354 lines
17 KiB
Plaintext
354 lines
17 KiB
Plaintext
LAMMPS (5 Dec 2010-ICMS)
|
|
# surface sputtering demo
|
|
|
|
# dimension variables
|
|
# box length in x and y
|
|
variable len index 20.0
|
|
# height of layer
|
|
variable hgt index 8.0
|
|
# delta between insert area and box
|
|
variable len0 index 0.1
|
|
# full length minus delta
|
|
variable len1 equal ${len}-${len0}
|
|
variable len1 equal 20.0-${len0}
|
|
variable len1 equal 20.0-0.1
|
|
# half length
|
|
variable len2 equal ${len}*0.5
|
|
variable len2 equal 20.0*0.5
|
|
|
|
units lj
|
|
atom_style atomic
|
|
boundary p p f
|
|
|
|
lattice fcc 0.85
|
|
Lattice spacing in x,y,z = 1.67577 1.67577 1.67577
|
|
region box block 0.0 ${len} 0.0 ${len} -1.0 40.0 units lattice
|
|
region box block 0.0 20.0 0.0 ${len} -1.0 40.0 units lattice
|
|
region box block 0.0 20.0 0.0 20.0 -1.0 40.0 units lattice
|
|
|
|
# particle density in z-direction is inhomogeneous:
|
|
# only do domain decomposition in x- and y-direction
|
|
processors * * 1
|
|
|
|
# two atom types: surface and sputter atoms
|
|
create_box 2 box
|
|
Created orthogonal box = (0 0 -1.67577) to (33.5153 33.5153 67.0307)
|
|
1 by 2 by 1 processor grid
|
|
|
|
region layer block 0.0 ${len} 0.0 ${len} 0.0 ${hgt}
|
|
region layer block 0.0 20.0 0.0 ${len} 0.0 ${hgt}
|
|
region layer block 0.0 20.0 0.0 20.0 0.0 ${hgt}
|
|
region layer block 0.0 20.0 0.0 20.0 0.0 8.0
|
|
create_atoms 1 region layer
|
|
Created 13600 atoms
|
|
mass 1 1.0
|
|
mass 2 3.0
|
|
|
|
region fixed block INF INF INF INF 0.0 0.1
|
|
group fixed region fixed
|
|
800 atoms in group fixed
|
|
group mobile subtract all fixed
|
|
12800 atoms in group mobile
|
|
|
|
|
|
pair_style lj/cut/opt 2.5
|
|
pair_coeff 1 1 1.0 1.0
|
|
pair_coeff 2 2 0.5 1.2
|
|
|
|
neighbor 0.3 bin
|
|
neigh_modify every 2 delay 6 check yes
|
|
|
|
minimize 1.0e-5 1.0e-8 1000 10000
|
|
WARNING: Resetting reneighboring criteria during minimization
|
|
Memory usage per processor = 4.96717 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 0 -6.5259752 0 -6.5259752 -1.2281195
|
|
36 0 -7.3412246 0 -7.3412246 -0.29303042
|
|
Loop time of 3.30338 on 2 procs for 36 steps with 13600 atoms
|
|
|
|
Minimization stats:
|
|
Stopping criterion = energy tolerance
|
|
Energy initial, next-to-last, final =
|
|
-6.52597518616 -7.34117366997 -7.34122455255
|
|
Force two-norm initial, final = 303.542 14.6837
|
|
Force max component initial, final = 7.48566 0.188904
|
|
Final line search alpha, max atom move = 0.00302967 0.000572317
|
|
Iterations, force evaluations = 36 111
|
|
|
|
Pair time (%) = 2.75307 (83.3409)
|
|
Neigh time (%) = 0.237482 (7.18905)
|
|
Comm time (%) = 0.243272 (7.36433)
|
|
Outpt time (%) = 0 (0)
|
|
Other time (%) = 0.0695615 (2.10576)
|
|
|
|
Nlocal: 6800 ave 6820 max 6780 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
Nghost: 3987 ave 4007 max 3967 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
