Merge branch 'clean-master2' of github.com:julient31/lammps into gneb_spin
This commit is contained in:
julient31
14
examples/USER/misc/electron_stopping/Si.Si.elstop
Normal file
14
examples/USER/misc/electron_stopping/Si.Si.elstop
Normal file
@ -0,0 +1,14 @@
|
||||
# Electronic stopping for Si in Si
|
||||
# Uses metal units
|
||||
# Kinetic energy in eV, stopping power in eV/A
|
||||
# For other atom types, add columns.
|
||||
|
||||
# energy Si in Si
|
||||
3918.2 6.541
|
||||
15672.9 13.091
|
||||
35263.9 19.660
|
||||
62691.5 26.257
|
||||
97955.4 32.889
|
||||
141055.9 39.566
|
||||
191992.0 46.292
|
||||
250766.1 53.074
|
||||
1
examples/USER/misc/electron_stopping/Si.sw
Symbolic link
1
examples/USER/misc/electron_stopping/Si.sw
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../potentials/Si.sw
|
||||
38
examples/USER/misc/electron_stopping/in.elstop
Normal file
38
examples/USER/misc/electron_stopping/in.elstop
Normal file
@ -0,0 +1,38 @@
|
||||
# Test case / example for fix electron/stopping
|
||||
# Perfect Si lattice with one primary knock-on atom.
|
||||
#
|
||||
# Also uses fix dt/reset, as one should when energies are high
|
||||
# enough to require electronic stopping.
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
timestep 0.0001
|
||||
|
||||
lattice fcc 5.431
|
||||
|
||||
region rbox block -10 10 -10 10 -10 10
|
||||
create_box 1 rbox
|
||||
|
||||
mass 1 28.0855
|
||||
|
||||
create_atoms 1 box
|
||||
|
||||
velocity all create 300 42534 mom yes rot yes
|
||||
|
||||
group gPKA id 1
|
||||
velocity gPKA set 1120 1620 389
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
|
||||
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
|
||||
fix fel all electron/stopping 1.0 Si.Si.elstop
|
||||
fix fnve all nve
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time dt f_fel
|
||||
|
||||
#compute ek all ke/atom
|
||||
#dump mydump all custom 200 elstop.dump id x y z vx vy vz fx fy fz c_ek
|
||||
|
||||
run 5000
|
||||
39
examples/USER/misc/electron_stopping/in.elstop.only
Normal file
39
examples/USER/misc/electron_stopping/in.elstop.only
Normal file
@ -0,0 +1,39 @@
|
||||
# Test case / example for fix electron/stopping
|
||||
# One fast atom, no other interactions.
|
||||
# Stopping only applied in a smaller box in the middle.
|
||||
#
|
||||
# Also uses fix dt/reset, as one should when energies are high
|
||||
# enough to require electronic stopping.
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
timestep 0.0001
|
||||
|
||||
lattice fcc 1
|
||||
|
||||
region rbox block -100 100 -100 100 -100 100
|
||||
region rsmallbox block -90 90 -90 90 -90 90
|
||||
|
||||
create_box 1 rbox
|
||||
|
||||
mass 1 28.0855
|
||||
|
||||
create_atoms 1 single 0 0 0
|
||||
velocity all set 1120 1620 389
|
||||
|
||||
pair_style zero 1
|
||||
pair_coeff * * 1
|
||||
|
||||
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
|
||||
fix fel all electron/stopping 1.0 Si.Si.elstop minneigh 0 region rsmallbox
|
||||
fix fnve all nve
|
||||
|
||||
compute ek all ke/atom
|
||||
compute ektot all reduce sum c_ek
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time dt f_fel c_ektot
|
||||
|
||||
#dump mydump all custom 200 elstop.only.dump id x y z vx vy vz fx fy fz c_ek
|
||||
|
||||
run 10000
|
||||
597
examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.1
Normal file
597
examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.1
Normal file
@ -0,0 +1,597 @@
|
||||
LAMMPS (28 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Test case / example for fix electron/stopping
|
||||
# Perfect Si lattice with one primary knock-on atom.
|
||||
#
|
||||
# Also uses fix dt/reset, as one should when energies are high
|
||||
# enough to require electronic stopping.
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
timestep 0.0001
|
||||
|
||||
lattice fcc 5.431
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region rbox block -10 10 -10 10 -10 10
|
||||
create_box 1 rbox
|
||||
Created orthogonal box = (-54.31 -54.31 -54.31) to (54.31 54.31 54.31)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
mass 1 28.0855
|
||||
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.00282311 secs
|
||||
|
||||
velocity all create 300 42534 mom yes rot yes
|
||||
|
||||
group gPKA id 1
|
||||
1 atoms in group gPKA
|
||||
velocity gPKA set 1120 1620 389
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
Reading potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
|
||||
fix fel all electron/stopping 1.0 Si.Si.elstop
|
||||
fix fnve all nve
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time dt f_fel
|
||||
|
||||
#compute ek all ke/atom
|
||||
#dump mydump all custom 200 elstop.dump id x y z vx vy vz fx fy fz c_ek
|
||||
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.77118
|
||||
ghost atom cutoff = 5.77118
|
||||
binsize = 2.88559, bins = 38 38 38
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) fix electron/stopping, occasional, copy from (1)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 10.89 | 10.89 | 10.89 Mbytes
|
||||
Step Time Dt f_fel
|
||||
0 0 4.98128e-05 0
|
||||
10 0.00030141297 7.4132113e-06 143.83504
|
||||
20 0.00035951427 6.0316944e-06 171.53673
|
||||
30 0.00057458971 3.5117251e-05 274.07596
|
||||
40 0.00086591312 5.8243334e-06 412.87446
|
||||
50 0.00090045701 2.1026443e-06 429.31458
|
||||
60 0.00091828462 1.5368285e-06 437.79421
|
||||
70 0.00093305888 1.4643253e-06 444.81982
|
||||
80 0.00094860749 1.7487528e-06 452.21378
|
||||
90 0.00097032161 3.0786693e-06 462.54244
|
||||
100 0.0010787914 4.9354535e-05 514.16832
|
||||
110 0.0012080771 2.321306e-06 575.68374
|
||||
120 0.0012239682 1.0510328e-06 583.23471
|
||||
130 0.0012325497 6.8272619e-07 587.30872
|
||||
140 0.0012385196 5.1205819e-07 590.14077
|
||||
150 0.001243165 4.1524338e-07 592.34294
|
||||
160 0.0012470201 3.5380824e-07 594.1694
|
||||
170 0.0012503578 3.1203776e-07 595.74992
|
||||
180 0.0012533367 2.8236408e-07 597.15986
|
||||
190 0.0012560575 2.6071908e-07 598.44711
|
||||
200 0.0012585888 2.4474123e-07 599.64431
|
||||
210 0.0012609803 2.3298466e-07 600.77504
|
||||
220 0.0012632696 2.2453464e-07 601.85726
|
||||
230 0.0012654871 2.1880713e-07 602.90531
|
||||
240 0.0012676582 2.1543942e-07 603.93128
|
||||
250 0.0012698054 2.1422997e-07 604.94591
|
||||
260 0.0012719499 2.1510772e-07 605.95925
|
||||
270 0.0012741128 2.1812163e-07 606.98126
|
||||
280 0.0012763159 2.2344765e-07 608.02243
|
||||
290 0.0012785839 2.3141489e-07 609.09436
|
||||
300 0.0012809453 2.425587e-07 610.21066
|
||||
310 0.0012834353 2.577174e-07 611.38806
|
||||
320 0.0012860996 2.7820843e-07 612.64822
|
||||
330 0.0012890001 3.0616141e-07 614.02061
|
||||
340 0.0012922261 3.4518994e-07 615.54764
|
||||
350 0.0012959145 4.0187423e-07 617.29438
|
||||
360 0.0013002933 4.894618e-07 619.36917
|
||||
370 0.0013057872 6.3886828e-07 621.97388
|
||||
380 0.0013133355 9.4153332e-07 625.55502
|
||||
390 0.0013257779 1.8246429e-06 631.46263
|
||||
400 0.0013651328 1.4820738e-05 650.16503
|
||||
410 0.0016916358 4.5528312e-05 805.3327
|
||||
420 0.0020836696 2.6189823e-05 991.45963
|
||||
430 0.002192113 5.1312984e-06 1042.8979
|
||||
440 0.0022530638 1.1643276e-05 1071.7967
|
||||
450 0.0025312898 1.5833134e-05 1203.6961
|
||||
460 0.0028677695 3.9078523e-05 1363.0792
|
||||
470 0.0032653301 3.9299497e-05 1551.2027
|
||||
480 0.0036647478 4.1100578e-05 1739.9906
|
||||
490 0.0040772194 3.6017871e-05 1934.7262
|
||||
500 0.004246426 1.1620229e-05 2014.5366
|
||||
510 0.0045410379 2.1151987e-05 2153.4172
|
||||
520 0.0048951987 4.2067206e-05 2320.2216
|
||||
530 0.0051251181 5.9152255e-06 2428.4156
|
||||
540 0.0051740847 5.0188036e-06 2451.4388
|
||||
550 0.0053207575 4.1618335e-05 2520.4067
|
||||
560 0.0054412772 2.3641932e-06 2577.0541
|
||||
570 0.005457552 1.0847369e-06 2584.6937
|
||||
580 0.0054664476 7.1198746e-07 2588.8658
|
||||
590 0.0054726999 5.3933302e-07 2591.796
|
||||
600 0.0054776139 4.4178461e-07 2594.0976
|
||||
610 0.0054817341 3.8039473e-07 2596.0263
|
||||
620 0.0054853401 3.3924667e-07 2597.7135
|
||||
630 0.0054885957 3.1069211e-07 2599.2361
|
||||
640 0.0054916066 2.9064829e-07 2600.6439
|
||||
650 0.0054944462 2.7678405e-07 2601.9712
|
||||
660 0.0054971697 2.6772348e-07 2603.244
|
||||
670 0.0054998211 2.6266505e-07 2604.4829
|
||||
680 0.0055024383 2.6119265e-07 2605.7058
|
||||
690 0.0055050563 2.6318733e-07 2606.929
|
||||
700 0.0055077103 2.6880326e-07 2608.1691
|
||||
710 0.0055104383 2.7849814e-07 2609.4439
|
||||
720 0.0055132846 2.9313007e-07 2610.7742
|
||||
730 0.0055163044 3.141612e-07 2612.186
|
||||
740 0.0055195719 3.4406726e-07 2613.714
|
||||
750 0.0055231932 3.8719688e-07 2615.4081
|
||||
760 0.0055273329 4.5174267e-07 2617.3455
|
||||
770 0.0055322712 5.5490406e-07 2619.6579
|
||||
780 0.0055385515 7.3934538e-07 2622.6004
|
||||
790 0.0055474645 1.1452909e-06 2626.7792
|
||||
800 0.0055635927 2.6160295e-06 2634.3465
|
||||
810 0.0057044835 3.9642931e-05 2700.5132
|
||||
820 0.0060307501 2.9394558e-05 2853.6539
|
||||
830 0.0063374404 8.5188148e-06 2997.4768
|
||||
840 0.0063740052 1.4828325e-06 3014.6052
|
||||
850 0.0063848364 7.5985425e-07 3019.6727
|
||||
860 0.0063911095 5.0258852e-07 3022.6045
|
||||
870 0.0063954921 3.7335256e-07 3024.6508
|
||||
880 0.0063988506 2.9643864e-07 3026.2175
|
||||
890 0.0064015712 2.4575869e-07 3027.4855
|
||||
900 0.0064038584 2.1001191e-07 3028.5506
|
||||
910 0.0064058333 1.8353805e-07 3029.4694
|
||||
920 0.006407573 1.6320008e-07 3030.2782
|
||||
930 0.0064091297 1.4712417e-07 3031.0014
|
||||
940 0.0064105403 1.3412445e-07 3031.6562
|
||||
950 0.0064118317 1.2341509e-07 3032.2552
|
||||
960 0.0064130243 1.1445544e-07 3032.808
|
||||
970 0.0064141337 1.0686175e-07 3033.3219
|
||||
980 0.0064151722 1.0035437e-07 3033.8027
|
||||
990 0.0064161498 9.4724852e-08 3034.2549
|
||||
1000 0.0064170744 8.9814769e-08 3034.6824
|
||||
1010 0.0064179527 8.5501639e-08 3035.0882
|
||||
1020 0.0064187902 8.1689338e-08 3035.475
|
||||
1030 0.0064195915 7.8301418e-08 3035.8449
|
||||
1040 0.0064203606 7.5276356e-08 3036.1997
|
||||
1050 0.0064211009 7.2564109e-08 3036.541
|
||||
1060 0.0064218154 7.0123584e-08 3036.8703
|
||||
1070 0.0064225065 6.7920744e-08 3037.1886
|
||||
1080 0.0064231766 6.5927178e-08 3037.4971
|
||||
1090 0.0064238276 6.4119002e-08 3037.7967
|
||||
1100 0.0064244613 6.2476011e-08 3038.0882
|
||||
1110 0.0064250792 6.0981016e-08 3038.3724
|
||||
1120 0.0064256828 5.9619315e-08 3038.6498
|
||||
1130 0.0064262733 5.8378279e-08 3038.9212
|
||||
1140 0.0064268519 5.7247013e-08 3039.1869
|
||||
1150 0.0064274196 5.6216088e-08 3039.4476
|
||||
1160 0.0064279775 5.5277318e-08 3039.7037
|
||||
1170 0.0064285264 5.4423582e-08 3039.9556
|
||||
1180 0.006429067 5.3648672e-08 3040.2036
|
||||
1190 0.0064296003 5.294717e-08 3040.4482
|
||||
1200 0.0064301269 5.2314351e-08 3040.6897
|
||||
1210 0.0064306474 5.1746091e-08 3040.9283
|
||||
1220 0.0064311625 5.1238802e-08 3041.1644
|
||||
1230 0.0064316729 5.0789368e-08 3041.3983
|
||||
1240 0.0064321789 5.0395101e-08 3041.6301
|
||||
1250 0.0064326813 5.0053692e-08 3041.8603
|
||||
1260 0.0064331805 4.9763183e-08 3042.0889
|
||||
1270 0.006433677 4.9521937e-08 3042.3163
|
||||
1280 0.0064341713 4.9328614e-08 3042.5427
|
||||
1290 0.0064346639 4.9182151e-08 3042.7682
|
||||
1300 0.0064351552 4.9081752e-08 3042.9931
|
||||
1310 0.0064356458 4.9026872e-08 3043.2177
|
||||
1320 0.006436136 4.9017214e-08 3043.4421
|
||||
1330 0.0064366262 4.9052721e-08 3043.6666
|
||||
1340 0.0064371171 4.9133581e-08 3043.8912
|
||||
1350 0.006437609 4.9260223e-08 3044.1164
|
||||
1360 0.0064381023 4.9433327e-08 3044.3422
|
||||
1370 0.0064385976 4.9653831e-08 3044.569
|
||||
1380 0.0064390953 4.9922944e-08 3044.7968
|
||||
1390 0.0064395959 5.0242164e-08 3045.0261
|
||||
1400 0.0064401 5.0613297e-08 3045.2568
|
||||
1410 0.006440608 5.1038483e-08 3045.4895
|
||||
1420 0.0064411205 5.1520228e-08 3045.7242
|
||||
1430 0.0064416381 5.2061443e-08 3045.9613
|
||||
1440 0.0064421614 5.2665486e-08 3046.201
|
||||
1450 0.006442691 5.3336219e-08 3046.4437
|
||||
1460 0.0064432276 5.4078074e-08 3046.6896
|
||||
1470 0.006443772 5.4896126e-08 3046.9392
|
||||
1480 0.0064443249 5.5796191e-08 3047.1927
|
||||
1490 0.0064448873 5.6784937e-08 3047.4506
|
||||
1500 0.0064454599 5.7870017e-08 3047.7132
|
||||
1510 0.0064460439 5.9060235e-08 3047.9812
|
||||
1520 0.0064466403 6.0365742e-08 3048.2549
|
||||
1530 0.0064472503 6.1798287e-08 3048.5349
|
||||
1540 0.0064478752 6.337151e-08 3048.822
|
||||
1550 0.0064485166 6.5101323e-08 3049.1166
|
||||
1560 0.006449176 6.7006371e-08 3049.4197
|
||||
1570 0.0064498554 6.9108623e-08 3049.732
|
||||
1580 0.0064505567 7.1434118e-08 3050.0546
|
||||
1590 0.0064512824 7.4013931e-08 3050.3885
|
||||
1600 0.0064520352 7.6885409e-08 3050.7351
|
||||
1610 0.0064528182 8.0093813e-08 3051.0957
|
||||
1620 0.006453635 8.3694486e-08 3051.472
|
||||
1630 0.0064544898 8.7755778e-08 3051.8661
|
||||
1640 0.0064553876 9.2363047e-08 3052.2802
|
||||
1650 0.0064563343 9.7624226e-08 3052.7171
|
||||
1660 0.0064573371 1.0367771e-07 3053.1801
|
||||
1670 0.0064584046 1.1070379e-07 3053.6733
|
||||
1680 0.0064595476 1.1894157e-07 3054.2017
|
||||
1690 0.0064607796 1.2871484e-07 3054.7716
|
||||
1700 0.0064621178 1.4047265e-07 3055.391
|
||||
1710 0.0064635847 1.5485559e-07 3056.0705
|
||||
1720 0.0064652106 1.7280864e-07 3056.8241
|
||||
1730 0.0064670371 1.9578361e-07 3057.6713
|
||||
1740 0.0064691241 2.261258e-07 3058.6401
|
||||
1750 0.0064715615 2.6787347e-07 3059.7724
|
||||
1760 0.0064744931 3.2858822e-07 3061.1353
|
||||
1770 0.0064781697 4.2416554e-07 3062.8461
|
||||
1780 0.0064830857 5.9426003e-07 3065.1356
|
||||
1790 0.0064904338 9.7042692e-07 3068.5608
|
||||
1800 0.006504521 2.3570057e-06 3075.1339
|
||||
1810 0.0066489551 2.5350137e-05 3142.596
|
||||
1820 0.0067263358 2.0982567e-06 3178.7218
|
||||
1830 0.0067413263 1.0389873e-06 3185.7117
|
||||
1840 0.0067499639 7.021379e-07 3189.736
|
||||
1850 0.0067561793 5.4125252e-07 3192.6298
|
||||
1860 0.00676114 4.4920623e-07 3194.938
|
||||
1870 0.0067653505 3.911598e-07 3196.8961
|
||||
1880 0.0067690759 3.5254253e-07 3198.6279
|
||||
1890 0.0067724748 3.2626983e-07 3200.2074
|
||||
1900 0.0067756518 3.0855768e-07 3201.6834
|
||||
1910 0.0067786819 2.9728199e-07 3203.0908
|
||||
1920 0.0067816236 2.9125633e-07 3204.457
|
||||
1930 0.0067845263 2.8989566e-07 3205.8049
|
||||
1940 0.0067874357 2.9306921e-07 3207.156
|
||||
1950 0.0067903982 3.0106889e-07 3208.5318
|
||||
1960 0.006793465 3.1467844e-07 3209.9563
|
||||
1970 0.0067966982 3.3537556e-07 3211.4583
|
||||
1980 0.0068001793 3.6577201e-07 3213.0759
|
||||
1990 0.0068040239 4.1056728e-07 3214.863
|
||||
2000 0.0068084116 4.7878365e-07 3216.9034
|
||||
2010 0.0068136505 5.897605e-07 3219.3409
|
||||
2020 0.0068203489 7.9292336e-07 3222.4591
|
||||
2030 0.0068300039 1.259738e-06 3226.9568
|
||||
2040 0.0068484332 3.1869606e-06 3235.5484
|
||||
2050 0.00704302 3.1308435e-05 3326.3332
|
||||
2060 0.0073582601 1.9393034e-05 3473.3099
|
||||
2070 0.0076291992 6.1118973e-06 3599.5265
|
||||
2080 0.0076591273 1.397136e-06 3613.4525
|
||||
2090 0.0076695786 7.5324795e-07 3618.31
|
||||
2100 0.0076758692 5.1095756e-07 3621.2308
|
||||
2110 0.0076803593 3.8613872e-07 3623.3137
|
||||
2120 0.0076838539 3.1077232e-07 3624.9334
|
||||
2130 0.0076867208 2.6065521e-07 3626.2611
|
||||
2140 0.0076891581 2.2509342e-07 3627.3889
|
||||
2150 0.007691284 1.9865679e-07 3628.372
|
||||
2160 0.0076931748 1.7830513e-07 3629.2457
|
||||
2170 0.0076948825 1.6220815e-07 3630.0343
|
||||
2180 0.0076964439 1.4920028e-07 3630.7548
|
||||
2190 0.0076978861 1.3850522e-07 3631.42
|
||||
2200 0.0076992297 1.2958672e-07 3632.0393
|
||||
2210 0.0077004907 1.2206289e-07 3632.6203
|
||||
2220 0.0077016817 1.1565477e-07 3633.1687
|
||||
2230 0.0077028128 1.1015407e-07 3633.6892
|
||||
2240 0.0077038924 1.0540234e-07 3634.1859
|
||||
2250 0.0077049274 1.0127711e-07 3634.6618
|
||||
2260 0.0077059236 9.7682361e-08 3635.1197
|
||||
2270 0.0077068859 9.454193e-08 3635.5619
|
||||
2280 0.0077078187 9.1794781e-08 3635.9903
