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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14610 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2016-02-15 18:06:11 +00:00
parent b1922ae7ca
commit bee7ffaee5
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225
examples/balance/log.15Feb16.balance.bond.fast.g++.1 Normal file
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LAMMPS (15 Feb 2016)
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
1 by 1 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
special_bonds lj/coul 0 1 1
0 = max # of 1-2 neighbors
1 = max # of special neighbors
create_bonds all all 1 1.0 1.5
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 42 29 1
Added 1014 bonds, new total = 1014
6 = max # of 1-2 neighbors
6 = max # of special neighbors
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
comm_modify cutoff 7.5
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 7.5
binsize = 1.4 -> bins = 42 29 1
Memory usage per processor = 4.44301 Mbytes
Step Temp E_pair Press 10[3] 10
0 25.701528 -2.2032569 3.1039469 1 1
100 27.623422 -6.228166 2.6542136 1 1
200 33.35302 -15.746749 3.2018248 1 1
300 39.17734 -24.1557 4.9116986 1 1
400 41.660701 -27.615203 8.6214678 1 1
500 37.154935 -24.096962 3.2656162 1 1
600 35.061294 -21.52655 2.3693223 1 1
700 37.204395 -22.313267 2.7108913 1 1
800 39.050704 -24.972147 5.5398741 1 1
900 38.37275 -24.777769 3.9291488 1 1
1000 39.147816 -26.003699 4.3586203 1 1
1100 36.084337 -24.88638 4.5496174 1 1
1200 32.404559 -20.810803 6.0760128 1 1
1300 32.625538 -19.709411 4.3718289 1 1
1400 32.246777 -18.785184 3.435959 1 1
1500 29.174368 -17.434726 2.2702916 1 1
1600 27.359273 -15.40756 1.033659 1 1
1700 26.046626 -14.318045 0.87714473 1 1
1800 24.540401 -13.017686 0.84464169 1 1
1900 26.259688 -12.777739 0.80954004 1 1
2000 27.491023 -13.363863 1.4519188 1 1
2100 27.839831 -13.709118 3.0184763 1 1
2200 26.669065 -12.710422 1.4560094 1 1
2300 26.86742 -12.730386 0.16986139 1 1
2400 26.375504 -12.476682 1.907352 1 1
2500 26.581263 -12.530908 1.5507765 1 1
2600 27.67091 -12.922702 2.0391206 1 1
2700 27.158784 -13.306789 3.7355268 1 1
2800 25.635671 -13.502047 2.9431633 1 1
2900 24.648357 -12.388002 0.44910075 1 1
3000 22.988768 -10.685349 0.37214853 1 1
3100 21.788719 -10.171928 -0.95734833 1 1
3200 22.707514 -9.6682633 -0.32868418 1 1
3300 22.907772 -10.612766 -0.024319089 1 1
3400 24.276426 -10.802246 0.44731188 1 1
3500 25.086959 -10.797849 2.3218091 1 1
3600 26.064365 -12.589537 1.2460738 1 1
3700 24.656426 -11.956895 0.57862216 1 1
3800 22.316856 -11.174148 -0.7567936 1 1
3900 22.590299 -9.5928781 0.4127727 1 1
4000 22.353461 -9.5887736 -0.34247396 1 1
4100 24.103395 -9.76584 0.98989862 1 1
4200 23.92261 -10.566828 -0.71536268 1 1
4300 24.44409 -11.358378 0.37166197 1 1
4400 24.772419 -11.324888 0.26732853 1 1
4500 23.150748 -11.309892 -0.43134573 1 1
4600 24.008361 -10.212365 0.43277527 1 1
4700 25.107401 -9.5753673 0.020406689 1 1
4800 23.658604 -8.9131426 0.46554745 1 1
4900 22.530251 -9.023311 -0.014405315 1 1
5000 23.110692 -9.6567397 0.9033234 1 1
5100 23.760144 -9.7623416 0.32059726 1 1
5200 25.048012 -9.6748253 0.66411561 1 1
5300 24.09835 -9.7867216 0.61128267 1 1
5400 22.984982 -9.9464053 0.28096544 1 1
5500 22.502003 -9.9294451 -0.53666181 1 1
5600 23.712298 -10.054318 0.64334761 1 1
5700 23.350796 -10.217344 2.1979894 1 1
5800 25.246549 -12.458753 0.055553025 1 1
5900 24.422272 -10.641177 0.82506839 1 1
6000 22.478315 -10.629525 -0.774321 1 1
6100 22.970846 -10.218868 0.59819592 1 1
6200 24.500063 -10.355481 0.55427078 1 1
6300 22.358071 -9.9041539 0.89500518 1 1
6400 23.924951 -11.121442 0.045999129 1 1
6500 24.83773 -10.464191 2.0048038 1 1
6600 24.752158 -9.9939162 0.53794465 1 1
6700 23.073765 -9.3662561 0.38618685 1 1
6800 21.940219 -8.4948475 -0.25184019 1 1
6900 22.23783 -8.8668868 0.0072863367 1 1
7000 25.667836 -10.473211 0.59852886 1 1
7100 23.352123 -9.0862268 0.85289283 1 1
7200 24.072107 -9.4020576 0.090222808 1 1
7300 22.806746 -8.4687857 -0.46892989 1 1
7400 24.798425 -9.1144357 -0.38738146 1 1
7500 24.748499 -9.1560558 0.94929896 1 1
7600 25.364753 -10.176533 0.2649225 1 1
7700 25.137988 -9.6617897 1.3920543 1 1
7800 25.502583 -10.320832 0.64812816 1 1
7900 24.5208 -9.9466543 -0.084071026 1 1
8000 24.653522 -10.312942 0.32535023 1 1
8100 23.129565 -9.6250435 0.016356303 1 1
8200 23.82421 -9.7608023 0.11631418 1 1
8300 25.081262 -9.3510452 0.92337854 1 1
8400 24.328205 -9.2875396 0.28266968 1 1
8500 25.041711 -11.254976 -0.21368615 1 1
8600 24.111473 -9.0389585 1.2102938 1 1
8700 23.50066 -9.0926498 0.78819229 1 1
8800 23.840962 -9.3434474 0.091313007 1 1
8900 23.081841 -9.0635966 0.56672001 1 1
9000 24.712103 -9.3243213 0.60301629 1 1
9100 24.457422 -9.439298 -0.60457515 1 1
9200 25.070662 -9.1945782 1.2399235 1 1
9300 25.019869 -8.7910068 0.42340497 1 1
9400 24.23662 -9.3111098 -0.75379175 1 1
9500 24.836827 -8.7324281 0.81857501 1 1
9600 24.901993 -8.6624128 0.84890877 1 1
9700 24.936686 -8.9869503 1.9627894 1 1
9800 25.393368 -9.8538595 0.45344428 1 1
9900 25.942336 -9.7854728 0.68352091 1 1
10000 24.636319 -9.3369442 0.62793231 1 1
Loop time of 1.67474 on 1 procs for 10000 steps with 361 atoms
Performance: 2579511.004 tau/day, 5971.090 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.47884 | 0.47884 | 0.47884 | 0.0 | 28.59
Bond | 0.24918 | 0.24918 | 0.24918 | 0.0 | 14.88
Neigh | 0.82974 | 0.82974 | 0.82974 | 0.0 | 49.54
Comm | 0.01265 | 0.01265 | 0.01265 | 0.0 | 0.76
Output | 0.00085878 | 0.00085878 | 0.00085878 | 0.0 | 0.05
Modify | 0.075636 | 0.075636 | 0.075636 | 0.0 | 4.52
Other | | 0.02783 | | | 1.66
Nlocal: 361 ave 361 max 361 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: 2421 ave 2421 max 2421 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2421
Ave neighs/atom = 6.70637
Ave special neighs/atom = 5.61773
Neighbor list builds = 4937
Dangerous builds = 5
Total wall time: 0:00:01

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examples/balance/log.15Feb16.balance.bond.fast.g++.4 Normal file
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LAMMPS (15 Feb 2016)
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
2 by 2 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
special_bonds lj/coul 0 1 1
0 = max # of 1-2 neighbors
1 = max # of special neighbors
create_bonds all all 1 1.0 1.5
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 42 29 1
Added 1014 bonds, new total = 1014
6 = max # of 1-2 neighbors
6 = max # of special neighbors
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
comm_modify cutoff 7.5
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 7.5
binsize = 1.4 -> bins = 42 29 1
Memory usage per processor = 4.49421 Mbytes
Step Temp E_pair Press 10[3] 10
0 25.701528 -2.2032569 3.1039469 3.2354571 1.0526316
100 27.623422 -6.228166 2.6542136 1.2631579 1.0083102
200 33.35302 -15.746749 3.2018248 1.2963989 1.0193906
300 39.17734 -24.1557 4.9116986 1.2963989 1.0193906
400 41.660701 -27.615203 8.6214679 1.3518006 1.0083102
500 37.154928 -24.096947 3.2656178 1.3296399 1.0193906
600 35.059889 -21.524279 2.372849 1.3296399 1.0083102
700 36.70516 -21.98396 3.2995108 1.3296399 1.0083102
800 39.53521 -25.672748 4.3257712 1.3961219 1.0083102
900 38.566797 -24.778382 4.1874914 1.3739612 1.0083102
1000 37.506157 -25.381025 5.6634589 1.4182825 1.0193906
1100 34.186888 -23.460558 5.2123037 1.2963989 1.0083102
1200 33.302788 -22.509552 4.9394032 1.1745152 1.0193906
1300 33.271956 -22.831342 4.5519649 1.1966759 1.0083102
1400 30.344677 -20.654604 4.1641375 1.0969529 1.0193906
1500 27.292624 -18.180523 1.0686706 1.1412742 1.0083102
1600 26.787948 -15.907011 1.7236133 1.1745152 1.0193906
1700 25.708419 -15.568774 0.73006531 1.1080332 1.0193906
1800 26.523196 -14.641077 0.78443231 1.1301939 1.0083102
1900 25.151151 -13.927975 1.1760729 1.1080332 1.0193906
2000 27.637036 -15.055467 1.5903524 1.1301939 1.0083102
2100 27.642772 -14.038356 2.4101976 1.2077562 1.0083102
2200 27.178261 -13.277262 1.9252291 1.1745152 1.0193906
2300 25.615526 -12.67851 0.88527229 1.1634349 1.0083102
2400 24.918218 -13.029669 0.95714212 1.1966759 1.0193906
2500 27.302154 -13.02629 1.3556788 1.1080332 1.0193906
2600 26.798157 -13.78042 2.703198 1.1855956 1.0083102
2700 27.24573 -16.504845 3.1771274 1.1523546 1.0193906
2800 24.592313 -14.795322 1.6473982 1.0969529 1.0193906
2900 22.803769 -13.043913 0.71978239 1.0969529 1.0083102
3000 21.388681 -13.323114 -1.3437735 1.0858726 1.0083102
3100 21.929044 -11.627262 -0.38509856 1.1191136 1.0083102
3200 22.350115 -10.438826 0.7833392 1.0526316 1.0083102
3300 22.619011 -9.9110914 1.4143766 1.1191136 1.0193906
3400 24.251234 -11.712256 1.4299187 1.0969529 1.0193906
3500 25.633796 -12.609976 1.4809529 1.0969529 1.0083102
3600 23.070279 -11.178798 0.35315388 1.1191136 1.0083102
3700 22.635771 -10.360523 0.060253018 1.1412742 1.0193906
3800 20.746426 -9.7066538 0.24549731 1.0526316 1.0083102
3900 22.467121 -10.469368 0.9854352 1.0969529 1.0193906
4000 22.658639 -10.781605 0.014232783 1.1191136 1.0083102
4100 22.839698 -10.528796 1.3995223 1.0526316 1.0083102
4200 23.52621 -12.150065 0.74863439 1.0747922 1.0193906
4300 24.401948 -11.703236 0.25019621 1.0637119 1.0193906
4400 22.769001 -11.763045 -0.033044917 1.1412742 1.0083102
4500 22.170178 -11.572473 -0.40444128 1.0526316 1.0083102
4600 22.409231 -10.761099 -0.012942618 1.0747922 1.0083102
4700 22.953641 -10.999181 0.17199357 1.0637119 1.0083102
4800 22.746977 -10.69943 -0.050664647 1.0526316 1.0083102
4900 23.784023 -10.353932 0.55400224 1.0747922 1.0304709
5000 23.250563 -11.567067 -0.23735032 1.0637119 1.0083102
5100 22.521138 -10.661998 0.50094359 1.0747922 1.0083102
5200 21.318659 -9.5996948 0.75683786 1.0637119 1.0193906
5300 21.603355 -10.042239 -0.2376815 1.0637119 1.0083102
5400 21.350407 -10.181041 -0.87085628 1.1745152 1.0193906
5500 22.430002 -10.535576 0.47962005 1.1191136 1.0193906
5600 22.459036 -11.914086 0.47719353 1.0858726 1.0193906
5700 23.348257 -12.888911 0.55511547 1.0858726 1.0193906
5800 23.357742 -12.328566 0.734193 1.0526316 1.0193906
5900 24.002277 -11.439187 0.23688862 1.0858726 1.0193906
6000 22.398563 -10.682615 0.28777592 1.0747922 1.0193906
6100 22.23883 -10.838986 -0.17956279 1.1080332 1.0083102
6200 21.930735 -11.182485 0.044031465 1.0526316 1.0193906
6300 22.658226 -11.142419 0.060550217 1.0526316 1.0193906
6400 22.375935 -11.1764 -0.027267206 1.0526316 1.0193906
6500 21.553541 -9.9609653 1.0562139 1.0858726 1.0193906
6600 23.339323 -10.988956 0.19462502 1.0526316 1.0083102
6700 22.506968 -11.276791 0.50225378 1.0969529 1.0083102
6800 22.991741 -10.292043 1.3278137 1.0858726 1.0193906
6900 22.716461 -10.540264 1.090723 1.0304709 1.0083102
7000 20.88433 -10.566053 -0.47976012 1.0969529 1.0193906
7100 22.034864 -10.27774 0.24169213 1.0193906 1.0083102
7200 23.107403 -10.304771 0.39888005 1.0969529 1.0304709
7300 22.734104 -9.8038963 1.1986757 1.0858726 1.0083102
7400 23.566402 -10.560548 1.0213434 1.1080332 1.0193906
7500 23.651346 -10.596902 1.290057 1.0969529 1.0083102
7600 23.181407 -10.247073 0.80701327 1.0526316 1.0083102
7700 23.778698 -10.659208 0.54327672 1.0304709 1.0193906
7800 22.655159 -10.183303 0.81382393 1.0747922 1.0193906
7900 22.897008 -10.849819 0.56424197 1.0415512 1.0083102
8000 23.698074 -10.398048 0.42170034 1.0747922 1.0083102
8100 22.726563 -9.8563277 0.30293638 1.0193906 1.0193906
8200 23.424699 -10.687885 0.54222367 1.0415512 1.0083102
8300 22.921826 -10.919492 0.55264172 1.0747922 1.0083102
8400 23.220159 -9.7725217 1.2872547 1.1080332 1.0083102
8500 23.606204 -9.7070499 1.0340181 1.0747922 1.0193906
8600 23.008166 -10.451507 -0.42524326 1.0747922 1.0083102
8700 22.4959 -10.278782 0.19535494 1.0858726 1.0083102
8800 25.153658 -10.757 1.5966743 1.0193906 1.0193906
8900 23.206798 -10.486994 1.2031737 1.0637119 1.0083102
9000 22.726684 -10.406196 0.10165144 1.0858726 1.0304709
9100 22.504045 -9.638919 -0.80560991 1.0747922 1.0083102
9200 21.431928 -9.073801 0.3773795 1.0415512 1.0193906
9300 23.596502 -11.045041 -0.3135787 1.0858726 1.0083102
9400 25.308669 -11.931174 1.3143518 1.0526316 1.0193906
9500 24.394499 -10.661499 0.82236963 1.0969529 1.0193906
9600 21.987451 -9.5632699 0.30728292 1.0858726 1.0193906
9700 22.150748 -9.5707928 -0.1239396 1.0526316 1.0193906
9800 23.347328 -9.7899306 0.29737715 1.0193906 1.0083102
9900 20.310207 -9.4839992 -1.2980277 1.0193906 1.0193906
10000 22.978427 -9.9593786 -0.45943368 1.0526316 1.0083102
Loop time of 0.815364 on 4 procs for 10000 steps with 361 atoms
Performance: 5298244.819 tau/day, 12264.456 timesteps/s
98.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12547 | 0.13632 | 0.14796 | 2.6 | 16.72
Bond | 0.05547 | 0.06023 | 0.064582 | 1.7 | 7.39
Neigh | 0.28201 | 0.28972 | 0.298 | 1.1 | 35.53
Comm | 0.16858 | 0.19467 | 0.22096 | 4.3 | 23.88
Output | 0.0017931 | 0.0019639 | 0.0023253 | 0.5 | 0.24
Modify | 0.039718 | 0.040559 | 0.041364 | 0.4 | 4.97
Other | | 0.09189 | | | 11.27
Nlocal: 90.25 ave 91 max 90 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 195.25 ave 202 max 185 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 629.5 ave 731 max 543 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 2518
Ave neighs/atom = 6.97507
Ave special neighs/atom = 5.61773
Neighbor list builds = 4874
Dangerous builds = 0
Total wall time: 0:00:00

524
examples/balance/log.15Feb16.balance.bond.slow.g++.1 Normal file
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LAMMPS (15 Feb 2016)
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
# careful not to slam into wall too hard
variable v index 0.3
variable w index 0.08
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
1 by 1 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 0.3 $w 0 sum yes
velocity all set 0.3 0.08 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
create_bonds all all 1 1.0 1.5
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 42 29 1
Added 1014 bonds, new total = 1014
6 = max # of 1-2 neighbors
30 = max # of 1-3 neighbors
180 = max # of 1-4 neighbors
36 = max # of special neighbors
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 40000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 42 29 1
Memory usage per processor = 6.31529 Mbytes
Step Temp E_pair Press 10[3] 10
0 0.57437856 0 0.26099453 1 1
100 0.29756515 0 0.10149401 1 1
200 0.35394813 0 0.075159099 1 1
300 0.39245849 0 0.033002384 1 1
400 0.34078347 0 -0.020825841 1 1
500 0.35201095 0 -0.062637506 1 1
600 0.34014717 0 -0.11122965 1 1
700 0.3323524 0 -0.11598015 1 1
800 0.35116047 0 -0.096162395 1 1
900 0.35695352 0 -0.01385176 1 1
1000 0.36986539 0 0.056772858 1 1
1100 0.34584644 0 0.084941323 1 1
1200 0.31921435 0 0.10545078 1 1
1300 0.32952819 0 0.124902 1 1
1400 0.34497365 0 0.12662081 1 1
1500 0.33429243 0 0.096230972 1 1
1600 0.33765387 0 0.025800542 1 1
1700 0.35134464 0 -0.04422593 1 1
1800 0.35003859 0 -0.096745576 1 1
1900 0.33839618 0 -0.095465943 1 1
2000 0.33732078 0 -0.094652802 1 1
2100 0.34552238 0 -0.076729261 1 1
2200 0.34893142 0 -0.036853228 1 1
2300 0.35379341 0 0.021124847 1 1
2400 0.34829744 0 0.09230184 1 1
2500 0.33038141 0 0.1399855 1 1
2600 0.30983019 0 0.12754742 1 1
2700 0.32992561 0 0.10485138 1 1
2800 0.34604747 0 0.066174138 1 1
2900 0.3444791 0 0.036590652 1 1
3000 0.34721342 0 -0.023793368 1 1
3100 0.33404314 0 -0.08374223 1 1
3200 0.33019355 0 -0.12715599 1 1
3300 0.33515177 0 -0.12217394 1 1
3400 0.33628481 0 -0.070877624 1 1
3500 0.34257038 0 -0.021612062 1 1
3600 0.32838009 0 0.030131228 1 1
3700 0.34462142 0 0.074586378 1 1
3800 0.30891825 0 0.10605673 1 1
3900 0.33847951 0 0.13956139 1 1
4000 0.32952079 0 0.12688129 1 1
4100 0.32646772 0 0.081089042 1 1
4200 0.35399503 0 0.013422873 1 1
4300 0.33154914 0 -0.050919508 1 1
4400 0.34113556 0 -0.083171 1 1
4500 0.32651708 0 -0.1063133 1 1
4600 0.34359609 0 -0.1076395 1 1
4700 0.34973537 0 -0.088231606 1 1
4800 0.35198515 0 -0.020901044 1 1
4900 0.35187284 0 0.043645941 1 1
5000 0.34887336 0 0.095698609 1 1
5100 0.30308163 0 0.11649328 1 1
5200 0.32401285 0 0.12072411 1 1
5300 0.33025072 0 0.10933161 1 1
5400 0.33288012 0 0.078356448 1 1
5500 0.35142492 0 0.036958063 1 1
5600 0.35125368 0 -0.041371343 1 1
5700 0.34547744 0 -0.096450846 1 1
5800 0.30939887 0 -0.12356656 1 1
5900 0.32315628 0 -0.11338676 1 1
6000 0.34117485 0 -0.066198961 1 1
6100 0.35298043 0 -0.016172816 1 1
6200 0.35130653 0 0.027660468 1 1
6300 0.35398766 0 0.087221238 1 1
6400 0.30963379 0 0.11990957 1 1
6500 0.3174541 0 0.14103528 1 1
6600 0.31989791 0 0.11575506 1 1
6700 0.33811477 0 0.060747353 1 1
6800 0.3424043 0 0.010357152 1 1
6900 0.34804319 0 -0.042621786 1 1
7000 0.35357865 0 -0.067248959 1 1
7100 0.33556885 0 -0.10983726 1 1
7200 0.33531101 0 -0.112179 1 1
7300 0.35742607 0 -0.078405267 1 1
7400 0.34577559 0 -0.01985432 1 1
7500 0.3498641 0 0.052289439 1 1
7600 0.33773715 0 0.092939035 1 1
7700 0.33093497 0 0.11924405 1 1
7800 0.31435814 0 0.12701724 1 1
7900 0.33132217 0 0.10793075 1 1
8000 0.33451798 0 0.077993125 1 1
8100 0.35188371 0 0.019929977 1 1
8200 0.33645742 0 -0.039302079 1 1
8300 0.3415632 0 -0.098067982 1 1
8400 0.30619282 0 -0.12952879 1 1
8500 0.34446484 0 -0.098084709 1 1
8600 0.33761673 0 -0.07069818 1 1
8700 0.34495452 0 -0.022458056 1 1
8800 0.33502983 0 0.027742411 1 1
8900 0.35418591 0 0.092390134 1 1
9000 0.31648387 0 0.12467398 1 1
9100 0.33994825 0 0.14460327 1 1
9200 0.33822571 0 0.11273284 1 1
9300 0.33260773 0 0.060063671 1 1
9400 0.36140305 0 0.021427642 1 1
9500 0.34273562 0 -0.034064202 1 1
9600 0.33867054 0 -0.089076906 1 1
9700 0.32088235 0 -0.12027075 1 1
9800 0.3320823 0 -0.11602794 1 1
9900 0.33916442 0 -0.080281044 1 1
10000 0.34852268 0 -0.01000914 1 1
10100 0.32955942 0 0.04258493 1 1
10200 0.34487898 0 0.086971308 1 1
10300 0.32325593 0 0.11558149 1 1
10400 0.30927871 0 0.12239437 1 1
10500 0.33176799 0 0.12285937 1 1
10600 0.35120027 0 0.084897432 1 1
10700 0.33129697 0 0.0053089279 1 1
10800 0.36028769 0 -0.04280715 1 1
10900 0.35552287 0 -0.084955999 1 1
11000 0.3406024 0 -0.096554577 1 1
11100 0.33041202 0 -0.10703492 1 1
11200 0.32442686 0 -0.084328121 1 1
11300 0.35952468 0 -0.020191965 1 1
11400 0.34610624 0 0.03440148 1 1
11500 0.3415612 0 0.1041929 1 1
11600 0.34040042 0 0.13215705 1 1
11700 0.33555094 0 0.12738686 1 1
11800 0.3458647 0 0.10963398 1 1
11900 0.33836678 0 0.067253864 1 1
12000 0.34853314 0 0.03201448 1 1
12100 0.34600048 0 -0.034833402 1 1
12200 0.33145631 0 -0.09865675 1 1
12300 0.32848884 0 -0.1248489 1 1
12400 0.3321344 0 -0.11266575 1 1
12500 0.32622305 0 -0.061634993 1 1
12600 0.36213537 0 -0.0090593315 1 1
12700 0.34673866 0 0.036734645 1 1
12800 0.34606618 0 0.086267678 1 1
12900 0.34271431 0 0.12415522 1 1
13000 0.31993287 0 0.13879926 1 1
13100 0.3422918 0 0.11978905 1 1
13200 0.33055236 0 0.062620483 1 1
13300 0.34652207 0 0.0043833459 1 1
13400 0.33574661 0 -0.04691024 1 1
13500 0.33940837 0 -0.074241604 1 1
13600 0.32093414 0 -0.1078027 1 1
13700 0.34336597 0 -0.10544097 1 1
13800 0.35806461 0 -0.072531559 1 1
13900 0.35209713 0 -0.018851408 1 1
14000 0.35702629 0 0.061046366 1 1
14100 0.33234093 0 0.094086465 1 1
14200 0.3459466 0 0.12186656 1 1
14300 0.3327428 0 0.11396572 1 1
14400 0.32409443 0 0.10658903 1 1
14500 0.35022184 0 0.083558031 1 1
14600 0.34823843 0 0.024605569 1 1
14700 0.35298973 0 -0.040418888 1 1
14800 0.33679845 0 -0.10067728 1 1
14900 0.32790966 0 -0.10925568 1 1
15000 0.34208495 0 -0.09568004 1 1
15100 0.33647529 0 -0.055652929 1 1
15200 0.35328398 0 -0.020236536 1 1
15300 0.34252669 0 0.026434179 1 1
15400 0.34409435 0 0.094410599 1 1
15500 0.32288994 0 0.12034455 1 1
15600 0.32109689 0 0.13645185 1 1
15700 0.33681572 0 0.098607746 1 1
15800 0.33635195 0 0.05570715 1 1
15900 0.34289757 0 0.013849092 1 1
16000 0.34225547 0 -0.035597548 1 1
16100 0.33660991 0 -0.076931881 1 1
16200 0.32802152 0 -0.12765884 1 1
16300 0.3469374 0 -0.10785455 1 1
16400 0.34053641 0 -0.070259853 1 1
16500 0.34610591 0 -0.014315306 1 1
16600 0.35109001 0 0.041251169 1 1
16700 0.34336905 0 0.077996627 1 1
16800 0.33277414 0 0.11053634 1 1
16900 0.32183338 0 0.11680626 1 1
17000 0.34044352 0 0.10806555 1 1
17100 0.32967873 0 0.067759786 1 1
17200 0.36172278 0 -0.0048631904 1 1
17300 0.35619435 0 -0.04215545 1 1
17400 0.34540936 0 -0.093994174 1 1
17500 0.33193585 0 -0.098831315 1 1
17600 0.3544756 0 -0.085660403 1 1
17700 0.34505209 0 -0.069640515 1 1
17800 0.36291124 0 -0.0063088133 1 1
17900 0.34255705 0 0.046794555 1 1
18000 0.34163238 0 0.11767705 1 1
18100 0.3466445 0 0.1351712 1 1
18200 0.33037668 0 0.12703659 1 1
18300 0.33677404 0 0.10956306 1 1
18400 0.34978954 0 0.087193072 1 1
18500 0.33354363 0 0.051095814 1 1
18600 0.34651729 0 0.0056245561 1 1
18700 0.32622232 0 -0.047319269 1 1
18800 0.32978847 0 -0.054929416 1 1
18900 0.34192451 0 -0.037252471 1 1
19000 0.34061294 0 -0.001167235 1 1
19100 0.34194478 0 0.016945224 1 1
19200 0.33321765 0 0.050665354 1 1
19300 0.33197783 0 0.080470585 1 1
19400 0.33284715 0 0.12423599 1 1
19500 0.33867856 0 0.12689524 1 1
19600 0.36092786 0 0.11417704 1 1
19700 0.34270183 0 0.069038291 1 1
19800 0.34880695 0 0.042483681 1 1
19900 0.33903644 0 0.034788638 1 1
20000 0.32590125 0 0.011383785 1 1
20100 0.30358859 0 0.0030743554 1 1
20200 0.31830224 0 0.017637826 1 1
20300 0.34195438 0 0.072811099 1 1
20400 0.31249563 0 0.10063541 1 1
20500 0.31544938 0 0.1405794 1 1
20600 0.30071644 0 0.12763486 1 1
20700 0.2890265 0 0.1136651 1 1
20800 0.28962296 0 0.094481978 1 1
20900 0.29447212 0 0.0967165 1 1
21000 0.31159961 0 0.067307231 1 1
21100 0.30490648 0 0.017689358 1 1
21200 0.30687262 0 -0.016055512 1 1
21300 0.30083286 0 -0.0014988997 1 1
21400 0.32070426 0 0.015960302 1 1
21500 0.31439311 0 0.038170385 1 1
21600 0.32617832 0 0.043263788 1 1
21700 0.35151793 0 0.066302727 1 1
21800 0.35912885 0 0.070099103 1 1
21900 0.32451958 0 0.068935768 1 1
22000 0.35219298 0 0.067161227 1 1
22100 0.34857705 0 0.032731746 1 1
22200 0.34750227 0 0.0056917695 1 1
22300 0.34766017 0 -0.0027090483 1 1
22400 0.33426062 0 -0.023196063 1 1
22500 0.34174625 0 -0.025019717 1 1
22600 0.3356145 0 -0.029707418 1 1
22700 0.3362653 0 -0.035815733 1 1
22800 0.33973405 0 -0.0024705835 1 1
22900 0.33813085 0 0.0077527467 1 1
23000 0.33339981 0 0.028340744 1 1
23100 0.34079832 0 0.018521302 1 1
23200 0.33074548 0 0.032378405 1 1
23300 0.32965664 0 0.035989589 1 1
23400 0.30927749 0 0.024581106 1 1
23500 0.32890632 0 0.01092479 1 1
23600 0.34137438 0 0.0094839745 1 1
23700 0.34512638 0 -0.012392771 1 1
23800 0.31781354 0 -0.012908449 1 1
23900 0.32405513 0 -0.015018071 1 1
24000 0.33549728 0 -0.012812915 1 1
24100 0.31368736 0 -0.020818372 1 1
24200 0.33533836 0 0.0056121057 1 1
24300 0.32530627 0 0.018183931 1 1
24400 0.31930662 0 0.027446878 1 1
24500 0.33540302 0 0.040307455 1 1
24600 0.34020431 0 0.027403921 1 1
24700 0.3291814 0 0.01204865 1 1
24800 0.31552604 0 0.019654111 1 1
24900 0.34727253 0 0.01670543 1 1
25000 0.35120105 0 0.0038617562 1 1
25100 0.32706871 0 -0.021196623 1 1
25200 0.32915282 0 -0.017146508 1 1
25300 0.32577518 0 -0.01312495 1 1
25400 0.33286855 0 0.0014726193 1 1
25500 0.33002601 0 0.0080974022 1 1
25600 0.34127655 0 0.014296091 1 1
25700 0.34048065 0 0.022513032 1 1
25800 0.33029079 0 0.038733531 1 1
25900 0.33031324 0 0.026156982 1 1
26000 0.32967371 0 0.028727383 1 1
26100 0.33775718 0 0.015607478 1 1
26200 0.35097144 0 0.012291703 1 1
26300 0.34303792 0 0.00094823191 1 1
26400 0.33632665 0 -0.0026904889 1 1
26500 0.33580127 0 -0.0074168555 1 1
26600 0.33063188 0 -0.020378601 1 1
26700 0.33581846 0 -0.00084397268 1 1
26800 0.32998532 0 0.015932208 1 1
26900 0.33825444 0 0.010428603 1 1
27000 0.32081518 0 0.019818223 1 1
27100 0.31448098 0 0.020093416 1 1
27200 0.32643684 0 0.021934917 1 1
27300 0.33289466 0 0.023713072 1 1
27400 0.32310744 0 0.024110945 1 1
27500 0.33115619 0 0.0025776713 1 1
27600 0.33295887 0 -0.010710764 1 1
27700 0.32968876 0 -0.0064595905 1 1
27800 0.34064581 0 -0.0086519116 1 1
27900 0.33559187 0 -0.0055753593 1 1
28000 0.32300727 0 -0.0004153384 1 1
28100 0.32147461 0 -0.0058543412 1 1
28200 0.35532383 0 0.013646951 1 1
28300 0.31507942 0 0.026532255 1 1
28400 0.32711006 0 0.033214981 1 1
28500 0.34472462 0 0.028050837 1 1
28600 0.33708059 0 0.019115676 1 1
28700 0.34478087 0 0.023743689 1 1
28800 0.34546686 0 0.0081772997 1 1
28900 0.34004886 0 0.017771865 1 1
29000 0.33604232 0 -0.010505671 1 1
29100 0.33541374 0 -0.016273261 1 1
29200 0.34347489 0 -0.010002306 1 1
29300 0.34083904 0 0.0089701784 1 1
29400 0.34846892 0 0.020765104 1 1
29500 0.3416255 0 0.022650856 1 1
29600 0.33725496 0 0.020693083 1 1
29700 0.34480638 0 0.024317128 1 1
29800 0.31459471 0 0.023097895 1 1
29900 0.33014448 0 0.03114046 1 1
30000 0.33741498 0 0.015624314 1 1
30100 0.32598657 0 -0.0018860541 1 1
30200 0.34855815 0 0.0017983372 1 1
30300 0.33375921 0 0.0010991235 1 1
30400 0.35008944 0 -0.0027316177 1 1
30500 0.33279729 0 -0.0035788551 1 1
30600 0.33868746 0 -0.0016249482 1 1
30700 0.33597034 0 -0.0014524001 1 1
30800 0.3227257 0 0.016353457 1 1
30900 0.32676516 0 0.027396654 1 1
31000 0.34083982 0 0.031606413 1 1
31100 0.32165238 0 0.013583368 1 1
31200 0.3428492 0 0.020486611 1 1
31300 0.32372541 0 0.01215566 1 1
31400 0.32734692 0 0.016229397 1 1
31500 0.33089262 0 0.0060426618 1 1
31600 0.34273493 0 -0.013456537 1 1
31700 0.32723905 0 -0.019243766 1 1
31800 0.33636488 0 0.0027814902 1 1
31900 0.32834805 0 0.00706877 1 1
32000 0.33995148 0 0.0018383309 1 1
32100 0.33412282 0 0.0076455933 1 1
32200 0.34334884 0 0.023586129 1 1
32300 0.32778925 0 0.020564321 1 1
32400 0.33163443 0 0.038878463 1 1
32500 0.32290345 0 0.022247461 1 1
32600 0.34113954 0 0.010966365 1 1
32700 0.33390633 0 0.0037777555 1 1
32800 0.34385341 0 0.010556575 1 1
32900 0.32137047 0 0.00022027143 1 1
33000 0.32079172 0 -0.017261272 1 1
33100 0.33570882 0 -0.0051942206 1 1
33200 0.34320894 0 -0.011515281 1 1
33300 0.32794746 0 -0.0018153673 1 1
33400 0.33060982 0 0.027118146 1 1
33500 0.33641809 0 0.02143035 1 1
33600 0.33643061 0 0.020833068 1 1
33700 0.3485949 0 0.030918751 1 1
33800 0.3283985 0 0.01947613 1 1
33900 0.31959761 0 0.021128147 1 1
34000 0.33897984 0 0.015270986 1 1
34100 0.32392267 0 0.0020130852 1 1
34200 0.33084514 0 -0.024316708 1 1
34300 0.3342259 0 -0.0059047764 1 1
34400 0.33385098 0 0.0063818721 1 1
34500 0.33255603 0 -0.01023837 1 1
34600 0.34766173 0 0.0056703013 1 1
34700 0.339822 0 0.0061648559 1 1
34800 0.33902329 0 0.030037037 1 1
34900 0.3216153 0 0.027996689 1 1
35000 0.32701056 0 0.024778517 1 1
35100 0.3124942 0 0.011316548 1 1
35200 0.34486416 0 0.011670127 1 1
35300 0.33275353 0 0.020491246 1 1
35400 0.33618763 0 0.014678874 1 1
35500 0.32352282 0 -0.018568683 1 1
35600 0.32617903 0 -0.012796912 1 1
35700 0.32378048 0 -0.021318585 1 1
35800 0.3371086 0 -0.0023678632 1 1
35900 0.33818476 0 0.011197742 1 1
36000 0.35142144 0 0.022520935 1 1
36100 0.35147297 0 0.020277852 1 1
36200 0.33489465 0 0.014564878 1 1
36300 0.33841515 0 0.036439962 1 1
36400 0.32301096 0 0.019966746 1 1
36500 0.35612028 0 0.036509556 1 1
36600 0.33841597 0 -0.0042180605 1 1
36700 0.34477654 0 -0.0052770853 1 1
36800 0.33804317 0 -0.013751733 1 1
36900 0.35003816 0 -0.0021184393 1 1
37000 0.32965041 0 -0.020900951 1 1
37100 0.34653095 0 -0.013667977 1 1
37200 0.35019871 0 -0.0071740923 1 1
37300 0.34859745 0 0.02006041 1 1
37400 0.35739859 0 0.020892822 1 1
37500 0.34128859 0 0.041072111 1 1
37600 0.33781905 0 0.023376738 1 1
37700 0.32961874 0 0.030953741 1 1
37800 0.343987 0 0.029579795 1 1
37900 0.33610448 0 0.036836828 1 1
38000 0.32757228 0 0.020902031 1 1
38100 0.32735808 0 0.019544751 1 1
38200 0.35646953 0 0.044607528 1 1
38300 0.32509773 0 0.03610738 1 1
38400 0.32111741 0 0.034474043 1 1
38500 0.30590608 0 0.053461212 1 1
38600 0.32322402 0 0.053453832 1 1
38700 0.33843057 0 0.076264534 1 1
38800 0.31350741 0 0.064733869 1 1
38900 0.31943061 0 0.067836769 1 1
39000 0.33775583 0 0.0788316 1 1
39100 0.34256036 0 0.075874935 1 1
39200 0.33128527 0 0.071610976 1 1
39300 0.34519653 0 0.046257301 1 1
39400 0.34351844 0 0.052422917 1 1
39500 0.35716037 0 0.048916058 1 1
39600 0.34000737 0 0.016149089 1 1
39700 0.34587892 0 0.021619621 1 1
39800 0.34878036 0 0.0092881327 1 1
39900 0.35225411 0 -0.011341599 1 1
40000 0.36309266 0 0.0050869295 1 1
Loop time of 1.94553 on 1 procs for 40000 steps with 361 atoms
Performance: 8881898.790 tau/day, 20559.951 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.068658 | 0.068658 | 0.068658 | 0.0 | 3.53
Bond | 0.9979 | 0.9979 | 0.9979 | 0.0 | 51.29
Neigh | 0.50428 | 0.50428 | 0.50428 | 0.0 | 25.92
Comm | 0.015341 | 0.015341 | 0.015341 | 0.0 | 0.79
Output | 0.0029466 | 0.0029466 | 0.0029466 | 0.0 | 0.15
Modify | 0.28324 | 0.28324 | 0.28324 | 0.0 | 14.56
Other | | 0.07317 | | | 3.76
Nlocal: 361 ave 361 max 361 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 31.0249
Neighbor list builds = 3079
Dangerous builds = 0
Total wall time: 0:00:01

524
examples/balance/log.15Feb16.balance.bond.slow.g++.4 Normal file
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LAMMPS (15 Feb 2016)
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
# careful not to slam into wall too hard
variable v index 0.3
variable w index 0.08
units lj
dimension 2
atom_style bond
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box bond/types 1 extra/bond/per/atom 6
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
2 by 2 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 0.3 $w 0 sum yes
velocity all set 0.3 0.08 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
bond_style harmonic
bond_coeff 1 10.0 1.2
create_bonds all all 1 1.0 1.5
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 42 29 1
Added 1014 bonds, new total = 1014
6 = max # of 1-2 neighbors
30 = max # of 1-3 neighbors
180 = max # of 1-4 neighbors
36 = max # of special neighbors
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom (c_1%10)+1
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 200 image.*.jpg v_p type bond atom 0.25 # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 40000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 42 29 1
Memory usage per processor = 6.41878 Mbytes
Step Temp E_pair Press 10[3] 10
0 0.57437856 0 0.26099453 3.2354571 1.0526316
100 0.29756515 0 0.10149401 1.0193906 1.0083102
200 0.35394813 0 0.075159099 1.0304709 1.0083102
300 0.39245849 0 0.033002384 1.0304709 1.0193906
400 0.34078347 0 -0.020825841 1.0304709 1.0083102
500 0.35201095 0 -0.062637506 1.0193906 1.0083102
600 0.34014717 0 -0.11122965 1.0415512 1.0083102
700 0.3323524 0 -0.11598015 1.0193906 1.0083102
800 0.35116047 0 -0.096162395 1.0083102 1.0193906
900 0.35695352 0 -0.01385176 1.0526316 1.0193906
1000 0.36986539 0 0.056772858 1.0083102 1.0083102
1100 0.34584644 0 0.084941323 1.0193906 1.0083102
1200 0.31921435 0 0.10545078 1.0415512 1.0193906
1300 0.32952819 0 0.124902 1.0083102 1.0083102
1400 0.34497365 0 0.12662081 1.0193906 1.0083102
1500 0.33429243 0 0.096230972 1.0526316 1.0193906
1600 0.33765387 0 0.025800542 1.0304709 1.0083102
1700 0.35134464 0 -0.04422593 1.0415512 1.0193906
1800 0.35003859 0 -0.096745576 1.0304709 1.0193906
1900 0.33839618 0 -0.095465943 1.0193906 1.0083102
2000 0.33732078 0 -0.094652802 1.0083102 1.0083102
2100 0.34552238 0 -0.076729261 1.0304709 1.0083102
2200 0.34893142 0 -0.036853228 1.0304709 1.0193906
2300 0.35379341 0 0.021124847 1.0304709 1.0304709
2400 0.34829744 0 0.09230184 1.0304709 1.0193906
2500 0.33038141 0 0.1399855 1.0193906 1.0193906
2600 0.30983019 0 0.12754742 1.0193906 1.0083102
2700 0.32992561 0 0.10485138 1.0415512 1.0304709
2800 0.34604747 0 0.066174138 1.0083102 1.0083102
2900 0.3444791 0 0.036590652 1.0193906 1.0193906
3000 0.34721342 0 -0.023793368 1.0193906 1.0083102
3100 0.33404314 0 -0.08374223 1.0415512 1.0083102
3200 0.33019355 0 -0.12715599 1.0083102 1.0083102
3300 0.33515177 0 -0.12217394 1.0193906 1.0083102
3400 0.33628481 0 -0.070877624 1.0193906 1.0083102
3500 0.34257038 0 -0.021612062 1.0304709 1.0083102
3600 0.32838009 0 0.030131228 1.0083102 1.0083102
3700 0.34462142 0 0.074586378 1.0415512 1.0083102
3800 0.30891825 0 0.10605673 1.0304709 1.0083102
3900 0.33847951 0 0.13956139 1.0415512 1.0193906
4000 0.32952079 0 0.12688129 1.0193906 1.0304709
4100 0.32646772 0 0.081089042 1.0304709 1.0193906
4200 0.35399503 0 0.013422873 1.0083102 1.0083102
4300 0.33154914 0 -0.050919508 1.0083102 1.0193906
4400 0.34113556 0 -0.083171 1.0415512 1.0083102
4500 0.32651708 0 -0.1063133 1.0193906 1.0083102
4600 0.34359609 0 -0.1076395 1.0083102 1.0193906
4700 0.34973537 0 -0.088231606 1.0415512 1.0083102
4800 0.35198515 0 -0.020901044 1.0415512 1.0083102
4900 0.35187284 0 0.043645941 1.0193906 1.0083102
5000 0.34887336 0 0.095698609 1.0193906 1.0083102
5100 0.30308163 0 0.11649328 1.0083102 1.0083102
5200 0.32401285 0 0.12072411 1.0193906 1.0083102
5300 0.33025072 0 0.10933161 1.0304709 1.0083102
5400 0.33288012 0 0.078356448 1.0083102 1.0193906
5500 0.35142492 0 0.036958063 1.0193906 1.0083102
5600 0.35125368 0 -0.041371343 1.0304709 1.0083102
5700 0.34547744 0 -0.096450846 1.0637119 1.0083102
5800 0.30939887 0 -0.12356656 1.0083102 1.0083102
5900 0.32315628 0 -0.11338676 1.0193906 1.0304709
6000 0.34117485 0 -0.066198961 1.0193906 1.0193906
6100 0.35298043 0 -0.016172816 1.0304709 1.0193906
6200 0.35130653 0 0.027660468 1.0415512 1.0083102
6300 0.35398766 0 0.087221238 1.0083102 1.0193906
6400 0.30963379 0 0.11990957 1.0193906 1.0083102
6500 0.3174541 0 0.14103528 1.0193906 1.0193906
6600 0.31989791 0 0.11575506 1.0415512 1.0193906
6700 0.33811477 0 0.060747353 1.0083102 1.0193906
6800 0.3424043 0 0.010357152 1.0304709 1.0083102
6900 0.34804319 0 -0.042621786 1.0193906 1.0083102
7000 0.35357865 0 -0.067248959 1.0304709 1.0083102
7100 0.33556885 0 -0.10983726 1.0193906 1.0083102
7200 0.33531101 0 -0.112179 1.0304709 1.0083102
7300 0.35742607 0 -0.078405267 1.0304709 1.0193906
7400 0.34577559 0 -0.01985432 1.0193906 1.0083102
7500 0.3498641 0 0.052289439 1.0526316 1.0083102
7600 0.33773715 0 0.092939035 1.0083102 1.0193906
7700 0.33093497 0 0.11924405 1.0193906 1.0083102
7800 0.31435814 0 0.12701724 1.0083102 1.0304709
7900 0.33132217 0 0.10793075 1.0193906 1.0083102
8000 0.33451798 0 0.077993125 1.0304709 1.0083102
8100 0.35188371 0 0.019929977 1.0193906 1.0193906
8200 0.33645742 0 -0.039302079 1.0193906 1.0193906
8300 0.3415632 0 -0.098067982 1.0304709 1.0083102
8400 0.30619282 0 -0.12952879 1.0193906 1.0193906
8500 0.34446484 0 -0.098084709 1.0083102 1.0083102
8600 0.33761673 0 -0.07069818 1.0193906 1.0083102
8700 0.34495452 0 -0.022458056 1.0193906 1.0083102
8800 0.33502983 0 0.027742411 1.0304709 1.0083102
8900 0.35418591 0 0.092390134 1.0083102 1.0193906
9000 0.31648387 0 0.12467398 1.0193906 1.0083102
9100 0.33994825 0 0.14460327 1.0193906 1.0083102
9200 0.33822571 0 0.11273284 1.0193906 1.0083102
9300 0.33260773 0 0.060063671 1.0083102 1.0193906
9400 0.36140305 0 0.021427642 1.0193906 1.0083102
9500 0.34273562 0 -0.034064202 1.0193906 1.0083102
9600 0.33867054 0 -0.089076906 1.0193906 1.0083102
9700 0.32088235 0 -0.12027075 1.0193906 1.0083102
9800 0.3320823 0 -0.11602794 1.0415512 1.0083102
9900 0.33916442 0 -0.080281044 1.0083102 1.0083102
10000 0.34852268 0 -0.01000914 1.0193906 1.0193906
10100 0.32955942 0 0.04258493 1.0083102 1.0083102
10200 0.34487898 0 0.086971308 1.0304709 1.0193906
10300 0.32325593 0 0.11558149 1.0304709 1.0193906
10400 0.30927871 0 0.12239437 1.0083102 1.0083102
10500 0.33176799 0 0.12285937 1.0193906 1.0193906
10600 0.35120027 0 0.084897432 1.0083102 1.0083102
10700 0.33129697 0 0.0053089279 1.0193906 1.0193906
10800 0.36028769 0 -0.04280715 1.0193906 1.0083102
10900 0.35552287 0 -0.084955999 1.0193906 1.0193906
11000 0.3406024 0 -0.096554577 1.0083102 1.0083102
11100 0.33041202 0 -0.10703492 1.0304709 1.0193906
11200 0.32442686 0 -0.084328121 1.0304709 1.0083102
11300 0.35952468 0 -0.020191965 1.0304709 1.0193906
11400 0.34610624 0 0.03440148 1.0193906 1.0083102
11500 0.3415612 0 0.1041929 1.0193906 1.0193906
11600 0.34040042 0 0.13215705 1.0304709 1.0193906
11700 0.33555094 0 0.12738686 1.0083102 1.0304709
11800 0.3458647 0 0.10963398 1.0193906 1.0193906
11900 0.33836678 0 0.067253864 1.0193906 1.0193906
12000 0.34853314 0 0.03201448 1.0193906 1.0083102
12100 0.34600048 0 -0.034833402 1.0304709 1.0083102
12200 0.33145631 0 -0.09865675 1.0193906 1.0193906
12300 0.32848884 0 -0.1248489 1.0193906 1.0193906
12400 0.3321344 0 -0.11266575 1.0083102 1.0083102
12500 0.32622305 0 -0.061634993 1.0304709 1.0083102
12600 0.36213537 0 -0.0090593315 1.0526316 1.0083102
12700 0.34673866 0 0.036734645 1.0193906 1.0083102
12800 0.34606618 0 0.086267678 1.0193906 1.0083102
12900 0.34271431 0 0.12415522 1.0304709 1.0083102
13000 0.31993287 0 0.13879926 1.0193906 1.0193906
13100 0.3422918 0 0.11978905 1.0083102 1.0083102
13200 0.33055236 0 0.062620483 1.0193906 1.0083102
13300 0.34652207 0 0.0043833459 1.0304709 1.0193906
13400 0.33574661 0 -0.04691024 1.0304709 1.0083102
13500 0.33940837 0 -0.074241604 1.0304709 1.0083102
13600 0.32093414 0 -0.1078027 1.0193906 1.0083102
13700 0.34336597 0 -0.10544097 1.0193906 1.0083102
13800 0.35806461 0 -0.072531559 1.0193906 1.0083102
13900 0.35209713 0 -0.018851408 1.0083102 1.0083102
14000 0.35702629 0 0.061046366 1.0083102 1.0083102
14100 0.33234093 0 0.094086465 1.0083102 1.0083102
14200 0.3459466 0 0.12186656 1.0193906 1.0083102
14300 0.3327428 0 0.11396572 1.0193906 1.0083102
14400 0.32409443 0 0.10658903 1.0193906 1.0193906
14500 0.35022184 0 0.083558031 1.0083102 1.0193906
14600 0.34823843 0 0.024605569 1.0083102 1.0083102
14700 0.35298973 0 -0.040418888 1.0193906 1.0083102
14800 0.33679845 0 -0.10067728 1.0193906 1.0193906
14900 0.32790966 0 -0.10925568 1.0193906 1.0083102
15000 0.34208495 0 -0.09568004 1.0193906 1.0083102
15100 0.33647529 0 -0.055652929 1.0083102 1.0193906
15200 0.35328398 0 -0.020236536 1.0193906 1.0193906
15300 0.34252669 0 0.026434179 1.0083102 1.0193906
15400 0.34409435 0 0.094410599 1.0304709 1.0083102
15500 0.32288994 0 0.12034455 1.0415512 1.0193906
15600 0.32109689 0 0.13645185 1.0193906 1.0193906
15700 0.33681572 0 0.098607746 1.0415512 1.0083102
15800 0.33635195 0 0.05570715 1.0193906 1.0193906
15900 0.34289757 0 0.013849092 1.0304709 1.0083102
16000 0.34225547 0 -0.035597548 1.0304709 1.0083102
16100 0.33660991 0 -0.076931881 1.0193906 1.0193906
16200 0.32802152 0 -0.12765884 1.0083102 1.0083102
16300 0.3469374 0 -0.10785455 1.0083102 1.0083102
16400 0.34053641 0 -0.070259853 1.0193906 1.0083102
16500 0.34610591 0 -0.014315306 1.0193906 1.0083102
16600 0.35109001 0 0.041251169 1.0304709 1.0083102
16700 0.34336905 0 0.077996627 1.0193906 1.0083102
16800 0.33277414 0 0.11053634 1.0083102 1.0083102
16900 0.32183338 0 0.11680626 1.0193906 1.0083102
17000 0.34044352 0 0.10806555 1.0193906 1.0083102
17100 0.32967873 0 0.067759786 1.0304709 1.0193906
17200 0.36172278 0 -0.0048631904 1.0304709 1.0083102
17300 0.35619435 0 -0.04215545 1.0193906 1.0083102
17400 0.34540936 0 -0.093994174 1.0193906 1.0193906
17500 0.33193585 0 -0.098831315 1.0083102 1.0193906
17600 0.3544756 0 -0.085660403 1.0193906 1.0083102
17700 0.34505209 0 -0.069640515 1.0304709 1.0193906
17800 0.36291124 0 -0.0063088133 1.0083102 1.0193906
17900 0.34255705 0 0.046794555 1.0304709 1.0083102
18000 0.34163238 0 0.11767705 1.0193906 1.0083102
18100 0.3466445 0 0.1351712 1.0415512 1.0193906
18200 0.33037668 0 0.12703659 1.0083102 1.0083102
18300 0.33677404 0 0.10956306 1.0083102 1.0304709
18400 0.34978954 0 0.087193072 1.0193906 1.0193906
18500 0.33354363 0 0.051095814 1.0526316 1.0193906
18600 0.34651729 0 0.0056245561 1.0304709 1.0193906
18700 0.32622232 0 -0.047319269 1.0083102 1.0193906
18800 0.32978847 0 -0.054929416 1.0304709 1.0193906
18900 0.34192451 0 -0.037252471 1.0193906 1.0083102
19000 0.34061294 0 -0.001167235 1.0083102 1.0083102
19100 0.34194478 0 0.016945224 1.0526316 1.0193906
19200 0.33321765 0 0.050665354 1.0526316 1.0083102
19300 0.33197783 0 0.080470585 1.0193906 1.0083102
19400 0.33284715 0 0.12423599 1.0304709 1.0304709
19500 0.33867856 0 0.12689524 1.0083102 1.0083102
19600 0.36092786 0 0.11417704 1.0193906 1.0083102
19700 0.34270183 0 0.069038291 1.0415512 1.0083102
19800 0.34880695 0 0.042483681 1.0193906 1.0083102
19900 0.33903644 0 0.034788638 1.0083102 1.0193906
20000 0.32590125 0 0.011383785 1.0193906 1.0083102
20100 0.30358859 0 0.0030743554 1.0526316 1.0083102
20200 0.31830224 0 0.017637826 1.0193906 1.0193906
20300 0.34195438 0 0.072811099 1.0304709 1.0193906
20400 0.31249563 0 0.10063541 1.0415512 1.0083102
20500 0.31544938 0 0.1405794 1.0083102 1.0083102
20600 0.30071644 0 0.12763486 1.0193906 1.0193906
20700 0.2890265 0 0.1136651 1.0083102 1.0083102
20800 0.28962296 0 0.094481978 1.0193906 1.0083102
20900 0.29447212 0 0.0967165 1.0193906 1.0193906
21000 0.31159961 0 0.067307231 1.0083102 1.0193906
21100 0.30490648 0 0.017689358 1.0083102 1.0304709
21200 0.30687262 0 -0.016055512 1.0193906 1.0193906
21300 0.30083286 0 -0.0014988997 1.0193906 1.0083102
21400 0.32070426 0 0.015960302 1.0083102 1.0083102
21500 0.31439311 0 0.038170385 1.0304709 1.0083102
21600 0.32617832 0 0.043263788 1.0083102 1.0083102
21700 0.35151793 0 0.066302727 1.0193906 1.0083102
21800 0.35912885 0 0.070099103 1.0193906 1.0083102
21900 0.32451958 0 0.068935768 1.0304709 1.0193906
22000 0.35219298 0 0.067161227 1.0193906 1.0193906
22100 0.34857705 0 0.032731746 1.0193906 1.0083102
22200 0.34750227 0 0.0056917695 1.0193906 1.0083102
22300 0.34766017 0 -0.0027090483 1.0193906 1.0083102
22400 0.33426062 0 -0.023196063 1.0304709 1.0193906
22500 0.34174625 0 -0.025019717 1.0083102 1.0083102
22600 0.3356145 0 -0.029707418 1.0304709 1.0193906
22700 0.3362653 0 -0.035815733 1.0193906 1.0193906
22800 0.33973405 0 -0.0024705835 1.0193906 1.0083102
22900 0.33813085 0 0.0077527467 1.0083102 1.0193906
23000 0.33339981 0 0.028340744 1.0193906 1.0083102
23100 0.34079832 0 0.018521302 1.0415512 1.0193906
23200 0.33074548 0 0.032378405 1.0193906 1.0083102
23300 0.32965664 0 0.035989589 1.0193906 1.0083102
23400 0.30927749 0 0.024581106 1.0193906 1.0083102
23500 0.32890632 0 0.01092479 1.0304709 1.0193906
23600 0.34137438 0 0.0094839745 1.0193906 1.0083102
23700 0.34512638 0 -0.012392771 1.0304709 1.0193906
23800 0.31781354 0 -0.012908449 1.0193906 1.0193906
23900 0.32405513 0 -0.015018071 1.0415512 1.0193906
24000 0.33549728 0 -0.012812915 1.0193906 1.0083102
24100 0.31368736 0 -0.020818372 1.0304709 1.0193906
24200 0.33533836 0 0.0056121057 1.0083102 1.0193906
24300 0.32530627 0 0.018183931 1.0415512 1.0083102
24400 0.31930662 0 0.027446878 1.0083102 1.0083102
24500 0.33540302 0 0.040307455 1.0304709 1.0083102
24600 0.34020431 0 0.027403921 1.0083102 1.0083102
24700 0.3291814 0 0.01204865 1.0193906 1.0083102
24800 0.31552604 0 0.019654111 1.0083102 1.0193906
24900 0.34727253 0 0.01670543 1.0193906 1.0083102
25000 0.35120105 0 0.0038617562 1.0193906 1.0083102
25100 0.32706871 0 -0.021196623 1.0415512 1.0193906
25200 0.32915282 0 -0.017146508 1.0193906 1.0083102
25300 0.32577518 0 -0.01312495 1.0193906 1.0304709
25400 0.33286855 0 0.0014726193 1.0193906 1.0193906
25500 0.33002601 0 0.0080974022 1.0193906 1.0083102
25600 0.34127655 0 0.014296091 1.0526316 1.0083102
25700 0.34048065 0 0.022513032 1.0193906 1.0193906
25800 0.33029079 0 0.038733531 1.0193906 1.0083102
25900 0.33031324 0 0.026156982 1.0304709 1.0193906
26000 0.32967371 0 0.028727383 1.0083102 1.0083102
26100 0.33775718 0 0.015607478 1.0083102 1.0193906
26200 0.35097144 0 0.012291703 1.0083102 1.0083102
26300 0.34303792 0 0.00094823191 1.0083102 1.0193906
26400 0.33632665 0 -0.0026904889 1.0193906 1.0193906
26500 0.33580127 0 -0.0074168555 1.0193906 1.0193906
26600 0.33063188 0 -0.020378601 1.0083102 1.0193906
26700 0.33581846 0 -0.00084397268 1.0083102 1.0193906
26800 0.32998532 0 0.015932208 1.0304709 1.0193906
26900 0.33825444 0 0.010428603 1.0304709 1.0083102
27000 0.32081518 0 0.019818223 1.0304709 1.0193906
27100 0.31448098 0 0.020093416 1.0193906 1.0083102
27200 0.32643684 0 0.021934917 1.0083102 1.0083102
27300 0.33289466 0 0.023713072 1.0415512 1.0083102
27400 0.32310744 0 0.024110945 1.0415512 1.0083102
27500 0.33115619 0 0.0025776713 1.0304709 1.0193906
27600 0.33295887 0 -0.010710764 1.0304709 1.0193906
27700 0.32968876 0 -0.0064595905 1.0193906 1.0193906
27800 0.34064581 0 -0.0086519116 1.0193906 1.0083102
27900 0.33559187 0 -0.0055753593 1.0083102 1.0083102
28000 0.32300727 0 -0.0004153384 1.0304709 1.0083102
28100 0.32147461 0 -0.0058543412 1.0083102 1.0083102
28200 0.35532383 0 0.013646951 1.0304709 1.0083102
28300 0.31507942 0 0.026532255 1.0415512 1.0193906
28400 0.32711006 0 0.033214981 1.0193906 1.0083102
28500 0.34472462 0 0.028050837 1.0304709 1.0193906
28600 0.33708059 0 0.019115676 1.0083102 1.0083102
28700 0.34478087 0 0.023743689 1.0304709 1.0083102
28800 0.34546686 0 0.0081772997 1.0304709 1.0193906
28900 0.34004886 0 0.017771865 1.0415512 1.0193906
29000 0.33604232 0 -0.010505671 1.0304709 1.0193906
29100 0.33541374 0 -0.016273261 1.0083102 1.0083102
29200 0.34347489 0 -0.010002306 1.0083102 1.0083102
29300 0.34083904 0 0.0089701784 1.0193906 1.0193906
29400 0.34846892 0 0.020765104 1.0083102 1.0083102
29500 0.3416255 0 0.022650856 1.0304709 1.0083102
29600 0.33725496 0 0.020693083 1.0193906 1.0193906
29700 0.34480638 0 0.024317128 1.0304709 1.0083102
29800 0.31459471 0 0.023097895 1.0083102 1.0083102
29900 0.33014448 0 0.03114046 1.0193906 1.0083102
30000 0.33741498 0 0.015624314 1.0083102 1.0193906
30100 0.32598657 0 -0.0018860541 1.0415512 1.0193906
30200 0.34855815 0 0.0017983372 1.0083102 1.0083102
30300 0.33375921 0 0.0010991235 1.0083102 1.0193906
30400 0.35008944 0 -0.0027316177 1.0415512 1.0083102
30500 0.33279729 0 -0.0035788551 1.0193906 1.0193906
30600 0.33868746 0 -0.0016249482 1.0083102 1.0193906
30700 0.33597034 0 -0.0014524001 1.0193906 1.0193906
30800 0.3227257 0 0.016353457 1.0415512 1.0193906
30900 0.32676516 0 0.027396654 1.0193906 1.0083102
31000 0.34083982 0 0.031606413 1.0415512 1.0193906
31100 0.32165238 0 0.013583368 1.0193906 1.0083102
31200 0.3428492 0 0.020486611 1.0304709 1.0193906
31300 0.32372541 0 0.01215566 1.0083102 1.0083102
31400 0.32734692 0 0.016229397 1.0083102 1.0083102
31500 0.33089262 0 0.0060426618 1.0083102 1.0083102
31600 0.34273493 0 -0.013456537 1.0083102 1.0083102
31700 0.32723905 0 -0.019243766 1.0193906 1.0083102
31800 0.33636488 0 0.0027814902 1.0083102 1.0083102
31900 0.32834805 0 0.00706877 1.0083102 1.0083102
32000 0.33995148 0 0.0018383309 1.0193906 1.0193906
32100 0.33412282 0 0.0076455933 1.0083102 1.0083102
32200 0.34334884 0 0.023586129 1.0083102 1.0083102
32300 0.32778925 0 0.020564321 1.0193906 1.0083102
32400 0.33163443 0 0.038878463 1.0193906 1.0083102
32500 0.32290345 0 0.022247461 1.0193906 1.0193906
32600 0.34113954 0 0.010966365 1.0304709 1.0083102
32700 0.33390633 0 0.0037777555 1.0193906 1.0083102
32800 0.34385341 0 0.010556575 1.0193906 1.0193906
32900 0.32137047 0 0.00022027143 1.0526316 1.0193906
33000 0.32079172 0 -0.017261272 1.0193906 1.0193906
33100 0.33570882 0 -0.0051942206 1.0083102 1.0083102
33200 0.34320894 0 -0.011515281 1.0304709 1.0083102
33300 0.32794746 0 -0.0018153673 1.0083102 1.0193906
33400 0.33060982 0 0.027118146 1.0193906 1.0083102
33500 0.33641809 0 0.02143035 1.0083102 1.0083102
33600 0.33643061 0 0.020833068 1.0193906 1.0083102
33700 0.3485949 0 0.030918751 1.0193906 1.0083102
33800 0.3283985 0 0.01947613 1.0193906 1.0083102
33900 0.31959761 0 0.021128147 1.0083102 1.0193906
34000 0.33897984 0 0.015270986 1.0193906 1.0083102
34100 0.32392267 0 0.0020130852 1.0304709 1.0193906
34200 0.33084514 0 -0.024316708 1.0193906 1.0193906
34300 0.3342259 0 -0.0059047764 1.0193906 1.0304709
34400 0.33385098 0 0.0063818721 1.0193906 1.0083102
34500 0.33255603 0 -0.01023837 1.0083102 1.0304709
34600 0.34766173 0 0.0056703013 1.0193906 1.0083102
34700 0.339822 0 0.0061648559 1.0083102 1.0193906
34800 0.33902329 0 0.030037037 1.0415512 1.0193906
34900 0.3216153 0 0.027996689 1.0304709 1.0083102
35000 0.32701056 0 0.024778517 1.0193906 1.0193906
35100 0.3124942 0 0.011316548 1.0193906 1.0304709
35200 0.34486416 0 0.011670127 1.0193906 1.0193906
35300 0.33275353 0 0.020491246 1.0193906 1.0193906
35400 0.33618763 0 0.014678874 1.0083102 1.0083102
35500 0.32352282 0 -0.018568683 1.0193906 1.0193906
35600 0.32617903 0 -0.012796912 1.0193906 1.0193906
35700 0.32378048 0 -0.021318585 1.0193906 1.0083102
35800 0.3371086 0 -0.0023678632 1.0193906 1.0193906
35900 0.33818476 0 0.011197742 1.0193906 1.0193906
36000 0.35142144 0 0.022520935 1.0083102 1.0193906
36100 0.35147297 0 0.020277852 1.0193906 1.0083102
36200 0.33489465 0 0.014564878 1.0415512 1.0083102
36300 0.33841515 0 0.036439962 1.0193906 1.0193906
36400 0.32301096 0 0.019966746 1.0304709 1.0083102
36500 0.35612028 0 0.036509556 1.0083102 1.0083102
36600 0.33841597 0 -0.0042180605 1.0193906 1.0193906
36700 0.34477654 0 -0.0052770853 1.0193906 1.0193906
36800 0.33804317 0 -0.013751733 1.0083102 1.0083102
36900 0.35003816 0 -0.0021184393 1.0083102 1.0193906
37000 0.32965041 0 -0.020900951 1.0193906 1.0083102
37100 0.34653095 0 -0.013667977 1.0193906 1.0083102
37200 0.35019871 0 -0.0071740923 1.0083102 1.0304709
37300 0.34859745 0 0.02006041 1.0304709 1.0083102
37400 0.35739859 0 0.020892822 1.0193906 1.0083102
37500 0.34128859 0 0.041072111 1.0193906 1.0193906
37600 0.33781905 0 0.023376738 1.0193906 1.0083102
37700 0.32961874 0 0.030953741 1.0193906 1.0083102
37800 0.343987 0 0.029579795 1.0083102 1.0083102
37900 0.33610448 0 0.036836828 1.0415512 1.0304709
38000 0.32757228 0 0.020902031 1.0193906 1.0193906
38100 0.32735808 0 0.019544751 1.0193906 1.0083102
38200 0.35646953 0 0.044607528 1.0083102 1.0304709
38300 0.32509773 0 0.03610738 1.0193906 1.0083102
38400 0.32111741 0 0.034474043 1.0193906 1.0193906
38500 0.30590608 0 0.053461212 1.0304709 1.0083102
38600 0.32322402 0 0.053453832 1.0193906 1.0304709
38700 0.33843057 0 0.076264534 1.0083102 1.0193906
38800 0.31350741 0 0.064733869 1.0415512 1.0083102
38900 0.31943061 0 0.067836769 1.0304709 1.0193906
39000 0.33775583 0 0.0788316 1.0193906 1.0193906
39100 0.34256036 0 0.075874935 1.0083102 1.0193906
39200 0.33128527 0 0.071610976 1.0193906 1.0083102
39300 0.34519653 0 0.046257301 1.0193906 1.0083102
39400 0.34351844 0 0.052422917 1.0304709 1.0304709
39500 0.35716037 0 0.048916058 1.0304709 1.0083102
39600 0.34000737 0 0.016149089 1.0304709 1.0083102
39700 0.34587892 0 0.021619621 1.0526316 1.0083102
39800 0.34878036 0 0.0092881327 1.0083102 1.0193906
39900 0.35225411 0 -0.011341599 1.0083102 1.0083102
40000 0.36309266 0 0.0050869295 1.0304709 1.0083102
Loop time of 1.06031 on 4 procs for 40000 steps with 361 atoms
Performance: 16297104.069 tau/day, 37724.778 timesteps/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.019866 | 0.021036 | 0.024189 | 1.3 | 1.98
Bond | 0.21436 | 0.24183 | 0.27259 | 5.1 | 22.81
Neigh | 0.16022 | 0.16068 | 0.16101 | 0.1 | 15.15
Comm | 0.2742 | 0.31331 | 0.3498 | 5.6 | 29.55
Output | 0.0070348 | 0.0075188 | 0.0087383 | 0.8 | 0.71
Modify | 0.14238 | 0.14861 | 0.15484 | 1.3 | 14.02
Other | | 0.1673 | | | 15.78
Nlocal: 90.25 ave 91 max 89 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 59.25 ave 61 max 56 min
Histogram: 1 0 0 0 0 0 0 0 2 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 = 31.0249
Neighbor list builds = 3079
Dangerous builds = 0
Total wall time: 0:00:01

