 105 ave 121 max 88 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 93.75 ave 102 max 84 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 952.75 ave 1150 max 759 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3811
Ave neighs/atom = 9.07381
Neighbor list builds = 13
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1000 1000
Memory usage per processor = 2.13417 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
777 0 -3.0047746 0 -2.4275389 2.30245 488.58251
780 0 -2.8947662 0 -2.7648906 3.2760992 488.58313
790 0 -2.8922178 0 -2.8552572 3.4749184 488.9907
800 0 -2.8997038 0 -2.8712066 3.4796289 489.36909
810 0 -2.902176 0 -2.8782065 3.4881184 489.89618
820 0 -2.9099852 0 -2.8915034 3.3342713 494.333
830 0 -2.9249749 0 -2.9075095 3.0348623 503.7551
840 0 -2.9421895 0 -2.9248611 2.5885038 511.66066
850 0 -2.9705134 0 -2.9566027 2.1604402 512.29096
860 0 -2.983166 0 -2.9715288 2.0550965 512.09303
870 0 -3.0022956 0 -2.9944909 2.0352125 509.02455
880 0 -3.0257602 0 -3.018125 1.8448712 510.86529
890 0 -3.0342452 0 -3.0255002 1.761039 510.97044
900 0 -3.0406548 0 -3.0316303 1.6443602 513.37976
910 0 -3.0517632 0 -3.0426532 1.4576879 514.63201
920 0 -3.0637404 0 -3.0545929 1.3334284 515.50851
930 0 -3.0683969 0 -3.0596546 1.3370449 515.29221
940 0 -3.0723501 0 -3.0632848 1.3237846 515.11444
950 0 -3.0738054 0 -3.0651295 1.3308782 515.95396
960 0 -3.0747293 0 -3.0657364 1.3207014 515.95396
970 0 -3.0750994 0 -3.0660707 1.3073068 516.11446
980 0 -3.0751645 0 -3.0661973 1.3050625 516.11446
985 0 -3.0751453 0 -3.0662144 1.3067705 516.11446
Loop time of 0.708511 on 4 procs for 208 steps with 420 atoms
Minimization stats:
E initial, next-to-last, final = -2.42754 -3.06621 -3.06621
Gradient 2-norm init/final= 483.567 0.68513
Gradient inf-norm init/final= 212.61 0.339518
Iterations = 208
Force evaluations = 766
Pair time (%) = 0.0414512 (5.85046)
Neigh time (%) = 0.00191033 (0.269626)
Comm time (%) = 0.294369 (41.5476)
Outpt time (%) = 0.0348218 (4.91479)
Other time (%) = 0.335958 (47.4175)
Nlocal: 105 ave 128 max 80 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 94 ave 108 max 81 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 894.75 ave 1160 max 631 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3579
Ave neighs/atom = 8.52143
Neighbor list builds = 38
Dangerous builds = 0

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@ -1,4 +1,4 @@
LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# Test of MEAM potential for SiC system
units metal
@ -37,13 +37,13 @@ Step Temp E_pair E_mol TotEng Press
80 2111.2748 -671.75001 0 -637.09124 -100964.78
90 2087.3167 -671.34241 0 -637.07694 -95316.087
100 1990.2171 -669.74712 0 -637.07564 -97755.737
Loop time of 0.127874 on 1 procs for 100 steps with 128 atoms
Loop time of 0.127763 on 1 procs for 100 steps with 128 atoms
Pair time (%) = 0.120988 (94.6152)
Neigh time (%) = 0.00319433 (2.49803)
Comm time (%) = 0.000864983 (0.676433)
Outpt time (%) = 0.00216031 (1.6894)
Other time (%) = 0.000666142 (0.520935)
Pair time (%) = 0.120687 (94.4612)
Neigh time (%) = 0.00334096 (2.61497)
Comm time (%) = 0.000868797 (0.680007)
Outpt time (%) = 0.00215125 (1.68378)
Other time (%) = 0.000715494 (0.560017)
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0

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@ -1,4 +1,4 @@
LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# Test of MEAM potential for SiC system
units metal
@ -37,13 +37,13 @@ Step Temp E_pair E_mol TotEng Press
80 2111.2748 -671.75001 0 -637.09124 -100964.78
90 2087.3167 -671.34241 0 -637.07694 -95316.087
100 1990.2171 -669.74712 0 -637.07564 -97755.737
Loop time of 0.164812 on 4 procs for 100 steps with 128 atoms
Loop time of 0.143319 on 4 procs for 100 steps with 128 atoms
Pair time (%) = 0.107879 (65.4556)
Neigh time (%) = 0.00101417 (0.61535)
Comm time (%) = 0.0441561 (26.7918)
Outpt time (%) = 0.0102268 (6.20515)
Other time (%) = 0.00153625 (0.932121)
Pair time (%) = 0.100818 (70.3452)
Neigh time (%) = 0.00115442 (0.805489)
Comm time (%) = 0.0315838 (22.0374)
Outpt time (%) = 0.00841707 (5.87294)
Other time (%) = 0.00134581 (0.93903)
Nlocal: 32 ave 35 max 29 min
Histogram: 1 0 0 1 0 0 1 0 0 1

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LAMMPS (21 May 2008)
# 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
timestep 0.001
run 100
Memory usage per processor = 6.09291 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 2.46606 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 2.43238 (98.6343)
Neigh time (%) = 0.0218449 (0.885821)
Comm time (%) = 0.00250888 (0.101736)
Outpt time (%) = 0.00022912 (0.00929095)
Other time (%) = 0.00909543 (0.368825)
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
reset_timestep 0
run 3000
Memory usage per processor = 6.34243 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300.50853 -8173.6884 0 -8137.8874 4994.9251 19886.554
100 292.0799 -8177.7235 0 -8142.9266 2567.6871 19863.778
200 306.71233 -8177.1504 0 -8140.6103 873.12617 20039.427
300 295.7806 -8172.9505 0 -8137.7127 -1054.1773 20083.875
400 309.18439 -8169.6374 0 -8132.8028 -1785.2352 20114.391
500 304.51122 -8163.9147 0 -8127.6369 -160.33189 20175.64
600 300 -8158.55 0 -8122.8096 1555.8342 20272.069
700 304.32794 -8149.4746 0 -8113.2185 3702.0205 20422.656
800 304.79621 -8138.8368 0 -8102.5249 3723.0289 20502.876
900 303.87706 -8128.16 0 -8091.9576 4388.821 20631.103
1000 300 -8113.4908 0 -8077.7503 6189.061 20747.117
1100 306.13486 -8097.1731 0 -8060.7018 8908.048 20871.68
1200 309.15672 -8081.8589 0 -8045.0276 10527.674 20988.916
1300 304.48415 -8064.5597 0 -8028.2851 10066.833 21118.364
1400 300 -8046.7607 0 -8011.0202 10976.597 21230.714
1500 300 -8041.3546 0 -8005.6141 11944.044 21366.268
1600 309.6032 -8035.2271 0 -7998.3426 11344.41 21522.036
1700 300 -8029.1688 0 -7993.4283 11303.056 21627.406
1800 300 -8034.2227 0 -7998.4823 9636.4113 21728.966
1900 307.85809 -8037.1065 0 -8000.4299 6167.5234 21849.865
2000 307.80945 -8029.9525 0 -7993.2817 3167.2857 22004.862
2100 300 -8032.7568 0 -7997.0163 1297.8408 22098.991
2200 300 -8042.2274 0 -8006.4869 1686.5561 22223.554
2300 309.41797 -8041.3421 0 -8004.4797 3429.6069 22335.905
2400 300 -8035.9622 0 -8000.2218 5397.5468 22461.689
2500 300 -8037.3252 0 -8001.5848 7036.8769 22589.915
2600 299.69899 -8035.7903 0 -8000.0857 9345.3265 22710.815
2700 300 -8037.7061 0 -8001.9657 8732.1782 22834.156
2800 300 -8039.9073 0 -8004.1669 8048.8501 22956.277
2900 300 -8039.6401 0 -8003.8996 7057.3819 23069.849
3000 300 -8038.195 0 -8002.4546 3400.007 23199.297
Loop time of 78.1257 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 76.7401 (98.2264)
Neigh time (%) = 0.942761 (1.20672)
Comm time (%) = 0.0805891 (0.103153)
Outpt time (%) = 0.0842321 (0.107816)
Other time (%) = 0.27803 (0.355876)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1657 ave 1657 max 1657 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23426 ave 23426 max 23426 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 46852 ave 46852 max 46852 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46852
Ave neighs/atom = 24.5042
Neighbor list builds = 221
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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
timestep 0.001
run 100
Memory usage per processor = 5.32801 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 0.738111 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.680541 (92.2004)
Neigh time (%) = 0.00550801 (0.74623)
Comm time (%) = 0.039358 (5.33226)
Outpt time (%) = 0.00177252 (0.240143)
Other time (%) = 0.0109315 (1.48101)
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
reset_timestep 0
run 3000
Memory usage per processor = 5.38726 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 292.28828 -8178.2806 0 -8143.4589 2992.7013 19964.244
100 301.02661 -8174.1628 0 -8138.3 441.39614 19947.951
200 290.97251 -8175.7136 0 -8141.0487 -438.32628 19981.719
300 304.4239 -8173.5555 0 -8137.288 -2447.7976 20067.185
400 305.76192 -8168.2982 0 -8131.8713 -814.70984 20153.166
500 304.73368 -8164.7296 0 -8128.4252 -963.99012 20227.497
600 300.12426 -8157.4957 0 -8121.7405 39.926198 20299.368
700 301.07583 -8150.7214 0 -8114.8528 2178.1731 20419.159
800 297.37471 -8139.56 0 -8104.1323 4209.733 20518.203
900 304.4007 -8127.6685 0 -8091.4038 6132.0576 20631.103
1000 306.98916 -8112.2064 0 -8075.6333 8585.8087 20758.108
1100 303.05268 -8097.0258 0 -8060.9217 9885.1628 20871.68
1200 300.37461 -8081.159 0 -8045.3739 9988.7374 20999.907
1300 307.55251 -8065.2275 0 -8028.5873 10516.036 21126.912
1400 303.2639 -8051.2915 0 -8015.1623 11668.072 21235.599
1500 300 -8039.6298 0 -8003.8893 12498.158 21361.383
1600 300 -8032.3339 0 -7996.5935 13558.655 21487.167
1700 300 -8021.6093 0 -7985.8689 13720.955 21608.067
1800 300 -8013.5338 0 -7977.7933 10671.999 21727.745
1900 300 -8014.5802 0 -7978.8398 6968.6003 21849.865
2000 300 -8026.6569 0 -7990.9165 3269.3318 21974.428
2100 300 -8033.1 0 -7997.3596 1537.5367 22102.655
2200 307.34939 -8028.6438 0 -7992.0278 3817.2972 22222.333
2300 300 -8027.8628 0 -7992.1223 3499.1613 22348.117
2400 300 -8035.3356 0 -7999.5951 2942.2954 22465.353
2500 303.62876 -8038.272 0 -8002.0993 1597.5261 22581.367
2600 300 -8036.5107 0 -8000.7702 2079.386 22714.478
2700 303.53313 -8037.4306 0 -8001.2693 1401.19 22832.935
2800 300 -8036.0227 0 -8000.2823 686.67133 22953.834
2900 300 -8033.2512 0 -7997.5108 76.040969 23067.406
3000 300 -8032.7731 0 -7997.0327 -170.54788 23202.96
Loop time of 23.4772 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 21.6076 (92.0366)
Neigh time (%) = 0.240626 (1.02493)
Comm time (%) = 1.2278 (5.22976)
Outpt time (%) = 0.10237 (0.436041)
Other time (%) = 0.298776 (1.27262)
Nlocal: 478 ave 516 max 442 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 787.25 ave 825 max 752 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 5769.5 ave 6126 max 5446 min
Histogram: 1 0 0 1 0 1 0 0 0 1
FullNghs: 11539 ave 12266 max 10876 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 46156
Ave neighs/atom = 24.1402
Neighbor list builds = 222
Dangerous builds = 0

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@ -1,163 +0,0 @@
LAMMPS (22 Jan 2008)
# 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
timestep 0.001
run 100
Memory usage per processor = 6.09291 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 2.46093 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 2.42762 (98.6468)
Neigh time (%) = 0.0215614 (0.87615)
Comm time (%) = 0.00257206 (0.104516)
Outpt time (%) = 0.000188828 (0.00767303)
Other time (%) = 0.00897908 (0.364866)
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
reset_timestep 0
run 3000
Memory usage per processor = 6.34243 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300.50853 -8173.6884 0 -8137.8874 4994.9251 19886.554
100 292.43462 -8178.5214 0 -8143.6823 2595.8245 19846.142
200 302.79029 -8177.5966 0 -8141.5238 928.09995 20038.569
300 291.68573 -8173.4974 0 -8138.7474 -1202.8487 20113.221
400 300 -8170.0629 0 -8134.3225 -1617.1537 20115.738
500 308.49792 -8164.7324 0 -8127.9796 -346.62656 20250.005
600 308.95879 -8159.1257 0 -8122.3179 1160.1349 20280.432
700 303.02599 -8150.2418 0 -8114.1409 2807.9227 20434.583
800 305.36804 -8140.8077 0 -8104.4278 3218.2338 20500.434
900 305.593 -8128.943 0 -8092.5363 3121.7248 20628.661
1000 308.39114 -8113.6413 0 -8076.9012 5180.0491 20758.108
1100 304.62199 -8096.7999 0 -8060.5088 8173.3445 20874.123
1200 293.41155 -8082.676 0 -8047.7205 9884.2082 20987.695
1300 303.32764 -8066.7733 0 -8030.6364 10196.38 21108.594
1400 304.17524 -8049.5115 0 -8013.2736 11518.936 21249.033
1500 300 -8038.1747 0 -8002.4343 12554.565 21361.383
1600 304.95664 -8030.581 0 -7994.25 12166.265 21483.504
1700 302.82085 -8019.1918 0 -7983.1153 11726.892 21604.403
1800 300 -8010.2023 0 -7974.4619 11039.364 21737.514
1900 309.75521 -7999.8484 0 -7962.9457 10360.853 21859.635
2000 304.01114 -7995.6108 0 -7959.3925 11104.967 21974.428
2100 300 -7998.317 0 -7962.5766 9661.15 22094.106
2200 300 -8008.5986 0 -7972.8581 7070.9315 22225.996
2300 300 -8012.1558 0 -7976.4153 6974.7608 22346.896
2400 309.62904 -8011.7107 0 -7974.8232 9446.6153 22470.237
2500 295.33175 -8007.0125 0 -7971.8282 10709.603 22576.482
2600 300 -8012.3194 0 -7976.579 9761.1868 22698.603
2700 300.71244 -8007.8295 0 -7972.0042 12262.62 22821.944
2800 306.97204 -8005.1205 0 -7968.5494 12418.816 22950.171
2900 300 -8004.8006 0 -7969.0601 10851.969 23074.734
3000 300 -8004.2168 0 -7968.4764 10301.261 23202.96
Loop time of 78.1421 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 76.7955 (98.2767)
Neigh time (%) = 0.911251 (1.16615)
Comm time (%) = 0.0806024 (0.103148)
Outpt time (%) = 0.0821629 (0.105145)
Other time (%) = 0.272587 (0.348835)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1661 ave 1661 max 1661 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23451 ave 23451 max 23451 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 46902 ave 46902 max 46902 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46902
Ave neighs/atom = 24.5303
Neighbor list builds = 216
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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
timestep 0.001
run 100
Memory usage per processor = 5.32801 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 0.743105 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.686752 (92.4165)
Neigh time (%) = 0.0055545 (0.747471)
Comm time (%) = 0.0390352 (5.25299)
Outpt time (%) = 0.00166398 (0.223923)
Other time (%) = 0.0100994 (1.35907)
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
reset_timestep 0
run 3000
Memory usage per processor = 5.38726 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 292.28828 -8178.2806 0 -8143.4589 2992.7013 19964.244
100 304.48468 -8173.0606 0 -8136.7859 425.54216 19949.638
200 292.7057 -8176.0355 0 -8141.1641 -420.37567 19967.921
300 300 -8174.2457 0 -8138.5052 -2225.0957 20035.454
400 301.8783 -8169.8228 0 -8133.8586 -954.54062 20072.806
500 297.3529 -8163.9704 0 -8128.5453 -636.90863 20224.627
600 300.21575 -8158.4937 0 -8122.7275 426.04354 20300.212
700 294.62668 -8149.3419 0 -8114.2416 2914.3315 20397.69
800 297.68293 -8140.221 0 -8104.7566 4382.9813 20500.434
900 307.34872 -8129.6288 0 -8093.0129 6273.2975 20626.218
1000 299.54856 -8114.9745 0 -8079.2878 9036.1509 20758.108
1100 298.61047 -8098.7531 0 -8063.1782 10485.79 20872.901
1200 293.03092 -8082.1069 0 -8047.1967 11405.523 21004.792
1300 307.76804 -8065.4274 0 -8028.7615 11979.925 21120.806
1400 300 -8051.592 0 -8015.8516 12466.401 21238.042
1500 308.53325 -8037.7116 0 -8000.9546 15186.116 21363.826
1600 300 -8031.8572 0 -7996.1168 16229.517 21487.167
1700 300 -8022.9422 0 -7987.2018 18187.816 21605.624
1800 300 -8009.2383 0 -7973.4979 18721.492 21735.072
1900 300.25537 -7997.9537 0 -7962.1828 18854.857 21848.644
2000 300 -7987.6026 0 -7951.8622 18713.498 21976.871
2100 300 -7996.2028 0 -7960.4624 16426.801 22100.212
2200 306.21818 -8006.9292 0 -7970.448 13195.382 22211.342
2300 300 -8010.9873 0 -7975.2468 11233.26 22342.011
2400 300 -8015.0713 0 -7979.3308 12014.401 22456.804
2500 300 -8015.6198 0 -7979.8793 11824.876 22578.925
2600 305.67337 -8008.4547 0 -7972.0384 11729.677 22705.93
2700 304.98465 -8007.1197 0 -7970.7855 9757.3741 22832.935
2800 300 -8008.3745 0 -7972.6341 8658.7198 22953.834
2900 300 -8007.6958 0 -7971.9554 7167.5651 23068.628
3000 300 -8007.8744 0 -7972.134 6613.2779 23202.96
Loop time of 23.8465 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 21.9333 (91.9771)
Neigh time (%) = 0.240415 (1.00818)
Comm time (%) = 1.26714 (5.31376)
Outpt time (%) = 0.113929 (0.477759)
Other time (%) = 0.291683 (1.22317)
Nlocal: 478 ave 517 max 446 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 784.5 ave 838 max 736 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 5844.5 ave 6271 max 5655 min
Histogram: 2 1 0 0 0 0 0 0 0 1
FullNghs: 11689 ave 12514 max 11309 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Total # of neighbors = 46756
Ave neighs/atom = 24.454
Neighbor list builds = 223
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# 3d Lennard-Jones melt
units lj
@ -36,13 +36,13 @@ Step Temp E_pair E_mol TotEng Press
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 1.26243 on 1 procs for 250 steps with 4000 atoms
Loop time of 1.2689 on 1 procs for 250 steps with 4000 atoms
Pair time (%) = 1.06787 (84.5881)
Neigh time (%) = 0.11483 (9.0959)
Comm time (%) = 0.020905 (1.65593)
Outpt time (%) = 0.028095 (2.22547)
Other time (%) = 0.0307348 (2.43457)
Pair time (%) = 1.07107 (84.4098)
Neigh time (%) = 0.116847 (9.20853)
Comm time (%) = 0.020932 (1.64962)
Outpt time (%) = 0.0287478 (2.26557)
Other time (%) = 0.0312967 (2.46645)
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