|
||||
2290 0.0077087255 8.9391579e-08 3636.4067
|
||||
2300 0.0077096098 8.7292175e-08 3636.8125
|
||||
2310 0.0077104742 8.5463727e-08 3637.2092
|
||||
2320 0.0077113216 8.3879281e-08 3637.598
|
||||
2330 0.007712154 8.2516693e-08 3637.9798
|
||||
2340 0.0077129738 8.1357804e-08 3638.3557
|
||||
2350 0.0077137829 8.0387796e-08 3638.7267
|
||||
2360 0.0077145831 7.9594705e-08 3639.0935
|
||||
2370 0.0077153761 7.8969036e-08 3639.457
|
||||
2380 0.0077161635 7.8503481e-08 3639.8178
|
||||
2390 0.007716947 7.8192701e-08 3640.1769
|
||||
2400 0.0077177281 7.8033171e-08 3640.5348
|
||||
2410 0.0077185083 7.8023089e-08 3640.8923
|
||||
2420 0.007719289 7.8162318e-08 3641.25
|
||||
2430 0.0077200718 7.8452384e-08 3641.6087
|
||||
2440 0.0077208582 7.8896522e-08 3641.9691
|
||||
2450 0.0077216498 7.9499759e-08 3642.3318
|
||||
2460 0.0077224481 8.026906e-08 3642.6977
|
||||
2470 0.0077232549 8.1213529e-08 3643.0675
|
||||
2480 0.0077240719 8.2344683e-08 3643.442
|
||||
2490 0.0077249012 8.3676812e-08 3643.8222
|
||||
2500 0.0077257448 8.5227445e-08 3644.209
|
||||
2510 0.0077266049 8.7017961e-08 3644.6035
|
||||
2520 0.0077274841 8.9074372e-08 3645.0068
|
||||
2530 0.0077283852 9.1428349e-08 3645.4203
|
||||
2540 0.0077293113 9.4118559e-08 3645.8454
|
||||
2550 0.0077302659 9.7192441e-08 3646.2837
|
||||
2560 0.0077312533 1.0070857e-07 3646.7372
|
||||
2570 0.0077322781 1.0473987e-07 3647.208
|
||||
2580 0.0077333458 1.0937801e-07 3647.6987
|
||||
2590 0.007734463 1.1473957e-07 3648.2124
|
||||
2600 0.0077356377 1.2097481e-07 3648.7528
|
||||
2610 0.0077368793 1.2828037e-07 3649.3242
|
||||
2620 0.0077381998 1.3691837e-07 3649.9322
|
||||
2630 0.0077396139 1.4724543e-07 3650.5836
|
||||
2640 0.0077411406 1.5975888e-07 3651.2873
|
||||
2650 0.0077428048 1.7517253e-07 3652.0548
|
||||
2660 0.0077446398 1.9454711e-07 3652.9016
|
||||
2670 0.0077466922 2.1952673e-07 3653.8493
|
||||
2680 0.0077490288 2.5279733e-07 3654.929
|
||||
2690 0.0077517515 2.9905194e-07 3656.188
|
||||
2700 0.0077550252 3.6725589e-07 3657.7029
|
||||
2710 0.0077591434 4.7681009e-07 3659.6101
|
||||
2720 0.0077647038 6.7839241e-07 3662.1874
|
||||
2730 0.007773234 1.1552111e-06 3666.1446
|
||||
2740 0.0077911374 3.3406902e-06 3674.458
|
||||
2750 0.0079702 8.4184292e-06 3757.6696
|
||||
2760 0.008006114 1.4496754e-06 3774.3449
|
||||
2770 0.0080166835 7.3926386e-07 3779.2462
|
||||
2780 0.0080227734 4.8640717e-07 3782.0672
|
||||
2790 0.0080270055 3.5945058e-07 3784.0255
|
||||
2800 0.0080302318 2.8394384e-07 3785.517
|
||||
2810 0.008032832 2.3422206e-07 3786.7179
|
||||
2820 0.0080350072 1.9916814e-07 3787.7215
|
||||
2830 0.0080368761 1.7321525e-07 3788.5831
|
||||
2840 0.0080385144 1.5327931e-07 3789.3377
|
||||
2850 0.0080399734 1.3751893e-07 3790.0091
|
||||
2860 0.0080412891 1.2476931e-07 3790.6141
|
||||
2870 0.0080424879 1.1425897e-07 3791.1649
|
||||
2880 0.0080435897 1.0545738e-07 3791.6707
|
||||
2890 0.0080446097 9.7988142e-08 3792.1386
|
||||
2900 0.0080455599 9.1577084e-08 3792.5741
|
||||
2910 0.00804645 8.6019912e-08 3792.9818
|
||||
2920 0.0080472879 8.1161402e-08 3793.3653
|
||||
2930 0.0080480798 7.6881575e-08 3793.7275
|
||||
2940 0.0080488311 7.3086284e-08 3794.0709
|
||||
2950 0.0080495465 6.9700651e-08 3794.3977
|
||||
2960 0.0080502295 6.666441e-08 3794.7094
|
||||
2970 0.0080508836 6.3928523e-08 3795.0078
|
||||
2980 0.0080515116 6.1452701e-08 3795.2941
|
||||
2990 0.0080521158 5.9203545e-08 3795.5694
|
||||
3000 0.0080526985 5.7153146e-08 3795.8346
|
||||
3010 0.0080532614 5.5278009e-08 3796.0908
|
||||
3020 0.0080538063 5.3558217e-08 3796.3386
|
||||
3030 0.0080543347 5.1976785e-08 3796.5788
|
||||
3040 0.0080548478 5.051914e-08 3796.8119
|
||||
3050 0.0080553469 4.9172716e-08 3797.0385
|
||||
3060 0.0080558329 4.7926619e-08 3797.2591
|
||||
3070 0.0080563069 4.6771366e-08 3797.4741
|
||||
3080 0.0080567697 4.5698662e-08 3797.6839
|
||||
3090 0.0080572222 4.4701228e-08 3797.8889
|
||||
3100 0.0080576649 4.3772647e-08 3798.0895
|
||||
3110 0.0080580987 4.2907247e-08 3798.2858
|
||||
3120 0.0080585241 4.2099999e-08 3798.4784
|
||||
3130 0.0080589417 4.1346425e-08 3798.6672
|
||||
3140 0.0080593519 4.0642535e-08 3798.8527
|
||||
3150 0.0080597554 3.9984758e-08 3799.0351
|
||||
3160 0.0080601524 3.9369895e-08 3799.2145
|
||||
3170 0.0080605435 3.8795073e-08 3799.3911
|
||||
3180 0.008060929 3.8257705e-08 3799.5651
|
||||
3190 0.0080613093 3.7755461e-08 3799.7368
|
||||
3200 0.0080616847 3.7286239e-08 3799.9062
|
||||
3210 0.0080620556 3.6848135e-08 3800.0734
|
||||
3220 0.0080624222 3.6439432e-08 3800.2387
|
||||
3230 0.0080627848 3.6058573e-08 3800.4022
|
||||
3240 0.0080631438 3.5704146e-08 3800.564
|
||||
3250 0.0080634994 3.5374876e-08 3800.7241
|
||||
3260 0.0080638517 3.5069606e-08 3800.8828
|
||||
3270 0.0080642011 3.4787289e-08 3801.0402
|
||||
3280 0.0080645478 3.4526978e-08 3801.1962
|
||||
3290 0.008064892 3.4287819e-08 3801.3511
|
||||
3300 0.0080652339 3.4069042e-08 3801.505
|
||||
3310 0.0080655736 3.3869955e-08 3801.6578
|
||||
3320 0.0080659115 3.368994e-08 3801.8098
|
||||
3330 0.0080662477 3.3528444e-08 3801.961
|
||||
3340 0.0080665823 3.3384981e-08 3802.1115
|
||||
3350 0.0080669156 3.3259123e-08 3802.2613
|
||||
3360 0.0080672476 3.3150499e-08 3802.4106
|
||||
3370 0.0080675787 3.305879e-08 3802.5594
|
||||
3380 0.008067909 3.2983732e-08 3802.7078
|
||||
3390 0.0080682385 3.2925108e-08 3802.8559
|
||||
3400 0.0080685676 3.288275e-08 3803.0038
|
||||
3410 0.0080688963 3.2856537e-08 3803.1515
|
||||
3420 0.0080692248 3.2846395e-08 3803.2991
|
||||
3430 0.0080695532 3.2852293e-08 3803.4466
|
||||
3440 0.0080698819 3.2874247e-08 3803.5943
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||||
3450 0.0080702108 3.2912319e-08 3803.742
|
||||
3460 0.0080705401 3.2966617e-08 3803.89
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||||
3470 0.0080708701 3.3037293e-08 3804.0382
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||||
3480 0.0080712008 3.312455e-08 3804.1868
|
||||
3490 0.0080715325 3.3228638e-08 3804.3358
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||||
3500 0.0080718653 3.3349858e-08 3804.4853
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||||
3510 0.0080721995 3.3488567e-08 3804.6355
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||||
3520 0.008072535 3.3645172e-08 3804.7862
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3530 0.0080728723 3.3820145e-08 3804.9378
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||||
3540 0.0080732113 3.4014016e-08 3805.0901
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||||
3550 0.0080735524 3.4227383e-08 3805.2434
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||||
3560 0.0080738957 3.4460914e-08 3805.3977
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||||
3570 0.0080742414 3.4715354e-08 3805.5532
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||||
3580 0.0080745898 3.4991532e-08 3805.7098
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||||
3590 0.0080749411 3.5290364e-08 3805.8677
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||||
3600 0.0080752954 3.5612865e-08 3806.0271
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||||
3610 0.0080756531 3.5960156e-08 3806.188
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||||
3620 0.0080760143 3.6333475e-08 3806.3505
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3630 0.0080763794 3.6734187e-08 3806.5148
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3640 0.0080767487 3.7163802e-08 3806.681
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3650 0.0080771224 3.7623985e-08 3806.8492
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3660 0.0080775008 3.8116577e-08 3807.0196
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||||
3670 0.0080778843 3.8643614e-08 3807.1924
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3680 0.0080782733 3.9207349e-08 3807.3676
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3690 0.008078668 3.9810283e-08 3807.5455
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3700 0.008079069 4.0455191e-08 3807.7262
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3710 0.0080794766 4.114516e-08 3807.91
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3720 0.0080798913 4.1883634e-08 3808.0971
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3730 0.0080803137 4.2674459e-08 3808.2877
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3740 0.0080807442 4.3521941e-08 3808.482
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3750 0.0080811834 4.4430917e-08 3808.6803
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3760 0.0080816321 4.5406834e-08 3808.883
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3770 0.0080820908 4.6455843e-08 3809.0902
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3780 0.0080825604 4.7584918e-08 3809.3025
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3790 0.0080830416 4.8801987e-08 3809.5201
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3800 0.0080835355 5.0116105e-08 3809.7436
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3810 0.0080840429 5.1537653e-08 3809.9733
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3820 0.0080845652 5.3078583e-08 3810.2097
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3830 0.0080851034 5.4752728e-08 3810.4535
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3840 0.008085659 5.6576175e-08 3810.7054
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3850 0.0080862335 5.8567743e-08 3810.9659
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3860 0.0080868289 6.0749572e-08 3811.236
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3870 0.008087447 6.3147889e-08 3811.5166
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3880 0.0080880901 6.5793981e-08 3811.8087
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3890 0.008088761 6.8725458e-08 3812.1136
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3900 0.0080894626 7.1987928e-08 3812.4327
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3910 0.0080901986 7.5637206e-08 3812.7675
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3920 0.008090973 7.9742316e-08 3813.1201
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3930 0.0080917909 8.4389592e-08 3813.4926
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3940 0.008092658 8.9688414e-08 3813.8879
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3950 0.0080935816 9.5779352e-08 3814.3091
|
||||
3960 0.0080945703 1.0284601e-07 3814.7604
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||||
3970 0.0080956349 1.1113264e-07 3815.2467
|
||||
3980 0.0080967891 1.2097115e-07 3815.7742
|
||||
3990 0.0080980502 1.3282379e-07 3816.3511
|
||||
4000 0.0080994413 1.4735308e-07 3816.9878
|
||||
4010 0.0081009931 1.6554202e-07 3817.6987
|
||||
4020 0.0081027486 1.8891116e-07 3818.5035
|
||||
4030 0.0081047696 2.1993774e-07 3819.4308
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4040 0.0081071501 2.6293325e-07 3820.524
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4050 0.0081100418 3.2608623e-07 3821.8531
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4060 0.0081137136 4.2695471e-07 3823.5422
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||||
4070 0.0081187073 6.1068659e-07 3825.8415
|
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4080 0.0081263808 1.0353843e-06 3829.3781
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4090 0.0081421033 2.8175459e-06 3836.6316
|
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4100 0.0083319479 3.0660994e-05 3924.296
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4110 0.0086521081 2.4031675e-05 4072.0381
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4120 0.0089367803 5.8263834e-06 4203.2922
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4130 0.0089679114 1.6262217e-06 4217.6293
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|
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4450 0.013251276 2.6649019e-06 6179.5172
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4460 0.013269544 1.2200106e-06 6187.8251
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4470 0.013279619 8.155501e-07 6192.4028
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4480 0.013286853 6.3300974e-07 6195.6879
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4490 0.01329269 5.3347649e-07 6198.3373
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||||
4500 0.013297735 4.7451627e-07 6200.6261
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||||
4510 0.013302306 4.392029e-07 6202.6992
|
||||
4520 0.013306599 4.1982963e-07 6204.6461
|
||||
4530 0.013310757 4.1285331e-07 6206.5311
|
||||
4540 0.013314895 4.1710029e-07 6208.4074
|
||||
4550 0.013319128 4.3324769e-07 6210.3267
|
||||
4560 0.013323586 4.6410935e-07 6212.348
|
||||
4570 0.013328439 5.1597347e-07 6214.5493
|
||||
4580 0.01333395 6.0235495e-07 6217.0498
|
||||
4590 0.013340584 7.5537668e-07 6220.0613
|
||||
4600 0.013349342 1.0699582e-06 6224.0388
|
||||
4610 0.013363183 1.98365e-06 6230.3293
|
||||
4620 0.013404081 1.4367775e-05 6248.9319
|
||||
4630 0.013593325 3.787203e-06 6335.0239
|
||||
4640 0.01361833 1.6441528e-06 6346.3866
|
||||
4650 0.013632159 1.1592769e-06 6352.6667
|
||||
4660 0.013642828 9.8623051e-07 6357.5101
|
||||
4670 0.013652418 9.4451692e-07 6361.8626
|
||||
4680 0.013662041 1.0034733e-06 6366.2295
|
||||
4690 0.013672824 1.2061779e-06 6371.1243
|
||||
4700 0.013686941 1.780995e-06 6377.5343
|
||||
4710 0.013713088 4.7634009e-06 6389.4131
|
||||
4720 0.013968014 3.9765415e-05 6505.2802
|
||||
4730 0.014228787 6.2632217e-06 6623.7185
|
||||
4740 0.014278333 4.7934169e-06 6646.2018
|
||||
4750 0.014382212 5.1069055e-05 6693.3424
|
||||
4760 0.014525205 2.0381123e-06 6758.2178
|
||||
4770 0.014538504 8.2250651e-07 6764.2412
|
||||
4780 0.014544984 4.9114353e-07 6767.1723
|
||||
4790 0.014549144 3.4212232e-07 6769.0518
|
||||
4800 0.014552156 2.589287e-07 6770.4109
|
||||
4810 0.014554491 2.0641662e-07 6771.4633
|
||||
4820 0.014556384 1.7052382e-07 6772.315
|
||||
4830 0.014557966 1.4457875e-07 6773.0262
|
||||
4840 0.014559319 1.250293e-07 6773.6339
|
||||
4850 0.014560498 1.09819e-07 6774.1626
|
||||
4860 0.014561539 9.7678962e-08 6774.629
|
||||
4870 0.01456247 8.7785899e-08 6775.0453
|
||||
4880 0.01456331 7.9583482e-08 6775.4205
|
||||
4890 0.014564074 7.2682934e-08 6775.7613
|
||||
4900 0.014564773 6.6804784e-08 6776.0732
|
||||
4910 0.014565418 6.1743238e-08 6776.3601
|
||||
4920 0.014566015 5.7343571e-08 6776.6256
|
||||
4930 0.014566571 5.3487327e-08 6776.8723
|
||||
4940 0.01456709 5.0082359e-08 6777.1026
|
||||
4950 0.014567577 4.7055963e-08 6777.3183
|
||||
4960 0.014568035 4.4350048e-08 6777.521
|
||||
4970 0.014568467 4.1917669e-08 6777.712
|
||||
4980 0.014568876 3.9720495e-08 6777.8926
|
||||
4990 0.014569265 3.7726941e-08 6778.0636
|
||||
5000 0.014569634 3.5910753e-08 6778.2261
|
||||
Loop time of 24.155 on 1 procs for 5000 steps with 32000 atoms
|
||||
|
||||
Performance: 0.001 ns/day, 37368.951 hours/ns, 206.996 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 15.795 | 15.795 | 15.795 | 0.0 | 65.39
|
||||
Neigh | 1.5182 | 1.5182 | 1.5182 | 0.0 | 6.29
|
||||
Comm | 0.58555 | 0.58555 | 0.58555 | 0.0 | 2.42
|
||||
Output | 0.0064323 | 0.0064323 | 0.0064323 | 0.0 | 0.03
|
||||
Modify | 5.619 | 5.619 | 5.619 | 0.0 | 23.26
|
||||
Other | | 0.6313 | | | 2.61
|
||||
|
||||
Nlocal: 32000 ave 32000 max 32000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 13556 ave 13556 max 13556 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: 576016 ave 576016 max 576016 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 576016
|
||||
Ave neighs/atom = 18.0005
|
||||
Neighbor list builds = 68
|
||||
Dangerous builds = 42
|
||||
Total wall time: 0:00:24
|
||||
597
examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.4
Normal file
597
examples/USER/misc/electron_stopping/log.20Mar19.elstop.g++.4
Normal file
@ -0,0 +1,597 @@
|
||||
LAMMPS (28 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Test case / example for fix electron/stopping
