forked from lijiext/lammps
402 lines
25 KiB
Groff
402 lines
25 KiB
Groff
LAMMPS (1 Feb 2014)
|
|
# Tethered nanorods
|
|
|
|
atom_style molecular
|
|
|
|
read_data data.rigid.tnr
|
|
orthogonal box = (-31.122 -31.122 -31.122) to (31.122 31.122 31.122)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
5600 atoms
|
|
scanning bonds ...
|
|
1 = max bonds/atom
|
|
reading bonds ...
|
|
1600 bonds
|
|
2 = max # of 1-2 neighbors
|
|
1 = max # of 1-3 neighbors
|
|
1 = max # of 1-4 neighbors
|
|
2 = max # of special neighbors
|
|
|
|
# Specify bond parameters
|
|
|
|
bond_style fene
|
|
bond_coeff 1 30.0 1.5 1.0 1.0
|
|
|
|
special_bonds fene
|
|
2 = max # of 1-2 neighbors
|
|
2 = max # of special neighbors
|
|
|
|
# Specify initial velocities
|
|
|
|
velocity all create 1.4 109345
|
|
|
|
# Specify rigid components
|
|
|
|
group rods type 2
|
|
4000 atoms in group rods
|
|
group tethers subtract all rods
|
|
1600 atoms in group tethers
|
|
|
|
neigh_modify exclude molecule rods delay 0 every 1
|
|
|
|
# Specify the pair potentials
|
|
|
|
pair_style lj/cut 2.5
|
|
pair_modify shift yes
|
|
pair_coeff * * 1.0 1.0 1.122
|
|
pair_coeff 2 2 1.0 1.0 2.5
|
|
|
|
# Specify output
|
|
|
|
thermo 100
|
|
thermo_style custom step temp pe etotal press enthalpy lx ly lz pxx pyy pzz
|
|
thermo_modify flush yes lost warn
|
|
|
|
timestep 0.005
|
|
|
|
fix 1 rods rigid molecule
|
|
800 rigid bodies with 4000 atoms
|
|
fix 2 tethers nve
|
|
fix 3 all langevin 1.4 1.4 1.0 437624
|
|
|
|
run 5000
|
|
Memory usage per processor = 6.39499 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
0 1.3963219 5.9478449 7.0445809 0.048565317 9.13595 62.244 62.244 62.244 0.0091983659 0.11850113 0.017996458
|
|
100 1.3418512 5.9671777 7.0211299 0.025020362 8.0985822 62.244 62.244 62.244 0.02036076 0.038265078 0.016435248
|
|
200 1.3730638 5.9750802 7.0535483 0.0053287535 7.2830205 62.244 62.244 62.244 -0.00054924195 0.0092396988 0.0072958036
|
|
300 1.376262 5.9821642 7.0631443 0.0055536521 7.3023013 62.244 62.244 62.244 0.0033577704 0.0069111861 0.0063919998
|
|
400 1.3782954 5.9983628 7.08094 0.0020507385 7.169251 62.244 62.244 62.244 -0.0060862717 0.0098998072 0.0023386801
|
|
500 1.386863 6.0053312 7.0946377 -0.0009847031 7.0522334 62.244 62.244 62.244 -0.0038708372 0.0005697804 0.00034694745
|
|
600 1.4069849 6.0035719 7.1086832 0.0047883912 7.3148858 62.244 62.244 62.244 0.001069365 0.0078059505 0.0054898581
|
|
700 1.4423187 5.9982171 7.1310812 0.012141001 7.6539093 62.244 62.244 62.244 0.0094765272 0.011007593 0.015938883
|
|
800 1.4303878 5.9968168 7.1203098 -0.00081349095 7.0852784 62.244 62.244 62.244 0.0011153812 0.00041597298 -0.0039718271
|
|
900 1.4140538 5.9838168 7.0944803 0.00207609 7.183883 62.244 62.244 62.244 0.00043409671 0.0022778944 0.0035162788
|
|
1000 1.3906567 5.988119 7.0804053 0.0022005856 7.1751692 62.244 62.244 62.244 0.0077268425 -0.0022042977 0.0010792119
|
|
1100 1.3921992 5.9892203 7.0827181 0.0035041977 7.2336194 62.244 62.244 62.244 -0.0037576823 0.0040827951 0.01018748
|
|
1200 1.3968803 5.9795846 7.0767592 -0.0031072146 6.9429532 62.244 62.244 62.244 -0.0077387449 0.0033056124 -0.0048885115
|
|
1300 1.3755848 5.9739757 7.0544239 0.0092247106 7.4516677 62.244 62.244 62.244 0.0092788748 0.010737194 0.0076580625
