clean up log files
This commit is contained in:
Steve Plimpton
@ -1,3 +1,4 @@
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!! DATE: 2022-07-05 UNITS: real
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parameters ./amoeba.prm
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parameters ./amoeba.prm
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verbose
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verbose
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neighbor-list
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neighbor-list
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@ -1,4 +1,5 @@
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parameters ./amoeba.prm
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!! DATE: 2022-07-05 UNITS: real
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parameters ./amoeba.prm
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digits 8
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digits 8
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@ -1,4 +1,5 @@
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parameters ./amoeba.prm
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!! DATE: 2022-07-05 UNITS: real
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parameters ./amoeba.prm
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digits 10
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digits 10
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openmp-threads 1
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openmp-threads 1
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@ -16,4 +17,3 @@ taper 6
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polar-eps 1e-5
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polar-eps 1e-5
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usolve-diag 1.0
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usolve-diag 1.0
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@ -1,4 +1,5 @@
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parameters ./hippo.prm
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!! DATE: 2022-07-05 UNITS: real
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parameters ./hippo.prm
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digits 8
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digits 8
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@ -1,4 +1,5 @@
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parameters ./hippo.prm
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!! DATE: 2022-07-05 UNITS: real
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parameters ./hippo.prm
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digits 8
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digits 8
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verbose
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verbose
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@ -19,4 +20,3 @@ taper 6
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polar-eps 1e-5
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polar-eps 1e-5
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usolve-diag 1.0
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usolve-diag 1.0
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@ -1,162 +0,0 @@
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LAMMPS (23 Jun 2022)
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# solvated ubiquitin molecule with AMOEBA force field
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units real
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boundary p p p
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atom_modify sort 0 0.0
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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 fourier
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improper_style amoeba
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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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fix pit all amoeba/pitorsion
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fix_modify pit energy yes
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fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
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fix_modify bit energy yes
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# read data file
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read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions
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Reading data file ...
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orthogonal box = (0 0 0) to (54.99 41.91 41.91)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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9737 atoms
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scanning bonds ...
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4 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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18 = max dihedrals/atom
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scanning impropers ...
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3 = max impropers/atom
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reading bonds ...
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6908 bonds
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reading angles ...
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5094 angles
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reading dihedrals ...
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3297 dihedrals
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reading impropers ...
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651 impropers
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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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4 = max # of 1-2 neighbors
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9 = max # of 1-3 neighbors
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19 = max # of 1-4 neighbors
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21 = max # of special neighbors
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special bonds CPU = 0.004 seconds
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read_data CPU = 0.077 seconds
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pair_style amoeba
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pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
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Reading potential file amoeba_ubiquitin.prm with DATE: 2022-07-05
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Skipping section: AMOEBA Protein Force Field Atom Classes
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Skipping section: Torsion-Torsion Parameters
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Skipping section: Biopolymer Atom Type Conversions
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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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4 = max # of 1-2 neighbors
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9 = max # of 1-3 neighbors
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19 = max # of 1-4 neighbors
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58 = max # of 1-5 neighbors
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21 = max # of special neighbors
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special bonds CPU = 0.006 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.ubiquitin 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 1
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run 10
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AMOEBA force field settings
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hal: cut 12 taper 10.8 vscale 0 0 1 1
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multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
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polar: cut 7 aewald 0.5 bsorder 5 FFT 60 48 48
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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 15 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 = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 8 6 6
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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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AMOEBA group count: 3196
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Per MPI rank memory allocation (min/avg/max) = 258.3 | 258.3 | 258.3 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 -35338.057 2856.5938 1955.5431 224.37609 65.00809 5101.5211 -30247.585 -6336.5196 -5795.4272 -6329.8149 -6884.3167 349.52657 77.164877 652.41925
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1 29.61379 -35356.153 2037.3541 1840.7883 223.90217 64.293945 4166.3385 -30341.522 -6486.773 -6452.8463 -6841.5982 -7386.1106 311.38025 120.72605 545.35513
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2 78.518242 -35383.65 825.39919 1538.3909 222.55095 62.191009 2648.5321 -30467.814 -5502.9841 -6410.2998 -6396.1829 -6937.8137 217.3515 210.76948 294.28051
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3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776
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4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224
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5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369
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6 118.24373 -36092.77 1166.179 815.59206 213.67399 44.022297 2239.4673 -30435.629 -1677.8051 -3988.2428 -2669.6848 -3247.7207 197.42472 285.87129 -162.35459
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7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786
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8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727
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9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705
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10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746
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Loop time of 24.1308 on 1 procs for 10 steps with 9737 atoms
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Performance: 0.036 ns/day, 670.300 hours/ns, 0.414 timesteps/s
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99.4% CPU use with 1 MPI tasks x no OpenMP threads
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AMOEBA timing breakdown:
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Init time: 0.0307243 0.13%
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Hal time: 7.7896 32.31%
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Mpole time: 2.35085 9.75%
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Induce time: 9.19392 38.14%
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Polar time: 4.74032 19.66%
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Total time: 24.1054
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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 | 24.105 | 24.105 | 24.105 | 0.0 | 99.90
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Bond | 0.016307 | 0.016307 | 0.016307 | 0.0 | 0.07
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0039483 | 0.0039483 | 0.0039483 | 0.0 | 0.02
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Output | 0.001034 | 0.001034 | 0.001034 | 0.0 | 0.00
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Modify | 0.0032551 | 0.0032551 | 0.0032551 | 0.0 | 0.01
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Other | | 0.00076 | | | 0.00
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Nlocal: 9737 ave 9737 max 9737 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 31511 ave 31511 max 31511 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5.6393e+06 ave 5.6393e+06 max 5.6393e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5639296
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Ave neighs/atom = 579.16155
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Ave special neighs/atom = 3.1364897
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:27
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@ -1,162 +0,0 @@
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LAMMPS (23 Jun 2022)
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# solvated ubiquitin molecule with AMOEBA force field
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units real
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boundary p p p
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atom_modify sort 0 0.0
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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 fourier
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||||||
improper_style amoeba
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|
||||||
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# per-atom properties required by AMOEBA or HIPPO
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||||||
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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
|
|
||||||
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
||||||
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|
||||||
fix pit all amoeba/pitorsion
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|
||||||
fix_modify pit energy yes
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|
||||||
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
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|
||||||
fix_modify bit energy yes
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|
||||||
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|
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# read data file
|
|
||||||
|
|
||||||
read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions
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|
||||||
Reading data file ...
|
|
||||||
orthogonal box = (0 0 0) to (54.99 41.91 41.91)
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|
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2 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
9737 atoms
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|
||||||
scanning bonds ...
|
|
||||||
4 = max bonds/atom
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|
||||||
scanning angles ...
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|
||||||
6 = max angles/atom
|
|
||||||
scanning dihedrals ...
|
|
||||||
18 = max dihedrals/atom
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|
||||||
scanning impropers ...
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|
||||||
3 = max impropers/atom
|
|
||||||
reading bonds ...
|
|
||||||
6908 bonds
|
|
||||||
reading angles ...
|
|
||||||
5094 angles
|
|
||||||
reading dihedrals ...
|
|
||||||
3297 dihedrals
|
|
||||||
reading impropers ...
