forked from lijiext/lammps
119 lines
4.9 KiB
Groff
119 lines
4.9 KiB
Groff
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LAMMPS (5 Oct 2016)
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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 0.4000E+01 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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run 0
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WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
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PPPM initialization ...
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WARNING: System is not charge neutral, net charge = -0.00064 (../kspace.cpp:297)
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
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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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3 neighbor list requests
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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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Memory usage per processor = 9.05502 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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Loop time of 4.52995e-06 on 4 procs for 0 steps with 384 atoms
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0.0% CPU use with 4 MPI tasks x no 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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---------------------------------------------------------------
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Pair | 0 | 0 | 0 | 0.0 | 0.00
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Bond | 0 | 0 | 0 | 0.0 | 0.00
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Kspace | 0 | 0 | 0 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0 | 0 | 0 | 0.0 | 0.00
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Output | 0 | 0 | 0 | 0.0 | 0.00
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 4.53e-06 | | |100.00
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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: 50927 ave 55516 max 46073 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Total # of neighbors = 203708
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Ave neighs/atom = 530.49
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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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