|
||||
# Perfect Si lattice with one primary knock-on atom.
|
||||
#
|
||||
# Also uses fix dt/reset, as one should when energies are high
|
||||
# enough to require electronic stopping.
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
timestep 0.0001
|
||||
|
||||
lattice fcc 5.431
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region rbox block -10 10 -10 10 -10 10
|
||||
create_box 1 rbox
|
||||
Created orthogonal box = (-54.31 -54.31 -54.31) to (54.31 54.31 54.31)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
mass 1 28.0855
|
||||
|
||||
create_atoms 1 box
|
||||
Created 32000 atoms
|
||||
create_atoms CPU = 0.000856161 secs
|
||||
|
||||
velocity all create 300 42534 mom yes rot yes
|
||||
|
||||
group gPKA id 1
|
||||
1 atoms in group gPKA
|
||||
velocity gPKA set 1120 1620 389
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
Reading potential file Si.sw with DATE: 2007-06-11
|
||||
|
||||
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
|
||||
fix fel all electron/stopping 1.0 Si.Si.elstop
|
||||
fix fnve all nve
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time dt f_fel
|
||||
|
||||
#compute ek all ke/atom
|
||||
#dump mydump all custom 200 elstop.dump id x y z vx vy vz fx fy fz c_ek
|
||||
|
||||
run 5000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5.77118
|
||||
ghost atom cutoff = 5.77118
|
||||
binsize = 2.88559, bins = 38 38 38
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair sw, perpetual
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) fix electron/stopping, occasional, copy from (1)
|
||||
attributes: full, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.825 | 3.825 | 3.825 Mbytes
|
||||
Step Time Dt f_fel
|
||||
0 0 4.98128e-05 0
|
||||
10 0.00030141235 7.4131221e-06 143.83474
|
||||
20 0.00035951242 6.0314282e-06 171.53584
|
||||
30 0.00057457861 3.511731e-05 274.07067
|
||||
40 0.00086591115 5.8248574e-06 412.87352
|
||||
50 0.00090045749 2.102773e-06 429.31482
|
||||
60 0.00091828633 1.5369556e-06 437.79502
|
||||
70 0.00093306208 1.4645168e-06 444.82135
|
||||
80 0.00094861336 1.7491631e-06 452.21657
|
||||
90 0.00097033523 3.0804023e-06 462.54893
|
||||
100 0.0010792154 4.9075683e-05 514.37014
|
||||
110 0.0012080866 2.3201427e-06 575.68827
|
||||
120 0.0012239719 1.0507964e-06 583.23648
|
||||
130 0.0012325518 6.8263389e-07 587.30975
|
||||
140 0.0012385211 5.1201217e-07 590.14147
|
||||
150 0.0012431661 4.1521773e-07 592.34347
|
||||
160 0.001247021 3.5379338e-07 594.16984
|
||||
170 0.0012503586 3.1202939e-07 595.75031
|
||||
180 0.0012533374 2.8236002e-07 597.16021
|
||||
190 0.0012560582 2.6071816e-07 598.44745
|
||||
200 0.0012585895 2.4474279e-07 599.64465
|
||||
210 0.001260981 2.3298831e-07 600.7754
|
||||
220 0.0012632704 2.2454021e-07 601.85763
|
||||
230 0.001265488 2.1881458e-07 602.90571
|
||||
240 0.0012676591 2.154488e-07 603.93173
|
||||
250 0.0012698064 2.1424147e-07 604.94641
|
||||
260 0.0012719511 2.1512161e-07 605.9598
|
||||
270 0.0012741141 2.1813836e-07 606.98189
|
||||
280 0.0012763174 2.2346783e-07 608.02314
|
||||
290 0.0012785856 2.3143942e-07 609.09518
|
||||
300 0.0012809473 2.4258888e-07 610.2116
|
||||
310 0.0012834376 2.5775518e-07 611.38916
|
||||
320 0.0012861023 2.7825685e-07 612.64953
|
||||
330 0.0012890034 3.062254e-07 614.02218
|
||||
340 0.0012922301 3.4527805e-07 615.54956
|
||||
350 0.0012959196 4.0200263e-07 617.29679
|
||||
360 0.0013003 4.8966484e-07 619.37233
|
||||
370 0.0013057965 6.3923294e-07 621.9783
|
||||
380 0.00131335 9.423535e-07 625.56194
|
||||
390 0.0013258073 1.8277087e-06 631.47661
|
||||
400 0.0013653313 1.4985239e-05 650.25939
|
||||
410 0.0016927117 4.5643592e-05 805.84388
|
||||
420 0.002085671 2.5698185e-05 992.40957
|
||||
430 0.0021935861 5.3102217e-06 1043.597
|
||||
440 0.0022614637 1.5788858e-05 1075.7807
|
||||
450 0.0025463923 1.6989456e-05 1210.8535
|
||||
460 0.0029095455 3.9205279e-05 1382.8591
|
||||
470 0.003309122 3.8882183e-05 1571.9128
|
||||
480 0.0037129772 4.0573389e-05 1762.7749
|
||||
490 0.004120209 2.7525742e-05 1955.0148
|
||||
500 0.0042711049 1.9373612e-05 2026.1805
|
||||
510 0.0045860203 2.4773305e-05 2174.6208
|
||||
520 0.004995259 3.8017877e-05 2367.3335
|
||||
530 0.0051457762 5.4205615e-06 2438.1475
|
||||
540 0.005203221 8.8625579e-06 2465.1577
|
||||
550 0.0054221421 5.7304442e-06 2568.0888
|
||||
560 0.0054524345 1.5599386e-06 2582.3169
|
||||
570 0.0054645073 9.1093243e-07 2587.9819
|
||||
580 0.0054723338 6.6033575e-07 2591.6518
|
||||
590 0.0054782965 5.3155858e-07 2594.446
|
||||
600 0.005483241 4.5581839e-07 2596.7619
|
||||
610 0.0054875675 4.0821885e-07 2598.7875
|
||||
620 0.0054915013 3.7775507e-07 2600.6287
|
||||
630 0.0054951861 3.5898561e-07 2602.3529
|
||||
640 0.0054987249 3.4911444e-07 2604.0086
|
||||
650 0.0055021998 3.4682698e-07 2605.6342
|
||||
660 0.0055056844 3.5182676e-07 2607.2643
|
||||
670 0.0055092538 3.6473743e-07 2608.9342
|
||||
680 0.0055129936 3.8730595e-07 2610.6841
|
||||
690 0.0055170145 4.2303997e-07 2612.566
|
||||
700 0.0055214749 4.7876507e-07 2614.6542
|
||||
710 0.0055266296 5.6863699e-07 2617.0684
|
||||
720 0.0055329452 7.2626141e-07 2620.0278
|
||||
730 0.0055414528 1.0527596e-06 2624.0166
|
||||
740 0.0055553208 2.0371511e-06 2630.523
|
||||
750 0.0056023478 2.2133456e-05 2652.6057
|
||||
760 0.0059007346 3.8610962e-05 2792.7168
|
||||
770 0.0062508505 3.9428337e-05 2956.9697
|
||||
780 0.0063682296 2.1223153e-06 3011.9927
|
||||
790 0.0063824196 9.0656948e-07 3018.6346
|
||||
800 0.0063896741 5.6137676e-07 3022.0266
|
||||
810 0.0063944906 4.0276465e-07 3024.2763
|
||||
820 0.0063980771 3.1284015e-07 3025.9499
|
||||
830 0.0064009279 2.5537602e-07 3027.2789
|
||||
840 0.006403292 2.1569057e-07 3028.3801
|
||||
850 0.0064053117 1.8674792e-07 3029.32
|
||||
860 0.0064070756 1.6477015e-07 3030.1402
|
||||
870 0.0064086425 1.4755386e-07 3030.8682
|
||||
880 0.0064100535 1.3373048e-07 3031.5232
|
||||
890 0.0064113381 1.2240666e-07 3032.1191
|
||||
900 0.0064125183 1.1297538e-07 3032.6662
|
||||
910 0.0064136112 1.0501022e-07 3033.1724
|
||||
920 0.0064146298 9.8203162e-08 3033.6439
|
||||
930 0.0064155847 9.2326368e-08 3034.0856
|
||||
940 0.0064164843 8.7207794e-08 3034.5015
|
||||
950 0.0064173357 8.2715188e-08 3034.8948
|
||||
960 0.0064181446 7.8745279e-08 3035.2682
|
||||
970 0.0064189159 7.5216291e-08 3035.6241
|
||||
980 0.0064196535 7.2062662e-08 3035.9642
|
||||
990 0.0064203612 6.9231241e-08 3036.2903
|
||||
1000 0.0064210418 6.6678502e-08 3036.6038
|
||||
1010 0.006421698 6.4368478e-08 3036.9059
|
||||
1020 0.0064223321 6.2271202e-08 3037.1976
|
||||
1030 0.0064229461 6.0361517e-08 3037.4799
|
||||
1040 0.0064235417 5.8618162e-08 3037.7537
|
||||
1050 0.0064241206 5.702305e-08 3038.0197
|
||||
1060 0.0064246841 5.556071e-08 3038.2784
|
||||
1070 0.0064252336 5.4217838e-08 3038.5306
|
||||
1080 0.0064257701 5.2982939e-08 3038.7768
|
||||
1090 0.0064262948 5.1846034e-08 3039.0174
|
||||
1100 0.0064268085 5.079843e-08 3039.2529
|
||||
1110 0.006427312 4.9832523e-08 3039.4837
|
||||
1120 0.0064278063 4.8941643e-08 3039.7101
|
||||
1130 0.0064282919 4.811992e-08 3039.9325
|
||||
1140 0.0064287697 4.7362175e-08 3040.1512
|
||||
1150 0.0064292401 4.6663831e-08 3040.3665
|
||||
1160 0.0064297038 4.6020833e-08 3040.5786
|
||||
1170 0.0064301613 4.5429586e-08 3040.7878
|
||||
1180 0.0064306131 4.4886899e-08 3040.9944
|
||||
1190 0.0064310597 4.4389937e-08 3041.1986
|
||||
1200 0.0064315016 4.3936183e-08 3041.4005
|
||||
1210 0.006431939 4.3523406e-08 3041.6003
|
||||
1220 0.0064323725 4.3149628e-08 3041.7984
|
||||
1230 0.0064328025 4.2813101e-08 3041.9947
|
||||
1240 0.0064332292 4.2512286e-08 3042.1896
|
||||
1250 0.0064336531 4.2245836e-08 3042.3831
|
||||
1260 0.0064340745 4.201258e-08 3042.5755
|
||||
1270 0.0064344937 4.1811507e-08 3042.7668
|
||||
1280 0.006434911 4.1641759e-08 3042.9572
|
||||
1290 0.0064353268 4.1502622e-08 3043.1469
|
||||
1300 0.0064357413 4.1393513e-08 3043.336
|
||||
1310 0.0064361549 4.1313982e-08 3043.5247
|
||||
1320 0.0064365678 4.1263699e-08 3043.713
|
||||
1330 0.0064369803 4.1242458e-08 3043.9012
|
||||
1340 0.0064373927 4.125017e-08 3044.0893
|
||||
1350 0.0064378054 4.1286866e-08 3044.2775
|
||||
1360 0.0064382185 4.1352691e-08 3044.466
|
||||
1370 0.0064386324 4.1447915e-08 3044.6548
|
||||
1380 0.0064390475 4.1572925e-08 3044.8441
|
||||
1390 0.0064394639 4.1728238e-08 3045.034
|
||||
1400 0.0064398819 4.1914501e-08 3045.2247
|
||||
1410 0.006440302 4.2132499e-08 3045.4163
|
||||
1420 0.0064407245 4.2383163e-08 3045.6091
|
||||
1430 0.0064411496 4.2667584e-08 3045.803
|
||||
1440 0.0064415776 4.2987016e-08 3045.9983
|
||||
1450 0.0064420091 4.33429e-08 3046.1952
|
||||
1460 0.0064424443 4.3736874e-08 3046.3938
|
||||
1470 0.0064428835 4.4170794e-08 3046.5944
|
||||
1480 0.0064433274 4.4646761e-08 3046.797
|
||||
1490 0.0064437761 4.5167139e-08 3047.0019
|
||||
1500 0.0064442303 4.5734596e-08 3047.2093
|
||||
1510 0.0064446904 4.6352132e-08 3047.4195
|
||||
1520 0.0064451569 4.7023127e-08 3047.6327
|
||||
1530 0.0064456303 4.7751389e-08 3047.849
|
||||
1540 0.0064461114 4.8541214e-08 3048.0689
|
||||
1550 0.0064466006 4.9397455e-08 3048.2926
|
||||
1560 0.0064470987 5.0325606e-08 3048.5204
|
||||
1570 0.0064476064 5.1331902e-08 3048.7527
|
||||
1580 0.0064481245 5.2423434e-08 3048.9899
|
||||
1590 0.006448654 5.3608296e-08 3049.2323
|
||||
1600 0.0064491958 5.4895757e-08 3049.4804
|
||||
1610 0.006449751 5.6296469e-08 3049.7347
|
||||
1620 0.0064503207 5.7822727e-08 3049.9959
|
||||
1630 0.0064509063 5.9488788e-08 3050.2644
|
||||
1640 0.0064515092 6.1311263e-08 3050.5409
|
||||
1650 0.0064521312 6.3309616e-08 3050.8263
|
||||
1660 0.006452774 6.5506785e-08 3051.1214
|
||||
1670 0.0064534398 6.7929981e-08 3051.4272
|
||||
1680 0.0064541309 7.0611714e-08 3051.7448
|
||||
1690 0.0064548502 7.3591127e-08 3052.0755
|
||||
1700 0.0064556007 7.6915753e-08 3052.4207
|
||||
1710 0.0064563863 8.064386e-08 3052.7823
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||||
1720 0.0064572113 8.4847627e-08 3053.1621
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1730 0.0064580807 8.9617502e-08 3053.5627
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||||
1740 0.0064590008 9.5068304e-08 3053.9869
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||||
1750 0.006459979 1.0134793e-07 3054.4381
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||||
1760 0.0064610244 1.0865003e-07 3054.9206
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||||
1770 0.0064621483 1.1723301e-07 3055.4397
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||||
1780 0.0064633651 1.2744917e-07 3056.0021
|
||||
1790 0.0064646931 1.3979108e-07 3056.6163
|
||||
1800 0.0064661566 1.5496815e-07 3057.2937
|
||||
1810 0.0064677883 1.7403894e-07 3058.0494
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||||
1820 0.006469634 1.9865267e-07 3058.9049
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1830 0.0064717601 2.3152064e-07 3059.8912
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1840 0.0064742682 2.7741818e-07 3061.0556
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||||
1850 0.0064773249 3.4556351e-07 3062.4759
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||||
1860 0.0064812294 4.5619653e-07 3064.2917
|
||||
1870 0.0064866019 6.6337441e-07 3066.7924
|
||||
1880 0.0064950748 1.1706786e-06 3070.7399
|
||||
1890 0.0065140322 3.7878566e-06 3079.5809
|
||||
1900 0.0066957122 6.7105464e-06 3164.3691
|
||||
1910 0.0067279909 1.493224e-06 3179.4195
|
||||
1920 0.0067392058 8.1410321e-07 3184.6428
|
||||
1930 0.0067460435 5.5996376e-07 3187.8246
|
||||
1940 0.0067509948 4.2936252e-07 3190.1267
|
||||
1950 0.0067549055 3.5072462e-07 3191.9436
|
||||
1960 0.0067581623 2.9865016e-07 3193.4556
|
||||
1970 0.0067609737 2.6192794e-07 3194.7601
|
||||
1980 0.0067634648 2.3486813e-07 3195.9153
|
||||
1990 0.0067657165 2.1428715e-07 3196.9589
|
||||
2000 0.0067677841 1.9827071e-07 3197.9167
|
||||
2010 0.0067697074 1.8560268e-07 3198.8073
|
||||
2020 0.006771516 1.7547663e-07 3199.6445
|
||||
2030 0.0067732327 1.6733961e-07 3200.4388
|
||||
2040 0.0067748755 1.6080268e-07 3201.1987
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||||
2050 0.0067764591 1.5558723e-07 3201.931
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2060 0.0067779957 1.5149159e-07 3202.6414
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||||
2070 0.0067794958 1.4836976e-07 3203.3348
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2080 0.0067809687 1.4611749e-07 3204.0155
|
||||
2090 0.0067824227 1.4466322e-07 3204.6874
|
||||
2100 0.0067838655 1.4396229e-07 3205.3542
|
||||
2110 0.0067853047 1.4399348e-07 3206.0191
|
||||
2120 0.0067867474 1.4475745e-07 3206.6858
|
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2130 0.0067882012 1.4627671e-07 3207.3576
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2140 0.0067896737 1.4859736e-07 3208.0381
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2150 0.0067911733 1.5179256e-07 3208.7311
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2160 0.0067927092 1.5596849e-07 3209.4411
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2170 0.0067942917 1.6127347e-07 3210.1728
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||||
2180 0.0067959331 1.6791214e-07 3210.9319
|
||||
2190 0.0067976479 1.7616698e-07 3211.7251
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||||
2200 0.0067994539 1.8643208e-07 3212.5608
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||||
2210 0.0068013736 1.9926751e-07 3213.4494
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||||
2220 0.0068034361 2.154897e-07 3214.4044
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||||
2230 0.0068056803 2.3632937e-07 3215.4441
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||||
2240 0.0068081604 2.6372257e-07 3216.5937
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2250 0.0068109549 3.0088625e-07 3217.8897
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2260 0.0068141846 3.5356212e-07 3219.3884
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2270 0.0068180485 4.330391e-07 3221.1825
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2280 0.0068229109 5.6479966e-07 3223.4417
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2290 0.0068295488 8.2016289e-07 3226.5284
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||||
2300 0.0068401389 1.4950446e-06 3231.4568
|
||||
2310 0.0068668194 6.4794351e-06 3243.8847
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||||
2320 0.0071339944 2.3817631e-05 3368.3827
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||||
2330 0.0074221156 3.4144405e-05 3502.5364
|
||||
2340 0.007650075 3.3142879e-06 3608.5998
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||||
2350 0.0076703526 1.1927138e-06 3618.0215
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||||
2360 0.0076797526 7.185434e-07 3622.3847
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2370 0.0076859146 5.1648342e-07 3625.2424
