forked from lijiext/lammps
131 lines
5.1 KiB
Groff
131 lines
5.1 KiB
Groff
LAMMPS (24 Jul 2017)
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using 1 OpenMP thread(s) per MPI task
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units metal
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atom_style full
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boundary p p p
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timestep 0.0001 # 0.1 fs
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read_data methane-box-8.data
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orthogonal box = (-0.499095 -0.270629 0.131683) to (8.4109 8.63937 9.04168)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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40 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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reading bonds ...
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32 bonds
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reading angles ...
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48 angles
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4 = max # of 1-2 neighbors
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3 = max # of 1-3 neighbors
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3 = max # of 1-4 neighbors
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4 = max # of special neighbors
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# DISCLAIMER: This potential mixes parameters from methane and silane
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# potentials and is NOT intended to be a realistic representation of either
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# system. It is meant to demonstrate the use of hybrid QUIP/LAMMPS potentials,
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# including the use of separate 'special_bonds' settings.
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pair_style hybrid/overlay lj/cut 8.0 quip
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# exclusion setting for quip; cannot be exactly 1.0 1.0 1.0,
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# since that would not flag 1-2, 1-3, and 1-4 pairs in lj/cut
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special_bonds lj/coul 0.999999999 0.999999999 0.999999999
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4 = max # of 1-2 neighbors
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3 = max # of 1-3 neighbors
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3 = max # of 1-4 neighbors
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4 = max # of special neighbors
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# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
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# Coulomb interactions ommitted for simplicity
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pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT
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pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC
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pair_coeff 1 2 lj/cut 0.0019295487 2.95
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pair_modify shift no
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# change exclusion settings for lj/cut only: exclude bonded pairs
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pair_modify pair lj/cut special lj/coul 0.0 0.0 0.0
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# Intramolecular
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# Tell QUIP to pretend this is silane (which is covered by the parameter file)
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pair_coeff * * quip sw_example.xml "IP SW" 14 1
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bond_style none
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angle_style none
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fix 1 all nve
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# Include diagnostics that allow us to compare to a pure QUIP run
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compute equip all pair quip
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compute evdw all pair lj/cut
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compute vir all pressure NULL virial
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thermo_style custom step epair ke etotal temp press c_vir c_evdw c_equip
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thermo 1
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# dump 1 all custom 1 dump.molecular id type x y z fx fy fz
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# dump_modify 1 sort id
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run 10
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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 = 10
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ghost atom cutoff = 10
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binsize = 5, bins = 2 2 2
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair lj/cut, perpetual, half/full from (2)
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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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(2) pair quip, perpetual
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attributes: full, newton on
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pair build: full/bin
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stencil: full/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 8.288 | 8.288 | 8.288 Mbytes
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Step E_pair KinEng TotEng Temp Press c_vir c_evdw c_equip
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0 -5.3530213 0 -5.3530213 0 518847.56 518847.56 -0.10904079 -5.2439805
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1 -5.9384459 0.58384822 -5.3545977 115.81657 517370.5 516488.87 -0.10783656 -5.8306093
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2 -7.669616 2.3104051 -5.3592109 458.30954 512986.36 509497.58 -0.10422283 -7.5653932
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3 -10.473314 5.1069211 -5.3663924 1013.0477 505833.04 498121.43 -0.098049469 -10.375264
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4 -14.234705 8.859182 -5.3755227 1757.3747 496127.44 482749.79 -0.089147485 -14.145557
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5 -18.806851 13.420941 -5.3859098 2662.28 484148.76 463882.72 -0.077305196 -18.729546
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6 -24.021727 18.625147 -5.3965797 3694.6259 470219.95 442095.39 -0.06194509 -23.959782
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7 -29.702647 24.295529 -5.4071176 4819.446 454683.57 417996.56 -0.042859727 -29.659787
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8 -35.67405 30.257258 -5.4167913 6002.0599 437887.03 392197.62 -0.019248651 -35.654801
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9 -41.771047 36.345757 -5.4252893 7209.8209 420163.51 365280.27 0.0096063065 -41.780653
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10 -47.845522 42.413161 -5.4323614 8413.3973 401821.91 337776.7 0.044743702 -47.890266
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Loop time of 0.0537777 on 1 procs for 10 steps with 40 atoms
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Performance: 1.607 ns/day, 14.938 hours/ns, 185.951 timesteps/s
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90.3% CPU use with 1 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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---------------------------------------------------------------
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Pair | 0.053478 | 0.053478 | 0.053478 | 0.0 | 99.44
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Bond | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 7.7724e-05 | 7.7724e-05 | 7.7724e-05 | 0.0 | 0.14
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Output | 0.00018263 | 0.00018263 | 0.00018263 | 0.0 | 0.34
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Modify | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 | 0.0 | 0.03
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Other | | 2.122e-05 | | | 0.04
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Nlocal: 40 ave 40 max 40 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1175 ave 1175 max 1175 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 4768 ave 4768 max 4768 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 9536 ave 9536 max 9536 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 9536
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Ave neighs/atom = 238.4
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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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Total wall time: 0:00:00
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