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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2966 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2009-07-02 20:23:49 +00:00
parent 15807776c8
commit f4cc5550f7
61 changed files with 1552 additions and 892 deletions
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26
examples/indent/log.indent.9Jan09.linux.1 → examples/indent/log.indent.7Jul09.linux.1
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LAMMPS (9 Jan 2009)
LAMMPS (7 Jul 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 4.3524 on 1 procs for 30000 steps with 420 atoms
Loop time of 4.37522 on 1 procs for 30000 steps with 420 atoms
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)
Pair time (%) = 3.37476 (77.1334)
Neigh time (%) = 0.0958061 (2.18974)
Comm time (%) = 0.0581815 (1.3298)
Outpt time (%) = 0.0787945 (1.80092)
Other time (%) = 0.767685 (17.5462)
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 4.04239 on 1 procs for 30000 steps with 420 atoms
Loop time of 4.06116 on 1 procs for 30000 steps with 420 atoms
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)
Pair time (%) = 3.34916 (82.4682)
Neigh time (%) = 0.097434 (2.39917)
Comm time (%) = 0.0584626 (1.43956)
Outpt time (%) = 0.0787721 (1.93965)
Other time (%) = 0.477326 (11.7534)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0

26
examples/indent/log.indent.9Jan09.linux.4 → examples/indent/log.indent.7Jul09.linux.4
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LAMMPS (9 Jan 2009)
LAMMPS (7 Jul 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 12.2128 on 4 procs for 30000 steps with 420 atoms
Loop time of 13.0055 on 4 procs for 30000 steps with 420 atoms
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)
Pair time (%) = 1.05029 (8.07573)
Neigh time (%) = 0.0304075 (0.233804)
Comm time (%) = 9.29519 (71.4711)
Outpt time (%) = 0.116246 (0.893821)
Other time (%) = 2.51339 (19.3255)
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 11.3223 on 4 procs for 30000 steps with 420 atoms
Loop time of 12.9245 on 4 procs for 30000 steps with 420 atoms
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)
Pair time (%) = 1.03264 (7.98985)
Neigh time (%) = 0.0303019 (0.234454)
Comm time (%) = 9.32815 (72.1744)
Outpt time (%) = 0.115188 (0.891241)
Other time (%) = 2.41817 (18.7101)
Nlocal: 105 ave 119 max 89 min
Histogram: 1 1 0 0 0 0 0 0 0 2

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LAMMPS (7 Jul 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 1.0e-6 1000 1000
Memory usage per processor = 2.36765 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5980059 444.44898
10 0 -3.1801584 0 -3.1801584 -1.3058039 441.04528
20 0 -3.1831474 0 -3.1831474 -1.2345239 438.53563
30 0 -3.1861452 0 -3.1861452 -1.0910037 438.78112
40 0 -3.1901049 0 -3.1901049 -0.84865219 435.53833
50 0 -3.1904808 0 -3.1904808 -0.81510177 435.53833
60 0 -3.1906458 0 -3.1906458 -0.78391532 435.53833
70 0 -3.190782 0 -3.190782 -0.75177925 435.53833
74 0 -3.1908431 0 -3.1908431 -0.7389172 435.53833
Loop time of 0.089426 on 1 procs for 74 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3.17275755126 -3.19084058014 -3.19084306149
Force two-norm initial, final = 6.74302 0.560739
Force max component initial, final = 1.46877 0.0659162
Final line search alpha, max atom move = 0.00643437 0.000424129
Iterations, force evaluations = 74 411
Pair time (%) = 0.074801 (83.6456)
Neigh time (%) = 0.000599623 (0.670524)
Comm time (%) = 0.000761271 (0.851285)
Outpt time (%) = 0.00557613 (6.23547)
Other time (%) = 0.00768805 (8.5971)
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 = 4
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 = 2.36765 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
74 0 -3.1908431 0 -2.0624125 -0.73821514 435.95254
80 0 -3.1521235 0 -3.1418193 -0.26108246 435.95258
90 0 -3.1725011 0 -3.1715059 -0.36505592 436.10565