202
examples/balance/log.15Feb16.balance.g++.1 Normal file
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LAMMPS (15 Feb 2016)
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style atomic
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
1 by 1 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom c_1%10
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 42 29 1
Memory usage per processor = 2.47688 Mbytes
Step Temp E_pair Press 10[3] 10
0 25.701528 -29.143179 -1.2407285 1 1
100 26.269576 -29.713313 7.9052334 1 1
200 26.368336 -29.809962 1.6412462 1 1
300 26.479082 -29.920083 2.3678653 1 1
400 26.522239 -29.965537 6.6787858 1 1
500 25.725591 -29.168034 0.67065285 1 1
600 26.247693 -29.692706 7.9887712 1 1
700 26.237368 -29.676926 1.5987214 1 1
800 25.889643 -29.431589 4.6160859 1 1
900 23.635295 -27.372963 9.029962 1 1
1000 22.571904 -25.87422 1.8936085 1 1
1100 17.493795 -21.447274 9.502619 1 1
1200 17.214459 -20.726964 6.3578933 1 1
1300 16.424366 -19.75746 3.9025348 1 1
1400 15.09282 -18.172384 1.7966088 1 1
1500 13.669129 -16.736191 1.3320876 1 1
1600 13.518191 -16.481254 2.2474968 1 1
1700 13.840191 -16.808798 1.848689 1 1
1800 12.705797 -15.654395 2.6658475 1 1
1900 12.560112 -15.376796 1.6651246 1 1
2000 12.11219 -14.943991 1.2347207 1 1
2100 11.681161 -14.453803 1.1856253 1 1
2200 11.380134 -14.15437 1.0983288 1 1
2300 11.404137 -14.206989 1.0886428 1 1
2400 11.267361 -14.00915 1.1353313 1 1
2500 11.086288 -13.866685 1.5189761 1 1
2600 11.241757 -14.031809 1.6088858 1 1
2700 10.741715 -13.522752 1.2648051 1 1
2800 10.594219 -13.461001 1.2068865 1 1
2900 10.497917 -13.243311 0.90549881 1 1
3000 9.8887944 -12.633322 1.2014467 1 1
3100 10.046064 -12.757462 0.72911664 1 1
3200 9.8202521 -12.544235 0.85793687 1 1
3300 9.9932983 -12.729524 1.3692879 1 1
3400 9.4389164 -12.132571 0.83559817 1 1
3500 9.4456791 -12.154808 1.2415677 1 1
3600 9.4291752 -12.13391 1.1892815 1 1
3700 9.2656145 -11.994284 0.93597208 1 1
3800 9.6833674 -12.407022 1.4696321 1 1
3900 9.2075262 -11.996657 1.0201833 1 1
4000 8.704708 -11.395839 1.5366945 1 1
4100 8.496226 -11.160512 0.98385093 1 1
4200 8.5566638 -11.241219 0.84428298 1 1
4300 8.3079987 -10.963542 0.96552044 1 1
4400 8.0878014 -10.695296 0.9598929 1 1
4500 7.8974753 -10.510996 0.67253552 1 1
4600 7.9008492 -10.511956 0.80200878 1 1
4700 7.8469401 -10.46341 0.91408186 1 1
4800 7.8237062 -10.478701 0.80709563 1 1
4900 7.9248576 -10.569715 0.93955604 1 1
5000 7.8285795 -10.450559 0.72760696 1 1
5100 7.8176003 -10.433727 1.0046395 1 1
5200 7.930586 -10.543139 1.1883254 1 1
5300 7.4014327 -10.200353 1.2717149 1 1
5400 7.3398704 -9.9377313 0.8277383 1 1
5500 7.9323894 -10.544566 0.58409181 1 1
5600 7.8256391 -10.452111 0.8371735 1 1
5700 7.5744223 -10.225985 0.56633204 1 1
5800 7.5149231 -10.128901 0.8877957 1 1
5900 7.2696456 -9.868796 1.0183026 1 1
6000 8.172964 -10.8046 0.82048799 1 1
6100 7.569911 -10.224271 0.85335085 1 1
6200 7.5498129 -10.158173 0.69550695 1 1
6300 7.0906227 -9.664124 0.38267058 1 1
6400 6.9720876 -9.556043 0.74772365 1 1
6500 7.2708269 -9.8393843 0.87493485 1 1
6600 7.0968522 -9.7557969 0.66499003 1 1
6700 7.1122649 -9.7305659 1.3152794 1 1
6800 6.9990684 -9.5808587 0.25569509 1 1
6900 7.2436468 -9.8205382 0.94441711 1 1
7000 7.0592104 -9.6306985 0.62683684 1 1
7100 6.7457928 -9.3199995 0.92851433 1 1
7200 7.0005278 -9.645515 0.79975493 1 1
7300 7.0106928 -9.5922649 0.78131757 1 1
7400 6.9425198 -9.5718261 0.3016744 1 1
7500 7.4193009 -9.9953487 0.55537513 1 1
7600 7.1870399 -9.7798145 0.94155142 1 1
7700 6.8261504 -9.3693292 0.78601298 1 1
7800 6.8794916 -9.4362689 0.9335562 1 1
7900 7.0068635 -9.5490666 0.53210657 1 1
8000 6.641609 -9.181226 0.80726821 1 1
8100 6.9290677 -9.4788963 1.1195905 1 1
8200 6.6497084 -9.197688 0.45616164 1 1
8300 6.6000864 -9.207368 0.46307403 1 1
8400 6.7434835 -9.3226196 0.78570419 1 1
8500 7.0766248 -9.5981608 0.48778261 1 1
8600 6.8206587 -9.3646115 0.76420951 1 1
8700 7.2009315 -9.7629817 0.69026433 1 1
8800 7.0581986 -9.636327 0.54467209 1 1
8900 7.2337543 -9.8210795 0.61604427 1 1
9000 6.7053026 -9.2552306 0.24196123 1 1
9100 6.7919694 -9.3561383 0.34320213 1 1
9200 6.8518231 -9.4142511 0.73735875 1 1
9300 6.5891178 -9.1414615 0.45262773 1 1
9400 6.4724853 -9.0217877 0.54837629 1 1
9500 6.3569528 -8.9201793 0.19617724 1 1
9600 6.3765498 -8.947548 0.85408461 1 1
9700 6.5652079 -9.1101844 0.74478711 1 1
9800 6.5099709 -9.0677449 0.69826809 1 1
9900 6.1773299 -8.7085595 0.69981004 1 1
10000 6.3999463 -8.9423632 0.42668066 1 1
Loop time of 0.675636 on 1 procs for 10000 steps with 361 atoms
Performance: 6393974.952 tau/day, 14800.868 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.29845 | 0.29845 | 0.29845 | 0.0 | 44.17
Neigh | 0.26869 | 0.26869 | 0.26869 | 0.0 | 39.77
Comm | 0.006007 | 0.006007 | 0.006007 | 0.0 | 0.89
Output | 0.00076938 | 0.00076938 | 0.00076938 | 0.0 | 0.11
Modify | 0.077204 | 0.077204 | 0.077204 | 0.0 | 11.43
Other | | 0.02452 | | | 3.63
Nlocal: 361 ave 361 max 361 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: 1191 ave 1191 max 1191 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1191
Ave neighs/atom = 3.29917
Neighbor list builds = 3609
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 2d circle of particles inside a box with LJ walls
variable b index 0
variable x index 50
variable y index 20
variable d index 20
variable v index 5
variable w index 2
units lj
dimension 2
atom_style atomic
boundary f f p
lattice hex 0.85
Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
region box block 0 $x 0 $y -0.5 0.5
region box block 0 50 0 $y -0.5 0.5
region box block 0 50 0 20 -0.5 0.5
create_box 1 box
Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
2 by 2 by 1 MPI processor grid
region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
region circle sphere 11 6.7735026918962581988 0.0 10
create_atoms 1 region circle
Created 361 atoms
mass 1 1.0
velocity all create 0.5 87287 loop geom
velocity all set $v $w 0 sum yes
velocity all set 5 $w 0 sum yes
velocity all set 5 2 0 sum yes
pair_style lj/cut 2.5
pair_coeff 1 1 10.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes
fix 1 all nve
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
comm_style tiled
fix 10 all balance 50 0.9 rcb
#compute 1 all property/atom proc
#variable p atom c_1%10
#dump 2 all custom 50 tmp.dump id v_p x y z
#dump 3 all image 50 image.*.jpg v_p type # adiam 1.0 view 0 0 zoom 1.8 subbox yes 0.02
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
thermo_style custom step temp epair press f_10[3] f_10
thermo 100
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 42 29 1
Memory usage per processor = 2.48839 Mbytes
Step Temp E_pair Press 10[3] 10
0 25.701528 -29.143179 -1.2407285 3.2354571 1.0526316
100 26.269576 -29.713313 7.9052334 1.2742382 1.0304709
200 26.368336 -29.809962 1.6412462 1.2520776 1.0083102
300 26.479082 -29.920083 2.3678653 1.2299169 1.0193906
400 26.522239 -29.965537 6.6787858 1.1855956 1.0083102
500 25.725591 -29.168034 0.67065285 1.2520776 1.0083102
600 26.247693 -29.692706 7.9887712 1.3074792 1.0083102
700 26.237368 -29.676926 1.5987214 1.2409972 1.0083102
800 25.889643 -29.431589 4.6160859 1.2631579 1.0083102
900 23.635295 -27.372963 9.029962 1.1634349 1.0083102
1000 22.571904 -25.87422 1.8936085 1.1301939 1.0193906
1100 17.493795 -21.447274 9.502619 1.0858726 1.0193906
1200 17.214459 -20.726965 6.3578917 1.0304709 1.0193906
1300 16.424154 -19.757386 3.9027133 1.1191136 1.0083102
1400 15.04233 -18.126227 1.7539398 1.0858726 1.0193906
1500 13.749022 -16.839766 1.4654778 1.0747922 1.0083102
1600 13.888812 -16.855703 1.8972035 1.0858726 1.0304709
1700 13.647879 -16.652436 1.5110481 1.0526316 1.0304709
1800 12.61308 -15.580445 2.1861667 1.0083102 1.0083102
1900 12.700272 -15.594505 1.6395684 1.0304709 1.0083102
2000 12.204319 -15.16754 1.6302417 1.1080332 1.0083102
2100 11.921129 -14.774621 1.4311256 1.0858726 1.0083102
2200 11.959274 -14.797326 1.4920985 1.0415512 1.0083102
2300 11.633606 -14.455284 1.4447243 1.1412742 1.0193906
2400 12.180014 -14.719121 1.4582702 1.0304709 1.0083102
2500 11.779995 -14.293633 1.2961686 1.0304709 1.0083102
2600 11.86013 -14.272853 1.1970414 1.0415512 1.0193906
2700 11.360658 -13.772549 1.192957 1.0526316 1.0083102
2800 11.045632 -13.438591 1.2007074 1.0083102 1.0193906
2900 10.689472 -13.127138 0.94544611 1.0193906 1.0193906
3000 10.445298 -12.809325 1.3035047 1.0304709 1.0193906
3100 10.22325 -12.599858 1.7838342 1.0304709 1.0083102
3200 10.226845 -12.602391 0.91456469 1.0304709 1.0193906
3300 9.8906692 -12.204654 1.4538962 1.0415512 1.0193906
3400 9.0246858 -11.627057 1.1929498 1.0304709 1.0193906
3500 9.4549317 -11.747347 0.92966653 1.0193906 1.0193906
3600 9.2467281 -11.534358 0.94959796 1.0415512 1.0083102
3700 9.1099307 -11.381318 1.2963887 1.0193906 1.0083102
3800 9.2236074 -11.483205 1.3510186 1.1080332 1.0193906
3900 8.6105519 -10.877844 1.3591509 1.0304709 1.0083102
4000 8.588698 -10.846126 0.76473884 1.0415512 1.0083102
4100 8.5960453 -10.831229 0.93758423 1.0747922 1.0193906
4200 8.1049344 -10.436054 0.74947412 1.0526316 1.0083102
4300 8.2606129 -10.471049 0.64465155 1.0193906 1.0193906
4400 8.0777962 -10.288476 1.1145052 1.0193906 1.0083102
4500 7.9202904 -10.10427 0.49016698 1.0304709 1.0083102
4600 8.2366755 -10.434942 0.65930769 1.0193906 1.0083102
4700 7.9313531 -10.13685 1.097861 1.0304709 1.0083102
4800 7.8637296 -10.085957 0.56015483 1.0304709 1.0193906
4900 7.3410322 -9.5357686 0.89340163 1.0304709 1.0193906
5000 7.6647481 -9.8529515 0.8283225 1.0193906 1.0193906
5100 7.4114006 -9.5917802 0.64812231 1.0083102 1.0193906
5200 7.6261959 -9.8178843 0.90517452 1.0193906 1.0083102
5300 7.6501619 -9.8428477 1.028077 1.0304709 1.0083102
5400 7.4694373 -9.6434672 0.38259983 1.0193906 1.0083102
5500 7.3111918 -9.4803007 0.47921149 1.0193906 1.0193906
5600 7.2132446 -9.3694039 0.71282856 1.0193906 1.0083102
5700 6.8349744 -9.0018958 0.85688618 1.0193906 1.0083102
5800 7.1978042 -9.3667457 0.61717818 1.0304709 1.0193906
5900 7.1441033 -9.3263118 0.32840394 1.0193906 1.0083102
6000 7.0943691 -9.2621241 1.3099316 1.0083102 1.0083102
6100 6.9547586 -9.1026607 0.44492974 1.0193906 1.0083102
6200 7.0932682 -9.2934579 0.93444691 1.0415512 1.0083102
6300 7.0536275 -9.2562193 0.57578551 1.0193906 1.0193906
6400 6.8839921 -9.0513091 0.65690774 1.0193906 1.0083102
6500 6.7618431 -8.9037814 0.6011838 1.0304709 1.0193906
6600 6.6600729 -8.7979286 0.73495903 1.0193906 1.0193906
6700 6.6544136 -8.8089155 0.41206297 1.0304709 1.0193906
6800 6.7935502 -8.9405122 1.022055 1.0193906 1.0083102
6900 6.6603594 -8.8085894 0.4271189 1.0526316 1.0193906
7000 6.4894888 -8.6794785 0.64389173 1.0526316 1.0193906
7100 6.6252776 -8.776746 1.3915989 1.0193906 1.0193906
7200 6.6680717 -8.8468379 0.60275261 1.0193906 1.0193906
7300 6.697874 -8.8458161 0.50887488 1.0637119 1.0083102
7400 6.2112277 -8.340139 0.45211042 1.0415512 1.0193906
7500 6.4923853 -8.6255862 0.79982162 1.0083102 1.0193906
7600 6.2922271 -8.4027197 0.33603817 1.0304709 1.0083102
7700 6.5744688 -8.7079756 0.51620003 1.0415512 1.0083102
7800 6.6730316 -8.8278613 1.2334484 1.0304709 1.0083102
7900 6.3831791 -8.4878853 0.49555781 1.0415512 1.0193906
8000 6.690559 -8.7918607 0.88102021 1.0415512 1.0083102
8100 6.5390375 -8.6612074 0.45605815 1.0304709 1.0193906
8200 6.6957638 -8.8406262 0.45001955 1.0193906 1.0083102
8300 6.8684401 -9.0293678 0.64215355 1.0083102 1.0083102
8400 6.4416293 -8.5841829 0.53513285 1.0193906 1.0193906
8500 6.6854101 -8.8269391 0.81750487 1.0637119 1.0083102
8600 6.588469 -8.7315753 0.33201251 1.0083102 1.0083102
8700 6.2974312 -8.4104697 0.57054382 1.0083102 1.0083102
8800 6.4691853 -8.5985479 0.95554418 1.0415512 1.0083102
8900 6.7437807 -8.8949865 0.69067866 1.0415512 1.0083102
9000 6.5681473 -8.6984555 0.88464065 1.0193906 1.0083102
9100 6.6158471 -8.7398687 0.72347757 1.0193906 1.0083102
9200 6.4521137 -8.6048511 0.75093363 1.0193906 1.0193906
9300 6.4179685 -8.5582051 1.0072192 1.0083102 1.0083102
9400 6.580258 -8.7234535 0.56842466 1.0193906 1.0193906
9500 6.4125418 -8.56348 0.36394135 1.0304709 1.0193906
9600 6.6723409 -8.8402798 0.56711277 1.0304709 1.0193906
9700 6.4522736 -8.594767 0.43495668 1.0193906 1.0083102
9800 6.2127437 -8.3329761 0.68977311 1.0304709 1.0193906
9900 6.4360513 -8.5839262 1.1702062 1.0304709 1.0193906
10000 6.3393653 -8.4396274 0.46277884 1.0304709 1.0193906
Loop time of 0.389322 on 4 procs for 10000 steps with 361 atoms
Performance: 11096205.412 tau/day, 25685.661 timesteps/s
98.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.061902 | 0.074659 | 0.098288 | 5.1 | 19.18
Neigh | 0.061993 | 0.067136 | 0.078793 | 2.6 | 17.24
Comm | 0.10335 | 0.13334 | 0.15511 | 5.6 | 34.25
Output | 0.0017662 | 0.0020409 | 0.0027893 | 1.0 | 0.52
Modify | 0.037374 | 0.038055 | 0.038669 | 0.2 | 9.77
Other | | 0.07409 | | | 19.03
Nlocal: 90.25 ave 92 max 88 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 36 ave 38 max 34 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 276.75 ave 448 max 153 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 1107
Ave neighs/atom = 3.06648
Neighbor list builds = 3472
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
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 1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
thermo 500
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65 -> bins = 12 12 1
Memory usage per processor = 3.95249 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.63799525 0 0.78760475 -0.15028724
500 1.5681124 -1.6060641 0 -0.053632801 0.23819933
1000 1.7596217 -1.7290976 0 0.012927885 0.12600944
1500 1.5746717 -1.5427933 0 0.016131762 0.21832857
2000 1.618761 -1.5563092 0 0.04626422 0.35910744
2500 1.7204861 -1.6946681 0 0.0086130985 0.24678557
3000 1.7361478 -1.7074239 0 0.011362383 0.28900802
3500 1.6065118 -1.5857229 0 0.0047237772 0.43793842
4000 1.8157912 -1.7310796 0 0.06655375 0.072835934
4500 1.7986098 -1.74424 0 0.036383686 0.25507425
5000 1.7182236 -1.7110892 0 -0.010047817 0.19846764
5500 1.6246782 -1.5532517 0 0.055179713 0.38134959
6000 1.5745671 -1.6393559 0 -0.08053447 0.52399765
6500 1.7556697 -1.8091946 0 -0.071081574 0.25253905
7000 1.6360783 -1.7317121 0 -0.11199463 0.19797181
7500 1.7873556 -1.6976635 0 0.071818533 0.18343875
8000 1.4168755 -1.5596513 0 -0.15694455 0.38638741
8500 1.659868 -1.6673176 0 -0.024048309 0.17576797
9000 1.7040724 -1.6906772 0 -0.0036454592 0.12467855
9500 1.6305347 -1.7599864 0 -0.14575703 0.11285404
10000 1.7422091 -1.8887509 0 -0.16396383 0.29065244
Loop time of 2.35255 on 1 procs for 10000 steps with 100 atoms
Performance: 1836307.682 tau/day, 4250.712 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1426 | 2.1426 | 2.1426 | 0.0 | 91.08
Neigh | 0.016685 | 0.016685 | 0.016685 | 0.0 | 0.71
Comm | 0.026507 | 0.026507 | 0.026507 | 0.0 | 1.13
Output | 0.00015068 | 0.00015068 | 0.00015068 | 0.0 | 0.01
Modify | 0.16023 | 0.16023 | 0.16023 | 0.0 | 6.81
Other | | 0.006348 | | | 0.27
Nlocal: 100 ave 100 max 100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 82 ave 82 max 82 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 428 ave 428 max 428 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 428
Ave neighs/atom = 4.28
Neighbor list builds = 776
Dangerous builds = 65
Total wall time: 0:00:02

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
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 1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
thermo 500
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65 -> bins = 12 12 1
Memory usage per processor = 3.93947 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -0.63799525 0 0.78760475 -0.15028724
500 1.5681124 -1.6060641 0 -0.053632801 0.23819933
1000 1.7596217 -1.7290976 0 0.012927885 0.12600944
1500 1.5746718 -1.5427933 0 0.016131767 0.21832856
2000 1.6187614 -1.5563097 0 0.046264104 0.35910742
2500 1.7210993 -1.6955088 0 0.0083794889 0.24522984
3000 1.7893309 -1.752166 0 0.019271611 0.1013425
3500 1.8922335 -1.7645965 0 0.10871463 0.51383163
4000 1.7068531 -1.6754593 0 0.014325271 0.31615632
4500 1.6924784 -1.7467381 0 -0.071184511 0.13138777
5000 1.7693873 -1.7177224 0 0.033971031 0.15253256
5500 1.6829564 -1.6729159 0 -0.0067890531 0.13745591
6000 1.9528594 -1.8229135 0 0.11041735 0.21444568
6500 1.8827185 -2.0037589 0 -0.13986752 0.044294616
7000 1.4723386 -1.6538512 0 -0.19623597 0.23973507
7500 1.7787216 -1.729955 0 0.030979334 0.15662931
8000 1.8821398 -1.8913154 0 -0.027996988 0.26972798
8500 1.7200393 -1.771927 0 -0.069088004 0.48600924
9000 1.6731944 -1.702556 0 -0.046093535 0.1259234
9500 1.7159449 -1.6430047 0 0.0557808 0.3620955
10000 1.4879693 -1.5303732 0 -0.057283589 0.34668456
Loop time of 0.853475 on 4 procs for 10000 steps with 100 atoms
Performance: 5061659.129 tau/day, 11716.804 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.48406 | 0.55202 | 0.69789 | 11.6 | 64.68
Neigh | 0.0044043 | 0.0046293 | 0.0049062 | 0.3 | 0.54
Comm | 0.091245 | 0.24104 | 0.30869 | 18.0 | 28.24
Output | 0.00033712 | 0.00036192 | 0.00039911 | 0.1 | 0.04
Modify | 0.040754 | 0.042422 | 0.044837 | 0.7 | 4.97
Other | | 0.013 | | | 1.52
Nlocal: 25 ave 29 max 20 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Nghost: 44 ave 45 max 43 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 104 ave 133 max 64 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 416
Ave neighs/atom = 4.16
Neighbor list builds = 773
Dangerous builds = 31
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
comm_modify mode 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 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.5
ghost atom cutoff = 13.5
binsize = 1.75 -> bins = 172 172 6
Memory usage per processor = 3.86192 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9572355 -0.00037176804 1.954689 0.017979461 98945.011
2000 2.0686234 -0.0010137498 2.0653112 0.01947028 96310.014
3000 2.1785689 0.0049562211 2.1811045 0.029298361 68537.78
4000 2.200053 0.00039100896 2.1979995 0.048071724 42672.579
5000 2.1407629 0.016107912 2.1544922 0.076141728 28576.1
6000 2.1131357 0.00050904012 2.1112969 0.095060602 21598.175
7000 2.0717026 0.013639823 2.0830406 0.11782618 17864.757
8000 2.0557671 0.015637275 2.0691201 0.13461012 15542.602
9000 2.052181 0.011294709 2.0611955 0.15150744 13852.149
10000 2.0531753 0.005995461 2.0568894 0.17005868 12487.961
11000 2.0458212 0.013960278 2.0575083 0.18853479 11391.15
12000 2.0405323 0.01846093 2.056726 0.20856764 10532.913
13000 2.0169788 0.041436672 2.0561744 0.23593917 9743.2413
14000 2.0381291 0.017030208 2.0528947 0.23907374 9093.804
15000 2.0400498 0.010140701 2.0479238 0.27667462 8571.3248
16000 2.0280005 0.024278921 2.0500261 0.31642444 8133.8701
17000 2.0330813 0.018237365 2.0490597 0.30128788 7764.8228
18000 2.0239878 0.02723825 2.0489771 0.30818234 7455.765
19000 2.0213402 0.035515393 2.0546096 0.39654991 7096.9286
20000 2.024466 0.032163441 2.0543801 0.37550172 6782.3498
21000 2.033932 0.017240839 2.0489129 0.39674508 6520.0345
22000 2.0204921 0.033630164 2.0518773 0.41617948 6306.7194
23000 2.0103922 0.046109389 2.0542679 0.44503939 6108.8439
24000 2.0063543 0.049507774 2.0536328 0.4949354 5923.2093
25000 1.9953872 0.066107231 2.0592773 0.5424389 5746.6695
26000 2.0416248 0.020853398 2.0602097 0.46642685 5593.8186
27000 2.0280574 0.037040684 2.0628447 0.49730884 5433.376
28000 2.0039648 0.055918617 2.0576568 0.56893257 5281.5584
29000 2.0042398 0.056161548 2.0581744 0.55361133 5164.0991
30000 2.031788 0.030776854 2.0603073 0.58478846 5056.2821
31000 2.0220647 0.044025601 2.0638435 0.60571441 4939.9798
32000 2.0115578 0.0548283 2.064151 0.62749615 4859.2601
33000 1.9905768 0.071616735 2.0599817 0.64066244 4787.7818
34000 2.0209823 0.052197269 2.0709341 0.68260584 4705.5825
35000 1.995165 0.078611977 2.0715601 0.69333031 4599.9346
36000 1.994471 0.079545726 2.0718006 0.7510532 4523.7494
37000 1.9939754 0.083417982 2.0751779 0.73746747 4449.8485
38000 1.9808613 0.098188975 2.0768493 0.89305039 4362.0588
39000 2.0056223 0.070537588 2.0739314 0.75049166 4320.201
40000 2.0490165 0.033488307 2.0802281 0.71809099 4259.8017
41000 2.0170375 0.066555481 2.0813519 0.80145545 4165.276
42000 2.034609 0.050123688 2.082472 0.7318767 4099.5342
43000 2.027217 0.053657298 2.0786218 0.79779536 4050.1962
44000 2.0107551 0.07427185 2.0827928 0.88949517 4022.2995
45000 2.035579 0.054511708 2.087829 0.85058092 3982.0592
46000 1.9855666 0.1079948 2.0913552 0.96268676 3937.279
47000 1.9938397 0.095380271 2.0870046 0.94036115 3882.9266
48000 2.0056151 0.087885527 2.0912722 0.94935203 3824.2309
49000 2.0079615 0.089440768 2.0951712 0.97596247 3781.8079
50000 1.9875181 0.10628651 2.0915963 1.1315334 3749.1501
Loop time of 8.47628 on 1 procs for 50000 steps with 900 atoms
Performance: 2548287.987 tau/day, 5898.815 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.0947 | 4.0947 | 4.0947 | 0.0 | 48.31
Neigh | 1.3526 | 1.3526 | 1.3526 | 0.0 | 15.96
Comm | 0.31602 | 0.31602 | 0.31602 | 0.0 | 3.73
Output | 0.0005331 | 0.0005331 | 0.0005331 | 0.0 | 0.01
Modify | 2.4242 | 2.4242 | 2.4242 | 0.0 | 28.60
Other | | 0.2882 | | | 3.40
Nlocal: 900 ave 900 max 900 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 548 ave 548 max 548 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6073 ave 6073 max 6073 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6073
Ave neighs/atom = 6.74778
Neighbor list builds = 3122
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:08

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LAMMPS (15 Feb 2016)
# 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
comm_modify mode 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 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
#dump_modify 3 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.5
ghost atom cutoff = 13.5
binsize = 1.75 -> bins = 172 172 6
Memory usage per processor = 3.76692 Mbytes
Step Temp E_pair TotEng Press Volume
0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
1000 1.9572355 -0.00037176804 1.954689 0.017979461 98945.011
2000 2.0686234 -0.0010137498 2.0653112 0.01947028 96310.014
3000 2.1785689 0.0049562211 2.1811045 0.029298361 68537.78
4000 2.200053 0.00039100896 2.1979995 0.048071724 42672.579
5000 2.1407629 0.016107891 2.1544922 0.076141723 28576.1
6000 2.1131348 0.00051000844 2.1112968 0.095061489 21598.174
7000 2.0735911 0.011894403 2.0831815 0.11729552 17864.933
8000 2.0619661 0.0060168177 2.0656919 0.1295732 15547.781
9000 2.0595354 0.0024157411 2.0596627 0.14657861 13836.694
10000 2.0425447 0.018278949 2.0585541 0.1740235 12474.354
11000 2.0460068 0.012079252 2.0558127 0.19227728 11392.874
12000 2.0372027 0.019110617 2.0540498 0.21648482 10523.896
13000 2.0416804 0.015790699 2.0552026 0.24604625 9785.1314
14000 2.0466943 0.0064454505 2.0508656 0.22777839 9165.8411
15000 2.0436536 0.015576669 2.0569595 0.28266826 8582.5053
16000 2.0335541 0.01998798 2.0512825 0.2894612 8114.5044
17000 2.0109406 0.039132968 2.0478392 0.34665262 7758.9312
18000 2.016964 0.038362354 2.0530852 0.37108874 7399.6774
19000 2.0399584 0.012731426 2.0504232 0.32979629 7081.8066
20000 2.0260154 0.027880228 2.0516445 0.36371005 6812.6037
21000 2.0321966 0.023814364 2.053753 0.36376888 6556.4552
22000 1.9850947 0.072749763 2.0556388 0.52542507 6293.5003
23000 2.0360536 0.02395391 2.0577452 0.42540507 6061.6557
24000 2.0237181 0.032711377 2.0541809 0.43998497 5883.2886
25000 2.0145711 0.042376354 2.0547091 0.54706192 5715.4423
26000 2.00533 0.049986982 2.0530888 0.55453953 5564.0132
27000 2.0266398 0.035044901 2.0594329 0.51842026 5431.0259
28000 2.0321757 0.029913711 2.0598314 0.49663872 5305.2909
29000 1.9964359 0.066498777 2.0607164 0.56461185 5174.9947
30000 1.982908 0.082624709 2.0633294 0.65815484 5046.1903
31000 2.0141773 0.049027808 2.0609671 0.58512256 4980.1474
32000 1.9938427 0.076695158 2.0683225 0.64309333 4844.0907
33000 2.012869 0.054851302 2.0654838 0.63073652 4749.9868
34000 1.9867827 0.083467738 2.0680429 0.7840696 4656.3038
35000 2.0013706 0.067630614 2.0667775 0.72991936 4566.7052
36000 2.0106349 0.063148106 2.071549 0.73927159 4495.7351
37000 2.0245299 0.053399546 2.07568 0.7189467 4423.018
38000 2.0133929 0.062427506 2.0735833 0.74002573 4351.9277
39000 1.9874796 0.088021324 2.0732926 0.79349127 4293.1815
40000 2.0240342 0.057908137 2.0796935 0.75182186 4235.9306
41000 1.9973584 0.077969812 2.0731089 0.83868109 4218.8397
42000 2.0034131 0.079826384 2.0810134 0.78010078 4179.2254
43000 2.0438594 0.047617472 2.0892059 0.77402823 4089.0577
44000 2.021871 0.066506327 2.0861308 0.82593265 3999.9932
45000 2.0052391 0.07876379 2.0817748 0.84100298 3958.8163
46000 2.0163501 0.073621087 2.0877308 0.8621767 3920.4982
47000 2.020619 0.067706551 2.0860804 0.92651509 3885.827
48000 2.0168306 0.082111421 2.0967011 0.9214563 3829.1155
49000 2.0007804 0.098241181 2.0967985 0.93140657 3755.3901
50000 2.0213773 0.071280328 2.0904116 0.9408025 3734.5105
Loop time of 3.62754 on 4 procs for 50000 steps with 900 atoms
Performance: 5954453.961 tau/day, 13783.458 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0162 | 1.0554 | 1.0927 | 2.9 | 29.09
Neigh | 0.33396 | 0.34264 | 0.35093 | 1.0 | 9.45
Comm | 0.73343 | 0.79932 | 0.87689 | 5.7 | 22.03
Output | 0.00097108 | 0.0010269 | 0.0011532 | 0.2 | 0.03
Modify | 1.1624 | 1.1976 | 1.2436 | 3.2 | 33.01
Other | | 0.2316 | | | 6.38
Nlocal: 225 ave 234 max 208 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 305.25 ave 313 max 299 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs: 1501.75 ave 1627 max 1408 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Total # of neighbors = 6007
Ave neighs/atom = 6.67444
Neighbor list builds = 3071
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

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LAMMPS (15 Feb 2016)
# 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
Reading potential file ffield.comb with DATE: 2011-02-22
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 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Cu
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Cu
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 3 3 3
Memory usage per processor = 6.4805 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 0.244377 on 1 procs for 10 steps with 256 atoms
Performance: 0.707 ns/day, 33.941 hours/ns, 40.920 timesteps/s
100.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.24393 | 0.24393 | 0.24393 | 0.0 | 99.82
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00022697 | 0.00022697 | 0.00022697 | 0.0 | 0.09
Output | 0.00011015 | 0.00011015 | 0.00011015 | 0.0 | 0.05
Modify | 4.6968e-05 | 4.6968e-05 | 4.6968e-05 | 0.0 | 0.02
Other | | 5.984e-05 | | | 0.02
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
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
Reading potential file ffield.comb with DATE: 2011-02-22
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 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Cu
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Cu
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 3 3 3
Memory usage per processor = 6.35565 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 0.0647703 on 4 procs for 10 steps with 256 atoms
Performance: 2.668 ns/day, 8.996 hours/ns, 154.392 timesteps/s
100.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.063009 | 0.063389 | 0.06358 | 0.1 | 97.87
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00075269 | 0.00095391 | 0.001322 | 0.7 | 1.47
Output | 0.00029755 | 0.00031668 | 0.00032735 | 0.1 | 0.49
Modify | 1.5736e-05 | 1.7047e-05 | 1.8835e-05 | 0.0 | 0.03
Other | | 9.34e-05 | | | 0.14
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
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
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
Reading potential file ffield.comb with DATE: 2011-02-22
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
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 6.39852 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -2.9288959 -2.9290251 -0.23839068 -2.6906344 0.79666672 -1.5933334 25.62 25.62 25.62 16816.568
1 1.0007128 -3.0464056 -3.0465348 0.40404394 -3.4505788 0.79666635 -1.5933327 25.62 25.62 25.62 16816.568
2 1.0028587 -3.0464056 -3.0465351 0.40404056 -3.4505757 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
Loop time of 0.690546 on 1 procs for 2 steps with 1296 atoms
Performance: 0.050 ns/day, 479.546 hours/ns, 2.896 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.27005 | 0.27005 | 0.27005 | 0.0 | 39.11
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00010324 | 0.00010324 | 0.00010324 | 0.0 | 0.01
Output | 4.9114e-05 | 4.9114e-05 | 4.9114e-05 | 0.0 | 0.01
Modify | 0.4203 | 0.4203 | 0.4203 | 0.0 | 60.86
Other | | 4.387e-05 | | | 0.01
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 not checked
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:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 8.27781 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 1.0028587 -3.0464056 -3.0465351 0.40403069 -3.4505658 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
3 1.0028587 -3.0917245 -3.091854 0.36260063 -3.4544547 0.79642968 -1.5928594 25.59438 25.59438 25.59438 16766.169
4 1.0028587 -3.1396788 -3.1398083 0.3165719 -3.4563802 0.7961845 -1.592369 25.56876 25.56876 25.56876 16715.871
5 1.0028587 -3.1898661 -3.1899956 0.26823211 -3.4582277 0.79593359 -1.5918672 25.54314 25.54314 25.54314 16665.673
6 1.0028587 -3.2418712 -3.2420007 0.21802935 -3.46003 0.79567997 -1.5913599 25.51752 25.51752 25.51752 16615.576
7 1.0028587 -3.2952659 -3.2953954 0.16641718 -3.4618126 0.79542651 -1.590853 25.4919 25.4919 25.4919 16565.579
8 1.0028587 -3.3496093 -3.3497388 0.11386046 -3.4635993 0.79517586 -1.5903517 25.46628 25.46628 25.46628 16515.683
9 1.0028587 -3.4044042 -3.4045337 0.060834938 -3.4653687 0.7949272 -1.5898544 25.44066 25.44066 25.44066 16465.887
10 1.0028587 -3.4591871 -3.4593166 0.0077994909 -3.4671161 0.79468287 -1.5893657 25.41504 25.41504 25.41504 16416.191
11 1.0028587 -3.513522 -3.5136516 -0.044749471 -3.4689021 0.79444783 -1.5888957 25.38942 25.38942 25.38942 16366.595
12 1.0028587 -3.5669229 -3.5670525 -0.096284014 -3.4707685 0.79422383 -1.5884477 25.3638 25.3638 25.3638 16317.099
13 1.0028587 -3.6188974 -3.6190269 -0.14629696 -3.4727299 0.79401234 -1.5880247 25.33818 25.33818 25.33818 16267.704
14 1.0028587 -3.6689504 -3.66908 -0.19428069 -3.4747993 0.79381468 -1.5876294 25.31256 25.31256 25.31256 16218.408
15 1.0028587 -3.7165899 -3.7167195 -0.23973186 -3.4769876 0.79363192 -1.5872638 25.28694 25.28694 25.28694 16169.211
16 1.0028587 -3.7613321 -3.7614616 -0.28215725 -3.4793044 0.79346499 -1.58693 25.26132 25.26132 25.26132 16120.114
17 1.0028587 -3.8027083 -3.8028378 -0.32108032 -3.4817575 0.79331465 -1.5866293 25.2357 25.2357 25.2357 16071.117
18 1.0028587 -3.8402726 -3.8404022 -0.35604832 -3.4843538 0.79318151 -1.586363 25.21008 25.21008 25.21008 16022.219
19 1.0028587 -3.873609 -3.8737385 -0.38663966 -3.4870989 0.79306609 -1.5861322 25.18446 25.18446 25.18446 15973.421
20 1.0028587 -3.9023636 -3.9024931 -0.41247128 -3.4900218 0.79297061 -1.5859412 25.15884 25.15884 25.15884 15924.721
21 1.0028587 -3.9264347 -3.9265643 -0.43319004 -3.4933742 0.7929094 -1.5858188 25.13322 25.13322 25.13322 15876.121
22 1.0028587 -3.9452897 -3.9454192 -0.44839149 -3.4970277 0.79287195 -1.5857439 25.1076 25.1076 25.1076 15827.62
23 1.0028587 -3.958699 -3.9588285 -0.45793805 -3.5008905 0.79285787 -1.5857157 25.08198 25.08198 25.08198 15779.217
24 1.0028587 -3.966498 -3.9666275 -0.4616679 -3.5049596 0.79285787 -1.5857157 25.05636 25.05636 25.05636 15730.913
25 1.0028587 -3.9686392 -3.9687687 -0.46014255 -3.5086261 0.79286937 -1.5857387 25.034573 25.034573 25.034573 15689.914
26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
Loop time of 29.9485 on 1 procs for 24 steps with 1296 atoms
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.04653512838 -3.96876869389 -3.96876869369
Force two-norm initial, final = 32801.4 117.257
Force max component initial, final = 18937.9 67.6917
Final line search alpha, max atom move = 9.01671e-10 6.10357e-08
Iterations, force evaluations = 24 53
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.6428 | 7.6428 | 7.6428 | 0.0 | 25.52
Neigh | 0.072307 | 0.072307 | 0.072307 | 0.0 | 0.24
Comm | 0.0033123 | 0.0033123 | 0.0033123 | 0.0 | 0.01
Output | 0.00073075 | 0.00073075 | 0.00073075 | 0.0 | 0.00
Modify | 22.217 | 22.217 | 22.217 | 0.0 | 74.18
Other | | 0.01276 | | | 0.04
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 3
Dangerous builds not checked
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 6.65281 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
27 0.98924824 -3.9686392 -3.9687669 -0.46018036 -3.5085866 0.79286575 -1.5857315 25.034573 25.034573 25.034573 15689.914
Loop time of 0.283693 on 1 procs for 1 steps with 1296 atoms
Performance: 0.061 ns/day, 394.018 hours/ns, 3.525 timesteps/s
100.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14656 | 0.14656 | 0.14656 | 0.0 | 51.66
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 5.8889e-05 | 5.8889e-05 | 5.8889e-05 | 0.0 | 0.02
Output | 2.8849e-05 | 2.8849e-05 | 2.8849e-05 | 0.0 | 0.01
Modify | 0.13702 | 0.13702 | 0.13702 | 0.0 | 48.30
Other | | 2.337e-05 | | | 0.01
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
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 NULL 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:680)
run 10
Memory usage per processor = 7.02781 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
27 25.034573 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
28 25.034823 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
29 25.035074 25.034573 25.034573 0 0 0 -87059995 -96445744 -96445673 -126501.16 -147663.09 -107878.31
30 25.035324 25.034573 25.034573 0 0 0 -68136799 -86908913 -86908841 -126497.63 -147658.05 -107874.8
31 25.035574 25.034573 25.034573 0 0 0 -49213405 -77372273 -77372200 -126494.09 -147653.02 -107871.3
32 25.035825 25.034573 25.034573 0 0 0 -30289818 -67835826 -67835753 -126490.56 -147647.98 -107867.79
33 25.036075 25.034573 25.034573 0 0 0 -11366046 -58299575 -58299501 -126487.03 -147642.95 -107864.28
34 25.036325 25.034573 25.034573 0 0 0 7557907.5 -48763524 -48763449 -126483.5 -147637.91 -107860.77
35 25.036576 25.034573 25.034573 0 0 0 26482035 -39227675 -39227600 -126479.96 -147632.87 -107857.27
36 25.036826 25.034573 25.034573 0 0 0 45406330 -29692031 -29691956 -126476.43 -147627.84 -107853.76
37 25.037076 25.034573 25.034573 0 0 0 64330788 -20156596 -20156520 -126472.9 -147622.8 -107850.25
Loop time of 1.61281 on 1 procs for 10 steps with 1296 atoms
Performance: 0.107 ns/day, 224.001 hours/ns, 6.200 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6096 | 1.6096 | 1.6096 | 0.0 | 99.80
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00054646 | 0.00054646 | 0.00054646 | 0.0 | 0.03
Output | 0.0023828 | 0.0023828 | 0.0023828 | 0.0 | 0.15
Modify | 0.00019932 | 0.00019932 | 0.00019932 | 0.0 | 0.01
Other | | 0.0001204 | | | 0.01
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom NULL 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 = 7.77781 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
37 25.037076 25.034573 25.034573 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
38 25.037076 25.034573 25.034823 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
39 25.037076 25.034573 25.035074 0 0 0 92791365 -1081679.6 8300643.1 -126464.81 -147612.37 -107844.24
40 25.037076 25.034573 25.035324 0 0 0 1.0232711e+08 8457831.4 27222756 -126460.25 -147606.97 -107841.74
41 25.037076 25.034573 25.035574 0 0 0 1.1186264e+08 17997157 46145038 -126455.7 -147601.57 -107839.24
42 25.037076 25.034573 25.035825 0 0 0 1.2139794e+08 27536295 65067481 -126451.14 -147596.17 -107836.73
43 25.037076 25.034573 25.036075 0 0 0 1.3093301e+08 37075242 83990081 -126446.58 -147590.78 -107834.23
44 25.037076 25.034573 25.036325 0 0 0 1.4046786e+08 46613995 1.0291283e+08 -126442.03 -147585.38 -107831.73
45 25.037076 25.034573 25.036576 0 0 0 1.5000248e+08 56152550 1.2183572e+08 -126437.47 -147579.98 -107829.23
46 25.037076 25.034573 25.036826 0 0 0 1.5953685e+08 65690906 1.4075876e+08 -126432.91 -147574.58 -107826.72
47 25.037076 25.034573 25.037076 0 0 0 1.69071e+08 75229058 1.5968192e+08 -126428.35 -147569.18 -107824.22
Loop time of 1.56349 on 1 procs for 10 steps with 1296 atoms
Performance: 0.111 ns/day, 217.151 hours/ns, 6.396 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5603 | 1.5603 | 1.5603 | 0.0 | 99.79
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0005424 | 0.0005424 | 0.0005424 | 0.0 | 0.03
Output | 0.0023627 | 0.0023627 | 0.0023627 | 0.0 | 0.15
Modify | 0.00018978 | 0.00018978 | 0.00018978 | 0.0 | 0.01
Other | | 0.0001137 | | | 0.01
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom NULL 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 = 8.54308 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
47 25.037076 25.034573 25.037076 0 0 0 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
48 25.037076 25.034573 25.037076 0 0 5.0074153e-07 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
49 25.037076 25.034573 25.037076 0 0 1.0014831e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -88830.837
50 25.037076 25.034573 25.037076 0 0 1.5022246e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -69839.957
51 25.037076 25.034573 25.037076 0 0 2.0029661e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.77 -50849.077
52 25.037076 25.034573 25.037076 0 0 2.5037076e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.76 -31858.197
53 25.037076 25.034573 25.037076 0 0 3.0044492e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.76 -12867.317
54 25.037076 25.034573 25.037076 0 0 3.5051907e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 6123.563
55 25.037076 25.034573 25.037076 0 0 4.0059322e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 25114.443
56 25.037076 25.034573 25.037076 0 0 4.5066738e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 44105.323
57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 63096.203
Loop time of 1.55801 on 1 procs for 10 steps with 1296 atoms
Performance: 0.111 ns/day, 216.390 hours/ns, 6.418 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.555 | 1.555 | 1.555 | 0.0 | 99.80
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00052738 | 0.00052738 | 0.00052738 | 0.0 | 0.03
Output | 0.0022299 | 0.0022299 | 0.0022299 | 0.0 | 0.14
Modify | 0.00018501 | 0.00018501 | 0.00018501 | 0.0 | 0.01
Other | | 0.0001023 | | | 0.01
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom NULL 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 = 9.29308 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
58 25.037076 25.034573 25.037076 5.0069146e-07 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
59 25.037076 25.034573 25.037076 1.0013829e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -107434.78 -147563.72 82087.087
60 25.037076 25.034573 25.037076 1.5020744e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -88445.781 -147563.72 82087.09
61 25.037076 25.034573 25.037076 2.0027658e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -69456.779 -147563.71 82087.094
62 25.037076 25.034573 25.037076 2.5034573e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -50467.776 -147563.71 82087.098
63 25.037076 25.034573 25.037076 3.0041488e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -31478.773 -147563.7 82087.101
64 25.037076 25.034573 25.037076 3.5048402e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -12489.77 -147563.7 82087.105
65 25.037076 25.034573 25.037076 4.0055317e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 6499.2334 -147563.69 82087.109
66 25.037076 25.034573 25.037076 4.5062231e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 25488.236 -147563.69 82087.113
67 25.037076 25.034573 25.037076 5.0069146e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 44477.239 -147563.68 82087.116
Loop time of 1.56044 on 1 procs for 10 steps with 1296 atoms
Performance: 0.111 ns/day, 216.728 hours/ns, 6.408 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.5574 | 1.5574 | 1.5574 | 0.0 | 99.80
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00051975 | 0.00051975 | 0.00051975 | 0.0 | 0.03
Output | 0.0022559 | 0.0022559 | 0.0022559 | 0.0 | 0.14
Modify | 0.00019503 | 0.00019503 | 0.00019503 | 0.0 | 0.01
Other | | 0.0001116 | | | 0.01
Nlocal: 1296 ave 1296 max 1296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8243 ave 8243 max 8243 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 862272 ave 862272 max 862272 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
Total wall time: 0:00:44

