109 lines
3.6 KiB
Plaintext
109 lines
3.6 KiB
Plaintext
LAMMPS (30 Aug 2013)
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units real
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atom_style atomic
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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 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
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boundary f p p
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create_box 1 mdRegion
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Created orthogonal box = (-64.86 -16.215 -16.215) to (64.86 16.215 16.215)
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4 by 1 by 1 MPI processor grid
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create_atoms 1 region mdRegion
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Created 3456 atoms
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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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# 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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velocity internal create 40 87287 mom yes loop geom # <<< NOTE
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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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ATC: constructing two_temperature coupling with parameter file Ar_ttm.mat
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ATC: version 2.0
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ATC: peratom PE compute created with ID: 3
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ATC: 2 materials defined from Ar_ttm.mat
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ATC: creating two_temperature extrinsic model
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ATC: 2 materials defined from Ar_ttm.mat
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fix_modify AtC mesh read gaussianIC1d_hex.mesh
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ATC: read 44 nodes
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ATC: read 10 HEX8 elements
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ATC: WARNING: mesh is not aligned with the coordinate directions atom-to-element mapping will be expensive
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# fix a temperature
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fix_modify AtC fix temperature all 20.0
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fix_modify AtC initial temperature all 20.0
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fix_modify AtC initial electron_temperature all gaussian 0 0 0 1 0 0 5 20 20
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fix_modify AtC 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 control thermal rescale 10
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# equilibrate MD field
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timestep 5.0
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thermo 10
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#output
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fix_modify AtC output gaussianIC1d_hexFE 10 text
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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# change thermostat
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fix_modify AtC unfix temperature all
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fix_modify AtC unfix electron_temperature all
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fix_modify AtC control thermal 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 100 # 400
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Setting up run ...
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Memory usage per processor = 52.9302 Mbytes
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Step Temp PotEng AtC[2] AtC[4]
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0 33.331404 -6667.7177 20 21.852118
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10 29.605914 -6628.8617 15.526061 21.823928
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20 20.144352 -6529.8249 4.1452637 21.728037
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30 10.661516 -6429.3908 -7.2917185 21.537517
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40 7.6716875 -6394.7484 -10.961235 21.28913
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50 11.012891 -6425.2214 -7.0020953 21.050343
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60 15.276591 -6465.7767 -1.8390571 20.85387
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70 17.15209 -6482.1581 0.55215503 20.688207
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80 17.028137 -6478.0796 0.55504167 20.530699
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90 16.865355 -6473.5664 0.41999569 20.372106
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100 17.920474 -6481.673 1.6267665 20.219157
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Loop time of 4.19774 on 4 procs for 100 steps with 3456 atoms
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Pair time (%) = 0.896439 (21.3553)
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Neigh time (%) = 0.408064 (9.72104)
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Comm time (%) = 0.161891 (3.85662)
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Outpt time (%) = 0.00701588 (0.167135)
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Other time (%) = 2.72433 (64.9)
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Nlocal: 864 ave 864 max 864 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 6741 ave 7924 max 5558 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 272828 ave 288265 max 257696 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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FullNghs: 545657 ave 575527 max 515800 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 2182628
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Ave neighs/atom = 631.547
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Neighbor list builds = 10
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Dangerous builds = 0
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