148 lines
7.2 KiB
Groff
148 lines
7.2 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.amoeba 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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1 by 1 by 1 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 = 0.007 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_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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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: 2
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Per MPI rank memory allocation (min/avg/max) = 48.33 | 48.33 | 48.33 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 -5.1627563 0.025695395 0.71581114 0 0 0.74150653 -4.4212497 -12260.522 -43226.042 39448.214 -33003.739 -85.160886 -28101.905 -72.971988
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10 1.1174766 -4.7928792 0.045080327 0.30848527 0 0 0.35356559 -4.4226587 -14728.416 11456.119 -52592.829 -3262.8454 70.868937 29494.268 57.977562
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20 3.0821934 -5.1387316 0.013108182 0.65694692 0 0 0.6700551 -4.4227393 3007.4148 -25925.326 49641.41 -15284.933 -79.726771 -29005.234 -68.530079
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30 3.461967 -4.8079248 0.013888863 0.31895667 0 0 0.33284554 -4.423482 8616.211 40027.877 -31134.295 16291.126 72.510013 23088.238 51.407946
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40 4.2181367 -5.0535921 0.0099009766 0.55796811 0 0 0.56786908 -4.4228557 24239.885 -5761.6967 62095.735 15576.675 -76.240192 -33057.385 -58.850871
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50 5.216657 -4.8012751 0.0053003148 0.29489399 0 0 0.30019431 -4.4233315 17728.056 44785.731 -21215.714 28613.715 66.24671 20292.137 51.010856
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60 9.45101 -5.0818046 0.0043357361 0.5118733 0 0 0.51620903 -4.4247372 16893.135 -15068.961 50111.11 13824.77 -75.966047 -34809.168 -52.83183
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70 10.385926 -4.8250769 0.022572262 0.22235766 0 0 0.24492992 -4.4253547 -1117.3665 19070.918 -36063.612 11648.813 61.067533 25754.59 53.919881
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80 12.797691 -5.123735 0.023756795 0.48275385 0 0 0.50651065 -4.4264869 -6491.9826 -28436.037 20681.908 -14176.121 -64.024669 -35737.052 -52.583533
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90 12.569481 -4.8303379 0.060369422 0.15670502 0 0 0.21707444 -4.4259273 -16762.536 1720.5855 -47624.986 -6793.7441 59.966729 30024.566 52.339671
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100 17.750788 -5.1195235 0.039885925 0.38711474 0 0 0.42700067 -4.4279642 -10817.92 -21833.456 4186.8301 -18211.329 -43.11086 -32664.671 -41.508916
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Loop time of 0.00539351 on 1 procs for 100 steps with 6 atoms
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Performance: 1601.925 ns/day, 0.015 hours/ns, 18540.802 timesteps/s
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97.1% CPU use with 1 MPI tasks x no OpenMP threads
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AMOEBA timing breakdown:
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Init time: 0.000111932 2.32%
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Hal time: 0.00045057 9.33%
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Mpole time: 0.00055958 11.59%
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Induce time: 0.00238881 49.46%
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Polar time: 0.0013042 27.00%
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Total time: 0.00482974
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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 | 0.0048575 | 0.0048575 | 0.0048575 | 0.0 | 90.06
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Bond | 9.4036e-05 | 9.4036e-05 | 9.4036e-05 | 0.0 | 1.74
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 1.3435e-05 | 1.3435e-05 | 1.3435e-05 | 0.0 | 0.25
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Output | 0.00034323 | 0.00034323 | 0.00034323 | 0.0 | 6.36
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Modify | 3.5435e-05 | 3.5435e-05 | 3.5435e-05 | 0.0 | 0.66
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Other | | 4.986e-05 | | | 0.92
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Nlocal: 6 ave 6 max 6 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: 15 ave 15 max 15 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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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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