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examples/comb/log.15Feb16.comb.Cu2O.elastic.g++.4 Normal file
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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
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
Reading potential file ffield.comb with DATE: 2011-02-22
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
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 6.28094 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
0 1 -2.9288959 -2.9290251 -0.23839068 -2.6906344 0.79666672 -1.5933334 25.62 25.62 25.62 16816.568
1 1.0007128 -3.0464056 -3.0465348 0.40404394 -3.4505788 0.79666635 -1.5933327 25.62 25.62 25.62 16816.568
2 1.0028587 -3.0464056 -3.0465351 0.40404056 -3.4505757 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
Loop time of 0.174112 on 4 procs for 2 steps with 1296 atoms
Performance: 0.198 ns/day, 120.911 hours/ns, 11.487 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.067018 | 0.067376 | 0.067552 | 0.1 | 38.70
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00030375 | 0.00049108 | 0.00085974 | 1.0 | 0.28
Output | 7.8678e-05 | 8.1301e-05 | 8.7023e-05 | 0.0 | 0.05
Modify | 0.10611 | 0.10612 | 0.10613 | 0.0 | 60.95
Other | | 4.166e-05 | | | 0.02
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 not checked
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:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 8.15594 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
2 1.0028587 -3.0464056 -3.0465351 0.40403069 -3.4505658 0.79666516 -1.5933303 25.62 25.62 25.62 16816.568
3 1.0028587 -3.0917245 -3.091854 0.36260063 -3.4544547 0.79642968 -1.5928594 25.59438 25.59438 25.59438 16766.169
4 1.0028587 -3.1396788 -3.1398083 0.3165719 -3.4563802 0.7961845 -1.592369 25.56876 25.56876 25.56876 16715.871
5 1.0028587 -3.1898661 -3.1899956 0.26823211 -3.4582277 0.79593359 -1.5918672 25.54314 25.54314 25.54314 16665.673
6 1.0028587 -3.2418712 -3.2420007 0.21802935 -3.46003 0.79567997 -1.5913599 25.51752 25.51752 25.51752 16615.576
7 1.0028587 -3.2952659 -3.2953954 0.16641718 -3.4618126 0.79542651 -1.590853 25.4919 25.4919 25.4919 16565.579
8 1.0028587 -3.3496093 -3.3497388 0.11386046 -3.4635993 0.79517586 -1.5903517 25.46628 25.46628 25.46628 16515.683
9 1.0028587 -3.4044042 -3.4045337 0.060834938 -3.4653687 0.7949272 -1.5898544 25.44066 25.44066 25.44066 16465.887
10 1.0028587 -3.4591871 -3.4593166 0.0077994909 -3.4671161 0.79468287 -1.5893657 25.41504 25.41504 25.41504 16416.191
11 1.0028587 -3.513522 -3.5136516 -0.044749471 -3.4689021 0.79444783 -1.5888957 25.38942 25.38942 25.38942 16366.595
12 1.0028587 -3.5669229 -3.5670525 -0.096284014 -3.4707685 0.79422383 -1.5884477 25.3638 25.3638 25.3638 16317.099
13 1.0028587 -3.6188974 -3.6190269 -0.14629696 -3.4727299 0.79401234 -1.5880247 25.33818 25.33818 25.33818 16267.704
14 1.0028587 -3.6689504 -3.66908 -0.19428069 -3.4747993 0.79381468 -1.5876294 25.31256 25.31256 25.31256 16218.408
15 1.0028587 -3.7165899 -3.7167195 -0.23973186 -3.4769876 0.79363192 -1.5872638 25.28694 25.28694 25.28694 16169.211
16 1.0028587 -3.7613321 -3.7614616 -0.28215725 -3.4793044 0.79346499 -1.58693 25.26132 25.26132 25.26132 16120.114
17 1.0028587 -3.8027083 -3.8028378 -0.32108032 -3.4817575 0.79331465 -1.5866293 25.2357 25.2357 25.2357 16071.117
18 1.0028587 -3.8402726 -3.8404022 -0.35604832 -3.4843538 0.79318151 -1.586363 25.21008 25.21008 25.21008 16022.219
19 1.0028587 -3.873609 -3.8737385 -0.38663966 -3.4870989 0.79306609 -1.5861322 25.18446 25.18446 25.18446 15973.421
20 1.0028587 -3.9023636 -3.9024931 -0.41247128 -3.4900218 0.79297061 -1.5859412 25.15884 25.15884 25.15884 15924.721
21 1.0028587 -3.9264347 -3.9265643 -0.43319004 -3.4933742 0.7929094 -1.5858188 25.13322 25.13322 25.13322 15876.121
22 1.0028587 -3.9452897 -3.9454192 -0.44839149 -3.4970277 0.79287195 -1.5857439 25.1076 25.1076 25.1076 15827.62
23 1.0028587 -3.958699 -3.9588285 -0.45793805 -3.5008905 0.79285787 -1.5857157 25.08198 25.08198 25.08198 15779.217
24 1.0028587 -3.966498 -3.9666275 -0.4616679 -3.5049596 0.79285787 -1.5857157 25.05636 25.05636 25.05636 15730.913
25 1.0028587 -3.9686392 -3.9687687 -0.46014255 -3.5086261 0.79286937 -1.5857387 25.034573 25.034573 25.034573 15689.914
26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
Loop time of 7.73864 on 4 procs for 24 steps with 1296 atoms
99.9% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-3.04653512838 -3.96876869389 -3.96876869369
Force two-norm initial, final = 32801.4 117.257
Force max component initial, final = 18937.9 67.6917
Final line search alpha, max atom move = 9.01671e-10 6.10357e-08
Iterations, force evaluations = 24 53
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8982 | 1.9386 | 1.9643 | 1.8 | 25.05
Neigh | 0.017612 | 0.017903 | 0.018068 | 0.1 | 0.23
Comm | 0.011921 | 0.037696 | 0.078263 | 13.0 | 0.49
Output | 0.00091124 | 0.00094914 | 0.0010424 | 0.2 | 0.01
Modify | 5.736 | 5.7361 | 5.7362 | 0.0 | 74.12
Other | | 0.007425 | | | 0.10
Nlocal: 324 ave 328 max 318 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 4943 ave 4949 max 4939 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 218192 max 211632 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 3
Dangerous builds not checked
min_modify dmax 0.2 line quadratic
unfix 1
fix 1 all nve
run 1
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 6.53094 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
26 1.0028587 -3.9686392 -3.9687687 -0.46018211 -3.5085866 0.79286471 -1.5857294 25.034573 25.034573 25.034573 15689.914
27 0.98924824 -3.9686392 -3.9687669 -0.46018036 -3.5085866 0.79286575 -1.5857315 25.034573 25.034573 25.034573 15689.914
Loop time of 0.0716895 on 4 procs for 1 steps with 1296 atoms
Performance: 0.241 ns/day, 99.569 hours/ns, 13.949 timesteps/s
100.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.035934 | 0.036807 | 0.03732 | 0.3 | 51.34
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00013494 | 0.00064868 | 0.0015209 | 2.1 | 0.90
Output | 3.6955e-05 | 3.8445e-05 | 4.1962e-05 | 0.0 | 0.05
Modify | 0.034179 | 0.034181 | 0.034182 | 0.0 | 47.68
Other | | 1.472e-05 | | | 0.02
Nlocal: 324 ave 328 max 318 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 4943 ave 4949 max 4939 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 218192 max 211632 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
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 NULL 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:680)
run 10
Memory usage per processor = 6.90594 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
27 25.034573 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
28 25.034823 25.034573 25.034573 0 0 0 -1.0598299e+08 -1.0598276e+08 -1.0598269e+08 -126504.69 -147668.13 -107881.81
29 25.035074 25.034573 25.034573 0 0 0 -87059995 -96445744 -96445673 -126501.16 -147663.09 -107878.31
30 25.035324 25.034573 25.034573 0 0 0 -68136799 -86908913 -86908841 -126497.63 -147658.05 -107874.8
31 25.035574 25.034573 25.034573 0 0 0 -49213405 -77372273 -77372200 -126494.09 -147653.02 -107871.3
32 25.035825 25.034573 25.034573 0 0 0 -30289818 -67835826 -67835753 -126490.56 -147647.98 -107867.79
33 25.036075 25.034573 25.034573 0 0 0 -11366046 -58299575 -58299501 -126487.03 -147642.95 -107864.28
34 25.036325 25.034573 25.034573 0 0 0 7557907.5 -48763524 -48763449 -126483.5 -147637.91 -107860.77
35 25.036576 25.034573 25.034573 0 0 0 26482035 -39227675 -39227600 -126479.96 -147632.87 -107857.27
36 25.036826 25.034573 25.034573 0 0 0 45406330 -29692031 -29691956 -126476.43 -147627.84 -107853.76
37 25.037076 25.034573 25.034573 0 0 0 64330788 -20156596 -20156520 -126472.9 -147622.8 -107850.25
Loop time of 0.40881 on 4 procs for 10 steps with 1296 atoms
Performance: 0.423 ns/day, 56.779 hours/ns, 24.461 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38885 | 0.39776 | 0.40386 | 1.0 | 97.30
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0020289 | 0.0081917 | 0.017143 | 7.1 | 2.00
Output | 0.0026636 | 0.0027153 | 0.0027769 | 0.1 | 0.66
Modify | 5.6982e-05 | 5.9664e-05 | 6.628e-05 | 0.0 | 0.01
Other | | 8.208e-05 | | | 0.02
Nlocal: 324 ave 328 max 318 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 4943 ave 4949 max 4939 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 218192 max 211632 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom NULL 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 = 7.65594 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
37 25.037076 25.034573 25.034573 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
38 25.037076 25.034573 25.034823 0 0 0 83255401 -10621373 -10621296 -126469.36 -147617.76 -107846.74
39 25.037076 25.034573 25.035074 0 0 0 92791365 -1081679.6 8300643.1 -126464.81 -147612.37 -107844.24
40 25.037076 25.034573 25.035324 0 0 0 1.0232711e+08 8457831.4 27222756 -126460.25 -147606.97 -107841.74
41 25.037076 25.034573 25.035574 0 0 0 1.1186264e+08 17997157 46145038 -126455.7 -147601.57 -107839.24
42 25.037076 25.034573 25.035825 0 0 0 1.2139794e+08 27536295 65067481 -126451.14 -147596.17 -107836.73
43 25.037076 25.034573 25.036075 0 0 0 1.3093301e+08 37075242 83990081 -126446.58 -147590.78 -107834.23
44 25.037076 25.034573 25.036325 0 0 0 1.4046786e+08 46613995 1.0291283e+08 -126442.03 -147585.38 -107831.73
45 25.037076 25.034573 25.036576 0 0 0 1.5000248e+08 56152550 1.2183572e+08 -126437.47 -147579.98 -107829.23
46 25.037076 25.034573 25.036826 0 0 0 1.5953685e+08 65690906 1.4075876e+08 -126432.91 -147574.58 -107826.72
47 25.037076 25.034573 25.037076 0 0 0 1.69071e+08 75229058 1.5968192e+08 -126428.35 -147569.18 -107824.22
Loop time of 0.407868 on 4 procs for 10 steps with 1296 atoms
Performance: 0.424 ns/day, 56.648 hours/ns, 24.518 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38874 | 0.39706 | 0.40377 | 0.9 | 97.35
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.001327 | 0.0080245 | 0.016345 | 6.6 | 1.97
Output | 0.0026383 | 0.0026469 | 0.0026655 | 0.0 | 0.65
Modify | 5.2929e-05 | 5.6744e-05 | 5.9128e-05 | 0.0 | 0.01
Other | | 7.844e-05 | | | 0.02
Nlocal: 324 ave 328 max 318 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 4943 ave 4949 max 4939 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 218192 max 211632 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom NULL 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 = 8.42123 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
47 25.037076 25.034573 25.037076 0 0 0 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
48 25.037076 25.034573 25.037076 0 0 5.0074153e-07 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.79 -107821.72
49 25.037076 25.034573 25.037076 0 0 1.0014831e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -88830.837
50 25.037076 25.034573 25.037076 0 0 1.5022246e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.78 -69839.957
51 25.037076 25.034573 25.037076 0 0 2.0029661e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.77 -50849.077
52 25.037076 25.034573 25.037076 0 0 2.5037076e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.76 -31858.197
53 25.037076 25.034573 25.037076 0 0 3.0044492e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.76 -12867.317
54 25.037076 25.034573 25.037076 0 0 3.5051907e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 6123.563
55 25.037076 25.034573 25.037076 0 0 4.0059322e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.75 25114.443
56 25.037076 25.034573 25.037076 0 0 4.5066738e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 44105.323
57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.74 63096.203
Loop time of 0.408682 on 4 procs for 10 steps with 1296 atoms
Performance: 0.423 ns/day, 56.761 hours/ns, 24.469 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38891 | 0.39738 | 0.40388 | 1.0 | 97.23
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0019937 | 0.0084969 | 0.016969 | 6.6 | 2.08
Output | 0.0026531 | 0.0026709 | 0.0026915 | 0.0 | 0.65
Modify | 5.1975e-05 | 5.6446e-05 | 5.9366e-05 | 0.0 | 0.01
Other | | 7.963e-05 | | | 0.02
Nlocal: 324 ave 328 max 318 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 4943 ave 4949 max 4939 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 218192 max 211632 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom NULL 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 = 9.17123 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
57 25.037076 25.034573 25.037076 0 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
58 25.037076 25.034573 25.037076 5.0069146e-07 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -126423.79 -147563.73 82087.083
59 25.037076 25.034573 25.037076 1.0013829e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -107434.78 -147563.72 82087.087
60 25.037076 25.034573 25.037076 1.5020744e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -88445.781 -147563.72 82087.09
61 25.037076 25.034573 25.037076 2.0027658e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -69456.779 -147563.71 82087.094
62 25.037076 25.034573 25.037076 2.5034573e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -50467.776 -147563.71 82087.098
63 25.037076 25.034573 25.037076 3.0041488e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -31478.773 -147563.7 82087.101
64 25.037076 25.034573 25.037076 3.5048402e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 -12489.77 -147563.7 82087.105
65 25.037076 25.034573 25.037076 4.0055317e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 6499.2334 -147563.69 82087.109
66 25.037076 25.034573 25.037076 4.5062231e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 25488.236 -147563.69 82087.113
67 25.037076 25.034573 25.037076 5.0069146e-06 0 5.0074153e-06 1.7860489e+08 84767004 1.7860521e+08 44477.239 -147563.68 82087.116
Loop time of 0.411159 on 4 procs for 10 steps with 1296 atoms
Performance: 0.420 ns/day, 57.105 hours/ns, 24.322 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.3889 | 0.39826 | 0.40584 | 1.1 | 96.86
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0024002 | 0.010008 | 0.019374 | 6.8 | 2.43
Output | 0.0027368 | 0.0027526 | 0.0027771 | 0.0 | 0.67
Modify | 5.6028e-05 | 5.8174e-05 | 6.0081e-05 | 0.0 | 0.01
Other | | 8.059e-05 | | | 0.02
Nlocal: 324 ave 328 max 318 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 4943 ave 4949 max 4939 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 215568 ave 218192 max 211632 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 862272
Ave neighs/atom = 665.333
Neighbor list builds = 0
Dangerous builds not checked
Total wall time: 0:00:11

235
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LAMMPS (15 Feb 2016)
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
reading atoms ...
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
Reading potential file ffield.comb with DATE: 2011-02-22
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
Neighbor list info ...
1 neighbor list requests
update every 10 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 6.13908 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -9.3995049 -9.3995049 5.256221 -14.655726 60985.254 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.169538 on 1 procs for 1 steps with 1500 atoms
Performance: 0.102 ns/day, 235.469 hours/ns, 5.898 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.16939 | 0.16939 | 0.16939 | 0.0 | 99.91
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 6.485e-05 | 6.485e-05 | 6.485e-05 | 0.0 | 0.04
Output | 2.9802e-05 | 2.9802e-05 | 2.9802e-05 | 0.0 | 0.02
Modify | 3.9101e-05 | 3.9101e-05 | 3.9101e-05 | 0.0 | 0.02
Other | | 1.717e-05 | | | 0.01
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 = 6.76408 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
2 0.13734003 -10.041396 -10.041413 2.7214902 -12.762903 -130794.11 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
3 0.2686308 -10.041388 -10.041423 2.7214912 -12.762914 -130800.39 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
4 0.44445358 -10.041379 -10.041436 2.7214924 -12.762929 -130808.63 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
5 0.66458606 -10.041367 -10.041453 2.7214941 -12.762947 -130818.84 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
Loop time of 1.16742 on 1 procs for 5 steps with 1500 atoms
Performance: 0.074 ns/day, 324.284 hours/ns, 4.283 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.85832 | 0.85832 | 0.85832 | 0.0 | 73.52
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00033593 | 0.00033593 | 0.00033593 | 0.0 | 0.03
Output | 0.00015116 | 0.00015116 | 0.00015116 | 0.0 | 0.01
Modify | 0.30852 | 0.30852 | 0.30852 | 0.0 | 26.43
Other | | 9.751e-05 | | | 0.01
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
# should minimize to higher tolerance in practice
#minimize 1.0e-12 1.0e-18 1000 10000
minimize 1.0e-4 1.0e-6 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 7.88908 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
7 0.92875014 -10.041833 -10.041953 2.7196698 -12.761623 -130754.01 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
Loop time of 0.64676 on 1 procs for 1 steps with 1500 atoms
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-10.0414727016 -10.0414727016 -10.0419532985
Force two-norm initial, final = 2625.99 2625.45
Force max component initial, final = 1915.33 1916.61
Final line search alpha, max atom move = 1.04421e-07 0.000200134
Iterations, force evaluations = 1 1
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.34047 | 0.34047 | 0.34047 | 0.0 | 52.64
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00012827 | 0.00012827 | 0.00012827 | 0.0 | 0.02
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.30579 | 0.30579 | 0.30579 | 0.0 | 47.28
Other | | 0.0003626 | | | 0.06
Nlocal: 1500 ave 1500 max 1500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10100 ave 10100 max 10100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1037500
Ave neighs/atom = 691.667
Neighbor list builds = 0
Dangerous builds = 0
min_modify dmax 0.005 line quadratic
#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 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Hf O
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Hf O
velocity all create 300.1 2398378
run 10
Neighbor list info ...
1 neighbor list requests
update every 10 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 6.76408 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
7 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
8 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
9 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
10 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
11 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
12 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
13 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
14 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
15 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
16 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
17 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
Loop time of 2.31943 on 1 procs for 10 steps with 1500 atoms
Performance: 0.075 ns/day, 322.143 hours/ns, 4.311 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7064 | 1.7064 | 1.7064 | 0.0 | 73.57
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00066495 | 0.00066495 | 0.00066495 | 0.0 | 0.03
Output | 0.00035143 | 0.00035143 | 0.00035143 | 0.0 | 0.02
Modify | 0.61178 | 0.61178 | 0.61178 | 0.0 | 26.38
Other | | 0.0002165 | | | 0.01
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
Total wall time: 0:00:10

235
examples/comb/log.15Feb16.comb.HfO2.g++.4 Normal file
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@ -0,0 +1,235 @@
LAMMPS (15 Feb 2016)
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
reading atoms ...
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
Reading potential file ffield.comb with DATE: 2011-02-22
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
Neighbor list info ...
1 neighbor list requests
update every 10 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 5.96686 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
0 0 -9.3995049 -9.3995049 5.256221 -14.655726 60985.254 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
Loop time of 0.0429993 on 4 procs for 1 steps with 1500 atoms
Performance: 0.402 ns/day, 59.721 hours/ns, 23.256 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.042339 | 0.042613 | 0.042762 | 0.1 | 99.10
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0001421 | 0.00029129 | 0.00056505 | 1.0 | 0.68
Output | 3.7909e-05 | 4.0174e-05 | 4.6015e-05 | 0.1 | 0.09
Modify | 2.4796e-05 | 2.4796e-05 | 2.4796e-05 | 0.0 | 0.06
Other | | 3.028e-05 | | | 0.07
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 = 6.59186 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
1 0.039315732 -9.3995035 -9.3995086 5.2562201 -14.655729 60983.797 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
2 0.13734003 -10.041396 -10.041413 2.7214902 -12.762903 -130794.11 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
3 0.2686308 -10.041388 -10.041423 2.7214912 -12.762914 -130800.39 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
4 0.44445358 -10.041379 -10.041436 2.7214924 -12.762929 -130808.63 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
5 0.66458606 -10.041367 -10.041453 2.7214941 -12.762947 -130818.84 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
Loop time of 0.290755 on 4 procs for 5 steps with 1500 atoms
Performance: 0.297 ns/day, 80.765 hours/ns, 17.197 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.21107 | 0.21252 | 0.21354 | 0.2 | 73.09
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00075912 | 0.001812 | 0.0032141 | 2.1 | 0.62
Output | 0.00020814 | 0.00021452 | 0.00023079 | 0.1 | 0.07
Modify | 0.07608 | 0.076133 | 0.076177 | 0.0 | 26.18
Other | | 7.701e-05 | | | 0.03
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
# should minimize to higher tolerance in practice
#minimize 1.0e-12 1.0e-18 1000 10000
minimize 1.0e-4 1.0e-6 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 7.71686 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
6 0.92875014 -10.041353 -10.041473 2.721496 -12.762969 -130831 17627.802 25.642 25.957 26.4845 -4.46691 3.3579959 -1.678998
7 0.92875014 -10.041833 -10.041953 2.7196698 -12.761623 -130754.01 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
Loop time of 0.161507 on 4 procs for 1 steps with 1500 atoms
100.0% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-10.0414727016 -10.0414727016 -10.0419532985
Force two-norm initial, final = 2625.99 2625.45
Force max component initial, final = 1915.33 1916.61
Final line search alpha, max atom move = 1.04421e-07 0.000200134
Iterations, force evaluations = 1 1
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.084314 | 0.085016 | 0.085468 | 0.2 | 52.64
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00030208 | 0.00076222 | 0.0014489 | 1.7 | 0.47
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0.075456 | 0.075471 | 0.07548 | 0.0 | 46.73
Other | | 0.0002575 | | | 0.16
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
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 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Hf O
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Hf O
velocity all create 300.1 2398378
run 10
Neighbor list info ...
1 neighbor list requests
update every 10 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 5 5
Memory usage per processor = 6.59186 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
7 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
8 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
9 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
10 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
11 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
12 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
13 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
14 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
15 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
16 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
17 300.1 -10.003188 -10.041953 2.7196698 -12.761623 -127240 17619.854 25.636872 25.952628 26.482314 -4.4665414 3.3577845 -1.6788923
Loop time of 0.581787 on 4 procs for 10 steps with 1500 atoms
Performance: 0.297 ns/day, 80.804 hours/ns, 17.188 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.42265 | 0.42528 | 0.42704 | 0.2 | 73.10
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0015607 | 0.0033906 | 0.0059152 | 2.7 | 0.58
Output | 0.00046325 | 0.00046599 | 0.00046873 | 0.0 | 0.08
Modify | 0.1524 | 0.15252 | 0.1526 | 0.0 | 26.22
Other | | 0.0001305 | | | 0.02
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
Total wall time: 0:00:02

333
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LAMMPS (15 Feb 2016)
# 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
Reading potential file ffield.comb with DATE: 2011-02-22
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:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 4 4 4
Memory usage per processor = 7.60455 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295965 -4.6297255 -4.6297255 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
4 1 -4.6295965 -4.6297255 -4.6297255 0
5 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.206087 on 1 procs for 5 steps with 512 atoms
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550325 -4.62972550325
Force two-norm initial, final = 5.86582 2.4862e-12
Force max component initial, final = 3.38663 2.10283e-12
Final line search alpha, max atom move = 1 2.10283e-12
Iterations, force evaluations = 5 10
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.2046 | 0.2046 | 0.2046 | 0.0 | 99.28
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00029564 | 0.00029564 | 0.00029564 | 0.0 | 0.14
Output | 3.0041e-05 | 3.0041e-05 | 3.0041e-05 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.001161 | | | 0.56
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 not checked
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 4 4 4
Memory usage per processor = 5.97955 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
5 1 -4.6295965 -4.6297255 -4.6297255 0
6 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.018579 on 1 procs for 1 steps with 512 atoms
Performance: 0.930 ns/day, 25.804 hours/ns, 53.824 timesteps/s
102.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.018534 | 0.018534 | 0.018534 | 0.0 | 99.76
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.7895e-05 | 2.7895e-05 | 2.7895e-05 | 0.0 | 0.15
Output | 9.0599e-06 | 9.0599e-06 | 9.0599e-06 | 0.0 | 0.05
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 7.868e-06 | | | 0.04
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 not checked
### 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 NULL 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:680)
run 10
Memory usage per processor = 6.72955 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
6 21.727916 21.727916 21.727916 0 0 0 -4.5569391e-06 -9.3041736e-06 -3.863262e-06 5.3686749e-06 -1.5078216e-06 5.1674734e-06
7 21.728133 21.727916 21.727916 0 0 0 -2.4800435e-06 -9.5067314e-06 -2.1562734e-06 5.5972954e-06 -2.3715124e-06 3.9555507e-06
8 21.72835 21.727916 21.727916 0 0 0 146204.17 77325.788 77325.788 3.5125695e-06 -1.9487795e-06 5.2972201e-06
9 21.728568 21.727916 21.727916 0 0 0 292407.63 154648.04 154648.04 5.6408383e-06 -2.4472325e-06 6.3046987e-06
10 21.728785 21.727916 21.727916 0 0 0 438610.37 231966.74 231966.74 5.5704989e-06 -1.8785254e-06 -1.4083956e-06
11 21.729002 21.727916 21.727916 0 0 0 584812.4 309281.91 309281.91 -1.2913749e-05 2.0544275e-06 7.547976e-06
12 21.729219 21.727916 21.727916 0 0 0 731013.71 386593.54 386593.54 6.0987798e-06 -2.0790709e-06 7.8755963e-06
13 21.729437 21.727916 21.727916 0 0 0 877214.3 463901.63 463901.63 5.2296156e-06 -2.2013505e-06 2.6034199e-06
14 21.729654 21.727916 21.727916 0 0 0 1023414.2 541206.18 541206.18 5.6537455e-06 -1.9222461e-06 4.3649131e-06
15 21.729871 21.727916 21.727916 0 0 0 1169613.3 618507.19 618507.19 5.5850663e-06 -2.204341e-06 6.1719985e-06
16 21.730089 21.727916 21.727916 0 0 0 1315811.8 695804.66 695804.66 -1.3406996e-05 2.5348334e-06 6.2581356e-06
Loop time of 0.203248 on 1 procs for 10 steps with 512 atoms
Performance: 0.850 ns/day, 28.229 hours/ns, 49.201 timesteps/s
99.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20165 | 0.20165 | 0.20165 | 0.0 | 99.21
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00027919 | 0.00027919 | 0.00027919 | 0.0 | 0.14
Output | 0.0011773 | 0.0011773 | 0.0011773 | 0.0 | 0.58
Modify | 8.1301e-05 | 8.1301e-05 | 8.1301e-05 | 0.0 | 0.04
Other | | 5.889e-05 | | | 0.03
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 not checked
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom NULL 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 = 7.47955 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
16 21.730089 21.727916 21.727916 0 0 0 1462009.5 773098.59 773098.59 4.2549849e-06 -8.3746497e-07 7.0310015e-06
17 21.730089 21.727916 21.728133 0 0 0 1462009.5 773098.59 773098.59 5.1784721e-06 -2.3038152e-06 5.7172699e-06
18 21.730089 21.727916 21.72835 0 0 0 1539307.6 850399.75 919275.09 9.5325273e-06 -6.4331187e-07 4.7453557e-06
19 21.730089 21.727916 21.728568 0 0 0 1616602.2 927697.36 1065450.9 1.3298468e-05 -1.8936338e-06 4.6426389e-06
20 21.730089 21.727916 21.728785 0 0 0 1693893.3 1004991.4 1211626 1.0653147e-05 -1.4284476e-06 6.3390661e-07
21 21.730089 21.727916 21.729002 0 0 0 1771180.8 1082282 1357800.3 9.0018044e-06 -1.2309518e-06 5.565611e-06
22 21.730089 21.727916 21.729219 0 0 0 1848464.7 1159569 1503974 7.5031694e-06 -2.7028978e-06 5.6324743e-06
23 21.730089 21.727916 21.729437 0 0 0 1925745.2 1236852.4 1650146.9 4.3439607e-06 -2.4393614e-06 5.5564577e-06
24 21.730089 21.727916 21.729654 0 0 0 2003022 1314132.4 1796319.1 2.3497113e-06 -2.3680104e-06 4.7932602e-06
25 21.730089 21.727916 21.729871 0 0 0 2080295.4 1391408.8 1942490.6 6.941166e-06 -1.1601937e-06 4.9355658e-06
26 21.730089 21.727916 21.730089 0 0 0 2157565.2 1468681.6 2088661.4 5.7633476e-06 -8.4264935e-07 4.0350137e-06
Loop time of 0.206357 on 1 procs for 10 steps with 512 atoms
Performance: 0.837 ns/day, 28.661 hours/ns, 48.460 timesteps/s
100.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20466 | 0.20466 | 0.20466 | 0.0 | 99.18
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00027633 | 0.00027633 | 0.00027633 | 0.0 | 0.13
Output | 0.0012765 | 0.0012765 | 0.0012765 | 0.0 | 0.62
Modify | 7.7963e-05 | 7.7963e-05 | 7.7963e-05 | 0.0 | 0.04
Other | | 6.175e-05 | | | 0.03
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 not checked
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom NULL 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 = 8.24482 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
26 21.730089 21.727916 21.730089 0 0 0 2234831.5 1545950.9 2234831.5 4.8476018e-06 4.2828413e-07 5.75372e-06
27 21.730089 21.727916 21.730089 0 0 4.3460177e-07 2234831.5 1545950.9 2234831.5 5.088922e-06 -2.3012471e-06 5.6950612e-06
28 21.730089 21.727916 21.730089 0 0 8.6920354e-07 2234831.5 1545950.9 2234831.5 4.7258447e-06 -1.3958256e-06 243.66105
29 21.730089 21.727916 21.730089 0 0 1.3038053e-06 2234831.5 1545950.9 2234831.5 4.7492097e-06 -2.8958095e-06 487.32212
30 21.730089 21.727916 21.730089 0 0 1.7384071e-06 2234831.5 1545950.9 2234831.5 4.8744538e-06 -2.3110563e-06 730.98324
31 21.730089 21.727916 21.730089 0 0 2.1730089e-06 2234831.5 1545950.9 2234831.5 4.3760082e-06 -8.3074269e-07 974.64423
32 21.730089 21.727916 21.730089 0 0 2.6076106e-06 2234831.5 1545950.9 2234831.5 4.7980741e-06 -5.7372478e-07 1218.3053
33 21.730089 21.727916 21.730089 0 0 3.0422124e-06 2234831.5 1545950.9 2234831.5 4.8822804e-06 -2.3433596e-06 1461.9664
34 21.730089 21.727916 21.730089 0 0 3.4768142e-06 2234831.5 1545950.9 2234831.5 4.8447261e-06 -1.9614792e-06 1705.6275
35 21.730089 21.727916 21.730089 0 0 3.911416e-06 2234831.5 1545950.9 2234831.5 5.1297449e-06 -2.114135e-06 1949.2885
36 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 4.5571577e-06 -1.8415232e-06 2192.9496
Loop time of 0.203569 on 1 procs for 10 steps with 512 atoms
Performance: 0.849 ns/day, 28.273 hours/ns, 49.123 timesteps/s
100.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20196 | 0.20196 | 0.20196 | 0.0 | 99.21
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00028515 | 0.00028515 | 0.00028515 | 0.0 | 0.14
Output | 0.0011783 | 0.0011783 | 0.0011783 | 0.0 | 0.58
Modify | 7.7724e-05 | 7.7724e-05 | 7.7724e-05 | 0.0 | 0.04
Other | | 6.366e-05 | | | 0.03
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 not checked
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom NULL 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 = 8.99482 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
36 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 5.1293854e-06 -1.6748595e-06 2436.6106
37 21.730089 21.727916 21.730089 4.3455832e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 5.1236563e-06 -3.3624188e-06 2436.6106
38 21.730089 21.727916 21.730089 8.6911663e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 243.64727 -0.00013232165 2436.6106
39 21.730089 21.727916 21.730089 1.3036749e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 487.29458 -0.0002652587 2436.6106
40 21.730089 21.727916 21.730089 1.7382333e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 730.9419 -0.00039565085 2436.6106
41 21.730089 21.727916 21.730089 2.1727916e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 974.58916 -0.00052768104 2436.6106
42 21.730089 21.727916 21.730089 2.6073499e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1218.2364 -0.00065822936 2436.6106
43 21.730089 21.727916 21.730089 3.0419082e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1461.8837 -0.0007889991 2436.6106
44 21.730089 21.727916 21.730089 3.4764665e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1705.531 -0.00091806693 2436.6106
45 21.730089 21.727916 21.730089 3.9110248e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1949.1783 -0.001049945 2436.6106
46 21.730089 21.727916 21.730089 4.3455832e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 2192.8256 -0.0011787861 2436.6106
Loop time of 0.204484 on 1 procs for 10 steps with 512 atoms
Performance: 0.845 ns/day, 28.401 hours/ns, 48.904 timesteps/s
100.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20272 | 0.20272 | 0.20272 | 0.0 | 99.14
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00029564 | 0.00029564 | 0.00029564 | 0.0 | 0.14
Output | 0.0013256 | 0.0013256 | 0.0013256 | 0.0 | 0.65
Modify | 7.844e-05 | 7.844e-05 | 7.844e-05 | 0.0 | 0.04
Other | | 6.27e-05 | | | 0.03
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 not checked
Total wall time: 0:00:01

331
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LAMMPS (15 Feb 2016)
# 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
Reading potential file ffield.comb with DATE: 2011-02-22
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:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 4 4 4
Memory usage per processor = 7.52233 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul
0 1 -4.6295947 -4.6297237 -4.6297237 0
1 1 -4.6295965 -4.6297255 -4.6297255 0
2 1 -4.6295965 -4.6297255 -4.6297255 0
3 1 -4.6295965 -4.6297255 -4.6297255 0
Loop time of 0.0429027 on 4 procs for 3 steps with 512 atoms
99.0% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-4.62972371535 -4.62972550325 -4.62972550325
Force two-norm initial, final = 5.86582 3.9583e-08
Force max component initial, final = 3.38663 2.28585e-08
Final line search alpha, max atom move = 1 2.28585e-08
Iterations, force evaluations = 3 6
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.026284 | 0.032657 | 0.041753 | 3.1 | 76.12
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00052333 | 0.0096034 | 0.015953 | 5.7 | 22.38
Output | 3.5048e-05 | 3.6538e-05 | 4.1008e-05 | 0.0 | 0.09
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0006061 | | | 1.41
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 not checked
min_modify dmax 0.2 line quadratic
unfix 1
run 1
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 4 4 4
Memory usage per processor = 5.89733 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 0.00605559 on 4 procs for 1 steps with 512 atoms
Performance: 2.854 ns/day, 8.411 hours/ns, 165.137 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0037332 | 0.0046489 | 0.00595 | 1.2 | 76.77
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.2002e-05 | 0.0013711 | 0.0022838 | 2.2 | 22.64
Output | 2.0027e-05 | 2.3484e-05 | 2.5988e-05 | 0.0 | 0.39
Modify | 0 | 2.3842e-07 | 9.5367e-07 | 0.1 | 0.00
Other | | 1.186e-05 | | | 0.20
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 not checked
### 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 NULL 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:680)
run 10
Memory usage per processor = 6.64733 Mbytes
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
4 21.727916 21.727916 21.727916 0 0 0 0.036618297 0.036625051 0.036618342 -1.7136998e-07 -3.2302114e-06 -1.7543151e-06
5 21.728133 21.727916 21.727916 0 0 0 0.036618988 0.036625612 0.036619564 -1.1309366e-06 -2.412817e-06 -2.6316468e-06
6 21.72835 21.727916 21.727916 0 0 0 146204.21 77325.824 77325.824 2.3636154e-06 -2.6955085e-06 -5.4243912e-06
7 21.728568 21.727916 21.727916 0 0 0 292407.66 154648.07 154648.07 -1.2891214e-06 -2.3607767e-06 -4.2545106e-06
8 21.728785 21.727916 21.727916 0 0 0 438610.41 231966.78 231966.78 -1.7378096e-06 -2.0714741e-06 -3.8921893e-06
9 21.729002 21.727916 21.727916 0 0 0 584812.43 309281.95 309281.95 2.5425006e-06 9.0454362e-06 -7.1598291e-06
10 21.729219 21.727916 21.727916 0 0 0 731013.74 386593.58 386593.58 -1.6897864e-06 -2.6139147e-06 -5.4137742e-06
11 21.729437 21.727916 21.727916 0 0 0 877214.34 463901.66 463901.66 -1.8806784e-06 -1.8704431e-06 -4.8350021e-06
12 21.729654 21.727916 21.727916 0 0 0 1023414.2 541206.21 541206.21 -9.1665744e-07 -1.59238e-06 -7.7617215e-06
13 21.729871 21.727916 21.727916 0 0 0 1169613.4 618507.22 618507.22 -1.1565806e-06 -2.0309366e-06 -6.6873647e-06
14 21.730089 21.727916 21.727916 0 0 0 1315811.8 695804.69 695804.69 1.8915845e-06 7.7289624e-06 -6.2492306e-06
Loop time of 0.0683999 on 4 procs for 10 steps with 512 atoms
Performance: 2.526 ns/day, 9.500 hours/ns, 146.199 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.041408 | 0.051284 | 0.065623 | 3.9 | 74.98
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0009675 | 0.015306 | 0.025153 | 7.1 | 22.38
Output | 0.0016904 | 0.0017211 | 0.001745 | 0.1 | 2.52
Modify | 2.4557e-05 | 2.9504e-05 | 3.4809e-05 | 0.1 | 0.04
Other | | 5.972e-05 | | | 0.09
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 not checked
## strain z, measure s_z: calculates C33
fix 2 all deform 1 z scale 1.0001 remap x
compute perfz all stress/atom NULL 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 = 7.39733 Mbytes
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
14 21.730089 21.727916 21.727916 0 0 0 1462009.6 773098.62 773098.62 -6.2271887e-07 -3.134065e-06 -1.4448086e-06
15 21.730089 21.727916 21.728133 0 0 0 1462009.6 773098.62 773098.62 -1.4749588e-06 -2.1972704e-06 -2.7974026e-06
16 21.730089 21.727916 21.72835 0 0 0 1539307.7 850399.78 919275.13 -1.1741349e-06 8.1321584e-06 -2.1634811e-06
17 21.730089 21.727916 21.728568 0 0 0 1616602.3 927697.4 1065450.9 9.2086349e-07 -2.6001292e-06 -2.9133823e-06
18 21.730089 21.727916 21.728785 0 0 0 1693893.3 1004991.5 1211626 1.3356364e-06 -2.794764e-06 -9.2778033e-06
19 21.730089 21.727916 21.729002 0 0 0 1771180.8 1082282 1357800.3 -8.7949961e-07 -3.4755821e-06 -7.1758788e-06
20 21.730089 21.727916 21.729219 0 0 0 1848464.8 1159569 1503974 1.674426e-06 -2.898863e-06 -2.1520562e-06
21 21.730089 21.727916 21.729437 0 0 0 1925745.2 1236852.5 1650146.9 -1.7524845e-06 -3.4851467e-06 -1.7806669e-06
22 21.730089 21.727916 21.729654 0 0 0 2003022.1 1314132.4 1796319.1 -2.1981227e-06 -2.7285159e-06 -2.0486576e-06
23 21.730089 21.727916 21.729871 0 0 0 2080295.4 1391408.8 1942490.6 -3.6986662e-06 -2.430512e-06 -2.6914988e-06
24 21.730089 21.727916 21.730089 0 0 0 2157565.2 1468681.6 2088661.4 -7.1345705e-06 -2.6113355e-06 -1.261254e-06
Loop time of 0.0679641 on 4 procs for 10 steps with 512 atoms
Performance: 2.543 ns/day, 9.439 hours/ns, 147.137 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.041426 | 0.05157 | 0.065353 | 3.8 | 75.88
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00090528 | 0.014692 | 0.024832 | 7.1 | 21.62
Output | 0.0016062 | 0.0016239 | 0.0016341 | 0.0 | 2.39
Modify | 1.9789e-05 | 2.6107e-05 | 3.4094e-05 | 0.1 | 0.04
Other | | 5.156e-05 | | | 0.08
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 not checked
## strain yz, measure s_yz: calculates C44
fix 2 all deform 1 yz erate 0.0001 remap x
compute perfyz all stress/atom NULL 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 = 8.16262 Mbytes
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
24 21.730089 21.727916 21.730089 0 0 0 2234831.5 1545950.9 2234831.5 -3.9610575e-06 -3.188829e-06 -5.7973926e-07
25 21.730089 21.727916 21.730089 0 0 4.3460177e-07 2234831.5 1545950.9 2234831.5 -4.4960939e-06 -2.549801e-06 -1.5603844e-06
26 21.730089 21.727916 21.730089 0 0 8.6920354e-07 2234831.5 1545950.9 2234831.5 -5.49227e-06 -4.2895969e-06 243.66104
27 21.730089 21.727916 21.730089 0 0 1.3038053e-06 2234831.5 1545950.9 2234831.5 -6.5461301e-06 -6.5635547e-06 487.32212
28 21.730089 21.727916 21.730089 0 0 1.7384071e-06 2234831.5 1545950.9 2234831.5 -6.2913987e-06 -6.8959666e-06 730.98323
29 21.730089 21.727916 21.730089 0 0 2.1730089e-06 2234831.5 1545950.9 2234831.5 -6.1650242e-06 -6.374019e-06 974.64422
30 21.730089 21.727916 21.730089 0 0 2.6076106e-06 2234831.5 1545950.9 2234831.5 -6.8112674e-06 -6.9206286e-06 1218.3053
31 21.730089 21.727916 21.730089 0 0 3.0422124e-06 2234831.5 1545950.9 2234831.5 -6.5914369e-06 -8.6480249e-06 1461.9664
32 21.730089 21.727916 21.730089 0 0 3.4768142e-06 2234831.5 1545950.9 2234831.5 -6.62009e-06 -8.621625e-06 1705.6275
33 21.730089 21.727916 21.730089 0 0 3.911416e-06 2234831.5 1545950.9 2234831.5 -6.712501e-06 -8.7315457e-06 1949.2885
34 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.3958831e-06 -7.1670331e-06 2192.9496
Loop time of 0.0681064 on 4 procs for 10 steps with 512 atoms
Performance: 2.537 ns/day, 9.459 hours/ns, 146.829 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.041511 | 0.051664 | 0.065403 | 3.8 | 75.86
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00090647 | 0.014658 | 0.024812 | 7.1 | 21.52
Output | 0.0016921 | 0.0017017 | 0.001713 | 0.0 | 2.50
Modify | 2.2173e-05 | 2.7835e-05 | 3.0994e-05 | 0.1 | 0.04
Other | | 5.496e-05 | | | 0.08
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 not checked
## strain xy, measure s_xy: calculates C66
fix 2 all deform 1 xy erate 0.0001 remap x
compute perfxy all stress/atom NULL 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 = 8.91262 Mbytes
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
34 21.730089 21.727916 21.730089 0 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.1581426e-06 -1.1350015e-05 2436.6106
35 21.730089 21.727916 21.730089 4.3455832e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 -6.7014652e-06 -1.1032048e-05 2436.6106
36 21.730089 21.727916 21.730089 8.6911663e-07 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 243.64726 -0.00014128194 2436.6106
37 21.730089 21.727916 21.730089 1.3036749e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 487.29457 -0.00027206674 2436.6106
38 21.730089 21.727916 21.730089 1.7382333e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 730.94189 -0.00040462289 2436.6106
39 21.730089 21.727916 21.730089 2.1727916e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 974.58915 -0.00053614117 2436.6106
40 21.730089 21.727916 21.730089 2.6073499e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1218.2364 -0.00066911336 2436.6106
41 21.730089 21.727916 21.730089 3.0419082e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1461.8837 -0.00080012128 2436.6106
42 21.730089 21.727916 21.730089 3.4764665e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1705.531 -0.00093156087 2436.6106
43 21.730089 21.727916 21.730089 3.9110248e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 1949.1783 -0.0010618138 2436.6106
44 21.730089 21.727916 21.730089 4.3455832e-06 0 4.3460177e-06 2234831.5 1545950.9 2234831.5 2192.8256 -0.0011926577 2436.6106
Loop time of 0.0681901 on 4 procs for 10 steps with 512 atoms
Performance: 2.534 ns/day, 9.471 hours/ns, 146.649 timesteps/s
100.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.041675 | 0.051819 | 0.065549 | 3.8 | 75.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00088024 | 0.014621 | 0.024764 | 7.2 | 21.44
Output | 0.0016496 | 0.0016653 | 0.0016737 | 0.0 | 2.44
Modify | 2.0027e-05 | 2.4855e-05 | 3.0756e-05 | 0.1 | 0.04
Other | | 6.02e-05 | | | 0.09
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 not checked
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
Reading potential file ffield.comb with DATE: 2011-02-22
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 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Si
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Si
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 4 4 4
Memory usage per processor = 6.47955 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 0.193527 on 1 procs for 10 steps with 512 atoms
Performance: 0.893 ns/day, 26.879 hours/ns, 51.672 timesteps/s
100.2% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.19296 | 0.19296 | 0.19296 | 0.0 | 99.71
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00025725 | 0.00025725 | 0.00025725 | 0.0 | 0.13
Output | 0.00012445 | 0.00012445 | 0.00012445 | 0.0 | 0.06
Modify | 8.3208e-05 | 8.3208e-05 | 8.3208e-05 | 0.0 | 0.04
Other | | 0.000104 | | | 0.05
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
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
Reading potential file ffield.comb with DATE: 2011-02-22
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 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 2 element Si
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 2 element Si
run 10
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 1 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 4 4 4
Memory usage per processor = 6.39352 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 0.0531193 on 4 procs for 10 steps with 512 atoms
Performance: 3.253 ns/day, 7.378 hours/ns, 188.255 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.046737 | 0.048466 | 0.051893 | 1.0 | 91.24
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00082636 | 0.0042595 | 0.0059838 | 3.2 | 8.02
Output | 0.00026178 | 0.00027215 | 0.0002954 | 0.1 | 0.51
Modify | 2.3842e-05 | 2.563e-05 | 2.8372e-05 | 0.0 | 0.05
Other | | 9.644e-05 | | | 0.18
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
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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 33.8162) with tilt (0 0 0)
1 by 1 by 1 MPI processor grid
reading atoms ...
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
Reading potential file lib.comb3 with DATE: 2014-02-01
Reading potential file ffield.comb3 with DATE: 2014-02-01
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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5 -> bins = 4 4 6
Memory usage per processor = 4.47117 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
0 300 -4.5167776 -4.5554988 -3.9875717 -0.56792713 -19801.669 17719.012 21.3 24.6 33.8162
10 467.10265 -4.5167723 -4.5770615 -4.0093169 -0.56774462 -15438.86 17719.012 21.3 24.6 33.8162
20 732.82159 -4.5169309 -4.6115167 -4.0435338 -0.56798291 -12197.607 17719.012 21.3 24.6 33.8162
30 906.42366 -4.517088 -4.6340807 -4.0657272 -0.56835345 -8825.2434 17719.012 21.3 24.6 33.8162
40 957.57065 -4.5172533 -4.6408475 -4.0717295 -0.56911807 -12551.812 17719.012 21.3 24.6 33.8162
50 920.31413 -4.517436 -4.6362215 -4.0660108 -0.57021068 -11911.093 17719.012 21.3 24.6 33.8162
60 1003.2 -4.5176403 -4.647124 -4.0757679 -0.57135607 1337.5658 17719.012 21.3 24.6 33.8162
70 1123.7779 -4.5178574 -4.6629041 -4.0904309 -0.57247327 7171.1488 17719.012 21.3 24.6 33.8162
80 1188.3196 -4.518095 -4.6714721 -4.0978283 -0.57364387 12411.934 17719.012 21.3 24.6 33.8162
90 1193.9207 -4.5183329 -4.672433 -4.0976379 -0.57479504 15405.848 17719.012 21.3 24.6 33.8162
100 1197.343 -4.5185478 -4.6730896 -4.0971431 -0.57594648 17853.038 17719.012 21.3 24.6 33.8162
Loop time of 45.764 on 1 procs for 100 steps with 682 atoms
Performance: 0.038 ns/day, 635.612 hours/ns, 2.185 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.987 | 10.987 | 10.987 | 0.0 | 24.01
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00317 | 0.00317 | 0.00317 | 0.0 | 0.01
Output | 0.0001812 | 0.0001812 | 0.0001812 | 0.0 | 0.00
Modify | 34.773 | 34.773 | 34.773 | 0.0 | 75.98
Other | | 0.001366 | | | 0.00
Nlocal: 682 ave 682 max 682 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4154 ave 4154 max 4154 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: 355216 ave 355216 max 355216 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 355216
Ave neighs/atom = 520.845
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:48

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LAMMPS (15 Feb 2016)
# 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 33.8162) with tilt (0 0 0)
1 by 2 by 2 MPI processor grid
reading atoms ...
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
Reading potential file lib.comb3 with DATE: 2014-02-01
Reading potential file ffield.comb3 with DATE: 2014-02-01
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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5 -> bins = 4 4 6
Memory usage per processor = 4.95436 Mbytes
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
0 300 -4.5167776 -4.5554988 -3.9875717 -0.56792713 -19801.669 17719.012 21.3 24.6 33.8162
10 467.10265 -4.5167723 -4.5770615 -4.0093169 -0.56774462 -15438.86 17719.012 21.3 24.6 33.8162
20 732.82159 -4.5169309 -4.6115167 -4.0435338 -0.56798291 -12197.607 17719.012 21.3 24.6 33.8162
30 906.42366 -4.517088 -4.6340807 -4.0657272 -0.56835345 -8825.2434 17719.012 21.3 24.6 33.8162
40 957.57065 -4.5172533 -4.6408475 -4.0717295 -0.56911807 -12551.812 17719.012 21.3 24.6 33.8162
50 920.31413 -4.517436 -4.6362215 -4.0660108 -0.57021068 -11911.093 17719.012 21.3 24.6 33.8162
60 1003.2 -4.5176403 -4.647124 -4.0757679 -0.57135607 1337.5658 17719.012 21.3 24.6 33.8162
70 1123.7779 -4.5178574 -4.6629041 -4.0904309 -0.57247327 7171.1488 17719.012 21.3 24.6 33.8162
80 1188.3196 -4.518095 -4.6714721 -4.0978283 -0.57364387 12411.934 17719.012 21.3 24.6 33.8162
90 1193.9207 -4.5183329 -4.672433 -4.0976379 -0.57479504 15405.848 17719.012 21.3 24.6 33.8162
100 1197.343 -4.5185478 -4.6730896 -4.0971431 -0.57594648 17853.038 17719.012 21.3 24.6 33.8162
Loop time of 20.7745 on 4 procs for 100 steps with 682 atoms
Performance: 0.083 ns/day, 288.534 hours/ns, 4.814 timesteps/s
98.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2393 | 3.5206 | 4.856 | 67.7 | 16.95
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.024316 | 1.3586 | 2.6388 | 108.8 | 6.54
Output | 0.00034308 | 0.00036204 | 0.00038791 | 0.1 | 0.00
Modify | 15.892 | 15.892 | 15.892 | 0.0 | 76.50
Other | | 0.002505 | | | 0.01
Nlocal: 170.5 ave 245 max 100 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 2872 ave 3583 max 2157 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: 88804 ave 131817 max 47999 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 355216
Ave neighs/atom = 520.845
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:21

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LAMMPS (15 Feb 2016)
# 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:445)
neigh_modify exclude type 2 3
#dump 1 all atom 500 dump.crack
#dump 2 all image 250 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 250 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
run 5000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 80 56 1
Memory usage per processor = 2.48017 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 7.03796 on 1 procs for 5000 steps with 8141 atoms
Performance: 184144.324 tau/day, 710.433 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.9472 | 5.9472 | 5.9472 | 0.0 | 84.50
Neigh | 0.36178 | 0.36178 | 0.36178 | 0.0 | 5.14
Comm | 0.0042093 | 0.0042093 | 0.0042093 | 0.0 | 0.06
Output | 0.00080466 | 0.00080466 | 0.00080466 | 0.0 | 0.01
Modify | 0.55 | 0.55 | 0.55 | 0.0 | 7.81
Other | | 0.1739 | | | 2.47
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
Total wall time: 0:00:07

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LAMMPS (15 Feb 2016)
# 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:445)
neigh_modify exclude type 2 3
#dump 1 all atom 500 dump.crack
#dump 2 all image 250 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 250 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
run 5000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 80 56 1
Memory usage per processor = 2.48163 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 1.91894 on 4 procs for 5000 steps with 8141 atoms
Performance: 675373.090 tau/day, 2605.606 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4786 | 1.5057 | 1.5343 | 2.0 | 78.47
Neigh | 0.094529 | 0.099406 | 0.1061 | 1.4 | 5.18
Comm | 0.071501 | 0.10352 | 0.13214 | 8.6 | 5.39
Output | 0.00072479 | 0.00076115 | 0.00084186 | 0.2 | 0.04
Modify | 0.13936 | 0.14058 | 0.14196 | 0.2 | 7.33
Other | | 0.06895 | | | 3.59
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
Total wall time: 0:00:01

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LAMMPS (15 Feb 2016)
# 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:445)
#dump 1 all atom 50 dump.deposit.atom
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65 -> bins = 3 3 6
Memory usage per processor = 2.54053 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 -0.52097006
2500 375 1.2269861 -5.4265984 -5.3038998 -0.49657196
2600 376 1.0399561 -5.476211 -5.3683432 -0.62204748
2700 377 1.0944051 -5.4078459 -5.2902772 -0.63977962
2800 378 1.0323162 -5.3957488 -5.281047 -0.62614071
2900 379 1.1065509 -5.3744068 -5.2474017 -0.57270098
3000 380 1.0280773 -5.3681364 -5.2463904 -0.66444652
3100 381 1.04368 -5.3317133 -5.2043351 -0.65414012
3200 382 1.0449176 -5.3088894 -5.1775909 -0.63418281
3300 383 1.1102316 -5.2604462 -5.1169568 -0.57913921
3400 384 1.2757372 -5.2904271 -5.1209933 -0.56059979
3500 385 1.0652825 -5.2267633 -5.0814975 -0.54269026
3600 386 1.0229877 -5.2277887 -5.0846764 -0.61796376
3700 387 0.96408893 -5.1769745 -5.0387137 -0.55113976
3800 388 1.0505509 -5.2197338 -5.0654003 -0.70804854
3900 389 0.95266837 -5.1605736 -5.017306 -0.52702995
4000 390 1.0413134 -5.2352309 -5.0750288 -0.66067611
4100 391 1.1486876 -5.2288717 -5.0481958 -0.65810366
4200 392 1.042156 -5.2716813 -5.1041919 -0.66967821
4300 393 0.9698966 -5.197189 -5.0380075 -0.46525386
4400 394 0.77874089 -5.257629 -5.12718 -0.67739426
4500 395 1.0157317 -5.2445238 -5.0709494 -0.5922696
4600 396 1.1447586 -5.2710072 -5.0715417 -0.62651602
4700 397 1.1902582 -5.311166 -5.0997978 -0.7459111
4800 398 0.95725223 -5.2619858 -5.0888146 -0.49253005
4900 399 1.0409188 -5.271542 -5.0797938 -0.56590831
5000 400 1.0870091 -5.2619328 -5.0581186 -0.61273172
5100 401 0.90909459 -5.3465255 -5.1730948 -0.61196826
5200 402 0.86456113 -5.2535951 -5.0858445 -0.47565663
5300 403 0.92212118 -5.27055 -5.0886427 -0.55555966
5400 404 0.96914771 -5.2702613 -5.075952 -0.58082428
5500 405 0.96828577 -5.263648 -5.0664046 -0.59818023
5600 406 1.0567855 -5.2988668 -5.0802215 -0.76787404
5700 407 1.0085537 -5.2053833 -4.9935127 -0.55232589
5800 408 0.86382168 -5.2038339 -5.0196367 -0.58471077
5900 409 0.98477929 -5.1862354 -4.9731475 -0.54570637
6000 410 1.0777582 -5.2410631 -5.004482 -0.6711063
6100 411 1.1113596 -5.1775001 -4.9300806 -0.54007427
6200 412 0.86878402 -5.1939794 -4.9978704 -0.64766373
6300 413 1.0174495 -5.2156346 -4.9828284 -0.60249161
6400 414 1.1184824 -5.2250149 -4.9656567 -0.64875897
6500 415 1.1607873 -5.2674286 -4.9947135 -0.65956525
6600 416 0.98987615 -5.2384031 -5.0028316 -0.66246801
6700 417 0.86291514 -5.2362314 -5.0282627 -0.56707491
6800 418 0.97203041 -5.2323576 -4.9951636 -0.54330037
6900 419 0.92972764 -5.2416508 -5.0119926 -0.58029478
7000 420 1.1472637 -5.3052417 -5.0184258 -0.64366532
7100 421 0.9275385 -5.3077824 -5.0731438 -0.54374736
7200 422 0.91492781 -5.3012606 -5.0671084 -0.55376032
7300 423 0.85621578 -5.3016071 -5.0799626 -0.56221777
7400 424 0.94571335 -5.2212917 -4.9737111 -0.52202896
7500 425 1.0819864 -5.2109452 -4.924537 -0.47511017
7600 426 1.1449289 -5.2138905 -4.9075011 -0.62518982
7700 427 0.98061711 -5.2129268 -4.9476779 -0.56003723
7800 428 1.0450011 -5.1652647 -4.8795985 -0.51780393
7900 429 0.98731276 -5.1520883 -4.879369 -0.46982802
8000 430 1.058201 -5.2605391 -4.9652272 -0.69798004
8100 431 1.1031976 -5.2428971 -4.9319029 -0.64564967
8200 432 0.99653694 -5.2790505 -4.9953143 -0.70353076
8300 433 1.2188348 -5.2664086 -4.9159584 -0.56779776
8400 434 1.0610032 -5.2291848 -4.9211516 -0.44040649
8500 435 0.88475193 -5.2938308 -5.034507 -0.70250793
8600 436 0.98427323 -5.2350748 -4.9438564 -0.54824635
8700 437 0.99048279 -5.2379591 -4.9421742 -0.68060327
8800 438 0.92407001 -5.1922203 -4.9137335 -0.67045436
8900 439 0.99630902 -5.1772321 -4.8742543 -0.66221601
9000 440 0.95766319 -5.1605694 -4.8667409 -0.68216304
9100 441 1.0231065 -5.1295203 -4.8128445 -0.52553274
9200 442 0.87783667 -5.1084284 -4.8343527 -0.54144063
9300 443 0.93581944 -5.1737089 -4.8790208 -0.68780812
9400 444 0.99373921 -5.1548474 -4.839268 -0.57996189
9500 445 0.95187515 -5.1408039 -4.8359899 -0.56491542
9600 446 0.91625338 -5.1555381 -4.8597074 -0.62931435
9700 447 0.9526195 -5.1025432 -4.7924624 -0.51046895
9800 448 0.97167962 -5.185173 -4.8663406 -0.56989109
9900 449 1.0038671 -5.1540302 -4.8220162 -0.56356384
10000 450 0.95642062 -5.2046982 -4.8858913 -0.70500643
Loop time of 5.66464 on 1 procs for 10000 steps with 450 atoms
Performance: 762626.084 tau/day, 1765.338 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.2197 | 3.2197 | 3.2197 | 0.0 | 56.84
Neigh | 2.1683 | 2.1683 | 2.1683 | 0.0 | 38.28
Comm | 0.11987 | 0.11987 | 0.11987 | 0.0 | 2.12
Output | 0.00085187 | 0.00085187 | 0.00085187 | 0.0 | 0.02
Modify | 0.11944 | 0.11944 | 0.11944 | 0.0 | 2.11
Other | | 0.03653 | | | 0.64
Nlocal: 450 ave 450 max 450 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1973 ave 1973 max 1973 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 29176 ave 29176 max 29176 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 29176
Ave neighs/atom = 64.8356
Neighbor list builds = 1143
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (15 Feb 2016)
# 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:445)
#dump 1 all atom 50 dump.deposit.atom
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65 -> bins = 3 3 6
Memory usage per processor = 2.60645 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 1.3599869 -5.5793818 -5.4691126 -0.44566809
2100 371 1.0007793 -5.585692 -5.5007201 -0.54221497
2200 372 1.1061185 -5.5172265 -5.4191031 -0.46551381
2300 373 0.99747278 -5.556485 -5.4642254 -0.55670256
2400 374 1.0990419 -5.5538566 -5.4480664 -0.63197307
2500 375 1.1415073 -5.5118583 -5.3977075 -0.51563393
2600 376 1.010645 -5.5221148 -5.4172873 -0.5495753
2700 377 1.0964314 -5.4985586 -5.3807722 -0.54042329
2800 378 0.93010494 -5.4391153 -5.3357703 -0.52395276
2900 379 0.93021935 -5.5144863 -5.4077197 -0.69409861
3000 380 1.0264349 -5.4314217 -5.3098702 -0.55798648
3100 381 1.1612003 -5.4088381 -5.2671168 -0.53167304
3200 382 1.087873 -5.4402561 -5.30356 -0.71158961
3300 383 1.048209 -5.4309208 -5.2954473 -0.67551183
3400 384 1.0275111 -5.4536819 -5.3172156 -0.73761551
3500 385 1.2716758 -5.4036871 -5.2302768 -0.63612803
3600 386 1.2154857 -5.4003006 -5.2302586 -0.61641823
3700 387 1.3376196 -5.4279619 -5.2361328 -0.59689863
3800 388 1.2523858 -5.358924 -5.1749395 -0.55321551
3900 389 1.1650111 -5.333714 -5.1585131 -0.55412715
4000 390 0.98352817 -5.2980477 -5.1467357 -0.68167218
4100 391 1.2779827 -5.297845 -5.0968324 -0.65191886
4200 392 1.0255535 -5.2295551 -5.064734 -0.4761042
4300 393 1.1237891 -5.2225392 -5.0381005 -0.52734107
4400 394 0.97683493 -5.2029168 -5.0392846 -0.59056934
4500 395 1.0041363 -5.1999674 -5.0283744 -0.72038887
4600 396 1.180431 -5.1922463 -4.9865652 -0.55948152
4700 397 1.0627588 -5.2298403 -5.0411136 -0.56208516
4800 398 1.1202971 -5.2121979 -5.0095311 -0.46793143
4900 399 1.2006424 -5.286657 -5.0654861 -0.63042465
5000 400 1.0893045 -5.2512329 -5.0469883 -0.6377186
5100 401 1.1454769 -5.2580965 -5.0395704 -0.59767673
5200 402 0.9467869 -5.249752 -5.0660471 -0.71059143
5300 403 0.96324471 -5.1724796 -4.9824599 -0.50261414
5400 404 1.1634679 -5.1969879 -4.9637184 -0.5555004
5500 405 0.99830529 -5.1678627 -4.9645042 -0.59796761
5600 406 1.0065294 -5.1718443 -4.9635968 -0.59208276
5700 407 0.97182891 -5.2110109 -5.0068552 -0.63948837
5800 408 1.1234056 -5.167964 -4.9284143 -0.53293706
5900 409 1.0124687 -5.1828555 -4.9637761 -0.4922831
6000 410 1.0804251 -5.2275621 -4.9903956 -0.52329411
6100 411 1.0772335 -5.26665 -5.0268279 -0.56252803
6200 412 1.0954219 -5.2051974 -4.9579299 -0.42238433
6300 413 1.0546562 -5.3045877 -5.0632681 -0.61171278
6400 414 1.0985486 -5.335815 -5.0810791 -0.67859848
6500 415 1.0416817 -5.2636237 -5.0188913 -0.61917889
6600 416 0.86231375 -5.1755229 -4.9703088 -0.51453403
6700 417 0.91939084 -5.2111481 -4.9895683 -0.5239181
6800 418 1.1242247 -5.240558 -4.9662256 -0.50836149
6900 419 1.0578099 -5.2020602 -4.9407635 -0.50665054
7000 420 0.98040609 -5.1860531 -4.9409516 -0.63496783
7100 421 0.99357521 -5.1989655 -4.9476216 -0.53673646
7200 422 1.1168255 -5.1850834 -4.8992607 -0.59194739
7300 423 1.0465199 -5.1485597 -4.877652 -0.4964202
7400 424 0.91999946 -5.1379187 -4.8970698 -0.45185782
7500 425 0.94098172 -5.2197403 -4.9706569 -0.6452508
7600 426 0.92305237 -5.2489345 -5.0019205 -0.67135987
7700 427 1.0692215 -5.2004352 -4.9112195 -0.60227676
7800 428 0.98946072 -5.2168971 -4.9464137 -0.61326494
7900 429 1.1578277 -5.2222386 -4.9024191 -0.6841757
8000 430 1.1057865 -5.2447073 -4.9361157 -0.57784399
8100 431 1.0527643 -5.2189715 -4.9221945 -0.5484357
8200 432 1.058862 -5.2236909 -4.9222094 -0.66008275
8300 433 1.0543331 -5.2105622 -4.907411 -0.60403808
8400 434 1.204621 -5.193864 -4.8441353 -0.57011085
8500 435 1.0247837 -5.1910294 -4.8906617 -0.6081565
8600 436 1.0314146 -5.1732662 -4.8680999 -0.59109692
8700 437 0.98196719 -5.144054 -4.8508121 -0.56483113
8800 438 1.1013378 -5.1980036 -4.8660936 -0.60785883
8900 439 1.1016903 -5.1251846 -4.7901603 -0.49838338
9000 440 1.0926008 -5.1360049 -4.8007751 -0.54767492
9100 441 1.1454324 -5.2217858 -4.8672472 -0.67308812
9200 442 1.059963 -5.1945332 -4.8635945 -0.54419884
9300 443 1.2168669 -5.2244149 -4.8412254 -0.49530257
9400 444 1.0656851 -5.1556938 -4.8172667 -0.41869179
9500 445 0.99794121 -5.2447091 -4.9251436 -0.638328
9600 446 1.1717194 -5.247915 -4.869602 -0.65769093
9700 447 1.2345494 -5.1717485 -4.7698985 -0.54917447
9800 448 1.187781 -5.1672598 -4.7775192 -0.55482592
9900 449 0.99538785 -5.1593424 -4.8301329 -0.5886329
10000 450 0.95030539 -5.1408028 -4.8240344 -0.4992403
Loop time of 4.67299 on 4 procs for 10000 steps with 450 atoms
Performance: 924461.293 tau/day, 2139.957 timesteps/s
98.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0024376 | 0.84903 | 2.165 | 97.5 | 18.17
Neigh | 0.0053134 | 0.57645 | 1.783 | 95.1 | 12.34
Comm | 0.54729 | 2.3753 | 4.0958 | 83.6 | 50.83
Output | 0.0022168 | 0.00986 | 0.028065 | 10.7 | 0.21
Modify | 0.0059755 | 0.037876 | 0.085638 | 16.4 | 0.81
Other | | 0.8245 | | | 17.64
Nlocal: 112.5 ave 250 max 9 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Nghost: 1522.75 ave 2248 max 440 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs: 7415.25 ave 17049 max 23 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 29661
Ave neighs/atom = 65.9133
Neighbor list builds = 1164
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (15 Feb 2016)
# 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
Read molecule dimer:
2 atoms with 3 types
1 bonds with 1 types
0 angles with 0 types
0 dihedrals with 0 types
0 impropers with 0 types
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:445)
#dump 1 all atom 50 dump.deposit.atom
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65 -> bins = 3 3 6
Memory usage per processor = 3.56565 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 0.84169616 -6.8174189 -6.7961324 -0.69200581
400 358 0.84705847 -6.785416 -6.7570071 -0.70386101
500 360 0.87562973 -6.7507562 -6.714217 -0.68491831
600 362 0.89546097 -6.7133515 -6.6684358 -0.68373096
700 364 0.86923875 -6.6724351 -6.6215093 -0.6663574
800 366 0.93007871 -6.6448092 -6.5816911 -0.68706422
900 368 1.0020611 -6.6164541 -6.540933 -0.66074734
1000 370 1.0082042 -6.5845669 -6.5014101 -0.69453732
1100 372 0.96783727 -6.5649235 -6.4753076 -0.6717256
1200 374 0.97597749 -6.5935771 -6.4925926 -0.69360182
1300 376 0.80208918 -6.5923852 -6.5033139 -0.64868248
1400 378 0.66705029 -6.582928 -6.5082634 -0.6111322
1500 380 0.67555528 -6.5640796 -6.4816473 -0.67638117
1600 382 0.65916245 -6.551728 -6.4662574 -0.62833932
1700 384 0.718469 -6.5624935 -6.4643654 -0.64737567
1800 386 0.59257091 -6.5604373 -6.4675604 -0.61982866
1900 388 0.63118529 -6.5638788 -6.467728 -0.63403973
2000 390 0.6013361 -6.571937 -6.473428 -0.62753885
2100 392 0.48508625 -6.5519559 -6.4663394 -0.66580902
2200 394 0.50266444 -6.5357335 -6.4395422 -0.71780255
2300 396 0.52557785 -6.5469569 -6.4355521 -0.65421156
2400 398 0.66055178 -6.5509266 -6.4186172 -0.65273326
2500 400 0.69210544 -6.5578062 -6.4211169 -0.68232818
2600 402 0.64576434 -6.6050398 -6.4574266 -0.64849208
2700 404 0.56298016 -6.6350083 -6.503562 -0.746185
2800 406 0.49149694 -6.6482516 -6.5155551 -0.76320999
2900 408 0.48366321 -6.6606024 -6.5257882 -0.65612432
3000 410 0.47356141 -6.6756446 -6.5312692 -0.70811639
3100 412 0.47568619 -6.6934709 -6.5474974 -0.72316681
3200 414 0.38708973 -6.6932142 -6.5659264 -0.73056797
3300 416 0.43665017 -6.6999962 -6.5567504 -0.75890315
3400 418 0.34923989 -6.7185629 -6.5909531 -0.66986444
3500 420 0.33999089 -6.6922536 -6.5729709 -0.70698979
3600 422 0.37659 -6.6827522 -6.5521249 -0.68796169
3700 424 0.34150483 -6.6973468 -6.5698573 -0.68312043
3800 426 0.41110243 -6.7043016 -6.5510735 -0.71352712
3900 428 0.40957994 -6.7172729 -6.5557011 -0.70233721
4000 430 0.42723175 -6.7170007 -6.5537357 -0.7497547
4100 432 0.37176212 -6.7218812 -6.5574518 -0.7098714
4200 434 0.33265381 -6.7082458 -6.5637164 -0.70399102
4300 436 0.43029564 -6.7142231 -6.5431037 -0.76230436
4400 438 0.38216708 -6.7315576 -6.5614315 -0.6674734
4500 440 0.35981631 -6.7496554 -6.583264 -0.73404044
4600 442 0.36073617 -6.7479258 -6.5907772 -0.71067075
4700 444 0.35705292 -6.7678184 -6.5973053 -0.75325156
4800 446 0.37426281 -6.7869581 -6.6010006 -0.67542828
4900 448 0.33524109 -6.7800476 -6.6026334 -0.66398211
5000 450 0.31770101 -6.7884069 -6.6064017 -0.74655689
5100 452 0.31791473 -6.7695361 -6.5901194 -0.77591531
5200 454 0.37320367 -6.7756559 -6.5809165 -0.76247336
5300 456 0.32228579 -6.7786007 -6.5856918 -0.67574614
5400 458 0.31274193 -6.7828483 -6.5928063 -0.72466782
5500 460 0.30708694 -6.7858555 -6.5973813 -0.76883863
5600 462 0.32849848 -6.7983978 -6.6021343 -0.76855876
5700 464 0.35124617 -6.8131288 -6.5975496 -0.78865946
5800 466 0.35055399 -6.8184367 -6.6060092 -0.70530424
5900 468 0.33326299 -6.8299034 -6.6095077 -0.68840817
6000 470 0.40104727 -6.8633145 -6.6132375 -0.77187971
6100 472 0.29105598 -6.8410097 -6.6311104 -0.7715889
6200 474 0.30288813 -6.8634336 -6.6428858 -0.78760673
6300 476 0.34293767 -6.9005784 -6.6534079 -0.74817698
6400 478 0.34963015 -6.9292987 -6.666687 -0.71175243
6500 480 0.319367 -6.9395521 -6.6743587 -0.76432283
6600 482 0.29016877 -6.9324045 -6.679475 -0.90715919
6700 484 0.35436305 -6.9551643 -6.6789059 -0.79939008
6800 486 0.327512 -6.9608693 -6.687362 -0.70392295
6900 488 0.32349315 -6.9513424 -6.6847712 -0.75205809
7000 490 0.35355467 -6.9907283 -6.7038887 -0.80881264
7100 492 0.32140685 -6.9979325 -6.7169278 -0.68673022
7200 494 0.32242041 -7.0116346 -6.728848 -0.79432529
7300 496 0.26266524 -6.9966902 -6.7334152 -0.86050198
7400 498 0.31564904 -7.0133015 -6.7158904 -0.81615792
7500 500 0.36973921 -7.0516561 -6.717083 -0.79423832
7600 502 0.33599186 -7.0516408 -6.7296713 -0.83610882
7700 504 0.29691416 -7.0495062 -6.738076 -0.83634675
7800 506 0.3244215 -7.0434148 -6.7342677 -0.7170135
7900 508 0.29167542 -7.0637209 -6.7576924 -0.78857188
8000 510 0.34198998 -7.1041546 -6.7635656 -0.83376311
8100 512 0.33068905 -7.1341746 -6.7960028 -0.78639771
8200 514 0.29688969 -7.136245 -6.8093036 -0.85753154
8300 516 0.29829676 -7.1313196 -6.8076328 -0.76960702
8400 518 0.31096049 -7.1559166 -6.8202327 -0.72775356
8500 520 0.26677854 -7.1413516 -6.8361967 -0.81908087
8600 522 0.28811568 -7.1390821 -6.8248702 -0.88515896
8700 524 0.27520272 -7.1501541 -6.8311651 -0.81462692
8800 526 0.28763152 -7.1525343 -6.8281253 -0.74124759
8900 528 0.29917883 -7.1547953 -6.8229151 -0.81440712
9000 530 0.28474306 -7.1612717 -6.8236771 -0.79150099
9100 532 0.29409713 -7.1748026 -6.8272211 -0.7916524
9200 534 0.26767862 -7.1646362 -6.8313179 -0.79362392
9300 536 0.27111075 -7.1719185 -6.8399556 -0.9578129
9400 538 0.33952348 -7.207044 -6.8368639 -0.89888939
9500 540 0.3284439 -7.2371916 -6.8625844 -0.7659201
9600 542 0.31256223 -7.2266123 -6.8655682 -0.82722861
9700 544 0.30268239 -7.2315617 -6.8705788 -0.81448482
9800 546 0.26835398 -7.2214231 -6.8757262 -0.86029096
9900 548 0.31676744 -7.264604 -6.884266 -0.74053962
10000 550 0.31368419 -7.2759575 -6.8979611 -0.76153366
Loop time of 6.58981 on 1 procs for 10000 steps with 550 atoms
Performance: 655557.606 tau/day, 1517.494 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.1313 | 4.1313 | 4.1313 | 0.0 | 62.69
Bond | 0.01234 | 0.01234 | 0.01234 | 0.0 | 0.19
Neigh | 2.1423 | 2.1423 | 2.1423 | 0.0 | 32.51
Comm | 0.13504 | 0.13504 | 0.13504 | 0.0 | 2.05
Output | 0.0010068 | 0.0010068 | 0.0010068 | 0.0 | 0.02
Modify | 0.12665 | 0.12665 | 0.12665 | 0.0 | 1.92
Other | | 0.0411 | | | 0.62
Nlocal: 550 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2349 ave 2349 max 2349 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39710 ave 39710 max 39710 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 39710
Ave neighs/atom = 72.2
Ave special neighs/atom = 0.363636
Neighbor list builds = 877
Dangerous builds = 0
Total wall time: 0:00:06

