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LAMMPS (30 Aug 2013)
units real
atom_style atomic
variable L equal 12
variable l2 equal 6
variable l equal 4
variable w equal 2
lattice fcc 5.405 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.405 5.405 5.405
region mdRegion cylinder z 0. 0. ${l2} -$w $w
region mdRegion cylinder z 0. 0. 6 -$w $w
region mdRegion cylinder z 0. 0. 6 -2 $w
region mdRegion cylinder z 0. 0. 6 -2 2
region mdInternal cylinder z 0. 0. $l -$w $w
region mdInternal cylinder z 0. 0. 4 -$w $w
region mdInternal cylinder z 0. 0. 4 -2 $w
region mdInternal cylinder z 0. 0. 4 -2 2
boundary f f f
pair_style lj/cut 13.5
read_data circle_temp.init
Reading data file ...
orthogonal box = (-64.86 -64.86 -10.81) to (64.86 64.86 10.81)
2 by 2 by 1 MPI processor grid
1792 atoms
1792 velocities
fix ZWALLS all wall/reflect zlo EDGE zhi EDGE
mass 1 39.95
pair_coeff 1 1 .238 3.405 13.5
group internal region mdInternal
832 atoms in group internal
group ghost subtract all internal
960 atoms in group ghost
fix AtC internal atc two_temperature Ar_ttm.mat
ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat
ATC: version 2.0
ATC: peratom PE compute created with ID: 3
ATC: 2 materials defined from Ar_ttm.mat
ATC: creating two_temperature extrinsic model
ATC: 2 materials defined from Ar_ttm.mat
# computational geometry
fix_modify AtC mesh read gaussianIC2d_hex.mesh
ATC: read 388 nodes
ATC: read 173 HEX8 elements
ATC: created nodeset 11 with 22 nodes
ATC: created nodeset 12 with 22 nodes
ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive
#fix_modify AtC mesh read gaussianIC2d_hex.exo
#fix_modify AtC mesh read gaussianIC2d_hex2.exo
#fix_modify AtC mesh read gaussianIC2d_hex2.mesh
fix_modify AtC mesh write parsed_gaussianIC2d_hex.mesh
fix_modify AtC mesh output gaussianIC2d_hexMESH
fix_modify AtC boundary ghost
# numerical parameters
fix_modify AtC time_integration fractional_step
fix_modify AtC internal_quadrature off
# initial conditions
fix_modify AtC fix temperature all 20.0
# NOTE this is only gaussian in x
fix_modify AtC fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
# thermostat
fix_modify AtC control thermal rescale 10
fix_modify AtC extrinsic exchange off
# run to equilibrate
thermo_style custom step temp pe f_AtC[2] f_AtC[4]
timestep 1.0
thermo 10
run 400
Setting up run ...
Memory usage per processor = 50.5401 Mbytes
Step Temp PotEng AtC[2] AtC[4]
0 18.559464 -2927.2438 20 22.619065
10 9.2908989 -2926.8636 20 22.619065
20 9.2908989 -2926.1076 20 22.619065
30 9.2908989 -2924.9455 20 22.619065
40 9.2908989 -2923.3809 20 22.619065
50 9.2908989 -2921.4179 20 22.619065
60 9.2908989 -2919.0624 20 22.619065
70 9.2908989 -2916.3227 20 22.619065
80 9.2908989 -2913.2105 20 22.619065
90 9.2908989 -2909.7421 20 22.619065
100 9.2908989 -2905.9396 20 22.619065
110 9.2908989 -2901.8364 20 22.619065
120 9.2908989 -2897.474 20 22.619065
130 9.2908989 -2892.8985 20 22.619065
140 9.2908989 -2888.1815 20 22.619065
150 9.2908989 -2883.3945 20 22.619065
160 9.2908989 -2878.6283 20 22.619065
170 9.2908989 -2873.9874 20 22.619065
180 9.2908989 -2869.5705 20 22.619065
190 9.2908989 -2865.4802 20 22.619065
200 9.2908989 -2861.8004 20 22.619065
210 9.2908989 -2858.6064 20 22.619065
220 9.2908989 -2855.9338 20 22.619065
230 9.2908989 -2853.7842 20 22.619065
240 9.2908989 -2852.155 20 22.619065
250 9.2908989 -2850.9801 20 22.619065
260 9.2908989 -2850.2014 20 22.619065
270 9.2908989 -2849.745 20 22.619065
