LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 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 CStemp all temp/cs cores shells compute thermo_press_lmp all pressure thermo_temp # press for correct kinetic scalar # 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 CStemp press thermo_press_lmp # velocity bias option velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CStemp Ewald initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:321) 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 ... 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/long/cs, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard velocity all scale 1427 temp CStemp # thermostating using the core/shell decoupling fix thermoberendsen all temp/berendsen 1427 1427 0.4 fix nve all nve fix_modify thermoberendsen temp CStemp # 2 fmsec timestep timestep 0.002 run 500 Ewald initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:321) 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 Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 0 -635.44099 -675.09865 39.657659 1427 -20613.612 -675.09865 1.6320365 1018.8211 -1695.5518 0 2.7895988e-14 3.594347e-15 13990.5 50 -634.17327 -666.17818 32.004909 1151.6314 -4029.8418 -667.9562 37.809071 989.23283 -1694.9981 1.7780231 9.7133792 2.191797 13990.5 100 -631.93507 -661.91226 29.977186 1078.6679 -3171.7799 -664.06719 39.33341 991.36934 -1694.7699 2.1549313 11.091423 2.1704389 13990.5 150 -630.16811 -663.12417 32.956056 1185.8565 143.26508 -665.48036 46.253769 982.97454 -1694.7087 2.3561935 11.467913 2.1652595 13990.5 200 -628.62323 -663.64922 35.025998 1260.3391 -1622.4126 -665.96878 41.661879 986.81675 -1694.4474 2.3195587 10.597709 2.9538262 13990.5 250 -627.31045 -662.01825 34.7078 1248.8894 -1509.6621 -664.50312 42.101718 987.90197 -1694.5068 2.4848739 10.392757 1.6933711 13990.5 300 -626.57622 -660.97494 34.39872 1237.7678 -1637.8094 -663.48087 41.653234 989.53228 -1694.6664 2.5059303 11.204361 2.2809738 13990.5 350 -625.91962 -665.35837 39.438749 1419.123 -1351.4779 -667.6167 41.582456 985.53382 -1694.733 2.2583289 10.83106 1.8963347 13990.5 400 -625.24849 -660.77642 35.527934 1278.4003 -424.45104 -663.12602 43.890331 987.75201 -1694.7684 2.3495966 11.521966 2.175931 13990.5 450 -624.67743 -662.88678 38.209353 1374.8857 1109.0155 -665.43212 46.964803 982.35208 -1694.749 2.5453383 11.002405 2.0014356 13990.5 500 -624.30215 -661.97859 37.676437 1355.7098 -998.57286 -664.60382 42.373117 987.59021 -1694.5671 2.625227 11.153883 2.8270306 13990.5 Loop time of 6.53907 on 1 procs for 500 steps with 432 atoms Performance: 13.213 ns/day, 1.816 hours/ns, 76.463 timesteps/s 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6198 | 5.6198 | 5.6198 | 0.0 | 85.94 Bond | 0.0020258 | 0.0020258 | 0.0020258 | 0.0 | 0.03 Kspace | 0.57813 | 0.57813 | 0.57813 | 0.0 | 8.84 Neigh | 0.23532 | 0.23532 | 0.23532 | 0.0 | 3.60 Comm | 0.086898 | 0.086898 | 0.086898 | 0.0 | 1.33 Output | 0.00044823 | 0.00044823 | 0.00044823 | 0.0 | 0.01 Modify | 0.012434 | 0.012434 | 0.012434 | 0.0 | 0.19 Other | | 0.004004 | | | 0.06 Nlocal: 432 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9338 ave 9338 max 9338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 297354 ave 297354 max 297354 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297354 Ave neighs/atom = 688.319 Ave special neighs/atom = 1 Neighbor list builds = 22 Dangerous builds = 0 unfix thermoberendsen # ------------------------ Dynamic Run ------------------------------- run 1000 Ewald initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:321) 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 Per MPI rank memory allocation (min/avg/max) = 17.29 | 17.29 | 17.29 Mbytes Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume 500 -624.30215 -661.97859 37.676437 1355.7098 -998.57286 -664.60382 42.373117 987.59021 -1694.5671 2.625227 11.153883 2.8270306 13990.5 550 -624.30709 -662.13368 37.826594 1361.1129 327.40639 -664.76823 45.306662 984.72847 -1694.8034 2.6345475 10.879928 1.9751611 13990.5 600 -624.30993 -661.84513 37.535201 1350.6277 -983.48045 -664.36158 42.366067 987.87918 -1694.6068 2.5164439 10.210733 1.7891188 13990.5 650 -624.30501 -659.20528 34.90027 1255.8151 556.10903 -661.96404 46.567866 986.0511 -1694.583 2.7587602 13.154392 2.1649995 13990.5 700 -624.30909 -661.85126 37.54217 1350.8784 -134.38128 -664.38499 44.382232 985.80624 -1694.5735 2.5337309 10.991718 2.0394718 13990.5 750 -624.30994 -660.52853 36.218591 1303.2522 1197.4475 -663.29728 47.437035 984.08807 -1694.8224 2.7687507 11.683138 2.075797 13990.5 800 -624.30475 -659.88119 35.576433 1280.1454 358.11619 -662.81702 45.487454 986.41325 -1694.7177 2.9358301 11.519677 3.7837385 13990.5 850 -624.3061 -663.63946 39.333359 1415.3307 -33.011248 -666.10531 44.296094 984.32445 -1694.7258 2.4658499 11.039607 1.9232237 13990.5 900 -624.3004 -659.038 34.737607 1249.962 373.33796 -662.10263 45.838541 986.93651 -1694.8777 3.0646238 12.13843 2.4692874 13990.5 950 -624.30802 -663.36014 39.052124 1405.2111 290.61832 -665.78004 45.269372 983.76386 -1694.8133 2.4198995 11.723515 2.0708786 13990.5 1000 -624.30213 -659.49404 35.191918 1266.3094 -920.00206 -662.25664 42.950066 989.20183 -1694.4085 2.7625985 11.442653 1.8492839 13990.5 1050 -624.30371 -659.3839 35.080191 1262.2891 284.04674 -662.15204 45.828093 986.77381 -1694.7539 2.7681351 12.123317 1.8741591 13990.5 1100 -624.3052 -660.69507 36.389872 1309.4153 -282.65356 -663.18011 44.45192 987.28618 -1694.9182 2.4850386 11.032596 1.9763392 13990.5 1150 -624.30478 -657.75327 33.448496 1203.5759 1331.9067 -660.51356 48.445972 985.91346 -1694.873 2.7602894 13.583395 2.4702797 13990.5 1200 -624.30892 -664.76096 40.452036 1455.5841 -1970.8297 -666.85506 39.983487 988.02113 -1694.8597 2.0941031 9.5654747 1.9888352 13990.5 1250 -624.30486 -661.48101 37.176152 1337.708 1864.8469 -664.22952 48.84895 981.57501 -1694.6535 2.7485121 11.090466 1.9610957 13990.5 1300 -624.3122 -662.74179 38.429588 1382.8104 1775.1061 -665.4945 48.300257 980.84489 -1694.6396 2.7527096 11.276872 1.7562916 13990.5 1350 -624.30198 -659.95211 35.65013 1282.7973 -154.85356 -662.68735 44.54654 987.24605 -1694.4799 2.7352371 11.229424 2.4657127 13990.5 1400 -624.30362 -659.14451 34.840882 1253.6781 -159.66669 -662.01516 44.455993 988.18506 -1694.6562 2.87065 11.536771 1.6678 13990.5 1450 -624.30238 -661.91803 37.615642 1353.5222 993.97328 -664.55469 46.579213 983.57987 -1694.7138 2.6366597 11.343434 2.3751981 13990.5 1500 -624.31198 -659.70757 35.395599 1273.6385 2948.584 -662.67607 51.30697 980.45677 -1694.4398 2.9684904 11.953269 2.2096873 13990.5 Loop time of 13.2154 on 1 procs for 1000 steps with 432 atoms Performance: 13.076 ns/day, 1.835 hours/ns, 75.669 timesteps/s 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.363 | 11.363 | 11.363 | 0.0 | 85.98 Bond | 0.0040638 | 0.0040638 | 0.0040638 | 0.0 | 0.03 Kspace | 1.1573 | 1.1573 | 1.1573 | 0.0 | 8.76 Neigh | 0.50039 | 0.50039 | 0.50039 | 0.0 | 3.79 Comm | 0.17365 | 0.17365 | 0.17365 | 0.0 | 1.31 Output | 0.00093961 | 0.00093961 | 0.00093961 | 0.0 | 0.01 Modify | 0.0068541 | 0.0068541 | 0.0068541 | 0.0 | 0.05 Other | | 0.009295 | | | 0.07 Nlocal: 432 ave 432 max 432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9380 ave 9380 max 9380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 296922 ave 296922 max 296922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296922 Ave neighs/atom = 687.319 Ave special neighs/atom = 1 Neighbor list builds = 47 Dangerous builds = 0 Total wall time: 0:00:19