|
|
||||||
651 impropers
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
4 = max # of 1-2 neighbors
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|
||||||
9 = max # of 1-3 neighbors
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|
||||||
19 = max # of 1-4 neighbors
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|
||||||
21 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.002 seconds
|
|
||||||
read_data CPU = 0.100 seconds
|
|
||||||
|
|
||||||
pair_style amoeba
|
|
||||||
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
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|
||||||
Reading potential file amoeba_ubiquitin.prm with DATE: 2022-07-05
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|
||||||
Skipping section: AMOEBA Protein Force Field Atom Classes
|
|
||||||
Skipping section: Torsion-Torsion Parameters
|
|
||||||
Skipping section: Biopolymer Atom Type Conversions
|
|
||||||
|
|
||||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.5 0.5 0.5
|
|
||||||
special bond factors coul: 0.5 0.5 0.5
|
|
||||||
4 = max # of 1-2 neighbors
|
|
||||||
9 = max # of 1-3 neighbors
|
|
||||||
19 = max # of 1-4 neighbors
|
|
||||||
58 = max # of 1-5 neighbors
|
|
||||||
21 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.002 seconds
|
|
||||||
|
|
||||||
# thermo output
|
|
||||||
|
|
||||||
compute virial all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
||||||
|
|
||||||
#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
thermo 1
|
|
||||||
run 10
|
|
||||||
AMOEBA force field settings
|
|
||||||
hal: cut 12 taper 10.8 vscale 0 0 1 1
|
|
||||||
multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
|
|
||||||
polar: cut 7 aewald 0.5 bsorder 5 FFT 60 48 48
|
|
||||||
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
|
|
||||||
precondition: cut 4.5
|
|
||||||
Generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 14
|
|
||||||
ghost atom cutoff = 14
|
|
||||||
binsize = 7, bins = 8 6 6
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair amoeba, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
AMOEBA group count: 3196
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.7 | 145.4 Mbytes
|
|
||||||
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]
|
|
||||||
0 0 -35338.057 2856.5938 1955.5431 224.37609 65.00809 5101.5211 -30247.585 -6336.5196 -5795.4272 -6329.8149 -6884.3167 349.52657 77.164877 652.41925
|
|
||||||
1 29.61379 -35356.153 2037.3541 1840.7883 223.90217 64.293945 4166.3385 -30341.522 -6486.773 -6452.8463 -6841.5982 -7386.1106 311.38025 120.72605 545.35513
|
|
||||||
2 78.518242 -35383.65 825.39919 1538.3909 222.55095 62.191009 2648.5321 -30467.814 -5502.9841 -6410.2998 -6396.1829 -6937.8137 217.3515 210.76948 294.28051
|
|
||||||
3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776
|
|
||||||
4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224
|
|
||||||
5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369
|
|
||||||
6 118.24373 -36092.77 1166.179 815.59206 213.67399 44.022297 2239.4673 -30435.629 -1677.8051 -3988.2428 -2669.6848 -3247.7207 197.42472 285.87129 -162.35459
|
|
||||||
7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786
|
|
||||||
8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727
|
|
||||||
9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705
|
|
||||||
10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746
|
|
||||||
Loop time of 6.07676 on 4 procs for 10 steps with 9737 atoms
|
|
||||||
|
|
||||||
Performance: 0.142 ns/day, 168.799 hours/ns, 1.646 timesteps/s
|
|
||||||
99.6% CPU use with 4 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
AMOEBA timing breakdown:
|
|
||||||
Init time: 0.0182673 0.30%
|
|
||||||
Hal time: 1.89506 31.24%
|
|
||||||
Mpole time: 0.649816 10.71%
|
|
||||||
Induce time: 2.27346 37.48%
|
|
||||||
Polar time: 1.22947 20.27%
|
|
||||||
Total time: 6.06608
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 6.0656 | 6.0662 | 6.067 | 0.0 | 99.83
|
|
||||||
Bond | 0.0030706 | 0.0035014 | 0.0039085 | 0.5 | 0.06
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.0045136 | 0.0052483 | 0.0058373 | 0.7 | 0.09
|
|
||||||
Output | 0.00065752 | 0.0007782 | 0.00099256 | 0.0 | 0.01
|
|
||||||
Modify | 0.00065468 | 0.0007142 | 0.00077861 | 0.0 | 0.01
|
|
||||||
Other | | 0.0003323 | | | 0.01
|
|
||||||
|
|
||||||
Nlocal: 2434.25 ave 2498 max 2390 min
|
|
||||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
|
||||||
Nghost: 16683.2 ave 16765 max 16568 min
|
|
||||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
|
||||||
Neighs: 1.40982e+06 ave 1.52088e+06 max 1.30717e+06 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
|
||||||
|
|
||||||
Total # of neighbors = 5639296
|
|
||||||
Ave neighs/atom = 579.16155
|
|
||||||
Ave special neighs/atom = 3.1364897
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:07
|
|
||||||
@ -1,145 +0,0 @@
|
|||||||
LAMMPS (23 Jun 2022)
|
|
||||||
# replicate water box with AMOEBA or HIPPO
|
|
||||||
|
|
||||||
units real
|
|
||||||
boundary p p p
|
|
||||||
|
|
||||||
atom_style amoeba
|
|
||||||
bond_style class2
|
|
||||||
angle_style amoeba
|
|
||||||
dihedral_style none
|
|
||||||
|
|
||||||
# per-atom properties required by AMOEBA or HIPPO
|
|
||||||
|
|
||||||
fix amtype all property/atom i_amtype ghost yes
|
|
||||||
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
|
|
||||||
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
||||||
|
|
||||||
# read data file
|
|
||||||
|
|
||||||
read_data data.water_box.amoeba fix amtype NULL "Tinker Types"
|
|
||||||
Reading data file ...
|
|
||||||
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
648 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
2 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
1 = max angles/atom
|
|
||||||
reading bonds ...
|
|
||||||
432 bonds
|
|
||||||
reading angles ...
|
|
||||||
216 angles
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
read_data CPU = 0.011 seconds
|
|
||||||
|
|
||||||
# force field
|
|
||||||
|
|
||||||
pair_style amoeba
|
|
||||||
pair_coeff * * amoeba_water.prm amoeba_water_box.key
|
|
||||||
Reading potential file amoeba_water.prm with DATE: 2022-07-05
|
|
||||||
|
|
||||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.5 0.5 0.5
|
|
||||||
special bond factors coul: 0.5 0.5 0.5
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of 1-5 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.001 seconds
|
|
||||||
|
|
||||||
# thermo output
|
|
||||||
|
|
||||||
compute virial all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
||||||
|
|
||||||
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
AMOEBA force field settings
|
|
||||||
hal: cut 7 taper 6 vscale 0 0 1 1
|
|
||||||
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
|
|
||||||
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
|
|
||||||
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
|
|
||||||
precondition: cut 4.5
|
|
||||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 9
|
|
||||||
ghost atom cutoff = 9
|
|
||||||
binsize = 4.5, bins = 5 5 5
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair amoeba, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
AMOEBA group count: 216
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 56.94 | 56.94 | 56.94 Mbytes
|
|
||||||
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]
|
|
||||||
0 0 -2172.0637 166.82637 83.732524 0 0 250.5589 -1921.5048 -6181.4178 -4772.1682 -6954.8414 -6817.2437 -272.19967 3173.3481 2229.9454
|
|
||||||
10 105.50186 -2373.7036 136.67877 106.86833 0 0 243.5471 -1926.6873 -8440.8076 -10450.396 -9513.7369 -9664.6007 -301.7395 322.28511 1917.0314
|
|
||||||
20 143.89822 -2358.363 70.950306 76.775658 0 0 147.72596 -1933.1172 -7370.2083 -7728.5515 -11580.39 -8675.2341 -806.78779 780.67516 2096.34
|
|
||||||
30 157.22465 -2375.4739 50.393531 87.108003 0 0 137.50153 -1934.7514 -4449.577 -6946.7795 -7865.2165 -4954.2358 -417.69587 -1004.2877 -36.388669
|
|
||||||
40 150.92481 -2354.1892 78.482464 53.798462 0 0 132.28093 -1930.8371 353.42948 -939.14353 -4636.5062 475.58057 -1073.8523 -1583.9471 -574.21807
|
|
||||||
50 153.0181 -2388.7322 100.20232 65.813823 0 0 166.01614 -1927.6078 3975.1981 1368.1361 425.64533 3886.0124 -1806.8586 -2534.5272 -2118.2395
|
|
||||||
60 155.01494 -2364.3168 92.946192 44.248949 0 0 137.19514 -1928.1623 5793.7546 3524.7523 1420.4096 6108.7958 -1536.5261 -2558.8204 -1501.5292
|
|
||||||
70 166.70755 -2383.503 76.491199 55.01988 0 0 131.51108 -1930.4824 4744.1583 1919.3954 2838.7666 2669.745 -169.21643 -188.08678 -2256.4142
|
|
||||||
80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412
|
|
||||||
90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604
|
|
||||||
100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924
|
|
||||||
Loop time of 13.2332 on 1 procs for 100 steps with 648 atoms
|
|
||||||
|
|
||||||
Performance: 0.653 ns/day, 36.759 hours/ns, 7.557 timesteps/s
|
|
||||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
AMOEBA timing breakdown:
|
|
||||||
Init time: 0.020242 0.15%
|
|
||||||
Hal time: 0.900253 6.81%
|
|
||||||
Mpole time: 1.29931 9.83%
|
|
||||||
Induce time: 8.37539 63.35%
|
|
||||||
Polar time: 2.62525 19.86%
|
|
||||||
Total time: 13.2205
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 13.221 | 13.221 | 13.221 | 0.0 | 99.90
|
|
||||||
Bond | 0.0027476 | 0.0027476 | 0.0027476 | 0.0 | 0.02
|
|
||||||
Neigh | 0.0055619 | 0.0055619 | 0.0055619 | 0.0 | 0.04
|
|
||||||
Comm | 0.002464 | 0.002464 | 0.002464 | 0.0 | 0.02
|
|
||||||
Output | 0.00041636 | 0.00041636 | 0.00041636 | 0.0 | 0.00
|
|
||||||
Modify | 0.00068882 | 0.00068882 | 0.00068882 | 0.0 | 0.01
|
|
||||||
Other | | 0.0007637 | | | 0.01
|
|
||||||
|
|
||||||
Nlocal: 648 ave 648 max 648 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 4290 ave 4290 max 4290 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 98545 ave 98545 max 98545 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 98545
|
|
||||||
Ave neighs/atom = 152.07562
|
|
||||||
Ave special neighs/atom = 2
|
|
||||||
Neighbor list builds = 2
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:13
|
|
||||||
@ -1,145 +0,0 @@
|
|||||||
LAMMPS (23 Jun 2022)
|
|
||||||
# replicate water box with AMOEBA or HIPPO
|
|
||||||
|
|
||||||
units real
|
|
||||||
boundary p p p
|
|
||||||
|
|
||||||
atom_style amoeba
|
|
||||||
bond_style class2
|
|
||||||
angle_style amoeba
|
|
||||||
dihedral_style none
|
|
||||||
|
|
||||||
# per-atom properties required by AMOEBA or HIPPO
|
|
||||||
|
|
||||||
fix amtype all property/atom i_amtype ghost yes
|
|
||||||
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
|
|
||||||
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
||||||
|
|
||||||
# read data file
|
|
||||||
|
|
||||||
read_data data.water_box.amoeba fix amtype NULL "Tinker Types"
|
|
||||||
Reading data file ...