280 9.2908989 -2849.5468 20 22.619065
290 9.2908989 -2849.5383 20 22.619065
300 9.2908989 -2849.6571 20 22.619065
310 9.2908989 -2849.8648 20 22.619065
320 9.2908989 -2850.1261 20 22.619065
330 9.2908989 -2850.4068 20 22.619065
340 9.2908989 -2850.6989 20 22.619065
350 9.2908989 -2850.9948 20 22.619065
360 9.2908989 -2851.2898 20 22.619065
370 9.2908989 -2851.5911 20 22.619065
380 9.2908989 -2851.9001 20 22.619065
390 9.2908989 -2852.2299 20 22.619065
400 9.2908989 -2852.6005 20 22.619065
Loop time of 16.0537 on 4 procs for 400 steps with 1792 atoms
Pair time (%) = 1.06738 (6.64882)
Neigh time (%) = 0 (0)
Comm time (%) = 0.113732 (0.708445)
Outpt time (%) = 0.00429314 (0.0267423)
Other time (%) = 14.8683 (92.616)
Nlocal: 448 ave 448 max 448 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 696 ave 696 max 696 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 51280 ave 52662 max 49886 min
Histogram: 1 1 0 0 0 0 0 0 0 2
FullNghs: 102560 ave 102560 max 102560 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 410240
Ave neighs/atom = 228.929
Neighbor list builds = 0
Dangerous builds = 0
# boundary conditions
fix_modify AtC unfix temperature all
fix_modify AtC unfix electron_temperature all
fix_modify AtC fix temperature 11 20.0
fix_modify AtC fix temperature 12 20.0
# numerical parameters
fix_modify AtC extrinsic electron_integration explicit 10
# thermostat
fix_modify AtC control thermal flux
fix_modify AtC extrinsic exchange on
# output
fix_modify AtC output gaussianIC2d_hexFE 10 full_text binary
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
dump D1 all atom 10 gaussianIC2d_hex.dmp
# relax the system
run 1000
Setting up run ...
Memory usage per processor = 55.345 Mbytes
Step Temp PotEng AtC[2] AtC[4]
400 9.2908989 -2852.6005 20 22.619065
410 9.3739709 -2853.0186 20.040932 22.611409
420 9.4777325 -2853.5491 20.093686 22.603893
430 9.603939 -2854.2014 20.159312 22.596534
440 9.7542127 -2854.9791 20.238859 22.589353
450 9.9295278 -2855.9033 20.332984 22.582373
460 10.130063 -2856.9771 20.441869 22.575614
470 10.35505 -2858.1731 20.565152 22.569098
480 10.602677 -2859.5024 20.701879 22.562845
490 10.870017 -2860.9396 20.85048 22.556874
500 11.153033 -2862.4773 21.008778 22.551199
510 11.446646 -2864.0797 21.174034 22.545832
520 11.744908 -2865.7188 21.343051 22.540779
530 12.041263 -2867.364 21.512313 22.53604
540 12.328877 -2868.9829 21.678162 22.531611
550 12.600994 -2870.5197 21.836981 22.527482
560 12.851303 -2871.9663 21.985384 22.523636
570 13.074293 -2873.2785 22.120399 22.520052
580 13.265513 -2874.4253 22.239594 22.516705
590 13.421751 -2875.3914 22.341174 22.513566
600 13.541109 -2876.1789 22.424015 22.510605
610 13.623016 -2876.7775 22.487675 22.507788
620 13.668152 -2877.1854 22.532362 22.505085
630 13.678331 -2877.4076 22.558874 22.502464
640 13.656332 -2877.4627 22.568531 22.499895
650 13.605722 -2877.3683 22.563078 22.497353
660 13.530708 -2877.1524 22.544625 22.494813
670 13.435942 -2876.8175 22.515544 22.492256
680 13.326383 -2876.406 22.478395 22.489667
690 13.207157 -2875.947 22.435845 22.487033
700 13.083403 -2875.4566 22.390572 22.484348
710 12.960144 -2874.9651 22.345189 22.48161
720 12.842152 -2874.501 22.302149 22.478818
730 12.73379 -2874.0887 22.263653 22.47598
740 12.638847 -2873.7524 22.231544 22.473103
750 12.560388 -2873.4976 22.207229 22.470197
760 12.500634 -2873.3389 22.191608 22.467277
770 12.46088 -2873.2928 22.185044 22.464357
780 12.441476 -2873.3551 22.187384 22.46145
