LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# Testsystem for core-shell model compared to Mitchel and Finchham
# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation.
# ------------------------ 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 2 by 2 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 ------------------------------
pair_style born/coul/wolf/cs 0.1 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
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 22
ghost atom cutoff = 22
binsize = 11, bins = 3 3 3
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair born/coul/wolf/cs, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
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
Per MPI rank memory allocation (min/avg/max) = 6.881 | 6.881 | 6.881 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -637.41039 -677.06805 39.657659 1427 -21302.622 -677.06805 1.6320365 -678.70009 0 0 1.3530839e-14 3.6429193e-15 13990.5
50 -635.62704 -667.67108 32.044047 1153.0397 -4532.6842 -669.45828 37.771018 -707.2293 0 1.787201 9.6848095 2.2028349 13990.5
100 -632.76343 -662.83014 30.066711 1081.8893 -3493.0827 -664.98212 39.195967 -704.17809 0 2.151977 11.060773 2.1578583 13990.5
150 -630.82533 -663.70172 32.876385 1182.9897 -75.706966 -666.12608 46.261038 -712.38712 0 2.4243598 11.746728 2.7663319 13990.5
200 -629.15463 -664.55009 35.395466 1273.6337 -1707.9185 -666.88117 41.794868 -708.67604 0 2.331082 10.596229 3.0031523 13990.5
250 -627.86625 -662.60876 34.742511 1250.1384 -1263.5726 -665.214 43.005742 -708.21974 0 2.6052329 10.572641 1.8416041 13990.5
300 -627.10829 -664.12159 37.013298 1331.8481 -1884.8587 -666.39136 40.786141 -707.1775 0 2.2697693 9.4160684 1.2472271 13990.5
350 -626.2729 -665.01858 38.745682 1394.1844 -1433.1302 -667.44315 41.864785 -709.30793 0 2.4245625 10.312641 1.9815612 13990.5
400 -625.54274 -661.84438 36.301638 1306.2404 -355.45544 -664.4483 44.370671 -708.81897 0 2.6039277 11.076154 2.1819702 13990.5
450 -624.88802 -661.12299 36.234964 1303.8413 -2356.6102 -663.6463 39.57847 -703.22477 0 2.523314 9.8995886 1.3113549 13990.5
500 -623.86344 -660.20235 36.338906 1307.5814 462.72863 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5
Loop time of 3.06159 on 4 procs for 500 steps with 432 atoms
Performance: 28.221 ns/day, 0.850 hours/ns, 163.314 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 | 2.3967 | 2.4786 | 2.5323 | 3.3 | 80.96
Bond | 0.00078011 | 0.00080734 | 0.00087595 | 0.0 | 0.03
Neigh | 0.065675 | 0.065807 | 0.06593 | 0.0 | 2.15
Comm | 0.43311 | 0.49538 | 0.58587 | 8.0 | 16.18
Output | 0.00041747 | 0.00060827 | 0.0011797 | 0.0 | 0.02
Modify | 0.0073676 | 0.016077 | 0.024872 | 6.9 | 0.53
Other | | 0.004283 | | | 0.14
Nlocal: 108 ave 112 max 106 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 6531.75 ave 6611 max 6460 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Neighs: 74316.2 ave 75641 max 72780 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Total # of neighbors = 297265
Ave neighs/atom = 688.113
Ave special neighs/atom = 1
Neighbor list builds = 21
Dangerous builds = 0
unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000
Per MPI rank memory allocation (min/avg/max) = 6.884 | 7.01 | 7.138 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -623.86344 -660.20235 36.338906 1307.5814 462.72863 -662.8515 45.983055 -708.83455 0 2.6491489 10.523732 1.6709561 13990.5