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2380 0.0076905359 4.0623045e-07 3627.3839
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||||
2390 0.0076942651 3.3753265e-07 3629.1108
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2400 0.0076974175 2.910504e-07 3630.5697
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||||
2410 0.0077001699 2.5780894e-07 3631.8426
|
||||
2420 0.007702631 2.3309498e-07 3632.9803
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||||
2430 0.007704873 2.1420535e-07 3634.0161
|
||||
2440 0.0077069459 1.9948463e-07 3634.9733
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||||
2450 0.0077088862 1.8786685e-07 3635.869
|
||||
2460 0.0077107216 1.7863849e-07 3636.716
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||||
2470 0.0077124736 1.713078e-07 3637.5242
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||||
2480 0.0077141595 1.6552875e-07 3638.3017
|
||||
2490 0.0077157937 1.6105508e-07 3639.0552
|
||||
2500 0.0077173883 1.5771154e-07 3639.7903
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||||
2510 0.0077189541 1.553756e-07 3640.5121
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2520 0.0077205008 1.539658e-07 3641.2249
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2530 0.0077220373 1.534345e-07 3641.933
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2540 0.0077235724 1.5376384e-07 3642.6405
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||||
2550 0.0077251148 1.5496427e-07 3643.3513
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||||
2560 0.0077266731 1.5707538e-07 3644.0695
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||||
2570 0.007728257 1.6016917e-07 3644.7995
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2580 0.0077298765 1.6435633e-07 3645.5461
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2590 0.0077315435 1.6979645e-07 3646.3147
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2600 0.0077332712 1.7671412e-07 3647.1115
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2610 0.0077350759 1.8542415e-07 3647.944
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2620 0.0077369773 1.9637153e-07 3648.8214
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2630 0.0077390006 2.1019669e-07 3649.7553
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2640 0.0077411783 2.2784614e-07 3650.7609
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2650 0.0077435548 2.5076917e-07 3651.8588
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2660 0.0077461922 2.8128932e-07 3653.0779
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||||
2670 0.0077491826 3.233607e-07 3654.4608
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||||
2680 0.0077526703 3.8426634e-07 3656.0746
|
||||
2690 0.0077569014 4.7896536e-07 3658.0337
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||||
2700 0.0077623476 6.435095e-07 3660.5572
|
||||
2710 0.0077700972 9.9066415e-07 3664.1508
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||||
2720 0.0077837321 2.1192489e-06 3670.4787
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||||
2730 0.0078537309 5.0478452e-05 3702.9978
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2740 0.0080019842 2.234588e-06 3771.8639
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2750 0.0080167983 9.3912008e-07 3778.7349
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2760 0.0080243022 5.7998894e-07 3782.2116
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2770 0.0080292782 4.1619434e-07 3784.5147
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||||
2780 0.0080329859 3.2365852e-07 3786.2291
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||||
2790 0.0080359374 2.6464667e-07 3787.5927
|
||||
2800 0.0080383893 2.2394834e-07 3788.7244
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||||
2810 0.0080404882 1.9429813e-07 3789.6924
|
||||
2820 0.0080423251 1.7180333e-07 3790.5389
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||||
2830 0.0080439606 1.5419708e-07 3791.292
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||||
2840 0.0080454366 1.4007294e-07 3791.9711
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||||
2850 0.0080467835 1.2851365e-07 3792.5904
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||||
2860 0.0080480239 1.1889632e-07 3793.1603
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||||
2870 0.0080491753 1.1078364e-07 3793.689
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||||
2880 0.0080502511 1.0385986e-07 3794.1826
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||||
2890 0.0080512621 9.7891518e-08 3794.6462
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||||
2900 0.0080522171 9.2702379e-08 3795.0838
|
||||
2910 0.0080531232 8.815703e-08 3795.4988
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||||
2920 0.0080539863 8.4149767e-08 3795.8939
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||||
2930 0.0080548115 8.0596927e-08 3796.2714
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||||
2940 0.0080556029 7.7431468e-08 3796.6332
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||||
2950 0.0080563642 7.4599072e-08 3796.9811
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||||
2960 0.0080570985 7.2055292e-08 3797.3166
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||||
2970 0.0080578086 6.9763432e-08 3797.6407
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||||
2980 0.0080584967 6.7692955e-08 3797.9548
|
||||
2990 0.0080591651 6.5818259e-08 3798.2596
|
||||
3000 0.0080598155 6.4117744e-08 3798.5562
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||||
3010 0.0080604496 6.2573076e-08 3798.8452
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||||
3020 0.0080610689 6.1168613e-08 3799.1273
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||||
3030 0.0080616747 5.9890948e-08 3799.4033
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||||
3040 0.0080622683 5.8728542e-08 3799.6735
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||||
3050 0.0080628507 5.7671429e-08 3799.9386
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||||
3060 0.0080634231 5.6710976e-08 3800.199
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3070 0.0080639862 5.5839691e-08 3800.4551
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||||
3080 0.008064541 5.5051058e-08 3800.7074
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3090 0.0080650882 5.4339406e-08 3800.9562
|
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3100 0.0080656287 5.3699803e-08 3801.2018
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||||
3110 0.008066163 5.3127961e-08 3801.4446
|
||||
3120 0.008066692 5.2620159e-08 3801.6849
|
||||
3130 0.0080672161 5.2173187e-08 3801.923
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||||
3140 0.0080677361 5.1784286e-08 3802.1591
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3150 0.0080682524 5.1451107e-08 3802.3936
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||||
3160 0.0080687656 5.1171678e-08 3802.6266
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||||
3170 0.0080692762 5.0944369e-08 3802.8584
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||||
3180 0.0080697848 5.0767875e-08 3803.0892
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||||
3190 0.0080702919 5.064119e-08 3803.3194
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||||
3200 0.0080707979 5.0563598e-08 3803.549
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||||
3210 0.0080713034 5.0534662e-08 3803.7784
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3220 0.0080718088 5.0554215e-08 3804.0077
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||||
3230 0.0080723146 5.0622362e-08 3804.2373
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||||
3240 0.0080728213 5.073948e-08 3804.4672
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||||
3250 0.0080733294 5.090622e-08 3804.6978
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3260 0.0080738394 5.1123521e-08 3804.9292
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3270 0.0080743518 5.139262e-08 3805.1618
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3280 0.0080748671 5.171507e-08 3805.3957
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3290 0.0080753859 5.2092761e-08 3805.6311
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3300 0.0080759088 5.2527952e-08 3805.8685
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3310 0.0080764362 5.3023303e-08 3806.1079
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3320 0.0080769689 5.3581914e-08 3806.3498
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3330 0.0080775075 5.4207378e-08 3806.5944
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3340 0.0080780526 5.4903844e-08 3806.842
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3350 0.0080786051 5.567608e-08 3807.093
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3360 0.0080791656 5.652957e-08 3807.3477
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3370 0.0080797351 5.7470611e-08 3807.6065
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3380 0.0080803144 5.8506444e-08 3807.8698
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3390 0.0080809045 5.9645402e-08 3808.1381
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3400 0.0080815065 6.0897097e-08 3808.412
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3410 0.0080821215 6.2272649e-08 3808.6918
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3420 0.0080827509 6.3784959e-08 3808.9782
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3430 0.0080833961 6.5449061e-08 3809.272
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3440 0.0080840587 6.7282544e-08 3809.5737
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3450 0.0080847405 6.9306098e-08 3809.8843
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3460 0.0080854434 7.1544197e-08 3810.2047
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3470 0.0080861698 7.402597e-08 3810.5359
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3480 0.0080869223 7.6786336e-08 3810.8791
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3490 0.0080877037 7.9867475e-08 3811.2357
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3500 0.0080885176 8.3320783e-08 3811.6073
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3510 0.0080893679 8.7209484e-08 3811.9957
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3520 0.0080902594 9.1612182e-08 3812.4031
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3530 0.0080911975 9.662777e-08 3812.8321
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4350 0.013714701 2.9652221e-06 6395.7088
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||||
4380 0.014504048 7.0683429e-06 6755.0394
|
||||
4390 0.014536871 1.4515319e-06 6769.9538
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||||
4400 0.014547629 7.6742092e-07 6774.8365
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||||
4410 0.01455401 5.1561918e-07 6777.7294
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||||
4420 0.014558528 3.8717171e-07 6779.7758
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4430 0.014562024 3.1004583e-07 6781.3579
|
||||
4440 0.014564879 2.5893679e-07 6782.6486
|
||||
4450 0.014567296 2.2275131e-07 6783.7406
|
||||
4460 0.014569397 1.9588676e-07 6784.6888
|
||||
4470 0.014571258 1.7521879e-07 6785.5285
|
||||
4480 0.014572934 1.5887218e-07 6786.2838
|
||||
4490 0.014574461 1.4565562e-07 6786.9717
|
||||
4500 0.014575867 1.3477717e-07 6787.6046
|
||||
4510 0.014577173 1.2569059e-07 6788.1919
|
||||
4520 0.014578394 1.1800737e-07 6788.741
|
||||
4530 0.014579544 1.1144387e-07 6789.2576
|
||||
4540 0.014580632 1.0578845e-07 6789.7464
|
||||
4550 0.014581667 1.0088007e-07 6790.2111
|
||||
4560 0.014582656 9.6594222e-08 6790.6548
|
||||
4570 0.014583605 9.283317e-08 6791.0802
|
||||
4580 0.014584518 8.9519251e-08 6791.4895
|
||||
4590 0.0145854 8.6590045e-08 6791.8845
|
||||
4600 0.014586254 8.3994895e-08 6792.267
|
||||
4610 0.014587083 8.1692339e-08 6792.6383
|
||||
4620 0.014587891 7.9648193e-08 6792.9997
|
||||
4630 0.014588679 7.7834097e-08 6793.3523
|
||||
4640 0.01458945 7.6226411e-08 6793.6971
|
||||
4650 0.014590205 7.4805352e-08 6794.035
|
||||
4660 0.014590948 7.3554327e-08 6794.3668
|
||||
4670 0.014591678 7.2459408e-08 6794.6932
|
||||
4680 0.014592398 7.1508917e-08 6795.015
|
||||
4690 0.01459311 7.0693097e-08 6795.3328
|
||||
4700 0.014593813 7.0003852e-08 6795.6471
|
||||
4710 0.014594511 6.9434537e-08 6795.9585
|
||||
4720 0.014595203 6.8979799e-08 6796.2676
|
||||
4730 0.014595891 6.8635445e-08 6796.5748
|
||||
4740 0.014596576 6.839835e-08 6796.8807
|
||||
4750 0.01459726 6.8266383e-08 6797.1857
|
||||
4760 0.014597942 6.823836e-08 6797.4903
|
||||
4770 0.014598625 6.8314021e-08 6797.795
|
||||
4780 0.014599309 6.849402e-08 6798.1003
|
||||
4790 0.014599995 6.8779943e-08 6798.4065
|
||||
4800 0.014600684 6.9174339e-08 6798.7143
|
||||
4810 0.014601378 6.9680779e-08 6799.0241
|
||||
4820 0.014602078 7.0303936e-08 6799.3364
|
||||
4830 0.014602784 7.1049693e-08 6799.6517
|
||||
4840 0.014603498 7.1925284e-08 6799.9707
|
||||
4850 0.014604222 7.2939475e-08 6800.294
|
||||
4860 0.014604956 7.4102791e-08 6800.6221
|
||||
4870 0.014605703 7.5427802e-08 6800.9557
|
||||
4880 0.014606464 7.6929481e-08 6801.2958
|
||||
4890 0.014607241 7.8625665e-08 6801.643
|
||||
4900 0.014608036 8.0537626e-08 6801.9983
|
||||
4910 0.01460885 8.2690811e-08 6802.3627
|
||||
4920 0.014609688 8.5115787e-08 6802.7374
|
||||
4930 0.014610551 8.7849474e-08 6803.1237
|
||||
4940 0.014611443 9.0936752e-08 6803.5231
|
||||
4950 0.014612368 9.4432608e-08 6803.9372
|
||||
4960 0.01461333 9.8405013e-08 6804.3681
|
||||
4970 0.014614334 1.0293885e-07 6804.8181
|
||||
4980 0.014615386 1.0814135e-07 6805.2899
|
||||
4990 0.014616494 1.1414984e-07 6805.7869
|
||||
5000 0.014617666 1.2114278e-07 6806.313
|
||||
Loop time of 9.26846 on 4 procs for 5000 steps with 32000 atoms
|
||||
|
||||
Performance: 0.006 ns/day, 4250.474 hours/ns, 539.464 timesteps/s
|
||||
96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.6281 | 4.7789 | 5.1937 | 11.0 | 51.56
|
||||
Neigh | 0.40488 | 0.41576 | 0.43895 | 2.1 | 4.49
|
||||
Comm | 0.8478 | 1.2799 | 1.4349 | 22.1 | 13.81
|
||||
Output | 0.0048099 | 0.016429 | 0.050251 | 15.2 | 0.18
|
||||
Modify | 2.1042 | 2.1347 | 2.1706 | 1.6 | 23.03
|
||||
Other | | 0.6427 | | | 6.93
|
||||
|
||||
Nlocal: 8000 ave 8033 max 7977 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Nghost: 6061.25 ave 6085 max 6028 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 144002 ave 144601 max 143596 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 576008
|
||||
Ave neighs/atom = 18.0003
|
||||
Neighbor list builds = 67
|
||||
Dangerous builds = 38
|
||||
Total wall time: 0:00:09
|
||||
@ -0,0 +1,196 @@
|
||||
LAMMPS (28 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Test case / example for fix electron/stopping
