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lammps/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1
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log.4May2017.g++.edip-Si-multi.1
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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 1 by 1 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/multi
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/multi, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1802.5039 -2372.6618 0 -2253.8359 12261.807
10 952.62744 -2316.428 0 -2253.6283 723.08194
20 549.13801 -2289.442 0 -2253.2413 -2444.5204
30 1047.0106 -2321.1523 0 -2252.1305 9013.201
40 663.46141 -2294.2083 0 -2250.4711 2942.5348
50 504.74535 -2282.849 0 -2249.5748 -461.44909
60 1019.2173 -2315.5639 0 -2248.3744 7706.4286
70 844.51195 -2302.5251 0 -2246.8526 3116.8302
80 814.90407 -2299.3372 0 -2245.6166 794.77455
90 1269.5636 -2327.4775 0 -2243.7845 7729.3968
100 977.61563 -2306.1118 0 -2241.6647 2969.9939
110 843.08539 -2295.6547 0 -2240.0763 1393.4039
120 1161.6968 -2314.6587 0 -2238.0766 7398.3492
130 918.19451 -2296.4321 0 -2235.9022 2537.3997
140 881.42548 -2292.2768 0 -2234.1709 1550.3339
150 1231.1005 -2313.1054 0 -2231.9479 8112.7566
160 967.01862 -2293.332 0 -2229.5836 3422.9627
170 833.51248 -2282.7489 0 -2227.8015 43.991459
180 1240.8488 -2307.3633 0 -2225.5632 6557.8651
190 1126.4621 -2297.1922 0 -2222.9328 4289.0067
200 947.59571 -2283.29 0 -2220.822 586.2811
210 1228.153 -2299.4702 0 -2218.5071 5315.0425
220 1215.4104 -2295.9408 0 -2215.8176 4870.3417
230 1112.436 -2286.7552 0 -2213.4204 2527.1879
240 1300.081 -2296.6013 0 -2210.8965 5738.3708
250 1192.5738 -2286.8463 0 -2208.2286 4076.49
260 1004.7055 -2272.1753 0 -2205.9424 359.37589
270 1241.2018 -2285.3632 0 -2203.5399 4160.5763
280 1360.1974 -2290.325 0 -2200.6572 5802.3902
290 1151.9365 -2273.9467 0 -2198.008 1418.8887
300 1174.3518 -2273.0089 0 -2195.5925 1998.229
310 1329.2727 -2280.5049 0 -2192.8757 4721.7297
320 1284.4414 -2274.7519 0 -2190.0781 2985.4674
330 1328.3761 -2274.9545 0 -2187.3844 4543.2109
340 1446.3847 -2279.8693 0 -2184.5198 6254.4059
350 1366.2165 -2271.7475 0 -2181.6828 3637.8335
360 1358.9609 -2268.5982 0 -2179.0118 3049.5798
370 1552.208 -2278.4802 0 -2176.1545 6334.0058
380 1562.5295 -2276.1793 0 -2173.1732 5787.5547
390 1415.5498 -2263.7824 0 -2170.4655 3438.5766
400 1323.1568 -2255.1641 0 -2167.938 2427.2294
410 1260.7186 -2248.5373 0 -2165.4273 1208.6299
420 1282.1118 -2247.3718 0 -2162.8516 462.65374
430 1451.944 -2255.7551 0 -2160.0391 2037.8025
440 1568.9415 -2260.417 0 -2156.9882 3531.1602
450 1565.8262 -2257.2396 0 -2154.0162 2586.7886
460 1677.7143 -2261.7214 0 -2151.122 4112.9756
470 1762.9071 -2264.4244 0 -2148.2089 5053.2139
480 1704.5898 -2257.8678 0 -2145.4967 4077.4626
490 1731.2619 -2257.1048 0 -2142.9753 4710.5263
500 1723.9777 -2254.161 0 -2140.5118 4760.7295
Loop time of 0.679564 on 1 procs for 500 steps with 511 atoms
Performance: 63.570 ns/day, 0.378 hours/ns, 735.765 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.65181 | 0.65181 | 0.65181 | 0.0 | 95.92
Neigh | 0.013857 | 0.013857 | 0.013857 | 0.0 | 2.04
Comm | 0.0033884 | 0.0033884 | 0.0033884 | 0.0 | 0.50
Output | 0.00070739 | 0.00070739 | 0.00070739 | 0.0 | 0.10
Modify | 0.0083694 | 0.0083694 | 0.0083694 | 0.0 | 1.23
Other | | 0.001432 | | | 0.21
Nlocal: 511 ave 511 max 511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 845 ave 845 max 845 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: 7902 ave 7902 max 7902 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 7902
Ave neighs/atom = 15.4638
Neighbor list builds = 19
Dangerous builds = 0
Total wall time: 0:00:00
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