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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2366 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2009-01-09 22:18:56 +00:00
parent 0f29eb20fe
commit c8632d65c6
72 changed files with 1528 additions and 2163 deletions
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14
examples/indent/in.indent.min
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@ -43,28 +43,28 @@ thermo 10
dump 1 all atom 10 dump.indent
dump_modify 1 scale no
minimize 1.0e-6 1.0e-6 1000 1000
minimize 1.0e-6 1000 1000
fix 4 all indent 5000.0 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
minimize 1.0e-6 1000 1000
fix 4 all indent 1000.0 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
minimize 1.0e-6 1000 1000
fix 4 all indent 1000.0 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
minimize 1.0e-6 1000 1000
fix 4 all indent 1000.0 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
minimize 1.0e-6 1000 1000
fix 4 all indent 1000.0 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
minimize 1.0e-6 1000 1000
fix 4 all indent 1000.0 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
minimize 1.0e-6 1000 1000

26
examples/indent/log.indent.21May08.linux.1 → examples/indent/log.indent.9Jan09.linux.1
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@ -1,4 +1,4 @@
LAMMPS (21 May 2008)
LAMMPS (9 Jan 2009)
# 2d indenter simulation
dimension 2
@ -91,13 +91,13 @@ Step Temp E_pair E_mol TotEng Press Volume
28000 0.10834261 -2.9909288 0 -2.8983217 1.4598621 471.38654
29000 0.11506991 -2.9815688 0 -2.8832114 1.6220695 475.78184
30000 0.1137611 -2.9910145 0 -2.8937758 1.5390363 476.49487
Loop time of 4.35277 on 1 procs for 30000 steps with 420 atoms
Loop time of 4.3524 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 3.3632 (77.2656)
Neigh time (%) = 0.0964704 (2.2163)
Comm time (%) = 0.056159 (1.29019)
Outpt time (%) = 0.0744166 (1.70964)
Other time (%) = 0.762532 (17.5183)
Pair time (%) = 3.35689 (77.1274)
Neigh time (%) = 0.0960853 (2.20764)
Comm time (%) = 0.0587516 (1.34987)
Outpt time (%) = 0.0790317 (1.81582)
Other time (%) = 0.761639 (17.4993)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -148,13 +148,13 @@ Step Temp E_pair E_mol TotEng Press Volume
58000 0.10977322 -3.0750653 0 -2.9812353 -0.13698023 483.43933
59000 0.11837611 -3.0824237 0 -2.9812403 -0.42226934 488.24864
60000 0.12513787 -3.0760063 0 -2.9690432 -0.27843098 488.02101
Loop time of 4.04106 on 1 procs for 30000 steps with 420 atoms
Loop time of 4.04239 on 1 procs for 30000 steps with 420 atoms
Pair time (%) = 3.33419 (82.5078)
Neigh time (%) = 0.0975268 (2.4134)
Comm time (%) = 0.0565064 (1.39831)
Outpt time (%) = 0.0741966 (1.83607)
Other time (%) = 0.478639 (11.8444)
Pair time (%) = 3.33166 (82.418)
Neigh time (%) = 0.0980058 (2.42445)
Comm time (%) = 0.0587137 (1.45245)
Outpt time (%) = 0.0790043 (1.9544)
Other time (%) = 0.475009 (11.7507)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0

26
examples/indent/log.indent.21May08.linux.4 → examples/indent/log.indent.9Jan09.linux.4
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@ -1,4 +1,4 @@
LAMMPS (21 May 2008)
LAMMPS (9 Jan 2009)
# 2d indenter simulation
dimension 2
@ -91,13 +91,13 @@ Step Temp E_pair E_mol TotEng Press Volume
28000 0.12123681 -3.0107629 0 -2.9071343 0.81020478 478.51729
29000 0.12528058 -3.01932 0 -2.912235 1.0826534 472.26351
30000 0.11527728 -3.0030382 0 -2.9045036 1.5931211 465.76942
Loop time of 12.2538 on 4 procs for 30000 steps with 420 atoms
Loop time of 12.2128 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 1.06251 (8.67087)