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LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# 3d Lennard-Jones melt
units lj
@ -36,13 +36,13 @@ Step Temp E_pair E_mol TotEng Press
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 0.504289 on 4 procs for 250 steps with 4000 atoms
Loop time of 0.505746 on 4 procs for 250 steps with 4000 atoms
Pair time (%) = 0.275774 (54.6857)
Neigh time (%) = 0.029693 (5.88809)
Comm time (%) = 0.153954 (30.5289)
Outpt time (%) = 0.0334665 (6.63636)
Other time (%) = 0.0114021 (2.26103)
Pair time (%) = 0.277338 (54.8375)
Neigh time (%) = 0.0297899 (5.89028)
Comm time (%) = 0.156375 (30.9197)
Outpt time (%) = 0.032173 (6.36149)
Other time (%) = 0.0100698 (1.99108)
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2

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LAMMPS (21 May 2008)
# 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 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 1.0 20.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all enforce2d
thermo 50
run 1000
Memory usage per processor = 1.84502 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 0.300502 on 1 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.202995 (67.5518)
Bond time (%) = 0.0206611 (6.87553)
Neigh time (%) = 0.0275362 (9.16338)
Comm time (%) = 0.00611711 (2.03563)
Outpt time (%) = 0.000581026 (0.193352)
Other time (%) = 0.0426121 (14.1803)
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
# 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 = 1.8908 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727615 0.058604601 -1.4645319 1.9982028
2000 0.43716482 -1.9789902 0.064175291 -1.4780144 1.8178005
3000 0.4652974 -2.0238585 0.067406181 -1.4915426 1.5369016
4000 0.4450276 -2.0120252 0.05904261 -1.5083259 1.4795779
5000 0.44249516 -2.0326528 0.06825332 -1.5222731 1.3463285
6000 0.44359067 -2.0236106 0.05661929 -1.5237703 1.2336671
7000 0.44829871 -2.053872 0.064049461 -1.5418974 1.2077943
8000 0.43835338 -2.0295717 0.063594195 -1.5279894 1.2702884
9000 0.46137509 -2.0331381 0.057420617 -1.5147269 1.293388
10000 0.45864575 -2.0647458 0.061160344 -1.5453219 1.091648
11000 0.43028298 -2.0528287 0.065356685 -1.5575476 1.0832846
12000 0.43770429 -2.0600447 0.06341501 -1.5592902 1.0777045
13000 0.46155652 -2.0506356 0.056176366 -1.5332873 1.2535564
14000 0.45157492 -2.0609489 0.061187063 -1.5485632 1.0797813
15000 0.46860396 -2.0810829 0.05900275 -1.5538667 1.0154193
16000 0.44657573 -2.0585991 0.064727245 -1.5476683 0.98186948
17000 0.43577692 -2.085853 0.064116312 -1.5863229 1.1138878
18000 0.45579186 -2.0928391 0.052663191 -1.5847639 0.77972989
19000 0.4638413 -2.1035558 0.05809772 -1.5820034 0.86184682
20000 0.44419341 -2.0904971 0.062276482 -1.5843973 0.71988805
21000 0.45600607 -2.097995 0.059849246 -1.5825197 0.78614854
22000 0.45943121 -2.1073469 0.061572162 -1.5867264 0.9111383
23000 0.45 -2.1088733 0.057406786 -1.6018415 0.68127639
24000 0.45200935 -2.0902016 0.065206229 -1.5733627 0.99578038
25000 0.45559026 -2.1000506 0.057458439 -1.5873816 0.76154574
26000 0.46839853 -2.1048288 0.056806361 -1.5800142 0.72250339
27000 0.45 -2.1126221 0.053370375 -1.6096267 0.78695915
28000 0.43926352 -2.0999927 0.060587004 -1.6005082 0.90396399
29000 0.44741081 -2.1167559 0.062267017 -1.6074509 0.72496134
30000 0.46565548 -2.1194308 0.057631518 -1.5965319 0.73222696
31000 0.46058458 -2.1102085 0.059770604 -1.5902371 0.79790524
32000 0.45349363 -2.1192242 0.064718489 -1.60139 0.68868895
33000 0.43945922 -2.1211684 0.056117328 -1.6259581 0.6127229
34000 0.45789468 -2.111049 0.054210912 -1.599325 0.66682436
35000 0.455467 -2.1261824 0.06685345 -1.6042415 0.54820231
36000 0.46511205 -2.1208942 0.058276998 -1.5978928 0.59296374
37000 0.44640964 -2.1143213 0.057944638 -1.610339 0.77242592
38000 0.44596116 -2.0946988 0.062196767 -1.5869125 0.85606153
39000 0.45745534 -2.1044294 0.054075498 -1.5932798 0.7490514
40000 0.46774599 -2.1141735 0.055820661 -1.5909966 0.68263873
41000 0.45209942 -2.1154203 0.069314198 -1.5943835 0.6331387
42000 0.44276955 -2.115384 0.063045461 -1.6099379 0.65679589
43000 0.44312295 -2.1028092 0.051688553 -1.608367 0.64527919
44000 0.44136077 -2.1121431 0.06255545 -1.6085947 0.64301583
45000 0.45549493 -2.1256992 0.054358465 -1.6162254 0.65053568
46000 0.44968532 -2.1025103 0.064024111 -1.5891756 0.69878466
47000 0.45751017 -2.1003604 0.054572612 -1.5886589 0.73343046
48000 0.46590931 -2.1166285 0.052436194 -1.5986713 0.73090893
49000 0.45210574 -2.1253492 0.058665633 -1.6149546 0.54736011
50000 0.43629064 -2.1279448 0.069771465 -1.6222463 0.54429106
51000 0.46639828 -2.1138965 0.061298663 -1.5865882 0.64577651
52000 0.43831593 -2.1123621 0.057043795 -1.6173676 0.74662964
53000 0.43501137 -2.1127324 0.075592639 -1.6024909 0.80359868
54000 0.45696335 -2.1226029 0.062928151 -1.6030923 0.64671682
55000 0.43593702 -2.127708 0.064441586 -1.6276927 0.62960269
56000 0.44913808 -2.1093471 0.055492835 -1.6050905 0.85024228
57000 0.44265459 -2.103588 0.054688319 -1.606614 0.71936833
58000 0.46008975 -2.1189366 0.059119033 -1.6001112 0.6781833
59000 0.45675715 -2.1231353 0.061231406 -1.6055274 0.62271773
60000 0.45937135 -2.1293456 0.068515696 -1.6018413 0.52284735
Loop time of 25.3203 on 1 procs for 60000 steps with 1200 atoms
Pair time (%) = 17.7009 (69.908)
Bond time (%) = 1.21589 (4.80203)
Neigh time (%) = 3.06021 (12.086)
Comm time (%) = 0.564598 (2.22982)
Outpt time (%) = 0.203498 (0.803696)
Other time (%) = 2.5752 (10.1705)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 425 ave 425 max 425 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9874 ave 9874 max 9874 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9874
Ave neighs/atom = 8.22833
Ave special neighs/atom = 0.5
Neighbor list builds = 4884
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 1.0 20.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all enforce2d
thermo 50
run 1000
Memory usage per processor = 2.07665 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 0.451741 on 4 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.055 (12.1751)
Bond time (%) = 0.0054844 (1.21406)
Neigh time (%) = 0.00761467 (1.68563)
Comm time (%) = 0.312935 (69.273)
Outpt time (%) = 0.00906777 (2.0073)
Other time (%) = 0.0616394 (13.6449)
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
# 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 = 2.08829 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727838 0.058618121 -1.4645407 1.9980741
2000 0.45 -2.0008971 0.06046133 -1.4908107 1.7505633
3000 0.46857989 -2.0062096 0.062600297 -1.4754199 1.4580464
4000 0.46655193 -2.0452235 0.063633136 -1.5154273 1.2266944
5000 0.44844443 -2.0305619 0.061707001 -1.5207842 1.2735298
6000 0.45 -2.0580878 0.062213978 -1.5462488 1.0224016
7000 0.4476022 -2.0378426 0.054638368 -1.535975 1.1284476
8000 0.4468407 -2.0267685 0.06891916 -1.511381 1.3309425
9000 0.45741983 -2.0597667 0.060064672 -1.5426633 1.0676372
10000 0.45865753 -2.0646248 0.063101783 -1.5432477 1.0898972
11000 0.4544539 -2.0523068 0.052930956 -1.5453006 1.0855721
12000 0.4495638 -2.0587133 0.058599459 -1.5509247 1.0857171
13000 0.46433272 -2.090385 0.059665091 -1.5667742 0.97090005
14000 0.44532862 -2.0655988 0.059393868 -1.5612474 1.1164806
15000 0.45523926 -2.0718246 0.056724666 -1.56024 1.0877035
16000 0.46244762 -2.0767037 0.064385121 -1.5502564 0.98812624
17000 0.46314908 -2.0857805 0.067070535 -1.5559468 0.94844275
18000 0.45 -2.1004858 0.062440373 -1.5884204 0.7444894
19000 0.45461444 -2.0745504 0.065328927 -1.5549859 0.9810655
20000 0.43132218 -2.0810153 0.063878005 -1.5861745 1.0115249
21000 0.45278155 -2.0976147 0.061040123 -1.5841704 0.87450921
22000 0.4413178 -2.0849706 0.05514809 -1.5888725 0.86794005
23000 0.4514062 -2.0698222 0.061531604 -1.5572605 1.0659691
24000 0.44685643 -2.0970941 0.057566091 -1.593044 0.88412737
25000 0.45304563 -2.1059193 0.067469611 -1.5857816 0.75590379
26000 0.43665864 -2.0781503 0.060302863 -1.5815527 1.0518426
27000 0.439842 -2.0820662 0.055355535 -1.5872352 1.02679
28000 0.45421836 -2.0958012 0.068552595 -1.5734087 0.93876409
29000 0.46710017 -2.0981517 0.054218079 -1.5772227 0.89764204
30000 0.43140661 -2.0930753 0.05639766 -1.6056305 0.75868765
31000 0.46278553 -2.1008921 0.05712374 -1.5813685 0.82007867
32000 0.46400002 -2.1263545 0.063574225 -1.599167 0.67935923
33000 0.43939072 -2.0940879 0.061376643 -1.5936867 0.78873715
34000 0.45175636 -2.1132311 0.062639359 -1.5992119 0.71670369
35000 0.44545357 -2.113453 0.065502953 -1.6028677 0.77337903
36000 0.43878041 -2.1101296 0.067575973 -1.6041389 0.5702654
37000 0.45726864 -2.0963464 0.063544674 -1.5759142 0.77408424
38000 0.46058278 -2.0960925 0.060468593 -1.5754249 0.91253803
39000 0.43612306 -2.088217 0.061585534 -1.5908718 0.80977481
40000 0.45643431 -2.1078785 0.061223384 -1.5906012 0.90050763
41000 0.45499013 -2.097803 0.060801097 -1.5823909 0.7724239
42000 0.44008414 -2.1073806 0.059385138 -1.6082781 0.76677042
43000 0.46520882 -2.1288778 0.053657089 -1.6103996 0.57206053
44000 0.44575963 -2.0863972 0.055762678 -1.5852464 0.92852911
45000 0.44272361 -2.1039527 0.05307631 -1.6085217 0.76464969
46000 0.44274241 -2.100733 0.065427251 -1.5929323 0.74550533
47000 0.44675956 -2.1111981 0.06130925 -1.6035016 0.72023447
48000 0.46850415 -2.1097324 0.052877281 -1.5887414 0.5836148
49000 0.46175146 -2.1056078 0.052122205 -1.5921189 0.73350989
50000 0.46143089 -2.0950096 0.05966393 -1.5742993 0.79335455
51000 0.44992091 -2.1092625 0.055443473 -1.604273 0.71374923
52000 0.44053251 -2.0903005 0.054677072 -1.595458 0.7414373
53000 0.44967972 -2.1071504 0.057337448 -1.6005079 0.63579953
54000 0.45717923 -2.1109235 0.055545674 -1.5985796 0.60432994
55000 0.4672155 -2.1209866 0.051378124 -1.6027823 0.70136422
56000 0.44691536 -2.1207875 0.058716627 -1.615528 0.72583043
57000 0.44378225 -2.1063669 0.056356727 -1.6065978 0.61593243
58000 0.44119675 -2.1123324 0.061570128 -1.6099332 0.80512516
59000 0.44879198 -2.0998451 0.052529358 -1.5988977 0.81118174
60000 0.46206126 -2.1178369 0.06448607 -1.5916746 0.63817566
Loop time of 30.5669 on 4 procs for 60000 steps with 1200 atoms
Pair time (%) = 4.76739 (15.5966)
Bond time (%) = 0.330764 (1.0821)
Neigh time (%) = 0.83275 (2.72435)
Comm time (%) = 20.1822 (66.0263)
Outpt time (%) = 0.245281 (0.80244)
Other time (%) = 4.20852 (13.7682)
Nlocal: 300 ave 304 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 207.5 ave 213 max 199 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 2404.5 ave 2529 max 2304 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 9618
Ave neighs/atom = 8.015
Ave special neighs/atom = 0.5
Neighbor list builds = 4886
Dangerous builds = 0