Neighs: 293600 ave 294742 max 292458 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
|
|
Total # of neighbors = 587200
|
|
Ave neighs/atom = 43.1765
|
|
Neighbor list builds = 8
|
|
Dangerous builds = 0
|
|
reset_timestep 0
|
|
|
|
velocity mobile create 0.4 87287
|
|
# use the temperature of the mobile layer atoms as reference
|
|
compute mtemp mobile temp
|
|
fix 1 mobile nve
|
|
fix 2 mobile langevin 0.2 0.2 5.0 982434
|
|
fix_modify 2 temp mtemp
|
|
|
|
thermo 100
|
|
thermo_style custom step atoms temp etotal
|
|
thermo_modify temp mtemp
|
|
WARNING: Temperature for thermo pressure is not for group all
|
|
|
|
dump id all xyz 200 sputter.xyz
|
|
|
|
# minimal equilibration
|
|
run 1000
|
|
Memory usage per processor = 4.23188 Mbytes
|
|
Step Atoms Temp TotEng
|
|
0 13600 0.4 -6.7765628
|
|
100 13600 0.20121051 -6.7800703
|
|
200 13600 0.20083791 -6.7814731
|
|
300 13600 0.20020268 -6.7841591
|
|
400 13600 0.20046153 -6.7837273
|
|
500 13600 0.19788085 -6.7821283
|
|
600 13600 0.1964279 -6.7773028
|
|
700 13600 0.20007955 -6.7764748
|
|
800 13600 0.20386935 -6.7780111
|
|
900 13600 0.20641972 -6.780506
|
|
1000 13600 0.20832321 -6.7844653
|
|
Loop time of 18.4513 on 2 procs for 1000 steps with 13600 atoms
|
|
|
|
Pair time (%) = 13.2945 (72.052)
|
|
Neigh time (%) = 2.13272 (11.5586)
|
|
Comm time (%) = 1.1551 (6.26028)
|
|
Outpt time (%) = 0.273862 (1.48425)
|
|
Other time (%) = 1.59509 (8.64487)
|
|
|
|
Nlocal: 6800 ave 6812 max 6788 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
Nghost: 3976 ave 3994 max 3958 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
Neighs: 273924 ave 274745 max 273104 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
|
|
Total # of neighbors = 547849
|
|
Ave neighs/atom = 40.283
|
|
Neighbor list builds = 62
|
|
Dangerous builds = 0
|
|
|
|
# define region for inserting particles
|
|
region sphere sphere ${len2} ${len2} 42.0 ${len2} units lattice
|
|
region sphere sphere 10 ${len2} 42.0 ${len2} units lattice
|
|
region sphere sphere 10 10 42.0 ${len2} units lattice
|
|
region sphere sphere 10 10 42.0 10 units lattice
|
|
region insert intersect 2 box sphere
|
|
|
|
# define group of inserted particles
|
|
group insert region insert
|
|
0 atoms in group insert
|
|
# deposite particles regularly into insert volume
|
|
fix insert insert deposit 50 2 200 12345 region insert vz -8.0 -9.0 target ${len2} ${len2} ${hgt} units lattice
|
|
fix insert insert deposit 50 2 200 12345 region insert vz -8.0 -9.0 target 10 ${len2} ${hgt} units lattice
|
|
fix insert insert deposit 50 2 200 12345 region insert vz -8.0 -9.0 target 10 10 ${hgt} units lattice
|
|
fix insert insert deposit 50 2 200 12345 region insert vz -8.0 -9.0 target 10 10 8.0 units lattice
|
|
neigh_modify every 1 delay 0 check yes
|
|
|
|
# time integrate inserted particles
|
|
fix 4 insert nve
|
|
|
|
# remove thermostat on layer atoms
|
|
unfix 2
|
|
|
|
variable nlayer equal count(mobile)+count(fixed)
|
|
variable ninsert equal count(insert)