|
||||
# One fast atom, no other interactions.
|
||||
# Stopping only applied in a smaller box in the middle.
|
||||
#
|
||||
# Also uses fix dt/reset, as one should when energies are high
|
||||
# enough to require electronic stopping.
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
timestep 0.0001
|
||||
|
||||
lattice fcc 1
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
|
||||
region rbox block -100 100 -100 100 -100 100
|
||||
region rsmallbox block -90 90 -90 90 -90 90
|
||||
|
||||
create_box 1 rbox
|
||||
Created orthogonal box = (-100 -100 -100) to (100 100 100)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
mass 1 28.0855
|
||||
|
||||
create_atoms 1 single 0 0 0
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 4.05312e-06 secs
|
||||
velocity all set 1120 1620 389
|
||||
|
||||
pair_style zero 1
|
||||
pair_coeff * * 1
|
||||
|
||||
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
|
||||
fix fel all electron/stopping 1.0 Si.Si.elstop minneigh 0 region rsmallbox
|
||||
fix fnve all nve
|
||||
|
||||
compute ek all ke/atom
|
||||
compute ektot all reduce sum c_ek
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time dt f_fel c_ektot
|
||||
|
||||
#dump mydump all custom 200 elstop.only.dump id x y z vx vy vz fx fy fz c_ek
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3
|
||||
ghost atom cutoff = 3
|
||||
binsize = 1.5, bins = 134 134 134
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) fix electron/stopping, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.31 | 13.31 | 13.31 Mbytes
|
||||
Step Time Dt f_fel c_ektot
|
||||
0 0 4.98128e-05 0 5865.5525
|
||||
100 0.0049972222 5.0137252e-05 76.048699 5789.883
|
||||
200 0.010027278 5.0467945e-05 151.67477 5714.2548
|
||||
300 0.015090636 5.0803375e-05 226.8806 5639.0469
|
||||
400 0.020187777 5.1143663e-05 301.6685 5564.2569
|
||||
500 0.025319192 5.1488933e-05 376.04082 5489.8825
|
||||
600 0.030485386 5.1839314e-05 449.99984 5415.9215
|
||||
700 0.035686876 5.2194938e-05 523.54788 5342.3714
|
||||
800 0.040924195 5.2555944e-05 596.68721 5269.23
|
||||
900 0.046197886 5.2922477e-05 669.42011 5196.4951
|
||||
1000 0.05150851 5.3294685e-05 741.74883 5124.1643
|
||||
1100 0.056856642 5.3672723e-05 813.67563 5052.2355
|
||||
1200 0.062229338 5.3731851e-05 824.43012 5041.1224
|
||||
1300 0.067602524 5.3731851e-05 824.43012 5041.1224
|
||||
1400 0.072978188 5.387166e-05 850.91948 5014.9907
|
||||
1500 0.07838447 5.425887e-05 922.23961 4943.6685
|
||||
1600 0.08382978 5.4652329e-05 993.16341 4872.7428
|
||||
1700 0.089299984 5.4705935e-05 1002.3545 4863.198
|
||||
1800 0.094770578 5.4705935e-05 1002.3545 4863.198
|
||||
1900 0.10024117 5.4705935e-05 1002.3545 4863.198
|
||||
2000 0.10571333 5.4819488e-05 1022.8338 4843.0716
|
||||
2100 0.11121515 5.5222127e-05 1093.1986 4772.7048
|
||||
2200 0.11675757 5.5631458e-05 1163.1724 4702.7291
|
||||
2300 0.12234126 5.6047675e-05 1232.7573 4633.1422
|
||||
2400 0.12796692 5.6470985e-05 1301.9555 4563.942
|
||||
2500 0.13363527 5.6901598e-05 1370.7692 4495.1264
|
||||
2600 0.13934706 5.7339739e-05 1439.2006 4426.6932
|
||||
2700 0.14510304 5.7785637e-05 1507.2516 4358.6403
|
||||
2800 0.150904 5.8239536e-05 1574.9245 4290.9655
|
||||
2900 0.15675076 5.8701688e-05 1642.2213 4223.6668
|
||||
3000 0.16264416 5.9172358e-05 1709.1441 4156.7422
|
||||
3100 0.16858505 5.9651822e-05 1775.695 4090.1894
|
||||
3200 0.17457434 6.0140369e-05 1841.8761 4024.0064
|
||||
3300 0.18061294 6.0638302e-05 1907.6894 3958.1913
|
||||
3400 0.18669814 6.0949329e-05 1947.6558 3917.8967
|
||||
3500 0.19279307 6.0949329e-05 1947.6558 3917.8967
|
||||
3600 0.198888 6.0949329e-05 1947.6558 3917.8967
|
||||
3700 0.20498294 6.0949329e-05 1947.6558 3917.8967
|
||||
3800 0.21107787 6.0949329e-05 1947.6558 3917.8967
|
||||
3900 0.2171728 6.0949329e-05 1947.6558 3917.8967
|
||||
4000 0.22326773 6.0949329e-05 1947.6558 3917.8967
|
||||
4100 0.22936267 6.0949329e-05 1947.6558 3917.8967
|
||||
4200 0.2354576 6.0949329e-05 1947.6558 3917.8967
|
||||
4300 0.24155253 6.0949329e-05 1947.6558 3917.8967
|
||||
4400 0.24764747 6.0949329e-05 1947.6558 3917.8967
|
||||
4500 0.2537424 6.0949329e-05 1947.6558 3917.8967
|
||||
4600 0.25983733 6.0949329e-05 1947.6558 3917.8967
|
||||
4700 0.26593227 6.0949329e-05 1947.6558 3917.8967
|
||||
4800 0.2720272 6.0949329e-05 1947.6558 3917.8967
|
||||
4900 0.27812213 6.0949329e-05 1947.6558 3917.8967
|
||||
5000 0.28421706 6.0949329e-05 1947.6558 3917.8967
|
||||
5100 0.290312 6.0949329e-05 1947.6558 3917.8967
|
||||
5200 0.29640693 6.0949329e-05 1947.6558 3917.8967
|
||||
5300 0.30250186 6.0949329e-05 1947.6558 3917.8967
|
||||
5400 0.3085968 6.0949329e-05 1947.6558 3917.8967
|
||||
5500 0.31469173 6.0949329e-05 1947.6558 3917.8967
|
||||
5600 0.32078666 6.0949329e-05 1947.6558 3917.8967
|
||||
5700 0.32688159 6.0949329e-05 1947.6558 3917.8967
|
||||
5800 0.33297653 6.0949329e-05 1947.6558 3917.8967
|
||||
5900 0.33907146 6.0949329e-05 1947.6558 3917.8967
|
||||
6000 0.34516639 6.0949329e-05 1947.6558 3917.8967
|
||||
6100 0.35126133 6.0949329e-05 1947.6558 3917.8967
|
||||
6200 0.35735626 6.0949329e-05 1947.6558 3917.8967
|
||||
6300 0.36345119 6.0949329e-05 1947.6558 3917.8967
|
||||
6400 0.36954612 6.0949329e-05 1947.6558 3917.8967
|
||||
6500 0.37564106 6.0949329e-05 1947.6558 3917.8967
|
||||
6600 0.38173599 6.0949329e-05 1947.6558 3917.8967
|
||||
6700 0.38783092 6.0949329e-05 1947.6558 3917.8967
|
||||
6800 0.39392586 6.0949329e-05 1947.6558 3917.8967
|
||||
6900 0.40002079 6.0949329e-05 1947.6558 3917.8967
|
||||
7000 0.40611572 6.0949329e-05 1947.6558 3917.8967
|
||||
7100 0.41221066 6.0949329e-05 1947.6558 3917.8967
|
||||
7200 0.41830559 6.0949329e-05 1947.6558 3917.8967
|
||||
7300 0.42440052 6.0949329e-05 1947.6558 3917.8967
|
||||
7400 0.43049545 6.0949329e-05 1947.6558 3917.8967
|
||||
7500 0.43659039 6.0949329e-05 1947.6558 3917.8967
|
||||
7600 0.44268532 6.0949329e-05 1947.6558 3917.8967
|
||||
7700 0.44878025 6.0949329e-05 1947.6558 3917.8967
|
||||
7800 0.45487519 6.0949329e-05 1947.6558 3917.8967
|
||||
7900 0.46097012 6.0949329e-05 1947.6558 3917.8967
|
||||
8000 0.46706505 6.0949329e-05 1947.6558 3917.8967
|
||||
8100 0.47315998 6.0949329e-05 1947.6558 3917.8967
|
||||
8200 0.47925492 6.0949329e-05 1947.6558 3917.8967
|
||||
8300 0.48534985 6.0949329e-05 1947.6558 3917.8967
|
||||
8400 0.49144478 6.0949329e-05 1947.6558 3917.8967
|
||||
8500 0.49753972 6.0949329e-05 1947.6558 3917.8967
|
||||
8600 0.50363465 6.0949329e-05 1947.6558 3917.8967
|
||||
8700 0.50972958 6.0949329e-05 1947.6558 3917.8967
|
||||
8800 0.51582452 6.0949329e-05 1947.6558 3917.8967
|
||||
8900 0.52191945 6.0949329e-05 1947.6558 3917.8967
|
||||
9000 0.52801438 6.0949329e-05 1947.6558 3917.8967
|
||||
9100 0.53410931 6.0949329e-05 1947.6558 3917.8967
|
||||
9200 0.54020425 6.0949329e-05 1947.6558 3917.8967
|
||||
9300 0.54629918 6.0949329e-05 1947.6558 3917.8967
|
||||
9400 0.55239411 6.0949329e-05 1947.6558 3917.8967
|
||||
9500 0.55848905 6.0949329e-05 1947.6558 3917.8967
|
||||
9600 0.56458398 6.0949329e-05 1947.6558 3917.8967
|
||||
9700 0.57067891 6.0949329e-05 1947.6558 3917.8967
|
||||
9800 0.57677384 6.0949329e-05 1947.6558 3917.8967
|
||||
9900 0.58286878 6.0949329e-05 1947.6558 3917.8967
|
||||
10000 0.58896371 6.0949329e-05 1947.6558 3917.8967
|
||||
Loop time of 1.25184 on 1 procs for 10000 steps with 1 atoms
|
||||
|
||||
Performance: 42.066 ns/day, 0.571 hours/ns, 7988.216 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 | 0.0005827 | 0.0005827 | 0.0005827 | 0.0 | 0.05
|
||||
Neigh | 1.2134 | 1.2134 | 1.2134 | 0.0 | 96.93
|
||||
Comm | 0.02822 | 0.02822 | 0.02822 | 0.0 | 2.25
|
||||
Output | 0.0017159 | 0.0017159 | 0.0017159 | 0.0 | 0.14
|
||||
Modify | 0.0052147 | 0.0052147 | 0.0052147 | 0.0 | 0.42
|
||||
Other | | 0.002664 | | | 0.21
|
||||
|
||||
Nlocal: 1 ave 1 max 1 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 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: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 960
|
||||
Dangerous builds = 568
|
||||
Total wall time: 0:00:01
|
||||
@ -0,0 +1,196 @@
|
||||
LAMMPS (28 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Test case / example for fix electron/stopping
|
||||
# One fast atom, no other interactions.
|
||||
# Stopping only applied in a smaller box in the middle.
|
||||
#
|
||||
# Also uses fix dt/reset, as one should when energies are high
|
||||
# enough to require electronic stopping.
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
timestep 0.0001
|
||||
|
||||
lattice fcc 1
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
|
||||
region rbox block -100 100 -100 100 -100 100
|
||||
region rsmallbox block -90 90 -90 90 -90 90
|
||||
|
||||
create_box 1 rbox
|
||||
Created orthogonal box = (-100 -100 -100) to (100 100 100)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
mass 1 28.0855
|
||||
|
||||
create_atoms 1 single 0 0 0
|
||||
Created 1 atoms
|
||||
create_atoms CPU = 1.19209e-05 secs
|
||||
velocity all set 1120 1620 389
|
||||
|
||||
pair_style zero 1
|
||||
pair_coeff * * 1
|
||||
|
||||
fix fdt all dt/reset 1 NULL 0.001 0.1 emax 20.0
|
||||
fix fel all electron/stopping 1.0 Si.Si.elstop minneigh 0 region rsmallbox
|
||||
fix fnve all nve
|
||||
|
||||
compute ek all ke/atom
|
||||
compute ektot all reduce sum c_ek
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time dt f_fel c_ektot
|
||||
|
||||
#dump mydump all custom 200 elstop.only.dump id x y z vx vy vz fx fy fz c_ek
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3
|
||||
ghost atom cutoff = 3
|
||||
binsize = 1.5, bins = 134 134 134
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) pair zero, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) fix electron/stopping, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin/atomonly
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.637 | 4.2 | 5.887 Mbytes
|
||||
Step Time Dt f_fel c_ektot
|
||||
0 0 4.98128e-05 0 5865.5525
|
||||
100 0.0049972222 5.0137252e-05 76.048699 5789.883
|
||||
200 0.010027278 5.0467945e-05 151.67477 5714.2548
|
||||
300 0.015090636 5.0803375e-05 226.8806 5639.0469
|
||||
400 0.020187777 5.1143663e-05 301.6685 5564.2569
|
||||
500 0.025319192 5.1488933e-05 376.04082 5489.8825
|
||||
600 0.030485386 5.1839314e-05 449.99984 5415.9215
|
||||
700 0.035686876 5.2194938e-05 523.54788 5342.3714
|
||||
800 0.040924195 5.2555944e-05 596.68721 5269.23
|
||||
900 0.046197886 5.2922477e-05 669.42011 5196.4951
|
||||
1000 0.05150851 5.3294685e-05 741.74883 5124.1643
|
||||
1100 0.056856642 5.3672723e-05 813.67563 5052.2355
|
||||
1200 0.062229338 5.3731851e-05 824.43012 5041.1224
|
||||
1300 0.067602524 5.3731851e-05 824.43012 5041.1224
|
||||
1400 0.072978188 5.387166e-05 850.91948 5014.9907
|
||||
1500 0.07838447 5.425887e-05 922.23961 4943.6685
|
||||
1600 0.08382978 5.4652329e-05 993.16341 4872.7428
|
||||
1700 0.089299984 5.4705935e-05 1002.3545 4863.198
|
||||
1800 0.094770578 5.4705935e-05 1002.3545 4863.198
|
||||
1900 0.10024117 5.4705935e-05 1002.3545 4863.198
|
||||
2000 0.10571333 5.4819488e-05 1022.8338 4843.0716
|
||||
2100 0.11121515 5.5222127e-05 1093.1986 4772.7048
|
||||
2200 0.11675757 5.5631458e-05 1163.1724 4702.7291
|
||||
2300 0.12234126 5.6047675e-05 1232.7573 4633.1422
|
||||
2400 0.12796692 5.6470985e-05 1301.9555 4563.942
|
||||
2500 0.13363527 5.6901598e-05 1370.7692 4495.1264
|
||||
2600 0.13934706 5.7339739e-05 1439.2006 4426.6932
|
||||
2700 0.14510304 5.7785637e-05 1507.2516 4358.6403
|
||||
2800 0.150904 5.8239536e-05 1574.9245 4290.9655
|
||||
2900 0.15675076 5.8701688e-05 1642.2213 4223.6668
|
||||
3000 0.16264416 5.9172358e-05 1709.1441 4156.7422
|
||||
3100 0.16858505 5.9651822e-05 1775.695 4090.1894
|
||||
3200 0.17457434 6.0140369e-05 1841.8761 4024.0064
|
||||
3300 0.18061294 6.0638302e-05 1907.6894 3958.1913
|
||||
3400 0.18669814 6.0949329e-05 1947.6558 3917.8967
|
||||
3500 0.19279307 6.0949329e-05 1947.6558 3917.8967
|
||||
3600 0.198888 6.0949329e-05 1947.6558 3917.8967
|
||||
3700 0.20498294 6.0949329e-05 1947.6558 3917.8967
|
||||
3800 0.21107787 6.0949329e-05 1947.6558 3917.8967
|
||||
3900 0.2171728 6.0949329e-05 1947.6558 3917.8967
|
||||
4000 0.22326773 6.0949329e-05 1947.6558 3917.8967
|
||||
4100 0.22936267 6.0949329e-05 1947.6558 3917.8967
|
||||
4200 0.2354576 6.0949329e-05 1947.6558 3917.8967
|
||||
4300 0.24155253 6.0949329e-05 1947.6558 3917.8967
|
||||
4400 0.24764747 6.0949329e-05 1947.6558 3917.8967
|
||||
4500 0.2537424 6.0949329e-05 1947.6558 3917.8967
|
||||
4600 0.25983733 6.0949329e-05 1947.6558 3917.8967
|
||||
4700 0.26593227 6.0949329e-05 1947.6558 3917.8967
|
||||
4800 0.2720272 6.0949329e-05 1947.6558 3917.8967
|
||||
4900 0.27812213 6.0949329e-05 1947.6558 3917.8967
|
||||
5000 0.28421706 6.0949329e-05 1947.6558 3917.8967
|
||||
5100 0.290312 6.0949329e-05 1947.6558 3917.8967
|
||||
5200 0.29640693 6.0949329e-05 1947.6558 3917.8967
|
||||
5300 0.30250186 6.0949329e-05 1947.6558 3917.8967
|
||||
5400 0.3085968 6.0949329e-05 1947.6558 3917.8967
|
||||
5500 0.31469173 6.0949329e-05 1947.6558 3917.8967
|
||||
5600 0.32078666 6.0949329e-05 1947.6558 3917.8967
|
||||
5700 0.32688159 6.0949329e-05 1947.6558 3917.8967
|
||||
5800 0.33297653 6.0949329e-05 1947.6558 3917.8967
|
||||
5900 0.33907146 6.0949329e-05 1947.6558 3917.8967
|
||||
6000 0.34516639 6.0949329e-05 1947.6558 3917.8967
|
||||
6100 0.35126133 6.0949329e-05 1947.6558 3917.8967
|
||||
6200 0.35735626 6.0949329e-05 1947.6558 3917.8967
|
||||
6300 0.36345119 6.0949329e-05 1947.6558 3917.8967
|
||||
6400 0.36954612 6.0949329e-05 1947.6558 3917.8967
|
||||
6500 0.37564106 6.0949329e-05 1947.6558 3917.8967
|
||||
6600 0.38173599 6.0949329e-05 1947.6558 3917.8967
|
||||
6700 0.38783092 6.0949329e-05 1947.6558 3917.8967
|
||||
6800 0.39392586 6.0949329e-05 1947.6558 3917.8967
|
||||
6900 0.40002079 6.0949329e-05 1947.6558 3917.8967
|
||||
7000 0.40611572 6.0949329e-05 1947.6558 3917.8967
|
||||
7100 0.41221066 6.0949329e-05 1947.6558 3917.8967
|
||||
7200 0.41830559 6.0949329e-05 1947.6558 3917.8967
|
||||
7300 0.42440052 6.0949329e-05 1947.6558 3917.8967
|
||||
7400 0.43049545 6.0949329e-05 1947.6558 3917.8967
|
||||
7500 0.43659039 6.0949329e-05 1947.6558 3917.8967
|
||||
7600 0.44268532 6.0949329e-05 1947.6558 3917.8967
|
||||
7700 0.44878025 6.0949329e-05 1947.6558 3917.8967
|
||||
7800 0.45487519 6.0949329e-05 1947.6558 3917.8967
|
||||
7900 0.46097012 6.0949329e-05 1947.6558 3917.8967
|
||||
8000 0.46706505 6.0949329e-05 1947.6558 3917.8967
|
||||
8100 0.47315998 6.0949329e-05 1947.6558 3917.8967
|
||||
8200 0.47925492 6.0949329e-05 1947.6558 3917.8967
|
||||
8300 0.48534985 6.0949329e-05 1947.6558 3917.8967
|
||||
8400 0.49144478 6.0949329e-05 1947.6558 3917.8967
|
||||
8500 0.49753972 6.0949329e-05 1947.6558 3917.8967
|
||||
8600 0.50363465 6.0949329e-05 1947.6558 3917.8967
|
||||
8700 0.50972958 6.0949329e-05 1947.6558 3917.8967
|
||||
8800 0.51582452 6.0949329e-05 1947.6558 3917.8967
|
||||
8900 0.52191945 6.0949329e-05 1947.6558 3917.8967
|
||||
9000 0.52801438 6.0949329e-05 1947.6558 3917.8967
|
||||
9100 0.53410931 6.0949329e-05 1947.6558 3917.8967
|
||||
9200 0.54020425 6.0949329e-05 1947.6558 3917.8967
|
||||
9300 0.54629918 6.0949329e-05 1947.6558 3917.8967
|
||||
9400 0.55239411 6.0949329e-05 1947.6558 3917.8967
|
||||
9500 0.55848905 6.0949329e-05 1947.6558 3917.8967
|
||||
9600 0.56458398 6.0949329e-05 1947.6558 3917.8967
|
||||
9700 0.57067891 6.0949329e-05 1947.6558 3917.8967
|
||||
9800 0.57677384 6.0949329e-05 1947.6558 3917.8967
|
||||
9900 0.58286878 6.0949329e-05 1947.6558 3917.8967
|
||||
