git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14610 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
225
examples/balance/log.15Feb16.balance.bond.fast.g++.1
Normal file
225
examples/balance/log.15Feb16.balance.bond.fast.g++.1
Normal file
@ -0,0 +1,225 @@
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LAMMPS (15 Feb 2016)
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# 2d circle of particles inside a box with LJ walls
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variable b index 0
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variable x index 50
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variable y index 20
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variable d index 20
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variable v index 5
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variable w index 2
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units lj
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dimension 2
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atom_style bond
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boundary f f p
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lattice hex 0.85
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Lattice spacing in x,y,z = 1.16553 2.01877 1.16553
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region box block 0 $x 0 $y -0.5 0.5
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region box block 0 50 0 $y -0.5 0.5
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region box block 0 50 0 20 -0.5 0.5
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create_box 1 box bond/types 1 extra/bond/per/atom 6
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Created orthogonal box = (0 0 -0.582767) to (58.2767 40.3753 0.582767)
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1 by 1 by 1 MPI processor grid
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region circle sphere $(v_d/2+1) $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
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region circle sphere 11 $(v_d/2/sqrt(3.0)+1) 0.0 $(v_d/2)
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region circle sphere 11 6.7735026918962581988 0.0 $(v_d/2)
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region circle sphere 11 6.7735026918962581988 0.0 10
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create_atoms 1 region circle
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Created 361 atoms
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mass 1 1.0
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velocity all create 0.5 87287 loop geom
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velocity all set $v $w 0 sum yes
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velocity all set 5 $w 0 sum yes
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velocity all set 5 2 0 sum yes
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pair_style lj/cut 2.5
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pair_coeff 1 1 10.0 1.0 2.5
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bond_style harmonic
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bond_coeff 1 10.0 1.2
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# need to preserve 1-3, 1-4 pairwise interactions during hard collisions
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special_bonds lj/coul 0 1 1
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0 = max # of 1-2 neighbors
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1 = max # of special neighbors
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create_bonds all all 1 1.0 1.5
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Neighbor list info ...
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2 neighbor list requests
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4 -> bins = 42 29 1
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Added 1014 bonds, new total = 1014
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6 = max # of 1-2 neighbors
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6 = max # of special neighbors
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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fix 1 all nve
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||||||
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fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi $x 1 1 2.5
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fix 2 all wall/lj93 xlo 0.0 1 1 2.5 xhi 50 1 1 2.5
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fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi $y 1 1 2.5
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fix 3 all wall/lj93 ylo 0.0 1 1 2.5 yhi 20 1 1 2.5
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comm_style tiled
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comm_modify cutoff 7.5
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fix 10 all balance 50 0.9 rcb
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#compute 1 all property/atom proc
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#variable p atom (c_1%10)+1
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#dump 2 all custom 50 tmp.dump id v_p x y z
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#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
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#variable colors string # "red green blue yellow white # purple pink orange lime gray"
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#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
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thermo_style custom step temp epair press f_10[3] f_10
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thermo 100
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run 10000
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Neighbor list info ...
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1 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 7.5
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binsize = 1.4 -> bins = 42 29 1
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Memory usage per processor = 4.44301 Mbytes
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Step Temp E_pair Press 10[3] 10
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0 25.701528 -2.2032569 3.1039469 1 1
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100 27.623422 -6.228166 2.6542136 1 1
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200 33.35302 -15.746749 3.2018248 1 1
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300 39.17734 -24.1557 4.9116986 1 1
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400 41.660701 -27.615203 8.6214678 1 1
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500 37.154935 -24.096962 3.2656162 1 1
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600 35.061294 -21.52655 2.3693223 1 1