200
examples/micelle/log.micelle.22Jan08.linux.1
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@ -1,200 +0,0 @@
LAMMPS (22 Jan 2008)
# 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 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 1.0 20.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all enforce2d
thermo 50
run 1000
Memory usage per processor = 1.84502 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84947453 0.78935018
50 0.47417944 0.67716204 0.057387153 1.2081359 1.3374428
100 0.45 0.73037684 0.054821983 1.2346363 2.3192865
150 0.67532546 0.72388376 0.043478036 1.4418431 2.8741848
200 0.45 0.78466058 0.076912805 1.3110109 3.0409372
250 0.66488946 0.69771453 0.081047682 1.4428206 3.6911924
300 0.45 0.76794745 0.066716745 1.2841017 3.7855266
350 0.67629601 0.62549506 0.072636862 1.3735826 4.2848322
400 0.45 0.68493339 0.090717081 1.225088 4.4713609
450 0.56732174 0.64322231 0.080690687 1.2905256 4.7372687
500 0.45 0.64764573 0.078468194 1.1755514 4.7911172
550 0.56476697 0.58160926 0.080519682 1.22619 4.9721793
600 0.45 0.58331363 0.088243449 1.1209946 5.131088
650 0.5229482 0.54530348 0.09321673 1.1608147 5.2637478
700 0.45 0.52374674 0.085166964 1.0583512 5.2922505
750 0.51528063 0.48974532 0.086434828 1.0908167 5.3858022
800 0.45 0.50467091 0.090255509 1.0443639 5.5801625
850 0.4950534 0.48512921 0.091950432 1.0715142 5.6661389
900 0.45 0.48352312 0.097223467 1.0301841 5.7149691
950 0.49451225 0.46619517 0.094098428 1.0541877 5.8766965
1000 0.45 0.46260893 0.10106179 1.0131082 5.8616912
Loop time of 0.307229 on 1 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.209812 (68.2917)
Bond time (%) = 0.0206535 (6.72251)
Neigh time (%) = 0.0273674 (8.90781)
Comm time (%) = 0.00643349 (2.09404)
Outpt time (%) = 0.000555038 (0.18066)
Other time (%) = 0.0424075 (13.8032)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 193 ave 193 max 193 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3176 ave 3176 max 3176 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3176
Ave neighs/atom = 2.64667
Ave special neighs/atom = 0.5
Neighbor list builds = 93
Dangerous builds = 0
# 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 = 1.8908 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.6864322 0.10106179 -1.1359329 3.7913551
1000 0.44913703 -1.9350593 0.071369049 -1.4151147 2.1470317
2000 0.46990408 -1.9863161 0.065077829 -1.4519216 1.6695179
3000 0.45096845 -2.0130162 0.061423646 -1.5011878 1.5489907
4000 0.4496134 -1.9991224 0.056693551 -1.4933774 1.5523766
5000 0.45935435 -2.0241729 0.065531769 -1.499861 1.3256492
6000 0.45626587 -2.0230661 0.060868899 -1.5065016 1.4541788
7000 0.46322362 -2.0578954 0.058349198 -1.5369017 1.2398016
8000 0.45253301 -2.0527631 0.069121572 -1.5316742 1.1230521
9000 0.45 -2.0616322 0.059639854 -1.5525549 1.0931151
10000 0.45473743 -2.0680168 0.062865722 -1.5509821 1.0393117
11000 0.46282597 -2.0645336 0.061660553 -1.5406256 1.0473486
12000 0.45729042 -2.0903864 0.053745705 -1.5799219 0.99522961
13000 0.45 -2.0993317 0.063786977 -1.5861073 0.81046383
14000 0.44464915 -2.0836131 0.061515258 -1.5780045 0.91036442
15000 0.45077322 -2.1026035 0.064321304 -1.5880724 0.72445371
16000 0.43806107 -2.0796558 0.056496971 -1.5856453 0.81980005
17000 0.44674015 -2.0942208 0.060106495 -1.5879326 0.88506041
18000 0.4517901 -2.0923656 0.051892418 -1.5892478 0.88650049
19000 0.45452903 -2.1066926 0.064413446 -1.5883183 0.70616051
20000 0.46590873 -2.1035695 0.049979109 -1.588264 0.68424889
21000 0.46952716 -2.1025765 0.05919241 -1.5744438 0.70616051
22000 0.4439583 -2.1004401 0.064237519 -1.5927993 0.70386205
23000 0.43508823 -2.0895563 0.067366868 -1.5876451 0.78908122
24000 0.43586625 -2.0944908 0.061850537 -1.5973188 0.75354904
25000 0.46055804 -2.0980569 0.057842949 -1.5802316 0.78832968
26000 0.44612123 -2.0803277 0.057849021 -1.5769151 0.88337838
27000 0.44546513 -2.0816879 0.060389445 -1.5763901 0.85808583
28000 0.43991361 -2.1030181 0.059409891 -1.6042445 0.71982555
29000 0.44356162 -2.1096901 0.052709226 -1.6139737 0.64555675
30000 0.43167655 -2.0778243 0.063810749 -1.5828766 0.94008105
31000 0.46020547 -2.0996246 0.055929654 -1.5840647 0.78413535
32000 0.44053792 -2.1146449 0.066783802 -1.6078738 0.80809122
33000 0.46051154 -2.1125835 0.054178744 -1.5984689 0.63733653
34000 0.4385451 -2.09542 0.058510448 -1.5989126 0.65064895
35000 0.44884027 -2.1147487 0.062438249 -1.6040312 0.74279786
36000 0.45524152 -2.1236253 0.056937704 -1.6120151 0.57159807
37000 0.45 -2.1085043 0.055110778 -1.603956 0.75114055
38000 0.43889198 -2.1102778 0.062986806 -1.6089476 0.63880845
39000 0.46777901 -2.1265214 0.053125894 -1.6062012 0.63053536
40000 0.45690015 -2.1199761 0.054748517 -1.6088985 0.68532972
41000 0.45311829 -2.0896266 0.051934484 -1.5851402 0.96365527
42000 0.45921622 -2.1034581 0.060948692 -1.5838672 0.73506328
43000 0.45 -2.1082479 0.056762774 -1.6020476 0.72674441
44000 0.4336231 -2.0956954 0.058341601 -1.6042727 0.74559009
45000 0.44994151 -2.1060939 0.057939004 -1.5987759 0.80070112
46000 0.44025695 -2.1197274 0.053721478 -1.6262993 0.6154191
47000 0.43248313 -2.1228046 0.062087253 -1.6287748 0.63193935
48000 0.44731445 -2.1105501 0.057531307 -1.6062635 0.67718731
49000 0.43994092 -2.1055833 0.05429976 -1.6118925 0.77492942
50000 0.44810318 -2.1233595 0.060967052 -1.6148494 0.59090715
51000 0.44881752 -2.102071 0.054986409 -1.5988281 0.59834463
52000 0.45426625 -2.1169037 0.058260039 -1.6049453 0.68188266
53000 0.45073048 -2.1230063 0.056513588 -1.6163256 0.62426353
54000 0.44959432 -2.1222829 0.063811706 -1.6094389 0.54386719
55000 0.45132261 -2.1279628 0.064303102 -1.6129012 0.64603693
56000 0.43984398 -2.1089368 0.073286695 -1.596356 0.68889946
57000 0.44087794 -2.1314477 0.062602042 -1.6285188 0.58345594
58000 0.45 -2.1366398 0.055525068 -1.6316773 0.46829877
59000 0.45897732 -2.1226343 0.055496441 -1.6087343 0.62440113
60000 0.46465277 -2.1313407 0.05734796 -1.6099208 0.4918466
Loop time of 25.4217 on 1 procs for 60000 steps with 1200 atoms
Pair time (%) = 17.848 (70.2078)
Bond time (%) = 1.20659 (4.74631)
Neigh time (%) = 3.04688 (11.9853)
Comm time (%) = 0.550053 (2.16371)
Outpt time (%) = 0.200696 (0.789469)
Other time (%) = 2.56947 (10.1074)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 402 ave 402 max 402 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9819 ave 9819 max 9819 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9819
Ave neighs/atom = 8.1825
Ave special neighs/atom = 0.5
Neighbor list builds = 4883
Dangerous builds = 0

200
examples/micelle/log.micelle.22Jan08.linux.4
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@ -1,200 +0,0 @@
LAMMPS (22 Jan 2008)
# 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 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 1.0 20.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all enforce2d
thermo 50
run 1000
Memory usage per processor = 2.07665 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 0.40003481 2.2200223e-06 0.84947453 0.78935018
50 0.47417944 0.67716204 0.057387153 1.2081359 1.3374428
100 0.45 0.73037684 0.054821983 1.2346363 2.3192865
150 0.67532546 0.72388376 0.043478036 1.4418431 2.8741848
200 0.45 0.78466058 0.076912805 1.3110109 3.0409372
250 0.66488946 0.69771453 0.081047682 1.4428206 3.6911924
300 0.45 0.76794745 0.066716745 1.2841017 3.7855266
350 0.67629601 0.62549506 0.072636862 1.3735826 4.2848322
400 0.45 0.68493339 0.090717081 1.225088 4.4713609
450 0.56732174 0.64322231 0.080690687 1.2905256 4.7372687
500 0.45 0.64764573 0.078468194 1.1755514 4.7911172
550 0.56476697 0.58160926 0.080519682 1.22619 4.9721793
600 0.45 0.58331363 0.088243449 1.1209946 5.131088
650 0.5229482 0.54530348 0.09321673 1.1608147 5.2637478
700 0.45 0.52374674 0.085166964 1.0583512 5.2922505
750 0.51528063 0.48974532 0.086434828 1.0908167 5.3858022
800 0.45 0.50467091 0.090255509 1.0443639 5.5801625
850 0.4950534 0.48512921 0.091950432 1.0715142 5.6661389
900 0.45 0.48352312 0.097223467 1.0301841 5.7149691
950 0.49451225 0.46619517 0.094098428 1.0541877 5.8766965
1000 0.45 0.46260893 0.10106179 1.0131082 5.8616912
Loop time of 0.490955 on 4 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.0608874 (12.4018)
Bond time (%) = 0.00615633 (1.25395)
Neigh time (%) = 0.00803632 (1.63687)
Comm time (%) = 0.342579 (69.7779)
Outpt time (%) = 0.00870401 (1.77287)
Other time (%) = 0.0645928 (13.1565)
Nlocal: 300 ave 302 max 294 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 101.75 ave 105 max 100 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 794 ave 811 max 774 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Total # of neighbors = 3176
Ave neighs/atom = 2.64667
Ave special neighs/atom = 0.5
Neighbor list builds = 93
Dangerous builds = 0
# 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 = 2.08821 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.6864322 0.10106179 -1.1359329 3.7913551
1000 0.44913925 -1.9350607 0.071368027 -1.4151148 2.1469799
2000 0.46330233 -2.0109066 0.060062476 -1.4881209 1.5324898
3000 0.45558043 -2.0007635 0.059797299 -1.4859552 1.5702601
4000 0.45220563 -2.0072356 0.056527027 -1.4990682 1.638398
5000 0.44785006 -2.0311932 0.060134137 -1.5237688 1.230184
6000 0.45771088 -2.0463288 0.069315928 -1.5198741 1.2460547
7000 0.46138508 -2.0487713 0.057977884 -1.529985 1.2468528
8000 0.44559611 -2.0638065 0.062625272 -1.5561421 1.20002
9000 0.45 -2.061874 0.056615058 -1.5558214 1.1272832
10000 0.45166111 -2.0830577 0.057737309 -1.5742238 0.97887077
11000 0.44698685 -2.069784 0.055068221 -1.5682876 1.0177951
12000 0.46301669 -2.0580068 0.055605722 -1.5399631 1.1559766
13000 0.44484462 -2.0819608 0.061742828 -1.5759295 0.93700282
14000 0.44041342 -2.0635971 0.057739522 -1.5659947 1.0577447
15000 0.44729718 -2.0913481 0.065605983 -1.579004 0.87294698
16000 0.44435529 -2.0663697 0.060050789 -1.5625191 1.0631116
17000 0.44386777 -2.0903336 0.059516752 -1.587504 0.81739013
18000 0.45689902 -2.0971983 0.054107571 -1.5867628 0.71897374
19000 0.4472909 -2.0884034 0.058274968 -1.5833967 0.95673839
20000 0.44814664 -2.0845781 0.048930184 -1.5880615 0.80827939
21000 0.44928982 -2.1002512 0.053169424 -1.5983536 0.87819514
22000 0.44789387 -2.0897931 0.052822646 -1.5896365 0.98715706
23000 0.4433766 -2.0885794 0.066555201 -1.5792019 0.89898598
24000 0.44312667 -2.0861432 0.063151224 -1.5804193 0.95502225
25000 0.44098155 -2.0862551 0.059710845 -1.5861139 0.91917278
26000 0.45495856 -2.1061747 0.062767897 -1.5890169 0.77211421
27000 0.4594986 -2.0958799 0.055287838 -1.5816679 0.71488348
28000 0.4575183 -2.1105669 0.057934393 -1.5956861 0.73787599
29000 0.45421662 -2.0756975 0.057553024 -1.5644956 0.74039524
30000 0.4585136 -2.1105471 0.065985026 -1.5866216 0.73259472
31000 0.44753589 -2.0917336 0.063360868 -1.5813962 0.84906857
32000 0.44032392 -2.0946933 0.062048876 -1.5928709 0.85477256
33000 0.46201854 -2.1053574 0.05975115 -1.5841652 0.83818932
34000 0.44113983 -2.0919028 0.057435684 -1.5938787 0.85594396
35000 0.44618448 -2.1018231 0.067168229 -1.5890281 0.83395278
36000 0.44369159 -2.1069618 0.062019195 -1.6018056 0.78846571
37000 0.45 -2.1114624 0.058110601 -1.6039143 0.7636489
38000 0.4467252 -2.1236195 0.05737899 -1.6200737 0.66412548
39000 0.45340978 -2.0949326 0.064106121 -1.5779835 0.78205295
40000 0.45764316 -2.1083827 0.067605249 -1.5837063 0.52832333
41000 0.44990529 -2.1093636 0.060159079 -1.5998616 0.73739844
42000 0.43206581 -2.11498 0.0601205 -1.6233338 0.62095123
43000 0.45994792 -2.1258732 0.066327507 -1.6001727 0.65184873
44000 0.44630971 -2.1233109 0.060169292 -1.6173898 0.40001409
45000 0.46411804 -2.0884843 0.059218361 -1.5657281 0.79695879
46000 0.43537118 -2.0998107 0.059065989 -1.6059177 0.81031265
47000 0.43358801 -2.0923508 0.063011733 -1.5962931 0.80685805
48000 0.43269029 -2.1137973 0.064359382 -1.6172885 0.58880044
49000 0.45152462 -2.1061598 0.051956693 -1.6032429 0.60144086
50000 0.44478646 -2.1149128 0.061234138 -1.6094482 0.6469632
51000 0.45019705 -2.1220268 0.060861152 -1.6115313 0.64270507
52000 0.43441062 -2.1002627 0.061381281 -1.6050138 0.59292368
53000 0.45987875 -2.1235389 0.061089767 -1.6031452 0.63069651
54000 0.46481074 -2.1279595 0.064073893 -1.5996559 0.51751117
55000 0.44094766 -2.1099173 0.060438881 -1.609082 0.74322185
56000 0.46544759 -2.1154714 0.05368944 -1.5969162 0.69683289
57000 0.44210658 -2.1087889 0.061886033 -1.6053489 0.74955564
58000 0.44315581 -2.1143795 0.062404579 -1.609373 0.69155981
59000 0.44795459 -2.120618 0.061673573 -1.6115498 0.70340021
60000 0.44468469 -2.1226864 0.068304275 -1.6102533 0.67010695
Loop time of 31.6764 on 4 procs for 60000 steps with 1200 atoms
Pair time (%) = 5.20959 (16.4463)
Bond time (%) = 0.359324 (1.13436)
Neigh time (%) = 0.83879 (2.648)
Comm time (%) = 20.8686 (65.8808)
Outpt time (%) = 0.261901 (0.826802)
Other time (%) = 4.13813 (13.0638)
Nlocal: 300 ave 308 max 294 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 221.75 ave 228 max 206 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 2402.25 ave 2457 max 2258 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Total # of neighbors = 9609
Ave neighs/atom = 8.0075
Ave special neighs/atom = 0.5
Neighbor list builds = 4871
Dangerous builds = 0

17
examples/min/in.min
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@ -2,7 +2,6 @@
units lj
dimension 2
boundary s s p
atom_style atomic
lattice sq2 0.8442
@ -14,21 +13,23 @@ 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
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 wall/reflect xlo xhi ylo yhi
fix 3 all enforce2d
fix 2 all enforce2d
dump 1 all atom 50 dump.min
dump 1 all atom 100 dump.min
thermo 100
run 500
run 1000
min_style cg
minimize 1.0e-16 1.0e-16 2000 20000
neigh_modify delay 0 every 1 check yes
dump_modify 1 every 25
thermo 50
minimize 1.0e-6 0.001 1000 10000

