mirror of https://github.com/lammps/lammps.git
199 lines
10 KiB
Groff
199 lines
10 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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units real
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atom_style full
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boundary p p p
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dielectric 1
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special_bonds lj/coul 0.0 0.0 1.0
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pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
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bond_style harmonic
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angle_style harmonic
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dihedral_style harmonic
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improper_style none
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kspace_style pppm 0.001
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read_data data.dreiding
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orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
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2 by 1 by 2 MPI processor grid
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reading atoms ...
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384 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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3 = max dihedrals/atom
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reading bonds ...
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320 bonds
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reading angles ...
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448 angles
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reading dihedrals ...
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192 dihedrals
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4 = max # of 1-2 neighbors
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3 = max # of 1-3 neighbors
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5 = max # of special neighbors
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pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
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pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
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pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
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pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
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pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
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pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
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pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
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pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
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pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
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pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
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pair_coeff 4 4 hbond/dreiding/lj 2 i 4.000 2.750000000000000 4
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pair_modify mix arithmetic
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neighbor 2.0 multi
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neigh_modify every 2 delay 4 check yes
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variable input index in.ch3oh.box.dreiding
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variable sname index ch3oh.box.dreiding
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compute hb all pair hbond/dreiding/lj
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variable C_hbond equal c_hb[1] #number hbonds
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variable E_hbond equal c_hb[2] #hbond energy
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thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
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thermo_modify line multi format float %14.6f
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fix 1 all nve
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thermo 10
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run 100
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PPPM initialization ...
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WARNING: System is not charge neutral, net charge = -0.00064 (src/kspace.cpp:302)
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.142073
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grid = 3 3 3
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stencil order = 5
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estimated absolute RMS force accuracy = 0.154715
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estimated relative force accuracy = 0.00046592
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using double precision FFTs
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3d grid and FFT values/proc = 392 12
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Neighbor list info ...
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update every 2 steps, delay 4 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 13.5
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ghost atom cutoff = 13.5
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binsize = 6.75, bins = 3 3 3
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3 neighbor lists, perpetual/occasional/extra = 3 0 0
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(1) pair hbond/dreiding/lj, perpetual, skip from (3)
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attributes: full, newton on
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pair build: skip
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stencil: none
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bin: none
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(2) pair lj/cut/coul/long, perpetual, half/full from (3)
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attributes: half, newton on
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pair build: halffull/newton
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stencil: none
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bin: none
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(3) neighbor class addition, perpetual
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attributes: full, newton on
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pair build: full/multi
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stencil: full/multi/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 10.17 | 10.17 | 10.17 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
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PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
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E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
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E_coul = 597.219740 E_long = -361.164864 v_E_hbond = -69.322152
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v_C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
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---------------- Step 10 ----- CPU = 0.0112 (sec) ----------------
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TotEng = 113.773202 KinEng = 1.537257 Temp = 1.346522
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PotEng = 112.235945 E_bond = 0.530880 E_angle = 1.407481
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E_dihed = 1.084172 E_impro = 0.000000 E_vdwl = -126.339883
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E_coul = 596.742306 E_long = -361.189011 v_E_hbond = -69.944278
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v_C_hbond = 240.000000 Press = -395.900496 Volume = 7447.236335
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---------------- Step 20 ----- CPU = 0.0206 (sec) ----------------