|
|
||||||
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
648 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
2 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
1 = max angles/atom
|
|
||||||
reading bonds ...
|
|
||||||
432 bonds
|
|
||||||
reading angles ...
|
|
||||||
216 angles
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.001 seconds
|
|
||||||
read_data CPU = 0.014 seconds
|
|
||||||
|
|
||||||
# force field
|
|
||||||
|
|
||||||
pair_style amoeba
|
|
||||||
pair_coeff * * amoeba_water.prm amoeba_water_box.key
|
|
||||||
Reading potential file amoeba_water.prm with DATE: 2022-07-05
|
|
||||||
|
|
||||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.5 0.5 0.5
|
|
||||||
special bond factors coul: 0.5 0.5 0.5
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of 1-5 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.001 seconds
|
|
||||||
|
|
||||||
# thermo output
|
|
||||||
|
|
||||||
compute virial all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
||||||
|
|
||||||
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
AMOEBA force field settings
|
|
||||||
hal: cut 7 taper 6 vscale 0 0 1 1
|
|
||||||
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
|
|
||||||
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
|
|
||||||
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
|
|
||||||
precondition: cut 4.5
|
|
||||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 9
|
|
||||||
ghost atom cutoff = 9
|
|
||||||
binsize = 4.5, bins = 5 5 5
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair amoeba, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
AMOEBA group count: 216
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 56.38 | 56.38 | 56.38 Mbytes
|
|
||||||
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]
|
|
||||||
0 0 -2172.0637 166.82637 83.732524 0 0 250.5589 -1921.5048 -6181.4178 -4772.1682 -6954.8414 -6817.2437 -272.19967 3173.3481 2229.9454
|
|
||||||
10 105.50186 -2373.7036 136.67877 106.86833 0 0 243.5471 -1926.6873 -8440.8076 -10450.396 -9513.7369 -9664.6007 -301.7395 322.28511 1917.0314
|
|
||||||
20 143.89822 -2358.363 70.950306 76.775658 0 0 147.72596 -1933.1172 -7370.2083 -7728.5515 -11580.39 -8675.2341 -806.78779 780.67516 2096.34
|
|
||||||
30 157.22465 -2375.4739 50.393531 87.108003 0 0 137.50153 -1934.7514 -4449.577 -6946.7795 -7865.2165 -4954.2358 -417.69587 -1004.2877 -36.388669
|
|
||||||
40 150.92481 -2354.1892 78.482464 53.798462 0 0 132.28093 -1930.8371 353.42948 -939.14353 -4636.5062 475.58057 -1073.8523 -1583.9471 -574.21807
|
|
||||||
50 153.0181 -2388.7322 100.20232 65.813823 0 0 166.01614 -1927.6078 3975.1981 1368.1361 425.64533 3886.0124 -1806.8586 -2534.5272 -2118.2395
|
|
||||||
60 155.01494 -2364.3168 92.946192 44.248949 0 0 137.19514 -1928.1623 5793.7546 3524.7523 1420.4096 6108.7958 -1536.5261 -2558.8204 -1501.5292
|
|
||||||
70 166.70755 -2383.503 76.491199 55.01988 0 0 131.51108 -1930.4824 4744.1583 1919.3954 2838.7666 2669.745 -169.21643 -188.08678 -2256.4142
|
|
||||||
80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412
|
|
||||||
90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604
|
|
||||||
100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924
|
|
||||||
Loop time of 5.51861 on 4 procs for 100 steps with 648 atoms
|
|
||||||
|
|
||||||
Performance: 1.566 ns/day, 15.329 hours/ns, 18.120 timesteps/s
|
|
||||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
AMOEBA timing breakdown:
|
|
||||||
Init time: 0.0236604 0.43%
|
|
||||||
Hal time: 0.257977 4.69%
|
|
||||||
Mpole time: 0.530078 9.63%
|
|
||||||
Induce time: 3.72129 67.60%
|
|
||||||
Polar time: 0.972013 17.66%
|
|
||||||
Total time: 5.50503
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 5.5047 | 5.5054 | 5.5063 | 0.0 | 99.76
|
|
||||||
Bond | 0.00080214 | 0.00087764 | 0.00092311 | 0.0 | 0.02
|
|
||||||
Neigh | 0.0016691 | 0.001675 | 0.0016849 | 0.0 | 0.03
|
|
||||||
Comm | 0.0083938 | 0.0092735 | 0.010026 | 0.7 | 0.17
|
|
||||||
Output | 0.000358 | 0.00041667 | 0.00056168 | 0.0 | 0.01
|
|
||||||
Modify | 0.00022011 | 0.00024519 | 0.00025818 | 0.0 | 0.00
|
|
||||||
Other | | 0.0007611 | | | 0.01
|
|
||||||
|
|
||||||
Nlocal: 162 ave 164 max 159 min
|
|
||||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
|
||||||
Nghost: 2568.5 ave 2585 max 2544 min
|
|
||||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
|
||||||
Neighs: 24636.2 ave 25226 max 23891 min
|
|
||||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 98545
|
|
||||||
Ave neighs/atom = 152.07562
|
|
||||||
Ave special neighs/atom = 2
|
|
||||||
Neighbor list builds = 2
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:05
|
|
||||||
@ -1,149 +0,0 @@
|
|||||||
LAMMPS (23 Jun 2022)
|
|
||||||
# water box with AMOEBA or HIPPO
|
|
||||||
|
|
||||||
units real
|
|
||||||
boundary p p p
|
|
||||||
|
|
||||||
atom_style amoeba
|
|
||||||
bond_style class2
|
|
||||||
angle_style amoeba
|
|
||||||
dihedral_style none
|
|
||||||
|
|
||||||
# per-atom properties required by AMOEBA or HIPPO
|
|
||||||
|
|
||||||
fix amtype all property/atom i_amtype ghost yes
|
|
||||||
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
|
|
||||||
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
||||||
|
|
||||||
# read data file
|
|
||||||
|
|
||||||
read_data data.water_box.hippo fix amtype NULL "Tinker Types"
|
|
||||||
Reading data file ...
|
|
||||||
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
648 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
2 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
1 = max angles/atom
|
|
||||||
reading bonds ...
|
|
||||||
432 bonds
|
|
||||||
reading angles ...