|
|
1400 1.3847985 5.9703631 7.0580481 0.0071703598 7.3668254 62.244 62.244 62.244 0.0080485848 0.012260474 0.001202021
|
|
1500 1.4190051 5.956946 7.0714985 0.0035992903 7.2264948 62.244 62.244 62.244 -0.0055125437 0.01038369 0.0059267242
|
|
1600 1.3980036 5.9671666 7.0652236 0.0061819851 7.3314385 62.244 62.244 62.244 0.0062429141 0.0035120077 0.0087910334
|
|
1700 1.4276062 5.9610381 7.0823462 0.007832375 7.4196319 62.244 62.244 62.244 0.0083316819 0.0058394293 0.009326014
|
|
1800 1.4112769 5.9630595 7.0715419 0.0068032101 7.3645087 62.244 62.244 62.244 0.0065502252 0.0062317255 0.0076276797
|
|
1900 1.4276973 5.9489341 7.0703139 0.008397746 7.4319462 62.244 62.244 62.244 0.0148941 0.0032963108 0.0070028268
|
|
2000 1.4056158 5.9564624 7.0604983 0.0090470732 7.4500926 62.244 62.244 62.244 0.011871718 0.0086681344 0.0066013673
|
|
2100 1.3924778 5.9483611 7.0420778 0.0088893819 7.4248814 62.244 62.244 62.244 0.010247454 0.0097830093 0.0066376825
|
|
2200 1.3760401 5.9435877 7.0243935 -0.0042972782 6.8393397 62.244 62.244 62.244 -0.0050064436 -0.0046216999 -0.0032636911
|
|
2300 1.4191937 5.9334036 7.0481042 0.0047000032 7.2505006 62.244 62.244 62.244 0.0057709636 0.0044949165 0.0038341296
|
|
2400 1.4213285 5.9472214 7.0635988 0.010197674 7.5027414 62.244 62.244 62.244 0.0083738259 0.0090537939 0.013165402
|
|
2500 1.4153808 5.9421661 7.0538718 0.00015906304 7.0607216 62.244 62.244 62.244 0.0023516208 -0.0019814985 0.00010706681
|
|
2600 1.4014223 5.9431386 7.0438807 0.0070733748 7.3484816 62.244 62.244 62.244 0.005414387 0.010055843 0.0057498949
|
|
2700 1.4138077 5.9369067 7.047377 0.0024268844 7.1518859 62.244 62.244 62.244 0.0052918441 0.0014960354 0.00049277387
|
|
2800 1.432192 5.9347676 7.0596777 0.0077670451 7.3941501 62.244 62.244 62.244 0.012668421 0.0059113035 0.0047214114
|
|
2900 1.3938659 5.921023 7.01583 0.00537512 7.2472989 62.244 62.244 62.244 0.0020490377 0.007656609 0.0064197131
|
|
3000 1.390221 5.9205014 7.0124455 -0.0010750979 6.9661485 62.244 62.244 62.244 0.0019519824 -0.0041878903 -0.00098938592
|
|
3100 1.4205722 5.9178284 7.0336117 0.009873547 7.4587965 62.244 62.244 62.244 0.0040973363 0.012167266 0.013356039
|
|
3200 1.398418 5.9150349 7.0134173 0.0061541829 7.278435 62.244 62.244 62.244 0.0067621803 0.011952562 -0.0002521939
|
|
3300 1.4269859 5.9148726 7.0356937 0.0060623983 7.2967588 62.244 62.244 62.244 0.012956243 -2.4795615e-05 0.0052557479
|
|
3400 1.434286 5.9356705 7.0622253 0.00027314048 7.0739876 62.244 62.244 62.244 -0.00054962139 0.0052526062 -0.0038835634
|
|
3500 1.4416809 5.9228152 7.0551783 0.0083382965 7.4142505 62.244 62.244 62.244 0.0073993829 0.0030328137 0.014582693
|
|
3600 1.4136063 5.9039442 7.0142563 0.001971221 7.099143 62.244 62.244 62.244 -0.00032316217 0.003503006 0.0027338193
|
|
3700 1.433382 5.9120101 7.0378549 0.0071287089 7.3448386 62.244 62.244 62.244 0.0064768154 0.0046765426 0.010232769
|
|
3800 1.3659482 5.9032871 6.9761662 -0.0054032435 6.7434863 62.244 62.244 62.244 -0.0073942825 -0.0082831048 -0.00053234334
|
|
3900 1.3963224 5.9042995 7.0010359 0.0053310327 7.2306062 62.244 62.244 62.244 0.0081855547 0.0048807072 0.0029268363
|
|
4000 1.4125479 5.9060668 7.0155474 0.0028451204 7.1380669 62.244 62.244 62.244 0.0052588116 0.00072372172 0.0025528279