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700 37.204395 -22.313267 2.7108913 1 1
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800 39.050704 -24.972147 5.5398741 1 1
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900 38.37275 -24.777769 3.9291488 1 1
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1000 39.147816 -26.003699 4.3586203 1 1
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1100 36.084337 -24.88638 4.5496174 1 1
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1200 32.404559 -20.810803 6.0760128 1 1
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1300 32.625538 -19.709411 4.3718289 1 1
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1400 32.246777 -18.785184 3.435959 1 1
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1500 29.174368 -17.434726 2.2702916 1 1
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1600 27.359273 -15.40756 1.033659 1 1
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1700 26.046626 -14.318045 0.87714473 1 1
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1800 24.540401 -13.017686 0.84464169 1 1
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1900 26.259688 -12.777739 0.80954004 1 1
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2000 27.491023 -13.363863 1.4519188 1 1
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2100 27.839831 -13.709118 3.0184763 1 1
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2200 26.669065 -12.710422 1.4560094 1 1
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2300 26.86742 -12.730386 0.16986139 1 1
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2400 26.375504 -12.476682 1.907352 1 1
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2500 26.581263 -12.530908 1.5507765 1 1
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2600 27.67091 -12.922702 2.0391206 1 1
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2700 27.158784 -13.306789 3.7355268 1 1
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2800 25.635671 -13.502047 2.9431633 1 1
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|
2900 24.648357 -12.388002 0.44910075 1 1
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3000 22.988768 -10.685349 0.37214853 1 1
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|
3100 21.788719 -10.171928 -0.95734833 1 1
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3200 22.707514 -9.6682633 -0.32868418 1 1
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3300 22.907772 -10.612766 -0.024319089 1 1
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3400 24.276426 -10.802246 0.44731188 1 1
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3500 25.086959 -10.797849 2.3218091 1 1
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3600 26.064365 -12.589537 1.2460738 1 1
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3700 24.656426 -11.956895 0.57862216 1 1
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3800 22.316856 -11.174148 -0.7567936 1 1
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|
3900 22.590299 -9.5928781 0.4127727 1 1
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4000 22.353461 -9.5887736 -0.34247396 1 1
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4100 24.103395 -9.76584 0.98989862 1 1
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4200 23.92261 -10.566828 -0.71536268 1 1
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4300 24.44409 -11.358378 0.37166197 1 1
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4400 24.772419 -11.324888 0.26732853 1 1
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4500 23.150748 -11.309892 -0.43134573 1 1
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4600 24.008361 -10.212365 0.43277527 1 1
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4700 25.107401 -9.5753673 0.020406689 1 1
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4800 23.658604 -8.9131426 0.46554745 1 1
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4900 22.530251 -9.023311 -0.014405315 1 1
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5000 23.110692 -9.6567397 0.9033234 1 1
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5100 23.760144 -9.7623416 0.32059726 1 1
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5200 25.048012 -9.6748253 0.66411561 1 1
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5300 24.09835 -9.7867216 0.61128267 1 1
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5400 22.984982 -9.9464053 0.28096544 1 1
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5500 22.502003 -9.9294451 -0.53666181 1 1
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5600 23.712298 -10.054318 0.64334761 1 1
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5700 23.350796 -10.217344 2.1979894 1 1
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5800 25.246549 -12.458753 0.055553025 1 1
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5900 24.422272 -10.641177 0.82506839 1 1
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6000 22.478315 -10.629525 -0.774321 1 1
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6100 22.970846 -10.218868 0.59819592 1 1
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6200 24.500063 -10.355481 0.55427078 1 1
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6300 22.358071 -9.9041539 0.89500518 1 1
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6400 23.924951 -11.121442 0.045999129 1 1
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6500 24.83773 -10.464191 2.0048038 1 1
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6600 24.752158 -9.9939162 0.53794465 1 1
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6700 23.073765 -9.3662561 0.38618685 1 1
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6800 21.940219 -8.4948475 -0.25184019 1 1
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6900 22.23783 -8.8668868 0.0072863367 1 1
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|
7000 25.667836 -10.473211 0.59852886 1 1
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|
7100 23.352123 -9.0862268 0.85289283 1 1
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7200 24.072107 -9.4020576 0.090222808 1 1
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7300 22.806746 -8.4687857 -0.46892989 1 1
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7400 24.798425 -9.1144357 -0.38738146 1 1
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7500 24.748499 -9.1560558 0.94929896 1 1
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7600 25.364753 -10.176533 0.2649225 1 1
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7700 25.137988 -9.6617897 1.3920543 1 1
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|
7800 25.502583 -10.320832 0.64812816 1 1
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|
7900 24.5208 -9.9466543 -0.084071026 1 1
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|
8000 24.653522 -10.312942 0.32535023 1 1
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|
