153 lines
7.2 KiB
Groff
153 lines
7.2 KiB
Groff
LAMMPS (24 Mar 2022)
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# water box with AMOEBA or HIPPO
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units real
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boundary p p p
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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_box.hippo fix amtype NULL "Tinker Types"
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Reading data file ...
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orthogonal box = (0 0 0) to (18.643 18.643 18.643)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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648 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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432 bonds
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reading angles ...
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216 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 = 0.012 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_box.key
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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 = 0.001 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_box id type x y z fx fy fz
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dump_modify 1 sort id
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# zero step run
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#run 0
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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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AMOEBA/HIPPO force field settings
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repulsion: cut 7 taper 6 rscale 0 0 1 1
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qxfer: cut 7 taper 6 mscale 0 0 0.4 1
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dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1
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multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
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polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
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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 = 9
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ghost atom cutoff = 9
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binsize = 4.5, bins = 5 5 5
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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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AMOEBA/HIPPO group count: 216
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Per MPI rank memory allocation (min/avg/max) = 57.8 | 57.8 | 57.8 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 -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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Loop time of 9.27469 on 1 procs for 100 steps with 648 atoms
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Performance: 0.932 ns/day, 25.763 hours/ns, 10.782 timesteps/s
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99.0% CPU use with 1 MPI tasks x no OpenMP threads
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AMEOBA/HIPPO timing breakdown:
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Init time: 0.012403 0.00134127
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Repulse time: 1.04474 11.2979
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Disp time: 0.83125 8.98919
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Mpole time: 1.66803 18.0382
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Induce time: 3.2846 35.5199
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Polar time: 2.12371 22.9659
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Qxfer time: 0.282486 3.05482
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Total time: 9.24722
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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 | 9.2473 | 9.2473 | 9.2473 | 0.0 | 99.70
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Bond | 0.0023727 | 0.0023727 | 0.0023727 | 0.0 | 0.03
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Neigh | 0.0055338 | 0.0055338 | 0.0055338 | 0.0 | 0.06
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Comm | 0.0021428 | 0.0021428 | 0.0021428 | 0.0 | 0.02
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Output | 0.016044 | 0.016044 | 0.016044 | 0.0 | 0.17
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Modify | 0.00059122 | 0.00059122 | 0.00059122 | 0.0 | 0.01
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Other | | 0.0006893 | | | 0.01
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Nlocal: 648 ave 648 max 648 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 4282 ave 4282 max 4282 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 98490 ave 98490 max 98490 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 98490
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Ave neighs/atom = 151.99074
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Ave special neighs/atom = 2
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Neighbor list builds = 2
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Dangerous builds = 0
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Total wall time: 0:00:09
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