ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11410 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2014-01-30 22:49:40 +00:00
parent b2e58866c4
commit abdec3cb5d
122 changed files with 0 additions and 49863 deletions
Download Patch File Download Diff File Expand all files Collapse all files

70
examples/body/log.body.18Feb13.linux.1
View File

@ -1,70 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d polygon nparticle bodies
units lj
dimension 2
atom_style body nparticle 2 6
read_data data.body
orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
1 by 1 by 1 MPI processor grid
100 atoms
100 bodies
velocity all create 1.44 87287 loop geom
pair_style body 5.0
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
fix 1 all nve/body
fix 2 all enforce2d
#compute 1 all body/local type 1 2 3
#dump 2 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
thermo 500
run 10000
Memory usage per processor = 3.13483 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.63799525 0 0.78760475 -0.15028724
500 1.5537157 -1.5243356 0 0.013843001 0.2654775
1000 1.5681616 -1.8003444 0 -0.2478644 0.07601415
1500 1.6994347 -1.7246456 0 -0.04220525 0.3664501
2000 1.6587022 -1.6970163 0 -0.054901081 0.10137795
2500 1.7859516 -1.8212698 0 -0.053177671 0.35400181
3000 1.7865459 -1.730183 0 0.038497352 0.28330983
3500 2.0521408 -1.98222 0 0.049399375 0.088928245
4000 1.721448 -1.7409775 0 -0.036743968 0.12815274
4500 1.6189244 -1.7257177 0 -0.12298249 0.21501422
5000 1.5828072 -1.6501894 0 -0.083210213 0.33447691
5500 1.8562352 -1.7632936 0 0.074379269 0.24273308
6000 1.4818079 -1.6942298 0 -0.22723999 0.22470999
6500 1.5229137 -1.6249423 0 -0.11725778 -0.043041211
7000 1.5930761 -1.5349749 0 0.04217044 0.072621368
7500 1.7251412 -1.7620322 0 -0.05414237 -0.052083575
8000 1.7843737 -1.6422594 0 0.12427062 0.3924994
8500 1.9344759 -1.7880774 0 0.12705368 0.32652919
9000 1.6338929 -1.6889133 0 -0.071359354 0.3793827
9500 1.5180082 -1.7729127 0 -0.27008457 0.27223707
10000 1.6133128 -1.7939587 0 -0.19677903 0.18983194
Loop time of 2.02483 on 1 procs for 10000 steps with 100 atoms
Pair time (%) = 1.79988 (88.8902)
Neigh time (%) = 0.0158422 (0.782395)
Comm time (%) = 0.0324693 (1.60355)
Outpt time (%) = 0.000159264 (0.00786552)
Other time (%) = 0.176485 (8.71602)
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 85 ave 85 max 85 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 424 ave 424 max 424 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 424
Ave neighs/atom = 4.24
Neighbor list builds = 795
Dangerous builds = 83

70
examples/body/log.body.18Feb13.linux.4
View File

@ -1,70 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d polygon nparticle bodies
units lj
dimension 2
atom_style body nparticle 2 6
read_data data.body
orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
2 by 2 by 1 MPI processor grid
100 atoms
100 bodies
velocity all create 1.44 87287 loop geom
pair_style body 5.0
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
fix 1 all nve/body
fix 2 all enforce2d
#compute 1 all body/local type 1 2 3
#dump 2 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
thermo 500
run 10000
Memory usage per processor = 3.10704 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.63799525 0 0.78760475 -0.15028724
500 1.5537157 -1.5243356 0 0.013843001 0.2654775
1000 1.5681616 -1.8003444 0 -0.2478644 0.07601415
1500 1.6994347 -1.7246456 0 -0.042205239 0.36645011
2000 1.6586974 -1.6970115 0 -0.054901078 0.10137999
2500 1.7878623 -1.8213737 0 -0.051390011 0.35530747
3000 1.7043715 -1.6613359 0 0.025991881 0.27048518
3500 1.6313416 -1.5250929 0 0.089935264 0.10510436
4000 1.5883641 -1.7692022 0 -0.1967218 0.50882304
4500 1.5897207 -1.5634198 0 0.010403642 0.24598267
5000 1.4849734 -1.5512049 0 -0.081081244 -0.028399888
5500 1.6074988 -1.7000582 0 -0.10863448 0.42879191
6000 1.6106093 -1.5850749 0 0.0094282394 0.4115976
6500 1.8169151 -1.7996899 0 -0.00094400747 0.21677584
7000 1.5487579 -1.6028263 0 -0.069555913 0.23742891
7500 1.7231927 -1.8001082 0 -0.094147408 -0.016712191
8000 1.5832288 -1.7242109 0 -0.15681439 0.33204
8500 1.9002455 -1.866332 0 0.014911066 0.28393405
9000 1.5916225 -1.6032424 0 -0.027536096 0.48213053
9500 1.6326075 -1.7974673 0 -0.18118584 0.078132294
10000 1.3851677 -1.49406 0 -0.12274404 0.18606978
Loop time of 0.705195 on 4 procs for 10000 steps with 100 atoms
Pair time (%) = 0.463261 (65.6926)
Neigh time (%) = 0.00452006 (0.640966)
Comm time (%) = 0.181194 (25.6941)
Outpt time (%) = 0.000352561 (0.0499949)
Other time (%) = 0.0558674 (7.92226)
Nlocal: 25 ave 25 max 25 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 43.75 ave 48 max 40 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Neighs: 101.5 ave 113 max 91 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 406
Ave neighs/atom = 4.06
Neighbor list builds = 805
Dangerous builds = 97

125
examples/colloid/log.colloid.18Feb13.linux.1
View File

@ -1,125 +0,0 @@
LAMMPS (18 Feb 2013)
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.01
Lattice spacing in x,y,z = 10 10 10
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -5) to (300 300 5)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
set type 1 mass 9
39 settings made for mass
set type 2 mass 1
861 settings made for mass
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0
communicate multi
# colloid potential
pair_style colloid 12.5
pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
#dump 1 all atom 1000 dump.colloid
#dump 1 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 1 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Memory usage per processor = 2.9658 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9558819 -0.00044998322 1.9532587 0.01784589 99146.35
2000 2.0558568 0.011295331 2.0648679 0.021858185 96654.425
3000 2.1809647 0.0091754217 2.1877168 0.031294876 68756.47
4000 2.1960934 0.0028186107 2.1964719 0.049318667 42974.984
5000 2.1463273 0.012748525 2.156691 0.073994939 28660.577
6000 2.1073992 0.0076702433 2.1127279 0.097655997 21544.211
7000 2.084579 -0.0022304831 2.0800323 0.11014552 17791.284
8000 2.0677538 0.00059800188 2.0660543 0.12718796 15494.44
9000 2.0545977 0.0064465732 2.0587614 0.15002732 13864.665
10000 2.0482054 0.010661731 2.0565913 0.17497885 12553.11
11000 2.0360539 0.022283053 2.0560747 0.18608443 11469.573
12000 2.0488819 0.012601482 2.0592068 0.20752397 10547.355
13000 2.0307724 0.027945421 2.0564614 0.23492616 9791.6008
14000 2.0291712 0.024760645 2.0516772 0.25749445 9166.0223
15000 2.0421329 0.011858836 2.0517227 0.26019128 8645.5059
16000 2.0321296 0.023089154 2.0529608 0.30100779 8173.8988
17000 2.0339883 0.020841935 2.0525702 0.31937035 7749.9866
18000 2.0165994 0.039101369 2.0534601 0.33206939 7399.5633
19000 2.0174571 0.03075954 2.045975 0.37582663 7115.1621
20000 2.0235743 0.033645074 2.054971 0.37789661 6779.655
21000 2.0086918 0.052575979 2.0590359 0.47587927 6468.3757
22000 2.0186512 0.035185664 2.0515939 0.39489244 6270.2423
23000 2.0159704 0.037209936 2.0509404 0.42372164 6090.2568
24000 2.0262103 0.034411154 2.0583702 0.46377965 5878.6019
25000 2.0136031 0.040396972 2.0517627 0.49998462 5706.6657
26000 2.0118123 0.04348596 2.0530629 0.52601904 5555.535
27000 2.0483861 0.010622163 2.0567323 0.46408289 5439.3763
28000 1.9775694 0.0880593 2.0634314 0.60451974 5303.7986
29000 2.0161573 0.051647461 2.0655645 0.55856521 5154.8346
30000 2.0154349 0.045614723 2.0588102 0.55640547 5067.2252
31000 2.0264636 0.042015926 2.0662279 0.58323212 4966.2146
32000 1.9946148 0.074464523 2.0668631 0.64405663 4840.3505
33000 2.016998 0.046624054 2.0613809 0.6520715 4765.5247
34000 2.0086574 0.060996501 2.067422 0.6530397 4666.4569
35000 2.0203252 0.05402663 2.0721071 0.69134002 4595.6514
36000 2.0271451 0.041489394 2.0663822 0.65114797 4526.2978
37000 2.0183469 0.064565854 2.0806701 0.70724758 4446.6465
38000 2.0049133 0.065280115 2.0679658 0.76328332 4389.5655
39000 2.0254497 0.05173788 2.0749371 0.75604831 4332.6535
40000 2.0019046 0.080413589 2.0800938 0.78175962 4254.5071
41000 2.0246809 0.05297341 2.0754047 0.77404015 4193.7093
42000 2.0254595 0.058651302 2.0818603 0.81823656 4135.9705
43000 2.0007241 0.083353246 2.0818543 0.82002543 4082.2245
44000 1.994415 0.089912333 2.0821113 0.98373573 4051.5787
45000 2.0130937 0.07986583 2.0907228 0.97054142 3991.453
46000 1.9997536 0.094509733 2.0920414 0.90955799 3926.3675
47000 2.0026833 0.086980098 2.0874382 1.1140455 3885.3495
48000 2.0217273 0.077640083 2.0971211 0.94719095 3829.7776
49000 1.9778606 0.11563852 2.0913015 1.1107597 3798.5114
50000 2.038067 0.060063696 2.0958661 1.0030415 3763.2003
Loop time of 8.78756 on 1 procs for 50000 steps with 900 atoms
Pair time (%) = 4.14849 (47.2086)
Neigh time (%) = 1.09428 (12.4526)
Comm time (%) = 0.430549 (4.89953)
Outpt time (%) = 0.00056386 (0.00641657)
Other time (%) = 3.11369 (35.4329)
Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 515 ave 515 max 515 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5990 ave 5990 max 5990 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5990
Ave neighs/atom = 6.65556
Neighbor list builds = 3145
Dangerous builds = 0

125
examples/colloid/log.colloid.18Feb13.linux.4
View File

@ -1,125 +0,0 @@
LAMMPS (18 Feb 2013)
# Big colloid particles and small LJ particles
units lj
atom_style sphere
dimension 2
lattice sq 0.01
Lattice spacing in x,y,z = 10 10 10
region box block 0 30 0 30 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -5) to (300 300 5)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 900 atoms
set group all type/fraction 2 0.96 23984
861 settings made for type/fraction
set type 1 mass 9
39 settings made for mass
set type 2 mass 1
861 settings made for mass
velocity all create 1.44 87287 loop geom
# multi neighbor and comm for efficiency
neighbor 1 multi
neigh_modify delay 0
communicate multi
# colloid potential
pair_style colloid 12.5
pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
#dump 1 all atom 1000 dump.colloid
#dump 1 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 1 pad 5 adiam 1 5.0 adiam 2 1.5
thermo_style custom step temp epair etotal press vol
thermo 1000
timestep 0.005
run 50000
Memory usage per processor = 2.8708 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9558819 -0.00044998322 1.9532587 0.01784589 99146.35
2000 2.0558568 0.011295331 2.0648679 0.021858185 96654.425
3000 2.1809647 0.0091754217 2.1877168 0.031294876 68756.47
4000 2.1960934 0.0028186107 2.1964719 0.049318667 42974.984
5000 2.1463273 0.01274853 2.156691 0.07399494 28660.577
6000 2.1073955 0.0076740311 2.112728 0.097657373 21544.21
7000 2.0843684 -0.001996932 2.0800555 0.11036967 17791.247
8000 2.0640518 0.0014998478 2.0632583 0.1290879 15498.836
9000 2.0466103 0.010705612 2.0550419 0.15352798 13893.115
10000 2.0318438 0.028356097 2.0579423 0.18270659 12603.157
11000 2.0483114 0.011317082 2.0573526 0.18793572 11521.407
12000 2.0465451 0.011178196 2.0554494 0.20917582 10593.908
13000 2.0339418 0.020973133 2.052655 0.22462811 9837.666
14000 2.0352875 0.021186021 2.054212 0.25973065 9169.0201
15000 2.0397627 0.016745562 2.0542419 0.26379715 8580.3575
16000 2.0306726 0.019939485 2.0483558 0.30415554 8135.4142
17000 2.0303715 0.023425678 2.0515413 0.29717285 7732.4398
18000 2.0091196 0.046353117 2.0532404 0.4201013 7321.9473
19000 2.0069004 0.044794224 2.0494648 0.37207191 7008.5252
20000 2.0293906 0.02286811 2.0500038 0.37743862 6770.2412
21000 2.0151565 0.035150252 2.0480677 0.42245372 6563.7655
22000 1.9931286 0.061233296 2.0521473 0.44215378 6387.0047
23000 2.0095257 0.04877004 2.0560629 0.4359382 6146.7894
24000 2.0244673 0.041537999 2.0637559 0.47433783 5904.2578
25000 2.0411374 0.014657985 2.0535275 0.42934196 5714.3163
26000 2.0101343 0.048931921 2.0568327 0.58433419 5557.1491
27000 2.010355 0.044833431 2.0529547 0.53172163 5441.607
28000 2.0075626 0.056527165 2.0618592 0.54811055 5312.0333
29000 2.0279913 0.036953425 2.0626914 0.53888357 5165.8026
30000 2.0014479 0.062210877 2.0614349 0.61283256 5028.4409
31000 2.0072038 0.060184255 2.0651578 0.62321627 4918.8388
32000 2.0250392 0.043276173 2.0660653 0.61454026 4822.6538
33000 2.0225382 0.041253335 2.0615443 0.61742775 4746.3484
34000 2.0079979 0.060100013 2.0658668 0.7196627 4668.3612
35000 1.9869444 0.081389753 2.0661264 0.69301002 4630.1772
36000 2.0080612 0.068966773 2.0747968 0.75807989 4524.4316
37000 2.016828 0.059785388 2.0743725 0.73797084 4436.8809
38000 1.9923438 0.084178865 2.074309 0.83179043 4358.5286
39000 2.0144256 0.058962222 2.0711496 0.72841391 4318.0019
40000 2.0205458 0.063834805 2.0821355 0.79611444 4233.3053
41000 1.9895557 0.088139599 2.0754847 0.77982219 4183.6801
42000 1.9862976 0.097665639 2.0817562 0.9527169 4136.6273
43000 1.9845679 0.10838021 2.0907431 0.84567001 4063.3971
44000 2.0058015 0.079068928 2.0826418 0.87879853 4013.8417
45000 2.01267 0.072607353 2.083041 0.84521964 3983.104
46000 2.0028119 0.088952749 2.0895393 0.86809738 3907.9426
47000 2.0219141 0.069213747 2.0888813 0.88288894 3868.029
48000 1.9820914 0.1111149 2.091004 1.0650645 3812.8502
49000 2.0161896 0.077389897 2.0913393 0.94940244 3771.6873
50000 2.0216994 0.071211384 2.0906645 0.99837694 3771.8545
Loop time of 3.74849 on 4 procs for 50000 steps with 900 atoms
Pair time (%) = 1.1053 (29.4865)
Neigh time (%) = 0.286503 (7.64317)
Comm time (%) = 0.876681 (23.3876)
Outpt time (%) = 0.000933409 (0.0249009)
Other time (%) = 1.47907 (39.4578)
Nlocal: 225 ave 251 max 199 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 295.25 ave 304 max 283 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 1477.25 ave 1684 max 1286 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 5909
Ave neighs/atom = 6.56556
Neighbor list builds = 3138
Dangerous builds = 0

73
examples/comb/log.comb.Cu.18Feb13.linux.1
View File

@ -1,73 +0,0 @@
LAMMPS (18 Feb 2013)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
#dump 1 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 2 element Cu
run 10
Memory usage per processor = 3.72504 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
1 10.099643 -3.5063151 -3.5076155 -3.5076155 0 27.512983 3023.4645 14.46 14.46 14.46 0
2 10.098572 -3.5063151 -3.5076153 -3.5076153 0 27.563765 3023.4645 14.46 14.46 14.46 0
3 10.096788 -3.5063151 -3.5076151 -3.5076151 0 27.64839 3023.4645 14.46 14.46 14.46 0
4 10.094291 -3.5063151 -3.5076148 -3.5076148 0 27.766843 3023.4645 14.46 14.46 14.46 0
5 10.09108 -3.5063151 -3.5076144 -3.5076144 0 27.919101 3023.4645 14.46 14.46 14.46 0
6 10.087158 -3.5063151 -3.5076139 -3.5076139 0 28.105138 3023.4645 14.46 14.46 14.46 0
7 10.082524 -3.5063151 -3.5076133 -3.5076133 0 28.324919 3023.4645 14.46 14.46 14.46 0
8 10.077179 -3.5063151 -3.5076126 -3.5076126 0 28.578403 3023.4645 14.46 14.46 14.46 0
9 10.071123 -3.5063151 -3.5076118 -3.5076118 0 28.865545 3023.4645 14.46 14.46 14.46 0
10 10.06436 -3.5063151 -3.5076109 -3.5076109 0 29.186292 3023.4645 14.46 14.46 14.46 0
Loop time of 0.181534 on 1 procs for 10 steps with 256 atoms
Pair time (%) = 0.180967 (99.6874)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000329018 (0.181243)
Outpt time (%) = 0.000129938 (0.0715778)
Other time (%) = 0.00010848 (0.0597576)
Nlocal: 256 ave 256 max 256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4375 ave 4375 max 4375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 172544 ave 172544 max 172544 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0

73
examples/comb/log.comb.Cu.18Feb13.linux.4
View File

@ -1,73 +0,0 @@
LAMMPS (18 Feb 2013)
# Pure Cu crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice fcc 3.615
Lattice spacing in x,y,z = 3.615 3.615 3.615
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256 atoms
mass 1 63.54
pair_style comb
pair_coeff * * ffield.comb Cu
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Cu
#dump 1 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 2 element Cu
run 10
Memory usage per processor = 3.21798 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
1 10.099638 -3.5063151 -3.5076155 -3.5076155 0 27.513531 3023.4645 14.46 14.46 14.46 0
2 10.098553 -3.5063151 -3.5076153 -3.5076153 0 27.565957 3023.4645 14.46 14.46 14.46 0
3 10.096744 -3.5063151 -3.5076151 -3.5076151 0 27.653322 3023.4645 14.46 14.46 14.46 0
4 10.094212 -3.5063151 -3.5076148 -3.5076148 0 27.775611 3023.4645 14.46 14.46 14.46 0
5 10.090958 -3.5063151 -3.5076144 -3.5076144 0 27.932801 3023.4645 14.46 14.46 14.46 0
6 10.086981 -3.5063151 -3.5076139 -3.5076139 0 28.124863 3023.4645 14.46 14.46 14.46 0
7 10.082283 -3.5063151 -3.5076132 -3.5076132 0 28.351761 3023.4645 14.46 14.46 14.46 0
8 10.076864 -3.5063151 -3.5076125 -3.5076125 0 28.613454 3023.4645 14.46 14.46 14.46 0
9 10.070725 -3.5063151 -3.5076118 -3.5076118 0 28.909893 3023.4645 14.46 14.46 14.46 0
10 10.063868 -3.5063151 -3.5076109 -3.5076109 0 29.241022 3023.4645 14.46 14.46 14.46 0
Loop time of 0.0491828 on 4 procs for 10 steps with 256 atoms
Pair time (%) = 0.046394 (94.3298)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00239462 (4.86881)
Outpt time (%) = 0.000263989 (0.536751)
Other time (%) = 0.000130177 (0.264679)
Nlocal: 64 ave 64 max 64 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 2971 ave 2971 max 2971 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 43136 ave 43136 max 43136 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 172544
Ave neighs/atom = 674
Neighbor list builds = 0
Dangerous builds = 0

315
examples/comb/log.comb.Cu2O.elastic.18Feb13.linux.1
View File

@ -1,315 +0,0 @@
LAMMPS (18 Feb 2013)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
1296 atoms
mass 1 63.54
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
432 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
#dump_modify 1 element Cu O
run 2
Memory usage per processor = 6.58849 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.7228352 -1.4456704 25.62 25.62 25.62 16816.568
1 0.99939067 -3.8453114 -3.8454405 -0.98378996 -2.8616505 0.72283606 -1.4456721 25.62 25.62 25.62 16816.568
2 0.9975671 -3.8453114 -3.8454402 -0.98378316 -2.8616571 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
Loop time of 0.303714 on 1 procs for 2 steps with 1296 atoms
Pair time (%) = 0.10212 (33.6237)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000129938 (0.042783)
Outpt time (%) = 5.00679e-05 (0.0164852)
Other time (%) = 0.201414 (66.317)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 8.03809 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 0.9975671 -3.8453114 -3.8454402 -0.98377395 -2.8616663 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
3 0.9975671 -3.8453323 -3.8454611 -0.98048803 -2.8649731 0.72283727 -1.4456745 25.59438 25.59438 25.59438 16766.169
4 0.9975671 -3.8453323 -3.8454611 -0.98048803 -2.8649731 0.72283727 -1.4456745 25.59438 25.59438 25.59438 16766.169
Loop time of 0.777246 on 1 procs for 2 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.84544021729 -3.84546110694 -3.84546110694
Force two-norm initial, final = 14.2445 25.7657
Force max component initial, final = 8.22308 14.8753
Final line search alpha, max atom move = 1.64125e-08 2.44141e-07
Iterations, force evaluations = 2 14
Pair time (%) = 0.77299 (99.4524)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000989199 (0.12727)
Outpt time (%) = 2.40803e-05 (0.00309815)
Other time (%) = 0.00324297 (0.417238)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 6.91773 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
4 0.9975671 -3.8453323 -3.8454611 -0.98048803 -2.8649731 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
5 0.99455526 -3.8453323 -3.8454607 -0.98046814 -2.8649926 0.72284124 -1.4456825 25.59438 25.59438 25.59438 16766.169
Loop time of 0.169949 on 1 procs for 1 steps with 1296 atoms
Pair time (%) = 0.0514941 (30.2997)
Neigh time (%) = 0 (0)
Comm time (%) = 6.67572e-05 (0.0392807)
Outpt time (%) = 2.5034e-05 (0.0147303)
Other time (%) = 0.118363 (69.6462)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
#undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (output.cpp:663)
run 10
Memory usage per processor = 7.17628 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
5 25.59438 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.965 -66762.055 -48486.82
6 25.594636 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.965 -66762.055 -48486.82
7 25.594892 25.59438 25.59438 0 0 0 -23480575 -23788468 -23788455 -57056.822 -66760.719 -48482.06
8 25.595148 25.59438 25.59438 0 0 0 -23151645 -23767428 -23767415 -57055.68 -66759.384 -48477.299
9 25.595404 25.59438 25.59438 0 0 0 -22822715 -23746393 -23746380 -57054.538 -66758.05 -48472.539
10 25.59566 25.59438 25.59438 0 0 0 -22493785 -23725364 -23725351 -57053.397 -66756.716 -48467.778
11 25.595916 25.59438 25.59438 0 0 0 -22164855 -23704340 -23704327 -57052.256 -66755.382 -48463.018
12 25.596172 25.59438 25.59438 0 0 0 -21835925 -23683322 -23683309 -57051.116 -66754.048 -48458.258
13 25.596428 25.59438 25.59438 0 0 0 -21506996 -23662310 -23662296 -57049.976 -66752.714 -48453.499
14 25.596684 25.59438 25.59438 0 0 0 -21178067 -23641302 -23641289 -57048.836 -66751.379 -48448.74
15 25.59694 25.59438 25.59438 0 0 0 -20849138 -23620300 -23620287 -57047.697 -66750.045 -48443.981
Loop time of 0.644403 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.64049 (99.3928)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000681877 (0.105815)
Outpt time (%) = 0.00294185 (0.456523)
Other time (%) = 0.000288963 (0.044842)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 7.69337 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
15 25.59694 25.59438 25.59438 0 0 0 -20520209 -23599304 -23599291 -57046.557 -66748.711 -48439.223
16 25.59694 25.59438 25.594636 0 0 0 -20520209 -23599304 -23599291 -57046.557 -66748.711 -48439.223
17 25.59694 25.59438 25.594892 0 0 0 -20499216 -23578254 -23270413 -57040.958 -66747.376 -48438.253
18 25.59694 25.59438 25.595148 0 0 0 -20478228 -23557209 -22941536 -57035.359 -66746.041 -48437.283
19 25.59694 25.59438 25.595404 0 0 0 -20457246 -23536169 -22612658 -57029.76 -66744.706 -48436.313
20 25.59694 25.59438 25.59566 0 0 0 -20436270 -23515135 -22283781 -57024.162 -66743.371 -48435.343
21 25.59694 25.59438 25.595916 0 0 0 -20415299 -23494106 -21954904 -57018.563 -66742.035 -48434.374
22 25.59694 25.59438 25.596172 0 0 0 -20394333 -23473083 -21626027 -57012.964 -66740.7 -48433.404
23 25.59694 25.59438 25.596428 0 0 0 -20373373 -23452065 -21297150 -57007.366 -66739.366 -48432.435
24 25.59694 25.59438 25.596684 0 0 0 -20352419 -23431053 -20968274 -57001.768 -66738.031 -48431.466
25 25.59694 25.59438 25.59694 0 0 0 -20331470 -23410046 -20639397 -56996.17 -66736.696 -48430.497
Loop time of 0.64448 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.640578 (99.3945)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000667572 (0.103583)
Outpt time (%) = 0.00293732 (0.455765)
Other time (%) = 0.000297308 (0.0461315)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 8.21046 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
25 25.59694 25.59438 25.59694 0 0 0 -20310526 -23389045 -20310521 -56990.572 -66735.361 -48429.528
26 25.59694 25.59438 25.59694 0 0 5.1193879e-07 -20310526 -23389045 -20310521 -56990.572 -66735.361 -48429.528
27 25.59694 25.59438 25.59694 0 0 1.0238776e-06 -20310526 -23389045 -20310521 -56990.566 -66735.355 -48165.06
28 25.59694 25.59438 25.59694 0 0 1.5358164e-06 -20310526 -23389045 -20310521 -56990.561 -66735.349 -47900.593
29 25.59694 25.59438 25.59694 0 0 2.0477552e-06 -20310526 -23389045 -20310521 -56990.555 -66735.343 -47636.125
30 25.59694 25.59438 25.59694 0 0 2.559694e-06 -20310526 -23389045 -20310521 -56990.549 -66735.337 -47371.657
31 25.59694 25.59438 25.59694 0 0 3.0716328e-06 -20310526 -23389045 -20310521 -56990.544 -66735.331 -47107.19
32 25.59694 25.59438 25.59694 0 0 3.5835716e-06 -20310526 -23389045 -20310521 -56990.538 -66735.325 -46842.722
33 25.59694 25.59438 25.59694 0 0 4.0955103e-06 -20310526 -23389045 -20310521 -56990.532 -66735.319 -46578.254
34 25.59694 25.59438 25.59694 0 0 4.6074491e-06 -20310526 -23389045 -20310521 -56990.527 -66735.313 -46313.787
35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.521 -66735.307 -46049.319
Loop time of 0.644405 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.640508 (99.3953)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00068593 (0.106444)
Outpt time (%) = 0.0029223 (0.453487)
Other time (%) = 0.000288725 (0.0448049)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 8.72755 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.515 -66735.301 -45784.851
36 25.59694 25.59438 25.59694 5.118876e-07 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.515 -66735.301 -45784.851
37 25.59694 25.59438 25.59694 1.0237752e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56726.109 -66735.297 -45784.844
38 25.59694 25.59438 25.59694 1.5356628e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56461.703 -66735.293 -45784.837
39 25.59694 25.59438 25.59694 2.0475504e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56197.297 -66735.289 -45784.83
40 25.59694 25.59438 25.59694 2.559438e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55932.891 -66735.285 -45784.823
41 25.59694 25.59438 25.59694 3.0713256e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55668.485 -66735.281 -45784.816
42 25.59694 25.59438 25.59694 3.5832132e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55404.079 -66735.277 -45784.809
43 25.59694 25.59438 25.59694 4.0951008e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55139.672 -66735.273 -45784.802
44 25.59694 25.59438 25.59694 4.6069884e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54875.266 -66735.269 -45784.795
45 25.59694 25.59438 25.59694 5.118876e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54610.86 -66735.265 -45784.788
Loop time of 0.64518 on 1 procs for 10 steps with 1296 atoms
Pair time (%) = 0.641236 (99.3887)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000692606 (0.107351)
Outpt time (%) = 0.00295544 (0.458079)
Other time (%) = 0.000295639 (0.0458227)
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 810432 ave 810432 max 810432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0

315
examples/comb/log.comb.Cu2O.elastic.18Feb13.linux.4
View File

@ -1,315 +0,0 @@
LAMMPS (18 Feb 2013)
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.Cu2O
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
1296 atoms
mass 1 63.54
group type1 type 1
864 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
432 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Cu O
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
thermo_modify norm yes
thermo 1
fix 1 all nve
fix 2 all qeq/comb 1 0.0001
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
#dump_modify 1 element Cu O
run 2
Memory usage per processor = 3.94168 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.7228352 -1.4456704 25.62 25.62 25.62 16816.568
1 0.99939067 -3.8453114 -3.8454405 -0.98378996 -2.8616505 0.72283606 -1.4456721 25.62 25.62 25.62 16816.568
2 0.9975671 -3.8453114 -3.8454402 -0.98378316 -2.8616571 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
Loop time of 0.0779197 on 4 procs for 2 steps with 1296 atoms
Pair time (%) = 0.0256954 (32.9768)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00067848 (0.870742)
Outpt time (%) = 6.35386e-05 (0.0815436)
Other time (%) = 0.0514823 (66.0709)
Nlocal: 324 ave 324 max 324 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 4943 ave 4943 max 4943 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 202608 max 202608 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.001
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 5.27942 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 0.9975671 -3.8453114 -3.8454402 -0.98377395 -2.8616663 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
3 0.9975671 -3.8453323 -3.8454611 -0.98048803 -2.8649731 0.72283727 -1.4456745 25.59438 25.59438 25.59438 16766.169
4 0.9975671 -3.8453323 -3.8454611 -0.98048803 -2.8649731 0.72283727 -1.4456745 25.59438 25.59438 25.59438 16766.169
Loop time of 0.202277 on 4 procs for 2 steps with 1296 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.84544021729 -3.84546110694 -3.84546110694
Force two-norm initial, final = 14.2445 25.7657
Force max component initial, final = 8.22308 14.8753
Final line search alpha, max atom move = 1.64125e-08 2.44141e-07
Iterations, force evaluations = 2 14
Pair time (%) = 0.194534 (96.1723)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00576496 (2.85004)
Outpt time (%) = 3.05772e-05 (0.0151165)
Other time (%) = 0.00194705 (0.962565)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Memory usage per processor = 4.25229 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
4 0.9975671 -3.8453323 -3.8454611 -0.98048803 -2.8649731 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
5 0.99455526 -3.8453323 -3.8454607 -0.98046814 -2.8649926 0.72284124 -1.4456825 25.59438 25.59438 25.59438 16766.169
Loop time of 0.0442772 on 4 procs for 1 steps with 1296 atoms
Pair time (%) = 0.013078 (29.5366)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000556648 (1.25719)
Outpt time (%) = 3.05772e-05 (0.0690585)
Other time (%) = 0.030612 (69.1372)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
unfix 2
#undump 1
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (output.cpp:663)
run 10
Memory usage per processor = 4.48932 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
5 25.59438 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.965 -66762.055 -48486.82
6 25.594636 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.965 -66762.055 -48486.82
7 25.594892 25.59438 25.59438 0 0 0 -23480575 -23788468 -23788455 -57056.822 -66760.719 -48482.06
8 25.595148 25.59438 25.59438 0 0 0 -23151645 -23767428 -23767415 -57055.68 -66759.384 -48477.299
9 25.595404 25.59438 25.59438 0 0 0 -22822715 -23746393 -23746380 -57054.538 -66758.05 -48472.539
10 25.59566 25.59438 25.59438 0 0 0 -22493785 -23725364 -23725351 -57053.397 -66756.716 -48467.778
11 25.595916 25.59438 25.59438 0 0 0 -22164855 -23704340 -23704327 -57052.256 -66755.382 -48463.018
12 25.596172 25.59438 25.59438 0 0 0 -21835925 -23683322 -23683309 -57051.116 -66754.048 -48458.258
13 25.596428 25.59438 25.59438 0 0 0 -21506996 -23662310 -23662296 -57049.976 -66752.714 -48453.499
14 25.596684 25.59438 25.59438 0 0 0 -21178067 -23641302 -23641289 -57048.836 -66751.379 -48448.74
15 25.59694 25.59438 25.59438 0 0 0 -20849138 -23620300 -23620287 -57047.697 -66750.045 -48443.981
Loop time of 0.166247 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.157497 (94.7364)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00575155 (3.45963)
Outpt time (%) = 0.00286341 (1.72238)
Other time (%) = 0.00013572 (0.0816372)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 4.96338 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
15 25.59694 25.59438 25.59438 0 0 0 -20520209 -23599304 -23599291 -57046.557 -66748.711 -48439.223
16 25.59694 25.59438 25.594636 0 0 0 -20520209 -23599304 -23599291 -57046.557 -66748.711 -48439.223
17 25.59694 25.59438 25.594892 0 0 0 -20499216 -23578254 -23270413 -57040.958 -66747.376 -48438.253
18 25.59694 25.59438 25.595148 0 0 0 -20478228 -23557209 -22941536 -57035.359 -66746.041 -48437.283
19 25.59694 25.59438 25.595404 0 0 0 -20457246 -23536169 -22612658 -57029.76 -66744.706 -48436.313
20 25.59694 25.59438 25.59566 0 0 0 -20436270 -23515135 -22283781 -57024.162 -66743.371 -48435.343
21 25.59694 25.59438 25.595916 0 0 0 -20415299 -23494106 -21954904 -57018.563 -66742.035 -48434.374
22 25.59694 25.59438 25.596172 0 0 0 -20394333 -23473083 -21626027 -57012.964 -66740.7 -48433.404
23 25.59694 25.59438 25.596428 0 0 0 -20373373 -23452065 -21297150 -57007.366 -66739.366 -48432.435
24 25.59694 25.59438 25.596684 0 0 0 -20352419 -23431053 -20968274 -57001.768 -66738.031 -48431.466
25 25.59694 25.59438 25.59694 0 0 0 -20331470 -23410046 -20639397 -56996.17 -66736.696 -48430.497
Loop time of 0.16598 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.157451 (94.8617)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00552714 (3.33001)
Outpt time (%) = 0.00287336 (1.73115)
Other time (%) = 0.00012809 (0.0771722)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 5.43744 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
25 25.59694 25.59438 25.59694 0 0 0 -20310526 -23389045 -20310521 -56990.572 -66735.361 -48429.528
26 25.59694 25.59438 25.59694 0 0 5.1193879e-07 -20310526 -23389045 -20310521 -56990.572 -66735.361 -48429.528
27 25.59694 25.59438 25.59694 0 0 1.0238776e-06 -20310526 -23389045 -20310521 -56990.566 -66735.355 -48165.06
28 25.59694 25.59438 25.59694 0 0 1.5358164e-06 -20310526 -23389045 -20310521 -56990.561 -66735.349 -47900.593
29 25.59694 25.59438 25.59694 0 0 2.0477552e-06 -20310526 -23389045 -20310521 -56990.555 -66735.343 -47636.125
30 25.59694 25.59438 25.59694 0 0 2.559694e-06 -20310526 -23389045 -20310521 -56990.549 -66735.337 -47371.657
31 25.59694 25.59438 25.59694 0 0 3.0716328e-06 -20310526 -23389045 -20310521 -56990.544 -66735.331 -47107.19
32 25.59694 25.59438 25.59694 0 0 3.5835716e-06 -20310526 -23389045 -20310521 -56990.538 -66735.325 -46842.722
33 25.59694 25.59438 25.59694 0 0 4.0955103e-06 -20310526 -23389045 -20310521 -56990.532 -66735.319 -46578.254
34 25.59694 25.59438 25.59694 0 0 4.6074491e-06 -20310526 -23389045 -20310521 -56990.527 -66735.313 -46313.787
35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.521 -66735.307 -46049.319
Loop time of 0.166387 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.158143 (95.0453)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00517648 (3.11111)
Outpt time (%) = 0.00292784 (1.75965)
Other time (%) = 0.000139594 (0.0838971)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 5.9115 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.515 -66735.301 -45784.851
36 25.59694 25.59438 25.59694 5.118876e-07 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.515 -66735.301 -45784.851
37 25.59694 25.59438 25.59694 1.0237752e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56726.109 -66735.297 -45784.844
38 25.59694 25.59438 25.59694 1.5356628e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56461.703 -66735.293 -45784.837
39 25.59694 25.59438 25.59694 2.0475504e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56197.297 -66735.289 -45784.83
40 25.59694 25.59438 25.59694 2.559438e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55932.891 -66735.285 -45784.823
41 25.59694 25.59438 25.59694 3.0713256e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55668.485 -66735.281 -45784.816
42 25.59694 25.59438 25.59694 3.5832132e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55404.079 -66735.277 -45784.809
43 25.59694 25.59438 25.59694 4.0951008e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55139.672 -66735.273 -45784.802
44 25.59694 25.59438 25.59694 4.6069884e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54875.266 -66735.269 -45784.795
45 25.59694 25.59438 25.59694 5.118876e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54610.86 -66735.265 -45784.788
Loop time of 0.166469 on 4 procs for 10 steps with 1296 atoms
Pair time (%) = 0.160847 (96.6229)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00259542 (1.5591)
Outpt time (%) = 0.00287849 (1.72914)
Other time (%) = 0.000147939 (0.0888686)
Nlocal: 324 ave 331 max 321 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 4943 ave 4946 max 4936 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 202608 ave 207074 max 200694 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 810432
Ave neighs/atom = 625.333
Neighbor list builds = 0
Dangerous builds = 0

259
examples/comb/log.comb.HfO2.18Feb13.linux.1
View File

@ -1,259 +0,0 @@
LAMMPS (18 Feb 2013)
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.m-HfO2
triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
1 by 1 by 1 MPI processor grid
1500 atoms
#read_data data.t-HfO2
#read_data data.c-HfO2
mass 1 178.0
group type1 type 1
500 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
1000 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Hf O
neighbor 0.5 bin
neigh_modify every 10 delay 10 check yes
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
thermo_modify norm yes
fix 1 all nvt temp 300.0 300.0 0.1
thermo 1
run 1
Memory usage per processor = 9.38262 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -9.5079733 -9.5079733 5.1477526 -14.655726 -137492.1 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.10158794 -9.5079736 -9.5079867 5.147743 -14.65573 -137441.67 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.121043 on 1 procs for 1 steps with 1500 atoms
Pair time (%) = 0.120863 (99.8511)
Neigh time (%) = 0 (0)
Comm time (%) = 8.4877e-05 (0.0701213)
Outpt time (%) = 3.31402e-05 (0.0273788)
Other time (%) = 6.22272e-05 (0.0514091)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
fix 2 all qeq/comb 1 0.003 file fq.out
run 5
Memory usage per processor = 10.508 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.10158794 -9.5079736 -9.5079867 5.147743 -14.65573 -137441.67 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
2 0.44611424 -10.177672 -10.17773 2.5152099 -12.69294 -408898.04 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
3 1.1091377 -10.177676 -10.17782 2.5151362 -12.692956 -408487.56 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
4 2.0744017 -10.177683 -10.177951 2.5150272 -12.692978 -407877.44 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
5 3.3393343 -10.177692 -10.178123 2.5148832 -12.693006 -407066.63 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
6 4.9005371 -10.177703 -10.178336 2.5147047 -12.693041 -406053.73 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
Loop time of 0.836517 on 1 procs for 5 steps with 1500 atoms
Pair time (%) = 0.604237 (72.2325)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000416756 (0.0498204)
Outpt time (%) = 0.000157833 (0.0188679)
Other time (%) = 0.231705 (27.6988)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.0002
minimize 1.0e-12 1.0e-18 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 11.9842 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 4.9005371 -10.177703 -10.178336 2.5147047 -12.693041 -406053.73 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
7 4.9005371 -10.179122 -10.179755 2.5134924 -12.693247 -399211.14 17620.846 25.636872 25.952767 26.483664 -4.4667689 3.3487003 -1.6743501
8 4.9005371 -10.180516 -10.181149 2.5123069 -12.693456 -392200.95 17613.885 25.631743 25.948534 26.482818 -4.4666263 3.3487003 -1.6743501
9 4.9005371 -10.181882 -10.182515 2.5111487 -12.693664 -385024.22 17606.918 25.626615 25.944298 26.481963 -4.4664821 3.3487003 -1.6743501
10 4.9005371 -10.18322 -10.183853 2.5100185 -12.693872 -377684.02 17599.945 25.621486 25.940062 26.481097 -4.4663361 3.3487003 -1.6743501
11 4.9005371 -10.184531 -10.185164 2.508917 -12.694081 -370183.53 17592.964 25.616358 25.935823 26.48022 -4.4661881 3.3487003 -1.6743501
12 4.9005371 -10.18581 -10.186443 2.5078447 -12.694287 -362524.12 17585.976 25.61123 25.931583 26.479331 -4.4660381 3.3487003 -1.6743501
13 4.9005371 -10.187061 -10.187694 2.5068022 -12.694496 -354711.13 17578.979 25.606101 25.927341 26.478428 -4.4658859 3.3487003 -1.6743501
14 4.9005371 -10.188281 -10.188914 2.5057902 -12.694704 -346745.81 17571.973 25.600973 25.923098 26.477512 -4.4657313 3.3487003 -1.6743501
15 4.9005371 -10.189469 -10.190102 2.5048092 -12.694911 -338631.19 17564.957 25.595844 25.918852 26.47658 -4.4655742 3.3487003 -1.6743501
16 4.9005371 -10.190627 -10.19126 2.5038597 -12.695119 -330371.37 17557.931 25.590716 25.914603 26.475632 -4.4654143 3.3487003 -1.6743501
17 4.9005371 -10.19175 -10.192383 2.5029424 -12.695325 -321967.67 17550.893 25.585588 25.910353 26.474666 -4.4652514 3.3487003 -1.6743501
18 4.9005371 -10.19284 -10.193473 2.5020578 -12.695531 -313424.33 17543.842 25.580459 25.906099 26.473681 -4.4650853 3.3487003 -1.6743501
19 4.9005371 -10.193897 -10.19453 2.5012064 -12.695737 -304744.97 17536.777 25.575331 25.901843 26.472676 -4.4649157 3.3487003 -1.6743501
20 4.9005371 -10.195049 -10.195682 2.5002594 -12.695942 -295752.55 17529.697 25.570202 25.897584 26.471648 -4.4647424 3.3487003 -1.6743501
21 4.9005371 -10.196037 -10.19667 2.4994765 -12.696146 -286810.19 17522.602 25.565074 25.893323 26.470598 -4.4645653 3.3487003 -1.6743501
22 4.9005371 -10.196988 -10.197621 2.4987283 -12.696349 -277740.46 17515.49 25.559946 25.889059 26.469523 -4.4643839 3.3487003 -1.6743501
23 4.9005371 -10.197903 -10.198536 2.4980153 -12.696552 -268547.09 17508.358 25.554817 25.88479 26.468418 -4.4641976 3.3487003 -1.6743501
24 4.9005371 -10.198782 -10.199415 2.497338 -12.696753 -259232.88 17501.204 25.549689 25.880518 26.467283 -4.4640061 3.3487003 -1.6743501
25 4.9005371 -10.199623 -10.200256 2.4966969 -12.696953 -249801.3 17494.027 25.54456 25.876241 26.466113 -4.4638088 3.3487003 -1.6743501
26 4.9005371 -10.200428 -10.201061 2.4960923 -12.697154 -240255.95 17486.823 25.539432 25.87196 26.464906 -4.4636052 3.3487003 -1.6743501
27 4.9005371 -10.201196 -10.201829 2.4955247 -12.697353 -230599.57 17479.589 25.534304 25.867673 26.463657 -4.4633945 3.3487003 -1.6743501
28 4.9005371 -10.201927 -10.20256 2.4949946 -12.697554 -220836.27 17472.324 25.529175 25.86338 26.462362 -4.4631762 3.3487003 -1.6743501
29 4.9005371 -10.20262 -10.203253 2.4945024 -12.697756 -210968.3 17465.022 25.524047 25.85908 26.461016 -4.4629492 3.3487003 -1.6743501
30 4.9005371 -10.203281 -10.203914 2.4940484 -12.697962 -201001.66 17457.679 25.518918 25.854774 26.459613 -4.4627126 3.3487003 -1.6743501
31 4.9005371 -10.203904 -10.204537 2.4936332 -12.69817 -190935.91 17450.29 25.51379 25.85046 26.458146 -4.4624651 3.3487003 -1.6743501
32 4.9005371 -10.204488 -10.205121 2.493257 -12.698378 -180773.29 17442.85 25.508662 25.846136 26.456606 -4.4622054 3.3487003 -1.6743501
33 4.9005371 -10.205037 -10.20567 2.4929204 -12.698591 -170517.54 17435.349 25.503533 25.841802 26.454984 -4.4619318 3.3487003 -1.6743501
34 4.9005371 -10.205549 -10.206182 2.4926237 -12.698806 -160169.44 17427.781 25.498405 25.837457 26.453266 -4.4616421 3.3487003 -1.6743501
35 4.9005371 -10.206023 -10.206656 2.4923673 -12.699023 -149728.79 17420.132 25.493276 25.833098 26.451438 -4.4613337 3.3487003 -1.6743501
36 4.9005371 -10.206456 -10.207089 2.4921518 -12.699241 -139194.99 17412.389 25.488148 25.828724 26.44948 -4.4610034 3.3487003 -1.6743501
37 4.9005371 -10.206852 -10.207486 2.4919775 -12.699463 -128568.57 17404.534 25.48302 25.824331 26.447367 -4.4606471 3.3487003 -1.6743501
38 4.9005371 -10.207211 -10.207844 2.491845 -12.699689 -117845.52 17396.543 25.477891 25.819915 26.445067 -4.4602591 3.3487003 -1.6743501
39 4.9005371 -10.20753 -10.208164 2.491755 -12.699918 -107020.01 17388.383 25.472763 25.815472 26.442534 -4.459832 3.3487003 -1.6743501
40 4.9005371 -10.207815 -10.208448 2.4917081 -12.700156 -96083.354 17380.008 25.467634 25.810993 26.439708 -4.4593554 3.3487003 -1.6743501
41 4.9005371 -10.208062 -10.208695 2.4917053 -12.700401 -85018.286 17371.351 25.462506 25.806467 26.436497 -4.4588137 3.3487003 -1.6743501
42 4.9005371 -10.208271 -10.208904 2.491748 -12.700652 -73793.674 17362.307 25.457378 25.801878 26.432756 -4.4581829 3.3487003 -1.6743501
43 4.9005371 -10.208446 -10.209079 2.4918382 -12.700917 -62360.119 17352.697 25.452249 25.797196 26.428245 -4.4574219 3.3487003 -1.6743501
44 4.9005371 -10.208582 -10.209215 2.491967 -12.701182 -51542.505 17343.008 25.447525 25.792747 26.422948 -4.4565285 3.3487003 -1.6743501
45 4.9005371 -10.208681 -10.209314 2.4920939 -12.701408 -43273.049 17334.863 25.44406 25.789315 26.417651 -4.4556351 3.3487003 -1.6743501
46 4.9005371 -10.208759 -10.209393 2.4922069 -12.701599 -36997.799 17327.922 25.441576 25.786676 26.412354 -4.4547418 3.3487003 -1.6743501
47 4.9005371 -10.208834 -10.209467 2.4923019 -12.701769 -32264.505 17321.909 25.439848 25.784649 26.407057 -4.4538484 3.3487003 -1.6743501
48 4.9005371 -10.208909 -10.209542 2.4923792 -12.701921 -28705.843 17316.601 25.438696 25.783087 26.40176 -4.452955 3.3487003 -1.6743501
49 4.9005371 -10.208986 -10.209619 2.4924408 -12.70206 -26035.132 17311.825 25.437979 25.781876 26.396463 -4.4520616 3.3487003 -1.6743501
50 4.9005371 -10.209067 -10.2097 2.4924894 -12.702189 -24030.259 17307.449 25.437586 25.780929 26.391166 -4.4511682 3.3487003 -1.6743501
51 4.9005371 -10.209153 -10.209786 2.4925278 -12.702314 -22521.401 17303.368 25.437435 25.780178 26.385869 -4.4502748 3.3487003 -1.6743501
52 4.9005371 -10.209241 -10.209874 2.4925582 -12.702432 -21377.916 17299.506 25.437463 25.779571 26.380573 -4.4493815 3.3487003 -1.6743501
53 4.9005371 -10.20933 -10.209963 2.4925827 -12.702546 -20503.155 17295.805 25.437622 25.779072 26.375276 -4.4484881 3.3487003 -1.6743501
54 4.9005371 -10.20942 -10.210053 2.4926026 -12.702655 -19825.084 17292.222 25.437876 25.77865 26.369979 -4.4475947 3.3487003 -1.6743501
55 4.9005371 -10.20951 -10.210143 2.4926193 -12.702762 -19290.332 17288.725 25.4382 25.778286 26.364682 -4.4467013 3.3487003 -1.6743501
56 4.9005371 -10.209601 -10.210234 2.4926335 -12.702867 -18859.558 17285.289 25.438575 25.777963 26.359385 -4.4458079 3.3487003 -1.6743501
57 4.9005371 -10.209691 -10.210324 2.4926461 -12.70297 -18503.909 17281.899 25.438986 25.77767 26.354088 -4.4449146 3.3487003 -1.6743501
58 4.9005371 -10.209782 -10.210415 2.4926574 -12.703072 -18202.31 17278.541 25.439423 25.777399 26.348791 -4.4440212 3.3487003 -1.6743501
59 4.9005371 -10.209872 -10.210505 2.4926678 -12.703173 -17939.44 17275.206 25.439879 25.777144 26.343494 -4.4431278 3.3487003 -1.6743501
60 4.9005371 -10.209962 -10.210595 2.4926777 -12.703272 -17704.202 17271.887 25.440348 25.776901 26.338197 -4.4422344 3.3487003 -1.6743501
61 4.9005371 -10.210051 -10.210684 2.4926871 -12.703371 -17488.592 17268.581 25.440826 25.776666 26.3329 -4.441341 3.3487003 -1.6743501
62 4.9005371 -10.21014 -10.210773 2.4926963 -12.703469 -17286.86 17265.282 25.441311 25.776436 26.327604 -4.4404476 3.3487003 -1.6743501
63 4.9005371 -10.210227 -10.21086 2.4927054 -12.703566 -17094.395 17261.99 25.441799 25.776211 26.322307 -4.4395543 3.3487003 -1.6743501
64 4.9005371 -10.210317 -10.21095 2.4927143 -12.703664 -16910.273 17258.701 25.442291 25.77599 26.31701 -4.4386609 3.3487003 -1.6743501
65 4.9005371 -10.210403 -10.211036 2.4927232 -12.703759 -16729.397 17255.416 25.442785 25.775771 26.311713 -4.4377675 3.3487003 -1.6743501
66 4.9005371 -10.210491 -10.211124 2.4927321 -12.703856 -16553.119 17252.132 25.443279 25.775553 26.306416 -4.4368741 3.3487003 -1.6743501
67 4.9005371 -10.210578 -10.211211 2.492741 -12.703952 -16378.985 17248.849 25.443775 25.775338 26.301119 -4.4359807 3.3487003 -1.6743501
68 4.9005371 -10.210665 -10.211298 2.49275 -12.704048 -16206.061 17245.568 25.44427 25.775123 26.295822 -4.4350874 3.3487003 -1.6743501
69 4.9005371 -10.210751 -10.211384 2.492759 -12.704143 -16034.089 17242.287 25.444765 25.77491 26.290525 -4.434194 3.3487003 -1.6743501
70 4.9005371 -10.210836 -10.211469 2.4927681 -12.704237 -15862.739 17239.006 25.44526 25.774697 26.285228 -4.4333006 3.3487003 -1.6743501
71 4.9005371 -10.210921 -10.211554 2.4927772 -12.704331 -15691.781 17235.726 25.445755 25.774485 26.279931 -4.4324072 3.3487003 -1.6743501
72 4.9005371 -10.211005 -10.211638 2.4927864 -12.704424 -15521.058 17232.446 25.44625 25.774275 26.274635 -4.4315138 3.3487003 -1.6743501
73 4.9005371 -10.211088 -10.211721 2.4927957 -12.704517 -15350.462 17229.166 25.446743 25.774065 26.269338 -4.4306204 3.3487003 -1.6743501
74 4.9005371 -10.211171 -10.211804 2.4928051 -12.704609 -15179.92 17225.886 25.447237 25.773855 26.264041 -4.4297271 3.3487003 -1.6743501
75 4.9005371 -10.211253 -10.211887 2.4928145 -12.704701 -15009.382 17222.606 25.447729 25.773647 26.258744 -4.4288337 3.3487003 -1.6743501
76 4.9005371 -10.211335 -10.211968 2.492824 -12.704792 -14838.814 17219.326 25.448221 25.773439 26.253447 -4.4279403 3.3487003 -1.6743501
77 4.9005371 -10.211416 -10.212049 2.4928336 -12.704883 -14668.193 17216.046 25.448713 25.773232 26.24815 -4.4270469 3.3487003 -1.6743501
78 4.9005371 -10.211495 -10.212128 2.4928433 -12.704971 -14496.606 17212.766 25.449203 25.773026 26.242853 -4.4261535 3.3487003 -1.6743501
79 4.9005371 -10.211574 -10.212207 2.492853 -12.70506 -14326.218 17209.486 25.449694 25.77282 26.237556 -4.4252602 3.3487003 -1.6743501
80 4.9005371 -10.211653 -10.212286 2.4928628 -12.705149 -14155.606 17206.206 25.450183 25.772616 26.232259 -4.4243668 3.3487003 -1.6743501
81 4.9005371 -10.211693 -10.212326 2.4928678 -12.705194 -14070.237 17204.566 25.450428 25.772514 26.229611 -4.4239201 3.3487003 -1.6743501
82 4.9005371 -10.211712 -10.212345 2.4928703 -12.705216 -14027.539 17203.746 25.45055 25.772463 26.228287 -4.4236967 3.3487003 -1.6743501
83 4.9005371 -10.211717 -10.21235 2.4928709 -12.705221 -14016.863 17203.541 25.45058 25.77245 26.227956 -4.4236409 3.3487003 -1.6743501
84 4.9005371 -10.21172 -10.212353 2.4928712 -12.705224 -14011.525 17203.438 25.450596 25.772444 26.22779 -4.423613 3.3487003 -1.6743501
85 4.9005371 -10.211721 -10.212354 2.4928714 -12.705225 -14008.856 17203.387 25.450603 25.772441 26.227707 -4.423599 3.3487003 -1.6743501
86 4.9005371 -10.211721 -10.212354 2.4928714 -12.705225 -14008.69 17203.384 25.450604 25.77244 26.227702 -4.4235981 3.3487003 -1.6743501
87 4.9005371 -10.211721 -10.212354 2.4928714 -12.705225 -14008.606 17203.382 25.450604 25.77244 26.2277 -4.4235977 3.3487003 -1.6743501
88 4.9005371 -10.211721 -10.212354 2.4928714 -12.705225 -14008.564 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3487003 -1.6743501
89 4.9005371 -10.211721 -10.212354 2.4928714 -12.705225 -14008.564 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3487003 -1.6743501
Loop time of 18.332 on 1 procs for 83 steps with 1500 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-10.178336106 -10.212354026 -10.212354026
Force two-norm initial, final = 8831.76 490.29
Force max component initial, final = 6793.35 484.808
Final line search alpha, max atom move = 5.03582e-11 2.44141e-08
Iterations, force evaluations = 83 147
Pair time (%) = 18.2365 (99.4787)
Neigh time (%) = 0.036432 (0.198734)
Comm time (%) = 0.0126019 (0.0687423)
Outpt time (%) = 0.00270295 (0.0147444)
Other time (%) = 0.0438213 (0.239042)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.051e+06 ave 1.051e+06 max 1.051e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1051000
Ave neighs/atom = 700.667
Neighbor list builds = 1
Dangerous builds = 0
min_modify dmax 0.005 line quadratic
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 element Hf O
#dump 1 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 2 element Hf O
velocity all create 300.1 2398378
run 10
Memory usage per processor = 10.5175 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
89 300.1 -10.173589 -10.212354 2.4928714 -12.705225 -10457.266 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
90 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
91 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
92 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
93 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
94 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
95 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
96 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
97 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
98 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
99 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
Loop time of 1.70632 on 1 procs for 10 steps with 1500 atoms
Pair time (%) = 1.23247 (72.23)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000850201 (0.0498267)
Outpt time (%) = 0.000328779 (0.0192684)
Other time (%) = 0.472666 (27.701)
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0585e+06 ave 1.0585e+06 max 1.0585e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1058500
Ave neighs/atom = 705.667
Neighbor list builds = 0
Dangerous builds = 0

259
examples/comb/log.comb.HfO2.18Feb13.linux.4
View File

@ -1,259 +0,0 @@
LAMMPS (18 Feb 2013)
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.m-HfO2
triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
1 by 2 by 2 MPI processor grid
1500 atoms
#read_data data.t-HfO2
#read_data data.c-HfO2
mass 1 178.0
group type1 type 1
500 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
mass 2 16.00
group type2 type 2
1000 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
pair_style comb
pair_coeff * * ffield.comb Hf O
neighbor 0.5 bin
neigh_modify every 10 delay 10 check yes
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
thermo_modify norm yes
fix 1 all nvt temp 300.0 300.0 0.1
thermo 1
run 1
Memory usage per processor = 3.77333 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -9.5079733 -9.5079733 5.1477526 -14.655726 -137492.1 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.10158794 -9.5079736 -9.5079867 5.147743 -14.65573 -137441.67 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.031365 on 4 procs for 1 steps with 1500 atoms
Pair time (%) = 0.0307955 (98.1844)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000482798 (1.53929)
Outpt time (%) = 3.77297e-05 (0.120293)
Other time (%) = 4.89354e-05 (0.156019)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
fix 2 all qeq/comb 1 0.003 file fq.out
run 5
Memory usage per processor = 4.3231 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.10158794 -9.5079736 -9.5079867 5.147743 -14.65573 -137441.67 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
2 0.44611424 -10.177672 -10.17773 2.5152099 -12.69294 -408898.04 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
3 1.1091377 -10.177676 -10.17782 2.5151362 -12.692956 -408487.56 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
4 2.0744017 -10.177683 -10.177951 2.5150272 -12.692978 -407877.44 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
5 3.3393343 -10.177692 -10.178123 2.5148832 -12.693006 -407066.63 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
6 4.9005371 -10.177703 -10.178336 2.5147047 -12.693041 -406053.73 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
Loop time of 0.21711 on 4 procs for 5 steps with 1500 atoms
Pair time (%) = 0.154565 (71.1923)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00278312 (1.2819)
Outpt time (%) = 0.000246465 (0.113521)
Other time (%) = 0.0595148 (27.4123)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 259375 ave 259375 max 259375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
unfix 1
fix 1 all box/relax aniso 0.0 vmax 0.0002
minimize 1.0e-12 1.0e-18 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 5.03804 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 4.9005371 -10.177703 -10.178336 2.5147047 -12.693041 -406053.73 17627.802 25.642 25.957 26.4845 -4.46691 3.3487003 -1.6743501
7 4.9005371 -10.179122 -10.179755 2.5134924 -12.693247 -399211.14 17620.846 25.636872 25.952767 26.483664 -4.4667689 3.3487003 -1.6743501
8 4.9005371 -10.180516 -10.181149 2.5123069 -12.693456 -392200.95 17613.885 25.631743 25.948534 26.482818 -4.4666263 3.3487003 -1.6743501
9 4.9005371 -10.181882 -10.182515 2.5111487 -12.693664 -385024.22 17606.918 25.626615 25.944298 26.481963 -4.4664821 3.3487003 -1.6743501
10 4.9005371 -10.18322 -10.183853 2.5100185 -12.693872 -377684.02 17599.945 25.621486 25.940062 26.481097 -4.4663361 3.3487003 -1.6743501
11 4.9005371 -10.184531 -10.185164 2.508917 -12.694081 -370183.53 17592.964 25.616358 25.935823 26.48022 -4.4661881 3.3487003 -1.6743501
12 4.9005371 -10.18581 -10.186443 2.5078447 -12.694287 -362524.12 17585.976 25.61123 25.931583 26.479331 -4.4660381 3.3487003 -1.6743501
13 4.9005371 -10.187061 -10.187694 2.5068022 -12.694496 -354711.13 17578.979 25.606101 25.927341 26.478428 -4.4658859 3.3487003 -1.6743501
14 4.9005371 -10.188281 -10.188914 2.5057902 -12.694704 -346745.81 17571.973 25.600973 25.923098 26.477512 -4.4657313 3.3487003 -1.6743501
15 4.9005371 -10.189469 -10.190102 2.5048092 -12.694911 -338631.19 17564.957 25.595844 25.918852 26.47658 -4.4655742 3.3487003 -1.6743501
16 4.9005371 -10.190627 -10.19126 2.5038597 -12.695119 -330371.37 17557.931 25.590716 25.914603 26.475632 -4.4654143 3.3487003 -1.6743501
17 4.9005371 -10.19175 -10.192383 2.5029424 -12.695325 -321967.67 17550.893 25.585588 25.910353 26.474666 -4.4652514 3.3487003 -1.6743501
18 4.9005371 -10.19284 -10.193473 2.5020578 -12.695531 -313424.33 17543.842 25.580459 25.906099 26.473681 -4.4650853 3.3487003 -1.6743501
19 4.9005371 -10.193897 -10.19453 2.5012064 -12.695737 -304744.97 17536.777 25.575331 25.901843 26.472676 -4.4649157 3.3487003 -1.6743501
20 4.9005371 -10.195049 -10.195682 2.5002594 -12.695942 -295752.55 17529.697 25.570202 25.897584 26.471648 -4.4647424 3.3487003 -1.6743501
21 4.9005371 -10.196037 -10.19667 2.4994765 -12.696146 -286810.19 17522.602 25.565074 25.893323 26.470598 -4.4645653 3.3487003 -1.6743501
22 4.9005371 -10.196988 -10.197621 2.4987283 -12.696349 -277740.46 17515.49 25.559946 25.889059 26.469523 -4.4643839 3.3487003 -1.6743501
23 4.9005371 -10.197903 -10.198536 2.4980153 -12.696552 -268547.09 17508.358 25.554817 25.88479 26.468418 -4.4641976 3.3487003 -1.6743501
24 4.9005371 -10.198782 -10.199415 2.497338 -12.696753 -259232.88 17501.204 25.549689 25.880518 26.467283 -4.4640061 3.3487003 -1.6743501
25 4.9005371 -10.199623 -10.200256 2.4966969 -12.696953 -249801.3 17494.027 25.54456 25.876241 26.466113 -4.4638088 3.3487003 -1.6743501
26 4.9005371 -10.200428 -10.201061 2.4960923 -12.697154 -240255.95 17486.823 25.539432 25.87196 26.464906 -4.4636052 3.3487003 -1.6743501
27 4.9005371 -10.201196 -10.201829 2.4955247 -12.697353 -230599.57 17479.589 25.534304 25.867673 26.463657 -4.4633945 3.3487003 -1.6743501
28 4.9005371 -10.201927 -10.20256 2.4949946 -12.697554 -220836.27 17472.324 25.529175 25.86338 26.462362 -4.4631762 3.3487003 -1.6743501
29 4.9005371 -10.20262 -10.203253 2.4945024 -12.697756 -210968.3 17465.022 25.524047 25.85908 26.461016 -4.4629492 3.3487003 -1.6743501
30 4.9005371 -10.203281 -10.203914 2.4940484 -12.697962 -201001.66 17457.679 25.518918 25.854774 26.459613 -4.4627126 3.3487003 -1.6743501
31 4.9005371 -10.203904 -10.204537 2.4936332 -12.69817 -190935.91 17450.29 25.51379 25.85046 26.458146 -4.4624651 3.3487003 -1.6743501
32 4.9005371 -10.204488 -10.205121 2.493257 -12.698378 -180773.29 17442.85 25.508662 25.846136 26.456606 -4.4622054 3.3487003 -1.6743501
33 4.9005371 -10.205037 -10.20567 2.4929204 -12.698591 -170517.54 17435.349 25.503533 25.841802 26.454984 -4.4619318 3.3487003 -1.6743501
34 4.9005371 -10.205549 -10.206182 2.4926237 -12.698806 -160169.44 17427.781 25.498405 25.837457 26.453266 -4.4616421 3.3487003 -1.6743501
35 4.9005371 -10.206023 -10.206656 2.4923673 -12.699023 -149728.79 17420.132 25.493276 25.833098 26.451438 -4.4613337 3.3487003 -1.6743501
36 4.9005371 -10.206456 -10.207089 2.4921518 -12.699241 -139194.99 17412.389 25.488148 25.828724 26.44948 -4.4610034 3.3487003 -1.6743501
37 4.9005371 -10.206852 -10.207486 2.4919775 -12.699463 -128568.57 17404.534 25.48302 25.824331 26.447367 -4.4606471 3.3487003 -1.6743501
38 4.9005371 -10.207211 -10.207844 2.491845 -12.699689 -117845.52 17396.543 25.477891 25.819915 26.445067 -4.4602591 3.3487003 -1.6743501
39 4.9005371 -10.20753 -10.208164 2.491755 -12.699918 -107020.01 17388.383 25.472763 25.815472 26.442534 -4.459832 3.3487003 -1.6743501
40 4.9005371 -10.207815 -10.208448 2.4917081 -12.700156 -96083.354 17380.008 25.467634 25.810993 26.439708 -4.4593554 3.3487003 -1.6743501
41 4.9005371 -10.208062 -10.208695 2.4917053 -12.700401 -85018.286 17371.351 25.462506 25.806467 26.436497 -4.4588137 3.3487003 -1.6743501
42 4.9005371 -10.208271 -10.208904 2.491748 -12.700652 -73793.674 17362.307 25.457378 25.801878 26.432756 -4.4581829 3.3487003 -1.6743501
43 4.9005371 -10.208446 -10.209079 2.4918382 -12.700917 -62360.119 17352.697 25.452249 25.797196 26.428245 -4.4574219 3.3487003 -1.6743501
44 4.9005371 -10.208582 -10.209215 2.491967 -12.701182 -51542.505 17343.008 25.447525 25.792747 26.422948 -4.4565285 3.3487003 -1.6743501
45 4.9005371 -10.208681 -10.209314 2.4920939 -12.701408 -43273.049 17334.863 25.44406 25.789315 26.417651 -4.4556351 3.3487003 -1.6743501
46 4.9005371 -10.208759 -10.209393 2.4922069 -12.701599 -36997.799 17327.922 25.441576 25.786676 26.412354 -4.4547418 3.3487003 -1.6743501
47 4.9005371 -10.208834 -10.209467 2.4923019 -12.701769 -32264.505 17321.909 25.439848 25.784649 26.407057 -4.4538484 3.3487003 -1.6743501
48 4.9005371 -10.208909 -10.209542 2.4923792 -12.701921 -28705.843 17316.601 25.438696 25.783087 26.40176 -4.452955 3.3487003 -1.6743501
49 4.9005371 -10.208986 -10.209619 2.4924408 -12.70206 -26035.132 17311.825 25.437979 25.781876 26.396463 -4.4520616 3.3487003 -1.6743501
50 4.9005371 -10.209067 -10.2097 2.4924894 -12.702189 -24030.259 17307.449 25.437586 25.780929 26.391166 -4.4511682 3.3487003 -1.6743501
51 4.9005371 -10.209153 -10.209786 2.4925278 -12.702314 -22521.401 17303.368 25.437435 25.780178 26.385869 -4.4502748 3.3487003 -1.6743501
52 4.9005371 -10.209241 -10.209874 2.4925582 -12.702432 -21377.916 17299.506 25.437463 25.779571 26.380573 -4.4493815 3.3487003 -1.6743501
53 4.9005371 -10.20933 -10.209963 2.4925827 -12.702546 -20503.155 17295.805 25.437622 25.779072 26.375276 -4.4484881 3.3487003 -1.6743501
54 4.9005371 -10.20942 -10.210053 2.4926026 -12.702655 -19825.084 17292.222 25.437876 25.77865 26.369979 -4.4475947 3.3487003 -1.6743501
55 4.9005371 -10.20951 -10.210143 2.4926193 -12.702762 -19290.332 17288.725 25.4382 25.778286 26.364682 -4.4467013 3.3487003 -1.6743501
56 4.9005371 -10.209601 -10.210234 2.4926335 -12.702867 -18859.558 17285.289 25.438575 25.777963 26.359385 -4.4458079 3.3487003 -1.6743501
57 4.9005371 -10.209691 -10.210324 2.4926461 -12.70297 -18503.909 17281.899 25.438986 25.77767 26.354088 -4.4449146 3.3487003 -1.6743501
58 4.9005371 -10.209782 -10.210415 2.4926574 -12.703072 -18202.31 17278.541 25.439423 25.777399 26.348791 -4.4440212 3.3487003 -1.6743501
59 4.9005371 -10.209872 -10.210505 2.4926678 -12.703173 -17939.44 17275.206 25.439879 25.777144 26.343494 -4.4431278 3.3487003 -1.6743501
60 4.9005371 -10.209962 -10.210595 2.4926777 -12.703272 -17704.202 17271.887 25.440348 25.776901 26.338197 -4.4422344 3.3487003 -1.6743501
61 4.9005371 -10.210051 -10.210684 2.4926871 -12.703371 -17488.592 17268.581 25.440826 25.776666 26.3329 -4.441341 3.3487003 -1.6743501
62 4.9005371 -10.21014 -10.210773 2.4926963 -12.703469 -17286.86 17265.282 25.441311 25.776436 26.327604 -4.4404476 3.3487003 -1.6743501
63 4.9005371 -10.210227 -10.21086 2.4927054 -12.703566 -17094.395 17261.99 25.441799 25.776211 26.322307 -4.4395543 3.3487003 -1.6743501
64 4.9005371 -10.210317 -10.21095 2.4927143 -12.703664 -16910.273 17258.701 25.442291 25.77599 26.31701 -4.4386609 3.3487003 -1.6743501
65 4.9005371 -10.210403 -10.211036 2.4927232 -12.703759 -16729.397 17255.416 25.442785 25.775771 26.311713 -4.4377675 3.3487003 -1.6743501
66 4.9005371 -10.210491 -10.211124 2.4927321 -12.703856 -16553.119 17252.132 25.443279 25.775553 26.306416 -4.4368741 3.3487003 -1.6743501
67 4.9005371 -10.210578 -10.211211 2.492741 -12.703952 -16378.985 17248.849 25.443775 25.775338 26.301119 -4.4359807 3.3487003 -1.6743501
68 4.9005371 -10.210665 -10.211298 2.49275 -12.704048 -16206.061 17245.568 25.44427 25.775123 26.295822 -4.4350874 3.3487003 -1.6743501
69 4.9005371 -10.210751 -10.211384 2.492759 -12.704143 -16034.089 17242.287 25.444765 25.77491 26.290525 -4.434194 3.3487003 -1.6743501
70 4.9005371 -10.210836 -10.211469 2.4927681 -12.704237 -15862.739 17239.006 25.44526 25.774697 26.285228 -4.4333006 3.3487003 -1.6743501
71 4.9005371 -10.210921 -10.211554 2.4927772 -12.704331 -15691.781 17235.726 25.445755 25.774485 26.279931 -4.4324072 3.3487003 -1.6743501
72 4.9005371 -10.211005 -10.211638 2.4927864 -12.704424 -15521.058 17232.446 25.44625 25.774275 26.274635 -4.4315138 3.3487003 -1.6743501
73 4.9005371 -10.211088 -10.211721 2.4927957 -12.704517 -15350.462 17229.166 25.446743 25.774065 26.269338 -4.4306204 3.3487003 -1.6743501
74 4.9005371 -10.211171 -10.211804 2.4928051 -12.704609 -15179.92 17225.886 25.447237 25.773855 26.264041 -4.4297271 3.3487003 -1.6743501
75 4.9005371 -10.211253 -10.211887 2.4928145 -12.704701 -15009.382 17222.606 25.447729 25.773647 26.258744 -4.4288337 3.3487003 -1.6743501
76 4.9005371 -10.211335 -10.211968 2.492824 -12.704792 -14838.814 17219.326 25.448221 25.773439 26.253447 -4.4279403 3.3487003 -1.6743501
77 4.9005371 -10.211416 -10.212049 2.4928336 -12.704883 -14668.193 17216.046 25.448713 25.773232 26.24815 -4.4270469 3.3487003 -1.6743501
78 4.9005371 -10.211495 -10.212128 2.4928433 -12.704971 -14496.606 17212.766 25.449203 25.773026 26.242853 -4.4261535 3.3487003 -1.6743501
79 4.9005371 -10.211574 -10.212207 2.492853 -12.70506 -14326.218 17209.486 25.449694 25.77282 26.237556 -4.4252602 3.3487003 -1.6743501
80 4.9005371 -10.211653 -10.212286 2.4928628 -12.705149 -14155.606 17206.206 25.450183 25.772616 26.232259 -4.4243668 3.3487003 -1.6743501
81 4.9005371 -10.211693 -10.212326 2.4928678 -12.705194 -14070.237 17204.566 25.450428 25.772514 26.229611 -4.4239201 3.3487003 -1.6743501
82 4.9005371 -10.211712 -10.212345 2.4928703 -12.705216 -14027.539 17203.746 25.45055 25.772463 26.228287 -4.4236967 3.3487003 -1.6743501
83 4.9005371 -10.211717 -10.21235 2.4928709 -12.705221 -14016.863 17203.541 25.45058 25.77245 26.227956 -4.4236409 3.3487003 -1.6743501
84 4.9005371 -10.21172 -10.212353 2.4928712 -12.705224 -14011.525 17203.438 25.450596 25.772444 26.22779 -4.423613 3.3487003 -1.6743501
85 4.9005371 -10.211721 -10.212354 2.4928714 -12.705225 -14008.856 17203.387 25.450603 25.772441 26.227707 -4.423599 3.3487003 -1.6743501
86 4.9005371 -10.211721 -10.212354 2.4928714 -12.705225 -14008.69 17203.384 25.450604 25.77244 26.227702 -4.4235981 3.3487003 -1.6743501
87 4.9005371 -10.211721 -10.212354 2.4928714 -12.705225 -14008.606 17203.382 25.450604 25.77244 26.2277 -4.4235977 3.3487003 -1.6743501
88 4.9005371 -10.211721 -10.212354 2.4928714 -12.705225 -14008.564 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3487003 -1.6743501
89 4.9005371 -10.211721 -10.212354 2.4928714 -12.705225 -14008.564 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3487003 -1.6743501
Loop time of 4.8661 on 4 procs for 83 steps with 1500 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-10.178336106 -10.212354026 -10.212354026
Force two-norm initial, final = 8831.76 490.29
Force max component initial, final = 6793.35 484.808
Final line search alpha, max atom move = 5.03582e-11 2.44141e-08
Iterations, force evaluations = 83 147
Pair time (%) = 4.62397 (95.024)
Neigh time (%) = 0.00863427 (0.177437)
Comm time (%) = 0.200844 (4.12742)
Outpt time (%) = 0.00380659 (0.0782267)
Other time (%) = 0.0288506 (0.592889)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 262750 ave 262750 max 262750 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1051000
Ave neighs/atom = 700.667
Neighbor list builds = 1
Dangerous builds = 0
min_modify dmax 0.005 line quadratic
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 element Hf O
#dump 1 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 2 element Hf O
velocity all create 300.1 2398378
run 10
Memory usage per processor = 4.32835 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
89 300.1 -10.173589 -10.212354 2.4928714 -12.705225 -10457.266 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
90 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
91 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
92 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
93 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
94 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
95 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
96 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
97 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
98 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
99 300.1 -10.174236 -10.213001 2.4010801 -12.614081 -16498.516 17203.381 25.450604 25.77244 26.227698 -4.4235975 3.3365845 -1.6682922
Loop time of 0.449717 on 4 procs for 10 steps with 1500 atoms
Pair time (%) = 0.312709 (69.5346)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0134462 (2.98991)
Outpt time (%) = 0.000474274 (0.105461)
Other time (%) = 0.123088 (27.37)
Nlocal: 375 ave 375 max 375 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 6075 ave 6075 max 6075 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 264625 ave 264625 max 264625 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1058500
Ave neighs/atom = 705.667
Neighbor list builds = 0
Dangerous builds = 0

