LAMMPS (24 Mar 2022) # water box with AMOEBA or HIPPO units real boundary p p p atom_style amoeba bond_style class2 angle_style amoeba dihedral_style none # per-atom properties required by AMOEBA or HIPPO fix amtype all property/atom i_amtype ghost yes fix extra all property/atom i_amgroup d_redID d_pval ghost yes fix extra2 all property/atom i_polaxe d2_xyzaxis 3 # read data file read_data data.water_box.hippo fix amtype NULL "Tinker Types" Reading data file ... orthogonal box = (0 0 0) to (18.643 18.643 18.643) 1 by 1 by 1 MPI processor grid reading atoms ... 648 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 432 bonds reading angles ... 216 angles Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of special neighbors special bonds CPU = 0.000 seconds read_data CPU = 0.012 seconds # force field pair_style hippo pair_coeff * * hippo_water.prm hippo_water_box.key special_bonds lj/coul 0.5 0.5 0.5 one/five yes Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0.5 0.5 0.5 special bond factors coul: 0.5 0.5 0.5 2 = max # of 1-2 neighbors 1 = max # of 1-3 neighbors 1 = max # of 1-4 neighbors 2 = max # of 1-5 neighbors 2 = max # of special neighbors special bonds CPU = 0.001 seconds # thermo output compute virial all pressure NULL virial thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] dump 1 all custom 10 dump.water_box id type x y z fx fy fz dump_modify 1 sort id # zero step run #run 0 # dynamics fix 1 all nve thermo 10 run 100 AMOEBA/HIPPO force field settings repulsion: cut 7 taper 6 rscale 0 0 1 1 qxfer: cut 7 taper 6 mscale 0 0 0.4 1 dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1 multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1 polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24 pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1 precondition: cut 4.5 generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair hippo, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard AMOEBA/HIPPO group count: 216 Per MPI rank memory allocation (min/avg/max) = 57.8 | 57.8 | 57.8 Mbytes Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6] 0 0 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578 10 100.94691 -2350.192 116.13156 88.56605 0 0 204.69761 -1950.8098 -11480.919 -13574.139 -12190.797 -12798.212 -263.77028 280.62864 1974.1486 20 153.91622 -2358.3058 36.396961 66.22466 0 0 102.62162 -1958.8438 -7778.4529 -8492.3868 -11999.431 -9125.9998 -917.99962 589.09064 1788.2094 30 145.5951 -2343.9956 39.651541 65.833248 0 0 105.48479 -1957.7184 -288.79965 -2574.4466 -3820.4824 -414.28285 -347.51491 -1147.3995 -126.71025 40 126.87801 -2340.2623 102.93951 43.896946 0 0 146.83646 -1948.7309 6766.15 5908.7048 1280.0961 7930.8191 -1085.6811 -1596.6859 -714.82888 50 134.52078 -2358.9232 107.49288 44.253826 0 0 151.74671 -1947.7419 8762.4348 6023.4661 5377.0189 9396.0316 -1629.1364 -1663.1666 -2381.51 60 173.10181 -2374.3854 51.097314 33.03646 0 0 84.133774 -1956.4102 4614.2907 1719.1989 505.79149 4552.3167 -1661.1714 -587.92108 -1380.6732 70 184.86849 -2391.6106 39.916931 35.978152 0 0 75.895083 -1959.1811 -2146.9339 -4993.4021 -4095.6729 -4897.5768 -833.09046 1542.411 -1539.5266 80 164.75795 -2406.3017 101.94229 33.067832 0 0 135.01013 -1953.542 -8779.3265 -10545.409 -10418.702 -12098.858 -1319.194 1750.3511 -275.1272 90 151.17491 -2434.6876 152.21826 41.301673 0 0 193.51993 -1949.6141 -13330.691 -15436.505 -13791.461 -16934.674 149.25497 2289.1026 976.14333 100 166.99163 -2452.5298 143.57768 35.341459 0 0 178.91914 -1951.5533 -14918.51 -16077.49 -17353.738 -18140.466 19.009088 1487.0469 1084.0231 Loop time of 9.27469 on 1 procs for 100 steps with 648 atoms Performance: 0.932 ns/day, 25.763 hours/ns, 10.782 timesteps/s 99.0% CPU use with 1 MPI tasks x no OpenMP threads AMEOBA/HIPPO timing breakdown: Init time: 0.012403 0.00134127 Repulse time: 1.04474 11.2979 Disp time: 0.83125 8.98919 Mpole time: 1.66803 18.0382 Induce time: 3.2846 35.5199 Polar time: 2.12371 22.9659 Qxfer time: 0.282486 3.05482 Total time: 9.24722 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.2473 | 9.2473 | 9.2473 | 0.0 | 99.70 Bond | 0.0023727 | 0.0023727 | 0.0023727 | 0.0 | 0.03 Neigh | 0.0055338 | 0.0055338 | 0.0055338 | 0.0 | 0.06 Comm | 0.0021428 | 0.0021428 | 0.0021428 | 0.0 | 0.02 Output | 0.016044 | 0.016044 | 0.016044 | 0.0 | 0.17 Modify | 0.00059122 | 0.00059122 | 0.00059122 | 0.0 | 0.01 Other | | 0.0006893 | | | 0.01 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4282 ave 4282 max 4282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98490 ave 98490 max 98490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98490 Ave neighs/atom = 151.99074 Ave special neighs/atom = 2 Neighbor list builds = 2 Dangerous builds = 0 Total wall time: 0:00:09