Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/examples/coreshell/log.coreshell.6Mar15.linux.1
d0bbf3fb9785efficient_neuronet

Last Change
Raw File

log.coreshell.6Mar15.linux.1
View Options

LAMMPS (5 Mar 2015)
# Testsystem for core-shell model compared to Mitchel and Finchham
# Hendrik Heenen, June 2014
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
1 by 1 by 1 MPI processor grid
reading atoms ...
432 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
216 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
kspace_style ewald 1.0e-6
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
compute CSequ all temp/cs cores shells
# output via chunk method
#compute prop all property/atom i_CSID
#compute cs_chunk all chunk/atom c_prop
#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CSequ
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
Ewald initialization ...
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 22
velocity all scale 1427 temp CSequ
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CSequ
# 2 fmsec timestep
timestep 0.002
run 500
Ewald initialization ...
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Memory usage per processor = 6.86279 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -628.35255 -668.0717 39.719144 1427 -20608.918 -668.0717 1.6320365 1025.8481 -1695.5518 0 3.4602128e-14 4.1910919e-15 13990.5
50 -632.83924 -664.88103 32.041787 1151.1736 -4098.5062 -668.28414 37.966205 988.74855 -1694.9989 3.4031081 25.060198 9.2894103 13990.5
100 -630.51517 -660.52949 30.014321 1078.3323 -3202.2416 -664.01378 39.505874 991.23277 -1694.7524 3.4842892 26.36833 10.674509 13990.5
150 -628.58401 -661.59121 33.007195 1185.8581 106.75378 -665.3449 46.400029 982.93422 -1694.6791 3.7536882 27.270427 10.826035 13990.5
200 -627.39592 -662.45902 35.063102 1259.7212 -1672.1319 -665.61583 41.658839 987.14579 -1694.4205 3.1568106 23.525213 6.58382 13990.5
250 -625.74143 -660.30023 34.558805 1241.6032 -1596.9927 -664.13159 42.148927 988.19127 -1694.4718 3.8313604 27.156726 8.5397995 13990.5
300 -625.07332 -659.68738 34.614061 1243.5884 -1525.4995 -663.38119 42.077062 989.22231 -1694.6806 3.6938081 26.233327 9.2896507 13990.5
350 -623.86869 -663.20518 39.336492 1413.2524 -1932.3573 -667.15923 40.519069 986.96395 -1694.6422 3.9540529 30.551213 14.69189 13990.5
400 -623.55169 -660.39199 36.840301 1323.5711 -1747.3638 -664.07907 41.004982 989.66515 -1694.7492 3.6870716 27.463501 11.288658 13990.5
450 -623.03498 -658.41209 35.377106 1271.0025 1243.4895 -662.14754 48.097573 984.42115 -1694.6663 3.735455 24.531264 6.5614635 13990.5
500 -622.34231 -660.50992 38.167608 1371.2576 -1301.9479 -664.26607 41.813817 988.57955 -1694.6594 3.7561473 23.595051 5.844275 13990.5
Loop time of 8.51483 on 1 procs for 500 steps with 432 atoms
Pair time (%) = 7.73226 (90.8093)
Bond time (%) = 0.00232315 (0.0272836)
Kspce time (%) = 0.518208 (6.08594)
Neigh time (%) = 0.17925 (2.10514)
Comm time (%) = 0.0653358 (0.767317)
Outpt time (%) = 0.000309229 (0.00363165)
Other time (%) = 0.0171449 (0.201354)
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9307 ave 9307 max 9307 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 297357 ave 297357 max 297357 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 297357
Ave neighs/atom = 688.326
Ave special neighs/atom = 1
Neighbor list builds = 21
Dangerous builds = 0
unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000
Ewald initialization ...