Neigh time (%) = 0.0298207 (0.243358)
Comm time (%) = 8.70494 (71.0387)
Outpt time (%) = 0.0981069 (0.800624)
Other time (%) = 2.35843 (19.2465)
Pair time (%) = 1.07248 (8.7816)
Neigh time (%) = 0.030852 (0.252621)
Comm time (%) = 8.66242 (70.9293)
Outpt time (%) = 0.112867 (0.92417)
Other time (%) = 2.33414 (19.1123)
Nlocal: 105 ave 112 max 97 min
Histogram: 1 0 1 0 0 0 0 0 1 1
@ -148,13 +148,13 @@ Step Temp E_pair E_mol TotEng Press Volume
58000 0.11671309 -3.0836904 0 -2.9839285 -0.17868279 485.62136
59000 0.10785966 -3.0761158 0 -2.9839215 -0.36413012 486.36951
60000 0.12108723 -3.0736236 0 -2.9701228 -0.30955784 486.51342
Loop time of 11.802 on 4 procs for 30000 steps with 420 atoms
Loop time of 11.3223 on 4 procs for 30000 steps with 420 atoms
Pair time (%) = 0.984152 (8.33884)
Neigh time (%) = 0.0291511 (0.247001)
Comm time (%) = 8.40175 (71.1891)
Outpt time (%) = 0.100835 (0.854389)
Other time (%) = 2.28613 (19.3707)
Pair time (%) = 1.06588 (9.41397)
Neigh time (%) = 0.0312169 (0.275711)
Comm time (%) = 8.04953 (71.0943)
Outpt time (%) = 0.11254 (0.993961)
Other time (%) = 2.06317 (18.2221)
Nlocal: 105 ave 119 max 89 min
Histogram: 1 1 0 0 0 0 0 0 0 2

372
examples/indent/log.indent.min.21May08.linux.1
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@ -1,372 +0,0 @@
LAMMPS (21 May 2008)
# 2d indenter simulation with minimization instead of dynamics
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 420 atoms
mass * 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
fix 2 lower setforce 0.0 0.0 0.0
# indenter
fix 5 all enforce2d
# minimize with indenter
thermo 10
dump 1 all atom 10 dump.indent
dump_modify 1 scale no
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.13877 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5980059 444.44898
10 0 -3.1805305 0 -3.1805305 -1.3022518 440.53426
20 0 -3.1852211 0 -3.1852211 -1.1504773 438.82144
30 0 -3.1897313 0 -3.1897313 -0.89994803 435.57358
40 0 -3.1905969 0 -3.1905969 -0.7983193 435.57358
50 0 -3.1908121 0 -3.1908121 -0.74804595 435.57358
60 0 -3.1909255 0 -3.1909255 -0.70168641 435.57358
61 0 -3.1909278 0 -3.1909278 -0.70198125 435.57358
Loop time of 0.070924 on 1 procs for 61 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3.17275755126 -3.19092554808 -3.19092776738
Force two-norm initial, final = 6.74302 0.339623
Force max component initial, final = 1.46877 0.0423087
Final line search alpha, max atom move = 0.00942043 0.000398566
Iterations, force evaluations = 61 330
Pair time (%) = 0.0604091 (85.1743)
Neigh time (%) = 0.000468254 (0.660219)
Comm time (%) = 0.00060463 (0.852503)
Outpt time (%) = 0.00444221 (6.26334)
Other time (%) = 0.00499988 (7.04962)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 95 ave 95 max 95 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3580 ave 3580 max 3580 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 3
Dangerous builds = 0
fix 4 all indent 5000.0 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.13877 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
61 0 -3.1909278 0 -2.1564188 -0.70185621 435.65118
70 0 -3.1660289 0 -3.1625401 -0.31636168 435.65027
80 0 -3.1770288 0 -3.1757599 -0.3483411 435.99856
90 0 -3.1793259 0 -3.1785215 -0.30052965 435.91274
100 0 -3.1800716 0 -3.1791754 -0.2910119 435.43352
110 0 -3.180909 0 -3.1800864 -0.2317541 434.78033
120 0 -3.181058 0 -3.1802803 -0.20711414 434.29941
130 0 -3.1812202 0 -3.1805012 -0.16291741 432.88397
135 0 -3.1812426 0 -3.1805375 -0.15669637 433.39974
Loop time of 0.088649 on 1 procs for 74 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.15641882135 -3.18053465436 -3.18053746811