8100 23.129565 -9.6250435 0.016356303 1 1
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|
8200 23.82421 -9.7608023 0.11631418 1 1
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|
8300 25.081262 -9.3510452 0.92337854 1 1
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|
8400 24.328205 -9.2875396 0.28266968 1 1
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|
8500 25.041711 -11.254976 -0.21368615 1 1
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8600 24.111473 -9.0389585 1.2102938 1 1
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|
8700 23.50066 -9.0926498 0.78819229 1 1
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|
8800 23.840962 -9.3434474 0.091313007 1 1
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|
8900 23.081841 -9.0635966 0.56672001 1 1
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|
9000 24.712103 -9.3243213 0.60301629 1 1
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|
9100 24.457422 -9.439298 -0.60457515 1 1
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|
9200 25.070662 -9.1945782 1.2399235 1 1
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|
9300 25.019869 -8.7910068 0.42340497 1 1
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|
9400 24.23662 -9.3111098 -0.75379175 1 1
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|
9500 24.836827 -8.7324281 0.81857501 1 1
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|
9600 24.901993 -8.6624128 0.84890877 1 1
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|
9700 24.936686 -8.9869503 1.9627894 1 1
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|
9800 25.393368 -9.8538595 0.45344428 1 1
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|
9900 25.942336 -9.7854728 0.68352091 1 1
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|
10000 24.636319 -9.3369442 0.62793231 1 1
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Loop time of 1.67474 on 1 procs for 10000 steps with 361 atoms
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|
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Performance: 2579511.004 tau/day, 5971.090 timesteps/s
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99.8% CPU use with 1 MPI tasks x no OpenMP threads
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|
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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|
---------------------------------------------------------------
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|
Pair | 0.47884 | 0.47884 | 0.47884 | 0.0 | 28.59
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Bond | 0.24918 | 0.24918 | 0.24918 | 0.0 | 14.88
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Neigh | 0.82974 | 0.82974 | 0.82974 | 0.0 | 49.54
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Comm | 0.01265 | 0.01265 | 0.01265 | 0.0 | 0.76
|
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Output | 0.00085878 | 0.00085878 | 0.00085878 | 0.0 | 0.05
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Modify | 0.075636 | 0.075636 | 0.075636 | 0.0 | 4.52
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Other | | 0.02783 | | | 1.66
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|
|
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|
Nlocal: 361 ave 361 max 361 min
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|
Histogram: 1 0 0 0 0 0 0 0 0 0
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|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
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||||||
|
Neighs: 2421 ave 2421 max 2421 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 2421
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||||||
|
Ave neighs/atom = 6.70637
|
||||||
|
Ave special neighs/atom = 5.61773
|
||||||
|
Neighbor list builds = 4937
|
||||||
|
Dangerous builds = 5
|
||||||
|
Total wall time: 0:00:01
|
||||||
225
examples/balance/log.15Feb16.balance.bond.fast.g++.4
Normal file
225
examples/balance/log.15Feb16.balance.bond.fast.g++.4
Normal file
@ -0,0 +1,225 @@
|
|||||||
|
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
524
examples/balance/log.15Feb16.balance.bond.slow.g++.1
Normal file
@ -0,0 +1,524 @@
|
|||||||
|
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
|
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3500 0.34257038 0 -0.021612062 1 1
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3600 0.32838009 0 0.030131228 1 1
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3700 0.34462142 0 0.074586378 1 1
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3800 0.30891825 0 0.10605673 1 1
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3900 0.33847951 0 0.13956139 1 1
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4000 0.32952079 0 0.12688129 1 1
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4100 0.32646772 0 0.081089042 1 1
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4200 0.35399503 0 0.013422873 1 1
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4300 0.33154914 0 -0.050919508 1 1
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4400 0.34113556 0 -0.083171 1 1
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4500 0.32651708 0 -0.1063133 1 1
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4600 0.34359609 0 -0.1076395 1 1
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4700 0.34973537 0 -0.088231606 1 1
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4800 0.35198515 0 -0.020901044 1 1
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4900 0.35187284 0 0.043645941 1 1
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5000 0.34887336 0 0.095698609 1 1
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5100 0.30308163 0 0.11649328 1 1
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5200 0.32401285 0 0.12072411 1 1
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5300 0.33025072 0 0.10933161 1 1
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5400 0.33288012 0 0.078356448 1 1
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5500 0.35142492 0 0.036958063 1 1
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5600 0.35125368 0 -0.041371343 1 1
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5700 0.34547744 0 -0.096450846 1 1
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5800 0.30939887 0 -0.12356656 1 1
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5900 0.32315628 0 -0.11338676 1 1
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6000 0.34117485 0 -0.066198961 1 1
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6100 0.35298043 0 -0.016172816 1 1
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6200 0.35130653 0 0.027660468 1 1
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6300 0.35398766 0 0.087221238 1 1
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6400 0.30963379 0 0.11990957 1 1
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6500 0.3174541 0 0.14103528 1 1