|
|
||||||
216 angles
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.001 seconds
|
|
||||||
read_data CPU = 0.012 seconds
|
|
||||||
|
|
||||||
# force field
|
|
||||||
|
|
||||||
pair_style hippo
|
|
||||||
pair_coeff * * hippo_water.prm hippo_water_box.key
|
|
||||||
Reading potential file hippo_water.prm with DATE: 2022-07-05
|
|
||||||
|
|
||||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.5 0.5 0.5
|
|
||||||
special bond factors coul: 0.5 0.5 0.5
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of 1-5 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.001 seconds
|
|
||||||
|
|
||||||
# thermo output
|
|
||||||
|
|
||||||
compute virial all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
||||||
|
|
||||||
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
HIPPO force field settings
|
|
||||||
repulsion: cut 7 taper 6 rscale 0 0 1 1
|
|
||||||
qxfer: cut 7 taper 6 mscale 0 0 0.4 1
|
|
||||||
dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1
|
|
||||||
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
|
|
||||||
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
|
|
||||||
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
|
|
||||||
precondition: cut 4.5
|
|
||||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 9
|
|
||||||
ghost atom cutoff = 9
|
|
||||||
binsize = 4.5, bins = 5 5 5
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair hippo, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
HIPPO group count: 216
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 56.46 | 56.46 | 56.46 Mbytes
|
|
||||||
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]
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
Loop time of 10.7228 on 1 procs for 100 steps with 648 atoms
|
|
||||||
|
|
||||||
Performance: 0.806 ns/day, 29.786 hours/ns, 9.326 timesteps/s
|
|
||||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
HIPPO timing breakdown:
|
|
||||||
Init time: 0.0153975 0.14%
|
|
||||||
Repulse time: 1.2388 11.57%
|
|
||||||
Disp time: 0.693631 6.48%
|
|
||||||
Mpole time: 2.01598 18.83%
|
|
||||||
Induce time: 3.8747 36.19%
|
|
||||||
Polar time: 2.52726 23.60%
|
|
||||||
Qxfer time: 0.341839 3.19%
|
|
||||||
Total time: 10.7076
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 10.708 | 10.708 | 10.708 | 0.0 | 99.86
|
|
||||||
Bond | 0.0028607 | 0.0028607 | 0.0028607 | 0.0 | 0.03
|
|
||||||
Neigh | 0.0073977 | 0.0073977 | 0.0073977 | 0.0 | 0.07
|
|
||||||
Comm | 0.0026424 | 0.0026424 | 0.0026424 | 0.0 | 0.02
|
|
||||||
Output | 0.00048358 | 0.00048358 | 0.00048358 | 0.0 | 0.00
|
|
||||||
Modify | 0.00077694 | 0.00077694 | 0.00077694 | 0.0 | 0.01
|
|
||||||
Other | | 0.0008999 | | | 0.01
|
|
||||||
|
|
||||||
Nlocal: 648 ave 648 max 648 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 4282 ave 4282 max 4282 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 98490 ave 98490 max 98490 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 98490
|
|
||||||
Ave neighs/atom = 151.99074
|
|
||||||
Ave special neighs/atom = 2
|
|
||||||
Neighbor list builds = 2
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:10
|
|
||||||
@ -1,149 +0,0 @@
|
|||||||
LAMMPS (23 Jun 2022)
|
|
||||||
# water box with AMOEBA or HIPPO
|
|
||||||
|
|
||||||
units real
|
|
||||||
boundary p p p
|
|
||||||
|
|
||||||
atom_style amoeba
|
|
||||||
bond_style class2
|
|
||||||
angle_style amoeba
|
|
||||||
dihedral_style none
|
|
||||||
|
|
||||||
# per-atom properties required by AMOEBA or HIPPO
|
|
||||||
|
|
||||||
fix amtype all property/atom i_amtype ghost yes
|
|
||||||
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
|
|
||||||
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
||||||
|
|
||||||
# read data file
|
|
||||||
|
|
||||||
read_data data.water_box.hippo fix amtype NULL "Tinker Types"
|
|
||||||
Reading data file ...
|
|
||||||
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
648 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
2 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
1 = max angles/atom
|
|
||||||
reading bonds ...
|
|
||||||
432 bonds
|
|
||||||
reading angles ...
|
|
||||||
216 angles
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
read_data CPU = 0.012 seconds
|
|
||||||
|
|
||||||
# force field
|
|
||||||
|
|
||||||
pair_style hippo
|
|
||||||
pair_coeff * * hippo_water.prm hippo_water_box.key
|
|
||||||
Reading potential file hippo_water.prm with DATE: 2022-07-05
|
|
||||||
|
|
||||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.5 0.5 0.5
|
|
||||||
special bond factors coul: 0.5 0.5 0.5
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of 1-5 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.001 seconds
|
|
||||||
|
|
||||||
# thermo output
|
|
||||||
|
|
||||||
compute virial all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
||||||
|
|
||||||
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
HIPPO force field settings
|
|
||||||
repulsion: cut 7 taper 6 rscale 0 0 1 1
|
|
||||||
qxfer: cut 7 taper 6 mscale 0 0 0.4 1
|
|
||||||
dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1
|
|
||||||
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
|
|
||||||
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
|
|
||||||
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
|
|
||||||
precondition: cut 4.5
|
|
||||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 9
|
|
||||||
ghost atom cutoff = 9
|
|
||||||
binsize = 4.5, bins = 5 5 5
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair hippo, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
HIPPO group count: 216
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 55.94 | 55.94 | 55.94 Mbytes
|
|
||||||
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]
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
Loop time of 3.56341 on 4 procs for 100 steps with 648 atoms
|
|
||||||
|
|
||||||
Performance: 2.425 ns/day, 9.898 hours/ns, 28.063 timesteps/s
|
|
||||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
HIPPO timing breakdown:
|
|
||||||
Init time: 0.0164761 0.47%
|
|
||||||
Repulse time: 0.329025 9.29%
|
|
||||||
Disp time: 0.240825 6.80%
|
|
||||||
Mpole time: 0.631085 17.81%
|
|
||||||
Induce time: 1.43692 40.56%
|
|
||||||
Polar time: 0.807046 22.78%
|
|
||||||
Qxfer time: 0.081509 2.30%
|
|
||||||
Total time: 3.5429
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 3.5358 | 3.5432 | 3.5499 | 0.3 | 99.43
|
|
||||||
Bond | 0.00065586 | 0.00073446 | 0.00079512 | 0.0 | 0.02
|
|
||||||
Neigh | 0.0016222 | 0.0016303 | 0.0016397 | 0.0 | 0.05
|
|
||||||
Comm | 0.0098332 | 0.016538 | 0.023936 | 4.9 | 0.46
|
|
||||||
Output | 0.00030555 | 0.00034729 | 0.00046611 | 0.0 | 0.01
|
|
||||||
Modify | 0.00020015 | 0.00022223 | 0.00025815 | 0.0 | 0.01
|
|
||||||
Other | | 0.0007117 | | | 0.02
|
|
||||||
|
|
||||||
Nlocal: 162 ave 166 max 160 min
|
|
||||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
|
||||||
Nghost: 2563.25 ave 2589 max 2535 min
|
|
||||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
|
||||||
Neighs: 24622.5 ave 25210 max 24056 min
|
|
||||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 98490
|
|
||||||
Ave neighs/atom = 151.99074
|
|
||||||
Ave special neighs/atom = 2
|
|
||||||
Neighbor list builds = 2
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:03
|
|
||||||
@ -1,146 +0,0 @@
|
|||||||
LAMMPS (23 Jun 2022)
|
|
||||||
# water dimer with AMOEBA or HIPPO
|
|
||||||
|
|
||||||
units real
|
|
||||||
boundary s s s
|
|
||||||
|
|
||||||
atom_style amoeba
|
|
||||||
bond_style class2
|
|
||||||
angle_style amoeba
|
|
||||||
dihedral_style none
|
|
||||||
|
|
||||||
# per-atom properties required by AMOEBA or HIPPO
|
|
||||||
|
|
||||||
fix amtype all property/atom i_amtype ghost yes
|
|
||||||
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
|
|
||||||
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
||||||
|
|
||||||
# read data file
|
|
||||||
|
|
||||||
read_data data.water_dimer.amoeba fix amtype NULL "Tinker Types"
|
|
||||||
Reading data file ...
|
|
||||||
orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
6 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
2 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
1 = max angles/atom
|
|
||||||
reading bonds ...
|
|
||||||
4 bonds
|
|
||||||
reading angles ...
