LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real dimension 3 boundary p p p atom_style atomic newton on timestep 1.0 read_data methanol.data orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635) 1 by 1 by 1 MPI processor grid reading atoms ... 968 atoms velocity all create 300.0 16802 dist gaussian pair_style table spline 15000 pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0 WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr. Should only be flagged at inflection points (src/pair_table.cpp:481) neigh_modify delay 0 every 1 check yes one 10000 neighbor 12.0 bin thermo 500 thermo_style custom step temp pe etotal press vol variable STEP equal step variable TEMP equal temp ## volume from cubic angstroms to cubic nm variable VOL equal vol/1000.0 ## pressure from atm to bar variable PRESS equal press*1.01325 variable PXX equal pxx*1.01325 variable PYY equal pyy*1.01325 variable PZZ equal pzz*1.01325 variable PXY equal pxy*1.01325 variable PXZ equal pxz*1.01325 variable PYZ equal pyz*1.01325 ## energy from kcal/mol to kJ/mol variable KE equal ke*4.184 variable PE equal pe*4.184 variable UVDW equal evdwl*4.184 ##### SPECIAL COMMANDS FOR FIX_BOCS ##### # ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2 fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20 # Report the modified pressure thermo_modify press 1_press ## Uncomment to save some data from simulation to files #fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no #fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no #fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no #fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no #fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no #fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no #fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no #fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no ## Prints a configuration to dump.txt every 500 steps #dump 1 all custom 500 dump.txt id type x y z fx fy fz # Write restart files to continue simulations #restart 10000 state1.restart state2.restart ## Run for this many steps run_style verlet run 10000 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 10000, page size: 100000 master list distance cutoff = 24 ghost atom cutoff = 24 binsize = 12, bins = 4 4 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair table, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes Step Temp PotEng TotEng Press Volume 0 300 1061.5961 1926.3291 107.006 66250.679 500 314.70267 1036.3305 1943.4431 205.83301 65603.85 1000 304.99804 1034.15 1913.2896 -79.521176 66268.87 1500 305.2621 996.9303 1876.831 -97.93992 67090.442 2000 311.29317 1083.9171 1981.2021 119.28085 65589.674 2500 305.51905 1051.59 1932.2314 -34.076658 66487.327 3000 291.76224 1053.524 1894.5121 45.522865 65879.535 3500 297.65795 1017.1028 1875.085 -79.41965 67185.19 4000 285.98779 1042.3622 1866.7058 88.549172 66357.051 4500 295.35 1071.4505 1922.7801 -16.75965 65378.949 5000 293.20958 1009.9943 1855.1543 -270.58058 67555.38 5500 292.40422 1085.3901 1928.2287 161.88502 65677.644 6000 318.79663 1012.4832 1931.3964 -65.692451 67458.05 6500 308.03807 1046.1413 1934.0436 249.70237 66052.045 7000 289.33716 1037.9657 1871.9636 47.662734 66782.578 7500 297.3092 1032.356 1889.3329 -24.049617 66129.95 8000 298.27827 1044.118 1903.8882 -26.61809 66720.381 8500 299.52706 1026.7068 1890.0766 -128.14995 67695.559 9000 304.67694 1018.2095 1896.4236 -61.360724 65942.4 9500 293.81117 1019.2221 1866.1162 -47.726496 66843.848 10000 309.9256 1043.5321 1936.875 -103.81403 66222.21 Loop time of 42.5056 on 1 procs for 10000 steps with 968 atoms Performance: 20.327 ns/day, 1.181 hours/ns, 235.263 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 40.972 | 40.972 | 40.972 | 0.0 | 96.39 Neigh | 0.18576 | 0.18576 | 0.18576 | 0.0 | 0.44 Comm | 0.71338 | 0.71338 | 0.71338 | 0.0 | 1.68 Output | 0.00050306 | 0.00050306 | 0.00050306 | 0.0 | 0.00 Modify | 0.52926 | 0.52926 | 0.52926 | 0.0 | 1.25 Other | | 0.1042 | | | 0.25 Nlocal: 968 ave 968 max 968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9215 ave 9215 max 9215 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 411837 ave 411837 max 411837 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411837 Ave neighs/atom = 425.451 Neighbor list builds = 13 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:42