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 2 by 2 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) = 6.881 | 6.881 | 6.881 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 1.5814015e-14 3.2317898e-15 13990.5
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50 -634.07021 -666.11867 32.048452 1153.1982 -4560.945 -668.28236 37.756542 -706.0389 0 2.163691 13.802484 3.022372 13990.5
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100 -631.97128 -662.02544 30.054164 1081.4378 -3497.564 -664.61825 39.275003 -703.89325 0 2.5928078 13.956833 2.5417699 13990.5
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150 -630.14953 -663.04215 32.892622 1183.5739 -88.43828 -665.63444 46.239965 -711.87441 0 2.5922927 14.667898 2.4964255 13990.5
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200 -628.52878 -663.9795 35.45072 1275.6219 -1755.9004 -666.73564 41.758052 -708.49369 0 2.7561421 14.230743 3.0924004 13990.5
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250 -627.27102 -662.025 34.753978 1250.5511 -1234.0918 -665.13519 43.170874 -708.30606 0 3.1101887 14.221086 1.941354 13990.5
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300 -626.5495 -663.74287 37.193368 1338.3275 -2049.3444 -666.45574 40.476148 -706.93188 0 2.7128711 13.330425 1.7756755 13990.5
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350 -625.87313 -665.21855 39.345421 1415.7647 -1543.1723 -667.90872 41.577366 -709.48609 0 2.6901682 13.541311 1.854662 13990.5
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400 -625.09344 -661.26404 36.1706 1301.5253 -729.96729 -664.10334 43.468765 -707.57211 0 2.8392963 13.663555 1.9067551 13990.5
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450 -624.46214 -660.01362 35.551477 1279.2474 -1617.7158 -663.06571 41.644856 -704.71057 0 3.0520921 14.527005 1.7280213 13990.5
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500 -623.49246 -659.2527 35.76024 1286.7593 -935.99238 -662.32953 43.038808 -705.36834 0 3.0768302 14.099593 1.9831106 13990.5
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Loop time of 2.44013 on 4 procs for 500 steps with 432 atoms
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Performance: 35.408 ns/day, 0.678 hours/ns, 204.907 timesteps/s
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98.6% CPU use with 4 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 | 2.0321 | 2.1124 | 2.1759 | 3.6 | 86.57
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Bond | 0.00069523 | 0.00071579 | 0.00074148 | 0.0 | 0.03
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Neigh | 0.060491 | 0.060606 | 0.060709 | 0.0 | 2.48
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Comm | 0.19263 | 0.25562 | 0.33556 | 10.4 | 10.48
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Output | 0.00041246 | 0.00057316 | 0.0010512 | 0.0 | 0.02
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Modify | 0.0059495 | 0.0062472 | 0.006577 | 0.4 | 0.26
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Other | | 0.00394 | | | 0.16
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Nlocal: 108 ave 114 max 105 min
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Histogram: 1 1 1 0 0 0 0 0 0 1
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Nghost: 6527 ave 6599 max 6472 min
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Histogram: 1 0 1 0 1 0 0 0 0 1
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Neighs: 74388.2 ave 75855 max 73680 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Total # of neighbors = 297553
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Ave neighs/atom = 688.78
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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) = 6.883 | 6.948 | 7.138 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 -623.49319 -659.2527 35.759511 1286.7331 -936.04802 -662.32953 43.038808 -705.36834 0 3.0768302 14.099593 1.9831106 13990.5
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550 -623.44059 -663.57938 40.138795 1444.3127 -935.73484 -666.2789 42.563337 -708.84224 0 2.6995167 13.918509 2.3189805 13990.5
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600 -623.4703 -660.01592 36.545618 1315.0196 1327.3492 -663.08845 47.985462 -711.07391 0 3.0725254 15.192713 2.4098428 13990.5
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650 -623.46796 -661.56776 38.099807 1370.9439 457.82439 -664.81976 45.495622 -710.31538 0 3.2519966 15.026057 1.8500226 13990.5
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700 -623.50158 -659.5131 36.011523 1295.8012 -460.03772 -663.1078 43.938203 -707.046 0 3.5946908 14.660979 2.4825518 13990.5
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750 -623.44787 -661.93353 38.485658 1384.8279 97.429626 -664.9551 45.083146 -710.03825 0 3.0215753 15.10043 2.3433897 13990.5
