151 lines
7.2 KiB
Groff
151 lines
7.2 KiB
Groff
LAMMPS (23 Jun 2022)
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# water hexamer with AMOEBA or HIPPO
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units real
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boundary s s s
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atom_style amoeba
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bond_style class2
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angle_style amoeba
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dihedral_style none
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# per-atom properties required by AMOEBA or HIPPO
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fix amtype all property/atom i_amtype ghost yes
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fix extra all property/atom i_amgroup d_redID d_pval ghost yes
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fix extra2 all property/atom i_polaxe d2_xyzaxis 3
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# read data file
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read_data data.water_hexamer.hippo fix amtype NULL "Tinker Types"
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Reading data file ...
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orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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18 atoms
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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12 bonds
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reading angles ...
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6 angles
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_data CPU = 0.007 seconds
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# force field
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pair_style hippo
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pair_coeff * * hippo_water.prm hippo_water.key
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Reading potential file hippo_water.prm with DATE: 2022-07-05
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Reading potential file hippo_water.key with DATE: 2022-07-05
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special_bonds lj/coul 0.5 0.5 0.5 one/five yes
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0.5 0.5 0.5
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special bond factors coul: 0.5 0.5 0.5
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of 1-5 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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# thermo output
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compute virial all pressure NULL virial
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thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
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#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
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#dump_modify 1 sort id
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# dynamics
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fix 1 all nve
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thermo 10
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run 100
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HIPPO force field settings
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repulsion: cut 10 taper 8 rscale 0 0 1 1
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qxfer: cut 10 taper 8 mscale 0 0 0.4 1
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dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
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multipole: cut 10 aewald 0 mscale 0 0 0.4 1
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polar: cut 10 aewald 0
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pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
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precondition: cut 4.5
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 1 1 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair hippo, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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HIPPO group count: 6
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Per MPI rank memory allocation (min/avg/max) = 47.84 | 47.84 | 47.84 Mbytes
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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]
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0 0 -47.362156 1.9820353 1.6634749 0 0 3.6455102 -43.716646 -34513.768 -42206.078 -31383.641 -29951.584 2850.1184 3579.9253 5768.3698
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10 11.52238 -45.959856 1.53397 0.085100522 0 0 1.6190706 -43.756903 -28644.676 -34867.94 -19324.955 -32842.522 -370.63233 -6452.0859 -4002.3535
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20 20.237283 -46.772008 0.54762833 1.3835192 0 0 1.9311476 -43.815361 -10546.356 -10116.359 -17063.425 -6393.701 -1166.7608 4243.6327 3493.9596
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30 20.666374 -45.011106 0.086797459 0.071122604 0 0 0.15792006 -43.805943 13150.762 15882.022 10964.553 10630.278 -6754.7642 -432.29165 -3783.115
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40 10.639014 -45.430939 0.18926921 0.96410995 0 0 1.1533792 -43.738441 33402.664 41252.58 19726.586 38211.875 -6166.03 6081.5692 1815.7739
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50 10.992432 -44.741108 0.19575431 0.25851128 0 0 0.45426559 -43.729815 37696.923 41572.466 33299.43 37168.141 -3254.5134 2.9639226 -1017.3669
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60 19.748633 -45.461264 0.035287281 0.63217389 0 0 0.66746117 -43.793065 26212.839 28825.788 16048.096 31876.925 3504.5461 135.3505 420.28566
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70 26.129957 -46.022729 0.30434543 0.56770169 0 0 0.87204711 -43.826579 3919.9866 -2755.6905 11500.428 517.54333 5626.9543 -2238.5786 86.305984
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80 17.768494 -46.309777 1.1680612 0.45551823 0 0 1.6235794 -43.785801 -18335.898 -22168.789 -14488.992 -20048.346 7343.173 -2646.2196 -2525.6625
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90 8.3822494 -47.063502 2.0182644 0.88875358 0 0 2.9070179 -43.731724 -33693.203 -43487.996 -15178.35 -43214.494 2412.6411 1993.0113 1780.7512
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100 8.6486333 -46.517402 1.9551958 0.38696887 0 0 2.3421647 -43.736979 -34734.97 -34372.659 -28372.146 -42286.799 226.18821 40.353457 -755.93912
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Loop time of 0.0384281 on 1 procs for 100 steps with 18 atoms
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Performance: 224.836 ns/day, 0.107 hours/ns, 2602.266 timesteps/s
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99.7% CPU use with 1 MPI tasks x no OpenMP threads
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HIPPO timing breakdown:
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Init time: 0.000296169 0.79%
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Repulse time: 0.00605807 16.08%
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Disp time: 0.00222186 5.90%
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Mpole time: 0.00734879 19.51%
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Induce time: 0.0128126 34.02%
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Polar time: 0.00749189 19.89%
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Qxfer time: 0.00142542 3.78%
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Total time: 0.0376635
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.037703 | 0.037703 | 0.037703 | 0.0 | 98.11
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Bond | 0.00016755 | 0.00016755 | 0.00016755 | 0.0 | 0.44
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 2.4711e-05 | 2.4711e-05 | 2.4711e-05 | 0.0 | 0.06
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Output | 0.00038288 | 0.00038288 | 0.00038288 | 0.0 | 1.00
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Modify | 6.4863e-05 | 6.4863e-05 | 6.4863e-05 | 0.0 | 0.17
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Other | | 8.521e-05 | | | 0.22
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Nlocal: 18 ave 18 max 18 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 153 ave 153 max 153 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 153
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Ave neighs/atom = 8.5
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Ave special neighs/atom = 2
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:00
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