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lammps/examples/USER/misc/edip/log.4May2017.g++.edip-Si.4
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log.4May2017.g++.edip-Si.4
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LAMMPS (4 May 2017)
using 1 OpenMP thread(s) per MPI task
units metal
atom_style atomic
atom_modify map array
boundary p p p
atom_modify sort 0 0.0
# temperature
variable t equal 1800.0
# coordination number cutoff
variable r equal 2.835
# minimization parameters
variable etol equal 1.0e-5
variable ftol equal 1.0e-5
variable maxiter equal 100
variable maxeval equal 100
variable dmax equal 1.0e-1
# diamond unit cell
variable a equal 5.431
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
lattice custom 5.431 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
Lattice spacing in x,y,z = 5.431 5.431 5.431
region myreg block 0 4 0 4 0 4
create_box 1 myreg
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
1 by 2 by 2 MPI processor grid
create_atoms 1 region myreg
Created 512 atoms
mass 1 28.06
group Si type 1
512 atoms in group Si
velocity all create $t 5287287 mom yes rot yes dist gaussian
velocity all create 1800 5287287 mom yes rot yes dist gaussian
# make a vacancy
group del id 300
1 atoms in group del
delete_atoms group del
Deleted 1 atoms, new total = 511
pair_style edip
pair_coeff * * Si.edip Si
Reading potential file Si.edip with DATE: 2011-09-15
thermo 10
fix 1 all nvt temp $t $t 0.1
fix 1 all nvt temp 1800 $t 0.1
fix 1 all nvt temp 1800 1800 0.1
timestep 1.0e-3
neighbor 1.0 bin
neigh_modify every 1 delay 10 check yes
# equilibrate
run 500
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 4.12138
ghost atom cutoff = 4.12138
binsize = 2.06069, bins = 11 11 11
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair edip, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1802.3816 -2372.6618 0 -2253.8439 12260.967
10 938.75954 -2315.5185 0 -2253.6329 558.21736
20 534.27232 -2288.4721 0 -2253.2514 -2710.767
30 1043.7796 -2320.9485 0 -2252.1398 8679.4385
40 658.09162 -2293.8597 0 -2250.4765 2165.3752
50 517.93008 -2283.7238 0 -2249.5805 -1124.9362
60 1063.3594 -2318.4409 0 -2248.3414 7277.853
70 868.14007 -2304.0133 0 -2246.7832 2050.2859
80 826.37803 -2300.0187 0 -2245.5416 91.100098
90 1289.6772 -2328.7151 0 -2243.6961 8180.7427
100 976.36211 -2305.9371 0 -2241.5727 3614.0511
110 810.81711 -2293.4705 0 -2240.0193 1359.3687
120 1165.707 -2314.9026 0 -2238.056 7336.4505
130 929.81248 -2297.139 0 -2235.8432 2793.8463
140 804.47872 -2287.2074 0 -2234.174 704.92524
150 1182.414 -2310.0266 0 -2232.0787 7822.2339
160 979.92395 -2294.2969 0 -2229.6977 3206.7474
170 830.14746 -2282.6079 0 -2227.8824 -296.87288
180 1271.1133 -2309.4274 0 -2225.6322 7199.614
190 1209.6006 -2302.6407 0 -2222.9006 5528.3799
200 954.67692 -2283.6621 0 -2220.7272 47.02925
210 1260.814 -2301.5582 0 -2218.442 4829.7879
220 1274.9954 -2299.7285 0 -2215.6774 5518.0611
230 1048.0074 -2282.398 0 -2213.3106 1754.4157
240 1261.7071 -2294.1107 0 -2210.9356 5233.2714
250 1272.6179 -2292.0793 0 -2208.1849 4795.934
260 989.14207 -2271.0278 0 -2205.8209 -820.18098
270 1212.0444 -2283.4212 0 -2203.52 3395.8631
280 1391.9572 -2292.3809 0 -2200.6194 6666.2464
290 1093.1205 -2270.0421 0 -2197.9807 206.94752
300 1159.483 -2272.102 0 -2195.6657 778.53823
310 1407.3528 -2285.6227 0 -2192.8463 5223.0487
320 1236.7164 -2271.5389 0 -2190.0112 1865.3963
330 1258.8275 -2270.4611 0 -2187.4758 2333.321
340 1507.9519 -2283.9906 0 -2184.5824 6775.546
350 1366.5116 -2271.7287 0 -2181.6446 3432.1175
360 1305.2828 -2265.1091 0 -2179.0614 1498.4079
370 1581.4334 -2280.4645 0 -2176.2122 6518.5598
380 1589.5319 -2277.9428 0 -2173.1566 6334.6527
390 1402.6782 -2262.9323 0 -2170.464 3278.3048
400 1374.9587 -2258.5717 0 -2167.9307 3608.7293
410 1295.7416 -2250.7752 0 -2165.3565 1877.5245
420 1278.6727 -2247.1099 0 -2162.8164 1599.4189
430 1508.1328 -2259.4245 0 -2160.0044 4300.2235
440 1624.2957 -2263.9806 0 -2156.9026 4432.6267
450 1597.3356 -2259.263 0 -2153.9623 3370.3829
460 1772.0921 -2267.9105 0 -2151.0895 5788.3219
470 1806.4047 -2267.304 0 -2148.221 5950.1188
480 1593.0406 -2250.7469 0 -2145.7294 2518.0601
490 1660.9766 -2252.894 0 -2143.398 4282.1654
500 1714.2831 -2253.9295 0 -2140.9194 5740.0268
Loop time of 0.109584 on 4 procs for 500 steps with 511 atoms
Performance: 394.220 ns/day, 0.061 hours/ns, 4562.726 timesteps/s
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.074678 | 0.077817 | 0.084705 | 1.4 | 71.01
Neigh | 0.0036662 | 0.0037943 | 0.0039661 | 0.2 | 3.46
Comm | 0.013665 | 0.020312 | 0.023178 | 2.7 | 18.54
Output | 0.0010247 | 0.0010931 | 0.0012922 | 0.3 | 1.00
Modify | 0.0043213 | 0.0047521 | 0.0051889 | 0.6 | 4.34
Other | | 0.001814 | | | 1.66
Nlocal: 127.75 ave 131 max 124 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 433.75 ave 441 max 426 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1979.5 ave 2040 max 1895 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Total # of neighbors = 7918
Ave neighs/atom = 15.4951
Neighbor list builds = 19
Dangerous builds = 0
Total wall time: 0:00:00
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