150 lines
6.1 KiB
Groff
150 lines
6.1 KiB
Groff
LAMMPS (23 Jun 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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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 = 0.004 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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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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# 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 1
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run 5
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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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1 7.1819351 -47.135822 1.4553325 1.5620463 0 0 3.0173788 -43.754508 -26763.923 -32046.377 -25919.73 -23012.16 1848.028 3578.5744 5396.0234
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2 18.776762 -46.526843 0.46636815 1.2906982 0 0 1.7570664 -43.818287 -6352.6601 -4602.4631 -11460.465 -4789.8629 -1296.5558 3625.7641 4391.7607
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3 19.013509 -45.750445 0.043880608 0.9336078 0 0 0.97748841 -43.809471 18351.549 29896.314 6275.5012 17065.39 -6055.8639 3664.6024 3015.6633
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4 11.017518 -45.12347 0.24124811 0.58878104 0 0 0.83002915 -43.735142 35358.63 54252.632 19050.919 31719.21 -9822.7607 3160.7845 1520.1368
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5 12.143149 -44.904245 0.22320916 0.3270434 0 0 0.55025256 -43.738653 35160.919 53395.572 20272.979 30653.482 -9511.0241 1392.4959 35.692826
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Loop time of 0.00117792 on 1 procs for 5 steps with 18 atoms
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Performance: 366.749 ns/day, 0.065 hours/ns, 4244.778 timesteps/s
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95.2% CPU use with 1 MPI tasks x 1 OpenMP threads
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HIPPO timing breakdown:
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Init time: 1.5876e-05 1.52%
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Repulse time: 0.000160405 15.32%
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Disp time: 5.1301e-05 4.90%
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Mpole time: 0.000219996 21.01%
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Induce time: 0.000352821 33.70%
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Polar time: 0.000218541 20.87%
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Qxfer time: 2.7842e-05 2.66%
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Total time: 0.00104695
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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 | 0.0010494 | 0.0010494 | 0.0010494 | 0.0 | 89.09
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Bond | 7.408e-06 | 7.408e-06 | 7.408e-06 | 0.0 | 0.63
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 1.032e-06 | 1.032e-06 | 1.032e-06 | 0.0 | 0.09
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Output | 0.00011139 | 0.00011139 | 0.00011139 | 0.0 | 9.46
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Modify | 2.647e-06 | 2.647e-06 | 2.647e-06 | 0.0 | 0.22
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Other | | 6.086e-06 | | | 0.52
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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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