10000 0.58896371 6.0949329e-05 1947.6558 3917.8967
|
||||
Loop time of 1.38891 on 4 procs for 10000 steps with 1 atoms
|
||||
|
||||
Performance: 37.915 ns/day, 0.633 hours/ns, 7199.876 timesteps/s
|
||||
94.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0004971 | 0.00060463 | 0.00069618 | 0.0 | 0.04
|
||||
Neigh | 1.1005 | 1.1507 | 1.2839 | 7.2 | 82.85
|
||||
Comm | 0.025918 | 0.026382 | 0.027041 | 0.3 | 1.90
|
||||
Output | 0.0016336 | 0.005001 | 0.01507 | 8.2 | 0.36
|
||||
Modify | 0.059378 | 0.20196 | 0.25453 | 18.3 | 14.54
|
||||
Other | | 0.00422 | | | 0.30
|
||||
|
||||
Nlocal: 0.25 ave 1 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 960
|
||||
Dangerous builds = 568
|
||||
Total wall time: 0:00:01
|
||||
@ -58,7 +58,7 @@ pair_coeff 1 4 1.0 1.0 1.12246
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
thermo 50
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
@ -69,4 +69,4 @@ thermo 1000
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
run 60000
|
||||
run 1000
|
||||
|
||||
87
examples/micelle/in.micelle-rigid
Normal file
87
examples/micelle/in.micelle-rigid
Normal file
@ -0,0 +1,87 @@
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
special_bonds fene
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 500
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 50
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
group solvent molecule 0
|
||||
group solute subtract all solvent
|
||||
unfix 1
|
||||
unfix 2
|
||||
unfix 4
|
||||
fix 1 solvent nve
|
||||
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
|
||||
fix 4 all enforce2d
|
||||
run 500
|
||||
unfix 2
|
||||
unfix 4
|
||||
unfix 5
|
||||
fix 5 solute rigid/small molecule
|
||||
fix 4 all enforce2d
|
||||
run 500
|
||||
@ -1,259 +0,0 @@
|
||||
LAMMPS (28 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000394821 secs
|
||||
read_data CPU = 0.00212336 secs
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.00018549 secs
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.113919 on 1 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 3792167.464 tau/day, 8778.165 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.076825 | 0.076825 | 0.076825 | 0.0 | 67.44
|
||||
Bond | 0.0041864 | 0.0041864 | 0.0041864 | 0.0 | 3.67
|
||||
Neigh | 0.017061 | 0.017061 | 0.017061 | 0.0 | 14.98
|
||||
Comm | 0.0019042 | 0.0019042 | 0.0019042 | 0.0 | 1.67
|
||||
Output | 0.00017285 | 0.00017285 | 0.00017285 | 0.0 | 0.15
|
||||
Modify | 0.011218 | 0.011218 | 0.011218 | 0.0 | 9.85
|
||||
Other | | 0.002551 | | | 2.24
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 195 ave 195 max 195 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3136 ave 3136 max 3136 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
run 60000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
|
||||
1000 0.45 -1.9727644 0.05860769 -1.4645317 1.9982326
|
||||
2000 0.46143408 -1.9889684 0.058103225 -1.4698156 1.7806269
|
||||
3000 0.44459291 -1.9997961 0.068724164 -1.4868496 1.4369618
|
||||
4000 0.46939549 -2.0330437 0.073499424 -1.4905399 1.3780016
|
||||
5000 0.44411088 -2.0339936 0.05862049 -1.5316323 1.2544164
|
||||
6000 0.44034597 -2.0265475 0.066481992 -1.5200864 1.2362891
|
||||
7000 0.45097378 -2.0331083 0.058467565 -1.5240428 1.2762333
|
||||
8000 0.45797632 -2.0330255 0.060048036 -1.5153828 1.3862396
|
||||
9000 0.45297811 -2.0383417 0.067056519 -1.5186845 1.2762554
|
||||
10000 0.45 -2.0628269 0.065650067 -1.5475518 1.0566213
|
||||
11000 0.44466757 -2.0593977 0.06190999 -1.5531907 1.1452469
|
||||
12000 0.46743534 -2.0684295 0.061056278 -1.5403274 1.0824225
|
||||
13000 0.45601091 -2.0689708 0.054868536 -1.5584713 0.96703283
|
||||
14000 0.44111882 -2.0553174 0.058249816 -1.5563164 1.0986427
|
||||
15000 0.43894405 -2.0866829 0.064117804 -1.5839869 0.90031836
|
||||
16000 0.43856814 -2.0879319 0.056024166 -1.593705 0.96387323
|
||||
17000 0.45977841 -2.103188 0.058097306 -1.5856955 0.83352919
|
||||
18000 0.43423341 -2.0813151 0.066623991 -1.5808196 0.98157638
|
||||
19000 0.44245939 -2.0851261 0.057637655 -1.5853978 0.84228341
|
||||
20000 0.43144678 -2.0895403 0.06536727 -1.5930858 0.88177768
|
||||
21000 0.45014968 -2.106686 0.059137572 -1.5977739 0.89408935
|
||||
22000 0.4575126 -2.1024115 0.063013023 -1.5822672 0.84886734
|
||||
23000 0.45 -2.10897 0.06724784 -1.5920971 0.66205013
|
||||
24000 0.43055602 -2.0894725 0.061566464 -1.5977089 0.81764789
|
||||
25000 0.4366384 -2.0926743 0.059609321 -1.5967905 0.85549875
|
||||
26000 0.4521714 -2.0963996 0.062031863 -1.5825731 0.80137118
|
||||
27000 0.45734834 -2.1060987 0.061712636 -1.5874188 0.82899415
|
||||
28000 0.44803467 -2.0859226 0.061871856 -1.5763894 0.97007526
|
||||
29000 0.45 -2.1106243 0.063825481 -1.5971738 0.63798376
|
||||
30000 0.44932806 -2.1006036 0.053053934 -1.598596 0.63907113
|
||||
31000 0.44713779 -2.1096164 0.066470416 -1.5963808 0.66832708
|
||||
32000 0.4373357 -2.0941237 0.058871613 -1.5982808 0.78176106
|
||||
33000 0.44030485 -2.105644 0.058804306 -1.6069017 0.66286458
|
||||
34000 0.43781175 -2.1233209 0.064611206 -1.6212628 0.56342584
|
||||
35000 0.45670132 -2.1059408 0.053049584 -1.5965705 0.73992396
|
||||
36000 0.45555427 -2.1149877 0.057627709 -1.6021854 0.85854939
|
||||
37000 0.44134236 -2.1106202 0.064444306 -1.6052013 0.74674603
|
||||
38000 0.44812623 -2.1003681 0.057266258 -1.5953491 0.78239359
|
||||
39000 0.44167062 -2.11141 0.055354 -1.6147534 0.7066385
|
||||
40000 0.46103176 -2.1166687 0.062155412 -1.5938657 0.73620955
|
||||
41000 0.44537102 -2.0993898 0.05631213 -1.5980778 0.87348756
|
||||
42000 0.44752506 -2.1115212 0.057506521 -1.6068625 0.72999561
|
||||
43000 0.4483886 -2.1184719 0.066943915 -1.6035131 0.78112063
|
||||
44000 0.45944897 -2.0916657 0.055242781 -1.5773568 0.98660473
|
||||
45000 0.46238513 -2.1163075 0.0530031 -1.6013046 0.74416054
|
||||
46000 0.45979064 -2.1165545 0.060657581 -1.5964895 0.63516974
|
||||
47000 0.45936546 -2.1140678 0.049931919 -1.6051532 0.76425182
|
||||
48000 0.45424613 -2.1122681 0.061885599 -1.5965149 0.71981142
|
||||
49000 0.44449524 -2.1147361 0.06626748 -1.6043438 0.78720467
|
||||
50000 0.4641185 -2.1114668 0.055104874 -1.5926302 0.70195865
|
||||
51000 0.44220655 -2.1075773 0.0589109 -1.6068283 0.73806859
|
||||
52000 0.43097906 -2.1189493 0.061502241 -1.6268271 0.69622593
|
||||
53000 0.45 -2.137688 0.053631829 -1.6344311 0.48269158
|
||||
54000 0.43777118 -2.1089246 0.047098534 -1.6244197 0.70423814
|
||||
55000 0.46061985 -2.1129502 0.062520353 -1.5901938 0.72492307
|
||||
56000 0.4524841 -2.1195648 0.06580089 -1.6016569 0.52709892
|
||||
57000 0.44914574 -2.1041993 0.061040876 -1.594387 0.7979988
|
||||
58000 0.46446286 -2.1181238 0.055741995 -1.598306 0.51009146
|
||||
59000 0.4632674 -2.1169321 0.050672678 -1.6033781 0.83110911
|
||||
60000 0.46340478 -2.122846 0.058485209 -1.6013422 0.69966471
|
||||
Loop time of 8.01683 on 1 procs for 60000 steps with 1200 atoms
|
||||
|
||||
Performance: 3233199.903 tau/day, 7484.259 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.4027 | 5.4027 | 5.4027 | 0.0 | 67.39
|
||||
Bond | 0.23585 | 0.23585 | 0.23585 | 0.0 | 2.94
|
||||
Neigh | 1.5188 | 1.5188 | 1.5188 | 0.0 | 18.95
|
||||
Comm | 0.14452 | 0.14452 | 0.14452 | 0.0 | 1.80
|
||||
Output | 0.00060487 | 0.00060487 | 0.00060487 | 0.0 | 0.01
|
||||
Modify | 0.56352 | 0.56352 | 0.56352 | 0.0 | 7.03
|
||||
Other | | 0.1508 | | | 1.88
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 395 ave 395 max 395 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9652 ave 9652 max 9652 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9652
|
||||
Ave neighs/atom = 8.04333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 4886
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:08
|
||||
@ -1,259 +0,0 @@
|
||||
LAMMPS (28 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000130415 secs
|
||||
read_data CPU = 0.00132132 secs
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 4.76837e-05 secs
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.0377742 on 4 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 11436375.633 tau/day, 26473.092 timesteps/s
|
||||
96.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.016871 | 0.017299 | 0.018185 | 0.4 | 45.80
|
||||
Bond | 0.0010128 | 0.0010633 | 0.001116 | 0.1 | 2.81
|
||||
Neigh | 0.004832 | 0.0048565 | 0.0048807 | 0.0 | 12.86
|
||||
Comm | 0.0066509 | 0.0077528 | 0.0084352 | 0.8 | 20.52
|
||||
Output | 0.00022054 | 0.00028259 | 0.00046587 | 0.0 | 0.75
|
||||
Modify | 0.0035386 | 0.0036086 | 0.0036943 | 0.1 | 9.55
|
||||
Other | | 0.002912 | | | 7.71
|
||||
|
||||
Nlocal: 300 ave 305 max 292 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 100.25 ave 108 max 93 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 784 ave 815 max 739 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
run 60000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
|
||||
1000 0.45 -1.9727652 0.058608073 -1.4645321 1.9982444
|
||||
2000 0.44428815 -1.9902282 0.064240544 -1.4820698 1.7051263
|
||||
3000 0.46641766 -1.9856844 0.065017468 -1.4546379 1.6939772
|
||||
4000 0.45734058 -2.0242583 0.070494626 -1.4968042 1.3474276
|
||||
5000 0.44904747 -2.0086954 0.058801142 -1.501221 1.4632351
|
||||
6000 0.44961405 -2.0334509 0.05721299 -1.5269985 1.3093586
|
||||
7000 0.45474928 -2.0453645 0.064725006 -1.5262692 1.1581035
|
||||
8000 0.44274767 -2.0375379 0.062216035 -1.5329431 1.312914
|
||||
9000 0.46176571 -2.0473031 0.065581966 -1.5203402 1.2013868
|
||||
10000 0.45046977 -2.0540466 0.065402724 -1.5385495 0.95819581
|
||||
11000 0.45016671 -2.0610028 0.056993955 -1.5542172 1.0433435
|
||||
12000 0.43823039 -2.073155 0.065171939 -1.5701178 1.1400059
|
||||
13000 0.44482161 -2.0678338 0.063901045 -1.5594819 0.97993813
|
||||
14000 0.45 -2.0892562 0.061753632 -1.5778776 0.89841778
|
||||
15000 0.44328626 -2.0859346 0.059956258 -1.5830615 0.90664821
|
||||
16000 0.45666508 -2.0859262 0.059582346 -1.5700593 0.9702235
|
||||
17000 0.44832038 -2.0762124 0.059153394 -1.5691122 0.93020504
|
||||
18000 0.4555831 -2.0844959 0.057986324 -1.5713062 0.87398232
|
||||
19000 0.45257867 -2.0671736 0.062190389 -1.5527816 0.89208496
|
||||
20000 0.44010419 -2.1020944 0.062053708 -1.6003033 0.84140973
|
||||
21000 0.45239369 -2.0820308 0.060981799 -1.5690323 0.98502522
|
||||
22000 0.44607468 -2.0820602 0.051731316 -1.5846259 0.86120529
|
||||
23000 0.45088473 -2.0865286 0.05727778 -1.5787418 1.1479844
|
||||
24000 0.45526919 -2.1086678 0.057378327 -1.5963997 0.86944138
|
||||
25000 0.46536624 -2.1055425 0.05665328 -1.5839108 0.72895438
|
||||
26000 0.46716668 -2.1035267 0.057498747 -1.5792505 0.85105386
|
||||
27000 0.44374699 -2.0932213 0.060937242 -1.5889069 0.93200759
|
||||
28000 0.45944001 -2.0968869 0.053052954 -1.5847768 0.78909249
|
||||
29000 0.4543632 -2.10493 0.061511018 -1.5894345 0.85862527
|
||||
30000 0.44987776 -2.0942536 0.062431086 -1.5823197 0.7349894
|
||||
31000 0.43829016 -2.0951259 0.060245682 -1.5969553 0.86702973
|
||||
32000 0.45416601 -2.0991679 0.055978905 -1.5894015 0.75777153
|
||||
33000 0.4605079 -2.1118364 0.058205688 -1.5935066 0.86041104
|
||||
34000 0.43638213 -2.0925345 0.067533519 -1.5889825 0.85100425
|
||||
35000 0.46912252 -2.1082718 0.051646432 -1.5878938 0.73613751
|
||||
36000 0.45 -2.0966442 0.052507159 -1.5945121 0.88722487
|
||||
37000 0.44970507 -2.1029685 0.065454263 -1.588184 0.76033821
|
||||
38000 0.44910233 -2.097751 0.05767009 -1.5913528 0.95830923
|
||||
39000 0.4322161 -2.1060426 0.062453704 -1.611733 0.74681695
|
||||
40000 0.46143858 -2.1328575 0.057333011 -1.6144704 0.58326322
|
||||
41000 0.43180549 -2.1070656 0.064150563 -1.6114694 0.82842684
|
||||
42000 0.46738909 -2.1067947 0.058017036 -1.5817781 0.73292362
|
||||
43000 0.43699124 -2.1171964 0.062817262 -1.6177521 0.73354741
|
||||
44000 0.45262916 -2.1281307 0.055228619 -1.6206502 0.64167946
|
||||
45000 0.43905419 -2.088789 0.055597999 -1.5945027 0.8002542
|
||||
46000 0.44485569 -2.1035061 0.067828181 -1.5911929 0.71861494
|
||||
47000 0.44496824 -2.0968296 0.0632326 -1.5889996 0.75202899
|
||||
48000 0.46567244 -2.1235948 0.061032118 -1.5972783 0.64094556
|
||||
49000 0.43202506 -2.0986097 0.053464022 -1.6134806 0.83857984
|
||||
50000 0.45454698 -2.1263344 0.058119708 -1.6140465 0.67030037
|
||||
51000 0.43702766 -2.1292347 0.074047424 -1.6185238 0.52896462
|
||||
52000 0.46367081 -2.1177288 0.06726625 -1.5871781 0.74343227
|
||||
53000 0.45 -2.1341074 0.062769314 -1.6217131 0.51130365
|
||||
54000 0.44862492 -2.1272108 0.057723381 -1.6212364 0.54735429
|
||||
55000 0.44926027 -2.1350444 0.066186625 -1.6199719 0.66821299
|
||||
56000 0.4544227 -2.1325537 0.065298628 -1.6132111 0.63597556
|
||||
57000 0.45697003 -2.1323238 0.053312855 -1.6224218 0.55572633
|
||||
58000 0.45698902 -2.1043208 0.055835989 -1.5918766 0.63502658
|
||||
59000 0.4425306 -2.1120353 0.056617261 -1.6132563 0.65681272
|
||||
60000 0.44319296 -2.1171981 0.058330294 -1.6160442 0.63602511
|
||||
Loop time of 2.63918 on 4 procs for 60000 steps with 1200 atoms
|
||||
|
||||
Performance: 9821248.084 tau/day, 22734.371 timesteps/s
|
||||
97.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1742 | 1.278 | 1.3471 | 5.9 | 48.43
|
||||
Bond | 0.046621 | 0.06565 | 0.081322 | 5.1 | 2.49
|
||||
Neigh | 0.46642 | 0.46917 | 0.47105 | 0.3 | 17.78
|
||||
Comm | 0.47295 | 0.55928 | 0.67758 | 10.5 | 21.19
|
||||
Output | 0.00073624 | 0.00173 | 0.0047016 | 4.1 | 0.07
|
||||
Modify | 0.14511 | 0.15226 | 0.15887 | 1.5 | 5.77
|
||||
Other | | 0.1131 | | | 4.28
|
||||
|
||||
Nlocal: 300 ave 309 max 281 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
Nghost: 232.75 ave 234 max 231 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Neighs: 2450.25 ave 2576 max 2179 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 1 2
|
||||
|
||||
Total # of neighbors = 9801
|
||||
Ave neighs/atom = 8.1675
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 4887
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
@ -1,290 +0,0 @@
|
||||
LAMMPS (28 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000271559 secs
|
||||
read_data CPU = 0.00115585 secs
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 8.39233e-05 secs
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.107201 on 1 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 4029800.456 tau/day, 9328.242 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.072035 | 0.072035 | 0.072035 | 0.0 | 67.20
|
||||
Bond | 0.0039918 | 0.0039918 | 0.0039918 | 0.0 | 3.72
|
||||
Neigh | 0.016078 | 0.016078 | 0.016078 | 0.0 | 15.00
|
||||
Comm | 0.0018375 | 0.0018375 | 0.0018375 | 0.0 | 1.71
|
||||
Output | 0.00016379 | 0.00016379 | 0.00016379 | 0.0 | 0.15
|
||||
Modify | 0.010665 | 0.010665 | 0.010665 | 0.0 | 9.95
|
||||
Other | | 0.002429 | | | 2.27
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 195 ave 195 max 195 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3136 ave 3136 max 3136 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
group solvent molecule 0
|
||||
750 atoms in group solvent
|
||||
group solute subtract all solvent
|
||||
450 atoms in group solute
|
||||
unfix 1
|
||||
unfix 2
|
||||
unfix 4
|
||||
fix 1 solvent nve
|
||||
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
|
||||
150 rigid bodies with 450 atoms
|
||||
fix 4 all enforce2d
|
||||
run 20000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736
|
||||
1000 0.46008168 -1.9040837 0.08808163 -1.4425691 0.93225457
|
||||
2000 0.44520658 -1.9317253 0.08808163 -1.4822843 3.8192896
|
||||
3000 0.43988556 -1.945898 0.08808163 -1.5007759 3.0371634
|
||||