100 0 -3.1770957 0 -3.1759313 -0.36790205 436.07344
110 0 -3.1790078 0 -3.177998 -0.33507478 436.17872
120 0 -3.1806189 0 -3.1797788 -0.25814928 436.17872
130 0 -3.1807519 0 -3.1799742 -0.24358133 434.54581
140 0 -3.18119 0 -3.1805338 -0.12889908 432.85282
143 0 -3.1812477 0 -3.1805537 -0.1274024 435.36966
Loop time of 0.0776429 on 1 procs for 69 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.06241249301 -3.18055125011 -3.1805537171
Force two-norm initial, final = 1731.02 0.50754
Force max component initial, final = 1265.65 0.134224
Final line search alpha, max atom move = 0.00356061 0.000477918
Iterations, force evaluations = 69 321
Pair time (%) = 0.0586853 (75.5836)
Neigh time (%) = 0.00300622 (3.87185)
Comm time (%) = 0.00072217 (0.930117)
Outpt time (%) = 0.00551438 (7.10224)
Other time (%) = 0.00971484 (12.5122)
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: 3592 ave 3592 max 3592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3592
Ave neighs/atom = 8.55238
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 = 2.36765 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
143 0 -3.1812477 0 -0.20603921 -0.12780422 434.00086
150 0 -2.9166198 0 -2.6416545 2.1362286 434.00451
160 0 -3.0353563 0 -3.008042 1.5943256 434.02366
170 0 -3.083974 0 -3.0715304 1.2922524 434.28347
180 0 -3.0944428 0 -3.0845539 1.2202659 434.39044
190 0 -3.1006452 0 -3.0921604 1.1820215 434.47518
200 0 -3.1015749 0 -3.0933672 1.1854353 434.07616
202 0 -3.1015946 0 -3.0933731 1.1852641 434.07616
Loop time of 0.0565 on 1 procs for 59 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.206039208467 -3.09337112336 -3.09337312876
Force two-norm initial, final = 1758.06 4.63149
Force max component initial, final = 925.071 1.21437
Final line search alpha, max atom move = 3.81154e-05 4.62863e-05
Iterations, force evaluations = 59 222
Pair time (%) = 0.0407476 (72.1198)
Neigh time (%) = 0.0030787 (5.44903)
Comm time (%) = 0.000559568 (0.990387)
Outpt time (%) = 0.00482178 (8.53413)
Other time (%) = 0.00729227 (12.9067)
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: 3684 ave 3684 max 3684 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3684
Ave neighs/atom = 8.77143
Neighbor list builds = 20
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 = 2.36765 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
202 0 -3.1015946 0 2.0766672 1.1844063 434.39055
210 0 -2.520913 0 -2.0690757 5.8013421 434.38134
220 0 -2.8039381 0 -2.7187821 4.1286417 439.67791
230 0 -2.8820548 0 -2.8528964 3.6796868 441.33006
240 0 -2.9261338 0 -2.9080962 3.2755112 445.24451
250 0 -2.9383137 0 -2.9266043 3.189536 444.61438
260 0 -2.9517388 0 -2.9424768 3.016748 445.58557
270 0 -2.9697366 0 -2.9619145 2.8041755 451.59439
280 0 -2.9968256 0 -2.9897502 2.4954221 454.90645
290 0 -3.013823 0 -3.0081202 2.4050739 454.15218
300 0 -3.0214909 0 -3.015636 2.2897823 455.93968
310 0 -3.0265359 0 -3.0204169 2.2635274 455.4861
320 0 -3.027514 0 -3.0214271 2.236737 455.17707
330 0 -3.0291397 0 -3.0228192 2.171714 456.01607
338 0 -3.0296169 0 -3.0231811 2.1574108 456.53101
Loop time of 0.120724 on 1 procs for 136 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
2.0766672396 -3.0231792545 -3.02318109385
Force two-norm initial, final = 2344.54 2.48756
Force max component initial, final = 1037.14 0.398868
Final line search alpha, max atom move = 0.000118496 4.72641e-05
Iterations, force evaluations = 136 481
Pair time (%) = 0.0887501 (73.5149)
Neigh time (%) = 0.00563741 (4.66967)
Comm time (%) = 0.00114322 (0.946968)
Outpt time (%) = 0.0102112 (8.45833)
Other time (%) = 0.014982 (12.4101)
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: 3777 ave 3777 max 3777 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3777
Ave neighs/atom = 8.99286
Neighbor list builds = 36
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 = 2.36765 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
