LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task units real atom_style full boundary p p p dielectric 1 special_bonds lj/coul 0.0 0.0 1.0 pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5 bond_style harmonic angle_style harmonic dihedral_style harmonic improper_style none kspace_style pppm 0.001 read_data data.dreiding orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697) 2 by 1 by 2 MPI processor grid reading atoms ... 384 atoms scanning bonds ... 4 = max bonds/atom scanning angles ... 6 = max angles/atom scanning dihedrals ... 3 = max dihedrals/atom reading bonds ... 320 bonds reading angles ... 448 angles reading dihedrals ... 192 dihedrals 4 = max # of 1-2 neighbors 3 = max # of 1-3 neighbors 5 = max # of special neighbors pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478 pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478 pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677 pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103 pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478 pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677 pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103 pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877 pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302 pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727 pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4 pair_modify mix arithmetic neighbor 2.0 multi neigh_modify every 2 delay 4 check yes variable input index in.ch3oh.box.dreiding variable sname index ch3oh.box.dreiding compute hb all pair hbond/dreiding/lj variable C_hbond equal c_hb[1] #number hbonds variable E_hbond equal c_hb[2] #hbond energy thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol thermo_modify line multi format float %14.6f fix 1 all nve thermo 10 run 100 PPPM initialization ... WARNING: System is not charge neutral, net charge = -0.00064 (src/kspace.cpp:302) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.142073 grid = 3 3 3 stencil order = 5 estimated absolute RMS force accuracy = 0.154715 estimated relative force accuracy = 0.00046592 using double precision FFTs 3d grid and FFT values/proc = 392 12 Neighbor list info ... update every 2 steps, delay 4 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.5 ghost atom cutoff = 13.5 binsize = 6.75, bins = 3 3 3 3 neighbor lists, perpetual/occasional/extra = 3 0 0 (1) pair hbond/dreiding/lj, perpetual, skip from (3) attributes: full, newton on pair build: skip stencil: none bin: none (2) pair lj/cut/coul/long, perpetual, half/full from (3) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (3) neighbor class addition, perpetual attributes: full, newton on pair build: full/multi stencil: full/multi/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 10.17 | 10.17 | 10.17 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000 PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880 E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324 E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152 v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335 ---------------- Step 10 ----- CPU = 0.0112 (sec) ---------------- TotEng = 113.773202 KinEng = 1.537257 Temp = 1.346522 PotEng = 112.235945 E_bond = 0.530880 E_angle = 1.407481 E_dihed = 1.084172 E_impro = 0.000000 E_vdwl = -126.339883 E_coul = 596.742306 E_long = -361.189011 v_E_hbond = -69.944278 v_C_hbond = 240.000000 Press = -395.900496 Volume = 7447.236335 ---------------- Step 20 ----- CPU = 0.0206 (sec) ---------------- TotEng = 113.879292 KinEng = 2.999580 Temp = 2.627407 PotEng = 110.879711 E_bond = 0.549156 E_angle = 1.323582 E_dihed = 1.357398 E_impro = 0.000000 E_vdwl = -127.482103 E_coul = 596.318729 E_long = -361.187051 v_E_hbond = -70.088343 v_C_hbond = 237.000000 Press = -487.150418 Volume = 7447.236335 ---------------- Step 30 ----- CPU = 0.0299 (sec) ---------------- TotEng = 113.587474 KinEng = 4.369566 Temp = 3.827412 PotEng = 109.217908 E_bond = 0.416485 E_angle = 1.294630 E_dihed = 1.710254 E_impro = 0.000000 E_vdwl = -128.565697 E_coul = 595.560846 E_long = -361.198612 v_E_hbond = -69.848068 v_C_hbond = 238.000000 Press = -423.966898 Volume = 7447.236335 ---------------- Step 40 ----- CPU = 0.0403 (sec) ---------------- TotEng = 113.915503 KinEng = 6.466349 Temp = 5.664037 PotEng = 107.449154 E_bond = 0.514530 E_angle = 1.342583 E_dihed = 1.536929 E_impro = 0.000000 E_vdwl = -129.858713 E_coul = 595.186400 E_long = -361.272576 v_E_hbond = -69.871393 v_C_hbond = 237.000000 Press = -498.152652 Volume = 7447.236335 ---------------- Step 50 ----- CPU = 0.0494 (sec) ---------------- TotEng = 113.787839 KinEng = 8.050614 Temp = 7.051734 PotEng = 105.737226 E_bond = 0.652153 E_angle = 1.416041 E_dihed = 1.363560 E_impro = 0.000000 E_vdwl = -130.513518 E_coul = 594.139769 E_long = -361.320780 v_E_hbond = -69.593967 v_C_hbond = 233.000000 Press = -557.299799 Volume = 7447.236335 ---------------- Step 60 ----- CPU = 0.0588 (sec) ---------------- TotEng = 114.120941 KinEng = 10.318793 Temp = 9.038489 PotEng = 103.802148 E_bond = 0.576578 E_angle = 1.285008 E_dihed = 1.123936 E_impro = 0.000000 E_vdwl = -131.268312 E_coul = 593.450009 E_long = -361.365070 v_E_hbond = -70.107165 v_C_hbond = 238.000000 Press = -571.907188 Volume = 7447.236335 ---------------- Step 70 ----- CPU = 0.0680 (sec) ---------------- TotEng = 113.836161 KinEng = 11.873184 Temp = 10.400019 PotEng = 101.962977 E_bond = 0.633521 E_angle = 1.315999 E_dihed = 1.055318 E_impro = 0.000000 E_vdwl = -131.673572 E_coul = 592.039194 E_long = -361.407483 v_E_hbond = -70.518544 v_C_hbond = 240.000000 Press = -576.731444 Volume = 7447.236335 ---------------- Step 80 ----- CPU = 0.0790 (sec) ---------------- TotEng = 113.589436 KinEng = 13.546467 Temp = 11.865689 PotEng = 100.042970 E_bond = 0.637759 E_angle = 1.439918 E_dihed = 1.020307 E_impro = 0.000000 E_vdwl = -131.980346 E_coul = 590.365879 E_long = -361.440548 v_E_hbond = -71.174370 v_C_hbond = 245.000000 Press = -735.254308 Volume = 7447.236335 ---------------- Step 90 ----- CPU = 0.0883 (sec) ---------------- TotEng = 114.100567 KinEng = 15.870735 Temp = 13.901574 PotEng = 98.229832 E_bond = 0.724671 E_angle = 1.435914 E_dihed = 1.028167 E_impro = 0.000000 E_vdwl = -132.680267 E_coul = 589.225626 E_long = -361.504279 v_E_hbond = -72.653223 v_C_hbond = 245.000000 Press = -820.598954 Volume = 7447.236335 ---------------- Step 100 ----- CPU = 0.0976 (sec) ---------------- TotEng = 113.670041 KinEng = 17.406803 Temp = 15.247054 PotEng = 96.263238 E_bond = 0.711253 E_angle = 1.338059 E_dihed = 1.474770 E_impro = 0.000000 E_vdwl = -132.917719 E_coul = 587.219020 E_long = -361.562145 v_E_hbond = -74.299795 v_C_hbond = 246.000000 Press = -786.245946 Volume = 7447.236335 Loop time of 0.0976357 on 4 procs for 100 steps with 384 atoms Performance: 88.492 ns/day, 0.271 hours/ns, 1024.215 timesteps/s 96.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055383 | 0.065178 | 0.07438 | 2.7 | 66.76 Bond | 0.00099874 | 0.0011503 | 0.001229 | 0.3 | 1.18 Kspace | 0.013823 | 0.022918 | 0.032308 | 4.4 | 23.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0064669 | 0.0072899 | 0.0078194 | 0.6 | 7.47 Output | 0.00039268 | 0.00043893 | 0.00056481 | 0.0 | 0.45 Modify | 0.000175 | 0.00019002 | 0.00020623 | 0.0 | 0.19 Other | | 0.0004706 | | | 0.48 Nlocal: 96 ave 104 max 87 min Histogram: 1 1 0 0 0 0 0 0 0 2 Nghost: 3063.25 ave 3108 max 3024 min Histogram: 1 0 1 0 0 0 1 0 0 1 Neighs: 25463.5 ave 28799 max 22471 min Histogram: 1 0 0 1 0 1 0 0 0 1 FullNghs: 1406 ave 1664 max 1237 min Histogram: 1 0 1 1 0 0 0 0 0 1 Total # of neighbors = 101854 Ave neighs/atom = 265.245 Ave special neighs/atom = 4 Neighbor list builds = 0 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:00