|
|
|
|
thermo_style custom step atoms v_nlayer v_ninsert temp etotal
|
|
WARNING: New thermo_style command, previous thermo_modify settings will be lost
|
|
thermo_modify temp mtemp
|
|
WARNING: Temperature for thermo pressure is not for group all
|
|
|
|
# handling of atoms the get bounced back from surface
|
|
# or sputtered off the surface.
|
|
thermo_modify lost ignore
|
|
|
|
run 15000
|
|
Memory usage per processor = 4.23398 Mbytes
|
|
Step Atoms nlayer ninsert Temp TotEng
|
|
1000 13600 13600 0 0.20832321 -6.7844653
|
|
1100 13601 13600 1 0.21058022 -6.7843547
|
|
1200 13601 13600 1 0.21340281 -6.784861
|
|
1300 13602 13600 2 0.21403698 -6.7845421
|
|
1400 13602 13600 2 0.21225101 -6.7844137
|
|
1500 13603 13600 3 0.2112857 -6.7836914
|
|
1600 13603 13600 3 0.20929795 -6.783739
|
|
1700 13604 13600 4 0.20751001 -6.7825912
|
|
1800 13604 13600 4 0.21300915 -6.7639251
|
|
1900 13605 13600 5 0.21176073 -6.7606992
|
|
2000 13605 13600 5 0.21404592 -6.7618863
|
|
2100 13606 13600 6 0.22238836 -6.7421581
|
|
2200 13606 13600 6 0.24216274 -6.7039303
|
|
2300 13607 13600 7 0.2417962 -6.6971856
|
|
2400 13607 13600 7 0.24042085 -6.6968129
|
|
2500 13608 13600 8 0.24045507 -6.6958318
|
|
2600 13608 13600 8 0.25176736 -6.6749343
|
|
2700 13609 13600 9 0.25900073 -6.6486764
|
|
2800 13609 13600 9 0.25015559 -6.6464785
|
|
2900 13610 13600 10 0.2439077 -6.6451635
|
|
3000 13610 13600 10 0.25658018 -6.6231917
|
|
3100 13611 13600 11 0.2613481 -6.602238
|
|
3200 13611 13600 11 0.25723347 -6.5982424
|
|
3300 13612 13600 12 0.26827614 -6.5821563
|
|
3400 13612 13600 12 0.27429368 -6.5772633
|
|
3500 13613 13600 13 0.27369134 -6.5771909
|
|
3600 13613 13600 13 0.28242118 -6.5597949
|
|
3700 13614 13600 14 0.28249581 -6.5538872
|
|
3800 13614 13600 14 0.28726974 -6.5316737
|
|
3900 13615 13600 15 0.28098713 -6.5306333
|
|
4000 13615 13600 15 0.29108569 -6.5083705
|
|
4100 13616 13600 16 0.28844946 -6.5066682
|
|
4200 13616 13600 16 0.28992033 -6.4976801
|
|
4300 13617 13600 17 0.2900645 -6.4841474
|
|
4400 13617 13600 17 0.29384833 -6.4842992
|
|
4500 13617 13599 18 0.30205092 -6.4664539
|
|
4600 13617 13599 18 0.30710089 -6.4659031
|
|
4700 13618 13599 19 0.30950759 -6.4464885
|
|
4800 13618 13599 19 0.3125975 -6.447011
|
|
4900 13619 13599 20 0.32026098 -6.4269473
|
|
5000 13619 13599 20 0.32731476 -6.4057706
|
|
5100 13620 13599 21 0.3325174 -6.382266
|
|
5200 13620 13599 21 0.33400486 -6.3755647
|
|
5300 13621 13599 22 0.32854612 -6.3747623
|
|
5400 13621 13599 22 0.33642524 -6.354324
|
|
5500 13622 13599 23 0.33014217 -6.3508996
|
|
5600 13622 13599 23 0.3365548 -6.338443
|
|
5700 13623 13599 24 0.34746859 -6.3074228
|
|
5800 13623 13599 24 0.34815069 -6.3026891
