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lammps/examples/sputter/log.sputter
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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
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