152 lines
7.3 KiB
Groff
152 lines
7.3 KiB
Groff
LAMMPS (23 Jun 2022)
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# water dimer 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_dimer.hippo fix amtype NULL "Tinker Types"
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Reading data file ...
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orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
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2 by 1 by 2 MPI processor grid
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reading atoms ...
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6 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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4 bonds
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reading angles ...
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2 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 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_dimer 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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WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
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HIPPO group count: 2
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Per MPI rank memory allocation (min/avg/max) = 47.91 | 48.04 | 48.18 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 -5.0101954 0.025695395 0.51472748 0 0 0.54042288 -4.4697726 -11875.159 -38149.178 29162.678 -26638.977 -70.63422 -24614.614 -58.505595
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10 0.75132894 -4.7952077 0.028216017 0.28494196 0 0 0.31315798 -4.4708519 -13243.822 12661.254 -49613.657 -2923.1497 69.449413 29456.684 56.087663
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20 2.1716525 -5.0036265 0.011809223 0.48875837 0 0 0.50056759 -4.4706925 4371.5298 -22102.532 47044.297 -12243.648 -74.588915 -28903.762 -64.48154
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30 2.9930198 -4.8261906 0.0091463366 0.30162756 0 0 0.3107739 -4.4708086 9992.4549 41973.539 -20985.339 8415.1715 67.458145 25027.414 40.261795
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40 3.312268 -4.9802484 0.010400667 0.45076258 0 0 0.46116325 -4.4697189 21565.307 -11602.414 65186.215 10476.902 -83.374203 -33222.094 -64.700001
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50 4.3187397 -4.8535614 0.0060313545 0.31244652 0 0 0.31847788 -4.4707168 11344.244 45839.35 -21073.749 8438.8954 73.345039 29422.636 43.897876
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60 4.9127902 -5.0035271 0.0070589202 0.45246538 0 0 0.4595243 -4.4707824 6529.9354 -37107.891 46740.24 9015.2973 -90.41111 -34402.095 -53.57079
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70 5.3145827 -4.8748857 0.025797484 0.29875503 0 0 0.32455252 -4.4711244 -10208.876 26324.134 -49272.688 -8697.2875 84.479942 36185.667 57.000355
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80 3.8409793 -5.0262066 0.027669388 0.47104466 0 0 0.49871405 -4.4702464 -9777.1809 -52088.554 28053.855 -6033.4555 -94.607853 -44638.417 -59.108505
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90 3.0683704 -4.8369716 0.035455716 0.28466932 0 0 0.32012503 -4.4711155 -10626.245 31066.635 -49425.925 -14107.889 87.765958 34632.905 52.101981
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100 3.5262799 -4.9906817 0.016687539 0.45011301 0 0 0.46680055 -4.4713252 5216.7691 -34991.221 43883.163 6082.1058 -95.830393 -48645.129 -64.784334
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Loop time of 0.0121417 on 4 procs for 100 steps with 6 atoms
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Performance: 711.596 ns/day, 0.034 hours/ns, 8236.062 timesteps/s
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99.4% CPU use with 4 MPI tasks x no OpenMP threads
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HIPPO timing breakdown:
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Init time: 0.000597179 5.89%
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Repulse time: 0.000498881 4.92%
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Disp time: 8.8931e-05 0.88%
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Mpole time: 0.000837487 8.26%
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Induce time: 0.00727381 71.77%
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Polar time: 0.000785393 7.75%
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Qxfer time: 4.87313e-05 0.48%
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Total time: 0.0101354
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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 | 0.010257 | 0.010374 | 0.01049 | 0.1 | 85.44
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Bond | 1.2833e-05 | 4.7018e-05 | 8.6931e-05 | 0.0 | 0.39
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0006916 | 0.00076578 | 0.00092404 | 0.0 | 6.31
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Output | 0.00040685 | 0.00049547 | 0.00057258 | 0.0 | 4.08
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Modify | 3.3096e-05 | 3.6004e-05 | 4.4046e-05 | 0.0 | 0.30
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Other | | 0.0004238 | | | 3.49
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Nlocal: 1.5 ave 3 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 4.5 ave 6 max 3 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 3.75 ave 12 max 0 min
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Histogram: 2 0 1 0 0 0 0 0 0 1
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Total # of neighbors = 15
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Ave neighs/atom = 2.5
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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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