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lammps/examples/USER/misc/edip/log.4May2017.g++.edip-Si.1
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log.4May2017.g++.edip-Si.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
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) = 2.979 | 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 723.08283
20 549.138 -2289.442 0 -2253.2413 -2444.5194
30 1047.0106 -2321.1522 0 -2252.1305 9013.2015
40 663.46143 -2294.2083 0 -2250.4711 2942.5358
50 504.74533 -2282.849 0 -2249.5748 -461.44817
60 1019.2173 -2315.5639 0 -2248.3744 7706.429
70 844.51197 -2302.5251 0 -2246.8526 3116.8313
80 814.90406 -2299.3372 0 -2245.6165 794.77536
90 1269.5635 -2327.4775 0 -2243.7845 7729.3971
100 977.61566 -2306.1118 0 -2241.6647 2969.9952
110 843.08538 -2295.6547 0 -2240.0763 1393.4046
120 1161.6968 -2314.6587 0 -2238.0766 7398.3495
130 918.19453 -2296.4321 0 -2235.9022 2537.4011
140 881.42546 -2292.2768 0 -2234.1709 1550.3345
150 1231.1005 -2313.1054 0 -2231.9479 8112.7568
160 967.01865 -2293.332 0 -2229.5836 3422.964
170 833.51246 -2282.7489 0 -2227.8015 43.99251
180 1240.8487 -2307.3633 0 -2225.5632 6557.8652
190 1126.4621 -2297.1922 0 -2222.9328 4289.0083
200 947.5957 -2283.29 0 -2220.8219 586.28203
210 1228.153 -2299.4702 0 -2218.5071 5315.0427
220 1215.4104 -2295.9407 0 -2215.8176 4870.343
230 1112.436 -2286.7552 0 -2213.4204 2527.1887
240 1300.081 -2296.6013 0 -2210.8965 5738.3711
250 1192.5739 -2286.8463 0 -2208.2286 4076.4913
260 1004.7055 -2272.1753 0 -2205.9424 359.3769
270 1241.2018 -2285.3632 0 -2203.5399 4160.5764
280 1360.1974 -2290.325 0 -2200.6572 5802.3912
290 1151.9366 -2273.9467 0 -2198.008 1418.8905
300 1174.3518 -2273.0089 0 -2195.5925 1998.2297
310 1329.2726 -2280.5049 0 -2192.8757 4721.7304
320 1284.4414 -2274.7519 0 -2190.0781 2985.4687
330 1328.3761 -2274.9545 0 -2187.3844 4543.2115
340 1446.3847 -2279.8693 0 -2184.5198 6254.4071
350 1366.2165 -2271.7475 0 -2181.6828 3637.8351
360 1358.9609 -2268.5982 0 -2179.0118 3049.5811
370 1552.2079 -2278.4802 0 -2176.1545 6334.0061
380 1562.5295 -2276.1793 0 -2173.1731 5787.5565
390 1415.5498 -2263.7823 0 -2170.4655 3438.5782
400 1323.1568 -2255.1641 0 -2167.938 2427.2311
410 1260.7186 -2248.5373 0 -2165.4273 1208.6316
420 1282.1118 -2247.3718 0 -2162.8516 462.65508
430 1451.9439 -2255.7551 0 -2160.0391 2037.8027
440 1568.9415 -2260.417 0 -2156.9882 3531.1613
450 1565.8261 -2257.2396 0 -2154.0161 2586.7896
460 1677.7143 -2261.7214 0 -2151.122 4112.976
470 1762.9071 -2264.4244 0 -2148.2089 5053.2148
480 1704.5898 -2257.8678 0 -2145.4966 4077.4649
490 1731.2619 -2257.1048 0 -2142.9753 4710.5276
500 1723.9777 -2254.161 0 -2140.5118 4760.7316
Loop time of 0.312472 on 1 procs for 500 steps with 511 atoms
Performance: 138.252 ns/day, 0.174 hours/ns, 1600.143 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.28525 | 0.28525 | 0.28525 | 0.0 | 91.29
Neigh | 0.013753 | 0.013753 | 0.013753 | 0.0 | 4.40
Comm | 0.0033333 | 0.0033333 | 0.0033333 | 0.0 | 1.07
Output | 0.00071096 | 0.00071096 | 0.00071096 | 0.0 | 0.23
Modify | 0.008044 | 0.008044 | 0.008044 | 0.0 | 2.57
Other | | 0.001385 | | | 0.44
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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