4000 0.4646519 -1.9753553 0.08808163 -1.5101312 -1.8041178
|
||||
5000 0.4362993 -1.9763715 0.08808163 -1.5341603 1.5037284
|
||||
6000 0.47007384 -1.9833154 0.08808163 -1.5136905 2.1227653
|
||||
7000 0.44854623 -1.9914288 0.08808163 -1.5392772 3.9458099
|
||||
8000 0.43841372 -1.9779603 0.08808163 -1.5340328 -4.5429769
|
||||
9000 0.4518303 -1.9834387 0.08808163 -1.5286215 4.4230447
|
||||
10000 0.43562904 -2.001471 0.08808163 -1.5598038 1.8919582
|
||||
11000 0.44014575 -1.9820611 0.08808163 -1.5367278 -2.1189418
|
||||
12000 0.44466956 -2.0134014 0.08808163 -1.5643963 -2.5218497
|
||||
13000 0.45274369 -2.021443 0.08808163 -1.5658844 2.4795173
|
||||
14000 0.44742645 -2.011108 0.08808163 -1.5598653 -0.74697767
|
||||
15000 0.4674843 -2.024737 0.08808163 -1.5572139 -1.9539999
|
||||
16000 0.45610154 -2.0401029 0.08808163 -1.5818189 -0.53082066
|
||||
17000 0.44679292 -2.0365577 0.08808163 -1.5858291 -6.5040295
|
||||
18000 0.44279107 -2.0500326 0.08808163 -1.6025522 -0.051597102
|
||||
19000 0.45603993 -2.0306289 0.08808163 -1.5723948 1.0986608
|
||||
20000 0.44519606 -2.0412229 0.08808163 -1.5917904 -1.0406746
|
||||
Loop time of 3.68102 on 1 procs for 20000 steps with 1200 atoms
|
||||
|
||||
Performance: 2347175.802 tau/day, 5433.277 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.7349 | 1.7349 | 1.7349 | 0.0 | 47.13
|
||||
Bond | 0.079483 | 0.079483 | 0.079483 | 0.0 | 2.16
|
||||
Neigh | 0.49063 | 0.49063 | 0.49063 | 0.0 | 13.33
|
||||
Comm | 0.049093 | 0.049093 | 0.049093 | 0.0 | 1.33
|
||||
Output | 0.00022578 | 0.00022578 | 0.00022578 | 0.0 | 0.01
|
||||
Modify | 1.273 | 1.273 | 1.273 | 0.0 | 34.58
|
||||
Other | | 0.05369 | | | 1.46
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 395 ave 395 max 395 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8915 ave 8915 max 8915 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8915
|
||||
Ave neighs/atom = 7.42917
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 1580
|
||||
Dangerous builds = 0
|
||||
unfix 5
|
||||
unfix 4
|
||||
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
|
||||
create bodies CPU = 0.00012517 secs
|
||||
150 rigid bodies with 450 atoms
|
||||
1.04536 = max distance from body owner to body atom
|
||||
fix 4 all enforce2d
|
||||
run 20000
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.633 | 8.633 | 8.633 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20000 0.44519606 -2.0412229 0.08808163 -1.5917904 1.3058893
|
||||
21000 0.4353376 -2.0483342 0.08808163 -1.6069035 0.53023317
|
||||
22000 0.44034324 -2.0416876 0.08808163 -1.5961941 4.0327077
|
||||
23000 0.4685403 -2.05295 0.08808163 -1.5845698 3.6792349
|
||||
24000 0.44872075 -2.0320623 0.08808163 -1.579769 -2.0476923
|
||||
25000 0.46829594 -2.0671408 0.08808163 -1.5989589 2.180811
|
||||
26000 0.45257544 -2.0418792 0.08808163 -1.5864572 3.3924018
|
||||
27000 0.44269664 -2.0409905 0.08808163 -1.5935868 -0.17012673
|
||||
28000 0.46961216 -2.0552479 0.08808163 -1.5859978 -7.2870888
|
||||
29000 0.46683129 -2.0438334 0.08808163 -1.5768404 3.0583141
|
||||
30000 0.44262228 -2.036737 0.08808163 -1.5893937 0.087520915
|
||||
31000 0.43517227 -2.0479672 0.08808163 -1.6066708 -0.3426009
|
||||
32000 0.44543779 -2.0538031 0.08808163 -1.6041744 -0.2093148
|
||||
33000 0.44629079 -2.0409901 0.08808163 -1.5906691 3.310113
|
||||
34000 0.43058831 -2.0713827 0.08808163 -1.6338069 0.14128843
|
||||
35000 0.44546512 -2.0427068 0.08808163 -1.593056 -3.1386697
|
||||
36000 0.42971129 -2.0527435 0.08808163 -1.6158795 -2.7334963
|
||||
37000 0.44707969 -2.0461803 0.08808163 -1.595219 -3.8777678
|
||||
38000 0.43150818 -2.0435276 0.08808163 -1.6052052 0.2905487
|
||||
39000 0.44463343 -2.0522113 0.08808163 -1.6032355 3.543123
|
||||
40000 0.44582593 -2.052213 0.08808163 -1.6022693 1.1486536
|
||||
Loop time of 3.69012 on 1 procs for 20000 steps with 1200 atoms
|
||||
|
||||
Performance: 2341388.948 tau/day, 5419.882 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.756 | 1.756 | 1.756 | 0.0 | 47.59
|
||||
Bond | 0.079221 | 0.079221 | 0.079221 | 0.0 | 2.15
|
||||
Neigh | 0.49085 | 0.49085 | 0.49085 | 0.0 | 13.30
|
||||
Comm | 0.048317 | 0.048317 | 0.048317 | 0.0 | 1.31
|
||||
Output | 0.0002315 | 0.0002315 | 0.0002315 | 0.0 | 0.01
|
||||
Modify | 1.2616 | 1.2616 | 1.2616 | 0.0 | 34.19
|
||||
Other | | 0.05386 | | | 1.46
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 393 ave 393 max 393 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9091 ave 9091 max 9091 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9091
|
||||
Ave neighs/atom = 7.57583
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 1582
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:07
|
||||
@ -1,290 +0,0 @@
|
||||
LAMMPS (28 Feb 2019)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000175714 secs
|
||||
read_data CPU = 0.00145626 secs
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 7.22408e-05 secs
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.0389124 on 4 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 11101855.138 tau/day, 25698.739 timesteps/s
|
||||
95.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.016776 | 0.017405 | 0.018435 | 0.5 | 44.73
|
||||
Bond | 0.0010033 | 0.0011995 | 0.0015519 | 0.6 | 3.08
|
||||
Neigh | 0.0044944 | 0.0045093 | 0.0045218 | 0.0 | 11.59
|
||||
Comm | 0.0080328 | 0.0093863 | 0.010242 | 0.9 | 24.12
|
||||
Output | 0.00021577 | 0.00027579 | 0.00045323 | 0.0 | 0.71
|
||||
Modify | 0.0034575 | 0.0036355 | 0.0040002 | 0.4 | 9.34
|
||||
Other | | 0.002501 | | | 6.43
|
||||
|
||||
Nlocal: 300 ave 305 max 292 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 100.25 ave 108 max 93 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 784 ave 815 max 739 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
group solvent molecule 0
|
||||
750 atoms in group solvent
|
||||
group solute subtract all solvent
|
||||
450 atoms in group solute
|
||||
unfix 1
|
||||
unfix 2
|
||||
unfix 4
|
||||
fix 1 solvent nve
|
||||
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
|
||||
150 rigid bodies with 450 atoms
|
||||
fix 4 all enforce2d
|
||||
run 20000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.44603578 -1.7056163 0.08808163 -1.2555023 3.4039736
|
||||
1000 0.46008163 -1.9040835 0.08808163 -1.4425689 0.93225869
|
||||
2000 0.44943348 -1.9355135 0.08808163 -1.4826417 3.8399671
|
||||
3000 0.4448437 -1.9480307 0.08808163 -1.4988842 2.5506553
|
||||
4000 0.46013872 -1.9783821 0.08808163 -1.5168212 -1.8963215
|
||||
5000 0.45520233 -1.9659462 0.08808163 -1.5083921 1.9238897
|
||||
6000 0.44942049 -1.9663403 0.08808163 -1.513479 3.0633512
|
||||
7000 0.45975758 -1.988462 0.08808163 -1.5272105 4.8267309
|
||||
8000 0.45125238 -1.9913522 0.08808163 -1.5370041 -4.6644852
|
||||
9000 0.45863606 -1.9792375 0.08808163 -1.5188962 4.3655071
|
||||
10000 0.46264541 -1.9864611 0.08808163 -1.5228656 2.2176464
|
||||
11000 0.45048361 -1.9907235 0.08808163 -1.5369994 -0.055360699
|
||||
12000 0.44536719 -2.012875 0.08808163 -1.5633037 -0.2583823
|
||||
13000 0.44212663 -2.0060111 0.08808163 -1.55907 3.3616171
|
||||
14000 0.44984353 -2.0335408 0.08808163 -1.5803361 -0.21585645
|
||||
15000 0.44896672 -2.0385265 0.08808163 -1.5860335 -4.6186206
|
||||
16000 0.46694997 -2.032795 0.08808163 -1.5657056 0.53443281
|
||||
17000 0.43208201 -2.0272255 0.08808163 -1.5884373 -6.5239975
|
||||
18000 0.43281873 -2.0331268 0.08808163 -1.5937406 -0.048319943
|
||||
19000 0.44704527 -2.0286742 0.08808163 -1.5777408 1.6356417
|
||||
20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -3.8337952
|
||||
Loop time of 1.71924 on 4 procs for 20000 steps with 1200 atoms
|
||||
|
||||
Performance: 5025468.853 tau/day, 11633.030 timesteps/s
|
||||
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.39864 | 0.40873 | 0.42192 | 1.6 | 23.77
|
||||
Bond | 0.02118 | 0.021816 | 0.022785 | 0.4 | 1.27
|
||||
Neigh | 0.13931 | 0.14031 | 0.14117 | 0.2 | 8.16
|
||||
Comm | 0.13974 | 0.15328 | 0.16884 | 3.3 | 8.92
|
||||
Output | 0.00026131 | 0.00044435 | 0.00099206 | 0.0 | 0.03
|
||||
Modify | 0.93275 | 0.94138 | 0.95072 | 0.7 | 54.76
|
||||
Other | | 0.05327 | | | 3.10
|
||||
|
||||
Nlocal: 300 ave 303 max 298 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Nghost: 218.5 ave 226 max 215 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 2258.75 ave 2283 max 2216 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 9035
|
||||
Ave neighs/atom = 7.52917
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 1580
|
||||
Dangerous builds = 0
|
||||
unfix 5
|
||||
unfix 4
|
||||
fix 5 solute rigid/small molecule langevin 0.45 0.45 0.5 112211
|
||||
create bodies CPU = 5.43594e-05 secs
|
||||
150 rigid bodies with 450 atoms
|
||||
0.916597 = max distance from body owner to body atom
|
||||
fix 4 all enforce2d
|
||||
run 20000
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.568 | 8.6 | 8.691 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20000 0.44279735 -2.0443561 0.08808163 -1.5968706 -1.033643
|
||||
21000 0.4529129 -2.049461 0.08808163 -1.5937651 0.93160285
|
||||
22000 0.45039188 -2.0530092 0.08808163 -1.5993595 -0.10608965
|
||||
23000 0.45261583 -2.0336042 0.08808163 -1.5781494 -2.5769871
|
||||
24000 0.4608331 -2.0404645 0.08808163 -1.57834 3.1931675
|
||||
25000 0.43479001 -2.0617104 0.08808163 -1.6207242 2.8190122
|
||||
26000 0.47009651 -2.0754873 0.08808163 -1.605844 -0.9158501
|
||||
27000 0.45002704 -2.0782104 0.08808163 -1.6248568 0.98629661
|
||||
28000 0.45126136 -2.0592619 0.08808163 -1.6049065 0.03305448
|
||||
29000 0.44355328 -2.0572858 0.08808163 -1.6091868 -6.0797989
|
||||
30000 0.45053899 -2.0530953 0.08808163 -1.5993261 0.38382951
|
||||
31000 0.46931923 -2.0718827 0.08808163 -1.6028703 2.2346891
|
||||
32000 0.45348857 -2.0744024 0.08808163 -1.6182393 4.5028966
|
||||
33000 0.44767742 -2.0597127 0.08808163 -1.6082662 -2.8021641
|
||||
34000 0.45287544 -2.0857303 0.08808163 -1.6300648 -5.384091
|
||||
35000 0.44743898 -2.0927246 0.08808163 -1.6414717 1.4800508
|
||||
36000 0.45627028 -2.0720546 0.08808163 -1.6136336 -2.9961696
|
||||
37000 0.4641334 -2.0701098 0.08808163 -1.6053065 8.4186854
|
||||
38000 0.45922901 -2.0962331 0.08808163 -1.6354106 0.38361763
|
||||
39000 0.4692834 -2.0573815 0.08808163 -1.5883982 -2.2177345
|
||||
40000 0.46206931 -2.057851 0.08808163 -1.5947231 -1.0405727
|
||||
Loop time of 1.25476 on 4 procs for 20000 steps with 1200 atoms
|
||||
|
||||
Performance: 6885775.862 tau/day, 15939.296 timesteps/s
|
||||
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.40627 | 0.43037 | 0.45515 | 2.6 | 34.30
|
||||
Bond | 0.020504 | 0.021573 | 0.022739 | 0.5 | 1.72
|
||||
Neigh | 0.14337 | 0.14438 | 0.1453 | 0.2 | 11.51
|
||||
Comm | 0.13776 | 0.16647 | 0.19351 | 5.0 | 13.27
|
||||
Output | 0.00025082 | 0.00052994 | 0.0013635 | 0.0 | 0.04
|
||||
Modify | 0.45467 | 0.45822 | 0.46259 | 0.5 | 36.52
|
||||
Other | | 0.03321 | | | 2.65
|
||||
|
||||
Nlocal: 300 ave 304 max 293 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Nghost: 215.25 ave 217 max 213 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Neighs: 2340 ave 2378 max 2290 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 9360
|
||||
Ave neighs/atom = 7.8
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 1579
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
260
examples/micelle/log.29Mar2019.micelle-rigid.g++.1
Normal file
260
examples/micelle/log.29Mar2019.micelle-rigid.g++.1
Normal file
@ -0,0 +1,260 @@
|
||||
LAMMPS (29 Mar 2019)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000473022 secs
|
||||
read_data CPU = 0.0024147 secs
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.00022316 secs
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
|
||||
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
|
||||
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
|
||||
200 0.45 1.01454 0.10663502 1.5708 4.7598476
|
||||
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
|
||||
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
|
||||
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
|
||||
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
|
||||
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
|
||||
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
|
||||
Loop time of 0.103162 on 1 procs for 500 steps with 1200 atoms
|
||||
|
||||
Performance: 2093802.885 tau/day, 4846.766 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.068308 | 0.068308 | 0.068308 | 0.0 | 66.21
|
||||
Bond | 0.004235 | 0.004235 | 0.004235 | 0.0 | 4.11
|
||||
Neigh | 0.014069 | 0.014069 | 0.014069 | 0.0 | 13.64
|
||||
Comm | 0.0019219 | 0.0019219 | 0.0019219 | 0.0 | 1.86
|
||||
Output | 0.00017262 | 0.00017262 | 0.00017262 | 0.0 | 0.17
|
||||
Modify | 0.011728 | 0.011728 | 0.011728 | 0.0 | 11.37
|
||||
Other | | 0.002726 | | | 2.64
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 197 ave 197 max 197 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3094 ave 3094 max 3094 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3094
|
||||
Ave neighs/atom = 2.57833
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 52
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 50
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
group solvent molecule 0
|
||||
750 atoms in group solvent
|
||||
group solute subtract all solvent
|
||||
450 atoms in group solute
|
||||
unfix 1
|
||||
unfix 2
|
||||
unfix 4
|
||||
fix 1 solvent nve
|
||||
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
|
||||
150 rigid bodies with 450 atoms
|
||||
fix 4 all enforce2d
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
|
||||
50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539
|
||||
100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696
|
||||
150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743
|
||||
200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793
|
||||
250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722
|
||||
300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794
|
||||
350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926
|
||||
400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858
|
||||
450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617
|
||||
500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061
|
||||
Loop time of 0.178806 on 1 procs for 500 steps with 1200 atoms
|
||||
|
||||
Performance: 1208012.705 tau/day, 2796.326 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.086131 | 0.086131 | 0.086131 | 0.0 | 48.17
|
||||
Bond | 0.0042472 | 0.0042472 | 0.0042472 | 0.0 | 2.38
|
||||
Neigh | 0.021317 | 0.021317 | 0.021317 | 0.0 | 11.92
|
||||
Comm | 0.0025985 | 0.0025985 | 0.0025985 | 0.0 | 1.45
|
||||
Output | 0.000175 | 0.000175 | 0.000175 | 0.0 | 0.10
|
||||
Modify | 0.061408 | 0.061408 | 0.061408 | 0.0 | 34.34
|
||||
Other | | 0.00293 | | | 1.64
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 416 ave 416 max 416 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8769 ave 8769 max 8769 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8769
|
||||
Ave neighs/atom = 7.3075
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 47
|
||||
Dangerous builds = 2
|
||||
unfix 2
|
||||
unfix 4
|
||||
unfix 5
|
||||
fix 5 solute rigid/small molecule
|
||||
create bodies CPU = 0.00015378 secs
|
||||
150 rigid bodies with 450 atoms
|
||||
1.30435 = max distance from body owner to body atom
|
||||
fix 4 all enforce2d
|
||||
run 500
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.64 | 8.64 | 8.64 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793
|
||||