Force two-norm initial, final = 1636.9 0.476876
Force max component initial, final = 1203.56 0.100932
Final line search alpha, max atom move = 0.00451872 0.000456084
Iterations, force evaluations = 74 382
Pair time (%) = 0.0699611 (78.9192)
Neigh time (%) = 0.00313973 (3.54176)
Comm time (%) = 0.000814438 (0.918722)
Outpt time (%) = 0.00523114 (5.90096)
Other time (%) = 0.00950265 (10.7194)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 97 ave 97 max 97 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3604 ave 3604 max 3604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3604
Ave neighs/atom = 8.58095
Neighbor list builds = 20
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.13877 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
135 0 -3.1812426 0 -0.19192458 -0.15631952 434.44459
140 0 -2.9513655 0 -2.3740533 1.7547425 434.44409
150 0 -3.0309712 0 -2.972253 1.5415829 434.4321
160 0 -3.0801925 0 -3.0643618 1.2777168 434.40824
170 0 -3.0957436 0 -3.0848812 1.1886307 434.74386
180 0 -3.1010658 0 -3.0927038 1.1609594 435.10251
190 0 -3.1021044 0 -3.0941231 1.1759758 435.10251
199 0 -3.1024981 0 -3.0945759 1.1898619 435.10251
Loop time of 0.0615499 on 1 procs for 64 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.191924575843 -3.09457566003 -3.09457586836
Force two-norm initial, final = 1762.19 1.91636
Force max component initial, final = 924.883 0.256442
Final line search alpha, max atom move = 2.37791e-05 6.09796e-06
Iterations, force evaluations = 64 260
Pair time (%) = 0.047811 (77.6785)
Neigh time (%) = 0.00175953 (2.8587)
Comm time (%) = 0.000551939 (0.896734)
Outpt time (%) = 0.00439906 (7.14715)
Other time (%) = 0.00702834 (11.4189)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 109 ave 109 max 109 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3650 ave 3650 max 3650 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3650
Ave neighs/atom = 8.69048
Neighbor list builds = 11
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.13877 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
199 0 -3.1024981 0 2.0734804 1.1926841 434.07296
200 0 -3.063514 0 0.94170308 1.558475 434.07296
210 0 -2.6525958 0 -2.3309877 5.0324928 434.04731
220 0 -2.8444394 0 -2.7762672 3.8808209 439.84976
230 0 -2.9010228 0 -2.8688771 3.50282 443.70029
240 0 -2.9360739 0 -2.9193447 3.2073694 446.22515
250 0 -2.9473458 0 -2.9348636 3.1112677 447.07394
260 0 -2.9582315 0 -2.9458551 2.9810138 452.72776
270 0 -2.9654484 0 -2.9536134 2.9095025 454.94634
280 0 -2.9684081 0 -2.9571448 2.850785 456.96062
290 0 -2.9876239 0 -2.9786657 2.5604167 462.68367
300 0 -3.0022762 0 -2.9940546 2.4239915 462.92227
310 0 -3.0281924 0 -3.0204026 2.0550802 465.91269
320 0 -3.0598503 0 -3.0525063 1.6608869 467.5867
330 0 -3.080703 0 -3.0750167 1.4336631 469.48895
340 0 -3.0942887 0 -3.0892328 1.2874725 470.07218
350 0 -3.1050593 0 -3.0995912 1.174125 469.84566
360 0 -3.1086036 0 -3.1025373 1.1315805 469.84566
370 0 -3.109772 0 -3.1035879 1.1092578 469.56239
371 0 -3.1097727 0 -3.1035884 1.109248 469.56239
Loop time of 0.151184 on 1 procs for 172 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
2.07348038848 -3.10358789808 -3.10358837139
Force two-norm initial, final = 2344.16 3.23869
Force max component initial, final = 1039.33 0.641102
Final line search alpha, max atom move = 1.87512e-05 1.20214e-05
Iterations, force evaluations = 172 621
Pair time (%) = 0.114722 (75.8823)
Neigh time (%) = 0.00551605 (3.64857)
Comm time (%) = 0.00139999 (0.926021)
Outpt time (%) = 0.0133951 (8.86012)