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6600 0.31989791 0 0.11575506 1 1
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6700 0.33811477 0 0.060747353 1 1
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6800 0.3424043 0 0.010357152 1 1
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6900 0.34804319 0 -0.042621786 1 1
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7000 0.35357865 0 -0.067248959 1 1
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7100 0.33556885 0 -0.10983726 1 1
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7200 0.33531101 0 -0.112179 1 1
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7300 0.35742607 0 -0.078405267 1 1
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7400 0.34577559 0 -0.01985432 1 1
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7500 0.3498641 0 0.052289439 1 1
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7600 0.33773715 0 0.092939035 1 1
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7700 0.33093497 0 0.11924405 1 1
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7800 0.31435814 0 0.12701724 1 1
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7900 0.33132217 0 0.10793075 1 1
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8000 0.33451798 0 0.077993125 1 1
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8100 0.35188371 0 0.019929977 1 1
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8200 0.33645742 0 -0.039302079 1 1
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8300 0.3415632 0 -0.098067982 1 1
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8400 0.30619282 0 -0.12952879 1 1
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8500 0.34446484 0 -0.098084709 1 1
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8600 0.33761673 0 -0.07069818 1 1
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8700 0.34495452 0 -0.022458056 1 1
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8800 0.33502983 0 0.027742411 1 1
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8900 0.35418591 0 0.092390134 1 1
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9000 0.31648387 0 0.12467398 1 1
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9100 0.33994825 0 0.14460327 1 1
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9200 0.33822571 0 0.11273284 1 1
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9300 0.33260773 0 0.060063671 1 1
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9400 0.36140305 0 0.021427642 1 1
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9500 0.34273562 0 -0.034064202 1 1
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9600 0.33867054 0 -0.089076906 1 1
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9700 0.32088235 0 -0.12027075 1 1
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9800 0.3320823 0 -0.11602794 1 1
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9900 0.33916442 0 -0.080281044 1 1
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10000 0.34852268 0 -0.01000914 1 1
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10100 0.32955942 0 0.04258493 1 1
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10200 0.34487898 0 0.086971308 1 1
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10300 0.32325593 0 0.11558149 1 1
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10400 0.30927871 0 0.12239437 1 1
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10500 0.33176799 0 0.12285937 1 1
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10600 0.35120027 0 0.084897432 1 1
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10700 0.33129697 0 0.0053089279 1 1
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10800 0.36028769 0 -0.04280715 1 1
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10900 0.35552287 0 -0.084955999 1 1
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11000 0.3406024 0 -0.096554577 1 1
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11100 0.33041202 0 -0.10703492 1 1
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11200 0.32442686 0 -0.084328121 1 1
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11300 0.35952468 0 -0.020191965 1 1
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11400 0.34610624 0 0.03440148 1 1
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11600 0.34040042 0 0.13215705 1 1
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11700 0.33555094 0 0.12738686 1 1
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11800 0.3458647 0 0.10963398 1 1
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11900 0.33836678 0 0.067253864 1 1
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12000 0.34853314 0 0.03201448 1 1
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12100 0.34600048 0 -0.034833402 1 1
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12200 0.33145631 0 -0.09865675 1 1
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12300 0.32848884 0 -0.1248489 1 1
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12400 0.3321344 0 -0.11266575 1 1
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12500 0.32622305 0 -0.061634993 1 1
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12700 0.34673866 0 0.036734645 1 1
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12800 0.34606618 0 0.086267678 1 1
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12900 0.34271431 0 0.12415522 1 1
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13000 0.31993287 0 0.13879926 1 1
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13100 0.3422918 0 0.11978905 1 1
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13200 0.33055236 0 0.062620483 1 1
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13300 0.34652207 0 0.0043833459 1 1
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13400 0.33574661 0 -0.04691024 1 1
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13500 0.33940837 0 -0.074241604 1 1
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13700 0.34336597 0 -0.10544097 1 1
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13900 0.35209713 0 -0.018851408 1 1
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14700 0.35298973 0 -0.040418888 1 1
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14800 0.33679845 0 -0.10067728 1 1
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14900 0.32790966 0 -0.10925568 1 1
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15200 0.35328398 0 -0.020236536 1 1
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15700 0.33681572 0 0.098607746 1 1
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15900 0.34289757 0 0.013849092 1 1
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16000 0.34225547 0 -0.035597548 1 1
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16100 0.33660991 0 -0.076931881 1 1
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16700 0.34336905 0 0.077996627 1 1
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16800 0.33277414 0 0.11053634 1 1
