147 lines
7.1 KiB
Groff
147 lines
7.1 KiB
Groff
LAMMPS (23 Jun 2022)
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# replicate water box with AMOEBA or HIPPO
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units real
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boundary p p p
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atom_style amoeba
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bond_style class2
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angle_style amoeba
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dihedral_style none
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# per-atom properties required by AMOEBA or HIPPO
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fix amtype all property/atom i_amtype ghost yes
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fix extra all property/atom i_amgroup d_redID d_pval ghost yes
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fix extra2 all property/atom i_polaxe d2_xyzaxis 3
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# read data file
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read_data data.water_box.amoeba fix amtype NULL "Tinker Types"
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Reading data file ...
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orthogonal box = (0 0 0) to (18.643 18.643 18.643)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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648 atoms
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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432 bonds
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reading angles ...
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216 angles
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.011 seconds
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# force field
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pair_style amoeba
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pair_coeff * * amoeba_water.prm amoeba_water_box.key
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Reading potential file amoeba_water.prm with DATE: 2022-07-05
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Reading potential file amoeba_water_box.key with DATE: 2022-07-05
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special_bonds lj/coul 0.5 0.5 0.5 one/five yes
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0.5 0.5 0.5
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special bond factors coul: 0.5 0.5 0.5
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of 1-5 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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# thermo output
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compute virial all pressure NULL virial
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thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
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#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
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#dump_modify 1 sort id
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# dynamics
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fix 1 all nve
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thermo 10
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run 100
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AMOEBA force field settings
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hal: cut 7 taper 6 vscale 0 0 1 1
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multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
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polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
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pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
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precondition: cut 4.5
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 9
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ghost atom cutoff = 9
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binsize = 4.5, bins = 5 5 5
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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: 216
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Per MPI rank memory allocation (min/avg/max) = 56.38 | 56.38 | 56.38 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 -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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Loop time of 5.22237 on 4 procs for 100 steps with 648 atoms
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Performance: 1.654 ns/day, 14.507 hours/ns, 19.148 timesteps/s
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100.0% CPU use with 4 MPI tasks x no OpenMP threads
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AMOEBA timing breakdown:
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Init time: 0.0217547 0.42%
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Hal time: 0.246901 4.74%
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Mpole time: 0.489975 9.41%
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Induce time: 3.54999 68.15%
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Polar time: 0.900374 17.28%
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Total time: 5.20901
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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 | 5.2084 | 5.2093 | 5.2114 | 0.1 | 99.75
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Bond | 0.00074127 | 0.00080769 | 0.00084525 | 0.0 | 0.02
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Neigh | 0.0014801 | 0.001481 | 0.0014832 | 0.0 | 0.03
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Comm | 0.007438 | 0.0095884 | 0.010526 | 1.3 | 0.18
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Output | 0.00028866 | 0.00033051 | 0.00044509 | 0.0 | 0.01
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Modify | 0.00020399 | 0.00020969 | 0.00021248 | 0.0 | 0.00
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Other | | 0.000658 | | | 0.01
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Nlocal: 162 ave 164 max 159 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 2568.5 ave 2585 max 2544 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Neighs: 24636.2 ave 25226 max 23891 min
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Histogram: 1 0 0 0 0 0 2 0 0 1
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Total # of neighbors = 98545
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Ave neighs/atom = 152.07562
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Ave special neighs/atom = 2
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Neighbor list builds = 2
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Dangerous builds = 0
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Total wall time: 0:00:05
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