73
examples/comb/log.comb.Si.18Feb13.linux.1
View File

@ -1,73 +0,0 @@
LAMMPS (18 Feb 2013)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
#dump 1 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 2 element Si
run 10
Memory usage per processor = 4.10655 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
1 10.097843 -4.6284152 -4.6297179 -4.6297179 0 1140.8131 10246.592 21.72 21.72 21.72 0
2 10.091376 -4.6284152 -4.6297171 -4.6297171 0 1140.8972 10246.592 21.72 21.72 21.72 0
3 10.080606 -4.6284152 -4.6297157 -4.6297157 0 1141.0373 10246.592 21.72 21.72 21.72 0
4 10.065546 -4.6284152 -4.6297137 -4.6297137 0 1141.233 10246.592 21.72 21.72 21.72 0
5 10.046214 -4.6284152 -4.6297113 -4.6297113 0 1141.4842 10246.592 21.72 21.72 21.72 0
6 10.022634 -4.6284152 -4.6297082 -4.6297082 0 1141.7906 10246.592 21.72 21.72 21.72 0
7 9.9948348 -4.6284152 -4.6297046 -4.6297046 0 1142.1515 10246.592 21.72 21.72 21.72 0
8 9.9628496 -4.6284152 -4.6297005 -4.6297005 0 1142.5666 10246.592 21.72 21.72 21.72 0
9 9.9267173 -4.6284152 -4.6296958 -4.6296958 0 1143.0353 10246.592 21.72 21.72 21.72 0
10 9.8864817 -4.6284152 -4.6296906 -4.6296906 0 1143.5568 10246.592 21.72 21.72 21.72 0
Loop time of 0.134755 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.134076 (99.4959)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000367403 (0.272645)
Outpt time (%) = 0.000136852 (0.101556)
Other time (%) = 0.000174999 (0.129865)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

73
examples/comb/log.comb.Si.18Feb13.linux.4
View File

@ -1,73 +0,0 @@
LAMMPS (18 Feb 2013)
# Pure Si crystal, structure created by LAMMPS, qeq off
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.43
Lattice spacing in x,y,z = 5.43 5.43 5.43
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
fix 1 all nve
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
thermo_modify norm yes
velocity all create 10.1 2398378
thermo 1
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
#dump_modify 1 append yes element Si
#dump 1 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 2 element Si
run 10
Memory usage per processor = 3.2561 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
1 10.097841 -4.6284152 -4.6297179 -4.6297179 0 1140.8134 10246.592 21.72 21.72 21.72 0
2 10.091367 -4.6284152 -4.6297171 -4.6297171 0 1140.8983 10246.592 21.72 21.72 21.72 0
3 10.080586 -4.6284152 -4.6297157 -4.6297157 0 1141.0397 10246.592 21.72 21.72 21.72 0
4 10.065511 -4.6284152 -4.6297137 -4.6297137 0 1141.2373 10246.592 21.72 21.72 21.72 0
5 10.046161 -4.6284152 -4.6297112 -4.6297112 0 1141.4909 10246.592 21.72 21.72 21.72 0
6 10.02256 -4.6284152 -4.6297082 -4.6297082 0 1141.8001 10246.592 21.72 21.72 21.72 0
7 9.9947353 -4.6284152 -4.6297046 -4.6297046 0 1142.1645 10246.592 21.72 21.72 21.72 0
8 9.9627224 -4.6284152 -4.6297005 -4.6297005 0 1142.5835 10246.592 21.72 21.72 21.72 0
9 9.9265602 -4.6284152 -4.6296958 -4.6296958 0 1143.0565 10246.592 21.72 21.72 21.72 0
10 9.8862927 -4.6284152 -4.6296906 -4.6296906 0 1143.5829 10246.592 21.72 21.72 21.72 0
Loop time of 0.0362901 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0342847 (94.474)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00158697 (4.37302)
Outpt time (%) = 0.000268877 (0.740909)
Other time (%) = 0.000149548 (0.41209)
Nlocal: 128 ave 128 max 128 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 3073 ave 3073 max 3073 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 53248 max 53248 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

274
examples/comb/log.comb.Si.elastic.18Feb13.linux.1
View File

@ -1,274 +0,0 @@
LAMMPS (18 Feb 2013)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box all triclinic
triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0)
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 4.79319 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295963 -4.6297253 -4.6297253 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.229323 on 1 procs for 3 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550036 -4.62972550036
Force two-norm initial, final = 5.86582 0.235602
Force max component initial, final = 3.38663 0.136025
Final line search alpha, max atom move = 0.000114869 1.5625e-05
Iterations, force evaluations = 3 16
Pair time (%) = 0.226666 (98.8416)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000636816 (0.277694)
Outpt time (%) = 1.90735e-05 (0.00831731)
Other time (%) = 0.00200057 (0.872381)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move (verlet.cpp:54)
Memory usage per processor = 3.80137 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.0133431 on 1 procs for 1 steps with 512 atoms
Pair time (%) = 0.013288 (99.5872)
Neigh time (%) = 0 (0)
Comm time (%) = 3.69549e-05 (0.276959)
Outpt time (%) = 1.00136e-05 (0.0750469)
Other time (%) = 8.10623e-06 (0.0607523)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (output.cpp:663)
run 10
Memory usage per processor = 4.25914 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 21.728073 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 4.2424409e-06 1.8970431e-06 5.2226895e-06
5 21.728291 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 3.0659899e-06 3.6846991e-06 4.9259641e-06
6 21.728508 21.728073 21.728073 0 0 0 364177.1 295296.39 295296.39 3.8875089e-06 2.372335e-06 4.6875974e-06
7 21.728725 21.728073 21.728073 0 0 0 510377.09 372612.84 372612.84 3.2832708e-06 3.8145125e-06 4.6443213e-06
8 21.728942 21.728073 21.728073 0 0 0 656576.36 449925.76 449925.76 4.0254046e-06 3.7666561e-06 1.4753812e-07
9 21.72916 21.728073 21.728073 0 0 0 802774.92 527235.13 527235.13 -5.7956471e-06 -1.771899e-06 2.0927452e-06
10 21.729377 21.728073 21.728073 0 0 0 948972.76 604540.97 604540.97 3.4378795e-06 3.6072928e-06 1.6693231e-06
11 21.729594 21.728073 21.728073 0 0 0 1095169.9 681843.26 681843.26 3.4064842e-06 3.1661348e-06 1.1859415e-06
12 21.729811 21.728073 21.728073 0 0 0 1241366.3 759142.02 759142.02 3.3766971e-06 3.2790869e-06 1.2694808e-06
13 21.730029 21.728073 21.728073 0 0 0 1387562 836437.23 836437.23 3.7553942e-06 3.4602587e-06 1.8958276e-06
14 21.730246 21.728073 21.728073 0 0 0 1533757 913728.91 913728.91 -5.8836668e-06 -5.4578803e-06 1.5156445e-06
Loop time of 0.16454 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.162362 (98.6762)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000379801 (0.230826)
Outpt time (%) = 0.00165915 (1.00836)
Other time (%) = 0.000139236 (0.0846216)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 4.7169 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 21.730246 21.728073 21.728073 0 0 0 1679951.2 991017.05 991017.05 4.4203553e-06 1.7546449e-06 3.8696804e-06
15 21.730246 21.728073 21.728291 0 0 0 1679951.2 991017.05 991017.05 3.4413815e-06 3.2045526e-06 3.765411e-06
16 21.730246 21.728073 21.728508 0 0 0 1757243.6 1068312.4 1137190.1 1.9121071e-06 7.2294681e-06 4.3210997e-06
17 21.730246 21.728073 21.728725 0 0 0 1834532.4 1145604.2 1283362.4 3.1284508e-06 3.8448888e-06 4.2955743e-06
18 21.730246 21.728073 21.728942 0 0 0 1911817.6 1222892.5 1429534 2.6951046e-06 3.4945075e-06 -4.5517214e-06
19 21.730246 21.728073 21.72916 0 0 0 1989099.3 1300177.3 1575704.9 -5.9762705e-07 3.542375e-06 -3.0529456e-06
20 21.730246 21.728073 21.729377 0 0 0 2066377.5 1377458.5 1721875.1 -6.9439231e-07 3.3859393e-06 4.3147517e-06
21 21.730246 21.728073 21.729594 0 0 0 2143652.1 1454736.2 1868044.5 -4.5695573e-07 3.4108162e-06 3.953809e-06
22 21.730246 21.728073 21.729811 0 0 0 2220923.2 1532010.3 2014213.3 -6.2504609e-07 4.0351804e-06 4.6966692e-06
23 21.730246 21.728073 21.730029 0 0 0 2298190.7 1609280.9 2160381.3 2.5898938e-07 4.0107779e-06 4.6632245e-06
24 21.730246 21.728073 21.730246 0 0 0 2375454.8 1686547.9 2306548.6 -4.5460256e-07 3.6194737e-06 3.412469e-06
Loop time of 0.16457 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.162394 (98.6779)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000376701 (0.2289)
Outpt time (%) = 0.00166512 (1.0118)
Other time (%) = 0.000133991 (0.0814189)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 5.17466 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 21.730246 21.728073 21.730246 0 0 0 2452715.2 1763811.4 2452715.2 3.1470723e-06 2.3932875e-06 3.3367488e-06
25 21.730246 21.728073 21.730246 0 0 4.3460492e-07 2452715.2 1763811.4 2452715.2 1.7837353e-06 4.8243295e-06 2.5146962e-06
26 21.730246 21.728073 21.730246 0 0 8.6920984e-07 2452715.2 1763811.4 2452715.2 2.8016568e-06 5.6512219e-06 243.65137
27 21.730246 21.728073 21.730246 0 0 1.3038148e-06 2452715.2 1763811.4 2452715.2 1.9900804e-06 4.0111151e-06 487.30277
28 21.730246 21.728073 21.730246 0 0 1.7384197e-06 2452715.2 1763811.4 2452715.2 1.762453e-06 6.1935142e-06 730.9542
29 21.730246 21.728073 21.730246 0 0 2.1730246e-06 2452715.2 1763811.4 2452715.2 2.3991797e-06 5.493982e-06 974.60552
30 21.730246 21.728073 21.730246 0 0 2.6076295e-06 2452715.2 1763811.4 2452715.2 2.2018322e-06 4.7607643e-06 1218.2569
31 21.730246 21.728073 21.730246 0 0 3.0422344e-06 2452715.2 1763811.4 2452715.2 2.8680162e-06 5.6568584e-06 1461.9083
32 21.730246 21.728073 21.730246 0 0 3.4768394e-06 2452715.2 1763811.4 2452715.2 2.2450268e-06 8.6579416e-06 1705.5598
33 21.730246 21.728073 21.730246 0 0 3.9114443e-06 2452715.2 1763811.4 2452715.2 1.9691724e-06 8.970813e-06 1949.2111
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.9802012e-06 8.483733e-06 2192.8625
Loop time of 0.164628 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.162457 (98.6812)
Neigh time (%) = 0 (0)
Comm time (%) = 0.000378132 (0.229689)
Outpt time (%) = 0.00165558 (1.00565)
Other time (%) = 0.000137329 (0.0834178)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 5.63243 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 3.1183118e-06 9.8932292e-06 2436.5139
35 21.730246 21.728073 21.730246 4.3456146e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.5429824e-06 1.089443e-05 2436.5139
36 21.730246 21.728073 21.730246 8.6912293e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 243.63759 -0.00011790196 2436.5139
37 21.730246 21.728073 21.730246 1.3036844e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 487.27523 -0.00024666123 2436.5139
38 21.730246 21.728073 21.730246 1.7382459e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 730.91287 -0.0003778327 2436.5139
39 21.730246 21.728073 21.730246 2.1728073e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 974.55045 -0.00050731605 2436.5139
40 21.730246 21.728073 21.730246 2.6073688e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1218.188 -0.00063724551 2436.5139
41 21.730246 21.728073 21.730246 3.0419303e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1461.8257 -0.00076799013 2436.5139
42 21.730246 21.728073 21.730246 3.4764917e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1705.4633 -0.00089693851 2436.5139
43 21.730246 21.728073 21.730246 3.9110532e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1949.1009 -0.0010276841 2436.5139
44 21.730246 21.728073 21.730246 4.3456146e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2192.7385 -0.0011569482 2436.5139
Loop time of 0.165023 on 1 procs for 10 steps with 512 atoms
Pair time (%) = 0.162837 (98.6753)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00037837 (0.229283)
Outpt time (%) = 0.00167394 (1.01437)
Other time (%) = 0.000133753 (0.081051)
Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4861 ave 4861 max 4861 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 212992 ave 212992 max 212992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

274
examples/comb/log.comb.Si.elastic.18Feb13.linux.4
View File

@ -1,274 +0,0 @@
LAMMPS (18 Feb 2013)
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
units metal
atom_style charge
dimension 3
boundary p p p
lattice diamond 5.431
Lattice spacing in x,y,z = 5.431 5.431 5.431
region box block 0 4 0 4 0 4
create_box 1 box
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 512 atoms
mass 1 29.0
change_box all triclinic
triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0)
velocity all create 1.0 277387
pair_style comb
pair_coeff * * ffield.comb Si
neighbor 0.5 bin
neigh_modify every 20 delay 0 check no
fix 1 all box/relax aniso 0.0 vmax 0.001
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
thermo_modify norm yes
thermo 1
minimize 1.0e-14 1.0e-20 1000 10000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 3.94669 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295963 -4.6297253 -4.6297253 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.0780766 on 4 procs for 3 steps with 512 atoms
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550036 -4.62972550036
Force two-norm initial, final = 5.86582 0.235602
Force max component initial, final = 3.38663 0.136025
Final line search alpha, max atom move = 0.000114869 1.5625e-05
Iterations, force evaluations = 3 16
Pair time (%) = 0.0592672 (75.9091)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0172435 (22.0854)
Outpt time (%) = 3.74317e-05 (0.0479423)
Other time (%) = 0.00152844 (1.95762)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move (verlet.cpp:54)
Memory usage per processor = 2.95487 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.00455427 on 4 procs for 1 steps with 512 atoms
Pair time (%) = 0.00345755 (75.9188)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00106198 (23.3182)
Outpt time (%) = 2.22921e-05 (0.489478)
Other time (%) = 1.24574e-05 (0.273532)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
### copy lines after this to any input script for elastic calculations ###
## Elastic constants calculations: strain box, measure box stress
## strain x, measure s_x, s_y, s_z, s_yz:
## calculates C11, C12, C13 and C14
fix 2 all deform 1 x scale 1.0001 remap x
compute perfx all stress/atom pair
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
WARNING: New thermo_style command, previous thermo_modify settings will be lost (output.cpp:663)
run 10
Memory usage per processor = 3.41263 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 21.728073 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 4.3524877e-06 1.8042579e-06 4.1896632e-06
5 21.728291 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 3.9149761e-06 3.2372561e-06 3.502927e-06
6 21.728508 21.728073 21.728073 0 0 0 364177.1 295296.39 295296.39 4.1166557e-06 -1.2651413e-06 4.8424433e-06
7 21.728725 21.728073 21.728073 0 0 0 510377.09 372612.84 372612.84 4.4157935e-06 3.4555783e-06 3.5524659e-06
8 21.728942 21.728073 21.728073 0 0 0 656576.36 449925.76 449925.76 3.5670296e-06 3.0278352e-06 -7.8505045e-07
9 21.72916 21.728073 21.728073 0 0 0 802774.92 527235.13 527235.13 -5.1605584e-06 -4.0956773e-06 1.1117963e-06
10 21.729377 21.728073 21.728073 0 0 0 948972.76 604540.97 604540.97 3.8245737e-06 2.4901528e-06 4.1996836e-07
11 21.729594 21.728073 21.728073 0 0 0 1095169.9 681843.26 681843.26 3.6820717e-06 2.7936078e-06 9.7033933e-07
12 21.729811 21.728073 21.728073 0 0 0 1241366.3 759142.02 759142.02 2.5991175e-06 2.4533026e-06 8.3157649e-08
13 21.730029 21.728073 21.728073 0 0 0 1387562 836437.23 836437.23 3.721416e-06 2.9778369e-06 1.060601e-06
14 21.730246 21.728073 21.728073 0 0 0 1533757 913728.91 913728.91 -4.9700036e-06 -5.1268692e-06 7.7885069e-07
Loop time of 0.0553849 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0413134 (74.5933)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0119895 (21.6477)
Outpt time (%) = 0.00200319 (3.61686)
Other time (%) = 7.87377e-05 (0.142165)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom pair
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
run 10
Memory usage per processor = 3.8704 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 21.730246 21.728073 21.728073 0 0 0 1679951.2 991017.05 991017.05 3.687345e-06 1.6819153e-06 4.1240524e-06
15 21.730246 21.728073 21.728291 0 0 0 1679951.2 991017.05 991017.05 3.3938808e-06 3.2093146e-06 3.3381904e-06
16 21.730246 21.728073 21.728508 0 0 0 1757243.6 1068312.4 1137190.1 2.8599709e-06 3.5571018e-07 3.402267e-06
17 21.730246 21.728073 21.728725 0 0 0 1834532.4 1145604.2 1283362.4 3.5833832e-06 3.2299854e-06 3.6621754e-06
18 21.730246 21.728073 21.728942 0 0 0 1911817.6 1222892.5 1429534 3.7053848e-06 3.4835013e-06 -3.9113334e-06
19 21.730246 21.728073 21.72916 0 0 0 1989099.3 1300177.3 1575704.9 -4.3298305e-08 3.1904447e-06 -3.1048376e-06
20 21.730246 21.728073 21.729377 0 0 0 2066377.5 1377458.5 1721875.1 -2.1040293e-07 3.325676e-06 3.9472127e-06
21 21.730246 21.728073 21.729594 0 0 0 2143652.1 1454736.2 1868044.5 4.8927752e-07 3.7764208e-06 4.2422297e-06
22 21.730246 21.728073 21.729811 0 0 0 2220923.2 1532010.3 2014213.3 3.4578611e-07 3.4348778e-06 3.5302571e-06
23 21.730246 21.728073 21.730029 0 0 0 2298190.7 1609280.9 2160381.3 2.7596926e-07 3.1082209e-06 3.2371412e-06
24 21.730246 21.728073 21.730246 0 0 0 2375454.8 1686547.9 2306548.6 6.5005639e-07 3.5157638e-06 3.3216552e-06
Loop time of 0.0553373 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0412204 (74.4894)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0120674 (21.8069)
Outpt time (%) = 0.00197399 (3.56719)
Other time (%) = 7.55191e-05 (0.13647)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom pair
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
run 10
Memory usage per processor = 4.32816 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 21.730246 21.728073 21.730246 0 0 0 2452715.2 1763811.4 2452715.2 2.7488902e-06 2.2403278e-06 2.9646035e-06
25 21.730246 21.728073 21.730246 0 0 4.3460492e-07 2452715.2 1763811.4 2452715.2 1.8018491e-06 4.5267444e-06 1.4167929e-06
26 21.730246 21.728073 21.730246 0 0 8.6920984e-07 2452715.2 1763811.4 2452715.2 2.2612618e-06 6.3053213e-06 243.65137
27 21.730246 21.728073 21.730246 0 0 1.3038148e-06 2452715.2 1763811.4 2452715.2 2.6450284e-06 5.3647504e-06 487.30277
28 21.730246 21.728073 21.730246 0 0 1.7384197e-06 2452715.2 1763811.4 2452715.2 2.1283355e-06 5.8925162e-06 730.9542
29 21.730246 21.728073 21.730246 0 0 2.1730246e-06 2452715.2 1763811.4 2452715.2 2.1488507e-06 2.9390226e-06 974.60552
30 21.730246 21.728073 21.730246 0 0 2.6076295e-06 2452715.2 1763811.4 2452715.2 2.8780366e-06 5.7299178e-06 1218.2569
31 21.730246 21.728073 21.730246 0 0 3.0422344e-06 2452715.2 1763811.4 2452715.2 2.7906173e-06 6.1777239e-06 1461.9083
32 21.730246 21.728073 21.730246 0 0 3.4768394e-06 2452715.2 1763811.4 2452715.2 3.1628404e-06 6.9745551e-06 1705.5598
33 21.730246 21.728073 21.730246 0 0 3.9114443e-06 2452715.2 1763811.4 2452715.2 2.6040944e-06 4.8739276e-06 1949.2111
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.3988573e-06 4.8943983e-06 2192.8625
Loop time of 0.0553365 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.0413296 (74.6877)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0119735 (21.6376)
Outpt time (%) = 0.00195616 (3.53503)
Other time (%) = 7.73072e-05 (0.139704)
Nlocal: 128 ave 164 max 100 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Nghost: 3073 ave 3101 max 3037 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 68224 max 41600 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom pair
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
run 10
Memory usage per processor = 4.78592 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.7629722e-06 6.2982358e-06 2436.5139
35 21.730246 21.728073 21.730246 4.3456146e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1.9222276e-06 7.9969235e-06 2436.5139
36 21.730246 21.728073 21.730246 8.6912293e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 243.63759 -0.00012183818 2436.5139
37 21.730246 21.728073 21.730246 1.3036844e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 487.27523 -0.00025103477 2436.5139
38 21.730246 21.728073 21.730246 1.7382459e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 730.91287 -0.00038377747 2436.5139
39 21.730246 21.728073 21.730246 2.1728073e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 974.55045 -0.000512822 2436.5139
40 21.730246 21.728073 21.730246 2.6073688e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1218.188 -0.00064353362 2436.5139
41 21.730246 21.728073 21.730246 3.0419303e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1461.8257 -0.00077379758 2436.5139
42 21.730246 21.728073 21.730246 3.4764917e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1705.4633 -0.00090375344 2436.5139
43 21.730246 21.728073 21.730246 3.9110532e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1949.1009 -0.0010335056 2436.5139
44 21.730246 21.728073 21.730246 4.3456146e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2192.7385 -0.0011635685 2436.5139
Loop time of 0.0511474 on 4 procs for 10 steps with 512 atoms
Pair time (%) = 0.041354 (80.8526)
Neigh time (%) = 0 (0)
Comm time (%) = 0.0077486 (15.1496)
Outpt time (%) = 0.00196868 (3.84904)
Other time (%) = 7.61151e-05 (0.148815)
Nlocal: 128 ave 152 max 112 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 3073 ave 3089 max 3049 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 53248 ave 63232 max 46592 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 212992
Ave neighs/atom = 416
Neighbor list builds = 0
Dangerous builds = 0

72
examples/comb/log.comb3.4Nov13.linux.1
View File

@ -1,72 +0,0 @@
LAMMPS (5 Nov 2013)
# Graphene-OH on Cu2O (110) surface
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.comb3-OHCCu
triclinic box = (0 0 0) to (21.3 24.6 23.8162) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
682 atoms
mass 1 16.0
mass 2 63.5
mass 3 1.00
mass 4 12.0
mass 5 12.0
pair_style comb3 polar_off
pair_coeff * * ffield.comb3 O Cu H C C
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
dump 1 all cfg 10 *.cfg mass type xs ys zs id type q
dump_modify 1 element O Cu H C C
fix 1 all nve
fix 2 all qeq/comb 10 1e-3 file fq.out
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz
thermo_modify norm yes
velocity all create 300.0 2398378
thermo 10
run 100
Memory usage per processor = 25.5933 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
0 300 -4.3728818 -4.411603 -3.8436746 -0.56792838 -21237.662 12479.212 21.3 24.6 23.8162
10 458.62564 -4.3728548 -4.4320499 -3.8642328 -0.56781711 -18048.055 12479.212 21.3 24.6 23.8162
20 744.81494 -4.3728588 -4.4689925 -3.9006671 -0.56832542 -17246.791 12479.212 21.3 24.6 23.8162
30 918.51338 -4.3729447 -4.4914978 -3.92258 -0.5689178 -18547.495 12479.212 21.3 24.6 23.8162
40 966.08747 -4.3732206 -4.4979141 -3.9280403 -0.56987377 -27675.956 12479.212 21.3 24.6 23.8162
50 953.7008 -4.3732162 -4.4963109 -3.9251828 -0.57112816 -23768.538 12479.212 21.3 24.6 23.8162
60 1051.9611 -4.3733738 -4.509151 -3.9367614 -0.57238959 2567.532 12479.212 21.3 24.6 23.8162
70 1182.0586 -4.3735982 -4.5261673 -3.9525774 -0.57358987 9288.2917 12479.212 21.3 24.6 23.8162
80 1247.345 -4.3738251 -4.5348207 -3.960019 -0.57480169 12178.117 12479.212 21.3 24.6 23.8162
90 1293.7474 -4.3741289 -4.5411137 -3.9651965 -0.57591714 17036.28 12479.212 21.3 24.6 23.8162
100 1320.6233 -4.3743569 -4.5448106 -3.9678065 -0.57700407 21564.551 12479.212 21.3 24.6 23.8162
Loop time of 18.5723 on 1 procs for 100 steps with 682 atoms
Pair time (%) = 8.42377 (45.3568)
Neigh time (%) = 0.0747871 (0.402682)
Comm time (%) = 0.00560045 (0.0301549)
Outpt time (%) = 0.0121541 (0.0654423)
Other time (%) = 10.0559 (54.145)
Nlocal: 682 ave 682 max 682 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6390 ave 6390 max 6390 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 365302 ave 365302 max 365302 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 365302
Ave neighs/atom = 535.633
Neighbor list builds = 1
Dangerous builds = 0

72
examples/comb/log.comb3.4Nov13.linux.4
View File

@ -1,72 +0,0 @@
LAMMPS (5 Nov 2013)
# Graphene-OH on Cu2O (110) surface
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.comb3-OHCCu
triclinic box = (0 0 0) to (21.3 24.6 23.8162) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
682 atoms
mass 1 16.0
mass 2 63.5
mass 3 1.00
mass 4 12.0
mass 5 12.0
pair_style comb3 polar_off
pair_coeff * * ffield.comb3 O Cu H C C
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
dump 1 all cfg 10 *.cfg mass type xs ys zs id type q
dump_modify 1 element O Cu H C C
fix 1 all nve
fix 2 all qeq/comb 10 1e-3 file fq.out
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz
thermo_modify norm yes
velocity all create 300.0 2398378
thermo 10
run 100
Memory usage per processor = 12.9876 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
0 300 -4.3728818 -4.411603 -3.8436746 -0.56792838 -21237.662 12479.212 21.3 24.6 23.8162
10 458.96416 -4.372855 -4.4320938 -3.8642394 -0.56785436 -18030.197 12479.212 21.3 24.6 23.8162
20 745.46506 -4.3728583 -4.4690759 -3.9006637 -0.56841223 -17209.979 12479.212 21.3 24.6 23.8162
30 919.42182 -4.3729439 -4.4916142 -3.9225611 -0.56905307 -18503.561 12479.212 21.3 24.6 23.8162
40 967.18839 -4.3732195 -4.4980551 -3.9280005 -0.57005462 -27594.263 12479.212 21.3 24.6 23.8162
50 954.87724 -4.373215 -4.4964616 -3.9251111 -0.57135052 -23703.989 12479.212 21.3 24.6 23.8162
60 1053.1861 -4.3733731 -4.5093085 -3.9366603 -0.57264818 2655.0236 12479.212 21.3 24.6 23.8162
70 1183.3656 -4.3735981 -4.5263358 -3.9524581 -0.57387771 9399.6669 12479.212 21.3 24.6 23.8162
80 1248.7675 -4.3738256 -4.5350047 -3.959893 -0.57511172 12251.912 12479.212 21.3 24.6 23.8162
90 1294.7086 -4.3741275 -4.5412364 -3.9649951 -0.57624126 17340.618 12479.212 21.3 24.6 23.8162
100 1322.3053 -4.3743594 -4.5450302 -3.9676954 -0.57733479 21593.239 12479.212 21.3 24.6 23.8162
Loop time of 8.25897 on 4 procs for 100 steps with 682 atoms
Pair time (%) = 3.15634 (38.2171)
Neigh time (%) = 0.0382928 (0.463651)
Comm time (%) = 0.7826 (9.47576)
Outpt time (%) = 0.0133025 (0.161067)
Other time (%) = 4.26844 (51.6824)
Nlocal: 170.5 ave 235 max 113 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 3861.75 ave 4575 max 3157 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 91328 ave 129873 max 56453 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 365312
Ave neighs/atom = 535.648
Neighbor list builds = 1
Dangerous builds = 0

135
examples/crack/log.crack.18Feb13.linux.1
View File

@ -1,135 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d LJ crack simulation
dimension 2
boundary s s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.93
Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
region box block 0 100 0 40 -0.25 0.25
create_box 5 box
Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 8141 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
mass 5 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
302 atoms in group lower
region 2 block INF INF 38.75 INF INF INF
group upper region 2
302 atoms in group upper
group boundary union lower upper
604 atoms in group boundary
group mobile subtract all boundary
7537 atoms in group mobile
region leftupper block INF 20 20 INF INF INF
region leftlower block INF 20 INF 20 INF INF
group leftupper region leftupper
841 atoms in group leftupper
group leftlower region leftlower
841 atoms in group leftlower
set group leftupper type 2
841 settings made for type
set group leftlower type 3
841 settings made for type
set group lower type 4
302 settings made for type
set group upper type 5
302 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.01 887723 temp new
velocity upper set 0.0 0.3 0.0
velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce NULL 0.0 0.0
# run
timestep 0.003
thermo 200
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
neigh_modify exclude type 2 3
#dump 1 all atom 500 dump.crack
#dump 1 all image 250 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 4
run 5000
Memory usage per processor = 2.09943 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.065651733 -3.2595015 0 -3.1987287 -0.036239172 8605.5917
200 0.060086376 -3.2531936 0 -3.1975725 -0.23125026 8638.8101
400 0.060533553 -3.2509973 0 -3.1949623 -0.4305406 8679.2464
600 0.06082965 -3.2466949 0 -3.1903858 -0.6028531 8716.7569
800 0.061677224 -3.2413215 0 -3.1842278 -0.7482749 8756.226
1000 0.062383731 -3.2349273 0 -3.1771796 -0.87425132 8793.1116
1200 0.063709246 -3.2276094 0 -3.1686347 -0.98020161 8828.8863
1400 0.065404552 -3.2196608 0 -3.1591168 -1.0695384 8866.4893
1600 0.067579602 -3.2110378 0 -3.1484804 -1.1456387 8900.6772
1800 0.069324241 -3.2018536 0 -3.1376812 -1.2020999 8933.017
2000 0.071014927 -3.1921108 0 -3.1263733 -1.2430105 8963.9853
2200 0.072992881 -3.1818701 0 -3.1143017 -1.2701297 9004.4136
2400 0.075000723 -3.1712313 0 -3.1018043 -1.2830866 9034.9991
2600 0.076843477 -3.1601004 0 -3.0889675 -1.27924 9072.1325
2800 0.078671706 -3.1487747 0 -3.0759495 -1.2659604 9103.9526
3000 0.080713586 -3.1373277 0 -3.0626123 -1.2440673 9134.552
3200 0.08309469 -3.1260242 0 -3.0491047 -1.214547 9169.0003
3400 0.085424766 -3.1146623 0 -3.0355859 -1.1839326 9206.909
3600 0.087396485 -3.1029493 0 -3.0220477 -1.143412 9233.783
3800 0.089007987 -3.090822 0 -3.0084286 -1.1000791 9259.0348
4000 0.089813071 -3.0794078 0 -2.9962692 -1.062847 9281.82
4200 0.08584753 -3.0668559 0 -2.9873882 -1.037972 9308.8113
4400 0.086197517 -3.0559678 0 -2.9761761 -1.028843 9328.9666
4600 0.086766447 -3.0437627 0 -2.9634443 -1.0208785 9361.9925
4800 0.088195149 -3.0328502 0 -2.9512093 -1.0272063 9395.6122
5000 0.089415266 -3.0228825 0 -2.9401122 -1.0215336 9436.1637
Loop time of 6.84719 on 1 procs for 5000 steps with 8141 atoms
Pair time (%) = 5.70829 (83.3669)
Neigh time (%) = 0.278341 (4.06504)
Comm time (%) = 0.0058105 (0.0848597)
Outpt time (%) = 0.000735044 (0.010735)
Other time (%) = 0.854015 (12.4725)
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

135
examples/crack/log.crack.18Feb13.linux.4
View File

@ -1,135 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d LJ crack simulation
dimension 2
boundary s s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.93
Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
region box block 0 100 0 40 -0.25 0.25
create_box 5 box
Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 8141 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
mass 5 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
302 atoms in group lower
region 2 block INF INF 38.75 INF INF INF
group upper region 2
302 atoms in group upper
group boundary union lower upper
604 atoms in group boundary
group mobile subtract all boundary
7537 atoms in group mobile
region leftupper block INF 20 20 INF INF INF
region leftlower block INF 20 INF 20 INF INF
group leftupper region leftupper
841 atoms in group leftupper
group leftlower region leftlower
841 atoms in group leftlower
set group leftupper type 2
841 settings made for type
set group leftlower type 3
841 settings made for type
set group lower type 4
302 settings made for type
set group upper type 5
302 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.01 887723 temp new
velocity upper set 0.0 0.3 0.0
velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce NULL 0.0 0.0
# run
timestep 0.003
thermo 200
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
neigh_modify exclude type 2 3
#dump 1 all atom 500 dump.crack
#dump 1 all image 250 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 4
run 5000
Memory usage per processor = 2.07747 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.065993465 -3.2595015 0 -3.1984123 -0.035939913 8605.5917
200 0.060035253 -3.2531886 0 -3.1976149 -0.22757684 8638.5331
400 0.06054278 -3.2510706 0 -3.1950271 -0.42811733 8677.8288
600 0.060576995 -3.246816 0 -3.1907408 -0.60017647 8717.6131
800 0.060802753 -3.2413477 0 -3.1850635 -0.74499308 8756.4512
1000 0.061812114 -3.2349942 0 -3.1777756 -0.87130079 8796.9575
1200 0.06317147 -3.2277552 0 -3.1692783 -0.98010628 8823.1488
1400 0.065125405 -3.2198031 0 -3.1595175 -1.0690179 8858.8358
1600 0.06725411 -3.2111272 0 -3.148871 -1.1440993 8892.6607
1800 0.069389572 -3.2019689 0 -3.137736 -1.199078 8933.7591
2000 0.071276448 -3.1921621 0 -3.1261826 -1.239553 8969.0463
2200 0.073243486 -3.1818809 0 -3.1140805 -1.264839 8997.6559
2400 0.075063494 -3.1711703 0 -3.1016851 -1.2772278 9038.4932
2600 0.076789207 -3.1600658 0 -3.0889832 -1.2754953 9073.4997
2800 0.07875979 -3.1487143 0 -3.0758075 -1.2637926 9106.2245
3000 0.080591853 -3.1372361 0 -3.0626334 -1.2388824 9142.7862
3200 0.08227693 -3.125423 0 -3.0492605 -1.2055283 9169.4322
3400 0.084289444 -3.1136554 0 -3.03563 -1.1672422 9204.8205
3600 0.086720297 -3.1021183 0 -3.0218427 -1.126381 9233.2656
3800 0.089264018 -3.0909262 0 -3.0082959 -1.0899774 9265.4143
4000 0.091377688 -3.0795096 0 -2.9949227 -1.0580229 9297.6799
4200 0.092665135 -3.0678736 0 -2.9820949 -1.0390124 9331.6135
4400 0.09055434 -3.0560482 0 -2.9722234 -1.0323741 9362.2075
4600 0.088763719 -3.0446018 0 -2.9624346 -1.027693 9391.6949
4800 0.089467982 -3.0337452 0 -2.950926 -1.0232092 9427.4155
5000 0.089910902 -3.0237571 0 -2.9405279 -1.0174796 9452.031
Loop time of 1.90609 on 4 procs for 5000 steps with 8141 atoms
Pair time (%) = 1.45986 (76.5892)
Neigh time (%) = 0.0753738 (3.95437)
Comm time (%) = 0.12308 (6.45722)
Outpt time (%) = 0.000668764 (0.0350857)
Other time (%) = 0.247107 (12.9641)
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 18247 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

178
examples/deposit/log.deposit.atom.17Dec13.linux.1
View File

@ -1,178 +0,0 @@
LAMMPS (16 Dec 2013)
# sample surface deposition script for atoms
units lj
atom_style atomic
boundary p p f
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region box block 0 5 0 5 0 10
create_box 2 box
Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
1 by 1 by 1 MPI processor grid
region substrate block INF INF INF INF INF 3
create_atoms 1 region substrate
Created 350 atoms
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 1.0 1.0 5.0
mass * 1.0
neigh_modify delay 0
group addatoms type 2
0 atoms in group addatoms
region mobile block 0 5 0 5 2 INF
group mobile region mobile
150 atoms in group mobile
compute add addatoms temp
compute_modify add dynamic yes extra 0
fix 1 addatoms nve
fix 2 mobile langevin 1.0 1.0 0.1 587283
fix 3 mobile nve
region slab block 0 5 0 5 8 9
fix 4 addatoms deposit 100 2 100 12345 region slab near 1.0 vz -1.0 -1.0
fix 5 addatoms wall/reflect zhi EDGE
thermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp add
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 50 dump.deposit.atom
#dump 1 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
#dump 1 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 2.12546 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 351 0.83994737 -6.3459678 -6.3423783 -0.12047746
200 352 0.83994737 -6.2377119 -6.2305533 -0.3420432
300 353 0.84063802 -6.102615 -6.0918986 -0.40610132
400 354 0.84248131 -6.0284461 -6.0141667 -0.46041042
500 355 0.84689832 -5.9201486 -5.9022564 -0.44565465
600 356 0.86694405 -5.8676653 -5.8457482 -0.45310439
700 357 0.93585062 -5.8080247 -5.7804997 -0.4235135
800 358 0.87721962 -5.7667317 -5.7373277 -0.47514081
900 359 0.98586832 -5.7397849 -5.7027118 -0.53506606
1000 360 1.1977372 -5.7043822 -5.6544765 -0.5143915
1100 361 0.86840339 -5.6974093 -5.6577177 -0.57133639
1200 362 0.91410157 -5.6449104 -5.5994579 -0.54863872
1300 363 1.0317704 -5.6108925 -5.5554668 -0.63480165
1400 364 0.78937966 -5.5995247 -5.5539836 -0.54633211
1500 365 1.0022364 -5.592367 -5.5305854 -0.61542058
1600 366 1.36861 -5.5602006 -5.4704557 -0.5557092
1700 367 1.2584928 -5.6125569 -5.5251139 -0.54474262
1800 368 1.2395052 -5.5575635 -5.4666216 -0.39432632
1900 369 1.4424114 -5.5511809 -5.4397751 -0.39219555
2000 370 1.0355115 -5.5657056 -5.4817452 -0.42684751
2100 371 1.0710232 -5.621664 -5.5307281 -0.60685079
2200 372 1.1723348 -5.5425772 -5.4385798 -0.53815496
2300 373 1.0854557 -5.6087637 -5.5083664 -0.6673737
2400 374 1.1021474 -5.5084817 -5.4023926 -0.52097008
2500 375 1.2269864 -5.4265984 -5.3038998 -0.49657202
2600 376 1.039955 -5.476211 -5.3683434 -0.62204764
2700 377 1.0944057 -5.407846 -5.2902772 -0.63977966
2800 378 1.0323171 -5.39575 -5.2810481 -0.62614235
2900 379 1.1065423 -5.3744087 -5.2474045 -0.57270499
3000 380 1.0281199 -5.3681406 -5.2463895 -0.66444016
3100 381 1.043599 -5.3317419 -5.2043735 -0.65417699
3200 382 1.0445598 -5.3089303 -5.1776767 -0.63427235
3300 383 1.1112429 -5.2607562 -5.117136 -0.57989768
3400 384 1.2829004 -5.2907632 -5.120378 -0.56018912
3500 385 1.0963306 -5.2325275 -5.0830279 -0.55177255
3600 386 1.0791899 -5.2303202 -5.0793455 -0.62981193
3700 387 0.94844753 -5.1732719 -5.0372543 -0.54632838
3800 388 1.0521937 -5.221439 -5.0668642 -0.66965407
3900 389 0.9826229 -5.2181425 -5.0703702 -0.63446515
4000 390 0.91368716 -5.181823 -5.0412558 -0.60085212
4100 391 0.89544864 -5.1919255 -5.0510813 -0.54221581
4200 392 0.75657889 -5.1831443 -5.0615513 -0.67325177
4300 393 0.93900487 -5.126951 -4.9728395 -0.48335997
4400 394 0.8593926 -5.2046256 -5.0606665 -0.61020127
4500 395 0.95412643 -5.2094621 -5.0464152 -0.66934949
4600 396 0.92666909 -5.2451094 -5.0836443 -0.60939327
4700 397 1.01953 -5.250453 -5.069403 -0.59800998
4800 398 0.79158616 -5.2564791 -5.1132776 -0.65741727
4900 399 1.0354176 -5.2890436 -5.0983088 -0.62373201
5000 400 1.0952161 -5.348647 -5.143294 -0.68192295
5100 401 0.93545388 -5.3669167 -5.1884573 -0.70799109
5200 402 1.1494382 -5.3432275 -5.1202022 -0.63752184
5300 403 0.99548049 -5.2792244 -5.0828455 -0.64833221
5400 404 1.1403496 -5.2690808 -5.0404463 -0.59847109
5500 405 1.1603116 -5.2594419 -5.0230821 -0.57039169
5600 406 1.0631193 -5.2339182 -5.0139625 -0.65214332
5700 407 0.96112361 -5.1115962 -4.9096894 -0.49296687
5800 408 1.0057273 -5.2149323 -5.0004758 -0.6288722
5900 409 1.0081842 -5.2677684 -5.0496161 -0.66956189
6000 410 1.1018378 -5.197239 -4.9553722 -0.56197903
6100 411 0.95491378 -5.2192405 -5.0066502 -0.57092889
6200 412 1.1257567 -5.2427379 -4.9886229 -0.60501573
6300 413 0.92515533 -5.2911514 -5.0794633 -0.71296835
6400 414 0.88193756 -5.2485519 -5.0440447 -0.62228066
6500 415 1.1421168 -5.258063 -4.9897344 -0.58398767
6600 416 1.1202205 -5.1905351 -4.9239442 -0.57396572
6700 417 0.95130512 -5.1665766 -4.9373053 -0.54725501
6800 418 1.1527843 -5.1757857 -4.8944842 -0.67073304
6900 419 1.0361942 -5.1545229 -4.8985656 -0.54846926
7000 420 0.99630188 -5.1619249 -4.9128494 -0.55694385
7100 421 0.9361364 -5.1977715 -4.9609579 -0.6844444
7200 422 1.0798692 -5.2022654 -4.9259007 -0.68276117
7300 423 1.1813674 -5.1407348 -4.8349198 -0.48578088
7400 424 1.172588 -5.1454198 -4.8384451 -0.56027825
7500 425 1.1057774 -5.1871818 -4.894476 -0.63993616
7600 426 1.1182194 -5.0981279 -4.7988861 -0.51535988
7700 427 1.2199143 -5.1427322 -4.8127554 -0.52888993
7800 428 1.1962566 -5.1524711 -4.825457 -0.48097947
7900 429 1.1264027 -5.171705 -4.8605658 -0.65075724
8000 430 1.1333818 -5.1429716 -4.826679 -0.66899357
8100 431 1.0571341 -5.0912822 -4.7932734 -0.59186526
8200 432 1.0064557 -5.1167265 -4.8301662 -0.59922344
8300 433 0.9988262 -5.1878937 -4.9007024 -0.65115476
8400 434 1.1031119 -5.1400663 -4.819808 -0.4893497
8500 435 1.1480133 -5.2265686 -4.8900819 -0.61178303
8600 436 1.1295109 -5.1695862 -4.8353961 -0.58399158
8700 437 1.0054231 -5.1692361 -4.8689896 -0.6618483
8800 438 0.97531325 -5.1627328 -4.8688028 -0.65722388
8900 439 1.0594641 -5.107595 -4.7854117 -0.62363978
9000 440 1.1400991 -5.1098088 -4.7600057 -0.58529871
9100 441 0.99798612 -5.0390174 -4.7301169 -0.46665264
9200 442 1.1110124 -5.1181538 -4.7712766 -0.71646157
9300 443 1.048379 -5.118944 -4.7888111 -0.57591241
9400 444 0.90506078 -5.1264418 -4.8390239 -0.76401152
9500 445 0.96451217 -5.0675273 -4.7586666 -0.64381165
9600 446 1.0823286 -5.0664171 -4.7169657 -0.5345442
9700 447 1.1847976 -5.1194594 -4.7338038 -0.62633623
9800 448 1.0307519 -5.1036157 -4.7654002 -0.59954885
9900 449 1.0182147 -5.0987073 -4.7619481 -0.58646377
10000 450 0.96233181 -5.146377 -4.8255998 -0.68930839
Loop time of 5.53702 on 1 procs for 10000 steps with 450 atoms
Pair time (%) = 3.04622 (55.0154)
Neigh time (%) = 2.15803 (38.9745)
Comm time (%) = 0.164064 (2.96303)
Outpt time (%) = 0.000992537 (0.0179255)
Other time (%) = 0.16772 (3.02906)
Nlocal: 450 ave 450 max 450 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1996 ave 1996 max 1996 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 28228 ave 28228 max 28228 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 28228
Ave neighs/atom = 62.7289
Neighbor list builds = 1143
Dangerous builds = 0

178
examples/deposit/log.deposit.atom.17Dec13.linux.4
View File

@ -1,178 +0,0 @@
LAMMPS (16 Dec 2013)
# sample surface deposition script for atoms
units lj
atom_style atomic
boundary p p f
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region box block 0 5 0 5 0 10
create_box 2 box
Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
1 by 1 by 4 MPI processor grid
region substrate block INF INF INF INF INF 3
create_atoms 1 region substrate
Created 350 atoms
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 1.0 1.0 5.0
mass * 1.0
neigh_modify delay 0
group addatoms type 2
0 atoms in group addatoms
region mobile block 0 5 0 5 2 INF
group mobile region mobile
150 atoms in group mobile
compute add addatoms temp
compute_modify add dynamic yes extra 0
fix 1 addatoms nve
fix 2 mobile langevin 1.0 1.0 0.1 587283
fix 3 mobile nve
region slab block 0 5 0 5 8 9
fix 4 addatoms deposit 100 2 100 12345 region slab near 1.0 vz -1.0 -1.0
fix 5 addatoms wall/reflect zhi EDGE
thermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp add
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 50 dump.deposit.atom
#dump 1 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
#dump 1 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 2.19138 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 351 0.83994737 -6.3596932 -6.3561037 -0.10696131
200 352 0.83994737 -6.3044678 -6.2973092 -0.38494392
300 353 0.84063802 -6.164881 -6.1541646 -0.41223901
400 354 0.84248131 -6.0388811 -6.0246018 -0.31496573
500 355 0.84688124 -6.0084178 -5.990526 -0.37482638
600 356 0.86681079 -6.0286531 -6.0067393 -0.54868509
700 357 0.93465165 -5.9564751 -5.9289854 -0.48728319
800 358 0.86905333 -5.8498868 -5.8207565 -0.4146325
900 359 0.90267243 -5.7844092 -5.7504647 -0.38165702
1000 360 0.92357983 -5.777549 -5.7390665 -0.38381524
1100 361 1.3481334 -5.7713272 -5.7097089 -0.44738093
1200 362 1.15494 -5.7155857 -5.6581577 -0.38961524
1300 363 0.97329529 -5.6445379 -5.5922534 -0.37655267
1400 364 1.2187161 -5.6818221 -5.6115115 -0.60238965
1500 365 1.2026123 -5.66813 -5.5939963 -0.56317155
1600 366 1.4012284 -5.6764268 -5.584543 -0.49098723
1700 367 1.3618781 -5.6121414 -5.517515 -0.47893702
1800 368 0.9670811 -5.5551479 -5.4841935 -0.3409573
1900 369 1.002089 -5.6037307 -5.5263336 -0.45325785
2000 370 1.3599868 -5.5793818 -5.4691126 -0.44566809
2100 371 1.0007794 -5.585692 -5.5007201 -0.54221497
2200 372 1.1061186 -5.5172266 -5.4191031 -0.46551394
2300 373 0.99747295 -5.556485 -5.4642255 -0.55670261
2400 374 1.0990417 -5.5538565 -5.4480664 -0.63197286
2500 375 1.1415126 -5.5118583 -5.3977071 -0.515634
2600 376 1.0106197 -5.5221131 -5.4172882 -0.54958102
2700 377 1.0964027 -5.4985654 -5.3807821 -0.54044665
2800 378 0.93035607 -5.4391662 -5.3357933 -0.52401636
2900 379 0.93052107 -5.5146104 -5.4078092 -0.69426617
3000 380 1.0256715 -5.4314645 -5.3100034 -0.55807748
3100 381 1.1165704 -5.441198 -5.3049236 -0.67260986
3200 382 1.0516479 -5.3743543 -5.2422101 -0.55726796
3300 383 1.3015716 -5.393488 -5.2252692 -0.55526352
3400 384 1.2021373 -5.4152522 -5.2555933 -0.63254327
3500 385 1.0712229 -5.3875667 -5.2414908 -0.53868713
3600 386 0.83109486 -5.3651207 -5.2488536 -0.65516002
3700 387 0.91939065 -5.3500756 -5.218225 -0.6090015
3800 388 1.1887187 -5.4422838 -5.2676524 -0.69893677
3900 389 1.0816342 -5.3817634 -5.2191012 -0.58777145
4000 390 0.85854697 -5.3988171 -5.2667329 -0.68550599
4100 391 1.0028015 -5.3760402 -5.2183106 -0.61280389
4200 392 1.1063074 -5.373048 -5.1952486 -0.69264824
4300 393 0.94803569 -5.2768075 -5.1212139 -0.4968846
4400 394 1.0358207 -5.2313016 -5.0577885 -0.47759843
4500 395 0.99463555 -5.2840763 -5.1141069 -0.65377832
4600 396 1.1336626 -5.2732108 -5.0756787 -0.68505207
4700 397 1.043989 -5.3177843 -5.1323907 -0.66352488
4800 398 1.1880124 -5.2919552 -5.0770384 -0.5760075
4900 399 1.03793 -5.2870595 -5.0958618 -0.42225723
5000 400 0.94525219 -5.3621262 -5.1848915 -0.57578045
5100 401 1.0012033 -5.2951115 -5.1041089 -0.49619424
5200 402 0.9093106 -5.323038 -5.1466046 -0.63808588
5300 403 1.0780126 -5.3297725 -5.1171125 -0.54697182
5400 404 1.1821134 -5.3408341 -5.1038263 -0.54142347
5500 405 1.0861151 -5.3794714 -5.1582257 -0.62078287
5600 406 0.99813873 -5.2575404 -5.051029 -0.46334991
5700 407 1.0024386 -5.3416556 -5.1310696 -0.67522177
5800 408 1.0499128 -5.2805967 -5.0567182 -0.51745165
5900 409 1.0175995 -5.2346622 -5.0144725 -0.56525137
6000 410 1.0580253 -5.3059195 -5.0736701 -0.72405837
6100 411 1.0301092 -5.2456791 -5.0163483 -0.63734034
6200 412 1.0936687 -5.2986069 -5.0517351 -0.65680297
6300 413 1.1588036 -5.2889356 -5.0237856 -0.68692669
6400 414 1.0738578 -5.2626417 -5.0136312 -0.61945759
6500 415 1.0799598 -5.2267416 -4.9730161 -0.54000165
6600 416 1.0654575 -5.2904664 -5.036908 -0.79867075
6700 417 1.1409741 -5.2288709 -4.953888 -0.61287225
6800 418 0.91721071 -5.2193327 -4.9955158 -0.67288058
6900 419 0.99562084 -5.2164082 -4.9704732 -0.59995412
7000 420 0.98493772 -5.1472091 -4.9009747 -0.5672666
7100 421 1.1650853 -5.1686492 -4.8739186 -0.65830934
7200 422 1.1058038 -5.1915304 -4.9085285 -0.71319305
7300 423 1.0695793 -5.1082351 -4.8313581 -0.47793146
7400 424 1.0205032 -5.1187042 -4.8515441 -0.45596744
7500 425 1.0509541 -5.119854 -4.8416602 -0.53998089
7600 426 0.94300051 -5.1572926 -4.9049403 -0.6117655
7700 427 0.97832544 -5.1763299 -4.9117009 -0.76832421
7800 428 0.99162405 -5.1076903 -4.8366155 -0.53958966
7900 429 1.0777105 -5.1240548 -4.8263655 -0.63632393
8000 430 1.0810155 -5.1582004 -4.8565216 -0.58803291
8100 431 1.0168798 -5.1415512 -4.8548902 -0.59356121
8200 432 1.1324612 -5.1323524 -4.8099155 -0.51666326
8300 433 1.0225017 -5.1357067 -4.841708 -0.53308683
8400 434 1.0938048 -5.1370091 -4.8194529 -0.50683321
8500 435 0.98749809 -5.1760393 -4.8866002 -0.63777967
8600 436 0.9696005 -5.1684071 -4.8815299 -0.60457804
8700 437 1.1714664 -5.2563529 -4.9065214 -0.64901375
8800 438 1.1068684 -5.1834342 -4.8498574 -0.448558
8900 439 1.048918 -5.2496241 -4.9306479 -0.51509876
9000 440 1.3045868 -5.2790483 -4.8787774 -0.63054863
9100 441 1.1505177 -5.2631527 -4.90704 -0.60158373
9200 442 1.0838443 -5.2358506 -4.8974558 -0.66026866
9300 443 0.99074033 -5.1267153 -4.8147328 -0.36508529
9400 444 1.120907 -5.2081858 -4.8522221 -0.70153485
9500 445 1.1571034 -5.2002705 -4.8297374 -0.39376803
9600 446 1.1427182 -5.1948759 -4.8259266 -0.50433867
9700 447 1.1386351 -5.1960248 -4.8253953 -0.55647471
9800 448 0.94339428 -5.1379682 -4.828417 -0.49931715
9900 449 0.9187318 -5.1851142 -4.8812575 -0.5929999
10000 450 1.1185411 -5.2444214 -4.8715743 -0.61322449
Loop time of 4.76332 on 4 procs for 10000 steps with 450 atoms
Pair time (%) = 0.82251 (17.2676)
Neigh time (%) = 0.589647 (12.3789)
Comm time (%) = 2.44321 (51.2921)
Outpt time (%) = 0.011445 (0.240274)
Other time (%) = 0.89651 (18.8211)
Nlocal: 112.5 ave 250 max 5 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 1496 ave 2221 max 416 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 7344.75 ave 16734 max 4 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 29379
Ave neighs/atom = 65.2867
Neighbor list builds = 1150
Dangerous builds = 0

184
examples/deposit/log.deposit.molecule.17Dec13.linux.1
View File

@ -1,184 +0,0 @@
LAMMPS (30 Dec 2013)
# sample surface deposition script for molecules
units lj
atom_style bond
boundary p p f
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region box block 0 5 0 5 0 10
create_box 3 box "bond types" 1 "extra bond per atom" 1
Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
1 by 1 by 1 MPI processor grid
region substrate block INF INF INF INF INF 3
create_atoms 1 region substrate
Created 350 atoms
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 1.0 1.0 5.0
mass * 1.0
bond_style harmonic
bond_coeff 1 5.0 1.0
neigh_modify delay 0
group addatoms type 2
0 atoms in group addatoms
region mobile block 0 5 0 5 2 INF
group mobile region mobile
150 atoms in group mobile
compute add addatoms temp
compute_modify add dynamic yes extra 0
fix 1 addatoms nve
fix 2 mobile langevin 0.1 0.1 0.1 587283
fix 3 mobile nve
molecule dimer molecule.dimer
region slab block 0 5 0 5 8 9
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0
fix 5 addatoms wall/reflect zhi EDGE
thermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 50 dump.deposit.atom
#dump 1 all movie 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
#dump 1 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 2.76078 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 352 0.83994737 -6.8875167 -6.8803581 -0.73353914
200 354 0.83994737 -6.8593854 -6.845149 -0.70414703
300 356 0.83994737 -6.8170634 -6.7958288 -0.69170868
400 358 0.84042015 -6.7849768 -6.756806 -0.70352248
500 360 0.84184269 -6.7489038 -6.7138265 -0.68386838
600 362 0.84581137 -6.7098504 -6.6677911 -0.6828296
700 364 0.87382946 -6.6715894 -6.6211265 -0.66625495
800 366 0.87689746 -6.6396776 -6.5813408 -0.68710928
900 368 0.89661715 -6.6072681 -6.5411455 -0.66320699
1000 370 1.00676 -6.5947268 -6.512331 -0.68611219
1100 372 0.86243824 -6.5866848 -6.5042223 -0.67174009
1200 374 0.84425239 -6.5636281 -6.479445 -0.69383244
1300 376 1.0078184 -6.550962 -6.4431087 -0.66633027
1400 378 1.0391938 -6.5969765 -6.4778058 -0.56558987
1500 380 0.74712353 -6.6166281 -6.5240793 -0.66003498
1600 382 0.58302452 -6.5997567 -6.5184528 -0.67167612
1700 384 0.56467802 -6.5776894 -6.4975516 -0.64668082
1800 386 0.71825353 -6.5726227 -6.4691096 -0.65076646
1900 388 0.53975986 -6.5613236 -6.4741837 -0.63639897
2000 390 0.59341094 -6.5769909 -6.4682541 -0.65193031
2100 392 0.68035001 -6.5827033 -6.4574143 -0.62788928
2200 394 0.57776644 -6.589353 -6.4761586 -0.69498055
2300 396 0.5318152 -6.5951551 -6.4885222 -0.60457555
2400 398 0.49568196 -6.6007559 -6.4881834 -0.69316627
2500 400 0.53409937 -6.6072399 -6.4763374 -0.69823432
2600 402 0.45633292 -6.6332159 -6.5034387 -0.65145273
2700 404 0.4892626 -6.6191003 -6.4911656 -0.66150699
2800 406 0.4586448 -6.6101924 -6.4821935 -0.71952986
2900 408 0.50133988 -6.6233932 -6.4820172 -0.69040381
3000 410 0.49942448 -6.6353753 -6.4859797 -0.6737426
3100 412 0.42190611 -6.6280489 -6.4885103 -0.71665975
3200 414 0.41178932 -6.621106 -6.4868768 -0.70387051
3300 416 0.46253061 -6.6361091 -6.4919436 -0.71264477
3400 418 0.42181868 -6.6317908 -6.4923081 -0.66171467
3500 420 0.41797099 -6.6287141 -6.4897821 -0.65879262
3600 422 0.36509229 -6.6214108 -6.4915707 -0.70324811
3700 424 0.39348534 -6.6179504 -6.4817297 -0.68426814
3800 426 0.39474314 -6.6086782 -6.4636684 -0.71591333
3900 428 0.45542305 -6.635636 -6.4706661 -0.68175206
4000 430 0.39042908 -6.6488343 -6.500435 -0.66366199
4100 432 0.39468368 -6.6585928 -6.49931 -0.76227835
4200 434 0.41142379 -6.6557126 -6.4903949 -0.73380042
4300 436 0.48160084 -6.6588571 -6.4749235 -0.71948887
4400 438 0.55431951 -6.698039 -6.4754774 -0.68067319
4500 440 0.4585125 -6.7096071 -6.5073393 -0.68190471
4600 442 0.44221158 -6.7238275 -6.5235013 -0.72486537
4700 444 0.3530253 -6.7116222 -6.5326725 -0.78475189
4800 446 0.39053263 -6.7192087 -6.5305763 -0.7500161
4900 448 0.39195928 -6.7304752 -6.5391648 -0.7414609
5000 450 0.39808899 -6.7364876 -6.5449794 -0.68624334
5100 452 0.40415767 -6.7520155 -6.5566586 -0.77799849
5200 454 0.32066094 -6.7478767 -6.5677968 -0.70955786
5300 456 0.3189586 -6.7748028 -6.5774312 -0.76013414
5400 458 0.28680679 -6.754829 -6.57373 -0.75077874
5500 460 0.3229394 -6.7693127 -6.565559 -0.76453959
5600 462 0.39545678 -6.7962985 -6.5645492 -0.75110236
5700 464 0.41518466 -6.8618036 -6.6026038 -0.79792247
5800 466 0.41117489 -6.8979481 -6.6272973 -0.68505301
5900 468 0.34391673 -6.8959897 -6.6377009 -0.67914717
6000 470 0.30168814 -6.8907915 -6.643955 -0.79643615
6100 472 0.30916205 -6.8885557 -6.6360589 -0.81599518
6200 474 0.35424257 -6.8990909 -6.6305161 -0.75613637
6300 476 0.35703296 -6.9174766 -6.6367178 -0.72950736
6400 478 0.37445271 -6.9445085 -6.6442671 -0.69659454
6500 480 0.329543 -6.9458858 -6.6609468 -0.75534893
6600 482 0.33963739 -6.947355 -6.6559786 -0.86232494
6700 484 0.34574376 -6.9518517 -6.6559314 -0.78159338
6800 486 0.38169407 -6.9787425 -6.6545343 -0.69654215
6900 488 0.36970486 -6.9727516 -6.6668784 -0.73296306
7000 490 0.32030483 -6.9604688 -6.6704554 -0.79884199
7100 492 0.34751955 -6.9885857 -6.6859115 -0.72531587
7200 494 0.34236112 -7.0019964 -6.700804 -0.81526247
7300 496 0.27559869 -7.0056964 -6.7192826 -0.77309778
7400 498 0.31846741 -7.0236162 -6.7200064 -0.84787873
7500 500 0.321674 -7.0382328 -6.7191195 -0.75690059
7600 502 0.31379969 -7.0541204 -6.7245415 -0.84134932
7700 504 0.33442098 -7.0824103 -6.7379709 -0.77808299
7800 506 0.31650445 -7.1121677 -6.7680346 -0.78541215
7900 508 0.30347752 -7.1100388 -6.7724658 -0.89260888
8000 510 0.31695084 -7.121996 -6.7701485 -0.80026292
8100 512 0.29991827 -7.133499 -6.779965 -0.77547985
8200 514 0.32128068 -7.1588222 -6.7891361 -0.85855005
8300 516 0.28103196 -7.1423077 -6.7970623 -0.76011418
8400 518 0.27077784 -7.150974 -6.8102547 -0.8189845
8500 520 0.29179445 -7.1717624 -6.8140245 -0.81319487
8600 522 0.29543603 -7.1666027 -6.8067797 -0.87228723
8700 524 0.27449088 -7.1899692 -6.824729 -0.86748792
8800 526 0.28192057 -7.1737434 -6.8131045 -0.80681355
8900 528 0.29164865 -7.1791336 -6.8042773 -0.83580175
9000 530 0.3473538 -7.2167575 -6.8110439 -0.84061628
9100 532 0.29792019 -7.211711 -6.8136015 -0.7023788
9200 534 0.2856865 -7.2088408 -6.8221795 -0.89143929
9300 536 0.27649993 -7.2299192 -6.8337365 -0.95862494
9400 538 0.29410309 -7.243419 -6.8486336 -0.91099619
9500 540 0.29981454 -7.2655451 -6.8556167 -0.79314135
9600 542 0.2972807 -7.2726656 -6.8578775 -0.77556553
9700 544 0.27946124 -7.2703884 -6.8622493 -0.78651169
9800 546 0.29668633 -7.2869601 -6.8663987 -0.86233713
9900 548 0.27596387 -7.2922319 -6.8749679 -0.78008994
10000 550 0.29155875 -7.2941724 -6.8764764 -0.76577583
Loop time of 6.55461 on 1 procs for 10000 steps with 550 atoms
Pair time (%) = 4.01151 (61.2013)
Bond time (%) = 0.0117879 (0.179841)
Neigh time (%) = 2.16259 (32.9935)
Comm time (%) = 0.187663 (2.86307)
Outpt time (%) = 0.000994444 (0.0151717)
Other time (%) = 0.18006 (2.74707)
Nlocal: 550 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2375 ave 2375 max 2375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39585 ave 39585 max 39585 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39585
Ave neighs/atom = 71.9727
Ave special neighs/atom = 0.363636
Neighbor list builds = 885
Dangerous builds = 0

