forked from lijiext/lammps
192 lines
11 KiB
Groff
192 lines
11 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# Testsystem for core-shell model compared to Mitchel and Finchham
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# Hendrik Heenen, June 2014
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# ------------------------ INITIALIZATION ----------------------------
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units metal
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dimension 3
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boundary p p p
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atom_style full
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# ----------------------- ATOM DEFINITION ----------------------------
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fix csinfo all property/atom i_CSID
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read_data data.coreshell fix csinfo NULL CS-Info
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orthogonal box = (0 0 0) to (24.096 24.096 24.096)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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432 atoms
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scanning bonds ...
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1 = max bonds/atom
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reading bonds ...
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216 bonds
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1 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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group cores type 1 2
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216 atoms in group cores
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group shells type 3 4
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216 atoms in group shells
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neighbor 2.0 bin
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comm_modify vel yes
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# ------------------------ FORCE FIELDS ------------------------------
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pair_style born/coul/dsf/cs 0.1 20.0 20.0 # A, rho, sigma=0, C, D
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pair_coeff * * 0.0 1.000 0.00 0.00 0.00
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pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
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pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
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pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
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bond_style harmonic
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bond_coeff 1 63.014 0.0
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bond_coeff 2 25.724 0.0
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# ------------------------ Equilibration Run -------------------------------
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reset_timestep 0
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thermo 50
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thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
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compute CSequ all temp/cs cores shells
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# output via chunk method
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#compute prop all property/atom i_CSID
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#compute cs_chunk all chunk/atom c_prop
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#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
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#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
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thermo_modify temp CSequ
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# velocity bias option
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velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 22
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ghost atom cutoff = 22
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binsize = 11, bins = 3 3 3
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair born/coul/dsf/cs, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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velocity all scale 1427 temp CSequ
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fix thermoberendsen all temp/berendsen 1427 1427 0.4
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fix nve all nve
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fix_modify thermoberendsen temp CSequ
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# 2 fmsec timestep
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timestep 0.002
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run 500
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Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes
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Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
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0 -635.80596 -675.46362 39.657659 1427 -21302.622 -675.46362 1.6320365 -677.09565 0 0 1.3517686e-14 2.942091e-15 13990.5
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50 -633.9898 -666.02679 32.03699 1152.7858 -4578.5681 -668.50431 37.800204 -706.30452 0 2.4775226 14.568073 4.3012389 13990.5
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100 -631.89604 -661.96148 30.065442 1081.8436 -3536.6738 -664.61798 39.18583 -703.80381 0 2.6564973 14.677968 3.9051029 13990.5
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150 -630.08723 -662.95879 32.871559 1182.816 -109.19506 -665.76772 46.247821 -712.01554 0 2.8089226 15.270039 2.9328953 13990.5
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200 -628.55895 -663.97376 35.414806 1274.3296 -1748.35 -666.58439 41.738552 -708.32294 0 2.6106349 14.148282 3.1047826 13990.5
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250 -627.28761 -661.92274 34.635123 1246.2743 -1280.4899 -664.917 43.045475 -707.96247 0 2.9942594 14.248617 2.4694705 13990.5
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300 -626.6163 -663.65651 37.040209 1332.8164 -1887.9043 -666.35215 40.84964 -707.20179 0 2.6956373 13.142643 1.9263242 13990.5
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350 -625.76781 -664.66441 38.896607 1399.6151 -1839.482 -667.47659 40.999206 -708.47579 0 2.8121749 13.601238 1.9262698 13990.5
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400 -625.02586 -661.46042 36.434568 1311.0236 -868.2031 -664.40231 43.21398 -707.61629 0 2.9418875 14.945389 2.7493413 13990.5
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450 -624.3278 -660.50844 36.180639 1301.8865 -2203.3944 -663.49896 40.008669 -703.50763 0 2.9905179 14.158866 1.7299899 13990.5
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500 -623.56254 -661.33839 37.775849 1359.2869 -810.50736 -664.11652 42.993999 -707.11052 0 2.7781274 13.68709 2.9115277 13990.5
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Loop time of 8.43387 on 1 procs for 500 steps with 432 atoms
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Performance: 10.244 ns/day, 2.343 hours/ns, 59.285 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 8.1175 | 8.1175 | 8.1175 | 0.0 | 96.25
