LAMMPS (23 Jun 2022) # replicate 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.amoeba 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 = 0.010 seconds # force field pair_style amoeba pair_coeff * * amoeba_water.prm amoeba_water_box.key Reading potential file amoeba_water.prm with DATE: 2022-07-05 Reading potential file amoeba_water_box.key with DATE: 2022-07-05 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 # dynamics fix 1 all nve thermo 10 run 100 AMOEBA force field settings hal: cut 7 taper 6 vscale 0 0 1 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 1 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 amoeba, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard AMOEBA group count: 216 Per MPI rank memory allocation (min/avg/max) = 56.94 | 56.94 | 56.94 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 -2172.0637 166.82637 83.732524 0 0 250.5589 -1921.5048 -6181.4178 -4772.1682 -6954.8414 -6817.2437 -272.19967 3173.3481 2229.9454 10 105.50186 -2373.7036 136.67877 106.86833 0 0 243.5471 -1926.6873 -8440.8076 -10450.396 -9513.7369 -9664.6007 -301.7395 322.28511 1917.0314 20 143.89822 -2358.363 70.950306 76.775658 0 0 147.72596 -1933.1172 -7370.2083 -7728.5515 -11580.39 -8675.2341 -806.78779 780.67516 2096.34 30 157.22465 -2375.4739 50.393531 87.108003 0 0 137.50153 -1934.7514 -4449.577 -6946.7795 -7865.2165 -4954.2358 -417.69587 -1004.2877 -36.388669 40 150.92481 -2354.1892 78.482464 53.798462 0 0 132.28093 -1930.8371 353.42948 -939.14353 -4636.5062 475.58057 -1073.8523 -1583.9471 -574.21807 50 153.0181 -2388.7322 100.20232 65.813823 0 0 166.01614 -1927.6078 3975.1981 1368.1361 425.64533 3886.0124 -1806.8586 -2534.5272 -2118.2395 60 155.01494 -2364.3168 92.946192 44.248949 0 0 137.19514 -1928.1623 5793.7546 3524.7523 1420.4096 6108.7958 -1536.5261 -2558.8204 -1501.5292 70 166.70755 -2383.503 76.491199 55.01988 0 0 131.51108 -1930.4824 4744.1583 1919.3954 2838.7666 2669.745 -169.21643 -188.08678 -2256.4142 80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412 90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604 100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924 Loop time of 14.5572 on 1 procs for 100 steps with 648 atoms Performance: 0.594 ns/day, 40.437 hours/ns, 6.869 timesteps/s 99.9% CPU use with 1 MPI tasks x no OpenMP threads AMOEBA timing breakdown: Init time: 0.0224497 0.15% Hal time: 1.00248 6.90% Mpole time: 1.42229 9.78% Induce time: 9.23983 63.55% Polar time: 2.8515 19.61% Total time: 14.5386 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.539 | 14.539 | 14.539 | 0.0 | 99.87 Bond | 0.0029302 | 0.0029302 | 0.0029302 | 0.0 | 0.02 Neigh | 0.010789 | 0.010789 | 0.010789 | 0.0 | 0.07 Comm | 0.0027888 | 0.0027888 | 0.0027888 | 0.0 | 0.02 Output | 0.00040039 | 0.00040039 | 0.00040039 | 0.0 | 0.00 Modify | 0.0007305 | 0.0007305 | 0.0007305 | 0.0 | 0.01 Other | | 0.0008703 | | | 0.01 Nlocal: 648 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4290 ave 4290 max 4290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 98545 ave 98545 max 98545 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98545 Ave neighs/atom = 152.07562 Ave special neighs/atom = 2 Neighbor list builds = 2 Dangerous builds = 0 Total wall time: 0:00:14