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Memory usage per processor = 6.86279 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -622.34231 -660.50992 38.167608 1371.2576 -1301.9479 -664.26607 41.813817 988.57955 -1694.6594 3.7561473 23.595051 5.844275 13990.5
550 -622.53283 -661.59223 39.059403 1403.2973 -385.2836 -664.93615 43.738024 985.8195 -1694.4937 3.3439143 21.675844 3.5834691 13990.5
600 -622.20391 -659.47921 37.275306 1339.1996 473.13042 -663.45898 46.093667 985.15793 -1694.7106 3.9797724 25.783443 9.4059533 13990.5
650 -622.3473 -660.85461 38.507306 1383.462 -1021.6262 -664.41457 42.581674 987.48335 -1694.4796 3.5599548 24.069859 6.9189396 13990.5
700 -621.9195 -660.92044 39.000937 1401.1968 71.427836 -664.81486 44.86887 985.26444 -1694.9482 3.894424 28.397753 9.3904596 13990.5
750 -622.28852 -658.93918 36.650662 1316.7579 -1249.2306 -662.31101 41.915549 990.48822 -1694.7148 3.3718339 24.259772 4.9454879 13990.5
800 -622.31982 -657.72021 35.400389 1271.839 254.0237 -661.60518 45.506498 987.48185 -1694.5935 3.8849638 24.386892 7.4962982 13990.5
850 -622.31623 -661.4936 39.177375 1407.5357 37.74414 -665.02673 44.380924 985.14989 -1694.5575 3.5331239 23.316952 5.5622744 13990.5
900 -621.83183 -660.10965 38.277816 1375.2171 1738.9676 -664.10328 48.428909 981.86752 -1694.3997 3.9936342 28.519154 11.384782 13990.5
950 -622.03652 -659.97862 37.942096 1363.1555 -49.888312 -663.91816 44.582637 986.15057 -1694.6514 3.9395363 27.011672 8.4915326 13990.5
1000 -621.71637 -660.69133 38.97496 1400.2635 -46.518055 -665.12412 44.669238 984.85534 -1694.6487 4.432789 29.799247 9.5235093 13990.5
1050 -621.90579 -658.42698 36.521187 1312.1062 27.913475 -662.80273 44.953547 986.65365 -1694.4099 4.3757505 28.035827 8.4898226 13990.5
1100 -621.92929 -661.57742 39.648126 1424.4485 820.11499 -665.35048 46.491843 982.84734 -1694.6897 3.7730563 27.803982 8.4955015 13990.5
1150 -622.36518 -659.3383 36.973112 1328.3426 -799.63876 -662.87451 43.109263 988.96432 -1694.9481 3.5362185 23.473216 4.2340288 13990.5
1200 -621.80278 -659.38996 37.587182 1350.4045 173.56518 -663.76385 45.4017 985.49478 -1694.6603 4.3738897 29.25765 11.540749 13990.5
1250 -621.89233 -658.13657 36.244239 1302.1562 -194.31216 -662.25387 44.600608 987.50208 -1694.3566 4.1173041 27.781148 11.737589 13990.5
1300 -622.01575 -659.4502 37.43445 1344.9172 419.91066 -663.67863 46.041458 984.96293 -1694.683 4.2284307 27.725967 9.666138 13990.5
1350 -621.64918 -658.52586 36.876681 1324.8781 -1542.8395 -662.92795 41.627963 989.87571 -1694.4316 4.4020823 30.153096 11.999079 13990.5
1400 -621.65713 -657.77765 36.120515 1297.7112 -2133.9795 -662.63382 40.620287 991.32101 -1694.5751 4.8561686 30.546416 11.476013 13990.5
1450 -621.92858 -659.45137 37.522795 1348.0912 217.78723 -663.34796 45.334127 985.96702 -1694.6491 3.8965883 27.625033 7.3805255 13990.5
1500 -621.9432 -657.57884 35.635634 1280.2907 632.02267 -661.89128 46.527064 986.00347 -1694.4218 4.3124408 28.010625 8.740067 13990.5
Loop time of 17.041 on 1 procs for 1000 steps with 432 atoms
Pair time (%) = 15.4577 (90.7085)
Bond time (%) = 0.00465488 (0.0273157)
Kspce time (%) = 1.03763 (6.08902)
Neigh time (%) = 0.390329 (2.29052)
Comm time (%) = 0.131336 (0.770706)
Outpt time (%) = 0.000611782 (0.00359005)
Other time (%) = 0.0188062 (0.110358)
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9406 ave 9406 max 9406 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 297120 ave 297120 max 297120 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 297120
Ave neighs/atom = 687.778
Ave special neighs/atom = 1
Neighbor list builds = 46
Dangerous builds = 0
c4science · Help