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LAMMPS (21 May 2008)
# 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 = 1.70423 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 3.2123658 -0.67642058 0 2.5319297 16.31058
800 3.3016845 -0.76574803 0 2.5318094 15.639063
900 3.4631643 -0.92710879 0 2.5317266 14.770503
1000 3.3142629 -0.77918518 0 2.5309349 15.655215
Loop time of 0.347704 on 1 procs for 1000 steps with 800 atoms
Pair time (%) = 0.232571 (66.8876)
Neigh time (%) = 0.0642586 (18.4808)
Comm time (%) = 0.00830054 (2.38724)
Outpt time (%) = 0.0115886 (3.33289)
Other time (%) = 0.0309854 (8.91142)
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: 7741 ave 7741 max 7741 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7741
Ave neighs/atom = 9.67625
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 = 2.16199 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.3142629 -0.77918518 0 2.5309349 15.655215
1050 3.3142629 -2.8169324 0 0.49318768 1.6991832
1100 3.3142629 -2.861172 0 0.4489481 1.6197458
1150 3.3142629 -2.8697401 0 0.44037994 1.6413078
1200 3.3142629 -2.8763859 0 0.4337342 1.5869118
1250 3.3142629 -2.8934188 0 0.41670128 1.5990139
1300 3.3142629 -2.8965883 0 0.41353175 1.654921
1350 3.3142629 -2.8980407 0 0.41207941 1.6792847
1400 3.3142629 -2.902264 0 0.40785611 1.6884403
1450 3.3142629 -2.9064602 0 0.40365988 1.7024527
1468 3.3142629 -2.9066747 0 0.40344535 1.7059968
Loop time of 0.777846 on 1 procs for 468 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.779185181879 -2.90667292007 -2.90667472402
Force two-norm initial, final = 1916.37 0.710061
Force max component initial, final = 301.855 0.315889
Final line search alpha, max atom move = 0.00526935 0.00166453
Iterations, force evaluations = 468 1861
Pair time (%) = 0.671168 (86.2855)
Neigh time (%) = 0.0293589 (3.77438)
Comm time (%) = 0.010078 (1.29562)
Outpt time (%) = 0.0204384 (2.62757)
Other time (%) = 0.0468025 (6.01694)
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: 7004 ave 7004 max 7004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7004
Ave neighs/atom = 8.755
Neighbor list builds = 93
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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 = 1.67966 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 3.2123644 -0.67641922 0 2.5319297 16.310586
800 3.3016549 -0.7657205 0 2.5318073 15.639175
900 3.4620767 -0.92601725 0 2.5317318 14.773629
1000 3.287472 -0.75213644 0 2.5312262 15.801806
Loop time of 0.540854 on 4 procs for 1000 steps with 800 atoms
Pair time (%) = 0.0630118 (11.6504)
Neigh time (%) = 0.017717 (3.27575)
Comm time (%) = 0.35042 (64.7901)
Outpt time (%) = 0.020339 (3.76053)
Other time (%) = 0.089366 (16.5231)
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 170.5 ave 177 max 167 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 1938 ave 1962 max 1890 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 7752
Ave neighs/atom = 9.69
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 = 2.1377 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.287472 -0.75213644 0 2.5312262 15.801806
1050 3.287472 -2.8165208 0 0.46684181 1.6792079
1100 3.287472 -2.8541112 0 0.42925141 1.6761282
1150 3.287472 -2.8666373 0 0.4167253 1.6812573
1200 3.287472 -2.8718121 0 0.41155051 1.6994149
1250 3.287472 -2.8734488 0 0.40991379 1.7128405
1300 3.287472 -2.877455 0 0.40590759 1.7118991
1326 3.287472 -2.8781184 0 0.40524418 1.710365
Loop time of 0.745146 on 4 procs for 326 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.752136436206 -2.87811588622 -2.8781184428
Force two-norm initial, final = 1981.45 0.760495
Force max component initial, final = 387.785 0.166498
Final line search alpha, max atom move = 0.00240665 0.000400702
Iterations, force evaluations = 326 1206
Pair time (%) = 0.112617 (15.1134)
Neigh time (%) = 0.00467056 (0.626798)
Comm time (%) = 0.36602 (49.1206)
Outpt time (%) = 0.019726 (2.64726)
Other time (%) = 0.242112 (32.4919)
Nlocal: 200 ave 204 max 197 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 172.25 ave 175 max 167 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Neighs: 1760.5 ave 1791 max 1732 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 7042
Ave neighs/atom = 8.8025
Neighbor list builds = 54
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
boundary s s p
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 841 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
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/reflect xlo xhi ylo yhi
fix 3 all enforce2d
dump 1 all atom 50 dump.min
thermo 100
run 500
Memory usage per processor = 1.69054 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 5 -2.3392224 0 2.6518596 5.2514392 947.65505
100 3.3097379 -0.63883378 0 2.6650009 17.070807 943.40014
200 3.3080762 -0.6288886 0 2.6732874 17.04277 941.19268
300 3.3787956 -0.69098843 0 2.6817808 16.831266 939.23341
400 3.3724983 -0.65871066 0 2.7077725 17.321124 935.66558
500 3.2655218 -0.53947527 0 2.7202221 17.961553 933.59779
Loop time of 0.178504 on 1 procs for 500 steps with 841 atoms
Pair time (%) = 0.115572 (64.7446)
Neigh time (%) = 0.0305917 (17.1378)
Comm time (%) = 0.000834465 (0.467477)
Outpt time (%) = 0.012027 (6.73768)
Other time (%) = 0.019479 (10.9124)
Nlocal: 841 ave 841 max 841 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: 7729 ave 7729 max 7729 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7729
Ave neighs/atom = 9.19025
Neighbor list builds = 100
Dangerous builds = 0
min_style cg
minimize 1.0e-16 1.0e-16 2000 20000
Memory usage per processor = 2.1483 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
500 3.2655218 -0.53947527 0 2.7202221 17.962424 933.55255
600 3.2655218 -2.7918184 0 0.467879 2.3687829 978.86967
700 3.2655218 -2.8484405 0 0.41125693 2.5617944 970.87845
800 3.2655218 -2.8653234 0 0.39437404 2.8341532 959.29931
900 3.2655218 -2.8709903 0 0.3887071 2.8615917 957.77926
1000 3.2655218 -2.875841 0 0.38385645 2.8424963 962.97893
1100 3.2655218 -2.8773559 0 0.38234149 2.8331831 966.27062
1200 3.2655218 -2.8779916 0 0.38170577 2.8383813 966.23993
1300 3.2655218 -2.877995 0 0.38170241 2.8377343 966.07015
1400 3.2655218 -2.8779951 0 0.38170231 2.8385866 965.76227
1500 3.2655218 -2.8779951 0 0.38170231 2.8358421 966.69888
Loop time of 2.96182 on 1 procs for 1000 steps with 841 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.5394752732 -2.87799510218 -2.87799510218
Force two-norm initial, final = 2031.66 4.61875e-05
Force max component initial, final = 297.987 7.7681e-06
Final line search alpha, max atom move = 1.40663e-08 1.09269e-13
Iterations, force evaluations = 1000 7616
Pair time (%) = 2.67288 (90.2446)
Neigh time (%) = 0.0491631 (1.65989)
Comm time (%) = 0.00455403 (0.153758)
Outpt time (%) = 0.0223653 (0.755121)
Other time (%) = 0.212854 (7.18659)
Nlocal: 841 ave 841 max 841 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: 7067 ave 7067 max 7067 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7067
Ave neighs/atom = 8.40309
Neighbor list builds = 159
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
boundary s s p
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 841 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
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/reflect xlo xhi ylo yhi
fix 3 all enforce2d
dump 1 all atom 50 dump.min
thermo 100
run 500
Memory usage per processor = 1.68047 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 5 -2.3392224 0 2.6518596 5.2514392 947.65505
100 3.3097379 -0.63883378 0 2.6650009 17.070807 943.40014
200 3.3080762 -0.6288886 0 2.6732874 17.04277 941.19268
300 3.3787956 -0.69098843 0 2.6817808 16.831266 939.23341
400 3.3724983 -0.65871066 0 2.7077725 17.321124 935.66558
500 3.2655218 -0.53947532 0 2.7202221 17.961553 933.5978
Loop time of 0.331249 on 4 procs for 500 steps with 841 atoms
Pair time (%) = 0.0336406 (10.1557)
Neigh time (%) = 0.00937784 (2.83105)
Comm time (%) = 0.21005 (63.4114)
Outpt time (%) = 0.0165854 (5.00693)
Other time (%) = 0.0615957 (18.595)
Nlocal: 210.25 ave 213 max 207 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 80.5 ave 85 max 78 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Neighs: 1932.25 ave 2011 max 1878 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 7729
Ave neighs/atom = 9.19025
Neighbor list builds = 100
Dangerous builds = 0
min_style cg
minimize 1.0e-16 1.0e-16 2000 20000
Memory usage per processor = 2.13823 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
500 3.2655218 -0.53947532 0 2.7202221 17.962423 933.55255
600 3.2655218 -2.7937912 0 0.46590627 2.3734536 977.59412
700 3.2655218 -2.8475351 0 0.41216236 2.6076008 966.90337
800 3.2655218 -2.8642481 0 0.39544933 2.8437164 954.79638
900 3.2655218 -2.8694679 0 0.39022957 2.8748519 952.24201
1000 3.2655218 -2.8750401 0 0.3846573 2.8381948 952.45791
1100 3.2655218 -2.8806997 0 0.37899774 2.8637062 955.32239
1200 3.2655218 -2.8828075 0 0.3768899 2.8570958 959.68528
1300 3.2655218 -2.8924026 0 0.36729488 2.8365883 960.6309
1400 3.2655218 -2.8930364 0 0.36666108 2.8441244 962.40489
1500 3.2655218 -2.9003629 0 0.35933455 2.8254524 962.68407
1600 3.2655218 -2.9070345 0 0.35266293 2.850024 963.46045
1700 3.2655218 -2.9075342 0 0.35216329 2.845873 963.37846
1800 3.2655218 -2.9075376 0 0.35215987 2.842893 964.32817
1900 3.2655218 -2.9075383 0 0.35215916 2.8397901 965.36065
2000 3.2655218 -2.9075383 0 0.35215911 2.8395142 965.44981
2100 3.2655218 -2.9075383 0 0.3521591 2.8436298 964.05174
2200 3.2655218 -2.9075383 0 0.3521591 2.842818 964.32681
2205 3.2655218 -2.9075383 0 0.3521591 2.842818 964.32681
Loop time of 9.216 on 4 procs for 1705 steps with 841 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.539475324067 -2.90753834001 -2.90753834001
Force two-norm initial, final = 2031.66 2.66327e-05
Force max component initial, final = 297.987 3.89961e-06
Final line search alpha, max atom move = 7.28834e-10 2.84217e-15
Iterations, force evaluations = 1705 13427
Pair time (%) = 1.36367 (14.7968)
Neigh time (%) = 0.031518 (0.341992)
Comm time (%) = 4.829 (52.398)
Outpt time (%) = 0.0586754 (0.636669)
Other time (%) = 2.93313 (31.8265)
Nlocal: 210.25 ave 216 max 203 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 85 ave 86 max 83 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 1762.75 ave 1856 max 1582 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 7051
Ave neighs/atom = 8.38407
Neighbor list builds = 333
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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 1.0 1.0 1.0
fix 2 all deform 1 xy erate 0.01 remap v
dump 1 all custom 500 dump.nemd tag type x y z
thermo 1000
run 50000
Memory usage per processor = 1.79413 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.431 1.2080502 189.52855
1000 1.201216 0.22081306 0 1.4145215 5.812072 189.52855
2000 1.1053634 0.34245325 0 1.4409081 7.2538039 189.52855
3000 1.0369584 0.33062855 0 1.361106 6.660302 189.52855
4000 1.0763793 0.2937252 0 1.3633772 6.8420884 189.52855
5000 0.99089378 0.28590111 0 1.2706018 6.429982 189.52855
6000 1.0307968 0.23016743 0 1.2545218 5.5964388 189.52855
7000 0.88642282 0.28517029 0 1.166053 6.0559882 189.52855
8000 0.95680641 0.19899612 0 1.1498225 4.9970284 189.52855
9000 0.82948739 0.23322237 0 1.0575255 6.1567415 189.52855
10000 0.8669664 0.21075772 0 1.0723056 5.530127 189.52855
11000 0.82083041 0.23243452 0 1.0481347 5.755917 189.52855
12000 0.87146711 0.19031553 0 1.056336 4.9189315 189.52855
13000 0.87563025 0.23281315 0 1.1029707 5.3535722 189.52855
14000 0.93356309 0.21105622 0 1.1387845 5.522022 189.52855
15000 0.90866689 0.25933437 0 1.1623221 6.0137405 189.52855
16000 1.0336736 0.24068668 0 1.2678999 6.0482803 189.52855
17000 1.0277848 0.25504818 0 1.2764093 6.2722003 189.52855
18000 1.0364869 0.26178553 0 1.2917944 5.7429124 189.52855
19000 0.94527034 0.38926601 0 1.3286284 6.5023984 189.52855
20000 1.0274028 0.31347493 0 1.3344564 7.0482764 189.52855
21000 1.1191047 0.25917341 0 1.3712837 5.6562822 189.52855
22000 1.0422655 0.34401979 0 1.3797711 6.3526729 189.52855
23000 1.0321083 0.29206781 0 1.3177254 6.2154608 189.52855
24000 1.0244771 0.32519735 0 1.3432715 6.6907816 189.52855
25000 1.0657586 0.33274044 0 1.3918381 6.8894346 189.52855
26000 1.1356479 0.23644778 0 1.3649979 5.4008811 189.52855
27000 1.0630847 0.28714545 0 1.3435858 6.648475 189.52855
28000 1.0803365 0.27113962 0 1.344724 6.7677826 189.52855
29000 1.1410108 0.20529094 0 1.3391704 5.982283 189.52855
30000 1.1917679 0.23409944 0 1.4184188 5.6963971 189.52855
31000 1.0831878 0.36265238 0 1.4390702 7.2461956 189.52855
32000 1.1345617 0.287766 0 1.4152367 6.4520365 189.52855
33000 0.99110806 0.36761581 0 1.3525294 7.1366759 189.52855
34000 1.078312 0.27340897 0 1.3449816 6.3911521 189.52855
35000 0.99660085 0.36948608 0 1.3598582 7.5812397 189.52855
36000 1.0144204 0.34392112 0 1.3520014 7.5639539 189.52855
37000 0.98694344 0.28582689 0 1.2666019 6.6959949 189.52855
38000 1.0024714 0.27282321 0 1.2690291 6.6264321 189.52855
39000 0.97207374 0.25235501 0 1.2183533 6.4007459 189.52855
40000 0.92812395 0.269067 0 1.1913902 6.3556929 189.52855
41000 0.97149408 0.279107 0 1.2445292 6.0646852 189.52855
42000 1.0134876 0.25321709 0 1.2603704 5.6813022 189.52855
43000 0.92625362 0.25866794 0 1.1791325 5.5152806 189.52855
44000 0.97786941 0.20193469 0 1.1736924 5.2346171 189.52855
45000 0.92077813 0.20916856 0 1.1241918 5.3582525 189.52855
46000 0.98568366 0.21767436 0 1.1971975 5.0698867 189.52855
47000 0.98658256 0.24457963 0 1.224996 5.5310436 189.52855
48000 1.0444714 0.24354858 0 1.281492 5.167352 189.52855
49000 1.0009963 0.28263617 0 1.2773762 6.3125521 189.52855
50000 1.0897606 0.2494605 0 1.3324101 6.4210283 189.52855
Loop time of 1.6234 on 1 procs for 50000 steps with 160 atoms
Pair time (%) = 0.317492 (19.5573)
Neigh time (%) = 0.18852 (11.6127)
Comm time (%) = 0.0984259 (6.06296)
Outpt time (%) = 0.0293596 (1.80853)
Other time (%) = 0.989599 (60.9585)
Nlocal: 160 ave 160 max 160 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 61 ave 61 max 61 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 361 ave 361 max 361 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 361
Ave neighs/atom = 2.25625
Neighbor list builds = 5054
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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 1.0 1.0 1.0
fix 2 all deform 1 xy erate 0.01 remap v
dump 1 all custom 500 dump.nemd tag type x y z
thermo 1000
run 50000
Memory usage per processor = 1.78793 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.431 1.2080502 189.52855
1000 1.1697926 0.21325256 0 1.3757339 5.2080616 189.52855
2000 1.0171912 0.29202538 0 1.3028591 6.2516963 189.52855
3000 0.99202333 0.30099879 0 1.286822 7.1377169 189.52855
4000 0.99232557 0.27498873 0 1.2611123 6.0634528 189.52855
5000 0.97745735 0.29346168 0 1.2648099 6.6231602 189.52855
6000 0.96324554 0.2806326 0 1.2378579 6.0791693 189.52855
7000 0.99859204 0.21058692 0 1.2029378 5.312413 189.52855
8000 1.0109566 0.19053005 0 1.1951682 5.114073 189.52855
9000 0.95156948 0.32960966 0 1.2752318 6.5200852 189.52855
10000 1.0191357 0.31557253 0 1.3283386 7.1244854 189.52855
11000 1.1018622 0.26166595 0 1.3566415 6.0071258 189.52855
12000 0.95953724 0.32378335 0 1.2773235 6.5580551 189.52855
13000 0.99604838 0.28112532 0 1.2709484 5.8429234 189.52855
14000 0.98563574 0.26169744 0 1.241173 6.4164311 189.52855
15000 0.92737672 0.33493597 0 1.2565166 6.6062138 189.52855
16000 0.95376077 0.33825777 0 1.2860575 7.4237304 189.52855
17000 1.1011389 0.22545271 0 1.3197095 5.7483214 189.52855
18000 0.99936019 0.34579596 0 1.3389102 6.5986774 189.52855
19000 1.0385827 0.34139906 0 1.3734906 7.3725224 189.52855
20000 1.0863768 0.25973407 0 1.3393211 5.719117 189.52855
21000 1.0292233 0.27151556 0 1.2943062 6.2598972 189.52855
22000 0.99429804 0.27141639 0 1.2595001 6.5580982 189.52855
23000 0.94958875 0.21465821 0 1.158312 5.8037305 189.52855
24000 0.88642624 0.20417299 0 1.0850591 5.4317389 189.52855
25000 0.91450961 0.1677748 0 1.0765687 4.817349 189.52855
26000 0.91751663 0.21347568 0 1.1252578 5.2020404 189.52855
27000 0.92235414 0.2743999 0 1.1909893 5.9318744 189.52855
28000 1.0147496 0.21738239 0 1.2257898 5.4243143 189.52855
29000 1.0423796 0.2177307 0 1.2535955 5.9015198 189.52855
30000 1.0918894 0.27418042 0 1.3592455 6.1376946 189.52855
31000 1.0808038 0.34889063 0 1.4229394 6.7579123 189.52855
32000 1.0621686 0.3810462 0 1.4365762 7.6754676 189.52855
33000 1.2846684 0.24383496 0 1.5204741 6.0921751 189.52855
34000 1.1516823 0.36346499 0 1.5079493 7.3192421 189.52855
35000 1.1268604 0.35725077 0 1.4770683 7.0260174 189.52855
36000 1.1843072 0.23214387 0 1.4090491 5.4136742 189.52855
37000 1.0516345 0.32002698 0 1.3650888 6.7995753 189.52855
38000 1.0383111 0.25289855 0 1.2847202 6.0240848 189.52855
39000 0.98462749 0.28564014 0 1.2641137 6.3777186 189.52855
40000 0.87538476 0.36557837 0 1.235492 6.8848323 189.52855
41000 0.98587871 0.26116271 0 1.2408797 6.4161684 189.52855
42000 0.97791927 0.27694735 0 1.2487546 6.3307714 189.52855
43000 0.99292488 0.23856305 0 1.2252821 5.6251966 189.52855
44000 0.84382228 0.3336851 0 1.1722335 6.706324 189.52855
45000 0.97000203 0.24195557 0 1.2058951 5.9593224 189.52855
46000 0.93260381 0.29811871 0 1.2248937 6.2647019 189.52855
47000 0.98928475 0.24566783 0 1.2287695 5.6042505 189.52855
48000 1.0089185 0.2711447 0 1.2737574 6.3042831 189.52855
49000 1.0584424 0.28195041 0 1.3337776 6.5027698 189.52855
50000 1.0404332 0.28577101 0 1.3197015 6.2419453 189.52855
Loop time of 22.236 on 4 procs for 50000 steps with 160 atoms
Pair time (%) = 0.117888 (0.530169)
Neigh time (%) = 0.0656884 (0.295415)
Comm time (%) = 14.7994 (66.5562)
Outpt time (%) = 0.0774301 (0.34822)
Other time (%) = 7.17555 (32.27)
Nlocal: 40 ave 41 max 39 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 38 ave 39 max 36 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 88.25 ave 92 max 84 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 353
Ave neighs/atom = 2.20625
Neighbor list builds = 5077
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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 1.0 1.0 1.0
fix 2 all deform 1 xy erate 0.01 remap v
dump 1 all custom 500 dump.nemd tag type x y z
thermo 1000
run 50000
Memory usage per processor = 1.79413 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.4265 1.2042513 189.52855
1000 1.1957714 0.24426867 0 1.4288297 5.6293729 189.52855
2000 1.0512544 0.36384346 0 1.4052424 7.4695343 189.52855
3000 1.1469734 0.23896893 0 1.3751894 5.6807214 189.52855
4000 1.0241419 0.33724993 0 1.3517905 7.6685283 189.52855
5000 1.0450738 0.3070054 0 1.3422817 6.5793804 189.52855
6000 1.0685486 0.28335604 0 1.341887 6.6844393 189.52855
7000 1.0897239 0.27389674 0 1.3534045 6.6481088 189.52855
8000 1.110529 0.22408733 0 1.3242051 5.6773903 189.52855
9000 1.0678619 0.29632567 0 1.3541763 6.3949916 189.52855
10000 1.1660924 0.22834951 0 1.3835098 5.5541843 189.52855
11000 1.0722384 0.27294548 0 1.3351317 6.4708617 189.52855
12000 1.0044103 0.32564577 0 1.3206397 7.2612801 189.52855
13000 0.99372325 0.28302395 0 1.2674311 6.7664165 189.52855
14000 0.92084625 0.35175684 0 1.2639702 6.8344289 189.52855
15000 1.0230407 0.23460993 0 1.2480596 5.8082977 189.52855
16000 1.0425501 0.2176758 0 1.250452 4.8674643 189.52855
17000 0.97012929 0.27885836 0 1.2398927 6.9865482 189.52855
18000 0.9831045 0.26127207 0 1.23516 6.3350937 189.52855
19000 0.98620312 0.21991389 0 1.1968714 5.5543736 189.52855
20000 1.01412 0.20446778 0 1.2090804 5.0827574 189.52855
21000 1.0010437 0.21376483 0 1.2054238 6.1091116 189.52855
22000 1.0127807 0.28721144 0 1.2904973 7.0634198 189.52855
23000 1.0813249 0.25976823 0 1.3309557 6.0306099 189.52855
24000 1.0802637 0.28544909 0 1.3555853 6.3827986 189.52855
25000 1.1518499 0.23206633 0 1.3731176 5.8921729 189.52855
26000 1.1108836 0.24930877 0 1.3497778 6.1708853 189.52855
27000 1.0607825 0.2234288 0 1.2742664 5.7632024 189.52855
28000 1.0391552 0.25691356 0 1.2863267 6.0416087 189.52855
29000 0.99095631 0.25778565 0 1.2394517 5.4705218 189.52855
30000 0.98637444 0.26105776 0 1.2381849 6.0167833 189.52855
31000 0.95692196 0.26393713 0 1.2118879 5.8106414 189.52855
32000 0.97151292 0.2510554 0 1.2134604 6.663016 189.52855
33000 1.0158087 0.26768531 0 1.2739708 6.5506448 189.52855
34000 0.95974388 0.31697173 0 1.267718 6.4849664 189.52855
35000 1.0527141 0.25903984 0 1.3018848 5.8715406 189.52855
36000 0.98256431 0.25872637 0 1.2320791 6.97778 189.52855
37000 1.0711558 0.2118975 0 1.2730112 5.5570897 189.52855
38000 1.0719782 0.21273864 0 1.274667 5.5745073 189.52855
39000 1.081957 0.20776531 0 1.279579 6.1207526 189.52855
40000 0.97959574 0.29250154 0 1.2629136 7.0039551 189.52855
41000 0.98177341 0.24070052 0 1.2132698 6.2770289 189.52855
42000 0.93713907 0.29565793 0 1.2240113 6.8009101 189.52855
43000 0.85994766 0.33876002 0 1.1906457 6.3808484 189.52855
44000 1.010351 0.24602983 0 1.2469088 6.0770182 189.52855
45000 0.98461752 0.25682126 0 1.232208 6.5865262 189.52855
46000 0.99366855 0.27489751 0 1.2592504 6.1331616 189.52855
47000 0.9723363 0.33478499 0 1.2980056 7.2892199 189.52855
48000 0.94450954 0.40945183 0 1.3451066 7.7632521 189.52855
49000 1.0821859 0.27329139 0 1.3453318 6.5206906 189.52855
50000 1.0229752 0.30045077 0 1.3138355 6.4390946 189.52855
Loop time of 1.4216 on 1 procs for 50000 steps with 160 atoms
Pair time (%) = 0.320149 (22.5203)
Neigh time (%) = 0.19033 (13.3884)
Comm time (%) = 0.0955777 (6.72324)
Outpt time (%) = 0.0293758 (2.06639)
Other time (%) = 0.78617 (55.3017)
Nlocal: 160 ave 160 max 160 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 71 ave 71 max 71 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 357 ave 357 max 357 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 357
Ave neighs/atom = 2.23125
Neighbor list builds = 5054
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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 1.0 1.0 1.0
fix 2 all deform 1 xy erate 0.01 remap v
dump 1 all custom 500 dump.nemd tag type x y z
thermo 1000
run 50000
Memory usage per processor = 1.78793 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.4265 1.2042513 189.52855
1000 1.1376326 0.2723749 0 1.3993422 6.0281618 189.52855
2000 1.1092867 0.30697161 0 1.4058587 6.5032573 189.52855
3000 1.1766842 0.22235709 0 1.3880098 5.8644335 189.52855
4000 1.0434686 0.34041502 0 1.3741011 7.0700722 189.52855
5000 1.1074638 0.22563765 0 1.322719 5.8819014 189.52855
6000 1.100945 0.2181433 0 1.3087669 6.0202699 189.52855
7000 0.97801661 0.33802096 0 1.3068687 7.5777517 189.52855
8000 1.0689837 0.23524351 0 1.2942054 5.85439 189.52855
9000 0.98697269 0.26366959 0 1.2413894 6.4300856 189.52855
10000 1.0108076 0.21921678 0 1.2205481 6.3955919 189.52855
11000 0.89800714 0.21444583 0 1.1040342 5.7539663 189.52855
12000 0.95992701 0.17693662 0 1.1278643 5.3022292 189.52855
13000 0.98389546 0.16326907 0 1.1379405 5.2203307 189.52855
14000 0.90861181 0.21504543 0 1.115139 4.9988336 189.52855
15000 0.85713034 0.19327642 0 1.0423712 5.3278582 189.52855
16000 0.8825445 0.23009835 0 1.104369 5.5304884 189.52855
17000 0.87611509 0.24874153 0 1.116643 6.43497 189.52855
18000 0.95591731 0.21548224 0 1.1624378 5.8740926 189.52855
19000 0.96623931 0.28660713 0 1.2437879 5.9965065 189.52855
20000 1.0307188 0.27291119 0 1.293967 6.2130706 189.52855
21000 1.058557 0.33094775 0 1.3795808 7.0034843 189.52855
22000 1.1038028 0.31323484 0 1.4066895 6.5357948 189.52855
23000 1.0332701 0.37233908 0 1.3959223 7.19646 189.52855
24000 1.1373415 0.2868604 0 1.4135393 6.512421 189.52855
25000 1.1251188 0.26998165 0 1.3845525 5.9383566 189.52855
26000 1.1495445 0.26242517 0 1.4011927 6.2097913 189.52855
27000 1.0710201 0.24813894 0 1.3091182 5.9469594 189.52855
28000 0.94089325 0.37721847 0 1.3092909 7.5991128 189.52855
29000 1.1245164 0.2012278 0 1.3152019 4.8980329 189.52855
30000 0.99392576 0.34334349 0 1.3279512 6.4315527 189.52855
31000 0.99011392 0.32648676 0 1.3073184 6.9984388 189.52855
32000 0.94636734 0.36450354 0 1.3019987 7.2324663 189.52855
33000 0.93907091 0.31264026 0 1.2429074 6.2071137 189.52855
34000 0.92196227 0.27866154 0 1.1919804 6.662139 189.52855
35000 0.9670411 0.25971717 0 1.2176923 5.8709837 189.52855
36000 0.94905466 0.30285469 0 1.243012 6.9870879 189.52855
37000 1.0027302 0.26550016 0 1.2588298 6.4022976 189.52855
38000 0.95341975 0.32978864 0 1.2742701 6.3304338 189.52855
39000 1.0930053 0.23648819 0 1.3192466 5.4154989 189.52855
40000 1.0943964 0.23898933 0 1.3231257 5.9056706 189.52855
41000 1.0267208 0.28983681 0 1.3069321 6.7084471 189.52855
42000 0.94374097 0.28271929 0 1.2176127 6.1336872 189.52855
43000 0.89703955 0.27637051 0 1.1650003 5.7892838 189.52855
44000 0.9145058 0.24114071 0 1.147073 5.7678354 189.52855
45000 0.98924374 0.24342035 0 1.2233899 5.8284458 189.52855
46000 0.97250668 0.23874128 0 1.2021307 6.56895 189.52855
47000 0.95124639 0.24487076 0 1.1871992 5.5045958 189.52855
48000 0.88977783 0.24482112 0 1.1262573 5.5189103 189.52855
49000 0.94390446 0.18400987 0 1.1190652 5.2014664 189.52855
50000 0.8982525 0.24633124 0 1.1361626 6.2422864 189.52855
Loop time of 24.1271 on 4 procs for 50000 steps with 160 atoms
Pair time (%) = 0.125436 (0.519896)
Neigh time (%) = 0.0702366 (0.291111)
Comm time (%) = 16.1323 (66.8637)
Outpt time (%) = 0.0769518 (0.318944)
Other time (%) = 7.72219 (32.0064)
Nlocal: 40 ave 41 max 39 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 36.5 ave 38 max 34 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 87.5 ave 92 max 82 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 350
Ave neighs/atom = 2.1875
Neighbor list builds = 5057
Dangerous builds = 0

