249 lines
12 KiB
Groff
249 lines
12 KiB
Groff
LAMMPS (13 Apr 2017)
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using 1 OpenMP thread(s) per MPI task
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#
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variable T_depart equal 300
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variable dt equal 0.0002
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variable a equal 4.5937
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variable c equal 2.9587
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variable ca equal ${c}/${a}
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variable ca equal 2.9587/${a}
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variable ca equal 2.9587/4.5937
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variable nx equal 6
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variable ny equal 6
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variable nz equal 11
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variable bx equal ${a}*${nx}
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variable bx equal 4.5937*${nx}
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variable bx equal 4.5937*6
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variable by equal ${a}*${ny}
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variable by equal 4.5937*${ny}
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variable by equal 4.5937*6
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variable bz equal ${c}*${nz}
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variable bz equal 2.9587*${nz}
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variable bz equal 2.9587*11
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# =======================================================================
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units metal
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atom_style atomic
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dimension 3
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boundary p p p
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lattice sc 1.0
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Lattice spacing in x,y,z = 1 1 1
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region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
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region box_vide prism 0 27.5622 0 ${by} 0 ${bz} 0.0 0.0 0.0
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region box_vide prism 0 27.5622 0 27.5622 0 ${bz} 0.0 0.0 0.0
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region box_vide prism 0 27.5622 0 27.5622 0 32.5457 0.0 0.0 0.0
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create_box 2 box_vide
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Created triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0)
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1 by 2 by 2 MPI processor grid
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#lattice sc 1.0
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#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz}
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# titanium atoms
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lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
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lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
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lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
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Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
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create_atoms 2 region box_vide
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Created 792 atoms
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# Oxygen atoms
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lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
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lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
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lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
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Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
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create_atoms 1 region box_vide
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Created 1584 atoms
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mass 1 16.00
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group Oxy type 1
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1584 atoms in group Oxy
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mass 2 47.867
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group Ti type 2
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792 atoms in group Ti
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velocity all create ${T_depart} 277387
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velocity all create 300 277387
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pair_style meam/spline
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pair_coeff * * TiO.meam.spline O Ti
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Reading potential file TiO.meam.spline with DATE: 2016-06-05
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neighbor 0.5 bin
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neigh_modify every 2 delay 0 check yes
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timestep ${dt}
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timestep 0.0002
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thermo_style custom step temp press pe ke etotal lx ly lz vol
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thermo 10
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#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
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fix 3 all nve
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run 100
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Neighbor list info ...
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update every 2 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 6
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ghost atom cutoff = 6
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binsize = 3, bins = 10 10 11
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair meam/spline, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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(2) pair meam/spline, perpetual, half/full from (1)
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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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Per MPI rank memory allocation (min/avg/max) = 3.922 | 3.922 | 3.922 Mbytes
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Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
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0 300 22403.656 -14374.073 92.097853 -14281.975 27.5622 27.5622 32.5457 24724.15
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10 301.16725 23582.084 -14374.431 92.456192 -14281.975 27.5622 27.5622 32.5457 24724.15
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20 304.58237 25059.749 -14375.479 93.504609 -14281.974 27.5622 27.5622 32.5457 24724.15
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30 312.41477 26504.358 -14377.883 95.9091 -14281.974 27.5622 27.5622 32.5457 24724.15
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40 327.67099 26687.057 -14382.566 100.59265 -14281.974 27.5622 27.5622 32.5457 24724.15
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50 352.32125 22677.292 -14390.134 108.1601 -14281.974 27.5622 27.5622 32.5457 24724.15
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60 388.40592 12472.705 -14401.211 119.23784 -14281.973 27.5622 27.5622 32.5457 24724.15
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70 439.97199 -1520.4694 -14417.04 135.06825 -14281.972 27.5622 27.5622 32.5457 24724.15
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80 513.34361 -16733.316 -14439.564 157.59282 -14281.971 27.5622 27.5622 32.5457 24724.15
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90 613.3542 -31099.591 -14470.267 188.29535 -14281.971 27.5622 27.5622 32.5457 24724.15
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100 741.02836 -42358.226 -14509.464 227.4904 -14281.973 27.5622 27.5622 32.5457 24724.15
