257 lines
13 KiB
Groff
257 lines
13 KiB
Groff
LAMMPS (24 Dec 2015)
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# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
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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 charge
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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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compute chargeOxy Oxy property/atom q
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compute q_Oxy Oxy reduce ave c_chargeOxy
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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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compute chargeTi Ti property/atom q
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compute q_Ti Ti reduce ave c_chargeTi
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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 smtbq
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pair_coeff * * ffield.smtbq.TiO2 O Ti
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Reading potential file ffield.smtbq.TiO2 with DATE: 2015-10-22
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neighbor 0.5 bin
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neigh_modify every 20 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 c_q_Ti c_q_Oxy lx ly lz vol
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thermo_modify flush yes
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thermo 1
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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 10
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Neighbor list info ...
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1 neighbor list requests
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update every 20 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 = 12.6744
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ghost atom cutoff = 12.6744
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binsize = 6.3372 -> bins = 5 5 6
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Memory usage per processor = 4.60415 Mbytes
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Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
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0 300 44365.066 -15815.239 92.097853 -15723.142 2.5521775 -1.2760888 27.5622 27.5622 32.5457 24724.15
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1 299.90799 44372.657 -15815.211 92.069608 -15723.142 2.5521771 -1.2760885 27.5622 27.5622 32.5457 24724.15
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2 299.64406 44386.645 -15815.13 91.988581 -15723.142 2.5521705 -1.2760852 27.5622 27.5622 32.5457 24724.15
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3 299.20863 44406.97 -15814.997 91.854908 -15723.142 2.5521584 -1.2760792 27.5622 27.5622 32.5457 24724.15
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4 298.60246 44433.509 -15814.812 91.668818 -15723.143 2.552141 -1.2760705 27.5622 27.5622 32.5457 24724.15
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5 297.82659 44466.206 -15814.574 91.430631 -15723.144 2.5521181 -1.276059 27.5622 27.5622 32.5457 24724.15
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6 296.88235 44505.016 -15814.285 91.140758 -15723.144 2.5520898 -1.2760449 27.5622 27.5622 32.5457 24724.15
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7 295.77139 44549.856 -15813.945 90.7997 -15723.145 2.5520562 -1.2760281 27.5622 27.5622 32.5457 24724.15
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8 294.49562 44600.663 -15813.555 90.408048 -15723.147 2.5520173 -1.2760087 27.5622 27.5622 32.5457 24724.15
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9 293.05725 44657.353 -15813.114 89.966478 -15723.148 2.5519732 -1.2759866 27.5622 27.5622 32.5457 24724.15
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10 291.45876 44719.821 -15812.625 89.475755 -15723.149 2.551924 -1.275962 27.5622 27.5622 32.5457 24724.15
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Loop time of 161.071 on 4 procs for 10 steps with 2376 atoms
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Performance: 0.001 ns/day, 22370.960 hours/ns, 0.062 timesteps/s
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99.8% 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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Pair | 161.07 | 161.07 | 161.07 | 0.0 |100.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0021119 | 0.0024694 | 0.0026705 | 0.4 | 0.00
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Output | 0.00060225 | 0.00070065 | 0.00098777 | 0.6 | 0.00
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Modify | 0.00012326 | 0.00013238 | 0.00014782 | 0.1 | 0.00
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Other | | 0.0001593 | | | 0.00
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Nlocal: 594 ave 630 max 558 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 7638 ave 7674 max 7602 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 492624 ave 522720 max 462528 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 1970496
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Ave neighs/atom = 829.333
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Neighbor list builds = 0
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Dangerous builds = 0
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unfix 3
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#thermo 15
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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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Neighbor list info ...