|
|
||||||
2 angles
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
read_data CPU = 0.007 seconds
|
|
||||||
|
|
||||||
# force field
|
|
||||||
|
|
||||||
pair_style amoeba
|
|
||||||
pair_coeff * * amoeba_water.prm amoeba_water.key
|
|
||||||
Reading potential file amoeba_water.prm with DATE: 2022-07-05
|
|
||||||
|
|
||||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.5 0.5 0.5
|
|
||||||
special bond factors coul: 0.5 0.5 0.5
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of 1-5 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
|
|
||||||
# thermo output
|
|
||||||
|
|
||||||
compute virial all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
||||||
|
|
||||||
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
AMOEBA force field settings
|
|
||||||
hal: cut 10 taper 8 vscale 0 0 1 1
|
|
||||||
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
|
|
||||||
polar: cut 10 aewald 0
|
|
||||||
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
|
|
||||||
precondition: cut 4.5
|
|
||||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 1 1 1
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair amoeba, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
|
|
||||||
AMOEBA group count: 2
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 48.33 | 48.33 | 48.33 Mbytes
|
|
||||||
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]
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
Loop time of 0.0054238 on 1 procs for 100 steps with 6 atoms
|
|
||||||
|
|
||||||
Performance: 1592.978 ns/day, 0.015 hours/ns, 18437.244 timesteps/s
|
|
||||||
98.9% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
AMOEBA timing breakdown:
|
|
||||||
Init time: 0.000115142 2.36%
|
|
||||||
Hal time: 0.000417554 8.56%
|
|
||||||
Mpole time: 0.000572556 11.74%
|
|
||||||
Induce time: 0.00241105 49.43%
|
|
||||||
Polar time: 0.0013468 27.61%
|
|
||||||
Total time: 0.00487742
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0049078 | 0.0049078 | 0.0049078 | 0.0 | 90.49
|
|
||||||
Bond | 8.5639e-05 | 8.5639e-05 | 8.5639e-05 | 0.0 | 1.58
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 1.3462e-05 | 1.3462e-05 | 1.3462e-05 | 0.0 | 0.25
|
|
||||||
Output | 0.00032702 | 0.00032702 | 0.00032702 | 0.0 | 6.03
|
|
||||||
Modify | 4.1776e-05 | 4.1776e-05 | 4.1776e-05 | 0.0 | 0.77
|
|
||||||
Other | | 4.812e-05 | | | 0.89
|
|
||||||
|
|
||||||
Nlocal: 6 ave 6 max 6 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 15 ave 15 max 15 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 15
|
|
||||||
Ave neighs/atom = 2.5
|
|
||||||
Ave special neighs/atom = 2
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -1,146 +0,0 @@
|
|||||||
LAMMPS (23 Jun 2022)
|
|
||||||
# water dimer with AMOEBA or HIPPO
|
|
||||||
|
|
||||||
units real
|
|
||||||
boundary s s s
|
|
||||||
|
|
||||||
atom_style amoeba
|
|
||||||
bond_style class2
|
|
||||||
angle_style amoeba
|
|
||||||
dihedral_style none
|
|
||||||
|
|
||||||
# per-atom properties required by AMOEBA or HIPPO
|
|
||||||
|
|
||||||
fix amtype all property/atom i_amtype ghost yes
|
|
||||||
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
|
|
||||||
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
||||||
|
|
||||||
# read data file
|
|
||||||
|
|
||||||
read_data data.water_dimer.amoeba fix amtype NULL "Tinker Types"
|
|
||||||
Reading data file ...
|
|
||||||
orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
|
|
||||||
2 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
6 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
2 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
1 = max angles/atom
|
|
||||||
reading bonds ...
|
|
||||||
4 bonds
|
|
||||||
reading angles ...
|
|
||||||
2 angles
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
read_data CPU = 0.009 seconds
|
|
||||||
|
|
||||||
# force field
|
|
||||||
|
|
||||||
pair_style amoeba
|
|
||||||
pair_coeff * * amoeba_water.prm amoeba_water.key
|
|
||||||
Reading potential file amoeba_water.prm with DATE: 2022-07-05
|
|
||||||
|
|
||||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.5 0.5 0.5
|
|
||||||
special bond factors coul: 0.5 0.5 0.5
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of 1-5 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.001 seconds
|
|
||||||
|
|
||||||
# thermo output
|
|
||||||
|
|
||||||
compute virial all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
||||||
|
|
||||||
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
AMOEBA force field settings
|
|
||||||
hal: cut 10 taper 8 vscale 0 0 1 1
|
|
||||||
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
|
|
||||||
polar: cut 10 aewald 0
|
|
||||||
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
|
|
||||||
precondition: cut 4.5
|
|
||||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 1 1 1
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair amoeba, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
|
|
||||||
AMOEBA group count: 2
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 48.35 | 48.48 | 48.62 Mbytes
|
|
||||||
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]
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
Loop time of 0.0160572 on 4 procs for 100 steps with 6 atoms
|
|
||||||
|
|
||||||
Performance: 538.077 ns/day, 0.045 hours/ns, 6227.743 timesteps/s
|
|
||||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
AMOEBA timing breakdown:
|
|
||||||
Init time: 0.000593411 4.20%
|
|
||||||
Hal time: 0.000115521 0.82%
|
|
||||||
Mpole time: 0.000734892 5.20%
|
|
||||||
Induce time: 0.0115567 81.83%
|
|
||||||
Polar time: 0.00110812 7.85%
|
|
||||||
Total time: 0.0141227
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.013932 | 0.014334 | 0.014559 | 0.2 | 89.27
|
|
||||||
Bond | 1.1551e-05 | 4.3997e-05 | 8.2514e-05 | 0.0 | 0.27
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.00064766 | 0.00080925 | 0.0012349 | 0.0 | 5.04
|
|
||||||
Output | 0.00037674 | 0.00043125 | 0.0005388 | 0.0 | 2.69
|
|
||||||
Modify | 2.9613e-05 | 3.9056e-05 | 4.4592e-05 | 0.0 | 0.24
|
|
||||||
Other | | 0.0003995 | | | 2.49
|
|
||||||
|
|
||||||
Nlocal: 1.5 ave 3 max 0 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
||||||
Nghost: 4.5 ave 6 max 3 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
||||||
Neighs: 3.75 ave 12 max 0 min
|
|
||||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 15
|
|
||||||
Ave neighs/atom = 2.5
|
|
||||||
Ave special neighs/atom = 2
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -1,150 +0,0 @@
|
|||||||
LAMMPS (23 Jun 2022)
|
|
||||||
# water dimer with AMOEBA or HIPPO
|
|
||||||
|
|
||||||
units real
|
|
||||||
boundary s s s
|
|
||||||
|
|
||||||
atom_style amoeba
|
|
||||||
bond_style class2
|
|
||||||
angle_style amoeba
|
|
||||||
dihedral_style none
|
|
||||||
|
|
||||||
# per-atom properties required by AMOEBA or HIPPO
|
|
||||||
|
|
||||||
fix amtype all property/atom i_amtype ghost yes
|
|
||||||
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
|
|
||||||
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
||||||
|
|
||||||
# read data file
|
|
||||||
|
|
||||||
read_data data.water_dimer.hippo fix amtype NULL "Tinker Types"
|
|
||||||
Reading data file ...
|
|
||||||
orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
6 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
2 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
1 = max angles/atom
|
|
||||||
reading bonds ...
|
|
||||||
4 bonds
|
|
||||||
reading angles ...
|
|
||||||
2 angles
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
read_data CPU = 0.007 seconds
|
|
||||||
|
|
||||||
# force field
|
|
||||||
|
|
||||||
pair_style hippo
|
|
||||||
pair_coeff * * hippo_water.prm hippo_water.key
|
|
||||||
Reading potential file hippo_water.prm with DATE: 2022-07-05
|
|
||||||
|
|
||||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.5 0.5 0.5
|
|
||||||
special bond factors coul: 0.5 0.5 0.5
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of 1-5 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
|
|
||||||
# thermo output
|
|
||||||
|
|
||||||
compute virial all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
||||||
|
|
||||||
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
HIPPO force field settings
|
|
||||||
repulsion: cut 10 taper 8 rscale 0 0 1 1
|
|
||||||
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
|
|
||||||
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
|
|
||||||
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
|
|
||||||
polar: cut 10 aewald 0
|
|
||||||
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
|
|
||||||
precondition: cut 4.5
|
|
||||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 1 1 1
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair hippo, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
|
|
||||||
HIPPO group count: 2
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 47.9 | 47.9 | 47.9 Mbytes
|
|
||||||
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]
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
Loop time of 0.00549002 on 1 procs for 100 steps with 6 atoms
|
|
||||||
|
|
||||||
Performance: 1573.763 ns/day, 0.015 hours/ns, 18214.853 timesteps/s
|
|
||||||
98.3% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
HIPPO timing breakdown:
|
|
||||||
Init time: 0.000118122 2.43%
|
|
||||||
Repulse time: 0.000596081 12.26%
|
|
||||||
Disp time: 0.000298407 6.14%
|
|
||||||
Mpole time: 0.000966546 19.89%
|
|
||||||
Induce time: 0.00167417 34.45%
|
|
||||||
Polar time: 0.00105479 21.70%
|
|
||||||
Qxfer time: 0.000147142 3.03%
|
|
||||||
Total time: 0.00486031
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0048915 | 0.0048915 | 0.0048915 | 0.0 | 89.10
|
|
||||||
Bond | 7.8835e-05 | 7.8835e-05 | 7.8835e-05 | 0.0 | 1.44
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 1.3993e-05 | 1.3993e-05 | 1.3993e-05 | 0.0 | 0.25
|
|
||||||
Output | 0.00039472 | 0.00039472 | 0.00039472 | 0.0 | 7.19
|
|
||||||
Modify | 4.5208e-05 | 4.5208e-05 | 4.5208e-05 | 0.0 | 0.82
|
|
||||||
Other | | 6.581e-05 | | | 1.20
|
|
||||||
|
|
||||||
Nlocal: 6 ave 6 max 6 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 15 ave 15 max 15 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 15
|
|
||||||
Ave neighs/atom = 2.5
|
|
||||||
Ave special neighs/atom = 2
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -1,150 +0,0 @@
|
|||||||
LAMMPS (23 Jun 2022)
|
|
||||||
# water dimer with AMOEBA or HIPPO
|
|
||||||
|
|
||||||
units real
|
|
||||||
boundary s s s
|
|
||||||
|
|
||||||
atom_style amoeba
|
|
||||||
bond_style class2
|
|
||||||
angle_style amoeba
|
|
||||||
dihedral_style none
|
|
||||||
|
|
||||||
# per-atom properties required by AMOEBA or HIPPO
|
|
||||||
|
|
||||||
fix amtype all property/atom i_amtype ghost yes
|
|
||||||
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
|
|
||||||
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
||||||
|
|
||||||
# read data file
|
|
||||||
|
|
||||||
read_data data.water_dimer.hippo fix amtype NULL "Tinker Types"
|
|
||||||
Reading data file ...