2
examples/obstacle/in.obstacle
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@ -43,7 +43,7 @@ fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Poisseuille flow
# Poiselle flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0

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LAMMPS (21 May 2008)
# 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
dump 1 all atom 100 dump.obstacle
#dump 1 all custom 100 dump.custom tag type x y z vx vy
run 25000
Memory usage per processor = 1.70365 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0027471 0 0 0.68849216 0.463265 1142.8674
1000 1 -0.33974838 0 0.3468576 1.3038702 1270.08
2000 1 -0.39015699 0 0.296449 1.3186607 1302.3377
3000 1 -0.46396059 0 0.22264539 1.4481737 1319.6122
4000 1 -0.5496054 0 0.13700058 1.4226554 1363.8627
5000 1 -0.48050604 0 0.20609995 1.2559184 1407.1184
6000 1 -0.48128066 0 0.20532532 1.269977 1433.5837
7000 1 -0.40707539 0 0.2795306 1.1836577 1441.9606
8000 1 -0.43843955 0 0.24816644 1.1680682 1445.6274
9000 1 -0.37805786 0 0.30854812 1.0549192 1453.6089
10000 1 -0.40408007 0 0.28252592 1.0810363 1446.2246
11000 1 -0.42972416 0 0.25688183 1.1044938 1443.9994
12000 1 -0.41545586 0 0.27115012 1.1307776 1447.7388
13000 1 -0.36928332 0 0.31732266 0.97287103 1456.3013
14000 1 -0.40912145 0 0.27748454 0.95493422 1459.6415
15000 1 -0.37477252 0 0.31183347 1.0249663 1468.7959
16000 1 -0.38531111 0 0.30129487 1.0220375 1462.2135
17000 1 -0.37376992 0 0.31283607 0.97728961 1461.4028
18000 1 -0.37434423 0 0.31226175 0.96886643 1463.9162
19000 1 -0.36998688 0 0.3166191 0.91573344 1462.3663
20000 1 -0.34624142 0 0.34036456 0.9870418 1458.2772
21000 1 -0.39671499 0 0.28989099 1.0313285 1453.5442
22000 1 -0.35842296 0 0.32818302 0.98937969 1454.5928
23000 1 -0.36252176 0 0.32408422 0.98605146 1457.477
24000 1 -0.38519815 0 0.30140784 1.0132503 1466.8342
25000 1 -0.38889832 0 0.29770766 0.99272161 1462.2441
Loop time of 3.01278 on 1 procs for 25000 steps with 769 atoms
Pair time (%) = 0.867625 (28.7981)
Neigh time (%) = 0.200178 (6.64429)
Comm time (%) = 0.0479047 (1.59005)
Outpt time (%) = 0.27641 (9.17456)
Other time (%) = 1.62067 (53.793)
Nlocal: 769 ave 769 max 769 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 45 ave 45 max 45 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1615 ave 1615 max 1615 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1615
Ave neighs/atom = 2.10013
Neighbor list builds = 1636
Dangerous builds = 0

134
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LAMMPS (21 May 2008)
# 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
dump 1 all atom 100 dump.obstacle
#dump 1 all custom 100 dump.custom tag type x y z vx vy
run 25000
Memory usage per processor = 1.6747 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0004177 0 0 0.68689281 0.46218884 1142.8674
1000 1 -0.31542378 0 0.3711822 1.175277 1269.5736
2000 1 -0.41219854 0 0.27440745 1.1491113 1299.751
3000 1 -0.47091634 0 0.21568964 1.5138975 1319.4646
4000 1 -0.53218028 0 0.1544257 1.4947487 1368.5894
5000 1 -0.46667863 0 0.21992736 1.2479263 1416.3743
6000 1 -0.48435058 0 0.20225541 1.1547645 1435.6664
7000 1 -0.45166298 0 0.23494301 1.2360154 1436.1059
8000 1 -0.42767328 0 0.2589327 1.0669461 1445.2577
9000 1 -0.3731244 0 0.31348158 1.0759192 1437.8863
10000 1 -0.38390694 0 0.30269904 1.0086513 1433.1836
11000 1 -0.38602215 0 0.30058383 0.97948448 1433.262
12000 1 -0.39324632 0 0.29335966 1.0627957 1439.8189
13000 1 -0.38406328 0 0.3025427 1.0506023 1450.2548
14000 1 -0.39923996 0 0.28736602 1.0593743 1453.5768
15000 1 -0.39243934 0 0.29416664 1.0295791 1451.2386
16000 1 -0.39115558 0 0.2954504 0.99442342 1452.2425
17000 1 -0.37672706 0 0.30987892 1.1334027 1446.7615
18000 1 -0.39587578 0 0.2907302 1.0416836 1451.6676
19000 1 -0.37159192 0 0.31501406 0.97004312 1453.7464
20000 1 -0.37573625 0 0.31086973 1.0174394 1456.2812
21000 1 -0.37788053 0 0.30872545 0.93039844 1468.4444
22000 1 -0.38096917 0 0.30563681 1.0034608 1464.2511
23000 1 -0.37098283 0 0.31562315 0.98141206 1460.3666
24000 1 -0.37160721 0 0.31499877 0.98831948 1462.133
25000 1 -0.39191532 0 0.29469067 1.0326092 1457.8187
Loop time of 7.66898 on 4 procs for 25000 steps with 769 atoms
Pair time (%) = 0.240548 (3.13664)
Neigh time (%) = 0.0541248 (0.705762)
Comm time (%) = 3.3025 (43.0631)
Outpt time (%) = 0.277801 (3.6224)
Other time (%) = 3.79401 (49.4721)
Nlocal: 192.25 ave 235 max 157 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 42.25 ave 46 max 38 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Neighs: 401.25 ave 540 max 283 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 1605
Ave neighs/atom = 2.08713
Neighbor list builds = 1636
Dangerous builds = 0