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TotEng = 113.879292 KinEng = 2.999580 Temp = 2.627407
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PotEng = 110.879711 E_bond = 0.549156 E_angle = 1.323582
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E_dihed = 1.357398 E_impro = 0.000000 E_vdwl = -127.482103
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E_coul = 596.318729 E_long = -361.187051 v_E_hbond = -70.088343
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v_C_hbond = 237.000000 Press = -487.150418 Volume = 7447.236335
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---------------- Step 30 ----- CPU = 0.0299 (sec) ----------------
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TotEng = 113.587474 KinEng = 4.369566 Temp = 3.827412
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PotEng = 109.217908 E_bond = 0.416485 E_angle = 1.294630
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E_dihed = 1.710254 E_impro = 0.000000 E_vdwl = -128.565697
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E_coul = 595.560846 E_long = -361.198612 v_E_hbond = -69.848068
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v_C_hbond = 238.000000 Press = -423.966898 Volume = 7447.236335
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---------------- Step 40 ----- CPU = 0.0403 (sec) ----------------
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TotEng = 113.915503 KinEng = 6.466349 Temp = 5.664037
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PotEng = 107.449154 E_bond = 0.514530 E_angle = 1.342583
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E_dihed = 1.536929 E_impro = 0.000000 E_vdwl = -129.858713
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E_coul = 595.186400 E_long = -361.272576 v_E_hbond = -69.871393
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v_C_hbond = 237.000000 Press = -498.152652 Volume = 7447.236335
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---------------- Step 50 ----- CPU = 0.0494 (sec) ----------------
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TotEng = 113.787839 KinEng = 8.050614 Temp = 7.051734
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PotEng = 105.737226 E_bond = 0.652153 E_angle = 1.416041
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E_dihed = 1.363560 E_impro = 0.000000 E_vdwl = -130.513518
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E_coul = 594.139769 E_long = -361.320780 v_E_hbond = -69.593967
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v_C_hbond = 233.000000 Press = -557.299799 Volume = 7447.236335
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---------------- Step 60 ----- CPU = 0.0588 (sec) ----------------
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TotEng = 114.120941 KinEng = 10.318793 Temp = 9.038489
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PotEng = 103.802148 E_bond = 0.576578 E_angle = 1.285008
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E_dihed = 1.123936 E_impro = 0.000000 E_vdwl = -131.268312
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E_coul = 593.450009 E_long = -361.365070 v_E_hbond = -70.107165
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v_C_hbond = 238.000000 Press = -571.907188 Volume = 7447.236335
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---------------- Step 70 ----- CPU = 0.0680 (sec) ----------------
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TotEng = 113.836161 KinEng = 11.873184 Temp = 10.400019
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PotEng = 101.962977 E_bond = 0.633521 E_angle = 1.315999
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E_dihed = 1.055318 E_impro = 0.000000 E_vdwl = -131.673572
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E_coul = 592.039194 E_long = -361.407483 v_E_hbond = -70.518544
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v_C_hbond = 240.000000 Press = -576.731444 Volume = 7447.236335
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---------------- Step 80 ----- CPU = 0.0790 (sec) ----------------
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TotEng = 113.589436 KinEng = 13.546467 Temp = 11.865689
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PotEng = 100.042970 E_bond = 0.637759 E_angle = 1.439918
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E_dihed = 1.020307 E_impro = 0.000000 E_vdwl = -131.980346
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E_coul = 590.365879 E_long = -361.440548 v_E_hbond = -71.174370
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v_C_hbond = 245.000000 Press = -735.254308 Volume = 7447.236335
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---------------- Step 90 ----- CPU = 0.0883 (sec) ----------------
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TotEng = 114.100567 KinEng = 15.870735 Temp = 13.901574
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PotEng = 98.229832 E_bond = 0.724671 E_angle = 1.435914
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E_dihed = 1.028167 E_impro = 0.000000 E_vdwl = -132.680267
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E_coul = 589.225626 E_long = -361.504279 v_E_hbond = -72.653223
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v_C_hbond = 245.000000 Press = -820.598954 Volume = 7447.236335
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---------------- Step 100 ----- CPU = 0.0976 (sec) ----------------
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TotEng = 113.670041 KinEng = 17.406803 Temp = 15.247054
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PotEng = 96.263238 E_bond = 0.711253 E_angle = 1.338059
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E_dihed = 1.474770 E_impro = 0.000000 E_vdwl = -132.917719
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E_coul = 587.219020 E_long = -361.562145 v_E_hbond = -74.299795
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v_C_hbond = 246.000000 Press = -786.245946 Volume = 7447.236335
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Loop time of 0.0976357 on 4 procs for 100 steps with 384 atoms
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Performance: 88.492 ns/day, 0.271 hours/ns, 1024.215 timesteps/s
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96.1% CPU use with 4 MPI tasks x 1 OpenMP threads
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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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Pair | 0.055383 | 0.065178 | 0.07438 | 2.7 | 66.76
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Bond | 0.00099874 | 0.0011503 | 0.001229 | 0.3 | 1.18
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Kspace | 0.013823 | 0.022918 | 0.032308 | 4.4 | 23.47
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0064669 | 0.0072899 | 0.0078194 | 0.6 | 7.47
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Output | 0.00039268 | 0.00043893 | 0.00056481 | 0.0 | 0.45
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Modify | 0.000175 | 0.00019002 | 0.00020623 | 0.0 | 0.19
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Other | | 0.0004706 | | | 0.48
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Nlocal: 96 ave 104 max 87 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Nghost: 3063.25 ave 3108 max 3024 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 25463.5 ave 28799 max 22471 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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FullNghs: 1406 ave 1664 max 1237 min
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Histogram: 1 0 1 1 0 0 0 0 0 1
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Total # of neighbors = 101854
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Ave neighs/atom = 265.245
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Ave special neighs/atom = 4
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Neighbor list builds = 0
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:00
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