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 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 ------------------------------ 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 = 6.15182 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 3.6635741e-14 5.3290705e-15 13990.5 50 -632.86102 -664.881 32.019982 1150.3902 -4100.2367 -668.28423 37.966091 988.74858 -1694.9989 3.403224 25.060809 9.2893842 13990.5 100 -630.51552 -660.52959 30.014075 1078.3235 -3202.4205 -664.01411 39.505563 991.23276 -1694.7524 3.4845198 26.369799 10.674421 13990.5 150 -628.58443 -661.59141 33.006978 1185.8503 106.65351 -665.34508 46.399848 982.93423 -1694.6792 3.7536698 27.270648 10.826129 13990.5 200 -627.39641 -662.45927 35.062861 1259.7125 -1672.2627 -665.61606 41.658596 987.1458 -1694.4205 3.1567877 23.525464 6.5838195 13990.5 250 -625.74093 -660.30053 34.559597 1241.6316 -1597.1305 -664.13208 42.148526 988.19121 -1694.4718 3.831555 27.157597 8.5399516 13990.5 300 -625.07349 -659.68703 34.613535 1243.5695 -1525.6663 -663.38085 42.076798 989.22292 -1694.6806 3.6938245 26.233967 9.2898941 13990.5 350 -623.86899 -663.20625 39.337263 1413.2801 -1933.067 -667.16008 40.51735 986.96485 -1694.6423 3.9538285 30.550701 14.691984 13990.5 400 -623.55154 -660.39034 36.838804 1323.5173 -1746.896 -664.07771 41.006288 989.66515 -1694.7492 3.687369 27.463762 11.289238 13990.5 450 -623.03522 -658.41494 35.37972 1271.0964 1245.1415 -662.15059 48.1009 984.41515 -1694.6666 3.7356529 24.533936 6.5615795 13990.5 500 -622.34349 -660.51826 38.174772 1371.515 -1306.7035 -664.27406 41.802611 988.58329 -1694.66 3.7557939 23.595131 5.801075 13990.5 Loop time of 2.53127 on 4 procs for 500 steps with 432 atoms Pair time (%) = 1.94114 (76.6863) Bond time (%) = 0.000725508 (0.0286618) Kspce time (%) = 0.353945 (13.9829) Neigh time (%) = 0.0488738 (1.9308) Comm time (%) = 0.17332 (6.84714) Outpt time (%) = 0.000516713 (0.0204132) Other time (%) = 0.012753 (0.503818) Nlocal: 108 ave 132 max 90 min Histogram: 1 0 1 0 1 0 0 0 0 1 Nghost: 6500 ave 6530 max 6448 min Histogram: 1 0 0 0 0 0 1 0 0 2 Neighs: 74339.8 ave 91261 max 61188 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 297359 Ave neighs/atom = 688.331 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 = 6.15373 Mbytes Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 500 -622.34349 -660.51826 38.174772 1371.515 -1306.7035 -664.27406 41.802611 988.58329 -1694.66 3.7557939 23.595131 5.801075 13990.5 550 -622.53431 -661.60445 39.070141 1403.6831 -388.25413 -664.94784 43.727803 985.81836 -1694.494 3.3433892 21.667306 3.5808033 13990.5 600 -622.20561 -659.56223 37.356624 1342.1211 428.9464 -663.53655 45.982645 985.19136 -1694.7106 3.974322 25.725869 9.3871295 13990.5 650 -622.35823 -660.82051 38.462275 1381.8442 -1009.0888 -664.38771 42.618521 987.47881 -1694.485 3.5671985 24.149905 7.00428 13990.5 700 -621.97407 -660.92034 38.946267 