169 lines
6.2 KiB
Plaintext
169 lines
6.2 KiB
Plaintext
LAMMPS (7 Jul 2009)
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#AtC Two temperature Coupling
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# DESCRIPTION:
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# full overlap of MD and FE regions w/ free ends & lateral periodic bcs
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# initial gaussian electron temperature profile and uniform phonon temperature
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# results in fast exchange followed by slower diffusion and finally relaxation
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# to equilibrium
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#
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echo both
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units real
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atom_style atomic
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# create domain
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#lattice type reduced density rho* = 4*(sigma/a)^3,
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# where N = 4 for fcc,
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# s = 3.405 A (Wagner)
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# a = 5.25 A (Ashcroft & Mermin, p. 70)
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# to create restart :
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# write_restart temp.bin
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# then : restart2data temp.bin temp.init
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#if {restart}
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boundary f p p
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pair_style lj/cut 13.5
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read_data temp.init
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orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215)
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1 by 1 by 1 processor grid
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3456 atoms
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3456 velocities
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#endif
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lattice fcc 5.405 origin 0.25 0.25 0.25
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Lattice spacing in x,y,z = 5.405 5.405 5.405
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region feRegion block -10 10 -3 3 -3 3
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region mdRegion block -12 12 -3 3 -3 3
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region mdInternal block -10 10 -3 3 -3 3
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# create atoms, NOTE commented out for restart
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#if !{restart}
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#boundary f p p
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#create_box 1 mdRegion
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#create_atoms 1 region mdRegion
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#mass 1 39.95
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#pair_style lj/cut 13.5
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#pair_coeff 1 1 .238 3.405 13.5
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#velocity internal create 40 87287 mom yes loop geom
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#endif
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# specify interal/ghost atoms
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group internal region mdInternal
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2880 atoms in group internal
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# do not define ghosts if outside fe region
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#group ghost subtract all internal
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neighbor 5. bin
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neigh_modify every 10 delay 0 check no
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# ID group atc PhysicsType ParameterFile
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fix AtC internal atc two_temperature Ar_ttm.mat
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# ID part keywords nx ny nz region
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fix_modify AtC fem create mesh 10 1 1 feRegion f p p
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# specify atom types
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#fix_modify AtC transfer internal type internal
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# fix a temperature
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fix_modify AtC transfer fix temperature all 20.0
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fix_modify AtC transfer initial temperature all 20.0
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fix_modify AtC transfer initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
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fix_modify AtC transfer fix electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
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# turn on thermostat
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fix_modify AtC extrinsic exchange off
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fix_modify AtC transfer thermal control rescale 10
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# equilibrate MD field
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timestep 5.0
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#timestep 0.1
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thermo 10
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#if !{restart}
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#run 1000
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#endif
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# write restart file (for atoms)
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#if !{restart}
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#write_restart gaussianT0.dat
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#endif
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#output
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fix_modify AtC transfer output gaussianIC_ttmFE 10 text
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# change thermostat
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fix_modify AtC transfer unfix temperature all
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fix_modify AtC transfer unfix electron_temperature all
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fix_modify AtC transfer thermal control flux
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fix_modify AtC extrinsic exchange on
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fix_modify AtC extrinsic electron_integration explicit 10
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# run with FE
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thermo_style custom step temp pe f_AtC[2] f_AtC[4]
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reset_timestep 0
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run 400
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Memory usage per processor = 20.4457 Mbytes
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Step Temp PotEng AtC[2] AtC[4]
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0 16.671491 -6505.7593 20 21.852118
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10 16.677475 -6505.5427 20.002541 21.837728
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20 16.576352 -6504.1927 19.867309 21.822847
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30 16.543006 -6503.5347 19.829679 21.807329
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40 16.606315 -6503.9098 19.948237 21.79227
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50 16.657241 -6504.1495 20.063768 21.77819
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60 16.632334 -6503.6282 20.043346 21.764516
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70 16.575817 -6502.7756 19.922594 21.750359
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80 16.582959 -6502.556 19.854482 21.735666
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90 16.619481 -6502.6709 19.843443 21.720989
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100 16.61416 -6502.3553 19.823604 21.706411
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110 16.63 -6502.2515 19.868881 21.692096
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120 16.693117 -6502.6546 19.982758 21.67865
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130 16.690721 -6502.395 19.998489 21.665851
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140 16.614049 -6501.3546 19.912824 21.652674
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150 16.61038 -6501.0505 19.922441 21.639146
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160 16.722799 -6501.9758 20.079964 21.626427
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170 16.770602 -6502.2509 20.17121 21.614856
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180 16.650892 -6500.7765 20.054544 21.603105
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190 16.541447 -6499.381 19.906876 21.590204
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200 16.645228 -6500.2039 19.964842 21.577132
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210 16.869527 -6502.3001 20.162483 21.565509
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220 16.964383 -6503.0601 20.257183 21.55523
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230 16.911611 -6502.3326 20.238311 21.545157
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240 16.817036 -6501.1565 20.182711 21.534754
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250 16.768709 -6500.4545 20.137714 21.524032
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260 16.815288 -6500.7352 20.15617 21.51338
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270 16.910049 -6501.5019 20.224357 21.50326
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280 16.977499 -6502.0383 20.29341 21.493767
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290 16.956659 -6501.6276 20.291231 21.484565
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300 16.835262 -6500.213 20.164202 21.474772
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310 16.71985 -6498.8264 20.004642 21.463806
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320 16.69098 -6498.3213 19.932827 21.452076
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330 16.761703 -6498.8528 20.012407 21.440668
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340 16.868998 -6499.7478 20.16924 21.430476
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350 16.984511 -6500.7709 20.340112 21.421697
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360 17.123542 -6502.0546 20.527447 21.414404
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370 17.196695 -6502.6994 20.623027 21.408269
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380 17.078535 -6501.3567 20.479029 21.401788
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390 16.82808 -6498.6218 20.180491 21.393274
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400 16.644633 -6496.5257 19.969187 21.382648
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Loop time of 38.0403 on 1 procs for 400 steps with 3456 atoms
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Pair time (%) = 11.5723 (30.4211)
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Neigh time (%) = 4.98386 (13.1015)
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Comm time (%) = 0.111562 (0.293273)
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Outpt time (%) = 0.00291038 (0.00765077)
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Other time (%) = 21.3697 (56.1764)
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Nlocal: 3456 ave 3456 max 3456 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 12768 ave 12768 max 12768 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.09177e+06 ave 1.09177e+06 max 1.09177e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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FullNghs: 2.18354e+06 ave 2.18354e+06 max 2.18354e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 2183544
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Ave neighs/atom = 631.812
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Neighbor list builds = 40
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Dangerous builds = 0
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