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16900 0.32183338 0 0.11680626 1 1
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17000 0.34044352 0 0.10806555 1 1
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17300 0.35619435 0 -0.04215545 1 1
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17900 0.34255705 0 0.046794555 1 1
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18100 0.3466445 0 0.1351712 1 1
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18200 0.33037668 0 0.12703659 1 1
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18300 0.33677404 0 0.10956306 1 1
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19000 0.34061294 0 -0.001167235 1 1
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19100 0.34194478 0 0.016945224 1 1
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19200 0.33321765 0 0.050665354 1 1
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19300 0.33197783 0 0.080470585 1 1
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19400 0.33284715 0 0.12423599 1 1
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19500 0.33867856 0 0.12689524 1 1
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19600 0.36092786 0 0.11417704 1 1
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19700 0.34270183 0 0.069038291 1 1
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19800 0.34880695 0 0.042483681 1 1
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19900 0.33903644 0 0.034788638 1 1
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20000 0.32590125 0 0.011383785 1 1
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20100 0.30358859 0 0.0030743554 1 1
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20200 0.31830224 0 0.017637826 1 1
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20300 0.34195438 0 0.072811099 1 1
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20400 0.31249563 0 0.10063541 1 1
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20500 0.31544938 0 0.1405794 1 1
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20700 0.2890265 0 0.1136651 1 1
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20900 0.29447212 0 0.0967165 1 1
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21000 0.31159961 0 0.067307231 1 1
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21100 0.30490648 0 0.017689358 1 1
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21200 0.30687262 0 -0.016055512 1 1
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21300 0.30083286 0 -0.0014988997 1 1
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21400 0.32070426 0 0.015960302 1 1
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21500 0.31439311 0 0.038170385 1 1
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21600 0.32617832 0 0.043263788 1 1
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21700 0.35151793 0 0.066302727 1 1
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21800 0.35912885 0 0.070099103 1 1
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21900 0.32451958 0 0.068935768 1 1
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22000 0.35219298 0 0.067161227 1 1
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22100 0.34857705 0 0.032731746 1 1
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22200 0.34750227 0 0.0056917695 1 1
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22300 0.34766017 0 -0.0027090483 1 1
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22400 0.33426062 0 -0.023196063 1 1
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22500 0.34174625 0 -0.025019717 1 1
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22700 0.3362653 0 -0.035815733 1 1
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22800 0.33973405 0 -0.0024705835 1 1
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22900 0.33813085 0 0.0077527467 1 1
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23000 0.33339981 0 0.028340744 1 1
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23100 0.34079832 0 0.018521302 1 1
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23200 0.33074548 0 0.032378405 1 1
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23300 0.32965664 0 0.035989589 1 1
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24000 0.33549728 0 -0.012812915 1 1
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24100 0.31368736 0 -0.020818372 1 1
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24200 0.33533836 0 0.0056121057 1 1
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24300 0.32530627 0 0.018183931 1 1
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24400 0.31930662 0 0.027446878 1 1
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24500 0.33540302 0 0.040307455 1 1
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24600 0.34020431 0 0.027403921 1 1
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24700 0.3291814 0 0.01204865 1 1
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24800 0.31552604 0 0.019654111 1 1
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24900 0.34727253 0 0.01670543 1 1
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25100 0.32706871 0 -0.021196623 1 1
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25500 0.33002601 0 0.0080974022 1 1
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25600 0.34127655 0 0.014296091 1 1
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26000 0.32967371 0 0.028727383 1 1
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26100 0.33775718 0 0.015607478 1 1
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26400 0.33632665 0 -0.0026904889 1 1
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26900 0.33825444 0 0.010428603 1 1
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27000 0.32081518 0 0.019818223 1 1
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27100 0.31448098 0 0.020093416 1 1
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27200 0.32643684 0 0.021934917 1 1
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27300 0.33289466 0 0.023713072 1 1
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27800 0.34064581 0 -0.0086519116 1 1
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27900 0.33559187 0 -0.0055753593 1 1
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28000 0.32300727 0 -0.0004153384 1 1
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28100 0.32147461 0 -0.0058543412 1 1
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28200 0.35532383 0 0.013646951 1 1
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28300 0.31507942 0 0.026532255 1 1
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28400 0.32711006 0 0.033214981 1 1
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28500 0.34472462 0 0.028050837 1 1
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28700 0.34478087 0 0.023743689 1 1
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29100 0.33541374 0 -0.016273261 1 1
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29500 0.3416255 0 0.022650856 1 1
