148 lines
7.2 KiB
Groff
148 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.amoeba 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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2 by 1 by 2 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 = 0.008 seconds
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# force field
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pair_style amoeba
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pair_coeff * * amoeba_water.prm amoeba_water.key
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Reading potential file amoeba_water.prm with DATE: 2022-07-05
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Reading potential file amoeba_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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AMOEBA force field settings
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hal: cut 10 taper 8 vscale 0 0 1 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 1 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 amoeba, 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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WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
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AMOEBA group count: 6
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Per MPI rank memory allocation (min/avg/max) = 48.3 | 48.3 | 48.3 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 -48.469664 1.9820353 2.2499329 0 0 4.2319683 -44.237696 -26322.671 -28303.103 -27669.614 -22995.296 1312.6688 2624.8394 4042.0489
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10 6.3616471 -46.626437 1.7910812 0.25704063 0 0 2.0481218 -44.255947 -23813.06 -24671.886 -17167.34 -30208.043 -474.208 -8339.5934 -5278.359
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20 15.149798 -48.177533 1.1130818 2.007499 0 0 3.1205807 -44.289255 -16468.855 -20150.975 -18596.629 -12107.083 885.52697 6320.1867 3064.949
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30 17.896968 -45.959274 0.54802739 0.19519937 0 0 0.74322676 -44.309141 -4749.0624 -9053.7792 -182.37209 -6721.7499 -2003.7641 -627.56998 -1658.1301
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40 16.203813 -46.840973 0.1371751 1.5793326 0 0 1.7165077 -44.303357 9267.4858 6108.7966 4116.4548 16028.336 380.03787 8468.0648 4492.3331
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50 11.584975 -45.166711 0.017120512 0.28622888 0 0 0.30334939 -44.276308 22189.511 21453.083 22339.471 21668.607 150.93139 1059.5253 200.0668
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60 10.002055 -45.994946 0.037889337 1.1987062 0 0 1.2365956 -44.251509 30944.004 35801.925 19832.696 36241.326 2042.3054 2320.5193 1660.0834
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70 11.272241 -45.411622 0.07431614 0.51778317 0 0 0.59209931 -44.248316 32055.564 39306.193 30181.52 25601.501 1373.4778 -4501.0686 -2570.4767
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80 14.011502 -46.081444 0.089688317 1.006928 0 0 1.0966163 -44.274812 25661.838 38836.598 12603.734 24205.867 -867.36437 -4211.9639 -2820.6725
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90 17.659498 -46.247295 0.21744649 0.82687716 0 0 1.0443237 -44.308098 12101.207 19426.995 14142.311 1046.299 -2157.5418 -2141.2454 -2621.456
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100 17.630532 -46.788272 0.61811601 0.9654966 0 0 1.5836126 -44.311254 -4455.3587 3961.5737 -11554.095 -7458.8012 -3120.9771 -1532.1706 -1499.0117
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Loop time of 0.0397428 on 4 procs for 100 steps with 18 atoms
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Performance: 217.398 ns/day, 0.110 hours/ns, 2516.180 timesteps/s
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100.0% CPU use with 4 MPI tasks x no OpenMP threads
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AMOEBA timing breakdown:
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Init time: 0.000772875 2.05%
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Hal time: 0.00114925 3.04%
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Mpole time: 0.00316129 8.37%
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Induce time: 0.0278156 73.61%
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Polar time: 0.0048762 12.90%
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Total time: 0.0377876
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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 | 0.03793 | 0.038002 | 0.038115 | 0.0 | 95.62
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Bond | 6.3821e-05 | 8.0969e-05 | 9.9652e-05 | 0.0 | 0.20
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00067584 | 0.00085989 | 0.0009896 | 0.0 | 2.16
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Output | 0.00035407 | 0.00040202 | 0.00051789 | 0.0 | 1.01
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Modify | 3.6589e-05 | 4.0916e-05 | 4.417e-05 | 0.0 | 0.10
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Other | | 0.0003569 | | | 0.90
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Nlocal: 4.5 ave 6 max 3 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Nghost: 13.5 ave 15 max 12 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Neighs: 38.25 ave 77 max 9 min
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Histogram: 2 0 0 0 0 0 1 0 0 1
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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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