|
|
4100 1.3943956 5.9040893 6.9993123 0.0058043569 7.2492654 62.244 62.244 62.244 0.0060576276 0.002478686 0.0088767572
|
|
4200 1.4249783 5.8906355 7.0098796 0.0030213234 7.1399869 62.244 62.244 62.244 0.0061743252 -0.0020791501 0.0049687951
|
|
4300 1.3899826 5.8966344 6.9883912 0.0057294842 7.2351201 62.244 62.244 62.244 0.0049055668 0.0021899931 0.010092893
|
|
4400 1.4414357 5.8986162 7.0307867 0.0050933157 7.2501203 62.244 62.244 62.244 0.0057939021 0.0037947176 0.0056913275
|
|
4500 1.4092608 5.892298 6.9991969 0.0012247406 7.0519379 62.244 62.244 62.244 0.0042876402 0.0014588188 -0.0020722372
|
|
4600 1.3779488 5.8928773 6.9751823 0.0020733584 7.0644674 62.244 62.244 62.244 0.0029285418 -0.0031642229 0.0064557564
|
|
4700 1.4084742 5.909909 7.0161901 -0.00053850548 6.9930004 62.244 62.244 62.244 -0.0018600331 -0.0018359559 0.0020804726
|
|
4800 1.4391588 5.9150069 7.0453891 0.015310705 7.7047142 62.244 62.244 62.244 0.014756643 0.018034492 0.013140978
|
|
4900 1.4496016 5.907877 7.0464614 0.0075305556 7.3707499 62.244 62.244 62.244 0.0091920128 0.0081340187 0.0052656353
|
|
5000 1.4293045 5.9102892 7.0329313 -0.0015935867 6.9643067 62.244 62.244 62.244 -0.0049858888 0.001820566 -0.0016154373
|
|
Loop time of 6.35156 on 1 procs for 5000 steps with 5600 atoms
|
|
|
|
Pair time (%) = 0.478212 (7.52904)
|
|
Bond time (%) = 0.222193 (3.49824)
|
|
Neigh time (%) = 1.2401 (19.5243)
|
|
Comm time (%) = 0.172963 (2.72315)
|
|
Outpt time (%) = 0.00360727 (0.0567935)
|
|
Other time (%) = 4.23449 (66.6685)
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 1351 ave 1351 max 1351 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 5255 ave 5255 max 5255 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 5255
|
|
Ave neighs/atom = 0.938393
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 766
|
|
Dangerous builds = 0
|
|
|
|
# Replace fix rigid and fix langevin with new ones
|
|
|
|
unfix 1
|
|
unfix 3
|
|
|
|
fix 3 tethers langevin 1.4 1.4 1.0 198450
|
|
|
|
# Test different integrators for rods
|
|
|
|
fix 1 rods rigid/nve molecule
|
|
800 rigid bodies with 4000 atoms
|
|
print "rigid/nve"
|
|
rigid/nve
|
|
run 1000
|
|
WARNING: Inconsistent image flags (../domain.cpp:645)
|
|
Memory usage per processor = 6.39499 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
5000 1.4293045 5.9102892 7.0329313 0.028061066 8.2413255 62.244 62.244 62.244 0.017765452 0.040562905 0.02585484
|
|
5100 1.4400998 5.9022414 7.0333627 0.0061821009 7.2995826 62.244 62.244 62.244 0.009770998 0.0030836918 0.0056916129
|
|
5200 1.4082657 5.9104139 7.0165312 0.0064210573 7.2930413 62.244 62.244 62.244 0.0080770492 0.0051169375 0.0060691852
|
|
5300 1.45649 5.8801752 7.0241701 0.0069092534 7.3217034 62.244 62.244 62.244 0.0065768895 0.0056877656 0.0084631052
|
|
5400 1.4233427 5.8824466 7.000406 0.0035507414 7.1533117 62.244 62.244 62.244 0.0033649256 -0.00080481231 0.0080921109
|
|
5500 1.4203908 5.8713513 6.9869921 0.0082802387 7.3435642 62.244 62.244 62.244 0.0073789675 0.0076306312 0.0098311173
|
|
5600 1.4100524 5.8744301 6.9819507 0.0025993542 7.0938867 62.244 62.244 62.244 -0.002226516 0.005551312 0.0044732667
|
|