Other time (%) = 0.016151 (10.683)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 107 ave 107 max 107 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3583 ave 3583 max 3583 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3583
Ave neighs/atom = 8.53095
Neighbor list builds = 34
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.13877 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
371 0 -3.1097727 0 5.4106439 1.1109825 468.82931
380 0 -2.4441636 0 -1.309673 6.0813907 467.93984
390 0 -2.6054951 0 -2.4413789 5.6157163 469.15728
400 0 -2.8131475 0 -2.7694356 4.3163689 472.06716
410 0 -2.880819 0 -2.8507992 3.7930669 477.45124
420 0 -2.9104468 0 -2.8924731 3.5295785 481.85712
430 0 -2.9319431 0 -2.9204061 3.1970102 489.06643
440 0 -2.9417286 0 -2.9310485 3.0830433 488.0347
450 0 -2.9510138 0 -2.9419933 2.9470967 489.59505
460 0 -2.9638809 0 -2.9561513 2.7401073 490.7871
470 0 -2.9729256 0 -2.9647313 2.6139212 491.76037
480 0 -2.9799518 0 -2.9702844 2.4823761 492.4931
490 0 -2.9891772 0 -2.9791221 2.3116927 492.96414
500 0 -2.9925408 0 -2.9822925 2.2882832 491.07477
506 0 -2.9926753 0 -2.9825662 2.2862105 491.07477
Loop time of 0.113422 on 1 procs for 135 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
5.41064387137 -2.9825647241 -2.9825661694
Force two-norm initial, final = 3145.19 3.37225
Force max component initial, final = 1382.98 0.92089
Final line search alpha, max atom move = 5.29869e-05 4.8795e-05
Iterations, force evaluations = 135 461
Pair time (%) = 0.085886 (75.7224)
Neigh time (%) = 0.00453472 (3.99809)
Comm time (%) = 0.00103426 (0.911868)
Outpt time (%) = 0.00957608 (8.44287)
Other time (%) = 0.0123911 (10.9248)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 111 ave 111 max 111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3784 ave 3784 max 3784 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3784
Ave neighs/atom = 9.00952
Neighbor list builds = 28
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.13885 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
506 0 -2.9926753 0 -2.4338838 2.2875269 490.79218
510 0 -2.9068666 0 -2.7797161 3.090576 490.79122
520 0 -2.8963094 0 -2.8573568 3.3001691 490.87676
530 0 -2.9247443 0 -2.910165 3.1750077 490.89395
540 0 -2.9559967 0 -2.9404145 2.9335435 491.0523
550 0 -2.9715115 0 -2.9588322 2.8116537 491.37201
560 0 -2.9927435 0 -2.9845363 2.6315408 491.74088
570 0 -3.0096677 0 -3.0017546 2.5066705 492.62943
580 0 -3.0209659 0 -3.0144942 2.4294681 492.15487
590 0 -3.0295431 0 -3.0230283 2.2922972 493.8197
600 0 -3.0369046 0 -3.0303653 2.2460976 494.37058
610 0 -3.0396447 0 -3.0330628 2.2112043 494.37058
620 0 -3.0428437 0 -3.0363283 2.1127716 497.10213
630 0 -3.0440196 0 -3.0372596 2.0844645 497.22845
633 0 -3.0441863 0 -3.0373734 2.0798762 497.22845
Loop time of 0.116155 on 1 procs for 127 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.43388381685 -3.03737140673 -3.03737337747
Force two-norm initial, final = 493.081 3.13221
Force max component initial, final = 230.445 1.12604
Final line search alpha, max atom move = 7.78733e-05 8.76885e-05
Iterations, force evaluations = 127 481
Pair time (%) = 0.0885282 (76.2156)
Neigh time (%) = 0.00443196 (3.81556)
Comm time (%) = 0.00115013 (0.99017)
Outpt time (%) = 0.00952411 (8.19949)
Other time (%) = 0.0125206 (10.7792)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 120 ave 120 max 120 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3677 ave 3677 max 3677 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3677
Ave neighs/atom = 8.75476
Neighbor list builds = 27
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.13885 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