184
examples/deposit/log.deposit.molecule.17Dec13.linux.4
View File

@ -1,184 +0,0 @@
LAMMPS (30 Dec 2013)
# sample surface deposition script for molecules
units lj
atom_style bond
boundary p p f
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region box block 0 5 0 5 0 10
create_box 3 box "bond types" 1 "extra bond per atom" 1
Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
1 by 1 by 4 MPI processor grid
region substrate block INF INF INF INF INF 3
create_atoms 1 region substrate
Created 350 atoms
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 1.0 1.0 5.0
mass * 1.0
bond_style harmonic
bond_coeff 1 5.0 1.0
neigh_modify delay 0
group addatoms type 2
0 atoms in group addatoms
region mobile block 0 5 0 5 2 INF
group mobile region mobile
150 atoms in group mobile
compute add addatoms temp
compute_modify add dynamic yes extra 0
fix 1 addatoms nve
fix 2 mobile langevin 0.1 0.1 0.1 587283
fix 3 mobile nve
molecule dimer molecule.dimer
region slab block 0 5 0 5 8 9
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0
fix 5 addatoms wall/reflect zhi EDGE
thermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 50 dump.deposit.atom
#dump 1 all movie 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
#dump 1 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 2.83497 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 352 0.83994737 -6.8946578 -6.8874992 -0.73775337
200 354 0.83994737 -6.8644786 -6.8502422 -0.69623155
300 356 0.83994737 -6.821588 -6.8003534 -0.69525265
400 358 0.84042015 -6.783499 -6.7553282 -0.68860116
500 360 0.84184269 -6.7432459 -6.7081686 -0.72724605
600 362 0.8458127 -6.7144697 -6.6724104 -0.66535013
700 364 0.87383242 -6.6725197 -6.6220566 -0.66071708
800 366 0.87696132 -6.6413623 -6.5830213 -0.66927232
900 368 0.89744792 -6.6071502 -6.5409657 -0.62868608
1000 370 0.99832562 -6.591423 -6.509704 -0.68145874
1100 372 0.83690497 -6.5836533 -6.5010396 -0.63926628
1200 374 0.88380837 -6.5576129 -6.4700582 -0.6448691
1300 376 0.93920197 -6.5480148 -6.4485844 -0.67509018
1400 378 1.0819467 -6.5984857 -6.4753138 -0.62854894
1500 380 0.72832384 -6.6161872 -6.5284826 -0.63429953
1600 382 0.63213539 -6.5990997 -6.5150252 -0.67037851
1700 384 0.5824052 -6.588541 -6.5069607 -0.69907025
1800 386 0.72529167 -6.5843125 -6.478207 -0.62283149
1900 388 0.57664201 -6.5677387 -6.4698656 -0.65451624
2000 390 0.65546977 -6.5676639 -6.4578769 -0.67432025
2100 392 0.69516646 -6.5858998 -6.4683877 -0.62289901
2200 394 0.56654159 -6.583766 -6.4770207 -0.70102083
2300 396 0.64110841 -6.598494 -6.4743096 -0.66950817
2400 398 0.52329199 -6.6104218 -6.4917721 -0.69664414
2500 400 0.55744613 -6.6221319 -6.4934736 -0.67790032
2600 402 0.46920185 -6.6192179 -6.5005058 -0.6830418
2700 404 0.56776413 -6.6299774 -6.4918044 -0.68598379
2800 406 0.44695801 -6.6053321 -6.4845111 -0.60979234
2900 408 0.51785351 -6.610722 -6.4741891 -0.62751234
3000 410 0.58665518 -6.6389279 -6.4792835 -0.64022876
3100 412 0.423824 -6.6194712 -6.4927699 -0.66450673
3200 414 0.45133153 -6.6230652 -6.4839389 -0.74364185
3300 416 0.51641116 -6.6567861 -6.49277 -0.64795831
3400 418 0.47621669 -6.6912734 -6.531463 -0.71160352
3500 420 0.38209486 -6.6823272 -6.5355428 -0.69351964
3600 422 0.44576071 -6.6807448 -6.5147154 -0.74737153
3700 424 0.41694154 -6.6822051 -6.5174366 -0.68130033
3800 426 0.40975915 -6.7048899 -6.5360548 -0.72002151
3900 428 0.48398461 -6.7282377 -6.5350708 -0.74439115
4000 430 0.36367577 -6.7208528 -6.5534139 -0.63650412
4100 432 0.34028562 -6.7242165 -6.5649615 -0.70137882
4200 434 0.33582497 -6.722058 -6.5514851 -0.76135001
4300 436 0.3825237 -6.7180169 -6.5381019 -0.70786373
4400 438 0.52062671 -6.7481686 -6.5135064 -0.73624603
4500 440 0.40436975 -6.7359486 -6.5304443 -0.79135494
4600 442 0.44491445 -6.7486865 -6.5249583 -0.76722101
4700 444 0.42190093 -6.7620999 -6.5568957 -0.68635283
4800 446 0.43599741 -6.7597134 -6.5440627 -0.77969628
4900 448 0.47851973 -6.7786447 -6.5458666 -0.74770553
5000 450 0.36262781 -6.8254599 -6.6092673 -0.71317359
5100 452 0.33856471 -6.8140502 -6.6072777 -0.70403037
5200 454 0.39260588 -6.835737 -6.6062808 -0.79831143
5300 456 0.31209864 -6.8230791 -6.6185118 -0.70136268
5400 458 0.31219166 -6.8170389 -6.6118122 -0.75454291
5500 460 0.33107044 -6.8102616 -6.5929746 -0.75347113
5600 462 0.40659306 -6.8413513 -6.5940668 -0.71199073
5700 464 0.35864173 -6.8618978 -6.6302942 -0.68000488
5800 466 0.35595504 -6.8739057 -6.637045 -0.72726368
5900 468 0.30133562 -6.8629749 -6.6404473 -0.79721111
6000 470 0.32080099 -6.860886 -6.631765 -0.79848812
6100 472 0.27961391 -6.8709022 -6.6465395 -0.71256878
6200 474 0.31406154 -6.8829903 -6.6410549 -0.7089865
6300 476 0.36004409 -6.9012979 -6.6442205 -0.77551843
6400 478 0.32635204 -6.8936662 -6.6413458 -0.6682556
6500 480 0.32068722 -6.8935855 -6.6453583 -0.7254097
6600 482 0.32713469 -6.9215037 -6.6558734 -0.76984099
6700 484 0.36721979 -6.9207471 -6.6473085 -0.75359037
6800 486 0.38350491 -6.9354455 -6.6470817 -0.79067926
6900 488 0.3250273 -6.9458853 -6.6769931 -0.67224329
7000 490 0.32830721 -6.9469844 -6.6778539 -0.7619618
7100 492 0.33730308 -6.9374197 -6.6588506 -0.78689069
7200 494 0.30775449 -6.9609022 -6.6952452 -0.67621108
7300 496 0.28573367 -6.9569147 -6.7028926 -0.67991253
7400 498 0.28191768 -6.988469 -6.7220227 -0.87179721
7500 500 0.31351279 -6.9987024 -6.7160563 -0.82937872
7600 502 0.28969341 -7.0254266 -6.7316544 -0.77890838
7700 504 0.28407599 -7.0337382 -6.7311947 -0.80238049
7800 506 0.29761165 -7.0326028 -6.731669 -0.8371957
7900 508 0.34677565 -7.0523551 -6.7260518 -0.8740631
8000 510 0.3118165 -7.0626608 -6.7450993 -0.77834874
8100 512 0.29761479 -7.0754729 -6.7620945 -0.74405688
8200 514 0.30483577 -7.0905149 -6.7644188 -0.85441065
8300 516 0.33684783 -7.1137001 -6.7534121 -0.82965734
8400 518 0.27961357 -7.0957286 -6.7677311 -0.78630354
8500 520 0.30612337 -7.1335883 -6.7809001 -0.83422091
8600 522 0.29624122 -7.1270458 -6.7835376 -0.84386217
8700 524 0.29657024 -7.1402335 -6.7844074 -0.69683349
8800 526 0.3086498 -7.137074 -6.7768455 -0.80569969
8900 528 0.26822775 -7.1262968 -6.7891397 -0.78344768
9000 530 0.29595187 -7.1836398 -6.8037091 -0.80740794
9100 532 0.27991165 -7.178976 -6.8079248 -0.71421566
9200 534 0.27664216 -7.1784888 -6.8037579 -0.84396547
9300 536 0.27879865 -7.2033389 -6.8100683 -0.64262205
9400 538 0.28514769 -7.1987974 -6.8126137 -0.7018808
9500 540 0.32951622 -7.2371185 -6.8151986 -0.88679168
9600 542 0.35683108 -7.2746833 -6.821215 -0.81047037
9700 544 0.29775774 -7.2584568 -6.8336125 -0.85576789
9800 546 0.29002392 -7.2763888 -6.8501209 -0.81455861
9900 548 0.31009857 -7.2950962 -6.852398 -0.93711055
10000 550 0.28745157 -7.3035265 -6.8657121 -0.90926429
Loop time of 5.64819 on 4 procs for 10000 steps with 550 atoms
Pair time (%) = 1.02706 (18.1839)
Bond time (%) = 0.00374371 (0.0662816)
Neigh time (%) = 0.562528 (9.95945)
Comm time (%) = 2.94816 (52.1966)
Outpt time (%) = 0.0134226 (0.237645)
Other time (%) = 1.09327 (19.3561)
Nlocal: 137.5 ave 298 max 3 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1917.25 ave 2722 max 455 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 9881.5 ave 24370 max 1 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 39526
Ave neighs/atom = 71.8655
Ave special neighs/atom = 0.363636
Neighbor list builds = 879
Dangerous builds = 0

210
examples/deposit/log.deposit.molecule.shake.31Dec13.linux.1
View File

@ -1,210 +0,0 @@
LAMMPS (30 Dec 2013)
# sample surface deposition script for molecules
units lj
atom_style bond
boundary p p f
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region box block 0 5 0 5 0 10
create_box 3 box "bond types" 1 "extra bond per atom" 1
Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
1 by 1 by 1 MPI processor grid
region substrate block INF INF INF INF INF 3
create_atoms 1 region substrate
Created 350 atoms
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 1.0 1.0 5.0
mass * 1.0
bond_style harmonic
bond_coeff 1 5.0 1.0
neigh_modify delay 0
group addatoms type 2
0 atoms in group addatoms
region mobile block 0 5 0 5 2 INF
group mobile region mobile
150 atoms in group mobile
compute add addatoms temp
compute_modify add dynamic yes extra 0
fix 1 addatoms nve
fix 2 mobile langevin 0.1 0.1 0.1 587283
fix 3 mobile nve
molecule dimer molecule.dimer.shake
region slab block 0 5 0 5 8 9
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 shake 6
fix 5 addatoms wall/reflect zhi EDGE
fix 6 all shake 0.0001 20 1000 b 1 mol dimer
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
0 = # of frozen angles
thermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 50 dump.deposit.atom
#dump 1 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
#dump 1 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 10000
SHAKE stats (type/ave/delta) on step 0
Memory usage per processor = 3.29483 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 352 0.83994737 -6.8875167 -6.8803581 -0.73353914
200 354 0.83994737 -6.8593854 -6.845149 -0.70414703
300 356 0.83994737 -6.8170634 -6.7958288 -0.69170868
400 358 0.84041725 -6.7849764 -6.756806 -0.7035216
500 360 0.84183519 -6.748903 -6.7138265 -0.68387035
600 362 0.8457626 -6.7098456 -6.6677911 -0.68283488
700 364 0.87175336 -6.6714189 -6.6211254 -0.66640179
800 366 0.89727068 -6.6401774 -6.58134 -0.6884522
900 368 0.8910839 -6.6065228 -6.5411444 -0.66350953
SHAKE stats (type/ave/delta) on step 1000
1 1 2.22045e-15
1000 370 0.91133967 -6.588373 -6.5144806 -0.66697456
1100 372 0.94335272 -6.5833353 -6.4996508 -0.67903461
1200 374 0.99444649 -6.5738934 -6.4781713 -0.69968884
1300 376 0.90431799 -6.5527637 -6.4589648 -0.65395726
1400 378 0.87224945 -6.5791233 -6.4822067 -0.59735159
1500 380 0.70715888 -6.5873408 -6.5035983 -0.66564852
1600 382 0.62213024 -6.5772707 -6.4990972 -0.64409364
1700 384 0.68070957 -6.5844244 -6.4940176 -0.64134987
1800 386 0.57401946 -6.5665002 -6.4861969 -0.67470049
1900 388 0.5881638 -6.5787142 -6.4923087 -0.63724246
SHAKE stats (type/ave/delta) on step 2000
1 1 1.9984e-15
2000 390 0.51745341 -6.5676275 -6.4880193 -0.64186008
2100 392 0.64333766 -6.5649026 -6.4615091 -0.69333804
2200 394 0.57593118 -6.5450453 -6.4485695 -0.68021805
2300 396 0.53492565 -6.5584624 -6.4652557 -0.62345783
2400 398 0.45661041 -6.544717 -6.4621142 -0.65654987
2500 400 0.58215641 -6.5446545 -6.4355002 -0.66883882
2600 402 0.43995697 -6.5607405 -6.4753757 -0.67436771
2700 404 0.4466557 -6.5533428 -6.4637906 -0.70117445
2800 406 0.42040295 -6.54221 -6.4552301 -0.72050093
2900 408 0.49200481 -6.5487677 -6.4438549 -0.67794849
SHAKE stats (type/ave/delta) on step 3000
1 1 1.66533e-15
3000 410 0.5342337 -6.5660827 -6.4488119 -0.68521246
3100 412 0.41569551 -6.5482164 -6.4543822 -0.65929253
3200 414 0.41434893 -6.5508493 -6.4547684 -0.73417701
3300 416 0.46561679 -6.574876 -6.4640682 -0.74107992
3400 418 0.39535512 -6.5649131 -6.4684388 -0.69006358
3500 420 0.39411087 -6.5718133 -6.4732856 -0.69106958
3600 422 0.37682035 -6.5696319 -6.4731945 -0.67828428
3700 424 0.37674329 -6.5708333 -6.4722048 -0.7295631
3800 426 0.37554504 -6.5551508 -6.4546528 -0.74098651
3900 428 0.47716365 -6.5863941 -6.4559545 -0.69775764
SHAKE stats (type/ave/delta) on step 4000
1 1 2.33147e-15
4000 430 0.39309652 -6.5839434 -6.474242 -0.67165044
4100 432 0.36137922 -6.5755863 -6.4726936 -0.75284168
4200 434 0.33665675 -6.5709582 -6.4732191 -0.70384507
4300 436 0.3946452 -6.5707735 -6.4540092 -0.69853666
4400 438 0.39629282 -6.5795369 -6.4601062 -0.67823491
4500 440 0.42475465 -6.6042384 -6.473916 -0.71292755
4600 442 0.34909419 -6.5857221 -6.4767288 -0.68062333
4700 444 0.33643716 -6.585937 -6.4790954 -0.71038994
4800 446 0.3811408 -6.5930525 -6.4699936 -0.74063911
4900 448 0.3779954 -6.6042774 -6.4802477 -0.70390914
SHAKE stats (type/ave/delta) on step 5000
1 1 2.66454e-15
5000 450 0.35790409 -6.6297715 -6.5104702 -0.67849435
5100 452 0.31862212 -6.6444655 -6.5366133 -0.69854773
5200 454 0.32789016 -6.6469195 -6.5342524 -0.77180002
5300 456 0.31629858 -6.6421111 -6.5318228 -0.68835335
5400 458 0.36152066 -6.6602984 -6.5324243 -0.66682577
5500 460 0.30603254 -6.6639673 -6.5541948 -0.75705636
5600 462 0.34658631 -6.6700688 -6.5440374 -0.75945094
5700 464 0.28458079 -6.6579566 -6.5530788 -0.7766899
5800 466 0.34190507 -6.6915819 -6.5639178 -0.6929815
5900 468 0.26172244 -6.6714593 -6.5724745 -0.70329441
SHAKE stats (type/ave/delta) on step 6000
1 1 2.88658e-15
6000 470 0.30325244 -6.6862834 -6.5701442 -0.82109242
6100 472 0.25803236 -6.6686757 -6.5686335 -0.75984602
6200 474 0.25736768 -6.6766546 -6.5756622 -0.67984915
6300 476 0.3530954 -6.7208307 -6.580631 -0.77335637
6400 478 0.3006363 -6.7044803 -6.5837227 -0.66974614
6500 480 0.27597377 -6.7071947 -6.5950803 -0.75642311
6600 482 0.2706662 -6.7070144 -6.5958279 -0.88321143
6700 484 0.27555986 -6.7058949 -6.5914578 -0.82283176
6800 486 0.2955121 -6.7016169 -6.5775747 -0.72199097
6900 488 0.2913952 -6.6993267 -6.5757226 -0.69282245
SHAKE stats (type/ave/delta) on step 7000
1 1 2.22045e-15
7000 490 0.27981191 -6.7009662 -6.5810468 -0.73943132
7100 492 0.31685264 -6.7152099 -6.5780359 -0.78601605
7200 494 0.26385909 -6.7026224 -6.5872508 -0.76508099
7300 496 0.2419927 -6.6912656 -6.584418 -0.89055484
7400 498 0.28044404 -6.6920358 -6.5670186 -0.79518453
7500 500 0.2762337 -6.7027512 -6.5784461 -0.76793505
7600 502 0.26902486 -6.6930632 -6.5708766 -0.80819618
7700 504 0.30012554 -6.7092162 -6.5716587 -0.83589424
7800 506 0.27717017 -6.718352 -6.5901745 -0.74594843
7900 508 0.28519942 -6.7259778 -6.5929221 -0.77889998
SHAKE stats (type/ave/delta) on step 8000
1 1 2.44249e-15
8000 510 0.28557016 -6.7262354 -6.5918494 -0.75257718
8100 512 0.32553601 -6.7486118 -6.5941094 -0.78328454
8200 514 0.28944387 -6.7379705 -6.5994429 -0.82277182
8300 516 0.28225288 -6.7447383 -6.6085349 -0.82524964
8400 518 0.29766781 -6.7537921 -6.6089808 -0.81172437
8500 520 0.28078531 -6.7473953 -6.6097025 -0.78667487
8600 522 0.29606157 -6.7504868 -6.6041575 -0.75691538
8700 524 0.28041746 -6.7552926 -6.615619 -0.79512658
8800 526 0.26962722 -6.7491997 -6.6138735 -0.8259819
8900 528 0.25123819 -6.7474166 -6.62037 -0.71869124
SHAKE stats (type/ave/delta) on step 9000
1 1 2.55351e-15
9000 530 0.24967063 -6.7564864 -6.6292957 -0.80484783
9100 532 0.255677 -6.7481047 -6.616902 -0.79613772
9200 534 0.24927075 -6.7427408 -6.6139042 -0.78203944
9300 536 0.24128001 -6.7505335 -6.6249418 -0.89696509
9400 538 0.23135126 -6.7432631 -6.6219972 -0.8704287
9500 540 0.24351964 -6.7393856 -6.6108613 -0.75482267
9600 542 0.26958835 -6.7406647 -6.5974148 -0.74586395
9700 544 0.29017813 -6.7545832 -6.5993592 -0.82279021
9800 546 0.28529127 -6.7509448 -6.5973264 -0.82084768
9900 548 0.28362819 -6.7624889 -6.6087707 -0.70739129
SHAKE stats (type/ave/delta) on step 10000
1 1 3.10862e-15
10000 550 0.26759148 -6.766521 -6.620562 -0.73792582
Loop time of 6.38249 on 1 procs for 10000 steps with 550 atoms
Pair time (%) = 3.88742 (60.9075)
Bond time (%) = 0.0116096 (0.181897)
Neigh time (%) = 2.05303 (32.1666)
Comm time (%) = 0.18659 (2.92347)
Outpt time (%) = 0.000954866 (0.0149607)
Other time (%) = 0.242887 (3.80551)
Nlocal: 550 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2367 ave 2367 max 2367 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 37090 ave 37090 max 37090 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 37090
Ave neighs/atom = 67.4364
Ave special neighs/atom = 0.363636
Neighbor list builds = 845
Dangerous builds = 0

210
examples/deposit/log.deposit.molecule.shake.31Dec13.linux.4
View File

@ -1,210 +0,0 @@
LAMMPS (30 Dec 2013)
# sample surface deposition script for molecules
units lj
atom_style bond
boundary p p f
lattice fcc 1.0
Lattice spacing in x,y,z = 1.5874 1.5874 1.5874
region box block 0 5 0 5 0 10
create_box 3 box "bond types" 1 "extra bond per atom" 1
Created orthogonal box = (0 0 0) to (7.93701 7.93701 15.874)
1 by 1 by 4 MPI processor grid
region substrate block INF INF INF INF INF 3
create_atoms 1 region substrate
Created 350 atoms
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 1 2 1.0 1.0 5.0
mass * 1.0
bond_style harmonic
bond_coeff 1 5.0 1.0
neigh_modify delay 0
group addatoms type 2
0 atoms in group addatoms
region mobile block 0 5 0 5 2 INF
group mobile region mobile
150 atoms in group mobile
compute add addatoms temp
compute_modify add dynamic yes extra 0
fix 1 addatoms nve
fix 2 mobile langevin 0.1 0.1 0.1 587283
fix 3 mobile nve
molecule dimer molecule.dimer.shake
region slab block 0 5 0 5 8 9
fix 4 addatoms deposit 100 0 100 12345 region slab near 1.0 mol dimer vz -1.0 -1.0 shake 6
fix 5 addatoms wall/reflect zhi EDGE
fix 6 all shake 0.0001 20 1000 b 1 mol dimer
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
0 = # of frozen angles
thermo_style custom step atoms temp epair etotal press
thermo 100
thermo_modify temp add lost/bond ignore lost warn
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
#dump 1 all atom 50 dump.deposit.atom
#dump 1 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
#dump 1 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 10000
SHAKE stats (type/ave/delta) on step 0
Memory usage per processor = 3.36903 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 352 0.83994737 -6.8946578 -6.8874992 -0.73775337
200 354 0.83994737 -6.8644786 -6.8502422 -0.69623155
300 356 0.83994737 -6.821588 -6.8003534 -0.69525265
400 358 0.84041725 -6.7834986 -6.7553282 -0.68860028
500 360 0.84183519 -6.7432451 -6.7081686 -0.72724802
600 362 0.84576393 -6.714465 -6.6724104 -0.66535527
700 364 0.8717559 -6.6683922 -6.6180986 -0.65401104
800 366 0.8972223 -6.6397054 -6.5808712 -0.6644064
900 368 0.89269075 -6.6040689 -6.5385725 -0.6293193
SHAKE stats (type/ave/delta) on step 1000
1 1 1.9984e-15
1000 370 0.8729371 -6.5843837 -6.513605 -0.66197956
1100 372 0.93342483 -6.5845128 -6.501709 -0.66278095
1200 374 0.91864917 -6.5632239 -6.4747977 -0.66231969
1300 376 0.88129406 -6.5508349 -6.4594241 -0.66330811
1400 378 0.88948953 -6.5759309 -6.4770988 -0.65591838
1500 380 0.66619538 -6.5716683 -6.4927768 -0.59010827
1600 382 0.64223132 -6.5753954 -6.4946962 -0.64796777
1700 384 0.71053601 -6.5931071 -6.498739 -0.71037238
1800 386 0.54790722 -6.5681884 -6.4915382 -0.63518672
1900 388 0.52085896 -6.5677463 -6.4912283 -0.67745991
SHAKE stats (type/ave/delta) on step 2000
1 1 2.22045e-15
2000 390 0.53994531 -6.563133 -6.4800645 -0.70555161
2100 392 0.64094961 -6.5675869 -6.4645772 -0.61019297
2200 394 0.50620722 -6.5592797 -6.4744836 -0.63511891
2300 396 0.6301209 -6.5760707 -6.4662769 -0.6545461
2400 398 0.53704268 -6.5642828 -6.4671294 -0.68416557
2500 400 0.64625918 -6.586831 -6.4656574 -0.68064342
2600 402 0.45719634 -6.5878773 -6.4991676 -0.72641767
2700 404 0.45430513 -6.5902202 -6.4991343 -0.64780429
2800 406 0.39401639 -6.5731811 -6.4916604 -0.63232952
2900 408 0.56403499 -6.5944647 -6.4741925 -0.66065801
SHAKE stats (type/ave/delta) on step 3000
1 1 1.88738e-15
3000 410 0.42366175 -6.5762728 -6.4832739 -0.58419502
3100 412 0.46961858 -6.597044 -6.4910379 -0.72500263
3200 414 0.45608063 -6.579384 -6.4736262 -0.66491063
3300 416 0.41525459 -6.6061269 -6.5073043 -0.7034034
3400 418 0.34167228 -6.5966324 -6.5132578 -0.69889479
3500 420 0.35438956 -6.5897102 -6.5011128 -0.69191247
3600 422 0.371945 -6.587433 -6.4922433 -0.74209613
3700 424 0.42415073 -6.5959033 -6.4848638 -0.70963735
3800 426 0.41039811 -6.5821598 -6.4723349 -0.77667535
3900 428 0.49077557 -6.6168589 -6.4826982 -0.73113384
SHAKE stats (type/ave/delta) on step 4000
1 1 2.10942e-15
4000 430 0.40203105 -6.6345318 -6.5223371 -0.71969376
4100 432 0.36787594 -6.6171373 -6.5123949 -0.76807348
4200 434 0.3261302 -6.6032025 -6.5085195 -0.74955499
4300 436 0.38926276 -6.6029583 -6.4877865 -0.72978015
4400 438 0.41086026 -6.621007 -6.4971861 -0.68550032
4500 440 0.3521118 -6.6242377 -6.5162034 -0.76756664
4600 442 0.38603968 -6.6293115 -6.5087832 -0.74258268
4700 444 0.34056733 -6.6415895 -6.5334364 -0.65780725
4800 446 0.37197114 -6.6416079 -6.5215096 -0.82603673
4900 448 0.30132362 -6.6363593 -6.5374874 -0.71862716
SHAKE stats (type/ave/delta) on step 5000
1 1 2.33147e-15
5000 450 0.28288619 -6.6354525 -6.5411571 -0.77201855
5100 452 0.26546305 -6.6297974 -6.5399393 -0.71006539
5200 454 0.30926196 -6.6267464 -6.5204801 -0.81320777
5300 456 0.32583739 -6.6465492 -6.5329349 -0.71621457
5400 458 0.32161442 -6.6474216 -6.5336628 -0.71056186
5500 460 0.34683164 -6.6587332 -6.5343262 -0.81507876
5600 462 0.33207554 -6.6707235 -6.5499688 -0.76405763
5700 464 0.30990462 -6.6765987 -6.5623882 -0.74469148
5800 466 0.38115342 -6.7114459 -6.5691268 -0.76594753
5900 468 0.3045191 -6.7224056 -6.6072349 -0.8010673
SHAKE stats (type/ave/delta) on step 6000
1 1 3.9968e-15
6000 470 0.29295042 -6.7112692 -6.5990754 -0.87488246
6100 472 0.28821962 -6.7201644 -6.6084183 -0.77836483
6200 474 0.27856084 -6.7228536 -6.6135449 -0.84000894
6300 476 0.27590056 -6.7303516 -6.6208028 -0.78812565
6400 478 0.25075258 -6.7209969 -6.6202762 -0.78937406
6500 480 0.2420497 -6.7100555 -6.6117228 -0.84935998
6600 482 0.24559955 -6.7058717 -6.6049822 -0.73869936
6700 484 0.26670092 -6.7106888 -6.5999308 -0.74058907
6800 486 0.27972148 -6.7095837 -6.5921698 -0.85599188
6900 488 0.27556092 -6.7181144 -6.6012268 -0.78080334
SHAKE stats (type/ave/delta) on step 7000
1 1 3.66374e-15
7000 490 0.31988812 -6.7171565 -6.5800616 -0.79439098
7100 492 0.28768419 -6.7050741 -6.5805279 -0.75103962
7200 494 0.27446382 -6.6965124 -6.5765039 -0.7254846
7300 496 0.27613579 -6.6951364 -6.5732136 -0.81917256
7400 498 0.28716597 -6.6931216 -6.5651078 -0.83063101
7500 500 0.29991456 -6.7065993 -6.5716377 -0.84995417
7600 502 0.30054942 -6.7057164 -6.5692119 -0.82453964
7700 504 0.33779908 -6.7355443 -6.5807197 -0.79378799
7800 506 0.27918017 -6.7440838 -6.6149767 -0.80343537
7900 508 0.27474528 -6.757924 -6.6297456 -0.9146801
SHAKE stats (type/ave/delta) on step 8000
1 1 3.21965e-15
8000 510 0.27352726 -6.7606902 -6.6319715 -0.83056014
8100 512 0.24483334 -6.7656728 -6.6494726 -0.81557302
8200 514 0.26136253 -6.776203 -6.6511151 -0.93698626
8300 516 0.22306201 -6.7512948 -6.6436544 -0.84185984
8400 518 0.23781328 -6.7617152 -6.6460223 -0.92614518
8500 520 0.26396807 -6.7687306 -6.6392847 -0.88122061
8600 522 0.27813101 -6.7722102 -6.6347431 -0.86382754
8700 524 0.28109538 -6.7747951 -6.6347838 -0.73669838
8800 526 0.25374762 -6.7712592 -6.643903 -0.81383179
8900 528 0.26572288 -6.7804903 -6.6461191 -0.88882544
SHAKE stats (type/ave/delta) on step 9000
1 1 2.55351e-15
9000 530 0.23242437 -6.7530647 -6.6346599 -0.82067326
9100 532 0.24597332 -6.7582807 -6.6320576 -0.89921536
9200 534 0.23307655 -6.7540042 -6.6335377 -0.94279835
9300 536 0.2252299 -6.7483888 -6.6311516 -0.72691575
9400 538 0.24036406 -6.7561763 -6.6301862 -0.79108419
9500 540 0.24443282 -6.7448693 -6.6158631 -0.89759125
9600 542 0.21936118 -6.725477 -6.6089161 -0.81388326
9700 544 0.24527855 -6.7404349 -6.6092289 -0.88469799
9800 546 0.26358125 -6.746269 -6.6043407 -0.94325913
9900 548 0.30133107 -6.7564789 -6.5931662 -0.95797751
SHAKE stats (type/ave/delta) on step 10000
1 1 2.77556e-15
10000 550 0.24849941 -6.7407813 -6.6052361 -0.88843235
Loop time of 6.0445 on 4 procs for 10000 steps with 550 atoms
Pair time (%) = 1.0029 (16.5919)
Bond time (%) = 0.0037064 (0.0613185)
Neigh time (%) = 0.542864 (8.98112)
Comm time (%) = 2.92824 (48.4448)
Outpt time (%) = 0.00355923 (0.0588838)
Other time (%) = 1.56323 (25.862)
Nlocal: 137.5 ave 298 max 4 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1913.75 ave 2692 max 538 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 9179.5 ave 22892 max 1 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 36718
Ave neighs/atom = 66.76
Ave special neighs/atom = 0.363636
Neighbor list builds = 848
Dangerous builds = 0

89
examples/dipole/log.dipole.18Feb13.linux.1
View File

@ -1,89 +0,0 @@
LAMMPS (18 Feb 2013)
# Point dipoles in a 2d box
units lj
atom_style hybrid sphere dipole
dimension 2
lattice sq2 0.7
Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
region box block 0 10 0 10 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 200 atoms
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
200 settings made for mass
set group all dipole/random 98934 0.75
200 settings made for dipole/random
velocity all create 0.0 87287 mom no
pair_style dipole/cut 2.5
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0
fix 1 all nve/sphere update dipole
fix 2 all enforce2d
timestep 0.005
compute erot all erotate/sphere
thermo_style custom step temp epair c_erot etotal press
thermo 500
#dump 1 all custom 500 dump.dipole id type x y z mux muy
#dump 1 all image 250 image.*.jpg mux type # zoom 1.6 adiam 1.2
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 3.28656 Mbytes
Step Temp E_pair erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
1500 0.42110221 -2.8019062 0.19532181 -2.3829095 0.18067141
2000 0.39019973 -2.7914873 0.22407026 -2.4032386 -0.40914143
2500 0.40242274 -2.8142159 0.24281467 -2.4138053 -0.3391299
3000 0.42771065 -2.8535488 0.25848739 -2.4279767 -0.2500108
3500 0.44706195 -2.7890555 0.18446345 -2.3442289 -0.1005632
4000 0.4041733 -2.7741037 0.22161024 -2.3719512 -0.13373446
4500 0.47549052 -2.8368758 0.21740299 -2.3637627 -0.14246916
5000 0.42071015 -2.7518085 0.20821432 -2.3332019 -0.047522754
5500 0.43520504 -2.8042986 0.24366805 -2.3712696 -0.22180582
6000 0.42802195 -2.7822398 0.24060881 -2.3563579 -0.35350862
6500 0.4479767 -2.8175363 0.25806495 -2.3717994 0.07885849
7000 0.39538519 -2.7246562 0.23766993 -2.331248 -0.098542228
7500 0.40716663 -2.7115371 0.21917238 -2.3064063 -0.14844207
8000 0.42814546 -2.7318282 0.23188976 -2.3058235 -0.37209482
8500 0.46175735 -2.7607768 0.23020837 -2.3013282 -0.33381513
9000 0.48360992 -2.758533 0.21927619 -2.2773411 -0.016767257
9500 0.47646809 -2.7812073 0.24046809 -2.3071216 -0.12582235
10000 0.48207466 -2.7437285 0.20973254 -2.2640642 0.51612253
Loop time of 1.02845 on 1 procs for 10000 steps with 200 atoms
Pair time (%) = 0.837266 (81.4103)
Neigh time (%) = 0.0349927 (3.40246)
Comm time (%) = 0.0476522 (4.6334)
Outpt time (%) = 0.000173092 (0.0168303)
Other time (%) = 0.108368 (10.537)
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 158 ave 158 max 158 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1673 ave 1673 max 1673 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1673
Ave neighs/atom = 8.365
Neighbor list builds = 679
Dangerous builds = 0

89
examples/dipole/log.dipole.18Feb13.linux.4
View File

@ -1,89 +0,0 @@
LAMMPS (18 Feb 2013)
# Point dipoles in a 2d box
units lj
atom_style hybrid sphere dipole
dimension 2
lattice sq2 0.7
Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
region box block 0 10 0 10 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 200 atoms
# need both mass settings due to hybrid atom style
mass 1 1.0
set group all mass 1.0
200 settings made for mass
set group all dipole/random 98934 0.75
200 settings made for dipole/random
velocity all create 0.0 87287 mom no
pair_style dipole/cut 2.5
pair_coeff * * 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0
fix 1 all nve/sphere update dipole
fix 2 all enforce2d
timestep 0.005
compute erot all erotate/sphere
thermo_style custom step temp epair c_erot etotal press
thermo 500
#dump 1 all custom 500 dump.dipole id type x y z mux muy
#dump 1 all image 250 image.*.jpg mux type # zoom 1.6 adiam 1.2
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 3.28531 Mbytes
Step Temp E_pair erot TotEng Press
0 0 -2.1909822 0 -2.1909822 -2.5750971
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
1500 0.42110221 -2.8019062 0.19532181 -2.3829095 0.18067141
2000 0.39019968 -2.7914873 0.22407029 -2.4032386 -0.4091395
2500 0.40237391 -2.8138968 0.24276582 -2.4135348 -0.33901619
3000 0.42595202 -2.8621684 0.26812111 -2.4383462 -0.19493812
3500 0.41153448 -2.8070419 0.23860803 -2.397565 -0.032395966
4000 0.40867238 -2.7790568 0.22331133 -2.3724278 0.014462986
4500 0.39803378 -2.7718651 0.23536245 -2.3758215 -0.25429533
5000 0.42736901 -2.8476039 0.2824171 -2.4223718 0.12187395
5500 0.41115816 -2.7810177 0.24508517 -2.3719153 -0.1925336
6000 0.43184788 -2.8015292 0.24726776 -2.3718406 -0.014489672
6500 0.45955478 -2.8340069 0.26105652 -2.3767499 -0.16015969
7000 0.43826613 -2.7488226 0.20031236 -2.3127478 0.071480756
7500 0.45738321 -2.7892162 0.23337255 -2.3341199 -0.17245012
8000 0.46107991 -2.7322063 0.18569571 -2.2734318 -0.21563894
8500 0.40367385 -2.7623279 0.27023252 -2.3606724 -0.038576129
9000 0.43104207 -2.7672424 0.25452132 -2.3383555 0.044351007
9500 0.38924411 -2.7231541 0.24926613 -2.3358562 -0.21910634
10000 0.44421944 -2.7677489 0.23376321 -2.3257506 0.034770807
Loop time of 0.47903 on 4 procs for 10000 steps with 200 atoms
Pair time (%) = 0.216013 (45.0939)
Neigh time (%) = 0.00924784 (1.93053)
Comm time (%) = 0.190206 (39.7065)
Outpt time (%) = 0.000464082 (0.0968794)
Other time (%) = 0.0630991 (13.1723)
Nlocal: 50 ave 55 max 41 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 87.75 ave 92 max 78 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 415 ave 481 max 301 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 1660
Ave neighs/atom = 8.3
Neighbor list builds = 671
Dangerous builds = 0

98
examples/dreiding/log.dreiding.18Feb13.linux.1
View File

@ -1,98 +0,0 @@
LAMMPS (18 Feb 2013)
units real
atom_style full
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
kspace_style pppm 0.001
read_data data.dreiding
4 = max bonds/atom
6 = max angles/atom
3 = max dihedrals/atom
0 = max impropers/atom
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
1 by 1 by 1 MPI processor grid
384 atoms
320 bonds
448 angles
192 dihedrals
0 impropers
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
5 = max # of special neighbors
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
variable input index in.ch3oh.box.dreiding
variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
run 0
WARNING: No fixes defined, atoms won't move (verlet.cpp:54)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (pppm.cpp:259)
G vector (1/distance) = 0.142073
grid = 3 3 3
stencil order = 5
estimated absolute RMS force accuracy = 0.154715
estimated relative force accuracy = 0.00046592
using double precision FFTs
3d grid and FFT values/proc = 512 27
Memory usage per processor = 7.97168 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 597.219740 E_long = -361.164864 E_hbond = -69.322152
C_hbond = 235.000000 Press = -847.550210 Volume = 7447.236335
Loop time of 2.14577e-06 on 1 procs for 0 steps with 384 atoms
Pair time (%) = 0 (0)
Bond time (%) = 0 (0)
Kspce time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 2.14577e-06 (100)
FFT time (% of Kspce) = 0 (0)
FFT Gflps 3d (1d only) = 0 0
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4637 ave 4637 max 4637 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 101854 ave 101854 max 101854 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 203708 ave 203708 max 203708 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 203708
Ave neighs/atom = 530.49
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0

98
examples/dreiding/log.dreiding.18Feb13.linux.4
View File

@ -1,98 +0,0 @@
LAMMPS (18 Feb 2013)
units real
atom_style full
boundary p p p
dielectric 1
special_bonds lj/coul 0.0 0.0 1.0
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
improper_style none
kspace_style pppm 0.001
read_data data.dreiding
4 = max bonds/atom
6 = max angles/atom
3 = max dihedrals/atom
0 = max impropers/atom
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
2 by 1 by 2 MPI processor grid
384 atoms
320 bonds
448 angles
192 dihedrals
0 impropers
4 = max # of 1-2 neighbors
3 = max # of 1-3 neighbors
5 = max # of special neighbors
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
pair_modify mix arithmetic
neighbor 2.0 multi
neigh_modify every 2 delay 4 check yes
variable input index in.ch3oh.box.dreiding
variable sname index ch3oh.box.dreiding
compute hb all pair hbond/dreiding/lj
variable C_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
thermo_modify line multi format float %14.6f
run 0
WARNING: No fixes defined, atoms won't move (verlet.cpp:54)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (pppm.cpp:259)
G vector (1/distance) = 0.142073
grid = 3 3 3
stencil order = 5
estimated absolute RMS force accuracy = 0.154715
estimated relative force accuracy = 0.00046592
using double precision FFTs
3d grid and FFT values/proc = 392 12
Memory usage per processor = 6.52757 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
E_coul = 597.219740 E_long = -361.164864 E_hbond = -69.322152
C_hbond = 235.000000 Press = -847.550210 Volume = 7447.236335
Loop time of 6.79493e-06 on 4 procs for 0 steps with 384 atoms
Pair time (%) = 0 (0)
Bond time (%) = 0 (0)
Kspce time (%) = 0 (0)
Neigh time (%) = 0 (0)
Comm time (%) = 0 (0)
Outpt time (%) = 0 (0)
Other time (%) = 6.79493e-06 (100)
FFT time (% of Kspce) = 0 (0)
FFT Gflps 3d (1d only) = 0 0
Nlocal: 96 ave 104 max 87 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 3063.25 ave 3108 max 3024 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 25463.5 ave 28799 max 22471 min
Histogram: 1 0 0 1 0 1 0 0 0 1
FullNghs: 50927 ave 55516 max 46073 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 203708
Ave neighs/atom = 530.49
Ave special neighs/atom = 4
Neighbor list builds = 0
Dangerous builds = 0

67
examples/eim/log.eim.18Feb13.linux.1
View File

@ -1,67 +0,0 @@
LAMMPS (18 Feb 2013)
# NaCl test problem for embedded atom method (EIM) potential
units metal
atom_style atomic
boundary p p p
lattice diamond 5.0
Lattice spacing in x,y,z = 5 5 5
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54)
1 by 1 by 1 MPI processor grid
2000 atoms
2000 velocities
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
neighbor 0.3 bin
neigh_modify delay 0
timestep 0.001
thermo_style custom step pe pxx pyy pzz temp
thermo 50
velocity all create 1400.0 43454 dist gaussian mom yes
fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
#dump id all atom 100 dump.eim
#dump 1 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3 element Na Cl
run 500
Memory usage per processor = 2.20266 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -5660.4738 -118151.29 -117613.39 -118064.41 1400
50 -5773.8661 889.73924 898.43321 703.5365 891.68472
100 -5742.8192 866.6183 817.86837 889.72898 838.77403
150 -5738.752 -335.23317 -345.69716 -123.3196 900.54672
200 -5704.2444 -172.01932 -508.83888 -654.45947 834.82705
250 -5724.4679 375.50199 546.99196 405.29298 966.14585
300 -5718.5442 428.47856 361.93998 752.00729 934.57116
350 -5722.7694 -409.40162 -484.53168 42.702482 865.13075
400 -5743.6862 173.43552 288.02324 107.96614 840.48912
450 -5751.3366 -752.54635 -762.07316 -591.45022 743.42176
500 -5780.5266 -157.23981 84.510897 -52.426827 712.64129
Loop time of 5.85191 on 1 procs for 500 steps with 2000 atoms
Pair time (%) = 5.38647 (92.0463)
Neigh time (%) = 0.367301 (6.2766)
Comm time (%) = 0.0237942 (0.406605)
Outpt time (%) = 0.000292301 (0.00499497)
Other time (%) = 0.0740573 (1.26552)
Nlocal: 2000 ave 2000 max 2000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4194 ave 4194 max 4194 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 99537 ave 99537 max 99537 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 99537
Ave neighs/atom = 49.7685
Neighbor list builds = 89
Dangerous builds = 10

67
examples/eim/log.eim.18Feb13.linux.4
View File

@ -1,67 +0,0 @@
LAMMPS (18 Feb 2013)
# NaCl test problem for embedded atom method (EIM) potential
units metal
atom_style atomic
boundary p p p
lattice diamond 5.0
Lattice spacing in x,y,z = 5 5 5
read_data data.eim
orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54)
1 by 2 by 2 MPI processor grid
2000 atoms
2000 velocities
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
neighbor 0.3 bin
neigh_modify delay 0
timestep 0.001
thermo_style custom step pe pxx pyy pzz temp
thermo 50
velocity all create 1400.0 43454 dist gaussian mom yes
fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
#dump id all atom 100 dump.eim
#dump 1 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3 element Na Cl
run 500
Memory usage per processor = 1.879 Mbytes
Step PotEng Pxx Pyy Pzz Temp
0 -5660.4738 -118151.29 -117613.39 -118064.41 1400
50 -5773.8661 889.73924 898.43321 703.5365 891.68472
100 -5742.8192 866.6183 817.86837 889.72898 838.77403
150 -5738.752 -335.23317 -345.69716 -123.3196 900.54672
200 -5704.2444 -172.01932 -508.83888 -654.45947 834.82705
250 -5724.4679 375.50199 546.99196 405.29298 966.14585
300 -5718.5442 428.47856 361.93998 752.00729 934.57116
350 -5722.7694 -409.40162 -484.53168 42.702482 865.13075
400 -5743.6862 173.43552 288.02324 107.96614 840.48912
450 -5751.3366 -752.54635 -762.07316 -591.45022 743.42176
500 -5780.5266 -157.23981 84.510897 -52.426827 712.64129
Loop time of 1.57123 on 4 procs for 500 steps with 2000 atoms
Pair time (%) = 1.39484 (88.774)
Neigh time (%) = 0.091349 (5.81387)
Comm time (%) = 0.0542217 (3.45092)
Outpt time (%) = 0.000287533 (0.0182999)
Other time (%) = 0.0305272 (1.94289)
Nlocal: 500 ave 501 max 498 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2179.25 ave 2182 max 2175 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 24884.2 ave 25164 max 24622 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 99537
Ave neighs/atom = 49.7685
Neighbor list builds = 89
Dangerous builds = 10

157
examples/ellipse/log.ellipse.gayberne.18Feb13.linux.1
View File

@ -1,157 +0,0 @@
LAMMPS (18 Feb 2013)
# GayBerne ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
compute q all property/atom quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.gayberne id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 1 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 1 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.89604 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1709963 -0.00050890768 2.2871782 0.066789189 13689.461
500 1.987484 -0.043660052 2.0342913 0.099199049 8475.4405
600 2.088535 -0.24318266 1.8270941 0.22391583 4674.8592
700 2.2604089 -0.73325761 1.481207 0.57184109 2507.095
800 1.8731398 -1.6161576 0.22080738 1.3049285 1420.4278
900 2.1404423 -3.0146759 -0.84039269 3.3566833 922.07169
1000 1.5927835 -4.5754144 -2.9697785 2.5493591 743.19289
1100 1.8380043 -4.8820159 -3.0604394 2.2950846 708.014
1200 2.05516 -4.5701279 -2.4718822 1.466469 753.52878
1300 2.0000364 -4.0755503 -2.031995 0.35675413 842.14053
1400 2.1055032 -3.7342781 -1.6632699 0.58193577 925.51606
1500 1.9241806 -3.582658 -1.639377 0.24973032 1006.7339
1600 2.125676 -3.4733166 -1.3572836 0.72069214 1061.1355
1700 1.8811354 -3.2933821 -1.4183258 0.59272021 1119.2646
1800 2.1014782 -3.1254259 -1.0248797 0.95254771 1162.1817
1900 1.8977855 -3.1905908 -1.2727444 0.7315737 1191.4876
2000 2.0794708 -3.253147 -1.2230906 0.49491309 1187.4615
Loop time of 0.744347 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.504503 (67.778)
Neigh time (%) = 0.0123847 (1.66383)
Comm time (%) = 0.0140009 (1.88096)
Outpt time (%) = 0.0178459 (2.39752)
Other time (%) = 0.195612 (26.2797)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 232 ave 232 max 232 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2868 ave 2868 max 2868 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2868
Ave neighs/atom = 7.17
Neighbor list builds = 138
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.90619 Mbytes
Step rot E_pair TotEng Press Volume
2000 2.0794708 -3.253147 -1.2230906 0.49491309 1187.4615
2100 2.0350673 -3.2084761 -1.1823685 0.33981994 1187.4615
2200 1.9674878 -3.1385619 -1.1467435 1.1720132 1187.4615
2300 2.0160349 -3.191283 -1.1652127 0.98222377 1187.4615
2400 2.1323062 -3.3152814 -1.1669961 0.76099841 1187.4615
2500 2.0866909 -3.2692047 -1.1766063 0.67971438 1187.4615
2600 2.0982853 -3.2774461 -1.1869918 0.9045362 1187.4615
2700 2.0482743 -3.2229418 -1.1928883 0.69426343 1187.4615
2800 1.9676269 -3.1400321 -1.1685787 0.7578428 1187.4615
2900 2.0421127 -3.2182014 -1.1866875 0.79386471 1187.4615
3000 2.1074286 -3.2870176 -1.2012732 0.18871121 1187.4615
3100 2.0466481 -3.2227223 -1.1821678 0.70482646 1187.4615
3200 2.1159694 -3.2976371 -1.1588561 0.52105755 1187.4615
3300 2.150544 -3.3366154 -1.179448 0.45837229 1187.4615
3400 2.1035378 -3.2868896 -1.1614884 0.72339226 1187.4615
3500 2.0665964 -3.2481259 -1.1351878 0.77887358 1187.4615
3600 2.0079794 -3.183204 -1.1647668 0.49419048 1187.4615
3700 2.0028597 -3.1740178 -1.1738107 0.38011763 1187.4615
3800 1.9501131 -3.1191211 -1.1785414 0.77609881 1187.4615
3900 2.0648034 -3.2412864 -1.1750708 0.55412858 1187.4615
4000 2.0161932 -3.1865719 -1.1939133 0.6656145 1187.4615
Loop time of 0.780147 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 0.621619 (79.6797)
Neigh time (%) = 0.00568986 (0.729332)
Comm time (%) = 0.0143819 (1.84348)
Outpt time (%) = 0.0179212 (2.29716)
Other time (%) = 0.120535 (15.4503)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 220 ave 220 max 220 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2901 ave 2901 max 2901 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2901
Ave neighs/atom = 7.2525
Neighbor list builds = 47
Dangerous builds = 0

157
examples/ellipse/log.ellipse.gayberne.18Feb13.linux.4
View File

@ -1,157 +0,0 @@
LAMMPS (18 Feb 2013)
# GayBerne ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
pair_style gayberne 1.0 3.0 1.0 4.0
pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
compute q all property/atom quatw quati quatj quatk
dump 1 all custom 100 dump.ellipse.gayberne id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 1 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 1 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.8645 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1709963 -0.00050890768 2.2871782 0.066789189 13689.461
500 1.987484 -0.043660052 2.0342913 0.099199049 8475.4405
600 2.088535 -0.24318266 1.8270941 0.22391583 4674.8592
700 2.2604089 -0.73325761 1.481207 0.57184109 2507.095
800 1.8731398 -1.6161576 0.22080738 1.3049285 1420.4278
900 2.1404423 -3.0146759 -0.84039269 3.3566833 922.07169
1000 1.5927835 -4.5754144 -2.9697785 2.5493591 743.19289
1100 1.8380043 -4.8820159 -3.0604394 2.2950846 708.014
1200 2.05516 -4.5701279 -2.4718822 1.466469 753.52878
1300 2.0000364 -4.0755503 -2.031995 0.35675413 842.14053
1400 2.1055032 -3.7342781 -1.6632699 0.58193577 925.51606
1500 1.9241806 -3.582658 -1.639377 0.24973032 1006.7339
1600 2.125676 -3.4733166 -1.3572836 0.72069214 1061.1355
1700 1.8811354 -3.2933821 -1.4183258 0.59272021 1119.2646
1800 2.1014782 -3.1254259 -1.0248797 0.9525477 1162.1817
1900 1.8977855 -3.1905908 -1.2727444 0.7315737 1191.4876
2000 2.0794708 -3.2531471 -1.2230906 0.49491309 1187.4615
Loop time of 0.266395 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.128512 (48.2411)
Neigh time (%) = 0.00328618 (1.23358)
Comm time (%) = 0.043604 (16.3682)
Outpt time (%) = 0.0182753 (6.86024)
Other time (%) = 0.0727174 (27.2969)
Nlocal: 100 ave 113 max 79 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 139.75 ave 151 max 132 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 717 ave 880 max 487 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 2868
Ave neighs/atom = 7.17
Neighbor list builds = 138
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.8665 Mbytes
Step rot E_pair TotEng Press Volume
2000 2.0794708 -3.2531471 -1.2230906 0.49491309 1187.4615
2100 2.0350673 -3.2084761 -1.1823685 0.33981993 1187.4615
2200 1.9674878 -3.1385619 -1.1467435 1.1720132 1187.4615
2300 2.0160349 -3.191283 -1.1652127 0.98222388 1187.4615
2400 2.1323062 -3.3152814 -1.1669961 0.76099822 1187.4615
2500 2.0866909 -3.2692048 -1.1766063 0.67971376 1187.4615
2600 2.098286 -3.2774469 -1.1869922 0.90453433 1187.4615
2700 2.0482737 -3.2229412 -1.1928882 0.69426669 1187.4615
2800 1.9676254 -3.1400305 -1.1685788 0.75785389 1187.4615
2900 2.0421207 -3.2182098 -1.1866861 0.79382733 1187.4615
3000 2.1074356 -3.2870234 -1.2012809 0.18867661 1187.4615
3100 2.0466079 -3.2226774 -1.1821925 0.7048821 1187.4615
3200 2.1158976 -3.2976855 -1.1589624 0.5209376 1187.4615
3300 2.1508115 -3.3368934 -1.1793489 0.45871464 1187.4615
3400 2.1046063 -3.2881336 -1.1615171 0.71895972 1187.4615
3500 2.066052 -3.2475413 -1.1359344 0.77760912 1187.4615
3600 2.0042504 -3.1791312 -1.1647191 0.50555439 1187.4615
3700 1.9888544 -3.1596354 -1.1679759 0.4059197 1187.4615
3800 1.9919683 -3.1636959 -1.1860197 0.70259722 1187.4615
3900 2.056542 -3.2325648 -1.1700712 0.43059703 1187.4615
4000 1.9958145 -3.1666798 -1.2556316 0.87469089 1187.4615
Loop time of 0.286178 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.157163 (54.9177)
Neigh time (%) = 0.00151408 (0.529068)
Comm time (%) = 0.0698599 (24.4113)
Outpt time (%) = 0.0182382 (6.37301)
Other time (%) = 0.0394036 (13.7689)
Nlocal: 100 ave 118 max 69 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 139 ave 156 max 130 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 729.75 ave 951 max 409 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 2919
Ave neighs/atom = 7.2975
Neighbor list builds = 47
Dangerous builds = 0

157
examples/ellipse/log.ellipse.resquared.18Feb13.linux.1
View File

@ -1,157 +0,0 @@
LAMMPS (18 Feb 2013)
# RESquared ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
pair_style resquared 4.0
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 1 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 1 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.41081 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1708604 -2.7650654e-05 2.2875165 0.066837495 13689.498
500 1.997512 0.016920625 2.0564634 0.11517748 8482.9706
600 2.0622304 0.078679437 2.0821362 0.28827312 4776.2481
700 2.1106581 0.19687916 2.326279 0.85203631 2756.4602
800 1.745752 0.29267549 1.978786 1.6290595 1832.812
900 1.7925965 0.24064027 2.0273447 1.7295568 1516.7688
1000 1.8280597 0.16642381 1.9844257 1.4314533 1517.3656
1100 2.157879 0.10561715 2.2607067 0.98795205 1744.9669
1200 1.7966771 0.057760855 1.8309261 0.54369976 2182.8259
1300 2.2982472 0.036382605 2.3348878 0.45715755 2731.1166
1400 1.7666501 0.038109497 1.7892555 0.32977405 3230.78
1500 2.3048922 0.081153096 2.376275 0.45835895 3431.9991
1600 1.8588345 0.067622658 1.9190878 0.39494686 3276.3398
1700 2.1798404 0.1400767 2.3395072 0.71093539 2829.7905
1800 1.9307392 0.14286145 2.0646696 0.84046137 2320.9547
1900 2.0667728 0.16459518 2.1859494 1.1672332 1900.3276
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
Loop time of 1.41227 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 1.19129 (84.3528)
Neigh time (%) = 0.011889 (0.841838)
Comm time (%) = 0.00994301 (0.704047)
Outpt time (%) = 0.000351429 (0.0248841)
Other time (%) = 0.198796 (14.0764)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 207 ave 207 max 207 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1886 ave 1886 max 1886 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1886
Ave neighs/atom = 4.715
Neighbor list builds = 179
Dangerous builds = 148
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.41283 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
2100 1.9516972 0.15050034 2.1113621 1.1750685 1657.9242
2200 1.9410444 0.1617683 2.122019 1.2634696 1657.9242
2300 1.918524 0.185457 2.1121008 1.3486177 1657.9242
2400 1.9148973 0.18929207 2.1281553 1.3450222 1657.9242
2500 1.8892245 0.21635013 2.1016576 1.5081781 1657.9242
2600 1.9450942 0.15744768 2.0838764 1.2106282 1657.9242
2700 1.9229729 0.18066635 2.1170011 1.3384024 1657.9242
2800 1.9512215 0.15099705 2.0988077 1.2134331 1657.9242
2900 1.9211263 0.18279158 2.0994515 1.3620719 1657.9242
3000 1.9067872 0.19775144 2.0931298 1.4157496 1657.9242
3100 1.9114595 0.19296361 2.1126574 1.4113475 1657.9242
3200 1.9427389 0.15998511 2.0865325 1.3075162 1657.9242
3300 1.9111626 0.19317346 2.1216597 1.430974 1657.9242
3400 1.9538368 0.14833057 2.1210144 1.2276261 1657.9242
3500 1.9244329 0.17929291 2.0825169 1.3186835 1657.9242
3600 1.9511869 0.15107062 2.1197982 1.2271623 1657.9242
3700 1.9369647 0.16601964 2.0970193 1.2813174 1657.9242
3800 1.9418163 0.16093067 2.1231369 1.2354415 1657.9242
3900 1.9450511 0.15759761 2.1394612 1.2392 1657.9242
4000 1.9350034 0.1681995 2.1142685 1.2676915 1657.9242
Loop time of 2.40524 on 1 procs for 2000 steps with 400 atoms
Pair time (%) = 2.26117 (94.0102)
Neigh time (%) = 0.00471711 (0.196118)
Comm time (%) = 0.0132644 (0.551481)
Outpt time (%) = 0.000371456 (0.0154436)
Other time (%) = 0.125716 (5.22677)
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 209 ave 209 max 209 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1903 ave 1903 max 1903 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1903
Ave neighs/atom = 4.7575
Neighbor list builds = 49
Dangerous builds = 0

157
examples/ellipse/log.ellipse.resquared.18Feb13.linux.4
View File

@ -1,157 +0,0 @@
LAMMPS (18 Feb 2013)
# RESquared ellipsoids in LJ background fluid
units lj
atom_style ellipsoid
dimension 2
lattice sq 0.02
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
region box block 0 20 0 20 -0.5 0.5
create_box 2 box
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 400 atoms
set group all type/fraction 2 0.1 95392
45 settings made for type/fraction
set type 1 mass 1.0
355 settings made for mass
set type 2 mass 1.5
45 settings made for mass
set type 1 shape 1 1 1
355 settings made for shape
set type 2 shape 3 1 1
45 settings made for shape
set group all quat/random 18238
400 settings made for quat/random
compute rot all temp/asphere
group spheroid type 1
355 atoms in group spheroid
variable dof equal count(spheroid)+2
compute_modify rot extra ${dof}
compute_modify rot extra 357
velocity all create 2.4 87287 loop geom
pair_style resquared 4.0
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
neighbor 0.8 bin
thermo_style custom step c_rot epair etotal press vol
thermo 100
timestep 0.002
compute q all property/atom quatw quati quatj quatk
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
#dump 1 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 1 pad 4 adiam 1 1.0 adiam 2 2.0
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
fix 2 all enforce2d
compute_modify 1_temp extra ${dof}
compute_modify 1_temp extra 357
# equilibrate to shrink box around dilute system
run 2000
Memory usage per processor = 3.39987 Mbytes
Step rot E_pair TotEng Press Volume
0 2.2718861 0 2.394 0.04788 20000
100 1.7443002 0 1.8380563 0.03576216 20558.672
200 2.2770454 0 2.3994366 0.046545139 20620.298
300 1.8573283 0 1.9571597 0.04240689 18460.771
400 2.1708604 -2.7650654e-05 2.2875165 0.066837495 13689.498
500 1.997512 0.016920625 2.0564634 0.11517748 8482.9706
600 2.0622304 0.078679437 2.0821362 0.28827312 4776.2481
700 2.1106581 0.19687916 2.326279 0.85203631 2756.4602
800 1.745752 0.29267549 1.978786 1.6290595 1832.812
900 1.7925965 0.24064027 2.0273447 1.7295568 1516.7688
1000 1.8280597 0.16642381 1.9844257 1.4314533 1517.3656
1100 2.157879 0.10561715 2.2607067 0.98795205 1744.9669
1200 1.7966771 0.057760855 1.8309261 0.54369976 2182.8259
1300 2.2982472 0.036382605 2.3348878 0.45715755 2731.1166
1400 1.7666501 0.038109497 1.7892555 0.32977405 3230.78
1500 2.3048922 0.081153096 2.376275 0.45835895 3431.9991
1600 1.8588345 0.067622658 1.9190878 0.39494686 3276.3398
1700 2.1798404 0.1400767 2.3395072 0.71093539 2829.7905
1800 1.9307392 0.14286145 2.0646696 0.84046137 2320.9547
1900 2.0667728 0.16459518 2.1859494 1.1672332 1900.3276
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
Loop time of 0.434882 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.304381 (69.9918)
Neigh time (%) = 0.00315994 (0.726621)
Comm time (%) = 0.0521417 (11.9899)
Outpt time (%) = 0.000434577 (0.09993)
Other time (%) = 0.0747641 (17.1918)
Nlocal: 100 ave 109 max 96 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Nghost: 116 ave 120 max 109 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 471.5 ave 499 max 455 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 1886
Ave neighs/atom = 4.715
Neighbor list builds = 179
Dangerous builds = 148
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 3.40071 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
2100 1.9516972 0.15050034 2.1113621 1.1750685 1657.9242
2200 1.9410444 0.1617683 2.122019 1.2634696 1657.9242
2300 1.918524 0.185457 2.1121008 1.3486177 1657.9242
2400 1.9148973 0.18929207 2.1281553 1.3450222 1657.9242
2500 1.8892245 0.21635014 2.1016576 1.5081781 1657.9242
2600 1.9450941 0.15744769 2.0838764 1.2106283 1657.9242
2700 1.9229729 0.18066636 2.1170012 1.3384025 1657.9242
2800 1.9512215 0.15099706 2.0988077 1.2134331 1657.9242
2900 1.9211263 0.18279161 2.0994515 1.362072 1657.9242
3000 1.9067874 0.19775131 2.0931298 1.415749 1657.9242
3100 1.9114597 0.1929634 2.1126573 1.4113467 1657.9242
3200 1.9427391 0.15998497 2.0865325 1.3075156 1657.9242
3300 1.9111628 0.19317321 2.1216596 1.4309722 1657.9242
3400 1.9538367 0.14833072 2.1210148 1.2276275 1657.9242
3500 1.9244321 0.17929374 2.0825174 1.3186878 1657.9242
3600 1.9511866 0.15107093 2.1197989 1.2271649 1657.9242
3700 1.9369592 0.16602536 2.0970215 1.2813456 1657.9242
3800 1.9418194 0.16092741 2.1231381 1.2354327 1657.9242
3900 1.9450474 0.15760145 2.1394611 1.2392217 1657.9242
4000 1.9350001 0.16820285 2.114271 1.2677094 1657.9242
Loop time of 0.696722 on 4 procs for 2000 steps with 400 atoms
Pair time (%) = 0.574434 (82.448)
Neigh time (%) = 0.00124782 (0.179099)
Comm time (%) = 0.0821022 (11.7841)
Outpt time (%) = 0.000450253 (0.0646245)
Other time (%) = 0.0384886 (5.52423)
Nlocal: 100 ave 107 max 97 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 117.5 ave 121 max 115 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 475.75 ave 511 max 446 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 1903
Ave neighs/atom = 4.7575
Neighbor list builds = 49
Dangerous builds = 0

127
examples/flow/log.flow.couette.18Feb13.linux.1
View File

@ -1,127 +0,0 @@
LAMMPS (18 Feb 2013)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
velocity lower set 0.0 0.0 0.0
velocity upper set 3.0 0.0 0.0
fix 3 boundary setforce 0.0 0.0 0.0
fix 4 all enforce2d
# Poiseuille flow
#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0
#fix 4 upper setforce 0.0 NULL 0.0
#fix 5 upper aveforce 0.0 -1.0 0.0
#fix 6 flow addforce 0.5 0.0 0.0
#fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
#dump 1 all atom 500 dump.flow
#dump 1 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.2
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 2.06376 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.52314537 571.54286
500 1.0644427 -0.31382888 0 0.44395296 3.0013076 571.54286
1000 1 -0.42965445 0 0.28225032 2.9612165 571.54286
1500 1.0739874 -0.41189772 0 0.35267901 2.5621951 571.54286
2000 1 -0.40814276 0 0.303762 2.9229578 571.54286
2500 1.193111 -0.38495952 0 0.46442186 2.8338993 571.54286
3000 1 -0.45584623 0 0.25605853 2.6569248 571.54286
3500 0.98858828 -0.44619629 0 0.25758441 2.6526913 571.54286
4000 1 -0.43273535 0 0.27916941 2.4570212 571.54286
4500 1.0805289 -0.34947719 0 0.41975647 2.5797635 571.54286
5000 1 -0.44623035 0 0.26567441 2.3488673 571.54286
5500 1.0821688 -0.41710054 0 0.35330058 2.6341553 571.54286
6000 1 -0.435398 0 0.27650676 2.496566 571.54286
6500 1.0788214 -0.46009514 0 0.30792295 2.3714035 571.54286
7000 1 -0.46345696 0 0.2484478 2.5780441 571.54286
7500 1.0331063 -0.436765 0 0.29870828 2.2415868 571.54286
8000 1 -0.42418776 0 0.287717 2.3469791 571.54286
8500 1.0898295 -0.42615905 0 0.3496958 2.6162262 571.54286
9000 1 -0.42341477 0 0.28849 2.5134824 571.54286
9500 1.0851884 -0.4442208 0 0.32833001 2.4872143 571.54286
10000 1 -0.39800556 0 0.3138992 2.5008138 571.54286
Loop time of 0.284207 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.126346 (44.4557)
Neigh time (%) = 0.0494514 (17.3998)
Comm time (%) = 0.00911665 (3.20775)
Outpt time (%) = 0.000174761 (0.0614907)
Other time (%) = 0.099118 (34.8753)
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: 943 ave 943 max 943 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 943
Ave neighs/atom = 2.24524
Neighbor list builds = 983
Dangerous builds = 0

127
examples/flow/log.flow.couette.18Feb13.linux.4
View File

@ -1,127 +0,0 @@
LAMMPS (18 Feb 2013)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
velocity lower set 0.0 0.0 0.0
velocity upper set 3.0 0.0 0.0
fix 3 boundary setforce 0.0 0.0 0.0
fix 4 all enforce2d
# Poiseuille flow
#velocity boundary set 0.0 0.0 0.0
#fix 3 lower setforce 0.0 0.0 0.0
#fix 4 upper setforce 0.0 NULL 0.0
#fix 5 upper aveforce 0.0 -1.0 0.0
#fix 6 flow addforce 0.5 0.0 0.0
#fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
#dump 1 all atom 500 dump.flow
#dump 1 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.2
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 2.06627 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.52314537 571.54286
500 1.0951876 -0.33403931 0 0.44562996 3.2502319 571.54286
1000 1 -0.3731019 0 0.33880286 2.8561715 571.54286
1500 1.0366879 -0.36031105 0 0.37771198 3.0196355 571.54286
2000 1 -0.41052955 0 0.30137522 2.865194 571.54286
2500 1.1228407 -0.37042187 0 0.4289338 2.9445246 571.54286
3000 1 -0.38445444 0 0.32745032 2.5935182 571.54286
3500 0.9837004 -0.45271556 0 0.24758544 2.7982195 571.54286
4000 1 -0.39733214 0 0.31457262 2.5610834 571.54286
4500 1.1185501 -0.40471335 0 0.39158777 2.4136693 571.54286
5000 1 -0.41474863 0 0.29715613 2.5475686 571.54286
5500 1.0417966 -0.3742507 0 0.36740927 2.4667154 571.54286
6000 1 -0.45012825 0 0.26177652 2.569894 571.54286
6500 1.1544519 -0.3964682 0 0.42539161 2.5635202 571.54286
7000 1 -0.44665963 0 0.26524513 2.4335307 571.54286
7500 0.97729968 -0.47377977 0 0.22196453 2.7482936 571.54286
8000 1 -0.42864525 0 0.28325951 2.3927949 571.54286
8500 1.0967901 -0.40513897 0 0.37567113 2.612602 571.54286
9000 1 -0.3847711 0 0.32713366 2.6900106 571.54286
9500 1.0085423 -0.4393538 0 0.27863229 2.4411599 571.54286
10000 1 -0.44847346 0 0.26343131 2.4997148 571.54286
Loop time of 0.160618 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.032594 (20.2929)
Neigh time (%) = 0.0132387 (8.24237)
Comm time (%) = 0.070047 (43.6109)
Outpt time (%) = 0.00035125 (0.218687)
Other time (%) = 0.044387 (27.6351)
Nlocal: 105 ave 115 max 94 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 40.25 ave 43 max 39 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Neighs: 235.75 ave 297 max 170 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 943
Ave neighs/atom = 2.24524
Neighbor list builds = 965
Dangerous builds = 0

127
examples/flow/log.flow.pois.18Feb13.linux.1
View File

@ -1,127 +0,0 @@
LAMMPS (18 Feb 2013)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
#velocity lower set 0.0 0.0 0.0
#velocity upper set 3.0 0.0 0.0
#fix 3 boundary setforce 0.0 0.0 0.0
#fix 4 all enforce2d
# Poiseuille flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -1.0 0.0
fix 6 flow addforce 0.5 0.0 0.0
fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
#dump 1 all atom 500 dump.flow
#dump 1 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 2.06376 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.52314537 571.54286
500 1.0990751 -0.36396768 0 0.41846911 2.522517 575.55806
1000 1 -0.34609791 0 0.36580685 1.9736175 584.67179
1500 1.2112861 -0.39062708 0 0.47169327 1.521881 587.24778
2000 1 -0.39956949 0 0.31233527 1.2496669 583.00676
2500 1.2236323 -0.40128446 0 0.46982521 1.4276891 570.03729
3000 1 -0.48849341 0 0.22341135 1.5091366 553.64637
3500 1.2404531 -0.63017461 0 0.25290984 1.7681313 535.22607
4000 1 -0.71551407 0 -0.003609313 2.2075137 516.73151
4500 1.2253143 -0.76279415 0 0.10951296 2.6154841 503.20466
5000 1 -0.79031519 0 -0.078410425 3.0914492 499.10917
5500 1.2025432 -0.74031121 0 0.115785 2.5889437 502.17138
6000 1 -0.64454518 0 0.067359583 2.0907022 510.47702
6500 1.2112733 -0.65703634 0 0.20527486 2.054449 515.41213
7000 1 -0.61856581 0 0.093338954 1.9843361 516.79512
7500 1.2212907 -0.67431193 0 0.19513077 1.9939559 517.17301
8000 1 -0.69966668 0 0.012238083 2.1559293 510.52934
8500 1.2245982 -0.73461969 0 0.13717758 2.4482542 506.2679
9000 1 -0.697338 0 0.014566762 2.4757604 503.86953
9500 1.1882 -0.66622491 0 0.17966032 2.3295348 505.67684
10000 1 -0.70364194 0 0.008262826 2.218568 507.64681
Loop time of 0.328633 on 1 procs for 10000 steps with 420 atoms
Pair time (%) = 0.139281 (42.3819)
Neigh time (%) = 0.028775 (8.75596)
Comm time (%) = 0.00759435 (2.31089)
Outpt time (%) = 0.000191689 (0.058329)
Other time (%) = 0.152791 (46.493)
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: 1116 ave 1116 max 1116 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1116
Ave neighs/atom = 2.65714
Neighbor list builds = 563
Dangerous builds = 0