205
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LAMMPS (15 Feb 2016)
# 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
Read molecule dimer:
2 atoms with 3 types
1 bonds with 1 types
0 angles with 0 types
0 dihedrals with 0 types
0 impropers with 0 types
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:445)
#dump 1 all atom 50 dump.deposit.atom
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65 -> bins = 3 3 6
Memory usage per processor = 3.63985 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 0.84169616 -6.8219435 -6.800657 -0.69554978
400 358 0.84705847 -6.7754627 -6.7470538 -0.67243811
500 360 0.87562973 -6.7314753 -6.6949361 -0.6950742
600 362 0.89546097 -6.710162 -6.6652463 -0.65981803
700 364 0.86924248 -6.6786002 -6.6276742 -0.66815906
800 366 0.93005193 -6.6524743 -6.5893578 -0.67112658
900 368 1.0019234 -6.6197846 -6.5442728 -0.63787501
1000 370 1.0088277 -6.5761382 -6.4929294 -0.68476387
1100 372 0.95920389 -6.5674754 -6.4791094 -0.6514881
1200 374 1.0580798 -6.5939034 -6.4854936 -0.64868897
1300 376 0.86424162 -6.5983754 -6.5057565 -0.63699331
1400 378 0.67483283 -6.5902961 -6.5114402 -0.65492911
1500 380 0.75360589 -6.5780719 -6.4817845 -0.68120797
1600 382 0.72620352 -6.569806 -6.4764019 -0.66989877
1700 384 0.70645024 -6.5716163 -6.4726668 -0.6613115
1800 386 0.69881235 -6.5763765 -6.4705405 -0.63092971
1900 388 0.55849097 -6.5759885 -6.4828798 -0.66382981
2000 390 0.61872265 -6.5695935 -6.4699984 -0.71796632
2100 392 0.5081592 -6.5617458 -6.4722443 -0.63479779
2200 394 0.48384274 -6.549079 -6.4615149 -0.66946296
2300 396 0.58288701 -6.5480033 -6.4412303 -0.71651424
2400 398 0.64008255 -6.5601944 -6.435487 -0.69102232
2500 400 0.69425764 -6.5828171 -6.4479527 -0.69066043
2600 402 0.64360746 -6.6331402 -6.4757801 -0.69090309
2700 404 0.49461099 -6.6579388 -6.5307976 -0.64409671
2800 406 0.55547146 -6.6714068 -6.5241964 -0.68541724
2900 408 0.50073205 -6.686261 -6.5339011 -0.62669192
3000 410 0.53038544 -6.6912316 -6.5383759 -0.66969696
3100 412 0.50129241 -6.7018519 -6.5548588 -0.68883024
3200 414 0.38030632 -6.6977772 -6.566269 -0.71750777
3300 416 0.46068514 -6.727184 -6.5662475 -0.68188023
3400 418 0.33822772 -6.7360772 -6.6016113 -0.72454552
3500 420 0.36453111 -6.724924 -6.5850647 -0.64608093
3600 422 0.36002968 -6.7121585 -6.5780413 -0.72223399
3700 424 0.36475294 -6.7260042 -6.5866143 -0.67031145
3800 426 0.36718557 -6.7217602 -6.5750235 -0.72937729
3900 428 0.37814959 -6.7263989 -6.5726951 -0.71591892
4000 430 0.40806996 -6.7375374 -6.5678266 -0.72678943
4100 432 0.38045271 -6.7361841 -6.568644 -0.73821367
4200 434 0.33066806 -6.7299457 -6.57638 -0.73722947
4300 436 0.41794011 -6.7644169 -6.579351 -0.73641289
4400 438 0.37024397 -6.7629482 -6.5884866 -0.71240322
4500 440 0.40320567 -6.7752853 -6.5850469 -0.77279245
4600 442 0.35772381 -6.7835099 -6.6013018 -0.73636644
4700 444 0.3651311 -6.7990539 -6.6175275 -0.66854139
4800 446 0.35091135 -6.802215 -6.6224615 -0.76162889
4900 448 0.36081012 -6.7989512 -6.6125569 -0.76016221
5000 450 0.31623339 -6.8039093 -6.6262913 -0.69115281
5100 452 0.31543867 -6.7941532 -6.6159299 -0.72205584
5200 454 0.36158004 -6.8038417 -6.5978895 -0.76776475
5300 456 0.32434144 -6.793123 -6.6082355 -0.72624243
5400 458 0.32124677 -6.793797 -6.6010261 -0.67741044
5500 460 0.32879658 -6.8125027 -6.6145418 -0.77045881
5600 462 0.33544185 -6.8282158 -6.6181936 -0.82298638
5700 464 0.31929648 -6.8312019 -6.617542 -0.77506457
5800 466 0.38513813 -6.8569307 -6.6094667 -0.72432147
5900 468 0.36275508 -6.8784065 -6.6183826 -0.71794686
6000 470 0.36550412 -6.8913174 -6.6280912 -0.73323549
6100 472 0.31989948 -6.8850192 -6.653122 -0.770755
6200 474 0.31533478 -6.8764261 -6.6470078 -0.81602846
6300 476 0.33764472 -6.9058038 -6.6574918 -0.70233823
6400 478 0.33629492 -6.9384728 -6.6676899 -0.750356
6500 480 0.329134 -6.9539905 -6.6660118 -0.76780643
6600 482 0.35893902 -6.9727388 -6.6687914 -0.79588633
6700 484 0.35256839 -6.980576 -6.6800042 -0.67119736
6800 486 0.3498406 -6.9854977 -6.6867156 -0.78135658
6900 488 0.31757914 -6.9609817 -6.6859771 -0.78048643
7000 490 0.40129918 -6.9903536 -6.6713072 -0.75727925
7100 492 0.33833658 -7.0145206 -6.6977622 -0.7587661
7200 494 0.35160231 -7.0237931 -6.7095634 -0.67933941
7300 496 0.28084778 -7.024433 -6.7195845 -0.82825025
7400 498 0.32213221 -7.0527945 -6.7230557 -0.84919299
7500 500 0.40905237 -7.1021905 -6.7203497 -0.93185466
7600 502 0.3609358 -7.1596615 -6.7690359 -0.64194099
7700 504 0.29253629 -7.1428432 -6.796613 -0.6976599
7800 506 0.31731365 -7.176045 -6.8068169 -0.87636485
7900 508 0.2905957 -7.1788367 -6.8119013 -0.75756081
8000 510 0.28404368 -7.1870361 -6.824287 -0.79842667
8100 512 0.34219804 -7.222691 -6.8386818 -0.75369138
8200 514 0.32055193 -7.2353127 -6.8551345 -0.78172901
8300 516 0.30120879 -7.2446887 -6.8672024 -0.83621194
8400 518 0.30883515 -7.2596909 -6.8762796 -0.71183282
8500 520 0.26204254 -7.2431895 -6.8834311 -0.83712537
8600 522 0.29103293 -7.2694658 -6.8867581 -0.82744948
8700 524 0.26753583 -7.2593959 -6.889244 -0.78004892
8800 526 0.26521096 -7.2599673 -6.8902608 -0.79408301
8900 528 0.28003646 -7.2530274 -6.8808417 -0.8606495
9000 530 0.26313192 -7.2628164 -6.8855381 -0.7707451
9100 532 0.2646514 -7.2830171 -6.893178 -0.76585646
9200 534 0.27846656 -7.2721664 -6.8861564 -0.89816607
9300 536 0.30560594 -7.2964254 -6.8845198 -0.72034116
9400 538 0.29262217 -7.3023252 -6.8913192 -0.62961985
9500 540 0.29718418 -7.3048523 -6.8949946 -0.87394403
9600 542 0.34146099 -7.349026 -6.9092212 -0.76789895
9700 544 0.28703519 -7.3161372 -6.9121067 -0.84885733
9800 546 0.28129876 -7.3140275 -6.9098746 -0.82726219
9900 548 0.28891495 -7.3235633 -6.9092268 -0.88128702
10000 550 0.29861445 -7.3507915 -6.9161229 -0.73192335
Loop time of 5.52188 on 4 procs for 10000 steps with 550 atoms
Performance: 782342.427 tau/day, 1810.978 timesteps/s
98.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0013716 | 1.0723 | 3.0973 | 122.1 | 19.42
Bond | 0.0012324 | 0.0039356 | 0.010944 | 6.5 | 0.07
Neigh | 0.0033538 | 0.5728 | 1.8205 | 98.1 | 10.37
Comm | 0.44758 | 2.8002 | 5.0381 | 103.8 | 50.71
Output | 0.0021229 | 0.01519 | 0.050854 | 16.7 | 0.28
Modify | 0.0069635 | 0.039662 | 0.076857 | 15.8 | 0.72
Other | | 1.018 | | | 18.43
Nlocal: 137.5 ave 299 max 2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1866.25 ave 2673 max 377 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 9891 ave 24535 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 39564
Ave neighs/atom = 71.9345
Ave special neighs/atom = 0.363636
Neighbor list builds = 884
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (15 Feb 2016)
# 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
Read molecule dimer:
2 atoms with 3 types
1 bonds with 1 types
0 angles with 0 types
0 dihedrals with 0 types
0 impropers with 0 types
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:445)
#dump 1 all atom 50 dump.deposit.atom
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65 -> bins = 3 3 6
SHAKE stats (type/ave/delta) on step 0
Memory usage per processor = 4.44065 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 352 1.0079368 -6.8875167 -6.8803581 -0.73353914
200 354 1.0079368 -6.8593854 -6.845149 -0.70414703
300 356 1.0098741 -6.8174079 -6.7961324 -0.691981
400 358 1.015821 -6.7853803 -6.7570054 -0.70383202
500 360 1.0431742 -6.7504367 -6.7142154 -0.68490175
600 362 1.0978772 -6.7139711 -6.6684789 -0.6851563
700 364 1.0536935 -6.6722083 -6.62155 -0.66701737
800 366 1.0615842 -6.6397391 -6.581729 -0.68874151
900 368 1.1690777 -6.6124387 -6.5409597 -0.6631748
SHAKE stats (type/ave/delta) on step 1000
1 1 2.33147e-15
1000 370 1.2238341 -6.5840994 -6.501408 -0.68752603
1100 372 1.0648652 -6.557204 -6.4784841 -0.67502685
1200 374 1.1172515 -6.5811189 -6.4914998 -0.67901522
1300 376 0.90409242 -6.5843683 -6.506222 -0.63816276
1400 378 0.7557157 -6.5929671 -6.5229934 -0.58917374
1500 380 0.84878624 -6.5750822 -6.4913204 -0.68236463
1600 382 0.7649257 -6.5590761 -6.4789792 -0.66149637
1700 384 0.7158335 -6.5532553 -6.4740289 -0.59288863
1800 386 0.71794608 -6.5599255 -6.4762271 -0.61004271
1900 388 0.65121754 -6.5536032 -6.4738794 -0.64961438
SHAKE stats (type/ave/delta) on step 2000
1 1 2.9976e-15
2000 390 0.69034633 -6.5451174 -6.4566114 -0.67204138
2100 392 0.64581391 -6.5535183 -6.4670253 -0.65563645
2200 394 0.65761022 -6.5431965 -6.4513982 -0.72677062
2300 396 0.6528782 -6.554984 -6.4601848 -0.64557524
2400 398 0.65836233 -6.5570075 -6.4577569 -0.69592521
2500 400 0.6411519 -6.5498234 -6.4496434 -0.72785753
2600 402 0.55292699 -6.5815848 -6.4921812 -0.64848109
2700 404 0.49353048 -6.5774182 -6.4949596 -0.72662195
2800 406 0.55912601 -6.5808134 -6.4844124 -0.75266257
2900 408 0.51233032 -6.571748 -6.4807089 -0.67844491
SHAKE stats (type/ave/delta) on step 3000
1 1 1.9984e-15
3000 410 0.47624368 -6.5904636 -6.5033458 -0.72887592
3100 412 0.45076116 -6.5887249 -6.5039336 -0.67815331
3200 414 0.50910708 -6.5995831 -6.501205 -0.78059594
3300 416 0.45275554 -6.5991184 -6.5093291 -0.71529909
3400 418 0.38977308 -6.6018891 -6.522629 -0.69785747
3500 420 0.43625362 -6.6049671 -6.5140809 -0.69363556
3600 422 0.48184349 -6.613181 -6.5104182 -0.72994587
3700 424 0.39971995 -6.5997664 -6.5125634 -0.68093342
3800 426 0.43158248 -6.6067065 -6.5104616 -0.7865976
3900 428 0.39156456 -6.591465 -6.5022651 -0.72788973
SHAKE stats (type/ave/delta) on step 4000
1 1 1.66533e-15
4000 430 0.45520202 -6.6043002 -6.4984393 -0.76339306
4100 432 0.37804217 -6.5825484 -6.4928509 -0.677846
4200 434 0.44408719 -6.6044968 -6.4970564 -0.72092913
4300 436 0.45187505 -6.6214439 -6.5100298 -0.71003531
4400 438 0.44634852 -6.6370982 -6.5250016 -0.7259646
4500 440 0.44774369 -6.6482048 -6.5337249 -0.75067855
4600 442 0.38004568 -6.6303883 -6.5315076 -0.70235189
4700 444 0.39828448 -6.6228295 -6.5174277 -0.78272067
4800 446 0.44085367 -6.6270343 -6.508419 -0.66562901
4900 448 0.47288585 -6.660755 -6.5314503 -0.74826687
SHAKE stats (type/ave/delta) on step 5000
1 1 1.77636e-15
5000 450 0.43761136 -6.6799555 -6.5583968 -0.78360367
5100 452 0.411973 -6.678564 -6.5623548 -0.70194168
5200 454 0.40797743 -6.6866303 -6.5698086 -0.80152835
5300 456 0.34469092 -6.6716537 -6.5714968 -0.67613535
5400 458 0.34013914 -6.6730911 -6.5728318 -0.76078338
5500 460 0.34154783 -6.6605085 -6.5584154 -0.77667767
5600 462 0.36897691 -6.659394 -6.5475828 -0.81373456
5700 464 0.3540965 -6.6625103 -6.553763 -0.78251629
5800 466 0.4082091 -6.6773565 -6.5503387 -0.70767517
5900 468 0.447614 -6.7033749 -6.5623 -0.71623466
SHAKE stats (type/ave/delta) on step 6000
1 1 2.9976e-15
6000 470 0.40113913 -6.679345 -6.5513219 -0.76250746
6100 472 0.42232629 -6.6963163 -6.5598656 -0.86594326
6200 474 0.39623605 -6.7100181 -6.5804473 -0.73732824
6300 476 0.37197778 -6.7159803 -6.5928994 -0.77305419
6400 478 0.33247467 -6.7128004 -6.6015118 -0.64546345
6500 480 0.34120281 -6.7088232 -6.5933119 -0.90961564
6600 482 0.3342529 -6.7056782 -6.5912555 -0.82385057
6700 484 0.34349872 -6.7152033 -6.5963272 -0.73664697
6800 486 0.33490767 -6.7243451 -6.6071963 -0.71978984
6900 488 0.36292075 -6.7126402 -6.5843536 -0.74097013
SHAKE stats (type/ave/delta) on step 7000
1 1 2.55351e-15
7000 490 0.37409279 -6.7221689 -6.5885643 -0.71570235
7100 492 0.3742131 -6.7256916 -6.5906859 -0.70045361
7200 494 0.35928736 -6.7227141 -6.5917997 -0.83125489
7300 496 0.31306304 -6.7132829 -6.5980934 -0.80568965
7400 498 0.381634 -6.7248419 -6.5830702 -0.81697798
7500 500 0.36301318 -6.7268458 -6.5907159 -0.78210607
7600 502 0.34015711 -6.7204559 -6.5917112 -0.81197949
7700 504 0.33268221 -6.7140074 -6.5869413 -0.80133
7800 506 0.32240031 -6.7139558 -6.5897106 -0.78091826
7900 508 0.28597508 -6.7091152 -6.5979339 -0.80994821
SHAKE stats (type/ave/delta) on step 8000
1 1 2.44249e-15
8000 510 0.3444676 -6.7275437 -6.5924583 -0.83444712
8100 512 0.34432983 -6.7402771 -6.604092 -0.79667718
8200 514 0.30652597 -6.7275717 -6.6053191 -0.79549578
8300 516 0.34347028 -6.7383117 -6.6001914 -0.81425668
8400 518 0.31465002 -6.7319759 -6.6044151 -0.77354562
8500 520 0.32120885 -6.7340886 -6.6028253 -0.83177871
8600 522 0.32040584 -6.71864 -6.5866721 -0.78525843
8700 524 0.34513435 -6.7414459 -6.5981888 -0.8520753
8800 526 0.32652464 -6.7316364 -6.5950672 -0.79191959
8900 528 0.29931888 -6.723678 -6.5975445 -0.86587625
SHAKE stats (type/ave/delta) on step 9000
1 1 2.10942e-15
9000 530 0.34199152 -6.7390429 -6.5938579 -0.8478443
9100 532 0.32986081 -6.7434023 -6.6023434 -0.8020183
9200 534 0.32008917 -6.7313919 -6.5935258 -0.73850848
9300 536 0.31879033 -6.745493 -6.6072118 -0.88838081
9400 538 0.31905323 -6.7359144 -6.596551 -0.90024213
9500 540 0.30837753 -6.7292799 -6.5936509 -0.81564405
9600 542 0.34603468 -6.7371426 -6.583917 -0.78921543
9700 544 0.31957585 -6.7248739 -6.582416 -0.76240549
9800 546 0.32315085 -6.7357573 -6.5907537 -0.92679394
9900 548 0.34107078 -6.7519889 -6.5979469 -0.73569227
SHAKE stats (type/ave/delta) on step 10000
1 1 2.44249e-15
10000 550 0.31059632 -6.7463923 -6.6052122 -0.75225652
Loop time of 6.33784 on 1 procs for 10000 steps with 550 atoms
Performance: 681620.330 tau/day, 1577.825 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.9751 | 3.9751 | 3.9751 | 0.0 | 62.72
Bond | 0.012007 | 0.012007 | 0.012007 | 0.0 | 0.19
Neigh | 2.0003 | 2.0003 | 2.0003 | 0.0 | 31.56
Comm | 0.13159 | 0.13159 | 0.13159 | 0.0 | 2.08
Output | 0.00095081 | 0.00095081 | 0.00095081 | 0.0 | 0.02
Modify | 0.17719 | 0.17719 | 0.17719 | 0.0 | 2.80
Other | | 0.04064 | | | 0.64
Nlocal: 550 ave 550 max 550 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2331 ave 2331 max 2331 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 36458 ave 36458 max 36458 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 36458
Ave neighs/atom = 66.2873
Ave special neighs/atom = 0.363636
Neighbor list builds = 839
Dangerous builds = 0
Total wall time: 0:00:06

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LAMMPS (15 Feb 2016)
# 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
Read molecule dimer:
2 atoms with 3 types
1 bonds with 1 types
0 angles with 0 types
0 dihedrals with 0 types
0 impropers with 0 types
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:445)
#dump 1 all atom 50 dump.deposit.atom
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 50 tmp.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 5.3
ghost atom cutoff = 5.3
binsize = 2.65 -> bins = 3 3 6
SHAKE stats (type/ave/delta) on step 0
Memory usage per processor = 4.51485 Mbytes
Step Atoms Temp E_pair TotEng Press
0 350 0 -6.9215833 -6.9215833 -1.0052629
100 352 1.0079368 -6.8946578 -6.8874992 -0.73775337
200 354 1.0079368 -6.8644786 -6.8502422 -0.69623155
300 356 1.0098741 -6.8219324 -6.800657 -0.69552497
400 358 1.015821 -6.775427 -6.7470521 -0.67240912
500 360 1.0431742 -6.7311558 -6.6949345 -0.69505765
600 362 1.0978772 -6.7107816 -6.6652895 -0.66124338
700 364 1.0536993 -6.6818292 -6.6311706 -0.67789771
800 366 1.0615655 -6.6354474 -6.5774383 -0.64710621
900 368 1.1688557 -6.614281 -6.5428156 -0.64842218
SHAKE stats (type/ave/delta) on step 1000
1 1 1.22125e-15
1000 370 1.2172009 -6.5772424 -6.4949991 -0.67942188
1100 372 1.1031034 -6.55895 -6.4774034 -0.65896897
1200 374 1.040192 -6.5874108 -6.503973 -0.62919433
1300 376 0.94890463 -6.5897148 -6.5076952 -0.63346087
1400 378 0.78945672 -6.5952649 -6.522167 -0.67613271
1500 380 0.82876461 -6.5798609 -6.4980749 -0.65306056
1600 382 0.73883758 -6.5591084 -6.4817432 -0.62749488
1700 384 0.73539709 -6.5556021 -6.4742105 -0.66817567
1800 386 0.67455206 -6.5535874 -6.474948 -0.57721026
1900 388 0.66352723 -6.5469905 -6.4657597 -0.69276627
SHAKE stats (type/ave/delta) on step 2000
1 1 2.22045e-15
2000 390 0.81013116 -6.5567994 -6.4529364 -0.71579948
2100 392 0.72889872 -6.5689128 -6.4712924 -0.65504494
2200 394 0.57901901 -6.552299 -6.4714715 -0.67723953
2300 396 0.59157803 -6.5485081 -6.4626098 -0.66397554
2400 398 0.70712699 -6.5593644 -6.4527623 -0.70641253
2500 400 0.7569242 -6.576119 -6.4578496 -0.69907756
2600 402 0.6662505 -6.6038869 -6.4961599 -0.66941055
2700 404 0.51455113 -6.6038412 -6.5178704 -0.69578494
2800 406 0.58401979 -6.6058664 -6.5051733 -0.70647457
2900 408 0.50129416 -6.6138934 -6.5248154 -0.64390758
SHAKE stats (type/ave/delta) on step 3000
1 1 2.66454e-15
3000 410 0.44807689 -6.6222658 -6.5403005 -0.68340233
3100 412 0.45962393 -6.6204312 -6.5339728 -0.66309459
3200 414 0.50182826 -6.6295842 -6.5326126 -0.74122586
3300 416 0.48471205 -6.6424495 -6.5463227 -0.69764601
3400 418 0.36856546 -6.6251783 -6.5502308 -0.76543921
3500 420 0.4203509 -6.6198957 -6.5323226 -0.64154608
3600 422 0.54795097 -6.6410801 -6.5242185 -0.7463818
3700 424 0.51183952 -6.6521145 -6.5404514 -0.70304908
3800 426 0.39414561 -6.6456807 -6.5577844 -0.74178922
3900 428 0.40589341 -6.6564647 -6.5640007 -0.78327027
SHAKE stats (type/ave/delta) on step 4000
1 1 1.88738e-15
4000 430 0.43166847 -6.6566443 -6.5562563 -0.73290988
4100 432 0.40408931 -6.6500622 -6.5541845 -0.73057986
4200 434 0.35377187 -6.6356255 -6.5500355 -0.76557381
4300 436 0.4291929 -6.657321 -6.5514993 -0.78608144
4400 438 0.43151668 -6.6494979 -6.5411262 -0.70820395
4500 440 0.44315446 -6.6596739 -6.5463674 -0.82000058
4600 442 0.41285261 -6.6553044 -6.547888 -0.76115447
4700 444 0.38354616 -6.6502515 -6.54875 -0.6954286
4800 446 0.39108666 -6.648355 -6.5431299 -0.72779836
4900 448 0.3799768 -6.6517925 -6.5478926 -0.79771549
SHAKE stats (type/ave/delta) on step 5000
1 1 3.10862e-15
5000 450 0.39260452 -6.6598567 -6.5507999 -0.76677324
5100 452 0.41475009 -6.6627963 -6.5458038 -0.70468384
5200 454 0.4115583 -6.6658575 -6.5480104 -0.78115993
5300 456 0.3753641 -6.6631393 -6.5540696 -0.78711192
5400 458 0.36565536 -6.6545908 -6.5468103 -0.74549556
5500 460 0.33271655 -6.6418893 -6.542436 -0.76780862
5600 462 0.36832168 -6.6440805 -6.5324679 -0.75143503
5700 464 0.39059076 -6.6481163 -6.5281612 -0.78380485
5800 466 0.36650802 -6.6430337 -6.5289916 -0.75502025
5900 468 0.35914314 -6.6418801 -6.5286886 -0.67704807
SHAKE stats (type/ave/delta) on step 6000
1 1 2.22045e-15
6000 470 0.39116517 -6.6612874 -6.5364474 -0.84800605
6100 472 0.38421704 -6.6693489 -6.545211 -0.78734456
6200 474 0.38216918 -6.6812774 -6.5563065 -0.81814647
6300 476 0.34722048 -6.6730701 -6.5581809 -0.77616674
6400 478 0.32907391 -6.6719973 -6.5618471 -0.7458085
6500 480 0.31094699 -6.6715976 -6.566329 -0.83282406
6600 482 0.35169592 -6.6680323 -6.5476384 -0.85138473
6700 484 0.36350925 -6.6706468 -6.5448456 -0.71970784
6800 486 0.38133383 -6.6922722 -6.5588839 -0.77339402
6900 488 0.34810579 -6.6746177 -6.551568 -0.77360649
SHAKE stats (type/ave/delta) on step 7000
1 1 3.66374e-15
7000 490 0.3590117 -6.683101 -6.5548825 -0.80004574
7100 492 0.38269726 -6.688913 -6.5508464 -0.81445922
7200 494 0.31934554 -6.6944357 -6.578075 -0.74069497
7300 496 0.32758627 -6.6955862 -6.5750529 -0.78679117
7400 498 0.3660502 -6.7111626 -6.5751801 -0.78104263
7500 500 0.32569889 -6.6953555 -6.5732185 -0.74496853
7600 502 0.33737271 -6.6971694 -6.5694785 -0.90240288
7700 504 0.35222518 -6.7006509 -6.5661204 -0.86220892
7800 506 0.31834385 -6.6988433 -6.5761614 -0.78723443
7900 508 0.35977076 -6.7264843 -6.5866128 -0.8568963
SHAKE stats (type/ave/delta) on step 8000
1 1 2.22045e-15
8000 510 0.35931856 -6.7266146 -6.5857054 -0.85544232
8100 512 0.36797798 -6.739034 -6.5934958 -0.82062699
8200 514 0.40277035 -6.7571847 -6.5965467 -0.82121365
8300 516 0.32568144 -6.7419653 -6.6109984 -0.78580816
8400 518 0.33705466 -6.7532799 -6.6166361 -0.83332745
8500 520 0.30158673 -6.7342587 -6.6110142 -0.8578352
8600 522 0.32525112 -6.7446972 -6.6107336 -0.96759
8700 524 0.32985772 -6.7480971 -6.611181 -0.78464535
8800 526 0.32397396 -6.7465569 -6.6110545 -0.81041129
8900 528 0.33669589 -6.7543874 -6.6125032 -0.87866197
SHAKE stats (type/ave/delta) on step 9000
1 1 3.88578e-15
9000 530 0.32538398 -6.7436298 -6.6054951 -0.79985713
9100 532 0.3336509 -6.7541485 -6.6114688 -0.84449566
9200 534 0.31516122 -6.7553334 -6.6195898 -0.88997909
9300 536 0.30963064 -6.7627673 -6.6284593 -0.75349544
9400 538 0.34228518 -6.7754099 -6.6258988 -0.77001741
9500 540 0.29032769 -6.7737667 -6.6460763 -0.85854407
9600 542 0.31033087 -6.7764458 -6.63903 -0.8553105
9700 544 0.33657054 -6.7798228 -6.629789 -0.91356823
9800 546 0.30235172 -6.7634263 -6.6277557 -0.92787364
9900 548 0.3446797 -6.7794717 -6.6237998 -0.88766558
SHAKE stats (type/ave/delta) on step 10000
1 1 2.55351e-15
10000 550 0.30296128 -6.7756768 -6.6379672 -0.84420968
Loop time of 5.79101 on 4 procs for 10000 steps with 550 atoms
Performance: 745983.597 tau/day, 1726.814 timesteps/s
98.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0016487 | 1.0205 | 2.974 | 120.1 | 17.62
Bond | 0.0012839 | 0.003953 | 0.010697 | 6.2 | 0.07
Neigh | 0.0035315 | 0.52893 | 1.691 | 94.9 | 9.13
Comm | 0.57816 | 2.7844 | 4.9123 | 99.7 | 48.08
Output | 0.0024757 | 0.0037841 | 0.0065219 | 2.7 | 0.07
Modify | 0.41353 | 1.2632 | 3.4168 | 111.3 | 21.81
Other | | 0.1862 | | | 3.22
Nlocal: 137.5 ave 300 max 2 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 1874.5 ave 2648 max 509 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 9185.75 ave 23231 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 36743
Ave neighs/atom = 66.8055
Ave special neighs/atom = 0.363636
Neighbor list builds = 833
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (15 Feb 2016)
# 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 lj/cut/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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 13 13 2
Memory usage per processor = 4.47689 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 0.39019964 -2.7914873 0.2240704 -2.4032387 -0.40914108
2500 0.40258219 -2.8140936 0.24274448 -2.4135243 -0.33941924
3000 0.41800133 -2.8282056 0.24466746 -2.4122942 -0.090527465
3500 0.40116089 -2.7573067 0.18791549 -2.3581517 -0.10988473
4000 0.44069383 -2.8320262 0.23306586 -2.3935358 -0.16090586
4500 0.39984934 -2.7780055 0.2316558 -2.3801554 -0.060493508
5000 0.38478499 -2.7506484 0.22192236 -2.3677873 -0.20522733
5500 0.41563657 -2.7772758 0.21967501 -2.3637174 -0.21224098
6000 0.4784307 -2.8050644 0.19178566 -2.3290259 -0.084370417
6500 0.45915752 -2.8043874 0.21761744 -2.3475257 0.044744498
7000 0.45492064 -2.7795535 0.20340455 -2.3269074 -0.027924625
7500 0.41266295 -2.7515872 0.22903767 -2.3409876 -0.43730101
8000 0.41905675 -2.7281536 0.19413869 -2.3111921 -0.020762772
8500 0.42951176 -2.7616497 0.22863785 -2.3342855 -0.18867239
9000 0.42532413 -2.748856 0.21378021 -2.3256584 0.015079949
9500 0.42237159 -2.7266142 0.20255034 -2.3063545 -0.15538561
10000 0.40758268 -2.778401 0.2746675 -2.3728562 -0.20811978
Loop time of 1.04484 on 1 procs for 10000 steps with 200 atoms
Performance: 4134616.221 tau/day, 9570.871 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.87532 | 0.87532 | 0.87532 | 0.0 | 83.78
Neigh | 0.037165 | 0.037165 | 0.037165 | 0.0 | 3.56
Comm | 0.034433 | 0.034433 | 0.034433 | 0.0 | 3.30
Output | 0.00014114 | 0.00014114 | 0.00014114 | 0.0 | 0.01
Modify | 0.083179 | 0.083179 | 0.083179 | 0.0 | 7.96
Other | | 0.0146 | | | 1.40
Nlocal: 200 ave 200 max 200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 162 ave 162 max 162 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1625 ave 1625 max 1625 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1625
Ave neighs/atom = 8.125
Neighbor list builds = 673
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (15 Feb 2016)
# 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 lj/cut/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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 13 13 2
Memory usage per processor = 4.47621 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 0.4211022 -2.8019061 0.19532181 -2.3829095 0.18067144
2000 0.39019893 -2.7914865 0.22407024 -2.4032385 -0.4091294
2500 0.40223098 -2.8137328 0.24270568 -2.4135129 -0.33712682
3000 0.43134251 -2.8297507 0.23156863 -2.4005649 -0.03874002
3500 0.4371177 -2.7992742 0.20071043 -2.3643421 -0.1177505
4000 0.40172237 -2.783663 0.22854198 -2.3839493 -0.016498497
4500 0.43131902 -2.8033297 0.22274751 -2.3741673 0.042304219
5000 0.43199785 -2.8317062 0.25487137 -2.4018684 -0.13863416
5500 0.45130496 -2.8225328 0.23220183 -2.3734843 0.11468611
6000 0.45365193 -2.8417511 0.24954005 -2.3903675 -0.12276716
6500 0.46129146 -2.8010207 0.21880638 -2.3420357 -0.13052608
7000 0.41700962 -2.7768891 0.25189185 -2.3619645 -0.41894812
7500 0.4156575 -2.7287605 0.21704468 -2.3151813 0.022065042
8000 0.43032108 -2.7802305 0.2541409 -2.352061 0.018040465
8500 0.47855371 -2.7877194 0.2130575 -2.3115585 -0.10958707
9000 0.42318631 -2.7600929 0.25229644 -2.3390225 0.36820391
9500 0.42857449 -2.6958592 0.18686752 -2.2694276 0.15379721
10000 0.43323126 -2.71981 0.22185737 -2.2887449 0.038354509
Loop time of 0.405458 on 4 procs for 10000 steps with 200 atoms
Performance: 10654618.438 tau/day, 24663.469 timesteps/s
99.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.17794 | 0.23423 | 0.25599 | 6.7 | 57.77
Neigh | 0.0083153 | 0.010322 | 0.011204 | 1.2 | 2.55
Comm | 0.086873 | 0.11001 | 0.17048 | 10.6 | 27.13
Output | 0.00028467 | 0.00030136 | 0.00034618 | 0.1 | 0.07
Modify | 0.021868 | 0.024962 | 0.026442 | 1.1 | 6.16
Other | | 0.02564 | | | 6.32
Nlocal: 50 ave 53 max 41 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Nghost: 89.75 ave 94 max 83 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 411.25 ave 459 max 307 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Total # of neighbors = 1645
Ave neighs/atom = 8.225
Neighbor list builds = 685
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
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
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
3 = max dihedrals/atom
reading bonds ...
320 bonds
reading angles ...
448 angles
reading dihedrals ...
192 dihedrals
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:55)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297)
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
Neighbor list info ...
3 neighbor list requests
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.5
ghost atom cutoff = 13.5
binsize = 6.75 -> bins = 3 3 3
Memory usage per processor = 8.70358 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 = -328.847347 Volume = 7447.236335
Loop time of 1.90735e-06 on 1 procs for 0 steps with 384 atoms
0.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Kspace | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.907e-06 | | |100.00
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
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
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
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
2 by 1 by 2 MPI processor grid
reading atoms ...
384 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
3 = max dihedrals/atom
reading bonds ...
320 bonds
reading angles ...
448 angles
reading dihedrals ...
192 dihedrals
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:55)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297)
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
Neighbor list info ...
3 neighbor list requests
update every 2 steps, delay 4 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13.5
ghost atom cutoff = 13.5
binsize = 6.75 -> bins = 3 3 3
Memory usage per processor = 8.55822 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 = -328.847347 Volume = 7447.236335
Loop time of 3.33786e-06 on 4 procs for 0 steps with 384 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Kspace | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 3.338e-06 | | |100.00
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
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
2000 atoms
reading velocities ...
2000 velocities
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
Reading potential file ffield.eim with DATE: 2010-08-31
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 2 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3 element Na Cl
#dump 3 all movie 25 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 element Na Cl
run 500
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.906
ghost atom cutoff = 7.906
binsize = 3.953 -> bins = 10 10 10
Memory usage per processor = 2.33063 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 5.98 on 1 procs for 500 steps with 2000 atoms
Performance: 7.224 ns/day, 3.322 hours/ns, 83.612 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.5037 | 5.5037 | 5.5037 | 0.0 | 92.04
Neigh | 0.38962 | 0.38962 | 0.38962 | 0.0 | 6.52
Comm | 0.01958 | 0.01958 | 0.01958 | 0.0 | 0.33
Output | 0.00030184 | 0.00030184 | 0.00030184 | 0.0 | 0.01
Modify | 0.058852 | 0.058852 | 0.058852 | 0.0 | 0.98
Other | | 0.007943 | | | 0.13
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
Total wall time: 0:00:06

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
2000 atoms
reading velocities ...
2000 velocities
pair_style eim
pair_coeff * * Na Cl ffield.eim Na Cl
Reading potential file ffield.eim with DATE: 2010-08-31
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 2 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3 element Na Cl
#dump 3 all movie 25 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 element Na Cl
run 500
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.906
ghost atom cutoff = 7.906
binsize = 3.953 -> bins = 10 10 10
Memory usage per processor = 2.21734 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 1.57729 on 4 procs for 500 steps with 2000 atoms
Performance: 27.389 ns/day, 0.876 hours/ns, 316.999 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3994 | 1.4083 | 1.4269 | 0.9 | 89.29
Neigh | 0.096567 | 0.096771 | 0.097035 | 0.1 | 6.14
Comm | 0.02714 | 0.045477 | 0.054307 | 5.0 | 2.88
Output | 0.00022769 | 0.0002473 | 0.00029278 | 0.2 | 0.02
Modify | 0.021543 | 0.021803 | 0.022018 | 0.1 | 1.38
Other | | 0.004696 | | | 0.30
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
Total wall time: 0:00:01

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LAMMPS (15 Feb 2016)
# 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 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.8
ghost atom cutoff = 4.8
binsize = 2.4 -> bins = 59 59 3
Memory usage per processor = 4.17878 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 2.1709732 -0.00046172705 2.2872012 0.066791266 13689.473
500 1.9712384 -0.014365021 2.0484832 0.12263116 8475.3548
600 2.0811163 -0.21654179 1.8340664 0.22433913 4685.3955
700 2.1578657 -0.68696192 1.3974517 0.60188995 2533.8873
800 1.8843124 -1.6343111 0.2143696 1.105687 1440.5961
900 2.1968489 -3.0749104 -0.92393949 3.2168763 924.62895
1000 1.4196808 -4.3944118 -2.972349 3.1895485 744.95136
1100 1.9354395 -4.9265904 -2.9959864 1.5434922 715.87574
1200 2.1063417 -4.5664569 -2.4467911 1.2012289 760.07454
1300 1.859493 -4.1043918 -2.2530918 0.35847277 846.54577
1400 2.1430322 -3.7414541 -1.6163368 0.7461639 928.96639
1500 1.9056885 -3.5118131 -1.5910333 0.35347839 1021.0387
1600 2.1297675 -3.2577617 -1.119554 0.73265236 1087.6271
1700 1.9341135 -3.2121534 -1.2832848 0.46406018 1140.8473
1800 2.0861201 -3.2382735 -1.1460071 0.6058924 1161.1051
1900 1.9976529 -3.2494581 -1.2698889 0.69257341 1151.4372
2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026
Loop time of 1.034 on 1 procs for 2000 steps with 400 atoms
Performance: 334235.078 tau/day, 1934.231 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.82535 | 0.82535 | 0.82535 | 0.0 | 79.82
Neigh | 0.01368 | 0.01368 | 0.01368 | 0.0 | 1.32
Comm | 0.011166 | 0.011166 | 0.011166 | 0.0 | 1.08
Output | 0.00032282 | 0.00032282 | 0.00032282 | 0.0 | 0.03
Modify | 0.17955 | 0.17955 | 0.17955 | 0.0 | 17.36
Other | | 0.003941 | | | 0.38
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 249 ave 249 max 249 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3031 ave 3031 max 3031 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3031
Ave neighs/atom = 7.5775
Neighbor list builds = 140
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 4.18892 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9791754 -3.3850065 -1.3653244 0.88473341 1121.7026
2100 2.0067383 -3.4164295 -1.402453 0.63163512 1121.7026
2200 2.0298976 -3.4415998 -1.4231421 0.91861985 1121.7026
2300 2.0418707 -3.4552616 -1.4277716 0.58834236 1121.7026
2400 2.0126621 -3.424202 -1.3839096 0.80723942 1121.7026
2500 1.9403964 -3.3489489 -1.3995215 0.79492719 1121.7026
2600 2.0459304 -3.4600931 -1.4229608 0.69699402 1121.7026
2700 2.0032293 -3.4126492 -1.429784 0.44210814 1121.7026
2800 1.9367905 -3.345688 -1.4171068 0.6872734 1121.7026
2900 1.9870908 -3.3983385 -1.4218501 0.42402247 1121.7026
3000 1.9654849 -3.3767671 -1.3835149 0.6611643 1121.7026
3100 1.9308462 -3.3343018 -1.3895992 0.45213534 1121.7026
3200 1.8924656 -3.2956948 -1.4157919 0.56524685 1121.7026
3300 1.8802888 -3.2822198 -1.4071878 0.86030365 1121.7026
3400 1.8847013 -3.2852796 -1.4162404 0.91660541 1121.7026
3500 1.9290452 -3.3332356 -1.3889879 0.70770119 1121.7026
3600 1.9223314 -3.32413 -1.3896278 0.56763748 1121.7026
3700 1.9185132 -3.3197222 -1.3913701 0.66889312 1121.7026
3800 1.877321 -3.2796045 -1.4050964 0.67335591 1121.7026
3900 1.9250447 -3.3313033 -1.3872185 0.64573122 1121.7026
4000 1.8574113 -3.2592142 -1.3807543 0.46117918 1121.7026
Loop time of 1.15469 on 1 procs for 2000 steps with 400 atoms
Performance: 299301.907 tau/day, 1732.071 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0251 | 1.0251 | 1.0251 | 0.0 | 88.77
Neigh | 0.0063124 | 0.0063124 | 0.0063124 | 0.0 | 0.55
Comm | 0.011792 | 0.011792 | 0.011792 | 0.0 | 1.02
Output | 0.00035834 | 0.00035834 | 0.00035834 | 0.0 | 0.03
Modify | 0.10537 | 0.10537 | 0.10537 | 0.0 | 9.13
Other | | 0.005782 | | | 0.50
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 219 ave 219 max 219 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3046 ave 3046 max 3046 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3046
Ave neighs/atom = 7.615
Neighbor list builds = 47
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

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LAMMPS (15 Feb 2016)
# 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 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.8
ghost atom cutoff = 4.8
binsize = 2.4 -> bins = 59 59 3
Memory usage per processor = 4.16784 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 2.1709732 -0.00046172705 2.2872012 0.066791266 13689.473
500 1.9712384 -0.014365021 2.0484832 0.12263116 8475.3548
600 2.0811163 -0.21654179 1.8340664 0.22433913 4685.3955
700 2.1578657 -0.68696192 1.3974517 0.60188995 2533.8873
800 1.8843124 -1.6343111 0.2143696 1.105687 1440.5961
900 2.1968489 -3.0749104 -0.92393949 3.2168763 924.62895
1000 1.4196808 -4.3944118 -2.972349 3.1895485 744.95136
1100 1.9354395 -4.9265904 -2.9959864 1.5434922 715.87574
1200 2.1063417 -4.5664569 -2.4467911 1.2012289 760.07454
1300 1.859493 -4.1043918 -2.2530918 0.35847277 846.54577
1400 2.1430322 -3.7414541 -1.6163368 0.7461639 928.96639
1500 1.9056885 -3.5118131 -1.5910333 0.35347839 1021.0387
1600 2.1297675 -3.2577617 -1.119554 0.73265236 1087.6271
1700 1.9341135 -3.2121534 -1.2832848 0.46406018 1140.8473
1800 2.0861201 -3.2382735 -1.1460071 0.6058924 1161.1051
1900 1.9976529 -3.2494581 -1.2698889 0.69257341 1151.4372
2000 1.9791754 -3.3850065 -1.3653244 0.88473343 1121.7026
Loop time of 0.513848 on 4 procs for 2000 steps with 400 atoms
Performance: 672572.269 tau/day, 3892.201 timesteps/s
88.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.19352 | 0.21426 | 0.23184 | 3.0 | 41.70
Neigh | 0.0034561 | 0.0036583 | 0.0038161 | 0.3 | 0.71
Comm | 0.10711 | 0.12693 | 0.14494 | 4.6 | 24.70
Output | 0.0016916 | 0.0017142 | 0.0017467 | 0.1 | 0.33
Modify | 0.14238 | 0.15759 | 0.16878 | 2.4 | 30.67
Other | | 0.009694 | | | 1.89
Nlocal: 100 ave 113 max 85 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 149.75 ave 160 max 141 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 757.75 ave 885 max 592 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 3031
Ave neighs/atom = 7.5775
Neighbor list builds = 140
Dangerous builds = 80
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 4.16867 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9791754 -3.3850065 -1.3653244 0.88473343 1121.7026
2100 2.0067383 -3.4164295 -1.402453 0.63163513 1121.7026
2200 2.0298976 -3.4415998 -1.4231421 0.91861985 1121.7026
2300 2.0418708 -3.4552617 -1.4277716 0.58834191 1121.7026
2400 2.0126625 -3.4242024 -1.3839097 0.80723766 1121.7026
2500 1.9403968 -3.3489494 -1.3995212 0.79492647 1121.7026
2600 2.0459318 -3.4600945 -1.4229599 0.69698729 1121.7026
2700 2.0032338 -3.4126541 -1.4297892 0.44208354 1121.7026
2800 1.9367789 -3.3456765 -1.4171038 0.6873665 1121.7026
2900 1.9870979 -3.3983434 -1.4218523 0.42398659 1121.7026
3000 1.965491 -3.376773 -1.3835208 0.66112051 1121.7026
3100 1.9307633 -3.3342121 -1.3895745 0.45224657 1121.7026
3200 1.8918453 -3.2949278 -1.4157216 0.56825582 1121.7026
3300 1.8824584 -3.2844031 -1.4066487 0.85795659 1121.7026
3400 1.8871451 -3.2878452 -1.4156691 0.91410213 1121.7026
3500 1.9297625 -3.3340904 -1.3901995 0.6754809 1121.7026
3600 1.8994197 -3.3009141 -1.3964162 0.58676937 1121.7026
3700 1.9181765 -3.3204193 -1.3956433 0.54632736 1121.7026
3800 1.9278078 -3.3300748 -1.3999307 0.48904879 1121.7026
3900 1.888321 -3.2896024 -1.3848249 0.49521159 1121.7026
4000 1.8372182 -3.2347372 -1.4091759 0.61895915 1121.7026
Loop time of 0.373834 on 4 procs for 2000 steps with 400 atoms
Performance: 924475.349 tau/day, 5349.973 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.25404 | 0.26703 | 0.29737 | 3.4 | 71.43
Neigh | 0.0014787 | 0.0016722 | 0.0018535 | 0.3 | 0.45
Comm | 0.036186 | 0.068545 | 0.082895 | 7.2 | 18.34
Output | 0.00050688 | 0.00052452 | 0.00055194 | 0.1 | 0.14
Modify | 0.025374 | 0.027727 | 0.030269 | 1.1 | 7.42
Other | | 0.008336 | | | 2.23
Nlocal: 100 ave 106 max 92 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Nghost: 148 ave 152 max 145 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 760.25 ave 815 max 713 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Total # of neighbors = 3041
Ave neighs/atom = 7.6025
Neighbor list builds = 46
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.8
ghost atom cutoff = 4.8
binsize = 2.4 -> bins = 59 59 3
Memory usage per processor = 4.17878 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 2.1708593 -2.5387568e-05 2.2875176 0.066837565 13689.499
500 2.012121 0.0083622744 2.0637959 0.10893231 8486.4241
600 2.1416108 0.08602656 2.2040317 0.34087235 4775.2723
700 2.0419962 0.17405962 2.1702488 0.78836378 2768.5757
800 1.9520613 0.31921669 2.2528751 1.813059 1823.5943
900 1.6291778 0.2415422 1.8569794 1.7008233 1518.2585
1000 1.9412761 0.13859576 2.1184352 1.3019342 1521.7058
1100 2.1016581 0.10912963 2.2356017 0.99454361 1756.0608
1200 1.7849978 0.049963029 1.8591867 0.54025938 2204.358
1300 2.3125867 0.046557089 2.3849986 0.47599584 2761.2014
1400 1.757077 0.026326047 1.7889269 0.28604209 3309.8144
1500 2.392565 0.048563131 2.4533846 0.37917665 3530.6855
1600 1.7590832 0.050490264 1.8168201 0.33612171 3313.4472
1700 2.252414 0.17372984 2.4394491 0.85851343 2716.0401
1800 1.7966767 0.28338104 2.0779465 1.4326114 2152.4099
1900 1.9682759 0.2168566 2.1183362 1.3383729 1806.7221
2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
Loop time of 1.79538 on 1 procs for 2000 steps with 400 atoms
Performance: 192494.490 tau/day, 1113.973 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.582 | 1.582 | 1.582 | 0.0 | 88.12
Neigh | 0.013545 | 0.013545 | 0.013545 | 0.0 | 0.75
Comm | 0.0087712 | 0.0087712 | 0.0087712 | 0.0 | 0.49
Output | 0.00034428 | 0.00034428 | 0.00034428 | 0.0 | 0.02
Modify | 0.18736 | 0.18736 | 0.18736 | 0.0 | 10.44
Other | | 0.003359 | | | 0.19
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 216 ave 216 max 216 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1929 ave 1929 max 1929 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1929
Ave neighs/atom = 4.8225
Neighbor list builds = 177
Dangerous builds = 146
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 4.18079 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
2100 1.978918 0.16562152 2.1632874 1.3092233 1654.9587
2200 1.9820406 0.16230289 2.1750657 1.2612976 1654.9587
2300 1.9577019 0.18791066 2.1531422 1.3478385 1654.9587
2400 2.0271146 0.11480565 2.1721336 1.0619428 1654.9587
2500 1.9894838 0.1544598 2.1329407 1.2325572 1654.9587
2600 1.998697 0.14468753 2.1485209 1.1903357 1654.9587
2700 1.9608664 0.18459944 2.1483889 1.3461095 1654.9587
2800 2.005755 0.13729992 2.1214078 1.1596182 1654.9587
2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587
3000 1.9606374 0.18480425 2.1301691 1.3280548 1654.9587
3100 1.9824235 0.16187644 2.1284432 1.2590072 1654.9587
3200 1.9389485 0.20774117 2.106322 1.4587341 1654.9587
3300 1.9849309 0.15929459 2.1301897 1.2415172 1654.9587
3400 1.9596863 0.18578944 2.1215072 1.3738214 1654.9587
3500 1.9671171 0.17804546 2.0934254 1.3147204 1654.9587
3600 1.9702641 0.17471582 2.1569255 1.3331099 1654.9587
3700 1.9103961 0.23792935 2.1305401 1.5832203 1654.9587
3800 1.9129619 0.23512654 2.1445946 1.5657403 1654.9587
3900 1.9868018 0.15725404 2.1658135 1.2582197 1654.9587
4000 2.0058784 0.13726837 2.1534352 1.1351359 1654.9587
Loop time of 3.05676 on 1 procs for 2000 steps with 400 atoms
Performance: 113061.044 tau/day, 654.288 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.9201 | 2.9201 | 2.9201 | 0.0 | 95.53
Neigh | 0.0051684 | 0.0051684 | 0.0051684 | 0.0 | 0.17
Comm | 0.011668 | 0.011668 | 0.011668 | 0.0 | 0.38
Output | 0.00038481 | 0.00038481 | 0.00038481 | 0.0 | 0.01
Modify | 0.1134 | 0.1134 | 0.1134 | 0.0 | 3.71
Other | | 0.00608 | | | 0.20
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 204 ave 204 max 204 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1857 ave 1857 max 1857 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1857
Ave neighs/atom = 4.6425
Neighbor list builds = 48
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (15 Feb 2016)
# 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 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
#dump_modify 3 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.8
ghost atom cutoff = 4.8
binsize = 2.4 -> bins = 59 59 3
Memory usage per processor = 4.16784 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 2.1708593 -2.5387568e-05 2.2875176 0.066837565 13689.499
500 2.012121 0.0083622744 2.0637959 0.10893231 8486.4241
600 2.1416108 0.08602656 2.2040317 0.34087235 4775.2723
700 2.0419962 0.17405962 2.1702488 0.78836378 2768.5757
800 1.9520613 0.31921669 2.2528751 1.813059 1823.5943
900 1.6291778 0.2415422 1.8569794 1.7008233 1518.2585
1000 1.9412761 0.13859576 2.1184352 1.3019342 1521.7058
1100 2.1016581 0.10912963 2.2356017 0.99454361 1756.0608
1200 1.7849978 0.049963029 1.8591867 0.54025938 2204.358
1300 2.3125867 0.046557089 2.3849986 0.47599584 2761.2014
1400 1.757077 0.026326047 1.7889269 0.28604209 3309.8144
1500 2.392565 0.048563131 2.4533846 0.37917665 3530.6855
1600 1.7590832 0.050490264 1.8168201 0.33612171 3313.4472
1700 2.252414 0.17372984 2.4394491 0.85851343 2716.0401
1800 1.7966767 0.28338104 2.0779465 1.4326114 2152.4099
1900 1.9682759 0.2168566 2.1183362 1.3383729 1806.7221
2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
Loop time of 0.543654 on 4 procs for 2000 steps with 400 atoms
Performance: 635698.342 tau/day, 3678.810 timesteps/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.38532 | 0.40127 | 0.41984 | 2.3 | 73.81
Neigh | 0.0035267 | 0.0035982 | 0.0036683 | 0.1 | 0.66
Comm | 0.039163 | 0.057053 | 0.072538 | 5.9 | 10.49
Output | 0.00048089 | 0.00050312 | 0.00056362 | 0.2 | 0.09
Modify | 0.076422 | 0.077282 | 0.078008 | 0.2 | 14.22
Other | | 0.003945 | | | 0.73
Nlocal: 100 ave 108 max 95 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost: 125.75 ave 128 max 123 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 482.25 ave 535 max 442 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 1929
Ave neighs/atom = 4.8225
Neighbor list builds = 177
Dangerous builds = 146
# run dynamics on dense system
unfix 1
fix 1 all nve/asphere
run 2000
Memory usage per processor = 4.16867 Mbytes
Step rot E_pair TotEng Press Volume
2000 1.9694503 0.17559901 2.14777 1.3281701 1654.9587
2100 1.978918 0.16562152 2.1632874 1.3092233 1654.9587
2200 1.9820406 0.16230289 2.1750657 1.2612976 1654.9587
2300 1.9577019 0.18791066 2.1531422 1.3478385 1654.9587
2400 2.0271146 0.11480565 2.1721336 1.0619428 1654.9587
2500 1.9894838 0.1544598 2.1329407 1.2325572 1654.9587
2600 1.998697 0.14468753 2.1485209 1.1903357 1654.9587
2700 1.9608664 0.18459944 2.1483889 1.3461096 1654.9587
2800 2.005755 0.13729992 2.1214078 1.1596183 1654.9587
2900 1.9080687 0.24019772 2.1661723 1.5974752 1654.9587
3000 1.9606373 0.18480426 2.1301691 1.3280548 1654.9587
3100 1.9824235 0.16187647 2.1284433 1.2590074 1654.9587
3200 1.9389485 0.20774113 2.1063219 1.4587339 1654.9587
3300 1.984931 0.15929453 2.1301897 1.2415169 1654.9587
3400 1.9596864 0.18578934 2.1215072 1.3738204 1654.9587
3500 1.9671165 0.17804604 2.0934256 1.3147236 1654.9587
3600 1.9702644 0.17471548 2.156925 1.3331072 1654.9587
3700 1.9104013 0.2379238 2.1305421 1.5831938 1654.9587
3800 1.9129623 0.23512612 2.1445951 1.565741 1654.9587
3900 1.9868116 0.15724371 2.1658058 1.2581725 1654.9587
4000 2.0058633 0.13728433 2.1534403 1.1352037 1654.9587
Loop time of 0.868601 on 4 procs for 2000 steps with 400 atoms
Performance: 397881.371 tau/day, 2302.554 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.71894 | 0.74023 | 0.79323 | 3.6 | 85.22
Neigh | 0.0012772 | 0.0013462 | 0.0014431 | 0.2 | 0.15
Comm | 0.037097 | 0.089266 | 0.10999 | 10.2 | 10.28
Output | 0.00050378 | 0.00052214 | 0.00055289 | 0.1 | 0.06
Modify | 0.027847 | 0.028882 | 0.030547 | 0.6 | 3.33
Other | | 0.008352 | | | 0.96
Nlocal: 100 ave 103 max 96 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 118 ave 122 max 115 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 464.25 ave 489 max 449 min
Histogram: 2 0 0 0 1 0 0 0 0 1
Total # of neighbors = 1857
Ave neighs/atom = 4.6425
Neighbor list builds = 48
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (15 Feb 2016)
# 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:445)
#dump 1 all atom 500 dump.flow
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.2
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.2
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123 -> bins = 37 32 1
Memory usage per processor = 2.47395 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 -0.40814263 0 0.30376214 2.9229587 571.54286
2500 1.1929729 -0.38735055 0 0.46193257 2.8337691 571.54286
3000 1 -0.44542386 0 0.2664809 2.7214531 571.54286
3500 1.1553179 -0.42687142 0 0.39560493 2.5109633 571.54286
4000 1 -0.40604742 0 0.30585734 2.7055928 571.54286
4500 1.1498154 -0.44055268 0 0.37800642 2.5561154 571.54286
5000 1 -0.41742254 0 0.29448222 2.4788457 571.54286
5500 1.014604 -0.42503236 0 0.29726906 2.579664 571.54286
6000 1 -0.41264837 0 0.29925639 2.5861705 571.54286
6500 1.1443238 -0.4392768 0 0.37537274 2.2801246 571.54286
7000 1 -0.38852754 0 0.32337722 2.3294037 571.54286
7500 1.0568142 -0.42350098 0 0.32885011 2.3953589 571.54286
8000 1 -0.39343 0 0.31847477 2.5701342 571.54286
8500 1.0872157 -0.46282796 0 0.3111661 2.2892446 571.54286
9000 1 -0.402333 0 0.30957177 2.4852035 571.54286
9500 0.99889786 -0.46870263 0 0.24241751 2.3763314 571.54286
10000 1 -0.43338695 0 0.27851782 2.405424 571.54286
Loop time of 0.271851 on 1 procs for 10000 steps with 420 atoms
Performance: 9534632.580 tau/day, 36784.848 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12448 | 0.12448 | 0.12448 | 0.0 | 45.79
Neigh | 0.054694 | 0.054694 | 0.054694 | 0.0 | 20.12
Comm | 0.0075622 | 0.0075622 | 0.0075622 | 0.0 | 2.78
Output | 0.00014329 | 0.00014329 | 0.00014329 | 0.0 | 0.05
Modify | 0.067663 | 0.067663 | 0.067663 | 0.0 | 24.89
Other | | 0.01731 | | | 6.37
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 46 ave 46 max 46 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 952 ave 952 max 952 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 952
Ave neighs/atom = 2.26667
Neighbor list builds = 996
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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:445)
#dump 1 all atom 500 dump.flow
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.2
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.2
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123 -> bins = 37 32 1
Memory usage per processor = 2.47768 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 -0.41052999 0 0.30137477 2.865191 571.54286
2500 1.1227078 -0.37036396 0 0.42889708 2.944809 571.54286
3000 1 -0.3831188 0 0.32878596 2.6840526 571.54286
3500 1.0822111 -0.42234615 0 0.34808509 2.8119594 571.54286
4000 1 -0.40805417 0 0.30385059 2.5977913 571.54286
4500 1.0910738 -0.37103658 0 0.40570404 2.3742519 571.54286
5000 1 -0.46702664 0 0.24487812 2.5666252 571.54286
5500 1.0411533 -0.40531814 0 0.33588386 2.5125963 571.54286
6000 1 -0.36183137 0 0.35007339 2.4382625 571.54286
6500 1.0533061 -0.38887062 0 0.360983 2.6032319 571.54286
7000 1 -0.49087253 0 0.22103223 2.4362009 571.54286
7500 1.056871 -0.42142263 0 0.33096887 2.5406254 571.54286
8000 1 -0.40440166 0 0.3075031 2.3664523 571.54286
8500 1.0340789 -0.36193981 0 0.37422586 2.4461942 571.54286
9000 1 -0.45171969 0 0.26018507 2.5525861 571.54286
9500 1.0322994 -0.40989898 0 0.32499991 2.6021234 571.54286
10000 1 -0.42489516 0 0.28700961 2.619505 571.54286
Loop time of 0.131903 on 4 procs for 10000 steps with 420 atoms
Performance: 19650813.964 tau/day, 75813.325 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.024203 | 0.030848 | 0.037153 | 3.6 | 23.39
Neigh | 0.013397 | 0.014826 | 0.016212 | 1.1 | 11.24
Comm | 0.039776 | 0.04867 | 0.05801 | 3.7 | 36.90
Output | 0.00026822 | 0.00028723 | 0.00034046 | 0.2 | 0.22
Modify | 0.018224 | 0.0192 | 0.020054 | 0.6 | 14.56
Other | | 0.01807 | | | 13.70
Nlocal: 105 ave 113 max 97 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 39.5 ave 43 max 36 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 236.75 ave 287 max 183 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 947
Ave neighs/atom = 2.25476
Neighbor list builds = 966
Dangerous builds = 0
Total wall time: 0:00:00

