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 2 by 2 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) = 3.37 | 3.37 | 3.371 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 -34.076657 66487.327 3000 291.76224 1053.524 1894.5121 45.522919 65879.535 3500 297.65792 1017.1041 1875.0862 -79.411904 67185.183 4000 285.99141 1042.379 1866.733 88.735986 66356.756 4500 295.34218 1071.2977 1922.6048 -17.479073 65381.597 5000 292.47 1012.3769 1855.405 -255.07433 67527.215 5500 294.04431 1080.4547 1928.0208 192.6588 65811.742 6000 300.45893 986.16669 1852.2225 -167.3405 67858.175 6500 305.59738 1022.5276 1903.3947 -116.41298 66612.704 7000 312.11968 1032.7392 1932.4065 152.17956 66016.299 7500 306.80585 1032.1157 1916.4662 51.07705 66875.727 8000 292.30957 1048.9003 1891.4661 61.280503 65894.103 8500 297.79592 1013.4061 1871.786 -133.01136 66842.574 9000 290.36753 1043.7732 1880.7412 65.208248 66010.86 9500 288.92211 1077.8835 1910.6851 46.291982 65674.639 10000 311.51608 1015.3567 1913.2842 -146.49492 66882.692 Loop time of 13.9823 on 4 procs for 10000 steps with 968 atoms Performance: 61.792 ns/day, 0.388 hours/ns, 715.190 timesteps/s 98.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.131 | 11.235 | 12.333 | 23.2 | 80.35 Neigh | 0.044854 | 0.046303 | 0.047541 | 0.5 | 0.33 Comm | 1.1939 | 2.2964 | 3.4087 | 51.7 | 16.42 Output | 0.0004735 | 0.0032033 | 0.01137 | 8.3 | 0.02 Modify | 0.30542 | 0.31846 | 0.32508 | 1.4 | 2.28 Other | | 0.08323 | | | 0.60 Nlocal: 242 ave 248 max 232 min Histogram: 1 0 0 0 0 0 1 0 1 1 Nghost: 5845.75 ave 5877 max 5808 min Histogram: 1 0 0 0 1 0 0 1 0 1 Neighs: 104313 ave 113860 max 95507 min Histogram: 1 1 0 0 0 0 0 1 0 1 Total # of neighbors = 417252 Ave neighs/atom = 431.045 Neighbor list builds = 13 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:14