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29700 0.34480638 0 0.024317128 1 1
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29800 0.31459471 0 0.023097895 1 1
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29900 0.33014448 0 0.03114046 1 1
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30000 0.33741498 0 0.015624314 1 1
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30100 0.32598657 0 -0.0018860541 1 1
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30200 0.34855815 0 0.0017983372 1 1
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30300 0.33375921 0 0.0010991235 1 1
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30400 0.35008944 0 -0.0027316177 1 1
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30700 0.33597034 0 -0.0014524001 1 1
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|
30800 0.3227257 0 0.016353457 1 1
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|
30900 0.32676516 0 0.027396654 1 1
|
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|
31000 0.34083982 0 0.031606413 1 1
|
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|
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
524
examples/balance/log.15Feb16.balance.bond.slow.g++.4
Normal file
@ -0,0 +1,524 @@
|
|||||||
|
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
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||||||
|
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
202
examples/balance/log.15Feb16.balance.g++.1
Normal file
@ -0,0 +1,202 @@
|
|||||||
|
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
|
||||||
202
examples/balance/log.15Feb16.balance.g++.4
Normal file
202
examples/balance/log.15Feb16.balance.g++.4
Normal file
@ -0,0 +1,202 @@
|
|||||||
|
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
|
||||||
86
examples/body/log.15Feb16.body.g++.1
Normal file
86
examples/body/log.15Feb16.body.g++.1
Normal file
@ -0,0 +1,86 @@
|
|||||||
|
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
|
||||||
86
examples/body/log.15Feb16.body.g++.4
Normal file
86
examples/body/log.15Feb16.body.g++.4
Normal file
@ -0,0 +1,86 @@
|
|||||||
|
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
|
||||||
146
examples/colloid/log.15Feb16.colloid.g++.1
Normal file
146
examples/colloid/log.15Feb16.colloid.g++.1
Normal file
@ -0,0 +1,146 @@
|
|||||||
|
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
|
||||||
146
examples/colloid/log.15Feb16.colloid.g++.4
Normal file
146
examples/colloid/log.15Feb16.colloid.g++.4
Normal file
@ -0,0 +1,146 @@
|
|||||||
|
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
|
||||||
92
examples/comb/log.15Feb16.comb.Cu.g++.1
Normal file
92
examples/comb/log.15Feb16.comb.Cu.g++.1
Normal file
@ -0,0 +1,92 @@
|
|||||||
|
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
|
||||||
92
examples/comb/log.15Feb16.comb.Cu.g++.4
Normal file
92
examples/comb/log.15Feb16.comb.Cu.g++.4
Normal file
@ -0,0 +1,92 @@
|
|||||||
|
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
|
||||||
409
examples/comb/log.15Feb16.comb.Cu2O.elastic.g++.1
Normal file
409
examples/comb/log.15Feb16.comb.Cu2O.elastic.g++.1
Normal file
@ -0,0 +1,409 @@
|
|||||||
|
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
|
||||||
409
examples/comb/log.15Feb16.comb.Cu2O.elastic.g++.4
Normal file
409
examples/comb/log.15Feb16.comb.Cu2O.elastic.g++.4
Normal file
@ -0,0 +1,409 @@
|
|||||||
|
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
examples/comb/log.15Feb16.comb.HfO2.g++.1
Normal file
235
examples/comb/log.15Feb16.comb.HfO2.g++.1
Normal file
@ -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 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
235
examples/comb/log.15Feb16.comb.HfO2.g++.4
Normal file
@ -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
examples/comb/log.15Feb16.comb.Si.elastic.g++.1
Normal file
333
examples/comb/log.15Feb16.comb.Si.elastic.g++.1
Normal file
@ -0,0 +1,333 @@
|
|||||||
|
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
examples/comb/log.15Feb16.comb.Si.elastic.g++.4
Normal file
331
examples/comb/log.15Feb16.comb.Si.elastic.g++.4
Normal file
@ -0,0 +1,331 @@
|
|||||||
|
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
|
||||||
92
examples/comb/log.15Feb16.comb.Si.g++.1
Normal file
92
examples/comb/log.15Feb16.comb.Si.g++.1
Normal file
@ -0,0 +1,92 @@
|
|||||||
|
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
|
||||||
92
examples/comb/log.15Feb16.comb.Si.g++.4
Normal file
92
examples/comb/log.15Feb16.comb.Si.g++.4
Normal file
@ -0,0 +1,92 @@
|
|||||||
|
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
|
||||||
90
examples/comb/log.15Feb16.comb3.g++.1
Normal file
90
examples/comb/log.15Feb16.comb3.g++.1
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
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
|
||||||
90
examples/comb/log.15Feb16.comb3.g++.4
Normal file
90
examples/comb/log.15Feb16.comb3.g++.4
Normal file
@ -0,0 +1,90 @@
|
|||||||
|
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
|
||||||
153
examples/crack/log.15Feb16.crack.g++.1
Normal file
153
examples/crack/log.15Feb16.crack.g++.1
Normal file
@ -0,0 +1,153 @@
|
|||||||
|
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
|
||||||
153
examples/crack/log.15Feb16.crack.g++.4
Normal file
153
examples/crack/log.15Feb16.crack.g++.4
Normal file
@ -0,0 +1,153 @@
|
|||||||
|
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
|
||||||
193
examples/deposit/log.15Feb16.deposit.atom.g++.1
Normal file
193
examples/deposit/log.15Feb16.deposit.atom.g++.1
Normal file
@ -0,0 +1,193 @@
|
|||||||
|
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
|
||||||
193
examples/deposit/log.15Feb16.deposit.atom.g++.4
Normal file
193
examples/deposit/log.15Feb16.deposit.atom.g++.4
Normal file
@ -0,0 +1,193 @@
|
|||||||
|
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
|
||||||
205
examples/deposit/log.15Feb16.deposit.molecule.g++.1
Normal file
205
examples/deposit/log.15Feb16.deposit.molecule.g++.1
Normal file
@ -0,0 +1,205 @@
|
|||||||
|
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
examples/deposit/log.15Feb16.deposit.molecule.g++.4
Normal file
205
examples/deposit/log.15Feb16.deposit.molecule.g++.4
Normal file
@ -0,0 +1,205 @@
|
|||||||
|
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
|
||||||
231
examples/deposit/log.15Feb16.deposit.molecule.shake.g++.1
Normal file
231
examples/deposit/log.15Feb16.deposit.molecule.shake.g++.1
Normal file
@ -0,0 +1,231 @@
|
|||||||
|
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
|
||||||
231
examples/deposit/log.15Feb16.deposit.molecule.shake.g++.4
Normal file
231
examples/deposit/log.15Feb16.deposit.molecule.shake.g++.4
Normal file
@ -0,0 +1,231 @@
|
|||||||
|
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
|
||||||
104
examples/dipole/log.15Feb16.dipole.g++.1
Normal file
104
examples/dipole/log.15Feb16.dipole.g++.1
Normal file
@ -0,0 +1,104 @@
|
|||||||
|
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