145
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LAMMPS (15 Feb 2016)
# 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:445)
#dump 1 all atom 500 dump.flow
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123 -> bins = 37 32 1
Memory usage per processor = 2.47395 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 -0.48849353 0 0.22341123 1.5091361 553.64637
3500 1.2404547 -0.63017551 0 0.25291012 1.768107 535.22599
4000 1 -0.71545964 0 -0.0035548789 2.2079822 516.73161
4500 1.2270239 -0.78740977 0 0.086114399 2.6094706 503.17906
5000 1 -0.8367971 0 -0.12489233 3.186175 498.73275
5500 1.2257721 -0.77200456 0 0.10062844 2.6369599 502.75573
6000 1 -0.6766551 0 0.035249665 2.2092944 512.08396
6500 1.2201203 -0.67876788 0 0.18984154 1.8784541 517.92079
7000 1 -0.68555696 0 0.026347797 1.8142356 516.44963
7500 1.2482526 -0.7345934 0 0.15404357 2.0253109 511.4042
8000 1 -0.70068231 0 0.011222455 2.1739831 504.55527
8500 1.2151375 -0.77680457 0 0.088257564 2.6264947 498.00946
9000 1 -0.74461165 0 -0.032706889 2.574656 498.14523
9500 1.2047533 -0.75768848 0 0.09998113 2.4174997 501.8877
10000 1 -0.67361996 0 0.038284798 2.2310948 507.57444
Loop time of 0.308209 on 1 procs for 10000 steps with 420 atoms
Performance: 8409879.284 tau/day, 32445.522 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13686 | 0.13686 | 0.13686 | 0.0 | 44.40
Neigh | 0.030894 | 0.030894 | 0.030894 | 0.0 | 10.02
Comm | 0.0063944 | 0.0063944 | 0.0063944 | 0.0 | 2.07
Output | 0.00016952 | 0.00016952 | 0.00016952 | 0.0 | 0.06
Modify | 0.11606 | 0.11606 | 0.11606 | 0.0 | 37.66
Other | | 0.01783 | | | 5.79
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: 1124 ave 1124 max 1124 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1124
Ave neighs/atom = 2.67619
Neighbor list builds = 561
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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:445)
#dump 1 all atom 500 dump.flow
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123 -> bins = 37 32 1
Memory usage per processor = 2.47768 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 -0.42381899 0 0.44989866 1.454461 570.15856
3000 1 -0.49143418 0 0.22047058 1.5345944 554.98632
3500 1.2444907 -0.59761906 0 0.28833979 1.8753537 537.01597
4000 1 -0.70389808 0 0.008006681 2.1377407 521.46953
4500 1.2086391 -0.73613601 0 0.12429994 2.8118471 507.60191
5000 1 -0.82025509 0 -0.10835033 2.9561662 501.69891
5500 1.2136337 -0.75490689 0 0.10908471 2.7434794 505.27439
6000 1 -0.69627045 0 0.015634317 2.4524175 508.59669
6500 1.207632 -0.68640835 0 0.17331064 2.2238608 515.69996
7000 1 -0.69036919 0 0.02153557 2.2262384 515.59362
7500 1.2071424 -0.70836083 0 0.15100956 2.1631657 513.88454
8000 1 -0.72087298 0 -0.0089682187 2.2520771 509.87373
8500 1.2046939 -0.75634562 0 0.10128171 2.2433251 505.69974
9000 1 -0.8200207 0 -0.10811593 2.6210027 502.60511
9500 1.2167146 -0.77385956 0 0.092325373 2.5938179 500.86068
10000 1 -0.73082779 0 -0.018923029 2.735112 505.69856
Loop time of 0.196428 on 4 procs for 10000 steps with 420 atoms
Performance: 13195670.685 tau/day, 50909.223 timesteps/s
99.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.033267 | 0.034629 | 0.035398 | 0.5 | 17.63
Neigh | 0.0084751 | 0.0087134 | 0.0089035 | 0.2 | 4.44
Comm | 0.063612 | 0.066345 | 0.06988 | 0.9 | 33.78
Output | 0.00033164 | 0.00035477 | 0.00041437 | 0.2 | 0.18
Modify | 0.056999 | 0.058513 | 0.061231 | 0.7 | 29.79
Other | | 0.02787 | | | 14.19
Nlocal: 105 ave 106 max 103 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 44.75 ave 47 max 44 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Neighs: 277 ave 296 max 255 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 1108
Ave neighs/atom = 2.6381
Neighbor list builds = 564
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
fix 4 all enforce2d
# Run
timestep 0.0025
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
#dump 1 all atom 500 dump.friction
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 20000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 41 31 1
Memory usage per processor = 2.47434 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 -3.0380599 0 -2.9968186 -0.32423949 2444.9333
8000 0.1 -3.0346451 0 -2.9934038 -0.38015467 2444.9333
9000 0.1 -3.0328231 0 -2.9915818 -0.43229228 2444.9333
10000 0.11715901 -3.0339975 0 -2.9856796 -0.32994136 2444.9333
11000 0.11489931 -3.0347978 0 -2.9874118 -0.45189608 2444.9333
12000 0.10977417 -3.0396002 0 -2.994328 -0.18902632 2444.9333
13000 0.1 -3.0460576 0 -3.0048163 -0.30636366 2444.9333
14000 0.10650444 -3.0498066 0 -3.0058827 -0.37168966 2444.9333
15000 0.11262528 -3.053675 0 -3.0072269 -0.32295729 2444.9333
16000 0.10822084 -3.0524308 0 -3.0077991 -0.25034257 2444.9333
17000 0.10833465 -3.0487557 0 -3.0040771 -0.4048054 2444.9333
18000 0.11599608 -3.0540506 0 -3.0062123 -0.30721348 2444.9333
19000 0.11303674 -3.0521905 0 -3.0055727 -0.29399612 2444.9333
20000 0.09925739 -3.0483895 0 -3.0074545 -0.34540139 2444.9333
Loop time of 5.95865 on 1 procs for 20000 steps with 1724 atoms
Performance: 724995.927 tau/day, 3356.463 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8617 | 4.8617 | 4.8617 | 0.0 | 81.59
Neigh | 0.33399 | 0.33399 | 0.33399 | 0.0 | 5.61
Comm | 0.036682 | 0.036682 | 0.036682 | 0.0 | 0.62
Output | 0.00041318 | 0.00041318 | 0.00041318 | 0.0 | 0.01
Modify | 0.57978 | 0.57978 | 0.57978 | 0.0 | 9.73
Other | | 0.1461 | | | 2.45
Nlocal: 1724 ave 1724 max 1724 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 145 ave 145 max 145 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 14387 ave 14387 max 14387 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 14387
Ave neighs/atom = 8.34513
Neighbor list builds = 726
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (15 Feb 2016)
# 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
fix 4 all enforce2d
# Run
timestep 0.0025
thermo 1000
thermo_modify temp new
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
#dump 1 all atom 500 dump.friction
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 20000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 41 31 1
Memory usage per processor = 2.47775 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 0.11937908 -3.0305561 0 -2.9813227 -0.3077312 2444.9333
9000 0.11110633 -3.0274042 0 -2.9815825 -0.52435329 2444.9333
10000 0.11593138 -3.0164989 0 -2.9686873 -0.36943466 2444.9333
11000 0.11066412 -3.0156369 0 -2.9699976 -0.46759658 2444.9333
12000 0.10383247 -3.0199664 0 -2.9771445 -0.27390498 2444.9333
13000 0.11288647 -3.027191 0 -2.9806352 -0.38261516 2444.9333
14000 0.10587004 -3.0302799 0 -2.9866177 -0.20888958 2444.9333
15000 0.11092262 -3.0308702 0 -2.9851243 -0.37310523 2444.9333
16000 0.11258624 -3.0421958 0 -2.9957638 -0.27895709 2444.9333
17000 0.10980848 -3.0388353 0 -2.9935488 -0.31492687 2444.9333
18000 0.11125763 -3.0392991 0 -2.993415 -0.30414022 2444.9333
19000 0.11673298 -3.0405242 0 -2.992382 -0.34902574 2444.9333
20000 0.11753441 -3.0437232 0 -2.9952505 -0.31244935 2444.9333
Loop time of 1.96189 on 4 procs for 20000 steps with 1724 atoms
Performance: 2201963.286 tau/day, 10194.274 timesteps/s
99.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0666 | 1.2376 | 1.4382 | 12.1 | 63.08
Neigh | 0.072524 | 0.085115 | 0.099557 | 3.4 | 4.34
Comm | 0.16011 | 0.38337 | 0.56903 | 24.0 | 19.54
Output | 0.00041413 | 0.00043744 | 0.0005033 | 0.2 | 0.02
Modify | 0.12679 | 0.14438 | 0.15946 | 3.2 | 7.36
Other | | 0.111 | | | 5.66
Nlocal: 431 ave 495 max 377 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost: 96 ave 125 max 74 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 3597.75 ave 4233 max 3149 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Total # of neighbors = 14391
Ave neighs/atom = 8.34745
Neighbor list builds = 704
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (15 Feb 2016)
# 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:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.84754
ghost atom cutoff = 1.84754
binsize = 0.923769 -> bins = 8 11 11
Memory usage per processor = 3.65406 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 -4.5005818e-13 -4.9677973e-13 -4.9219424e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.083575 on 1 procs for 134 steps with 1000 atoms
100.5% CPU use with 1 MPI tasks x no OpenMP threads
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 5.83329e-10
Force max component initial, final = 1960.27 3.42093e-10
Final line search alpha, max atom move = 1 3.42093e-10
Iterations, force evaluations = 134 137
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.068495 | 0.068495 | 0.068495 | 0.0 | 81.96
Neigh | 0.00106 | 0.00106 | 0.00106 | 0.0 | 1.27
Comm | 0.0014729 | 0.0014729 | 0.0014729 | 0.0 | 1.76
Output | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 | 0.0 | 0.02
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01253 | | | 14.99
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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.84754
ghost atom cutoff = 1.84754
binsize = 0.923769 -> bins = 8 11 11
# Start Run #1
log log.nodrag

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LAMMPS (15 Feb 2016)
# 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:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.84754
ghost atom cutoff = 1.84754
binsize = 0.923769 -> bins = 8 11 11
Memory usage per processor = 3.63062 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 -4.5046204e-13 -4.92206e-13 -4.9610344e-13 6.9780266 9.8684199 9.8684199
Loop time of 0.0294001 on 4 procs for 134 steps with 1000 atoms
99.5% CPU use with 4 MPI tasks x no OpenMP threads
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 5.80609e-10
Force max component initial, final = 1960.27 3.41627e-10
Final line search alpha, max atom move = 1 3.41627e-10
Iterations, force evaluations = 134 137
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.015008 | 0.017768 | 0.020491 | 1.5 | 60.43
Neigh | 0.00022388 | 0.0002709 | 0.00032783 | 0.2 | 0.92
Comm | 0.0022066 | 0.0049043 | 0.0076346 | 2.8 | 16.68
Output | 1.5974e-05 | 1.6928e-05 | 1.9789e-05 | 0.0 | 0.06
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.00644 | | | 21.91
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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.84754
ghost atom cutoff = 1.84754
binsize = 0.923769 -> bins = 8 11 11
# Start Run #1
log log.nodrag

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LAMMPS (15 Feb 2016)
# 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 882.849286914813 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:445)
#dump 1 all atom 250 dump.indent
#dump 2 all image 1000 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 30000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 17 15 1
Memory usage per processor = 2.4697 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 0.66485023 441.13781
13000 0.1194298 -3.0579575 0 -2.9558734 1.0884087 437.72805
14000 0.12310404 -3.051382 0 -2.9461573 0.87077685 445.54012
15000 0.11148458 -3.0402208 0 -2.944928 1.0040641 451.9079
16000 0.12322323 -3.041552 0 -2.9362254 0.7581871 456.90367
17000 0.12311085 -3.0300334 0 -2.9248029 1.0483261 452.91646
18000 0.12062509 -3.0261636 0 -2.9230579 1.3983564 451.71896
19000 0.11957854 -3.0142948 0 -2.9120836 1.3961883 457.92501
20000 0.12230825 -3.0015681 0 -2.8970237 1.1238267 470.13177
21000 0.1206722 -3.0280371 0 -2.9248911 0.77173089 472.88673
22000 0.11522969 -3.0159631 0 -2.9174691 0.58945089 474.56136
23000 0.1169292 -3.0257398 0 -2.9257932 0.90016236 473.58055
24000 0.11814748 -3.0288882 0 -2.9279002 0.85469502 469.82134
25000 0.11141357 -3.0218783 0 -2.9266463 1.0469177 471.01085
26000 0.11159246 -3.0122701 0 -2.9168851 1.1216321 471.99194
27000 0.10918089 -3.0045635 0 -2.9112398 1.2920286 474.41152
28000 0.1183178 -3.0017823 0 -2.9006488 1.3477212 474.08453
29000 0.118332 -2.9855957 0 -2.88445 1.4002777 478.49231
30000 0.11691453 -2.9721091 0 -2.872175 1.6266108 479.0394
Loop time of 2.46597 on 1 procs for 30000 steps with 420 atoms
Performance: 3153322.983 tau/day, 12165.598 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8479 | 1.8479 | 1.8479 | 0.0 | 74.94
Neigh | 0.078045 | 0.078045 | 0.078045 | 0.0 | 3.16
Comm | 0.026873 | 0.026873 | 0.026873 | 0.0 | 1.09
Output | 0.00028443 | 0.00028443 | 0.00028443 | 0.0 | 0.01
Modify | 0.44704 | 0.44704 | 0.44704 | 0.0 | 18.13
Other | | 0.06581 | | | 2.67
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 111 ave 111 max 111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3711 ave 3711 max 3711 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3711
Ave neighs/atom = 8.83571
Neighbor list builds = 614
Dangerous builds = 0
# run without indenter
unfix 4
run 30000
Memory usage per processor = 2.46978 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.11691453 -2.9721091 0 -2.872175 1.6267079 479.0108
31000 0.10925212 -3.0270482 0 -2.9336637 -0.33277278 488.93429
32000 0.11439597 -2.9975157 0 -2.8997344 -0.41937391 489.30458
33000 0.1202415 -3.0272086 0 -2.9244307 0.45435486 481.29876
34000 0.12236916 -3.0291826 0 -2.9245861 0.060773047 480.57112
35000 0.10701052 -3.0155083 0 -2.9240398 -0.32828426 491.34913
36000 0.11671309 -3.0501978 0 -2.9504359 0.17774604 480.03548
37000 0.11311041 -3.0472325 0 -2.9505501 -0.096250401 480.52043
38000 0.11671309 -3.0386964 0 -2.9389345 -0.26914235 481.1656
39000 0.127378 -3.0478959 0 -2.9390181 -0.11503417 478.38488
40000 0.11422635 -3.0479185 0 -2.9502821 -0.11840551 479.29223
41000 0.11339443 -3.0470107 0 -2.9500855 -0.36658233 484.33262
42000 0.11750945 -3.0506884 0 -2.9502458 -0.18687218 482.18706
43000 0.10968886 -3.0433967 0 -2.9496388 -0.23827778 483.87888
44000 0.11163929 -3.0449886 0 -2.9495636 -0.2241347 482.09898
45000 0.11726053 -3.0498339 0 -2.9496041 -0.03707734 480.27988
46000 0.10971187 -3.0434544 0 -2.9496769 -0.311219 482.26813
47000 0.11448154 -3.0476146 0 -2.9497602 -0.10374643 480.75372
48000 0.11796515 -3.0503583 0 -2.9495262 -0.18534074 479.03433
49000 0.11331324 -3.0464609 0 -2.9496051 -0.38382421 483.23363
50000 0.1102072 -3.043921 0 -2.94972 -0.11678189 481.28121
51000 0.11169997 -3.0449271 0 -2.9494503 -0.22869529 483.39421
52000 0.1052379 -3.0396306 0 -2.9496773 -0.264831 479.77275
53000 0.12170796 -3.0536766 0 -2.9496453 -0.14056206 482.58519
54000 0.11347849 -3.0465613 0 -2.9495642 -0.23137478 481.27
55000 0.115223 -3.0480538 0 -2.9495655 -0.32336031 485.15401
56000 0.11115417 -3.044689 0 -2.9496787 -0.066353134 481.37281
57000 0.10783414 -3.0418895 0 -2.949717 -0.20380917 482.14483
58000 0.10703451 -3.04105 0 -2.949561 -0.2673909 482.03847
59000 0.11041464 -3.0439806 0 -2.9496023 -0.17616699 481.33957
60000 0.12014097 -3.05226 0 -2.949568 -0.21176633 481.15213
Loop time of 2.13712 on 1 procs for 30000 steps with 420 atoms
Performance: 3638544.822 tau/day, 14037.596 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7832 | 1.7832 | 1.7832 | 0.0 | 83.44
Neigh | 0.074649 | 0.074649 | 0.074649 | 0.0 | 3.49
Comm | 0.02573 | 0.02573 | 0.02573 | 0.0 | 1.20
Output | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.01
Modify | 0.19673 | 0.19673 | 0.19673 | 0.0 | 9.21
Other | | 0.05655 | | | 2.65
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 106 ave 106 max 106 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3578 ave 3578 max 3578 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3578
Ave neighs/atom = 8.51905
Neighbor list builds = 617
Dangerous builds = 0
Total wall time: 0:00:04

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LAMMPS (15 Feb 2016)
# 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 882.849286914813 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:445)
#dump 1 all atom 250 dump.indent
#dump 2 all image 1000 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 30000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 17 15 1
Memory usage per processor = 2.47636 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 0.1084272 -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 0.85709169 442.10189
15000 0.11934084 -3.0498848 0 -2.9478768 1.0392201 451.74396
16000 0.12576913 -3.045218 0 -2.9377154 1.3479479 441.2702
17000 0.11546579 -3.0348367 0 -2.9361409 1.631821 439.48441
18000 0.12148869 -3.0221152 0 -2.9182713 1.6088855 449.25443
19000 0.11883863 -3.0036777 0 -2.902099 1.5201108 447.12736
20000 0.11163567 -3.0038144 0 -2.9083924 1.4078554 461.76339
21000 0.11361999 -2.9900869 0 -2.8929688 1.1334192 473.91362
22000 0.12696379 -3.0207381 0 -2.9122143 0.83288039 473.02925
23000 0.1188706 -3.01731 0 -2.915704 1.1482286 468.57874
24000 0.11820885 -3.0098527 0 -2.9088123 0.98884958 472.75675
25000 0.11671309 -3.0101308 0 -2.9103689 1.2402973 469.77097
26000 0.11965934 -3.0091118 0 -2.9068315 0.94844832 469.04458
27000 0.12147721 -3.0085715 0 -2.9047374 1.2363584 474.98572
28000 0.11718062 -2.993818 0 -2.8936565 1.143781 478.94786
29000 0.10922042 -2.9873887 0 -2.8940313 1.6184815 473.13968
30000 0.11475456 -2.9749758 0 -2.876888 1.8682946 472.49357
Loop time of 1.12298 on 4 procs for 30000 steps with 420 atoms
Performance: 6924409.691 tau/day, 26714.544 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.41457 | 0.4817 | 0.52191 | 6.4 | 42.89
Neigh | 0.017548 | 0.01979 | 0.022012 | 1.5 | 1.76
Comm | 0.22983 | 0.30219 | 0.38513 | 12.2 | 26.91
Output | 0.00051403 | 0.00054651 | 0.00063753 | 0.2 | 0.05
Modify | 0.1947 | 0.2007 | 0.20671 | 1.3 | 17.87
Other | | 0.1181 | | | 10.51
Nlocal: 105 ave 115 max 90 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 96.25 ave 104 max 87 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 931.25 ave 1078 max 743 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 3725
Ave neighs/atom = 8.86905
Neighbor list builds = 608
Dangerous builds = 0
# run without indenter
unfix 4
run 30000
Memory usage per processor = 2.47641 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
30000 0.11475456 -2.9749758 0 -2.876888 1.8675667 472.67773
31000 0.11574891 -3.0442299 0 -2.9452921 -0.72600606 489.16618
32000 0.11316772 -3.0299575 0 -2.933226 -0.74912451 483.50803
33000 0.12321675 -3.052617 0 -2.947296 0.29368262 473.07336
34000 0.11671309 -3.0470741 0 -2.9473122 -0.46988097 480.59621
35000 0.11671309 -3.0456501 0 -2.9458882 -0.74504498 475.07349
36000 0.11980973 -3.0797043 0 -2.9772955 0.083053833 461.14624
37000 0.10992033 -3.0712499 0 -2.9772942 -0.6447083 468.1598
38000 0.11831288 -3.0676136 0 -2.9664842 -0.59676518 469.61724
39000 0.11663782 -3.0775961 0 -2.9778985 0.21776888 460.87504
40000 0.10805913 -3.0688733 0 -2.9765084 -0.59632811 469.15555
41000 0.12118734 -3.0800988 0 -2.9765125 -0.32401944 466.81124
42000 0.12373313 -3.0822746 0 -2.9765123 -0.0033603954 462.85792
43000 0.1078275 -3.0686759 0 -2.976509 -0.71758451 469.60392
44000 0.12315017 -3.0787716 0 -2.9735076 -0.05619902 463.06786
45000 0.11564078 -3.0833684 0 -2.9845231 -0.36953273 465.92986
46000 0.10640706 -3.0654913 0 -2.9745386 -0.53685976 469.3539
47000 0.11810977 -3.0754985 0 -2.9745428 0.088083121 463.20699
48000 0.11241387 -3.0828874 0 -2.9868003 -0.54828531 466.25548
49000 0.11679121 -3.0748686 0 -2.9750399 -0.33781022 465.50451
50000 0.11656344 -3.07471 0 -2.9750761 -0.054088803 461.22814
51000 0.12060058 -3.0781622 0 -2.9750774 -0.55815121 468.81379
52000 0.11936306 -3.0876851 0 -2.9856581 -0.34773758 464.10154
53000 0.11032135 -3.0799138 0 -2.9856153 -0.1735616 465.533
54000 0.12365261 -3.0737021 0 -2.9680086 -0.52954909 468.29003
55000 0.12763641 -3.0771061 0 -2.9680074 -0.17884875 464.79749
56000 0.12638245 -3.0879132 0 -2.9798863 -0.2754242 464.35767
57000 0.11481136 -3.0780176 0 -2.9798812 -0.45547532 468.09393
58000 0.11858604 -3.0812503 0 -2.9798874 -0.17502776 463.2168
59000 0.11344551 -3.0768536 0 -2.9798847 -0.32382437 465.29204
60000 0.11637998 -3.0793607 0 -2.9798836 -0.45942931 466.04868
Loop time of 0.939672 on 4 procs for 30000 steps with 420 atoms
Performance: 8275230.111 tau/day, 31926.042 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.40284 | 0.47452 | 0.51851 | 6.7 | 50.50
Neigh | 0.017638 | 0.020592 | 0.023174 | 1.7 | 2.19
Comm | 0.21243 | 0.28882 | 0.37711 | 12.8 | 30.74
Output | 0.00049996 | 0.00052589 | 0.00059867 | 0.2 | 0.06
Modify | 0.052075 | 0.056787 | 0.061078 | 1.7 | 6.04
Other | | 0.09843 | | | 10.47
Nlocal: 105 ave 112 max 98 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 92.5 ave 96 max 89 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 892.25 ave 1003 max 788 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 3569
Ave neighs/atom = 8.49762
Neighbor list builds = 634
Dangerous builds = 0
Total wall time: 0:00:02

452
examples/indent/log.15Feb16.indent.min.g++.1 Normal file
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LAMMPS (15 Feb 2016)
# 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 2 all image 25 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 25 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 17 15 1
Memory usage per processor = 3.5947 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333
10 0 -3.1815908 0 -3.1815908 -1.1226904 440.57558
20 0 -3.1895471 0 -3.1895471 -0.86027602 436.93033
30 0 -3.1908366 0 -3.1908366 -0.72179223 436.93033
35 0 -3.1909386 0 -3.1909386 -0.69788745 433.53082
Loop time of 0.00924516 on 1 procs for 35 steps with 420 atoms
97.3% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3.17275755126 -3.19093697812 -3.19093855395
Force two-norm initial, final = 6.74302 0.230475
Force max component initial, final = 1.46877 0.0236603
Final line search alpha, max atom move = 1 0.0236603
Iterations, force evaluations = 35 70
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0078757 | 0.0078757 | 0.0078757 | 0.0 | 85.19
Neigh | 0.0004518 | 0.0004518 | 0.0004518 | 0.0 | 4.89
Comm | 8.0109e-05 | 8.0109e-05 | 8.0109e-05 | 0.0 | 0.87
Output | 2.5749e-05 | 2.5749e-05 | 2.5749e-05 | 0.0 | 0.28
Modify | 0.00010729 | 0.00010729 | 0.00010729 | 0.0 | 1.16
Other | | 0.0007045 | | | 7.62
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 4414.24643457407 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:168)
Memory usage per processor = 3.5947 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
35 0 -3.1909386 0 -2.174369 -0.6944516 435.67574
40 0 -3.1462704 0 -3.1261242 -0.20646557 435.67534
50 0 -3.174757 0 -3.173603 -0.34916248 436.00326
60 0 -3.1789904 0 -3.1780198 -0.31146423 436.06053
70 0 -3.1800572 0 -3.1792392 -0.27664904 436.09293
80 0 -3.1808315 0 -3.1799813 -0.24091474 435.00572
90 0 -3.1810856 0 -3.1803991 -0.1771392 433.03804
100 0 -3.1812307 0 -3.1805381 -0.15305004 434.96379
110 0 -3.1812588 0 -3.1805938 -0.12504604 432.50683
111 0 -3.1812728 0 -3.1805961 -0.12407116 432.50683
Loop time of 0.0215449 on 1 procs for 76 steps with 420 atoms
102.1% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.17436899358 -3.18059381924 -3.18059607055
Force two-norm initial, final = 1618.56 0.444006
Force max component initial, final = 1191.42 0.168708
Final line search alpha, max atom move = 0.428869 0.0723538
Iterations, force evaluations = 76 147
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.016444 | 0.016444 | 0.016444 | 0.0 | 76.33
Neigh | 0.0022733 | 0.0022733 | 0.0022733 | 0.0 | 10.55
Comm | 0.0001955 | 0.0001955 | 0.0001955 | 0.0 | 0.91
Output | 5.7459e-05 | 5.7459e-05 | 5.7459e-05 | 0.0 | 0.27
Modify | 0.00096774 | 0.00096774 | 0.00096774 | 0.0 | 4.49
Other | | 0.001607 | | | 7.46
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: 3596 ave 3596 max 3596 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3596
Ave neighs/atom = 8.5619
Neighbor list builds = 19
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.5 0 6.0
fix 4 all indent 882.849286914813 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:168)
Memory usage per processor = 3.5947 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
111 0 -3.1812728 0 -0.21796953 -0.12362158 434.07977
120 0 -2.9592755 0 -2.8003562 1.9418398 434.0832
130 0 -3.0632093 0 -3.0453082 1.4275815 434.09622
140 0 -3.0947739 0 -3.0852867 1.2276154 434.51983
150 0 -3.1008901 0 -3.0931811 1.1938163 434.52998
160 0 -3.1026159 0 -3.0950306 1.2229151 434.35672
170 0 -3.1032959 0 -3.0962512 1.3134391 432.20445
180 0 -3.1041304 0 -3.0969544 1.3751461 430.37017
190 0 -3.1043441 0 -3.0970791 1.392095 430.37017
193 0 -3.1043345 0 -3.0970891 1.3934777 430.37017
Loop time of 0.022316 on 1 procs for 82 steps with 420 atoms
103.1% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.217969533586 -3.09708660422 -3.09708908043
Force two-norm initial, final = 1754.38 0.648372
Force max component initial, final = 924.68 0.156564
Final line search alpha, max atom move = 0.961384 0.150518
Iterations, force evaluations = 82 156
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.017607 | 0.017607 | 0.017607 | 0.0 | 78.90
Neigh | 0.0018115 | 0.0018115 | 0.0018115 | 0.0 | 8.12
Comm | 0.00016046 | 0.00016046 | 0.00016046 | 0.0 | 0.72
Output | 5.8413e-05 | 5.8413e-05 | 5.8413e-05 | 0.0 | 0.26
Modify | 0.0010521 | 0.0010521 | 0.0010521 | 0.0 | 4.71
Other | | 0.001626 | | | 7.29
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: 3666 ave 3666 max 3666 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3666
Ave neighs/atom = 8.72857
Neighbor list builds = 14
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.0 0 6.0
fix 4 all indent 882.849286914813 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:168)
Memory usage per processor = 3.5947 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
193 0 -3.1043345 0 2.0111862 1.3910056 431.13503
200 0 -2.5918177 0 -1.931934 5.51119 430.91952
210 0 -2.8122285 0 -2.7440908 4.2686845 440.18379
220 0 -2.9102892 0 -2.8879734 3.5957736 444.98944
230 0 -2.9492295 0 -2.9335905 3.2079493 451.92209
240 0 -2.9611099 0 -2.9486963 3.1240398 452.59159
250 0 -2.9644912 0 -2.9549723 3.0493724 455.54273
260 0 -2.9716881 0 -2.9621479 2.8585653 458.29826
270 0 -3.0142839 0 -3.0048107 2.1183076 462.48471
280 0 -3.0666108 0 -3.0590819 1.4342986 470.61174
290 0 -3.1004306 0 -3.0944504 1.1550298 472.70399
300 0 -3.1107855 0 -3.1043751 1.0663324 470.76888
310 0 -3.1124671 0 -3.1059633 1.0375877 473.02275
316 0 -3.1126981 0 -3.1061297 1.0266662 473.02275
Loop time of 0.0393021 on 1 procs for 123 steps with 420 atoms
99.2% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
2.01118618013 -3.10612971775 -3.10612971775
Force two-norm initial, final = 2329.79 2.56384
Force max component initial, final = 1038.4 0.558457
Final line search alpha, max atom move = 6.21371e-07 3.47009e-07
Iterations, force evaluations = 123 270
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.030668 | 0.030668 | 0.030668 | 0.0 | 78.03
Neigh | 0.0037498 | 0.0037498 | 0.0037498 | 0.0 | 9.54
Comm | 0.00033641 | 0.00033641 | 0.00033641 | 0.0 | 0.86
Output | 8.6069e-05 | 8.6069e-05 | 8.6069e-05 | 0.0 | 0.22
Modify | 0.0017693 | 0.0017693 | 0.0017693 | 0.0 | 4.50
Other | | 0.002692 | | | 6.85
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: 3583 ave 3583 max 3583 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3583
Ave neighs/atom = 8.53095
Neighbor list builds = 29
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.4 0 6.0
fix 4 all indent 882.849286914813 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:168)
Memory usage per processor = 3.5947 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
316 0 -3.1126981 0 5.3552772 1.0307152 471.16452
320 0 -2.7131804 0 0.70918694 3.910187 471.16482
330 0 -2.5180572 0 -2.2327154 5.9511047 472.82589
340 0 -2.8183947 0 -2.790733 4.18655 477.34785
350 0 -2.9132456 0 -2.8943586 3.4322048 481.94491
360 0 -2.9337359 0 -2.9225123 3.2341233 484.63169
370 0 -2.9463892 0 -2.9382426 3.0071366 485.20235
380 0 -2.9682176 0 -2.9597318 2.6056737 490.5653
390 0 -2.9878255 0 -2.974755 2.3632883 491.02616
400 0 -3.0033473 0 -2.9915257 2.205124 490.20353
410 0 -3.0130231 0 -3.001125 2.0531631 492.78365
420 0 -3.0146089 0 -3.0030496 1.9865701 492.35543
430 0 -3.0344603 0 -3.0225619 1.6795534 494.30371
440 0 -3.03943 0 -3.0271752 1.64578 494.30371
450 0 -3.0420658 0 -3.0294992 1.6461313 493.96169
460 0 -3.0443144 0 -3.0312966 1.6701433 493.56812
465 0 -3.0444584 0 -3.0313908 1.6713796 493.56812
Loop time of 0.0470922 on 1 procs for 149 steps with 420 atoms
99.8% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
5.35527716926 -3.03139082546 -3.03139082546
Force two-norm initial, final = 3151.59 4.64631
Force max component initial, final = 1384.28 2.19626
Final line search alpha, max atom move = 1.88135e-07 4.13193e-07
Iterations, force evaluations = 149 323
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.036967 | 0.036967 | 0.036967 | 0.0 | 78.50
Neigh | 0.004194 | 0.004194 | 0.004194 | 0.0 | 8.91
Comm | 0.00037503 | 0.00037503 | 0.00037503 | 0.0 | 0.80
Output | 0.00010633 | 0.00010633 | 0.00010633 | 0.0 | 0.23
Modify | 0.002212 | 0.002212 | 0.002212 | 0.0 | 4.70
Other | | 0.003238 | | | 6.88
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 113 ave 113 max 113 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3693 ave 3693 max 3693 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3693
Ave neighs/atom = 8.79286
Neighbor list builds = 33
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.2 0 6.0
fix 4 all indent 882.849286914813 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:168)
Memory usage per processor = 3.59478 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
465 0 -3.0444584 0 -2.5580192 1.6715946 493.50462
470 0 -2.9426683 0 -2.8814986 2.6421083 493.54443
480 0 -2.9569251 0 -2.9256743 2.6206554 493.55709
490 0 -2.961805 0 -2.9376884 2.6095523 493.40001
500 0 -2.9651536 0 -2.9450214 2.6314399 493.06356
510 0 -2.9667772 0 -2.9489178 2.6710408 492.70775
520 0 -2.9728188 0 -2.9566496 2.7182742 492.38186
530 0 -2.9791224 0 -2.9651707 2.7038256 493.19977
540 0 -2.9968316 0 -2.984276 2.5920672 495.29778
550 0 -3.0029515 0 -2.9915532 2.4491025 500.52622
560 0 -3.0160794 0 -3.0057787 2.0399831 513.34527
570 0 -3.0363001 0 -3.0306173 1.6834763 520.40445
580 0 -3.0548101 0 -3.0490935 1.501103 521.5353
590 0 -3.0640876 0 -3.0585539 1.3888581 520.17883
600 0 -3.0713144 0 -3.0649318 1.3341898 518.99349
610 0 -3.0727361 0 -3.0662278 1.2983097 519.87058
620 0 -3.0732598 0 -3.0671664 1.2611866 520.9829
630 0 -3.076528 0 -3.069576 1.1930176 520.18857
640 0 -3.0778611 0 -3.0710808 1.1946248 520.31492
650 0 -3.0781525 0 -3.0715363 1.2031624 520.31492
651 0 -3.0781525 0 -3.0715363 1.2031624 520.31492
Loop time of 0.057997 on 1 procs for 186 steps with 420 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-2.55801918976 -3.07153633363 -3.07153633363
Force two-norm initial, final = 440.856 1.45625
Force max component initial, final = 245.987 0.411517
Final line search alpha, max atom move = 1.25651e-06 5.17073e-07
Iterations, force evaluations = 186 403
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.045592 | 0.045592 | 0.045592 | 0.0 | 78.61
Neigh | 0.0050173 | 0.0050173 | 0.0050173 | 0.0 | 8.65
Comm | 0.00052071 | 0.00052071 | 0.00052071 | 0.0 | 0.90
Output | 0.00014472 | 0.00014472 | 0.00014472 | 0.0 | 0.25
Modify | 0.0027096 | 0.0027096 | 0.0027096 | 0.0 | 4.67
Other | | 0.004013 | | | 6.92
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: 3622 ave 3622 max 3622 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3622
Ave neighs/atom = 8.62381
Neighbor list builds = 39
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.0 0 6.0
fix 4 all indent 882.849286914813 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:168)
Memory usage per processor = 3.59487 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
651 0 -3.0781525 0 -2.6488207 1.2032064 520.29591
660 0 -3.0085949 0 -2.9796645 1.9715308 520.26872
670 0 -3.014536 0 -2.9989599 2.0077209 520.35057
680 0 -3.0193861 0 -3.0073499 2.0050119 520.52555
690 0 -3.0214256 0 -3.0087927 2.0056587 520.37174
700 0 -3.0218644 0 -3.0095894 2.0386389 520.05804
710 0 -3.0262571 0 -3.0142277 2.1356802 520.14691
720 0 -3.0325017 0 -3.0216037 2.1065924 521.43634
730 0 -3.0400735 0 -3.0302631 2.0146233 523.09133
740 0 -3.048476 0 -3.0386288 1.9305047 523.14231
750 0 -3.0523937 0 -3.042131 1.9025403 522.0453
760 0 -3.0544932 0 -3.044222 1.9106706 521.73287
770 0 -3.0587698 0 -3.048907 1.9552463 521.6899
780 0 -3.065994 0 -3.0566273 1.931796 521.52157
790 0 -3.0675084 0 -3.0577936 1.9283059 520.99202
799 0 -3.0677005 0 -3.057959 1.9288603 520.99202
Loop time of 0.046221 on 1 procs for 148 steps with 420 atoms
99.5% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-2.64882068661 -3.05795898949 -3.05795898949
Force two-norm initial, final = 420.333 1.17649
Force max component initial, final = 194.656 0.28552
Final line search alpha, max atom move = 1.95857e-06 5.5921e-07
Iterations, force evaluations = 148 327
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.036542 | 0.036542 | 0.036542 | 0.0 | 79.06
Neigh | 0.0038009 | 0.0038009 | 0.0038009 | 0.0 | 8.22
Comm | 0.00038958 | 0.00038958 | 0.00038958 | 0.0 | 0.84
Output | 9.8705e-05 | 9.8705e-05 | 9.8705e-05 | 0.0 | 0.21
Modify | 0.0021958 | 0.0021958 | 0.0021958 | 0.0 | 4.75
Other | | 0.003194 | | | 6.91
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 122 ave 122 max 122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3612 ave 3612 max 3612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3612
Ave neighs/atom = 8.6
Neighbor list builds = 30
Dangerous builds = 0
Total wall time: 0:00:00

445
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LAMMPS (15 Feb 2016)
# 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 2 all image 25 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 25 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
minimize 1.0e-6 1.0e-6 1000 1000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 17 15 1
Memory usage per processor = 3.60136 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333
10 0 -3.1815908 0 -3.1815908 -1.1226904 440.57558
20 0 -3.1895471 0 -3.1895471 -0.86027602 436.93033
30 0 -3.1908366 0 -3.1908366 -0.72179223 436.93033
35 0 -3.1909386 0 -3.1909386 -0.69788745 433.53082
Loop time of 0.00339699 on 4 procs for 35 steps with 420 atoms
95.7% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3.17275755126 -3.19093697812 -3.19093855395
Force two-norm initial, final = 6.74302 0.230475
Force max component initial, final = 1.46877 0.0236603
Final line search alpha, max atom move = 1 0.0236603
Iterations, force evaluations = 35 70
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0019855 | 0.002022 | 0.0020628 | 0.1 | 59.52
Neigh | 0.00012016 | 0.00012463 | 0.00012922 | 0.0 | 3.67
Comm | 0.00034857 | 0.00041682 | 0.00048089 | 0.3 | 12.27
Output | 3.7909e-05 | 4.0412e-05 | 4.6968e-05 | 0.1 | 1.19
Modify | 3.2663e-05 | 3.8743e-05 | 4.4823e-05 | 0.1 | 1.14
Other | | 0.0007544 | | | 22.21
Nlocal: 105 ave 111 max 99 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 84 ave 90 max 78 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 895 ave 999 max 798 min
Histogram: 2 0 0 0 0 0 0 0 0 2
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 4414.24643457407 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:168)
Memory usage per processor = 3.60136 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
35 0 -3.1909386 0 -2.174369 -0.6944516 435.67574
40 0 -3.1462704 0 -3.1261242 -0.20646557 435.67534
50 0 -3.174757 0 -3.173603 -0.34916248 436.00326
60 0 -3.1789904 0 -3.1780198 -0.31146423 436.06053
70 0 -3.1800572 0 -3.1792392 -0.27664904 436.09293
80 0 -3.1808315 0 -3.1799813 -0.24091474 435.00572
90 0 -3.1810856 0 -3.1803991 -0.17713919 433.03804
100 0 -3.1812307 0 -3.1805381 -0.15305002 434.96379
110 0 -3.1812588 0 -3.1805938 -0.12504601 432.50683
111 0 -3.1812728 0 -3.1805961 -0.12407115 432.50683
Loop time of 0.00934356 on 4 procs for 76 steps with 420 atoms
91.0% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.17436899358 -3.18059381928 -3.18059607058
Force two-norm initial, final = 1618.56 0.444005
Force max component initial, final = 1191.42 0.168709
Final line search alpha, max atom move = 0.428871 0.0723543
Iterations, force evaluations = 76 147
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0039222 | 0.0042289 | 0.0045605 | 0.5 | 45.26
Neigh | 0.00056624 | 0.00060999 | 0.00065136 | 0.2 | 6.53
Comm | 0.0011964 | 0.0017179 | 0.0022454 | 1.1 | 18.39
Output | 0.00011611 | 0.0001232 | 0.000139 | 0.1 | 1.32
Modify | 0.00025821 | 0.00028563 | 0.0003078 | 0.1 | 3.06
Other | | 0.002378 | | | 25.45
Nlocal: 105 ave 111 max 99 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 87 ave 90 max 84 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 899 ave 1001 max 797 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 3596
Ave neighs/atom = 8.5619
Neighbor list builds = 19
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.5 0 6.0
fix 4 all indent 882.849286914813 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:168)
Memory usage per processor = 3.60136 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
111 0 -3.1812728 0 -0.21796955 -0.12362156 434.07977
120 0 -2.9592755 0 -2.8003562 1.9418398 434.0832
130 0 -3.0632093 0 -3.0453082 1.4275815 434.09622
140 0 -3.0947739 0 -3.0852867 1.2276154 434.51983
150 0 -3.1008901 0 -3.0931811 1.1938163 434.52998
160 0 -3.1026159 0 -3.0950306 1.2229151 434.35672
170 0 -3.1032959 0 -3.0962512 1.3134388 432.20444
180 0 -3.1041304 0 -3.0969544 1.3751455 430.37021
190 0 -3.1043441 0 -3.0970791 1.3920926 430.37021
193 0 -3.1043346 0 -3.0970891 1.3934753 430.37021
Loop time of 0.0095458 on 4 procs for 82 steps with 420 atoms
94.3% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.217969552445 -3.09708660005 -3.09708907864
Force two-norm initial, final = 1754.38 0.649535
Force max component initial, final = 924.68 0.156756
Final line search alpha, max atom move = 0.962047 0.150807
Iterations, force evaluations = 82 156
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0040784 | 0.0045295 | 0.00495 | 0.6 | 47.45
Neigh | 0.00041556 | 0.00045681 | 0.0004952 | 0.2 | 4.79
Comm | 0.0011504 | 0.0016876 | 0.0022304 | 1.2 | 17.68
Output | 0.00012088 | 0.00012857 | 0.000144 | 0.1 | 1.35
Modify | 0.00027156 | 0.00029528 | 0.00032377 | 0.1 | 3.09
Other | | 0.002448 | | | 25.65
Nlocal: 105 ave 112 max 98 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 94 ave 97 max 91 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 916.5 ave 1013 max 831 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 3666
Ave neighs/atom = 8.72857
Neighbor list builds = 14
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 12.0 0 6.0
fix 4 all indent 882.849286914813 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:168)
Memory usage per processor = 3.60136 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
193 0 -3.1043346 0 2.0111873 1.3910032 431.13505
200 0 -2.5918062 0 -1.93191 5.511262 430.91953
210 0 -2.8122299 0 -2.7440894 4.2686747 440.18337
220 0 -2.910295 0 -2.8879715 3.5956981 444.98997
230 0 -2.949231 0 -2.9335905 3.2079519 451.9225
240 0 -2.9611012 0 -2.9486911 3.1241334 452.5907
250 0 -2.9644798 0 -2.9549529 3.0499305 455.51712
260 0 -2.9716705 0 -2.9621358 2.8593553 458.27346
270 0 -3.0143454 0 -3.0048234 2.1158458 462.52748
280 0 -3.0656896 0 -3.0590412 1.4428324 470.69566
290 0 -3.1008608 0 -3.0951203 1.1487473 472.80734
300 0 -3.1109522 0 -3.1046995 1.064904 470.50807
310 0 -3.1123989 0 -3.105985 1.0430839 470.40952
313 0 -3.1125022 0 -3.1060453 1.0390872 470.40952
Loop time of 0.0165539 on 4 procs for 120 steps with 420 atoms
92.1% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
2.01118731028 -3.10604533837 -3.10604533837
Force two-norm initial, final = 2329.79 2.39232
Force max component initial, final = 1038.4 0.571422
Final line search alpha, max atom move = 7.76258e-07 4.43571e-07
Iterations, force evaluations = 120 264
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0066144 | 0.0077118 | 0.0089424 | 1.2 | 46.59
Neigh | 0.0008266 | 0.00094324 | 0.0010567 | 0.3 | 5.70
Comm | 0.0018625 | 0.0032995 | 0.0045738 | 2.2 | 19.93
Output | 0.00018287 | 0.00019288 | 0.00021982 | 0.1 | 1.17
Modify | 0.00045705 | 0.00051093 | 0.00056267 | 0.2 | 3.09
Other | | 0.003896 | | | 23.53
Nlocal: 105 ave 123 max 90 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 91 ave 100 max 85 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Neighs: 892.25 ave 1107 max 699 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 3569
Ave neighs/atom = 8.49762
Neighbor list builds = 28
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.4 0 6.0
fix 4 all indent 882.849286914813 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:168)
Memory usage per processor = 3.60136 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
313 0 -3.1125022 0 5.3341053 1.0377311 471.02427
320 0 -2.402824 0 -0.86170235 6.1550233 471.02943
330 0 -2.5964265 0 -2.4563494 5.5893601 473.87197
340 0 -2.857458 0 -2.8325789 3.9156904 478.37268
350 0 -2.923244 0 -2.9056267 3.3461026 481.81668
360 0 -2.9355414 0 -2.924236 3.2437289 484.05209
370 0 -2.9486011 0 -2.9405396 2.9295065 487.64545
380 0 -2.9695687 0 -2.9616077 2.5116249 491.53648
390 0 -2.991356 0 -2.9786736 2.2788393 491.056
400 0 -3.0098108 0 -2.9963408 2.0798685 490.87751
410 0 -3.0142937 0 -3.0017605 2.0015139 491.52711
417 0 -3.0148998 0 -3.0024932 1.9909706 492.48053
Loop time of 0.0134063 on 4 procs for 104 steps with 420 atoms
95.1% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
5.33410533222 -3.00249023582 -3.00249317367
Force two-norm initial, final = 3147.64 2.97401
Force max component initial, final = 1384.36 0.679769
Final line search alpha, max atom move = 0.14124 0.0960107
Iterations, force evaluations = 104 200
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0046661 | 0.0059155 | 0.0071743 | 1.5 | 44.13
Neigh | 0.00073218 | 0.00090402 | 0.0010717 | 0.5 | 6.74
Comm | 0.001442 | 0.0029395 | 0.0044417 | 2.5 | 21.93
Output | 0.00014901 | 0.00015819 | 0.00018287 | 0.1 | 1.18
Modify | 0.0003469 | 0.00039375 | 0.0004406 | 0.2 | 2.94
Other | | 0.003095 | | | 23.09
Nlocal: 105 ave 121 max 89 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 93.5 ave 101 max 86 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 936 ave 1121 max 741 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3744
Ave neighs/atom = 8.91429
Neighbor list builds = 27
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.2 0 6.0
fix 4 all indent 882.849286914813 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:168)
Memory usage per processor = 3.60141 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
417 0 -3.0148998 0 -2.4816986 1.9918498 492.26314
420 0 -2.9209943 0 -2.7871779 2.8201475 492.26417
430 0 -2.9210322 0 -2.8866221 3.0115293 492.22119
440 0 -2.930174 0 -2.9072946 3.0289241 491.74253
450 0 -2.9423694 0 -2.9251127 3.0269322 491.55578
460 0 -2.9595882 0 -2.9424058 2.8769376 491.29122
470 0 -2.9716874 0 -2.9531385 2.7820875 491.71167
480 0 -2.9967793 0 -2.9798492 2.5135722 493.20335
490 0 -3.0077594 0 -2.9927399 2.3652753 495.90598
500 0 -3.0156527 0 -3.0064227 2.2002124 502.94121
510 0 -3.0389075 0 -3.0316863 1.8518803 512.1298
520 0 -3.0533374 0 -3.0444153 1.6968184 511.35747
530 0 -3.0643133 0 -3.0573978 1.5165159 516.34223
540 0 -3.0958216 0 -3.0905446 1.0627598 519.02979
550 0 -3.1051578 0 -3.1009512 1.0050567 517.17039
560 0 -3.1119271 0 -3.1069923 0.92711525 515.78315
570 0 -3.114104 0 -3.1090684 0.9237051 515.34157
580 0 -3.114576 0 -3.1094219 0.9181339 515.34157
590 0 -3.114722 0 -3.1095528 0.90665975 515.99746
600 0 -3.1149189 0 -3.1096744 0.88783587 515.99746
605 0 -3.1149612 0 -3.1097106 0.88187936 515.99746
Loop time of 0.0259686 on 4 procs for 188 steps with 420 atoms
100.1% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-2.48169863396 -3.10971061979 -3.10971061979
Force two-norm initial, final = 470.636 1.194
Force max component initial, final = 222.162 0.376608
Final line search alpha, max atom move = 2.92234e-06 1.10058e-06
Iterations, force evaluations = 188 401
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0087585 | 0.011606 | 0.014545 | 2.6 | 44.69
Neigh | 0.00098324 | 0.0012714 | 0.0015543 | 0.8 | 4.90
Comm | 0.0028691 | 0.006242 | 0.0094991 | 4.1 | 24.04
Output | 0.00028014 | 0.00029546 | 0.00033355 | 0.1 | 1.14
Modify | 0.00066638 | 0.00077331 | 0.00089598 | 0.4 | 2.98
Other | | 0.005781 | | | 22.26
Nlocal: 105 ave 125 max 84 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 94.25 ave 104 max 84 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 895.75 ave 1159 max 648 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3583
Ave neighs/atom = 8.53095
Neighbor list builds = 38
Dangerous builds = 0
fix 4 all indent ${k1} sphere 10 11.0 0 6.0
fix 4 all indent 882.849286914813 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:168)
Memory usage per processor = 3.60141 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
605 0 -3.1149612 0 -2.7562264 0.88153856 516.19694
610 0 -3.0480145 0 -3.0046036 1.5377628 516.18952
620 0 -3.0581364 0 -3.0393996 1.5790644 516.23694
630 0 -3.058957 0 -3.0461523 1.6279637 515.82575
640 0 -3.0608654 0 -3.0476936 1.631809 515.82575
650 0 -3.059954 0 -3.0488507 1.7016953 514.58992
660 0 -3.0601043 0 -3.0495387 1.7749452 513.2301
670 0 -3.0600329 0 -3.0503272 1.8525614 512.87295
680 0 -3.0618342 0 -3.0532875 1.9461671 512.7735
690 0 -3.0681709 0 -3.0588644 1.8339583 513.83989
700 0 -3.0723671 0 -3.0624663 1.7080165 515.99424
710 0 -3.0738836 0 -3.0635305 1.6674853 516.40455
720 0 -3.0744809 0 -3.0640016 1.6430059 516.40455
729 0 -3.074692 0 -3.0641622 1.6351234 517.12194
Loop time of 0.0175288 on 4 procs for 124 steps with 420 atoms
99.8% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = linesearch alpha is zero
Energy initial, next-to-last, final =
-2.75622643697 -3.06416218566 -3.06416218566
Force two-norm initial, final = 387.971 1.75423
Force max component initial, final = 226.888 0.425447
Final line search alpha, max atom move = 9.47831e-07 4.03252e-07
Iterations, force evaluations = 124 275
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0053589 | 0.0078858 | 0.010479 | 2.7 | 44.99
Neigh | 0.00037146 | 0.00052333 | 0.00067759 | 0.6 | 2.99
Comm | 0.0017581 | 0.0046017 | 0.0073204 | 3.9 | 26.25
Output | 0.00017619 | 0.00018531 | 0.00021076 | 0.1 | 1.06
Modify | 0.00044012 | 0.00054049 | 0.00064754 | 0.4 | 3.08
Other | | 0.003792 | | | 21.63
Nlocal: 105 ave 131 max 78 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 97.25 ave 110 max 84 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 900.25 ave 1197 max 607 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3601
Ave neighs/atom = 8.57381
Neighbor list builds = 16
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
128 atoms
pair_style meam
pair_coeff * * library.meam Si C SiC.meam Si C
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file SiC.meam with DATE: 2007-06-11
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 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3 element Si C
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 element Si C
run 100
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15 -> bins = 6 6 6
Memory usage per processor = 6.89445 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 0.0991108 on 1 procs for 100 steps with 128 atoms
Performance: 87.175 ns/day, 0.275 hours/ns, 1008.971 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.09579 | 0.09579 | 0.09579 | 0.0 | 96.65
Neigh | 0.0022409 | 0.0022409 | 0.0022409 | 0.0 | 2.26
Comm | 0.00058365 | 0.00058365 | 0.00058365 | 0.0 | 0.59
Output | 9.6083e-05 | 9.6083e-05 | 9.6083e-05 | 0.0 | 0.10
Modify | 0.000283 | 0.000283 | 0.000283 | 0.0 | 0.29
Other | | 0.0001168 | | | 0.12
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
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
128 atoms
pair_style meam
pair_coeff * * library.meam Si C SiC.meam Si C
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file SiC.meam with DATE: 2007-06-11
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 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3 element Si C
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 element Si C
run 100
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15 -> bins = 6 6 6
Memory usage per processor = 6.82006 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 0.0386363 on 4 procs for 100 steps with 128 atoms
Performance: 223.624 ns/day, 0.107 hours/ns, 2588.242 timesteps/s
99.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.034338 | 0.034685 | 0.0351 | 0.1 | 89.77
Neigh | 0.00057364 | 0.00061846 | 0.00071192 | 0.2 | 1.60
Comm | 0.0023026 | 0.0027502 | 0.003161 | 0.6 | 7.12
Output | 0.00025105 | 0.00029814 | 0.00041199 | 0.4 | 0.77
Modify | 8.9169e-05 | 0.00010341 | 0.00012875 | 0.1 | 0.27
Other | | 0.0001808 | | | 0.47
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
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file Ni.meam with DATE: 2007-06-11
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:445)
timestep 0.001
run 100
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15 -> bins = 27 17 5
Memory usage per processor = 8.55725 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 1.81808 on 1 procs for 100 steps with 1912 atoms
Performance: 4.752 ns/day, 5.050 hours/ns, 55.003 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7962 | 1.7962 | 1.7962 | 0.0 | 98.80
Neigh | 0.014991 | 0.014991 | 0.014991 | 0.0 | 0.82
Comm | 0.0016303 | 0.0016303 | 0.0016303 | 0.0 | 0.09
Output | 6.5804e-05 | 6.5804e-05 | 6.5804e-05 | 0.0 | 0.00
Modify | 0.0041728 | 0.0041728 | 0.0041728 | 0.0 | 0.23
Other | | 0.001022 | | | 0.06
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 2 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 2 pad 4
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 3 pad 4
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
reset_timestep 0
run 3000
Memory usage per processor = 8.73384 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 6186.7018 20755.029
1100 306.13486 -8097.1731 0 -8060.7018 8904.6621 20879.616
1200 309.15669 -8081.8589 0 -8045.0276 10523.683 20996.875
1300 304.48415 -8064.5597 0 -8028.2851 10063.03 21126.348
1400 300 -8046.7607 0 -8011.0203 10972.459 21238.721
1500 300 -8041.3546 0 -8005.6142 11939.555 21374.301
1600 309.60207 -8035.2265 0 -7998.3422 11340.176 21530.099
1700 300 -8029.1685 0 -7993.4281 11298.745 21635.488
1800 300 -8034.2271 0 -7998.4867 9629.3065 21738.292
1900 307.84886 -8037.1066 0 -8000.4311 6166.9669 21857.993
2000 307.82172 -8029.9182 0 -7993.246 3178.6607 22013.016
2100 300 -8032.5982 0 -7996.8578 1354.4696 22107.168
2200 300 -8040.9505 0 -8005.2101 1872.6686 22231.755
2300 300 -8044.4439 0 -8008.7035 3214.7865 22355.121
2400 304.60017 -8038.5216 0 -8002.2331 5092.8026 22477.266
2500 308.48504 -8034.0394 0 -7997.2881 7280.4765 22596.967
2600 308.46083 -8037.9984 0 -8001.25 9860.0578 22717.89
2700 305.72597 -8038.4481 0 -8002.0255 10620.389 22837.592
2800 308.33801 -8043.0579 0 -8006.3241 8184.9538 22957.293
2900 300 -8042.671 0 -8006.9306 6691.6548 23085.545
3000 305.66039 -8041.7651 0 -8005.3503 3816.3815 23204.025
Loop time of 57.0164 on 1 procs for 3000 steps with 1912 atoms
Performance: 4.546 ns/day, 5.279 hours/ns, 52.616 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 56.168 | 56.168 | 56.168 | 0.0 | 98.51
Neigh | 0.64021 | 0.64021 | 0.64021 | 0.0 | 1.12
Comm | 0.051842 | 0.051842 | 0.051842 | 0.0 | 0.09
Output | 0.00062251 | 0.00062251 | 0.00062251 | 0.0 | 0.00
Modify | 0.1245 | 0.1245 | 0.1245 | 0.0 | 0.22
Other | | 0.03095 | | | 0.05
Nlocal: 1912 ave 1912 max 1912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1662 ave 1662 max 1662 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 23535 ave 23535 max 23535 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 47070 ave 47070 max 47070 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 47070
Ave neighs/atom = 24.6182
Neighbor list builds = 223
Dangerous builds = 0
Total wall time: 0:00:58