|
|
5900 13624 13599 25 0.34779043 -6.3018994
|
|
6000 13624 13599 25 0.34785697 -6.3020403
|
|
6100 13625 13599 26 0.35678241 -6.2765048
|
|
6200 13625 13599 26 0.36339634 -6.260885
|
|
6300 13626 13599 27 0.36162866 -6.2585204
|
|
6400 13626 13599 27 0.36114131 -6.258271
|
|
6500 13627 13599 28 0.36972629 -6.2431921
|
|
6600 13627 13599 28 0.37440147 -6.2190753
|
|
6700 13628 13599 29 0.36867416 -6.2124175
|
|
6800 13628 13599 29 0.3700442 -6.2030189
|
|
6900 13629 13599 30 0.37885383 -6.1916269
|
|
7000 13629 13599 30 0.37772273 -6.1895715
|
|
7100 13630 13599 31 0.3839563 -6.1732165
|
|
7200 13630 13599 31 0.39196673 -6.1529669
|
|
7300 13631 13599 32 0.393845 -6.1480924
|
|
7400 13631 13599 32 0.39881509 -6.146092
|
|
7500 13632 13599 33 0.4079294 -6.1257628
|
|
7600 13632 13599 33 0.41107484 -6.1045312
|
|
7700 13633 13599 34 0.40835826 -6.0991979
|
|
7800 13633 13599 34 0.41450904 -6.0798907
|
|
7900 13634 13599 35 0.40791093 -6.0774146
|
|
8000 13634 13599 35 0.41276541 -6.0608485
|
|
8100 13635 13599 36 0.41057353 -6.0547596
|
|
8200 13634 13598 36 0.40873687 -6.0537089
|
|
8300 13635 13598 37 0.41552214 -6.0358319
|
|
8400 13635 13598 37 0.425368 -6.0216733
|
|
8500 13636 13598 38 0.425068 -6.0140163
|
|
8600 13636 13598 38 0.44531917 -5.9936724
|
|
8700 13637 13598 39 0.43327704 -5.989434
|
|
8800 13637 13598 39 0.43516665 -5.9849514
|
|
8900 13638 13598 40 0.44728126 -5.9672792
|
|
9000 13638 13598 40 0.43967925 -5.9657483
|
|
9100 13639 13598 41 0.44772275 -5.9438221
|
|
9200 13639 13598 41 0.45074179 -5.9250545
|
|
9300 13640 13598 42 0.45273687 -5.913662
|
|
9400 13640 13598 42 0.45072012 -5.9020303
|
|
9500 13641 13598 43 0.44556267 -5.8981662
|
|
9600 13641 13598 43 0.45466918 -5.881651
|
|
9700 13642 13598 44 0.45327111 -5.8745981
|
|
9800 13642 13598 44 0.46467321 -5.8525411
|
|
9900 13643 13598 45 0.47756597 -5.8344292
|
|
10000 13643 13598 45 0.47554676 -5.8300508
|
|
10100 13644 13598 46 0.47699644 -5.8283877
|
|
10200 13644 13598 46 0.48308309 -5.8146058
|
|
10300 13645 13598 47 0.49182207 -5.7927428
|
|
10400 13645 13598 47 0.48611494 -5.7842182
|
|
10500 13646 13598 48 0.49601147 -5.7603372
|
|
10600 13646 13598 48 0.48890039 -5.7567369
|
|
10700 13647 13598 49 0.48721712 -5.7535371
|
|
10800 13647 13598 49 0.49062265 -5.7365295
|
|
10900 13647 13597 50 0.49149207 -5.7183349
|
|
11000 13646 13596 50 0.49196107 -5.7194844
|
|
11100 13646 13596 50 0.49227515 -5.7095232
|
|
11200 13646 13596 50 0.49086426 -5.708591
|
|
11300 13646 13596 50 0.4999325 -5.690973
|
|
11400 13645 13595 50 0.5087244 -5.676373
|
|
11500 13645 13595 50 0.51158471 -5.6699749
|
|
11600 13645 13595 50 0.51837942 -5.6660993
|
|