127
examples/flow/log.flow.pois.18Feb13.linux.4
View File

@ -1,127 +0,0 @@
LAMMPS (18 Feb 2013)
# 2-d LJ flow simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
60 atoms in group upper
group boundary union lower upper
120 atoms in group boundary
group flow subtract all boundary
300 atoms in group flow
set group lower type 2
60 settings made for type
set group upper type 3
60 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Couette flow
#velocity lower set 0.0 0.0 0.0
#velocity upper set 3.0 0.0 0.0
#fix 3 boundary setforce 0.0 0.0 0.0
#fix 4 all enforce2d
# Poiseuille flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -1.0 0.0
fix 6 flow addforce 0.5 0.0 0.0
fix 7 all enforce2d
# Run
timestep 0.003
thermo 500
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
#dump 1 all atom 500 dump.flow
#dump 1 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 10000
Memory usage per processor = 2.06627 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1 0 0 0.71190476 0.52314537 571.54286
500 1.0758737 -0.36090417 0 0.40501541 2.7822308 575.0659
1000 1 -0.35701441 0 0.35489035 2.0575313 585.71407
1500 1.2368663 -0.37709732 0 0.50343367 1.4865879 587.193
2000 1 -0.39362939 0 0.31827537 1.4236 578.9418
2500 1.2272957 -0.423819 0 0.44989866 1.454461 570.15856
3000 1 -0.49143403 0 0.22047073 1.5345951 554.98633
3500 1.2444908 -0.59761803 0 0.28834092 1.875379 537.01606
4000 1 -0.70133161 0 0.010573147 2.1395416 521.46845
4500 1.2212352 -0.74763375 0 0.1217694 2.7598268 507.63512
5000 1 -0.7889135 0 -0.077008742 2.9809426 501.21601
5500 1.1965673 -0.78262115 0 0.069220825 2.8192028 505.3984
6000 1 -0.71434201 0 -0.0024372499 2.346053 512.05291
6500 1.203859 -0.67621716 0 0.18081576 2.1621043 518.624
7000 1 -0.66493592 0 0.046968842 1.8459166 519.01312
7500 1.2065975 -0.69903932 0 0.15994317 2.0439995 515.42888
8000 1 -0.71320172 0 -0.0012969589 2.1303566 511.98833
8500 1.2146567 -0.72062191 0 0.144098 2.4268382 504.80659
9000 1 -0.74806158 0 -0.036156822 2.5758196 502.43487
9500 1.1970932 -0.73220717 0 0.1200092 2.585169 504.06803
10000 1 -0.71105178 0 0.00085297794 2.3528576 507.92052
Loop time of 0.230103 on 4 procs for 10000 steps with 420 atoms
Pair time (%) = 0.0363874 (15.8136)
Neigh time (%) = 0.00789845 (3.43258)
Comm time (%) = 0.0856229 (37.2107)
Outpt time (%) = 0.000398636 (0.173243)
Other time (%) = 0.0997953 (43.3699)
Nlocal: 105 ave 107 max 103 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 42.75 ave 46 max 37 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 276.5 ave 295 max 257 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 1106
Ave neighs/atom = 2.63333
Neighbor list builds = 564
Dangerous builds = 0

145
examples/friction/log.friction.18Feb13.linux.1
View File

@ -1,145 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d friction simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 50 0 22 -0.25 0.25
create_box 4 box
Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
1 by 1 by 1 MPI processor grid
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
# atom regions
region lo-fixed block INF INF INF 1.1 INF INF
region lo-slab block INF INF INF 7 INF INF
region above-lo block INF INF INF 7 INF INF side out
region hi-fixed block INF INF 20.9 INF INF INF
region hi-slab block INF INF 15 INF INF INF
region below-hi block INF INF 15 INF INF INF side out
region lo-asperity sphere 32 7 0 8
region hi-asperity sphere 18 15 0 8
region lo-half-sphere intersect 2 lo-asperity above-lo
region hi-half-sphere intersect 2 hi-asperity below-hi
# create 2 surfaces with asperities
create_atoms 1 region lo-slab
Created 750 atoms
create_atoms 1 region hi-slab
Created 750 atoms
create_atoms 2 region lo-half-sphere
Created 112 atoms
create_atoms 3 region hi-half-sphere
Created 112 atoms
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
group lo region lo-slab
750 atoms in group lo
group lo type 2
862 atoms in group lo
group hi region hi-slab
750 atoms in group hi
group hi type 3
862 atoms in group hi
group lo-fixed region lo-fixed
150 atoms in group lo-fixed
group hi-fixed region hi-fixed
150 atoms in group hi-fixed
group boundary union lo-fixed hi-fixed
300 atoms in group boundary
group mobile subtract all boundary
1424 atoms in group mobile
set group lo-fixed type 4
150 settings made for type
set group hi-fixed type 4
150 settings made for type
# initial velocities
compute new mobile temp/partial 0 1 0
velocity mobile create 0.1 482748 temp new
velocity hi set 1.0 0.0 0.0 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
fix_modify 3 temp new
# Run
timestep 0.0025
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
#dump 1 all atom 500 dump.friction
#dump 1 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 20000
Memory usage per processor = 2.06912 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1333672 0 -3.0921259 -1.1437867 2444.9333
1000 0.1 -3.0915465 0 -3.0503052 0.010015559 2444.9333
2000 0.1 -3.0826487 0 -3.0414074 -0.42012889 2444.9333
3000 0.089819692 -3.07584 0 -3.0387972 -0.25252108 2444.9333
4000 0.098489874 -3.0667093 0 -3.0260907 -0.25506538 2444.9333
5000 0.11379986 -3.0557087 0 -3.0087762 -0.080871179 2444.9333
6000 0.11269179 -3.04532 0 -2.9988445 -0.33381202 2444.9333
7000 0.1 -3.0380598 0 -2.9968185 -0.32423909 2444.9333
8000 0.1 -3.0346453 0 -2.993404 -0.38015347 2444.9333
9000 0.1 -3.0324305 0 -2.9911892 -0.42940009 2444.9333
10000 0.11811429 -3.0334969 0 -2.984785 -0.32538147 2444.9333
11000 0.11627653 -3.0344827 0 -2.9865288 -0.45037424 2444.9333
12000 0.11250787 -3.0472157 0 -3.000816 -0.27347069 2444.9333
13000 0.11429889 -3.0455404 0 -2.9984021 -0.28832736 2444.9333
14000 0.11292741 -3.0466673 0 -3.0000946 -0.38939496 2444.9333
15000 0.11239299 -3.0460428 0 -2.9996905 -0.35437935 2444.9333
16000 0.11775554 -3.0457709 0 -2.997207 -0.14263984 2444.9333
17000 0.11456908 -3.0459128 0 -2.998663 -0.3686153 2444.9333
18000 0.1165453 -3.0454305 0 -2.9973657 -0.3572725 2444.9333
19000 0.11403056 -3.0440495 0 -2.9970218 -0.25462158 2444.9333
20000 0.11801421 -3.0462201 0 -2.9975495 -0.23484136 2444.9333
Loop time of 5.71207 on 1 procs for 20000 steps with 1724 atoms
Pair time (%) = 4.62848 (81.0298)
Neigh time (%) = 0.305739 (5.35251)
Comm time (%) = 0.0428324 (0.749857)
Outpt time (%) = 0.000311375 (0.00545117)
Other time (%) = 0.73471 (12.8624)
Nlocal: 1724 ave 1724 max 1724 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: 14384 ave 14384 max 14384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14384
Ave neighs/atom = 8.34339
Neighbor list builds = 723
Dangerous builds = 0

145
examples/friction/log.friction.18Feb13.linux.4
View File

@ -1,145 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d friction simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 50 0 22 -0.25 0.25
create_box 4 box
Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
2 by 2 by 1 MPI processor grid
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
# atom regions
region lo-fixed block INF INF INF 1.1 INF INF
region lo-slab block INF INF INF 7 INF INF
region above-lo block INF INF INF 7 INF INF side out
region hi-fixed block INF INF 20.9 INF INF INF
region hi-slab block INF INF 15 INF INF INF
region below-hi block INF INF 15 INF INF INF side out
region lo-asperity sphere 32 7 0 8
region hi-asperity sphere 18 15 0 8
region lo-half-sphere intersect 2 lo-asperity above-lo
region hi-half-sphere intersect 2 hi-asperity below-hi
# create 2 surfaces with asperities
create_atoms 1 region lo-slab
Created 750 atoms
create_atoms 1 region hi-slab
Created 750 atoms
create_atoms 2 region lo-half-sphere
Created 112 atoms
create_atoms 3 region hi-half-sphere
Created 112 atoms
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
group lo region lo-slab
750 atoms in group lo
group lo type 2
862 atoms in group lo
group hi region hi-slab
750 atoms in group hi
group hi type 3
862 atoms in group hi
group lo-fixed region lo-fixed
150 atoms in group lo-fixed
group hi-fixed region hi-fixed
150 atoms in group hi-fixed
group boundary union lo-fixed hi-fixed
300 atoms in group boundary
group mobile subtract all boundary
1424 atoms in group mobile
set group lo-fixed type 4
150 settings made for type
set group hi-fixed type 4
150 settings made for type
# initial velocities
compute new mobile temp/partial 0 1 0
velocity mobile create 0.1 482748 temp new
velocity hi set 1.0 0.0 0.0 sum yes
# fixes
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
fix_modify 3 temp new
# Run
timestep 0.0025
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
#dump 1 all atom 500 dump.friction
#dump 1 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 20000
Memory usage per processor = 2.06744 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.1 -3.1333672 0 -3.0921259 -1.1437867 2444.9333
1000 0.081958665 -3.0927273 0 -3.0589265 -0.021846131 2444.9333
2000 0.082641883 -3.0850764 0 -3.0509938 -0.44960195 2444.9333
3000 0.092293442 -3.0748001 0 -3.0367371 -0.25353161 2444.9333
4000 0.096012911 -3.0565129 0 -3.0169159 -0.027669541 2444.9333
5000 0.1 -3.0465555 0 -3.0053142 -0.099323956 2444.9333
6000 0.11642983 -3.0390782 0 -2.991061 -0.21034609 2444.9333
7000 0.11597774 -3.0331763 0 -2.9853456 -0.46345898 2444.9333
8000 0.11937899 -3.0305561 0 -2.9813226 -0.30773083 2444.9333
9000 0.111108 -3.0274067 0 -2.9815843 -0.5243749 2444.9333
10000 0.11666452 -3.0170603 0 -2.9689463 -0.37436916 2444.9333
11000 0.11005147 -3.0140407 0 -2.9686541 -0.46293236 2444.9333
12000 0.11286668 -3.0174735 0 -2.9709258 -0.28406396 2444.9333
13000 0.11280782 -3.0238036 0 -2.9772802 -0.41208934 2444.9333
14000 0.1 -3.0332072 0 -2.9919659 -0.1785001 2444.9333
15000 0.1148413 -3.0339717 0 -2.9866096 -0.4418584 2444.9333
16000 0.11194137 -3.0322089 0 -2.9860428 -0.29354474 2444.9333
17000 0.10699902 -3.0395654 0 -2.9954376 -0.37176577 2444.9333
18000 0.11091428 -3.0400366 0 -2.9942941 -0.19329155 2444.9333
19000 0.1094118 -3.0432032 0 -2.9980803 -0.38516174 2444.9333
20000 0.11137857 -3.0442022 0 -2.9982683 -0.37419199 2444.9333
Loop time of 1.97972 on 4 procs for 20000 steps with 1724 atoms
Pair time (%) = 1.18649 (59.9324)
Neigh time (%) = 0.0773743 (3.90835)
Comm time (%) = 0.432971 (21.8703)
Outpt time (%) = 0.000461817 (0.0233274)
Other time (%) = 0.282418 (14.2656)
Nlocal: 431 ave 493 max 377 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 96 ave 125 max 77 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 3596 ave 4228 max 3139 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 14384
Ave neighs/atom = 8.34339
Neighbor list builds = 700
Dangerous builds = 0

77
examples/gpu/log.gpu.melt.2.5.18Feb13.linux.1
View File

@ -1,77 +0,0 @@
LAMMPS (18 Feb 2013)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut/gpu 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 46.8462 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733685 0 -4.6133769 -5.0196738
100 0.75865618 -5.760326 0 -4.6223462 0.19586078
200 0.75643081 -5.7572862 0 -4.6226445 0.22641252
300 0.74927357 -5.7463992 0 -4.6224932 0.2973801
400 0.7404924 -5.7329247 0 -4.6221905 0.37767073
500 0.73092032 -5.7182616 0 -4.6218854 0.46900679
600 0.72315678 -5.706314 0 -4.621583 0.5348031
700 0.71597165 -5.6952207 0 -4.6212675 0.59549602
800 0.71194748 -5.6889042 0 -4.6209871 0.63784817
900 0.70596464 -5.6796285 0 -4.6206857 0.68573109
1000 0.70323336 -5.67534 0 -4.6204941 0.7069076
Loop time of 19.9863 on 1 procs for 1000 steps with 256000 atoms
Pair time (%) = 12.3568 (61.8261)
Neigh time (%) = 7.41482e-05 (0.000370995)
Comm time (%) = 1.09925 (5.50003)
Outpt time (%) = 0.0106428 (0.0532503)
Other time (%) = 6.51958 (32.6202)
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 69905 ave 69905 max 69905 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0

77
examples/gpu/log.gpu.melt.2.5.18Feb13.linux.4
View File

@ -1,77 +0,0 @@
LAMMPS (18 Feb 2013)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut/gpu 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 14.5208 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733685 0 -4.6133769 -5.0196738
100 0.75865619 -5.7603258 0 -4.622346 0.19586113
200 0.75643076 -5.7572857 0 -4.6226439 0.22641355
300 0.74927365 -5.7463989 0 -4.6224928 0.29738053
400 0.74049513 -5.7329265 0 -4.6221881 0.37765479
500 0.73092165 -5.7182628 0 -4.6218846 0.46899675
600 0.72307341 -5.7061845 0 -4.6215786 0.53536825
700 0.71593631 -5.6951696 0 -4.6212694 0.59644919
800 0.71106107 -5.6875486 0 -4.6209611 0.6450072
900 0.70789378 -5.6825117 0 -4.6206752 0.67079907
1000 0.70324302 -5.6753075 0 -4.6204471 0.71004301
Loop time of 7.94848 on 4 procs for 1000 steps with 256000 atoms
Pair time (%) = 4.79772 (60.3603)
Neigh time (%) = 5.11408e-05 (0.000643403)
Comm time (%) = 1.32216 (16.6341)
Outpt time (%) = 0.0349077 (0.439174)
Other time (%) = 1.79364 (22.5658)
Nlocal: 64000 ave 64090 max 63900 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 30521 ave 30604 max 30461 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0

77
examples/gpu/log.gpu.melt.5.0.18Feb13.linux.1
View File

@ -1,77 +0,0 @@
LAMMPS (18 Feb 2013)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1 threads_per_atom 8
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 256000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut/gpu 5.0
pair_coeff 1 1 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 58.5717 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -7.1616924 0 -5.0017009 -5.6743468
100 0.7599844 -6.1430228 0 -5.0030506 -0.43702259
200 0.75772866 -6.1397323 0 -5.0031437 -0.40563906
300 0.75029981 -6.1286575 0 -5.0032122 -0.33104595
400 0.73999172 -6.1132482 0 -5.003265 -0.24002804
500 0.73224839 -6.101694 0 -5.0033257 -0.16523398
600 0.72448053 -6.0900827 0 -5.0033661 -0.099467461
700 0.71878931 -6.0815935 0 -5.0034138 -0.044377743
800 0.71440115 -6.0750377 0 -5.0034401 -0.008074032
900 0.70942787 -6.0675896 0 -5.0034519 0.032869143
1000 0.70453362 -6.0602662 0 -5.0034699 0.069294492
Loop time of 43.6376 on 1 procs for 1000 steps with 256000 atoms
Pair time (%) = 35.9388 (82.3573)
Neigh time (%) = 7.1764e-05 (0.000164454)
Comm time (%) = 1.41024 (3.23171)
Outpt time (%) = 0.0104296 (0.0239005)
Other time (%) = 6.27813 (14.387)
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 141796 ave 141796 max 141796 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0

77
examples/gpu/log.gpu.melt.5.0.18Feb13.linux.4
View File

@ -1,77 +0,0 @@
LAMMPS (18 Feb 2013)
# 3d Lennard-Jones melt
newton off
package gpu force/neigh 0 1 1 threads_per_atom 8
variable x index 2
variable y index 2
variable z index 2
variable xx equal 20*$x
variable xx equal 20*2
variable yy equal 20*$y
variable yy equal 20*2
variable zz equal 20*$z
variable zz equal 20*2
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 ${xx} 0 ${yy} 0 ${zz}
region box block 0 40 0 ${yy} 0 ${zz}
region box block 0 40 0 40 0 ${zz}
region box block 0 40 0 40 0 40
create_box 1 box
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 256000 atoms
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut/gpu 5.0
pair_coeff 1 1 1.0 1.0 5.0
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
thermo 100
run 1000
Memory usage per processor = 20.382 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -7.1616924 0 -5.0017009 -5.6743468
100 0.75998442 -6.1430228 0 -5.0030506 -0.43702261
200 0.75772866 -6.1397323 0 -5.0031437 -0.40563886
300 0.75029993 -6.1286577 0 -5.0032122 -0.33104749
400 0.73999255 -6.1132496 0 -5.0032651 -0.24002869
500 0.73223505 -6.1016739 0 -5.0033256 -0.16512851
600 0.72450374 -6.090118 0 -5.0033666 -0.099412819
700 0.71914115 -6.082123 0 -5.0034155 -0.04585998
800 0.71391558 -6.0743087 0 -5.0034395 -0.0061018629
900 0.70919683 -6.0672408 0 -5.0034497 0.033186808
1000 0.7053422 -6.0614666 0 -5.0034575 0.062941897
Loop time of 21.0469 on 4 procs for 1000 steps with 256000 atoms
Pair time (%) = 17.4649 (82.9807)
Neigh time (%) = 5.51939e-05 (0.000262242)
Comm time (%) = 1.69517 (8.05425)
Outpt time (%) = 0.0226806 (0.107762)
Other time (%) = 1.86413 (8.85702)
Nlocal: 64000 ave 64103 max 63848 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 64417.2 ave 64486 max 64349 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 50
Dangerous builds = 0

75
examples/gpu/log.gpu.phosphate.18Feb13.linux.1
View File

@ -1,75 +0,0 @@
LAMMPS (18 Feb 2013)
# GI-System
units metal
newton off
package gpu force/neigh 0 1 1
atom_style charge
read_data data.phosphate
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
1 by 1 by 1 MPI processor grid
10950 atoms
10950 velocities
replicate 3 3 3
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
1 by 1 by 1 MPI processor grid
295650 atoms
pair_style lj/cut/coul/long/gpu 15.0
pair_coeff 1 1 0.0 0.29
pair_coeff 1 2 0.0 0.29
pair_coeff 1 3 0.000668 2.5738064
pair_coeff 2 2 0.0 0.29
pair_coeff 2 3 0.004251 1.91988674
pair_coeff 3 3 0.012185 2.91706967
kspace_style pppm/gpu 1e-5
neighbor 2.0 bin
thermo 100
timestep 0.001
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
run 200
PPPM initialization ...
G vector (1/distance) = 0.210051
grid = 108 108 108
stencil order = 5
estimated absolute RMS force accuracy = 0.000178801
estimated relative force accuracy = 1.24171e-05
using double precision FFTs
3d grid and FFT values/proc = 1520875 1259712
Memory usage per processor = 266.927 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 400.30257 -2381941.6 0 -2366643.8 -449.97088 4242016.4
100 411.69681 -2392428.5 0 -2376695.3 7046.6795 4308883.5
200 401.284 -2394152.5 0 -2378817.2 3243.274 4334284.4
Loop time of 156.48 on 1 procs for 200 steps with 295650 atoms
Pair time (%) = 12.2461 (7.82602)
Kspce time (%) = 81.8041 (52.2777)
Neigh time (%) = 0.0129185 (0.00825567)
Comm time (%) = 0.346706 (0.221566)
Outpt time (%) = 0.00171018 (0.0010929)
Other time (%) = 62.0683 (39.6654)
FFT time (% of Kspce) = 57.1943 (69.9162)
FFT Gflps 3d (1d only) = 1.23749 2.95335
Nlocal: 295650 ave 295650 max 295650 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 226982 ave 226982 max 226982 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 6
Dangerous builds = 0
unfix 1

75
examples/gpu/log.gpu.phosphate.18Feb13.linux.4
View File

@ -1,75 +0,0 @@
LAMMPS (18 Feb 2013)
# GI-System
units metal
newton off
package gpu force/neigh 0 1 1
atom_style charge
read_data data.phosphate
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
1 by 2 by 2 MPI processor grid
10950 atoms
10950 velocities
replicate 3 3 3
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
2 by 1 by 2 MPI processor grid
295650 atoms
pair_style lj/cut/coul/long/gpu 15.0
pair_coeff 1 1 0.0 0.29
pair_coeff 1 2 0.0 0.29
pair_coeff 1 3 0.000668 2.5738064
pair_coeff 2 2 0.0 0.29
pair_coeff 2 3 0.004251 1.91988674
pair_coeff 3 3 0.012185 2.91706967
kspace_style pppm/gpu 1e-5
neighbor 2.0 bin
thermo 100
timestep 0.001
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
run 200
PPPM initialization ...
G vector (1/distance) = 0.210051
grid = 108 108 108
stencil order = 5
estimated absolute RMS force accuracy = 0.000178801
estimated relative force accuracy = 1.24171e-05
using double precision FFTs
3d grid and FFT values/proc = 427915 314928
Memory usage per processor = 80.0769 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 400.30257 -2381941.6 0 -2366643.8 -449.971 4242016.4
100 411.6968 -2392428.5 0 -2376695.3 7046.6956 4308883.5
200 401.28397 -2394152.5 0 -2378817.2 3243.2753 4334284.4
Loop time of 64.6184 on 4 procs for 200 steps with 295650 atoms
Pair time (%) = 5.24801 (8.12154)
Kspce time (%) = 42.7106 (66.0967)
Neigh time (%) = 0.00641513 (0.00992772)
Comm time (%) = 0.553393 (0.856402)
Outpt time (%) = 0.000457346 (0.000707766)
Other time (%) = 16.0995 (24.9147)
FFT time (% of Kspce) = 22.695 (53.1367)
FFT Gflps 3d (1d only) = 3.11864 11.5832
Nlocal: 73912.5 ave 74223 max 73638 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nghost: 105257 ave 105797 max 104698 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 6
Dangerous builds = 0
unfix 1

122
examples/gpu/log.gpu.rhodo.18Feb13.linux.1
View File

@ -1,122 +0,0 @@
LAMMPS (18 Feb 2013)
# Rhodopsin model
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long/gpu 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm/gpu 1e-4
read_data data.rhodo
4 = max bonds/atom
18 = max angles/atom
40 = max dihedrals/atom
4 = max impropers/atom
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
1 by 1 by 1 MPI processor grid
32000 atoms
32000 velocities
27723 bonds
40467 angles
56829 dihedrals
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
replicate $x $y $z
replicate 2 $y $z
replicate 2 2 $z
replicate 2 2 2
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
1 by 1 by 1 MPI processor grid
256000 atoms
221784 bonds
323736 angles
454632 dihedrals
8272 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
12936 = # of size 2 clusters
29064 = # of size 3 clusters
5976 = # of size 4 clusters
33864 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 100
thermo_style multi
timestep 2.0
run 200
PPPM initialization ...
G vector (1/distance) = 0.245959
grid = 48 64 60
stencil order = 5
estimated absolute RMS force accuracy = 0.0410392
estimated relative force accuracy = 0.000123588
using double precision FFTs
3d grid and FFT values/proc = 237705 184320
Memory usage per processor = 760.048 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 157024.0524 KinEng = 172792.6155 Temp = 301.1796
PotEng = -15768.5631 E_bond = 28164.9917 E_angle = 117224.0742
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
E_coul = 1894295.6653 E_long = -2130488.8032 Press = 9562.1554
Volume = 2457390.7959
---------------- Step 100 ----- CPU = 36.9731 (sec) ----------------
TotEng = -233301.5647 KinEng = 123222.8702 Temp = 214.7790
PotEng = -356524.4350 E_bond = 13098.4680 E_angle = 56766.9162
E_dihed = 45556.8237 E_impro = 1313.9365 E_vdwl = -40863.9296
E_coul = 1705084.9441 E_long = -2137481.5939 Press = -1634.3724
Volume = 2522232.6324
---------------- Step 200 ----- CPU = 71.7796 (sec) ----------------
TotEng = -308341.5902 KinEng = 108937.0512 Temp = 189.8786
PotEng = -417278.6414 E_bond = 9579.0189 E_angle = 47373.5018
E_dihed = 39847.3805 E_impro = 967.6494 E_vdwl = -23632.3384
E_coul = 1646631.2737 E_long = -2138045.1272 Press = -1185.5582
Volume = 2554682.9557
Loop time of 71.7796 on 1 procs for 200 steps with 256000 atoms
Pair time (%) = 10.4771 (14.5962)
Bond time (%) = 27.3962 (38.1671)
Kspce time (%) = 7.23529 (10.0799)
Neigh time (%) = 5.6228 (7.83343)
Comm time (%) = 0.678451 (0.945186)
Outpt time (%) = 0.001441 (0.00200754)
Other time (%) = 20.3683 (28.3762)
FFT time (% of Kspce) = 5.21147 (72.0284)
FFT Gflps 3d (1d only) = 1.71528 2.99119
Nlocal: 256000 ave 256000 max 256000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 161665 ave 161665 max 161665 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 7.43187
Neighbor list builds = 31
Dangerous builds = 12

122
examples/gpu/log.gpu.rhodo.18Feb13.linux.4
View File

@ -1,122 +0,0 @@
LAMMPS (18 Feb 2013)
# Rhodopsin model
newton off
package gpu force/neigh 0 1 1
variable x index 2
variable y index 2
variable z index 2
units real
neigh_modify delay 5 every 1
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/long/gpu 8.0 10.0
pair_modify mix arithmetic
kspace_style pppm/gpu 1e-4
read_data data.rhodo
4 = max bonds/atom
18 = max angles/atom
40 = max dihedrals/atom
4 = max impropers/atom
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
1 by 2 by 2 MPI processor grid
32000 atoms
32000 velocities
27723 bonds
40467 angles
56829 dihedrals
1034 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
replicate $x $y $z
replicate 2 $y $z
replicate 2 2 $z
replicate 2 2 2
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
1 by 2 by 2 MPI processor grid
256000 atoms
221784 bonds
323736 angles
454632 dihedrals
8272 impropers
4 = max # of 1-2 neighbors
12 = max # of 1-3 neighbors
24 = max # of 1-4 neighbors
26 = max # of special neighbors
fix 1 all shake 0.0001 5 0 m 1.0 a 232
12936 = # of size 2 clusters
29064 = # of size 3 clusters
5976 = # of size 4 clusters
33864 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo 100
thermo_style multi
timestep 2.0
run 200
PPPM initialization ...
G vector (1/distance) = 0.245959
grid = 48 64 60
stencil order = 5
estimated absolute RMS force accuracy = 0.0410392
estimated relative force accuracy = 0.000123588
using double precision FFTs
3d grid and FFT values/proc = 68635 46080
Memory usage per processor = 250.358 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 157024.0492 KinEng = 172792.6155 Temp = 301.1796
PotEng = -15768.5663 E_bond = 28164.9917 E_angle = 117224.0742
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324
E_coul = 1894295.6622 E_long = -2130488.8032 Press = 9562.1554
Volume = 2457390.7959
---------------- Step 100 ----- CPU = 12.1280 (sec) ----------------
TotEng = -233301.6590 KinEng = 123222.8183 Temp = 214.7789
PotEng = -356524.4772 E_bond = 13098.4683 E_angle = 56766.9228
E_dihed = 45556.8211 E_impro = 1313.9369 E_vdwl = -40863.9000
E_coul = 1705084.8591 E_long = -2137481.5855 Press = -1634.3808
Volume = 2522232.6313
---------------- Step 200 ----- CPU = 23.3169 (sec) ----------------
TotEng = -308342.2597 KinEng = 108936.8553 Temp = 189.8783
PotEng = -417279.1150 E_bond = 9579.0042 E_angle = 47373.6037
E_dihed = 39847.3737 E_impro = 967.6451 E_vdwl = -23631.6382
E_coul = 1646630.1738 E_long = -2138045.2773 Press = -1185.5491
Volume = 2554682.9808
Loop time of 23.3169 on 4 procs for 200 steps with 256000 atoms
Pair time (%) = 4.29395 (18.4156)
Bond time (%) = 6.57406 (28.1944)
Kspce time (%) = 4.75311 (20.3848)
Neigh time (%) = 1.32057 (5.66359)
Comm time (%) = 0.555436 (2.38212)
Outpt time (%) = 0.000431776 (0.00185177)
Other time (%) = 5.81936 (24.9577)
FFT time (% of Kspce) = 1.78333 (37.5192)
FFT Gflps 3d (1d only) = 5.0126 11.639
Nlocal: 64000 ave 64003 max 63997 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 70636.8 ave 70640 max 70632 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 7.43187
Neighbor list builds = 31
Dangerous builds = 12

90
examples/hugoniostat/log.hugoniostat.18Feb13.linux.1
View File

@ -1,90 +0,0 @@
LAMMPS (18 Feb 2013)
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.41421 2 2
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0 0 0) to (7.07107 10 10)
1 by 1 by 1 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.80048 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
134 0 -6.3344257 -6.3344257 -4.4827806e-13 -4.9289339e-13 -4.9887818e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.0826018 on 1 procs for 134 steps with 1000 atoms
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.2937539309 -6.33442568056 -6.33442568056
Force two-norm initial, final = 3395.29 5.85376e-10
Force max component initial, final = 1960.27 3.43538e-10
Final line search alpha, max atom move = 1 3.43538e-10
Iterations, force evaluations = 134 137
Pair time (%) = 0.0648637 (78.5258)
Neigh time (%) = 0.00100684 (1.21891)
Comm time (%) = 0.00205088 (2.48285)
Outpt time (%) = 2.00272e-05 (0.0242454)
Other time (%) = 0.0146604 (17.7482)
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21000 ave 21000 max 21000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
# Start Run #1
log log.nodrag

90
examples/hugoniostat/log.hugoniostat.18Feb13.linux.4
View File

@ -1,90 +0,0 @@
LAMMPS (18 Feb 2013)
# This script reproduces stress trajectories from Fig. 1 in
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
#
# Three thermostatting scenarios are visited: undamped (nodrag),
# damped (drag) and Nose-Hoover chain (nhchains).
#
# The axial and shear stress trajectories are printed to the
# file "stress_vs_t.dat". For the damped case, the original figure
# seems to be a plot of 2*tau, rather than tau.
#
# The script also demonstrates how to
# orient a crystal along <110>,
# and how to use the lj/cubic pair style.
units lj
boundary p p p
atom_style atomic
# Set up FCC lattice with z axis along <110>
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
Lattice spacing in x,y,z = 1.41421 2 2
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
create_box 1 mycell
Created orthogonal box = (0 0 0) to (7.07107 10 10)
1 by 2 by 2 MPI processor grid
mass * 1.0
create_atoms 1 box
Created 1000 atoms
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
pair_style lj/cubic
pair_coeff * * 1.0 0.8908987
# Relax box dimensions
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
thermo 100
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.77704 Mbytes
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
134 0 -6.3344257 -6.3344257 -4.4436885e-13 -4.8889278e-13 -4.8955934e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.0323071 on 4 procs for 134 steps with 1000 atoms
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-6.2937539309 -6.33442568056 -6.33442568056
Force two-norm initial, final = 3395.29 5.75073e-10
Force max component initial, final = 1960.27 3.37121e-10
Final line search alpha, max atom move = 1 3.37121e-10
Iterations, force evaluations = 134 137
Pair time (%) = 0.0166269 (51.4651)
Neigh time (%) = 0.000261307 (0.80882)
Comm time (%) = 0.00654018 (20.2438)
Outpt time (%) = 2.61664e-05 (0.0809927)
Other time (%) = 0.0088526 (27.4014)
Nlocal: 250 ave 305 max 205 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 829 ave 874 max 774 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 5250 ave 6445 max 4305 min
Histogram: 1 0 0 2 0 0 0 0 0 1
Total # of neighbors = 21000
Ave neighs/atom = 21
Neighbor list builds = 1
Dangerous builds = 0
# Define initial velocity
velocity all create 0.01 87287 mom yes rot yes dist gaussian
write_restart restart.equil
# Start Run #1
log log.nodrag

176
examples/indent/log.indent.18Feb13.linux.1
View File

@ -1,176 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d indenter simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.2 482748 temp new
fix 1 all nve
fix 2 lower setforce 0.0 0.0 0.0
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
# run with indenter
timestep 0.003
variable k equal 1000.0/xlat
variable y equal "13.0*ylat - step*dt*0.02*ylat"
fix 4 all indent $k sphere 10 v_y 0 5.0
fix 4 all indent 882.84928691481343321 sphere 10 v_y 0 5.0
fix 5 all enforce2d
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
#dump 1 all atom 250 dump.indent
#dump 1 all image 1000 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 30000
Memory usage per processor = 2.05951 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.2 -3.1727576 0 -3.0018052 -1.436185 444.53333
1000 0.11974254 -3.0876892 0 -2.9853378 -0.037059247 440.78771
2000 0.12086797 -3.0886512 0 -2.9853378 -0.39883289 444.3556
3000 0.11671309 -3.0840074 0 -2.9842455 -0.34859991 442.95428
4000 0.12339115 -3.1000529 0 -2.9945828 -0.049696765 438.99297
5000 0.10860594 -3.0866045 0 -2.9937722 -0.47973882 443.99855
6000 0.11839788 -3.0929689 0 -2.9917669 -0.033454196 442.70339
7000 0.12194527 -3.0835584 0 -2.9793242 -0.13981611 443.36261
8000 0.11671309 -3.0862884 0 -2.9865265 0.073952568 441.71327
9000 0.12449823 -3.0880806 0 -2.9816643 0.28647997 439.28167
10000 0.12475263 -3.0830722 0 -2.9764384 0.38101457 440.50309
11000 0.11198118 -3.0743549 0 -2.9786377 0.67583952 438.50252
12000 0.10823034 -3.0621355 0 -2.9696244 0.66485024 441.13781
13000 0.1194298 -3.0579575 0 -2.9558734 1.0884087 437.72805
14000 0.12310403 -3.051382 0 -2.9461573 0.87077702 445.54011
15000 0.11148462 -3.0402208 0 -2.944928 1.0040645 451.90788
16000 0.12322336 -3.041552 0 -2.9362254 0.75818852 456.90372
17000 0.12311109 -3.030034 0 -2.9248033 1.0483105 452.91666
18000 0.12062529 -3.0261654 0 -2.9230595 1.3983601 451.71885
19000 0.11959344 -3.0143076 0 -2.9120837 1.3960449 457.9261
20000 0.12233862 -3.0015922 0 -2.8970218 1.1237129 470.124
21000 0.12097317 -3.0284929 0 -2.9250896 0.76635797 472.92527
22000 0.11569678 -3.0270581 0 -2.9281649 0.5809488 474.70546
23000 0.1108732 -3.0266318 0 -2.9318616 0.98885909 471.32905
24000 0.12620366 -3.0324956 0 -2.9246215 1.0953962 467.09873
25000 0.12180898 -3.0158998 0 -2.9117821 1.0327326 468.77165
26000 0.11188975 -3.0111933 0 -2.9155542 1.0566079 475.00383
27000 0.11592811 -3.0033529 0 -2.9042619 1.0702439 475.46225
28000 0.12257955 -2.9963958 0 -2.8916195 1.3711735 474.37327
29000 0.11235575 -2.9779653 0 -2.8819279 1.5993236 472.45721
30000 0.11564816 -2.9764576 0 -2.877606 1.7153154 475.9608
Loop time of 2.3314 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 1.73976 (74.6228)
Neigh time (%) = 0.0687068 (2.94702)
Comm time (%) = 0.0318851 (1.36764)
Outpt time (%) = 0.000296593 (0.0127217)
Other time (%) = 0.490756 (21.0498)
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: 3729 ave 3729 max 3729 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3729
Ave neighs/atom = 8.87857
Neighbor list builds = 619
Dangerous builds = 0
# run without indenter
unfix 4
run 30000
Memory usage per processor = 2.05959 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.11564816 -2.9764576 0 -2.877606 1.7186102 475.04831
31000 0.11109883 -3.0337933 0 -2.9388303 -0.62530288 488.2277
32000 0.1188179 -3.0275826 0 -2.9260216 -0.66828105 485.94533
33000 0.11802002 -3.0512943 0 -2.9504153 0.25566016 476.02668
34000 0.10576299 -3.0406973 0 -2.9502951 -0.52852395 476.92361
35000 0.11793262 -3.0680565 0 -2.9672522 -0.4355881 468.95111
36000 0.12287931 -3.0867004 0 -2.9816678 0.062228809 461.41252
37000 0.11137578 -3.0739118 0 -2.978712 -0.71966265 470.33395
38000 0.11463317 -3.0653157 0 -2.9673316 -0.26573651 468.14603
39000 0.11376942 -3.0832959 0 -2.9860501 -0.015297443 460.99165
40000 0.11547074 -3.0745917 0 -2.9758917 -0.65392557 471.44699
41000 0.12353792 -3.0814892 0 -2.9758937 -0.2846897 464.57095
42000 0.11025924 -3.0833464 0 -2.989101 -0.092947795 462.24163
43000 0.11612511 -3.0669276 0 -2.9676682 -0.57569445 468.19807
44000 0.12120248 -3.0818096 0 -2.9782103 0.005877698 462.28926
45000 0.11846418 -3.0794698 0 -2.9782112 -0.27859792 465.42685
46000 0.11315369 -3.0749275 0 -2.978208 -0.65492669 469.71888
47000 0.11170116 -3.073688 0 -2.9782101 0.069117813 463.8082
48000 0.11853841 -3.0795346 0 -2.9782125 -0.64585424 467.42305
49000 0.10976733 -3.0727734 0 -2.9789485 -0.34654008 466.39102
50000 0.11671309 -3.0787137 0 -2.9789518 -0.10105418 462.8133
51000 0.10907083 -3.0715934 0 -2.9783638 -0.5708327 467.88839
52000 0.12514884 -3.0753206 0 -2.9683482 -0.20691236 464.84118
53000 0.12024322 -3.0851757 0 -2.9823964 -0.17603398 462.1454
54000 0.1194586 -3.0713797 0 -2.9692711 -0.44966799 466.03415
55000 0.12751859 -3.0782662 0 -2.9692682 -0.30626509 464.20394
56000 0.11163288 -3.0776391 0 -2.9822196 -0.27414403 466.07964
57000 0.12313114 -3.0705777 0 -2.9653298 -0.51276983 469.08858
58000 0.12589682 -3.084674 0 -2.9770622 -0.28711084 464.73702
59000 0.10936357 -3.0705365 0 -2.9770567 -0.33561843 464.63316
60000 0.12149574 -3.0809095 0 -2.9770596 -0.3776745 465.8276
Loop time of 2.10947 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 1.71534 (81.3161)
Neigh time (%) = 0.0708265 (3.35755)
Comm time (%) = 0.0313859 (1.48786)
Outpt time (%) = 0.00027895 (0.0132237)
Other time (%) = 0.291641 (13.8253)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3569 ave 3569 max 3569 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3569
Ave neighs/atom = 8.49762
Neighbor list builds = 641
Dangerous builds = 0

176
examples/indent/log.indent.18Feb13.linux.4
View File

@ -1,176 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d indenter simulation
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass 1 1.0
mass 2 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
compute new mobile temp
velocity mobile create 0.2 482748 temp new
fix 1 all nve
fix 2 lower setforce 0.0 0.0 0.0
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
# run with indenter
timestep 0.003
variable k equal 1000.0/xlat
variable y equal "13.0*ylat - step*dt*0.02*ylat"
fix 4 all indent $k sphere 10 v_y 0 5.0
fix 4 all indent 882.84928691481343321 sphere 10 v_y 0 5.0
fix 5 all enforce2d
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
#dump 1 all atom 250 dump.indent
#dump 1 all image 1000 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 30000
Memory usage per processor = 2.06495 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0.2 -3.1727576 0 -3.0018052 -1.436185 444.53333
1000 0.11573595 -3.0964873 0 -2.9975606 -0.20448672 441.83732
2000 0.11519605 -3.0960246 0 -2.9975594 -0.38133491 442.33058
3000 0.11367906 -3.0839597 0 -2.9867912 -0.42579765 444.59119
4000 0.11618844 -3.0860897 0 -2.9867762 -0.041580916 439.84614
5000 0.11327789 -3.0848614 0 -2.9880358 -0.48898867 446.19202
6000 0.12058424 -3.0869438 0 -2.983873 0.011477134 440.56887
7000 0.11772522 -3.0833477 0 -2.9827207 -0.090378245 442.56787
8000 0.12533514 -3.0970033 0 -2.9898715 0.13263189 441.23478
9000 0.1198683 -3.0867062 0 -2.9842473 0.34046664 439.4706
10000 0.12234014 -3.0835007 0 -2.9789291 0.28399731 441.94307
11000 0.11082436 -3.0754796 0 -2.9807511 0.62194284 441.32012
12000 0.10842719 -3.0646379 0 -2.9719584 0.65383569 442.64668
13000 0.11686417 -3.0600388 0 -2.9601477 1.0041123 438.50135
14000 0.12557378 -3.0570017 0 -2.949666 0.85709167 442.10189
15000 0.11934084 -3.0498848 0 -2.9478768 1.0392199 451.74396
16000 0.12576904 -3.0452178 0 -2.9377152 1.3479499 441.27019
17000 0.11546522 -3.0348362 0 -2.936141 1.6318206 439.4846
18000 0.12148311 -3.0221147 0 -2.9182755 1.6088802 449.25447
19000 0.118843 -3.003677 0 -2.9020946 1.5201603 447.11853
20000 0.11165592 -3.0037968 0 -2.9083575 1.4074727 461.75512
21000 0.11360385 -2.9898251 0 -2.8927209 1.1326435 473.96384
22000 0.12150985 -3.0248097 0 -2.9209477 0.78906514 473.4399
23000 0.11900756 -3.0140794 0 -2.9123563 1.2011762 469.94964
24000 0.12144629 -3.0209952 0 -2.9171876 0.75868599 473.27056
25000 0.12502653 -3.0209271 0 -2.9140592 0.69048742 484.86502
26000 0.12040444 -3.021456 0 -2.9185388 0.21874131 486.96835
27000 0.11960292 -3.0422633 0 -2.9400313 0.37183014 486.93936
28000 0.11652365 -3.0437678 0 -2.9441678 0.65795683 483.2875
29000 0.11671309 -3.044343 0 -2.9445811 0.81258278 482.40921
30000 0.1220056 -3.0408195 0 -2.9365338 0.8072655 486.26501
Loop time of 0.963257 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 0.449727 (46.6882)
Neigh time (%) = 0.0182621 (1.89587)
Comm time (%) = 0.241803 (25.1026)
Outpt time (%) = 0.000499487 (0.051854)
Other time (%) = 0.252965 (26.2614)
Nlocal: 105 ave 120 max 89 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 91.5 ave 98 max 85 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 904 ave 1090 max 721 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3616
Ave neighs/atom = 8.60952
Neighbor list builds = 615
Dangerous builds = 0
# run without indenter
unfix 4
run 30000
Memory usage per processor = 2.065 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.1220056 -3.0408195 0 -2.9365338 0.80726384 486.26601
31000 0.11523899 -3.0452254 0 -2.9467235 -0.45196679 488.03016
32000 0.11671309 -3.0341159 0 -2.934354 -0.43181326 492.18636
33000 0.1222407 -3.0522595 0 -2.9477728 0.0026848443 483.854
34000 0.11512572 -3.0460203 0 -2.9476152 -0.21245818 493.13647
35000 0.12254508 -3.0524445 0 -2.9476977 -0.40908297 491.35424
36000 0.11662073 -3.0476077 0 -2.9479248 -0.00681441 487.04397
37000 0.12068279 -3.0633798 0 -2.9602248 -0.42268002 479.44382
38000 0.11671309 -3.0719801 0 -2.9722182 -0.37892984 481.83063
39000 0.12550174 -3.0797649 0 -2.9724908 -0.20439104 462.53227
40000 0.11787623 -3.0733224 0 -2.9725663 -0.34034574 467.47074
41000 0.11527048 -3.0710921 0 -2.9725633 -0.34310742 466.58893
42000 0.11312036 -3.0799073 0 -2.9832163 -0.19115407 463.84361
43000 0.12076996 -3.0752802 0 -2.9720506 -0.45925901 466.21436
44000 0.12008601 -3.0854737 0 -2.9828287 -0.42730211 465.06031
45000 0.11523031 -3.0813219 0 -2.9828274 -0.25270677 464.6103
46000 0.11474818 -3.0809077 0 -2.9828253 -0.42749761 466.13298
47000 0.11255445 -3.0789955 0 -2.9827882 -0.21266892 464.50422
48000 0.11846657 -3.0840872 0 -2.9828265 -0.26492346 464.59321
49000 0.11649089 -3.0718217 0 -2.9722497 -0.42141906 467.89742
50000 0.11857682 -3.0736036 0 -2.9722486 -0.1389822 464.85208
51000 0.12327382 -3.0776206 0 -2.9722508 -0.30974423 465.46077
52000 0.11600223 -3.0823411 0 -2.9831868 -0.45359158 465.40117
53000 0.11363768 -3.080283 0 -2.9831499 -0.24565163 464.66219
54000 0.11563656 -3.0820291 0 -2.9831873 -0.52399163 465.73246
55000 0.10932144 -3.07663 0 -2.9831862 -0.28497633 464.77274
56000 0.11442216 -3.0809919 0 -2.9831882 -0.24532139 465.43717
57000 0.11466454 -3.0811996 0 -2.9831888 -0.44276747 467.24929
58000 0.12266453 -3.0880404 0 -2.9831915 -0.24936044 464.24984
59000 0.10932278 -3.0766304 0 -2.9831854 -0.24813701 465.04486
60000 0.11984215 -3.0856269 0 -2.9831904 -0.38791762 465.21812
Loop time of 0.850555 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 0.43598 (51.2583)
Neigh time (%) = 0.0184039 (2.16375)
Comm time (%) = 0.251242 (29.5386)
Outpt time (%) = 0.000487506 (0.0573163)
Other time (%) = 0.144442 (16.9821)
Nlocal: 105 ave 110 max 96 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 96 ave 99 max 92 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 892.75 ave 999 max 763 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 3571
Ave neighs/atom = 8.50238
Neighbor list builds = 631
Dangerous builds = 0

386
examples/indent/log.indent.min.18Feb13.linux.1
View File

@ -1,386 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d indenter simulation with minimization instead of dynamics
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass * 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
fix 2 lower setforce 0.0 0.0 0.0
# indenter
fix 5 all enforce2d
# minimize with indenter
thermo 10
#dump 1 all atom 10 dump.indent
#dump 1 all image 25 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 4
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74074 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333
10 0 -3.1801584 0 -3.1801584 -1.3055542 441.12964
20 0 -3.1831474 0 -3.1831474 -1.2342864 438.61999
30 0 -3.1861452 0 -3.1861452 -1.090794 438.86547
40 0 -3.1901049 0 -3.1901049 -0.84848785 435.62268
50 0 -3.1904808 0 -3.1904808 -0.81494392 435.62268
60 0 -3.1906458 0 -3.1906458 -0.7837635 435.62268
70 0 -3.190782 0 -3.190782 -0.75163367 435.62268
74 0 -3.1908431 0 -3.1908431 -0.73877396 435.62268
Loop time of 0.0420349 on 1 procs for 74 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3.17275755126 -3.19084058073 -3.19084306284
Force two-norm initial, final = 6.74302 0.560627
Force max component initial, final = 1.46877 0.0659033
Final line search alpha, max atom move = 0.00643442 0.00042405
Iterations, force evaluations = 74 411
Pair time (%) = 0.0375848 (89.4134)
Neigh time (%) = 0.000423908 (1.00847)
Comm time (%) = 0.000356674 (0.84852)
Outpt time (%) = 6.46114e-05 (0.153709)
Other time (%) = 0.00360489 (8.57595)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3580 ave 3580 max 3580 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 4
Dangerous builds = 0
variable k equal 5000.0/xlat
variable k1 equal 1000.0/xlat
fix 4 all indent $k sphere 10 13.0 0 6.0
fix 4 all indent 4414.2464345740672798 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74074 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
74 0 -3.1908431 0 -2.0624129 -0.73807217 436.03689
80 0 -3.1521235 0 -3.1418193 -0.26103179 436.03693
90 0 -3.172501 0 -3.1715058 -0.36498503 436.19
100 0 -3.1770944 0 -3.1759303 -0.36782131 436.15772
110 0 -3.179003 0 -3.1778726 -0.34159509 436.07263
120 0 -3.1801625 0 -3.1792123 -0.29559493 435.77089
130 0 -3.1809815 0 -3.1802941 -0.20023407 434.94204
140 0 -3.1811433 0 -3.1804117 -0.18406939 434.72448
150 0 -3.1811799 0 -3.1804818 -0.1702338 433.59385
153 0 -3.1811948 0 -3.1804962 -0.16741701 434.21648
Loop time of 0.0456018 on 1 procs for 79 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.06241291025 -3.1804948246 -3.18049620256
Force two-norm initial, final = 1731.02 0.685103
Force max component initial, final = 1265.65 0.414535
Final line search alpha, max atom move = 0.00404562 0.00167705
Iterations, force evaluations = 79 395
Pair time (%) = 0.0360727 (79.1037)
Neigh time (%) = 0.00304174 (6.67022)
Comm time (%) = 0.00048399 (1.06134)
Outpt time (%) = 7.51019e-05 (0.16469)
Other time (%) = 0.00592828 (13.0001)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 97 ave 97 max 97 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3588 ave 3588 max 3588 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3588
Ave neighs/atom = 8.54286
Neighbor list builds = 28
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.5 0 6.0
fix 4 all indent 882.84928691481343321 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74074 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
153 0 -3.1811948 0 -0.18603384 -0.16723721 434.68332
160 0 -2.9090761 0 -2.6333579 2.1447602 434.68072
170 0 -3.0415034 0 -3.0104612 1.5042735 434.66633
180 0 -3.0884003 0 -3.0765732 1.2355426 434.76276
190 0 -3.0994422 0 -3.0898461 1.1641889 435.42255
200 0 -3.1014094 0 -3.0931133 1.1599923 435.3953
210 0 -3.1020409 0 -3.0941305 1.1794559 435.3953
218 0 -3.1023729 0 -3.0947356 1.2073015 432.67331
Loop time of 0.0292969 on 1 procs for 65 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.186033840731 -3.09473282421 -3.09473557651
Force two-norm initial, final = 1763.65 6.09015
Force max component initial, final = 923.948 2.61452
Final line search alpha, max atom move = 4.46936e-05 0.000116852
Iterations, force evaluations = 65 254
Pair time (%) = 0.0235493 (80.3817)
Neigh time (%) = 0.00143504 (4.89827)
Comm time (%) = 0.000310421 (1.05957)
Outpt time (%) = 5.36442e-05 (0.183105)
Other time (%) = 0.00394845 (13.4774)
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: 3643 ave 3643 max 3643 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3643
Ave neighs/atom = 8.67381
Neighbor list builds = 13
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.0 0 6.0
fix 4 all indent 882.84928691481343321 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74074 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
218 0 -3.1023729 0 2.0539539 1.2036101 434.00028
220 0 -2.922584 0 0.072390064 2.6056454 433.99932
230 0 -2.668658 0 -2.4566172 5.0165208 434.08769
240 0 -2.8499593 0 -2.7922824 3.8545046 440.80557
250 0 -2.9028377 0 -2.8796686 3.5239894 443.03741
260 0 -2.9342094 0 -2.9178605 3.2300832 445.68299
270 0 -2.9475355 0 -2.9337224 3.1109551 447.72032
280 0 -2.9613325 0 -2.947947 2.9571654 454.25603
290 0 -2.9663049 0 -2.9542667 2.8897107 457.30309
300 0 -2.9704157 0 -2.9592155 2.8023958 459.42996
310 0 -2.9756423 0 -2.968638 2.7521429 459.34867
320 0 -2.9978861 0 -2.9890592 2.4949523 461.5362
330 0 -3.0142422 0 -3.005417 2.2846994 464.66312
340 0 -3.0568662 0 -3.0480922 1.6364098 468.52301
350 0 -3.0828602 0 -3.0768519 1.3802145 469.91193
360 0 -3.0972929 0 -3.0932153 1.2324673 470.94192
370 0 -3.1047044 0 -3.1008857 1.1293681 472.52295
380 0 -3.1135319 0 -3.1102574 1.0420821 472.12091
390 0 -3.1175222 0 -3.1142918 0.97965377 472.97795
400 0 -3.1187338 0 -3.1153334 0.94435659 472.69321
405 0 -3.1187791 0 -3.1154874 0.94071059 473.02633
Loop time of 0.0786171 on 1 procs for 187 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
2.05395386014 -3.11548504008 -3.11548737402
Force two-norm initial, final = 2336.86 2.49306
Force max component initial, final = 1033.24 0.56375
Final line search alpha, max atom move = 0.000144903 8.16887e-05
Iterations, force evaluations = 187 666
Pair time (%) = 0.0623558 (79.3158)
Neigh time (%) = 0.00473833 (6.0271)
Comm time (%) = 0.000860453 (1.09449)
Outpt time (%) = 0.000171661 (0.218351)
Other time (%) = 0.0104909 (13.3443)
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: 3595 ave 3595 max 3595 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3595
Ave neighs/atom = 8.55952
Neighbor list builds = 41
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.4 0 6.0
fix 4 all indent 882.84928691481343321 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74074 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
405 0 -3.1187791 0 4.1010512 0.94105309 472.85417
410 0 -2.7453992 0 -0.76524543 3.787259 472.85546
420 0 -2.7371457 0 -2.6599871 4.6557516 474.64255
430 0 -2.892462 0 -2.8511282 3.5775445 478.67373
440 0 -2.9476659 0 -2.9278211 3.0983273 483.03769
450 0 -2.9727004 0 -2.9579624 2.8084683 486.47809
460 0 -2.9786493 0 -2.9647184 2.7312126 486.86678
470 0 -2.9807767 0 -2.9687015 2.673796 487.8298
480 0 -3.0392825 0 -3.0345542 2.0383409 492.60498
490 0 -3.0662881 0 -3.0621098 1.883644 492.10824
500 0 -3.0724601 0 -3.0676281 1.8280565 492.3841
510 0 -3.075659 0 -3.0702097 1.7459651 495.44987
520 0 -3.0809152 0 -3.0737087 1.5680112 496.06645
530 0 -3.0810409 0 -3.0741347 1.5607276 496.06645
531 0 -3.0810434 0 -3.074137 1.5606178 496.06645
Loop time of 0.050755 on 1 procs for 126 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
4.10105120882 -3.07413473436 -3.07413697818
Force two-norm initial, final = 2883.88 1.27518
Force max component initial, final = 1390.55 0.348204
Final line search alpha, max atom move = 0.00053786 0.000187285
Iterations, force evaluations = 126 428
Pair time (%) = 0.0400298 (78.8686)
Neigh time (%) = 0.00321174 (6.32792)
Comm time (%) = 0.000584602 (1.15181)
Outpt time (%) = 0.000118732 (0.233932)
Other time (%) = 0.00681019 (13.4178)
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: 3627 ave 3627 max 3627 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3627
Ave neighs/atom = 8.63571
Neighbor list builds = 28
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.2 0 6.0
fix 4 all indent 882.84928691481343321 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74082 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
531 0 -3.0810434 0 -2.5600032 1.559876 496.30236
540 0 -2.9988642 0 -2.9589658 2.4125155 496.35337
550 0 -3.0017228 0 -2.982818 2.4470621 496.37549
560 0 -3.0046874 0 -2.9925555 2.453411 496.3319
570 0 -3.0168302 0 -3.0055389 2.3718472 496.33107
580 0 -3.0242316 0 -3.0138915 2.3381241 496.05165
590 0 -3.0305673 0 -3.0205301 2.3109477 496.05561
600 0 -3.0356362 0 -3.025277 2.2764986 496.30016
609 0 -3.0369089 0 -3.0269096 2.2676135 496.60403
Loop time of 0.033392 on 1 procs for 78 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.56000317525 -3.02690830486 -3.02690956016
Force two-norm initial, final = 489.426 2.96134
Force max component initial, final = 235.033 0.826103
Final line search alpha, max atom move = 5.90513e-05 4.87825e-05
Iterations, force evaluations = 78 288
Pair time (%) = 0.027077 (81.0883)
Neigh time (%) = 0.00139165 (4.16762)
Comm time (%) = 0.000361204 (1.08171)
Outpt time (%) = 6.8903e-05 (0.206346)
Other time (%) = 0.00449324 (13.456)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 119 ave 119 max 119 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3738 ave 3738 max 3738 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3738
Ave neighs/atom = 8.9
Neighbor list builds = 12
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.0 0 6.0
fix 4 all indent 882.84928691481343321 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74082 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
609 0 -3.0369089 0 -2.5275208 2.268159 496.48459
610 0 -2.9943277 0 -2.7104758 2.6279836 496.48459
620 0 -2.959651 0 -2.910638 3.1184732 496.5361
630 0 -2.9557819 0 -2.932758 3.2024498 496.64951
640 0 -2.9630829 0 -2.9423137 3.1385711 497.26793
650 0 -2.9626746 0 -2.9444066 3.1379819 497.89111
660 0 -2.9647438 0 -2.9465018 3.1073974 498.18875
662 0 -2.9646671 0 -2.9465373 3.1089922 498.05818
Loop time of 0.028291 on 1 procs for 53 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.52752080275 -2.94653627582 -2.94653726672
Force two-norm initial, final = 465.896 4.03098
Force max component initial, final = 202.702 0.934056
Final line search alpha, max atom move = 2.52001e-05 2.35383e-05
Iterations, force evaluations = 53 234
Pair time (%) = 0.0224955 (79.5148)
Neigh time (%) = 0.00176501 (6.23878)
Comm time (%) = 0.000309467 (1.09387)
Outpt time (%) = 5.36442e-05 (0.189616)
Other time (%) = 0.00366735 (12.963)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 119 ave 119 max 119 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3890 ave 3890 max 3890 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3890
Ave neighs/atom = 9.2619
Neighbor list builds = 15
Dangerous builds = 0

383
examples/indent/log.indent.min.18Feb13.linux.4
View File

@ -1,383 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d indenter simulation with minimization instead of dynamics
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 420 atoms
mass * 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
fix 2 lower setforce 0.0 0.0 0.0
# indenter
fix 5 all enforce2d
# minimize with indenter
thermo 10
#dump 1 all atom 10 dump.indent
#dump 1 all image 25 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 4
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74739 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333
10 0 -3.1801584 0 -3.1801584 -1.3055542 441.12964
20 0 -3.1831474 0 -3.1831474 -1.2342864 438.61999
30 0 -3.1861452 0 -3.1861452 -1.090794 438.86547
40 0 -3.1901049 0 -3.1901049 -0.84848785 435.62268
50 0 -3.1904808 0 -3.1904808 -0.81494392 435.62268
60 0 -3.1906458 0 -3.1906458 -0.78376348 435.62268
70 0 -3.190782 0 -3.190782 -0.75163367 435.62268
74 0 -3.1908431 0 -3.1908431 -0.73877366 435.62268
Loop time of 0.0185711 on 4 procs for 74 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3.17275755126 -3.19084058192 -3.19084306553
Force two-norm initial, final = 6.74302 0.560405
Force max component initial, final = 1.46877 0.0658777
Final line search alpha, max atom move = 0.00643452 0.000423891
Iterations, force evaluations = 74 411
Pair time (%) = 0.00969809 (52.2215)
Neigh time (%) = 0.000124156 (0.668547)
Comm time (%) = 0.00429964 (23.1523)
Outpt time (%) = 0.000114322 (0.61559)
Other time (%) = 0.00433487 (23.342)
Nlocal: 105 ave 110 max 99 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 84 ave 90 max 79 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 895 ave 909 max 887 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 4
Dangerous builds = 0
variable k equal 5000.0/xlat
variable k1 equal 1000.0/xlat
fix 4 all indent $k sphere 10 13.0 0 6.0
fix 4 all indent 4414.2464345740672798 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74739 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
74 0 -3.1908431 0 -2.0624137 -0.73807188 436.03689
80 0 -3.1521235 0 -3.1418193 -0.26103149 436.03693
90 0 -3.1725009 0 -3.1715057 -0.36498447 436.19
100 0 -3.1770919 0 -3.1759284 -0.3678025 436.15756
110 0 -3.1795983 0 -3.1785044 -0.32326426 436.06295
120 0 -3.180804 0 -3.180035 -0.20918127 435.18508
130 0 -3.1809911 0 -3.1802835 -0.19952206 435.02873
140 0 -3.1812658 0 -3.1804986 -0.15366344 433.51948
146 0 -3.1812455 0 -3.1805445 -0.14836947 435.0937
Loop time of 0.0166457 on 4 procs for 72 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.06241374157 -3.18054133059 -3.18054446743
Force two-norm initial, final = 1731.02 0.676007
Force max component initial, final = 1265.65 0.173903
Final line search alpha, max atom move = 0.00387145 0.000673254
Iterations, force evaluations = 72 345
Pair time (%) = 0.00802875 (48.2332)
Neigh time (%) = 0.000551105 (3.3108)
Comm time (%) = 0.00351822 (21.136)
Outpt time (%) = 0.000110805 (0.665669)
Other time (%) = 0.00443679 (26.6543)
Nlocal: 105 ave 112 max 100 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 90 ave 91 max 87 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 898.5 ave 1008 max 803 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 3594
Ave neighs/atom = 8.55714
Neighbor list builds = 19
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.5 0 6.0
fix 4 all indent 882.84928691481343321 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74739 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
146 0 -3.1812455 0 -0.19421025 -0.14862682 434.34034
150 0 -3.014014 0 -2.150849 1.2736554 434.34067
160 0 -3.0201036 0 -2.9704071 1.6338013 434.34322
170 0 -3.0776968 0 -3.0613388 1.3031997 434.34364
180 0 -3.0967588 0 -3.0866334 1.185812 434.57417
190 0 -3.1005652 0 -3.0919539 1.1735235 435.17752
196 0 -3.1017505 0 -3.0934822 1.1681854 435.17752
Loop time of 0.00841713 on 4 procs for 50 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.194210248978 -3.09347927442 -3.09348223433
Force two-norm initial, final = 1761.49 4.17181
Force max component initial, final = 925.173 0.656203
Final line search alpha, max atom move = 6.95708e-05 4.56525e-05
Iterations, force evaluations = 50 167
Pair time (%) = 0.00394958 (46.9232)
Neigh time (%) = 0.000289381 (3.438)
Comm time (%) = 0.00179011 (21.2674)
Outpt time (%) = 7.65324e-05 (0.909245)
Other time (%) = 0.00231153 (27.4622)
Nlocal: 105 ave 112 max 100 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 94.5 ave 97 max 93 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 917 ave 1007 max 843 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 3668
Ave neighs/atom = 8.73333
Neighbor list builds = 10
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.0 0 6.0
fix 4 all indent 882.84928691481343321 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74739 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
196 0 -3.1017505 0 2.1127939 1.1697142 434.60875
200 0 -2.7394854 0 -1.0892906 4.0022866 434.60573
210 0 -2.7544814 0 -2.577826 4.4044049 436.48892
220 0 -2.8579353 0 -2.8074636 3.7797411 439.87258
230 0 -2.9022246 0 -2.8784961 3.4815054 443.63873
240 0 -2.9305421 0 -2.9126522 3.231004 445.10785
250 0 -2.9448077 0 -2.9342638 3.1031101 445.46452
260 0 -2.9566418 0 -2.9487878 2.9442714 447.34888
270 0 -2.9806907 0 -2.9726111 2.6656874 451.60358
280 0 -3.013399 0 -3.0078799 2.3761456 454.60159
288 0 -3.0156794 0 -3.0100369 2.3561703 454.47086
Loop time of 0.0147963 on 4 procs for 92 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
2.11279386005 -3.01003409316 -3.01003689972
Force two-norm initial, final = 2354.19 10.6992
Force max component initial, final = 1030.75 2.3669
Final line search alpha, max atom move = 1.01822e-05 2.41002e-05
Iterations, force evaluations = 92 281
Pair time (%) = 0.00680196 (45.9708)
Neigh time (%) = 0.00072515 (4.9009)
Comm time (%) = 0.00309056 (20.8874)
Outpt time (%) = 0.000139892 (0.945456)
Other time (%) = 0.00403869 (27.2954)
Nlocal: 105 ave 112 max 100 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 96.5 ave 103 max 92 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 944.25 ave 1053 max 860 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 3777
Ave neighs/atom = 8.99286
Neighbor list builds = 24
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.4 0 6.0
fix 4 all indent 882.84928691481343321 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74739 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
288 0 -3.0156794 0 7.1171473 2.355068 454.68358
290 0 -2.8452078 0 3.5864588 3.6837591 454.68269
300 0 -2.4748788 0 -2.0951207 7.152968 454.65604
310 0 -2.6443354 0 -2.5599454 6.2206133 455.36549
320 0 -2.7292243 0 -2.6964225 5.5582308 460.64087
330 0 -2.843175 0 -2.8202032 4.6449932 462.86057
340 0 -2.8828279 0 -2.8618415 4.2245783 464.4721
350 0 -2.9314767 0 -2.9140209 3.6424349 466.8869
360 0 -2.951292 0 -2.9358399 3.4517327 467.05453
370 0 -2.9671005 0 -2.9510401 3.2998677 468.38052
380 0 -2.973776 0 -2.957996 3.230072 468.91123
390 0 -2.9835714 0 -2.9670369 3.1601977 468.84333
400 0 -2.9932702 0 -2.977073 3.0661142 469.96757
410 0 -2.9973126 0 -2.9803761 3.0064502 470.35978
420 0 -2.9984004 0 -2.9811103 2.9742432 471.20047
422 0 -2.9983819 0 -2.981117 2.9743994 471.20047
Loop time of 0.0254161 on 4 procs for 134 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
7.11714730709 -2.98111566909 -2.9811169746
Force two-norm initial, final = 3561.96 4.0693
Force max component initial, final = 1428.53 0.756423
Final line search alpha, max atom move = 3.21187e-05 2.42953e-05
Iterations, force evaluations = 134 463
Pair time (%) = 0.0113537 (44.6711)
Neigh time (%) = 0.00104672 (4.11832)
Comm time (%) = 0.00635916 (25.0202)
Outpt time (%) = 0.0002473 (0.973003)
Other time (%) = 0.00640929 (25.2174)
Nlocal: 105 ave 121 max 90 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 95.5 ave 104 max 88 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs: 967.75 ave 1191 max 736 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3871
Ave neighs/atom = 9.21667
Neighbor list builds = 34
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.2 0 6.0
fix 4 all indent 882.84928691481343321 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74739 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
422 0 -2.9983819 0 -2.4247091 2.9762147 470.91305
430 0 -2.8725327 0 -2.7997215 4.0925928 470.95669
440 0 -2.8860983 0 -2.8443512 4.0556536 471.30395
450 0 -2.8837107 0 -2.8563971 4.0876009 472.28454
460 0 -2.8868229 0 -2.8612818 4.042484 472.6945
468 0 -2.8890509 0 -2.8626462 4.0096607 473.44277
Loop time of 0.01213 on 4 procs for 46 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.42470908136 -2.86264581787 -2.86264619706
Force two-norm initial, final = 508.719 7.57495
Force max component initial, final = 211.612 1.10056
Final line search alpha, max atom move = 2.77182e-06 3.05057e-06
Iterations, force evaluations = 46 222
Pair time (%) = 0.00546134 (45.0233)
Neigh time (%) = 0.000517488 (4.26617)
Comm time (%) = 0.00317794 (26.199)
Outpt time (%) = 6.56247e-05 (0.541011)
Other time (%) = 0.00290763 (23.9706)
Nlocal: 105 ave 123 max 88 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 95.5 ave 106 max 86 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 1004 ave 1271 max 753 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 4016
Ave neighs/atom = 9.5619
Neighbor list builds = 17
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.0 0 6.0
fix 4 all indent 882.84928691481343321 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (min.cpp:173)
Memory usage per processor = 2.74739 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
468 0 -2.8890509 0 -2.0764903 4.0180938 472.44912
470 0 -2.7914459 0 -2.3905312 4.7967051 472.46115
480 0 -2.7374378 0 -2.674199 5.4568225 472.70395
490 0 -2.7641101 0 -2.7357867 5.3643096 473.39917
500 0 -2.8122727 0 -2.7926853 4.9786461 476.90111
510 0 -2.8299101 0 -2.8085767 4.8165377 477.93893
520 0 -2.8372309 0 -2.8152964 4.7547052 477.58292
530 0 -2.8458557 0 -2.8231473 4.6583621 478.4087
540 0 -2.8526532 0 -2.8288639 4.5400358 479.19239
550 0 -2.860019 0 -2.8344544 4.3930149 480.37372
560 0 -2.8650984 0 -2.8392003 4.281231 481.26478
570 0 -2.866992 0 -2.8408512 4.2365878 481.90908
580 0 -2.8755764 0 -2.8483339 4.1011751 482.2041
590 0 -2.8840238 0 -2.8553253 4.0171782 482.71323
600 0 -2.8862663 0 -2.8575807 3.9798586 482.98348
610 0 -2.8866507 0 -2.8579501 3.9731951 482.98348
620 0 -2.886874 0 -2.8582838 3.9636254 482.98348
630 0 -2.8870022 0 -2.8583814 3.9532999 482.98348
636 0 -2.8869652 0 -2.8584222 3.9529206 482.98348
Loop time of 0.0376098 on 4 procs for 168 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.07649028348 -2.85842008708 -2.85842218639
Force two-norm initial, final = 599.704 0.654213
Force max component initial, final = 247.322 0.0812675
Final line search alpha, max atom move = 0.000673498 5.47335e-05
Iterations, force evaluations = 168 730
Pair time (%) = 0.0181205 (48.1802)
Neigh time (%) = 0.000626683 (1.66628)
Comm time (%) = 0.0094232 (25.0552)
Outpt time (%) = 0.000270963 (0.720457)
Other time (%) = 0.00916851 (24.378)
Nlocal: 105 ave 121 max 88 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 95.5 ave 105 max 85 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 1018 ave 1248 max 793 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 4072
Ave neighs/atom = 9.69524
Neighbor list builds = 20
Dangerous builds = 0