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LAMMPS (15 Feb 2016)
# 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
Reading potential file library.meam with DATE: 2012-06-29
Reading potential file Ni.meam with DATE: 2007-06-11
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:445)
timestep 0.001
run 100
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.3
ghost atom cutoff = 4.3
binsize = 2.15 -> bins = 27 17 5
Memory usage per processor = 7.74146 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 0.491613 on 4 procs for 100 steps with 1912 atoms
Performance: 17.575 ns/day, 1.366 hours/ns, 203.412 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.4688 | 0.47596 | 0.48111 | 0.7 | 96.82
Neigh | 0.003762 | 0.003863 | 0.0039828 | 0.2 | 0.79
Comm | 0.0044096 | 0.0096632 | 0.016901 | 5.3 | 1.97
Output | 0.00011063 | 0.0001418 | 0.00019789 | 0.3 | 0.03
Modify | 0.001152 | 0.0011944 | 0.0012844 | 0.2 | 0.24
Other | | 0.0007868 | | | 0.16
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 2 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 2 pad 4
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
#dump_modify 3 pad 4
thermo 100
thermo_modify temp new2d
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:445)
reset_timestep 0
run 3000
Memory usage per processor = 7.78572 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 7921.3464 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 9586.4761 21255.821
1500 300 -8041.9686 0 -8006.2281 9655.7305 21365.751
1600 308.48003 -8031.9004 0 -7995.1497 10878.457 21496.446
1700 300 -8018.8868 0 -7983.1463 11313.287 21610.04
1800 300 -8011.8184 0 -7976.0779 11545.113 21730.963
1900 300 -8008.9215 0 -7973.1811 9196.3325 21861.658
2000 300 -8013.4567 0 -7977.7163 5843.9738 21977.695
2100 300 -8023.8599 0 -7988.1195 1292.526 22107.168
2200 300 -8036.0201 0 -8000.2797 711.97062 22221.984
2300 300 -8041.9948 0 -8006.2544 898.57229 22344.128
2400 300 -8048.658 0 -8012.9175 -389.36413 22478.487
2500 300 -8050.0812 0 -8014.3408 -1981.1849 22592.082
2600 307.46028 -8046.847 0 -8010.2178 -2034.1541 22713.005
2700 293.56734 -8041.2081 0 -8006.2341 -2496.4019 22837.592
2800 295.42272 -8035.3079 0 -8000.1128 -1331.5373 22953.629
2900 300 -8033.3512 0 -7997.6107 -2171.4081 23089.209
3000 300 -8029.6279 0 -7993.8875 -672.58255 23197.918
Loop time of 15.7189 on 4 procs for 3000 steps with 1912 atoms
Performance: 16.490 ns/day, 1.455 hours/ns, 190.853 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.034 | 15.188 | 15.303 | 2.8 | 96.62
Neigh | 0.16167 | 0.16592 | 0.17044 | 0.8 | 1.06
Comm | 0.19007 | 0.30646 | 0.46393 | 20.5 | 1.95
Output | 0.00079918 | 0.00091255 | 0.0012419 | 0.6 | 0.01
Modify | 0.033848 | 0.035817 | 0.037596 | 0.8 | 0.23
Other | | 0.02219 | | | 0.14
Nlocal: 478 ave 515 max 444 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 786.25 ave 835 max 748 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 5779.5 ave 6212 max 5416 min
Histogram: 1 0 1 0 0 1 0 0 0 1
FullNghs: 11559 ave 12371 max 10859 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Total # of neighbors = 46236
Ave neighs/atom = 24.182
Neighbor list builds = 221
Dangerous builds = 0
Total wall time: 0:00:16

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LAMMPS (15 Feb 2016)
# 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 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 12 12 12
Memory usage per processor = 2.19271 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 0.739 on 1 procs for 250 steps with 4000 atoms
Performance: 146143.468 tau/day, 338.295 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.62778 | 0.62778 | 0.62778 | 0.0 | 84.95
Neigh | 0.083963 | 0.083963 | 0.083963 | 0.0 | 11.36
Comm | 0.01149 | 0.01149 | 0.01149 | 0.0 | 1.55
Output | 0.00010991 | 0.00010991 | 0.00010991 | 0.0 | 0.01
Modify | 0.01251 | 0.01251 | 0.01251 | 0.0 | 1.69
Other | | 0.003146 | | | 0.43
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 not checked
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 50
run 250
Neighbor list info ...
1 neighbor list requests
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 12 12 12
Memory usage per processor = 2.10344 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 0.214556 on 4 procs for 250 steps with 4000 atoms
Performance: 503365.139 tau/day, 1165.197 timesteps/s
98.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.16133 | 0.16562 | 0.1711 | 1.0 | 77.19
Neigh | 0.021791 | 0.022137 | 0.022399 | 0.2 | 10.32
Comm | 0.016056 | 0.022041 | 0.026695 | 2.9 | 10.27
Output | 0.00012183 | 0.0001328 | 0.00014186 | 0.1 | 0.06
Modify | 0.0032513 | 0.0033011 | 0.0033648 | 0.1 | 1.54
Other | | 0.001321 | | | 0.62
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 not checked
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123 -> bins = 51 51 1
Memory usage per processor = 2.98958 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 0.188732 on 1 procs for 1000 steps with 1200 atoms
Performance: 2288961.113 tau/day, 5298.521 timesteps/s
100.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13192 | 0.13192 | 0.13192 | 0.0 | 69.90
Bond | 0.0065749 | 0.0065749 | 0.0065749 | 0.0 | 3.48
Neigh | 0.021622 | 0.021622 | 0.021622 | 0.0 | 11.46
Comm | 0.003341 | 0.003341 | 0.003341 | 0.0 | 1.77
Output | 0.00019431 | 0.00019431 | 0.00019431 | 0.0 | 0.10
Modify | 0.020563 | 0.020563 | 0.020563 | 0.0 | 10.90
Other | | 0.004518 | | | 2.39
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 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 26 26 1
Memory usage per processor = 2.98958 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727655 0.058608718 -1.4645318 1.9982299
2000 0.4661092 -1.9963233 0.067084121 -1.4635184 1.5676107
3000 0.44946688 -2.0126501 0.070702998 -1.4928548 1.5636132
4000 0.45269674 -1.9944702 0.05825464 -1.4838961 1.6015127
5000 0.46281924 -2.0302807 0.058318349 -1.5095288 1.3929421
6000 0.45409991 -2.0339156 0.061724414 -1.5184697 1.1978692
7000 0.44058968 -2.0436374 0.060141133 -1.5432738 1.1877802
8000 0.4429781 -2.0508103 0.061300632 -1.5469007 1.1825472
9000 0.44909024 -2.0620769 0.063430248 -1.5499306 1.1841529
10000 0.44709728 -2.0337047 0.059176633 -1.5278033 1.1906481
11000 0.46222813 -2.0666276 0.053626157 -1.5511585 0.99322264
12000 0.45722371 -2.0527602 0.062728903 -1.5331886 1.1135813
13000 0.44844353 -2.0672473 0.07057216 -1.5486053 0.9416127
14000 0.44211202 -2.0804052 0.056164487 -1.5824971 0.99700319
15000 0.45659943 -2.0711771 0.059428792 -1.5555294 1.1123211
16000 0.45113626 -2.0895625 0.057848795 -1.5809534 1.0015991
17000 0.44423013 -2.0840859 0.06718595 -1.57304 0.92034012
18000 0.45279338 -2.0644167 0.058541719 -1.5534589 1.1560585
19000 0.44673847 -2.0729637 0.061474462 -1.565123 0.99627228
20000 0.44428193 -2.0937135 0.066588799 -1.583213 0.86154418
21000 0.45902797 -2.0821041 0.057286828 -1.5661718 0.76853595
22000 0.45733559 -2.0962718 0.064103239 -1.5752141 0.90967955
23000 0.44617227 -2.070896 0.061562573 -1.5635329 0.92864876
24000 0.45569898 -2.0843503 0.061015469 -1.5680156 0.90170833
25000 0.45952666 -2.0892064 0.058901296 -1.5711614 0.9123274
26000 0.44773853 -2.0896169 0.065994021 -1.5762575 0.8887526
27000 0.43541542 -2.0893237 0.060387783 -1.5938834 0.97604018
28000 0.44025187 -2.0937721 0.066174764 -1.5877124 0.98394478
29000 0.44695847 -2.0966733 0.064980967 -1.5851064 0.78278706
30000 0.44848319 -2.1017012 0.053308469 -1.6002833 0.85185298
31000 0.45215181 -2.0927324 0.057875178 -1.5830822 0.77068692
32000 0.44586981 -2.0962193 0.056970051 -1.593751 0.85672441
33000 0.43591379 -2.1069871 0.064934652 -1.6065019 0.87081371
34000 0.44153683 -2.0967535 0.061537811 -1.5940468 0.75497708
35000 0.45482946 -2.1045277 0.060250612 -1.5898266 0.80290163
36000 0.45 -2.1154856 0.052206018 -1.6136546 0.67520748
37000 0.44973679 -2.1076496 0.067371347 -1.5909163 0.83319072
38000 0.45549751 -2.1044983 0.061863351 -1.587517 0.6786145
39000 0.43927254 -2.1159446 0.057855173 -1.6191829 0.66483475
40000 0.43711657 -2.0941837 0.063039594 -1.5943918 0.90680301
41000 0.43992749 -2.0931285 0.063772204 -1.5897954 0.7538478
42000 0.44374588 -2.1029745 0.061963499 -1.5976349 0.74793466
43000 0.45 -2.0916744 0.055058096 -1.5869913 0.86069235
44000 0.45381626 -2.0984483 0.059995477 -1.5850147 0.74948091
45000 0.44547409 -2.1217483 0.058753101 -1.6178924 0.57348898
46000 0.43283033 -2.1054695 0.059343099 -1.6136567 0.77490901
47000 0.44310217 -2.1215687 0.066613901 -1.6122219 0.73014542
48000 0.44611257 -2.118313 0.05944897 -1.6131232 0.59077782
49000 0.44114725 -2.0911126 0.065639368 -1.5846936 0.78309201
50000 0.44572124 -2.0892024 0.065540869 -1.5783117 0.87647821
51000 0.4460699 -2.1142274 0.061090043 -1.6074391 0.61721581
52000 0.44799203 -2.1122931 0.056821256 -1.6078531 0.70734576
53000 0.44819437 -2.1098838 0.058117987 -1.6039449 0.71349136
54000 0.45 -2.1384776 0.051012047 -1.6378405 0.4810217
55000 0.43931842 -2.1053055 0.061275315 -1.6050778 0.58268948
56000 0.44126963 -2.1133637 0.057474037 -1.6149877 0.68063945
57000 0.45823746 -2.1205329 0.065224217 -1.5974531 0.73788456
58000 0.437031 -2.0998724 0.051717885 -1.6114877 0.86071379
59000 0.45070454 -2.1115874 0.053721754 -1.6075367 0.62358834
60000 0.44181643 -2.1243164 0.060489492 -1.6223786 0.6992428
Loop time of 13.7021 on 1 procs for 60000 steps with 1200 atoms
Performance: 1891674.479 tau/day, 4378.876 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.5222 | 9.5222 | 9.5222 | 0.0 | 69.49
Bond | 0.39977 | 0.39977 | 0.39977 | 0.0 | 2.92
Neigh | 2.1261 | 2.1261 | 2.1261 | 0.0 | 15.52
Comm | 0.26046 | 0.26046 | 0.26046 | 0.0 | 1.90
Output | 0.00084543 | 0.00084543 | 0.00084543 | 0.0 | 0.01
Modify | 1.1202 | 1.1202 | 1.1202 | 0.0 | 8.18
Other | | 0.2726 | | | 1.99
Nlocal: 1200 ave 1200 max 1200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 417 ave 417 max 417 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9495 ave 9495 max 9495 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9495
Ave neighs/atom = 7.9125
Ave special neighs/atom = 0.5
Neighbor list builds = 4885
Dangerous builds = 0
Total wall time: 0:00:13

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LAMMPS (15 Feb 2016)
# 2d micelle simulation
dimension 2
neighbor 0.3 bin
neigh_modify delay 5
atom_style bond
# Soft potential push-off
read_data data.micelle
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
2 by 2 by 1 MPI processor grid
reading atoms ...
1200 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123 -> bins = 51 51 1
Memory usage per processor = 3.55365 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 0.0662177 on 4 procs for 1000 steps with 1200 atoms
Performance: 6523939.295 tau/day, 15101.711 timesteps/s
98.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.03338 | 0.034415 | 0.035278 | 0.4 | 51.97
Bond | 0.0016546 | 0.0017538 | 0.001863 | 0.2 | 2.65
Neigh | 0.0062997 | 0.0064718 | 0.0066252 | 0.2 | 9.77
Comm | 0.011654 | 0.012875 | 0.013857 | 0.8 | 19.44
Output | 0.00039363 | 0.00041753 | 0.00046754 | 0.1 | 0.63
Modify | 0.0067155 | 0.0069018 | 0.0072353 | 0.3 | 10.42
Other | | 0.003383 | | | 5.11
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 2 all image 2000 image.*.jpg type type zoom 1.6
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
reset_timestep 0
run 60000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 26 26 1
Memory usage per processor = 3.55365 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
1000 0.45 -1.9727663 0.058608449 -1.4645328 1.9982389
2000 0.45428051 -1.9704547 0.062434911 -1.4541178 1.7134222
3000 0.46748648 -2.0088544 0.065086237 -1.4766712 1.4648627
4000 0.45608936 -2.032563 0.057148422 -1.5197053 1.3833681
5000 0.46134038 -2.0250107 0.061983009 -1.5020718 1.3378201
6000 0.45254634 -2.0414745 0.071656389 -1.5176489 1.2670697
7000 0.46380932 -2.0463598 0.060057501 -1.5228795 1.1029258
8000 0.46495917 -2.0570216 0.058074076 -1.5343758 1.1187483
9000 0.45771237 -2.0510911 0.061803881 -1.5319563 1.1540073
10000 0.45 -2.0568306 0.06114562 -1.54606 1.128504
11000 0.43977142 -2.0442503 0.061128391 -1.543717 1.2268919
12000 0.4412548 -2.051046 0.065150223 -1.5450087 1.0681597
13000 0.46384147 -2.0657072 0.064678941 -1.5375734 0.99078604
14000 0.43330137 -2.0693058 0.06542588 -1.5709397 1.0252118
15000 0.44825078 -2.078972 0.059800283 -1.5712944 0.76305383
16000 0.45607271 -2.085101 0.058347214 -1.5710611 0.99903698
17000 0.45329523 -2.0865426 0.057674526 -1.5759505 0.90245709
18000 0.46719329 -2.076619 0.062698678 -1.5471164 0.95433376
19000 0.45253889 -2.0741652 0.06154596 -1.5604575 1.0606446
20000 0.43708811 -2.1005493 0.063453064 -1.6003723 0.65980174
21000 0.43630563 -2.0780131 0.05595505 -1.586116 0.86690426
22000 0.44050783 -2.0766368 0.057980992 -1.578515 0.99638367
23000 0.44657992 -2.0731942 0.058890194 -1.5680963 0.92620975
24000 0.45645869 -2.0957688 0.065464986 -1.5742255 0.88631971
25000 0.46007071 -2.0928226 0.058133397 -1.5750019 0.75468418
26000 0.46316546 -2.0945456 0.064110354 -1.5676557 0.84437166
27000 0.44780223 -2.0966995 0.063284428 -1.585986 0.89645525
28000 0.43945645 -2.0909433 0.062357411 -1.5894957 0.92336874
29000 0.44332217 -2.0885003 0.063832997 -1.5817146 0.86508766
30000 0.44865024 -2.0899642 0.057319345 -1.5843685 0.76862889
31000 0.45702135 -2.0941006 0.059669304 -1.5777908 0.76171188
32000 0.46630168 -2.1066612 0.051622888 -1.5891252 0.72214981
33000 0.44966822 -2.1086408 0.061298737 -1.5980486 0.7056562
34000 0.45599464 -2.11216 0.045835595 -1.6107098 0.75827582
35000 0.44021366 -2.1082791 0.066290667 -1.6021416 0.85079438
36000 0.46531913 -2.1228506 0.054779097 -1.6031402 0.60391389
37000 0.44777064 -2.1193684 0.062074675 -1.6098962 0.68654583
38000 0.46608897 -2.1243843 0.052889984 -1.6057938 0.6517974
39000 0.44921432 -2.1050268 0.059790015 -1.5963968 0.74248261
40000 0.44407222 -2.0930539 0.055687841 -1.5936639 0.69821332
41000 0.4377755 -2.0929451 0.056403441 -1.599131 0.90040574
42000 0.46403029 -2.1245032 0.058491534 -1.6023681 0.6984091
43000 0.45456147 -2.0966395 0.055922733 -1.5865341 0.86499812
44000 0.45619203 -2.1150101 0.054818604 -1.6043796 0.71197595
45000 0.44806278 -2.1067617 0.057539822 -1.6015324 0.7644258
46000 0.46326243 -2.1204997 0.060566953 -1.5970563 0.68822898
47000 0.43464277 -2.1257611 0.069053137 -1.6224273 0.60024032
48000 0.46986944 -2.1245871 0.058768355 -1.5963409 0.58191819
49000 0.4428734 -2.1203847 0.059089451 -1.6187909 0.60806508
50000 0.43813854 -2.12123 0.066218857 -1.6172377 0.42860822
51000 0.4514578 -2.1304644 0.057932769 -1.62145 0.62355123
52000 0.44155257 -2.1248047 0.062563155 -1.6210569 0.81276016
53000 0.4467801 -2.1254575 0.056774655 -1.6222751 0.6115287
54000 0.43972332 -2.1036785 0.061427338 -1.6028943 0.75225909
55000 0.44933771 -2.104883 0.058556755 -1.5973629 0.75480805
56000 0.45 -2.1212286 0.057392665 -1.614211 0.56759345
57000 0.43127001 -2.0978236 0.04986292 -1.61705 0.71828346
58000 0.43621486 -2.1097172 0.056706821 -1.617159 0.80497906
59000 0.44446312 -2.1103931 0.055606397 -1.610694 0.79904859
60000 0.43177211 -2.0985468 0.049687241 -1.6174473 0.81094066
Loop time of 4.44409 on 4 procs for 60000 steps with 1200 atoms
Performance: 5832469.978 tau/day, 13501.088 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3453 | 2.4228 | 2.4713 | 3.0 | 54.52
Bond | 0.084212 | 0.10413 | 0.11722 | 3.8 | 2.34
Neigh | 0.61098 | 0.61843 | 0.62485 | 0.7 | 13.92
Comm | 0.72832 | 0.81507 | 0.94114 | 9.7 | 18.34
Output | 0.0012789 | 0.0013777 | 0.0016506 | 0.4 | 0.03
Modify | 0.2745 | 0.28888 | 0.31551 | 3.0 | 6.50
Other | | 0.1934 | | | 4.35
Nlocal: 300 ave 305 max 293 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Nghost: 211 ave 215 max 205 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Neighs: 2448.75 ave 2531 max 2414 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 9795
Ave neighs/atom = 8.1625
Ave special neighs/atom = 0.5
Neighbor list builds = 4880
Dangerous builds = 0
Total wall time: 0:00:04

553
examples/min/log.15Feb16.min.box.g++.1 Normal file
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LAMMPS (15 Feb 2016)
# 2d Lennard-Jones melt and subsequent energy minimization,
# followed by box relaxation to a target stress state
#
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 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
thermo 100
run 1000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 22 22 1
Memory usage per processor = 2.47843 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 -0.85213743 0 2.532518 15.162759
700 3.2123675 -0.67642318 0 2.5319289 16.310565
800 3.3016275 -0.76569171 0 2.5318087 15.639335
900 3.4639203 -0.92788002 0 2.5317104 14.765912
1000 3.3256788 -0.79078181 0 2.5307399 15.599298
Loop time of 0.200459 on 1 procs for 1000 steps with 800 atoms
Performance: 2155054.114 tau/day, 4988.551 timesteps/s
99.3% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12873 | 0.12873 | 0.12873 | 0.0 | 64.22
Neigh | 0.050699 | 0.050699 | 0.050699 | 0.0 | 25.29
Comm | 0.0045221 | 0.0045221 | 0.0045221 | 0.0 | 2.26
Output | 8.5354e-05 | 8.5354e-05 | 8.5354e-05 | 0.0 | 0.04
Modify | 0.011955 | 0.011955 | 0.011955 | 0.0 | 5.96
Other | | 0.00447 | | | 2.23
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 317 ave 317 max 317 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7743 ave 7743 max 7743 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7743
Ave neighs/atom = 9.67875
Neighbor list builds = 203
Dangerous builds = 0
# perform the box relaxation by progressively
# adding more degrees of freedom, for smoother
# convergence
neigh_modify delay 0 every 1 check yes
velocity all create 0.0 1
thermo 50
# atoms only
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 3.60343 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0 -0.79078181 0 -0.79078181 12.79527
1050 0 -2.8361415 0 -2.8361415 -1.1950285
1100 0 -2.8661626 0 -2.8661626 -1.1864964
1150 0 -2.8783275 0 -2.8783275 -1.1746571
1200 0 -2.8838202 0 -2.8838202 -1.1647075
1250 0 -2.8956657 0 -2.8956657 -1.1991876
1300 0 -2.9039122 0 -2.9039122 -1.1445553
1350 0 -2.9100776 0 -2.9100776 -1.1036121
1400 0 -2.9131297 0 -2.9131297 -1.0962069
1450 0 -2.9167506 0 -2.9167506 -1.0259809
1475 0 -2.9169436 0 -2.9169436 -1.0125744
Loop time of 0.239637 on 1 procs for 475 steps with 800 atoms
100.1% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.790781812776 -2.9169407756 -2.91694356781
Force two-norm initial, final = 1905.47 0.794548
Force max component initial, final = 343.392 0.268404
Final line search alpha, max atom move = 0.347566 0.0932881
Iterations, force evaluations = 475 940
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.19656 | 0.19656 | 0.19656 | 0.0 | 82.02
Neigh | 0.021103 | 0.021103 | 0.021103 | 0.0 | 8.81
Comm | 0.0028365 | 0.0028365 | 0.0028365 | 0.0 | 1.18
Output | 6.6996e-05 | 6.6996e-05 | 6.6996e-05 | 0.0 | 0.03
Modify | 0.002048 | 0.002048 | 0.002048 | 0.0 | 0.85
Other | | 0.01702 | | | 7.10
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 329 ave 329 max 329 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6957 ave 6957 max 6957 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6957
Ave neighs/atom = 8.69625
Neighbor list builds = 85
Dangerous builds = 0
# isotropic volume relaxation to hydrostatic target
fix 3 all box/relax iso 1.5 vmax 1.0e-3
variable emin equal pe+f_3/atoms
thermo_style custom step temp pe pxx pyy pxy f_3 v_emin
# anisotropic volume relaxation to hydrostatic target
minimize 0.0 10.0e0 10000 100000
Memory usage per processor = 3.60343 Mbytes
Step Temp PotEng Pxx Pyy Pxy 3 emin
1475 0 -2.9169436 -1.0208231 -1.0043256 0.042048233 0 -2.9169436
1500 0 -2.9112018 1.4420862 1.4721681 0.065929095 -0.087730988 -2.9989327
1550 0 -2.9169778 1.5234769 1.5850923 0.063502312 -0.11432538 -3.0313032
1600 0 -2.924265 1.4545702 1.5281333 0.053590255 -0.12032598 -3.044591
1650 0 -2.9289538 1.4528452 1.5692678 0.038096542 -0.12516914 -3.054123
1699 0 -2.9334511 1.4447667 1.5587557 0.044510608 -0.12731783 -3.060769
Loop time of 0.112636 on 1 procs for 224 steps with 800 atoms
100.3% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-2.91694356781 -3.06076807543 -3.060768969
Force two-norm initial, final = 4762.05 8.66905
Force max component initial, final = 4762.05 3.21614
Final line search alpha, max atom move = 6.88085e-05 0.000221298
Iterations, force evaluations = 224 409
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.090125 | 0.090125 | 0.090125 | 0.0 | 80.01
Neigh | 0.0039701 | 0.0039701 | 0.0039701 | 0.0 | 3.52
Comm | 0.0010481 | 0.0010481 | 0.0010481 | 0.0 | 0.93
Output | 9.6798e-05 | 9.6798e-05 | 9.6798e-05 | 0.0 | 0.09
Modify | 0.00088024 | 0.00088024 | 0.00088024 | 0.0 | 0.78
Other | | 0.01652 | | | 14.66
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 338 ave 338 max 338 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7313 ave 7313 max 7313 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7313
Ave neighs/atom = 9.14125
Neighbor list builds = 16
Dangerous builds = 0
fix 3 all box/relax aniso 1.5 vmax 1.0e-3
minimize 0.0 10.0 10000 100000
Memory usage per processor = 3.60343 Mbytes
Step Temp PotEng Pxx Pyy Pxy 3 emin
1699 0 -2.9334511 1.4447667 1.5587557 0.044510608 0 -2.9334511
1700 0 -2.9335996 1.4982915 1.4969508 0.044657372 9.09619e-05 -2.9335086
Loop time of 0.000809908 on 1 procs for 1 steps with 800 atoms
123.5% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-2.93345114337 -2.93345114337 -2.93350862414
Force two-norm initial, final = 71.3983 8.74381
Force max component initial, final = 51.6897 2.68015
Final line search alpha, max atom move = 1.93462e-05 5.18508e-05
Iterations, force evaluations = 1 2
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00066304 | 0.00066304 | 0.00066304 | 0.0 | 81.87
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 6.9141e-06 | 6.9141e-06 | 6.9141e-06 | 0.0 | 0.85
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 6.4373e-06 | 6.4373e-06 | 6.4373e-06 | 0.0 | 0.79
Other | | 0.0001335 | | | 16.49
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 338 ave 338 max 338 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7301 ave 7301 max 7301 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7301
Ave neighs/atom = 9.12625
Neighbor list builds = 0
Dangerous builds = 0
# anisotropic volume relaxation to non-hydrostatic target
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3
minimize 0.0 10.0 10000 100000
Memory usage per processor = 3.60343 Mbytes
Step Temp PotEng Pxx Pyy Pxy 3 emin
1700 0 -2.9335996 1.4982915 1.4969508 0.044657372 -3.5527137e-17 -2.9335996
1750 0 -2.9306696 0.95043712 1.984164 0.04474671 -0.014282691 -2.9449523
1800 0 -2.9328947 1.0034263 1.9908351 0.043891947 -0.017255878 -2.9501506
1850 0 -2.935585 0.98224846 1.9920507 0.047038767 -0.021070874 -2.9566559
1900 0 -2.9380757 0.96811097 1.9677247 0.068809483 -0.024274947 -2.9623506
1913 0 -2.9391305 0.98238419 1.9782761 0.074400364 -0.025108208 -2.9642387
Loop time of 0.100323 on 1 procs for 213 steps with 800 atoms
100.7% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-2.93359958604 -2.96406714389 -2.96423867812
Force two-norm initial, final = 622.999 9.93502
Force max component initial, final = 442.577 5.00802
Final line search alpha, max atom move = 0.000369148 0.0018487
Iterations, force evaluations = 213 356
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.079344 | 0.079344 | 0.079344 | 0.0 | 79.09
Neigh | 0.0028028 | 0.0028028 | 0.0028028 | 0.0 | 2.79
Comm | 0.00087476 | 0.00087476 | 0.00087476 | 0.0 | 0.87
Output | 0.00012708 | 0.00012708 | 0.00012708 | 0.0 | 0.13
Modify | 0.00077343 | 0.00077343 | 0.00077343 | 0.0 | 0.77
Other | | 0.0164 | | | 16.35
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 337 ave 337 max 337 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7344 ave 7344 max 7344 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7344
Ave neighs/atom = 9.18
Neighbor list builds = 11
Dangerous builds = 0
minimize 0.0 1.0 10000 100000
Memory usage per processor = 3.60343 Mbytes
Step Temp PotEng Pxx Pyy Pxy 3 emin
1913 0 -2.9391305 0.98238419 1.9782761 0.074400364 7.1054274e-17 -2.9391305
1950 0 -2.9397224 0.98880561 2.0105792 0.10042798 -0.0026601558 -2.9423825
2000 0 -2.9426513 0.99541675 1.9727175 0.13793826 -0.0055993834 -2.9482507
2050 0 -2.9422932 1.0135462 2.062652 0.15208716 -0.0090986322 -2.9513919
2100 0 -2.9452654 0.98891373 1.9917349 0.17178076 -0.0088814224 -2.9541468
2150 0 -2.9479511 1.0054525 1.9938996 0.19677305 -0.012189723 -2.9601408
2200 0 -2.9524854 0.92417794 1.9670411 0.21283803 -0.014527245 -2.9670127
2250 0 -2.9546681 0.94388065 1.9485987 0.26294591 -0.016606496 -2.9712746
2300 0 -2.9562108 0.97059342 2.0096507 0.26715603 -0.018777368 -2.9749882
2350 0 -2.9568148 1.0327203 2.0192612 0.28381119 -0.019537293 -2.9763521
2400 0 -2.9587001 1.0106008 1.9969503 0.30603661 -0.019408356 -2.9781085
2450 0 -2.9590843 0.98958837 2.0224183 0.31018833 -0.020232067 -2.9793164
2500 0 -2.9605371 1.0129369 2.0118845 0.31896899 -0.0206348 -2.9811719
2550 0 -2.96203 1.0088756 1.9950565 0.31619508 -0.020741018 -2.982771
2600 0 -2.9640352 1.0260949 1.9708112 0.32681194 -0.020520418 -2.9845557
2650 0 -2.9660094 1.0023933 1.9418952 0.32890865 -0.020061429 -2.9860709
2700 0 -2.9665094 0.99813752 1.9545648 0.33001828 -0.020784521 -2.9872939
2750 0 -2.9670182 1.0109981 1.9548987 0.33172056 -0.021377228 -2.9883954
2800 0 -2.9664869 1.0258673 2.0006802 0.31745442 -0.022943731 -2.9894306
2850 0 -2.9667139 0.97403389 2.0113279 0.30412138 -0.023501638 -2.9902156
2900 0 -2.9680973 0.9828473 1.9525815 0.28059505 -0.023126582 -2.9912239
2950 0 -2.9682294 0.94859438 1.9938632 0.25025064 -0.024655342 -2.9928848
3000 0 -2.969822 0.95834394 2.0063727 0.21932668 -0.025262588 -2.9950845
3050 0 -2.9707839 1.0391399 2.0683958 0.16283029 -0.027043589 -2.9978275
3100 0 -2.9758409 0.95391478 1.9747899 0.15833517 -0.025149181 -3.0009901
3150 0 -2.9768939 0.97373082 2.0001007 0.15841842 -0.025677624 -3.0025715
3200 0 -2.9777485 0.99736666 2.0198069 0.15135627 -0.025930613 -3.0036792
3250 0 -2.9797804 1.0301449 1.9779232 0.14660973 -0.025016253 -3.0047966
3300 0 -2.9820171 0.94285548 1.96158 0.13286429 -0.024090816 -3.0061079
3350 0 -2.9817184 0.98345019 2.006374 0.11946654 -0.025223277 -3.0069417
3400 0 -2.9812891 1.0291774 2.0523043 0.11233996 -0.026572014 -3.0078611
3450 0 -2.9835185 1.0204667 2.0006849 0.10950044 -0.025913625 -3.0094321
3500 0 -2.9846522 1.0357247 1.9956135 0.11397223 -0.02596945 -3.0106216
3550 0 -2.9849965 1.0465415 2.0034542 0.10529073 -0.026768999 -3.0117655
3600 0 -2.9854932 1.0100248 2.0061519 0.08830457 -0.027590513 -3.0130837
3650 0 -2.9857647 0.98930272 2.0182283 0.087267346 -0.028614885 -3.0143796
3700 0 -2.9858424 0.98968749 2.0513509 0.10976845 -0.030020766 -3.0158632
3750 0 -2.9898376 1.0094545 1.9684317 0.12012512 -0.02962014 -3.0194577
3800 0 -2.9909385 0.99283062 1.9564888 0.12537594 -0.030015407 -3.0209539
3850 0 -2.9926048 0.98361678 1.9819742 0.16313881 -0.030948861 -3.0235536
3900 0 -2.9932922 0.98225201 1.9919792 0.18301585 -0.031158418 -3.0244506
3950 0 -2.993953 0.99909161 1.9914448 0.19489054 -0.03131767 -3.0252706
4000 0 -2.9938341 0.98065126 2.0201506 0.19082331 -0.032058718 -3.0258928
4050 0 -2.9950536 0.9785676 1.9774178 0.16443738 -0.031591517 -3.0266451
4100 0 -2.9953218 1.0069483 1.9925044 0.14079031 -0.031936209 -3.027258
4150 0 -2.9963656 0.97761728 1.9845911 0.11288389 -0.031595867 -3.0279614
4200 0 -2.9964199 0.98359583 2.0139525 0.095496549 -0.032163052 -3.028583
4250 0 -2.9972591 0.993874 2.0143705 0.091692668 -0.03194206 -3.0292011
4300 0 -2.9982807 0.98492505 2.012554 0.11938807 -0.031454431 -3.0297351
4350 0 -2.9999398 0.98784549 1.9881272 0.12507612 -0.031022256 -3.0309621
4400 0 -3.0001304 0.99616457 1.9945789 0.12453613 -0.031177114 -3.0313075
4450 0 -3.0004497 1.0000329 1.9931979 0.1270167 -0.031009688 -3.0314594
4500 0 -3.0005789 0.99179213 1.9969317 0.13667693 -0.030980836 -3.0315598
4550 0 -3.0007423 1.0041962 1.9941677 0.15252242 -0.031006633 -3.0317489
4600 0 -3.0010569 1.0057204 1.9817944 0.15946073 -0.030819514 -3.0318765
4650 0 -3.0014825 0.98469354 2.0019354 0.16598597 -0.030622748 -3.0321052
4700 0 -3.0018368 1.0158862 2.0017724 0.17909232 -0.030557071 -3.0323939
4750 0 -3.0024201 0.9960973 2.0134985 0.16196409 -0.030652485 -3.0330726
4800 0 -3.0046547 0.99511822 1.9709749 0.11634573 -0.029985363 -3.03464
4850 0 -3.0057898 0.9840066 2.0608646 0.10865238 -0.032240795 -3.0380306
4900 0 -3.0073588 1.0457338 2.016365 0.11066013 -0.031987734 -3.0393466
4950 0 -3.0090739 1.0131698 1.9782205 0.1141775 -0.031538332 -3.0406122
5000 0 -3.0101274 1.0065972 1.9526686 0.11953597 -0.031347107 -3.0414745
5050 0 -3.0102918 1.0154549 1.9752505 0.1220875 -0.031756469 -3.0420483
5100 0 -3.0108263 1.0025509 2.0124654 0.13973674 -0.032101781 -3.0429281
5150 0 -3.0148407 0.95927344 1.8896916 0.16214187 -0.030046018 -3.0448867
5200 0 -3.0150313 0.95062265 2.0075523 0.17001319 -0.032059324 -3.0470906
5250 0 -3.0175735 0.97218401 1.959978 0.14895932 -0.031263777 -3.0488372
5300 0 -3.016581 1.0802252 2.05308 0.12479188 -0.034297458 -3.0508785
5350 0 -3.0218616 0.92814595 1.9346365 0.11066894 -0.032101217 -3.0539628
5400 0 -3.0230864 1.0009537 1.9581426 0.10072265 -0.033417491 -3.0565039
5450 0 -3.0229488 0.97989404 2.0379675 0.085383544 -0.03507026 -3.0580191
5500 0 -3.0253542 0.966137 1.971244 0.082518184 -0.033935405 -3.0592896
5550 0 -3.0257839 1.0012734 2.0297929 0.088881743 -0.034859305 -3.0606432
5600 0 -3.0285415 1.0069584 1.9971527 0.060161704 -0.034365808 -3.0629073
5650 0 -3.0309829 1.0001688 2.0107095 0.042774249 -0.034976624 -3.0659595
5700 0 -3.0346459 1.0148121 1.9812613 0.057797039 -0.034875301 -3.0695212
5750 0 -3.034967 0.99889543 2.0007332 0.062522099 -0.035508727 -3.0704757
5800 0 -3.0354193 0.99309448 1.9905175 0.058723802 -0.035599394 -3.0710187
5850 0 -3.0377114 0.95244639 1.8862163 0.036564194 -0.034423714 -3.0721351
5900 0 -3.0374037 0.9409737 1.9685026 0.020781029 -0.036371599 -3.0737753
5950 0 -3.037355 1.0040584 1.9975884 0.029471446 -0.037134087 -3.0744891
6000 0 -3.0377611 0.97903528 1.9912525 0.030018934 -0.036958151 -3.0747193
6050 0 -3.0377435 1.0026599 1.9926518 0.03268008 -0.037097365 -3.0748408
6100 0 -3.0376857 0.99774066 2.0011206 0.032339746 -0.037203823 -3.0748895
6150 0 -3.0378018 0.99312254 1.9976029 0.033591679 -0.037118029 -3.0749198
6200 0 -3.0378621 0.99757283 1.9947742 0.033965158 -0.037072763 -3.0749349
6250 0 -3.0378032 0.99964291 1.9971778 0.033045048 -0.037140636 -3.0749439
6300 0 -3.0377782 0.9965492 1.9980669 0.032201395 -0.037170252 -3.0749485
6314 0 -3.0377854 0.99649081 1.9975871 0.032243768 -0.037163869 -3.0749493
Loop time of 2.34844 on 1 procs for 4401 steps with 800 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-2.93913047033 -3.07494921994 -3.07494925979
Force two-norm initial, final = 25.9452 0.920316
Force max component initial, final = 19.0294 0.548784
Final line search alpha, max atom move = 0.000841982 0.000462066
Iterations, force evaluations = 4401 8540
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9026 | 1.9026 | 1.9026 | 0.0 | 81.01
Neigh | 0.027466 | 0.027466 | 0.027466 | 0.0 | 1.17
Comm | 0.020059 | 0.020059 | 0.020059 | 0.0 | 0.85
Output | 0.0028694 | 0.0028694 | 0.0028694 | 0.0 | 0.12
Modify | 0.018381 | 0.018381 | 0.018381 | 0.0 | 0.78
Other | | 0.3771 | | | 16.06
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 342 ave 342 max 342 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7244 ave 7244 max 7244 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7244
Ave neighs/atom = 9.055
Neighbor list builds = 109
Dangerous builds = 0
minimize 0.0 1.0e-2 10000 100000
Memory usage per processor = 3.60343 Mbytes
Step Temp PotEng Pxx Pyy Pxy 3 emin
6314 0 -3.0377854 0.99649081 1.9975871 0.032243768 3.5527137e-17 -3.0377854
6350 0 -3.0377426 0.9995618 1.9997582 0.032364722 -4.5395813e-05 -3.037788
6400 0 -3.0377432 0.99984154 1.9998786 0.032403541 -4.5666168e-05 -3.0377889
6450 0 -3.0377267 0.99999473 2.0002343 0.032176487 -6.317327e-05 -3.0377899
6500 0 -3.0377343 1.0000023 1.9999491 0.032228066 -5.6306704e-05 -3.0377906
6550 0 -3.0377346 1.0001343 1.9999711 0.032298354 -5.6111747e-05 -3.0377907
6600 0 -3.0377349 1.0002038 1.9999408 0.032324674 -5.5966675e-05 -3.0377908
6650 0 -3.0377306 1.0004192 2.0000469 0.032324741 -6.0315852e-05 -3.0377909
6700 0 -3.0377323 1.0000441 2.000009 0.032302097 -5.8641949e-05 -3.037791
6750 0 -3.0377303 1.0000605 2.0000938 0.032293244 -6.0671758e-05 -3.037791
6800 0 -3.0377231 1.0004525 2.0003454 0.032282004 -6.7960388e-05 -3.0377911
6850 0 -3.0377314 0.99987595 1.9999542 0.032227371 -5.9796937e-05 -3.0377912
6900 0 -3.0377256 0.99344819 2.0011607 0.031344595 -6.9303736e-05 -3.0377949
6950 0 -3.0373578 0.99761743 2.0225249 0.030185311 -0.00050004148 -3.0378578
7000 0 -3.0378367 1.0018764 1.9978072 0.032669355 -6.3346776e-05 -3.0379001
7050 0 -3.037828 1.0008325 1.9993554 0.033274825 -7.6731821e-05 -3.0379047
7100 0 -3.0378259 0.99929476 2.000522 0.033459662 -8.1578573e-05 -3.0379074
7150 0 -3.0378481 1.0010779 1.9992842 0.0335711 -6.0551519e-05 -3.0379087
7200 0 -3.0378388 0.99931209 2.0002124 0.033322503 -7.0644382e-05 -3.0379094
7250 0 -3.0378359 1.0003652 1.9999793 0.033413223 -7.4037459e-05 -3.0379099
7300 0 -3.0378373 0.99974121 2.0001941 0.03354157 -7.2831065e-05 -3.0379102
7350 0 -3.0378405 1.000399 1.9998044 0.033708545 -6.9814263e-05 -3.0379103
7400 0 -3.0378346 0.99989677 2.0001045 0.03373625 -7.5817257e-05 -3.0379104
7450 0 -3.0378359 1.0001255 1.9999563 0.033756091 -7.4569461e-05 -3.0379105
7500 0 -3.0378358 0.99994381 2.0000901 0.033790565 -7.4692471e-05 -3.0379105
7550 0 -3.0378365 1.0001569 2.0000048 0.033810907 -7.3987385e-05 -3.0379105
7600 0 -3.0378378 0.99995421 1.9999929 0.033778739 -7.2688901e-05 -3.0379105
7650 0 -3.0378356 1.0000328 2.0000725 0.033750734 -7.4891228e-05 -3.0379105
7700 0 -3.0378356 1.0000928 2.000025 0.033739518 -7.492587e-05 -3.0379105
7750 0 -3.037836 1.000026 2.0000007 0.033743007 -7.4483428e-05 -3.0379105
7800 0 -3.0378354 1.0000164 2.0000445 0.033752032 -7.5086586e-05 -3.0379105
7850 0 -3.0378352 1.0000397 2.0000524 0.033753896 -7.5318252e-05 -3.0379105
7900 0 -3.0378354 1.0000486 2.0000488 0.033742064 -7.5113089e-05 -3.0379105
7904 0 -3.0378356 1.0000321 2.0000425 0.033740786 -7.491864e-05 -3.0379105
Loop time of 0.858773 on 1 procs for 1590 steps with 800 atoms
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-3.03778539031 -3.0379105126 -3.03791051261
Force two-norm initial, final = 3.7074 0.00953997
Force max component initial, final = 3.0105 0.0052229
Final line search alpha, max atom move = 0.0789456 0.000412325
Iterations, force evaluations = 1590 3180
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.70479 | 0.70479 | 0.70479 | 0.0 | 82.07
Neigh | 0.00049901 | 0.00049901 | 0.00049901 | 0.0 | 0.06
Comm | 0.0068367 | 0.0068367 | 0.0068367 | 0.0 | 0.80
Output | 0.00099421 | 0.00099421 | 0.00099421 | 0.0 | 0.12
Modify | 0.0066617 | 0.0066617 | 0.0066617 | 0.0 | 0.78
Other | | 0.139 | | | 16.19
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 340 ave 340 max 340 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7246 ave 7246 max 7246 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7246
Ave neighs/atom = 9.0575
Neighbor list builds = 2
Dangerous builds = 0
# Final refinement uses nreset to eliminate stress offset
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3 nreset 100
minimize 0.0 1.0e-4 10000 100000
Memory usage per processor = 3.60343 Mbytes
Step Temp PotEng Pxx Pyy Pxy 3 emin
7904 0 -3.0378356 1.0000321 2.0000425 0.033740786 0 -3.0378356
7950 0 -3.0378364 1.000001 2.0000015 0.03373689 8.3404927e-07 -3.0378356
8000 0 -3.0378364 0.99999791 2.0000025 0.033733241 8.1782018e-07 -3.0378356
8050 0 -3.0378364 1.0000013 1.9999999 0.033727555 1.0952852e-07 -3.0378363
8100 0 -3.0378364 0.99999975 1.9999993 0.03372457 1.1467852e-07 -3.0378363
8150 0 -3.0378364 0.99999962 1.9999999 0.033723065 -1.6306321e-08 -3.0378364
8200 0 -3.0378364 1.0000001 1.9999991 0.033723385 -9.8605362e-09 -3.0378364
8250 0 -3.0378364 0.9999999 1.9999999 0.033724134 1.6533658e-08 -3.0378364
8300 0 -3.0378364 0.99999987 1.9999999 0.033724908 2.416758e-08 -3.0378364
8350 0 -3.0378364 1 1.9999991 0.0337256 1.2773347e-08 -3.0378364
8400 0 -3.0378364 0.9999998 1.9999999 0.033725946 -1.1867813e-08 -3.0378364
8450 0 -3.0378364 0.99999995 1.9999999 0.033726404 -1.3134768e-08 -3.0378364
8500 0 -3.0378364 0.99999967 1.9999999 0.033726454 -1.1481639e-08 -3.0378364
8550 0 -3.0378364 0.99999998 1.9999998 0.033726207 2.9756123e-09 -3.0378364
8600 0 -3.0378364 0.99999979 1.9999999 0.033726113 4.7253467e-09 -3.0378364
8650 0 -3.0378364 0.99999993 1.9999999 0.033725878 -1.9054681e-10 -3.0378364
8700 0 -3.0378364 1 1.9999997 0.033725586 4.9116894e-09 -3.0378364
8750 0 -3.0378364 0.99999991 2 0.033725386 7.3634181e-10 -3.0378364
8753 0 -3.0378364 1 2 0.033725385 -1.0901182e-09 -3.0378364
Loop time of 0.461345 on 1 procs for 849 steps with 800 atoms
99.7% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-3.03783559397 -3.03783642331 -3.03783642331
Force two-norm initial, final = 0.0462457 9.79399e-05
Force max component initial, final = 0.0364742 4.124e-05
Final line search alpha, max atom move = 1 4.124e-05
Iterations, force evaluations = 849 1698
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.37917 | 0.37917 | 0.37917 | 0.0 | 82.19
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0035837 | 0.0035837 | 0.0035837 | 0.0 | 0.78
Output | 0.00053287 | 0.00053287 | 0.00053287 | 0.0 | 0.12
Modify | 0.0036094 | 0.0036094 | 0.0036094 | 0.0 | 0.78
Other | | 0.07445 | | | 16.14
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 342 ave 342 max 342 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7245 ave 7245 max 7245 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7245
Ave neighs/atom = 9.05625
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:04

542
examples/min/log.15Feb16.min.box.g++.4 Normal file
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LAMMPS (15 Feb 2016)
# 2d Lennard-Jones melt and subsequent energy minimization,
# followed by box relaxation to a target stress state
#
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 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
thermo 100
run 1000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 22 22 1
Memory usage per processor = 2.47676 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 3.3136053 -0.77935264 0 2.5301106 15.833296
600 3.3888915 -0.85213737 0 2.532518 15.162759
700 3.2123636 -0.67641846 0 2.5319297 16.31059
800 3.3016408 -0.76570603 0 2.5318077 15.639259
900 3.4621697 -0.92610292 0 2.5317391 14.773473
1000 3.3058424 -0.77076863 0 2.5309414 15.708171
Loop time of 0.0697336 on 4 procs for 1000 steps with 800 atoms
Performance: 6195003.241 tau/day, 14340.285 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.033633 | 0.034047 | 0.03476 | 0.2 | 48.82
Neigh | 0.01311 | 0.01343 | 0.013635 | 0.2 | 19.26
Comm | 0.014188 | 0.014708 | 0.015157 | 0.4 | 21.09
Output | 0.00019526 | 0.00020427 | 0.00022554 | 0.1 | 0.29
Modify | 0.0031531 | 0.0032287 | 0.0034115 | 0.2 | 4.63
Other | | 0.004116 | | | 5.90
Nlocal: 200 ave 202 max 196 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Nghost: 170.25 ave 174 max 167 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 1934.75 ave 1972 max 1873 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 7739
Ave neighs/atom = 9.67375
Neighbor list builds = 203
Dangerous builds = 0
# perform the box relaxation by progressively
# adding more degrees of freedom, for smoother
# convergence
neigh_modify delay 0 every 1 check yes
velocity all create 0.0 1
thermo 50
# atoms only
minimize 1.0e-6 0.001 1000 10000
Memory usage per processor = 3.60176 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 0 -0.77076863 0 -0.77076863 12.920868
1050 0 -2.8318266 0 -2.8318266 -1.1892931
1100 0 -2.8658339 0 -2.8658339 -1.0859975
1150 0 -2.8788056 0 -2.8788056 -1.1017533
1200 0 -2.8831122 0 -2.8831122 -1.1004001
1250 0 -2.8877971 0 -2.8877971 -1.0596414
1300 0 -2.8887969 0 -2.8887969 -1.0448381
Loop time of 0.0555401 on 4 procs for 300 steps with 800 atoms
99.5% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.770768629298 -2.88879411525 -2.88879694984
Force two-norm initial, final = 1950.95 0.825241
Force max component initial, final = 374.098 0.224821
Final line search alpha, max atom move = 0.410301 0.0922441
Iterations, force evaluations = 300 595
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.032524 | 0.033133 | 0.033955 | 0.3 | 59.66
Neigh | 0.0036891 | 0.0038166 | 0.0038748 | 0.1 | 6.87
Comm | 0.0073385 | 0.0081375 | 0.0089004 | 0.6 | 14.65
Output | 8.5831e-05 | 9.042e-05 | 0.0001018 | 0.1 | 0.16
Modify | 0.00034714 | 0.0003776 | 0.00040054 | 0.1 | 0.68
Other | | 0.009985 | | | 17.98
Nlocal: 200 ave 202 max 196 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 172.5 ave 175 max 169 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 1757 ave 1793 max 1721 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 7028
Ave neighs/atom = 8.785
Neighbor list builds = 59
Dangerous builds = 0
# isotropic volume relaxation to hydrostatic target
fix 3 all box/relax iso 1.5 vmax 1.0e-3
variable emin equal pe+f_3/atoms
thermo_style custom step temp pe pxx pyy pxy f_3 v_emin
# anisotropic volume relaxation to hydrostatic target
minimize 0.0 10.0e0 10000 100000
Memory usage per processor = 3.60176 Mbytes
Step Temp PotEng Pxx Pyy Pxy 3 emin
1300 0 -2.8887969 -0.93904343 -1.1506328 -0.0037265764 0 -2.8887969
1350 0 -2.889313 1.555657 1.4414453 -0.025585726 -0.10933729 -2.9986503
1400 0 -2.8958621 1.5320803 1.476774 0.0041557664 -0.1208966 -3.0167587
1403 0 -2.8962558 1.5290172 1.4743135 0.00471395 -0.12088872 -3.0171446
Loop time of 0.0181124 on 4 procs for 103 steps with 800 atoms
93.8% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-2.88879694984 -3.01714081772 -3.01714455432
Force two-norm initial, final = 4823.19 9.6427
Force max component initial, final = 4823.19 3.04698
Final line search alpha, max atom move = 2.87851e-05 8.77075e-05
Iterations, force evaluations = 103 161
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0093105 | 0.0095073 | 0.009722 | 0.1 | 52.49
Neigh | 0.0010061 | 0.00104 | 0.0010571 | 0.1 | 5.74
Comm | 0.0019989 | 0.0022128 | 0.0024509 | 0.3 | 12.22
Output | 7.2956e-05 | 7.4506e-05 | 7.9155e-05 | 0.0 | 0.41
Modify | 8.9645e-05 | 0.00010043 | 0.00010562 | 0.1 | 0.55
Other | | 0.005177 | | | 28.58
Nlocal: 200 ave 202 max 198 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 178.25 ave 181 max 175 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Neighs: 1854.75 ave 1878 max 1822 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 7419
Ave neighs/atom = 9.27375
Neighbor list builds = 16
Dangerous builds = 0
fix 3 all box/relax aniso 1.5 vmax 1.0e-3
minimize 0.0 10.0 10000 100000
Memory usage per processor = 3.60176 Mbytes
Step Temp PotEng Pxx Pyy Pxy 3 emin
1403 0 -2.8962558 1.5290172 1.4743135 0.00471395 0 -2.8962558
1404 0 -2.8963678 1.49615 1.499767 0.0037848845 9.6365079e-05 -2.8962714
Loop time of 0.000356197 on 4 procs for 1 steps with 800 atoms
0.0% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-2.8962558314 -2.8962558314 -2.89627142801
Force two-norm initial, final = 35.4271 9.77898
Force max component initial, final = 25.6271 3.39863
Final line search alpha, max atom move = 3.90213e-05 0.000132619
Iterations, force evaluations = 1 2
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00017381 | 0.0001772 | 0.00018167 | 0.0 | 49.75
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 3.314e-05 | 3.7372e-05 | 4.0054e-05 | 0.0 | 10.49
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 2.1458e-06 | 2.6226e-06 | 3.0994e-06 | 0.0 | 0.74
Other | | 0.000139 | | | 39.02
Nlocal: 200 ave 202 max 197 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 178.25 ave 180 max 176 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 1847 ave 1872 max 1822 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 7388
Ave neighs/atom = 9.235
Neighbor list builds = 0
Dangerous builds = 0
# anisotropic volume relaxation to non-hydrostatic target
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3
minimize 0.0 10.0 10000 100000
Memory usage per processor = 3.60176 Mbytes
Step Temp PotEng Pxx Pyy Pxy 3 emin
1404 0 -2.8963678 1.49615 1.499767 0.0037848845 -7.1054274e-17 -2.8963678
1450 0 -2.8925305 0.94584654 2.0945709 -0.029336194 -0.016086454 -2.9086169
1500 0 -2.8975934 1.0123866 2.009477 -0.036498498 -0.01841842 -2.9160118
1550 0 -2.903576 1.0046986 1.9380791 -0.037683327 -0.020970768 -2.9245468
1592 0 -2.9061298 0.98518925 1.9835783 -0.048932212 -0.024234721 -2.9303646
Loop time of 0.0329762 on 4 procs for 188 steps with 800 atoms
100.1% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-2.89636779309 -2.93027409874 -2.93036456323
Force two-norm initial, final = 622.345 9.97488
Force max component initial, final = 441.816 3.5534
Final line search alpha, max atom move = 4.49831e-05 0.000159843
Iterations, force evaluations = 188 295
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.017398 | 0.017577 | 0.017932 | 0.2 | 53.30
Neigh | 0.00051427 | 0.00052792 | 0.00054002 | 0.0 | 1.60
Comm | 0.0033214 | 0.0037473 | 0.0040131 | 0.4 | 11.36
Output | 0.00013399 | 0.00013644 | 0.00014377 | 0.0 | 0.41
Modify | 0.00018668 | 0.00020236 | 0.00021911 | 0.1 | 0.61
Other | | 0.01079 | | | 32.71
Nlocal: 200 ave 202 max 196 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Nghost: 179.5 ave 183 max 176 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 1862.5 ave 1893 max 1821 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Total # of neighbors = 7450
Ave neighs/atom = 9.3125
Neighbor list builds = 8
Dangerous builds = 0
minimize 0.0 1.0 10000 100000
Memory usage per processor = 3.60176 Mbytes
Step Temp PotEng Pxx Pyy Pxy 3 emin
1592 0 -2.9061298 0.98518925 1.9835783 -0.048932212 3.5527137e-17 -2.9061298
1600 0 -2.9046586 1.0529014 2.0593731 -0.050860896 -0.0020973121 -2.9067559
1650 0 -2.9077781 0.98217454 2.0557227 -0.053762924 -0.0037318755 -2.91151
1700 0 -2.911189 0.94319026 2.0024059 -0.048920328 -0.0038748811 -2.9150639
1750 0 -2.9164651 0.94353792 1.9550633 -0.029155121 -0.0061062511 -2.9225713
1800 0 -2.9184486 0.98650677 2.0009524 -0.0078670444 -0.0093780731 -2.9278267
1850 0 -2.9212867 1.0498564 1.9603902 0.010111603 -0.010488406 -2.9317751
1900 0 -2.9213403 0.99740355 2.0425934 0.026161958 -0.014050539 -2.9353909
1950 0 -2.9266889 0.99152482 1.9933997 0.03409256 -0.015614063 -2.942303
2000 0 -2.9285908 1.0350107 2.0275013 0.033065933 -0.019303075 -2.9478939
2050 0 -2.9304105 0.96637822 1.9834345 0.026336793 -0.020013699 -2.9504242
2100 0 -2.9330357 0.97845141 1.9025015 0.021574938 -0.019779787 -2.9528155
2150 0 -2.9331851 0.99675158 2.0074323 -0.0065532256 -0.02481578 -2.9580009
2200 0 -2.9368641 0.98438888 1.9246359 -0.019231932 -0.025247992 -2.962112
2250 0 -2.939513 1.0279353 1.9269466 -0.023572931 -0.027689455 -2.9672025
2300 0 -2.942156 0.94637839 2.0082098 -0.021822127 -0.031345014 -2.973501
2350 0 -2.948735 0.93651267 1.9760466 -0.022735061 -0.032992594 -2.9817275
2400 0 -2.9511278 0.99314345 1.9385123 -0.016972758 -0.032842878 -2.9839707
2450 0 -2.9533012 0.97729639 2.0154201 -0.015641052 -0.035591247 -2.9888925
2500 0 -2.954422 1.0349465 2.0120139 -0.019420841 -0.036210665 -2.9906327
2550 0 -2.9575726 0.99530485 1.9284884 -0.016807344 -0.034822839 -2.9923955
2600 0 -2.9573298 0.97329576 2.0164988 -0.01795058 -0.036637536 -2.9939673
2650 0 -2.9593898 1.0203573 1.9464484 -0.020216394 -0.035748408 -2.9951382
2700 0 -2.960177 0.96566571 2.0425296 0.0035371639 -0.037754691 -2.9979317
2750 0 -2.9629231 1.0117643 1.9542228 0.02632338 -0.036929577 -2.9998526
2800 0 -2.9657029 0.92990254 1.937087 0.017338918 -0.037267648 -3.0029706
2850 0 -2.9658958 0.91635927 1.9894507 0.019284324 -0.038677428 -3.0045732
2900 0 -2.965953 0.9735388 2.0220848 0.02052448 -0.040410779 -3.0063638
2950 0 -2.9674506 1.0026034 1.9615451 0.018621661 -0.040233908 -3.0076845
3000 0 -2.9681703 0.95627387 1.9536224 0.012057729 -0.041412351 -3.0095827
3050 0 -2.9686102 0.94751435 1.9576194 0.0092272739 -0.042069932 -3.0106801
3100 0 -2.9688024 0.94009207 1.9632077 0.00083680762 -0.04264597 -3.0114483
3150 0 -2.9689839 0.94565802 1.967564 -0.00031007068 -0.0432371 -3.012221
3200 0 -2.9694532 0.95670917 1.9517533 0.004846097 -0.043402976 -3.0128562
3250 0 -2.9691757 0.98229076 1.944547 0.0041700186 -0.044427988 -3.0136037
3300 0 -2.9688471 1.0032058 1.9262141 -0.026504883 -0.046396712 -3.0152438
3350 0 -2.9696022 0.95533401 2.0105577 -0.025342982 -0.049074731 -3.0186769
3400 0 -2.9731784 0.98985638 1.94557 -0.02748758 -0.050096034 -3.0232744
3450 0 -2.974309 1.0513691 1.9998728 -0.020391151 -0.053374636 -3.0276836
3500 0 -2.9765721 0.92595096 1.9633667 -0.020063084 -0.052822995 -3.0293951
3550 0 -2.9777457 0.93450229 1.9995925 -0.013662027 -0.055309483 -3.0330551
3600 0 -2.9806963 0.97640261 1.9283298 -0.0027545827 -0.05512979 -3.0358261
3650 0 -2.9807118 0.93736872 1.9944251 0.0082873538 -0.056469091 -3.0371809
3700 0 -2.9831586 1.0685131 2.0595128 0.06305966 -0.059015668 -3.0421743
3750 0 -2.9875796 0.91547454 2.0024827 0.065982869 -0.058535211 -3.0461148
3800 0 -2.9898449 0.93958431 1.9413764 0.05523992 -0.058407873 -3.0482528
3850 0 -2.9903134 0.93830475 1.9849576 0.045612541 -0.059283499 -3.0495969
3900 0 -2.9909848 0.9648608 1.994041 0.029853801 -0.059730698 -3.0507155
3950 0 -2.9920567 1.0174164 1.9831331 0.02751284 -0.060321142 -3.0523778
4000 0 -2.9931559 1.054449 2.0273684 0.025820071 -0.061814098 -3.05497
4050 0 -2.9967814 1.0336441 1.9607185 0.0080753355 -0.061169081 -3.0579505
4100 0 -2.996981 0.97811615 1.9997583 -0.0019083765 -0.062392266 -3.0593732
4150 0 -2.9983301 0.991139 1.9758294 -0.016110953 -0.062441222 -3.0607713
4200 0 -2.9995915 1.0106869 1.94477 -0.031095458 -0.062510217 -3.0621017
4250 0 -3.0001063 1.0128218 1.9591959 -0.040593262 -0.063330573 -3.0634368
4300 0 -3.0004474 1.0307974 2.0014391 -0.02845165 -0.064737002 -3.0651844
4350 0 -3.0023551 0.94191501 1.9833078 -0.025720298 -0.064657395 -3.0670125
4400 0 -3.0034901 0.92627522 1.9930372 -0.029253399 -0.065165877 -3.068656
4450 0 -3.0043084 0.94822317 1.9935963 -0.031195651 -0.065572365 -3.0698807
4500 0 -3.0046609 0.96345675 2.0190707 -0.039549039 -0.066952817 -3.0716137
4550 0 -3.0065584 1.0311919 1.9866639 -0.038624939 -0.067227259 -3.0737856
4600 0 -3.0087629 0.92310969 1.9583359 -0.035110538 -0.066754503 -3.0755174
4650 0 -3.0091217 1.0423151 1.9721517 -0.034927703 -0.068388691 -3.0775104
4700 0 -3.0114997 0.99672323 1.9830988 -0.048241072 -0.070376893 -3.0818766
4750 0 -3.0157144 0.93005562 1.9478873 -0.041212478 -0.070661825 -3.0863762
4800 0 -3.0170643 0.94982686 1.9707107 -0.016217397 -0.071816245 -3.0888806
4850 0 -3.0187449 0.96472623 1.9601211 -0.015502505 -0.072690566 -3.0914355
4900 0 -3.0187912 0.96300066 1.9632806 -0.013507355 -0.073036437 -3.0918277
4950 0 -3.0186022 0.95642396 1.9621686 0.00054760573 -0.073428768 -3.0920309
5000 0 -3.0183836 0.9494408 1.9520187 0.015769055 -0.074225535 -3.0926091
5050 0 -3.0182793 0.94895214 1.9567982 0.013131143 -0.074585191 -3.0928645
5100 0 -3.0181701 0.94187261 1.9560213 0.0077456348 -0.074917521 -3.0930876
5150 0 -3.0177645 0.93541836 1.96018 -0.0071875906 -0.075709553 -3.0934741
5200 0 -3.0178922 0.92272827 1.9365084 0.00055102294 -0.076432947 -3.0943251
5250 0 -3.0196541 0.99625947 1.9913119 -0.031679622 -0.078732819 -3.0983869
5300 0 -3.0244724 0.93077516 1.9153792 -0.028418358 -0.077643158 -3.1021155
5350 0 -3.025691 0.95290818 1.9263259 0.0018721029 -0.078001949 -3.103693
5400 0 -3.0256873 0.95659054 1.9606014 -0.010278289 -0.079028106 -3.1047154
5450 0 -3.0254641 0.9498986 1.9647294 -0.014184683 -0.07984313 -3.1053072
5500 0 -3.0246542 0.95996989 1.9814976 -0.018179831 -0.080970098 -3.1056243
5550 0 -3.0239232 0.98579742 1.9735322 -0.025560182 -0.082383595 -3.1063068
5600 0 -3.0237848 0.9479909 2.0195426 0.0030195864 -0.084189849 -3.1079746
5650 0 -3.0268106 0.94766402 1.964692 0.010752186 -0.083892975 -3.1107036
5700 0 -3.0278767 0.97021681 1.9671324 0.027681234 -0.084443887 -3.1123206
5750 0 -3.0303934 0.96494193 1.9497379 0.039647978 -0.084344583 -3.114738
5800 0 -3.0306454 0.9752013 1.9521019 0.05693752 -0.084567064 -3.1152124
5850 0 -3.0310671 0.95652383 1.9572113 0.068831395 -0.084556099 -3.1156232
5900 0 -3.0313081 0.95538786 1.9578087 0.07883359 -0.084550262 -3.1158584
5950 0 -3.0314843 0.95333099 1.9487315 0.085926517 -0.084409813 -3.1158941
6000 0 -3.0314748 0.9544137 1.9511524 0.10185896 -0.084510085 -3.1159848
6050 0 -3.0313105 0.9590106 1.959899 0.10814531 -0.084790331 -3.1161008
6100 0 -3.0313244 0.9580272 1.9605104 0.10879691 -0.08493735 -3.1162617
6130 0 -3.0313384 0.95532497 1.9595324 0.10924759 -0.084945274 -3.1162837
Loop time of 0.917613 on 4 procs for 4538 steps with 800 atoms
99.6% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-2.90612984251 -3.11628366855 -3.11628369961
Force two-norm initial, final = 21.7981 0.937604
Force max component initial, final = 14.4511 0.431389
Final line search alpha, max atom move = 0.000547499 0.000236185
Iterations, force evaluations = 4538 8462
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.49716 | 0.5033 | 0.51238 | 0.9 | 54.85
Neigh | 0.0065906 | 0.0068512 | 0.0069604 | 0.2 | 0.75
Comm | 0.094408 | 0.10467 | 0.11346 | 2.5 | 11.41
Output | 0.0040958 | 0.0041735 | 0.0043962 | 0.2 | 0.45
Modify | 0.0052106 | 0.0053825 | 0.0055635 | 0.2 | 0.59
Other | | 0.2932 | | | 31.96
Nlocal: 200 ave 203 max 197 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 181.5 ave 183 max 181 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Neighs: 1814.25 ave 1838 max 1768 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 7257
Ave neighs/atom = 9.07125
Neighbor list builds = 104
Dangerous builds = 0
minimize 0.0 1.0e-2 10000 100000
Memory usage per processor = 3.60176 Mbytes
Step Temp PotEng Pxx Pyy Pxy 3 emin
6130 0 -3.0313384 0.95532497 1.9595324 0.10924759 -3.5527137e-17 -3.0313384
6150 0 -3.0304428 0.9947235 1.9969091 0.10935746 -0.00091797415 -3.0313608
6200 0 -3.0303022 1.0001878 2.000297 0.10984247 -0.0010859161 -3.0313882
6250 0 -3.0303474 0.99938469 1.9997606 0.10892851 -0.0010447278 -3.0313921
6300 0 -3.030364 0.99909678 1.9994518 0.10814831 -0.0010293495 -3.0313933
6350 0 -3.0303717 0.99985291 1.9992837 0.1079772 -0.0010221246 -3.0313938
6400 0 -3.0303643 0.99996396 1.9996376 0.10768185 -0.0010298963 -3.0313942
6450 0 -3.0303548 1.0000119 1.9998057 0.10740047 -0.0010396613 -3.0313944
6500 0 -3.0303565 0.99994354 1.9997054 0.10745687 -0.0010380365 -3.0313945
6550 0 -3.0303597 0.99997619 1.99973 0.10757709 -0.0010348341 -3.0313946
6600 0 -3.0303627 0.99989601 1.9997112 0.10753202 -0.0010319717 -3.0313947
6650 0 -3.0303601 0.99996966 1.9998692 0.10746847 -0.0010345994 -3.0313947
6700 0 -3.0303593 0.9999198 1.9999738 0.10750063 -0.001035439 -3.0313948
6750 0 -3.030358 0.99984873 1.9999385 0.10758609 -0.0010368344 -3.0313948
6800 0 -3.0303557 0.99989034 1.999929 0.10766313 -0.0010390742 -3.0313948
6850 0 -3.0303539 0.99997112 1.9999636 0.10767624 -0.0010409153 -3.0313948
6900 0 -3.0303556 0.99996801 1.9998614 0.10770653 -0.0010392495 -3.0313948
6950 0 -3.0303537 0.99999067 1.999933 0.10772838 -0.0010411386 -3.0313949
7000 0 -3.0303521 0.99997861 1.9999979 0.1077447 -0.001042745 -3.0313949
7050 0 -3.0303524 0.99996541 1.9999799 0.1077349 -0.0010424959 -3.0313949
7100 0 -3.0303525 0.99999438 1.9999815 0.10775527 -0.0010423842 -3.0313949
7150 0 -3.0303535 0.99998124 1.9999354 0.10775281 -0.0010413311 -3.0313949
7200 0 -3.0303532 0.99999763 1.9999874 0.10772418 -0.001041638 -3.0313949
7250 0 -3.0303539 0.99996105 1.9999842 0.10772361 -0.001041024 -3.0313949
7300 0 -3.0303535 0.99998962 1.9999966 0.10770842 -0.001041396 -3.0313949
7350 0 -3.0303535 1.0000095 1.9999958 0.10769735 -0.0010413981 -3.0313949
7400 0 -3.0303541 1.0000005 1.9999858 0.1076965 -0.0010408177 -3.0313949
7450 0 -3.030354 1.000003 1.9999931 0.10769929 -0.0010409352 -3.0313949
7500 0 -3.0303537 1.0000034 1.9999885 0.10769864 -0.0010411458 -3.0313949
7550 0 -3.0303533 1.0000018 1.9999949 0.10769873 -0.0010415749 -3.0313949
7600 0 -3.0303529 1.0000017 2.0000034 0.10770161 -0.0010419517 -3.0313949
7607 0 -3.0303527 1.0000104 2.0000131 0.10770259 -0.0010421819 -3.0313949
Loop time of 0.320295 on 4 procs for 1477 steps with 800 atoms
99.5% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-3.03133842556 -3.03139488756 -3.03139488756
Force two-norm initial, final = 51.7975 0.00951208
Force max component initial, final = 38.3845 0.00429369
Final line search alpha, max atom move = 0.165786 0.000711832
Iterations, force evaluations = 1477 2954
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.16982 | 0.17493 | 0.18263 | 1.2 | 54.61
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.032802 | 0.041339 | 0.047369 | 2.7 | 12.91
Output | 0.0013659 | 0.0013915 | 0.0014555 | 0.1 | 0.43
Modify | 0.0018022 | 0.0019018 | 0.0019994 | 0.2 | 0.59
Other | | 0.1007 | | | 31.45
Nlocal: 200 ave 203 max 197 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 181.5 ave 183 max 181 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Neighs: 1815.5 ave 1838 max 1771 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 7262
Ave neighs/atom = 9.0775
Neighbor list builds = 0
Dangerous builds = 0
# Final refinement uses nreset to eliminate stress offset
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-3 nreset 100
minimize 0.0 1.0e-4 10000 100000
Memory usage per processor = 3.60176 Mbytes
Step Temp PotEng Pxx Pyy Pxy 3 emin
7607 0 -3.0303527 1.0000104 2.0000131 0.10770259 3.5527137e-17 -3.0303527
7650 0 -3.030353 0.9999904 2.0000076 0.10770145 2.9878713e-07 -3.0303527
7700 0 -3.0303532 1.0000001 1.9999991 0.10770283 4.6315231e-07 -3.0303527
7750 0 -3.0303531 1.0000061 2.0000052 0.10770517 2.2696958e-08 -3.0303531
7800 0 -3.0303533 0.99999944 1.999999 0.10770496 1.5707701e-07 -3.0303531
7850 0 -3.0303533 0.99999877 1.9999985 0.10770396 4.6999275e-08 -3.0303532
7900 0 -3.0303533 0.99999936 2 0.10770371 6.8328929e-09 -3.0303532
7950 0 -3.0303532 0.99999993 2.0000004 0.10770354 -1.6637037e-08 -3.0303533
8000 0 -3.0303532 1.0000004 2.0000006 0.10770361 -2.6542248e-08 -3.0303533
8050 0 -3.0303532 1.0000003 2.0000002 0.1077037 1.7569483e-10 -3.0303532
8100 0 -3.0303532 1.0000002 2.0000001 0.10770386 3.0847712e-09 -3.0303532
8150 0 -3.0303532 1.0000003 2.0000002 0.10770398 -1.4421314e-09 -3.0303532
8200 0 -3.0303532 1.0000001 2.0000001 0.10770407 7.0744514e-10 -3.0303532
8201 0 -3.0303532 0.99999993 2 0.10770406 3.9670625e-09 -3.0303532
Loop time of 0.129254 on 4 procs for 594 steps with 800 atoms
99.8% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = force tolerance
Energy initial, next-to-last, final =
-3.03035270564 -3.0303532347 -3.0303532347
Force two-norm initial, final = 0.0165847 8.42164e-05
Force max component initial, final = 0.0112809 5.39223e-05
Final line search alpha, max atom move = 1 5.39223e-05
Iterations, force evaluations = 594 1188
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.068712 | 0.07072 | 0.073833 | 0.7 | 54.71
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.01326 | 0.016652 | 0.019008 | 1.7 | 12.88
Output | 0.00053024 | 0.00053924 | 0.00056386 | 0.1 | 0.42
Modify | 0.00071311 | 0.00077671 | 0.00081825 | 0.2 | 0.60
Other | | 0.04057 | | | 31.39
Nlocal: 200 ave 203 max 197 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 181.5 ave 183 max 181 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Neighs: 1816.25 ave 1841 max 1772 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 7265
Ave neighs/atom = 9.08125
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:01