134
examples/obstacle/log.obstacle.22Jan08.linux.1
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@ -1,134 +0,0 @@
LAMMPS (22 Jan 2008)
# 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
dump 1 all atom 100 dump.obstacle
#dump 1 all custom 100 dump.custom tag type x y z vx vy
run 25000
Memory usage per processor = 1.70365 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0028598 0 0 0.68791746 0.4628783 1142.8674
1000 1 -0.37328511 0 0.31267068 1.3684627 1268.502
2000 1 -0.37505949 0 0.3108963 1.1534403 1304.1442
3000 1 -0.47919489 0 0.20676089 1.4549832 1322.0606
4000 1 -0.48849092 0 0.19746486 1.4619445 1361.4653
5000 1 -0.5158306 0 0.17012519 1.3415433 1399.8571
6000 1 -0.46839183 0 0.21756396 1.1363632 1433.3799
7000 1 -0.4934634 0 0.19249239 1.1974639 1438.8597
8000 1 -0.43365481 0 0.25230098 1.1237932 1444.8858
9000 1 -0.38250014 0 0.30345564 1.0808676 1445.4458
10000 1 -0.41296265 0 0.27299313 1.0868711 1444.8934
11000 1 -0.3906263 0 0.29532949 1.0008831 1443.6394
12000 1 -0.41935827 0 0.26659752 1.0104839 1435.183
13000 1 -0.35477192 0 0.33118387 0.94488941 1440.5498
14000 1 -0.39497861 0 0.29097718 1.072787 1435.3595
15000 1 -0.38656691 0 0.29938888 1.05116 1442.1287
16000 1 -0.37132523 0 0.31463056 1.0827132 1450.8796
17000 1 -0.37146616 0 0.31448963 1.1724883 1450.3808
18000 1 -0.38747606 0 0.29847973 1.0753661 1455.6913
19000 1 -0.37206204 0 0.31389375 1.0665364 1450.8326
20000 1 -0.39878843 0 0.28716736 1.0958347 1453.0454
21000 1 -0.36006462 0 0.32589117 0.92452983 1459.3281
22000 1 -0.36787908 0 0.3180767 0.9659935 1465.6707
23000 1 -0.36909747 0 0.31685831 0.9769748 1470.1647
24000 1 -0.38163837 0 0.30431741 0.99582238 1458.5709
25000 1 -0.38524202 0 0.30071376 0.96693615 1458.596
Loop time of 2.95816 on 1 procs for 25000 steps with 769 atoms
Pair time (%) = 0.863224 (29.1811)
Neigh time (%) = 0.197628 (6.68078)
Comm time (%) = 0.0466022 (1.57538)
Outpt time (%) = 0.271423 (9.17539)
Other time (%) = 1.57928 (53.3874)
Nlocal: 769 ave 769 max 769 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 43 ave 43 max 43 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1642 ave 1642 max 1642 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1642
Ave neighs/atom = 2.13524
Neighbor list builds = 1639
Dangerous builds = 0

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examples/obstacle/log.obstacle.22Jan08.linux.4
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@ -1,134 +0,0 @@
LAMMPS (22 Jan 2008)
# 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
dump 1 all atom 100 dump.obstacle
#dump 1 all custom 100 dump.custom tag type x y z vx vy
run 25000
Memory usage per processor = 1.6747 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0005301 0 0 0.68631944 0.46180304 1142.8674
1000 1 -0.2948784 0 0.39107738 1.1626002 1268.8767
2000 1 -0.34841619 0 0.3375396 1.1178514 1300.3744
3000 1 -0.45198006 0 0.23397572 1.5104251 1319.535
4000 1 -0.4930904 0 0.19286538 1.5054789 1359.7954
5000 1 -0.49437088 0 0.19158491 1.5038965 1397.2548
6000 1 -0.4538845 0 0.23207128 1.2100734 1429.6759
7000 1 -0.46715598 0 0.2187998 1.1832386 1441.9733
8000 1 -0.4490541 0 0.23690168 1.1504605 1441.328
9000 1 -0.41648732 0 0.26946847 1.1453723 1437.0673
10000 1 -0.3776725 0 0.30828328 1.080226 1434.3847
11000 1 -0.4189651 0 0.26699069 1.0496379 1435.2496
12000 1 -0.39688957 0 0.28906621 1.0443611 1440.7218
13000 1 -0.38977976 0 0.29617602 1.0309823 1460.2618
14000 1 -0.38124839 0 0.30470739 1.0195507 1463.0566
15000 1 -0.35208681 0 0.33386897 0.93784921 1466.2431
16000 1 -0.41112084 0 0.27483495 1.0717681 1465.3625
17000 1 -0.36742687 0 0.31852892 1.0452766 1466.8819
18000 1 -0.38418683 0 0.30176896 0.94933535 1464.1674
19000 1 -0.38168345 0 0.30427234 0.97892386 1457.3935
20000 1 -0.37778426 0 0.30817153 1.0205159 1452.8383
21000 1 -0.3778136 0 0.30814218 1.07933 1449.0972
22000 1 -0.36663586 0 0.31931993 0.93798261 1452.0117
23000 1 -0.39885464 0 0.28710115 1.0286456 1449.9107
24000 1 -0.40766765 0 0.27828813 1.138272 1451.4717
25000 1 -0.36180623 0 0.32414956 0.91494742 1464.0945
Loop time of 9.24974 on 4 procs for 25000 steps with 769 atoms
Pair time (%) = 0.269292 (2.91135)
Neigh time (%) = 0.0605692 (0.654821)
Comm time (%) = 4.36665 (47.2083)
Outpt time (%) = 0.31033 (3.35502)
Other time (%) = 4.2429 (45.8705)
Nlocal: 192.25 ave 244 max 151 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 43 ave 45 max 41 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 399.25 ave 566 max 263 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 1597
Ave neighs/atom = 2.07672
Neighbor list builds = 1638
Dangerous builds = 0

34
examples/peptide/log.peptide.22Jan08.linux.1 → examples/peptide/log.peptide.21May08.linux.1
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@ -1,4 +1,4 @@
LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# Solvated 5-mer peptide
units real
@ -70,7 +70,7 @@ TotEng = -5237.4580 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 = -845.4767
---------------- Step 50 ----- CPU = 1.9580 (sec) ----------------
---------------- Step 50 ----- CPU = 1.9220 (sec) ----------------
TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752
PotEng = -6379.9512 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1773
@ -84,12 +84,12 @@ SHAKE stats (type/ave/delta) on step 100
14 0.96 0
18 0.957201 5.38003e-06
31 104.52 0.000502302
---------------- Step 100 ----- CPU = 3.9176 (sec) ----------------
---------------- Step 100 ----- CPU = 3.8466 (sec) ----------------
TotEng = -5257.9998 KinEng = 1078.0523 Temp = 267.9656
PotEng = -6336.0521 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3270
E_coul = 26786.2252 E_long = -33906.1028 Press = -648.6625
---------------- Step 150 ----- CPU = 5.9178 (sec) ----------------
---------------- Step 150 ----- CPU = 5.8126 (sec) ----------------
TotEng = -5287.2845 KinEng = 1098.6038 Temp = 273.0740
PotEng = -6385.8884 E_bond = 17.4924 E_angle = 32.8594
E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9699
@ -103,12 +103,12 @@ SHAKE stats (type/ave/delta) on step 200
14 0.96 0
18 0.957201 3.59691e-06
31 104.52 0.000388135
---------------- Step 200 ----- CPU = 7.8301 (sec) ----------------
---------------- Step 200 ----- CPU = 7.6880 (sec) ----------------
TotEng = -5308.4506 KinEng = 1100.5139 Temp = 273.5487
PotEng = -6408.9645 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3197
E_coul = 26735.6532 E_long = -33901.9330 Press = -1470.4759
---------------- Step 250 ----- CPU = 9.8341 (sec) ----------------
---------------- Step 250 ----- CPU = 9.6620 (sec) ----------------
TotEng = -5294.1810 KinEng = 1071.1657 Temp = 266.2538
PotEng = -6365.3468 E_bond = 14.2024 E_angle = 39.1969
E_dihed = 19.4546 E_impro = 3.1388 E_vdwl = 753.6297
@ -122,23 +122,23 @@ SHAKE stats (type/ave/delta) on step 300
14 0.96 0
18 0.957202 7.62681e-06
31 104.52 0.000805945
---------------- Step 300 ----- CPU = 11.8338 (sec) ----------------
---------------- Step 300 ----- CPU = 11.6334 (sec) ----------------
TotEng = -5251.4412 KinEng = 1123.4657 Temp = 279.2537
PotEng = -6374.9069 E_bond = 14.2235 E_angle = 38.4664
E_dihed = 18.1383 E_impro = 2.3705 E_vdwl = 715.5989
E_coul = 26744.9563 E_long = -33908.6606 Press = -467.2646
Loop time of 11.8338 on 1 procs for 300 steps with 2004 atoms
Loop time of 11.6334 on 1 procs for 300 steps with 2004 atoms
Pair time (%) = 9.14838 (77.307)
Bond time (%) = 0.0331497 (0.280127)
Kspce time (%) = 1.27265 (10.7543)
Neigh time (%) = 1.18564 (10.0191)
Comm time (%) = 0.0640588 (0.541319)
Outpt time (%) = 0.00577974 (0.0488409)
Other time (%) = 0.124176 (1.04933)
Pair time (%) = 8.95694 (76.9933)
Bond time (%) = 0.0339992 (0.292255)
Kspce time (%) = 1.24836 (10.7308)
Neigh time (%) = 1.1949 (10.2713)
Comm time (%) = 0.0653448 (0.5617)
Outpt time (%) = 0.00594068 (0.0510657)
Other time (%) = 0.127918 (1.09957)
FFT time (% of Kspce) = 0.134997 (10.6076)
FFT Gflps 3d 1d-only = 1.21865 1.86907
FFT time (% of Kspce) = 0.136571 (10.94)
FFT Gflps 3d 1d-only = 1.20461 1.854
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0

34
examples/peptide/log.peptide.22Jan08.linux.4 → examples/peptide/log.peptide.21May08.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# Solvated 5-mer peptide
units real
@ -70,7 +70,7 @@ TotEng = -5237.4580 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 = -845.4767
---------------- Step 50 ----- CPU = 0.6428 (sec) ----------------
---------------- Step 50 ----- CPU = 0.6366 (sec) ----------------
TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752
PotEng = -6379.9512 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1773
@ -84,12 +84,12 @@ SHAKE stats (type/ave/delta) on step 100
14 0.96 0
18 0.957201 5.38003e-06
31 104.52 0.000502302
---------------- Step 100 ----- CPU = 1.2863 (sec) ----------------
---------------- Step 100 ----- CPU = 1.2804 (sec) ----------------
TotEng = -5257.9998 KinEng = 1078.0523 Temp = 267.9656
PotEng = -6336.0521 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3270
E_coul = 26786.2252 E_long = -33906.1028 Press = -648.6625
---------------- Step 150 ----- CPU = 1.9373 (sec) ----------------
---------------- Step 150 ----- CPU = 1.9476 (sec) ----------------
TotEng = -5287.2845 KinEng = 1098.6039 Temp = 273.0740
PotEng = -6385.8883 E_bond = 17.4924 E_angle = 32.8594
E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9699
@ -103,12 +103,12 @@ SHAKE stats (type/ave/delta) on step 200
14 0.96 0
18 0.957201 3.59691e-06
31 104.52 0.000388135
---------------- Step 200 ----- CPU = 2.5714 (sec) ----------------
---------------- Step 200 ----- CPU = 2.5921 (sec) ----------------
TotEng = -5308.4506 KinEng = 1100.5139 Temp = 273.5487
PotEng = -6408.9645 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3197
E_coul = 26735.6532 E_long = -33901.9330 Press = -1470.4761
---------------- Step 250 ----- CPU = 3.2272 (sec) ----------------
---------------- Step 250 ----- CPU = 3.2541 (sec) ----------------
TotEng = -5294.1811 KinEng = 1071.1657 Temp = 266.2538
PotEng = -6365.3467 E_bond = 14.2024 E_angle = 39.1969
E_dihed = 19.4546 E_impro = 3.1388 E_vdwl = 753.6297
@ -122,23 +122,23 @@ SHAKE stats (type/ave/delta) on step 300
14 0.96 0
18 0.957202 7.62685e-06
31 104.52 0.000805946
---------------- Step 300 ----- CPU = 3.8863 (sec) ----------------
---------------- Step 300 ----- CPU = 3.9119 (sec) ----------------
TotEng = -5251.4403 KinEng = 1123.4658 Temp = 279.2538
PotEng = -6374.9062 E_bond = 14.2235 E_angle = 38.4663
E_dihed = 18.1383 E_impro = 2.3705 E_vdwl = 715.5987
E_coul = 26744.9572 E_long = -33908.6606 Press = -467.2532
Loop time of 3.88697 on 4 procs for 300 steps with 2004 atoms
Loop time of 3.91243 on 4 procs for 300 steps with 2004 atoms
Pair time (%) = 2.10925 (54.2645)
Bond time (%) = 0.00993025 (0.255475)
Kspce time (%) = 0.813088 (20.9183)
Neigh time (%) = 0.259184 (6.66801)
Comm time (%) = 0.390454 (10.0452)
Outpt time (%) = 0.019382 (0.49864)
Other time (%) = 0.285689 (7.34991)
Pair time (%) = 2.14349 (54.7867)
Bond time (%) = 0.0107697 (0.275269)
Kspce time (%) = 0.751045 (19.1964)
Neigh time (%) = 0.26354 (6.73596)
Comm time (%) = 0.415519 (10.6205)
Outpt time (%) = 0.0160949 (0.411378)
Other time (%) = 0.31197 (7.97382)
FFT time (% of Kspce) = 0.243359 (29.9302)
FFT Gflps 3d 1d-only = 0.676015 5.55305
FFT time (% of Kspce) = 0.2215 (29.4923)
FFT Gflps 3d 1d-only = 0.742726 5.19614
Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1

4
examples/pour/in.pour
View File

@ -25,8 +25,8 @@ fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
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
compute erot all erotate/sphere
thermo_style custom step atoms ke c_erot vol
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

4
examples/pour/in.pour.2d
View File

@ -30,8 +30,8 @@ fix ins all pour 1000 1 4767548 vol 0.4 10 &
fix 3 all enforce2d
compute erot all erotate/sphere
thermo_style custom step atoms ke c_erot vol
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

39
examples/pour/log.pour.22Jan08.linux.1 → examples/pour/log.pour.21May08.linux.1
View File

@ -1,4 +1,4 @@
LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# Pour granular particles into chute container, then induce flow
atom_style granular
@ -21,7 +21,7 @@ neigh_modify delay 0
pair_style gran/history 2000.0 50.0 0.5 0
timestep 0.001
fix 1 all nve/gran
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
@ -29,15 +29,16 @@ 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
thermo_style granular
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore
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 = 3.27422 Mbytes
Step Atoms KinEng RotKEgrn Volume
Step Atoms KinEng 1 Volume
0 0 -0 0 6600
1000 402 779.98578 0 6600
2000 402 1424.4252 0 6600
@ -64,13 +65,13 @@ Step Atoms KinEng RotKEgrn Volume
23000 3000 422.1483 32.45423 6600
24000 3000 365.17401 21.632169 6600
25000 3000 220.87181 24.123943 6600
Loop time of 20.7499 on 1 procs for 25000 steps with 3000 atoms
Loop time of 20.231 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 13.5449 (65.2771)
Neigh time (%) = 1.67646 (8.07935)
Comm time (%) = 0.364293 (1.75563)
Outpt time (%) = 0.0648448 (0.312507)
Other time (%) = 5.09938 (24.5754)
Pair time (%) = 13.4518 (66.4912)
Neigh time (%) = 1.66174 (8.21387)
Comm time (%) = 0.362025 (1.78946)
Outpt time (%) = 0.066838 (0.330375)
Other time (%) = 4.68855 (23.1751)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -87,8 +88,8 @@ Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Memory usage per processor = 10.1398 Mbytes
Step Atoms KinEng RotKEgrn Volume
Memory usage per processor = 9.91094 Mbytes
Step Atoms KinEng 1 Volume
25000 3000 220.87181 24.123943 6600
26000 3000 108.79862 20.458515 6600
27000 3000 112.95727 12.664104 6600
@ -115,13 +116,13 @@ Step Atoms KinEng RotKEgrn Volume
48000 3000 16081.514 219.64212 6600
49000 3000 17731.002 236.51098 6600
50000 3000 19431.348 255.96964 6600
Loop time of 40.4029 on 1 procs for 25000 steps with 3000 atoms
Loop time of 39.3461 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 28.6386 (70.8825)
Neigh time (%) = 2.64738 (6.55244)
Comm time (%) = 0.784085 (1.94067)
Outpt time (%) = 0.108553 (0.268677)
Other time (%) = 8.22431 (20.3558)
Pair time (%) = 28.4144 (72.2164)
Neigh time (%) = 2.58973 (6.58193)
Comm time (%) = 0.766247 (1.94745)
Outpt time (%) = 0.107744 (0.273835)
Other time (%) = 7.46804 (18.9804)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

