168 lines
7.7 KiB
Groff
168 lines
7.7 KiB
Groff
LAMMPS (4 May 2017)
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using 1 OpenMP thread(s) per MPI task
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units metal
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atom_style atomic
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atom_modify map array
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boundary p p p
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atom_modify sort 0 0.0
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# temperature
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variable t equal 1800.0
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# coordination number cutoff
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variable r equal 2.835
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# minimization parameters
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variable etol equal 1.0e-5
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variable ftol equal 1.0e-5
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variable maxiter equal 100
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variable maxeval equal 100
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variable dmax equal 1.0e-1
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# diamond unit cell
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variable a equal 5.431
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lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
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lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
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Lattice spacing in x,y,z = 5.431 5.431 5.431
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region myreg block 0 4 0 4 0 4
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create_box 1 myreg
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Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
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1 by 2 by 2 MPI processor grid
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create_atoms 1 region myreg
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Created 512 atoms
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mass 1 28.06
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group Si type 1
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512 atoms in group Si
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velocity all create $t 5287287 mom yes rot yes dist gaussian
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velocity all create 1800 5287287 mom yes rot yes dist gaussian
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# make a vacancy
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group del id 300
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1 atoms in group del
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delete_atoms group del
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Deleted 1 atoms, new total = 511
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pair_style edip/multi
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pair_coeff * * Si.edip Si
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Reading potential file Si.edip with DATE: 2011-09-15
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thermo 10
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fix 1 all nvt temp $t $t 0.1
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fix 1 all nvt temp 1800 $t 0.1
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fix 1 all nvt temp 1800 1800 0.1
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timestep 1.0e-3
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neighbor 1.0 bin
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neigh_modify every 1 delay 10 check yes
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# equilibrate
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run 500
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Neighbor list info ...
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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 = 4.12138
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ghost atom cutoff = 4.12138
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binsize = 2.06069, bins = 11 11 11
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair edip/multi, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1802.3816 -2372.6618 0 -2253.844 12260.967
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10 938.75954 -2315.5185 0 -2253.6329 558.21646
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20 534.27233 -2288.4721 0 -2253.2514 -2710.768
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30 1043.7796 -2320.9485 0 -2252.1398 8679.4381
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40 658.0916 -2293.8597 0 -2250.4765 2165.3742
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50 517.93009 -2283.7238 0 -2249.5805 -1124.9373
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60 1063.3594 -2318.4409 0 -2248.3414 7277.8526
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70 868.14006 -2304.0134 0 -2246.7832 2050.2848
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80 826.37805 -2300.0187 0 -2245.5416 91.099408
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90 1289.6772 -2328.7151 0 -2243.6961 8180.7423
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100 976.36208 -2305.9371 0 -2241.5727 3614.0499
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110 810.81713 -2293.4705 0 -2240.0193 1359.368
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120 1165.707 -2314.9026 0 -2238.056 7336.45
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130 929.81245 -2297.139 0 -2235.8432 2793.8451
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140 804.47874 -2287.2074 0 -2234.174 704.92455
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150 1182.4141 -2310.0266 0 -2232.0787 7822.2337
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160 979.92391 -2294.2969 0 -2229.6977 3206.7458
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170 830.14748 -2282.6079 0 -2227.8824 -296.87377
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180 1271.1133 -2309.4274 0 -2225.6322 7199.614
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190 1209.6006 -2302.6407 0 -2222.9006 5528.3784
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200 954.67693 -2283.6621 0 -2220.7273 47.02795
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210 1260.814 -2301.5582 0 -2218.442 4829.788
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220 1274.9954 -2299.7285 0 -2215.6774 5518.0597
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230 1048.0074 -2282.398 0 -2213.3106 1754.4144
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240 1261.7072 -2294.1108 0 -2210.9356 5233.2712
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250 1272.6178 -2292.0793 0 -2208.1849 4795.9325
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260 989.14205 -2271.0278 0 -2205.8209 -820.1828
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270 1212.0445 -2283.4212 0 -2203.52 3395.8634
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280 1391.9572 -2292.3809 0 -2200.6194 6666.2451
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290 1093.1204 -2270.0421 0 -2197.9807 206.94523
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300 1159.4831 -2272.102 0 -2195.6657 778.53806
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310 1407.3528 -2285.6228 0 -2192.8463 5223.048
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320 1236.7163 -2271.5389 0 -2190.0113 1865.3943
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330 1258.8275 -2270.4611 0 -2187.4758 2333.3209
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340 1507.9519 -2283.9906 0 -2184.5824 6775.5456
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350 1366.5116 -2271.7287 0 -2181.6446 3432.115
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360 1305.2829 -2265.1092 0 -2179.0614 1498.4073
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370 1581.4335 -2280.4645 0 -2176.2122 6518.5597
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380 1589.5319 -2277.9428 0 -2173.1567 6334.6506
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390 1402.6781 -2262.9323 0 -2170.464 3278.3038
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400 1374.9587 -2258.5717 0 -2167.9307 3608.7284
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410 1295.7416 -2250.7752 0 -2165.3565 1877.5222
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420 1278.6727 -2247.1099 0 -2162.8164 1599.4181
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430 1508.1328 -2259.4245 0 -2160.0044 4300.2224
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440 1624.2957 -2263.9806 0 -2156.9026 4432.625
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450 1597.3356 -2259.263 0 -2153.9624 3370.3816
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460 1772.0922 -2267.9106 0 -2151.0895 5788.3214
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470 1806.4047 -2267.304 0 -2148.221 5950.1166
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480 1593.0406 -2250.7469 0 -2145.7294 2518.0576
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490 1660.9767 -2252.894 0 -2143.398 4282.1643
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500 1714.283 -2253.9295 0 -2140.9194 5740.0247
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Loop time of 0.205398 on 4 procs for 500 steps with 511 atoms
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Performance: 210.324 ns/day, 0.114 hours/ns, 2434.304 timesteps/s
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99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
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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 | 0.16285 | 0.1688 | 0.17446 | 1.1 | 82.18
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Neigh | 0.0035172 | 0.0036234 | 0.0038214 | 0.2 | 1.76
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Comm | 0.018727 | 0.024851 | 0.030996 | 2.9 | 12.10
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Output | 0.0013061 | 0.0014012 | 0.0015635 | 0.3 | 0.68
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Modify | 0.0046582 | 0.0048603 | 0.0050988 | 0.2 | 2.37
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Other | | 0.001861 | | | 0.91
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Nlocal: 127.75 ave 131 max 124 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Nghost: 433.75 ave 441 max 426 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 1979.5 ave 2040 max 1895 min
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Histogram: 1 0 0 0 1 0 0 0 0 2
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Total # of neighbors = 7918
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Ave neighs/atom = 15.4951
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Neighbor list builds = 19
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Dangerous builds = 0
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Total wall time: 0:00:00
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