141
examples/min/log.15Feb16.min.g++.1 Normal file
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LAMMPS (15 Feb 2016)
# 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 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
thermo 100
run 1000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 22 22 1
Memory usage per processor = 2.47843 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 -0.85213743 0 2.532518 15.162759
700 3.2123675 -0.67642318 0 2.5319289 16.310565
800 3.3016275 -0.76569171 0 2.5318087 15.639335
900 3.4639203 -0.92788002 0 2.5317104 14.765912
1000 3.3256788 -0.79078181 0 2.5307399 15.599298
Loop time of 0.200054 on 1 procs for 1000 steps with 800 atoms
Performance: 2159417.710 tau/day, 4998.652 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12834 | 0.12834 | 0.12834 | 0.0 | 64.15
Neigh | 0.051023 | 0.051023 | 0.051023 | 0.0 | 25.50
Comm | 0.0045159 | 0.0045159 | 0.0045159 | 0.0 | 2.26
Output | 9.2268e-05 | 9.2268e-05 | 9.2268e-05 | 0.0 | 0.05
Modify | 0.011642 | 0.011642 | 0.011642 | 0.0 | 5.82
Other | | 0.004437 | | | 2.22
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 317 ave 317 max 317 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 7743 ave 7743 max 7743 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7743
Ave neighs/atom = 9.67875
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 = 3.60343 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.3256788 -0.79078181 0 2.5307399 15.599298
1050 3.3256788 -2.8361415 0 0.48538014 1.6090001
1100 3.3256788 -2.8661626 0 0.45535906 1.6175322
1150 3.3256788 -2.8783275 0 0.44319421 1.6293715
1200 3.3256788 -2.8838202 0 0.43770144 1.6393211
1250 3.3256788 -2.8956657 0 0.42585599 1.604841
1300 3.3256788 -2.9039122 0 0.41760945 1.6594733
1350 3.3256788 -2.9100776 0 0.4114441 1.7004165
1400 3.3256788 -2.9131297 0 0.40839199 1.7078217
1450 3.3256788 -2.9167506 0 0.40477104 1.7780477
1475 3.3256788 -2.9169436 0 0.4045781 1.7914542
Loop time of 0.241237 on 1 procs for 475 steps with 800 atoms
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.790781812776 -2.9169407756 -2.91694356781
Force two-norm initial, final = 1905.47 0.794548
Force max component initial, final = 343.392 0.268404
Final line search alpha, max atom move = 0.347566 0.0932881
Iterations, force evaluations = 475 940
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.1979 | 0.1979 | 0.1979 | 0.0 | 82.04
Neigh | 0.021076 | 0.021076 | 0.021076 | 0.0 | 8.74
Comm | 0.0028479 | 0.0028479 | 0.0028479 | 0.0 | 1.18
Output | 8.9169e-05 | 8.9169e-05 | 8.9169e-05 | 0.0 | 0.04
Modify | 0.002037 | 0.002037 | 0.002037 | 0.0 | 0.84
Other | | 0.01728 | | | 7.16
Nlocal: 800 ave 800 max 800 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 329 ave 329 max 329 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6957 ave 6957 max 6957 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6957
Ave neighs/atom = 8.69625
Neighbor list builds = 85
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 4
thermo 100
run 1000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 22 22 1
Memory usage per processor = 2.47676 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 3.3136053 -0.77935264 0 2.5301106 15.833296
600 3.3888915 -0.85213737 0 2.532518 15.162759
700 3.2123636 -0.67641846 0 2.5319297 16.31059
800 3.3016408 -0.76570603 0 2.5318077 15.639259
900 3.4621697 -0.92610292 0 2.5317391 14.773473
1000 3.3058424 -0.77076863 0 2.5309414 15.708171
Loop time of 0.0792709 on 4 procs for 1000 steps with 800 atoms
Performance: 5449666.950 tau/day, 12614.970 timesteps/s
94.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.033109 | 0.03398 | 0.035743 | 0.6 | 42.87
Neigh | 0.013423 | 0.013508 | 0.013607 | 0.1 | 17.04
Comm | 0.019584 | 0.022177 | 0.023639 | 1.0 | 27.98
Output | 0.0001688 | 0.00018328 | 0.00020313 | 0.1 | 0.23
Modify | 0.0031462 | 0.0032172 | 0.0032594 | 0.1 | 4.06
Other | | 0.006205 | | | 7.83
Nlocal: 200 ave 202 max 196 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Nghost: 170.25 ave 174 max 167 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 1934.75 ave 1972 max 1873 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 7739
Ave neighs/atom = 9.67375
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 = 3.60176 Mbytes
Step Temp E_pair E_mol TotEng Press
1000 3.3058424 -0.77076863 0 2.5309414 15.708171
1050 3.3058424 -2.8318266 0 0.46988351 1.5980106
1100 3.3058424 -2.8658339 0 0.43587618 1.7013061
1150 3.3058424 -2.8788056 0 0.42290443 1.6855503
1200 3.3058424 -2.8831122 0 0.41859789 1.6869035
1250 3.3058424 -2.8877971 0 0.413913 1.7276622
1300 3.3058424 -2.8887969 0 0.41291311 1.7424655
Loop time of 0.053865 on 4 procs for 300 steps with 800 atoms
98.4% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.770768629298 -2.88879411525 -2.88879694984
Force two-norm initial, final = 1950.95 0.825241
Force max component initial, final = 374.098 0.224821
Final line search alpha, max atom move = 0.410301 0.0922441
Iterations, force evaluations = 300 595
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.032029 | 0.032993 | 0.034442 | 0.5 | 61.25
Neigh | 0.0037003 | 0.0038341 | 0.0038917 | 0.1 | 7.12
Comm | 0.0051906 | 0.0071514 | 0.0082016 | 1.4 | 13.28
Output | 8.1778e-05 | 8.5294e-05 | 9.5844e-05 | 0.1 | 0.16
Modify | 0.00035262 | 0.00036818 | 0.00039029 | 0.1 | 0.68
Other | | 0.009433 | | | 17.51
Nlocal: 200 ave 202 max 196 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 172.5 ave 175 max 169 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 1757 ave 1793 max 1721 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 7028
Ave neighs/atom = 8.785
Neighbor list builds = 59
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 17 17 17
Memory usage per processor = 7.53726 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 3.56196 on 1 procs for 100 steps with 23328 atoms
Performance: 4.851 ns/day, 4.947 hours/ns, 28.074 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.404 | 3.404 | 3.404 | 0.0 | 95.56
Neigh | 0.069748 | 0.069748 | 0.069748 | 0.0 | 1.96
Comm | 0.020276 | 0.020276 | 0.020276 | 0.0 | 0.57
Output | 0.00094318 | 0.00094318 | 0.00094318 | 0.0 | 0.03
Modify | 0.03792 | 0.03792 | 0.03792 | 0.0 | 1.06
Other | | 0.02909 | | | 0.82
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 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 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 = 7.54369 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 4.87683 on 1 procs for 100 steps with 23328 atoms
Performance: 3.543 ns/day, 6.773 hours/ns, 20.505 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.4604 | 3.4604 | 3.4604 | 0.0 | 70.96
Neigh | 0.13708 | 0.13708 | 0.13708 | 0.0 | 2.81
Comm | 0.018285 | 0.018285 | 0.018285 | 0.0 | 0.37
Output | 0.01176 | 0.01176 | 0.01176 | 0.0 | 0.24
Modify | 1.219 | 1.219 | 1.219 | 0.0 | 25.00
Other | | 0.03037 | | | 0.62
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
Total wall time: 0:00:08

160
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LAMMPS (15 Feb 2016)
# 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 17 17 17
Memory usage per processor = 4.74184 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 0.933348 on 4 procs for 100 steps with 23328 atoms
Performance: 18.514 ns/day, 1.296 hours/ns, 107.141 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.86277 | 0.86536 | 0.87057 | 0.3 | 92.72
Neigh | 0.017456 | 0.017565 | 0.017691 | 0.1 | 1.88
Comm | 0.026787 | 0.033015 | 0.037011 | 2.1 | 3.54
Output | 0.00049233 | 0.00060636 | 0.00074911 | 0.4 | 0.06
Modify | 0.0094292 | 0.0099058 | 0.010101 | 0.3 | 1.06
Other | | 0.0069 | | | 0.74
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 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 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 = 4.74184 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 1.2639 on 4 procs for 100 steps with 23328 atoms
Performance: 13.672 ns/day, 1.755 hours/ns, 79.120 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.86747 | 0.87285 | 0.87567 | 0.3 | 69.06
Neigh | 0.035299 | 0.03557 | 0.035746 | 0.1 | 2.81
Comm | 0.028839 | 0.031931 | 0.038177 | 2.0 | 2.53
Output | 0.0037065 | 0.0037336 | 0.0038128 | 0.1 | 0.30
Modify | 0.31184 | 0.31328 | 0.31455 | 0.2 | 24.79
Other | | 0.006528 | | | 0.52
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
Total wall time: 0:00:02

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LAMMPS (15 Feb 2016)
# test of NB3B pair style with pair hybrid and KSpace solver
units real
atom_style full
bond_style morse
angle_style none
dihedral_style none
improper_style none
read_data data.nb3b
orthogonal box = (0 0 0) to (22.5907 22.359 23.4708)
1 by 1 by 1 MPI processor grid
reading atoms ...
1400 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
560 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
pair_style hybrid/overlay nb3b/harmonic lj/cut/coul/long 10.0
pair_coeff * * nb3b/harmonic MOH.nb3b.harmonic M O H
Reading potential file MOH.nb3b.harmonic with DATE: 2013-06-28
pair_modify mix arithmetic
pair_coeff 1 1 lj/cut/coul/long 0.000000903 5.264325869
pair_coeff 1 2 lj/cut/coul/long 0.000374621 4.214922978
pair_coeff 1 3 lj/cut/coul/long 0 2.632162934
pair_coeff 2 2 lj/cut/coul/long 0.155416412 3.165520088
pair_coeff 2 3 lj/cut/coul/long 0 1.582760044
pair_coeff 3 3 lj/cut/coul/long 0 0
kspace_style ewald/disp 0.0001
neighbor 2.0 bin
neigh_modify delay 5
special_bonds lj/coul 0.0 0.0 1.0
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
1 = max # of special neighbors
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press lx ly lz xy xz yz vol
timestep 1.0
run_style respa 2 2 pair 1 kspace 2
Respa levels:
1 = bond angle dihedral improper pair
2 = kspace
thermo 50
### Minimize forces in structure ###
minimize 1.0e-06 1.0e-08 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 4 4 4
vectors: nbox = 6, nkvec = 478
Memory usage per processor = 16.5817 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
0 -61505.983 0 0 -61505.983 198.11978 0 0 0 5426.6842 -20935.868 -46194.919 979.72809 22.5907 22.359 23.4708 0 0 0 11855.229
4 -61506.604 0 0 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 1657.4299 22.5907 22.359 23.4708 0 0 0 11855.229
Loop time of 0.848486 on 1 procs for 4 steps with 1400 atoms
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-61505.9829 -61506.5882212 -61506.6041431
Force two-norm initial, final = 17.893 3.40908
Force max component initial, final = 0.757547 0.131738
Final line search alpha, max atom move = 0.394559 0.0519786
Iterations, force evaluations = 4 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.77228 | 0.77228 | 0.77228 | 0.0 | 91.02
Bond | 0.00031042 | 0.00031042 | 0.00031042 | 0.0 | 0.04
Kspace | 0.074903 | 0.074903 | 0.074903 | 0.0 | 8.83
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00057626 | 0.00057626 | 0.00057626 | 0.0 | 0.07
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0004158 | | | 0.05
Nlocal: 1400 ave 1400 max 1400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10804 ave 10804 max 10804 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 596960 ave 596960 max 596960 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.19392e+06 ave 1.19392e+06 max 1.19392e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1193920
Ave neighs/atom = 852.8
Ave special neighs/atom = 0.8
Neighbor list builds = 0
Dangerous builds = 0
### Run NVE to equilibrate velocities ###
velocity all create 298.0 4928459 mom yes rot yes dist gaussian
fix 1 all nve
fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0
run 100
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 4 4 4
Memory usage per processor = 16.2067 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
4 -60263.898 1242.7057 298 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 6449.147 22.5907 22.359 23.4708 0 0 0 11855.229
50 -58769.885 1186.4036 284.49881 -59956.289 309.92499 0 0 0 6168.8458 -20249.062 -46185.998 21737.807 22.5907 22.359 23.4708 0 0 0 11855.229
100 -58865.196 1242.7057 298 -60107.902 371.56168 0 0 0 6422.4016 -20716.005 -46185.86 22887.006 22.5907 22.359 23.4708 0 0 0 11855.229
104 -58865.334 1260.1244 302.177 -60125.458 386.24491 0 0 0 6377.3686 -20705.327 -46183.745 19154.01 22.5907 22.359 23.4708 0 0 0 11855.229
Loop time of 17.467 on 1 procs for 100 steps with 1400 atoms
Performance: 0.495 ns/day, 48.519 hours/ns, 5.725 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 16.477 | 16.477 | 16.477 | 0.0 | 94.33
Bond | 0.0069525 | 0.0069525 | 0.0069525 | 0.0 | 0.04
Kspace | 0.84704 | 0.84704 | 0.84704 | 0.0 | 4.85
Neigh | 0.10518 | 0.10518 | 0.10518 | 0.0 | 0.60
Comm | 0.015078 | 0.015078 | 0.015078 | 0.0 | 0.09
Output | 0.00010085 | 0.00010085 | 0.00010085 | 0.0 | 0.00
Modify | 0.0071354 | 0.0071354 | 0.0071354 | 0.0 | 0.04
Other | | 0.008824 | | | 0.05
Nlocal: 1400 ave 1400 max 1400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 10843 ave 10843 max 10843 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 595307 ave 595307 max 595307 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.19061e+06 ave 1.19061e+06 max 1.19061e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1190614
Ave neighs/atom = 850.439
Ave special neighs/atom = 0.8
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:18

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LAMMPS (15 Feb 2016)
# test of NB3B pair style with pair hybrid and KSpace solver
units real
atom_style full
bond_style morse
angle_style none
dihedral_style none
improper_style none
read_data data.nb3b
orthogonal box = (0 0 0) to (22.5907 22.359 23.4708)
2 by 1 by 2 MPI processor grid
reading atoms ...
1400 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
560 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
pair_style hybrid/overlay nb3b/harmonic lj/cut/coul/long 10.0
pair_coeff * * nb3b/harmonic MOH.nb3b.harmonic M O H
Reading potential file MOH.nb3b.harmonic with DATE: 2013-06-28
pair_modify mix arithmetic
pair_coeff 1 1 lj/cut/coul/long 0.000000903 5.264325869
pair_coeff 1 2 lj/cut/coul/long 0.000374621 4.214922978
pair_coeff 1 3 lj/cut/coul/long 0 2.632162934
pair_coeff 2 2 lj/cut/coul/long 0.155416412 3.165520088
pair_coeff 2 3 lj/cut/coul/long 0 1.582760044
pair_coeff 3 3 lj/cut/coul/long 0 0
kspace_style ewald/disp 0.0001
neighbor 2.0 bin
neigh_modify delay 5
special_bonds lj/coul 0.0 0.0 1.0
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
1 = max # of special neighbors
thermo_style custom step etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong press lx ly lz xy xz yz vol
timestep 1.0
run_style respa 2 2 pair 1 kspace 2
Respa levels:
1 = bond angle dihedral improper pair
2 = kspace
thermo 50
### Minimize forces in structure ###
minimize 1.0e-06 1.0e-08 1000 10000
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 4 4 4
vectors: nbox = 6, nkvec = 478
Memory usage per processor = 16.9507 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
0 -61505.983 0 0 -61505.983 198.11978 0 0 0 5426.6842 -20935.868 -46194.919 979.72809 22.5907 22.359 23.4708 0 0 0 11855.229
4 -61506.604 0 0 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 1657.4299 22.5907 22.359 23.4708 0 0 0 11855.229
Loop time of 0.254354 on 4 procs for 4 steps with 1400 atoms
99.0% CPU use with 4 MPI tasks x no OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-61505.9829 -61506.5882212 -61506.6041431
Force two-norm initial, final = 17.893 3.40908
Force max component initial, final = 0.757547 0.131738
Final line search alpha, max atom move = 0.394559 0.0519786
Iterations, force evaluations = 4 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.07247 | 0.17424 | 0.22771 | 14.9 | 68.50
Bond | 8.5115e-05 | 9.495e-05 | 0.0001049 | 0.1 | 0.04
Kspace | 0.024093 | 0.07615 | 0.17696 | 22.2 | 29.94
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0019753 | 0.0034024 | 0.0047915 | 2.0 | 1.34
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0004643 | | | 0.18
Nlocal: 350 ave 399 max 305 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 6602 ave 6647 max 6553 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 149240 ave 170954 max 129384 min
Histogram: 1 1 0 0 0 0 0 1 0 1
FullNghs: 298480 ave 340157 max 260160 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Total # of neighbors = 1193920
Ave neighs/atom = 852.8
Ave special neighs/atom = 0.8
Neighbor list builds = 0
Dangerous builds = 0
### Run NVE to equilibrate velocities ###
velocity all create 298.0 4928459 mom yes rot yes dist gaussian
fix 1 all nve
fix 2 all temp/rescale 10 298.0 298.0 25.0 1.0
run 100
EwaldDisp initialization ...
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
G vector = 0.269426
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (../pair.cpp:220)
Neighbor list info ...
4 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 4 4 4
Memory usage per processor = 16.5757 Mbytes
Step TotEng KinEng Temp PotEng E_bond E_angle E_dihed E_impro E_vdwl E_coul E_long Press Lx Ly Lz Xy Xz Yz Volume
4 -60263.898 1242.7057 298 -61506.604 198.69671 0 0 0 5460.0893 -20970.348 -46195.042 6449.147 22.5907 22.359 23.4708 0 0 0 11855.229
50 -58769.885 1186.4036 284.49881 -59956.289 309.92499 0 0 0 6168.8458 -20249.062 -46185.998 21737.807 22.5907 22.359 23.4708 0 0 0 11855.229
100 -58865.196 1242.7057 298 -60107.902 371.56168 0 0 0 6422.4016 -20716.005 -46185.86 22887.006 22.5907 22.359 23.4708 0 0 0 11855.229
104 -58865.334 1260.1244 302.177 -60125.458 386.24491 0 0 0 6377.3686 -20705.327 -46183.745 19154.01 22.5907 22.359 23.4708 0 0 0 11855.229
Loop time of 4.80696 on 4 procs for 100 steps with 1400 atoms
Performance: 1.797 ns/day, 13.353 hours/ns, 20.803 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.4587 | 3.5531 | 4.4418 | 64.9 | 73.91
Bond | 0.0018251 | 0.0019184 | 0.0019794 | 0.1 | 0.04
Kspace | 0.21553 | 0.22335 | 0.231 | 1.4 | 4.65
Neigh | 0.026918 | 0.02694 | 0.026957 | 0.0 | 0.56
Comm | 0.096146 | 0.98534 | 3.08 | 123.3 | 20.50
Output | 0.00012541 | 0.00017965 | 0.00030398 | 0.5 | 0.00
Modify | 0.0023086 | 0.0030754 | 0.0038064 | 1.2 | 0.06
Other | | 0.0131 | | | 0.27
Nlocal: 350 ave 357 max 340 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6639.25 ave 6657 max 6627 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 148827 ave 152055 max 145212 min
Histogram: 1 0 0 0 0 2 0 0 0 1
FullNghs: 297654 ave 303283 max 288784 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Total # of neighbors = 1190614
Ave neighs/atom = 850.439
Ave special neighs/atom = 0.8
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (15 Feb 2016)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 4327.2753 2746.3378 0.3387091 5.0075576 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969
100 0.10482184 0.085218486 0.014588241 0.066178594 0.19602237 0.0070900402 0.0022691875 2.3031875 0 -3.0535967 0.31839181 -3.0473647 0.63987598 -3.0465067 1 -3.0487759
111 0.096708467 0.07803707 0.013922973 0.05417562 0.2023467 0.0070871172 0.0022668002 2.3052945 0 -3.0535968 0.31853431 -3.0473633 0.64178871 -3.0465096 1 -3.0487764
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
111 0.2023467 0.1777038 0.013922973 0.05417562 0.2023467 0.0070871172 0.0022668002 2.3052945 0 -3.0535968 0.31853431 -3.0473633 0.64178871 -3.0465096 1 -3.0487764
179 0.096874474 0.090676856 0.01040177 0.023364005 0.096874474 0.0071047642 0.0022856172 2.3122768 0 -3.0535969 0.31577311 -3.0473955 0.61798541 -3.0464922 1 -3.0487778

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LAMMPS (15 Feb 2016)
Running on 4 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 14.104748 10.419633 0.24852044 5.0039071 8.2116049 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305
100 0.24646695 0.10792196 0.01781018 0.098854684 0.63725646 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923
200 0.061777741 0.050288749 0.012466513 0.020420207 0.88741041 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938
300 0.056346766 0.030000618 0.0093152917 0.013765031 1.0101529 0.0014069751 0.0014068154 1.1699608 0 -3.0514942 0.30992449 -3.0502613 0.64174291 -3.0500873 1 -3.0514941
400 0.025589489 0.015671005 0.0061287063 0.008588518 1.1136424 0.001370987 0.0013709154 1.1704204 0 -3.0514943 0.32016645 -3.0502198 0.65324019 -3.0501233 1 -3.0514943
500 0.014778626 0.0092108366 0.0042668521 0.0059963914 1.1636579 0.0013527466 0.0013527072 1.1706283 0 -3.0514944 0.32550275 -3.0501993 0.65875414 -3.0501416 1 -3.0514943
600 0.08786211 0.020876327 0.0031421548 0.0051657363 1.1898894 0.0013430848 0.0013430599 1.1707681 0 -3.0514944 0.32831927 -3.0501889 0.66160681 -3.0501513 1 -3.0514944
633 0.0098132678 0.0055392541 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
Climbing replica = 3
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
633 1.1924486 1.1648685 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944
733 0.095331134 0.089136608 0.0021551441 0.0031844438 0.043042998 0.0016022317 0.0016022168 1.170789 0 -3.0514944 0.29157063 -3.0503375 0.50358402 -3.0498922 1 -3.0514944
833 0.10539135 0.030724373 0.0013749699 0.002221013 0.10539135 0.0016019798 0.001601971 1.1732118 0 -3.0514944 0.26249002 -3.0504848 0.50415223 -3.0498924 1 -3.0514944
933 0.01883894 0.011496399 0.0011058925 0.0018178041 0.014621806 0.0016018934 0.0016018865 1.173866 0 -3.0514944 0.25788763 -3.0505113 0.50466375 -3.0498925 1 -3.0514944
996 0.0082457876 0.0036336551 0.00077325986 0.0013910671 0.0068823708 0.0016018293 0.0016018244 1.174511 0 -3.0514944 0.2544553 -3.0505324 0.50520462 -3.0498926 1 -3.0514944

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LAMMPS (15 Feb 2016)
Running on 3 partitions of processors
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959
10 0.27332818 0.040944923 0.039164338 0.27332818 0.17804882 0.51235911 0.497084 1.6790474 0 -2213.3364 0.49024121 -2212.824 1 -2213.3211
20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347
30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364
40 0.042139318 0.0037035773 0.011737071 0.042139318 0.026104737 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371
50 0.025904252 0.0022808801 0.008105847 0.025904252 0.016908971 0.5101712 0.51008591 1.7391431 0 -2213.3373 0.49923347 -2212.8272 1 -2213.3373
Climbing replica = 2
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
50 0.025904252 0.0044134315 0.008105847 0.025904252 0.016908971 0.5101712 0.51008591 1.7391431 0 -2213.3373 0.49923347 -2212.8272 1 -2213.3373
60 0.011518317 0.0013089596 0.0054472815 0.011518317 0.0091629734 0.51014415 0.51010903 1.7406815 0 -2213.3374 0.50065207 -2212.8272 1 -2213.3373
61 0.0089525108 0.0012703829 0.0052524345 0.0088142351 0.0089525108 0.51014321 0.51010962 1.7407173 0 -2213.3374 0.50065779 -2212.8272 1 -2213.3373

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LAMMPS (15 Feb 2016)
# 2d NEMD simulation
units lj
atom_style atomic
dimension 2
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 2 all image 1000 image.*.jpg type type adiam 1.2
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type adiam 1.2
#dump_modify 3 pad 5
thermo 1000
run 50000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65 -> bins = 24 19 3
Memory usage per processor = 2.49357 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.431 1.2080502 189.52855
1000 1.1326992 0.25863754 0 1.3842573 6.0588079 189.52855
2000 1.0158438 0.33502643 0 1.3445212 7.2638652 189.52855
3000 1.0968167 0.3149227 0 1.4048843 7.0653223 189.52855
4000 1.0070993 0.40611915 0 1.4069241 7.7283521 189.52855
5000 1.1153133 0.2674828 0 1.3758254 6.2949171 189.52855
6000 1.0170665 0.25843673 0 1.2691466 6.049412 189.52855
7000 1.0224605 0.20974914 0 1.2258193 5.5104976 189.52855
8000 0.96149374 0.24035439 0 1.1958388 5.4179146 189.52855
9000 0.87759014 0.2590493 0 1.1311545 5.8711239 189.52855
10000 0.83791968 0.23477897 0 1.0674617 5.666904 189.52855
11000 0.87702487 0.22958877 0 1.1011322 5.9068062 189.52855
12000 0.81507294 0.26375817 0 1.0737369 5.9166925 189.52855
13000 0.85655284 0.24676491 0 1.0979643 5.6918734 189.52855
14000 0.84369293 0.27818471 0 1.1166046 6.4146184 189.52855
15000 0.90052173 0.19836095 0 1.0932544 5.2690913 189.52855
16000 0.83836874 0.26921637 0 1.1023453 5.9579526 189.52855
17000 0.90492897 0.21933098 0 1.1186041 5.6042194 189.52855
18000 0.90113412 0.24880908 0 1.1443111 6.0634846 189.52855
19000 1.0160445 0.17252962 0 1.1822239 5.3149334 189.52855
20000 0.96217234 0.2414377 0 1.1975965 5.476653 189.52855
21000 0.98229664 0.27569118 0 1.2518485 5.9340174 189.52855
22000 1.0551763 0.26997615 0 1.3185576 6.2094112 189.52855
23000 1.051999 0.34076639 0 1.3861904 7.082385 189.52855
24000 1.1350071 0.23701844 0 1.3649317 6.1829742 189.52855
25000 1.0946409 0.33366032 0 1.4214597 7.1907559 189.52855
26000 1.1511799 0.24626808 0 1.3902531 5.8469984 189.52855
27000 1.1009203 0.25653085 0 1.3505704 6.1504287 189.52855
28000 1.0521302 0.2876798 0 1.3332342 5.9906187 189.52855
29000 1.0518465 0.21853 0 1.2638025 5.6577549 189.52855
30000 0.97264625 0.28758145 0 1.2541487 6.5769804 189.52855
31000 1.0133579 0.31575837 0 1.3227828 6.6650893 189.52855
32000 1.0714324 0.28757036 0 1.3523063 6.2682059 189.52855
33000 1.0739451 0.28062459 0 1.3478575 6.6862746 189.52855
34000 1.0056867 0.38289586 0 1.382297 7.1120131 189.52855
35000 1.0911349 0.26370939 0 1.3480247 6.1476048 189.52855
36000 1.0618618 0.28269593 0 1.3379211 6.9414608 189.52855
37000 1.0704991 0.29974994 0 1.3635585 7.0834346 189.52855
38000 1.1087507 0.2682201 0 1.3700411 5.8506019 189.52855
39000 1.1303733 0.22362416 0 1.3469326 5.2500269 189.52855
40000 1.0174248 0.28956571 0 1.3006316 6.4491571 189.52855
41000 0.95981887 0.29162143 0 1.2454414 6.4658646 189.52855
42000 0.88302144 0.30432252 0 1.1818251 6.7401923 189.52855
43000 0.93164419 0.25110308 0 1.1769245 5.9067383 189.52855
44000 0.98352598 0.23322873 0 1.2106077 5.5606585 189.52855
45000 1.0247245 0.26503082 0 1.2833508 6.533394 189.52855
46000 0.93004532 0.32277782 0 1.2470104 6.4689179 189.52855
47000 1.0653176 0.29185413 0 1.3505135 6.9534569 189.52855
48000 1.0401524 0.3420245 0 1.3756759 6.8016042 189.52855
49000 1.0023407 0.31833091 0 1.314407 6.7385662 189.52855
50000 1.0566272 0.28657142 0 1.3365947 6.261203 189.52855
Loop time of 1.1489 on 1 procs for 50000 steps with 160 atoms
Performance: 18800575.740 tau/day, 43519.851 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.20048 | 0.20048 | 0.20048 | 0.0 | 17.45
Neigh | 0.16117 | 0.16117 | 0.16117 | 0.0 | 14.03
Comm | 0.048121 | 0.048121 | 0.048121 | 0.0 | 4.19
Output | 0.00054765 | 0.00054765 | 0.00054765 | 0.0 | 0.05
Modify | 0.67693 | 0.67693 | 0.67693 | 0.0 | 58.92
Other | | 0.06166 | | | 5.37
Nlocal: 160 ave 160 max 160 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 71 ave 71 max 71 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 362 ave 362 max 362 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 362
Ave neighs/atom = 2.2625
Neighbor list builds = 5256
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (15 Feb 2016)
# 2d NEMD simulation
units lj
atom_style atomic
dimension 2
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 2 all image 1000 image.*.jpg type type adiam 1.2
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type adiam 1.2
#dump_modify 3 pad 5
thermo 1000
run 50000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.3
ghost atom cutoff = 1.3
binsize = 0.65 -> bins = 24 19 3
Memory usage per processor = 2.49198 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 1.44 0 0 1.431 1.2080502 189.52855
1000 1.1682693 0.24486562 0 1.4058332 5.8092954 189.52855
2000 1.0928734 0.27609364 0 1.3621366 6.2237017 189.52855
3000 1.0895801 0.24812344 0 1.3308937 5.6987334 189.52855
4000 1.0231536 0.23938192 0 1.2561408 5.6395384 189.52855
5000 0.92980496 0.29549086 0 1.2194845 6.7361058 189.52855
6000 0.94654468 0.27175873 0 1.2123875 6.1830354 189.52855
7000 1.04513 0.19555104 0 1.234149 5.3099904 189.52855
8000 0.90165043 0.33774203 0 1.2337571 6.8441345 189.52855
9000 1.0559475 0.21527383 0 1.2646217 5.3936713 189.52855
10000 1.0316023 0.25162907 0 1.2767839 6.0630699 189.52855
11000 1.0057873 0.1929355 0 1.1924366 5.1939416 189.52855
12000 0.95976424 0.23631857 0 1.1900843 5.1197849 189.52855
13000 0.96228689 0.2359206 0 1.1921932 5.8485377 189.52855
14000 0.92347491 0.28934379 0 1.207047 6.7279587 189.52855
15000 0.98798195 0.25310368 0 1.2349107 5.5744542 189.52855
16000 0.93800257 0.39455603 0 1.3266961 7.5939651 189.52855
17000 1.1781148 0.21856228 0 1.3893138 5.8347428 189.52855
18000 1.1292943 0.26429204 0 1.3865283 6.0510955 189.52855
19000 1.1047406 0.37926848 0 1.4771045 8.1596576 189.52855
20000 1.1716353 0.34662527 0 1.5109379 7.4616642 189.52855
21000 1.1630831 0.35981763 0 1.5156314 7.1024447 189.52855
22000 1.1249714 0.28308559 0 1.4010259 6.4004855 189.52855
23000 1.1062056 0.28618757 0 1.3854794 6.4957851 189.52855
24000 1.0588756 0.31727536 0 1.369533 6.987661 189.52855
25000 1.0379506 0.30773124 0 1.3391947 6.3814122 189.52855
26000 1.0316899 0.25596718 0 1.281209 6.4851096 189.52855
27000 0.95909019 0.32282679 0 1.2759227 6.480673 189.52855
28000 1.0224651 0.24795447 0 1.2640291 5.5846145 189.52855
29000 0.98739892 0.24878333 0 1.230011 5.6749101 189.52855
30000 1.0099165 0.22964407 0 1.2332486 5.3791167 189.52855
31000 0.93350481 0.2879577 0 1.2156281 6.2148818 189.52855
32000 0.99089487 0.22340991 0 1.2081117 5.639 189.52855
33000 0.89519123 0.26943351 0 1.1590298 6.3869898 189.52855
34000 0.891093 0.28473528 0 1.1702589 6.0284238 189.52855
35000 0.83575157 0.25811245 0 1.0886406 6.4030425 189.52855
36000 0.81108815 0.26558543 0 1.0716043 6.3037393 189.52855
37000 0.92476501 0.18404704 0 1.1030323 5.3793557 189.52855
38000 0.85121163 0.2792429 0 1.1251345 5.9668051 189.52855
39000 0.90345348 0.2399627 0 1.1377696 6.1440023 189.52855
40000 0.93871579 0.2217328 0 1.1545816 4.9454727 189.52855
41000 1.0132854 0.25226008 0 1.2592124 6.2541531 189.52855
42000 0.98600788 0.27213553 0 1.2519809 6.0321859 189.52855
43000 1.0635948 0.27086236 0 1.3278097 6.6622232 189.52855
44000 1.0332292 0.36613701 0 1.3929085 7.4935675 189.52855
45000 1.1168224 0.3374366 0 1.4472788 7.3625776 189.52855
46000 1.0725949 0.37916007 0 1.4450513 6.8897095 189.52855
47000 1.0940234 0.35474661 0 1.4419324 7.4781317 189.52855
48000 1.1093597 0.26705754 0 1.3694837 5.8401116 189.52855
49000 1.0803976 0.29555751 0 1.3692026 6.4769008 189.52855
50000 1.0150244 0.29822696 0 1.3069075 6.4417197 189.52855
Loop time of 1.04457 on 4 procs for 50000 steps with 160 atoms
Performance: 20678409.528 tau/day, 47866.689 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.049384 | 0.050257 | 0.051119 | 0.4 | 4.81
Neigh | 0.043314 | 0.043914 | 0.044468 | 0.3 | 4.20
Comm | 0.35483 | 0.40496 | 0.45232 | 5.9 | 38.77
Output | 0.0010872 | 0.0012692 | 0.0017776 | 0.8 | 0.12
Modify | 0.30946 | 0.35542 | 0.40435 | 6.0 | 34.03
Other | | 0.1887 | | | 18.07
Nlocal: 40 ave 42 max 38 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 35.5 ave 37 max 34 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 88.75 ave 96 max 79 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 355
Ave neighs/atom = 2.21875
Neighbor list builds = 5284
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (15 Feb 2016)
# 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:445)
#dump 1 all atom 100 dump.obstacle
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 25000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123 -> bins = 73 32 1
Memory usage per processor = 2.47903 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 -0.52004759 0 0.16655839 1.417774 1324.489
4000 1 -0.5052153 0 0.18139068 1.4877209 1370.8743
5000 1 -0.49501138 0 0.1915946 1.2415582 1408.4993
6000 1 -0.45834057 0 0.22826542 1.2577643 1433.2191
7000 1 -0.44788351 0 0.23872247 1.1057853 1452.7011
8000 1 -0.42511924 0 0.26148674 1.1445522 1453.2588
9000 1 -0.35807547 0 0.32853051 1.0527564 1449.2608
10000 1 -0.38692228 0 0.2996837 1.0338935 1447.9561
11000 1 -0.38893457 0 0.29767141 1.0095645 1451.1231
12000 1 -0.35706485 0 0.32954114 1.0796623 1453.0879
13000 1 -0.39551125 0 0.29109474 1.0390286 1453.2992
14000 1 -0.38153043 0 0.30507555 0.98105926 1452.5639
15000 1 -0.38762689 0 0.29897909 1.1442417 1452.0174
16000 1 -0.3685331 0 0.31807289 1.0032132 1458.431
17000 1 -0.36299809 0 0.32360789 0.93727845 1460.2986
18000 1 -0.35752931 0 0.32907667 0.98337283 1458.583
19000 1 -0.38350344 0 0.30310254 1.0148373 1458.9749
20000 1 -0.35659703 0 0.33000895 1.0264431 1460.0031
21000 1 -0.36878002 0 0.31782596 1.0877739 1455.1053
22000 1 -0.37986917 0 0.30673681 1.129754 1455.0258
23000 1 -0.39249509 0 0.29411089 0.97187435 1459.6771
24000 1 -0.33410442 0 0.35250156 0.93960021 1463.5903
25000 1 -0.37437615 0 0.31222983 0.9644765 1464.9391
Loop time of 1.65987 on 1 procs for 25000 steps with 769 atoms
Performance: 3903929.372 tau/day, 15061.456 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.52106 | 0.52106 | 0.52106 | 0.0 | 31.39
Neigh | 0.16143 | 0.16143 | 0.16143 | 0.0 | 9.73
Comm | 0.023438 | 0.023438 | 0.023438 | 0.0 | 1.41
Output | 0.00032663 | 0.00032663 | 0.00032663 | 0.0 | 0.02
Modify | 0.87449 | 0.87449 | 0.87449 | 0.0 | 52.68
Other | | 0.07912 | | | 4.77
Nlocal: 769 ave 769 max 769 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 45 ave 45 max 45 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1618 ave 1618 max 1618 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1618
Ave neighs/atom = 2.10403
Neighbor list builds = 1622
Dangerous builds = 0
Total wall time: 0:00:01

155
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LAMMPS (15 Feb 2016)
# 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:445)
#dump 1 all atom 100 dump.obstacle
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 25000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.42246
ghost atom cutoff = 1.42246
binsize = 0.71123 -> bins = 73 32 1
Memory usage per processor = 2.47142 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 -0.49062369 0 0.19598229 1.5239334 1322.2627
4000 1 -0.50088987 0 0.18571611 1.4614192 1367.6511
5000 1 -0.47747975 0 0.20912623 1.3417367 1405.501
6000 1 -0.47477948 0 0.21182651 1.3061542 1432.0778
7000 1 -0.44736042 0 0.23924556 1.1332701 1441.4911
8000 1 -0.42748547 0 0.25912051 1.0531138 1443.7226
9000 1 -0.41433123 0 0.27227475 1.0997172 1450.1414
10000 1 -0.38722477 0 0.29938121 1.0652717 1456.2877
11000 1 -0.40216239 0 0.28444359 1.1152975 1459.2764
12000 1 -0.38520467 0 0.30140132 0.94109687 1463.6094
13000 1 -0.38233942 0 0.30426656 1.0184283 1461.2151
14000 1 -0.38106329 0 0.3055427 0.93372261 1459.276
15000 1 -0.36896962 0 0.31763636 1.0015053 1456.4295
16000 1 -0.38669413 0 0.29991185 0.99320514 1460.5925
17000 1 -0.3879857 0 0.29862028 0.95908906 1461.1978
18000 1 -0.37448688 0 0.3121191 0.96871256 1460.7159
19000 1 -0.39700052 0 0.28960547 1.0770396 1458.2596
20000 1 -0.36125976 0 0.32534622 0.86282353 1466.9129
21000 1 -0.38882675 0 0.29777923 0.9877477 1457.4909
22000 1 -0.38158333 0 0.30502266 1.0184682 1454.5247
23000 1 -0.37327871 0 0.31332728 1.0623185 1453.1342
24000 1 -0.40040333 0 0.28620265 0.94983886 1459.4461
25000 1 -0.37645924 0 0.31014674 1.0526044 1458.7191
Loop time of 0.801717 on 4 procs for 25000 steps with 769 atoms
Performance: 8082654.578 tau/day, 31183.081 timesteps/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.066442 | 0.13097 | 0.21239 | 16.1 | 16.34
Neigh | 0.03235 | 0.042894 | 0.056734 | 4.4 | 5.35
Comm | 0.14225 | 0.21218 | 0.28481 | 11.2 | 26.47
Output | 0.0005331 | 0.00056887 | 0.00064301 | 0.2 | 0.07
Modify | 0.27222 | 0.31224 | 0.33583 | 4.6 | 38.95
Other | | 0.1029 | | | 12.83
Nlocal: 192.25 ave 243 max 151 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Nghost: 41.75 ave 43 max 39 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 408.5 ave 575 max 266 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 1634
Ave neighs/atom = 2.12484
Neighbor list builds = 1631
Dangerous builds = 1
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
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 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 2 pad 3
#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 3 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5
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 = 15.1545 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 = 1.0068 (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 = -1331.7980
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80799e-07
6 0.997 1.06209e-06
8 1.08 6.20485e-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 = 2.0247 (sec) ----------------
TotEng = -5257.9972 KinEng = 1078.0556 Temp = 267.9664
PotEng = -6336.0528 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
E_coul = 26786.6841 E_long = -33906.5620 Press = -648.6637
---------------- Step 150 ----- CPU = 3.0615 (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 = 736.9686
E_coul = 26717.2583 E_long = -33907.2812 Press = -333.1888
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50855e-07
8 1.08 6.58342e-08
10 1.111 5.5535e-07
12 1.08 1.99243e-07
14 0.96 0
18 0.957201 3.59666e-06
31 104.52 0.000388186
---------------- Step 200 ----- CPU = 4.0675 (sec) ----------------
TotEng = -5308.4527 KinEng = 1100.5055 Temp = 273.5467
PotEng = -6408.9582 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3264
E_coul = 26736.1130 E_long = -33902.3928 Press = -1470.3831
---------------- Step 250 ----- CPU = 5.1252 (sec) ----------------
TotEng = -5294.1807 KinEng = 1071.1619 Temp = 266.2529
PotEng = -6365.3426 E_bond = 14.2022 E_angle = 39.1953
E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5416
E_coul = 26713.8467 E_long = -33908.7226 Press = -188.8007
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78262e-06
6 0.997001 3.50131e-06
8 1.08 2.0932e-06
10 1.111 5.64324e-06
12 1.08 2.10399e-06
14 0.96 0
18 0.957202 7.67973e-06
31 104.52 0.000806336
---------------- Step 300 ----- CPU = 6.1883 (sec) ----------------
TotEng = -5251.4333 KinEng = 1123.6266 Temp = 279.2937
PotEng = -6375.0599 E_bond = 14.2249 E_angle = 38.4712
E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4550
E_coul = 26745.4115 E_long = -33909.1249 Press = -469.5254
Loop time of 6.18835 on 1 procs for 300 steps with 2004 atoms
Performance: 8.377 ns/day, 2.865 hours/ns, 48.478 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8942 | 4.8942 | 4.8942 | 0.0 | 79.09
Bond | 0.015213 | 0.015213 | 0.015213 | 0.0 | 0.25
Kspace | 0.49706 | 0.49706 | 0.49706 | 0.0 | 8.03
Neigh | 0.67515 | 0.67515 | 0.67515 | 0.0 | 10.91
Comm | 0.029536 | 0.029536 | 0.029536 | 0.0 | 0.48
Output | 0.00019145 | 0.00019145 | 0.00019145 | 0.0 | 0.00
Modify | 0.070009 | 0.070009 | 0.070009 | 0.0 | 1.13
Other | | 0.006974 | | | 0.11
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: 708029 ave 708029 max 708029 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708029
Ave neighs/atom = 353.308
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0
Total wall time: 0:00:06

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LAMMPS (15 Feb 2016)
# 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
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 2 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
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 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 2 pad 3
#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
#dump_modify 3 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
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 5 5 5
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 = 14.4096 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 = 0.2819 (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 = 0.5649 (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 = 0.8549 (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 = 26717.2583 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 = 1.1354 (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 = 1.4311 (sec) ----------------
TotEng = -5294.1809 KinEng = 1071.1623 Temp = 266.2530
PotEng = -6365.3432 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 = -188.8077
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78266e-06
6 0.997001 3.50137e-06
8 1.08 2.09322e-06
10 1.111 5.64331e-06
12 1.08 2.10401e-06
14 0.96 0
18 0.957202 7.67991e-06
31 104.52 0.000806336
---------------- Step 300 ----- CPU = 1.7306 (sec) ----------------
TotEng = -5251.4350 KinEng = 1123.6256 Temp = 279.2935
PotEng = -6375.0606 E_bond = 14.2249 E_angle = 38.4712
E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4557
E_coul = 26745.4100 E_long = -33909.1249 Press = -469.5450
Loop time of 1.73061 on 4 procs for 300 steps with 2004 atoms
Performance: 29.955 ns/day, 0.801 hours/ns, 173.349 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2122 | 1.2332 | 1.2511 | 1.6 | 71.26
Bond | 0.0012589 | 0.0043506 | 0.007498 | 4.2 | 0.25
Kspace | 0.1673 | 0.18692 | 0.20947 | 4.0 | 10.80
Neigh | 0.17076 | 0.17102 | 0.17129 | 0.0 | 9.88
Comm | 0.068879 | 0.070616 | 0.071993 | 0.5 | 4.08
Output | 0.00030756 | 0.00032926 | 0.00038385 | 0.2 | 0.02
Modify | 0.059337 | 0.059592 | 0.059881 | 0.1 | 3.44
Other | | 0.004566 | | | 0.26
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
Total wall time: 0:00:01

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LAMMPS (15 Feb 2016)
# 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 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.0025001
ghost atom cutoff = 0.0025001
binsize = 0.00125005 -> bins = 9 5 9
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Memory usage per processor = 26.6858 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 2407361.6 0 8.994088e+08 2.3787786e+14 2.5138992e-06
900 1.2358395e+28 4532520.6 0 8.9673706e+08 1.9097312e+14 3.1145903e-06
1000 1.2341057e+28 3219939.5 0 8.9417279e+08 1.5968597e+14 3.7196039e-06
Loop time of 20.9881 on 1 procs for 1000 steps with 3487 atoms
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 20.268 | 20.268 | 20.268 | 0.0 | 96.57
Neigh | 0.59991 | 0.59991 | 0.59991 | 0.0 | 2.86
Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 0.01
Output | 0.0002439 | 0.0002439 | 0.0002439 | 0.0 | 0.00
Modify | 0.10321 | 0.10321 | 0.10321 | 0.0 | 0.49
Other | | 0.01511 | | | 0.07
Nlocal: 3487 ave 3487 max 3487 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 567140 ave 567140 max 567140 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1209076
Ave neighs/atom = 346.738
Neighbor list builds = 46
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:21

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LAMMPS (15 Feb 2016)
# 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 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 2 pad 4
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
#dump_modify 3 pad 4
run 1000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0.0025001
ghost atom cutoff = 0.0025001
binsize = 0.00125005 -> bins = 9 5 9
Peridynamic bonds:
total # of bonds = 335966
bonds/atom = 96.3482
Memory usage per processor = 26.9049 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 2407361.5 0 8.994088e+08 2.3787786e+14 2.5138992e-06
900 1.2358395e+28 4532520.1 0 8.9673706e+08 1.9097312e+14 3.1145903e-06
1000 1.2341057e+28 3219974.3 0 8.9417286e+08 1.5968598e+14 3.7196039e-06
Loop time of 5.93611 on 4 procs for 1000 steps with 3487 atoms
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.6969 | 5.0667 | 5.4557 | 15.1 | 85.35
Neigh | 0.11722 | 0.15148 | 0.18695 | 8.1 | 2.55
Comm | 0.24957 | 0.67644 | 1.083 | 45.2 | 11.40
Output | 0.00026965 | 0.00032377 | 0.00040698 | 0.3 | 0.01
Modify | 0.02939 | 0.029681 | 0.030176 | 0.2 | 0.50
Other | | 0.01153 | | | 0.19
Nlocal: 871.75 ave 920 max 824 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 1343.25 ave 1391 max 1295 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 141785 ave 170754 max 115891 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
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:05