633 0 -3.0441863 0 -2.579812 2.0845158 496.12175
640 0 -2.9619387 0 -2.9193336 2.9399685 496.15811
650 0 -2.9754885 0 -2.9486959 2.8967918 496.27037
660 0 -2.9780194 0 -2.9578621 2.8898564 496.39733
670 0 -2.9937222 0 -2.9767902 2.7261813 496.77066
680 0 -2.9993112 0 -2.9838808 2.6840597 497.14933
690 0 -3.0135704 0 -2.9960465 2.6099984 497.08567
700 0 -3.018956 0 -3.0043211 2.5993674 496.98092
709 0 -3.0198905 0 -3.005157 2.5960149 496.81307
Loop time of 0.075793 on 1 procs for 76 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.57981199808 -3.00515693209 -3.00515698891
Force two-norm initial, final = 450.585 2.66944
Force max component initial, final = 213.273 0.45537
Final line search alpha, max atom move = 3.34725e-06 1.52424e-06
Iterations, force evaluations = 76 318
Pair time (%) = 0.058588 (77.3)
Neigh time (%) = 0.00277781 (3.665)
Comm time (%) = 0.00077343 (1.02045)
Outpt time (%) = 0.00515795 (6.80531)
Other time (%) = 0.00849581 (11.2092)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 119 ave 119 max 119 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3734 ave 3734 max 3734 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3734
Ave neighs/atom = 8.89048
Neighbor list builds = 17
Dangerous builds = 0

374
examples/indent/log.indent.min.21May08.linux.4
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@ -1,374 +0,0 @@
LAMMPS (21 May 2008)
# 2d indenter simulation with minimization instead of dynamics
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
2 by 2 by 1 processor grid
create_atoms 1 box
Created 420 atoms
mass * 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
fix 2 lower setforce 0.0 0.0 0.0
# indenter
fix 5 all enforce2d
# minimize with indenter
thermo 10
dump 1 all atom 10 dump.indent
dump_modify 1 scale no
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.13359 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5980059 444.44898
10 0 -3.1805305 0 -3.1805305 -1.3022518 440.53426
20 0 -3.1852211 0 -3.1852211 -1.1504773 438.82144
30 0 -3.1897313 0 -3.1897313 -0.89994803 435.57358
40 0 -3.1905969 0 -3.1905969 -0.79831934 435.57358
50 0 -3.1908121 0 -3.1908121 -0.74804622 435.57358
60 0 -3.1909265 0 -3.1909265 -0.69982255 435.57358
62 0 -3.1909324 0 -3.1909324 -0.69984937 435.57358
Loop time of 0.195302 on 4 procs for 62 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3.17275755126 -3.19093059349 -3.19093241947
Force two-norm initial, final = 6.74302 0.389376
Force max component initial, final = 1.46877 0.0465566
Final line search alpha, max atom move = 0.00891891 0.000415234
Iterations, force evaluations = 62 337
Pair time (%) = 0.0169503 (8.67903)
Neigh time (%) = 0.000139177 (0.0712624)
Comm time (%) = 0.102262 (52.3607)
Outpt time (%) = 0.00876337 (4.48709)
Other time (%) = 0.0671875 (34.4019)
Nlocal: 105 ave 113 max 98 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost: 84 ave 91 max 76 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 895 ave 916 max 868 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 3
Dangerous builds = 0
fix 4 all indent 5000.0 sphere 10 13.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.1337 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
62 0 -3.1909324 0 -2.1616994 -0.69975283 435.63367
70 0 -3.1623092 0 -3.1567788 -0.29850166 435.63305
80 0 -3.1762926 0 -3.1748715 -0.35755222 435.96901
90 0 -3.1789632 0 -3.1779258 -0.32349148 435.69881
100 0 -3.1799259 0 -3.1789996 -0.29722727 435.53439
110 0 -3.1806761 0 -3.1797642 -0.25692976 435.13697
120 0 -3.1809142 0 -3.1801529 -0.22277366 434.45467
130 0 -3.1812045 0 -3.1804711 -0.17432467 434.93849
133 0 -3.1811808 0 -3.180483 -0.17028649 434.93849