29
examples/kim/log.kim.lj.26Jul13.mac_mpi.1
View File

@ -1,29 +0,0 @@
LAMMPS (7 Aug 2013)
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Setting up run ...
Memory usage per processor = 18.2361 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -741.55469 0 85.684388 -34.939092
100 108.37517 -362.56658 0 85.694308 3963.7892
Loop time of 5.53531 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 4.7712 (86.1957)
Neigh time (%) = 0.655387 (11.8401)
Comm time (%) = 0.0243204 (0.439368)
Outpt time (%) = 0.000120163 (0.00217084)
Other time (%) = 0.0842826 (1.52264)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 20131 ave 20131 max 20131 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.09236e+06 ave 2.09236e+06 max 2.09236e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2092355
Ave neighs/atom = 65.3861
Neighbor list builds = 5
Dangerous builds = 0

29
examples/kim/log.kim.lj.26Jul13.mac_mpi.4
View File

@ -1,29 +0,0 @@
LAMMPS (7 Aug 2013)
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Setting up run ...
Memory usage per processor = 5.52322 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -741.55469 0 85.684388 -34.939092
100 108.37517 -362.56658 0 85.694308 3963.7892
Loop time of 1.69624 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 1.40092 (82.5896)
Neigh time (%) = 0.189553 (11.1749)
Comm time (%) = 0.0761309 (4.48821)
Outpt time (%) = 5.59688e-05 (0.00329957)
Other time (%) = 0.0295833 (1.74405)
Nlocal: 8000 ave 8010 max 7989 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 9240.25 ave 9249 max 9228 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 555266 ave 555920 max 554805 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 2221065
Ave neighs/atom = 69.4083
Neighbor list builds = 5
Dangerous builds = 0

29
examples/kim/log.kim.lj.lmp.26Jul13.mac_mpi.1
View File

@ -1,29 +0,0 @@
LAMMPS (7 Aug 2013)
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Setting up run ...
Memory usage per processor = 16.8628 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -741.55469 0 85.684388 -34.939092
100 108.37517 -362.56658 0 85.694308 3963.7892
Loop time of 4.71197 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 4.16929 (88.4831)
Neigh time (%) = 0.434233 (9.21553)
Comm time (%) = 0.0237658 (0.504371)
Outpt time (%) = 0.000121117 (0.0025704)
Other time (%) = 0.084554 (1.79445)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 20131 ave 20131 max 20131 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.88909e+06 ave 1.88909e+06 max 1.88909e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1889091
Ave neighs/atom = 59.0341
Neighbor list builds = 5
Dangerous builds = 0

29
examples/kim/log.kim.lj.lmp.26Jul13.mac_mpi.4
View File

@ -1,29 +0,0 @@
LAMMPS (7 Aug 2013)
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Setting up run ...
Memory usage per processor = 5.06545 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 -741.55469 0 85.684388 -34.939092
100 108.37517 -362.56658 0 85.694308 3963.7892
Loop time of 1.37841 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 1.15367 (83.696)
Neigh time (%) = 0.117947 (8.5567)
Comm time (%) = 0.0773094 (5.60859)
Outpt time (%) = 5.93066e-05 (0.00430254)
Other time (%) = 0.0294212 (2.13443)
Nlocal: 8000 ave 8010 max 7989 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 9240.25 ave 9249 max 9228 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 472273 ave 473390 max 471652 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Total # of neighbors = 1889091
Ave neighs/atom = 59.0341
Neighbor list builds = 5
Dangerous builds = 0

63
examples/meam/log.meam.18Feb13.linux.1
View File

@ -1,63 +0,0 @@
LAMMPS (18 Feb 2013)
# Test of MEAM potential for SiC system
units metal
boundary p p p
atom_style atomic
read_data data.meam
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
1 by 1 by 1 MPI processor grid
128 atoms
pair_style meam
pair_coeff * * library.meam Si C SiC.meam Si C
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
#dump 1 all atom 50 dump.meam
#dump 1 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3 element Si C
run 100
Memory usage per processor = 5.10826 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.38121 0 -636.38121 -76571.819
10 1807.8862 -666.21959 0 -636.54126 -150571.49
20 1932.4467 -668.2581 0 -636.53498 -120223.52
30 1951.3652 -668.58139 0 -636.54771 -100508.4
40 2172.5974 -672.22715 0 -636.5617 -110753.34
50 2056.9149 -670.33108 0 -636.56468 -105418.07
60 1947.9564 -668.52788 0 -636.55015 -111413.04
70 1994.7712 -669.28849 0 -636.54225 -109645.76
80 2126.0903 -671.43755 0 -636.53557 -97475.831
90 2065.755 -670.4349 0 -636.52338 -95858.837
100 2051.4553 -670.20799 0 -636.53122 -107068.9
Loop time of 0.0824008 on 1 procs for 100 steps with 128 atoms
Pair time (%) = 0.0791755 (96.0858)
Neigh time (%) = 0.00218797 (2.65527)
Comm time (%) = 0.000564575 (0.685157)
Outpt time (%) = 0.000112295 (0.136279)
Other time (%) = 0.000360489 (0.437482)
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 543 ave 543 max 543 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1526 ave 1526 max 1526 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 3052 ave 3052 max 3052 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3052
Ave neighs/atom = 23.8438
Neighbor list builds = 10
Dangerous builds = 10

63
examples/meam/log.meam.18Feb13.linux.4
View File

@ -1,63 +0,0 @@
LAMMPS (18 Feb 2013)
# Test of MEAM potential for SiC system
units metal
boundary p p p
atom_style atomic
read_data data.meam
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
1 by 2 by 2 MPI processor grid
128 atoms
pair_style meam
pair_coeff * * library.meam Si C SiC.meam Si C
neighbor 0.3 bin
neigh_modify delay 10
fix 1 all nve
thermo 10
timestep 0.001
#dump 1 all atom 50 dump.meam
#dump 1 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3 element Si C
run 100
Memory usage per processor = 4.99308 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -636.38121 0 -636.38121 -76571.819
10 1807.8862 -666.21959 0 -636.54126 -150571.49
20 1932.4467 -668.2581 0 -636.53498 -120223.52
30 1951.3652 -668.58139 0 -636.54771 -100508.4
40 2172.5974 -672.22715 0 -636.5617 -110753.34
50 2056.9149 -670.33108 0 -636.56468 -105418.07
60 1947.9564 -668.52788 0 -636.55015 -111413.04
70 1994.7712 -669.28849 0 -636.54225 -109645.76
80 2126.0903 -671.43755 0 -636.53557 -97475.831
90 2065.755 -670.4349 0 -636.52338 -95858.837
100 2051.4553 -670.20799 0 -636.53122 -107068.9
Loop time of 0.0363526 on 4 procs for 100 steps with 128 atoms
Pair time (%) = 0.0321491 (88.437)
Neigh time (%) = 0.00059098 (1.62569)
Comm time (%) = 0.00310814 (8.55)
Outpt time (%) = 0.000262499 (0.722092)
Other time (%) = 0.000241816 (0.665196)
Nlocal: 32 ave 36 max 30 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Nghost: 293.75 ave 305 max 285 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 381.5 ave 413 max 334 min
Histogram: 1 0 0 0 1 0 0 0 0 2
FullNghs: 763 ave 866 max 678 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 3052
Ave neighs/atom = 23.8438
Neighbor list builds = 10
Dangerous builds = 10

169
examples/meam/log.meam.shear.18Feb13.linux.1
View File

@ -1,169 +0,0 @@
LAMMPS (18 Feb 2013)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
1 by 1 by 1 MPI processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1 box
Created 1912 atoms
pair_style meam
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
timestep 0.001
run 100
Memory usage per processor = 6.78767 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
25 222.78953 -8188.1215 0 -8148.2941 9095.9008 19547.02
50 300 -8149.7654 0 -8096.1353 10633.141 19684.382
75 304.80657 -8163.4557 0 -8108.9665 7045.457 19759.745
100 300 -8173.6884 0 -8120.0584 5952.521 19886.589
Loop time of 1.5859 on 1 procs for 100 steps with 1912 atoms
Pair time (%) = 1.56483 (98.6714)
Neigh time (%) = 0.0144849 (0.913355)
Comm time (%) = 0.00155544 (0.0980796)
Outpt time (%) = 6.19888e-05 (0.00390875)
Other time (%) = 0.0049684 (0.313286)
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 500 dump.meam.shear
#dump 1 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 1 pad 4
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
reset_timestep 0
run 3000
Memory usage per processor = 6.96425 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300.50853 -8173.6884 0 -8137.8874 4992.9811 19894.297
100 292.0799 -8177.7235 0 -8142.9266 2566.6872 19871.516
200 306.71233 -8177.1504 0 -8140.6103 872.78764 20047.2
300 295.7806 -8172.9505 0 -8137.7127 -1053.769 20091.657
400 309.18439 -8169.6374 0 -8132.8028 -1784.5443 20122.178
500 304.51122 -8163.9147 0 -8127.6369 -160.26993 20183.44
600 300 -8158.55 0 -8122.8096 1555.2344 20279.887
700 304.32794 -8149.4746 0 -8113.2185 3700.5984 20430.504
800 304.79621 -8138.8368 0 -8102.5249 3721.6015 20510.74
900 303.87706 -8128.16 0 -8091.9576 4387.1435 20638.992
1000 300 -8113.4908 0 -8077.7503 6186.7017 20755.029
1100 306.13485 -8097.1731 0 -8060.7018 8904.6623 20879.616
1200 309.15674 -8081.8589 0 -8045.0276 10523.683 20996.875
1300 304.48415 -8064.5597 0 -8028.2851 10063.026 21126.348
1400 300 -8046.7606 0 -8011.0202 10972.46 21238.721
1500 300 -8041.3545 0 -8005.614 11939.553 21374.301
1600 309.60382 -8035.2271 0 -7998.3425 11340.231 21530.1
1700 300 -8029.1688 0 -7993.4284 11298.984 21635.492
1800 300 -8034.2178 0 -7998.4773 9635.8998 21737.07
1900 299.69156 -8037.3123 0 -8001.6086 6094.2811 21857.993
2000 308.23519 -8030.0074 0 -7993.2859 3176.5086 21983.182
2100 300 -8031.5977 0 -7995.8573 1352.4566 22112.054
2200 300 -8039.3918 0 -8003.6514 2078.9229 22231.755
2300 305.77226 -8038.7518 0 -8002.3237 3408.6101 22345.35
2400 300 -8034.7719 0 -7999.0314 5324.2456 22468.716
2500 300 -8034.9187 0 -7999.1782 7770.9385 22588.417
2600 300 -8034.3037 0 -7998.5633 10402.367 22709.34
2700 304.22676 -8032.9652 0 -7996.7213 11603.947 22840.035
2800 306.55646 -8032.2292 0 -7995.7077 10585.627 22959.736
2900 304.12756 -8031.7372 0 -7995.505 7574.3331 23087.988
3000 301.87833 -8033.9958 0 -7998.0316 4111.4578 23197.918
Loop time of 50.5684 on 1 procs for 3000 steps with 1912 atoms
Pair time (%) = 49.7489 (98.3795)
Neigh time (%) = 0.619643 (1.22536)
Comm time (%) = 0.0495932 (0.0980715)
Outpt time (%) = 0.000526667 (0.00104149)
Other time (%) = 0.149708 (0.29605)
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: 23337 ave 23337 max 23337 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 46674 ave 46674 max 46674 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46674
Ave neighs/atom = 24.4111
Neighbor list builds = 219
Dangerous builds = 0

169
examples/meam/log.meam.shear.18Feb13.linux.4
View File

@ -1,169 +0,0 @@
LAMMPS (18 Feb 2013)
# 3d metal shear simulation
units metal
boundary s s p
atom_style atomic
lattice fcc 3.52
Lattice spacing in x,y,z = 3.52 3.52 3.52
region box block 0 16.0 0 10.0 0 2.828427
create_box 3 box
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
2 by 2 by 1 MPI processor grid
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
create_atoms 1 box
Created 1912 atoms
pair_style meam
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
neighbor 0.3 bin
neigh_modify delay 5
region lower block INF INF INF 0.9 INF INF
region upper block INF INF 6.1 INF INF INF
group lower region lower
264 atoms in group lower
group upper region upper
264 atoms in group upper
group boundary union lower upper
528 atoms in group boundary
group mobile subtract all boundary
1384 atoms in group mobile
set group lower type 2
264 settings made for type
set group upper type 3
264 settings made for type
# void
#region void cylinder z 8 5 2.5 INF INF
#delete_atoms region void
# temp controllers
compute new3d mobile temp
compute new2d mobile temp/partial 0 1 1
# equilibrate
velocity mobile create 300.0 5812775 temp new3d
fix 1 all nve
fix 2 boundary setforce 0.0 0.0 0.0
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
fix_modify 3 temp new3d
thermo 25
thermo_modify temp new3d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
timestep 0.001
run 100
Memory usage per processor = 5.9664 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
25 221.59546 -8187.6813 0 -8148.0673 9100.4509 19547.02
50 300 -8150.0685 0 -8096.4384 10317.407 19685.743
75 307.76021 -8164.6669 0 -8109.6496 6289.7138 19757.814
100 300 -8176.5141 0 -8122.884 4162.2559 19873.327
Loop time of 0.435571 on 4 procs for 100 steps with 1912 atoms
Pair time (%) = 0.421216 (96.7044)
Neigh time (%) = 0.00371981 (0.854007)
Comm time (%) = 0.00860035 (1.9745)
Outpt time (%) = 8.96454e-05 (0.0205811)
Other time (%) = 0.00194496 (0.446531)
Nlocal: 478 ave 492 max 465 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 809 ave 822 max 795 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 5916 ave 6133 max 5658 min
Histogram: 1 0 0 1 0 0 0 0 1 1
FullNghs: 11832 ave 12277 max 11299 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 47328
Ave neighs/atom = 24.7531
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 500 dump.meam.shear
#dump 1 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 1 pad 4
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
reset_timestep 0
run 3000
Memory usage per processor = 6.01067 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 295.42794 -8176.5141 0 -8141.3183 3169.3113 19886.93
100 292.02876 -8176.5475 0 -8141.7567 -826.45881 19918.758
200 306.10676 -8176.7837 0 -8140.3158 -1371.1065 19948.794
300 300 -8172.6378 0 -8136.8974 -1736.2602 20086.712
400 306.48529 -8168.4581 0 -8131.9451 -957.8783 20111.985
500 309.89005 -8166.3097 0 -8129.391 -1024.7828 20200.517
600 302.35862 -8157.8008 0 -8121.7794 540.69714 20316.092
700 292.46062 -8149.9463 0 -8115.1041 1709.248 20448.424
800 306.03297 -8139.326 0 -8102.8669 4197.3195 20522.955
900 302.01714 -8127.2712 0 -8091.2905 6337.0018 20634.106
1000 300 -8112.4155 0 -8076.675 7383.2425 20759.915
1100 303.06207 -8097.0321 0 -8060.9268 7921.3462 20879.616
1200 300.99295 -8079.4118 0 -8043.5531 10534.001 20995.654
1300 300 -8065.6269 0 -8029.8865 10683.83 21125.127
1400 300 -8050.6108 0 -8014.8704 9586.4735 21255.821
1500 300 -8041.9686 0 -8006.2281 9655.7424 21365.751
1600 308.48003 -8031.9005 0 -7995.1498 10878.449 21496.446
1700 300 -8018.8868 0 -7983.1463 11313.466 21610.04
1800 300 -8011.819 0 -7976.0786 11545.414 21730.963
1900 300 -8008.9295 0 -7973.1891 9195.9922 21861.658
2000 300 -8013.4803 0 -7977.7399 5835.8211 21977.695
2100 300 -8024.1289 0 -7988.3885 1247.1291 22107.168
2200 300 -8035.3879 0 -7999.6475 755.15155 22219.541
2300 300 -8039.784 0 -8004.0436 990.04968 22355.121
2400 300 -8044.0207 0 -8008.2803 -798.93073 22469.937
2500 300 -8045.7015 0 -8009.9611 -2282.7 22588.417
2600 309.16599 -8043.0604 0 -8006.228 -1333.726 22713.005
2700 297.78976 -8035.0476 0 -7999.5705 -1819.5883 22842.478
2800 306.30156 -8029.889 0 -7993.3979 -155.02495 22962.179
2900 300 -8028.0102 0 -7992.2698 731.08083 23083.102
3000 300 -8025.8905 0 -7990.15 2169.2725 23200.361
Loop time of 13.8874 on 4 procs for 3000 steps with 1912 atoms
Pair time (%) = 13.3529 (96.1508)
Neigh time (%) = 0.161529 (1.16313)
Comm time (%) = 0.316078 (2.276)
Outpt time (%) = 0.000714779 (0.00514694)
Other time (%) = 0.0562313 (0.404907)
Nlocal: 478 ave 511 max 445 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 787.5 ave 833 max 753 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 5805 ave 6124 max 5486 min
Histogram: 1 1 0 0 0 0 0 0 1 1
FullNghs: 11610 ave 12225 max 11027 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 46440
Ave neighs/atom = 24.2887
Neighbor list builds = 222
Dangerous builds = 0

60
examples/melt/log.melt.18Feb13.linux.1
View File

@ -1,60 +0,0 @@
LAMMPS (18 Feb 2013)
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 1 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
thermo 50
run 250
Memory usage per processor = 2.37286 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
Loop time of 0.722158 on 1 procs for 250 steps with 4000 atoms
Pair time (%) = 0.609933 (84.4598)
Neigh time (%) = 0.0793972 (10.9944)
Comm time (%) = 0.0139024 (1.92512)
Outpt time (%) = 9.27448e-05 (0.0128427)
Other time (%) = 0.0188324 (2.6078)
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 151513 ave 151513 max 151513 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Neighbor list builds = 12
Dangerous builds = 0

60
examples/melt/log.melt.18Feb13.linux.4
View File

@ -1,60 +0,0 @@
LAMMPS (18 Feb 2013)
# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region box block 0 10 0 10 0 10
create_box 1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no
fix 1 all nve
#dump id all atom 50 dump.melt
#dump 1 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
thermo 50
run 250
Memory usage per processor = 1.89067 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 0.214934 on 4 procs for 250 steps with 4000 atoms
Pair time (%) = 0.159902 (74.3957)
Neigh time (%) = 0.021036 (9.78721)
Comm time (%) = 0.0281214 (13.0837)
Outpt time (%) = 0.000122249 (0.0568775)
Other time (%) = 0.00575262 (2.67646)
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 37915.5 ave 39239 max 36193 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 151662
Ave neighs/atom = 37.9155
Neighbor list builds = 12
Dangerous builds = 0

209
examples/micelle/log.micelle.18Feb13.linux.1
View File

@ -1,209 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
1 = max bonds/atom
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
1200 atoms
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Memory usage per processor = 2.4798 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 0.16137 on 1 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.103494 (64.1344)
Bond time (%) = 0.00649524 (4.02506)
Neigh time (%) = 0.0191967 (11.8961)
Comm time (%) = 0.00400829 (2.48391)
Outpt time (%) = 0.000231028 (0.143166)
Other time (%) = 0.027945 (17.3174)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 195 ave 195 max 195 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3136 ave 3136 max 3136 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 1 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Memory usage per processor = 2.63239 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727753 0.058614052 -1.4645362 1.9980678
2000 0.45 -2.001583 0.074586381 -1.4773716 1.677722
3000 0.45 -2.01376 0.065369685 -1.4987654 1.5672632
4000 0.44978364 -2.0284623 0.069543994 -1.5095095 1.3255914
5000 0.4515788 -2.0213579 0.063453981 -1.5067015 1.2898067
6000 0.44084238 -2.0220208 0.059857725 -1.5216881 1.3664878
7000 0.45280746 -2.0465582 0.056091161 -1.538037 1.1247107
8000 0.45575503 -2.0556878 0.056250977 -1.5440615 1.2847641
9000 0.45541476 -2.0383734 0.062759047 -1.5205791 1.4205644
10000 0.43553889 -2.0491499 0.064724759 -1.5492492 1.2479479
11000 0.46199123 -2.0775949 0.05294824 -1.5630404 0.91003048
12000 0.45116812 -2.0484232 0.065204884 -1.5324262 1.1225658
13000 0.44686952 -2.0599878 0.049287713 -1.564203 1.1154998
14000 0.45212998 -2.0625951 0.058683349 -1.5521586 0.98441931
15000 0.4556105 -2.0756197 0.059200748 -1.5611881 0.95502443
16000 0.45043625 -2.0824009 0.064992475 -1.5673475 1.1101553
17000 0.44547914 -2.0937506 0.063134923 -1.5855078 1.0387966
18000 0.44560114 -2.0932092 0.063158377 -1.584821 0.92976825
19000 0.46409216 -2.0998691 0.063095466 -1.5730682 0.74222038
20000 0.43356947 -2.079761 0.058993704 -1.5875591 0.98809322
21000 0.43970509 -2.0772972 0.063415284 -1.5745433 1.1679023
22000 0.45439796 -2.0869643 0.060942539 -1.5720025 0.95309247
23000 0.46436648 -2.0865877 0.062283763 -1.5603244 0.82847808
24000 0.45179512 -2.099375 0.057554155 -1.5904022 0.81341216
25000 0.45 -2.1028977 0.053292072 -1.5999806 0.8167413
26000 0.44379478 -2.0953332 0.065257482 -1.5866508 0.79986647
27000 0.45233801 -2.0995326 0.060977813 -1.5865937 0.8732284
28000 0.45416333 -2.0995467 0.051944425 -1.5938174 0.84546945
29000 0.44235173 -2.0819112 0.063209787 -1.5767183 0.7973497
30000 0.463297 -2.1019723 0.052828108 -1.5862333 0.83736896
31000 0.46237603 -2.114332 0.059492046 -1.5928492 0.6791076
32000 0.46010313 -2.1067583 0.06500768 -1.5820309 0.73245227
33000 0.45581512 -2.106217 0.054623133 -1.5961586 0.77209258
34000 0.46132621 -2.1005582 0.063679478 -1.5759369 0.79365061
35000 0.44457465 -2.1009737 0.063096958 -1.5936726 0.77684088
36000 0.46892599 -2.1283119 0.063349886 -1.5964267 0.66757096
37000 0.43919893 -2.117133 0.061828288 -1.6164718 0.82728955
38000 0.46347483 -2.1095945 0.053697761 -1.5928082 0.6018967
39000 0.46560699 -2.134901 0.051889552 -1.6177925 0.61468453
40000 0.45486545 -2.1082829 0.05921023 -1.5945863 0.67314005
41000 0.46926414 -2.1056671 0.052918097 -1.5838759 0.72673846
42000 0.44801848 -2.1122598 0.053198288 -1.6114163 0.7515948
43000 0.44733537 -2.1143993 0.048691802 -1.6187449 0.64883126
44000 0.44330158 -2.0946395 0.063057453 -1.5886499 0.74170615
45000 0.44616358 -2.1212538 0.054840602 -1.6206214 0.72390736
46000 0.43298663 -2.0977927 0.063259619 -1.6019073 0.75151063
47000 0.45 -2.093575 0.062292347 -1.5816576 0.83230853
48000 0.43668769 -2.1011039 0.055608008 -1.6091721 0.81680002
49000 0.43402566 -2.1180572 0.0705711 -1.6138221 0.61733524
50000 0.45870183 -2.1234461 0.061839249 -1.6032873 0.71893984
51000 0.46897063 -2.1240109 0.056638825 -1.5987922 0.57223633
52000 0.44547026 -2.114712 0.066830872 -1.6027821 0.88042497
53000 0.45698191 -2.1088353 0.055900552 -1.5963336 0.73302935
54000 0.46105819 -2.1164732 0.053844244 -1.6019549 0.52305471
55000 0.46526131 -2.1168922 0.053629683 -1.5983889 0.74647219
56000 0.4610805 -2.1203778 0.060044544 -1.5996369 0.56764901
57000 0.43539083 -2.1162246 0.058878039 -1.6223185 0.63599171
58000 0.45613812 -2.1341668 0.059717309 -1.6186914 0.5752578
59000 0.45035503 -2.1066421 0.056509876 -1.6001524 0.69875083
60000 0.46528439 -2.1306197 0.058828427 -1.6068946 0.47995479
Loop time of 13.4627 on 1 procs for 60000 steps with 1200 atoms
Pair time (%) = 9.23657 (68.6086)
Bond time (%) = 0.391739 (2.90981)
Neigh time (%) = 1.90366 (14.1403)
Comm time (%) = 0.341246 (2.53475)
Outpt time (%) = 0.000712633 (0.00529339)
Other time (%) = 1.58877 (11.8013)
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 450 ave 450 max 450 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9799 ave 9799 max 9799 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9799
Ave neighs/atom = 8.16583
Ave special neighs/atom = 0.5
Neighbor list builds = 4876
Dangerous builds = 0

209
examples/micelle/log.micelle.18Feb13.linux.4
View File

@ -1,209 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
1 = max bonds/atom
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
1200 atoms
300 bonds
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special_bonds fene
2 = max # of 1-2 neighbors
2 = max # of special neighbors
pair_style soft 1.12246
pair_coeff * * 0.0 1.12246
bond_style harmonic
bond_coeff 1 50.0 0.75
velocity all create 0.45 2349852
variable prefactor equal ramp(1.0,20.0)
fix 1 all nve
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
fix 3 all adapt 1 pair soft a * * v_prefactor
fix 4 all enforce2d
thermo 50
run 1000
Memory usage per processor = 2.79958 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 0.0598879 on 4 procs for 1000 steps with 1200 atoms
Pair time (%) = 0.0267262 (44.6271)
Bond time (%) = 0.00173765 (2.90151)
Neigh time (%) = 0.00505728 (8.44456)
Comm time (%) = 0.0149809 (25.0149)
Outpt time (%) = 0.000514269 (0.858719)
Other time (%) = 0.0108716 (18.1532)
Nlocal: 300 ave 305 max 292 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 100.25 ave 108 max 93 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 784 ave 815 max 739 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 3136
Ave neighs/atom = 2.61333
Ave special neighs/atom = 0.5
Neighbor list builds = 92
Dangerous builds = 0
unfix 3
# Main run
pair_style lj/cut 2.5
# solvent/head - full-size and long-range
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 2.5
# tail/tail - size-averaged and long-range
pair_coeff 3 3 1.0 0.75 2.5
pair_coeff 4 4 1.0 0.50 2.5
pair_coeff 3 4 1.0 0.67 2.5
# solvent/tail - full-size and repulsive
pair_coeff 1 3 1.0 1.0 1.12246
pair_coeff 1 4 1.0 1.0 1.12246
# head/tail - size-averaged and repulsive
pair_coeff 2 3 1.0 0.88 1.12246
pair_coeff 2 4 1.0 0.75 1.12246
thermo 1000
#dump 1 all atom 2000 dump.micelle
#dump 1 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 1 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Memory usage per processor = 2.79958 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727852 0.0586182 -1.464542 1.9980664
2000 0.46082446 -1.977605 0.057039794 -1.4601247 1.726013
3000 0.45 -2.0006402 0.05562923 -1.495386 1.511225
4000 0.4623338 -2.0091993 0.059138048 -1.4881127 1.3542907
5000 0.45 -2.0395585 0.061066034 -1.5288674 1.1830193
6000 0.45905159 -2.0634848 0.058991931 -1.5458239 1.1082099
7000 0.45 -2.0508705 0.061559594 -1.5396859 1.2020831
8000 0.44666556 -2.0397402 0.066632486 -1.5268144 1.2612013
9000 0.45034184 -2.03446 0.064174681 -1.5203188 1.1644088
10000 0.44920732 -2.0856804 0.059525789 -1.5773216 0.93583471
11000 0.45896474 -2.063989 0.064678373 -1.5407284 1.0732096
12000 0.45848122 -2.0752398 0.061533665 -1.555607 1.0281395
13000 0.46738009 -2.0629007 0.067132245 -1.5287778 0.96711354
14000 0.44988856 -2.062354 0.062693783 -1.5501466 1.0123189
15000 0.45098377 -2.072531 0.051120563 -1.5708025 0.97044948
16000 0.45 -2.1017479 0.064909547 -1.5872134 0.90299146
17000 0.4552102 -2.0765865 0.056648474 -1.5651072 0.91280438
18000 0.44824933 -2.0828037 0.058978706 -1.5759492 0.92795752
19000 0.44079166 -2.0556475 0.059088524 -1.5561347 1.1454216
20000 0.44463382 -2.0859907 0.057486911 -1.5842405 0.92599126
21000 0.44406551 -2.0826296 0.056776522 -1.5821577 0.99925665
22000 0.44911834 -2.0711967 0.059641892 -1.5628107 0.95834342
23000 0.43655144 -2.0909928 0.062696368 -1.5921088 0.91119509
24000 0.44867934 -2.1018259 0.055592487 -1.597928 0.76348634
25000 0.45260844 -2.0937068 0.059149636 -1.5823259 0.89135412
26000 0.44898273 -2.1016995 0.066566046 -1.5865249 0.74284381
27000 0.43221936 -2.084773 0.062900549 -1.5900132 0.87821534
28000 0.46292457 -2.0965745 0.055816359 -1.5782193 0.74158202
29000 0.45 -2.1306418 0.063790424 -1.6172264 0.53967764
30000 0.44871717 -2.0907319 0.055486729 -1.586902 0.99873528
31000 0.46125755 -2.0755203 0.056517719 -1.5581294 0.9347469
32000 0.45941056 -2.0914092 0.057505763 -1.5748757 0.89468013
33000 0.46026614 -2.0984679 0.056646234 -1.5819391 0.80740251
34000 0.46916633 -2.1193229 0.054211886 -1.5963356 0.61039936
35000 0.43884901 -2.0922975 0.061924634 -1.5918896 0.79377862
36000 0.43947177 -2.0909805 0.053228588 -1.5986464 0.90484301
37000 0.45414812 -2.1030789 0.055686423 -1.5936228 0.87060399
38000 0.44280127 -2.0908535 0.058003408 -1.5904178 0.8046892
39000 0.45516585 -2.1008067 0.058183565 -1.5878366 0.6089312
40000 0.43067796 -2.0848319 0.062869447 -1.5916434 0.74412702
41000 0.44165418 -2.1259603 0.064019775 -1.6206544 0.6221064
42000 0.43982239 -2.1055547 0.064067567 -1.6020312 0.62130789
43000 0.46586098 -2.1382757 0.05819116 -1.6146118 0.54791918
44000 0.45469796 -2.1328327 0.066699087 -1.6118146 0.52752596
45000 0.45358824 -2.1251041 0.063138554 -1.6087553 0.64714368
46000 0.44191865 -2.1041137 0.059520035 -1.6030433 0.62417966
47000 0.45804456 -2.1075048 0.066124313 -1.5837176 0.82334648
48000 0.45700413 -2.1298865 0.065741607 -1.6075216 0.58174639
49000 0.45842123 -2.1362735 0.056849019 -1.6213852 0.51934277
50000 0.44239274 -2.1182037 0.053635135 -1.6225444 0.59636555
51000 0.45869721 -2.1176213 0.059785615 -1.5995207 0.62467419
52000 0.45 -2.1136347 0.062713868 -1.6012959 0.71773796
53000 0.44480469 -2.1070829 0.061995737 -1.6006531 0.72790523
54000 0.45834924 -2.1352139 0.056517736 -1.6207289 0.64257865
55000 0.44776128 -2.1167768 0.051321782 -1.6180669 0.52184371
56000 0.46087785 -2.1186123 0.059414538 -1.598704 0.72628855
57000 0.44514743 -2.1107461 0.062138072 -1.6038315 0.68847034
58000 0.44897344 -2.1218568 0.056966905 -1.6162906 0.66787759
59000 0.43532599 -2.1262526 0.062848971 -1.6284404 0.61398862
60000 0.44623012 -2.105934 0.05919675 -1.600879 0.73556885
Loop time of 4.45718 on 4 procs for 60000 steps with 1200 atoms
Pair time (%) = 2.33901 (52.4774)
Bond time (%) = 0.0977297 (2.19264)
Neigh time (%) = 0.49103 (11.0166)
Comm time (%) = 1.01247 (22.7155)
Outpt time (%) = 0.00150865 (0.0338477)
Other time (%) = 0.51543 (11.564)
Nlocal: 300 ave 320 max 287 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 218.75 ave 232 max 205 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 2461 ave 2617 max 2321 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 9844
Ave neighs/atom = 8.20333
Ave special neighs/atom = 0.5
Neighbor list builds = 4879
Dangerous builds = 0

115
examples/min/log.min.18Feb13.linux.1
View File

@ -1,115 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
#dump 1 all atom 100 dump.min
#dump 1 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 4
thermo 100
run 1000
Memory usage per processor = 2.06282 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
200 3.3041082 -0.77000277 0 2.5299752 15.602653
300 3.3840228 -0.84859211 0 2.5312006 15.188203
400 3.3916063 -0.85694601 0 2.5304208 15.383853
500 3.3136052 -0.77935263 0 2.5301106 15.833296
600 3.3888915 -0.85213741 0 2.532518 15.162759
700 3.2123662 -0.67642106 0 2.5319297 16.310578
800 3.3016847 -0.76574936 0 2.5318082 15.639067
900 3.463125 -0.92707601 0 2.5317201 14.770608
1000 3.3134849 -0.7783474 0 2.5309957 15.658702
Loop time of 0.198333 on 1 procs for 1000 steps with 800 atoms
Pair time (%) = 0.127439 (64.2553)
Neigh time (%) = 0.0468309 (23.6123)
Comm time (%) = 0.00531244 (2.67855)
Outpt time (%) = 0.000103712 (0.052292)
Other time (%) = 0.0186465 (9.40161)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 316 ave 316 max 316 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7747 ave 7747 max 7747 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
#dump_modify 1 every 25
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.74947 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.3134849 -0.7783474 0 2.5309957 15.658702
1050 3.3134849 -2.808351 0 0.50099208 1.7334413
1100 3.3134849 -2.8586611 0 0.45068195 1.6058414
1150 3.3134849 -2.8712625 0 0.43808058 1.6049732
1200 3.3134849 -2.8785429 0 0.43080018 1.5883814
1250 3.3134849 -2.8832131 0 0.42612994 1.6155122
1300 3.3134849 -2.8882533 0 0.42108976 1.6323994
1350 3.3134849 -2.8953262 0 0.41401689 1.5991374
1365 3.3134849 -2.895477 0 0.41386606 1.5988878
Loop time of 0.27736 on 1 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.778347402608 -2.89547454669 -2.89547702741
Force two-norm initial, final = 1921.37 0.684479
Force max component initial, final = 298.456 0.229696
Final line search alpha, max atom move = 0.00501944 0.00115295
Iterations, force evaluations = 365 1305
Pair time (%) = 0.231267 (83.3816)
Neigh time (%) = 0.0190115 (6.85445)
Comm time (%) = 0.00438023 (1.57926)
Outpt time (%) = 6.41346e-05 (0.0231232)
Other time (%) = 0.0226369 (8.16156)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 319 ave 319 max 319 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7040 ave 7040 max 7040 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7040
Ave neighs/atom = 8.8
Neighbor list builds = 83
Dangerous builds = 0

115
examples/min/log.min.18Feb13.linux.4
View File

@ -1,115 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
#dump 1 all atom 100 dump.min
#dump 1 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 4
thermo 100
run 1000
Memory usage per processor = 2.06116 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
200 3.3041082 -0.77000277 0 2.5299752 15.602653
300 3.3840228 -0.84859211 0 2.5312006 15.188203
400 3.3916063 -0.85694601 0 2.5304208 15.383853
500 3.3136052 -0.77935264 0 2.5301106 15.833296
600 3.3888915 -0.85213742 0 2.532518 15.162759
700 3.2123632 -0.67641807 0 2.5319297 16.310592
800 3.3016497 -0.76571656 0 2.531806 15.639198
900 3.4621454 -0.9260857 0 2.531732 14.772965
1000 3.2803075 -0.74465936 0 2.5315477 15.835597
Loop time of 0.067068 on 4 procs for 1000 steps with 800 atoms
Pair time (%) = 0.0325241 (48.4942)
Neigh time (%) = 0.0122744 (18.3014)
Comm time (%) = 0.0142534 (21.2521)
Outpt time (%) = 0.000184894 (0.275681)
Other time (%) = 0.00783122 (11.6765)
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 170.25 ave 176 max 167 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 1936.75 ave 1963 max 1896 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
#dump_modify 1 every 25
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.7478 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.2803075 -0.74465936 0 2.5315477 15.835597
1050 3.2803075 -2.8198371 0 0.45636995 1.6553949
1100 3.2803075 -2.8554989 0 0.42070813 1.6571551
1150 3.2803075 -2.8646695 0 0.41153758 1.7045388
1200 3.2803075 -2.8688213 0 0.40738582 1.6922085
1250 3.2803075 -2.8764988 0 0.39970826 1.6948532
1300 3.2803075 -2.8776606 0 0.39854651 1.6821387
1350 3.2803075 -2.8789379 0 0.39726915 1.6715024
1365 3.2803075 -2.879076 0 0.3971311 1.66923
Loop time of 0.103431 on 4 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.744659361981 -2.87907436106 -2.8790759758
Force two-norm initial, final = 2006.88 0.477401
Force max component initial, final = 395.193 0.0879763
Final line search alpha, max atom move = 0.00334856 0.000294593
Iterations, force evaluations = 365 1437
Pair time (%) = 0.0645013 (62.3616)
Neigh time (%) = 0.0046317 (4.47805)
Comm time (%) = 0.0178814 (17.2882)
Outpt time (%) = 0.000117421 (0.113526)
Other time (%) = 0.0162994 (15.7587)
Nlocal: 200 ave 204 max 194 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 171.75 ave 173 max 170 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 1762.75 ave 1797 max 1711 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 7051
Ave neighs/atom = 8.81375
Neighbor list builds = 78
Dangerous builds = 0

353
examples/min/log.min.box.18Feb13.linux.1
View File

@ -1,353 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
#dump 1 all atom 500 dump.min
#dump 1 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 4
thermo 100
run 1000
Memory usage per processor = 2.06282 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
200 3.3041082 -0.77000277 0 2.5299752 15.602653
300 3.3840228 -0.84859211 0 2.5312006 15.188203
400 3.3916063 -0.85694601 0 2.5304208 15.383853
500 3.3136052 -0.77935263 0 2.5301106 15.833296
600 3.3888915 -0.85213741 0 2.532518 15.162759
700 3.2123662 -0.67642106 0 2.5319297 16.310578
800 3.3016847 -0.76574936 0 2.5318082 15.639067
900 3.463125 -0.92707601 0 2.5317201 14.770608
1000 3.3134849 -0.7783474 0 2.5309957 15.658702
Loop time of 0.198071 on 1 procs for 1000 steps with 800 atoms
Pair time (%) = 0.12724 (64.2398)
Neigh time (%) = 0.0467253 (23.5902)
Comm time (%) = 0.00525904 (2.65513)
Outpt time (%) = 0.000102282 (0.0516388)
Other time (%) = 0.018744 (9.46327)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 316 ave 316 max 316 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7747 ave 7747 max 7747 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
velocity all create 0.0 1
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.75634 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0 -0.7783474 0 -0.7783474 12.864955
1050 0 -2.808351 0 -2.808351 -1.0603061
1100 0 -2.8586611 0 -2.8586611 -1.1879061
1150 0 -2.8712625 0 -2.8712625 -1.1887742
1200 0 -2.8785429 0 -2.8785429 -1.205366
1250 0 -2.8832131 0 -2.8832131 -1.1782352
1300 0 -2.8882533 0 -2.8882533 -1.1613481
1350 0 -2.8953262 0 -2.8953262 -1.19461
1365 0 -2.895477 0 -2.895477 -1.1948596
Loop time of 0.277047 on 1 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.778347402608 -2.89547454669 -2.89547702741
Force two-norm initial, final = 1921.37 0.684479
Force max component initial, final = 298.456 0.229696
Final line search alpha, max atom move = 0.00501944 0.00115295
Iterations, force evaluations = 365 1305
Pair time (%) = 0.231153 (83.4348)
Neigh time (%) = 0.0189683 (6.84662)
Comm time (%) = 0.00435162 (1.57071)
Outpt time (%) = 6.58035e-05 (0.0237518)
Other time (%) = 0.0225077 (8.12414)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 319 ave 319 max 319 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7040 ave 7040 max 7040 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7040
Ave neighs/atom = 8.8
Neighbor list builds = 83
Dangerous builds = 0
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-4 nreset 100
thermo_style custom step temp pe pxx pyy pxy
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
Memory usage per processor = 2.75634 Mbytes
Step Temp PotEng Pxx Pyy Pxy
1365 0 -2.895477 -1.2253391 -1.16438 0.0029844696
1400 0 -2.9030976 -1.037803 -0.93005749 0.0031404612
1450 0 -2.9111551 -0.7499331 -0.56417894 0.0034000612
1500 0 -2.9156519 -0.43747438 -0.15725876 0.0035241132
1550 0 -2.9163188 -0.10113405 0.29275665 0.0032578192
1600 0 -2.9129142 0.25786755 0.78857369 0.0031418378
1650 0 -2.9052907 0.63122126 1.3305275 0.0027036138
1700 0 -2.8938515 0.97940259 1.9066628 0.0017474185
1750 0 -2.8934608 0.9929599 1.9909561 0.0022591527
1800 0 -2.8938899 1.0037689 2.0049399 0.0031549929
1850 0 -2.8950206 0.99253195 1.9899581 0.0044014083
1900 0 -2.8954835 0.99574288 1.9942509 0.0052643914
1950 0 -2.8957658 1.0003472 2.0004684 0.0058490005
2000 0 -2.8970438 0.97690958 1.9714991 0.0067217987
2050 0 -2.897073 0.99072137 1.9920898 0.0072873033
2100 0 -2.8972746 0.99651146 1.995402 0.0075817227
2150 0 -2.8975964 0.99381046 1.991681 0.007627454
2200 0 -2.8979803 0.99274725 1.9904104 0.007749339
2250 0 -2.8982086 0.99172995 1.9905936 0.0077177074
2300 0 -2.8983994 0.99377061 1.9899673 0.0076946648
2350 0 -2.8985769 0.99172845 1.9896457 0.0074117889
2400 0 -2.8986693 0.99578192 1.992246 0.0071806046
2450 0 -2.8988819 0.99128252 1.9903378 0.0069177704
2500 0 -2.8989812 0.99522115 1.991489 0.0068121239
2550 0 -2.8991564 0.99146083 1.990657 0.0065352609
2600 0 -2.8992555 0.99538317 1.9914926 0.0062558371
2650 0 -2.8994204 0.99157917 1.9907942 0.0059727799
2700 0 -2.8995111 0.9953798 1.9917332 0.0057516669
2750 0 -2.899661 0.9919244 1.9913158 0.005332134
2800 0 -2.8997549 0.99504761 1.9916688 0.0050046256
2850 0 -2.8999018 0.99193526 1.9912547 0.004492394
2900 0 -2.8999871 0.99565899 1.9922087 0.0040528402
2950 0 -2.9001422 0.99213366 1.9916425 0.0035862563
3000 0 -2.9002325 0.99582487 1.9924604 0.0032829497
3050 0 -2.9003895 0.99227644 1.9918388 0.0029100217
3100 0 -2.9004934 0.9954142 1.9922624 0.0026581626
3150 0 -2.9006459 0.99232395 1.9918443 0.0023680976
3200 0 -2.9007414 0.99623688 1.99297 0.0020662395
3250 0 -2.9009264 0.99256898 1.991983 0.0018040717
3300 0 -2.9009986 0.99800399 1.9945846 0.0015930444
3350 0 -2.9011372 0.99321268 1.9969898 0.001407703
3400 0 -2.9013641 0.99622318 1.9930656 0.0014563979
3450 0 -2.9015832 0.99282311 1.9924118 0.0014454286
3500 0 -2.9017596 0.99595378 1.992875 0.0016105573
3550 0 -2.9020182 0.99269026 1.9918179 0.0017633837
3600 0 -2.9022093 0.99607639 1.9930845 0.0020441612
3650 0 -2.9024948 0.99278561 1.9922635 0.0022606286
3700 0 -2.9027328 0.99606872 1.9930129 0.0026414228
3750 0 -2.9030541 0.99270955 1.9922055 0.0030676238
3800 0 -2.9033283 0.99509621 1.9917886 0.0034492628
3850 0 -2.9036436 0.99265445 1.9918333 0.0039194462
3900 0 -2.9039245 0.99611739 1.9930579 0.0043794142
3950 0 -2.9043033 0.99262403 1.9918954 0.0048733419
4000 0 -2.9046124 0.99585905 1.9928584 0.0054448584
4050 0 -2.9050077 0.99265871 1.9918589 0.0059527585
4100 0 -2.9053408 0.99596017 1.992967 0.0066819293
4150 0 -2.9057612 0.99271888 1.9920143 0.0074538661
4200 0 -2.9061208 0.99585342 1.9928494 0.0083030126
4250 0 -2.9065583 0.99276056 1.9921715 0.0091760837
4300 0 -2.9069587 0.99569608 1.9928109 0.010563215
4350 0 -2.9074386 0.99294112 1.9923317 0.012242263
4400 0 -2.9079159 0.99617793 1.9929836 0.014425511
4450 0 -2.9084828 0.99335369 1.9912818 0.017137841
4500 0 -2.9088005 0.99954722 1.9956616 0.019873686
4550 0 -2.9092238 0.99844962 1.9944461 0.022380697
4600 0 -2.9096299 0.99300644 1.9925264 0.024687168
4650 0 -2.9100061 0.99370577 1.9934207 0.027508267
4700 0 -2.9104263 0.99565636 1.9926298 0.030664353
4750 0 -2.9109614 0.99284169 1.9919846 0.034334378
4800 0 -2.9114155 0.9960171 1.9931707 0.038040635
4850 0 -2.9119649 0.99287594 1.9919796 0.041618415
4900 0 -2.9125125 0.99631202 1.9935981 0.046177605
4950 0 -2.9134822 0.99545012 1.9963436 0.055551769
5000 0 -2.9138087 1.0016464 1.9978697 0.059129043
5050 0 -2.9138895 1.0005328 2.0066685 0.060919794
5100 0 -2.9144557 0.99415884 1.9925195 0.062934069
5150 0 -2.9143897 0.99900082 2.0070401 0.06446803
5200 0 -2.9150165 0.99737915 1.9943189 0.066857536
5250 0 -2.9154332 0.9999712 2.0021875 0.069632138
5300 0 -2.9157558 0.99795158 1.9974044 0.070422281
5350 0 -2.9158439 1.0016699 2.0035502 0.071049397
5400 0 -2.9164666 0.99255654 1.9908929 0.071776886
5450 0 -2.9168846 1.0018915 1.9938812 0.072677356
5500 0 -2.9173241 0.99707078 1.9957969 0.072868177
5550 0 -2.9179842 0.99391224 1.9978813 0.073182143
5600 0 -2.9184699 0.99532518 1.9933732 0.073208315
5650 0 -2.9188477 1.0063118 2.0052442 0.073258803
5700 0 -2.919468 1.0026929 2.0041254 0.073010391
5750 0 -2.9202844 1.0035994 2.0008607 0.072352512
5800 0 -2.9204309 1.0072764 2.008335 0.072056645
5850 0 -2.9213742 0.99720824 1.9925634 0.071173036
5900 0 -2.9216129 1.0000335 2.001122 0.070609448
5950 0 -2.9223916 1.0003501 2.0032975 0.069559273
6000 0 -2.9227892 1.0043807 2.0050332 0.069077943
6050 0 -2.9233982 1.004802 2.0050324 0.068450588
6100 0 -2.9237721 1.0066363 2.0070477 0.06823504
6150 0 -2.9245074 1.0063392 2.0068761 0.068112243
6200 0 -2.9258589 0.99455185 1.9953413 0.06865518
6250 0 -2.9261201 1.0042987 2.0031819 0.069636648
6300 0 -2.9270045 0.99564956 1.9901358 0.071020033
6350 0 -2.9270282 1.007771 2.0049483 0.072360652
6400 0 -2.9279953 0.99228232 1.9927028 0.074781454
6450 0 -2.9280616 1.0017566 2.0022453 0.076142216
6500 0 -2.9288249 0.99408967 1.9888019 0.078305191
6550 0 -2.9286973 1.0065411 2.0049519 0.079618619
6600 0 -2.9291183 0.99372953 1.9985414 0.080448942
6650 0 -2.9292204 1.0023178 2.0050015 0.081907164
6700 0 -2.9301292 0.99992006 2.0016415 0.085917352
6750 0 -2.9302372 1.00613 2.004525 0.086946884
6800 0 -2.9305702 1.0074557 1.9965127 0.087976601
6850 0 -2.9313326 1.0050252 2.0080944 0.092584504
6900 0 -2.9317498 1.0087999 1.9958456 0.094058095
6950 0 -2.9318279 0.99688134 2.002508 0.094400121
7000 0 -2.9318978 1.0034321 2.0052797 0.095451664
7050 0 -2.9322652 0.99758568 2.0037109 0.097238969
7100 0 -2.9327121 0.99815697 1.9914701 0.098802948
7150 0 -2.9327437 1.0038622 2.0011895 0.10050304
7200 0 -2.9329063 1.004612 2.0032044 0.10185804
7250 0 -2.9335997 0.98168701 1.9864884 0.10300105
7300 0 -2.9336515 0.99279141 1.992742 0.10470943
7350 0 -2.9337138 1.003092 2.000106 0.10653676
7400 0 -2.9340414 1.0023845 1.9946755 0.10808147
7450 0 -2.9342536 0.99920061 1.9983417 0.10966697
7500 0 -2.9344657 0.99656006 2.002306 0.11134193
7550 0 -2.9346812 1.0009774 2.0059445 0.11345836
7600 0 -2.9352073 0.99664019 2.0028997 0.116237
7650 0 -2.9355092 1.0067299 2.0052137 0.11889963
7700 0 -2.9359369 1.000096 2.0038144 0.12089102
7750 0 -2.936237 1.0071591 2.0077241 0.12334687
7800 0 -2.9367687 1.0047286 2.0037322 0.12562793
7850 0 -2.9372513 0.99839299 2.0008738 0.1271966
7900 0 -2.93781 1.0013489 1.9924309 0.12900725
7950 0 -2.9382206 0.99271028 1.9910513 0.12995672
8000 0 -2.9385111 0.99261038 1.9917151 0.13094744
8050 0 -2.9388605 0.99256847 1.9933576 0.13194246
8100 0 -2.9391752 0.99421545 1.9941225 0.13291935
8150 0 -2.9394092 0.9997332 1.9965286 0.13397127
8200 0 -2.939821 0.99876146 1.9939496 0.13501447
8250 0 -2.9403015 0.99313692 1.9903144 0.13588404
8300 0 -2.9406524 0.99504174 1.9916891 0.13709102
8350 0 -2.9411077 0.99272049 1.9917049 0.13823709
8400 0 -2.9414976 0.99650126 1.9935111 0.13948558
8450 0 -2.9419844 0.9928859 1.9921827 0.14058516
8500 0 -2.9424055 0.9957698 1.9928898 0.14199174
8550 0 -2.9428963 0.99297812 1.9922564 0.14329168
8600 0 -2.9431968 0.99693087 1.9947462 0.14458722
8650 0 -2.9435631 0.99940154 1.9944064 0.14582129
8700 0 -2.9441466 0.99396641 1.9935763 0.14733962
8750 0 -2.9449093 0.99592155 1.9932061 0.15025209
8800 0 -2.9461707 0.99237436 1.9925136 0.15595847
8850 0 -2.9462853 1.000815 2.007233 0.15828028
8900 0 -2.9469511 1.0000829 1.9986375 0.16055827
8950 0 -2.9473161 1.0004185 1.9954916 0.16178098
9000 0 -2.9476848 1.0002902 1.9955333 0.16283909
9050 0 -2.9476782 1.0024581 2.0035957 0.16324604
9100 0 -2.9477989 1.0030916 2.0059473 0.16365445
9150 0 -2.9482536 0.99281175 1.9946546 0.16370039
9200 0 -2.9481416 1.00865 2.0073808 0.16435272
9250 0 -2.9486901 0.99494204 1.9953024 0.16410446
9300 0 -2.9486493 0.99953893 2.0056513 0.16419403
9350 0 -2.949079 1.003429 1.997895 0.16444925
9400 0 -2.9491509 1.0064853 2.0082985 0.16432267
9450 0 -2.9494699 1.0048863 2.001313 0.16433478
9500 0 -2.9496103 1.0059455 2.0060809 0.16420418
9550 0 -2.9499432 1.0037986 1.9989587 0.16406824
9600 0 -2.9501927 1.0010447 2.0005638 0.16375939
9650 0 -2.9511285 0.98322543 1.9801177 0.16290463
9700 0 -2.9506509 1.0102419 2.0082163 0.16328052
9750 0 -2.9511779 0.99511265 1.9950262 0.16251764
9800 0 -2.9512164 0.99608392 2.0052439 0.16186521
9850 0 -2.9517206 0.99656506 1.9966162 0.16144425
9900 0 -2.9519451 1.0066635 2.0043954 0.16101155
9950 0 -2.9520952 1.0051178 2.0087197 0.16058558
10000 0 -2.9531155 1.0041379 2.0031534 0.15982682
10050 0 -2.9537418 0.99448829 1.9904993 0.15928106
10100 0 -2.9540875 1.0000256 1.9948928 0.1590648
10150 0 -2.9545724 0.99595476 1.9920689 0.15859113
10200 0 -2.9550866 0.9945366 1.9940695 0.15788443
10250 0 -2.955721 0.99319075 1.9905041 0.15710363
10300 0 -2.9560458 0.99598109 1.9939645 0.15650198
10350 0 -2.9565093 0.99480453 1.9979782 0.15542386
10400 0 -2.9570486 0.99396171 1.9942613 0.15473357
10450 0 -2.9576457 0.99301571 1.9922208 0.1541236
10500 0 -2.9583596 0.9956042 1.992646 0.15365553
10550 0 -2.9591414 0.99318206 1.9923162 0.15326877
10600 0 -2.959942 0.99596727 1.9933176 0.15282597
10650 0 -2.9609186 0.99353471 1.9930306 0.1521666
10700 0 -2.9620307 0.99594782 1.9932886 0.1508232
10750 0 -2.9637166 0.99482397 1.9947588 0.14649906
10800 0 -2.9662462 0.99407822 1.9953083 0.13351206
10850 0 -2.9665593 1.0027673 1.9995492 0.13140588
10900 0 -2.9667709 1.0023406 2.0013835 0.12981724
10950 0 -2.9670159 1.0033354 2.0040861 0.12797651
11000 0 -2.9672441 1.0037572 2.004755 0.12647524
11050 0 -2.967593 0.99874092 1.9995822 0.12495147
11100 0 -2.9681165 0.99125559 1.9863869 0.1236617
11150 0 -2.9679478 1.0024409 2.0014347 0.12298067
11200 0 -2.968096 1.0083556 2.0040025 0.12211851
11250 0 -2.96854 0.99060368 1.9933029 0.12097655
11300 0 -2.968643 0.99899132 2.0034915 0.11986456
11350 0 -2.9687697 1.0018133 2.0075949 0.11899469
11365 0 -2.9688638 1.0116402 2.005578 0.11895715
Loop time of 2.59322 on 1 procs for 10000 steps with 800 atoms
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2.89547702741 -2.96928950062 -2.96886378746
Force two-norm initial, final = 3665.97 11.745
Force max component initial, final = 2998.7 10.1406
Final line search alpha, max atom move = 6.36291e-05 0.00064524
Iterations, force evaluations = 10000 10063
Pair time (%) = 1.93249 (74.5208)
Neigh time (%) = 0.00828385 (0.319442)
Comm time (%) = 0.0284746 (1.09804)
Outpt time (%) = 0.00297451 (0.114703)
Other time (%) = 0.621 (23.947)
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 330 ave 330 max 330 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7336 ave 7336 max 7336 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7336
Ave neighs/atom = 9.17
Neighbor list builds = 36
Dangerous builds = 0

353
examples/min/log.min.box.18Feb13.linux.4
View File

@ -1,353 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d Lennard-Jones melt and subsequent energy minimization
units lj
dimension 2
atom_style atomic
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box block 0 20 0 20 -0.1 0.1
create_box 1 box
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 800 atoms
mass 1 1.0
velocity all create 5.0 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_modify shift yes
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all enforce2d
#dump 1 all atom 500 dump.min
#dump 1 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 4
thermo 100
run 1000
Memory usage per processor = 2.06116 Mbytes
Step Temp E_pair E_mol TotEng Press
0 5 -2.461717 0 2.532033 5.0190509
100 3.2788864 -0.74311698 0 2.5316708 15.912832
200 3.3041082 -0.77000277 0 2.5299752 15.602653
300 3.3840228 -0.84859211 0 2.5312006 15.188203
400 3.3916063 -0.85694601 0 2.5304208 15.383853
500 3.3136052 -0.77935264 0 2.5301106 15.833296
600 3.3888915 -0.85213742 0 2.532518 15.162759
700 3.2123632 -0.67641807 0 2.5319297 16.310592
800 3.3016497 -0.76571656 0 2.531806 15.639198
900 3.4621454 -0.9260857 0 2.531732 14.772965
1000 3.2803075 -0.74465936 0 2.5315477 15.835597
Loop time of 0.0670121 on 4 procs for 1000 steps with 800 atoms
Pair time (%) = 0.0326686 (48.7503)
Neigh time (%) = 0.0121983 (18.2032)
Comm time (%) = 0.0145113 (21.6547)
Outpt time (%) = 0.000176668 (0.263636)
Other time (%) = 0.0074572 (11.1281)
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 170.25 ave 176 max 167 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Neighs: 1936.75 ave 1963 max 1896 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 7747
Ave neighs/atom = 9.68375
Neighbor list builds = 203
Dangerous builds = 0
neigh_modify delay 0 every 1 check yes
velocity all create 0.0 1
thermo 50
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 2.75239 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0 -0.74465936 0 -0.74465936 13.069823
1050 0 -2.8198371 0 -2.8198371 -1.1103791
1100 0 -2.8554989 0 -2.8554989 -1.1086189
1150 0 -2.8646695 0 -2.8646695 -1.0612352
1200 0 -2.8688213 0 -2.8688213 -1.0735655
1250 0 -2.8764988 0 -2.8764988 -1.0709208
1300 0 -2.8776606 0 -2.8776606 -1.0836353
1350 0 -2.8789379 0 -2.8789379 -1.0942716
1365 0 -2.879076 0 -2.879076 -1.096544
Loop time of 0.102816 on 4 procs for 365 steps with 800 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.744659361981 -2.87907436106 -2.8790759758
Force two-norm initial, final = 2006.88 0.477401
Force max component initial, final = 395.193 0.0879763
Final line search alpha, max atom move = 0.00334856 0.000294593
Iterations, force evaluations = 365 1437
Pair time (%) = 0.06445 (62.685)
Neigh time (%) = 0.00459725 (4.47135)
Comm time (%) = 0.0176167 (17.1343)
Outpt time (%) = 0.0001086 (0.105626)
Other time (%) = 0.0160431 (15.6037)
Nlocal: 200 ave 204 max 194 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 171.75 ave 173 max 170 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 1762.75 ave 1797 max 1711 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 7051
Ave neighs/atom = 8.81375
Neighbor list builds = 78
Dangerous builds = 0
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-4 nreset 100
thermo_style custom step temp pe pxx pyy pxy
min_modify line quadratic
minimize 0.0 1.0e-6 10000 100000
Memory usage per processor = 2.75239 Mbytes
Step Temp PotEng Pxx Pyy Pxy
1365 0 -2.879076 -1.0493949 -1.1436932 0.037565201
1400 0 -2.8859021 -0.86433583 -0.91383427 0.038857701
1450 0 -2.8929425 -0.58254768 -0.55566103 0.040538566
1500 0 -2.8966088 -0.28118754 -0.15988163 0.042020855
1550 0 -2.8967125 0.036820191 0.27480302 0.04324269
1600 0 -2.8931249 0.36718787 0.74943653 0.044424741
1650 0 -2.8858731 0.69688815 1.2623711 0.044835267
1700 0 -2.8755822 0.98073679 1.7977638 0.043907813
1750 0 -2.8722618 0.99796906 1.9978937 0.040932086
1800 0 -2.8731203 0.9972851 1.9960832 0.039723601
1850 0 -2.8733692 1.0063823 2.0084146 0.038402341
1900 0 -2.8747209 0.98521911 1.9798435 0.03629572
1950 0 -2.874625 1.0055823 2.0075042 0.034193545
2000 0 -2.8752902 0.99350208 1.9911933 0.03326557
2050 0 -2.8752769 1.0018946 2.0024682 0.03231859
2100 0 -2.8758319 0.99169935 1.9887983 0.031437471
2150 0 -2.8761892 0.99301192 1.9906401 0.029831022
2200 0 -2.8765018 0.99825416 1.9982587 0.027754052
2250 0 -2.8768461 0.99326761 1.9910275 0.027115046
2300 0 -2.8767423 1.0035487 2.0046857 0.026126393
2350 0 -2.8770655 0.99795811 1.9973107 0.025614851
2400 0 -2.877445 0.99163396 1.9870033 0.025156704
2450 0 -2.8774865 0.99148327 1.9905808 0.024719242
2500 0 -2.8775546 0.9950178 1.9915017 0.024486868
2550 0 -2.877691 0.9916018 1.9905624 0.02421693
2600 0 -2.8777627 0.99470414 1.9910618 0.023930399
2650 0 -2.8778782 0.99170595 1.9907118 0.023475253
2700 0 -2.877945 0.99480447 1.9913566 0.023271004
2750 0 -2.8780803 0.99164504 1.9902596 0.023000125
2800 0 -2.8781378 0.99501379 1.9915144 0.022773904
2850 0 -2.8782474 0.99219164 1.9915607 0.022481218
2900 0 -2.8783151 0.99550644 1.9921431 0.022359954
2950 0 -2.8784484 0.99224048 1.9913612 0.022193155
3000 0 -2.8785175 0.99532849 1.9920577 0.021941569
3050 0 -2.8786568 0.99222235 1.9910476 0.021737518
3100 0 -2.8787309 0.99525548 1.9920127 0.021688272
3150 0 -2.8788689 0.99228052 1.9913905 0.021446146
3200 0 -2.8789303 0.99616583 1.992901 0.021394358
3250 0 -2.8790946 0.99232091 1.9915574 0.02118161
3300 0 -2.8791847 0.99541221 1.9921056 0.021194771
3350 0 -2.8793341 0.9922686 1.9915267 0.021013055
3400 0 -2.8794452 0.99516725 1.9917199 0.021036976
3450 0 -2.8795969 0.99227386 1.9913259 0.021052828
3500 0 -2.8797075 0.99538375 1.9920724 0.02124209
3550 0 -2.8798796 0.99230271 1.9914458 0.021226686
3600 0 -2.8800015 0.99546439 1.9922124 0.02149345
3650 0 -2.880188 0.99227706 1.9913914 0.021617113
3700 0 -2.880312 0.99546322 1.9922772 0.021954501
3750 0 -2.8805126 0.99224941 1.991302 0.02213367
3800 0 -2.8806831 0.99459806 1.9906732 0.022675671
3850 0 -2.8808636 0.9921438 1.9909899 0.022992462
3900 0 -2.8810051 0.99533223 1.9921709 0.023485422
3950 0 -2.881225 0.99232174 1.9914377 0.023944603
4000 0 -2.8813892 0.99554805 1.992182 0.024545033
4050 0 -2.8816257 0.99218933 1.9910408 0.025105298
4100 0 -2.8817867 0.99546861 1.9923568 0.025863634
4150 0 -2.8820302 0.99242518 1.9914814 0.026365444
4200 0 -2.8822192 0.99526027 1.9919315 0.027062527
4250 0 -2.8824692 0.99223247 1.9913085 0.027610787
4300 0 -2.8826625 0.99537467 1.9921185 0.028217161
4350 0 -2.882922 0.99239179 1.9914342 0.028679998
4400 0 -2.8831241 0.99556357 1.9922663 0.029235596
4450 0 -2.8833989 0.9921938 1.9912448 0.029596184
4500 0 -2.8836067 0.99557381 1.9922188 0.030181
4550 0 -2.8838874 0.99214405 1.9912047 0.030371361
4600 0 -2.8840891 0.99568228 1.9925689 0.030873328
4650 0 -2.8843766 0.99222214 1.991537 0.031107839
4700 0 -2.8846039 0.99540851 1.9920535 0.031397701
4750 0 -2.8849039 0.99221886 1.9907361 0.031483457
4800 0 -2.8851163 0.99551704 1.9923517 0.031579764
4850 0 -2.8854144 0.99225442 1.9913169 0.031526446
4900 0 -2.8856452 0.99550052 1.9922005 0.031417289
4950 0 -2.8859485 0.99210587 1.9910919 0.03118115
5000 0 -2.8861801 0.99535546 1.9921671 0.030985542
5050 0 -2.8864881 0.99209875 1.9911885 0.030438838
5100 0 -2.8867336 0.99520939 1.9919538 0.029911151
5150 0 -2.8870413 0.99225176 1.9913023 0.029087623
5200 0 -2.8873039 0.99488953 1.9914722 0.0283991
5250 0 -2.8876062 0.99228521 1.991158 0.027574033
5300 0 -2.8878541 0.99556088 1.9922986 0.026813081
5350 0 -2.8881769 0.99220208 1.9912481 0.025847812
5400 0 -2.8884304 0.99556208 1.9922152 0.02492658
5450 0 -2.8887574 0.99219343 1.9912168 0.023790678
5500 0 -2.8890085 0.99566139 1.9925529 0.022691755
5550 0 -2.8893435 0.99223125 1.9912108 0.021332027
5600 0 -2.8895985 0.99555806 1.9925205 0.019969308
5650 0 -2.8899325 0.99238332 1.9915515 0.018334611
5700 0 -2.8902024 0.9950743 1.9920344 0.016688965
5750 0 -2.8905116 0.99266165 1.9920244 0.014675128
5800 0 -2.8907908 0.99538343 1.9922424 0.012898355
5850 0 -2.8911238 0.99274659 1.9916141 0.010718854
5900 0 -2.891395 0.99586743 1.992946 0.0084079793
5950 0 -2.8917377 0.99323184 1.9923269 0.0058847015
6000 0 -2.8920318 0.99618703 1.9931886 0.0031743443
6050 0 -2.8924173 0.99312644 1.9919607 0.00036370652
6100 0 -2.8927403 0.99609392 1.9932028 -0.0023282997
6150 0 -2.8931582 0.99334969 1.9924865 -0.0052253296
6200 0 -2.8931737 1.0044374 2.0036405 -0.0073374891
6250 0 -2.8933601 1.0053494 2.0084308 -0.0095543493
6300 0 -2.8937021 1.0040228 2.0072436 -0.011528379
6350 0 -2.8941162 1.0040963 2.0067291 -0.014066056
6400 0 -2.8946376 1.0056964 2.0065238 -0.016998255
6450 0 -2.8952383 1.002655 2.0052962 -0.019179448
6500 0 -2.8957747 1.0053824 2.0058467 -0.020794074
6550 0 -2.8963468 1.0031095 2.0056915 -0.021771701
6600 0 -2.8968938 1.0056478 2.0062435 -0.021988194
6650 0 -2.8976105 1.0027738 2.0056577 -0.022097734
6700 0 -2.8985813 1.0049044 2.0041091 -0.022978826
6750 0 -2.8993763 1.0013212 2.0046643 -0.024685401
6800 0 -2.8999352 0.99348555 1.9941849 -0.024745246
6850 0 -2.9002761 0.99611648 1.9915352 -0.024953484
6900 0 -2.9002655 1.0044443 2.0034446 -0.025004427
6950 0 -2.9006942 1.0038737 2.0062629 -0.024954287
7000 0 -2.9012609 1.0022744 2.0036566 -0.024819334
7050 0 -2.9016604 1.0051803 2.0055167 -0.024458964
7100 0 -2.9021771 1.0033287 2.0059127 -0.024041683
7150 0 -2.9026446 1.0051909 2.0057434 -0.023513487
7200 0 -2.9030997 1.003201 2.0057931 -0.022955905
7250 0 -2.9035001 1.0053534 2.006177 -0.022222879
7300 0 -2.9039398 1.003141 2.0056512 -0.021526869
7350 0 -2.9043194 1.0053552 2.0062897 -0.020600969
7400 0 -2.9047554 1.0029275 2.0053735 -0.019798089
7450 0 -2.9051394 1.0050723 2.0057785 -0.018810517
7500 0 -2.9055639 1.0030839 2.0056435 -0.018085221
7550 0 -2.9059506 1.00542 2.006424 -0.01743443
7600 0 -2.906389 1.0034617 2.0060075 -0.017038562
7650 0 -2.9068088 1.0052048 2.0059319 -0.01659861
7700 0 -2.907256 1.0032841 2.0057462 -0.016390423
7750 0 -2.9076758 1.0050008 2.0056173 -0.01606256
7800 0 -2.9081063 1.0033321 2.0058403 -0.016036071
7850 0 -2.9085325 1.0050458 2.0057159 -0.015738035
7900 0 -2.9089602 1.0033725 2.0057939 -0.015561818
7950 0 -2.9093746 1.00496 2.0055106 -0.015498031
8000 0 -2.9097997 1.0034291 2.0058947 -0.015471401
8050 0 -2.9102208 1.0049791 2.0055274 -0.015258479
8100 0 -2.9106489 1.0035304 2.0060557 -0.015178684
8150 0 -2.9110829 1.0052492 2.0060114 -0.014964657
8200 0 -2.9115393 1.0037164 2.006322 -0.014718896
8250 0 -2.9120088 1.0051472 2.0058765 -0.014430597
8300 0 -2.912515 1.0035172 2.0062174 -0.014197457
8350 0 -2.9130749 1.0054557 2.0059921 -0.013814584
8400 0 -2.9137199 1.0035594 2.0063641 -0.013128137
8450 0 -2.914514 1.0053008 2.0055891 -0.012076819
8500 0 -2.9153923 1.0020887 2.0048249 -0.010873863
8550 0 -2.9161681 1.005124 2.0041437 -0.009983199
8600 0 -2.9166232 1.0035103 2.0031583 -0.0098656588
8650 0 -2.9168935 1.0017735 2.0032739 -0.010137246
8700 0 -2.9176075 0.99350983 1.9942491 -0.010568888
8750 0 -2.9176655 1.0037509 2.0042507 -0.010929755
8800 0 -2.9180335 1.0034837 2.0006008 -0.011388
8850 0 -2.9184726 0.99722599 1.9972524 -0.012308771
8900 0 -2.9185896 1.0070137 2.0062244 -0.012981266
8950 0 -2.9189395 0.99775846 2.0046927 -0.013843916
9000 0 -2.9194348 0.99994718 1.9961545 -0.01430817
9050 0 -2.9199623 0.99913876 1.9945451 -0.015066366
9100 0 -2.9200915 1.0053667 2.0015458 -0.015628169
9150 0 -2.9203602 1.0029844 1.9981877 -0.015943776
9200 0 -2.9204472 1.007234 2.0012475 -0.01621898
9250 0 -2.9207559 1.0000323 1.9994854 -0.01673357
9300 0 -2.9208476 1.0070892 2.004772 -0.016969206
9350 0 -2.9212065 0.9954353 2.002531 -0.017293607
9400 0 -2.9213536 1.011464 1.9987715 -0.016468707
9450 0 -2.9216568 1.0004584 1.992812 -0.016331783
9500 0 -2.9215087 1.0030182 2.006723 -0.016328481
9550 0 -2.9218914 1.0097858 1.9978241 -0.01513886
9600 0 -2.9221223 1.0064187 1.9937476 -0.014411434
9650 0 -2.9224212 1.0060439 1.9885122 -0.013032442
9700 0 -2.9220952 1.00799 2.0115738 -0.012619136
9750 0 -2.9226088 0.99323702 1.9948387 -0.011548183
9800 0 -2.9225553 0.99626951 2.0047326 -0.010162452
9850 0 -2.9227332 1.006235 2.0036748 -0.0075392887
9900 0 -2.9232122 0.98911031 1.9917417 -0.0055326528
9950 0 -2.9231491 0.99681615 1.9994126 -0.0037310254
10000 0 -2.9235123 0.9884299 1.9875481 -0.0021912307
10050 0 -2.9237223 0.9999364 1.9825867 0.00099300384
10100 0 -2.9235973 0.99000996 1.9970993 0.0021504958
10150 0 -2.9233485 1.0077913 2.0121611 0.004525478
10200 0 -2.9236768 1.0032927 2.0035362 0.007071254
10250 0 -2.9238478 1.0002834 2.003131 0.0096263035
10300 0 -2.9240364 0.99131539 2.0026965 0.011952105
10350 0 -2.9242833 0.99641849 1.9947521 0.014575055
10400 0 -2.9244439 0.99508819 1.9965681 0.018000688
10450 0 -2.9243187 1.0124534 2.0090192 0.021804357
10500 0 -2.9246558 0.99263574 2.0030149 0.023531827
10550 0 -2.9250009 0.99916756 1.9950546 0.027624091
10600 0 -2.9248637 1.0079577 2.0069131 0.02964918
10650 0 -2.9253535 1.0010931 1.994458 0.032931815
10700 0 -2.925576 0.99564043 1.9973125 0.03610588
10750 0 -2.9255597 1.0108614 2.0075111 0.0396819
10800 0 -2.9261759 0.9865698 1.9969888 0.0427848
10850 0 -2.9265088 0.99539121 1.9933442 0.046588103
10900 0 -2.9270268 0.9946174 1.9930678 0.052105624
10950 0 -2.9270626 1.0042522 2.0070013 0.055801296
11000 0 -2.9274337 1.0073265 2.0057225 0.059701269
11050 0 -2.927977 0.99674096 1.9951088 0.062406122
11100 0 -2.9280496 1.0088979 2.0105292 0.066470787
11150 0 -2.928782 0.99018003 1.990749 0.068640734
11200 0 -2.9290447 0.99949136 2.0055469 0.073700453
11250 0 -2.9297585 1.0015608 1.9941199 0.078090219
11300 0 -2.929934 1.0057572 2.0034521 0.080757029
11350 0 -2.9305123 0.99951982 1.9941245 0.083214206
11365 0 -2.9302543 1.0058576 2.0105109 0.083648804
Loop time of 1.04051 on 4 procs for 10000 steps with 800 atoms
Minimization stats:
Stopping criterion = max iterations
Energy initial, next-to-last, final =
-2.8790759758 -2.93081588364 -2.93025426371
Force two-norm initial, final = 3556.23 12.2587
Force max component initial, final = 2979.1 9.18102
Final line search alpha, max atom move = 2.99243e-05 0.000274736
Iterations, force evaluations = 10000 10062
Pair time (%) = 0.499169 (47.9735)
Neigh time (%) = 0.00172853 (0.166124)
Comm time (%) = 0.124863 (12.0002)
Outpt time (%) = 0.00372344 (0.357848)
Other time (%) = 0.411025 (39.5023)
Nlocal: 200 ave 205 max 194 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 178 ave 181 max 173 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 1857.25 ave 1884 max 1824 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 7429
Ave neighs/atom = 9.28625
Neighbor list builds = 29
Dangerous builds = 0