338 0 -3.0296169 0 6.961911 2.1609896 455.77497
340 0 -2.8586172 0 3.4274844 3.4930046 455.77548
350 0 -2.304443 0 -2.0147753 8.1347595 455.82935
360 0 -2.6395219 0 -2.5815108 6.1050134 457.95769
370 0 -2.7821529 0 -2.7562487 4.9838644 463.79818
380 0 -2.8608313 0 -2.8356522 4.3574266 464.8841
390 0 -2.8864591 0 -2.8638843 4.0677888 464.84671
400 0 -2.9390045 0 -2.9225692 3.4493421 469.61713
410 0 -2.9595506 0 -2.9439395 3.295113 468.52735
420 0 -2.9680709 0 -2.9519988 3.2145507 469.64
430 0 -2.9725693 0 -2.9563543 3.1767655 469.60893
440 0 -2.9843733 0 -2.9680525 3.0830944 470.37202
450 0 -2.9946883 0 -2.9781239 2.9958694 470.99594
460 0 -2.9970525 0 -2.9805938 2.9608762 472.16068
470 0 -2.9983522 0 -2.9814143 2.9400748 471.95229
472 0 -2.9983603 0 -2.9814207 2.9398944 471.95229
Loop time of 0.121973 on 1 procs for 134 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
6.96191096541 -2.98142046882 -2.98142066081
Force two-norm initial, final = 3554.26 1.67097
Force max component initial, final = 1417.97 0.211357
Final line search alpha, max atom move = 2.88431e-05 6.09618e-06
Iterations, force evaluations = 134 481
Pair time (%) = 0.0894356 (73.3241)
Neigh time (%) = 0.00557256 (4.56868)
Comm time (%) = 0.00115991 (0.950953)
Outpt time (%) = 0.0109332 (8.96359)
Other time (%) = 0.0148718 (12.1927)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 115 ave 115 max 115 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3838 ave 3838 max 3838 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3838
Ave neighs/atom = 9.1381
Neighbor list builds = 35
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 = 2.36765 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
472 0 -2.9983603 0 -2.4280353 2.9444196 471.22697
480 0 -2.8863925 0 -2.7990921 3.9536272 471.26019
490 0 -2.8863751 0 -2.8438685 4.0283513 471.37872
500 0 -2.8874137 0 -2.8553934 4.0257436 472.13493
510 0 -2.8891518 0 -2.8680243 3.9855761 473.29808
520 0 -2.892536 0 -2.8708711 3.903257 476.05078
530 0 -2.895889 0 -2.875555 3.8192823 476.37839
539 0 -2.8963524 0 -2.8766806 3.8020824 476.98607
Loop time of 0.075753 on 1 procs for 67 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.42803525652 -2.87667971779 -2.87668061174
Force two-norm initial, final = 505.843 4.76344
Force max component initial, final = 209.948 1.46556
Final line search alpha, max atom move = 1.63098e-05 2.39029e-05
Iterations, force evaluations = 67 313
Pair time (%) = 0.0584297 (77.1319)
Neigh time (%) = 0.00240541 (3.17533)
Comm time (%) = 0.000724316 (0.956155)
Outpt time (%) = 0.00472283 (6.23452)
Other time (%) = 0.0094707 (12.5021)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 117 ave 117 max 117 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4020 ave 4020 max 4020 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4020
Ave neighs/atom = 9.57143
Neighbor list builds = 15
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 = 2.36773 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
539 0 -2.8963524 0 -2.1448516 3.8101192 475.97994
540 0 -2.8284353 0 -2.3728207 4.3388795 475.97994
550 0 -2.7618007 0 -2.7173482 5.1686742 476.1911
560 0 -2.7775101 0 -2.7536284 5.1254483 476.0715
570 0 -2.8018137 0 -2.7801844 4.875653 479.07433
580 0 -2.8348619 0 -2.8106477 4.6622148 479.08037
590 0 -2.8478953 0 -2.8242027 4.5831784 478.89146
600 0 -2.8561474 0 -2.8313225 4.4709421 479.12303
610 0 -2.8607838 0 -2.8355791 4.3763977 480.83847
620 0 -2.8644617 0 -2.838614 4.3067029 481.24727
630 0 -2.8661483 0 -2.8401307 4.2724321 481.24727
640 0 -2.8729811 0 -2.845837 4.1671583 481.57706
650 0 -2.8819751 0 -2.8539942 4.0710845 481.94034
660 0 -2.8847714 0 -2.8566531 4.0337696 482.16244
670 0 -2.8862614 0 -2.8578008 4.0074194 482.16244
676 0 -2.8863082 0 -2.8579227 4.0016092 482.42577
Loop time of 0.133903 on 1 procs for 137 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.14485156833 -2.8579216319 -2.85792271133