|
||||||
104
examples/dipole/log.15Feb16.dipole.g++.4
Normal file
104
examples/dipole/log.15Feb16.dipole.g++.4
Normal file
@ -0,0 +1,104 @@
|
|||||||
|
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
|
||||||
117
examples/dreiding/log.15Feb16.dreiding.g++.1
Normal file
117
examples/dreiding/log.15Feb16.dreiding.g++.1
Normal file
@ -0,0 +1,117 @@
|
|||||||
|
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
|
||||||
117
examples/dreiding/log.15Feb16.dreiding.g++.4
Normal file
117
examples/dreiding/log.15Feb16.dreiding.g++.4
Normal file
@ -0,0 +1,117 @@
|
|||||||
|
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
|
||||||
88
examples/eim/log.15Feb16.eim.g++.1
Normal file
88
examples/eim/log.15Feb16.eim.g++.1
Normal file
@ -0,0 +1,88 @@
|
|||||||
|
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
|
||||||
88
examples/eim/log.15Feb16.eim.g++.4
Normal file
88
examples/eim/log.15Feb16.eim.g++.4
Normal file
@ -0,0 +1,88 @@
|
|||||||
|
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
|
||||||
185
examples/ellipse/log.15Feb16.ellipse.gayberne.g++.1
Normal file
185
examples/ellipse/log.15Feb16.ellipse.gayberne.g++.1
Normal file
@ -0,0 +1,185 @@
|
|||||||
|
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
|
||||||
185
examples/ellipse/log.15Feb16.ellipse.gayberne.g++.4
Normal file
185
examples/ellipse/log.15Feb16.ellipse.gayberne.g++.4
Normal file
@ -0,0 +1,185 @@
|
|||||||
|
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
|
||||||
182
examples/ellipse/log.15Feb16.ellipse.resquared.g++.1
Normal file
182
examples/ellipse/log.15Feb16.ellipse.resquared.g++.1
Normal file
@ -0,0 +1,182 @@
|
|||||||
|
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
|
||||||
182
examples/ellipse/log.15Feb16.ellipse.resquared.g++.4
Normal file
182
examples/ellipse/log.15Feb16.ellipse.resquared.g++.4
Normal file
@ -0,0 +1,182 @@
|
|||||||
|
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
|
||||||
145
examples/flow/log.15Feb16.flow.couette.g++.1
Normal file
145
examples/flow/log.15Feb16.flow.couette.g++.1
Normal file
@ -0,0 +1,145 @@
|
|||||||
|
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
|
||||||
145
examples/flow/log.15Feb16.flow.couette.g++.4
Normal file
145
examples/flow/log.15Feb16.flow.couette.g++.4
Normal file
@ -0,0 +1,145 @@
|
|||||||
|
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
examples/flow/log.15Feb16.flow.pois.g++.1
Normal file
145
examples/flow/log.15Feb16.flow.pois.g++.1
Normal file
@ -0,0 +1,145 @@
|
|||||||
|
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
|
||||||
145
examples/flow/log.15Feb16.flow.pois.g++.4
Normal file
145
examples/flow/log.15Feb16.flow.pois.g++.4
Normal file
@ -0,0 +1,145 @@
|
|||||||
|
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
|
||||||
164
examples/friction/log.15Feb16.friction.g++.1
Normal file
164
examples/friction/log.15Feb16.friction.g++.1
Normal file
@ -0,0 +1,164 @@
|
|||||||
|
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
|
||||||
164
examples/friction/log.15Feb16.friction.g++.4
Normal file
164
examples/friction/log.15Feb16.friction.g++.4
Normal file
@ -0,0 +1,164 @@
|
|||||||
|
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
|
||||||
110
examples/hugoniostat/log.15Feb16.hugoniostat.g++.1
Normal file
110
examples/hugoniostat/log.15Feb16.hugoniostat.g++.1
Normal file
@ -0,0 +1,110 @@
|
|||||||
|
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
|
||||||
110
examples/hugoniostat/log.15Feb16.hugoniostat.g++.4
Normal file
110
examples/hugoniostat/log.15Feb16.hugoniostat.g++.4
Normal file
@ -0,0 +1,110 @@
|
|||||||
|
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
|
||||||
201
examples/indent/log.15Feb16.indent.g++.1
Normal file
201
examples/indent/log.15Feb16.indent.g++.1
Normal file
@ -0,0 +1,201 @@
|
|||||||
|
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
|
||||||
201
examples/indent/log.15Feb16.indent.g++.4
Normal file
201
examples/indent/log.15Feb16.indent.g++.4
Normal file
@ -0,0 +1,201 @@
|
|||||||
|
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
452
examples/indent/log.15Feb16.indent.min.g++.1
Normal file
@ -0,0 +1,452 @@
|
|||||||
|
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
examples/indent/log.15Feb16.indent.min.g++.4
Normal file
445
examples/indent/log.15Feb16.indent.min.g++.4
Normal file
@ -0,0 +1,445 @@
|
|||||||
|
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
|
||||||
84
examples/meam/log.15Feb16.meam.icc.1
Normal file
84
examples/meam/log.15Feb16.meam.icc.1
Normal file
@ -0,0 +1,84 @@
|
|||||||
|
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
|
||||||
84
examples/meam/log.15Feb16.meam.icc.4
Normal file
84
examples/meam/log.15Feb16.meam.icc.4
Normal file
@ -0,0 +1,84 @@
|
|||||||
|
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
|
||||||
196
examples/meam/log.15Feb16.meam.shear.icc.1
Normal file
196
examples/meam/log.15Feb16.meam.shear.icc.1
Normal file
@ -0,0 +1,196 @@
|
|||||||
|
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
|
||||||
196
examples/meam/log.15Feb16.meam.shear.icc.4
Normal file
196
examples/meam/log.15Feb16.meam.shear.icc.4
Normal file
@ -0,0 +1,196 @@
|
|||||||
|
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
|
||||||
78
examples/melt/log.15Feb16.melt.g++.1
Normal file
78
examples/melt/log.15Feb16.melt.g++.1
Normal file
@ -0,0 +1,78 @@
|
|||||||
|
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
|
||||||
78
examples/melt/log.15Feb16.melt.g++.4
Normal file
78
examples/melt/log.15Feb16.melt.g++.4
Normal file
@ -0,0 +1,78 @@
|
|||||||
|
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
|
||||||
244
examples/micelle/log.15Feb16.micelle.g++.1
Normal file
244
examples/micelle/log.15Feb16.micelle.g++.1
Normal file
@ -0,0 +1,244 @@
|
|||||||
|
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
|
||||||
244
examples/micelle/log.15Feb16.micelle.g++.4
Normal file
244
examples/micelle/log.15Feb16.micelle.g++.4
Normal file
@ -0,0 +1,244 @@
|
|||||||
|
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
553
examples/min/log.15Feb16.min.box.g++.1
Normal file
@ -0,0 +1,553 @@
|
|||||||
|
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
542
examples/min/log.15Feb16.min.box.g++.4
Normal file
@ -0,0 +1,542 @@
|
|||||||
|
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
141
examples/min/log.15Feb16.min.g++.1
Normal file
@ -0,0 +1,141 @@
|
|||||||
|
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
|
||||||
137
examples/min/log.15Feb16.min.g++.4
Normal file
137
examples/min/log.15Feb16.min.g++.4
Normal file
@ -0,0 +1,137 @@
|
|||||||
|
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
|
||||||
160
examples/msst/log.15Feb16.msst.g++.1
Normal file
160
examples/msst/log.15Feb16.msst.g++.1
Normal file
@ -0,0 +1,160 @@
|
|||||||
|
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
examples/msst/log.15Feb16.msst.g++.4
Normal file
160
examples/msst/log.15Feb16.msst.g++.4
Normal file
@ -0,0 +1,160 @@
|
|||||||
|
