168 lines
7.7 KiB
Groff
168 lines
7.7 KiB
Groff
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
|