1399.2327 142.95891 -664.75916 45.033131 985.16618 -1694.9585 3.8388194 27.934663 8.7392159 13990.5 750 -622.29209 -658.81919 36.527095 1312.3185 -952.526 -662.17886 42.618062 989.9262 -1694.7231 3.3596669 24.324239 4.9087128 13990.5 800 -622.33521 -658.14785 35.812637 1286.6499 135.34005 -661.96381 45.178323 987.39314 -1694.5353 3.815955 24.107767 7.0978979 13990.5 850 -622.37957 -660.474 38.094424 1368.6283 857.3439 -663.9925 46.509627 984.19258 -1694.6947 3.5185004 23.581763 5.0835354 13990.5 900 -622.29844 -660.66771 38.369271 1378.5028 2861.462 -664.35013 50.97682 979.13332 -1694.4603 3.6824207 24.493416 6.3661215 13990.5 950 -622.35097 -659.43438 37.083412 1332.3054 705.55718 -663.24413 46.294781 984.74433 -1694.2832 3.8097517 24.11493 4.1360943 13990.5 1000 -622.08622 -658.28773 36.201516 1300.6213 421.181 -662.27058 45.865645 986.51483 -1694.6511 3.98285 26.774991 7.4172909 13990.5 1050 -622.10558 -657.21399 35.108408 1261.3489 -464.31761 -661.46995 44.291275 988.69737 -1694.4586 4.2559609 25.983762 5.4926993 13990.5 1100 -622.29369 -658.21246 35.918767 1290.4629 123.81951 -662.20344 45.651482 986.92119 -1694.7761 3.990985 25.85199 5.2327524 13990.5 1150 -621.98418 -658.28218 36.297998 1304.0876 546.02432 -662.38868 46.194374 985.7826 -1694.3657 4.1065008 27.128736 6.901853 13990.5 1200 -621.76032 -658.36996 36.60964 1315.2841 198.92215 -662.79546 45.536182 986.45023 -1694.7819 4.4255014 30.59935 9.4790152 13990.5 1250 -621.77583 -657.79539 36.019569 1294.0844 521.16569 -662.12132 46.16971 986.26128 -1694.5523 4.3259289 29.294668 9.6073346 13990.5 1300 -622.0461 -659.54559 37.499494 1347.2541 -854.68333 -663.33538 42.882224 988.27569 -1694.4933 3.7897892 26.707354 8.861147 13990.5 1350 -621.7984 -657.10932 35.310914 1268.6244 -1010.1044 -661.35487 42.90716 990.41696 -1694.679 4.2455538 29.623565 10.702495 13990.5 1400 -622.2597 -660.89426 38.634556 1388.0337 2292.235 -664.36487 49.907981 980.3269 -1694.5997 3.4706065 25.34727 6.8458703 13990.5 1450 -622.36952 -660.43856 38.069033 1367.716 199.44207 -664.44407 45.483438 984.89046 -1694.818 4.0055092 24.149259 3.9431126 13990.5 1500 -621.84913 -659.73606 37.886922 1361.1733 -1274.5089 -663.96475 42.049386 988.31676 -1694.3309 4.2286938 28.927291 10.527466 13990.5 Loop time of 5.06693 on 4 procs for 1000 steps with 432 atoms Pair time (%) = 3.90916 (77.1504) Bond time (%) = 0.00148368 (0.0292816) Kspce time (%) = 0.657798 (12.9822) Neigh time (%) = 0.108943 (2.15008) Comm time (%) = 0.373417 (7.36968) Outpt time (%) = 0.00109911 (0.0216918) Other time (%) = 0.0150309 (0.296647) Nlocal: 108 ave 113 max 100 min Histogram: 1 0 0 0 1 0 0 0 0 2 Nghost: 6461 ave 6519 max 6372 min Histogram: 1 0 0 0 1 0 0 0 0 2 Neighs: 74316.8 ave 77778 max 69869 min Histogram: 1 0 0 0 0 1 0 1 0 1 Total # of neighbors = 297267 Ave neighs/atom = 688.118 Ave special neighs/atom = 1 Neighbor list builds = 46 Dangerous builds = 0