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Loop time of 8.92317 on 4 procs for 100 steps with 2376 atoms
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Performance: 0.194 ns/day, 123.933 hours/ns, 11.207 timesteps/s
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99.5% 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 | 8.8912 | 8.9 | 8.9064 | 0.2 | 99.74
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Neigh | 0.0027034 | 0.0028808 | 0.0032032 | 0.4 | 0.03
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Comm | 0.010964 | 0.017648 | 0.026568 | 5.0 | 0.20
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Output | 0.00037575 | 0.00047809 | 0.00053835 | 0.0 | 0.01
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Modify | 0.00099134 | 0.001001 | 0.0010085 | 0.0 | 0.01
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Other | | 0.001162 | | | 0.01
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Nlocal: 594 ave 599 max 589 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Nghost: 2290.25 ave 2296 max 2282 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Neighs: 26671.5 ave 26934 max 26495 min
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Histogram: 1 0 0 2 0 0 0 0 0 1
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FullNghs: 53343 ave 53828 max 52922 min
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Histogram: 1 0 0 0 2 0 0 0 0 1
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Total # of neighbors = 213372
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Ave neighs/atom = 89.803
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Neighbor list builds = 1
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Dangerous builds = 0
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unfix 3
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fix 1 all box/relax tri 0.0 vmax 0.001
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minimize 1.0e-3 1.0e-5 1000 10000
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WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
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Per MPI rank memory allocation (min/avg/max) = 5.047 | 5.047 | 5.047 Mbytes
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Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
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100 741.02836 -42358.226 -14509.464 227.4904 -14281.973 27.5622 27.5622 32.5457 24724.15
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101 741.02836 -39686.588 -14515.398 227.4904 -14287.907 27.569587 27.569656 32.513154 24712.729
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Loop time of 0.193516 on 4 procs for 1 steps with 2376 atoms
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99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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-14509.46351 -14509.46351 -14515.3978891
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Force two-norm initial, final = 5602.69 5487.77
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Force max component initial, final = 5235.27 5113.06
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Final line search alpha, max atom move = 1.91012e-07 0.000976657
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Iterations, force evaluations = 1 1
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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 | 0.19287 | 0.19299 | 0.19318 | 0.0 | 99.73
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00014043 | 0.00033247 | 0.00045896 | 0.0 | 0.17
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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 | | 0.0001886 | | | 0.10
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Nlocal: 594 ave 601 max 586 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Nghost: 2263.25 ave 2271 max 2251 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Neighs: 26425.8 ave 26807 max 26121 min
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Histogram: 1 0 0 1 1 0 0 0 0 1
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FullNghs: 52851.5 ave 53580 max 52175 min
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Histogram: 1 0 0 0 2 0 0 0 0 1
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Total # of neighbors = 211406
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Ave neighs/atom = 88.9756
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Neighbor list builds = 0
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Dangerous builds = 0
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unfix 1
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reset_timestep 0
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thermo 50
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fix 3 all npt temp 300 300 0.1 aniso 1.0 1.0 1.0
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run 500
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Per MPI rank memory allocation (min/avg/max) = 3.937 | 3.937 | 3.937 Mbytes
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Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
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0 741.02836 -39686.588 -14515.398 227.4904 -14287.907 27.569587 27.569656 32.513154 24712.729
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50 1157.347 29332.549 -14679.321 355.29725 -14324.024 27.60903 27.609325 32.375509 24678.772
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100 777.55858 101883.12 -14674.854 238.70492 -14436.149 27.778518 27.777373 32.017262 24704.976
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150 945.49014 -18305.383 -14806.687 290.25871 -14516.428 27.998313 27.99535 31.670225 24823.838
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200 427.46608 -4045.0095 -14674.887 131.22903 -14543.658 28.130283 28.127147 31.431578 24869.438
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250 362.82166 -7283.1332 -14669.07 111.38365 -14557.687 28.225232 28.222707 31.238451 24884.314
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300 626.2858 7228.0309 -14760.128 192.26526 -14567.862 28.302384 28.299949 31.070038 24885.734
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350 859.84293 30084.735 -14845.064 263.96563 -14581.099 28.372349 28.369334 30.934424 24899.261
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400 755.26136 54745.408 -14830.701 231.85983 -14598.842 28.450301 28.448361 30.836159 24957.691
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450 802.52344 5690.2863 -14860.193 246.36895 -14613.824 28.542311 28.541672 30.773339 25069.354
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500 631.84734 -31473.795 -14816.101 193.97261 -14622.128 28.605857 28.605891 30.737955 25152.746
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Loop time of 39.7881 on 4 procs for 500 steps with 2376 atoms
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Performance: 0.217 ns/day, 110.522 hours/ns, 12.567 timesteps/s
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99.4% 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 | 39.617 | 39.633 | 39.653 | 0.2 | 99.61
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Neigh | 0.043624 | 0.046792 | 0.051708 | 1.4 | 0.12
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Comm | 0.05215 | 0.072616 | 0.092142 | 5.6 | 0.18
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Output | 0.00042915 | 0.00045079 | 0.00051546 | 0.0 | 0.00
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Modify | 0.029836 | 0.030341 | 0.03094 | 0.2 | 0.08
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Other | | 0.004489 | | | 0.01
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Nlocal: 594 ave 606 max 582 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Nghost: 2226 ave 2238 max 2214 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Neighs: 25652.8 ave 26129 max 25153 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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FullNghs: 51305.5 ave 52398 max 50251 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Total # of neighbors = 205222
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Ave neighs/atom = 86.3729
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Neighbor list builds = 16
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Dangerous builds = 0
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Total wall time: 0:00:49
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