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
|
||||||
173
examples/nb3b/log.15Feb16.nb3b.g++.1
Normal file
173
examples/nb3b/log.15Feb16.nb3b.g++.1
Normal file
@ -0,0 +1,173 @@
|
|||||||
|
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
|
||||||
173
examples/nb3b/log.15Feb16.nb3b.g++.4
Normal file
173
examples/nb3b/log.15Feb16.nb3b.g++.4
Normal file
@ -0,0 +1,173 @@
|
|||||||
|
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
|
||||||
10
examples/neb/log.15Feb16.neb.hop1.g++.4
Normal file
10
examples/neb/log.15Feb16.neb.hop1.g++.4
Normal file
@ -0,0 +1,10 @@
|
|||||||
|
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
|
||||||
18
examples/neb/log.15Feb16.neb.hop2.g++.4
Normal file
18
examples/neb/log.15Feb16.neb.hop2.g++.4
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
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
|
||||||
14
examples/neb/log.15Feb16.neb.sivac.g++.3
Normal file
14
examples/neb/log.15Feb16.neb.sivac.g++.3
Normal file
@ -0,0 +1,14 @@
|
|||||||
|
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
|
||||||
130
examples/nemd/log.15Feb16.nemd.g++.1
Normal file
130
examples/nemd/log.15Feb16.nemd.g++.1
Normal file
@ -0,0 +1,130 @@
|
|||||||
|
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
|
||||||
130
examples/nemd/log.15Feb16.nemd.g++.4
Normal file
130
examples/nemd/log.15Feb16.nemd.g++.4
Normal file
@ -0,0 +1,130 @@
|
|||||||
|
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
|
||||||
155
examples/obstacle/log.15Feb16.obstacle.g++.1
Normal file
155
examples/obstacle/log.15Feb16.obstacle.g++.1
Normal file
@ -0,0 +1,155 @@
|
|||||||
|
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
examples/obstacle/log.15Feb16.obstacle.g++.4
Normal file
155
examples/obstacle/log.15Feb16.obstacle.g++.4
Normal file
@ -0,0 +1,155 @@
|
|||||||
|
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
|
||||||
189
examples/peptide/log.15Feb16.peptide.g++.1
Normal file
189
examples/peptide/log.15Feb16.peptide.g++.1
Normal file
@ -0,0 +1,189 @@
|
|||||||
|
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
|
||||||
189
examples/peptide/log.15Feb16.peptide.g++.4
Normal file
189
examples/peptide/log.15Feb16.peptide.g++.4
Normal file
@ -0,0 +1,189 @@
|
|||||||
|
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
|
||||||
104
examples/peri/log.15Feb16.peri.g++.1
Normal file
104
examples/peri/log.15Feb16.peri.g++.1
Normal file
@ -0,0 +1,104 @@
|
|||||||
|
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
|
||||||
104
examples/peri/log.15Feb16.peri.g++.4
Normal file
104
examples/peri/log.15Feb16.peri.g++.4
Normal file
@ -0,0 +1,104 @@
|
|||||||
|
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
|
||||||
115
examples/pour/log.15Feb16.pour.2d.g++.1
Normal file
115
examples/pour/log.15Feb16.pour.2d.g++.1
Normal file
@ -0,0 +1,115 @@
|
|||||||
|
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
|
||||||
115
examples/pour/log.15Feb16.pour.2d.g++.4
Normal file
115
examples/pour/log.15Feb16.pour.2d.g++.4
Normal file
@ -0,0 +1,115 @@
|
|||||||
|
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
|
||||||
136
examples/pour/log.15Feb16.pour.2d.molecule.g++.1
Normal file
136
examples/pour/log.15Feb16.pour.2d.molecule.g++.1
Normal file
@ -0,0 +1,136 @@
|
|||||||
|
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
|
||||||
136
examples/pour/log.15Feb16.pour.2d.molecule.g++.4
Normal file
136
examples/pour/log.15Feb16.pour.2d.molecule.g++.4
Normal file
@ -0,0 +1,136 @@
|
|||||||
|
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
|
||||||
169
examples/pour/log.15Feb16.pour.g++.1
Normal file
169
examples/pour/log.15Feb16.pour.g++.1
Normal file
@ -0,0 +1,169 @@
|
|||||||
|
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
|
||||||
169
examples/pour/log.15Feb16.pour.g++.4
Normal file
169
examples/pour/log.15Feb16.pour.g++.4
Normal file
@ -0,0 +1,169 @@
|
|||||||
|
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
|
||||||
22
examples/prd/log.15Feb16.prd.g++.4
Normal file
22
examples/prd/log.15Feb16.prd.g++.4
Normal file
@ -0,0 +1,22 @@
|
|||||||
|
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
|
||||||
105
examples/qeq/log.15Feb16.qeq.buck.g++.1
Normal file
105
examples/qeq/log.15Feb16.qeq.buck.g++.1
Normal file
@ -0,0 +1,105 @@
|
|||||||
|
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
|
||||||
105
examples/qeq/log.15Feb16.qeq.buck.g++.4
Normal file
105
examples/qeq/log.15Feb16.qeq.buck.g++.4
Normal file
@ -0,0 +1,105 @@
|
|||||||
|
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
|
||||||
105
examples/qeq/log.15Feb16.qeq.reaxc.g++.1
Normal file
105
examples/qeq/log.15Feb16.qeq.reaxc.g++.1
Normal file
@ -0,0 +1,105 @@
|
|||||||
|
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
|
||||||
105
examples/qeq/log.15Feb16.qeq.reaxc.g++.4
Normal file
105
examples/qeq/log.15Feb16.qeq.reaxc.g++.4
Normal file
@ -0,0 +1,105 @@
|
|||||||
|
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
|
||||||
101
examples/reax/log.15Feb16.reax.rdx.g++.1
Normal file
101
examples/reax/log.15Feb16.reax.rdx.g++.1
Normal file
@ -0,0 +1,101 @@
|
|||||||
|
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
|
||||||
101
examples/reax/log.15Feb16.reax.rdx.g++.4
Normal file
101
examples/reax/log.15Feb16.reax.rdx.g++.4
Normal file
@ -0,0 +1,101 @@
|
|||||||
|
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
|
||||||
97
examples/reax/log.15Feb16.reax.tatb.g++.1
Normal file
97
examples/reax/log.15Feb16.reax.tatb.g++.1
Normal file
@ -0,0 +1,97 @@
|
|||||||
|
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
|
||||||
97
examples/reax/log.15Feb16.reax.tatb.g++.4
Normal file
97
examples/reax/log.15Feb16.reax.tatb.g++.4
Normal file
@ -0,0 +1,97 @@
|
|||||||
|
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
|
||||||
104
examples/reax/log.15Feb16.reaxc.rdx.g++.1
Normal file
104
examples/reax/log.15Feb16.reaxc.rdx.g++.1
Normal file
@ -0,0 +1,104 @@
|
|||||||
|
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
|
||||||
104
examples/reax/log.15Feb16.reaxc.rdx.g++.4
Normal file
104
examples/reax/log.15Feb16.reaxc.rdx.g++.4
Normal file
@ -0,0 +1,104 @@
|
|||||||
|
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
|
||||||
102
examples/reax/log.15Feb16.reaxc.tatb.g++.1
Normal file
102
examples/reax/log.15Feb16.reaxc.tatb.g++.1
Normal file
@ -0,0 +1,102 @@
|
|||||||
|
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
|
||||||
102
examples/reax/log.15Feb16.reaxc.tatb.g++.4
Normal file
102
examples/reax/log.15Feb16.reaxc.tatb.g++.4
Normal file
@ -0,0 +1,102 @@
|
|||||||
|
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
|
||||||
329
examples/rigid/log.15Feb16.rigid.g++.1
Normal file
329
examples/rigid/log.15Feb16.rigid.g++.1
Normal file
@ -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 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
329
examples/rigid/log.15Feb16.rigid.g++.4
Normal file
@ -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
|
||||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user