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800 -623.48215 -659.50655 36.024402 1296.2647 1097.3866 -662.61124 47.251998 -709.86324 0 3.1046914 14.556382 2.0543766 13990.5
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850 -623.45868 -661.13782 37.679134 1355.8068 -1802.1624 -664.41257 40.70845 -705.12102 0 3.2747525 14.691444 2.2054332 13990.5
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900 -623.43556 -663.59137 40.155815 1444.9251 534.99197 -666.71877 45.601619 -712.32039 0 3.127395 14.741411 2.5807895 13990.5
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950 -623.51318 -661.57916 38.06598 1369.7267 -678.12625 -664.37535 43.207862 -707.58322 0 2.7961988 14.430307 2.3936105 13990.5
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1000 -623.47287 -661.22274 37.749874 1358.3523 634.7979 -664.42973 46.373361 -710.80309 0 3.2069879 15.891192 2.4042765 13990.5
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1050 -623.48133 -661.52868 38.047347 1369.0562 -583.15228 -664.6098 43.618772 -708.22857 0 3.081116 14.806856 2.3447613 13990.5
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1100 -623.47867 -661.83761 38.358946 1380.2685 -868.9779 -664.8826 42.84846 -707.73106 0 3.044983 14.69567 2.399143 13990.5
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1150 -623.44713 -661.21299 37.765857 1358.9274 405.14554 -664.09567 45.578739 -709.6744 0 2.8826753 15.437367 3.1381305 13990.5
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1200 -623.46549 -660.91706 37.451568 1347.6183 699.78996 -664.0883 46.36297 -710.45127 0 3.1712473 15.109665 1.8891886 13990.5
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1250 -623.49296 -658.2218 34.728838 1249.6464 1061.0154 -661.29052 47.668699 -708.95922 0 3.0687228 14.901367 2.3964137 13990.5
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1300 -623.49837 -660.91022 37.411844 1346.1889 226.99512 -664.35989 45.352287 -709.71217 0 3.4496704 15.161542 2.2137993 13990.5
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1350 -623.46718 -658.80365 35.336469 1271.5108 1039.6469 -662.16908 47.565671 -709.73475 0 3.3654314 15.892516 2.7888426 13990.5
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1400 -623.47124 -661.45375 37.982513 1366.7233 -379.56023 -664.6321 43.788306 -708.42041 0 3.1783497 14.251126 1.7415409 13990.5
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1450 -623.46671 -660.17518 36.708464 1320.8792 -374.37056 -662.92706 44.083648 -707.01071 0 2.7518803 15.210167 1.9984277 13990.5
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1500 -623.50515 -659.06488 35.559725 1279.5442 260.37822 -662.39548 45.779764 -708.17524 0 3.3306005 14.682396 2.4201107 13990.5
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Loop time of 5.16152 on 4 procs for 1000 steps with 432 atoms
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Performance: 33.478 ns/day, 0.717 hours/ns, 193.741 timesteps/s
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98.3% CPU use with 4 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 | 4.0761 | 4.2795 | 4.6259 | 10.9 | 82.91
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Bond | 0.0013907 | 0.0014481 | 0.0015037 | 0.1 | 0.03
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Neigh | 0.13612 | 0.13618 | 0.13624 | 0.0 | 2.64
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Comm | 0.38391 | 0.73074 | 0.93346 | 26.3 | 14.16
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Output | 0.00096703 | 0.0014517 | 0.0028937 | 2.2 | 0.03
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Modify | 0.0022988 | 0.0024452 | 0.0025537 | 0.2 | 0.05
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Other | | 0.009786 | | | 0.19
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Nlocal: 108 ave 114 max 94 min
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Histogram: 1 0 0 0 0 0 0 0 1 2
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Nghost: 6512.25 ave 6586 max 6456 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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Neighs: 74248.2 ave 77441 max 65858 min
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Histogram: 1 0 0 0 0 0 0 0 0 3
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Total # of neighbors = 296993
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Ave neighs/atom = 687.484
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Ave special neighs/atom = 1
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Neighbor list builds = 46
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Dangerous builds = 0
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Total wall time: 0:00:07
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