790 12.441898 -2873.5323 22.198021 22.458571
800 12.46082 -2873.805 22.215988 22.455733
810 12.49627 -2874.168 22.240082 22.452947
820 12.545761 -2874.6084 22.268974 22.450223
830 12.606442 -2875.1154 22.30132 22.447568
840 12.675209 -2875.662 22.335827 22.444987
850 12.748831 -2876.2487 22.37131 22.442482
860 12.82405 -2876.8458 22.406711 22.440055
870 12.897672 -2877.4308 22.441104 22.437705
880 12.966664 -2877.9918 22.473679 22.435429
890 13.028239 -2878.5162 22.503727 22.433223
900 13.079989 -2878.9972 22.530647 22.431081
910 13.120007 -2879.4076 22.553961 22.428997
920 13.147015 -2879.7527 22.573337 22.426963
930 13.16047 -2880.0242 22.58862 22.424972
940 13.160646 -2880.2274 22.59987 22.423016
950 13.148646 -2880.3654 22.607373 22.421086
960 13.126349 -2880.4343 22.611652 22.419177
970 13.096257 -2880.4731 22.613422 22.417282
980 13.061264 -2880.4808 22.61352 22.415397
990 13.024335 -2880.4734 22.612794 22.413521
1000 12.988154 -2880.4712 22.611974 22.411652
1010 12.954832 -2880.4752 22.61156 22.409791
1020 12.925706 -2880.5039 22.611782 22.407939
1030 12.901268 -2880.5535 22.612583 22.406098
1040 12.88122 -2880.6284 22.613671 22.404269
1050 12.864638 -2880.7185 22.614595 22.402454
1060 12.850161 -2880.8186 22.614818 22.400653
1070 12.836182 -2880.9229 22.613762 22.398864
1080 12.820975 -2881.0195 22.610813 22.397087
1090 12.802812 -2881.1106 22.605315 22.395317
1100 12.780035 -2881.173 22.596564 22.39355
1110 12.751178 -2881.197 22.583861 22.391781
1120 12.715144 -2881.1906 22.566647 22.390003
1130 12.671396 -2881.1397 22.544644 22.388208
1140 12.620084 -2881.0462 22.517962 22.386389
1150 12.562182 -2880.9131 22.487201 22.384538
1160 12.499543 -2880.7564 22.453506 22.382651
1170 12.434887 -2880.5794 22.418573 22.380722
1180 12.371719 -2880.4084 22.384601 22.378752
1190 12.314101 -2880.2706 22.354147 22.376742
1200 12.266306 -2880.174 22.329904 22.374701
1210 12.232344 -2880.154 22.31439 22.372639
1220 12.215387 -2880.2186 22.309572 22.370571
1230 12.217218 -2880.3818 22.316512 22.368514
1240 12.237824 -2880.6446 22.335104 22.366485
1250 12.275283 -2880.9982 22.36402 22.364503
1260 12.325989 -2881.4247 22.400878 22.362581
1270 12.385157 -2881.8965 22.442588 22.360729
1280 12.447441 -2882.39 22.485773 22.358953
1290 12.507528 -2882.8684 22.527171 22.357252
1300 12.560627 -2883.3106 22.563936 22.355622
1310 12.602763 -2883.7013 22.59382 22.354054
1320 12.630896 -2884.014 22.615213 22.352535
1330 12.642918 -2884.2415 22.627102 22.351052
1340 12.63759 -2884.376 22.628986 22.349588
1350 12.614465 -2884.4144 22.620781 22.348128
1360 12.573824 -2884.3577 22.602735 22.346656
1370 12.516666 -2884.2059 22.575396 22.345156
1380 12.444674 -2883.9691 22.539592 22.343613
1390 12.360208 -2883.6693 22.496432 22.342016
1400 12.266237 -2883.307 22.447301 22.340354
Loop time of 98.8153 on 4 procs for 1000 steps with 1792 atoms
Pair time (%) = 2.6955 (2.72782)
Neigh time (%) = 0.012054 (0.0121985)
Comm time (%) = 0.181319 (0.183493)
Outpt time (%) = 0.986294 (0.998119)
Other time (%) = 94.9401 (96.0784)
Nlocal: 448 ave 448 max 448 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 696 ave 696 max 696 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 52292.2 ave 52503 max 52099 min
Histogram: 2 0 0 0 0 0 0 0 1 1
FullNghs: 104584 ave 104823 max 104416 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Total # of neighbors = 418338
Ave neighs/atom = 233.448
Neighbor list builds = 2
Dangerous builds = 0
|