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1 neighbor list requests
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update every 1 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 = 12.6744
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ghost atom cutoff = 12.6744
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binsize = 6.3372 -> bins = 5 5 6
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Memory usage per processor = 5.97915 Mbytes
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Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
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10 291.45876 44719.821 -15812.625 89.475755 -15723.149 2.551924 -1.275962 27.5622 27.5622 32.5457 24724.15
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11 291.45876 38966.735 -15814.114 89.475755 -15724.638 2.5514114 -1.2757057 27.582769 27.582778 32.578246 24785.835
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Loop time of 22.3212 on 4 procs for 1 steps with 2376 atoms
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99.9% CPU use with 4 MPI tasks x no 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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-15812.6250198 -15812.6250198 -15814.1138993
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Force two-norm initial, final = 1103.27 950.466
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Force max component initial, final = 758.704 657.184
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Final line search alpha, max atom move = 1.31804e-06 0.000866193
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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 | 22.32 | 22.32 | 22.32 | 0.0 |100.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00042605 | 0.00043178 | 0.00043893 | 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 | | 0.0004204 | | | 0.00
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Nlocal: 594 ave 600 max 587 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Nghost: 7638 ave 7645 max 7632 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 492126 ave 497133 max 486366 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Total # of neighbors = 1968506
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Ave neighs/atom = 828.496
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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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thermo 1
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fix 3 all nve
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run 10
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Neighbor list info ...
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1 neighbor list requests
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update every 20 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 = 12.6744
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ghost atom cutoff = 12.6744
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binsize = 6.3372 -> bins = 5 5 6
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Memory usage per processor = 4.85415 Mbytes
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Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
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11 291.45876 38966.735 -15814.114 89.475755 -15724.638 2.5514114 -1.2757057 27.582769 27.582778 32.578246 24785.835
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12 289.71602 39034.428 -15813.58 88.940745 -15724.639 2.5513568 -1.2756784 27.582769 27.582778 32.578246 24785.835
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13 287.81994 39107.705 -15813 88.358662 -15724.641 2.5512976 -1.2756488 27.582769 27.582778 32.578246 24785.835
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14 285.77378 39186.429 -15812.373 87.730505 -15724.642 2.5512335 -1.2756168 27.582769 27.582778 32.578246 24785.835
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15 283.58105 39270.434 -15811.702 87.057353 -15724.644 2.5511647 -1.2755824 27.582769 27.582778 32.578246 24785.835
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16 281.24552 39359.544 -15810.986 86.340362 -15724.646 2.5510913 -1.2755457 27.582769 27.582778 32.578246 24785.835
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17 278.77119 39453.574 -15810.229 85.580761 -15724.648 2.5510134 -1.2755067 27.582769 27.582778 32.578246 24785.835
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18 276.16232 39552.323 -15809.43 84.779855 -15724.65 2.5509311 -1.2754655 27.582769 27.582778 32.578246 24785.835
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19 273.42337 39655.586 -15808.592 83.939017 -15724.652 2.5508445 -1.2754223 27.582769 27.582778 32.578246 24785.835
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20 270.55904 39763.139 -15807.715 83.05969 -15724.655 2.5507538 -1.2753769 27.582769 27.582778 32.578246 24785.835
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21 267.57425 39874.754 -15806.801 82.14338 -15724.658 2.5506591 -1.2753296 27.582769 27.582778 32.578246 24785.835
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Loop time of 170.172 on 4 procs for 10 steps with 2376 atoms
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Performance: 0.001 ns/day, 23634.979 hours/ns, 0.059 timesteps/s
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99.9% 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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Pair | 170.17 | 170.17 | 170.17 | 0.0 |100.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.0025029 | 0.0028628 | 0.0030224 | 0.4 | 0.00
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Output | 0.00063372 | 0.00081372 | 0.0011685 | 0.7 | 0.00
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Modify | 0.00012541 | 0.0001539 | 0.00021005 | 0.3 | 0.00
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Other | | 0.0001655 | | | 0.00
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Nlocal: 594 ave 600 max 587 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Nghost: 7638 ave 7645 max 7632 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Neighs: 0 ave 0 max 0 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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FullNghs: 490100 ave 495079 max 484284 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Total # of neighbors = 1960398
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Ave neighs/atom = 825.083
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:06:39
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