11700 13645 13595 50 0.52060372 -5.6512303
|
|
11800 13645 13595 50 0.51649441 -5.649488
|
|
11900 13645 13595 50 0.51069584 -5.6478531
|
|
12000 13645 13595 50 0.50684316 -5.6451634
|
|
12100 13645 13595 50 0.50498726 -5.6458569
|
|
12200 13645 13595 50 0.50560556 -5.6450684
|
|
12300 13645 13595 50 0.5035552 -5.6450399
|
|
12400 13645 13595 50 0.50402115 -5.6439875
|
|
12500 13645 13595 50 0.49890249 -5.6445616
|
|
12600 13644 13594 50 0.501075 -5.648631
|
|
12700 13644 13594 50 0.50683173 -5.65101
|
|
12800 13644 13594 50 0.51043653 -5.6508532
|
|
12900 13644 13594 50 0.51154851 -5.6505932
|
|
13000 13644 13594 50 0.51138889 -5.6505739
|
|
13100 13644 13594 50 0.51682645 -5.6509008
|
|
13200 13644 13594 50 0.51338525 -5.6516941
|
|
13300 13644 13594 50 0.50921613 -5.6511795
|
|
13400 13644 13594 50 0.51245321 -5.6498126
|
|
13500 13644 13594 50 0.51002695 -5.6509423
|
|
13600 13644 13594 50 0.50688879 -5.6497583
|
|
13700 13644 13594 50 0.5083792 -5.6495744
|
|
13800 13644 13594 50 0.50691706 -5.6497556
|
|
13900 13644 13594 50 0.50461476 -5.649312
|
|
14000 13644 13594 50 0.50973646 -5.6497581
|
|
14100 13644 13594 50 0.5092232 -5.6504694
|
|
14200 13644 13594 50 0.51307881 -5.6499432
|
|
14300 13644 13594 50 0.51593536 -5.6511145
|
|
14400 13643 13593 50 0.50940383 -5.651823
|
|
14500 13642 13592 50 0.51533411 -5.6528822
|
|
14600 13642 13592 50 0.52389431 -5.6529784
|
|
14700 13642 13592 50 0.52160091 -5.6539425
|
|
14800 13642 13592 50 0.51759686 -5.6529695
|
|
14900 13642 13592 50 0.51695824 -5.65242
|
|
15000 13641 13591 50 0.5146085 -5.6539402
|
|
15100 13640 13590 50 0.51108108 -5.6539714
|
|
15200 13640 13590 50 0.50982199 -5.6541109
|
|
15300 13640 13590 50 0.5099508 -5.6536099
|
|
15400 13640 13590 50 0.51324068 -5.6532432
|
|
15500 13640 13590 50 0.5147851 -5.6534988
|
|
15600 13640 13590 50 0.51818529 -5.6530576
|
|
15700 13640 13590 50 0.51838253 -5.6538436
|
|
15800 13638 13588 50 0.5196605 -5.6552535
|
|
15900 13637 13587 50 0.5212409 -5.6570219
|
|
16000 13637 13587 50 0.5169173 -5.6569506
|
|
Loop time of 370.179 on 2 procs for 15000 steps with 13637 atoms
|
|
|
|
Pair time (%) = 189.401 (51.1648)
|
|
Neigh time (%) = 145.628 (39.3399)
|
|
Comm time (%) = 21.6744 (5.85511)
|
|
Outpt time (%) = 4.05343 (1.09499)
|
|
Other time (%) = 9.42176 (2.54519)
|
|
|
|
Nlocal: 6818.5 ave 6830 max 6807 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
Nghost: 3942 ave 3959 max 3925 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
Neighs: 256816 ave 257886 max 255747 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
|
|
Total # of neighbors = 513633
|
|
Ave neighs/atom = 37.6647
|
|
Neighbor list builds = 4402
|
|
Dangerous builds = 0
|