|
|
||||||
orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
|
|
||||||
2 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
6 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
2 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
1 = max angles/atom
|
|
||||||
reading bonds ...
|
|
||||||
4 bonds
|
|
||||||
reading angles ...
|
|
||||||
2 angles
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
read_data CPU = 0.007 seconds
|
|
||||||
|
|
||||||
# force field
|
|
||||||
|
|
||||||
pair_style hippo
|
|
||||||
pair_coeff * * hippo_water.prm hippo_water.key
|
|
||||||
Reading potential file hippo_water.prm with DATE: 2022-07-05
|
|
||||||
|
|
||||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.5 0.5 0.5
|
|
||||||
special bond factors coul: 0.5 0.5 0.5
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of 1-5 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
|
|
||||||
# thermo output
|
|
||||||
|
|
||||||
compute virial all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
||||||
|
|
||||||
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
HIPPO force field settings
|
|
||||||
repulsion: cut 10 taper 8 rscale 0 0 1 1
|
|
||||||
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
|
|
||||||
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
|
|
||||||
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
|
|
||||||
polar: cut 10 aewald 0
|
|
||||||
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
|
|
||||||
precondition: cut 4.5
|
|
||||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 1 1 1
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair hippo, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
|
|
||||||
HIPPO group count: 2
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 47.91 | 48.04 | 48.18 Mbytes
|
|
||||||
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]
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
Loop time of 0.0111155 on 4 procs for 100 steps with 6 atoms
|
|
||||||
|
|
||||||
Performance: 777.294 ns/day, 0.031 hours/ns, 8996.461 timesteps/s
|
|
||||||
98.1% CPU use with 4 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
HIPPO timing breakdown:
|
|
||||||
Init time: 0.000522591 5.56%
|
|
||||||
Repulse time: 0.000518986 5.52%
|
|
||||||
Disp time: 7.85217e-05 0.84%
|
|
||||||
Mpole time: 0.000799739 8.51%
|
|
||||||
Induce time: 0.00666551 70.95%
|
|
||||||
Polar time: 0.000761531 8.11%
|
|
||||||
Qxfer time: 4.34115e-05 0.46%
|
|
||||||
Total time: 0.00939447
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.0093886 | 0.0095904 | 0.009719 | 0.1 | 86.28
|
|
||||||
Bond | 1.1102e-05 | 3.5048e-05 | 6.4101e-05 | 0.0 | 0.32
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.00058179 | 0.0007073 | 0.00089017 | 0.0 | 6.36
|
|
||||||
Output | 0.00033655 | 0.00038862 | 0.00047709 | 0.0 | 3.50
|
|
||||||
Modify | 2.5893e-05 | 3.3791e-05 | 3.9341e-05 | 0.0 | 0.30
|
|
||||||
Other | | 0.0003603 | | | 3.24
|
|
||||||
|
|
||||||
Nlocal: 1.5 ave 3 max 0 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
||||||
Nghost: 4.5 ave 6 max 3 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
||||||
Neighs: 3.75 ave 12 max 0 min
|
|
||||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 15
|
|
||||||
Ave neighs/atom = 2.5
|
|
||||||
Ave special neighs/atom = 2
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -1,145 +0,0 @@
|
|||||||
LAMMPS (23 Jun 2022)
|
|
||||||
# water hexamer with AMOEBA or HIPPO
|
|
||||||
|
|
||||||
units real
|
|
||||||
boundary s s s
|
|
||||||
|
|
||||||
atom_style amoeba
|
|
||||||
bond_style class2
|
|
||||||
angle_style amoeba
|
|
||||||
dihedral_style none
|
|
||||||
|
|
||||||
# per-atom properties required by AMOEBA or HIPPO
|
|
||||||
|
|
||||||
fix amtype all property/atom i_amtype ghost yes
|
|
||||||
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
|
|
||||||
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
||||||
|
|
||||||
# read data file
|
|
||||||
|
|
||||||
read_data data.water_hexamer.amoeba fix amtype NULL "Tinker Types"
|
|
||||||
Reading data file ...
|
|
||||||
orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
18 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
2 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
1 = max angles/atom
|
|
||||||
reading bonds ...
|
|
||||||
12 bonds
|
|
||||||
reading angles ...
|
|
||||||
6 angles
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
read_data CPU = 0.007 seconds
|
|
||||||
|
|
||||||
# force field
|
|
||||||
|
|
||||||
pair_style amoeba
|
|
||||||
pair_coeff * * amoeba_water.prm amoeba_water.key
|
|
||||||
Reading potential file amoeba_water.prm with DATE: 2022-07-05
|
|
||||||
|
|
||||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.5 0.5 0.5
|
|
||||||
special bond factors coul: 0.5 0.5 0.5
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of 1-5 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
|
|
||||||
# thermo output
|
|
||||||
|
|
||||||
compute virial all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
||||||
|
|
||||||
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
AMOEBA force field settings
|
|
||||||
hal: cut 10 taper 8 vscale 0 0 1 1
|
|
||||||
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
|
|
||||||
polar: cut 10 aewald 0
|
|
||||||
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
|
|
||||||
precondition: cut 4.5
|
|
||||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 1 1 1
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair amoeba, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
AMOEBA group count: 6
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 48.28 | 48.28 | 48.28 Mbytes
|
|
||||||
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]
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
Loop time of 0.0422729 on 1 procs for 100 steps with 18 atoms
|
|
||||||
|
|
||||||
Performance: 204.386 ns/day, 0.117 hours/ns, 2365.584 timesteps/s
|
|
||||||
99.1% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
AMOEBA timing breakdown:
|
|
||||||
Init time: 0.000326361 0.79%
|
|
||||||
Hal time: 0.00514709 12.41%
|
|
||||||
Mpole time: 0.00443325 10.69%
|
|
||||||
Induce time: 0.0203454 49.05%
|
|
||||||
Polar time: 0.0112122 27.03%
|
|
||||||
Total time: 0.0414795
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.041518 | 0.041518 | 0.041518 | 0.0 | 98.21
|
|
||||||
Bond | 0.00021732 | 0.00021732 | 0.00021732 | 0.0 | 0.51
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 1.4363e-05 | 1.4363e-05 | 1.4363e-05 | 0.0 | 0.03
|
|
||||||
Output | 0.00037904 | 0.00037904 | 0.00037904 | 0.0 | 0.90
|
|
||||||
Modify | 7.8692e-05 | 7.8692e-05 | 7.8692e-05 | 0.0 | 0.19
|
|
||||||
Other | | 6.519e-05 | | | 0.15
|
|
||||||
|
|
||||||
Nlocal: 18 ave 18 max 18 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 153 ave 153 max 153 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 153
|
|
||||||
Ave neighs/atom = 8.5
|
|
||||||
Ave special neighs/atom = 2
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -1,146 +0,0 @@
|
|||||||
LAMMPS (23 Jun 2022)
|
|
||||||
# water hexamer with AMOEBA or HIPPO
|
|
||||||
|
|
||||||
units real
|
|
||||||
boundary s s s
|
|
||||||
|
|
||||||
atom_style amoeba
|
|
||||||
bond_style class2
|
|
||||||
angle_style amoeba
|
|
||||||
dihedral_style none
|
|
||||||
|
|
||||||
# per-atom properties required by AMOEBA or HIPPO
|
|
||||||
|
|
||||||
fix amtype all property/atom i_amtype ghost yes
|
|
||||||
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
|
|
||||||
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
||||||
|
|
||||||
# read data file
|
|
||||||
|
|
||||||
read_data data.water_hexamer.amoeba fix amtype NULL "Tinker Types"
|
|
||||||
Reading data file ...
|
|
||||||
orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
|
|
||||||
2 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
18 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
2 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
1 = max angles/atom
|
|
||||||
reading bonds ...
|
|
||||||
12 bonds
|
|
||||||
reading angles ...