135
examples/msst/log.msst.18Feb13.linux.1
View File

@ -1,135 +0,0 @@
LAMMPS (18 Feb 2013)
# LJ test of msst shock dynamics
# Energy in eV, time in ps, distance in angstroms.
units metal
boundary p p p
atom_style atomic
timestep 1e-03
lattice fcc 5.3589
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
## Specify the box as a given number of unit cells.
region box1 block 0 18 0 18 0 18 units lattice
## Instantiate the system.
create_box 1 box1
Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
1 by 1 by 1 MPI processor grid
create_atoms 1 region box1
Created 23328 atoms
mass 1 40.00
# Initial velocities correspond to around 300K.
velocity all create 600.0 9999
pair_style lj/cut 10
pair_coeff 1 1 0.01032 3.405
timestep 2e-3
# Equilibrate the system
fix 2 all nve
thermo 10
run 100
Memory usage per processor = 17.232 Mbytes
Step Temp E_pair E_mol TotEng Press
0 600 -1943.9014 0 -134.75058 992.06384
10 586.44651 -1917.3971 0 -149.11346 1306.17
20 539.94305 -1778.786 0 -150.72199 2492.7873
30 449.49509 -1506.4706 0 -151.12989 4667.6248
40 331.86049 -1151.7344 0 -151.09164 7379.764
50 258.27083 -929.8024 0 -151.05092 9103.558
60 256.1869 -923.58742 0 -151.1195 9252.9158
70 281.76061 -1000.7367 0 -151.1576 8739.2518
80 300.28534 -1056.589 0 -151.15321 8324.8812
90 305.83368 -1073.3097 0 -151.14426 8175.2478
100 304.06857 -1067.9843 0 -151.14112 8191.234
Loop time of 3.41779 on 1 procs for 100 steps with 23328 atoms
Pair time (%) = 3.27187 (95.7305)
Neigh time (%) = 0.0658 (1.92522)
Comm time (%) = 0.0221024 (0.646685)
Outpt time (%) = 0.000823975 (0.0241084)
Other time (%) = 0.0571954 (1.67346)
Nlocal: 23328 ave 23328 max 23328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22235 ave 22235 max 22235 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.18372e+06 ave 2.18372e+06 max 2.18372e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2183715
Ave neighs/atom = 93.6092
Neighbor list builds = 1
Dangerous builds = 0
unfix 2
# MSST fix
fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
MSST parameters:
Shock in z direction
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.00000e+02
Shock velocity = 2.80000e+01
Artificial viscosity (units of mass/length/time) = 3.00000e+02
Initial pressure calculated on first step
Initial volume calculated on first step
Initial energy calculated on first step
# this is needed to make etotal equal the MSST conserved quantity
fix_modify msst energy yes
variable dhug equal f_msst[1]
variable dray equal f_msst[2]
variable lgr_vel equal f_msst[3]
variable lgr_pos equal f_msst[4]
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
#dump id all atom 50 dump.msst
#dump 1 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
run 100
Fix MSST v0 = 8.97521e+05
Fix MSST p0 = 8.10679e+03
Fix MSST e0 = to be -1.51141e+02
Fix MSST initial strain rate of -3.20112e-02 established by reducing temperature by factor of 1.00000e-02
Memory usage per processor = 17.2384 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng dhug dray lgr_vel lgr_pos msst
100 301.02788 907.67474 -1058.8159 96.4602 96.4602 96.4602 8242.1214 8202.9779 8095.8693 -151.14112 1.5203428 -10.919311 0 0 9.1684318
110 297.71411 897.68288 -1048.8859 96.4602 96.4602 96.399397 8347.6253 8303.7121 8220.7572 -151.20299 1.439058 28.652258 0.017649501 -0.55980494 5.7336721
120 295.64308 891.43821 -1042.72 96.4602 96.4602 96.340496 8431.6742 8379.2441 8331.5304 -151.28174 1.3655893 56.776734 0.034747125 -1.119263 2.3808018
130 296.02228 892.5816 -1043.9407 96.4602 96.4602 96.283468 8456.2492 8412.6368 8392.5853 -151.35912 1.2945465 37.811981 0.05130089 -1.6783851 -0.87840575
140 298.19024 899.11855 -1050.5482 96.4602 96.4602 96.228236 8430.5151 8415.6802 8414.2537 -151.42965 1.2243399 -18.01985 0.067333442 -2.2371818 -4.0330712
150 300.86421 907.18122 -1058.6966 96.4602 96.4602 96.174681 8399.4697 8396.2236 8420.9004 -151.51534 1.1598278 -86.5197 0.082879112 -2.7956634 -7.0824881
160 303.34119 914.64996 -1066.2388 96.4602 96.4602 96.122673 8388.3438 8360.5024 8428.751 -151.58881 1.0977647 -151.64553 0.097975827 -3.353839 -10.033902
170 304.87769 919.28288 -1070.961 96.4602 96.4602 96.072088 8408.8694 8333.4337 8449.5665 -151.67812 1.044322 -201.80899 0.11265931 -3.9117174 -12.897768
180 304.99 919.62151 -1071.3588 96.4602 96.4602 96.022824 8461.5542 8343.1436 8484.9824 -151.73733 0.99203387 -235.51793 0.12695926 -4.4693063 -15.685622
190 305.1148 919.99782 -1071.7807 96.4602 96.4602 95.9748 8498.7562 8371.4217 8514.4473 -151.78288 0.93937416 -273.43964 0.1408996 -5.0266132 -18.403999
200 306.45829 924.0488 -1075.8787 96.4602 96.4602 95.927931 8488.9509 8385.2408 8529.6443 -151.82991 0.88654815 -324.00777 0.15450451 -5.583645 -21.055149
Loop time of 4.36974 on 1 procs for 100 steps with 23328 atoms
Pair time (%) = 3.28512 (75.1789)
Neigh time (%) = 0.132638 (3.03538)
Comm time (%) = 0.0216973 (0.496535)
Outpt time (%) = 0.0132208 (0.302553)
Other time (%) = 0.917059 (20.9866)
Nlocal: 23328 ave 23328 max 23328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22205 ave 22205 max 22205 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.18349e+06 ave 2.18349e+06 max 2.18349e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2183494
Ave neighs/atom = 93.5997
Neighbor list builds = 2
Dangerous builds = 0

135
examples/msst/log.msst.18Feb13.linux.4
View File

@ -1,135 +0,0 @@
LAMMPS (18 Feb 2013)
# LJ test of msst shock dynamics
# Energy in eV, time in ps, distance in angstroms.
units metal
boundary p p p
atom_style atomic
timestep 1e-03
lattice fcc 5.3589
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
## Specify the box as a given number of unit cells.
region box1 block 0 18 0 18 0 18 units lattice
## Instantiate the system.
create_box 1 box1
Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
1 by 2 by 2 MPI processor grid
create_atoms 1 region box1
Created 23328 atoms
mass 1 40.00
# Initial velocities correspond to around 300K.
velocity all create 600.0 9999
pair_style lj/cut 10
pair_coeff 1 1 0.01032 3.405
timestep 2e-3
# Equilibrate the system
fix 2 all nve
thermo 10
run 100
Memory usage per processor = 5.55383 Mbytes
Step Temp E_pair E_mol TotEng Press
0 600 -1943.9014 0 -134.75058 992.06384
10 586.47212 -1917.4465 0 -149.08565 1305.7368
20 540.13678 -1779.3375 0 -150.68935 2488.8545
30 450.11466 -1508.2891 0 -151.08028 4655.1306
40 332.99843 -1155.1208 0 -151.04685 7357.5162
50 259.2571 -932.72753 0 -151.0022 9086.2087
60 256.22581 -923.67654 0 -151.0913 9257.1571
70 281.12085 -998.79866 0 -151.14863 8759.7887
80 299.37658 -1053.8476 0 -151.1519 8352.9467
90 304.24026 -1068.4941 0 -151.13319 8218.1594
100 301.9683 -1061.6332 0 -151.12284 8244.1277
Loop time of 0.921801 on 4 procs for 100 steps with 23328 atoms
Pair time (%) = 0.834578 (90.5377)
Neigh time (%) = 0.0168348 (1.82629)
Comm time (%) = 0.0523829 (5.68267)
Outpt time (%) = 0.000578165 (0.0627212)
Other time (%) = 0.0174276 (1.8906)
Nlocal: 5832 ave 5850 max 5813 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 10571 ave 10590 max 10553 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 545762 ave 548069 max 543643 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Total # of neighbors = 2183047
Ave neighs/atom = 93.5805
Neighbor list builds = 1
Dangerous builds = 0
unfix 2
# MSST fix
fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
MSST parameters:
Shock in z direction
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.00000e+02
Shock velocity = 2.80000e+01
Artificial viscosity (units of mass/length/time) = 3.00000e+02
Initial pressure calculated on first step
Initial volume calculated on first step
Initial energy calculated on first step
# this is needed to make etotal equal the MSST conserved quantity
fix_modify msst energy yes
variable dhug equal f_msst[1]
variable dray equal f_msst[2]
variable lgr_vel equal f_msst[3]
variable lgr_pos equal f_msst[4]
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
#dump id all atom 50 dump.msst
#dump 1 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
run 100
Fix MSST v0 = 8.97521e+05
Fix MSST p0 = 8.18624e+03
Fix MSST e0 = to be -1.51123e+02
Fix MSST initial strain rate of -3.19005e-02 established by reducing temperature by factor of 1.00000e-02
Memory usage per processor = 5.55383 Mbytes
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng dhug dray lgr_vel lgr_pos msst
100 298.94862 901.40524 -1052.5281 96.4602 96.4602 96.4602 8270.9151 8253.4662 8175.4946 -151.12284 1.5098415 -10.744684 0 0 9.1051034
110 296.49826 894.01679 -1045.224 96.4602 96.4602 96.399609 8338.4937 8340.5504 8294.9909 -151.20723 1.4327442 23.73173 0.017588167 -0.55980562 5.6560557
120 295.97607 892.44225 -1043.7239 96.4602 96.4602 96.340904 8377.6797 8385.921 8378.3042 -151.28169 1.3584606 24.672199 0.034628719 -1.1192655 2.2953307
130 297.34893 896.58179 -1047.945 96.4602 96.4602 96.284029 8379.2516 8394.8806 8416.2669 -151.36322 1.2881444 -17.170168 0.051138087 -1.6783905 -0.96527961
140 299.71946 903.72952 -1055.1787 96.4602 96.4602 96.22888 8357.0358 8388.6743 8424.3188 -151.44922 1.221125 -86.501161 0.067146366 -2.2371908 -4.1195182
150 301.79241 909.97998 -1061.4976 96.4602 96.4602 96.175327 8332.7118 8393.7027 8434.6177 -151.51765 1.1560248 -151.34689 0.082691635 -2.7956762 -7.172084
160 303.18249 914.17141 -1065.7667 96.4602 96.4602 96.123244 8321.1154 8413.1248 8454.5596 -151.59527 1.0977348 -204.4864 0.097810061 -3.3538554 -10.134387
170 304.34089 917.66428 -1069.3198 96.4602 96.4602 96.072522 8327.6227 8431.1177 8467.92 -151.65554 1.0390628 -262.29751 0.11253339 -3.9117366 -13.01442
180 305.86343 922.25514 -1073.9633 96.4602 96.4602 96.023049 8345.1853 8432.5201 8461.3276 -151.70813 0.97863988 -338.30793 0.12689398 -4.4693274 -15.815462
190 307.44054 927.01052 -1078.7892 96.4602 96.4602 95.9747 8368.4081 8427.5109 8450.584 -151.77867 0.92329631 -416.89333 0.1409285 -5.0266346 -18.541801
200 308.43619 930.01265 -1081.8521 96.4602 96.4602 95.927349 8393.2058 8443.1265 8454.6733 -151.83947 0.8723277 -479.24592 0.1546734 -5.5836644 -21.20378
Loop time of 1.17268 on 4 procs for 100 steps with 23328 atoms
Pair time (%) = 0.841547 (71.7624)
Neigh time (%) = 0.0342548 (2.92106)
Comm time (%) = 0.0479164 (4.08604)
Outpt time (%) = 0.00436926 (0.372586)
Other time (%) = 0.244597 (20.8579)
Nlocal: 5832 ave 5874 max 5803 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 10563.8 ave 10588 max 10526 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 545708 ave 550787 max 542668 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 2182834
Ave neighs/atom = 93.5714
Neighbor list builds = 2
Dangerous builds = 0

11
examples/neb/log.neb.hop1.18Feb13.linux.4
View File

@ -1,11 +0,0 @@
LAMMPS (18 Feb 2013)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 4394.415 2794.6751 0.41279209 4.8987813 4588.501 0.43598632 0.42993506 1.8911387 0 -3.053578 0.33333333 -2.6175917 0.66666667 -2.7448543 1 -3.0475267
100 0.16491797 0.11704265 0.073253678 0.15376032 0.16852504 0.0070973947 0.0022716577 2.2924235 0 -3.0535878 0.32028055 -3.0473424 0.63279844 -3.0464904 1 -3.0487621
167 0.099489681 0.075645838 0.058144199 0.074832649 0.20958916 0.0070828454 0.0022622141 2.3072232 0 -3.053591 0.31925954 -3.0473496 0.64307831 -3.0465082 1 -3.0487704
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
167 0.20958916 0.18030355 0.058144199 0.074832649 0.20958916 0.0070828454 0.0022622141 2.3072232 0 -3.053591 0.31925954 -3.0473496 0.64307831 -3.0465082 1 -3.0487704
267 0.15398043 0.13842303 0.053188236 0.064560479 0.15398043 0.0070933391 0.0022732427 2.3091348 0 -3.053592 0.31934334 -3.047352 0.63302643 -3.0464987 1 -3.0487719
339 0.099312103 0.088450672 0.042522861 0.048330586 0.099312103 0.0071036621 0.002284228 2.3132329 0 -3.0535938 0.31606593 -3.0473883 0.61753222 -3.0464901 1 -3.0487743

19
examples/neb/log.neb.hop2.18Feb13.linux.4
View File

@ -1,19 +0,0 @@
LAMMPS (18 Feb 2013)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 14.470556 10.654221 0.40467815 5.0039317 14.654382 0.0018497549 0.00068389874 0.98392852 0 -3.0514828 0.33333333 -3.0496331 0.66666667 -3.049639 1 -3.050317
100 0.30693642 0.14214612 0.064540435 0.18992386 0.55839627 0.0015370681 0.0015317937 1.155908 0 -3.0514877 0.28786213 -3.0503592 0.58937589 -3.0499507 1 -3.0514825
200 0.10867436 0.057454792 0.043842067 0.051490038 0.84846595 0.0014585096 0.001457658 1.1692143 0 -3.051491 0.29660843 -3.050316 0.62299493 -3.0500325 1 -3.0514902
300 0.11662168 0.030516737 0.030666311 0.034651023 1.0116774 0.0014064671 0.0014060807 1.1700677 0 -3.0514927 0.30984279 -3.05026 0.64188282 -3.0500862 1 -3.0514923
400 0.057106221 0.016512887 0.020989339 0.023348884 1.1072181 0.0013732957 0.0013731118 1.1704502 0 -3.0514936 0.31945381 -3.0502218 0.65251914 -3.0501203 1 -3.0514934
500 0.093684293 0.021481358 0.014823818 0.01669741 1.1580507 0.0013547017 0.0013546054 1.1706327 0 -3.051494 0.32491587 -3.0502011 0.65816371 -3.0501393 1 -3.0514939
600 0.02560367 0.0056944922 0.0095793714 0.010672043 1.1952184 0.0013409641 0.0013409194 1.1708165 0 -3.0514942 0.32892103 -3.0501865 0.6622228 -3.0501532 1 -3.0514941
700 0.053702771 0.012476635 0.0068206548 0.0077241137 1.2464658 0.0013348463 0.0013348207 1.1708921 0 -3.0514943 0.33065695 -3.0501803 0.66397271 -3.0501594 1 -3.0514942
720 0.0093868547 0.0029986965 0.0065969518 0.0073833131 1.2468529 0.0013343964 0.0013343722 1.1709106 0 -3.0514943 0.33077105 -3.0501798 0.66408416 -3.0501599 1 -3.0514943
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
720 1.2468529 1.2166503 0.0065969518 0.0073833131 1.2468529 0.0013343964 0.0013343722 1.1709106 0 -3.0514943 0.33077105 -3.0501798 0.66408416 -3.0501599 1 -3.0514943
820 0.14126642 0.078847007 0.0044950467 0.0051237953 0.14126642 0.0016023457 0.0016023321 1.1716496 0 -3.0514943 0.28575219 -3.0503638 0.50149409 -3.049892 1 -3.0514943
920 0.043110818 0.038638164 0.003579024 0.0040777949 0.012030411 0.0016020443 0.0016020343 1.1725483 0 -3.0514943 0.26947368 -3.0504461 0.50334153 -3.0498923 1 -3.0514943
1020 0.030296371 0.011719629 0.0024503979 0.002861026 0.030296371 0.0016019293 0.001601923 1.1739155 0 -3.0514943 0.25797318 -3.0505101 0.50450691 -3.0498924 1 -3.0514943
1102 0.0092997898 0.0056166831 0.0018951803 0.0022471504 0.0078955098 0.0016018729 0.0016018682 1.1743883 0 -3.0514943 0.25524857 -3.0505268 0.50492227 -3.0498925 1 -3.0514943

112
examples/nemd/log.nemd.18Feb13.linux.1
View File

@ -1,112 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d NEMD simulation
units lj
atom_style atomic
dimension 2d
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box prism 0 10 0 8 -0.5 0.5 0 0 0
create_box 2 box
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 160 atoms
mass * 1.0
velocity all create 1.44 87287 loop geom
region slice block 4 6 INF INF INF INF
set region slice type 2
40 settings made for type
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
fix 2 all deform 1 xy erate 0.01 remap v
#dump 1 all custom 5000 dump.nemd id type x y z
#dump 1 all image 1000 image.*.jpg type type adiam 1.2
#dump_modify 1 pad 5
thermo 1000
run 50000
Memory usage per processor = 2.0627 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.431 1.2080502 189.52855
1000 1.1132807 0.27905278 0 1.3853755 6.5147704 189.52855
2000 1.0443617 0.2588631 0 1.2966975 5.8123077 189.52855
3000 0.99740048 0.30663122 0 1.2977979 6.7893948 189.52855
4000 1.0452154 0.2549558 0 1.2936386 5.9682721 189.52855
5000 1.0446171 0.24804329 0 1.2861316 6.0510081 189.52855
6000 0.99414736 0.27672942 0 1.2646634 6.1314117 189.52855
7000 0.98222339 0.25264497 0 1.2287295 5.835047 189.52855
8000 1.0949044 0.21576814 0 1.3038294 5.491461 189.52855
9000 1.0926686 0.24221385 0 1.3280532 6.3130763 189.52855
10000 1.076097 0.2855754 0 1.3549468 5.8734258 189.52855
11000 0.99180114 0.32327904 0 1.3088814 6.7664177 189.52855
12000 0.92157563 0.3649801 0 1.2807959 7.1346057 189.52855
13000 1.0357975 0.24757954 0 1.2769033 5.1431799 189.52855
14000 1.0007104 0.23333402 0 1.22779 5.7856096 189.52855
15000 0.99137134 0.24780673 0 1.232982 6.1361025 189.52855
16000 0.94735806 0.285215 0 1.2266521 6.5489235 189.52855
17000 0.92947519 0.35111458 0 1.2747806 6.8906691 189.52855
18000 0.93468492 0.30314528 0 1.2319884 6.7846869 189.52855
19000 0.97664561 0.22133285 0 1.1918744 5.1668518 189.52855
20000 0.92288444 0.24361535 0 1.1607318 5.8575076 189.52855
21000 0.95982212 0.23711835 0 1.1909416 6.1133698 189.52855
22000 0.94710657 0.30873344 0 1.2499206 6.7011709 189.52855
23000 0.95315902 0.25917016 0 1.2063719 6.436954 189.52855
24000 0.92248708 0.25883982 0 1.1755614 6.7367986 189.52855
25000 0.90317019 0.26834925 0 1.1658746 5.8271823 189.52855
26000 0.91432206 0.29952864 0 1.2081362 7.2639988 189.52855
27000 1.0070883 0.25437551 0 1.2551695 5.9319042 189.52855
28000 0.90757676 0.33894646 0 1.2408509 6.5341369 189.52855
29000 0.93635654 0.27447038 0 1.2049747 5.7410459 189.52855
30000 1.0260914 0.26547724 0 1.2851555 6.7175944 189.52855
31000 1.0885528 0.22068838 0 1.3024377 5.9614548 189.52855
32000 0.99983894 0.26432646 0 1.2579164 5.6537115 189.52855
33000 0.98254278 0.25012552 0 1.2265274 6.00352 189.52855
34000 1.0461448 0.239846 0 1.2794524 5.8594944 189.52855
35000 1.0600085 0.32706153 0 1.3804449 7.1757696 189.52855
36000 1.0293724 0.37370741 0 1.3966463 7.1818303 189.52855
37000 0.99724062 0.35645069 0 1.3474586 7.3712517 189.52855
38000 1.1355196 0.23285267 0 1.3612752 5.9101916 189.52855
39000 1.0750755 0.31068535 0 1.3790417 6.7523098 189.52855
40000 1.0269017 0.38361397 0 1.4040975 7.532356 189.52855
41000 0.98265149 0.34340216 0 1.3199121 6.9652101 189.52855
42000 0.95262128 0.36420847 0 1.3108759 7.5380723 189.52855
43000 1.0124646 0.25137287 0 1.2575095 6.6275506 189.52855
44000 0.95142407 0.29804153 0 1.2435192 5.9780096 189.52855
45000 0.99724723 0.19281581 0 1.1838302 5.4332418 189.52855
46000 0.90112949 0.29935892 0 1.1948564 7.0600659 189.52855
47000 0.8786086 0.34312007 0 1.2162374 6.4678979 189.52855
48000 1.0516991 0.17931414 0 1.2244401 5.5158284 189.52855
49000 0.98386816 0.26044721 0 1.2381662 5.8913908 189.52855
50000 1.0316312 0.19654107 0 1.2217246 5.2461518 189.52855
Loop time of 1.12043 on 1 procs for 50000 steps with 160 atoms
Pair time (%) = 0.199276 (17.7856)
Neigh time (%) = 0.139233 (12.4267)
Comm time (%) = 0.0540705 (4.82586)
Outpt time (%) = 0.000417948 (0.0373023)
Other time (%) = 0.727435 (64.9245)
Nlocal: 160 ave 160 max 160 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 66 ave 66 max 66 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 351 ave 351 max 351 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 351
Ave neighs/atom = 2.19375
Neighbor list builds = 5281
Dangerous builds = 0

112
examples/nemd/log.nemd.18Feb13.linux.4
View File

@ -1,112 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d NEMD simulation
units lj
atom_style atomic
dimension 2d
lattice sq2 0.8442
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
region box prism 0 10 0 8 -0.5 0.5 0 0 0
create_box 2 box
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
2 by 2 by 1 MPI processor grid
create_atoms 1 box
Created 160 atoms
mass * 1.0
velocity all create 1.44 87287 loop geom
region slice block 4 6 INF INF INF INF
set region slice type 2
40 settings made for type
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
fix 2 all deform 1 xy erate 0.01 remap v
#dump 1 all custom 5000 dump.nemd id type x y z
#dump 1 all image 1000 image.*.jpg type type adiam 1.2
#dump_modify 1 pad 5
thermo 1000
run 50000
Memory usage per processor = 2.06108 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.431 1.2080502 189.52855
1000 1.124295 0.28924371 0 1.4065119 7.0530596 189.52855
2000 0.95544082 0.41610026 0 1.3655696 8.2906389 189.52855
3000 1.0379332 0.3006166 0 1.3320627 6.6571959 189.52855
4000 1.0384606 0.21868978 0 1.25066 5.5810527 189.52855
5000 0.94117133 0.28986466 0 1.2251537 6.7004134 189.52855
6000 0.8855088 0.29250925 0 1.1724836 6.0234641 189.52855
7000 0.89371735 0.22907448 0 1.1172061 6.0996491 189.52855
8000 0.91424769 0.21379978 0 1.1223334 5.3165508 189.52855
9000 0.90042293 0.21884136 0 1.1136366 5.488714 189.52855
10000 0.85048519 0.25030732 0 1.095477 5.6995459 189.52855
11000 0.84698813 0.26740545 0 1.1090999 6.0227022 189.52855
12000 0.84154976 0.27476871 0 1.1110588 6.1957407 189.52855
13000 0.95858623 0.24922085 0 1.2018159 6.1788034 189.52855
14000 1.0214286 0.21791039 0 1.2329551 5.4418702 189.52855
15000 1.0398737 0.2633112 0 1.2966857 6.4069155 189.52855
16000 1.0064086 0.32204447 0 1.322163 6.9037595 189.52855
17000 0.95972629 0.32803912 0 1.2817671 6.816773 189.52855
18000 0.97474673 0.27514532 0 1.2437999 6.5619061 189.52855
19000 0.98058523 0.29730787 0 1.2717644 6.3947579 189.52855
20000 1.0096005 0.29191846 0 1.2952089 6.5005373 189.52855
21000 1.0340906 0.30603597 0 1.3336635 6.6365016 189.52855
22000 1.0986576 0.25246406 0 1.3442551 6.3254116 189.52855
23000 1.0118481 0.31753984 0 1.3230639 6.0921359 189.52855
24000 1.0766759 0.20245452 0 1.2724012 5.4505434 189.52855
25000 1.1081144 0.1941749 0 1.2953635 5.4769844 189.52855
26000 1.0100198 0.29200311 0 1.2957102 6.4496868 189.52855
27000 1.0780229 0.22518995 0 1.2964752 5.4742933 189.52855
28000 0.95411135 0.30374431 0 1.2518925 6.4759593 189.52855
29000 0.89919125 0.33340443 0 1.2269757 7.2806173 189.52855
30000 1.0252498 0.21740235 0 1.2362443 6.0225096 189.52855
31000 0.94842379 0.29574176 0 1.2382379 6.6857537 189.52855
32000 0.98564692 0.28884608 0 1.2683327 5.8893159 189.52855
33000 1.0203197 0.25128893 0 1.2652316 6.3876672 189.52855
34000 0.92927072 0.35791559 0 1.2813784 6.9518532 189.52855
35000 1.0595999 0.2526221 0 1.3055995 6.3468891 189.52855
36000 1.0080572 0.3373598 0 1.3391167 6.8836622 189.52855
37000 1.0371553 0.39107985 0 1.421753 7.8264775 189.52855
38000 1.1399348 0.32003125 0 1.4528415 6.7472192 189.52855
39000 1.1719539 0.28244065 0 1.4470698 6.1962707 189.52855
40000 1.160549 0.2692168 0 1.4225124 6.4898037 189.52855
41000 1.082068 0.31445471 0 1.3897598 7.1045082 189.52855
42000 1.1200126 0.24056295 0 1.3535754 6.1401582 189.52855
43000 1.1131393 0.25879245 0 1.3649747 5.6653752 189.52855
44000 1.0584865 0.28294496 0 1.3348159 6.7007718 189.52855
45000 1.1250306 0.22801778 0 1.346017 5.5953791 189.52855
46000 1.0799948 0.25829243 0 1.3315373 6.2101875 189.52855
47000 1.0466019 0.30437314 0 1.3444338 6.5602361 189.52855
48000 0.99707221 0.2760815 0 1.266922 6.3946457 189.52855
49000 0.96261953 0.29992833 0 1.2565315 6.7358834 189.52855
50000 0.91044957 0.33413644 0 1.2388957 6.7732395 189.52855
Loop time of 0.875128 on 4 procs for 50000 steps with 160 atoms
Pair time (%) = 0.0523399 (5.98083)
Neigh time (%) = 0.0384604 (4.39483)
Comm time (%) = 0.346787 (39.6271)
Outpt time (%) = 0.000826657 (0.0944613)
Other time (%) = 0.436714 (49.9028)
Nlocal: 40 ave 42 max 38 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 36.25 ave 42 max 34 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Neighs: 91 ave 103 max 84 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 364
Ave neighs/atom = 2.275
Neighbor list builds = 5274
Dangerous builds = 0

137
examples/obstacle/log.obstacle.18Feb13.linux.1
View File

@ -1,137 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d LJ obstacle flow
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 40 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 840 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
120 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
120 atoms in group upper
group boundary union lower upper
240 atoms in group boundary
group flow subtract all boundary
600 atoms in group flow
set group lower type 2
120 settings made for type
set group upper type 3
120 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Poiselle flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
# 2 obstacles
region void1 sphere 10 4 0 3
delete_atoms region void1
Deleted 36 atoms, new total = 804
region void2 sphere 20 7 0 3
delete_atoms region void2
Deleted 35 atoms, new total = 769
fix 7 flow indent 100 sphere 10 4 0 4
fix 8 flow indent 100 sphere 20 7 0 4
fix 9 all enforce2d
# Run
timestep 0.003
thermo 1000
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
#dump 1 all atom 100 dump.obstacle
#dump 1 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 25000
Memory usage per processor = 2.07044 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0027471 0 0 0.68849216 0.46317653 1143.0857
1000 1 -0.33689286 0 0.34971312 1.2905426 1286.7728
2000 1 -0.36746164 0 0.31914434 1.1668828 1313.44
3000 1 -0.52004751 0 0.16655848 1.4177739 1324.489
4000 1 -0.50683869 0 0.17976729 1.4851498 1370.896
5000 1 -0.49074513 0 0.19586085 1.2870129 1411.5513
6000 1 -0.45051896 0 0.23608702 1.2173953 1441.7581
7000 1 -0.44428914 0 0.24231685 1.2136189 1451.7268
8000 1 -0.41943736 0 0.26716862 1.0476856 1463.0805
9000 1 -0.42143857 0 0.26516741 1.1040812 1449.7584
10000 1 -0.40181705 0 0.28478893 0.97148485 1448.5974
11000 1 -0.4088962 0 0.27770978 1.1761219 1440.3567
12000 1 -0.38630717 0 0.30029881 1.0593811 1444.9934
13000 1 -0.37152911 0 0.31507687 0.98075952 1448.0726
14000 1 -0.37370096 0 0.31290502 1.0046443 1449.4749
15000 1 -0.39915937 0 0.28744662 1.0240313 1452.3583
16000 1 -0.37562636 0 0.31097963 1.0053468 1452.3514
17000 1 -0.35736161 0 0.32924437 1.070682 1452.898
18000 1 -0.38767402 0 0.29893196 1.0418661 1456.1288
19000 1 -0.38489181 0 0.30171417 1.0361798 1446.8804
20000 1 -0.39521864 0 0.29138735 1.0754044 1447.4619
21000 1 -0.37845983 0 0.30814615 1.0072922 1453.8721
22000 1 -0.40926684 0 0.27733914 1.0929362 1452.8181
23000 1 -0.3586683 0 0.32793768 1.006092 1459.6104
24000 1 -0.38908821 0 0.29751777 0.95291948 1464.8522
25000 1 -0.38890426 0 0.29770172 0.95284427 1455.9361
Loop time of 1.73023 on 1 procs for 25000 steps with 769 atoms
Pair time (%) = 0.509133 (29.4258)
Neigh time (%) = 0.144696 (8.36287)
Comm time (%) = 0.02689 (1.55413)
Outpt time (%) = 0.000263929 (0.015254)
Other time (%) = 1.04924 (60.6419)
Nlocal: 769 ave 769 max 769 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: 1624 ave 1624 max 1624 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1624
Ave neighs/atom = 2.11183
Neighbor list builds = 1642
Dangerous builds = 0

137
examples/obstacle/log.obstacle.18Feb13.linux.4
View File

@ -1,137 +0,0 @@
LAMMPS (18 Feb 2013)
# 2d LJ obstacle flow
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.7
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
region box block 0 40 0 10 -0.25 0.25
create_box 3 box
Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
4 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 840 atoms
mass 1 1.0
mass 2 1.0
mass 3 1.0
# LJ potentials
pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
120 atoms in group lower
region 2 block INF INF 8.75 INF INF INF
group upper region 2
120 atoms in group upper
group boundary union lower upper
240 atoms in group boundary
group flow subtract all boundary
600 atoms in group flow
set group lower type 2
120 settings made for type
set group upper type 3
120 settings made for type
# initial velocities
compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile
# Poiselle flow
velocity boundary set 0.0 0.0 0.0
fix 3 lower setforce 0.0 0.0 0.0
fix 4 upper setforce 0.0 NULL 0.0
fix 5 upper aveforce 0.0 -0.5 0.0
fix 6 flow addforce 1.0 0.0 0.0
# 2 obstacles
region void1 sphere 10 4 0 3
delete_atoms region void1
Deleted 36 atoms, new total = 804
region void2 sphere 20 7 0 3
delete_atoms region void2
Deleted 35 atoms, new total = 769
fix 7 flow indent 100 sphere 10 4 0 4
fix 8 flow indent 100 sphere 20 7 0 4
fix 9 all enforce2d
# Run
timestep 0.003
thermo 1000
thermo_modify temp mobile
WARNING: Temperature for thermo pressure is not for group all (thermo.cpp:436)
#dump 1 all atom 100 dump.obstacle
#dump 1 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 25000
Memory usage per processor = 2.06043 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.0004177 0 0 0.68689281 0.46210058 1143.0857
1000 1 -0.32494012 0 0.36166587 1.2240503 1282.5239
2000 1 -0.37815616 0 0.30844982 1.0642877 1312.5691
3000 1 -0.49062349 0 0.1959825 1.5239344 1322.2627
4000 1 -0.50104941 0 0.18555657 1.4605776 1367.6505
5000 1 -0.4655479 0 0.22105808 1.3317864 1406.9197
6000 1 -0.50936502 0 0.17724096 1.2130158 1424.3621
7000 1 -0.44959207 0 0.23701391 1.1070391 1443.1
8000 1 -0.42617261 0 0.26043338 1.2005043 1444.8955
9000 1 -0.41192389 0 0.2746821 1.0022569 1450.9691
10000 1 -0.40940409 0 0.27720189 0.98653582 1447.7805
11000 1 -0.4093125 0 0.27729348 1.0625786 1446.6852
12000 1 -0.41948268 0 0.26712331 1.1166793 1449.6135
13000 1 -0.38874722 0 0.29785877 0.99617473 1456.1633
14000 1 -0.40067763 0 0.28592835 0.98191459 1454.6009
15000 1 -0.39026612 0 0.29633987 1.0245506 1452.7783
16000 1 -0.39139643 0 0.29520955 1.0281029 1451.2662
17000 1 -0.37821271 0 0.30839327 1.0108601 1454.1047
18000 1 -0.37382372 0 0.31278227 0.93743647 1457.2083
19000 1 -0.3737367 0 0.31286928 1.0333603 1458.6131
20000 1 -0.37232139 0 0.31428459 1.0471568 1448.6511
21000 1 -0.40114891 0 0.28545707 1.0045402 1455.5644
22000 1 -0.36552339 0 0.32108259 0.99841802 1459.4723
23000 1 -0.35573934 0 0.33086665 0.89283563 1460.8941
24000 1 -0.3608262 0 0.32577978 1.0097641 1453.0004
25000 1 -0.36649381 0 0.32011217 0.98366691 1451.5444
Loop time of 0.818261 on 4 procs for 25000 steps with 769 atoms
Pair time (%) = 0.130597 (15.9603)
Neigh time (%) = 0.0388979 (4.75373)
Comm time (%) = 0.20022 (24.469)
Outpt time (%) = 0.000515699 (0.0630239)
Other time (%) = 0.44803 (54.754)
Nlocal: 192.25 ave 242 max 159 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Nghost: 43 ave 45 max 39 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 414 ave 588 max 284 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 1656
Ave neighs/atom = 2.15345
Neighbor list builds = 1641
Dangerous builds = 1

164
examples/peptide/log.peptide.18Feb13.linux.1
View File

@ -1,164 +0,0 @@
LAMMPS (18 Feb 2013)
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
3 = max bonds/atom
6 = max angles/atom
14 = max dihedrals/atom
1 = max impropers/atom
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 MPI processor grid
2004 atoms
2004 velocities
1365 bonds
786 angles
207 dihedrals
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style multi
thermo 50
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
#dump 1 peptide atom 10 dump.peptide
#dump 1 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 1 pad 3
#compute bnd all property/local btype batom1 batom2
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
run 300
PPPM initialization ...
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 10648 3375
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 22.911 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2646 E_long = -33907.9271 Press = -845.4774
---------------- Step 50 ----- CPU = 0.9730 (sec) ----------------
TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748
PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771
E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7981
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80799e-07
6 0.997 1.06209e-06
8 1.08 6.20484e-07
10 1.111 6.23445e-07
12 1.08 2.68063e-07
14 0.96 0
18 0.957201 5.38018e-06
31 104.52 0.000502316
---------------- Step 100 ----- CPU = 1.9571 (sec) ----------------
TotEng = -5257.9973 KinEng = 1078.0556 Temp = 267.9664
PotEng = -6336.0529 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
E_coul = 26786.6840 E_long = -33906.5620 Press = -648.6639
---------------- Step 150 ----- CPU = 2.9714 (sec) ----------------
TotEng = -5287.2844 KinEng = 1098.6036 Temp = 273.0739
PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
E_coul = 26717.2584 E_long = -33907.2812 Press = -333.1895
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50856e-07
8 1.08 6.58343e-08
10 1.111 5.55349e-07
12 1.08 1.99243e-07
14 0.96 0
18 0.957201 3.59666e-06
31 104.52 0.000388184
---------------- Step 200 ----- CPU = 3.9411 (sec) ----------------
TotEng = -5308.4528 KinEng = 1100.5056 Temp = 273.5467
PotEng = -6408.9584 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3261
E_coul = 26736.1131 E_long = -33902.3928 Press = -1470.3871
---------------- Step 250 ----- CPU = 4.9633 (sec) ----------------
TotEng = -5294.1808 KinEng = 1071.1623 Temp = 266.2530
PotEng = -6365.3431 E_bond = 14.2022 E_angle = 39.1953
E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5411
E_coul = 26713.8466 E_long = -33908.7226 Press = -188.8083
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78266e-06
6 0.997001 3.50137e-06
8 1.08 2.09323e-06
10 1.111 5.64331e-06
12 1.08 2.10401e-06
14 0.96 0
18 0.957202 7.67992e-06
31 104.52 0.000806336
---------------- Step 300 ----- CPU = 5.9858 (sec) ----------------
TotEng = -5251.4349 KinEng = 1123.6255 Temp = 279.2934
PotEng = -6375.0604 E_bond = 14.2249 E_angle = 38.4712
E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4556
E_coul = 26745.4104 E_long = -33909.1249 Press = -469.5456
Loop time of 5.98579 on 1 procs for 300 steps with 2004 atoms
Pair time (%) = 4.5748 (76.4277)
Bond time (%) = 0.0121517 (0.203009)
Kspce time (%) = 0.65928 (11.0141)
Neigh time (%) = 0.635301 (10.6135)
Comm time (%) = 0.0336189 (0.561646)
Outpt time (%) = 0.000190973 (0.00319044)
Other time (%) = 0.0704458 (1.17688)
FFT time (% of Kspce) = 0.0800959 (12.149)
FFT Gflps 3d (1d only) = 2.05396 3.32443
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11181 ave 11181 max 11181 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708028 ave 708028 max 708028 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708028
Ave neighs/atom = 353.307
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0

164
examples/peptide/log.peptide.18Feb13.linux.4
View File

@ -1,164 +0,0 @@
LAMMPS (18 Feb 2013)
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
3 = max bonds/atom
6 = max angles/atom
14 = max dihedrals/atom
1 = max impropers/atom
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 MPI processor grid
2004 atoms
2004 velocities
1365 bonds
786 angles
207 dihedrals
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style multi
thermo 50
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
#dump 1 peptide atom 10 dump.peptide
#dump 1 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 1 pad 3
#compute bnd all property/local btype batom1 batom2
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
run 300
PPPM initialization ...
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 4312 960
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 10.3307 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2646 E_long = -33907.9271 Press = -845.4774
---------------- Step 50 ----- CPU = 0.2826 (sec) ----------------
TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748
PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771
E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7981
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80799e-07
6 0.997 1.06209e-06
8 1.08 6.20484e-07
10 1.111 6.23445e-07
12 1.08 2.68063e-07
14 0.96 0
18 0.957201 5.38018e-06
31 104.52 0.000502316
---------------- Step 100 ----- CPU = 0.5630 (sec) ----------------
TotEng = -5257.9973 KinEng = 1078.0556 Temp = 267.9664
PotEng = -6336.0529 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
E_coul = 26786.6840 E_long = -33906.5620 Press = -648.6639
---------------- Step 150 ----- CPU = 0.8510 (sec) ----------------
TotEng = -5287.2845 KinEng = 1098.6036 Temp = 273.0739
PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
E_coul = 26717.2583 E_long = -33907.2812 Press = -333.1895
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50856e-07
8 1.08 6.58343e-08
10 1.111 5.55349e-07
12 1.08 1.99243e-07
14 0.96 0
18 0.957201 3.59666e-06
31 104.52 0.000388184
---------------- Step 200 ----- CPU = 1.1296 (sec) ----------------
TotEng = -5308.4528 KinEng = 1100.5056 Temp = 273.5467
PotEng = -6408.9584 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3261
E_coul = 26736.1131 E_long = -33902.3928 Press = -1470.3869
---------------- Step 250 ----- CPU = 1.4237 (sec) ----------------
TotEng = -5294.1808 KinEng = 1071.1623 Temp = 266.2530
PotEng = -6365.3431 E_bond = 14.2022 E_angle = 39.1953
E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5412
E_coul = 26713.8465 E_long = -33908.7226 Press = -188.8075
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78266e-06
6 0.997001 3.50139e-06
8 1.08 2.09322e-06
10 1.111 5.6433e-06
12 1.08 2.10401e-06
14 0.96 0
18 0.957202 7.6799e-06
31 104.52 0.000806335
---------------- Step 300 ----- CPU = 1.7161 (sec) ----------------
TotEng = -5251.4350 KinEng = 1123.6255 Temp = 279.2935
PotEng = -6375.0605 E_bond = 14.2249 E_angle = 38.4712
E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4558
E_coul = 26745.4101 E_long = -33909.1248 Press = -469.5428
Loop time of 1.71616 on 4 procs for 300 steps with 2004 atoms
Pair time (%) = 1.18558 (69.0834)
Bond time (%) = 0.00336462 (0.196056)
Kspce time (%) = 0.247925 (14.4465)
Neigh time (%) = 0.158655 (9.24477)
Comm time (%) = 0.0626211 (3.64892)
Outpt time (%) = 0.000257373 (0.0149971)
Other time (%) = 0.0577542 (3.36533)
FFT time (% of Kspce) = 0.0315048 (12.7074)
FFT Gflps 3d (1d only) = 5.22186 11.7303
Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6586.25 ave 6628 max 6548 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 177007 ave 180562 max 170212 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 708028
Ave neighs/atom = 353.307
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0

84
examples/peri/log.peri.18Feb13.linux.1
View File

@ -1,84 +0,0 @@
LAMMPS (18 Feb 2013)
# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
1 by 1 by 1 MPI processor grid
create_atoms 1 region target
Created 3487 atoms
pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
set group all density 2200
3487 settings made for density
set group all volume 1.25e-10
3487 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 1 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 1 pad 4
run 1000
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Memory usage per processor = 24.2471 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07
100 1.7890585e+24 552721.8 0 681881.47 1.7210968e+11 5.0030006e-07
200 1.3549879e+27 3097027.6 0 1.0091931e+08 1.1829272e+14 5.5130066e-07
300 3.3009625e+27 6331254.8 0 2.4464163e+08 1.9647265e+14 8.0862953e-07
400 3.815184e+27 6225081.7 0 2.8165928e+08 1.8189267e+14 1.0095118e-06
500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06
600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06
700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06
800 1.2424839e+28 2407365.2 0 8.994088e+08 2.3787786e+14 2.5138992e-06
900 1.2358398e+28 4532421.1 0 8.9673716e+08 1.9097317e+14 3.1145903e-06
1000 1.2341036e+28 3219688.2 0 8.9417102e+08 1.596857e+14 3.7196039e-06
Loop time of 20.46 on 1 procs for 1000 steps with 3487 atoms
Pair time (%) = 19.7808 (96.6808)
Neigh time (%) = 0.563618 (2.75474)
Comm time (%) = 0.0018146 (0.00886905)
Outpt time (%) = 0.000224829 (0.00109887)
Other time (%) = 0.113445 (0.554473)
Nlocal: 3487 ave 3487 max 3487 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 567135 ave 567135 max 567135 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1209076
Ave neighs/atom = 346.738
Neighbor list builds = 46
Dangerous builds = 0

84
examples/peri/log.peri.18Feb13.linux.4
View File

@ -1,84 +0,0 @@
LAMMPS (18 Feb 2013)
# small Peridynamic cylinder hit by projectile
units si
boundary s s s
atom_style peri
atom_modify map array
neighbor 0.0010 bin
# small target
lattice sc 0.0005
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
create_box 1 target
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
2 by 1 by 2 MPI processor grid
create_atoms 1 region target
Created 3487 atoms
pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
set group all density 2200
3487 settings made for density
set group all volume 1.25e-10
3487 settings made for volume
velocity all set 0.0 0.0 0.0 sum no units box
fix 1 all nve
# spherical indenter to shatter target
variable y0 equal 0.00155
variable vy equal -100
variable y equal "v_y0 + step*dt*v_vy"
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
compute 1 all damage/atom
timestep 1.0e-7
thermo 100
#dump 1 all custom 100 dump.peri id type x y z c_1
#dump 1 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 1 pad 4
run 1000
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Memory usage per processor = 18.744 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 0 0 0 0 5.0030006e-07
100 1.7890585e+24 552721.8 0 681881.47 1.7210968e+11 5.0030006e-07
200 1.3549879e+27 3097027.6 0 1.0091931e+08 1.1829272e+14 5.5130066e-07
300 3.3009625e+27 6331254.8 0 2.4464163e+08 1.9647265e+14 8.0862953e-07
400 3.815184e+27 6225081.7 0 2.8165928e+08 1.8189267e+14 1.0095118e-06
500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06
600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06
700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06
800 1.2424839e+28 2407365.3 0 8.994088e+08 2.3787786e+14 2.5138992e-06
900 1.2358398e+28 4532419.8 0 8.9673716e+08 1.9097317e+14 3.1145903e-06
1000 1.2341036e+28 3219727.8 0 8.9417105e+08 1.596857e+14 3.7196039e-06
Loop time of 5.76524 on 4 procs for 1000 steps with 3487 atoms
Pair time (%) = 4.99867 (86.7035)
Neigh time (%) = 0.14311 (2.48229)
Comm time (%) = 0.577355 (10.0144)
Outpt time (%) = 0.000337362 (0.00585166)
Other time (%) = 0.0457699 (0.793894)
Nlocal: 871.75 ave 910 max 835 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Nghost: 1343.25 ave 1380 max 1305 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 141784 ave 170146 max 116083 min
Histogram: 1 1 0 0 0 0 0 1 0 1
FullNghs: 302269 ave 346070 max 260820 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Total # of neighbors = 1209076
Ave neighs/atom = 346.738
Neighbor list builds = 46
Dangerous builds = 0

144
examples/pour/log.pour.18Feb13.linux.1
View File

@ -1,144 +0,0 @@
LAMMPS (18 Feb 2013)
# Pour granular particles into chute container, then induce flow
atom_style sphere
boundary p p fm
newton off
communicate single vel yes
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
1 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
#dump id all atom 1000 dump.pour
#dump 1 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 25000
Memory usage per processor = 9.46169 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 6600
1000 402 779.98578 0 6600
2000 402 1424.4252 0 6600
3000 402 1425.0863 12.9927 6600
4000 804 1724.8532 47.325647 6600
5000 804 1598.6681 64.779741 6600
6000 804 1364.8231 61.75911 6600
7000 1206 1519.7287 69.028648 6600
8000 1206 1409.6162 62.604936 6600
9000 1206 1243.5299 53.012812 6600
10000 1608 1400.2632 57.300035 6600
11000 1608 1226.4327 53.185401 6600
12000 1608 1190.754 41.207269 6600
13000 2010 1309.6301 51.508727 6600
14000 2010 1182.74 46.857423 6600
15000 2010 985.17177 43.141534 6600
16000 2412 1041.1301 47.314349 6600
17000 2412 1038.3663 39.508439 6600
18000 2412 916.06571 39.312699 6600
19000 2814 1021.9901 42.073133 6600
20000 2814 959.466 41.811414 6600
21000 2814 761.2927 41.364383 6600
22000 2814 521.07124 40.192029 6600
23000 3000 423.49186 37.34074 6600
24000 3000 362.28297 22.586628 6600
25000 3000 223.45694 22.976343 6600
Loop time of 9.28813 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 5.36181 (57.7276)
Neigh time (%) = 1.04765 (11.2794)
Comm time (%) = 0.25077 (2.6999)
Outpt time (%) = 0.000460148 (0.00495415)
Other time (%) = 2.62743 (28.2881)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 669 ave 669 max 669 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13650 ave 13650 max 13650 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13650
Ave neighs/atom = 4.55
Neighbor list builds = 1153
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Memory usage per processor = 10.2619 Mbytes
Step Atoms KinEng 1 Volume
25000 3000 223.45694 22.976343 6600
26000 3000 113.473 17.666374 6600
27000 3000 102.76936 12.540567 6600
28000 3000 179.07068 11.501122 6600
29000 3000 289.11251 14.028808 6600
30000 3000 461.92265 17.681677 6600
31000 3000 710.67032 23.209353 6600
32000 3000 991.22981 30.179598 6600
33000 3000 1366.0205 36.321028 6600
34000 3000 1817.0366 45.963988 6600
35000 3000 2329.5052 51.957397 6600
36000 3000 2938.7862 59.654677 6600
37000 3000 3662.828 70.399596 6600
38000 3000 4375.2295 78.906063 6600
39000 3000 5250.4031 92.018452 6600
40000 3000 6032.6969 100.23325 6600
41000 3000 7053.8661 115.73204 6600
42000 3000 8063.1636 122.38643 6600
43000 3000 9181.8348 143.39138 6600
44000 3000 10270.31 149.34715 6600
45000 3000 11434.53 161.47217 6600
46000 3000 12731.277 171.19811 6600
47000 3000 13938.907 170.91903 6600
48000 3000 15244.449 192.6018 6600
49000 3000 16627.76 195.3851 6600
50000 3000 17863.962 213.64088 6600
Loop time of 18.2656 on 1 procs for 25000 steps with 3000 atoms
Pair time (%) = 11.864 (64.9527)
Neigh time (%) = 1.57208 (8.60681)
Comm time (%) = 0.539768 (2.95511)
Outpt time (%) = 0.000703335 (0.0038506)
Other time (%) = 4.28904 (23.4816)
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 755 ave 755 max 755 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13875 ave 13875 max 13875 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13875
Ave neighs/atom = 4.625
Neighbor list builds = 803
Dangerous builds = 0

144
examples/pour/log.pour.18Feb13.linux.4
View File

@ -1,144 +0,0 @@
LAMMPS (18 Feb 2013)
# Pour granular particles into chute container, then induce flow
atom_style sphere
boundary p p fm
newton off
communicate single vel yes
region reg block -10 10 -10 10 -0.5 16 units box
create_box 1 reg
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
2 by 2 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
pair_style gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix zlower all wall/gran 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
Particle insertion: 402 every 3162 steps, 3000 by step 22135
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
#dump id all atom 1000 dump.pour
#dump 1 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 1 pad 5
run 25000
Memory usage per processor = 9.33682 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 6600
1000 402 779.98578 0 6600
2000 402 1424.4252 0 6600
3000 402 1425.0863 12.9927 6600
4000 804 1724.8627 47.36161 6600
5000 804 1599.9516 63.808734 6600
6000 804 1359.1774 63.495338 6600
7000 1206 1532.7896 68.602762 6600
8000 1206 1403.0157 62.695772 6600
9000 1206 1247.1412 52.224384 6600
10000 1608 1386.1699 50.718814 6600
11000 1608 1228.7495 56.267861 6600
12000 1608 1189.1544 43.443594 6600
13000 2010 1317.573 51.491142 6600
14000 2010 1185.3306 43.927099 6600
15000 2010 985.99454 42.308206 6600
16000 2412 1044.9221 43.454386 6600
17000 2412 1039.7494 36.063243 6600
18000 2412 911.55352 38.525857 6600
19000 2814 1013.9593 33.512188 6600
20000 2814 959.68861 39.700347 6600
21000 2814 744.30153 45.796008 6600
22000 2814 518.78148 40.865035 6600
23000 3000 418.32473 34.643341 6600
24000 3000 364.52165 21.06497 6600
25000 3000 216.23449 24.600132 6600
Loop time of 2.82073 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 1.36596 (48.4257)
Neigh time (%) = 0.273009 (9.67867)
Comm time (%) = 0.360224 (12.7706)
Outpt time (%) = 0.000543416 (0.0192651)
Other time (%) = 0.820993 (29.1057)
Nlocal: 750 ave 760 max 738 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 388 ave 390 max 387 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 3566.5 ave 3594 max 3538 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Total # of neighbors = 14266
Ave neighs/atom = 4.75533
Neighbor list builds = 1153
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Memory usage per processor = 10.1159 Mbytes
Step Atoms KinEng 1 Volume
25000 3000 216.23449 24.600132 6600
26000 3000 108.39805 20.034719 6600
27000 3000 103.08805 11.62627 6600
28000 3000 193.88384 11.945176 6600
29000 3000 320.96581 14.507685 6600
30000 3000 490.74134 19.09055 6600
31000 3000 755.89878 24.20335 6600
32000 3000 1093.7602 32.036876 6600
33000 3000 1447.6165 37.970427 6600
34000 3000 1879.1719 41.830611 6600
35000 3000 2350.6451 54.069915 6600
36000 3000 2943.3616 63.590846 6600
37000 3000 3655.4973 69.25479 6600
38000 3000 4351.899 72.183547 6600
39000 3000 5056.2313 81.96612 6600
40000 3000 5833.5917 101.79198 6600
41000 3000 6698.392 107.53934 6600
42000 3000 7602.7265 119.87878 6600
43000 3000 8669.6298 134.41156 6600
44000 3000 9749.5781 144.67 6600
45000 3000 10835.643 160.22694 6600
46000 3000 11992.67 155.62346 6600
47000 3000 13262.167 178.56213 6600
48000 3000 14489.853 198.13017 6600
49000 3000 15940.443 200.18228 6600
50000 3000 17238.955 209.40216 6600
Loop time of 5.38506 on 4 procs for 25000 steps with 3000 atoms
Pair time (%) = 3.04231 (56.4954)
Neigh time (%) = 0.41015 (7.61644)
Comm time (%) = 0.572889 (10.6385)
Outpt time (%) = 0.000714064 (0.0132601)
Other time (%) = 1.359 (25.2364)
Nlocal: 750 ave 755 max 744 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 405.25 ave 416 max 400 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Neighs: 3625.5 ave 3698 max 3577 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 14502
Ave neighs/atom = 4.834
Neighbor list builds = 807
Dangerous builds = 0

97
examples/pour/log.pour.2d.18Feb13.linux.1
View File

@ -1,97 +0,0 @@
LAMMPS (18 Feb 2013)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
boundary f fm p
newton off
communicate single vel yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
1 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
#dump id all atom 250 dump.pour
#dump 1 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 25000
Memory usage per processor = 9.58 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 224 185.87695 0 5000
2000 224 348.08417 0 5000
3000 224 565.2162 0 5000
4000 448 1042.9716 0 5000
5000 448 1542.0614 0 5000
6000 448 1766.5136 41.192729 5000
7000 672 1846.4596 67.352592 5000
8000 672 1814.3429 92.898167 5000
9000 672 1662.3643 111.88767 5000
10000 896 1654.7184 91.390546 5000
11000 896 1532.7703 69.886692 5000
12000 896 1470.9688 66.246593 5000
13000 1000 1471.1825 60.129537 5000
14000 1000 1355.6479 59.801716 5000
15000 1000 1132.1071 52.624027 5000
16000 1000 773.40416 42.626873 5000
17000 1000 461.51805 37.889877 5000
18000 1000 338.7731 28.037959 5000
19000 1000 166.73672 26.940654 5000
20000 1000 45.061374 18.328659 5000
21000 1000 24.350861 10.312694 5000
22000 1000 18.811191 8.8044879 5000
23000 1000 15.483854 5.3046832 5000
24000 1000 11.962946 5.0549062 5000
25000 1000 9.0369801 3.2724609 5000
Loop time of 2.88655 on 1 procs for 25000 steps with 1000 atoms
Pair time (%) = 1.22176 (42.3259)
Neigh time (%) = 0.303655 (10.5196)
Comm time (%) = 0.0110941 (0.384337)
Outpt time (%) = 0.000306368 (0.0106136)
Other time (%) = 1.34974 (46.7595)
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: 2330 ave 2330 max 2330 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2330
Ave neighs/atom = 2.33
Neighbor list builds = 2001
Dangerous builds = 0

97
examples/pour/log.pour.2d.18Feb13.linux.4
View File

@ -1,97 +0,0 @@
LAMMPS (18 Feb 2013)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
boundary f fm p
newton off
communicate single vel yes
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
4 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 1 all nve/sphere
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
fix ins all pour 1000 1 4767548 vol 0.4 10 diam 0.5 1.0 region slab
Particle insertion: 224 every 3000 steps, 1000 by step 12001
fix 3 all enforce2d
compute 1 all erotate/sphere
thermo_style custom step atoms ke c_1 vol
thermo 1000
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes
#dump id all atom 250 dump.pour
#dump 1 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 25000
Memory usage per processor = 9.54554 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 224 185.87695 0 5000
2000 224 348.08417 0 5000
3000 224 565.2162 0 5000
4000 448 1042.9716 0 5000
5000 448 1542.0614 0 5000
6000 448 1766.5136 41.192729 5000
7000 672 1846.4596 67.352592 5000
8000 672 1814.3429 92.898167 5000
9000 672 1662.3643 111.88767 5000
10000 896 1652.8654 91.325153 5000
11000 896 1541.4417 70.862864 5000
12000 896 1474.3165 61.956769 5000
13000 1000 1463.9007 59.436066 5000
14000 1000 1355.973 51.999639 5000
15000 1000 1130.5891 49.13995 5000
16000 1000 787.89487 46.05549 5000
17000 1000 462.83858 40.678165 5000
18000 1000 325.64118 32.743319 5000
19000 1000 155.22607 30.549487 5000
20000 1000 43.494925 22.262581 5000
21000 1000 23.694914 15.061018 5000
22000 1000 20.580126 10.477019 5000
23000 1000 16.06558 7.3034265 5000
24000 1000 12.026429 6.0665971 5000
25000 1000 11.818403 5.4542268 5000
Loop time of 0.908638 on 4 procs for 25000 steps with 1000 atoms
Pair time (%) = 0.304472 (33.5086)
Neigh time (%) = 0.0796848 (8.76969)
Comm time (%) = 0.0719426 (7.91763)
Outpt time (%) = 0.000483155 (0.0531735)
Other time (%) = 0.452056 (49.7509)
Nlocal: 250 ave 252 max 248 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 18 ave 25 max 12 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 604.25 ave 614 max 589 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 2417
Ave neighs/atom = 2.417
Neighbor list builds = 2023
Dangerous builds = 0

106
examples/pour/log.pour.2d.molecule.31Dec13.linux.1
View File

@ -1,106 +0,0 @@
LAMMPS (30 Dec 2013)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
atom_modify map array
boundary f fm p
newton off
communicate single vel yes cutoff 2.5
fix prop all property/atom mol
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
1 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
molecule object molecule.vshape
fix 3 all rigid/small molecule mol object
0 rigid bodies with 0 atoms
2.23607 = max distance from body owner to body atom
# insure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3
Particle insertion: 26 every 3000 steps, 500 by step 57001
fix 4 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 100 tmp.dump
#dump 1 all image 250 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 25000
Memory usage per processor = 8.8613 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 130 208.5324 0.0022531902 5000
2000 130 395.40215 0.0022531902 5000
3000 130 647.2719 0.0022531902 5000
4000 260 1159.1081 0.0026224951 5000
5000 260 1718.8157 0.0026515989 5000
6000 260 2031.535 10.691958 5000
7000 390 2065.2783 21.015337 5000
8000 390 1911.4694 10.935944 5000
9000 390 1884.4332 7.8649255 5000
10000 520 2109.7343 6.3162072 5000
11000 520 2055.0964 9.2024202 5000
12000 520 1737.7978 3.8651428 5000
13000 650 1827.8021 5.4025759 5000
14000 650 1714.9891 5.1408637 5000
15000 650 1460.3591 1.9883146 5000
16000 780 1656.7752 2.6070722 5000
17000 780 1487.906 2.9690473 5000
18000 780 1508.32 2.4036266 5000
19000 910 1508.0974 5.3892045 5000
20000 910 1310.8002 4.8125827 5000
21000 910 1044.281 2.4533982 5000
22000 1040 1188.4887 1.8312293 5000
23000 1040 1405.6437 2.4849983 5000
24000 1040 1287.8333 2.4405773 5000
25000 1170 1190.5047 2.8533518 5000
Loop time of 3.1821 on 1 procs for 25000 steps with 1170 atoms
Pair time (%) = 0.846852 (26.613)
Neigh time (%) = 0.207832 (6.53126)
Comm time (%) = 0.013463 (0.423086)
Outpt time (%) = 0.000284433 (0.00893853)
Other time (%) = 2.11367 (66.4237)
Nlocal: 1170 ave 1170 max 1170 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: 1707 ave 1707 max 1707 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1707
Ave neighs/atom = 1.45897
Neighbor list builds = 1751
Dangerous builds = 0

106
examples/pour/log.pour.2d.molecule.31Dec13.linux.4
View File

@ -1,106 +0,0 @@
LAMMPS (30 Dec 2013)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
atom_modify map array
boundary f fm p
newton off
communicate single vel yes cutoff 2.5
fix prop all property/atom mol
region reg block 0 100 0 50 -0.5 0.5 units box
create_box 1 reg
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
4 by 1 by 1 MPI processor grid
neighbor 0.2 bin
neigh_modify delay 0
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
# are used in this example file to produce a quick simulation and movie.
# More appropriate values for realistic simulations would be
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
timestep 0.001
fix 2 all gravity 1.0 spherical 0.0 -180.0
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
molecule object molecule.vshape
fix 3 all rigid/small molecule mol object
0 rigid bodies with 0 atoms
2.23607 = max distance from body owner to body atom
# insure region size + molecule size does not overlap wall
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3
Particle insertion: 26 every 3000 steps, 500 by step 57001
fix 4 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 100 tmp.dump
#dump 1 all image 250 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 1 pad 5
run 25000
Memory usage per processor = 8.82364 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 130 208.5324 0.0022531902 5000
2000 130 395.40215 0.0022531902 5000
3000 130 647.2719 0.0022531902 5000
4000 260 1159.1081 0.0026224951 5000
5000 260 1718.8157 0.0026515989 5000
6000 260 2031.535 10.691958 5000
7000 390 2065.2783 21.015337 5000
8000 390 1911.4694 10.935944 5000
9000 390 1884.4332 7.8649255 5000
10000 520 2109.7343 6.3162072 5000
11000 520 2055.0964 9.2024202 5000
12000 520 1737.7978 3.8651428 5000
13000 650 1835.9412 5.4696261 5000
14000 650 1705.5968 4.6127934 5000
15000 650 1458.6093 2.3324994 5000
16000 780 1663.1206 3.4762842 5000
17000 780 1448.6268 2.5272414 5000
18000 780 1439.06 2.3644535 5000
19000 910 1353.2736 3.4079237 5000
20000 910 1303.0395 4.7540237 5000
21000 910 1037.3662 2.6725377 5000
22000 1040 1225.3222 2.0920106 5000
23000 1040 1306.8689 2.4710217 5000
24000 1040 1304.5309 2.5544338 5000
25000 1170 1181.4033 4.5232994 5000
Loop time of 1.19572 on 4 procs for 25000 steps with 1170 atoms
Pair time (%) = 0.217633 (18.2011)
Neigh time (%) = 0.0619622 (5.18202)
Comm time (%) = 0.0785548 (6.56969)
Outpt time (%) = 0.000421941 (0.0352878)
Other time (%) = 0.837144 (70.012)
Nlocal: 292.5 ave 312 max 278 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Nghost: 44.5 ave 60 max 28 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 427.5 ave 451 max 399 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 1710
Ave neighs/atom = 1.46154
Neighbor list builds = 1769
Dangerous builds = 0