Loop time of 0.244739 on 4 procs for 71 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.16169943481 -3.18048036213 -3.18048296345
Force two-norm initial, final = 1631.5 0.578482
Force max component initial, final = 1199.98 0.329125
Final line search alpha, max atom move = 0.00349203 0.00114931
Iterations, force evaluations = 71 355
Pair time (%) = 0.017894 (7.31145)
Neigh time (%) = 0.0011586 (0.4734)
Comm time (%) = 0.112865 (46.1166)
Outpt time (%) = 0.0102966 (4.20717)
Other time (%) = 0.102525 (41.8914)
Nlocal: 105 ave 111 max 97 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nghost: 87.5 ave 94 max 83 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 899.5 ave 999 max 780 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 3598
Ave neighs/atom = 8.56667
Neighbor list builds = 26
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 12.5 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.1337 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
133 0 -3.1811808 0 -0.18671581 -0.17039738 434.65545
140 0 -2.9568412 0 -2.6132958 1.8016846 434.65108
150 0 -3.0386882 0 -2.9999474 1.4984083 434.62898
160 0 -3.0826407 0 -3.0685811 1.2551644 434.57947
170 0 -3.0981887 0 -3.088612 1.1595488 434.77255
180 0 -3.1008782 0 -3.092831 1.1609479 435.01081
190 0 -3.1020574 0 -3.0940645 1.1745346 433.50297
Loop time of 0.151218 on 4 procs for 57 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.186715805594 -3.09406360571 -3.09406448654
Force two-norm initial, final = 1763.46 2.8639
Force max component initial, final = 923.871 0.542549
Final line search alpha, max atom move = 4.44737e-05 2.41292e-05
Iterations, force evaluations = 57 213
Pair time (%) = 0.0106732 (7.05812)
Neigh time (%) = 0.000609338 (0.402953)
Comm time (%) = 0.0673354 (44.5286)
Outpt time (%) = 0.00733972 (4.85372)
Other time (%) = 0.0652606 (43.1566)
Nlocal: 105 ave 111 max 100 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 95 ave 97 max 94 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 919.25 ave 1002 max 841 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 3677
Ave neighs/atom = 8.75476
Neighbor list builds = 14
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 12.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.1337 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
190 0 -3.1020574 0 2.0879207 1.1717514 434.53266
200 0 -2.6526837 0 -2.2204899 4.9402286 434.50195
210 0 -2.8249714 0 -2.7487333 3.9661938 440.62768
220 0 -2.8949553 0 -2.8686149 3.5486763 442.64135
230 0 -2.9341012 0 -2.918716 3.2037914 445.61973
240 0 -2.945263 0 -2.9321043 3.1039145 447.45331
250 0 -2.951342 0 -2.9386967 3.0244918 449.75516
260 0 -2.9621939 0 -2.9504774 2.8850797 454.0499
270 0 -2.9688775 0 -2.9574839 2.8368447 456.93443
280 0 -2.9734478 0 -2.96335 2.7700408 459.48311
290 0 -2.9847809 0 -2.9764627 2.6320292 459.48311
300 0 -3.0040805 0 -2.9959046 2.3950577 463.79192
310 0 -3.0341912 0 -3.0273837 1.9732267 467.79314
320 0 -3.0731303 0 -3.0655636 1.4582214 468.69565
330 0 -3.0926057 0 -3.0874424 1.319003 469.93704
340 0 -3.107211 0 -3.1011349 1.1546194 469.95306
350 0 -3.1108793 0 -3.1046768 1.1127509 470.06157
360 0 -3.1117881 0 -3.1054768 1.082638 470.06157
364 0 -3.1119921 0 -3.1056 1.0764114 470.64428
Loop time of 0.442124 on 4 procs for 174 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
2.0879207472 -3.10559786164 -3.1056000465
Force two-norm initial, final = 2347.57 1.55187
Force max component initial, final = 1040.59 0.272401
Final line search alpha, max atom move = 0.000362691 9.87974e-05
Iterations, force evaluations = 174 627