39
examples/pour/log.pour.22Jan08.linux.4 → examples/pour/log.pour.21May08.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# Pour granular particles into chute container, then induce flow
atom_style granular
@ -21,7 +21,7 @@ neigh_modify delay 0
pair_style gran/history 2000.0 50.0 0.5 0
timestep 0.001
fix 1 all nve/gran
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran zplane 0.0 2000.0 50.0 0.5
@ -29,15 +29,16 @@ 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
thermo_style granular
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore
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 = 3.14935 Mbytes
Step Atoms KinEng RotKEgrn Volume
Step Atoms KinEng 1 Volume
0 0 -0 0 6600
1000 402 779.98578 0 6600
2000 402 1424.4252 0 6600
@ -64,13 +65,13 @@ Step Atoms KinEng RotKEgrn Volume
23000 3000 438.80433 35.866677 6600
24000 3000 350.60693 23.380222 6600
25000 3000 232.00186 22.76523 6600
Loop time of 13.1865 on 4 procs for 25000 steps with 3000 atoms
Loop time of 12.3364 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 3.85555 (29.2386)
Neigh time (%) = 0.421859 (3.19917)
Comm time (%) = 5.00618 (37.9644)
Outpt time (%) = 0.0909717 (0.689884)
Other time (%) = 3.81195 (28.908)
Pair time (%) = 3.62034 (29.3469)
Neigh time (%) = 0.423409 (3.4322)
Comm time (%) = 4.89279 (39.6614)
Outpt time (%) = 0.0863795 (0.700201)
Other time (%) = 3.31347 (26.8593)
Nlocal: 750 ave 763 max 730 min
Histogram: 1 0 0 0 1 0 0 0 0 2
@ -87,8 +88,8 @@ Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Memory usage per processor = 9.90906 Mbytes
Step Atoms KinEng RotKEgrn Volume
Memory usage per processor = 9.68018 Mbytes
Step Atoms KinEng 1 Volume
25000 3000 232.00186 22.76523 6600
26000 3000 106.03482 19.110968 6600
27000 3000 117.35702 11.863221 6600
@ -115,13 +116,13 @@ Step Atoms KinEng RotKEgrn Volume
48000 3000 17394.628 231.95039 6600
49000 3000 19056.668 255.27889 6600
50000 3000 20908.007 287.26263 6600
Loop time of 19.7873 on 4 procs for 25000 steps with 3000 atoms
Loop time of 18.252 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 8.2543 (41.7152)
Neigh time (%) = 0.681514 (3.44421)
Comm time (%) = 5.89918 (29.813)
Outpt time (%) = 0.13265 (0.670383)
Other time (%) = 4.81962 (24.3572)
Pair time (%) = 7.67562 (42.0535)
Neigh time (%) = 0.668073 (3.66027)
Comm time (%) = 5.45432 (29.8833)
Outpt time (%) = 0.128624 (0.704711)
Other time (%) = 4.3254 (23.6982)
Nlocal: 750 ave 760 max 743 min
Histogram: 1 0 1 1 0 0 0 0 0 1

90
examples/pour/log.pour.2d.21May08.linux.1 Normal file
View File

@ -0,0 +1,90 @@
LAMMPS (21 May 2008)
# Pour 2d granular particles into container
dimension 2
atom_style granular
boundary f fm p
newton off
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 (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/hertzian 2000.0 50.0 0.5 0
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran xplane 0 100 50 0
fix ywalls all wall/gran yplane 0 NULL 50 0
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 = 3.12551 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 224 348.20549 0 5000
2000 224 650.98655 0 5000
3000 224 1056.0039 0 5000
4000 448 1941.6817 0 5000
5000 448 2869.092 0 5000
6000 448 3244.0285 59.709037 5000
7000 672 3381.9514 72.635418 5000
8000 672 3209.9845 135.37739 5000
9000 672 3037.2686 125.65507 5000
10000 896 2983.0247 113.16927 5000
11000 896 2808.8482 72.058343 5000
12000 896 2750.718 73.383261 5000
13000 1000 2726.6048 65.657144 5000
14000 1000 2512.3122 60.161228 5000
15000 1000 2081.7342 49.717007 5000
16000 1000 1454.4989 55.593577 5000
17000 1000 838.42356 47.392952 5000
18000 1000 591.78268 31.70284 5000
19000 1000 267.16614 26.169498 5000
20000 1000 39.186825 15.992488 5000
21000 1000 25.943515 7.3119929 5000
22000 1000 15.094337 4.2244747 5000
23000 1000 8.3263828 2.7944168 5000
24000 1000 4.0127427 1.5742141 5000
25000 1000 1.6900361 0.87976982 5000
Loop time of 6.8258 on 1 procs for 25000 steps with 1000 atoms
Pair time (%) = 3.86265 (56.5889)
Neigh time (%) = 0.370904 (5.43385)
Comm time (%) = 0.0147769 (0.216486)
Outpt time (%) = 0.113987 (1.66994)
Other time (%) = 2.46349 (36.0908)
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: 2475 ave 2475 max 2475 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2475
Ave neighs/atom = 2.475
Neighbor list builds = 1627
Dangerous builds = 0

90
examples/pour/log.pour.2d.21May08.linux.4 Normal file
View File

@ -0,0 +1,90 @@
LAMMPS (21 May 2008)
# Pour 2d granular particles into container
dimension 2
atom_style granular
boundary f fm p
newton off
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 (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/hertzian 2000.0 50.0 0.5 0
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran xplane 0 100 50 0
fix ywalls all wall/gran yplane 0 NULL 50 0
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 = 3.09867 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 224 348.20549 0 5000
2000 224 650.98655 0 5000
3000 224 1056.0039 0 5000
4000 448 1941.6817 0 5000
5000 448 2869.092 0 5000
6000 448 3244.0285 59.709037 5000
7000 672 3381.9514 72.635418 5000
8000 672 3209.9845 135.37739 5000
9000 672 3037.2686 125.65507 5000
10000 896 2983.0247 113.16927 5000
11000 896 2808.8482 72.058343 5000
12000 896 2750.718 73.383261 5000
13000 1000 2726.6044 65.656874 5000
14000 1000 2512.4219 59.997862 5000
15000 1000 2086.6017 51.808696 5000
16000 1000 1465.7682 53.531804 5000
17000 1000 830.37814 47.232643 5000
18000 1000 598.17657 29.282204 5000
19000 1000 253.30511 31.894452 5000
20000 1000 37.347525 17.140954 5000
21000 1000 20.803138 8.8531328 5000
22000 1000 15.095346 4.8904454 5000
23000 1000 8.7452294 2.3928721 5000
24000 1000 5.0388199 1.1642031 5000
25000 1000 3.4373452 0.74346362 5000
Loop time of 9.49783 on 4 procs for 25000 steps with 1000 atoms
Pair time (%) = 1.01844 (10.7229)
Neigh time (%) = 0.101886 (1.07273)
Comm time (%) = 3.84115 (40.4424)
Outpt time (%) = 0.142735 (1.50282)
Other time (%) = 4.39362 (46.2592)
Nlocal: 250 ave 505 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: 627.25 ave 1265 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 2509
Ave neighs/atom = 2.509
Neighbor list builds = 1627
Dangerous builds = 0

89
examples/pour/log.pour.2d.22Jan08.linux.1
View File

@ -1,89 +0,0 @@
LAMMPS (22 Jan 2008)
# Pour 2d granular particles into container
dimension 2
atom_style granular
boundary f fm p
newton off
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 (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/hertzian 2000.0 50.0 0.5 0
timestep 0.001
fix 1 all nve/gran
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran xplane 0 100 50 0
fix ywalls all wall/gran yplane 0 NULL 50 0
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
thermo_style granular
thermo 1000
thermo_modify lost ignore
compute_modify thermo_temp dynamic yes
dump id all atom 250 dump.pour
run 25000
Memory usage per processor = 3.12551 Mbytes
Step Atoms KinEng RotKEgrn Volume
0 0 -0 0 5000
1000 224 348.20549 0 5000
2000 224 650.98655 0 5000
3000 224 1056.0039 0 5000
4000 448 1941.6817 0 5000
5000 448 2869.092 0 5000
6000 448 3240.26 51.002089 5000
7000 672 3375.857 86.854847 5000
8000 672 3218.9668 120.74194 5000
9000 672 3042.428 99.125781 5000
10000 896 2986.9987 88.589831 5000
11000 896 2829.33 66.164478 5000
12000 896 2741.8245 63.121028 5000
13000 1000 2712.5291 62.754703 5000
14000 1000 2476.3302 60.318998 5000
15000 1000 2074.2112 55.107868 5000
16000 1000 1441.07 57.502968 5000
17000 1000 837.81119 47.509652 5000
18000 1000 606.38794 34.97416 5000
19000 1000 267.8998 34.474186 5000
20000 1000 38.669262 19.982355 5000
21000 1000 21.342125 11.876372 5000
22000 1000 14.57957 5.6091923 5000
23000 1000 8.3300727 3.1535324 5000
24000 1000 5.3845351 1.4196696 5000
25000 1000 3.436019 0.90458586 5000
Loop time of 7.10731 on 1 procs for 25000 steps with 1000 atoms
Pair time (%) = 3.94757 (55.5425)
Neigh time (%) = 0.374912 (5.27501)
Comm time (%) = 0.0137208 (0.193051)
Outpt time (%) = 0.114302 (1.60824)
Other time (%) = 2.6568 (37.3812)
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: 2464 ave 2464 max 2464 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2464
Ave neighs/atom = 2.464
Neighbor list builds = 1615
Dangerous builds = 0

89
examples/pour/log.pour.2d.22Jan08.linux.4
View File

@ -1,89 +0,0 @@
LAMMPS (22 Jan 2008)
# Pour 2d granular particles into container
dimension 2
atom_style granular
boundary f fm p
newton off
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 (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/hertzian 2000.0 50.0 0.5 0
timestep 0.001
fix 1 all nve/gran
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran xplane 0 100 50 0
fix ywalls all wall/gran yplane 0 NULL 50 0
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
thermo_style granular
thermo 1000
thermo_modify lost ignore
compute_modify thermo_temp dynamic yes
dump id all atom 250 dump.pour
run 25000
Memory usage per processor = 3.09867 Mbytes
Step Atoms KinEng RotKEgrn Volume
0 0 -0 0 5000
1000 224 348.20549 0 5000
2000 224 650.98655 0 5000
3000 224 1056.0039 0 5000
4000 448 1941.6817 0 5000
5000 448 2869.092 0 5000
6000 448 3240.26 51.002089 5000
7000 672 3375.857 86.854847 5000
8000 672 3218.9668 120.74194 5000
9000 672 3042.428 99.125781 5000
10000 896 2986.9987 88.589831 5000
11000 896 2829.33 66.164478 5000
12000 896 2741.8245 63.121034 5000
13000 1000 2712.6085 62.756506 5000
14000 1000 2481.4123 60.427347 5000
15000 1000 2061.8464 56.399834 5000
16000 1000 1452.1851 54.458544 5000
17000 1000 833.03811 44.980618 5000
18000 1000 585.79885 36.672365 5000
19000 1000 276.7811 30.881939 5000
20000 1000 30.566489 17.571585 5000
21000 1000 18.21801 9.3358364 5000
22000 1000 11.354764 5.1520478 5000
23000 1000 7.4178622 2.1905651 5000
24000 1000 4.6531861 1.0674461 5000
25000 1000 2.6666049 0.68062336 5000
Loop time of 9.60115 on 4 procs for 25000 steps with 1000 atoms
Pair time (%) = 1.08202 (11.2697)
Neigh time (%) = 0.110134 (1.14709)
Comm time (%) = 3.93212 (40.9546)
Outpt time (%) = 0.141791 (1.47682)
Other time (%) = 4.33509 (45.1518)
Nlocal: 250 ave 503 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 6.25 ave 13 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 621.75 ave 1244 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 2487
Ave neighs/atom = 2.487
Neighbor list builds = 1607
Dangerous builds = 0

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@ -1,4 +1,4 @@
LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# Simple rigid body system
units lj
@ -285,13 +285,13 @@ Step Temp E_pair E_mol TotEng Press
9900 16738.489 -0.00024984585 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 0.235085 on 1 procs for 10000 steps with 81 atoms
Loop time of 0.236778 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0157146 (6.68466)
Neigh time (%) = 0.0421674 (17.9371)
Comm time (%) = 0.0163469 (6.95363)
Outpt time (%) = 0.0261998 (11.1448)
Other time (%) = 0.134656 (57.2798)
Pair time (%) = 0.0151129 (6.38272)
Neigh time (%) = 0.0427065 (18.0365)
Comm time (%) = 0.0166826 (7.04568)
Outpt time (%) = 0.0264668 (11.1779)
Other time (%) = 0.135809 (57.3572)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0

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@ -1,4 +1,4 @@
LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# Simple rigid body system
units lj
@ -285,13 +285,13 @@ Step Temp E_pair E_mol TotEng Press
9900 16738.489 -0.00024984583 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 4.3193 on 4 procs for 10000 steps with 81 atoms
Loop time of 4.06518 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.00839633 (0.194391)
Neigh time (%) = 0.0188292 (0.435933)
Comm time (%) = 3.17395 (73.4829)
Outpt time (%) = 0.168198 (3.89411)
Other time (%) = 0.949927 (21.9926)
Pair time (%) = 0.00766569 (0.18857)
Neigh time (%) = 0.0178966 (0.440241)
Comm time (%) = 2.97041 (73.0696)
Outpt time (%) = 0.147557 (3.62977)
Other time (%) = 0.921653 (22.6719)
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1

14
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@ -1,4 +1,4 @@
LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# Simple rigid body system
units lj
@ -285,13 +285,13 @@ Step Temp E_pair E_mol TotEng Press
9900 19690.077 396.95803 0 3678.6375 1.6169288
9950 20574.352 249.26902 0 3678.3277 5.9594646
10000 20861.51 201.85286 0 3678.7712 -0.64028741
Loop time of 7.25136 on 1 procs for 10000 steps with 81 atoms
Loop time of 7.26124 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.280846 (3.87301)
Neigh time (%) = 0.125411 (1.72948)
Comm time (%) = 0.0173204 (0.238857)
Outpt time (%) = 0.0274284 (0.378252)
Other time (%) = 6.80035 (93.7804)
Pair time (%) = 0.280442 (3.86218)
Neigh time (%) = 0.121096 (1.6677)
Comm time (%) = 0.0176237 (0.242709)
Outpt time (%) = 0.0308731 (0.425176)
Other time (%) = 6.8112 (93.8022)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0

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@ -1,4 +1,4 @@
LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# Simple rigid body system
units lj
@ -285,13 +285,13 @@ Step Temp E_pair E_mol TotEng Press
9900 20831.124 213.97543 0 3685.8294 -23.250883
9950 20257.767 308.71666 0 3685.0111 -9.1959081
10000 21123.35 164.53453 0 3685.0929 2.4217121
Loop time of 11.8231 on 4 procs for 10000 steps with 81 atoms
Loop time of 11.1702 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0847651 (0.716943)
Neigh time (%) = 0.0420694 (0.355823)
Comm time (%) = 3.50799 (29.6706)
Outpt time (%) = 0.162343 (1.3731)
Other time (%) = 8.02595 (67.8835)
Pair time (%) = 0.0751896 (0.673126)
Neigh time (%) = 0.0374737 (0.335479)
Comm time (%) = 3.20709 (28.7111)
Outpt time (%) = 0.17948 (1.60678)
Other time (%) = 7.67097 (68.6735)
Nlocal: 20.25 ave 72 max 0 min
Histogram: 2 1 0 0 0 0 0 0 0 1

14
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@ -1,4 +1,4 @@
LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# Simple rigid body system
units lj
@ -286,13 +286,13 @@ Step Temp E_pair E_mol TotEng Press
9900 19741.039 106.38351 0 3762.1314 -0.15155351
9950 17199.878 577.88679 0 3763.0494 13.40024
10000 18985.433 246.5308 0 3762.3518 0.62625708
Loop time of 7.54982 on 1 procs for 10000 steps with 81 atoms
Loop time of 7.52498 on 1 procs for 10000 steps with 81 atoms
Pair time (%) = 0.212344 (2.81257)
Neigh time (%) = 0.0943768 (1.25005)
Comm time (%) = 0.0214007 (0.283459)
Outpt time (%) = 0.0292683 (0.387668)
Other time (%) = 7.19243 (95.2663)
Pair time (%) = 0.212854 (2.82864)
Neigh time (%) = 0.0927372 (1.23239)
Comm time (%) = 0.0216842 (0.288163)
Outpt time (%) = 0.0303783 (0.4037)
Other time (%) = 7.16732 (95.2471)
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0

14
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@ -1,4 +1,4 @@
LAMMPS (22 Jan 2008)
LAMMPS (21 May 2008)
# Simple rigid body system
units lj
@ -286,13 +286,13 @@ Step Temp E_pair E_mol TotEng Press
9900 19205.165 207.15936 0 3763.6714 7.5682042
9950 18962.217 252.13659 0 3763.6582 -1.4248706
10000 19978.362 63.931872 0 3763.6285 5.7744071
Loop time of 12.4183 on 4 procs for 10000 steps with 81 atoms
Loop time of 12.0971 on 4 procs for 10000 steps with 81 atoms
Pair time (%) = 0.0675793 (0.54419)
Neigh time (%) = 0.034472 (0.27759)
Comm time (%) = 3.23596 (26.0579)
Outpt time (%) = 0.162251 (1.30655)
Other time (%) = 8.91806 (71.8137)
Pair time (%) = 0.0632877 (0.523162)
Neigh time (%) = 0.0323215 (0.267182)
Comm time (%) = 3.17539 (26.2491)
Outpt time (%) = 0.149343 (1.23453)
Other time (%) = 8.6768 (71.726)
Nlocal: 20.25 ave 39 max 0 min
Histogram: 1 1 0 0 0 0 0 0 0 2

159
examples/shear/log.shear.21May08.linux.1 Normal file
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@ -0,0 +1,159 @@
LAMMPS (21 May 2008)
# 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
timestep 0.001
run 100
Memory usage per processor = 1.98543 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 0.467599 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 0.443526 (94.8517)
Neigh time (%) = 0.0121951 (2.60803)
Comm time (%) = 0.00291872 (0.624193)
Outpt time (%) = 0.00022912 (0.0489993)
Other time (%) = 0.00873041 (1.86707)
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
reset_timestep 0
run 3000
Memory usage per processor = 2.06028 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 77.151949 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 14.379 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 13.2702 (92.2892)
Neigh time (%) = 0.67312 (4.68129)
Comm time (%) = 0.0920188 (0.639955)
Outpt time (%) = 0.081636 (0.567746)
Other time (%) = 0.261964 (1.82186)
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