|
|
||||||
6 angles
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
read_data CPU = 0.008 seconds
|
|
||||||
|
|
||||||
# force field
|
|
||||||
|
|
||||||
pair_style amoeba
|
|
||||||
pair_coeff * * amoeba_water.prm amoeba_water.key
|
|
||||||
Reading potential file amoeba_water.prm with DATE: 2022-07-05
|
|
||||||
|
|
||||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.5 0.5 0.5
|
|
||||||
special bond factors coul: 0.5 0.5 0.5
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of 1-5 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
|
|
||||||
# thermo output
|
|
||||||
|
|
||||||
compute virial all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
||||||
|
|
||||||
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
AMOEBA force field settings
|
|
||||||
hal: cut 10 taper 8 vscale 0 0 1 1
|
|
||||||
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
|
|
||||||
polar: cut 10 aewald 0
|
|
||||||
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
|
|
||||||
precondition: cut 4.5
|
|
||||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 1 1 1
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair amoeba, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
|
|
||||||
AMOEBA group count: 6
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 48.3 | 48.3 | 48.3 Mbytes
|
|
||||||
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]
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
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
|
|
||||||
Loop time of 0.0414203 on 4 procs for 100 steps with 18 atoms
|
|
||||||
|
|
||||||
Performance: 208.593 ns/day, 0.115 hours/ns, 2414.273 timesteps/s
|
|
||||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
AMOEBA timing breakdown:
|
|
||||||
Init time: 0.000755971 1.92%
|
|
||||||
Hal time: 0.00126807 3.22%
|
|
||||||
Mpole time: 0.00372714 9.45%
|
|
||||||
Induce time: 0.0278954 70.76%
|
|
||||||
Polar time: 0.00576419 14.62%
|
|
||||||
Total time: 0.0394242
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.039586 | 0.039644 | 0.039746 | 0.0 | 95.71
|
|
||||||
Bond | 6.0994e-05 | 8.2233e-05 | 9.988e-05 | 0.0 | 0.20
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.00069921 | 0.00087777 | 0.001002 | 0.0 | 2.12
|
|
||||||
Output | 0.00035764 | 0.00040122 | 0.00052238 | 0.0 | 0.97
|
|
||||||
Modify | 4.6185e-05 | 5.6938e-05 | 6.2738e-05 | 0.0 | 0.14
|
|
||||||
Other | | 0.0003586 | | | 0.87
|
|
||||||
|
|
||||||
Nlocal: 4.5 ave 6 max 3 min
|
|
||||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
|
||||||
Nghost: 13.5 ave 15 max 12 min
|
|
||||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
|
||||||
Neighs: 38.25 ave 77 max 9 min
|
|
||||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 153
|
|
||||||
Ave neighs/atom = 8.5
|
|
||||||
Ave special neighs/atom = 2
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -1,149 +0,0 @@
|
|||||||
LAMMPS (23 Jun 2022)
|
|
||||||
# water hexamer with AMOEBA or HIPPO
|
|
||||||
|
|
||||||
units real
|
|
||||||
boundary s s s
|
|
||||||
|
|
||||||
atom_style amoeba
|
|
||||||
bond_style class2
|
|
||||||
angle_style amoeba
|
|
||||||
dihedral_style none
|
|
||||||
|
|
||||||
# per-atom properties required by AMOEBA or HIPPO
|
|
||||||
|
|
||||||
fix amtype all property/atom i_amtype ghost yes
|
|
||||||
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
|
|
||||||
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
||||||
|
|
||||||
# read data file
|
|
||||||
|
|
||||||
read_data data.water_hexamer.hippo fix amtype NULL "Tinker Types"
|
|
||||||
Reading data file ...
|
|
||||||
orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
18 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
2 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
1 = max angles/atom
|
|
||||||
reading bonds ...
|
|
||||||
12 bonds
|
|
||||||
reading angles ...
|
|
||||||
6 angles
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
read_data CPU = 0.007 seconds
|
|
||||||
|
|
||||||
# force field
|
|
||||||
|
|
||||||
pair_style hippo
|
|
||||||
pair_coeff * * hippo_water.prm hippo_water.key
|
|
||||||
Reading potential file hippo_water.prm with DATE: 2022-07-05
|
|
||||||
|
|
||||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.5 0.5 0.5
|
|
||||||
special bond factors coul: 0.5 0.5 0.5
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of 1-5 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
|
|
||||||
# thermo output
|
|
||||||
|
|
||||||
compute virial all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
||||||
|
|
||||||
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
HIPPO force field settings
|
|
||||||
repulsion: cut 10 taper 8 rscale 0 0 1 1
|
|
||||||
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
|
|
||||||
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
|
|
||||||
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
|
|
||||||
polar: cut 10 aewald 0
|
|
||||||
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
|
|
||||||
precondition: cut 4.5
|
|
||||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 1 1 1
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair hippo, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
HIPPO group count: 6
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 47.84 | 47.84 | 47.84 Mbytes
|
|
||||||
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]
|
|
||||||
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
|
|
||||||
10 11.52238 -45.959856 1.53397 0.085100522 0 0 1.6190706 -43.756903 -28644.676 -34867.94 -19324.955 -32842.522 -370.63233 -6452.0859 -4002.3535
|
|
||||||
20 20.237283 -46.772008 0.54762833 1.3835192 0 0 1.9311476 -43.815361 -10546.356 -10116.359 -17063.425 -6393.701 -1166.7608 4243.6327 3493.9596
|
|
||||||
30 20.666374 -45.011106 0.086797459 0.071122604 0 0 0.15792006 -43.805943 13150.762 15882.022 10964.553 10630.278 -6754.7642 -432.29165 -3783.115
|
|
||||||
40 10.639014 -45.430939 0.18926921 0.96410995 0 0 1.1533792 -43.738441 33402.664 41252.58 19726.586 38211.875 -6166.03 6081.5692 1815.7739
|
|
||||||
50 10.992432 -44.741108 0.19575431 0.25851128 0 0 0.45426559 -43.729815 37696.923 41572.466 33299.43 37168.141 -3254.5134 2.9639226 -1017.3669
|
|
||||||
60 19.748633 -45.461264 0.035287281 0.63217389 0 0 0.66746117 -43.793065 26212.839 28825.788 16048.096 31876.925 3504.5461 135.3505 420.28566
|
|
||||||
70 26.129957 -46.022729 0.30434543 0.56770169 0 0 0.87204711 -43.826579 3919.9866 -2755.6905 11500.428 517.54333 5626.9543 -2238.5786 86.305984
|
|
||||||
80 17.768494 -46.309777 1.1680612 0.45551823 0 0 1.6235794 -43.785801 -18335.898 -22168.789 -14488.992 -20048.346 7343.173 -2646.2196 -2525.6625
|
|
||||||
90 8.3822494 -47.063502 2.0182644 0.88875358 0 0 2.9070179 -43.731724 -33693.203 -43487.996 -15178.35 -43214.494 2412.6411 1993.0113 1780.7512
|
|
||||||
100 8.6486333 -46.517402 1.9551958 0.38696887 0 0 2.3421647 -43.736979 -34734.97 -34372.659 -28372.146 -42286.799 226.18821 40.353457 -755.93912
|
|
||||||
Loop time of 0.0380494 on 1 procs for 100 steps with 18 atoms
|
|
||||||
|
|
||||||
Performance: 227.073 ns/day, 0.106 hours/ns, 2628.163 timesteps/s
|
|
||||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
HIPPO timing breakdown:
|
|
||||||
Init time: 0.000298991 0.80%
|
|
||||||
Repulse time: 0.00610364 16.36%
|
|
||||||
Disp time: 0.00215934 5.79%
|
|
||||||
Mpole time: 0.00717983 19.24%
|
|
||||||
Induce time: 0.0128706 34.49%
|
|
||||||
Polar time: 0.00726207 19.46%
|
|
||||||
Qxfer time: 0.00143879 3.86%
|
|
||||||
Total time: 0.0373178
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.037354 | 0.037354 | 0.037354 | 0.0 | 98.17
|
|
||||||
Bond | 0.0001712 | 0.0001712 | 0.0001712 | 0.0 | 0.45
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 1.5977e-05 | 1.5977e-05 | 1.5977e-05 | 0.0 | 0.04
|
|
||||||
Output | 0.00036487 | 0.00036487 | 0.00036487 | 0.0 | 0.96
|
|
||||||
Modify | 6.9428e-05 | 6.9428e-05 | 6.9428e-05 | 0.0 | 0.18
|
|
||||||
Other | | 7.438e-05 | | | 0.20
|
|
||||||
|
|
||||||
Nlocal: 18 ave 18 max 18 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 153 ave 153 max 153 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 153
|
|
||||||
Ave neighs/atom = 8.5
|
|
||||||
Ave special neighs/atom = 2
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -1,150 +0,0 @@
|
|||||||
LAMMPS (23 Jun 2022)
|
|
||||||
# water hexamer with AMOEBA or HIPPO
|
|
||||||
|
|
||||||
units real
|
|
||||||
boundary s s s
|
|
||||||
|
|
||||||
atom_style amoeba
|
|
||||||
bond_style class2
|
|
||||||
angle_style amoeba
|
|
||||||
dihedral_style none
|
|
||||||
|
|
||||||
# per-atom properties required by AMOEBA or HIPPO
|
|
||||||
|
|
||||||
fix amtype all property/atom i_amtype ghost yes
|
|
||||||
fix extra all property/atom i_amgroup d_redID d_pval ghost yes
|
|
||||||
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
|
|
||||||
|
|
||||||
# read data file
|
|
||||||
|
|
||||||
read_data data.water_hexamer.hippo fix amtype NULL "Tinker Types"
|
|
||||||
Reading data file ...