Force two-norm initial, final = 575.194 2.83836
Force max component initial, final = 246.366 0.900012
Final line search alpha, max atom move = 5.35906e-05 4.82321e-05
Iterations, force evaluations = 137 541
Pair time (%) = 0.101857 (76.0677)
Neigh time (%) = 0.00354767 (2.64944)
Comm time (%) = 0.00121427 (0.906826)
Outpt time (%) = 0.0110219 (8.23123)
Other time (%) = 0.0162623 (12.1449)
Nlocal: 420 ave 420 max 420 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 117 ave 117 max 117 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4067 ave 4067 max 4067 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4067
Ave neighs/atom = 9.68333
Neighbor list builds = 22
Dangerous builds = 0

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LAMMPS (7 Jul 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 1.0e-6 1000 1000
Memory usage per processor = 2.36247 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
0 0 -3.1727576 0 -3.1727576 -1.5980059 444.44898
10 0 -3.1801584 0 -3.1801584 -1.3058039 441.04528
20 0 -3.1831474 0 -3.1831474 -1.2345239 438.53563
30 0 -3.1861452 0 -3.1861452 -1.0910037 438.78112
40 0 -3.1901049 0 -3.1901049 -0.84865219 435.53833
50 0 -3.1904808 0 -3.1904808 -0.81510177 435.53833
60 0 -3.1906458 0 -3.1906458 -0.78391529 435.53833
70 0 -3.190782 0 -3.190782 -0.75177925 435.53833
74 0 -3.1908431 0 -3.1908431 -0.73891689 435.53833
Loop time of 0.215456 on 4 procs for 74 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3.17275755126 -3.19084058139 -3.19084306435
Force two-norm initial, final = 6.74302 0.560503
Force max component initial, final = 1.46877 0.0658891
Final line search alpha, max atom move = 0.00643447 0.000423962
Iterations, force evaluations = 74 411
Pair time (%) = 0.022081 (10.2485)
Neigh time (%) = 0.000195861 (0.0909054)
Comm time (%) = 0.107793 (50.0301)
Outpt time (%) = 0.0101855 (4.72744)
Other time (%) = 0.0752007 (34.9031)
Nlocal: 105 ave 111 max 99 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 84 ave 90 max 78 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 895 ave 911 max 888 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Total # of neighbors = 3580
Ave neighs/atom = 8.52381
Neighbor list builds = 4
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 = 2.36251 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
74 0 -3.1908431 0 -2.0624134 -0.73821482 435.95253
80 0 -3.1521235 0 -3.1418193 -0.26108213 435.95257
90 0 -3.1725009 0 -3.1715057 -0.36505532 436.10564
100 0 -3.177093 0 -3.1759292 -0.36788198 436.07327
110 0 -3.1795715 0 -3.1784814 -0.32383634 435.95359
120 0 -3.1802472 0 -3.1794125 -0.28110358 435.12253
130 0 -3.1808946 0 -3.1801058 -0.22616311 434.75819
140 0 -3.1811811 0 -3.1804555 -0.16882959 433.62172
148 0 -3.1812301 0 -3.1805215 -0.16062302 434.1409
Loop time of 0.224046 on 4 procs for 74 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.06241337528 -3.18051942016 -3.18052152763
Force two-norm initial, final = 1731.02 0.458909
Force max component initial, final = 1265.65 0.221751
Final line search alpha, max atom move = 0.00250114 0.00055463
Iterations, force evaluations = 74 356
Pair time (%) = 0.0191688 (8.55574)
Neigh time (%) = 0.00120753 (0.538965)
Comm time (%) = 0.100357 (44.7932)
Outpt time (%) = 0.0105996 (4.731)
Other time (%) = 0.0927126 (41.3811)
Nlocal: 105 ave 111 max 99 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 87 ave 90 max 84 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 896 ave 999 max 791 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Total # of neighbors = 3584
Ave neighs/atom = 8.53333
Neighbor list builds = 27
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 = 2.36251 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
148 0 -3.1812301 0 -0.18956754 -0.1604829 434.51995
150 0 -3.095721 0 -1.4570917 0.56252386 434.51977
160 0 -3.0094505 0 -2.8879891 1.6056155 434.51159