159
examples/shear/log.shear.21May08.linux.4 Normal file
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@ -0,0 +1,159 @@
LAMMPS (21 May 2008)
# 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
timestep 0.001
run 100
Memory usage per processor = 1.88566 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 0.193502 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.145985 (75.4434)
Neigh time (%) = 0.00310105 (1.60259)
Comm time (%) = 0.03407 (17.607)
Outpt time (%) = 0.0012731 (0.657923)
Other time (%) = 0.00907356 (4.68912)
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
reset_timestep 0
run 3000
Memory usage per processor = 1.90439 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 6.09161 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 4.41471 (72.4719)
Neigh time (%) = 0.170875 (2.80508)
Comm time (%) = 1.11289 (18.2692)
Outpt time (%) = 0.104965 (1.7231)
Other time (%) = 0.288174 (4.73068)
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

159
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@ -1,159 +0,0 @@
LAMMPS (22 Jan 2008)
# 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
timestep 0.001
run 100
Memory usage per processor = 1.98543 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 0.467166 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 0.443394 (94.9114)
Neigh time (%) = 0.0120709 (2.58386)
Comm time (%) = 0.00285816 (0.611809)
Outpt time (%) = 0.000116348 (0.0249051)
Other time (%) = 0.0087266 (1.86799)
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
reset_timestep 0
run 3000
Memory usage per processor = 2.06028 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 298.53339 -8245.8191 0 -8210.2533 8059.4154 19778.399
100 300 -8263.5777 0 -8227.8373 2795.3643 19788.083
200 295.48797 -8257.8787 0 -8222.6759 2179.0845 19913.732
300 292.48667 -8250.5584 0 -8215.7131 2.9847512 20043.736
400 304.93883 -8245.9033 0 -8209.5745 179.50544 20125.384
500 294.27283 -8241.2854 0 -8206.2272 829.41012 20145.713
600 302.25208 -8230.3821 0 -8194.3734 4273.5024 20285.46
700 300 -8223.3443 0 -8187.6038 6565.4269 20406.893
800 303.62781 -8211.0391 0 -8174.8665 8116.0638 20515.088
900 297.87427 -8197.7869 0 -8162.2997 10317.159 20621.333
1000 300 -8181.081 0 -8145.3406 13621.801 20748.339
1100 307.26338 -8166.9162 0 -8130.3105 17420.976 20877.786
1200 300.29796 -8153.8084 0 -8118.0325 20385.904 20986.474
1300 300 -8147.0071 0 -8111.2667 21178.857 21115.921
1400 300 -8137.1276 0 -8101.3872 21423.889 21246.59
1500 308.75316 -8131.6139 0 -8094.8306 20067.792 21365.047
1600 300 -8133.2906 0 -8097.5501 16682.824 21477.398
1700 308.52741 -8149.3473 0 -8112.5909 11697.908 21599.518
1800 300 -8152.6978 0 -8116.9573 9550.2281 21737.514
1900 308.57591 -8146.2494 0 -8109.4873 9662.4382 21859.635
2000 308.26812 -8146.4139 0 -8109.6884 9661.2057 21976.871
2100 302.17107 -8146.0627 0 -8110.0636 8521.2058 22094.106
2200 305.08447 -8151.7703 0 -8115.4241 4427.9711 22218.669
2300 300 -8166.2097 0 -8130.4693 -1334.8828 22346.896
2400 304.42128 -8165.4861 0 -8129.219 -931.52307 22464.131
2500 291.59698 -8160.1078 0 -8125.3684 2248.0287 22592.358
2600 304.33702 -8161.3244 0 -8125.0673 3566.8213 22704.709
2700 308.4539 -8163.6628 0 -8126.9152 1887.5801 22825.608
2800 309.42404 -8163.7723 0 -8126.9092 -395.06509 22946.507
2900 307.81471 -8165.3682 0 -8128.6967 -3460.652 23077.176
3000 299.7731 -8165.3688 0 -8129.6554 -5437.2745 23191.969
Loop time of 14.364 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 13.2885 (92.5126)
Neigh time (%) = 0.644948 (4.49003)
Comm time (%) = 0.0909958 (0.633499)
Outpt time (%) = 0.0792053 (0.551416)
Other time (%) = 0.260347 (1.8125)
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2089 ave 2089 max 2089 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 45088 ave 45088 max 45088 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45088
Ave neighs/atom = 23.5816
Neighbor list builds = 216
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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
timestep 0.001
run 100
Memory usage per processor = 1.88566 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 0.211954 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.152662 (72.0261)
Neigh time (%) = 0.0030964 (1.46088)
Comm time (%) = 0.0420393 (19.8341)
Outpt time (%) = 0.00200987 (0.948256)
Other time (%) = 0.0121462 (5.7306)
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
reset_timestep 0
run 3000
Memory usage per processor = 1.90439 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 292.46783 -8250.5856 0 -8215.7425 5714.7972 19847.781
100 297.48776 -8255.7637 0 -8220.3225 1519.5936 19869.252
200 300 -8259.5191 0 -8223.7786 407.14026 19843.233
300 306.85093 -8252.9546 0 -8216.3979 -1452.8459 19987.791
400 303.87074 -8246.296 0 -8210.0945 1276.3308 20128.061
500 299.00581 -8241.6473 0 -8206.0253 943.44685 20226.281
600 300 -8228.0773 0 -8192.3369 3740.0009 20307.41
700 302.55478 -8222.4773 0 -8186.4325 6034.1752 20412.441
800 291.55934 -8208.4477 0 -8173.7129 9870.4071 20534.96
900 300.04405 -8197.8106 0 -8162.0649 11858.874 20635.988
1000 303.4363 -8185.1721 0 -8149.0223 15860.089 20755.666
1100 300 -8172.7372 0 -8136.9967 19064.863 20868.017
1200 300 -8163.6948 0 -8127.9543 20503.74 20997.464
1300 300 -8157.774 0 -8122.0336 19017.48 21108.594
1400 301.23169 -8148.1245 0 -8112.2373 19838.433 21245.369
1500 300 -8137.0376 0 -8101.2972 19618.234 21361.383
1600 300 -8129.5673 0 -8093.8269 17832.316 21493.274
1700 300 -8131.9086 0 -8096.1682 15651.56 21609.288
1800 300 -8154.2629 0 -8118.5225 9602.8973 21725.302
1900 300 -8166.6747 0 -8130.9342 7079.4166 21855.971
2000 297.56913 -8164.1963 0 -8128.7455 6008.7168 21970.765
2100 307.18117 -8162.4989 0 -8125.903 5339.1594 22100.212
2200 307.91443 -8165.8526 0 -8129.1693 4903.917 22218.669
2300 307.29809 -8166.6561 0 -8130.0463 4057.1866 22343.232
2400 306.14212 -8165.725 0 -8129.2529 4381.5236 22462.91
2500 306.62123 -8166.8443 0 -8130.3151 2924.8251 22583.809
2600 300 -8166.6003 0 -8130.8598 2179.9998 22701.045
2700 309.89171 -8168.2224 0 -8131.3035 3044.4626 22836.599
2800 305.74412 -8166.2652 0 -8129.8404 1099.7498 22952.613
2900 301.2671 -8170.7739 0 -8134.8825 -2699.4417 23073.512
3000 300 -8171.8299 0 -8136.0895 -3656.4591 23189.527
Loop time of 6.35133 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 4.57768 (72.0743)
Neigh time (%) = 0.167127 (2.63138)
Comm time (%) = 1.18119 (18.5976)
Outpt time (%) = 0.113077 (1.78037)
Other time (%) = 0.312252 (4.91633)
Nlocal: 478 ave 508 max 449 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 1006.75 ave 1064 max 959 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 11284 ave 12171 max 10415 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Total # of neighbors = 45136
Ave neighs/atom = 23.6067
Neighbor list builds = 216
Dangerous builds = 0

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LAMMPS (21 May 2008)
# 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
timestep 0.001
run 100
Memory usage per processor = 1.96813 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 0.404765 on 1 procs for 100 steps with 1708 atoms
Pair time (%) = 0.383371 (94.7145)
Neigh time (%) = 0.0106142 (2.6223)
Comm time (%) = 0.00265503 (0.655943)
Outpt time (%) = 0.000173807 (0.0429402)
Other time (%) = 0.00795102 (1.96435)
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
reset_timestep 0
run 3000
Memory usage per processor = 2.03328 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 12.4157 on 1 procs for 3000 steps with 1708 atoms
Pair time (%) = 11.4629 (92.3256)
Neigh time (%) = 0.556271 (4.48038)
Comm time (%) = 0.0828254 (0.667103)
Outpt time (%) = 0.0738423 (0.59475)
Other time (%) = 0.239896 (1.9322)
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 (21 May 2008)
# 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
timestep 0.001
run 100
Memory usage per processor = 1.87344 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 0.176328 on 4 procs for 100 steps with 1708 atoms
Pair time (%) = 0.1287 (72.9894)
Neigh time (%) = 0.00338066 (1.91726)
Comm time (%) = 0.033612 (19.0622)
Outpt time (%) = 0.00139475 (0.790998)
Other time (%) = 0.00923985 (5.24016)
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
reset_timestep 0
run 3000
Memory usage per processor = 1.89003 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 5.30706 on 4 procs for 3000 steps with 1708 atoms
Pair time (%) = 3.79223 (71.4564)
Neigh time (%) = 0.135778 (2.55845)
Comm time (%) = 0.98511 (18.5623)
Outpt time (%) = 0.097142 (1.83043)
Other time (%) = 0.296796 (5.59247)
Nlocal: 427 ave 441 max 411 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 777.25 ave 826 max 727 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 9559.25 ave 10062 max 9128 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 38237
Ave neighs/atom = 22.387
Neighbor list builds = 210
Dangerous builds = 0

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examples/shear/log.shear.void.22Jan08.linux.1
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LAMMPS (22 Jan 2008)
# 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
timestep 0.001
run 100
Memory usage per processor = 1.96813 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 0.40687 on 1 procs for 100 steps with 1708 atoms
Pair time (%) = 0.385552 (94.7605)
Neigh time (%) = 0.0105622 (2.59596)
Comm time (%) = 0.00262928 (0.646221)
Outpt time (%) = 0.000127792 (0.0314086)
Other time (%) = 0.0079987 (1.96591)
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
reset_timestep 0
run 3000
Memory usage per processor = 2.03328 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 296.81549 -7297.4174 0 -7267.2741 786.10955 19771.704
100 300 -7311.9184 0 -7281.4518 -5944.573 19791.679
200 298.46333 -7306.5409 0 -7276.2304 -6669.0732 19903.341
300 298.05646 -7303.4774 0 -7273.2081 -10334.9 20033.654
400 297.71277 -7298.5998 0 -7268.3655 -7644.8753 20112.791
500 300 -7301.3145 0 -7270.8479 -6327.722 20143.842
600 306.29328 -7291.192 0 -7260.0863 -1482.3063 20281.66
700 308.44794 -7289.4349 0 -7258.1103 -3026.5046 20394.034
800 300 -7282.5733 0 -7252.1067 -3555.2034 20513.867
900 300 -7273.9966 0 -7243.53 -1850.9526 20622.554
1000 300 -7266.6095 0 -7236.1429 -1119.6046 20741.011
1100 301.26482 -7261.9024 0 -7231.3073 -1647.8612 20874.123
1200 299.17066 -7259.2281 0 -7228.8457 -1938.4437 20998.686
1300 300 -7263.9553 0 -7233.4887 -3376.9235 21112.258
1400 300 -7270.1139 0 -7239.6473 -5846.3511 21249.033
1500 307.98903 -7273.6991 0 -7242.4211 -6121.5944 21366.268
1600 300 -7278.9972 0 -7248.5306 -9389.2139 21484.725
1700 300 -7279.8403 0 -7249.3737 -14440.631 21615.394
1800 309.55921 -7284.1875 0 -7252.7501 -14795.954 21727.745
1900 299.29406 -7282.5749 0 -7252.18 -15392.232 21848.644
2000 299.964 -7271.7156 0 -7241.2526 -19451.05 21968.322
2100 308.54552 -7272.2334 0 -7240.8989 -23685.178 22100.212
2200 308.49102 -7271.1314 0 -7239.8025 -20630.136 22219.89
2300 290.31543 -7268.9828 0 -7239.4997 -19028.307 22342.011
2400 299.15433 -7259.7686 0 -7229.3878 -14272.769 22459.246
2500 299.15088 -7260.7963 0 -7230.4159 -14923.448 22576.482
2600 301.27999 -7258.5805 0 -7227.9839 -15706.203 22702.266
2700 307.83121 -7254.9828 0 -7223.7209 -19761.07 22830.493
2800 300 -7254.6086 0 -7224.142 -23849.892 22944.065
2900 303.23126 -7256.0886 0 -7225.2938 -23451.705 23080.84
3000 290.86402 -7255.5292 0 -7225.9904 -20678.136 23202.96
Loop time of 12.3962 on 1 procs for 3000 steps with 1708 atoms
Pair time (%) = 11.4662 (92.4971)
Neigh time (%) = 0.539913 (4.35546)
Comm time (%) = 0.0821109 (0.662385)
Outpt time (%) = 0.0712039 (0.574399)
Other time (%) = 0.23685 (1.91066)
Nlocal: 1708 ave 1708 max 1708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1882 ave 1882 max 1882 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 38801 ave 38801 max 38801 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 38801
Ave neighs/atom = 22.7172
Neighbor list builds = 205
Dangerous builds = 0

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LAMMPS (22 Jan 2008)
# 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
timestep 0.001
run 100
Memory usage per processor = 1.87344 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 0.185206 on 4 procs for 100 steps with 1708 atoms
Pair time (%) = 0.134434 (72.5863)
Neigh time (%) = 0.00337529 (1.82245)
Comm time (%) = 0.035861 (19.3627)
Outpt time (%) = 0.00149727 (0.808433)
Other time (%) = 0.0100384 (5.42011)
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
reset_timestep 0
run 3000
Memory usage per processor = 1.89003 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 303.68338 -7300.0537 0 -7269.213 396.12256 19807.521
100 307.23986 -7307.219 0 -7276.0171 -5006.3499 19862.724
200 300 -7309.7515 0 -7279.2849 -9319.6187 19862.401
300 298.46847 -7303.3937 0 -7273.0826 -9727.416 20012.256
400 298.27255 -7299.2458 0 -7268.9546 -7916.7896 20056.15
500 297.5947 -7299.7495 0 -7269.5271 -6499.9287 20136.515
600 299.11571 -7294.7189 0 -7264.342 -4738.4592 20278.808
700 299.12204 -7285.1912 0 -7254.8138 -1900.5818 20396.287
800 300 -7279.6074 0 -7249.1408 -601.56409 20516.31
900 300 -7272.2062 0 -7241.7396 372.01695 20624.997
1000 297.17814 -7265.7734 0 -7235.5934 -1620.5152 20750.781
1100 300 -7257.7175 0 -7227.2509 -1422.3295 20870.459
1200 300 -7254.9538 0 -7224.4872 -2924.6246 20990.137
1300 300 -7257.9757 0 -7227.5091 -4069.1414 21123.248
1400 300 -7265.0693 0 -7234.6027 -6549.1146 21249.033
1500 305.40659 -7268.4 0 -7237.3844 -9980.0284 21360.162
1600 307.73328 -7272.8967 0 -7241.6447 -12845.156 21479.84
1700 308.89481 -7272.8308 0 -7241.4609 -14742.73 21599.518
1800 301.22537 -7272.7599 0 -7242.1688 -15363.965 21736.293
1900 294.08915 -7269.2219 0 -7239.3555 -17918.885 21854.75
2000 300 -7267.3723 0 -7236.9057 -22110.158 21970.765
2100 303.71749 -7266.6269 0 -7235.7828 -24452.593 22103.876
2200 305.09813 -7260.5568 0 -7229.5724 -22990.432 22219.89
2300 302.38637 -7258.8153 0 -7228.1063 -21646.154 22335.905
2400 305.66165 -7262.3039 0 -7231.2623 -21131.332 22458.025
2500 298.90421 -7257.9905 0 -7227.6352 -21269.206 22592.358
2600 300.16888 -7256.8469 0 -7226.3631 -23698.687 22699.824
2700 296.33302 -7251.3734 0 -7221.2792 -26655.74 22826.829
2800 296.22091 -7248.3427 0 -7218.2599 -30008.453 22947.728
2900 301.32756 -7250.3222 0 -7219.7207 -28370.97 23080.84
3000 300 -7252.9148 0 -7222.4482 -28938.171 23201.739
Loop time of 5.54083 on 4 procs for 3000 steps with 1708 atoms
Pair time (%) = 3.99282 (72.0617)
Neigh time (%) = 0.141571 (2.55505)
Comm time (%) = 1.02782 (18.55)
Outpt time (%) = 0.102889 (1.85692)
Other time (%) = 0.275728 (4.9763)
Nlocal: 427 ave 441 max 415 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 784 ave 845 max 718 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 9597.25 ave 10151 max 9269 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 38389
Ave neighs/atom = 22.476
Neighbor list builds = 211
Dangerous builds = 0