Pair time (%) = 0.0312243 (7.06233)
Neigh time (%) = 0.00168264 (0.380581)
Comm time (%) = 0.194638 (44.0235)
Outpt time (%) = 0.0250429 (5.66422)
Other time (%) = 0.189536 (42.8694)
Nlocal: 105 ave 124 max 88 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Nghost: 91 ave 101 max 83 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Neighs: 895.75 ave 1115 max 701 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 3583
Ave neighs/atom = 8.53095
Neighbor list builds = 37
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.4 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.13412 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
364 0 -3.1119921 0 5.298237 1.0771566 470.31871
370 0 -2.4706074 0 -0.46762265 5.6645357 470.32512
380 0 -2.5654967 0 -2.2868489 5.7091963 472.21069
390 0 -2.7900999 0 -2.7382868 4.3936563 475.50311
400 0 -2.8964643 0 -2.8678983 3.6413245 478.51257
410 0 -2.9215437 0 -2.9039148 3.4292005 481.10502
420 0 -2.932025 0 -2.9189824 3.3118799 481.94612
430 0 -2.9441386 0 -2.9331795 3.0690119 486.08079
440 0 -2.9535012 0 -2.9448517 2.894999 486.93505
450 0 -2.9655482 0 -2.9565479 2.764485 487.55059
460 0 -2.9781289 0 -2.9685763 2.6237204 488.19495
470 0 -2.9855619 0 -2.9749667 2.5373271 488.87918
480 0 -2.9979445 0 -2.9871212 2.4094118 488.39681
490 0 -3.0061397 0 -2.9952104 2.3160128 488.96413
500 0 -3.0277451 0 -3.0182291 2.1035708 489.43065
510 0 -3.0325642 0 -3.0225811 2.0403541 489.96211
520 0 -3.036465 0 -3.0258406 1.9813961 490.66038
Loop time of 0.398392 on 4 procs for 156 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
5.29823695273 -3.02584005386 -3.02584061747
Force two-norm initial, final = 3139.62 3.91937
Force max component initial, final = 1384.24 0.791964
Final line search alpha, max atom move = 1.53242e-05 1.21362e-05
Iterations, force evaluations = 156 554
Pair time (%) = 0.0276904 (6.95053)
Neigh time (%) = 0.0014354 (0.360298)
Comm time (%) = 0.177661 (44.5945)
Outpt time (%) = 0.0231554 (5.81222)
Other time (%) = 0.16845 (42.2825)
Nlocal: 105 ave 120 max 88 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 93.75 ave 101 max 86 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 932.5 ave 1122 max 719 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 3730
Ave neighs/atom = 8.88095
Neighbor list builds = 32
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.2 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.13417 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
520 0 -3.036465 0 -2.5645975 1.9835257 490.13358
530 0 -2.9573732 0 -2.9070091 2.8284983 490.25643
540 0 -2.9588212 0 -2.9314259 2.8725676 490.27534
550 0 -2.9610691 0 -2.9402566 2.8788187 489.96007
555 0 -2.961503 0 -2.9405195 2.8746792 490.02321
Loop time of 0.102779 on 4 procs for 35 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.56459752176 -2.94051952347 -2.94051952521
Force two-norm initial, final = 435.594 4.76669
Force max component initial, final = 239.583 0.740992
Final line search alpha, max atom move = 3.21755e-08 2.38418e-08
Iterations, force evaluations = 35 162
Pair time (%) = 0.00810117 (7.88211)
Neigh time (%) = 0.000264108 (0.256967)
Comm time (%) = 0.0478805 (46.5859)
Outpt time (%) = 0.00421453 (4.10057)
Other time (%) = 0.0423188 (41.1745)
Nlocal: 105 ave 122 max 87 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 94.25 ave 103 max 85 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 967.5 ave 1175 max 732 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 3870
Ave neighs/atom = 9.21429
Neighbor list builds = 6
Dangerous builds = 0
fix 4 all indent 1000.0 sphere 10 11.0 0 6.0
fix_modify 4 energy yes