550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065
|
||||
600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965
|
||||
650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319
|
||||
700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351
|
||||
750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907
|
||||
800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431
|
||||
850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157
|
||||
900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056
|
||||
950 0.48351943 -1.9162485 0.13695201 -1.3868399 2.1891332
|
||||
1000 0.49033701 -1.9115165 0.13695201 -1.3765742 2.1508141
|
||||
Loop time of 0.166502 on 1 procs for 500 steps with 1200 atoms
|
||||
|
||||
Performance: 1297278.008 tau/day, 3002.958 timesteps/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.085767 | 0.085767 | 0.085767 | 0.0 | 51.51
|
||||
Bond | 0.0042562 | 0.0042562 | 0.0042562 | 0.0 | 2.56
|
||||
Neigh | 0.018039 | 0.018039 | 0.018039 | 0.0 | 10.83
|
||||
Comm | 0.0024002 | 0.0024002 | 0.0024002 | 0.0 | 1.44
|
||||
Output | 0.00018239 | 0.00018239 | 0.00018239 | 0.0 | 0.11
|
||||
Modify | 0.052717 | 0.052717 | 0.052717 | 0.0 | 31.66
|
||||
Other | | 0.003141 | | | 1.89
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 415 ave 415 max 415 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8743 ave 8743 max 8743 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8743
|
||||
Ave neighs/atom = 7.28583
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 40
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
260
examples/micelle/log.29Mar2019.micelle-rigid.g++.4
Normal file
260
examples/micelle/log.29Mar2019.micelle-rigid.g++.4
Normal file
@ -0,0 +1,260 @@
|
||||
LAMMPS (29 Mar 2019)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000422001 secs
|
||||
read_data CPU = 0.00473404 secs
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000183344 secs
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.54981866 0.93548899 0.068440043 1.5532895 1.9232786
|
||||
100 0.45 0.99659327 0.079228519 1.5254468 3.2135679
|
||||
150 0.86965411 0.90456016 0.07493355 1.8484231 4.3821925
|
||||
200 0.45 1.01454 0.10663502 1.5708 4.7598476
|
||||
250 0.79636561 0.82567712 0.12105337 1.7424325 5.4983899
|
||||
300 0.45 0.86475538 0.11819875 1.4325791 5.8554758
|
||||
350 0.72135464 0.70693069 0.10912636 1.5368106 6.0388247
|
||||
400 0.45 0.75067331 0.14165013 1.3419484 6.3840708
|
||||
450 0.64839221 0.62402486 0.14173679 1.4136135 6.4791009
|
||||
500 0.45 0.66669513 0.13695201 1.2532721 6.807146
|
||||
Loop time of 0.0426326 on 4 procs for 500 steps with 1200 atoms
|
||||
|
||||
Performance: 5066547.720 tau/day, 11728.120 timesteps/s
|
||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.016784 | 0.019254 | 0.022154 | 1.5 | 45.16
|
||||
Bond | 0.0010612 | 0.0012558 | 0.0014153 | 0.4 | 2.95
|
||||
Neigh | 0.0046048 | 0.0046697 | 0.0047245 | 0.1 | 10.95
|
||||
Comm | 0.0064592 | 0.0097114 | 0.012527 | 2.4 | 22.78
|
||||
Output | 0.00022507 | 0.00026393 | 0.00033951 | 0.0 | 0.62
|
||||
Modify | 0.0041659 | 0.0048084 | 0.0053945 | 0.8 | 11.28
|
||||
Other | | 0.002669 | | | 6.26
|
||||
|
||||
Nlocal: 300 ave 304 max 292 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
Nghost: 103.5 ave 108 max 98 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Neighs: 773.5 ave 792 max 735 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
|
||||
Total # of neighbors = 3094
|
||||
Ave neighs/atom = 2.57833
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 52
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 50
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
group solvent molecule 0
|
||||
750 atoms in group solvent
|
||||
group solute subtract all solvent
|
||||
450 atoms in group solute
|
||||
unfix 1
|
||||
unfix 2
|
||||
unfix 4
|
||||
fix 1 solvent nve
|
||||
fix 2 solvent temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 5 solute rigid molecule langevin 0.45 0.45 0.5 112211
|
||||
150 rigid bodies with 450 atoms
|
||||
fix 4 all enforce2d
|
||||
run 500
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.251 | 5.282 | 5.374 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45318168 -1.3753652 0.13695201 -0.8705807 1.975423
|
||||
50 0.77871641 -1.6955252 0.13695201 -0.92651507 0.64222539
|
||||
100 0.5336062 -1.7124572 0.13695201 -1.1423948 -0.11959696
|
||||
150 0.58789067 -1.7926109 0.13695201 -1.1784877 1.2592743
|
||||
200 0.47864796 -1.8040298 0.13695201 -1.2785752 3.6739793
|
||||
250 0.51124651 -1.8614797 0.13695201 -1.309566 2.5817722
|
||||
300 0.45695639 -1.8708384 0.13695201 -1.3629901 3.0833794
|
||||
350 0.477504 -1.8924359 0.13695201 -1.3679098 -5.1605926
|
||||
400 0.45328205 -1.87754 0.13695201 -1.372674 -4.0355858
|
||||
450 0.47465031 -1.9071924 0.13695201 -1.3849826 3.1949617
|
||||
500 0.45533691 -1.9072316 0.13695201 -1.4006978 0.48079061
|
||||
Loop time of 0.0887392 on 4 procs for 500 steps with 1200 atoms
|
||||
|
||||
Performance: 2434100.210 tau/day, 5634.491 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.022611 | 0.022839 | 0.023082 | 0.1 | 25.74
|
||||
Bond | 0.0010793 | 0.0011569 | 0.0012515 | 0.2 | 1.30
|
||||
Neigh | 0.0064609 | 0.0064996 | 0.0065265 | 0.0 | 7.32
|
||||
Comm | 0.0071712 | 0.0073687 | 0.0077734 | 0.3 | 8.30
|
||||
Output | 0.00023389 | 0.00025356 | 0.00030327 | 0.0 | 0.29
|
||||
Modify | 0.047258 | 0.047683 | 0.048503 | 0.2 | 53.73
|
||||
Other | | 0.002938 | | | 3.31
|
||||
|
||||
Nlocal: 300 ave 309 max 291 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Nghost: 218.75 ave 223 max 216 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Neighs: 2192.25 ave 2251 max 2113 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 8769
|
||||
Ave neighs/atom = 7.3075
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 47
|
||||
Dangerous builds = 2
|
||||
unfix 2
|
||||
unfix 4
|
||||
unfix 5
|
||||
fix 5 solute rigid/small molecule
|
||||
create bodies CPU = 7.70092e-05 secs
|
||||
150 rigid bodies with 450 atoms
|
||||
1.30435 = max distance from body owner to body atom
|
||||
fix 4 all enforce2d
|
||||
run 500
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.565 | 8.597 | 8.69 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
500 0.45533691 -1.9072316 0.13695201 -1.4006978 2.4545793
|
||||
550 0.45627282 -1.912409 0.13695201 -1.4051155 2.1845065
|
||||
600 0.44734553 -1.8890695 0.13695201 -1.389022 2.3458965
|
||||
650 0.46444648 -1.9042462 0.13695201 -1.3903185 2.1609319
|
||||
700 0.47113236 -1.8977576 0.13695201 -1.3784032 2.2420351
|
||||
750 0.48554548 -1.9253545 0.13695201 -1.3943015 2.143907
|
||||
800 0.46350091 -1.8865749 0.13695201 -1.3734146 2.294431
|
||||
850 0.4766104 -1.9094039 0.13695201 -1.3856031 2.2077157
|
||||
900 0.48988467 -1.9051538 0.13695201 -1.3705787 2.0107056
|
||||
950 0.48351942 -1.9162485 0.13695201 -1.3868399 2.1891332
|
||||
1000 0.490337 -1.9115164 0.13695201 -1.3765742 2.1508141
|
||||
Loop time of 0.0588261 on 4 procs for 500 steps with 1200 atoms
|
||||
|
||||
Performance: 3671840.233 tau/day, 8499.630 timesteps/s
|
||||
98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.022407 | 0.022631 | 0.0229 | 0.1 | 38.47
|
||||
Bond | 0.0010669 | 0.0011355 | 0.0012124 | 0.2 | 1.93
|
||||
Neigh | 0.0052333 | 0.00528 | 0.0053182 | 0.0 | 8.98
|
||||
Comm | 0.0063677 | 0.0066406 | 0.0068488 | 0.2 | 11.29
|
||||
Output | 0.00023055 | 0.00024778 | 0.00028086 | 0.0 | 0.42
|
||||
Modify | 0.020577 | 0.020651 | 0.020834 | 0.1 | 35.11
|
||||
Other | | 0.00224 | | | 3.81
|
||||
|
||||
Nlocal: 300 ave 303 max 295 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 219 ave 224 max 215 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
Neighs: 2185.75 ave 2244 max 2143 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 8743
|
||||
Ave neighs/atom = 7.28583
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 40
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
218
examples/micelle/log.29Mar2019.micelle.g++.1
Normal file
218
examples/micelle/log.29Mar2019.micelle.g++.1
Normal file
@ -0,0 +1,218 @@
|
||||
LAMMPS (29 Mar 2019)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.00037837 secs
|
||||
read_data CPU = 0.00206876 secs
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000177383 secs
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.799 | 3.799 | 3.799 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.208895 on 1 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 2068027.282 tau/day, 4787.100 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.14142 | 0.14142 | 0.14142 | 0.0 | 67.70
|
||||
Bond | 0.008441 | 0.008441 | 0.008441 | 0.0 | 4.04
|
||||
Neigh | 0.025716 | 0.025716 | 0.025716 | 0.0 | 12.31
|
||||
Comm | 0.0036864 | 0.0036864 | 0.0036864 | 0.0 | 1.76
|
||||
Output | 0.0003562 | 0.0003562 | 0.0003562 | 0.0 | 0.17
|
||||
Modify | 0.023699 | 0.023699 | 0.023699 | 0.0 | 11.35
|
||||
Other | | 0.00558 | | | 2.67
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 195 ave 195 max 195 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3136 ave 3136 max 3136 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 50
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.024 | 4.024 | 4.024 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
|
||||
50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557
|
||||
100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661
|
||||
150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373
|
||||
200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655
|
||||
250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682
|
||||
300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947
|
||||
350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532
|
||||
400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066
|
||||
450 0.47220236 -1.9468502 0.065625624 -1.4094157 2.0984288
|
||||
500 0.4684673 -1.9444333 0.076696283 -1.3996601 2.0528682
|
||||
550 0.47683128 -1.958676 0.070589719 -1.4116523 2.0856022
|
||||
600 0.46851243 -1.9338267 0.07060548 -1.3950992 2.26405
|
||||
650 0.46874142 -1.9462493 0.069134685 -1.4087638 2.1070263
|
||||
700 0.46437384 -1.9309953 0.071977522 -1.3950309 2.2256923
|
||||
750 0.47326225 -1.9484255 0.075435845 -1.4001218 2.0880254
|
||||
800 0.45 -1.9646005 0.064159585 -1.4508159 2.0612696
|
||||
850 0.46748307 -1.970559 0.060384874 -1.4430806 1.9472879
|
||||
900 0.46909484 -1.953723 0.062470295 -1.4225488 2.0222909
|
||||
950 0.45631531 -1.9387753 0.067536568 -1.4153037 2.0638421
|
||||
1000 0.45 -1.9727646 0.058607721 -1.4645318 1.9982315
|
||||
Loop time of 0.252254 on 1 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 1712557.882 tau/day, 3964.254 timesteps/s
|
||||
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17177 | 0.17177 | 0.17177 | 0.0 | 68.09
|
||||
Bond | 0.0084555 | 0.0084555 | 0.0084555 | 0.0 | 3.35
|
||||
Neigh | 0.03991 | 0.03991 | 0.03991 | 0.0 | 15.82
|
||||
Comm | 0.0049119 | 0.0049119 | 0.0049119 | 0.0 | 1.95
|
||||
Output | 0.00039077 | 0.00039077 | 0.00039077 | 0.0 | 0.15
|
||||
Modify | 0.021131 | 0.021131 | 0.021131 | 0.0 | 8.38
|
||||
Other | | 0.005685 | | | 2.25
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 415 ave 415 max 415 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8586 ave 8586 max 8586 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 8586
|
||||
Ave neighs/atom = 7.155
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 86
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
218
examples/micelle/log.29Mar2019.micelle.g++.4
Normal file
218
examples/micelle/log.29Mar2019.micelle.g++.4
Normal file
@ -0,0 +1,218 @@
|
||||
LAMMPS (29 Mar 2019)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000413656 secs
|
||||
read_data CPU = 0.00487924 secs
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.000178576 secs
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.42246
|
||||
ghost atom cutoff = 1.42246
|
||||
binsize = 0.71123, bins = 51 51 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair soft, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.758 | 3.85 | 4.126 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.0906248 on 4 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 4766906.584 tau/day, 11034.506 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.036572 | 0.039266 | 0.041216 | 1.0 | 43.33
|
||||
Bond | 0.0023205 | 0.0024512 | 0.0025697 | 0.2 | 2.70
|
||||
Neigh | 0.0088909 | 0.0089301 | 0.0089679 | 0.0 | 9.85
|
||||
Comm | 0.022308 | 0.024047 | 0.027175 | 1.3 | 26.53
|
||||
Output | 0.00057411 | 0.00061274 | 0.00071025 | 0.0 | 0.68
|
||||
Modify | 0.0083182 | 0.0092374 | 0.0098341 | 0.6 | 10.19
|
||||
Other | | 0.006081 | | | 6.71
|
||||
|
||||
Nlocal: 300 ave 305 max 292 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 100.25 ave 108 max 93 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 784 ave 815 max 739 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 50
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
run 1000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.8
|
||||
ghost atom cutoff = 2.8
|
||||
binsize = 1.4, bins = 26 26 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.001 | 4.032 | 4.124 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
|
||||
50 0.59734982 -1.8103783 0.076066922 -1.1374593 3.2770557
|
||||
100 0.45 -1.8347112 0.093132329 -1.2919539 3.024661
|
||||
150 0.51924311 -1.8943977 0.076004124 -1.2995832 2.5570373
|
||||
200 0.45 -1.8918672 0.082422107 -1.3598201 2.5629655
|
||||
250 0.50281134 -1.920406 0.074011331 -1.3440023 2.3518682
|
||||
300 0.45 -1.9351047 0.075337265 -1.4101424 2.3249947
|
||||
350 0.47650026 -1.9313687 0.072115117 -1.3831504 2.1987532
|
||||
400 0.45 -1.9554318 0.081603939 -1.4242028 2.0787066
|
||||
450 0.47220236 -1.9468502 0.065625625 -1.4094157 2.0984288
|
||||
500 0.4684673 -1.9444333 0.076696285 -1.3996601 2.0528682
|
||||
550 0.47683128 -1.958676 0.070589721 -1.4116523 2.0856023
|
||||
600 0.46851245 -1.9338267 0.070605469 -1.3950992 2.26405
|
||||
650 0.46874143 -1.9462493 0.069134686 -1.4087638 2.1070262
|
||||
700 0.4643739 -1.9309953 0.071977511 -1.3950309 2.225692
|
||||
750 0.47326259 -1.9484258 0.075435808 -1.4001218 2.0880235
|
||||
800 0.45 -1.9646003 0.06415956 -1.4508158 2.0612703
|
||||
850 0.46748278 -1.9705588 0.06038513 -1.4430804 1.9472884
|
||||
900 0.46909438 -1.9537221 0.062470305 -1.4225483 2.0223008
|
||||
950 0.45631508 -1.9387742 0.067536066 -1.4153033 2.063854
|
||||
1000 0.45 -1.9727651 0.058608085 -1.464532 1.9982447
|
||||
Loop time of 0.0878521 on 4 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Performance: 4917357.613 tau/day, 11382.772 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.043517 | 0.044455 | 0.046903 | 0.7 | 50.60
|
||||
Bond | 0.0020199 | 0.0022303 | 0.0024347 | 0.4 | 2.54
|
||||
Neigh | 0.012207 | 0.012335 | 0.012512 | 0.1 | 14.04
|
||||
Comm | 0.014938 | 0.018265 | 0.020068 | 1.5 | 20.79
|
||||
Output | 0.00061369 | 0.00064814 | 0.00073504 | 0.0 | 0.74
|
||||
Modify | 0.0052264 | 0.0053691 | 0.0055039 | 0.2 | 6.11
|
||||
Other | | 0.00455 | | | 5.18
|
||||
|
||||
Nlocal: 300 ave 305 max 296 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
Nghost: 219.5 ave 228 max 214 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
Neighs: 2146.5 ave 2201 max 2114 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 8586
|
||||
Ave neighs/atom = 7.155
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 86
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:00
|
||||
Reference in New Issue
Block a user