|
|
||||||
orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
|
|
||||||
2 by 1 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
18 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
2 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
1 = max angles/atom
|
|
||||||
reading bonds ...
|
|
||||||
12 bonds
|
|
||||||
reading angles ...
|
|
||||||
6 angles
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0 0 0
|
|
||||||
special bond factors coul: 0 0 0
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.000 seconds
|
|
||||||
read_data CPU = 0.008 seconds
|
|
||||||
|
|
||||||
# force field
|
|
||||||
|
|
||||||
pair_style hippo
|
|
||||||
pair_coeff * * hippo_water.prm hippo_water.key
|
|
||||||
Reading potential file hippo_water.prm with DATE: 2022-07-05
|
|
||||||
|
|
||||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
|
||||||
Finding 1-2 1-3 1-4 neighbors ...
|
|
||||||
special bond factors lj: 0.5 0.5 0.5
|
|
||||||
special bond factors coul: 0.5 0.5 0.5
|
|
||||||
2 = max # of 1-2 neighbors
|
|
||||||
1 = max # of 1-3 neighbors
|
|
||||||
1 = max # of 1-4 neighbors
|
|
||||||
2 = max # of 1-5 neighbors
|
|
||||||
2 = max # of special neighbors
|
|
||||||
special bonds CPU = 0.001 seconds
|
|
||||||
|
|
||||||
# thermo output
|
|
||||||
|
|
||||||
compute virial all pressure NULL virial
|
|
||||||
|
|
||||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
|
|
||||||
|
|
||||||
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
|
|
||||||
#dump_modify 1 sort id
|
|
||||||
|
|
||||||
# dynamics
|
|
||||||
|
|
||||||
fix 1 all nve
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
run 100
|
|
||||||
HIPPO force field settings
|
|
||||||
repulsion: cut 10 taper 8 rscale 0 0 1 1
|
|
||||||
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
|
|
||||||
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
|
|
||||||
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
|
|
||||||
polar: cut 10 aewald 0
|
|
||||||
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
|
|
||||||
precondition: cut 4.5
|
|
||||||
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 1 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 1 1 1
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair hippo, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/newton
|
|
||||||
stencil: half/bin/3d
|
|
||||||
bin: standard
|
|
||||||
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
|
|
||||||
HIPPO group count: 6
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 47.86 | 47.86 | 47.86 Mbytes
|
|
||||||
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]
|
|
||||||
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
|
|
||||||
10 11.52238 -45.959856 1.53397 0.085100522 0 0 1.6190706 -43.756903 -28644.676 -34867.94 -19324.955 -32842.522 -370.63233 -6452.0859 -4002.3535
|
|
||||||
20 20.237283 -46.772008 0.54762833 1.3835192 0 0 1.9311476 -43.815361 -10546.356 -10116.359 -17063.425 -6393.701 -1166.7608 4243.6327 3493.9596
|
|
||||||
30 20.666374 -45.011106 0.086797459 0.071122604 0 0 0.15792006 -43.805943 13150.762 15882.022 10964.553 10630.278 -6754.7642 -432.29165 -3783.115
|
|
||||||
40 10.639014 -45.430939 0.18926921 0.96410995 0 0 1.1533792 -43.738441 33402.664 41252.58 19726.586 38211.875 -6166.03 6081.5692 1815.7739
|
|
||||||
50 10.992432 -44.741108 0.19575431 0.25851128 0 0 0.45426559 -43.729815 37696.923 41572.466 33299.43 37168.141 -3254.5134 2.9639226 -1017.3669
|
|
||||||
60 19.748633 -45.461264 0.035287281 0.63217389 0 0 0.66746117 -43.793065 26212.839 28825.788 16048.096 31876.925 3504.5461 135.3505 420.28566
|
|
||||||
70 26.129957 -46.022729 0.30434543 0.56770169 0 0 0.87204711 -43.826579 3919.9866 -2755.6905 11500.428 517.54333 5626.9543 -2238.5786 86.305984
|
|
||||||
80 17.768494 -46.309777 1.1680612 0.45551823 0 0 1.6235794 -43.785801 -18335.898 -22168.789 -14488.992 -20048.346 7343.173 -2646.2196 -2525.6625
|
|
||||||
90 8.3822494 -47.063502 2.0182644 0.88875358 0 0 2.9070179 -43.731724 -33693.203 -43487.996 -15178.35 -43214.494 2412.6411 1993.0113 1780.7512
|
|
||||||
100 8.6486333 -46.517402 1.9551958 0.38696887 0 0 2.3421647 -43.736979 -34734.97 -34372.659 -28372.146 -42286.799 226.18821 40.353457 -755.93912
|
|
||||||
Loop time of 0.0319956 on 4 procs for 100 steps with 18 atoms
|
|
||||||
|
|
||||||
Performance: 270.038 ns/day, 0.089 hours/ns, 3125.434 timesteps/s
|
|
||||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
HIPPO timing breakdown:
|
|
||||||
Init time: 0.000692588 2.32%
|
|
||||||
Repulse time: 0.00294464 9.88%
|
|
||||||
Disp time: 0.000526361 1.77%
|
|
||||||
Mpole time: 0.00377225 12.66%
|
|
||||||
Induce time: 0.0178884 60.04%
|
|
||||||
Polar time: 0.00361349 12.13%
|
|
||||||
Qxfer time: 0.000349507 1.17%
|
|
||||||
Total time: 0.0297917
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.029692 | 0.029996 | 0.030382 | 0.2 | 93.75
|
|
||||||
Bond | 5.5693e-05 | 6.9151e-05 | 8.2812e-05 | 0.0 | 0.22
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.00066534 | 0.0011191 | 0.0014774 | 1.0 | 3.50
|
|
||||||
Output | 0.00036537 | 0.00040732 | 0.00052168 | 0.0 | 1.27
|
|
||||||
Modify | 4.6407e-05 | 5.1041e-05 | 5.4068e-05 | 0.0 | 0.16
|
|
||||||
Other | | 0.0003526 | | | 1.10
|
|
||||||
|
|
||||||
Nlocal: 4.5 ave 6 max 3 min
|
|
||||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
|
||||||
Nghost: 13.5 ave 15 max 12 min
|
|
||||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
|
||||||
Neighs: 38.25 ave 77 max 9 min
|
|
||||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 153
|
|
||||||
Ave neighs/atom = 8.5
|
|
||||||
Ave special neighs/atom = 2
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:00
|
|
||||||
@ -847,7 +847,7 @@ void PairAmoeba::file_ffield(const std::vector<std::string> &words, int nline)
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
void PairAmoeba::file_literature(const std::vector<std::string> &words, int /*nline*/)
|
void PairAmoeba::file_literature(const std::vector<std::string> & /*words*/, int /*nline*/)
|
||||||
{
|
{
|
||||||
// do nothing, this section is skipped
|
// do nothing, this section is skipped
|
||||||
}
|
}
|
||||||
@ -1185,7 +1185,7 @@ void PairAmoeba::file_charge_penetration(const std::vector<std::string> &words,
|
|||||||
|
|
||||||
void PairAmoeba::file_dippolar(const std::vector<std::string> &words, int nline)
|
void PairAmoeba::file_dippolar(const std::vector<std::string> &words, int nline)
|
||||||
{
|
{
|
||||||
const int ndipparams = amoeba ? 4 : 3;
|
const std::size_t ndipparams = amoeba ? 4 : 3;
|
||||||
if (words[0] != "polarize")
|
if (words[0] != "polarize")
|
||||||
error->all(FLERR, "{} PRM file dipole polariability line {} has invalid format: {}",
|
error->all(FLERR, "{} PRM file dipole polariability line {} has invalid format: {}",
|
||||||
utils::uppercase(mystyle), nline, utils::join_words(words, " "));
|
utils::uppercase(mystyle), nline, utils::join_words(words, " "));
|
||||||
|
|||||||
Reference in New Issue
Block a user