minimize 1.0e-6 1.0e-6 1000 1000
Memory usage per processor = 2.13417 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
555 0 -2.961503 0 -2.2877493 2.8751077 489.95017
560 0 -2.8344545 0 -2.7178932 4.0070178 489.9685
570 0 -2.8416708 0 -2.7942509 4.0898832 489.94064
580 0 -2.8533166 0 -2.8157525 4.037354 490.08268
590 0 -2.8684931 0 -2.8438659 3.9512523 491.28069
600 0 -2.8931986 0 -2.873389 3.6795318 495.68999
610 0 -2.9185227 0 -2.9031181 3.4245451 501.20762
620 0 -2.9459421 0 -2.9340958 3.1457774 506.56569
630 0 -2.9664702 0 -2.9555106 2.9687571 508.81195
640 0 -2.9825303 0 -2.972447 2.8299588 511.123
650 0 -2.9898857 0 -2.9793125 2.7459514 512.06965
660 0 -2.9972242 0 -2.9861323 2.6336573 513.79477
670 0 -3.0011334 0 -2.9898313 2.5703138 514.08613
680 0 -3.0047158 0 -2.9928666 2.5186384 514.30437
690 0 -3.006177 0 -2.9941837 2.5029598 513.35582
700 0 -3.0070307 0 -2.99484 2.4844535 513.35582
710 0 -3.0085036 0 -2.9958931 2.4321016 514.61101
720 0 -3.0091542 0 -2.9962012 2.3910347 517.24803
730 0 -3.0092026 0 -2.9963461 2.3934124 515.38352
740 0 -3.0095191 0 -2.9964638 2.3793318 515.38352
748 0 -3.0095449 0 -2.9965397 2.3669912 517.32503
Loop time of 0.552679 on 4 procs for 193 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.28774930201 -2.99653743495 -2.99653965384
Force two-norm initial, final = 527.637 0.855847
Force max component initial, final = 237.878 0.232991
Final line search alpha, max atom move = 0.00111439 0.000259642
Iterations, force evaluations = 193 821
Pair time (%) = 0.0397109 (7.18517)
Neigh time (%) = 0.00146961 (0.265907)
Comm time (%) = 0.267403 (48.3831)
Outpt time (%) = 0.0289575 (5.23948)
Other time (%) = 0.215138 (38.9263)
Nlocal: 105 ave 132 max 79 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 96.5 ave 112 max 82 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 928.25 ave 1222 max 648 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3713
Ave neighs/atom = 8.84048
Neighbor list builds = 33
Dangerous builds = 0

55
examples/indent/log.indent.min.9Jan09.linux.1 Normal file
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LAMMPS (9 Jan 2009)
# 2d indenter simulation with minimization instead of dynamics
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
1 by 1 by 1 processor grid
create_atoms 1 box
Created 420 atoms
mass * 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
fix 2 lower setforce 0.0 0.0 0.0
# indenter
fix 5 all enforce2d
# minimize with indenter
thermo 10
dump 1 all atom 10 dump.indent
dump_modify 1 scale no
minimize 1.0e-6 1000 1000
ERROR: Illegal minimize command

55
examples/indent/log.indent.min.9Jan09.linux.4 Normal file
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@ -0,0 +1,55 @@
LAMMPS (9 Jan 2009)
# 2d indenter simulation with minimization instead of dynamics
dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5
# create geometry
lattice hex 0.9
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
region box block 0 20 0 10 -0.25 0.25
create_box 2 box
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
2 by 2 by 1 processor grid
create_atoms 1 box
Created 420 atoms
mass * 1.0
# LJ potentials
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5
# define groups
region 1 block INF INF INF 1.25 INF INF
group lower region 1
60 atoms in group lower
group mobile subtract all lower
360 atoms in group mobile
set group lower type 2
60 settings made for type
# initial velocities
fix 2 lower setforce 0.0 0.0 0.0
# indenter
fix 5 all enforce2d
# minimize with indenter
thermo 10
dump 1 all atom 10 dump.indent
dump_modify 1 scale no
minimize 1.0e-6 1000 1000
ERROR: Illegal minimize command