5700 1.4094008 5.8740942 6.981103 0.001858876 7.0611518 62.244 62.244 62.244 -0.00080782471 -0.00061623499 0.0070006878
|
|
5800 1.4017129 5.8875092 6.9884795 0.0010380104 7.0331794 62.244 62.244 62.244 0.0043974934 -0.0033700586 0.0020865964
|
|
5900 1.3979088 5.8861057 6.9840882 0.0019969425 7.0700826 62.244 62.244 62.244 -0.002580911 0.0061245675 0.0024471709
|
|
6000 1.4274747 5.8829671 7.004172 0.00018898098 7.0123101 62.244 62.244 62.244 0.0019071211 -0.0011893793 -0.00015079887
|
|
Loop time of 1.27908 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Pair time (%) = 0.137631 (10.7602)
|
|
Bond time (%) = 0.0451553 (3.53029)
|
|
Neigh time (%) = 0.276716 (21.634)
|
|
Comm time (%) = 0.0356052 (2.78366)
|
|
Outpt time (%) = 0.000710726 (0.0555654)
|
|
Other time (%) = 0.783261 (61.2363)
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 1380 ave 1380 max 1380 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 5416 ave 5416 max 5416 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 5416
|
|
Ave neighs/atom = 0.967143
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 153
|
|
Dangerous builds = 0
|
|
unfix 1
|
|
|
|
fix 1 rods rigid/nvt molecule temp 1.4 1.4 1.0
|
|
800 rigid bodies with 4000 atoms
|
|
print "rigid/nvt"
|
|
rigid/nvt
|
|
run 1000
|
|
WARNING: Inconsistent image flags (../domain.cpp:645)
|
|
Memory usage per processor = 6.39499 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
6000 1.4274747 5.8829671 7.004172 -0.02124798 6.0891699 62.244 62.244 62.244 -0.0035029341 -0.035545622 -0.024695385
|
|
6100 1.4047816 5.8827162 6.9860969 0.0039973389 7.1582344 62.244 62.244 62.244 0.0038546201 0.0038745986 0.0042627978
|
|
6200 1.4013195 5.8723518 6.9730132 0.0055794243 7.21328 62.244 62.244 62.244 0.0052298684 0.006566317 0.0049420874
|
|
6300 1.4164814 5.8699858 6.982556 0.0046834632 7.18424 62.244 62.244 62.244 0.0042595662 0.0075687542 0.0022220694
|
|
6400 1.4008382 5.8754385 6.9757219 0.0057855428 7.2248648 62.244 62.244 62.244 0.011229504 0.0035917167 0.0025354077
|
|
6500 1.3961747 5.8821344 6.9787548 0.0054798914 7.2147355 62.244 62.244 62.244 0.0079746581 0.0012807952 0.007184221
|
|
6600 1.3989989 5.8839851 6.9828238 0.0078068029 7.3190083 62.244 62.244 62.244 0.0075737438 0.01001737 0.0058292953
|
|
6700 1.3944424 5.8846079 6.9798678 0.0025837202 7.0911306 62.244 62.244 62.244 0.001801077 0.0043727527 0.0015773308
|
|
6800 1.3886249 5.8876899 6.9783804 0.0083096819 7.3362204 62.244 62.244 62.244 0.0057252172 0.0080731664 0.011130662
|
|
6900 1.4128008 5.8873288 6.9970082 -0.0017879625 6.9200131 62.244 62.244 62.244 0.0032920311 -0.0044843856 -0.004171533
|
|
7000 1.4296767 5.8776376 7.0005721 0.0028980535 7.125371 62.244 62.244 62.244 0.0020944649 0.002732346 0.0038673497
|
|
Loop time of 1.30653 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Pair time (%) = 0.140375 (10.7442)
|
|
Bond time (%) = 0.0453455 (3.47069)
|
|
Neigh time (%) = 0.278969 (21.3519)
|
|
Comm time (%) = 0.0354125 (2.71043)
|
|
Outpt time (%) = 0.000714064 (0.0546535)
|
|
Other time (%) = 0.805712 (61.6681)
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 1365 ave 1365 max 1365 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 5888 ave 5888 max 5888 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 5888
|
|
Ave neighs/atom = 1.05143