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Bond | 0.0019796 | 0.0019796 | 0.0019796 | 0.0 | 0.02
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Neigh | 0.21242 | 0.21242 | 0.21242 | 0.0 | 2.52
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Comm | 0.085533 | 0.085533 | 0.085533 | 0.0 | 1.01
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Output | 0.00041103 | 0.00041103 | 0.00041103 | 0.0 | 0.00
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Modify | 0.012187 | 0.012187 | 0.012187 | 0.0 | 0.14
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Other | | 0.003863 | | | 0.05
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Nlocal: 432 ave 432 max 432 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 9280 ave 9280 max 9280 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 297636 ave 297636 max 297636 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 297636
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Ave neighs/atom = 688.972
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Ave special neighs/atom = 1
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Neighbor list builds = 20
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Dangerous builds = 0
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unfix thermoberendsen
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# ------------------------ Dynamic Run -------------------------------
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run 1000
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Per MPI rank memory allocation (min/avg/max) = 8.59 | 8.59 | 8.59 Mbytes
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Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
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500 -623.56254 -661.33839 37.775849 1359.2869 -810.50736 -664.11652 42.993999 -707.11052 0 2.7781274 13.68709 2.9115277 13990.5
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550 -623.5004 -660.74472 37.244326 1340.1611 -1413.4326 -663.99669 41.875014 -705.8717 0 3.2519651 15.097948 2.278405 13990.5
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600 -623.46963 -659.61729 36.147655 1300.6997 -521.50578 -662.54994 43.956071 -706.50601 0 2.9326492 14.99649 2.6334959 13990.5
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650 -623.49291 -661.50698 38.014069 1367.8588 -1230.0925 -664.21074 42.027844 -706.23859 0 2.7037578 13.982308 1.6247207 13990.5
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700 -623.4913 -660.11564 36.62434 1317.8522 -727.89052 -663.24921 43.413397 -706.66261 0 3.1335699 15.009937 2.0563966 13990.5
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750 -623.50292 -657.95982 34.4569 1239.8613 636.46644 -661.16971 46.539267 -707.70898 0 3.2098934 15.25993 2.1864622 13990.5
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800 -623.5176 -659.92032 36.402711 1309.8773 -912.75799 -662.84989 42.668309 -705.5182 0 2.9295708 13.577516 2.0006099 13990.5
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850 -623.44098 -660.92727 37.486295 1348.8679 -550.40358 -664.08308 43.667245 -707.75033 0 3.1558098 14.836208 2.279198 13990.5
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900 -623.46361 -661.21737 37.753765 1358.4923 1267.8647 -664.52195 47.67284 -712.19479 0 3.3045765 15.058502 1.886141 13990.5
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950 -623.50114 -660.58464 37.083492 1334.3739 1754.7359 -663.48186 48.70363 -712.18549 0 2.897226 15.519042 2.2654928 13990.5
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1000 -623.50161 -660.02915 36.527539 1314.369 228.76104 -663.31152 45.374099 -708.68562 0 3.2823685 14.783709 2.4201134 13990.5
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1050 -623.45985 -660.57417 37.114321 1335.4832 -1490.604 -663.75391 41.258878 -705.01279 0 3.1797391 14.250262 2.3153255 13990.5
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1100 -623.51051 -661.20338 37.692871 1356.3011 1791.7899 -664.01042 48.626451 -712.63687 0 2.807039 15.559872 3.184101 13990.5
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1150 -623.51067 -663.19545 39.684776 1427.9758 1023.0584 -666.07723 46.5628 -712.64003 0 2.8817804 13.895322 2.3950292 13990.5
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1200 -623.49625 -659.6715 36.175253 1301.6927 1600.2805 -662.62259 48.522365 -711.14495 0 2.9510854 15.567834 2.1677651 13990.5
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1250 -623.48282 -660.56735 37.084533 1334.4113 -871.67341 -663.86673 42.560699 -706.42743 0 3.2993759 14.569539 2.0093709 13990.5
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1300 -623.47744 -663.63125 40.153811 1444.853 1343.7147 -666.39564 47.104842 -713.50048 0 2.7643857 14.186019 1.4599359 13990.5
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1350 -623.49121 -661.42731 37.936096 1365.0531 589.73669 -664.46099 45.947687 -710.40867 0 3.0336821 14.801223 2.7486556 13990.5
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1400 -623.50803 -660.03912 36.53109 1314.4968 362.97431 -663.24909 45.772904 -709.02199 0 3.2099708 14.566488 1.9170714 13990.5
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1450 -623.51243 -659.65548 36.143052 1300.534 2853.0755 -663.0534 51.355353 -714.40875 0 3.3979157 15.890282 2.5251359 13990.5
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1500 -623.51621 -661.87741 38.361201 1380.3496 740.04973 -665.00896 46.208742 -711.2177 0 3.1315492 15.168927 2.4710846 13990.5
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Loop time of 16.907 on 1 procs for 1000 steps with 432 atoms
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Performance: 10.221 ns/day, 2.348 hours/ns, 59.147 timesteps/s
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99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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Pair | 16.247 | 16.247 | 16.247 | 0.0 | 96.09
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Bond | 0.0039518 | 0.0039518 | 0.0039518 | 0.0 | 0.02
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Neigh | 0.46795 | 0.46795 | 0.46795 | 0.0 | 2.77
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Comm | 0.17146 | 0.17146 | 0.17146 | 0.0 | 1.01
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Output | 0.00082397 | 0.00082397 | 0.00082397 | 0.0 | 0.00
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Modify | 0.0065799 | 0.0065799 | 0.0065799 | 0.0 | 0.04
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Other | | 0.009467 | | | 0.06
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Nlocal: 432 ave 432 max 432 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 9318 ave 9318 max 9318 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 297131 ave 297131 max 297131 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 297131
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Ave neighs/atom = 687.803
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Ave special neighs/atom = 1
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Neighbor list builds = 44
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Dangerous builds = 0
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Total wall time: 0:00:25
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