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LAMMPS (15 Feb 2016)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
boundary f fm p
newton off
comm_modify 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 range 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 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 25000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6 -> bins = 167 84 2
Memory usage per processor = 2.75187 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 224 201.77464 0 5000
2000 224 372.42868 0 5000
3000 224 599.60221 0 5000
4000 448 1084.3752 0 5000
5000 448 1592.4543 0 5000
6000 448 1763.3153 37.274939 5000
7000 672 1805.206 89.331853 5000
8000 672 1778.0015 111.58381 5000
9000 672 1592.6805 97.550311 5000
10000 896 1631.962 76.905078 5000
11000 896 1590.1527 68.644552 5000
12000 896 1564.4707 60.119562 5000
13000 1000 1490.072 56.982972 5000
14000 1000 1266.4669 57.579371 5000
15000 1000 1034.1055 46.079374 5000
16000 1000 748.70283 43.933154 5000
17000 1000 462.65166 37.522016 5000
18000 1000 327.40481 29.450285 5000
19000 1000 223.24319 31.981144 5000
20000 1000 54.792042 23.449101 5000
21000 1000 25.805484 16.352528 5000
22000 1000 20.617765 11.756965 5000
23000 1000 16.115382 7.9435503 5000
24000 1000 11.971003 5.9411126 5000
25000 1000 10.404117 4.3811155 5000
Loop time of 3.04462 on 1 procs for 25000 steps with 1000 atoms
Performance: 709447.910 tau/day, 8211.203 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2896 | 1.2896 | 1.2896 | 0.0 | 42.36
Neigh | 0.40714 | 0.40714 | 0.40714 | 0.0 | 13.37
Comm | 0.0080216 | 0.0080216 | 0.0080216 | 0.0 | 0.26
Output | 0.00042129 | 0.00042129 | 0.00042129 | 0.0 | 0.01
Modify | 1.2178 | 1.2178 | 1.2178 | 0.0 | 40.00
Other | | 0.1217 | | | 4.00
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: 2374 ave 2374 max 2374 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2374
Ave neighs/atom = 2.374
Neighbor list builds = 2089
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (15 Feb 2016)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
boundary f fm p
newton off
comm_modify 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 range 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 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5
run 25000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6 -> bins = 167 84 2
Memory usage per processor = 2.71741 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 224 201.77464 0 5000
2000 224 372.42868 0 5000
3000 224 599.60221 0 5000
4000 448 1084.3752 0 5000
5000 448 1592.4543 0 5000
6000 448 1763.3153 37.274939 5000
7000 672 1805.206 89.331853 5000
8000 672 1778.0015 111.58381 5000
9000 672 1592.6805 97.550311 5000
10000 896 1630.8521 79.742572 5000
11000 896 1593.1588 67.633788 5000
12000 896 1562.2084 65.097236 5000
13000 1000 1504.1203 63.468934 5000
14000 1000 1266.5724 55.837334 5000
15000 1000 1041.8665 48.938774 5000
16000 1000 766.27305 43.846151 5000
17000 1000 466.30103 43.206188 5000
18000 1000 320.50154 26.84775 5000
19000 1000 207.91453 29.183522 5000
20000 1000 52.447982 19.30378 5000
21000 1000 22.027641 10.395933 5000
22000 1000 15.395099 6.7003289 5000
23000 1000 11.97674 5.2548063 5000
24000 1000 7.8974699 3.7396899 5000
25000 1000 6.1288038 2.2056805 5000
Loop time of 0.977215 on 4 procs for 25000 steps with 1000 atoms
Performance: 2210364.086 tau/day, 25582.918 timesteps/s
98.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.30766 | 0.33267 | 0.35001 | 3.1 | 34.04
Neigh | 0.094669 | 0.1019 | 0.10693 | 1.6 | 10.43
Comm | 0.060945 | 0.078421 | 0.097028 | 5.5 | 8.02
Output | 0.00042653 | 0.00045699 | 0.00049639 | 0.1 | 0.05
Modify | 0.2936 | 0.30701 | 0.31712 | 1.7 | 31.42
Other | | 0.1568 | | | 16.04
Nlocal: 250 ave 267 max 232 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Nghost: 18 ave 23 max 14 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 606 ave 664 max 559 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Total # of neighbors = 2424
Ave neighs/atom = 2.424
Neighbor list builds = 2060
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
atom_modify map array
boundary f fm p
newton off
comm_modify vel yes cutoff 2.5
fix prop all property/atom mol ghost 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 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
Read molecule object:
5 atoms with 1 types
0 bonds with 0 types
0 angles with 0 types
0 dihedrals with 0 types
0 impropers with 0 types
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
compute Tsphere all temp/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify lost ignore norm no temp Tsphere
compute_modify Tsphere dynamic yes
thermo 1000
#dump id all atom 100 tmp.dump
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol2 atom mol%10
#dump 2 all image 250 image.*.jpg v_mol2 type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5 amap 0 10 sa 1 10 ${colors}
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol3 atom mol%10
#dump 3 all movie 250 movie.mpg v_mol3 type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
run 25000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 2.5
binsize = 0.6 -> bins = 167 84 2
Memory usage per processor = 2.75807 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 130 259.24123 2.3772821e-30 5000
2000 130 465.39775 9.5010246e-30 5000
3000 130 736.55426 2.1365791e-29 5000
4000 260 1274.295 6.045774e-05 5000
5000 260 1855.4991 0.0021687846 5000
6000 260 1936.8934 6.9705094 5000
7000 390 1909.1519 11.402993 5000
8000 390 1958.2549 10.910611 5000
9000 390 1968.6293 14.080709 5000
10000 520 2278.4559 8.2512574 5000
11000 520 1952.4436 6.8525602 5000
12000 520 1391.9826 3.6742003 5000
13000 650 1608.9033 2.2121034 5000
14000 650 1562.8758 2.9284792 5000
15000 650 1549.101 2.432552 5000
16000 780 1718.9486 2.339785 5000
17000 780 1646.7053 5.1414663 5000
18000 780 1441.0842 3.7040072 5000
19000 910 1546.6435 2.5109623 5000
20000 910 1379.5416 4.2028322 5000
21000 910 1155.2864 2.05953 5000
22000 1040 1237.0246 3.0494101 5000
23000 1040 1160.8301 3.0040354 5000
24000 1040 1192.673 1.6310726 5000
25000 1170 1128.3916 3.3745733 5000
Loop time of 3.24674 on 1 procs for 25000 steps with 1170 atoms
Performance: 665282.302 tau/day, 7700.027 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.90701 | 0.90701 | 0.90701 | 0.0 | 27.94
Neigh | 0.25099 | 0.25099 | 0.25099 | 0.0 | 7.73
Comm | 0.010076 | 0.010076 | 0.010076 | 0.0 | 0.31
Output | 0.00050974 | 0.00050974 | 0.00050974 | 0.0 | 0.02
Modify | 1.9744 | 1.9744 | 1.9744 | 0.0 | 60.81
Other | | 0.1038 | | | 3.20
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: 1699 ave 1699 max 1699 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1699
Ave neighs/atom = 1.45214
Neighbor list builds = 1737
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (15 Feb 2016)
# Pour 2d granular particles into container
dimension 2
atom_style sphere
atom_modify map array
boundary f fm p
newton off
comm_modify vel yes cutoff 2.5
fix prop all property/atom mol ghost 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 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
Read molecule object:
5 atoms with 1 types
0 bonds with 0 types
0 angles with 0 types
0 dihedrals with 0 types
0 impropers with 0 types
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
compute Tsphere all temp/sphere
thermo_style custom step atoms ke c_1 vol
thermo_modify lost ignore norm no temp Tsphere
compute_modify Tsphere dynamic yes
thermo 1000
#dump id all atom 100 tmp.dump
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol2 atom mol%10
#dump 2 all image 250 image.*.jpg v_mol2 type # zoom 1.6 adiam 1.5
#dump_modify 2 pad 5 amap 0 10 sa 1 10 ${colors}
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
#variable mol3 atom mol%10
#dump 3 all movie 250 movie.mpg v_mol3 type # zoom 1.6 adiam 1.5
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
run 25000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 2.5
binsize = 0.6 -> bins = 167 84 2
Memory usage per processor = 2.72041 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 5000
1000 130 259.24123 2.3773387e-30 5000
2000 130 465.39775 9.5010816e-30 5000
3000 130 736.55426 2.1365846e-29 5000
4000 260 1274.295 6.045774e-05 5000
5000 260 1855.4991 0.0021687846 5000
6000 260 1936.8934 6.9705094 5000
7000 390 1909.1519 11.402993 5000
8000 390 1958.2549 10.910611 5000
9000 390 1968.6293 14.080709 5000
10000 520 2278.4559 8.2512574 5000
11000 520 1952.4436 6.8525602 5000
12000 520 1391.9826 3.6742003 5000
13000 650 1608.8924 2.2123232 5000
14000 650 1562.872 2.9306477 5000
15000 650 1548.2428 2.4495128 5000
16000 780 1712.8658 2.2773941 5000
17000 780 1649.1423 4.9833774 5000
18000 780 1421.6645 4.0064802 5000
19000 910 1574.37 2.4833854 5000
20000 910 1354.8838 5.1248395 5000
21000 910 1156.7385 2.5239056 5000
22000 1040 1233.7916 2.9364978 5000
23000 1040 1150.2238 2.5059515 5000
24000 1040 1224.372 1.6145537 5000
25000 1170 1202.871 2.6775319 5000
Loop time of 1.18423 on 4 procs for 25000 steps with 1170 atoms
Performance: 1823968.216 tau/day, 21110.743 timesteps/s
99.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.22024 | 0.23723 | 0.25431 | 2.6 | 20.03
Neigh | 0.057575 | 0.064853 | 0.070241 | 1.8 | 5.48
Comm | 0.068985 | 0.082663 | 0.097154 | 3.9 | 6.98
Output | 0.00060296 | 0.00069225 | 0.0009203 | 0.5 | 0.06
Modify | 0.67185 | 0.6862 | 0.69518 | 1.1 | 57.94
Other | | 0.1126 | | | 9.51
Nlocal: 292.5 ave 304 max 278 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 42.5 ave 58 max 27 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 427 ave 456 max 388 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 1708
Ave neighs/atom = 1.45983
Neighbor list builds = 1732
Dangerous builds = 0
Total wall time: 0:00:01

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LAMMPS (15 Feb 2016)
# Pour granular particles into chute container, then induce flow
atom_style sphere
boundary p p fm
newton off
comm_modify 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 2 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 25000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6 -> bins = 34 34 28
Memory usage per processor = 2.90017 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 6600
1000 402 768.04606 0 6600
2000 402 1407.1714 0 6600
3000 402 1373.819 15.59952 6600
4000 804 1737.1399 39.311164 6600
5000 804 1571.3184 67.501382 6600
6000 804 1318.6439 77.636174 6600
7000 1206 1522.1986 68.863683 6600
8000 1206 1387.2223 64.067846 6600
9000 1206 1265.9044 51.726525 6600
10000 1608 1460.3212 48.844763 6600
11000 1608 1310.2001 53.532609 6600
12000 1608 1134.4592 48.567743 6600
13000 2010 1182.5037 45.620614 6600
14000 2010 1192.4303 39.066935 6600
15000 2010 967.05968 42.363789 6600
16000 2412 1119.8304 39.217157 6600
17000 2412 1063.7921 45.71714 6600
18000 2412 855.28326 42.745948 6600
19000 2814 970.7019 40.155896 6600
20000 2814 923.94347 34.590568 6600
21000 2814 793.75092 36.707509 6600
22000 2814 543.4546 37.669131 6600
23000 3000 446.47658 39.719019 6600
24000 3000 331.57201 24.034747 6600
25000 3000 239.90493 18.457205 6600
Loop time of 9.98164 on 1 procs for 25000 steps with 3000 atoms
Performance: 216397.236 tau/day, 2504.598 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.5892 | 5.5892 | 5.5892 | 0.0 | 55.99
Neigh | 1.5595 | 1.5595 | 1.5595 | 0.0 | 15.62
Comm | 0.21001 | 0.21001 | 0.21001 | 0.0 | 2.10
Output | 0.00055695 | 0.00055695 | 0.00055695 | 0.0 | 0.01
Modify | 2.3514 | 2.3514 | 2.3514 | 0.0 | 23.56
Other | | 0.271 | | | 2.71
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 658 ave 658 max 658 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13479 ave 13479 max 13479 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13479
Ave neighs/atom = 4.493
Neighbor list builds = 1149
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Memory usage per processor = 7.37566 Mbytes
Step Atoms KinEng 1 Volume
25000 3000 239.90493 18.457205 6600
26000 3000 86.453151 19.990229 6600
27000 3000 104.03763 12.243926 6600
28000 3000 187.74939 11.703132 6600
29000 3000 316.59921 14.610301 6600
30000 3000 520.76149 18.82089 6600
31000 3000 821.71283 25.266473 6600
32000 3000 1153.8578 30.714985 6600
33000 3000 1520.1476 38.247011 6600
34000 3000 2006.3144 44.480026 6600
35000 3000 2556.4751 55.768118 6600
36000 3000 3160.9914 63.728696 6600
37000 3000 3877.5537 71.484742 6600
38000 3000 4675.4987 79.37485 6600
39000 3000 5479.8489 94.281786 6600
40000 3000 6350.6439 106.39353 6600
41000 3000 7245.0837 113.40306 6600
42000 3000 8227.1726 129.62268 6600
43000 3000 9422.0189 144.63991 6600
44000 3000 10616.036 149.84326 6600
45000 3000 11908.182 169.96204 6600
46000 3000 13257.313 184.73533 6600
47000 3000 14765.4 201.20237 6600
48000 3000 16184.643 202.00907 6600
49000 3000 17573.204 215.30429 6600
50000 3000 19117.749 232.28939 6600
Loop time of 19.1635 on 1 procs for 25000 steps with 3000 atoms
Performance: 112714.075 tau/day, 1304.561 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.221 | 12.221 | 12.221 | 0.0 | 63.77
Neigh | 2.2719 | 2.2719 | 2.2719 | 0.0 | 11.86
Comm | 0.44526 | 0.44526 | 0.44526 | 0.0 | 2.32
Output | 0.00094628 | 0.00094628 | 0.00094628 | 0.0 | 0.00
Modify | 3.7599 | 3.7599 | 3.7599 | 0.0 | 19.62
Other | | 0.4643 | | | 2.42
Nlocal: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 742 ave 742 max 742 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 13997 ave 13997 max 13997 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 13997
Ave neighs/atom = 4.66567
Neighbor list builds = 836
Dangerous builds = 0
Total wall time: 0:00:29

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LAMMPS (15 Feb 2016)
# Pour granular particles into chute container, then induce flow
atom_style sphere
boundary p p fm
newton off
comm_modify 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 2 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 2 pad 5
#dump 3 all movie 1000 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
#dump_modify 3 pad 5
run 25000
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 1.2
ghost atom cutoff = 1.2
binsize = 0.6 -> bins = 34 34 28
Memory usage per processor = 2.77531 Mbytes
Step Atoms KinEng 1 Volume
0 0 -0 0 6600
1000 402 768.04606 0 6600
2000 402 1407.1714 0 6600
3000 402 1373.819 15.59952 6600
4000 804 1737.1399 39.311164 6600
5000 804 1571.3184 67.501382 6600
6000 804 1318.6439 77.636174 6600
7000 1206 1521.8348 69.010381 6600
8000 1206 1391.0761 64.407583 6600
9000 1206 1264.98 50.32567 6600
10000 1608 1462.7175 49.903609 6600
11000 1608 1317.5878 52.401196 6600
12000 1608 1120.9416 46.067058 6600
13000 2010 1200.1517 49.662302 6600
14000 2010 1180.2805 38.850379 6600
15000 2010 970.23519 39.121533 6600
16000 2412 1101.3888 44.051087 6600
17000 2412 1054.4967 43.489619 6600
18000 2412 850.25959 42.296696 6600
19000 2814 959.68841 42.757546 6600
20000 2814 933.72206 42.668586 6600
21000 2814 779.2842 42.116934 6600
22000 2814 537.68477 35.113909 6600
23000 3000 456.26221 36.394458 6600
24000 3000 334.38331 26.256087 6600
25000 3000 233.7217 18.768345 6600
Loop time of 2.97699 on 4 procs for 25000 steps with 3000 atoms
Performance: 725563.868 tau/day, 8397.730 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3818 | 1.4161 | 1.4613 | 2.9 | 47.57
Neigh | 0.39047 | 0.40059 | 0.40954 | 1.3 | 13.46
Comm | 0.30601 | 0.31937 | 0.33453 | 2.2 | 10.73
Output | 0.00056505 | 0.00065571 | 0.00070286 | 0.2 | 0.02
Modify | 0.60454 | 0.61377 | 0.62323 | 1.1 | 20.62
Other | | 0.2265 | | | 7.61
Nlocal: 750 ave 765 max 730 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 390.75 ave 393 max 385 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Neighs: 3548 ave 3643 max 3454 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 14192
Ave neighs/atom = 4.73067
Neighbor list builds = 1152
Dangerous builds = 0
unfix ins
fix 2 all gravity 1.0 chute 26.0
run 25000
Memory usage per processor = 7.22932 Mbytes
Step Atoms KinEng 1 Volume
25000 3000 233.7217 18.768345 6600
26000 3000 80.58756 21.114703 6600
27000 3000 112.90794 11.760837 6600
28000 3000 211.68857 11.667711 6600
29000 3000 368.27114 15.483397 6600
30000 3000 611.33941 21.023859 6600
31000 3000 902.04662 29.663904 6600
32000 3000 1188.6213 31.996848 6600
33000 3000 1626.3144 38.244424 6600
34000 3000 2068.1939 45.793779 6600
35000 3000 2654.4292 55.900641 6600
36000 3000 3212.0662 64.492942 6600
37000 3000 3942.9079 73.557353 6600
38000 3000 4710.2169 84.24051 6600
39000 3000 5513.597 93.737814 6600
40000 3000 6367.338 112.43633 6600
41000 3000 7417.7889 130.70338 6600
42000 3000 8428.2678 124.66302 6600
43000 3000 9498.0121 136.37107 6600
44000 3000 10680.269 149.21074 6600
45000 3000 11852.03 154.67802 6600
46000 3000 12896.699 167.10324 6600
47000 3000 14218.465 196.70386 6600
48000 3000 15555.796 204.40316 6600
49000 3000 16694.338 208.98934 6600
50000 3000 17936.665 192.19442 6600
Loop time of 5.6096 on 4 procs for 25000 steps with 3000 atoms
Performance: 385054.499 tau/day, 4456.649 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0572 | 3.1012 | 3.1483 | 1.8 | 55.28
Neigh | 0.57694 | 0.58054 | 0.5881 | 0.6 | 10.35
Comm | 0.52065 | 0.53928 | 0.55884 | 1.8 | 9.61
Output | 0.00074744 | 0.00090379 | 0.0011649 | 0.5 | 0.02
Modify | 0.94697 | 0.95569 | 0.96864 | 0.9 | 17.04
Other | | 0.432 | | | 7.70
Nlocal: 750 ave 758 max 741 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 404 ave 417 max 395 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Neighs: 3603.75 ave 3695 max 3528 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 14415
Ave neighs/atom = 4.805
Neighbor list builds = 827
Dangerous builds = 0
Total wall time: 0:00:08

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LAMMPS (15 Feb 2016)
Running on 4 partitions of processors
Step CPU Clock Event Correlated Coincident Replica
100 0.000 0 0 0 0 0
100 0.539 0 0 0 0 0
100 0.694 0 0 0 0 0
100 0.850 0 0 0 0 0
100 0.928 0 0 0 0 0
200 1.555 400 1 0 4 1
300 1.924 500 2 1 1 1
500 3.495 772 3 0 2 2
800 5.446 1328 4 0 2 2
1000 7.037 1636 5 0 1 3
1000 7.989 1636 5 0 1 3
1200 8.838 1908 6 0 1 2
1300 9.212 2008 7 1 1 2
1900 12.291 4024 8 0 1 3
1900 12.832 4024 8 0 1 3
1900 13.157 4024 8 0 1 3
1900 13.320 4024 8 0 1 3
2100 14.090 4220 9 0 2 3
Loop time of 14.0941 on 4 procs for 2000 steps with 511 atoms

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LAMMPS (15 Feb 2016)
# This example demonstrates the use of various fix qeq variants with
# that defines and uses charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
1 by 1 by 1 MPI processor grid
reading atoms ...
1200 atoms
replicate 2 2 2
orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405)
1 by 1 by 1 MPI processor grid
9600 atoms
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
kspace_style ewald 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
3200 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
6400 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot spcpu
thermo 10
timestep 0.0001
velocity all create 300.0 1281937
fix 1 all nve
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2
fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
run 100
Ewald initialization ...
G vector (1/distance) = 0.305064
estimated absolute RMS force accuracy = 2.07629e-05
estimated relative force accuracy = 1.44191e-06
KSpace vectors: actual max1d max3d = 13556 20 34460
kxmax kymax kzmax = 18 18 20
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5 -> bins = 8 8 9
Memory usage per processor = 70.3977 Mbytes
Step PotEng q1 q2 qtot S/CPU
0 -27457.219 0.85227886 -0.42613943 -2.1827873e-10 0
10 -27626.057 0.85486228 -0.42743114 -2.14186e-10 0.65299981
20 -27975.085 0.85968531 -0.42984266 -9.5496944e-11 0.55284542
30 -28552.628 0.86755661 -0.4337783 -2.7284841e-11 0.52549773
40 -29133.643 0.87426387 -0.43713193 -1.8098945e-10 0.52418671
50 -29697.011 0.8794039 -0.43970195 -7.4578566e-11 0.51636783
60 -30342.001 0.88478594 -0.44239297 -1.200533e-10 0.52492361
70 -31081.138 0.8906973 -0.44534865 5.7752914e-11 0.56248275
80 -31792.732 0.89506635 -0.44753317 2.2782842e-10 0.59687627
90 -32424.749 0.89714841 -0.44857421 2.3510438e-10 0.58629238
100 -32998.353 0.89755721 -0.44877861 1.5006663e-11 0.60415017
Loop time of 178.066 on 1 procs for 100 steps with 9600 atoms
Performance: 0.005 ns/day, 4946.280 hours/ns, 0.562 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.335 | 15.335 | 15.335 | 0.0 | 8.61
Kspace | 96.45 | 96.45 | 96.45 | 0.0 | 54.17
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.022512 | 0.022512 | 0.022512 | 0.0 | 0.01
Output | 0.0019941 | 0.0019941 | 0.0019941 | 0.0 | 0.00
Modify | 66.247 | 66.247 | 66.247 | 0.0 | 37.20
Other | | 0.01012 | | | 0.01
Nlocal: 9600 ave 9600 max 9600 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 22125 ave 22125 max 22125 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.9408e+06 ave 2.9408e+06 max 2.9408e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2940800
Ave neighs/atom = 306.333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:03:02

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LAMMPS (15 Feb 2016)
# This example demonstrates the use of various fix qeq variants with
# that defines and uses charges, in this case pair_style buck/coul/long
units metal
atom_style charge
read_data data.aC
orthogonal box = (0 0 0) to (25.1583 25.1583 28.0203)
1 by 2 by 2 MPI processor grid
reading atoms ...
1200 atoms
replicate 2 2 2
orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405)
1 by 2 by 2 MPI processor grid
9600 atoms
pair_style buck/coul/long 12.0
pair_coeff 2 2 1388.77 .3623188 175.0
pair_coeff 1 2 18003 .2052124 133.5381
pair_coeff 1 1 0 .1 0
kspace_style ewald 1e-6
neighbor 1.0 bin
neigh_modify delay 0 every 1 check yes
group type1 type 1
3200 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
6400 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
variable qtot equal count(type1)*c_q1+count(type2)*c_q2
thermo_style custom step pe c_q1 c_q2 v_qtot spcpu
thermo 10
timestep 0.0001
velocity all create 300.0 1281937
fix 1 all nve
#fix 2 all qeq/point 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/shielded 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/slater 1 10 1.0e-6 100 param.qeq2
#fix 2 all qeq/dynamic 1 10 1.0e-4 100 param.qeq2
fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
run 100
Ewald initialization ...
G vector (1/distance) = 0.305064
estimated absolute RMS force accuracy = 2.07629e-05
estimated relative force accuracy = 1.44191e-06
KSpace vectors: actual max1d max3d = 13556 20 34460
kxmax kymax kzmax = 18 18 20
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 13
ghost atom cutoff = 13
binsize = 6.5 -> bins = 8 8 9
Memory usage per processor = 22.8544 Mbytes
Step PotEng q1 q2 qtot S/CPU
0 -27457.215 0.85227886 -0.42613943 2.1373125e-11 0
10 -27626.057 0.85486228 -0.42743114 2.4556357e-11 2.5540579
20 -27975.085 0.85968531 -0.42984266 6.0481398e-11 2.1404073
30 -28552.627 0.86755661 -0.4337783 1.3278623e-10 2.0419173
40 -29133.643 0.87426387 -0.43713193 6.3664629e-11 2.0338224
50 -29697.01 0.8794039 -0.43970195 8.5492502e-11 2.0248457
60 -30342 0.88478594 -0.44239297 1.3096724e-10 2.0459077
70 -31081.139 0.89069733 -0.44534866 1.5188562e-10 2.1726062
80 -31792.732 0.89506635 -0.44753317 1.3960744e-10 2.3350176
90 -32424.752 0.89714841 -0.44857421 1.1641532e-10 2.2406318
100 -32998.353 0.89755721 -0.44877861 8.0035534e-11 2.3247991
Loop time of 45.8779 on 4 procs for 100 steps with 9600 atoms
Performance: 0.019 ns/day, 1274.386 hours/ns, 2.180 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.9256 | 4.0039 | 4.0664 | 2.6 | 8.73
Kspace | 24.225 | 24.347 | 24.445 | 1.6 | 53.07
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.12152 | 0.21473 | 0.28551 | 14.7 | 0.47
Output | 0.0010197 | 0.0011217 | 0.0011744 | 0.2 | 0.00
Modify | 17.303 | 17.304 | 17.304 | 0.0 | 37.72
Other | | 0.007412 | | | 0.02
Nlocal: 2400 ave 2400 max 2400 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 11550 ave 11550 max 11550 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 735200 ave 740758 max 729642 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 2940800
Ave neighs/atom = 306.333
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:46

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LAMMPS (15 Feb 2016)
# This example demonstrates the use of various fix qeq variants with pair reax/c
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reax/c, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reax/c.
units real
atom_style charge
read_data data.CHO
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
105 atoms
pair_style reax/c NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 1 bin
neigh_modify every 1 delay 0 check yes
group type1 type 1
60 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
25 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
group type3 type 3
20 atoms in group type3
compute charge3 type3 property/atom q
compute q3 type3 reduce ave c_charge3
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
thermo 1
velocity all create 300.0 1281937
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
timestep 0.25
run 10
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5 -> bins = 5 5 5
Memory usage per processor = 15.3036 Mbytes
Step PotEng q1 q2 q3 qtot
0 -10226.557 0.095634063 -0.15658793 -0.091167279 4.4408921e-16
1 -10225.799 0.095649584 -0.1566219 -0.091171371 7.1054274e-15
2 -10223.656 0.095669731 -0.15666714 -0.091175264 -6.4392935e-15
3 -10220.276 0.095691257 -0.15671597 -0.091178813 2.6645353e-15
4 -10215.894 0.095714363 -0.15676887 -0.091182006 -3.1086245e-15
5 -10210.804 0.095733863 -0.15681398 -0.09118412 6.6613381e-16
6 -10205.342 0.095751253 -0.15685427 -0.091185918 -1.110223e-15
7 -10199.848 0.095762028 -0.1568795 -0.091186707 8.8817842e-15
8 -10194.646 0.095767243 -0.15689184 -0.091186932 -2.4424907e-15
9 -10190.016 0.095760528 -0.15687664 -0.091185782 -4.4408921e-16
10 -10186.168 0.095748006 -0.15684815 -0.09118383 1.110223e-15
Loop time of 0.0423889 on 1 procs for 10 steps with 105 atoms
Performance: 5.096 ns/day, 4.710 hours/ns, 235.911 timesteps/s
99.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.037234 | 0.037234 | 0.037234 | 0.0 | 87.84
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 4.1485e-05 | 4.1485e-05 | 4.1485e-05 | 0.0 | 0.10
Output | 0.00019646 | 0.00019646 | 0.00019646 | 0.0 | 0.46
Modify | 0.0048897 | 0.0048897 | 0.0048897 | 0.0 | 11.54
Other | | 2.766e-05 | | | 0.07
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3417 ave 3417 max 3417 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3417
Ave neighs/atom = 32.5429
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# This example demonstrates the use of various fix qeq variants with pair reax/c
# You can comment in/out various versions below
#
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
# used with pair_style reax/c, provided that the QEq parameters are the same.
#
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
# the QEq parameters are the same. These two styles can also be used with
# pair_style reax/c.
units real
atom_style charge
read_data data.CHO
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
105 atoms
pair_style reax/c NULL checkqeq no
pair_coeff * * ffield.reax.cho H C O
Reading potential file ffield.reax.cho with DATE: 2011-02-18
neighbor 1 bin
neigh_modify every 1 delay 0 check yes
group type1 type 1
60 atoms in group type1
compute charge1 type1 property/atom q
compute q1 type1 reduce ave c_charge1
group type2 type 2
25 atoms in group type2
compute charge2 type2 property/atom q
compute q2 type2 reduce ave c_charge2
group type3 type 3
20 atoms in group type3
compute charge3 type3 property/atom q
compute q3 type3 reduce ave c_charge3
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
thermo 1
velocity all create 300.0 1281937
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
timestep 0.25
run 10
Neighbor list info ...
2 neighbor list requests
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 11
ghost atom cutoff = 11
binsize = 5.5 -> bins = 5 5 5
Memory usage per processor = 11.1055 Mbytes
Step PotEng q1 q2 q3 qtot
0 -10226.557 0.095633919 -0.15658765 -0.091167194 1.7763568e-15
1 -10225.799 0.0956503 -0.15662357 -0.09117143 2.8865799e-15
2 -10223.656 0.095669684 -0.15666698 -0.091175327 1.110223e-15
3 -10220.276 0.095691296 -0.15671615 -0.091178696 0
4 -10215.894 0.09571384 -0.15676787 -0.091181678 8.8817842e-16
5 -10210.804 0.095734178 -0.15681468 -0.09118418 1.3322676e-15
6 -10205.342 0.095751126 -0.15685409 -0.091185769 4.4408921e-16
7 -10199.848 0.095762403 -0.15688037 -0.091186751 0
8 -10194.646 0.095766449 -0.15689014 -0.091186673 -4.4408921e-16
9 -10190.016 0.095761078 -0.15687818 -0.09118551 -4.4408921e-16
10 -10186.168 0.095747223 -0.15684634 -0.091183742 0
Loop time of 0.0712105 on 4 procs for 10 steps with 105 atoms
Performance: 3.033 ns/day, 7.912 hours/ns, 140.429 timesteps/s
72.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.014191 | 0.015309 | 0.016687 | 0.7 | 21.50
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0013485 | 0.010136 | 0.018539 | 7.8 | 14.23
Output | 0.0023825 | 0.002628 | 0.0029249 | 0.4 | 3.69
Modify | 0.035412 | 0.042747 | 0.050082 | 3.5 | 60.03
Other | | 0.0003899 | | | 0.55
Nlocal: 26.25 ave 35 max 15 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 300 ave 357 max 239 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 1025.25 ave 1468 max 405 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 4101
Ave neighs/atom = 39.0571
Neighbor list builds = 0
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
21 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
WARNING: pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c (../pair_reax.cpp:48)
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 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
1 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 3 3 3
Memory usage per processor = 2.95105 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 -244.79971 0 168.88435
10 1281.7558 -1989.1322 -1912.7188 -19609.913 -2733.8828 -15.775275 0.20055725 0 55.020231 3.1070522 -77.710916 0 14.963568 -5.8082204 843.41939 -180.17724 0 107.5115
20 516.83079 -1941.677 -1910.8655 -12525.41 -2801.8626 7.4107974 0.073134188 0 81.986982 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574158
30 467.2641 -1940.978 -1913.1215 -35957.487 -2755.021 -6.9179959 0.049322439 0 78.853175 0.13604392 -51.653634 0 19.862872 -9.7098575 853.79334 -151.232 0 80.861768
40 647.45541 -1951.1994 -1912.6006 -5883.7147 -2798.3556 17.334807 0.15102863 0 63.23512 0.18070931 -54.598962 0 17.325008 -12.052277 883.01667 -164.21335 0 96.777422
50 716.38057 -1949.4749 -1906.767 5473.2085 -2800.931 9.2056917 0.15413274 0 85.371449 3.2986106 -78.253597 0 34.861773 -8.5531236 882.01435 -193.85275 0 117.2096
60 1175.2707 -1975.9611 -1905.8959 -1939.4971 -2726.5816 -11.651982 0.24296788 0 48.320663 7.1799636 -75.363641 0 16.520132 -4.8869463 844.754 -194.23296 0 119.73837
70 1156.7 -1975.3486 -1906.3905 24628.344 -2880.5223 25.652478 0.26894312 0 83.724884 7.1049303 -68.700942 0 24.750744 -8.6338218 911.20067 -183.4058 0 113.21158
80 840.23687 -1955.4768 -1905.3851 -17731.383 -2755.7295 -8.0168306 0.13867962 0 86.14748 2.2387306 -76.945841 0 23.595858 -7.2609645 853.6346 -167.88289 0 94.603895
90 365.79169 -1926.406 -1904.5989 898.37155 -2842.183 47.368211 0.23109 0 92.288131 0.38031313 -61.361483 0 18.476377 -12.255472 900.24202 -186.48056 0 116.88831
100 801.32078 -1953.4177 -1905.646 -2417.5518 -2802.7244 4.6676973 0.18046558 0 76.730114 5.4177372 -77.102556 0 24.997234 -7.7554179 898.67306 -196.8912 0 120.38952
Loop time of 0.523648 on 1 procs for 100 steps with 21 atoms
Performance: 16.500 ns/day, 1.455 hours/ns, 190.968 timesteps/s
99.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.52205 | 0.52205 | 0.52205 | 0.0 | 99.70
Neigh | 0.00072503 | 0.00072503 | 0.00072503 | 0.0 | 0.14
Comm | 0.00039506 | 0.00039506 | 0.00039506 | 0.0 | 0.08
Output | 0.00027037 | 0.00027037 | 0.00027037 | 0.0 | 0.05
Modify | 7.2956e-05 | 7.2956e-05 | 7.2956e-05 | 0.0 | 0.01
Other | | 0.0001328 | | | 0.03
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 not checked
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
21 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
WARNING: pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c (../pair_reax.cpp:48)
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 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
1 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 3 3 3
Memory usage per processor = 3.0718 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 -180.17725 0 107.51148
20 516.8308 -1941.677 -1910.8655 -12525.411 -2801.8626 7.4107973 0.07313419 0 81.986982 0.2281551 -57.494871 0 30.656735 -10.102557 877.78696 -158.93385 0 88.574155
30 467.26411 -1940.978 -1913.1215 -35957.487 -2755.021 -6.9179966 0.049322437 0 78.853175 0.13604391 -51.653634 0 19.862872 -9.7098574 853.79333 -151.232 0 80.861765
40 647.45584 -1951.1994 -1912.6006 -5883.7102 -2798.3557 17.334812 0.15102857 0 63.235124 0.18070914 -54.598951 0 17.325006 -12.052278 883.01674 -164.21335 0 96.777418
50 716.38108 -1949.4679 -1906.76 5473.1803 -2800.9311 9.2057064 0.15413272 0 85.371443 3.2986124 -78.253597 0 34.861778 -8.5531235 882.01441 -193.85213 0 117.21596
60 1175.2703 -1975.9632 -1905.898 -1939.6676 -2726.5815 -11.652032 0.24296779 0 48.320636 7.1799647 -75.363643 0 16.520124 -4.8869416 844.75396 -194.25563 0 119.75889
70 1156.7016 -1975.3469 -1906.3887 24628.125 -2880.5225 25.65252 0.26894309 0 83.724869 7.1048931 -68.700978 0 24.750754 -8.6338341 911.20067 -183.41947 0 113.22722
80 840.3323 -1955.4867 -1905.3893 -17732.956 -2755.7336 -8.0168615 0.13869303 0 86.143454 2.2388975 -76.946365 0 23.594977 -7.2608903 853.63682 -167.88599 0 94.604168
90 365.75853 -1926.4192 -1904.6141 902.29004 -2842.1715 47.360077 0.23110905 0 92.28805 0.38040356 -61.364192 0 18.473252 -12.253964 900.23128 -186.47889 0 116.88518
100 801.64661 -1953.4392 -1905.6481 -2464.5533 -2802.6922 4.6510183 0.18048786 0 76.715675 5.41849 -77.102069 0 24.987058 -7.7531389 898.65974 -196.87724 0 120.37303
Loop time of 0.433318 on 4 procs for 100 steps with 21 atoms
Performance: 19.939 ns/day, 1.204 hours/ns, 230.777 timesteps/s
97.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.16821 | 0.25684 | 0.42837 | 20.0 | 59.27
Neigh | 4.0293e-05 | 0.00022489 | 0.00054836 | 1.3 | 0.05
Comm | 0.0036013 | 0.17559 | 0.26447 | 24.3 | 40.52
Output | 0.00044513 | 0.00048918 | 0.00056028 | 0.2 | 0.11
Modify | 3.4571e-05 | 6.1274e-05 | 8.2731e-05 | 0.2 | 0.01
Other | | 0.0001184 | | | 0.03
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 not checked
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
384 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
WARNING: pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c (../pair_reax.cpp:48)
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 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 2 all reax/bonds 25 bonds.reax.tatb
run 25
Neighbor list info ...
1 neighbor list requests
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 4 3
Memory usage per processor = 6.61277 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 0.63682807 -44767.737 -44767.01 8391.5966 -61118.763 486.82916 4.723415 0 1567.835 20.768662 -278.20804 -1557.6962 252.64683 -655.74117 18859.328 -8738.2727 0 6388.8127
10 2.4306957 -44769.41 -44766.635 11717.369 -61113.142 487.89093 4.7227063 0 1567.2936 20.705084 -274.37509 -1560.8546 252.87219 -655.43578 18850.19 -8731.0713 0 6381.7946
15 5.0590478 -44772.63 -44766.854 17125.033 -61103.34 489.28007 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.3112 0 6370.4665
20 8.0678579 -44775.923 -44766.713 24620.824 -61088.791 490.42346 4.7193467 0 1565.5541 20.415031 -260.38512 -1574.1001 253.39805 -654.26837 18815.312 -8703.3104 0 6355.1097
25 10.975539 -44777.231 -44764.701 34381.278 -61068.889 490.53149 4.7164093 0 1566.5715 20.169755 -251.2311 -1582.8552 253.88696 -653.46042 18790.855 -8683.8362 0 6336.3099
Loop time of 7.52359 on 1 procs for 25 steps with 384 atoms
Performance: 0.018 ns/day, 1337.526 hours/ns, 3.323 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.4675 | 7.4675 | 7.4675 | 0.0 | 99.25
Neigh | 0.052319 | 0.052319 | 0.052319 | 0.0 | 0.70
Comm | 0.0021715 | 0.0021715 | 0.0021715 | 0.0 | 0.03
Output | 0.00026178 | 0.00026178 | 0.00026178 | 0.0 | 0.00
Modify | 0.0010068 | 0.0010068 | 0.0010068 | 0.0 | 0.01
Other | | 0.000315 | | | 0.00
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 not checked
Total wall time: 0:00:07

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
384 atoms
# reax args: hbcut hbnewflag tripflag precision
pair_style reax 6.0 1 1 1.0e-6
WARNING: pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c (../pair_reax.cpp:48)
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 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 2 all reax/bonds 25 bonds.reax.tatb
run 25
Neighbor list info ...
1 neighbor list requests
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 4 3
Memory usage per processor = 4.03843 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 -44767.816 -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 6388.86
10 2.4306905 -44769.408 -44766.633 11717.247 -61113.142 487.89094 4.7227063 0 1567.2936 20.705084 -274.3751 -1560.8546 252.87219 -655.43578 18850.19 -8731.0965 0 6381.8216
15 5.0590422 -44772.626 -44766.85 17124.943 -61103.34 489.2801 4.7214008 0 1566.4744 20.590604 -268.28963 -1566.5961 252.97781 -654.93836 18835.335 -8719.3383 0 6370.4973
20 8.0678512 -44775.934 -44766.723 24620.531 -61088.791 490.42349 4.7193467 0 1565.5541 20.415031 -260.38513 -1574.1001 253.39804 -654.26837 18815.312 -8703.4033 0 6355.1921
25 10.97553 -44777.231 -44764.701 34381.242 -61068.889 490.53154 4.7164093 0 1566.5715 20.169755 -251.23111 -1582.8552 253.88696 -653.46042 18790.855 -8683.8451 0 6336.3185
Loop time of 3.35853 on 4 procs for 25 steps with 384 atoms
Performance: 0.040 ns/day, 597.072 hours/ns, 7.444 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.1029 | 3.2261 | 3.3401 | 5.3 | 96.06
Neigh | 0.011399 | 0.011589 | 0.011772 | 0.1 | 0.35
Comm | 0.0055692 | 0.11938 | 0.24261 | 27.6 | 3.55
Output | 0.00039721 | 0.0005976 | 0.00081921 | 0.7 | 0.02
Modify | 0.00036359 | 0.00061446 | 0.00086737 | 0.8 | 0.02
Other | | 0.0002854 | | | 0.01
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 not checked
Total wall time: 0:00:03

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
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 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 3 3 3
Memory usage per processor = 14.4462 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 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396
10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935
20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379
30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727
40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096
50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995
60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413
70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648
80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398
90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068717 0.2433807 0 96.181613 0.96184887 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141
100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961
Loop time of 0.372956 on 1 procs for 100 steps with 21 atoms
Performance: 23.166 ns/day, 1.036 hours/ns, 268.128 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.35299 | 0.35299 | 0.35299 | 0.0 | 94.65
Neigh | 0.008096 | 0.008096 | 0.008096 | 0.0 | 2.17
Comm | 0.00043416 | 0.00043416 | 0.00043416 | 0.0 | 0.12
Output | 0.00021172 | 0.00021172 | 0.00021172 | 0.0 | 0.06
Modify | 0.011089 | 0.011089 | 0.011089 | 0.0 | 2.97
Other | | 0.0001314 | | | 0.04
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 not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
21 atoms
pair_style reax/c control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
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 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
Neighbor list info ...
2 neighbor list requests
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 3 3 3
Memory usage per processor = 12.531 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 1288.6115 -1989.6644 -1912.8422 -19456.354 -2734.6769 -15.60722 0.2017796 0 54.629558 3.1252288 -77.7067 0 14.933901 -5.8108542 843.92073 -180.43321 0 107.75934
20 538.95831 -1942.7037 -1910.5731 -10725.671 -2803.7395 7.9078306 0.077926651 0 81.610051 0.22951926 -57.557099 0 30.331204 -10.178049 878.99014 -159.69268 0 89.316921
30 463.09502 -1933.5765 -1905.9685 -33255.512 -2749.8591 -8.015455 0.027628766 0 81.6274 0.11972393 -50.262275 0 20.820315 -9.6327041 851.88722 -149.49498 0 79.205714
40 885.49378 -1958.9125 -1906.1228 -4814.644 -2795.644 9.1506485 0.13747497 0 70.948 0.24360511 -57.862677 0 19.076502 -11.141216 873.73898 -159.99393 0 92.43409
50 861.16297 -1954.4602 -1903.1209 -1896.8002 -2784.8451 3.8270162 0.157933 0 79.851673 3.3492148 -78.066132 0 32.628944 -7.9565368 872.81852 -190.98572 0 114.76001
60 1167.7835 -1971.8433 -1902.2245 -3482.8296 -2705.8635 -17.121613 0.2274909 0 44.507674 7.85602 -74.788998 0 16.256483 -4.6046575 835.83058 -188.33691 0 114.19414
70 1439.9939 -1989.3026 -1903.4556 23846.042 -2890.7893 31.958672 0.26671708 0 85.758381 3.1804035 -71.002944 0 24.357195 -10.311284 905.8679 -175.38487 0 106.79661
80 502.39535 -1930.7548 -1900.8039 -20356.194 -2703.8126 -18.662209 0.11286005 0 99.803849 2.0329206 -76.171278 0 19.23716 -6.2787147 826.47505 -166.03123 0 92.539386
90 749.07874 -1946.9841 -1902.3269 17798.394 -2863.7576 42.068612 0.24338059 0 96.181423 0.96185061 -69.95542 0 24.615344 -11.582758 903.68812 -190.13826 0 120.69124
100 1109.6904 -1968.5879 -1902.4323 -4490.0667 -2755.8991 -7.1224194 0.21757691 0 61.805857 7.0827218 -75.645383 0 20.115437 -6.23727 863.56487 -198.56975 0 122.09963
Loop time of 0.301445 on 4 procs for 100 steps with 21 atoms
Performance: 28.662 ns/day, 0.837 hours/ns, 331.736 timesteps/s
99.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.2505 | 0.25132 | 0.25322 | 0.2 | 83.37
Neigh | 0.0036662 | 0.0049902 | 0.006367 | 1.4 | 1.66
Comm | 0.0030849 | 0.0049003 | 0.0058699 | 1.5 | 1.63
Output | 0.00038004 | 0.00043535 | 0.00049639 | 0.2 | 0.14
Modify | 0.038152 | 0.03968 | 0.041151 | 0.5 | 13.16
Other | | 0.0001191 | | | 0.04
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 not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

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LAMMPS (15 Feb 2016)
# 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
reading atoms ...
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
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
fix 4 all reax/c/bonds 5 bonds.reaxc
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 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Neighbor list info ...
2 neighbor list requests
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 4 3
Memory usage per processor = 155.82 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 7827.7879 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274
5 0.61603942 -44761.698 -44760.994 8934.6281 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691
10 2.3525551 -44763.227 -44760.541 12288.607 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9688 0 6381.7066
15 4.9013326 -44766.36 -44760.764 17717.015 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.237 0 6370.4033
20 7.829471 -44769.686 -44760.747 25205.558 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5091 0 6355.2604
25 10.697926 -44772.904 -44760.691 34232.793 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3608 0 6336.8416
Loop time of 4.39835 on 1 procs for 25 steps with 384 atoms
Performance: 0.031 ns/day, 781.929 hours/ns, 5.684 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.5683 | 3.5683 | 3.5683 | 0.0 | 81.13
Neigh | 0.40996 | 0.40996 | 0.40996 | 0.0 | 9.32
Comm | 0.0022433 | 0.0022433 | 0.0022433 | 0.0 | 0.05
Output | 0.00019693 | 0.00019693 | 0.00019693 | 0.0 | 0.00
Modify | 0.41718 | 0.41718 | 0.41718 | 0.0 | 9.49
Other | | 0.0004306 | | | 0.01
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 not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:04

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LAMMPS (15 Feb 2016)
# 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 2 by 2 MPI processor grid
reading atoms ...
384 atoms
pair_style reax/c control.reax_c.tatb
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
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
fix 4 all reax/c/bonds 5 bonds.reaxc
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 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb
run 25
Neighbor list info ...
2 neighbor list requests
update every 5 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12.5
ghost atom cutoff = 12.5
binsize = 6.25 -> bins = 5 4 3
Memory usage per processor = 105.386 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 7827.7867 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6397 0 6391.0277
5 0.61603967 -44761.698 -44760.994 8934.6339 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1905 0 6388.6665
10 2.3525545 -44763.227 -44760.541 12288.586 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.714
15 4.9013281 -44766.36 -44760.764 17716.982 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2476 0 6370.4138
20 7.8294637 -44769.686 -44760.747 25205.512 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.518 0 6355.2692
25 10.697905 -44772.904 -44760.691 34232.815 -61069.308 490.25887 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3481 0 6336.829
Loop time of 2.68044 on 4 procs for 25 steps with 384 atoms
Performance: 0.050 ns/day, 476.523 hours/ns, 9.327 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.255 | 2.2552 | 2.2557 | 0.0 | 84.13
Neigh | 0.22861 | 0.22899 | 0.22971 | 0.1 | 8.54
Comm | 0.005641 | 0.006301 | 0.0065787 | 0.5 | 0.24
Output | 0.00036383 | 0.002835 | 0.0036614 | 2.7 | 0.11
Modify | 0.18515 | 0.18673 | 0.18977 | 0.4 | 6.97
Other | | 0.0004016 | | | 0.01
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 not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:02

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LAMMPS (15 Feb 2016)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 1 by 1 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 18 18 18
Memory usage per processor = 3.15778 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.972284e-05 0 5269.5046 14.510657
2650 16733.017 1.7051479 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419352 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.8460621 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706558 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.0002211587 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690666 0 5269.5189 12.011706
8500 16738.481 -0.0034646804 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532811 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652434 0 5269.5216 12.011692
9550 16738.493 -0.005315616 0 5269.5203 12.011611
9600 16738.549 -0.026814368 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589885 0 5269.4979 12.062708
9750 16738.013 0.13550123 0 5269.5101 11.407245
9800 16738.512 -0.011620328 0 5269.5201 11.394974
9850 16738.489 -0.00067270523 0 5269.5237 11.395098
9900 16738.489 -0.00024984554 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.122539 on 1 procs for 10000 steps with 81 atoms
Performance: 705081.398 tau/day, 81606.643 timesteps/s
100.4% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0094028 | 0.0094028 | 0.0094028 | 0.0 | 7.67
Neigh | 0.03594 | 0.03594 | 0.03594 | 0.0 | 29.33
Comm | 0.00758 | 0.00758 | 0.00758 | 0.0 | 6.19
Output | 0.0011275 | 0.0011275 | 0.0011275 | 0.0 | 0.92
Modify | 0.065143 | 0.065143 | 0.065143 | 0.0 | 53.16
Other | | 0.003345 | | | 2.73
Nlocal: 81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 84 ave 84 max 84 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

329
examples/rigid/log.15Feb16.rigid.g++.4 Normal file
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@ -0,0 +1,329 @@
LAMMPS (15 Feb 2016)
# Simple rigid body system
units lj
atom_style atomic
pair_style lj/cut 2.5
read_data data.rigid
orthogonal box = (-12 -12 -12) to (12 12 12)
1 by 2 by 2 MPI processor grid
reading atoms ...
81 atoms
velocity all create 100.0 4928459
# unconnected bodies
group clump1 id <> 1 9
9 atoms in group clump1
group clump2 id <> 10 18
9 atoms in group clump2
group clump3 id <> 19 27
9 atoms in group clump3
group clump4 id <> 28 36
9 atoms in group clump4
group clump5 id <> 37 45
9 atoms in group clump5
group clump6 id <> 46 54
9 atoms in group clump6
group clump7 id <> 55 63
9 atoms in group clump7
group clump8 id <> 64 72
9 atoms in group clump8
group clump9 id <> 73 81
9 atoms in group clump9
fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 clump6 clump7 clump8 clump9
9 rigid bodies with 81 atoms
# 1 chain of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 36 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 # clump6 clump7 clump8 clump9
# 2 chains of connected bodies
#group clump1 id <> 1 9
#group clump2 id <> 9 18
#group clump3 id <> 18 27
#group clump4 id <> 27 36
#group clump5 id <> 37 45
#group clump6 id <> 45 54
#group clump7 id <> 54 63
#group clump8 id <> 63 72
#group clump9 id <> 72 81
#fix 1 all poems group clump1 clump2 clump3 clump4
#fix 2 all poems group clump5 clump6 clump7 clump8 clump9
neigh_modify exclude group clump1 clump1
neigh_modify exclude group clump2 clump2
neigh_modify exclude group clump3 clump3
neigh_modify exclude group clump4 clump4
neigh_modify exclude group clump5 clump5
neigh_modify exclude group clump6 clump6
neigh_modify exclude group clump7 clump7
neigh_modify exclude group clump8 clump8
neigh_modify exclude group clump9 clump9
thermo 100
#dump 1 all atom 50 dump.rigid
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 5
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 5
timestep 0.0001
thermo 50
run 10000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4 -> bins = 18 18 18
Memory usage per processor = 3.1287 Mbytes
Step Temp E_pair E_mol TotEng Press
0 115.29439 5235.9179 0 5272.2142 -2.7403788
50 14910.685 571.71558 0 5265.82 32.006171
100 16298.442 136.66184 0 5267.653 16.444229
150 16682.606 17.490511 0 5269.4219 14.900344
200 16733.929 1.372872 0 5269.4617 14.569267
250 16738.853 -0.15252816 0 5269.4864 14.496404
300 16738.588 -0.055171335 0 5269.5002 14.496025
350 16738.492 -0.017444677 0 5269.5077 14.496446
400 16738.464 -0.0060102023 0 5269.5104 14.496618
450 16738.455 -0.0012713351 0 5269.5124 14.496701
500 16738.455 -0.00081068621 0 5269.5128 14.496709
550 16738.455 -0.00083203497 0 5269.5129 14.496707
600 16738.455 -0.00058355356 0 5269.5131 14.496709
650 16738.455 -0.00047226704 0 5269.5131 14.496708
700 16738.455 0 0 5269.5136 14.496713
750 16738.455 0 0 5269.5136 14.49671
800 16738.455 0 0 5269.5137 14.496709
850 16738.455 0 0 5269.5137 14.49671
900 16738.456 0 0 5269.5138 14.496713
950 16738.462 -0.0035323872 0 5269.5122 14.496671
1000 16738.586 -0.051135144 0 5269.5036 14.496229
1050 16737.358 0.32995057 0 5269.4981 14.525763
1100 16737.892 0.16210246 0 5269.4984 14.531983
1150 16738.703 -0.089235095 0 5269.5025 14.509899
1200 16738.466 -0.0075446243 0 5269.5096 14.510615
1250 16738.456 0 0 5269.514 14.510704
1300 16738.457 0 0 5269.5141 14.510701
1350 16738.457 0 0 5269.5141 14.510699
1400 16738.457 -0.00044736511 0 5269.5138 14.510693
1450 16738.458 -0.0010971179 0 5269.5134 14.510687
1500 16738.458 -0.00057885428 0 5269.5139 14.510698
1550 16738.457 0 0 5269.5143 14.51071
1600 16738.457 0 0 5269.5144 14.510712
1650 16738.457 0 0 5269.5144 14.510712
1700 16738.458 0 0 5269.5144 14.51071
1750 16738.458 0 0 5269.5145 14.510708
1800 16738.458 0 0 5269.5145 14.510706
1850 16738.458 0 0 5269.5146 14.510705
1900 16738.458 0 0 5269.5146 14.510706
1950 16738.465 -0.0031733615 0 5269.5134 14.510659
2000 16738.491 -0.013255268 0 5269.5117 14.510532
2050 16738.556 -0.0365811 0 5269.5087 14.51029
2100 16738.633 -0.063209659 0 5269.5065 14.510219
2150 16738.607 -0.05601761 0 5269.5055 14.510231
2200 16738.557 -0.038423032 0 5269.5072 14.510404
2250 16738.515 -0.023709918 0 5269.5088 14.510539
2300 16738.489 -0.013249035 0 5269.5111 14.510621
2350 16738.468 -0.0045563719 0 5269.5131 14.510714
2400 16738.46 -0.00052194273 0 5269.5146 14.510771
2450 16738.464 -0.0023259756 0 5269.514 14.510746
2500 16738.468 -0.0051929186 0 5269.5127 14.510731
2550 16738.581 -0.044940117 0 5269.5085 14.510315
2600 16738.427 -7.9722832e-05 0 5269.5046 14.510657
2650 16733.017 1.705148 0 5269.5067 14.596295
2700 16738.761 -0.10614946 0 5269.5038 14.499584
2750 16733.973 1.4038179 0 5269.5064 14.598107
2800 16738.585 -0.046813448 0 5269.5076 14.511073
2850 16738.487 -0.012558719 0 5269.5111 14.510111
2900 16738.465 -0.0026252725 0 5269.514 14.510277
2950 16738.476 -0.0082220764 0 5269.512 14.510223
3000 16738.66 -0.071284779 0 5269.507 14.509758
3050 16715.332 7.2419351 0 5269.476 14.870305
3100 16653.226 26.818761 0 5269.5009 14.496764
3150 16739.351 -0.30690375 0 5269.4886 13.643904
3200 16733.238 1.6025328 0 5269.4737 12.016934
3250 16734.374 1.2554429 0 5269.4841 11.963561
3300 16732.156 1.9585967 0 5269.4893 12.234024
3350 16738.655 -0.079693236 0 5269.497 12.092757
3400 16738.543 -0.042215005 0 5269.4991 12.092809
3450 16738.591 -0.059327511 0 5269.4972 12.092536
3500 16738.759 -0.11761245 0 5269.4918 12.09203
3550 16713.405 7.846062 0 5269.4737 12.389816
3600 16734.939 1.0821936 0 5269.4891 12.173591
3650 16738.808 -0.13663194 0 5269.4882 12.027009
3700 16738.602 -0.070934368 0 5269.4889 12.025288
3750 16737.731 0.20706557 0 5269.4927 12.061948
3800 16738.578 -0.05582043 0 5269.4965 12.035665
3850 16738.471 -0.016307928 0 5269.5024 12.035302
3900 16738.449 -0.0058182199 0 5269.5059 12.035401
3950 16738.439 -0.0012027325 0 5269.5074 12.035461
4000 16738.436 -0.00020698452 0 5269.5075 12.035469
4050 16738.437 0 0 5269.5078 12.035454
4100 16738.437 0 0 5269.508 12.035435
4150 16738.438 0 0 5269.5081 12.035426
4200 16738.438 0 0 5269.5083 12.035432
4250 16738.439 0 0 5269.5085 12.035447
4300 16738.439 0 0 5269.5086 12.035463
4350 16738.44 0 0 5269.5087 12.035474
4400 16738.44 0 0 5269.5088 12.035478
4450 16738.44 0 0 5269.5089 12.035474
4500 16738.44 0 0 5269.509 12.035462
4550 16738.441 0 0 5269.5092 12.035449
4600 16738.441 0 0 5269.5093 12.035445
4650 16738.442 0 0 5269.5095 12.035451
4700 16738.442 0 0 5269.5096 12.03546
4750 16738.443 0 0 5269.5097 12.035465
4800 16738.443 0 0 5269.5098 12.035466
4850 16738.443 0 0 5269.51 12.035463
4900 16738.444 0 0 5269.5101 12.035456
4950 16738.444 0 0 5269.5102 12.035447
5000 16738.445 0 0 5269.5104 12.03544
5050 16738.445 0 0 5269.5105 12.035442
5100 16738.446 0 0 5269.5107 12.035455
5150 16738.446 0 0 5269.5108 12.03547
5200 16738.446 0 0 5269.5109 12.035479
5250 16738.447 0 0 5269.511 12.035479
5300 16738.447 0 0 5269.5111 12.03547
5350 16738.447 0 0 5269.5112 12.035454
5400 16738.448 0 0 5269.5113 12.035434
5450 16738.448 0 0 5269.5115 12.03542
5500 16738.449 0 0 5269.5117 12.035422
5550 16738.457 -0.0030919234 0 5269.5111 12.035383
5600 16738.51 -0.021618357 0 5269.5092 12.035106
5650 16738.622 -0.059214788 0 5269.507 12.035694
5700 16395.28 108.06942 0 5269.5463 24.369038
5750 16738.544 -0.033973429 0 5269.5077 12.011261
5800 16738.456 -0.0037013529 0 5269.5102 12.011675
5850 16738.451 0 0 5269.5123 12.011709
5900 16738.451 -0.00022115871 0 5269.5122 12.011687
5950 16738.452 -0.00024253349 0 5269.5124 12.011678
6000 16738.452 0 0 5269.5128 12.011688
6050 16738.453 0 0 5269.513 12.011702
6100 16738.453 0 0 5269.5131 12.011716
6150 16738.454 0 0 5269.5132 12.011725
6200 16738.454 0 0 5269.5133 12.011728
6250 16738.454 0 0 5269.5134 12.011723
6300 16738.455 0 0 5269.5135 12.011712
6350 16738.455 0 0 5269.5137 12.0117
6400 16738.456 0 0 5269.5138 12.011697
6450 16738.456 0 0 5269.514 12.011704
6500 16738.456 0 0 5269.5141 12.011714
6550 16738.457 0 0 5269.5142 12.011719
6600 16738.457 0 0 5269.5143 12.011718
6650 16738.458 0 0 5269.5144 12.011713
6700 16738.458 0 0 5269.5146 12.011705
6750 16738.459 0 0 5269.5147 12.011696
6800 16738.459 0 0 5269.5149 12.01169
6850 16738.46 0 0 5269.515 12.011695
6900 16738.46 0 0 5269.5152 12.01171
6950 16738.46 0 0 5269.5153 12.011726
7000 16738.461 0 0 5269.5154 12.011736
7050 16738.461 0 0 5269.5155 12.011737
7100 16738.461 0 0 5269.5155 12.011728
7150 16738.461 0 0 5269.5156 12.011712
7200 16738.462 0 0 5269.5158 12.011691
7250 16738.463 0 0 5269.516 12.011676
7300 16738.463 0 0 5269.5162 12.011677
7350 16738.464 0 0 5269.5164 12.011693
7400 16738.464 0 0 5269.5165 12.011713
7450 16738.465 0 0 5269.5166 12.011729
7500 16738.465 0 0 5269.5167 12.011736
7550 16738.465 0 0 5269.5168 12.011734
7600 16738.465 0 0 5269.5168 12.011722
7650 16738.466 0 0 5269.517 12.011704
7700 16738.466 0 0 5269.5171 12.011687
7750 16738.467 0 0 5269.5173 12.011681
7800 16738.467 0 0 5269.5175 12.011687
7850 16738.468 0 0 5269.5176 12.0117
7900 16738.468 0 0 5269.5178 12.011712
7950 16738.469 0 0 5269.5179 12.011721
8000 16738.469 0 0 5269.518 12.011724
8050 16738.469 0 0 5269.5181 12.01172
8100 16738.47 0 0 5269.5182 12.011709
8150 16738.47 0 0 5269.5183 12.0117
8200 16738.47 0 0 5269.5185 12.0117
8250 16738.471 0 0 5269.5186 12.011709
8300 16738.471 0 0 5269.5187 12.011719
8350 16738.472 0 0 5269.5189 12.011723
8400 16738.472 0 0 5269.519 12.01172
8450 16738.473 -0.00039690663 0 5269.5189 12.011706
8500 16738.481 -0.0034646803 0 5269.5182 12.011643
8550 16738.483 -0.0045307409 0 5269.5178 12.011621
8600 16738.474 -0.00076532813 0 5269.5189 12.011681
8650 16738.474 0 0 5269.5197 12.011699
8700 16738.475 0 0 5269.5199 12.011715
8750 16738.475 0 0 5269.52 12.011732
8800 16738.475 0 0 5269.52 12.011743
8850 16738.476 0 0 5269.5201 12.011744
8900 16738.476 0 0 5269.5202 12.011735
8950 16738.476 0 0 5269.5203 12.011719
9000 16738.477 0 0 5269.5205 12.011698
9050 16738.477 0 0 5269.5206 12.011683
9100 16738.478 0 0 5269.5208 12.011684
9150 16738.479 0 0 5269.521 12.011701
9200 16738.479 0 0 5269.5212 12.011722
9250 16738.479 0 0 5269.5213 12.011738
9300 16738.48 0 0 5269.5214 12.011746
9350 16738.48 0 0 5269.5214 12.011744
9400 16738.48 0 0 5269.5215 12.011732
9450 16738.48 0 0 5269.5216 12.011715
9500 16738.481 -0.00037652438 0 5269.5216 12.011692
9550 16738.493 -0.0053156163 0 5269.5203 12.011611
9600 16738.549 -0.026814371 0 5269.5163 12.011415
9650 16738.765 -0.10191523 0 5269.5092 12.011013
9700 16735.041 1.0589894 0 5269.4979 12.062708
9750 16738.013 0.13550109 0 5269.5101 11.407246
9800 16738.512 -0.011620327 0 5269.5201 11.394974
9850 16738.489 -0.00067270507 0 5269.5237 11.395098
9900 16738.489 -0.00024984555 0 5269.5242 11.395085
9950 16738.49 0 0 5269.5245 11.395076
10000 16738.49 0 0 5269.5246 11.395075
Loop time of 0.187163 on 4 procs for 10000 steps with 81 atoms
Performance: 461628.979 tau/day, 53429.280 timesteps/s
95.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0022814 | 0.0031556 | 0.0039577 | 1.1 | 1.69
Neigh | 0.010708 | 0.011337 | 0.012736 | 0.8 | 6.06
Comm | 0.084257 | 0.090435 | 0.10014 | 2.1 | 48.32
Output | 0.003355 | 0.0035859 | 0.0039752 | 0.4 | 1.92
Modify | 0.062852 | 0.072432 | 0.07759 | 2.1 | 38.70
Other | | 0.006218 | | | 3.32
Nlocal: 20.25 ave 38 max 3 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 27.25 ave 48 max 13 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Neighbor list builds = 998
Dangerous builds = 997
Total wall time: 0:00:00

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