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 151
|
|
Dangerous builds = 0
|
|
unfix 1
|
|
|
|
compute myTemp all temp
|
|
|
|
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 iso 0.05 0.05 1.0 dilate all
|
|
800 rigid bodies with 4000 atoms
|
|
print "rigid/npt iso"
|
|
rigid/npt iso
|
|
fix_modify 1 temp myTemp
|
|
|
|
run 1000
|
|
WARNING: Inconsistent image flags (../domain.cpp:645)
|
|
Memory usage per processor = 6.39499 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
7000 1.4296767 5.8776376 7.0005721 0.012931516 7.5574422 62.244 62.244 62.244 -0.033811545 0.071351891 0.0012542007
|
|
7100 1.4257807 5.8661379 6.9860122 0.0063203866 7.2286059 59.901999 59.901999 59.901999 0.0075682964 0.0028831604 0.0085097032
|
|
7200 1.407746 5.857124 6.962833 0.0084753318 7.2534913 57.694979 57.694979 57.694979 0.010202527 0.0094388943 0.005784574
|
|
7300 1.3925246 5.8467137 6.9404672 0.014254002 7.3803203 55.699712 55.699712 55.699712 0.010958166 0.015538449 0.01626539
|
|
7400 1.3876126 5.8261824 6.9160778 0.011565854 7.238709 53.8566 53.8566 53.8566 0.010074234 0.013288968 0.011334359
|
|
7500 1.4080244 5.8243986 6.9303263 0.013237792 7.2665719 52.200705 52.200705 52.200705 0.014684708 0.015549417 0.0094792517
|
|
7600 1.4024992 5.8202266 6.9218146 0.0087754412 7.1257639 50.677331 50.677331 50.677331 0.012762778 0.0046632388 0.0089003068
|
|
7700 1.4053227 5.79557 6.8993757 0.017894387 7.2814436 49.264862 49.264862 49.264862 0.017455799 0.011081333 0.02514603
|
|
7800 1.3626299 5.7913047 6.8615775 -0.0027715764 6.8070755 47.931898 47.931898 47.931898 -0.00096112659 -0.00022698058 -0.0071266219
|
|
7900 1.3811061 5.7611338 6.8459187 0.022417792 7.2542129 46.722152 46.722152 46.722152 0.017429453 0.023217068 0.026606854
|
|
8000 1.3909989 5.7527072 6.8452623 0.0050901754 6.9314891 45.607102 45.607102 45.607102 0.0033084213 0.0050773514 0.0068847534
|
|
Loop time of 2.1421 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Pair time (%) = 0.243607 (11.3723)
|
|
Bond time (%) = 0.067399 (3.1464)
|
|
Neigh time (%) = 0.578037 (26.9846)
|
|
Comm time (%) = 0.0550971 (2.5721)
|
|
Outpt time (%) = 0.000721693 (0.0336909)
|
|
Other time (%) = 1.19724 (55.8909)
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 1964 ave 1964 max 1964 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 11395 ave 11395 max 11395 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 11395
|
|
Ave neighs/atom = 2.03482
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 263
|
|
Dangerous builds = 0
|
|
unfix 1
|
|
|
|
fix 1 rods rigid/npt molecule temp 1.4 1.4 1.0 x 0.05 0.05 1.0 dilate all
|
|
800 rigid bodies with 4000 atoms
|
|
print "rigid/npt x"
|
|
rigid/npt x
|
|
run 1000
|
|
WARNING: Inconsistent image flags (../domain.cpp:645)
|
|
Memory usage per processor = 6.39499 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
8000 1.3909989 5.7527072 6.8452623 -0.013693646 6.6132941 45.607102 45.607102 45.607102 -0.043122633 -0.045235911 0.047277607
|
|
8100 1.3859992 5.7541236 6.8427517 0.025001526 7.2534745 44.228819 45.607102 45.607102 0.034466544 0.018726978 0.021811058
|
|
8200 1.3854121 5.741923 6.83009 0.00064570832 6.8403853 42.926629 45.607102 45.607102 0.0027453757 0.0012726672 -0.002080918