170 0 -3.0712576 0 -3.0461099 1.3150004 434.48634
180 0 -3.0919922 0 -3.0805103 1.2089866 434.4778
190 0 -3.1001557 0 -3.091098 1.1597663 434.92027
192 0 -3.1001613 0 -3.0911135 1.1597453 434.92027
Loop time of 0.0922478 on 4 procs for 44 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-0.189567544179 -3.09111043936 -3.09111351567
Force two-norm initial, final = 1762.82 7.39274
Force max component initial, final = 924.443 2.0665
Final line search alpha, max atom move = 2.33508e-05 4.82545e-05
Iterations, force evaluations = 44 130
Pair time (%) = 0.00678003 (7.3498)
Neigh time (%) = 0.000626624 (0.679283)
Comm time (%) = 0.0388998 (42.1689)
Outpt time (%) = 0.00712276 (7.72133)
Other time (%) = 0.0388185 (42.0807)
Nlocal: 105 ave 111 max 98 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 93.5 ave 96 max 92 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 918 ave 999 max 823 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 3672
Ave neighs/atom = 8.74286
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 = 2.36251 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
192 0 -3.1001613 0 2.1397449 1.1596258 434.96505
200 0 -2.5007873 0 -1.92419 5.8474143 434.96
210 0 -2.7571181 0 -2.6183912 4.3908294 436.40494
220 0 -2.8469394 0 -2.7899856 3.8274551 440.10986
230 0 -2.9049319 0 -2.8826176 3.4460145 443.45437
240 0 -2.9276486 0 -2.9111566 3.2520705 444.18526
250 0 -2.9445729 0 -2.9354012 3.0848831 443.92809
260 0 -2.9641063 0 -2.9564606 2.8101826 451.23574
270 0 -2.9903407 0 -2.9832949 2.5127065 453.82669
280 0 -3.0140859 0 -3.0083556 2.3384981 456.42508
290 0 -3.0184171 0 -3.0127622 2.3081304 454.69284
300 0 -3.0268999 0 -3.0208085 2.2262732 455.83178
310 0 -3.0279478 0 -3.0218766 2.2095343 454.93707
311 0 -3.0279511 0 -3.0218794 2.2095092 454.93707
Loop time of 0.25761 on 4 procs for 119 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
2.13974493524 -3.02187658409 -3.02187944028
Force two-norm initial, final = 2364.71 5.58912
Force max component initial, final = 1047.79 1.30644
Final line search alpha, max atom move = 3.71246e-05 4.8501e-05
Iterations, force evaluations = 119 376
Pair time (%) = 0.0203169 (7.8867)
Neigh time (%) = 0.00125414 (0.486838)
Comm time (%) = 0.108068 (41.9502)
Outpt time (%) = 0.0182751 (7.0941)
Other time (%) = 0.109696 (42.5822)
Nlocal: 105 ave 110 max 98 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 96 ave 100 max 90 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 941.25 ave 1025 max 839 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 3765
Ave neighs/atom = 8.96429
Neighbor list builds = 26
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 = 2.36255 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
311 0 -3.0279511 0 6.9389112 2.2069729 455.45989
320 0 -2.2777436 0 -1.4982915 8.0579872 455.4549
330 0 -2.5894029 0 -2.4615958 6.423689 456.60369
340 0 -2.721932 0 -2.6874426 5.4815336 460.86823
350 0 -2.840306 0 -2.8167483 4.5352584 466.35175
360 0 -2.8777332 0 -2.8546042 4.2030136 465.89752
370 0 -2.9346094 0 -2.9190825 3.5036472 467.98916
380 0 -2.9530714 0 -2.9366932 3.3587171 468.16677
390 0 -2.9623386 0 -2.9455153 3.2827574 468.16677
400 0 -2.9695202 0 -2.9530478 3.2196447 469.09638
410 0 -2.9852569 0 -2.9686584 3.0770278 470.62895
420 0 -2.9953623 0 -2.9793025 2.9909952 470.8922
430 0 -2.9975757 0 -2.9809236 2.9604675 471.57978
436 0 -2.9985868 0 -2.9813144 2.9474782 471.23734
Loop time of 0.289543 on 4 procs for 125 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
6.93891120218 -2.98131311316 -2.981314398
Force two-norm initial, final = 3550.67 6.45366
Force max component initial, final = 1419.72 1.884
Final line search alpha, max atom move = 1.2714e-05 2.39531e-05
Iterations, force evaluations = 125 434
Pair time (%) = 0.0238197 (8.22666)
Neigh time (%) = 0.00136173 (0.470303)
Comm time (%) = 0.125435 (43.3219)
Outpt time (%) = 0.0180767 (6.24318)
Other time (%) = 0.120849 (41.738)