550 -623.95339 -660.07946 36.126069 1299.9229 -362.67285 -662.8047 44.180832 -706.98553 0 2.725239 11.07199 2.0461376 13990.5
600 -624.04508 -661.27298 37.227902 1339.5701 110.39822 -663.90927 45.166569 -709.07584 0 2.6362911 11.747923 2.1846828 13990.5
650 -623.9608 -661.50573 37.544934 1350.9779 -1594.4701 -663.91531 41.226571 -705.14188 0 2.4095736 10.022027 1.6264014 13990.5
700 -624.00658 -663.55636 39.549777 1423.1181 -588.98052 -665.88666 43.124023 -709.01068 0 2.3302979 9.9245872 2.1027837 13990.5
750 -623.99813 -659.97694 35.978814 1294.6243 -364.14087 -662.75959 43.973558 -706.73315 0 2.782646 11.487833 1.8799696 13990.5
800 -624.01235 -661.04908 37.03673 1332.6912 -85.65751 -663.49204 44.570113 -708.06215 0 2.4429544 11.213146 1.6792935 13990.5
850 -624.02581 -659.39932 35.373517 1272.8439 -1090.9176 -662.11969 42.375065 -704.49476 0 2.7203674 11.21463 2.2907477 13990.5
900 -624.09244 -663.33388 39.241435 1412.0231 303.76293 -666.00594 45.332457 -711.3384 0 2.6720661 11.89718 2.0599025 13990.5
950 -624.04544 -661.11578 37.070343 1333.9007 1637.6353 -663.61305 48.6589 -712.27195 0 2.4972693 12.343765 2.4292305 13990.5
1000 -623.95457 -661.51817 37.563599 1351.6495 -851.76774 -663.83595 42.813476 -706.64943 0 2.3177804 10.251415 1.6922809 13990.5
1050 -623.98731 -662.01986 38.032541 1368.5235 -2123.915 -664.72608 39.917367 -704.64345 0 2.7062234 9.6008351 1.7364324 13990.5
1100 -623.9653 -659.3203 35.355002 1272.1777 -436.97572 -662.14462 44.05761 -706.20223 0 2.8243234 11.267511 2.6807914 13990.5
1150 -624.02272 -665.13875 41.116028 1479.4764 -128.02349 -667.47666 44.014064 -711.49073 0 2.337912 10.406786 1.5105446 13990.5
1200 -623.97327 -663.08066 39.107391 1407.1997 -539.90459 -665.67972 43.318696 -708.99842 0 2.5990577 10.632743 1.4609102 13990.5
1250 -623.92529 -661.81994 37.894649 1363.5617 1707.6307 -664.63708 48.39571 -713.03279 0 2.8171362 11.368475 1.8834293 13990.5
1300 -623.99279 -662.19655 38.203765 1374.6846 -820.5362 -664.34485 42.656892 -707.00174 0 2.1482931 10.187738 1.7086422 13990.5
1350 -623.99805 -658.70847 34.710418 1248.9836 775.25351 -662.01721 46.922474 -708.93969 0 3.3087449 12.454651 2.5036539 13990.5
1400 -623.96952 -662.16086 38.191338 1374.2374 880.29949 -664.90588 46.628569 -711.53444 0 2.7450171 11.920421 3.0464811 13990.5
1450 -623.9503 -662.26105 38.310754 1378.5344 -394.54404 -664.76894 43.635444 -708.40439 0 2.5078923 10.460115 1.8699789 13990.5
1500 -624.00558 -661.4861 37.480516 1348.66 438.34419 -664.32045 45.721579 -710.04203 0 2.8343497 11.655942 2.0688262 13990.5
Loop time of 6.53617 on 4 procs for 1000 steps with 432 atoms
Performance: 26.438 ns/day, 0.908 hours/ns, 152.995 timesteps/s
93.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8738 | 5.0908 | 5.4162 | 10.1 | 77.89
Bond | 0.0016415 | 0.0017839 | 0.0019331 | 0.3 | 0.03
Neigh | 0.15882 | 0.15886 | 0.15894 | 0.0 | 2.43
Comm | 0.93524 | 1.2478 | 1.4524 | 19.3 | 19.09
Output | 0.00097799 | 0.0018684 | 0.0036883 | 2.5 | 0.03
Modify | 0.0027459 | 0.0028836 | 0.0030859 | 0.2 | 0.04
Other | | 0.03211 | | | 0.49
Nlocal: 108 ave 116 max 102 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 6504.5 ave 6624 max 6380 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 74267.8 ave 79232 max 70988 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 297071
Ave neighs/atom = 687.664
Ave special neighs/atom = 1
Neighbor list builds = 45
Dangerous builds = 0
Total wall time: 0:00:09