|
|
8300 1.4154816 5.7503811 6.8621661 0.0142623 7.0833894 41.760381 45.607102 45.607102 0.011045171 0.01999352 0.011748208
|
|
8400 1.3809342 5.7526615 6.8373114 0.010034961 6.9882285 40.489828 45.607102 45.607102 0.013514677 0.009127176 0.0074630301
|
|
8500 1.377763 5.7274882 6.8096473 0.010601881 6.9645838 39.345393 45.607102 45.607102 0.011511215 0.00061614599 0.019678283
|
|
8600 1.431011 5.716086 6.8400685 0.0082177641 6.9567982 38.242914 45.607102 45.607102 0.017556217 0.0072745279 -0.00017745274
|
|
8700 1.4088268 5.7023605 6.8089185 0.014325516 7.006943 37.216169 45.607102 45.607102 0.030284184 0.0090717286 0.0036206352
|
|
8800 1.4053586 5.7019319 6.8057658 0.004331614 6.8641135 36.265817 45.607102 45.607102 0.0075148755 0.012823387 -0.0073434199
|
|
8900 1.4159123 5.7005178 6.812641 0.013485111 6.9893826 35.286383 45.607102 45.607102 0.025461313 0.0051541371 0.0098398833
|
|
9000 1.4232531 5.6865082 6.8043973 0.014588857 6.9910378 34.44354 45.607102 45.607102 0.016849826 0.025113792 0.0018029545
|
|
Loop time of 2.23572 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Pair time (%) = 0.329728 (14.7482)
|
|
Bond time (%) = 0.0679741 (3.04037)
|
|
Neigh time (%) = 0.547063 (24.4692)
|
|
Comm time (%) = 0.0531805 (2.37867)
|
|
Outpt time (%) = 0.000710964 (0.0318003)
|
|
Other time (%) = 1.23706 (55.3317)
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 2374 ave 2374 max 2374 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 14730 ave 14730 max 14730 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 14730
|
|
Ave neighs/atom = 2.63036
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 190
|
|
Dangerous builds = 0
|
|
unfix 1
|
|
|
|
fix 1 rods rigid/nph molecule iso 0.05 0.05 1.0 dilate all
|
|
800 rigid bodies with 4000 atoms
|
|
print "rigid/nph iso"
|
|
rigid/nph iso
|
|
run 1000
|
|
WARNING: Inconsistent image flags (../domain.cpp:645)
|
|
Memory usage per processor = 6.39499 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
9000 1.4232531 5.6865082 6.8043973 -0.045897712 6.2172112 34.44354 45.607102 45.607102 -0.13827955 -0.060145768 0.060732183
|
|
9100 1.4046189 5.689947 6.7931999 0.025063166 7.0966586 33.816926 44.777394 44.777394 0.026506621 0.026941055 0.021741822
|
|
9200 1.4514944 5.6439353 6.7840064 0.010043669 6.8992028 33.212004 43.97641 43.97641 0.013456849 0.016567864 0.00010629292
|
|
9300 1.4577939 5.655083 6.800102 0.010672001 6.9162857 32.639692 43.218605 43.218605 0.026259683 -0.0039439335 0.0097002517
|
|
9400 1.4990612 5.6382783 6.8157106 0.0044191075 6.8615643 32.121265 42.53215 42.53215 -0.0025936629 0.022212724 -0.0063617388
|
|
9500 1.4578238 5.6474926 6.7925351 0.011187763 6.9033093 31.623599 41.873184 41.873184 0.026402116 0.012016515 -0.0048553414
|
|
9600 1.4618782 5.6455953 6.7938223 0.040647445 7.17882 31.159311 41.258416 41.258416 0.030007882 0.037188739 0.054745715
|
|
9700 1.472894 5.6140659 6.7709452 0.031213864 7.0543129 30.721834 40.679146 40.679146 0.030150709 0.023805303 0.03968558
|
|
9800 1.4853035 5.5879969 6.7546233 0.019089748 6.920651 30.285846 40.101849 40.101849 -0.001882924 0.030361407 0.02879076
|
|
9900 1.4922807 5.5739043 6.7460109 0.034454036 7.033471 29.869325 39.55033 39.55033 0.037756787 0.037488603 0.028116717