631
examples/prd/log.prd.0.18Feb13.linux.4
View File

@ -1,631 +0,0 @@
LAMMPS (18 Feb 2013)
Processor partition = 0
# Parallel replica dynamics model for a single vacancy in bulk Si
# events occur when a neighboring atom diffuses to the vacant site
# run this on multiple partitions as
# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
#log none
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.4310000000000000497 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg
Created 512 atoms
mass 1 28.06
group Si type 1
512 atoms in group Si
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511
pair_style sw
pair_coeff * * Si.sw Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
# equilibrate
run 100
Memory usage per processor = 2.0318 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1802.5039 -2211.666 0 -2092.8401 12351.692
10 996.01982 -2158.3093 0 -2092.649 14285.475
20 590.09928 -2131.1531 0 -2092.2521 12113.964
30 1033.01 -2159.2522 0 -2091.1534 6860.4116
40 724.76581 -2137.281 0 -2089.5025 5999.4372
50 489.66604 -2120.8082 0 -2088.5281 6403.4234
60 960.70653 -2150.7394 0 -2087.407 5687.324
70 908.41498 -2145.7665 0 -2085.8813 8220.9655
80 796.82286 -2137.1227 0 -2084.5941 11307.153
90 1245.9045 -2164.9841 0 -2082.8507 11282.071
100 1083.0647 -2152.0805 0 -2080.682 12015.018
Loop time of 0.199255 on 1 procs for 100 steps with 511 atoms
Pair time (%) = 0.19512 (97.9246)
Neigh time (%) = 0.00134087 (0.67294)
Comm time (%) = 0.000883102 (0.443202)
Outpt time (%) = 7.98702e-05 (0.0400844)
Other time (%) = 0.00183153 (0.91919)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13996 ave 13996 max 13996 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13996
Ave neighs/atom = 27.3894
Neighbor list builds = 2
Dangerous builds = 0
# only output atoms near vacancy
compute coord all coord/atom $r
compute coord all coord/atom 2.8349999999999999645
#dump events all custom 1 dump.prd id type x y z
#dump_modify events thresh c_coord != 4
compute patom all pe/atom
compute pe all reduce sum c_patom
compute satom all stress/atom
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp pe c_pe press v_press
compute 1 all event/displace 0.5
prd 2000 100 10 10 100 1 54985 temp $t min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 1.0000000000000000818e-05 ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 1.0000000000000000818e-05 100 ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 1.0000000000000000818e-05 100 100 vel all uniform
WARNING: Resetting reneighboring criteria during PRD (prd.cpp:201)
Memory usage per processor = 3.74842 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1083.0647 -2211.0684 -2211.0684 7372.2593 -7372.2593
119 1083.0647 -2211.6557 -2211.6557 7411.1722 -7411.1722
Loop time of 0.054491 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1453.2509 -2126.4979 -2126.4979 16449.583 -16449.583
120 1640.3958 -2113.5727 -2113.5727 18469.616 -18469.616
130 1765.8167 -2109.1554 -2109.1554 19438.152 -19438.152
140 1727.5983 -2102.4557 -2102.4557 18703.763 -18703.763
150 1873.8652 -2105.5049 -2105.5049 18700.015 -18700.015
160 1740.1521 -2099.9445 -2099.9445 17850.695 -17850.695
170 1854.5372 -2101.9702 -2101.9702 17723.367 -17723.367
180 1788.5252 -2099.7644 -2099.7644 17796.757 -17796.757
190 1782.0313 -2097.2111 -2097.2111 17085.932 -17085.932
200 1761.1774 -2093.3215 -2093.3215 16509.756 -16509.756
Loop time of 0.218751 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
100 1761.1774 -2093.3215 -2093.3215 16509.756 -16509.756
110 1739.6511 -2090.6077 -2090.6077 15948.63 -15948.63
120 1712.9864 -2087.5346 -2087.5346 16028.758 -16028.758
130 1632.023 -2080.8455 -2080.8455 16292.761 -16292.761
140 1733.3057 -2086.0742 -2086.0742 15090.31 -15090.31
150 1739.3938 -2084.9124 -2084.9124 15081.918 -15081.918
160 1656.2093 -2077.9071 -2077.9071 16611.003 -16611.003
170 1734.9792 -2081.5311 -2081.5311 16511.598 -16511.598
180 1867.0258 -2088.5786 -2088.5786 16517.663 -16517.663
190 1859.2979 -2086.5014 -2086.5014 15835.134 -15835.134
200 1868.7353 -2085.7395 -2085.7395 15039.302 -15039.302
Loop time of 0.226467 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
200 1868.7353 -2085.7395 -2085.7395 15039.302 -15039.302
216 1868.7353 -2213.2677 -2213.2677 9444.9178 -9444.9178
Loop time of 0.0422311 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
200 1868.7353 -2083.245 -2083.245 15572.348 -15572.348
210 1881.8867 -2082.857 -2082.857 15333.566 -15333.566
220 1935.757 -2085.3056 -2085.3056 15507.872 -15507.872
230 1912.3683 -2082.841 -2082.841 14338.661 -14338.661
240 1753.2588 -2071.6079 -2071.6079 13605.421 -13605.421
250 1728.2117 -2069.2341 -2069.2341 12820.588 -12820.588
260 1835.1212 -2075.4787 -2075.4787 11970.037 -11970.037
270 1760.8425 -2069.7609 -2069.7609 13431.399 -13431.399
280 1819.1145 -2072.7978 -2072.7978 13843.416 -13843.416
290 1931.6502 -2079.3975 -2079.3975 14257.316 -14257.316
300 1991.315 -2082.6543 -2082.6543 15669.782 -15669.782
Loop time of 0.231256 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
300 1991.315 -2082.6543 -2082.6543 15669.782 -15669.782
318 1991.315 -2213.2946 -2213.2946 10290.671 -10290.671
Loop time of 0.048367 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
300 1991.315 -2082.6543 -2082.6543 15669.782 -15669.782
310 1912.141 -2083.3513 -2083.3513 14100.457 -14100.457
320 1767.1362 -2080.7508 -2080.7508 13738.15 -13738.15
330 1893.2627 -2086.4709 -2086.4709 13308.437 -13308.437
340 1779.3615 -2084.7222 -2084.7222 11290.367 -11290.367
350 1840.5794 -2087.0052 -2087.0052 12245.306 -12245.306
360 1712.927 -2080.8869 -2080.8869 11630.287 -11630.287
370 1795.1829 -2080.1542 -2080.1542 11903.52 -11903.52
380 1828.9719 -2081.6588 -2081.6588 12611.779 -12611.779
390 1860.397 -2085.2626 -2085.2626 11645.979 -11645.979
400 1720.6814 -2079.6644 -2079.6644 10689.828 -10689.828
Loop time of 0.231485 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
300 1720.6814 -2079.6644 -2079.6644 10689.828 -10689.828
310 1717.6388 -2079.0268 -2079.0268 10581.957 -10581.957
320 1789.9235 -2083.2531 -2083.2531 11258.441 -11258.441
330 1764.9794 -2081.0181 -2081.0181 11462.171 -11462.171
340 1726.7798 -2077.8759 -2077.8759 11685.977 -11685.977
350 1794.5158 -2081.6454 -2081.6454 11583.204 -11583.204
360 1808.19 -2081.8003 -2081.8003 12387.732 -12387.732
370 1858.3457 -2084.3825 -2084.3825 13197.68 -13197.68
380 1906.8872 -2086.92 -2086.92 13054.839 -13054.839
390 1848.16 -2082.5114 -2082.5114 13515.286 -13515.286
400 1820.8925 -2080.2663 -2080.2663 13488.79 -13488.79
Loop time of 0.231938 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
400 1820.8925 -2080.2663 -2080.2663 13488.79 -13488.79
417 1820.8925 -2213.2897 -2213.2897 9117.3067 -9117.3067
Loop time of 0.0437009 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
400 1820.8925 -2080.2663 -2080.2663 13488.79 -13488.79
410 1847.8771 -2081.6391 -2081.6391 12838.569 -12838.569
420 1782.8346 -2076.9831 -2076.9831 12294.226 -12294.226
430 1758.055 -2074.9742 -2074.9742 11409.107 -11409.107
440 1849.7159 -2080.6063 -2080.6063 11615.729 -11615.729
450 1869.1231 -2081.506 -2081.506 12455.826 -12455.826
460 1790.313 -2075.9994 -2075.9994 13049.633 -13049.633
470 1815.1995 -2077.3516 -2077.3516 13045.061 -13045.061
480 1880.6611 -2081.396 -2081.396 11970.764 -11970.764
490 1815.7853 -2076.9102 -2076.9102 12251.974 -12251.974
500 1864.8064 -2080.0034 -2080.0034 11181.614 -11181.614
Loop time of 0.233857 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
500 1864.8064 -2080.0034 -2080.0034 11181.614 -11181.614
517 1864.8064 -2213.2124 -2213.2124 9411.2128 -9411.2128
Loop time of 0.0432351 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
500 1864.8064 -2080.0034 -2080.0034 11181.614 -11181.614
510 1834.5308 -2077.9186 -2077.9186 12623.531 -12623.531
520 1821.9414 -2077.0496 -2077.0496 13905.708 -13905.708
530 1926.5524 -2083.9748 -2083.9748 14022.223 -14022.223
540 1900.0475 -2082.3932 -2082.3932 13519.516 -13519.516
550 1844.7474 -2079.0522 -2079.0522 13017.172 -13017.172
560 1851.9925 -2079.9135 -2079.9135 12830.136 -12830.136
570 1817.9413 -2078.1133 -2078.1133 12446.332 -12446.332
580 1765.4615 -2075.1011 -2075.1011 11172.734 -11172.734
590 1841.9645 -2080.5964 -2080.5964 11252.344 -11252.344
600 1832.5281 -2080.4681 -2080.4681 13212.158 -13212.158
Loop time of 0.233282 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
600 1832.5281 -2080.4681 -2080.4681 13212.158 -13212.158
619 1832.5281 -2213.2705 -2213.2705 9195.2704 -9195.2704
Loop time of 0.0451121 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
600 1832.5281 -2080.4681 -2080.4681 13212.158 -13212.158
610 1787.5429 -2078.0256 -2078.0256 13240.463 -13240.463
620 1823.7995 -2080.9486 -2080.9486 12375.051 -12375.051
630 1853.2062 -2083.4589 -2083.4589 12983.625 -12983.625
640 1834.2035 -2082.851 -2082.851 13067.13 -13067.13
650 1789.0195 -2080.5378 -2080.5378 12947.796 -12947.796
660 1805.2876 -2082.2756 -2082.2756 12528.317 -12528.317
670 1839.5253 -2085.2087 -2085.2087 12508.998 -12508.998
680 1819.135 -2084.6004 -2084.6004 12615.631 -12615.631
690 1742.0477 -2080.2199 -2080.2199 12867.541 -12867.541
700 1771.846 -2082.8491 -2082.8491 11627.605 -11627.605
Loop time of 0.232503 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
700 1771.846 -2082.8491 -2082.8491 11627.605 -11627.605
716 1771.846 -2213.2414 -2213.2414 8780.9495 -8780.9495
Loop time of 0.036931 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
700 1771.846 -2088.3939 -2088.3939 12152.346 -12152.346
710 1762.7562 -2088.4048 -2088.4048 11588.828 -11588.828
720 1677.307 -2083.3065 -2083.3065 10323.038 -10323.038
730 1638.8947 -2081.1322 -2081.1322 10662.708 -10662.708
740 1733.4188 -2087.5736 -2087.5736 11190.078 -11190.078
750 1745.235 -2088.4473 -2088.4473 12275.541 -12275.541
760 1799.948 -2092.108 -2092.108 13287.26 -13287.26
770 1805.9054 -2092.5319 -2092.5319 14221.436 -14221.436
780 1802.4038 -2092.3583 -2092.3583 13453.411 -13453.411
790 1728.5017 -2087.5173 -2087.5173 12749.412 -12749.412
800 1695.7727 -2085.3213 -2085.3213 12245.9 -12245.9
Loop time of 0.230922 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
800 1695.7727 -2085.3213 -2085.3213 12245.9 -12245.9
817 1695.7727 -2213.2643 -2213.2643 8256.0666 -8256.0666
Loop time of 0.0461409 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
800 1695.7727 -2085.3213 -2085.3213 12245.9 -12245.9
810 1723.8878 -2077.4775 -2077.4775 14056.576 -14056.576
820 1819.4569 -2078.5591 -2078.5591 14126.224 -14126.224
830 1857.684 -2082.1666 -2082.1666 13988.119 -13988.119
840 1817.2451 -2083.1231 -2083.1231 13507.31 -13507.31
850 1801.7367 -2083.0485 -2083.0485 13398.987 -13398.987
860 1800.2129 -2082.8677 -2082.8677 13538.068 -13538.068
870 1829.4598 -2084.6232 -2084.6232 13353.506 -13353.506
880 1713.8058 -2078.7287 -2078.7287 12668.351 -12668.351
890 1801.1051 -2078.5303 -2078.5303 12620.955 -12620.955
900 1878.837 -2083.4562 -2083.4562 12162.469 -12162.469
Loop time of 0.232426 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
800 1878.837 -2083.4562 -2083.4562 12162.469 -12162.469
810 1875.9494 -2083.067 -2083.067 12404.086 -12404.086
820 1765.2324 -2075.6435 -2075.6435 12708.749 -12708.749
830 1805.1712 -2078.1447 -2078.1447 12187.198 -12187.198
840 1899.9714 -2084.2726 -2084.2726 12555.644 -12555.644
850 1823.6926 -2079.2062 -2079.2062 12933.086 -12933.086
860 1809.2646 -2078.2623 -2078.2623 11742.131 -11742.131
870 1909.7967 -2084.9627 -2084.9627 11229.754 -11229.754
880 1764.4244 -2075.5143 -2075.5143 11457.095 -11457.095
890 1771.6808 -2076.1399 -2076.1399 11453.854 -11453.854
900 1865.5698 -2082.4582 -2082.4582 11659.558 -11659.558
Loop time of 0.234094 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
900 1865.5698 -2082.4582 -2082.4582 11659.558 -11659.558
919 1865.5698 -2213.3124 -2213.3124 9426.4803 -9426.4803
Loop time of 0.049902 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
900 1865.5698 -2081.8053 -2081.8053 13628.128 -13628.128
910 1841.8133 -2080.4515 -2080.4515 13654.3 -13654.3
920 1749.7144 -2074.6188 -2074.6188 12839.204 -12839.204
930 1821.6017 -2079.6013 -2079.6013 12167.782 -12167.782
940 1780.9248 -2077.1578 -2077.1578 12235.554 -12235.554
950 1762.8345 -2076.2012 -2076.2012 11833.919 -11833.919
960 1806.203 -2079.2727 -2079.2727 12022.387 -12022.387
970 1804.2459 -2079.3716 -2079.3716 12365.406 -12365.406
980 1761.8387 -2076.7964 -2076.7964 12458.703 -12458.703
990 1836.2958 -2081.9304 -2081.9304 12598.164 -12598.164
1000 1865.0257 -2084.1008 -2084.1008 13918.459 -13918.459
Loop time of 0.232142 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1000 1865.0257 -2084.1008 -2084.1008 13918.459 -13918.459
1017 1865.0257 -2213.2668 -2213.2668 9416.317 -9416.317
Loop time of 0.044035 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1000 1865.0257 -2084.1008 -2084.1008 13918.459 -13918.459
1010 1761.782 -2083.3408 -2083.3408 12613.089 -12613.089
1020 1770.1696 -2081.6751 -2081.6751 12434.518 -12434.518
1030 1768.5769 -2079.8994 -2079.8994 12854.085 -12854.085
1040 1792.1357 -2079.6761 -2079.6761 12773.174 -12773.174
1050 1806.4749 -2080.3993 -2080.3993 13958.637 -13958.637
1060 1845.1324 -2083.7096 -2083.7096 13427.182 -13427.182
1070 1876.1853 -2089.1565 -2089.1565 12775.944 -12775.944
1080 1765.8044 -2087.3727 -2087.3727 12387.705 -12387.705
1090 1838.2298 -2090.426 -2090.426 12939.571 -12939.571
1100 1704.553 -2084.6714 -2084.6714 12988.172 -12988.172
Loop time of 0.233263 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1000 1704.553 -2084.6714 -2084.6714 12988.172 -12988.172
1010 1772.8609 -2089.6666 -2089.6666 12540.188 -12540.188
1020 1770.1379 -2089.9786 -2089.9786 12184.488 -12184.488
1030 1656.6786 -2082.9255 -2082.9255 12022.316 -12022.316
1040 1702.4827 -2086.2684 -2086.2684 10641.654 -10641.654
1050 1674.8977 -2084.6421 -2084.6421 11257.979 -11257.979
1060 1676.1205 -2084.7766 -2084.7766 12111.764 -12111.764
1070 1778.8497 -2091.4724 -2091.4724 12971.534 -12971.534
1080 1779.3081 -2091.3613 -2091.3613 12566.776 -12566.776
1090 1668.192 -2083.8243 -2083.8243 12813.326 -12813.326
1100 1754.5887 -2089.1711 -2089.1711 13090.818 -13090.818
Loop time of 0.230267 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1100 1754.5887 -2089.1711 -2089.1711 13090.818 -13090.818
1116 1754.5887 -2213.2659 -2213.2659 8660.0106 -8660.0106
Loop time of 0.041208 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1100 1754.5887 -2089.1711 -2089.1711 13090.818 -13090.818
1110 1848.3952 -2094.8662 -2094.8662 12871.151 -12871.151
1120 1738.0586 -2087.0603 -2087.0603 13998.616 -13998.616
1130 1728.3695 -2085.8036 -2085.8036 14319.362 -14319.362
1140 1841.826 -2092.4967 -2092.4967 13691.837 -13691.837
1150 1797.9782 -2088.7251 -2088.7251 13942.683 -13942.683
1160 1783.6033 -2086.8622 -2086.8622 13738.416 -13738.416
1170 1807.3027 -2087.4147 -2087.4147 13420.976 -13420.976
1180 1815.9792 -2086.9303 -2086.9303 12722.057 -12722.057
1190 1739.4179 -2080.8105 -2080.8105 12854.023 -12854.023
1200 1761.8697 -2081.1857 -2081.1857 12092.665 -12092.665
Loop time of 0.227404 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1200 1761.8697 -2081.1857 -2081.1857 12092.665 -12092.665
1218 1761.8697 -2213.3017 -2213.3017 8713.6317 -8713.6317
Loop time of 0.0471811 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1200 1761.8697 -2081.1857 -2081.1857 12092.665 -12092.665
1210 1760.7244 -2079.9528 -2079.9528 12012.593 -12012.593
1220 1752.9287 -2078.2871 -2078.2871 11916.806 -11916.806
1230 1838.3629 -2082.7918 -2082.7918 12841.149 -12841.149
1240 1870.3467 -2083.881 -2083.881 13974.686 -13974.686
1250 1781.4455 -2077.1866 -2077.1866 13743.967 -13743.967
1260 1829.5891 -2079.6638 -2079.6638 12847.61 -12847.61
1270 1859.3421 -2081.0235 -2081.0235 12227.579 -12227.579
1280 1778.2976 -2075.2099 -2075.2099 12092.041 -12092.041
1290 1802.5006 -2076.4007 -2076.4007 12166.805 -12166.805
1300 1858.5552 -2079.7352 -2079.7352 12469.68 -12469.68
Loop time of 0.22974 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1300 1858.5552 -2079.7352 -2079.7352 12469.68 -12469.68
1319 1858.5552 -2213.2905 -2213.2905 9377.5263 -9377.5263
Loop time of 0.0523369 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1300 1858.5552 -2079.7352 -2079.7352 12469.68 -12469.68
1310 1883.892 -2081.1414 -2081.1414 13154.969 -13154.969
1320 1918.1413 -2083.2747 -2083.2747 14133.403 -14133.403
1330 1939.2365 -2084.7147 -2084.7147 14302.027 -14302.027
1340 1866.4525 -2080.1222 -2080.1222 14374.257 -14374.257
1350 1810.4562 -2076.7079 -2076.7079 12997.156 -12997.156
1360 1814.6292 -2077.2746 -2077.2746 11910.098 -11910.098
1370 1755.1167 -2073.6137 -2073.6137 11855.888 -11855.888
1380 1782.5531 -2075.6399 -2075.6399 12156.35 -12156.35
1390 1816.7724 -2078.0849 -2078.0849 12765.305 -12765.305
1400 1837.2515 -2079.6383 -2079.6383 13124.564 -13124.564
Loop time of 0.22733 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1400 1837.2515 -2079.6383 -2079.6383 13124.564 -13124.564
1418 1837.2515 -2213.2909 -2213.2909 9231.4256 -9231.4256
Loop time of 0.045197 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1400 1837.2515 -2083.1407 -2083.1407 12986.943 -12986.943
1410 1822.713 -2082.4248 -2082.4248 14004.789 -14004.789
1420 1832.5229 -2083.3398 -2083.3398 15470.52 -15470.52
1430 1914.5807 -2089.0996 -2089.0996 15354.125 -15354.125
1440 1857.9286 -2085.8454 -2085.8454 13988.104 -13988.104
1450 1754.4226 -2079.5406 -2079.5406 13819.892 -13819.892
1460 1818.444 -2084.2673 -2084.2673 12996.924 -12996.924
1470 1825.4699 -2085.2741 -2085.2741 12289.466 -12289.466
1480 1723.4843 -2079.0743 -2079.0743 12726.17 -12726.17
1490 1818.4232 -2085.8377 -2085.8377 12243.424 -12243.424
1500 1808.3404 -2085.6948 -2085.6948 11928.53 -11928.53
Loop time of 0.229424 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1500 1808.3404 -2085.6948 -2085.6948 11928.53 -11928.53
1519 1808.3404 -2213.302 -2213.302 9037.7704 -9037.7704
Loop time of 0.05199 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1500 1808.3404 -2088.1491 -2088.1491 13315.668 -13315.668
1510 1935.1323 -2097.1896 -2097.1896 13464.858 -13464.858
1520 1678.3356 -2081.0029 -2081.0029 13813.289 -13813.289
1530 1740.6495 -2085.7701 -2085.7701 12852.328 -12852.328
1540 1858.7458 -2094.2425 -2094.2425 11105.92 -11105.92
1550 1599.0288 -2077.7804 -2077.7804 10438.389 -10438.389
1560 1555.965 -2075.3756 -2075.3756 11066.476 -11066.476
1570 1782.1645 -2090.5618 -2090.5618 11513.89 -11513.89
1580 1639.6945 -2081.3242 -2081.3242 13028.031 -13028.031
1590 1706.6709 -2085.7625 -2085.7625 13989.78 -13989.78
1600 2022.0741 -2106.5216 -2106.5216 14373.472 -14373.472
Loop time of 0.228021 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1600 2022.0741 -2106.5216 -2106.5216 14373.472 -14373.472
1617 2022.0741 -2213.2036 -2213.2036 10476.808 -10476.808
Loop time of 0.0426509 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1600 2022.0741 -2106.5216 -2106.5216 14373.472 -14373.472
1610 1709.9018 -2082.1738 -2082.1738 11779.399 -11779.399
1620 1843.2806 -2085.0227 -2085.0227 12079.368 -12079.368
1630 1781.7944 -2083.8272 -2083.8272 11339.308 -11339.308
1640 1858.9199 -2087.7445 -2087.7445 11680.172 -11680.172
1650 1676.4808 -2079.6354 -2079.6354 10807.862 -10807.862
1660 1784.4381 -2078.5909 -2078.5909 10825.528 -10825.528
1670 1797.7974 -2078.4044 -2078.4044 11402.613 -11402.613
1680 1832.5315 -2080.5079 -2080.5079 12031.263 -12031.263
1690 1859.9425 -2084.4511 -2084.4511 12027.239 -12027.239
1700 1746.6608 -2080.9402 -2080.9402 11194.592 -11194.592
Loop time of 0.227506 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1600 1746.6608 -2080.9402 -2080.9402 11194.592 -11194.592
1610 1719.0554 -2079.054 -2079.054 11178.847 -11178.847
1620 1785.874 -2083.3136 -2083.3136 11151.584 -11151.584
1630 1709.212 -2078.0262 -2078.0262 11909.487 -11909.487
1640 1724.909 -2078.7337 -2078.7337 12338.207 -12338.207
1650 1851.0445 -2086.6016 -2086.6016 13182.101 -13182.101
1660 1877.9938 -2087.9289 -2087.9289 13545.96 -13545.96
1670 1859.7098 -2086.3587 -2086.3587 13586.735 -13586.735
1680 1856.0077 -2085.8266 -2085.8266 13326.439 -13326.439
1690 1852.5537 -2085.3781 -2085.3781 12829.132 -12829.132
1700 1781.9012 -2080.5479 -2080.5479 11799.182 -11799.182
Loop time of 0.23015 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1700 1781.9012 -2080.5479 -2080.5479 11799.182 -11799.182
1719 1781.9012 -2213.2828 -2213.2828 8850.0906 -8850.0906
Loop time of 0.0428729 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1700 1781.9012 -2080.5479 -2080.5479 11799.182 -11799.182
1710 1744.9008 -2077.9268 -2077.9268 11732.091 -11732.091
1720 1752.0816 -2078.1361 -2078.1361 11741.531 -11741.531
1730 1828.2888 -2082.842 -2082.842 11720.773 -11720.773
1740 1786.3351 -2079.7361 -2079.7361 12450.459 -12450.459
1750 1778.8339 -2078.8936 -2078.8936 13103.956 -13103.956
1760 1869.5607 -2084.4952 -2084.4952 13328.105 -13328.105
1770 1901.6696 -2086.2777 -2086.2777 13723.6 -13723.6
1780 1863.4556 -2083.5556 -2083.5556 14468.139 -14468.139
1790 1783.3884 -2078.1381 -2078.1381 14221.764 -14221.764
1800 1808.5452 -2079.6622 -2079.6622 12177.545 -12177.545
Loop time of 0.228004 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1800 1808.5452 -2079.6622 -2079.6622 12177.545 -12177.545
1819 1808.5452 -2213.309 -2213.309 9036.9782 -9036.9782
Loop time of 0.0528128 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1800 1808.5452 -2076.1141 -2076.1141 12641.91 -12641.91
1810 1782.0254 -2074.2029 -2074.2029 11987.656 -11987.656
1820 1834.1279 -2077.4569 -2077.4569 11478.352 -11478.352
1830 1791.6785 -2074.4904 -2074.4904 11268.276 -11268.276
1840 1710.0109 -2068.909 -2068.909 10673.193 -10673.193
1850 1793.8245 -2074.1497 -2074.1497 11497.954 -11497.954
1860 1876.3222 -2079.2504 -2079.2504 12338.777 -12338.777
1870 1854.3831 -2077.5204 -2077.5204 13414.981 -13414.981
1880 1873.4141 -2078.5705 -2078.5705 13586.534 -13586.534
1890 1905.1875 -2080.5343 -2080.5343 13730.745 -13730.745
1900 1928.0686 -2082.0735 -2082.0735 13195.816 -13195.816
Loop time of 0.229921 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1900 1928.0686 -2082.0735 -2082.0735 13195.816 -13195.816
1920 1928.0686 -2213.2849 -2213.2849 9852.9888 -9852.9888
Loop time of 0.0549979 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1900 1928.0686 -2082.0735 -2082.0735 13195.816 -13195.816
1910 1792.83 -2084.9923 -2084.9923 14194.264 -14194.264
1920 1848.1085 -2088.3062 -2088.3062 14021.427 -14021.427
1930 1801.6152 -2088.6097 -2088.6097 12402.211 -12402.211
1940 1728.0714 -2084.0635 -2084.0635 12172.687 -12172.687
1950 1873.5978 -2089.1424 -2089.1424 12450.15 -12450.15
1960 1750.3387 -2086.13 -2086.13 11887.665 -11887.665
1970 1810.8301 -2087.1529 -2087.1529 12874.661 -12874.661
1980 1698.2365 -2080.73 -2080.73 12126.298 -12126.298
1990 1825.6087 -2082.7204 -2082.7204 12862.535 -12862.535
2000 1743.674 -2079.3142 -2079.3142 12724.32 -12724.32
Loop time of 0.226812 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1900 1743.674 -2079.3142 -2079.3142 12724.32 -12724.32
1910 1792.7661 -2082.8528 -2082.8528 12367.878 -12367.878
1920 1800.2311 -2083.6545 -2083.6545 11883.087 -11883.087
1930 1804.2647 -2084.2645 -2084.2645 12020.625 -12020.625
1940 1854.7421 -2088.0162 -2088.0162 12265.553 -12265.553
1950 1748.1756 -2081.4807 -2081.4807 12398.959 -12398.959
1960 1715.3022 -2079.7847 -2079.7847 11986.482 -11986.482
1970 1809.2371 -2086.4247 -2086.4247 11679.461 -11679.461
1980 1800.4344 -2086.3399 -2086.3399 12025.457 -12025.457
1990 1697.0311 -2080.0216 -2080.0216 12687.338 -12687.338
2000 1742.3339 -2083.4435 -2083.4435 11879.588 -11879.588
Loop time of 0.226868 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
2000 1742.3339 -2083.4435 -2083.4435 11879.588 -11879.588
2019 1742.3339 -2213.2888 -2213.2888 8577.2768 -8577.2768
Loop time of 0.0516479 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
2000 1742.3339 -2083.4435 -2083.4435 11879.588 -11879.588
2010 1819.1825 -2088.9481 -2088.9481 10969.804 -10969.804
2020 1688.1794 -2080.7333 -2080.7333 12075.819 -12075.819
2030 1742.9277 -2084.7042 -2084.7042 12353.472 -12353.472
2040 1852.3585 -2092.2678 -2092.2678 12215.689 -12215.689
2050 1752.6535 -2086.0967 -2086.0967 12274.557 -12274.557
2060 1678.177 -2081.5424 -2081.5424 12559.192 -12559.192
2070 1796.9922 -2089.6689 -2089.6689 12144.946 -12144.946
2080 1801.5169 -2090.2547 -2090.2547 12446.852 -12446.852
2090 1759.1092 -2087.7653 -2087.7653 12345.933 -12345.933
2100 1761.5053 -2088.2279 -2088.2279 12750.987 -12750.987
Loop time of 0.230455 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
2100 1761.5053 -2088.2279 -2088.2279 12750.987 -12750.987
2117 1761.5053 -2213.3069 -2213.3069 8711.9275 -8711.9275
Loop time of 0.0469959 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
2100 1761.5053 -2081.5748 -2081.5748 11355.026 -11355.026
Loop time of 7.17835 on 1 procs for 17 steps with 511 atoms
PRD stats:
Dephase time (%) = 1.37024 (19.0885)
Dynamics time (%) = 4.60404 (64.1379)
Quench time (%) = 0.929547 (12.9493)
Other time (%) = 0.0735519 (1.02463)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13354 ave 13354 max 13354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13354
Ave neighs/atom = 26.1331
Neighbor list builds = 96
Dangerous builds = 0

631
examples/prd/log.prd.1.18Feb13.linux.4
View File

@ -1,631 +0,0 @@
LAMMPS (18 Feb 2013)
Processor partition = 1
# Parallel replica dynamics model for a single vacancy in bulk Si
# events occur when a neighboring atom diffuses to the vacant site
# run this on multiple partitions as
# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
#log none
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.4310000000000000497 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg
Created 512 atoms
mass 1 28.06
group Si type 1
512 atoms in group Si
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511
pair_style sw
pair_coeff * * Si.sw Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
# equilibrate
run 100
Memory usage per processor = 2.0318 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1802.5039 -2211.666 0 -2092.8401 12351.692
10 996.01982 -2158.3093 0 -2092.649 14285.475
20 590.09928 -2131.1531 0 -2092.2521 12113.964
30 1033.01 -2159.2522 0 -2091.1534 6860.4116
40 724.76581 -2137.281 0 -2089.5025 5999.4372
50 489.66604 -2120.8082 0 -2088.5281 6403.4234
60 960.70653 -2150.7394 0 -2087.407 5687.324
70 908.41498 -2145.7665 0 -2085.8813 8220.9655
80 796.82286 -2137.1227 0 -2084.5941 11307.153
90 1245.9045 -2164.9841 0 -2082.8507 11282.071
100 1083.0647 -2152.0805 0 -2080.682 12015.018
Loop time of 0.194795 on 1 procs for 100 steps with 511 atoms
Pair time (%) = 0.190662 (97.8783)
Neigh time (%) = 0.00133681 (0.686267)
Comm time (%) = 0.000878572 (0.451024)
Outpt time (%) = 7.72476e-05 (0.0396559)
Other time (%) = 0.00184035 (0.944765)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13996 ave 13996 max 13996 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13996
Ave neighs/atom = 27.3894
Neighbor list builds = 2
Dangerous builds = 0
# only output atoms near vacancy
compute coord all coord/atom $r
compute coord all coord/atom 2.8349999999999999645
#dump events all custom 1 dump.prd id type x y z
#dump_modify events thresh c_coord != 4
compute patom all pe/atom
compute pe all reduce sum c_patom
compute satom all stress/atom
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp pe c_pe press v_press
compute 1 all event/displace 0.5
prd 2000 100 10 10 100 1 54985 temp $t min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 1.0000000000000000818e-05 ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 1.0000000000000000818e-05 100 ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 1.0000000000000000818e-05 100 100 vel all uniform
WARNING: Resetting reneighboring criteria during PRD (prd.cpp:201)
Memory usage per processor = 3.74842 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1083.0647 -2211.0684 -2211.0684 7372.2593 -7372.2593
119 1083.0647 -2211.6557 -2211.6557 7411.1722 -7411.1722
Loop time of 0.0537591 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1407.6264 -2123.5255 -2123.5255 16796.664 -16796.664
120 1740.5244 -2117.1258 -2117.1258 18709.166 -18709.166
130 1713.1995 -2109.2989 -2109.2989 18919.818 -18919.818
140 1779.4809 -2106.0183 -2106.0183 18935.633 -18935.633
150 1774.6703 -2102.5814 -2102.5814 18566.259 -18566.259
160 1764.4555 -2098.5966 -2098.5966 18247.113 -18247.113
170 1807.273 -2097.5073 -2097.5073 19262.305 -19262.305
180 1802.9051 -2096.2207 -2096.2207 18967.398 -18967.398
190 1818.8653 -2096.042 -2096.042 18419.673 -18419.673
200 1807.602 -2095.1974 -2095.1974 18165.399 -18165.399
Loop time of 0.21852 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
100 1807.602 -2095.1974 -2095.1974 18165.399 -18165.399
110 1745.3032 -2089.8161 -2089.8161 17154.684 -17154.684
120 1759.657 -2089.5011 -2089.5011 15296.251 -15296.251
130 1716.433 -2085.3645 -2085.3645 14320.132 -14320.132
140 1665.0731 -2080.6773 -2080.6773 13663.224 -13663.224
150 1673.2986 -2079.8264 -2079.8264 13049.78 -13049.78
160 1748.3061 -2083.2698 -2083.2698 13797.007 -13797.007
170 1765.6267 -2082.8476 -2082.8476 15017.251 -15017.251
180 1819.2949 -2084.8604 -2084.8604 15341.074 -15341.074
190 1856.6017 -2085.841 -2085.841 15232.338 -15232.338
200 1837.7362 -2083.245 -2083.245 15359.444 -15359.444
Loop time of 0.228085 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
200 1837.7362 -2083.245 -2083.245 15359.444 -15359.444
222 1837.7362 -2213.2958 -2213.2958 9231.1053 -9231.1053
Loop time of 0.0511508 on 1 procs for 22 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
200 1837.7362 -2083.245 -2083.245 15359.444 -15359.444
210 1840.6293 -2082.2033 -2082.2033 14844.948 -14844.948
220 1876.4513 -2083.4211 -2083.4211 14044.573 -14044.573
230 1830.1329 -2079.331 -2079.331 13271.066 -13271.066
240 1796.9539 -2076.207 -2076.207 13181.701 -13181.701
250 1815.7837 -2076.5264 -2076.5264 13920.64 -13920.64
260 1864.2627 -2078.8288 -2078.8288 14446.65 -14446.65
270 1823.3876 -2075.3079 -2075.3079 14537.612 -14537.612
280 1819.1185 -2074.2612 -2074.2612 14161.795 -14161.795
290 1917.7731 -2080.0422 -2080.0422 14106.458 -14106.458
300 1873.3899 -2076.5024 -2076.5024 15178.622 -15178.622
Loop time of 0.22907 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
300 1873.3899 -2076.5024 -2076.5024 15178.622 -15178.622
320 1873.3899 -2213.3069 -2213.3069 9479.7746 -9479.7746
Loop time of 0.0571311 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
300 1873.3899 -2076.5024 -2076.5024 15178.622 -15178.622
310 1774.8865 -2074.3353 -2074.3353 15109.591 -15109.591
320 1909.8713 -2081.0651 -2081.0651 14297.983 -14297.983
330 1831.1736 -2082.648 -2082.648 13911.946 -13911.946
340 1782.9014 -2081.0633 -2081.0633 12948.277 -12948.277
350 1824.5061 -2082.2008 -2082.2008 12862.649 -12862.649
360 1872.7321 -2086.5367 -2086.5367 12420.995 -12420.995
370 1688.5932 -2078.7564 -2078.7564 11683.93 -11683.93
380 1864.9804 -2082.5641 -2082.5641 11669.845 -11669.845
390 1781.3406 -2080.8891 -2080.8891 11392.404 -11392.404
400 1754.9942 -2077.4471 -2077.4471 11538.936 -11538.936
Loop time of 0.228898 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
300 1754.9942 -2077.4471 -2077.4471 11538.936 -11538.936
310 1849.1709 -2083.1493 -2083.1493 11171.322 -11171.322
320 1830.1419 -2081.4047 -2081.4047 11369.031 -11369.031
330 1763.0288 -2076.5299 -2076.5299 12094.669 -12094.669
340 1878.1833 -2083.6662 -2083.6662 13264.506 -13264.506
350 1917.2697 -2085.8435 -2085.8435 13291.842 -13291.842
360 1795.9824 -2077.5749 -2077.5749 13016.539 -13016.539
370 1837.3619 -2080.0809 -2080.0809 11654.708 -11654.708
380 1885.8321 -2083.0993 -2083.0993 10923.765 -10923.765
390 1745.3951 -2073.7224 -2073.7224 11432.075 -11432.075
400 1739.6563 -2073.1992 -2073.1992 10901.087 -10901.087
Loop time of 0.228805 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
400 1739.6563 -2073.1992 -2073.1992 10901.087 -10901.087
420 1739.6563 -2213.2706 -2213.2706 8556.9364 -8556.9364
Loop time of 0.057143 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
400 1739.6563 -2073.1992 -2073.1992 10901.087 -10901.087
410 1865.528 -2081.2965 -2081.2965 11369.72 -11369.72
420 1817.039 -2077.9231 -2077.9231 12284.358 -12284.358
430 1841.0037 -2079.3779 -2079.3779 12199.662 -12199.662
440 1933.3949 -2085.4168 -2085.4168 12571.997 -12571.997
450 1824.2691 -2078.3022 -2078.3022 12475.107 -12475.107
460 1742.7526 -2073.0352 -2073.0352 13123.36 -13123.36
470 1904.6385 -2083.8117 -2083.8117 12367.287 -12367.287
480 1900.8084 -2083.7693 -2083.7693 11586.764 -11586.764
490 1765.8738 -2075.1817 -2075.1817 11148.626 -11148.626
500 1818.1562 -2078.9363 -2078.9363 11026.721 -11026.721
Loop time of 0.228196 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
500 1818.1562 -2078.9363 -2078.9363 11026.721 -11026.721
520 1818.1562 -2213.3028 -2213.3028 9100.7638 -9100.7638
Loop time of 0.0550539 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
500 1818.1562 -2078.9363 -2078.9363 11026.721 -11026.721
510 1855.4317 -2081.7363 -2081.7363 10646.37 -10646.37
520 1767.2976 -2076.3 -2076.3 11298.884 -11298.884
530 1800.7868 -2078.8762 -2078.8762 10799.285 -10799.285
540 1817.9627 -2080.3797 -2080.3797 10703.952 -10703.952
550 1790.4703 -2078.9532 -2078.9532 11128.572 -11128.572
560 1808.189 -2080.5096 -2080.5096 10652.116 -10652.116
570 1830.4747 -2082.3843 -2082.3843 10627.271 -10627.271
580 1816.8801 -2081.9375 -2081.9375 10664.365 -10664.365
590 1746.6186 -2077.7546 -2077.7546 11742.416 -11742.416
600 1761.9264 -2079.1576 -2079.1576 12420.9 -12420.9
Loop time of 0.229456 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
600 1761.9264 -2079.1576 -2079.1576 12420.9 -12420.9
620 1761.9264 -2213.3164 -2213.3164 8715.1081 -8715.1081
Loop time of 0.050993 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
600 1761.9264 -2079.1576 -2079.1576 12420.9 -12420.9
610 1830.7639 -2084.073 -2084.073 11771.278 -11771.278
620 1769.7037 -2080.4252 -2080.4252 11979.886 -11979.886
630 1822.9172 -2084.3132 -2084.3132 11300.932 -11300.932
640 1824.3493 -2084.8166 -2084.8166 10829.863 -10829.863
650 1733.4412 -2079.2284 -2079.2284 11599.031 -11599.031
660 1789.5315 -2083.281 -2083.281 12317.055 -12317.055
670 1854.9044 -2087.957 -2087.957 12396.242 -12396.242
680 1770.0585 -2082.762 -2082.762 12312.359 -12312.359
690 1791.3498 -2084.5474 -2084.5474 11710.405 -11710.405
700 1879.1336 -2090.7525 -2090.7525 10706.781 -10706.781
Loop time of 0.228524 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
700 1879.1336 -2090.7525 -2090.7525 10706.781 -10706.781
718 1879.1336 -2213.3003 -2213.3003 9517.1887 -9517.1887
Loop time of 0.046026 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
700 1879.1336 -2088.3939 -2088.3939 12889.204 -12889.204
710 1814.1237 -2084.5974 -2084.5974 12285.032 -12285.032
720 1755.5486 -2081.2365 -2081.2365 12206.775 -12206.775
730 1775.9721 -2083.0461 -2083.0461 12733.094 -12733.094
740 1774.9985 -2083.4078 -2083.4078 12653.923 -12653.923
750 1775.7013 -2083.8599 -2083.8599 12379.764 -12379.764
760 1776.7454 -2084.2994 -2084.2994 12627.379 -12627.379
770 1819.9834 -2087.5129 -2087.5129 11631.061 -11631.061
780 1809.3834 -2087.2039 -2087.2039 11047.665 -11047.665
790 1714.0167 -2081.2937 -2081.2937 11340.179 -11340.179
800 1712.7589 -2081.4883 -2081.4883 11330.776 -11330.776
Loop time of 0.228822 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
800 1712.7589 -2081.4883 -2081.4883 11330.776 -11330.776
818 1712.7589 -2213.2955 -2213.2955 8376.1803 -8376.1803
Loop time of 0.0475512 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
800 1712.7589 -2081.4883 -2081.4883 11330.776 -11330.776
810 1792.7684 -2082.4358 -2082.4358 13429.873 -13429.873
820 1739.1918 -2078.6129 -2078.6129 13178.104 -13178.104
830 1864.638 -2083.0747 -2083.0747 12836.897 -12836.897
840 1765.781 -2081.0309 -2081.0309 13384.756 -13384.756
850 1752.7636 -2078.0967 -2078.0967 14021.396 -14021.396
860 1855.6782 -2081.935 -2081.935 13079.266 -13079.266
870 1819.6679 -2083.4249 -2083.4249 12377.61 -12377.61
880 1847.0607 -2086.7402 -2086.7402 13476.796 -13476.796
890 1788.2771 -2086.2175 -2086.2175 12947.672 -12947.672
900 1765.1941 -2084.1493 -2084.1493 12560.819 -12560.819
Loop time of 0.226878 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
800 1765.1941 -2084.1493 -2084.1493 12560.819 -12560.819
810 1817.715 -2087.8364 -2087.8364 11341.557 -11341.557
820 1719.0788 -2081.5392 -2081.5392 10897.597 -10897.597
830 1676.1893 -2078.8268 -2078.8268 11397.802 -11397.802
840 1780.9587 -2085.7277 -2085.7277 10862.292 -10862.292
850 1819.7436 -2088.2381 -2088.2381 11156.469 -11156.469
860 1718.1718 -2081.4821 -2081.4821 12556.104 -12556.104
870 1759.3307 -2084.0658 -2084.0658 13115.925 -13115.925
880 1878.3559 -2091.7336 -2091.7336 12178.258 -12178.258
890 1807.6117 -2086.9376 -2086.9376 11895.674 -11895.674
900 1746.8208 -2082.8174 -2082.8174 11298.18 -11298.18
Loop time of 0.228365 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
900 1746.8208 -2082.8174 -2082.8174 11298.18 -11298.18
920 1746.8208 -2213.2983 -2213.2983 8611.3134 -8611.3134
Loop time of 0.0548692 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
900 1746.8208 -2081.8053 -2081.8053 12812.552 -12812.552
910 1792.6751 -2084.6689 -2084.6689 12725.248 -12725.248
920 1789.7336 -2084.2674 -2084.2674 11813.766 -11813.766
930 1783.4345 -2083.6379 -2083.6379 11831.318 -11831.318
940 1713.795 -2078.7772 -2078.7772 11723.525 -11723.525
950 1711.3789 -2078.256 -2078.256 11640.181 -11640.181
960 1711.9374 -2077.7861 -2077.7861 12079.854 -12079.854
970 1759.9375 -2080.3175 -2080.3175 12605.261 -12605.261
980 1794.9009 -2081.8774 -2081.8774 13293.854 -13293.854
990 1839.5283 -2084.0415 -2084.0415 14232.329 -14232.329
1000 1891.8985 -2086.7244 -2086.7244 13901.493 -13901.493
Loop time of 0.230243 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1000 1891.8985 -2086.7244 -2086.7244 13901.493 -13901.493
1018 1891.8985 -2213.3115 -2213.3115 9611.9555 -9611.9555
Loop time of 0.0496509 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1000 1891.8985 -2086.7244 -2086.7244 13901.493 -13901.493
1010 1807.931 -2085.4113 -2085.4113 13673.347 -13673.347
1020 1848.8179 -2087.9387 -2087.9387 12159.14 -12159.14
1030 1783.9124 -2086.2028 -2086.2028 12085.317 -12085.317
1040 1802.125 -2085.6618 -2085.6618 13060.527 -13060.527
1050 1866.9247 -2089.4183 -2089.4183 12550.017 -12550.017
1060 1727.9726 -2084.048 -2084.048 12894.09 -12894.09
1070 1797.1898 -2083.1976 -2083.1976 13473.224 -13473.224
1080 1798.1026 -2082.3986 -2082.3986 13076.343 -13076.343
1090 1902.6166 -2088.501 -2088.501 13792.144 -13792.144
1100 1698.3979 -2081.1883 -2081.1883 12986.81 -12986.81
Loop time of 0.226919 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1000 1698.3979 -2081.1883 -2081.1883 12986.81 -12986.81
1010 1750.2024 -2083.9278 -2083.9278 12435.817 -12435.817
1020 1790.2529 -2085.7919 -2085.7919 12295.779 -12295.779
1030 1770.1234 -2083.6823 -2083.6823 12925.751 -12925.751
1040 1766.3321 -2082.6385 -2082.6385 13147.877 -13147.877
1050 1791.6431 -2083.5004 -2083.5004 13631.61 -13631.61
1060 1829.9027 -2085.2288 -2085.2288 14240.689 -14240.689
1070 1859.399 -2086.4419 -2086.4419 14082.458 -14082.458
1080 1885.6176 -2087.5558 -2087.5558 14640.987 -14640.987
1090 1886.2609 -2087.1345 -2087.1345 15532.317 -15532.317
1100 1790.9433 -2080.5091 -2080.5091 14768.821 -14768.821
Loop time of 0.227847 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1100 1790.9433 -2080.5091 -2080.5091 14768.821 -14768.821
1118 1790.9433 -2213.2987 -2213.2987 8913.1864 -8913.1864
Loop time of 0.0482619 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1100 1790.9433 -2080.5091 -2080.5091 14768.821 -14768.821
1110 1814.3939 -2081.769 -2081.769 13689.839 -13689.839
1120 1833.7192 -2082.7815 -2082.7815 13519.243 -13519.243
1130 1796.837 -2080.1348 -2080.1348 14072.965 -14072.965
1140 1818.7494 -2081.3921 -2081.3921 13916.101 -13916.101
1150 1818.9994 -2081.2488 -2081.2488 13140.548 -13140.548
1160 1761.0556 -2077.2848 -2077.2848 13308.506 -13308.506
1170 1805.8494 -2080.0847 -2080.0847 13471.127 -13471.127
1180 1865.5836 -2083.8741 -2083.8741 14278.524 -14278.524
1190 1890.5694 -2085.4621 -2085.4621 15255.857 -15255.857
1200 1871.5608 -2084.2639 -2084.2639 15821.347 -15821.347
Loop time of 0.23167 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1200 1871.5608 -2084.2639 -2084.2639 15821.347 -15821.347
1219 1871.5608 -2213.3158 -2213.3158 9468.276 -9468.276
Loop time of 0.0493429 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1200 1871.5608 -2084.2639 -2084.2639 15821.347 -15821.347
1210 1868.7203 -2084.2286 -2084.2286 14757.029 -14757.029
1220 1845.9795 -2082.9747 -2082.9747 13416.768 -13416.768
1230 1721.0072 -2074.9829 -2074.9829 12653.426 -12653.426
1240 1728.2984 -2075.6335 -2075.6335 11904.94 -11904.94
1250 1760.6468 -2077.838 -2077.838 12363.743 -12363.743
1260 1790.6407 -2079.8354 -2079.8354 13772.489 -13772.489
1270 1855.4774 -2084.1181 -2084.1181 14259.348 -14259.348
1280 1909.5179 -2087.7772 -2087.7772 14969.305 -14969.305
1290 1843.272 -2083.6147 -2083.6147 15655.108 -15655.108
1300 1850.0586 -2084.346 -2084.346 15667.554 -15667.554
Loop time of 0.231307 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1300 1850.0586 -2084.346 -2084.346 15667.554 -15667.554
1320 1850.0586 -2213.3195 -2213.3195 9322.6568 -9322.6568
Loop time of 0.052731 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1300 1850.0586 -2084.346 -2084.346 15667.554 -15667.554
1310 1901.2957 -2088.0828 -2088.0828 14348.338 -14348.338
1320 1845.8424 -2084.9061 -2084.9061 13222.237 -13222.237
1330 1703.2439 -2075.9846 -2075.9846 13160.468 -13160.468
1340 1759.3432 -2080.0715 -2080.0715 12678.444 -12678.444
1350 1848.0856 -2086.283 -2086.283 12513.213 -12513.213
1360 1766.9936 -2081.3221 -2081.3221 13413.575 -13413.575
1370 1759.0589 -2081.1569 -2081.1569 14027.4 -14027.4
1380 1854.7078 -2087.8131 -2087.8131 13488.284 -13488.284
1390 1861.4274 -2088.694 -2088.694 13755.794 -13755.794
1400 1786.8881 -2084.3111 -2084.3111 14765.79 -14765.79
Loop time of 0.230063 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1400 1786.8881 -2084.3111 -2084.3111 14765.79 -14765.79
1418 1786.8881 -2213.2846 -2213.2846 8886.069 -8886.069
Loop time of 0.0461609 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1400 1786.8881 -2083.1407 -2083.1407 12641.043 -12641.043
1410 1812.2443 -2085.4259 -2085.4259 13130.596 -13130.596
1420 1781.5601 -2084.1148 -2084.1148 13794.095 -13794.095
1430 1816.6843 -2087.3261 -2087.3261 14262.13 -14262.13
1440 1776.0284 -2085.8037 -2085.8037 13506.678 -13506.678
1450 1747.7998 -2085.4471 -2085.4471 13056.821 -13056.821
1460 1778.5134 -2089.39 -2089.39 13266.78 -13266.78
1470 1840.1712 -2095.8688 -2095.8688 13524.008 -13524.008
1480 1746.1558 -2092.2341 -2092.2341 12369.096 -12369.096
1490 1661.5852 -2088.7904 -2088.7904 11360.287 -11360.287
1500 1655.5694 -2089.9177 -2089.9177 10972.565 -10972.565
Loop time of 0.230808 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1500 1655.5694 -2089.9177 -2089.9177 10972.565 -10972.565
1519 1655.5694 -2213.2819 -2213.2819 7982.3333 -7982.3333
Loop time of 0.0530219 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1500 1655.5694 -2088.1491 -2088.1491 12266.426 -12266.426
1510 1858.3169 -2102.6683 -2102.6683 11486.74 -11486.74
1520 1589.6231 -2085.7524 -2085.7524 12341.834 -12341.834
1530 1569.3501 -2084.7933 -2084.7933 11907.599 -11907.599
1540 1796.1688 -2099.8918 -2099.8918 10462.273 -10462.273
1550 1603.8116 -2087.2233 -2087.2233 11406.623 -11406.623
1560 1542.9429 -2083.0325 -2083.0325 12076.743 -12076.743
1570 1817.7406 -2100.7606 -2100.7606 11813.995 -11813.995
1580 1646.4361 -2088.9642 -2088.9642 13492.322 -13492.322
1590 1632.6599 -2087.4811 -2087.4811 14603.481 -14603.481
1600 2009.4138 -2111.5732 -2111.5732 13852.416 -13852.416
Loop time of 0.229462 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1600 2009.4138 -2111.5732 -2111.5732 13852.416 -13852.416
1619 2009.4138 -2213.2965 -2213.2965 10413.156 -10413.156
Loop time of 0.0547919 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1600 2009.4138 -2111.5732 -2111.5732 13852.416 -13852.416
1610 1697.1733 -2080.6515 -2080.6515 12137.525 -12137.525
1620 1884.5359 -2085.4978 -2085.4978 12301.761 -12301.761
1630 1799.0114 -2084.7875 -2084.7875 13001.402 -13001.402
1640 1822.4374 -2085.6471 -2085.6471 12188.808 -12188.808
1650 1813.8575 -2085.9718 -2085.9718 11877.305 -11877.305
1660 1784.9861 -2084.4001 -2084.4001 12331.077 -12331.077
1670 1847.3065 -2086.9388 -2086.9388 13451.768 -13451.768
1680 1758.4974 -2083.6409 -2083.6409 12744.573 -12744.573
1690 1865.6773 -2087.3989 -2087.3989 13885.825 -13885.825
1700 1807.1864 -2087.345 -2087.345 12271.996 -12271.996
Loop time of 0.225691 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1600 1807.1864 -2087.345 -2087.345 12271.996 -12271.996
1610 1781.1589 -2085.0991 -2085.0991 11779.473 -11779.473
1620 1751.0492 -2082.5729 -2082.5729 12098.338 -12098.338
1630 1750.1596 -2081.9145 -2081.9145 11669.766 -11669.766
1640 1799.536 -2084.5103 -2084.5103 12073.924 -12073.924
1650 1788.3038 -2083.0848 -2083.0848 12401.815 -12401.815
1660 1706.9461 -2077.0226 -2077.0226 11867.225 -11867.225
1670 1769.7603 -2080.398 -2080.398 11782.054 -11782.054
1680 1855.9414 -2085.2452 -2085.2452 11953.771 -11953.771
1690 1794.599 -2080.4156 -2080.4156 12986.207 -12986.207
1700 1796.6882 -2079.8178 -2079.8178 13336.358 -13336.358
Loop time of 0.227775 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1700 1796.6882 -2079.8178 -2079.8178 13336.358 -13336.358
1717 1796.6882 -2213.286 -2213.286 8952.1586 -8952.1586
Loop time of 0.041846 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1700 1796.6882 -2079.8178 -2079.8178 13336.358 -13336.358
1710 1908.9407 -2086.4998 -2086.4998 13426.557 -13426.557
1720 1895.1818 -2084.9898 -2084.9898 14259.836 -14259.836
1730 1821.3737 -2079.6705 -2079.6705 14430.721 -14430.721
1740 1891.4293 -2083.9221 -2083.9221 12809.819 -12809.819
1750 1839.7569 -2080.2332 -2080.2332 12449.372 -12449.372
1760 1742.4817 -2073.6038 -2073.6038 12438.333 -12438.333
1770 1747.721 -2073.6808 -2073.6808 12684.968 -12684.968
1780 1840.5898 -2079.4792 -2079.4792 12821.365 -12821.365
1790 1835.8529 -2078.8524 -2078.8524 12445.058 -12445.058
1800 1839.1137 -2078.7997 -2078.7997 12888.228 -12888.228
Loop time of 0.229002 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1800 1839.1137 -2078.7997 -2078.7997 12888.228 -12888.228
1820 1839.1137 -2213.3043 -2213.3043 9252.8762 -9252.8762
Loop time of 0.05351 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1800 1839.1137 -2076.1141 -2076.1141 12851.856 -12851.856
1810 1847.1948 -2076.4193 -2076.4193 12095.243 -12095.243
1820 1852.6203 -2076.6095 -2076.6095 12588.549 -12588.549
1830 1834.9309 -2075.3368 -2075.3368 12532.297 -12532.297
1840 1781.6431 -2071.7471 -2071.7471 11609.17 -11609.17
1850 1762.9842 -2070.4212 -2070.4212 11879.69 -11879.69
1860 1835.9552 -2075.0851 -2075.0851 12540.983 -12540.983
1870 1921.2641 -2080.5952 -2080.5952 13447.361 -13447.361
1880 1908.7351 -2079.7868 -2079.7868 13484.028 -13484.028
1890 1893.6986 -2078.9917 -2078.9917 13954.252 -13954.252
1900 1883.1217 -2078.6692 -2078.6692 14081.928 -14081.928
Loop time of 0.23346 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1900 1883.1217 -2078.6692 -2078.6692 14081.928 -14081.928
1921 1883.1217 -2213.3197 -2213.3197 9553.4902 -9553.4902
Loop time of 0.058414 on 1 procs for 21 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1900 1883.1217 -2078.6692 -2078.6692 14081.928 -14081.928
1910 1784.5237 -2084.6905 -2084.6905 13389.919 -13389.919
1920 1731.1905 -2080.6963 -2080.6963 12970.939 -12970.939
1930 1850.3131 -2084.6718 -2084.6718 13719.542 -13719.542
1940 1831.2993 -2087.5516 -2087.5516 13434.958 -13434.958
1950 1743.2339 -2084.7246 -2084.7246 14362.929 -14362.929
1960 1853.8244 -2089.3655 -2089.3655 13929.842 -13929.842
1970 1699.1334 -2083.859 -2083.859 13684.756 -13684.756
1980 1812.1618 -2085.8552 -2085.8552 14478.969 -14478.969
1990 1802.7775 -2087.2555 -2087.2555 14695.415 -14695.415
2000 1839.2685 -2091.105 -2091.105 14707.233 -14707.233
Loop time of 0.231524 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1900 1839.2685 -2091.105 -2091.105 14707.233 -14707.233
1910 1758.6133 -2087.016 -2087.016 13616.046 -13616.046
1920 1700.711 -2084.2588 -2084.2588 12824.655 -12824.655
1930 1751.7857 -2088.5085 -2088.5085 12349.562 -12349.562
1940 1754.9537 -2089.478 -2089.478 12280.371 -12280.371
1950 1685.603 -2085.509 -2085.509 13197.034 -13197.034
1960 1713.2304 -2087.7626 -2087.7626 13267.547 -13267.547
1970 1760.9078 -2091.2137 -2091.2137 13458.047 -13458.047
1980 1752.4605 -2090.8824 -2090.8824 14025.525 -14025.525
1990 1783.2844 -2093.0833 -2093.0833 13878.972 -13878.972
2000 1795.4952 -2094.0299 -2094.0299 13749.599 -13749.599
Loop time of 0.230699 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
2000 1795.4952 -2094.0299 -2094.0299 13749.599 -13749.599
2017 1795.4952 -2213.2891 -2213.2891 8939.1137 -8939.1137
Loop time of 0.0422771 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
2000 1795.4952 -2094.0299 -2094.0299 13749.599 -13749.599
2010 1716.471 -2088.9279 -2088.9279 13720.493 -13720.493
2020 1648.4001 -2084.439 -2084.439 13359.443 -13359.443
2030 1677.6114 -2086.2033 -2086.2033 13113.177 -13113.177
2040 1698.0201 -2087.2241 -2087.2241 13276.862 -13276.862
2050 1732.5808 -2089.0495 -2089.0495 13460.966 -13460.966
2060 1779.8938 -2091.6181 -2091.6181 13393.474 -13393.474
2070 1764.0047 -2089.9669 -2089.9669 14040.691 -14040.691
2080 1777.9135 -2090.2448 -2090.2448 14162.157 -14162.157
2090 1772.5816 -2089.2159 -2089.2159 13499.045 -13499.045
2100 1714.5393 -2084.6691 -2084.6691 13396.984 -13396.984
Loop time of 0.232635 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
2100 1714.5393 -2084.6691 -2084.6691 13396.984 -13396.984
2118 1714.5393 -2213.2509 -2213.2509 8384.1471 -8384.1471
Loop time of 0.0486701 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
2100 1714.5393 -2081.5748 -2081.5748 11032.46 -11032.46
Loop time of 7.1784 on 1 procs for 18 steps with 511 atoms
PRD stats:
Dephase time (%) = 1.35843 (18.9238)
Dynamics time (%) = 4.59429 (64.0016)
Quench time (%) = 1.0186 (14.1897)
Other time (%) = 0.0765398 (1.06625)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13354 ave 13354 max 13354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13354
Ave neighs/atom = 26.1331
Neighbor list builds = 95
Dangerous builds = 0

12
examples/prd/log.prd.18Feb13.linux.4
View File

@ -1,12 +0,0 @@
LAMMPS (18 Feb 2013)
Running on 4 partitions of processors
Step CPU Clock Event Correlated Coincident Replica
100 0.000 0 0 0 0 0
200 0.505 400 1 0 4 1
700 2.194 2100 2 0 2 3
900 3.005 2600 3 0 1 3
1400 4.683 4300 4 0 1 2
1500 4.974 4400 5 1 1 2
1800 6.067 5300 6 0 2 3
2100 7.175 6200 7 0 1 3
Loop time of 7.17835 on 4 procs for 2000 steps with 511 atoms