Nlocal: 105 ave 121 max 88 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 95.5 ave 104 max 86 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Neighs: 966.5 ave 1191 max 735 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3866
Ave neighs/atom = 9.20476
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 = 2.36293 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
436 0 -2.9985868 0 -2.4239206 2.9478011 471.18571
440 0 -2.8166144 0 -2.7382486 4.3967122 471.19197
450 0 -2.8764026 0 -2.8310192 4.0942123 471.21606
460 0 -2.8805925 0 -2.8478712 4.0748546 472.00217
470 0 -2.8864852 0 -2.8605778 4.0312192 472.67989
480 0 -2.8898248 0 -2.8678631 3.9542855 475.03785
490 0 -2.893791 0 -2.8710437 3.8965844 474.2549
500 0 -2.8955486 0 -2.8767179 3.803347 477.13514
510 0 -2.8970704 0 -2.8807102 3.7328017 478.68259
520 0 -2.9005241 0 -2.884383 3.6654603 478.68259
530 0 -2.9058489 0 -2.8923006 3.5085931 480.92479
540 0 -2.910759 0 -2.8955936 3.3712074 484.42745
550 0 -2.9164927 0 -2.9013938 3.3385686 482.53381
560 0 -2.9516699 0 -2.9366584 2.9939337 486.68956
570 0 -2.9994108 0 -2.9879038 2.5947902 492.89309
580 0 -3.0095975 0 -2.9989197 2.5157328 493.76136
590 0 -3.0194304 0 -3.0080499 2.3401785 495.56145
600 0 -3.0211052 0 -3.0098256 2.3243561 495.56145
610 0 -3.0325078 0 -3.0223848 2.1752451 495.48473
620 0 -3.035681 0 -3.025198 2.1414912 495.33905
630 0 -3.0370734 0 -3.0266573 2.104713 496.55651
640 0 -3.0374264 0 -3.0271748 2.1054757 495.93844
643 0 -3.0374266 0 -3.027195 2.1055236 495.93844
Loop time of 0.57116 on 4 procs for 207 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.42392055478 -3.02719421293 -3.02719500834
Force two-norm initial, final = 509.654 2.21767
Force max component initial, final = 213.307 0.721585
Final line search alpha, max atom move = 6.72413e-05 4.85203e-05
Iterations, force evaluations = 207 910
Pair time (%) = 0.0498471 (8.72733)
Neigh time (%) = 0.00203168 (0.355712)
Comm time (%) = 0.254625 (44.5803)
Outpt time (%) = 0.0316057 (5.53359)
Other time (%) = 0.233051 (40.803)
Nlocal: 105 ave 123 max 88 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 99 ave 107 max 90 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 934.75 ave 1156 max 712 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3739
Ave neighs/atom = 8.90238
Neighbor list builds = 42
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 = 2.36309 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
643 0 -3.0374266 0 -2.460799 2.1045374 496.17084
650 0 -2.9185333 0 -2.8659901 3.1963665 496.16373
660 0 -2.9409566 0 -2.9037554 3.0951938 496.34856
670 0 -2.941145 0 -2.9159259 3.1327325 496.53636
680 0 -2.9427263 0 -2.9183455 3.1295139 496.33168
681 0 -2.9427264 0 -2.9183458 3.1295136 496.33168
Loop time of 0.109531 on 4 procs for 38 steps with 420 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2.46079895643 -2.9183454976 -2.91834578686
Force two-norm initial, final = 513.774 9.82806
Force max component initial, final = 247.058 2.42683
Final line search alpha, max atom move = 1.25538e-06 3.04659e-06
Iterations, force evaluations = 38 173
Pair time (%) = 0.00946778 (8.64389)
Neigh time (%) = 0.000327587 (0.29908)
Comm time (%) = 0.0487782 (44.5335)
Outpt time (%) = 0.00580919 (5.30367)
Other time (%) = 0.0451487 (41.2199)
Nlocal: 105 ave 125 max 86 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 98.5 ave 107 max 88 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Neighs: 966 ave 1210 max 717 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 3864
Ave neighs/atom = 9.2
Neighbor list builds = 7
Dangerous builds = 0

55
examples/indent/log.indent.min.9Jan09.linux.1
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@ -1,55 +0,0 @@
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
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@ -1,55 +0,0 @@
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