|
|
10000 1.4702912 5.5609742 6.7158092 0.02974948 6.9548436 29.496685 39.056912 39.056912 0.048495581 0.026126614 0.014626246
|
|
Loop time of 2.46339 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Pair time (%) = 0.418965 (17.0077)
|
|
Bond time (%) = 0.0689692 (2.79977)
|
|
Neigh time (%) = 0.69069 (28.0382)
|
|
Comm time (%) = 0.0612285 (2.48554)
|
|
Outpt time (%) = 0.00073576 (0.0298677)
|
|
Other time (%) = 1.2228 (49.639)
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 2884 ave 2884 max 2884 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 21437 ave 21437 max 21437 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 21437
|
|
Ave neighs/atom = 3.82804
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 190
|
|
Dangerous builds = 0
|
|
unfix 1
|
|
|
|
fix 1 rods rigid/nph molecule x 0.05 0.05 1.0 y 0.05 0.05 1.0 couple xy dilate all
|
|
800 rigid bodies with 4000 atoms
|
|
print "rigid/nph xy couple"
|
|
rigid/nph xy couple
|
|
run 1000
|
|
WARNING: Inconsistent image flags (../domain.cpp:645)
|
|
Memory usage per processor = 6.39881 Mbytes
|
|
Step Temp PotEng TotEng Press Enthalpy Lx Ly Lz Pxx Pyy Pzz
|
|
10000 1.4702912 5.5609742 6.7158092 0.072285735 7.2966186 29.496685 39.056912 39.056912 0.0517015 0.12420995 0.040945755
|
|
10100 1.4573097 5.5587677 6.7034064 0.044500854 7.0509833 29.081982 38.507799 39.056912 0.044350384 0.023335488 0.06581669
|
|
10200 1.4979402 5.529745 6.7062968 0.020491404 6.8628393 28.761597 38.083573 39.056912 0.027897265 0.011514546 0.0220624
|
|
10300 1.5172843 5.5187731 6.7105187 0.02641776 6.9082543 28.469328 37.696576 39.056912 0.036912371 0.030960772 0.011380138
|
|
10400 1.4760818 5.5254938 6.684877 0.0091876447 6.7521031 28.14814 37.271288 39.056912 0.015300105 0.02827069 -0.016007861
|
|
10500 1.5146302 5.5026001 6.692261 0.021789385 6.8479527 27.815895 36.831359 39.056912 0.015592969 0.032547229 0.017227956
|
|
10600 1.4679788 5.4885912 6.64161 0.011753224 6.7237238 27.505044 36.419757 39.056912 0.010721153 0.010926592 0.013611926
|
|
10700 1.4667245 5.4720863 6.6241198 0.0043905713 6.6539747 27.135001 35.929779 39.056912 -0.03606819 0.013643937 0.035595967
|
|
10800 1.4647544 5.4559859 6.606472 0.036718423 6.8501768 26.80851 35.497468 39.056912 0.044497798 0.031324763 0.034332708
|
|
10900 1.4580432 5.4564769 6.6016918 0.065478135 7.0263115 26.499317 35.088061 39.056912 0.08229008 0.052793688 0.061350637
|
|
11000 1.4700915 5.4471801 6.6018582 -0.016382922 6.4976429 26.245381 34.751822 39.056912 -0.0093025128 -0.034580288 -0.005265964
|
|
Loop time of 2.65811 on 1 procs for 1000 steps with 5600 atoms
|
|
|
|
Pair time (%) = 0.524128 (19.7181)
|
|
Bond time (%) = 0.068589 (2.58037)
|
|
Neigh time (%) = 0.759783 (28.5836)
|
|
Comm time (%) = 0.0634546 (2.38721)
|
|
Outpt time (%) = 0.000737429 (0.0277426)
|
|
Other time (%) = 1.24142 (46.7031)
|
|
|
|
Nlocal: 5600 ave 5600 max 5600 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 3289 ave 3289 max 3289 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 27077 ave 27077 max 27077 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 27077
|
|
Ave neighs/atom = 4.83518
|
|
Ave special neighs/atom = 0.571429
|
|
Neighbor list builds = 170
|
|
Dangerous builds = 0
|
|
|