631
examples/prd/log.prd.2.18Feb13.linux.4
View File

@ -1,631 +0,0 @@
LAMMPS (18 Feb 2013)
Processor partition = 2
# Parallel replica dynamics model for a single vacancy in bulk Si
# events occur when a neighboring atom diffuses to the vacant site
# run this on multiple partitions as
# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
#log none
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.4310000000000000497 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg
Created 512 atoms
mass 1 28.06
group Si type 1
512 atoms in group Si
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511
pair_style sw
pair_coeff * * Si.sw Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
# equilibrate
run 100
Memory usage per processor = 2.0318 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1802.5039 -2211.666 0 -2092.8401 12351.692
10 996.01982 -2158.3093 0 -2092.649 14285.475
20 590.09928 -2131.1531 0 -2092.2521 12113.964
30 1033.01 -2159.2522 0 -2091.1534 6860.4116
40 724.76581 -2137.281 0 -2089.5025 5999.4372
50 489.66604 -2120.8082 0 -2088.5281 6403.4234
60 960.70653 -2150.7394 0 -2087.407 5687.324
70 908.41498 -2145.7665 0 -2085.8813 8220.9655
80 796.82286 -2137.1227 0 -2084.5941 11307.153
90 1245.9045 -2164.9841 0 -2082.8507 11282.071
100 1083.0647 -2152.0805 0 -2080.682 12015.018
Loop time of 0.200207 on 1 procs for 100 steps with 511 atoms
Pair time (%) = 0.196045 (97.9214)
Neigh time (%) = 0.00137591 (0.687246)
Comm time (%) = 0.000874281 (0.436689)
Outpt time (%) = 6.96182e-05 (0.0347731)
Other time (%) = 0.00184178 (0.91994)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13996 ave 13996 max 13996 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13996
Ave neighs/atom = 27.3894
Neighbor list builds = 2
Dangerous builds = 0
# only output atoms near vacancy
compute coord all coord/atom $r
compute coord all coord/atom 2.8349999999999999645
#dump events all custom 1 dump.prd id type x y z
#dump_modify events thresh c_coord != 4
compute patom all pe/atom
compute pe all reduce sum c_patom
compute satom all stress/atom
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp pe c_pe press v_press
compute 1 all event/displace 0.5
prd 2000 100 10 10 100 1 54985 temp $t min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 1.0000000000000000818e-05 ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 1.0000000000000000818e-05 100 ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 1.0000000000000000818e-05 100 100 vel all uniform
WARNING: Resetting reneighboring criteria during PRD (prd.cpp:201)
Memory usage per processor = 3.74842 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1083.0647 -2211.0684 -2211.0684 7372.2593 -7372.2593
119 1083.0647 -2211.6557 -2211.6557 7411.1722 -7411.1722
Loop time of 0.0556271 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1453.0014 -2126.4815 -2126.4815 17039.938 -17039.938
120 1712.5747 -2118.2811 -2118.2811 19245.699 -19245.699
130 1816.1055 -2117.2078 -2117.2078 19172.109 -19172.109
140 1741.5479 -2111.5113 -2111.5113 18643.317 -18643.317
150 1779.1262 -2108.4242 -2108.4242 18055.809 -18055.809
160 1708.5416 -2100.8014 -2100.8014 18706.608 -18706.608
170 1810.3199 -2099.9306 -2099.9306 18691.592 -18691.592
180 1805.675 -2098.8187 -2098.8187 17517.611 -17517.611
190 1827.5401 -2099.2194 -2099.2194 17130.547 -17130.547
200 1726.2196 -2093.025 -2093.025 16774.098 -16774.098
Loop time of 0.218774 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
100 1726.2196 -2093.025 -2093.025 16774.098 -16774.098
110 1740.3774 -2092.6139 -2092.6139 15523.606 -15523.606
120 1781.5972 -2093.9535 -2093.9535 14428.677 -14428.677
130 1684.5193 -2086.1781 -2086.1781 14825.487 -14825.487
140 1613.5723 -2080.1384 -2080.1384 14868.993 -14868.993
150 1755.5164 -2087.9807 -2087.9807 13748.119 -13748.119
160 1738.7712 -2085.2666 -2085.2666 14802.112 -14802.112
170 1674.8255 -2079.507 -2079.507 15674.35 -15674.35
180 1760.9622 -2083.599 -2083.599 15769.066 -15769.066
190 1899.9806 -2091.1229 -2091.1229 16231.019 -16231.019
200 1814.7529 -2083.9976 -2083.9976 17122.298 -17122.298
Loop time of 0.228664 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
200 1814.7529 -2083.9976 -2083.9976 17122.298 -17122.298
217 1814.7529 -2213.2613 -2213.2613 9069.1206 -9069.1206
Loop time of 0.0372241 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
200 1814.7529 -2083.245 -2083.245 15201.593 -15201.593
210 1801.6419 -2081.0472 -2081.0472 15342.659 -15342.659
220 1881.8236 -2085.0669 -2085.0669 14755.087 -14755.087
230 1866.0873 -2082.8539 -2082.8539 13894.752 -13894.752
240 1792.3297 -2076.96 -2076.96 13354.538 -13354.538
250 1787.3004 -2075.652 -2075.652 13316.541 -13316.541
260 1830.871 -2077.5427 -2077.5427 12617.353 -12617.353
270 1791.7089 -2074.006 -2074.006 13195.786 -13195.786
280 1849.0237 -2076.8667 -2076.8667 13418.75 -13418.75
290 1929.6949 -2081.3067 -2081.3067 14728.325 -14728.325
300 1879.9418 -2077.2916 -2077.2916 16541.913 -16541.913
Loop time of 0.22818 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
300 1879.9418 -2077.2916 -2077.2916 16541.913 -16541.913
317 1879.9418 -2213.2283 -2213.2283 9516.969 -9516.969
Loop time of 0.044373 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
300 1879.9418 -2077.2916 -2077.2916 16541.913 -16541.913
310 1838.8029 -2078.0409 -2078.0409 14753.009 -14753.009
320 1789.8725 -2076.7713 -2076.7713 15560.98 -15560.98
330 1950.1614 -2086.0999 -2086.0999 13361.512 -13361.512
340 1759.3354 -2082.9137 -2082.9137 12750.26 -12750.26
350 1857.8525 -2086.2264 -2086.2264 13541.869 -13541.869
360 1873.6249 -2090.6161 -2090.6161 12790.402 -12790.402
370 1704.2028 -2083.8532 -2083.8532 12022.063 -12022.063
380 1824.0288 -2084.9296 -2084.9296 13078.149 -13078.149
390 1823.8695 -2086.0185 -2086.0185 12394.039 -12394.039
400 1826.7938 -2087.3212 -2087.3212 11456.443 -11456.443
Loop time of 0.228451 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
300 1826.7938 -2087.3212 -2087.3212 11456.443 -11456.443
310 1790.3054 -2084.4713 -2084.4713 11190.448 -11190.448
320 1732.854 -2080.2375 -2080.2375 11020.269 -11020.269
330 1679.9775 -2076.2292 -2076.2292 10476.6 -10476.6
340 1706.236 -2077.3108 -2077.3108 10973.286 -10973.286
350 1798.7321 -2082.6213 -2082.6213 12099.734 -12099.734
360 1827.8354 -2083.7164 -2083.7164 12269.553 -12269.553
370 1803.5781 -2081.3205 -2081.3205 11882.622 -11882.622
380 1831.5584 -2082.4022 -2082.4022 11868.591 -11868.591
390 1865.1115 -2083.8776 -2083.8776 12451.163 -12451.163
400 1885.8707 -2084.5972 -2084.5972 12777.133 -12777.133
Loop time of 0.22865 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
400 1885.8707 -2084.5972 -2084.5972 12777.133 -12777.133
421 1885.8707 -2213.3072 -2213.3072 9565.3643 -9565.3643
Loop time of 0.058778 on 1 procs for 21 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
400 1885.8707 -2084.5972 -2084.5972 12777.133 -12777.133
410 1840.8997 -2081.0851 -2081.0851 13049.359 -13049.359
420 1860.5306 -2081.9195 -2081.9195 12866.668 -12866.668
430 1842.0725 -2080.3072 -2080.3072 11967.296 -11967.296
440 1778.5284 -2075.7716 -2075.7716 11672.911 -11672.911
450 1792.767 -2076.3662 -2076.3662 11362.562 -11362.562
460 1812.368 -2077.2861 -2077.2861 11982.449 -11982.449
470 1805.4534 -2076.4744 -2076.4744 11355.668 -11355.668
480 1771.7109 -2073.8789 -2073.8789 11574.724 -11574.724
490 1895.5684 -2081.6811 -2081.6811 10875.512 -10875.512
500 1863.4356 -2079.2626 -2079.2626 12022.062 -12022.062
Loop time of 0.228616 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
500 1863.4356 -2079.2626 -2079.2626 12022.062 -12022.062
519 1863.4356 -2213.2964 -2213.2964 9413.3063 -9413.3063
Loop time of 0.051645 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
500 1863.4356 -2079.2626 -2079.2626 12022.062 -12022.062
510 1811.0452 -2075.5953 -2075.5953 12654.915 -12654.915
520 1939.3016 -2083.9091 -2083.9091 12699.136 -12699.136
530 1865.6263 -2079.0274 -2079.0274 13205.704 -13205.704
540 1840.8195 -2077.4842 -2077.4842 13607.888 -13607.888
550 1910.185 -2082.2276 -2082.2276 13164.337 -13164.337
560 1897.5018 -2081.7046 -2081.7046 12541.871 -12541.871
570 1805.2364 -2076.0408 -2076.0408 12518.288 -12518.288
580 1820.8895 -2077.5197 -2077.5197 12510.55 -12510.55
590 1880.7209 -2081.9748 -2081.9748 11279.988 -11279.988
600 1774.2632 -2075.5235 -2075.5235 10905.347 -10905.347
Loop time of 0.229592 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
600 1774.2632 -2075.5235 -2075.5235 10905.347 -10905.347
621 1774.2632 -2213.3211 -2213.3211 8802.4378 -8802.4378
Loop time of 0.0593848 on 1 procs for 21 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
600 1774.2632 -2075.5235 -2075.5235 10905.347 -10905.347
610 1776.4519 -2076.2072 -2076.2072 11432.057 -11432.057
620 1866.4889 -2082.7151 -2082.7151 11939.587 -11939.587
630 1757.9348 -2076.135 -2076.135 12794.432 -12794.432
640 1821.0434 -2080.8738 -2080.8738 12398.818 -12398.818
650 1878.4228 -2085.2725 -2085.2725 13017.551 -13017.551
660 1874.4782 -2085.7432 -2085.7432 13297.304 -13297.304
670 1796.8744 -2081.4171 -2081.4171 12112.746 -12112.746
680 1789.2824 -2081.7003 -2081.7003 11627.391 -11627.391
690 1769.7646 -2081.1645 -2081.1645 12468.2 -12468.2
700 1781.4831 -2082.6368 -2082.6368 12878.838 -12878.838
Loop time of 0.227894 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
700 1781.4831 -2082.6368 -2082.6368 12878.838 -12878.838
720 1781.4831 -2213.249 -2213.249 8849.8358 -8849.8358
Loop time of 0.0444601 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
700 1781.4831 -2088.3939 -2088.3939 12218.534 -12218.534
710 1724.4898 -2085.2684 -2085.2684 11903.569 -11903.569
720 1764.7152 -2088.4829 -2088.4829 11526.3 -11526.3
730 1724.9813 -2086.3524 -2086.3524 12129.067 -12129.067
740 1711.2186 -2085.8354 -2085.8354 12875.329 -12875.329
750 1774.7765 -2090.326 -2090.326 12385.579 -12385.579
760 1787.964 -2091.4692 -2091.4692 11889.535 -11889.535
770 1711.6992 -2086.6713 -2086.6713 12283.555 -12283.555
780 1717.7443 -2087.2139 -2087.2139 11537.044 -11537.044
790 1683.3367 -2084.9743 -2084.9743 10800.126 -10800.126
800 1631.6415 -2081.4408 -2081.4408 10616.296 -10616.296
Loop time of 0.228734 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
800 1631.6415 -2081.4408 -2081.4408 10616.296 -10616.296
819 1631.6415 -2213.3087 -2213.3087 7818.8075 -7818.8075
Loop time of 0.048811 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
800 1631.6415 -2081.4408 -2081.4408 10616.296 -10616.296
810 1790.007 -2081.8313 -2081.8313 13202.119 -13202.119
820 1849.219 -2084.8387 -2084.8387 12576.218 -12576.218
830 1792.8687 -2084.1604 -2084.1604 11392.768 -11392.768
840 1731.9467 -2079.4445 -2079.4445 12892.679 -12892.679
850 1785.6213 -2078.2286 -2078.2286 13776.917 -13776.917
860 1831.1149 -2080.0094 -2080.0094 12904.24 -12904.24
870 1819.41 -2081.0253 -2081.0253 12547.946 -12547.946
880 1758.8325 -2078.0286 -2078.0286 12618.106 -12618.106
890 1763.5444 -2075.2871 -2075.2871 13398.793 -13398.793
900 1808.5838 -2075.4917 -2075.4917 13281.327 -13281.327
Loop time of 0.228458 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
800 1808.5838 -2075.4917 -2075.4917 13281.327 -13281.327
810 1851.8312 -2077.9782 -2077.9782 12015.32 -12015.32
820 1808.4808 -2074.7871 -2074.7871 11857.883 -11857.883
830 1828.2295 -2075.7871 -2075.7871 11715.86 -11715.86
840 1836.1989 -2076.03 -2076.03 12095.951 -12095.951
850 1806.7992 -2073.8356 -2073.8356 12485.462 -12485.462
860 1889.8731 -2079.0926 -2079.0926 12485.696 -12485.696
870 1879.6457 -2078.2828 -2078.2828 13039.623 -13039.623
880 1832.0939 -2075.1105 -2075.1105 12938.4 -12938.4
890 1875.4331 -2078.0004 -2078.0004 12216.702 -12216.702
900 1914.4276 -2080.7098 -2080.7098 12144.748 -12144.748
Loop time of 0.230588 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
900 1914.4276 -2080.7098 -2080.7098 12144.748 -12144.748
919 1914.4276 -2213.3188 -2213.3188 9764.087 -9764.087
Loop time of 0.0494659 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
900 1914.4276 -2081.8053 -2081.8053 13963.686 -13963.686
910 1810.633 -2075.2099 -2075.2099 14043.827 -14043.827
920 1839.0572 -2077.3907 -2077.3907 13195.428 -13195.428
930 1875.3856 -2080.1678 -2080.1678 12550.917 -12550.917
940 1774.6978 -2073.9954 -2073.9954 12878.164 -12878.164
950 1739.4586 -2072.1025 -2072.1025 12381.741 -12381.741
960 1860.7393 -2080.5553 -2080.5553 11340.855 -11340.855
970 1675.5209 -2068.7733 -2068.7733 12264.795 -12264.795
980 1794.0159 -2076.9546 -2076.9546 12079.272 -12079.272
990 1965.1199 -2088.653 -2088.653 12866.959 -12866.959
1000 1860.4796 -2082.3648 -2082.3648 14940.447 -14940.447
Loop time of 0.230387 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1000 1860.4796 -2082.3648 -2082.3648 14940.447 -14940.447
1016 1860.4796 -2213.2478 -2213.2478 9385.9786 -9385.9786
Loop time of 0.04182 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1000 1860.4796 -2082.3648 -2082.3648 14940.447 -14940.447
1010 1725.5676 -2081.2141 -2081.2141 12659.195 -12659.195
1020 1776.6517 -2080.2782 -2080.2782 14283.292 -14283.292
1030 1892.8575 -2087.068 -2087.068 14207.132 -14207.132
1040 1779.8487 -2086.4423 -2086.4423 13177.279 -13177.279
1050 1827.1799 -2088.9648 -2088.9648 12860.512 -12860.512
1060 1788.3529 -2088.9653 -2088.9653 12121.719 -12121.719
1070 1710.9667 -2083.8206 -2083.8206 12445.746 -12445.746
1080 1828.553 -2086.433 -2086.433 12715.209 -12715.209
1090 1823.9802 -2088.7607 -2088.7607 12059.344 -12059.344
1100 1792.7229 -2089.0486 -2089.0486 11500.622 -11500.622
Loop time of 0.225763 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1000 1792.7229 -2089.0486 -2089.0486 11500.622 -11500.622
1010 1699.0134 -2083.5757 -2083.5757 11300.601 -11300.601
1020 1628.0232 -2079.447 -2079.447 11165.976 -11165.976
1030 1649.3552 -2081.1852 -2081.1852 11327.923 -11327.923
1040 1780.5559 -2090.032 -2090.032 11432.453 -11432.453
1050 1757.6796 -2088.6549 -2088.6549 11052.281 -11052.281
1060 1707.3484 -2085.4178 -2085.4178 11557.124 -11557.124
1070 1740.6914 -2087.5927 -2087.5927 12294.274 -12294.274
1080 1770.6598 -2089.4669 -2089.4669 12907.34 -12907.34
1090 1742.39 -2087.4355 -2087.4355 13144.749 -13144.749
1100 1806.4889 -2091.4432 -2091.4432 12589.891 -12589.891
Loop time of 0.229148 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1100 1806.4889 -2091.4432 -2091.4432 12589.891 -12589.891
1116 1806.4889 -2213.2741 -2213.2741 9022.1362 -9022.1362
Loop time of 0.042588 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1100 1806.4889 -2091.4432 -2091.4432 12589.891 -12589.891
1110 1759.3742 -2088.0631 -2088.0631 12373.16 -12373.16
1120 1741.0508 -2086.5288 -2086.5288 11902.565 -11902.565
1130 1752.2435 -2086.8177 -2086.8177 11844.496 -11844.496
1140 1786.7182 -2088.5202 -2088.5202 11401.503 -11401.503
1150 1760.1379 -2086.0667 -2086.0667 11634.293 -11634.293
1160 1737.621 -2083.7432 -2083.7432 12261.472 -12261.472
1170 1706.1721 -2080.6152 -2080.6152 11900.384 -11900.384
1180 1692.9524 -2078.4392 -2078.4392 11857.894 -11857.894
1190 1845.4734 -2086.9009 -2086.9009 12368.868 -12368.868
1200 1931.9798 -2090.8563 -2090.8563 13231.297 -13231.297
Loop time of 0.227931 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1200 1931.9798 -2090.8563 -2090.8563 13231.297 -13231.297
1217 1931.9798 -2213.2743 -2213.2743 9876.9115 -9876.9115
Loop time of 0.0442169 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1200 1931.9798 -2090.8563 -2090.8563 13231.297 -13231.297
1210 1844.6662 -2083.5459 -2083.5459 13676.012 -13676.012
1220 1823.5246 -2080.8506 -2080.8506 13754.811 -13754.811
1230 1855.1817 -2081.8069 -2081.8069 13072.56 -13072.56
1240 1817.3161 -2078.3873 -2078.3873 13440.344 -13440.344
1250 1846.7917 -2079.601 -2079.601 13176.331 -13176.331
1260 1879.5517 -2081.1956 -2081.1956 12521.935 -12521.935
1270 1856.8093 -2079.3203 -2079.3203 12606.391 -12606.391
1280 1802.8957 -2075.5089 -2075.5089 13433.639 -13433.639
1290 1858.5815 -2079.0007 -2079.0007 11938.06 -11938.06
1300 1855.8203 -2078.7061 -2078.7061 11790.601 -11790.601
Loop time of 0.230682 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1300 1855.8203 -2078.7061 -2078.7061 11790.601 -11790.601
1320 1855.8203 -2213.31 -2213.31 9361.0005 -9361.0005
Loop time of 0.0519319 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1300 1855.8203 -2078.7061 -2078.7061 11790.601 -11790.601
1310 1874.9965 -2079.9692 -2079.9692 11644.669 -11644.669
1320 1769.8025 -2073.0867 -2073.0867 11913.24 -11913.24
1330 1767.7322 -2072.9816 -2072.9816 11519.778 -11519.778
1340 1877.3892 -2080.2309 -2080.2309 11401.149 -11401.149
1350 1832.5468 -2077.3496 -2077.3496 11388.096 -11388.096
1360 1824.2863 -2076.9333 -2076.9333 13175.108 -13175.108
1370 1878.976 -2080.7152 -2080.7152 13742.012 -13742.012
1380 1853.0704 -2079.2587 -2079.2587 13419.479 -13419.479
1390 1879.4579 -2081.3358 -2081.3358 13342.696 -13342.696
1400 1900.1245 -2083.1407 -2083.1407 13418.759 -13418.759
Loop time of 0.228864 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1400 1900.1245 -2083.1407 -2083.1407 13418.759 -13418.759
1418 1900.1245 -2213.3012 -2213.3012 9665.7068 -9665.7068
Loop time of 0.0449259 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1400 1900.1245 -2083.1407 -2083.1407 13418.759 -13418.759
1410 1901.6666 -2083.8299 -2083.8299 13518.235 -13518.235
1420 1818.6697 -2079.0462 -2079.0462 13733.805 -13733.805
1430 1760.3629 -2075.8907 -2075.8907 13140.244 -13140.244
1440 1797.4632 -2078.982 -2078.982 11102.802 -11102.802
1450 1787.354 -2078.9476 -2078.9476 11338.448 -11338.448
1460 1762.8326 -2077.925 -2077.925 11770.958 -11770.958
1470 1798.49 -2080.8371 -2080.8371 11559.353 -11559.353
1480 1811.1557 -2082.2118 -2082.2118 13113.303 -13113.303
1490 1874.659 -2086.985 -2086.985 13079.855 -13079.855
1500 1882.075 -2088.1491 -2088.1491 13822.082 -13822.082
Loop time of 0.230282 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1500 1882.075 -2088.1491 -2088.1491 13822.082 -13822.082
1519 1882.075 -2213.3023 -2213.3023 9541.1899 -9541.1899
Loop time of 0.0428538 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1500 1882.075 -2088.1491 -2088.1491 13822.082 -13822.082
1510 1847.5745 -2086.6473 -2086.6473 13865.395 -13865.395
1520 1776.4045 -2082.7466 -2082.7466 12604.819 -12604.819
1530 1744.8455 -2081.3864 -2081.3864 11823.185 -11823.185
1540 1769.32 -2083.6389 -2083.6389 10753.254 -10753.254
1550 1767.1256 -2084.0617 -2084.0617 10187.637 -10187.637
1560 1736.4738 -2082.5362 -2082.5362 11049.891 -11049.891
1570 1700.4926 -2080.5399 -2080.5399 12042.247 -12042.247
1580 1696.0678 -2080.4908 -2080.4908 11552.055 -11552.055
1590 1720.0071 -2082.1654 -2082.1654 11110.307 -11110.307
1600 1810.361 -2088.1464 -2088.1464 11402.751 -11402.751
Loop time of 0.229181 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1600 1810.361 -2088.1464 -2088.1464 11402.751 -11402.751
1617 1810.361 -2213.2909 -2213.2909 9047.1326 -9047.1326
Loop time of 0.0454371 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1600 1810.361 -2088.1464 -2088.1464 11402.751 -11402.751
1610 1738.2296 -2084.0656 -2084.0656 11367.025 -11367.025
1620 1732.2548 -2079.551 -2079.551 11352.482 -11352.482
1630 1823.6067 -2081.0447 -2081.0447 11759.019 -11759.019
1640 1747.0418 -2077.4773 -2077.4773 11967.929 -11967.929
1650 1811.7099 -2078.1627 -2078.1627 11353.138 -11353.138
1660 1706.9977 -2071.9188 -2071.9188 10638.169 -10638.169
1670 1829.7223 -2073.7338 -2073.7338 11869.478 -11869.478
1680 1811.4357 -2074.3495 -2074.3495 12307.737 -12307.737
1690 1714.1408 -2068.5122 -2068.5122 13422.716 -13422.716
1700 1889.8094 -2074.2435 -2074.2435 13671.805 -13671.805
Loop time of 0.226494 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1600 1889.8094 -2074.2435 -2074.2435 13671.805 -13671.805
1610 1960.8575 -2078.866 -2078.866 12934.864 -12934.864
1620 1923.6166 -2076.54 -2076.54 14112.707 -14112.707
1630 1944.7555 -2078.2457 -2078.2457 13865.325 -13865.325
1640 1902.2989 -2075.9002 -2075.9002 13297.512 -13297.512
1650 1849.5907 -2072.9273 -2072.9273 13933.385 -13933.385
1660 1926.326 -2078.5135 -2078.5135 13981.854 -13981.854
1670 1920.9614 -2078.7358 -2078.7358 13767.146 -13767.146
1680 1850.6527 -2074.6766 -2074.6766 13812.372 -13812.372
1690 1863.9535 -2076.0517 -2076.0517 12782.004 -12782.004
1700 1893.9231 -2078.4898 -2078.4898 12720.592 -12720.592
Loop time of 0.228946 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1700 1893.9231 -2078.4898 -2078.4898 12720.592 -12720.592
1716 1893.9231 -2213.2837 -2213.2837 9620.0072 -9620.0072
Loop time of 0.0387161 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1700 1893.9231 -2078.4898 -2078.4898 12720.592 -12720.592
1710 1875.7299 -2077.7377 -2077.7377 13345.116 -13345.116
1720 1898.0515 -2079.6613 -2079.6613 14132.452 -14132.452
1730 1882.8777 -2079.146 -2079.146 13699.059 -13699.059
1740 1816.9287 -2075.2717 -2075.2717 13073.965 -13073.965
1750 1862.4091 -2078.7296 -2078.7296 12789.163 -12789.163
1760 1893.0397 -2081.2522 -2081.2522 13312.699 -13312.699
1770 1834.7444 -2077.9575 -2077.9575 14033.233 -14033.233
1780 1864.6391 -2080.5104 -2080.5104 13228.094 -13228.094
1790 1854.6185 -2080.4852 -2080.4852 12156.34 -12156.34
1800 1783.2906 -2076.4283 -2076.4283 12334.453 -12334.453
Loop time of 0.228757 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1800 1783.2906 -2076.4283 -2076.4283 12334.453 -12334.453
1817 1783.2906 -2213.2924 -2213.2924 8858.239 -8858.239
Loop time of 0.0428009 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1800 1783.2906 -2076.1141 -2076.1141 12468.46 -12468.46
1810 1845.4581 -2080.8627 -2080.8627 12506.58 -12506.58
1820 1801.3296 -2078.6098 -2078.6098 13055.572 -13055.572
1830 1777.9523 -2077.7188 -2077.7188 12729.867 -12729.867
1840 1758.541 -2077.0154 -2077.0154 12518.443 -12518.443
1850 1828.6136 -2082.1861 -2082.1861 11837.329 -11837.329
1860 1826.6839 -2082.6205 -2082.6205 12848.747 -12848.747
1870 1848.9771 -2084.6985 -2084.6985 14273.245 -14273.245
1880 1859.0854 -2086.037 -2086.037 13956.23 -13956.23
1890 1826.3509 -2084.6002 -2084.6002 13737.356 -13737.356
1900 1856.0966 -2087.3351 -2087.3351 13759.117 -13759.117
Loop time of 0.228033 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1900 1856.0966 -2087.3351 -2087.3351 13759.117 -13759.117
1921 1856.0966 -2213.3256 -2213.3256 9364.6843 -9364.6843
Loop time of 0.0563731 on 1 procs for 21 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1900 1856.0966 -2087.3351 -2087.3351 13759.117 -13759.117
1910 1732.1651 -2081.2025 -2081.2025 13648.771 -13648.771
1920 1791.3554 -2081.3056 -2081.3056 13652.014 -13652.014
1930 1824.4855 -2083.5698 -2083.5698 13761.469 -13761.469
1940 1789.0389 -2083.4838 -2083.4838 12938.14 -12938.14
1950 1754.5722 -2081.062 -2081.062 13678.133 -13678.133
1960 1790.0373 -2080.9357 -2080.9357 13972.404 -13972.404
1970 1815.9084 -2082.4892 -2082.4892 13423.516 -13423.516
1980 1741.0456 -2079.056 -2079.056 13024.446 -13024.446
1990 1845.2042 -2082.4853 -2082.4853 12369.149 -12369.149
2000 1726.2212 -2078.0219 -2078.0219 12670.669 -12670.669
Loop time of 0.228263 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1900 1726.2212 -2078.0219 -2078.0219 12670.669 -12670.669
1910 1859.235 -2087.1634 -2087.1634 12382.624 -12382.624
1920 1859.3456 -2087.6091 -2087.6091 12482.545 -12482.545
1930 1748.0548 -2080.7392 -2080.7392 13217.457 -13217.457
1940 1876.5822 -2089.6972 -2089.6972 12827.369 -12827.369
1950 1858.9549 -2089.1237 -2089.1237 12267.563 -12267.563
1960 1661.6597 -2076.6976 -2076.6976 13069.247 -13069.247
1970 1739.6756 -2082.3166 -2082.3166 13000.655 -13000.655
1980 1831.8527 -2088.8393 -2088.8393 11823.386 -11823.386
1990 1661.818 -2078.0492 -2078.0492 12159.308 -12159.308
2000 1700.7919 -2080.912 -2080.912 11889.457 -11889.457
Loop time of 0.230409 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
2000 1700.7919 -2080.912 -2080.912 11889.457 -11889.457
2019 1700.7919 -2213.3012 -2213.3012 8294.8879 -8294.8879
Loop time of 0.0511601 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
2000 1700.7919 -2080.912 -2080.912 11889.457 -11889.457
2010 1861.3608 -2091.7401 -2091.7401 11627.567 -11627.567
2020 1723.5921 -2082.9109 -2082.9109 11679.426 -11679.426
2030 1715.155 -2082.5582 -2082.5582 12295.003 -12295.003
2040 1850.4844 -2091.6449 -2091.6449 12563.959 -12563.959
2050 1761.29 -2085.9529 -2085.9529 13011.92 -13011.92
2060 1706.9101 -2082.541 -2082.541 13421.673 -13421.673
2070 1819.5707 -2090.0959 -2090.0959 12744.935 -12744.935
2080 1798.901 -2088.8739 -2088.8739 12477.746 -12477.746
2090 1722.8968 -2084.0198 -2084.0198 12266.395 -12266.395
2100 1780.5329 -2087.9446 -2087.9446 12351.983 -12351.983
Loop time of 0.228013 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
2100 1780.5329 -2087.9446 -2087.9446 12351.983 -12351.983
2118 1780.5329 -2213.3048 -2213.3048 8843.7542 -8843.7542
Loop time of 0.0483091 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
2100 1780.5329 -2081.5748 -2081.5748 11485.708 -11485.708
Loop time of 7.17718 on 1 procs for 18 steps with 511 atoms
PRD stats:
Dephase time (%) = 1.3562 (18.896)
Dynamics time (%) = 4.58155 (63.835)
Quench time (%) = 0.945275 (13.1706)
Other time (%) = 0.0760477 (1.05958)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13354 ave 13354 max 13354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13354
Ave neighs/atom = 26.1331
Neighbor list builds = 98
Dangerous builds = 0

631
examples/prd/log.prd.3.18Feb13.linux.4
View File

@ -1,631 +0,0 @@
LAMMPS (18 Feb 2013)
Processor partition = 3
# Parallel replica dynamics model for a single vacancy in bulk Si
# events occur when a neighboring atom diffuses to the vacant site
# run this on multiple partitions as
# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
#log none
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.4310000000000000497 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 1 by 1 MPI processor grid
create_atoms 1 region myreg
Created 512 atoms
mass 1 28.06
group Si type 1
512 atoms in group Si
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511
pair_style sw
pair_coeff * * Si.sw Si
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
# equilibrate
run 100
Memory usage per processor = 2.0318 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1802.5039 -2211.666 0 -2092.8401 12351.692
10 996.01982 -2158.3093 0 -2092.649 14285.475
20 590.09928 -2131.1531 0 -2092.2521 12113.964
30 1033.01 -2159.2522 0 -2091.1534 6860.4116
40 724.76581 -2137.281 0 -2089.5025 5999.4372
50 489.66604 -2120.8082 0 -2088.5281 6403.4234
60 960.70653 -2150.7394 0 -2087.407 5687.324
70 908.41498 -2145.7665 0 -2085.8813 8220.9655
80 796.82286 -2137.1227 0 -2084.5941 11307.153
90 1245.9045 -2164.9841 0 -2082.8507 11282.071
100 1083.0647 -2152.0805 0 -2080.682 12015.018
Loop time of 0.199962 on 1 procs for 100 steps with 511 atoms
Pair time (%) = 0.195804 (97.9207)
Neigh time (%) = 0.00138426 (0.692261)
Comm time (%) = 0.000849485 (0.424824)
Outpt time (%) = 6.74725e-05 (0.0337427)
Other time (%) = 0.00185657 (0.92846)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13996 ave 13996 max 13996 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13996
Ave neighs/atom = 27.3894
Neighbor list builds = 2
Dangerous builds = 0
# only output atoms near vacancy
compute coord all coord/atom $r
compute coord all coord/atom 2.8349999999999999645
#dump events all custom 1 dump.prd id type x y z
#dump_modify events thresh c_coord != 4
compute patom all pe/atom
compute pe all reduce sum c_patom
compute satom all stress/atom
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
thermo_style custom step temp pe c_pe press v_press
compute 1 all event/displace 0.5
prd 2000 100 10 10 100 1 54985 temp $t min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 ${ftol} ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 1.0000000000000000818e-05 ${maxiter} ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 1.0000000000000000818e-05 100 ${maxeval} vel all uniform
prd 2000 100 10 10 100 1 54985 temp 1800 min 1.0000000000000000818e-05 1.0000000000000000818e-05 100 100 vel all uniform
WARNING: Resetting reneighboring criteria during PRD (prd.cpp:201)
Memory usage per processor = 3.74842 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1083.0647 -2211.0684 -2211.0684 7372.2593 -7372.2593
119 1083.0647 -2211.6557 -2211.6557 7411.1722 -7411.1722
Loop time of 0.0556021 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
110 1495.0763 -2129.2427 -2129.2427 17292.034 -17292.034
120 1695.6936 -2119.9568 -2119.9568 19395.276 -19395.276
130 1720.2165 -2112.5918 -2112.5918 19379.647 -19379.647
140 1792.9012 -2110.2027 -2110.2027 20162.681 -20162.681
150 1826.4633 -2110.1906 -2110.1906 19821.473 -19821.473
160 1707.1346 -2102.4592 -2102.4592 19283.638 -19283.638
170 1889.7308 -2106.7875 -2106.7875 19121.04 -19121.04
180 1726.1399 -2100.5051 -2100.5051 17912.961 -17912.961
190 1725.2909 -2094.183 -2094.183 17836.706 -17836.706
200 1797.4072 -2092.6159 -2092.6159 17749.283 -17749.283
Loop time of 0.219582 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
100 1797.4072 -2092.6159 -2092.6159 17749.283 -17749.283
110 1749.1865 -2088.09 -2088.09 17886.987 -17886.987
120 1730.091 -2085.5138 -2085.5138 16298.238 -16298.238
130 1725.5695 -2083.8602 -2083.8602 14810.515 -14810.515
140 1742.8337 -2083.604 -2083.604 14304.4 -14304.4
150 1755.1691 -2082.9974 -2082.9974 14289.749 -14289.749
160 1730.1652 -2079.9294 -2079.9294 14796.483 -14796.483
170 1746.47 -2079.5667 -2079.5667 14891.286 -14891.286
180 1867.6791 -2086.0994 -2086.0994 15143.089 -15143.089
190 1826.3577 -2081.9693 -2081.9693 14842.324 -14842.324
200 1890.4086 -2084.9324 -2084.9324 15298.464 -15298.464
Loop time of 0.228683 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
200 1890.4086 -2084.9324 -2084.9324 15298.464 -15298.464
218 1890.4086 -2213.3051 -2213.3051 9595.2117 -9595.2117
Loop time of 0.0460262 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
200 1890.4086 -2083.245 -2083.245 15721.201 -15721.201
210 1895.0321 -2082.3794 -2082.3794 16182.652 -16182.652
220 1967.6529 -2086.173 -2086.173 15532.872 -15532.872
230 1820.3126 -2075.6591 -2075.6591 15093.435 -15093.435
240 1713.4056 -2067.9324 -2067.9324 14623.702 -14623.702
250 1806.5325 -2073.3192 -2073.3192 13241.861 -13241.861
260 1838.2185 -2074.62 -2074.62 12793.039 -12793.039
270 1796.1907 -2071.1002 -2071.1002 13382.202 -13382.202
280 1855.3253 -2074.2821 -2074.2821 14014.125 -14014.125
290 1915.1832 -2077.5543 -2077.5543 15817.805 -15817.805
300 1943.8007 -2078.9069 -2078.9069 17664.976 -17664.976
Loop time of 0.233072 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
300 1943.8007 -2078.9069 -2078.9069 17664.976 -17664.976
320 1943.8007 -2213.3262 -2213.3262 9968.2615 -9968.2615
Loop time of 0.0541098 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
300 1943.8007 -2078.9069 -2078.9069 17664.976 -17664.976
310 1830.358 -2077.8168 -2077.8168 14980.856 -14980.856
320 1816.8748 -2078.525 -2078.525 14548.875 -14548.875
330 1812.5384 -2078.949 -2078.949 13614.012 -13614.012
340 1854.3003 -2082.1223 -2082.1223 13185.902 -13185.902
350 1853.1764 -2085.2567 -2085.2567 12110.408 -12110.408
360 1853.1119 -2088.4344 -2088.4344 12224.055 -12224.055
370 1837.6042 -2090.6376 -2090.6376 11312.576 -11312.576
380 1790.0042 -2089.7364 -2089.7364 11726.39 -11726.39
390 1704.071 -2083.1405 -2083.1405 11697.254 -11697.254
400 1828.0893 -2084.6844 -2084.6844 12331.728 -12331.728
Loop time of 0.226976 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
300 1828.0893 -2084.6844 -2084.6844 12331.728 -12331.728
310 1818.7058 -2083.7777 -2083.7777 13364.201 -13364.201
320 1784.6932 -2081.2738 -2081.2738 13319.356 -13319.356
330 1781.3136 -2080.7661 -2080.7661 12726.586 -12726.586
340 1850.504 -2085.0411 -2085.0411 12804.72 -12804.72
350 1806.9896 -2081.9086 -2081.9086 12799.418 -12799.418
360 1797.0754 -2081.008 -2081.008 12932.182 -12932.182
370 1939.3485 -2090.1815 -2090.1815 12022.081 -12022.081
380 1833.459 -2083.0989 -2083.0989 12722.114 -12722.114
390 1767.2468 -2078.7079 -2078.7079 12994.83 -12994.83
400 1840.9497 -2083.5253 -2083.5253 12470.362 -12470.362
Loop time of 0.227942 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
400 1840.9497 -2083.5253 -2083.5253 12470.362 -12470.362
418 1840.9497 -2213.3059 -2213.3059 9257.8757 -9257.8757
Loop time of 0.046737 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
400 1840.9497 -2083.5253 -2083.5253 12470.362 -12470.362
410 1825.8375 -2082.5217 -2082.5217 12012.844 -12012.844
420 1723.3215 -2075.7602 -2075.7602 11394.557 -11394.557
430 1764.1446 -2078.4055 -2078.4055 9429.6621 -9429.6621
440 1722.8256 -2075.5423 -2075.5423 10622.932 -10622.932
450 1746.9424 -2076.92 -2076.92 11529.679 -11529.679
460 1837.7686 -2082.6258 -2082.6258 12192.008 -12192.008
470 1853.9148 -2083.4249 -2083.4249 13244.632 -13244.632
480 1853.6885 -2083.2159 -2083.2159 14116.299 -14116.299
490 1915.2224 -2087.1642 -2087.1642 14632.565 -14632.565
500 1936.7625 -2088.6317 -2088.6317 14188.134 -14188.134
Loop time of 0.226231 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
500 1936.7625 -2088.6317 -2088.6317 14188.134 -14188.134
519 1936.7625 -2213.3032 -2213.3032 9913.4596 -9913.4596
Loop time of 0.0458939 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
500 1936.7625 -2088.6317 -2088.6317 14188.134 -14188.134
510 1834.5516 -2082.0916 -2082.0916 13945.662 -13945.662
520 1805.8538 -2080.48 -2080.48 11915.304 -11915.304
530 1719.5829 -2075.0416 -2075.0416 10641.83 -10641.83
540 1700.9425 -2073.9843 -2073.9843 10638.084 -10638.084
550 1721.0296 -2075.3479 -2075.3479 10855.732 -10855.732
560 1792.256 -2080.0028 -2080.0028 10718.277 -10718.277
570 1816.469 -2081.5215 -2081.5215 12281.721 -12281.721
580 1898.1645 -2086.8779 -2086.8779 13891.519 -13891.519
590 1909.9896 -2087.7381 -2087.7381 15407.945 -15407.945
600 1905.9376 -2087.7136 -2087.7136 15536.218 -15536.218
Loop time of 0.228947 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
600 1905.9376 -2087.7136 -2087.7136 15536.218 -15536.218
620 1905.9376 -2213.3226 -2213.3226 9705.2581 -9705.2581
Loop time of 0.0514681 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
600 1905.9376 -2087.7136 -2087.7136 15536.218 -15536.218
610 1898.495 -2087.6161 -2087.6161 13863.644 -13863.644
620 1873.699 -2086.5202 -2086.5202 11778.817 -11778.817
630 1744.3676 -2078.5837 -2078.5837 11019.865 -11019.865
640 1681.2181 -2074.9263 -2074.9263 9815.9404 -9815.9404
650 1707.9678 -2077.065 -2077.065 10236.708 -10236.708
660 1719.4888 -2078.0855 -2078.0855 10716.295 -10716.295
670 1694.7476 -2076.6002 -2076.6002 10237.649 -10237.649
680 1773.8128 -2081.8591 -2081.8591 12034.22 -12034.22
690 1832.6905 -2085.7381 -2085.7381 12268.403 -12268.403
700 1872.2418 -2088.3939 -2088.3939 12841.871 -12841.871
Loop time of 0.227463 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
700 1872.2418 -2088.3939 -2088.3939 12841.871 -12841.871
718 1872.2418 -2213.2732 -2213.2732 9469.3455 -9469.3455
Loop time of 0.0468318 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
700 1872.2418 -2088.3939 -2088.3939 12841.871 -12841.871
710 1856.1726 -2087.4734 -2087.4734 12587.6 -12587.6
720 1809.0844 -2084.5719 -2084.5719 11962.825 -11962.825
730 1813.7498 -2085.1228 -2085.1228 12275.918 -12275.918
740 1778.4404 -2083.0339 -2083.0339 12609.945 -12609.945
750 1793.7621 -2084.2846 -2084.2846 12022.021 -12022.021
760 1756.218 -2082.0146 -2082.0146 11970.105 -11970.105
770 1788.1399 -2084.3038 -2084.3038 11486.204 -11486.204
780 1752.5386 -2082.1061 -2082.1061 11773.768 -11773.768
790 1737.5719 -2081.2139 -2081.2139 12812.397 -12812.397
800 1760.5292 -2082.7503 -2082.7503 13832.216 -13832.216
Loop time of 0.229003 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
800 1760.5292 -2082.7503 -2082.7503 13832.216 -13832.216
817 1760.5292 -2213.2818 -2213.2818 8701.2542 -8701.2542
Loop time of 0.0445819 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
800 1760.5292 -2082.7503 -2082.7503 13832.216 -13832.216
810 1824.7855 -2084.3929 -2084.3929 13668.719 -13668.719
820 1712.4425 -2078.6074 -2078.6074 12847.66 -12847.66
830 1875.2236 -2083.5586 -2083.5586 12721.192 -12721.192
840 1802.2145 -2083.7392 -2083.7392 11989.282 -11989.282
850 1820.2177 -2085.1324 -2085.1324 11057.193 -11057.193
860 1730.3595 -2080.5914 -2080.5914 11507.405 -11507.405
870 1809.9784 -2081.2823 -2081.2823 12298.894 -12298.894
880 1803.9222 -2081.5723 -2081.5723 11947.359 -11947.359
890 1757.0085 -2078.7491 -2078.7491 12561.76 -12561.76
900 1809.447 -2079.3762 -2079.3762 12554.534 -12554.534
Loop time of 0.229334 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
800 1809.447 -2079.3762 -2079.3762 12554.534 -12554.534
810 1806.5101 -2079.1895 -2079.1895 11903.119 -11903.119
820 1785.2438 -2077.8038 -2077.8038 11702.485 -11702.485
830 1781.1685 -2077.5303 -2077.5303 12703.961 -12703.961
840 1863.47 -2082.9537 -2082.9537 13361.794 -13361.794
850 1879.7765 -2084.0849 -2084.0849 14480.503 -14480.503
860 1906.2551 -2086.0185 -2086.0185 14752.263 -14752.263
870 1882.1344 -2084.7545 -2084.7545 15091.996 -15091.996
880 1868.6595 -2084.3355 -2084.3355 14227.917 -14227.917
890 1806.8883 -2080.8098 -2080.8098 13418.625 -13418.625
900 1813.034 -2081.8053 -2081.8053 13267.308 -13267.308
Loop time of 0.228557 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
900 1813.034 -2081.8053 -2081.8053 13267.308 -13267.308
917 1813.034 -2213.2328 -2213.2328 9058.7627 -9058.7627
Loop time of 0.0433311 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
900 1813.034 -2081.8053 -2081.8053 13267.308 -13267.308
910 1790.47 -2080.925 -2080.925 13187.347 -13187.347
920 1773.8688 -2080.4392 -2080.4392 12634.894 -12634.894
930 1785.9855 -2081.8252 -2081.8252 12561.505 -12561.505
940 1801.3588 -2083.4277 -2083.4277 12028.691 -12028.691
950 1778.6138 -2082.521 -2082.521 12646.355 -12646.355
960 1764.4699 -2082.1518 -2082.1518 11945.626 -11945.626
970 1778.2914 -2083.5962 -2083.5962 11676.59 -11676.59
980 1763.0077 -2083.0977 -2083.0977 12675.07 -12675.07
990 1724.8156 -2081.0275 -2081.0275 12706.385 -12706.385
1000 1789.1021 -2085.6571 -2085.6571 12733.814 -12733.814
Loop time of 0.228717 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1000 1789.1021 -2085.6571 -2085.6571 12733.814 -12733.814
1019 1789.1021 -2213.3142 -2213.3142 8903.9364 -8903.9364
Loop time of 0.0541492 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1000 1789.1021 -2085.6571 -2085.6571 12733.814 -12733.814
1010 1803.5662 -2086.2788 -2086.2788 12296.832 -12296.832
1020 1721.4631 -2081.4632 -2081.4632 12617.022 -12617.022
1030 1901.5059 -2088.5616 -2088.5616 13322.949 -13322.949
1040 1790.4919 -2088.3943 -2088.3943 11842.661 -11842.661
1050 1728.9375 -2084.1491 -2084.1491 11186.843 -11186.843
1060 1822.9805 -2086.1115 -2086.1115 11654.623 -11654.623
1070 1793.5987 -2086.1655 -2086.1655 11565.879 -11565.879
1080 1774.9684 -2085.0099 -2085.0099 11788.082 -11788.082
1090 1875.45 -2090.5357 -2090.5357 12023.082 -12023.082
1100 1770.2149 -2089.1678 -2089.1678 11314.012 -11314.012
Loop time of 0.228125 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1000 1770.2149 -2089.1678 -2089.1678 11314.012 -11314.012
1010 1751.5551 -2088.5144 -2088.5144 11418.611 -11418.611
1020 1783.4529 -2091.1906 -2091.1906 11869.563 -11869.563
1030 1724.468 -2087.853 -2087.853 11660.095 -11660.095
1040 1700.0952 -2086.721 -2086.721 10696.55 -10696.55
1050 1760.1423 -2091.0982 -2091.0982 9178.1354 -9178.1354
1060 1644.0734 -2083.7826 -2083.7826 9093.1125 -9093.1125
1070 1613.8056 -2081.9631 -2081.9631 9591.8493 -9591.8493
1080 1709.8502 -2088.2878 -2088.2878 9538.5577 -9538.5577
1090 1676.8021 -2085.9346 -2085.9346 10766.925 -10766.925
1100 1718.403 -2088.3484 -2088.3484 10949.517 -10949.517
Loop time of 0.227946 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1100 1718.403 -2088.3484 -2088.3484 10949.517 -10949.517
1117 1718.403 -2213.2587 -2213.2587 8409.3544 -8409.3544
Loop time of 0.045167 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1100 1718.403 -2088.3484 -2088.3484 10949.517 -10949.517
1110 1765.1951 -2090.924 -2090.924 10989.261 -10989.261
1120 1739.4922 -2088.58 -2088.58 11689.558 -11689.558
1130 1727.0447 -2086.942 -2086.942 12283.035 -12283.035
1140 1785.7915 -2089.784 -2089.784 11818.431 -11818.431
1150 1809.8869 -2090.1546 -2090.1546 10879.76 -10879.76
1160 1744.4121 -2084.5197 -2084.5197 11286.034 -11286.034
1170 1757.7394 -2084.0004 -2084.0004 11548.282 -11548.282
1180 1821.8601 -2086.7401 -2086.7401 11282.746 -11282.746
1190 1801.9718 -2084.0004 -2084.0004 11879.914 -11879.914
1200 1778.413 -2081.1797 -2081.1797 11763.504 -11763.504
Loop time of 0.228988 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1200 1778.413 -2081.1797 -2081.1797 11763.504 -11763.504
1220 1778.413 -2213.2935 -2213.2935 8826.8778 -8826.8778
Loop time of 0.056355 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1200 1778.413 -2081.1797 -2081.1797 11763.504 -11763.504
1210 1779.9735 -2080.1523 -2080.1523 11767.914 -11767.914
1220 1761.523 -2077.9508 -2077.9508 12102.479 -12102.479
1230 1799.751 -2079.6111 -2079.6111 11976.738 -11976.738
1240 1852.8341 -2082.3812 -2082.3812 12122.449 -12122.449
1250 1835.3624 -2080.6598 -2080.6598 12594.439 -12594.439
1260 1822.3142 -2079.3754 -2079.3754 12980.571 -12980.571
1270 1824.7898 -2079.2048 -2079.2048 13133.515 -13133.515
1280 1835.3097 -2079.6291 -2079.6291 13141.016 -13141.016
1290 1918.3152 -2084.9315 -2084.9315 12831.552 -12831.552
1300 1872.0268 -2081.8383 -2081.8383 12855.872 -12855.872
Loop time of 0.229217 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1300 1872.0268 -2081.8383 -2081.8383 12855.872 -12855.872
1320 1872.0268 -2213.3016 -2213.3016 9471.4837 -9471.4837
Loop time of 0.0549281 on 1 procs for 20 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1300 1872.0268 -2081.8383 -2081.8383 12855.872 -12855.872
1310 1842.2091 -2079.9447 -2079.9447 11930.547 -11930.547
1320 1839.1324 -2079.8702 -2079.8702 11520.211 -11520.211
1330 1781.5944 -2076.2294 -2076.2294 12517.772 -12517.772
1340 1808.2791 -2078.1377 -2078.1377 12331.797 -12331.797
1350 1825.5011 -2079.4214 -2079.4214 12959.817 -12959.817
1360 1805.1617 -2078.2612 -2078.2612 12283.097 -12283.097
1370 1794.2198 -2077.7174 -2077.7174 11854.379 -11854.379
1380 1856.0315 -2081.9959 -2081.9959 12222.656 -12222.656
1390 1830.6929 -2080.5837 -2080.5837 12676.219 -12676.219
1400 1787.3453 -2078.0218 -2078.0218 12795.723 -12795.723
Loop time of 0.229278 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1400 1787.3453 -2078.0218 -2078.0218 12795.723 -12795.723
1419 1787.3453 -2213.3099 -2213.3099 8888.2838 -8888.2838
Loop time of 0.0524161 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1400 1787.3453 -2083.1407 -2083.1407 12644.184 -12644.184
1410 1858.6264 -2088.1699 -2088.1699 13665.536 -13665.536
1420 1836.7078 -2087.1342 -2087.1342 13718.627 -13718.627
1430 1761.5946 -2082.6238 -2082.6238 13729.715 -13729.715
1440 1825.9335 -2087.3258 -2087.3258 13009.414 -13009.414
1450 1817.7629 -2087.2906 -2087.2906 12876.965 -12876.965
1460 1773.2189 -2084.9022 -2084.9022 12124.77 -12124.77
1470 1742.8153 -2083.4385 -2083.4385 11686.602 -11686.602
1480 1741.4145 -2083.843 -2083.843 11494.225 -11494.225
1490 1765.3668 -2085.8995 -2085.8995 11215.781 -11215.781
1500 1760.2197 -2086.0116 -2086.0116 11232.652 -11232.652
Loop time of 0.228275 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1500 1760.2197 -2086.0116 -2086.0116 11232.652 -11232.652
1517 1760.2197 -2213.245 -2213.245 8696.1847 -8696.1847
Loop time of 0.0442488 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1500 1760.2197 -2088.1491 -2088.1491 12985.172 -12985.172
1510 1927.1878 -2099.7308 -2099.7308 12023.236 -12023.236
1520 1616.4053 -2079.8776 -2079.8776 12507.037 -12507.037
1530 1598.2599 -2079.1598 -2079.1598 11597.301 -11597.301
1540 1792.8199 -2092.3519 -2092.3519 10302.629 -10302.629
1550 1633.2272 -2082.1258 -2082.1258 11028.733 -11028.733
1560 1596.4787 -2079.8411 -2079.8411 11401.206 -11401.206
1570 1803.3749 -2093.4571 -2093.4571 11211.847 -11211.847
1580 1632.0154 -2081.9939 -2081.9939 13381.635 -13381.635
1590 1718.3971 -2087.372 -2087.372 14772.258 -14772.258
1600 2048.734 -2108.6472 -2108.6472 14338.8 -14338.8
Loop time of 0.229118 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1600 2048.734 -2108.6472 -2108.6472 14338.8 -14338.8
1618 2048.734 -2213.2799 -2213.2799 10685.447 -10685.447
Loop time of 0.03898 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1600 2048.734 -2108.6472 -2108.6472 14338.8 -14338.8
1610 1699.675 -2080.9037 -2080.9037 11840.386 -11840.386
1620 1817.4828 -2081.4111 -2081.4111 13490.885 -13490.885
1630 1813.0686 -2081.5266 -2081.5266 13881.909 -13881.909
1640 1779.9893 -2079.3276 -2079.3276 13857.386 -13857.386
1650 1937.4396 -2087.3853 -2087.3853 13788.514 -13788.514
1660 1762.8309 -2083.9296 -2083.9296 12151.903 -12151.903
1670 1791.277 -2082.2407 -2082.2407 12210.144 -12210.144
1680 1803.435 -2081.2765 -2081.2765 12398.317 -12398.317
1690 1802.7286 -2080.2585 -2080.2585 12311.1 -12311.1
1700 1825.8738 -2080.7812 -2080.7812 12487.488 -12487.488
Loop time of 0.229152 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1600 1825.8738 -2080.7812 -2080.7812 12487.488 -12487.488
1610 1818.7567 -2079.2051 -2079.2051 12961.247 -12961.247
1620 1853.2617 -2080.4774 -2080.4774 13334.998 -13334.998
1630 1845.6923 -2079.1003 -2079.1003 14024.126 -14024.126
1640 1842.4692 -2078.142 -2078.142 13972.69 -13972.69
1650 1932.9485 -2083.4976 -2083.4976 13927.397 -13927.397
1660 1891.8513 -2080.3519 -2080.3519 14382.688 -14382.688
1670 1871.3356 -2078.7396 -2078.7396 15250.018 -15250.018
1680 1889.0458 -2079.7669 -2079.7669 14923.552 -14923.552
1690 1896.2267 -2080.2296 -2080.2296 13037.903 -13037.903
1700 1836.5539 -2076.3875 -2076.3875 12688.151 -12688.151
Loop time of 0.22974 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1700 1836.5539 -2076.3875 -2076.3875 12688.151 -12688.151
1716 1836.5539 -2213.2588 -2213.2588 9221.7377 -9221.7377
Loop time of 0.042166 on 1 procs for 16 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1700 1836.5539 -2076.3875 -2076.3875 12688.151 -12688.151
1710 1859.5138 -2078.0746 -2078.0746 12410.243 -12410.243
1720 1819.1932 -2075.6335 -2075.6335 12724.601 -12724.601
1730 1813.3698 -2075.501 -2075.501 12702.894 -12702.894
1740 1840.4368 -2077.5556 -2077.5556 13145.533 -13145.533
1750 1872.195 -2079.983 -2079.983 13220.848 -13220.848
1760 1847.9633 -2078.804 -2078.804 13870.064 -13870.064
1770 1887.8505 -2081.9384 -2081.9384 15041.963 -15041.963
1780 1967.1648 -2087.8474 -2087.8474 14594.014 -14594.014
1790 1866.7002 -2082.0986 -2082.0986 13615.248 -13615.248
1800 1761.77 -2076.1141 -2076.1141 12320.655 -12320.655
Loop time of 0.229012 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1800 1761.77 -2076.1141 -2076.1141 12320.655 -12320.655
1819 1761.77 -2213.2705 -2213.2705 8712.9668 -8712.9668
Loop time of 0.042516 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1800 1761.77 -2076.1141 -2076.1141 12320.655 -12320.655
1810 1703.4947 -2073.1063 -2073.1063 12008.391 -12008.391
1820 1780.1034 -2078.8985 -2078.8985 11424.159 -11424.159
1830 1792.3191 -2080.4109 -2080.4109 11527.375 -11527.375
1840 1740.7982 -2077.6542 -2077.6542 13041.565 -13041.565
1850 1860.8658 -2086.1706 -2086.1706 14356.817 -14356.817
1860 1942.1014 -2092.2204 -2092.2204 14527.618 -14527.618
1870 1830.8975 -2085.683 -2085.683 15024.292 -15024.292
1880 1809.0262 -2085.0269 -2085.0269 14356.631 -14356.631
1890 1832.6706 -2087.3315 -2087.3315 13353.932 -13353.932
1900 1791.352 -2085.3156 -2085.3156 12909.588 -12909.588
Loop time of 0.228083 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
1900 1791.352 -2085.3156 -2085.3156 12909.588 -12909.588
1917 1791.352 -2213.2561 -2213.2561 8912.2973 -8912.2973
Loop time of 0.044138 on 1 procs for 17 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1900 1791.352 -2085.3156 -2085.3156 12909.588 -12909.588
1910 1839.8996 -2088.5949 -2088.5949 13946.912 -13946.912
1920 1728.8047 -2084.4404 -2084.4404 13398.47 -13398.47
1930 1844.6379 -2087.8523 -2087.8523 12606.037 -12606.037
1940 1750.4698 -2084.9552 -2084.9552 12830.245 -12830.245
1950 1777.4189 -2083.7326 -2083.7326 12890.868 -12890.868
1960 1757.0139 -2081.0743 -2081.0743 12928.49 -12928.49
1970 1815.4975 -2082.2189 -2082.2189 12590.606 -12590.606
1980 1820.5692 -2083.6914 -2083.6914 11259.175 -11259.175
1990 1760.8482 -2081.178 -2081.178 12204.966 -12204.966
2000 1888.8176 -2087.1036 -2087.1036 12717.455 -12717.455
Loop time of 0.226744 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
1900 1888.8176 -2087.1036 -2087.1036 12717.455 -12717.455
1910 1835.8382 -2083.7475 -2083.7475 13543.202 -13543.202
1920 1838.6207 -2084.1142 -2084.1142 13995.434 -13995.434
1930 1844.8228 -2084.7395 -2084.7395 14254.28 -14254.28
1940 1809.1821 -2082.6216 -2082.6216 14113.256 -14113.256
1950 1866.6498 -2086.6639 -2086.6639 13152.916 -13152.916
1960 1854.176 -2086.1617 -2086.1617 11993.967 -11993.967
1970 1710.438 -2077.0061 -2077.0061 12356.799 -12356.799
1980 1713.8796 -2077.4442 -2077.4442 12066.558 -12066.558
1990 1830.1984 -2085.2536 -2085.2536 11224.423 -11224.423
2000 1745.1241 -2079.7516 -2079.7516 12000.282 -12000.282
Loop time of 0.228773 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
2000 1745.1241 -2079.7516 -2079.7516 12000.282 -12000.282
2018 1745.1241 -2213.2723 -2213.2723 8595.2359 -8595.2359
Loop time of 0.047271 on 1 procs for 18 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
2000 1745.1241 -2079.7516 -2079.7516 12000.282 -12000.282
2010 1764.5303 -2081.1092 -2081.1092 12533.707 -12533.707
2020 1803.9081 -2083.7299 -2083.7299 12751.448 -12751.448
2030 1839.3617 -2086.0949 -2086.0949 12814.216 -12814.216
2040 1868.2548 -2088.0926 -2088.0926 13020.533 -13020.533
2050 1793.5586 -2083.3252 -2083.3252 13251.553 -13251.553
2060 1775.5342 -2082.3028 -2082.3028 12783.678 -12783.678
2070 1851.6766 -2087.482 -2087.482 12508.389 -12508.389
2080 1855.9094 -2087.9994 -2087.9994 12382.735 -12382.735
2090 1728.9486 -2079.9079 -2079.9079 12119.774 -12119.774
2100 1750.5079 -2081.5748 -2081.5748 11279.495 -11279.495
Loop time of 0.225841 on 1 procs for 100 steps with 511 atoms
Memory usage per processor = 4.28247 Mbytes
Step Temp PotEng pe Press press
2100 1750.5079 -2081.5748 -2081.5748 11279.495 -11279.495
2119 1750.5079 -2213.2837 -2213.2837 8634.903 -8634.903
Loop time of 0.0530138 on 1 procs for 19 steps with 511 atoms
Memory usage per processor = 3.59583 Mbytes
Step Temp PotEng pe Press press
2100 1750.5079 -2081.5748 -2081.5748 11279.495 -11279.495
Loop time of 7.17719 on 1 procs for 19 steps with 511 atoms
PRD stats:
Dephase time (%) = 1.35991 (18.9477)
Dynamics time (%) = 4.57289 (63.7142)
Quench time (%) = 0.954329 (13.2967)
Other time (%) = 0.0748234 (1.04252)
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1017 ave 1017 max 1017 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 13354 ave 13354 max 13354 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13354
Ave neighs/atom = 26.1331
Neighbor list builds = 98
Dangerous builds = 0

81
examples/reax/log.reax.rdx.18Feb13.linux.1
View File

@ -1,81 +0,0 @@
LAMMPS (18 Feb 2013)
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
21 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
#dump 1 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
run 100
Memory usage per processor = 2.21677 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.8843
10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082204 843.41939 -180.17724 0 107.5115
20 516.83079 -1941.677 -1910.8655 -12525.411 -2801.8626 7.4107972 0.073134187 0 81.986983 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574159
30 467.2641 -1940.978 -1913.1215 -35957.488 -2755.021 -6.9179958 0.049322445 0 78.853174 0.13604392 -51.653635 0 19.862871 -9.7098575 853.79334 -151.232 0 80.861769
40 647.45542 -1951.1994 -1912.6006 -5883.714 -2798.3556 17.33481 0.15102863 0 63.235118 0.18070929 -54.59896 0 17.325008 -12.052278 883.01668 -164.21335 0 96.777423
50 716.38085 -1949.4707 -1906.7628 5473.2048 -2800.931 9.2056931 0.1541327 0 85.37148 3.2986104 -78.253597 0 34.86177 -8.5531232 882.01439 -193.8522 0 117.21316
60 1175.2706 -1975.961 -1905.8958 -1939.4802 -2726.5818 -11.651983 0.24296785 0 48.320653 7.1799711 -75.363637 0 16.520124 -4.8869434 844.75415 -194.23296 0 119.73842
70 1156.7 -1975.3463 -1906.3882 24628.243 -2880.5226 25.652536 0.26894314 0 83.724875 7.1049199 -68.70095 0 24.750741 -8.6338272 911.20093 -183.41949 0 113.22771
80 840.23792 -1955.4773 -1905.3855 -17731.433 -2755.7299 -8.0168345 0.13867988 0 86.147409 2.2387302 -76.945849 0 23.595809 -7.2609612 853.63488 -167.88294 0 94.603642
90 365.79009 -1926.4058 -1904.5988 898.4147 -2842.1833 47.368255 0.23109012 0 92.288131 0.38031335 -61.361504 0 18.476365 -12.255471 900.24235 -186.48053 0 116.88854
100 801.32068 -1953.4184 -1905.6467 -2417.7238 -2802.725 4.6677502 0.18046561 0 76.730118 5.4177141 -77.102576 0 24.997222 -7.7554226 898.67346 -196.89124 0 120.38907
Loop time of 0.419315 on 1 procs for 100 steps with 21 atoms
Pair time (%) = 0.417611 (99.5936)
Neigh time (%) = 0.000760555 (0.18138)
Comm time (%) = 0.000501871 (0.119688)
Outpt time (%) = 0.000254154 (0.0606118)
Other time (%) = 0.000187635 (0.0447481)
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1106 ave 1106 max 1106 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1106
Ave neighs/atom = 52.6667
Neighbor list builds = 10
Dangerous builds = 0

81
examples/reax/log.reax.rdx.18Feb13.linux.4
View File

@ -1,81 +0,0 @@
LAMMPS (18 Feb 2013)
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
21 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all custom 10 dump.reax.rdx id type q xs ys zs
#dump 1 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
run 100
Memory usage per processor = 2.43839 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -1885.1268 -1885.1268 27233.074 -2958.4712 79.527715 0.31082031 0 97.771125 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79972 0 168.88429
10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070523 -77.710916 0 14.963568 -5.8082203 843.41939 -180.17724 0 107.51149
20 516.8308 -1941.677 -1910.8655 -12525.411 -2801.8626 7.4107974 0.073134189 0 81.986982 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574158
30 467.26409 -1940.978 -1913.1215 -35957.487 -2755.021 -6.9179961 0.049322431 0 78.853175 0.13604389 -51.653632 0 19.862872 -9.7098575 853.79334 -151.232 0 80.861771
40 647.45569 -1951.1994 -1912.6005 -5883.7069 -2798.3557 17.334815 0.15102853 0 63.235128 0.18070898 -54.598942 0 17.325005 -12.052278 883.01681 -164.21333 0 96.77741
50 716.38166 -1949.473 -1906.765 5473.1746 -2800.931 9.205706 0.15413271 0 85.371465 3.2986143 -78.253598 0 34.861779 -8.5531229 882.0144 -193.85134 0 117.21005
60 1175.2704 -1975.9608 -1905.8956 -1939.4947 -2726.5814 -11.65205 0.24296778 0 48.320632 7.1799754 -75.363634 0 16.520121 -4.8869383 844.75394 -194.2328 0 119.73838
70 1156.7034 -1975.3496 -1906.3913 24628.204 -2880.5226 25.652517 0.26894307 0 83.724905 7.1048781 -68.700983 0 24.750747 -8.6338357 911.20075 -183.40571 0 113.21084
80 840.23678 -1955.4782 -1905.3864 -17731.413 -2755.7299 -8.0168177 0.13867967 0 86.147442 2.2387235 -76.945834 0 23.595799 -7.2609676 853.63482 -167.88302 0 94.602852
90 365.78801 -1926.4068 -1904.5999 898.3745 -2842.1832 47.368114 0.23109 0 92.288102 0.38031195 -61.361481 0 18.476353 -12.25546 900.24227 -186.48059 0 116.88762
100 801.3241 -1953.4184 -1905.6465 -2417.969 -2802.7245 4.667552 0.18046595 0 76.729919 5.4177255 -77.102568 0 24.997105 -7.7553985 898.67327 -196.8912 0 120.38931
Loop time of 2.72973 on 4 procs for 100 steps with 21 atoms
Pair time (%) = 1.78805 (65.5027)
Neigh time (%) = 0.000213504 (0.00782141)
Comm time (%) = 0.940931 (34.4697)
Outpt time (%) = 0.000394046 (0.0144353)
Other time (%) = 0.000147998 (0.00542171)
Nlocal: 5.25 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 301.25 ave 827 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1205
Ave neighs/atom = 57.381
Neighbor list builds = 10
Dangerous builds = 0

77
examples/reax/log.reax.tatb.18Feb13.linux.1
View File

@ -1,77 +0,0 @@
LAMMPS (18 Feb 2013)
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 1 by 1 MPI processor grid
384 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reax.tatb id type q x y z
#dump 1 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
fix 2 all reax/bonds 25 bonds.reax.tatb
run 25
Memory usage per processor = 6.71069 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.0231
5 0.63682726 -44767.817 -44767.09 8391.1654 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3993 0 6388.8594
10 2.4306905 -44769.41 -44766.635 11717.27 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.0893 0 6381.8126
15 5.0590385 -44772.631 -44766.856 17125.213 -61103.34 489.2801 4.7214008 0 1566.4744 20.590604 -268.28964 -1566.5961 252.97781 -654.93836 18835.335 -8719.2621 0 6370.4157
20 8.0678464 -44775.934 -44766.723 24620.53 -61088.791 490.4235 4.7193467 0 1565.5541 20.415031 -260.38514 -1574.1001 253.39804 -654.26838 18815.312 -8703.4032 0 6355.1922
25 10.975525 -44777.233 -44764.703 34381.132 -61068.889 490.53155 4.7164093 0 1566.5715 20.169755 -251.23112 -1582.8552 253.88696 -653.46042 18790.855 -8683.8775 0 6336.3489
Loop time of 5.81471 on 1 procs for 25 steps with 384 atoms
Pair time (%) = 5.76028 (99.0638)
Neigh time (%) = 0.050385 (0.866509)
Comm time (%) = 0.0024991 (0.042979)
Outpt time (%) = 0.00028801 (0.00495312)
Other time (%) = 0.00126314 (0.0217232)
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 286828
Ave neighs/atom = 746.948
Neighbor list builds = 5
Dangerous builds = 0

77
examples/reax/log.reax.tatb.18Feb13.linux.4
View File

@ -1,77 +0,0 @@
LAMMPS (18 Feb 2013)
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 2 by 2 MPI processor grid
384 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reax.tatb id type q x y z
#dump 1 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
fix 2 all reax/bonds 25 bonds.reax.tatb
run 25
Memory usage per processor = 3.32017 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -44767.08 -44767.08 7294.6353 -61120.591 486.4378 4.7236377 0 1568.024 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6378 0 6391.023
5 0.63682726 -44767.816 -44767.089 8391.165 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.3995 0 6388.8607
10 2.4306932 -44769.412 -44766.637 11717.214 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.1085 0 6381.8302
15 5.0590454 -44772.631 -44766.856 17124.962 -61103.34 489.28008 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.3321 0 6370.4856
20 8.0678552 -44775.923 -44766.712 24620.829 -61088.791 490.42348 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39805 -654.26837 18815.312 -8703.3072 0 6355.1072
25 10.975535 -44777.231 -44764.7 34381.277 -61068.889 490.53152 4.7164093 0 1566.5715 20.169755 -251.2311 -1582.8552 253.88697 -653.46042 18790.855 -8683.8355 0 6336.3093
Loop time of 2.52987 on 4 procs for 25 steps with 384 atoms
Pair time (%) = 2.46087 (97.2726)
Neigh time (%) = 0.0108202 (0.427696)
Comm time (%) = 0.0567853 (2.2446)
Outpt time (%) = 0.000581682 (0.0229926)
Other time (%) = 0.000812888 (0.0321317)
Nlocal: 96 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 319016
Ave neighs/atom = 830.771
Neighbor list builds = 5
Dangerous builds = 0

81
examples/reax/log.reaxc.rdx.18Feb13.linux.1
View File

@ -1,81 +0,0 @@
LAMMPS (18 Feb 2013)
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 1 by 1 MPI processor grid
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 1 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
run 100
Memory usage per processor = 3.52479 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -1884.3081 -1884.3081 27186.179 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79962 0 168.88427
10 1288.6115 -1989.6644 -1912.8422 -19456.351 -2734.6769 -15.607219 0.20177961 0 54.629555 3.1252294 -77.7067 0 14.933901 -5.8108541 843.92074 -180.43321 0 107.75935
20 538.95844 -1942.7037 -1910.5731 -10725.667 -2803.7395 7.907833 0.077926684 0 81.610046 0.22951933 -57.557103 0 30.331203 -10.178049 878.99015 -159.69268 0 89.316919
30 463.09509 -1933.5765 -1905.9685 -33255.505 -2749.8591 -8.0154611 0.027628698 0 81.627409 0.11972389 -50.262271 0 20.820317 -9.6327034 851.88721 -149.49498 0 79.20571
40 885.49513 -1958.9125 -1906.1227 -4814.654 -2795.644 9.1506168 0.13747487 0 70.948047 0.24360542 -57.862691 0 19.076512 -11.141212 873.73895 -159.99391 0 92.434069
50 861.16162 -1954.4602 -1903.121 -1896.7715 -2784.845 3.8269557 0.15793308 0 79.851627 3.349211 -78.066131 0 32.628923 -7.9565308 872.81849 -190.98571 0 114.76
60 1167.7833 -1971.8435 -1902.2247 -3482.8295 -2705.864 -17.121533 0.22749088 0 44.507695 7.8560068 -74.789008 0 16.256504 -4.6046686 835.83079 -188.33691 0 114.19415
70 1439.9922 -1989.3026 -1903.4557 23845.829 -2890.7894 31.958655 0.26671714 0 85.758299 3.1804114 -71.002957 0 24.357196 -10.311281 905.86803 -175.38497 0 106.7967
80 502.39806 -1930.7551 -1900.804 -20356.294 -2703.8118 -18.66249 0.11286116 0 99.803602 2.0329432 -76.171314 0 19.236971 -6.2786743 826.47466 -166.0314 0 92.539547
90 749.08048 -1946.9839 -1902.3266 17798.53 -2863.7581 42.068713 0.24338045 0 96.181555 0.96183463 -69.955449 0 24.615403 -11.582762 903.68851 -190.13823 0 120.69122
100 1109.6933 -1968.5879 -1902.4322 -4490.3588 -2755.8988 -7.1225497 0.21757669 0 61.806016 7.0826283 -75.645461 0 20.115364 -6.2372642 863.56468 -198.56954 0 122.09943
Loop time of 0.264553 on 1 procs for 100 steps with 21 atoms
Pair time (%) = 0.245092 (92.6439)
Neigh time (%) = 0.00887609 (3.35512)
Comm time (%) = 0.00054431 (0.205747)
Outpt time (%) = 0.000228405 (0.0863362)
Other time (%) = 0.00981188 (3.70885)
Nlocal: 21 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1096 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.1905
Neighbor list builds = 10
Dangerous builds = 0

81
examples/reax/log.reaxc.rdx.18Feb13.linux.4
View File

@ -1,81 +0,0 @@
LAMMPS (18 Feb 2013)
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real
atom_style charge
read_data data.rdx
orthogonal box = (35 35 35) to (48 48 48)
1 by 2 by 2 MPI processor grid
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx
#dump 1 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
run 100
Memory usage per processor = 3.59594 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -1884.3081 -1884.3081 27186.18 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79953 0 168.88418
10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.60722 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934
20 538.95822 -1942.7037 -1910.5731 -10725.635 -2803.7394 7.9078291 0.077926697 0 81.610051 0.22951943 -57.557107 0 30.331207 -10.178049 878.9901 -159.68963 0 89.313877
30 463.09523 -1933.5765 -1905.9685 -33255.535 -2749.859 -8.0154756 0.027628846 0 81.627404 0.11972406 -50.262287 0 20.820307 -9.6327017 851.88715 -149.49499 0 79.205722
40 885.49345 -1958.9125 -1906.1228 -4814.6579 -2795.6439 9.1506373 0.1374749 0 70.948017 0.24360495 -57.862671 0 19.076505 -11.141215 873.73891 -159.99392 0 92.434084
50 861.16061 -1954.4602 -1903.1211 -1896.7508 -2784.8451 3.8270211 0.15793303 0 79.851614 3.3492088 -78.06613 0 32.628946 -7.9565395 872.81855 -190.98572 0 114.76
60 1167.7828 -1971.8434 -1902.2247 -3482.8488 -2705.8638 -17.121551 0.227491 0 44.507677 7.8559987 -74.789014 0 16.256493 -4.6046659 835.83066 -188.33693 0 114.19417
70 1439.9917 -1989.3026 -1903.4558 23846.315 -2890.7893 31.958613 0.26671709 0 85.75826 3.1804345 -71.002976 0 24.357232 -10.311269 905.86798 -175.385 0 106.79673
80 502.39502 -1930.755 -1900.8041 -20356.14 -2703.813 -18.662112 0.11286018 0 99.803696 2.0329323 -76.171277 0 19.237208 -6.2787216 826.47527 -166.03126 0 92.539416
90 749.07195 -1946.9842 -1902.3273 17798.308 -2863.7576 42.068592 0.24338053 0 96.18133 0.9618479 -69.955394 0 24.615347 -11.58276 903.68813 -190.13817 0 120.69115
100 1109.687 -1968.5881 -1902.4328 -4490.0888 -2755.9001 -7.1221876 0.21757676 0 61.805736 7.082699 -75.645404 0 20.115587 -6.2372974 863.56536 -198.56966 0 122.09956
Loop time of 0.236897 on 4 procs for 100 steps with 21 atoms
Pair time (%) = 0.172669 (72.8878)
Neigh time (%) = 0.00515354 (2.17543)
Comm time (%) = 0.00553721 (2.33739)
Outpt time (%) = 0.000409842 (0.173004)
Other time (%) = 0.0531276 (22.4264)
Nlocal: 5.25 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.5 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 298.75 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1195
Ave neighs/atom = 56.9048
Neighbor list builds = 10
Dangerous builds = 0

79
examples/reax/log.reaxc.tatb.18Feb13.linux.1
View File

@ -1,79 +0,0 @@
LAMMPS (18 Feb 2013)
# ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real
atom_style charge
read_data data.tatb
triclinic box = (0 0 0) to (13.624 17.1149 15.1826) with tilt (-5.75316 -6.32547 7.42573)
1 by 1 by 1 MPI processor grid
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax 1 2 3 4
compute reax all pair reax/c
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c
thermo 5
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq
timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z
#dump 1 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 1 pad 3
fix 3 all reax/c/bonds 1 1 25 bonds.reaxc.tatb
run 25
Memory usage per processor = 23.0386 Mbytes
Step Temp E_pair TotEng Press eb ea elp emol ev epen ecoa ehb et eco ew ep efi eqeq
0 0 -44760.998 -44760.998 7827.7865 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0278
5 0.61603967 -44761.698 -44760.994 8934.6346 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671
10 2.3525552 -44763.227 -44760.541 12288.583 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.7139
15 4.9013321 -44766.36 -44760.764 17716.956 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2549 0 6370.4211
20 7.829462 -44769.686 -44760.747 25205.546 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5195 0 6355.2708
25 10.697905 -44772.904 -44760.691 34232.775 -61069.308 490.25888 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3691 0 6336.8499
Loop time of 3.50117 on 1 procs for 25 steps with 384 atoms
Pair time (%) = 2.71245 (77.4727)
Neigh time (%) = 0.40859 (11.6701)
Comm time (%) = 0.00248218 (0.0708956)
Outpt time (%) = 0.000218868 (0.00625129)
Other time (%) = 0.377427 (10.78)
Nlocal: 384 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 286828
Ave neighs/atom = 746.948
Neighbor list builds = 5
Dangerous builds = 0

Some files were not shown because too many files have changed in this diff Show More