5302074b3f
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10709 f3b2605a-c512-4ea7-a41b-209d697bcdaa
160 lines
7.0 KiB
Plaintext
160 lines
7.0 KiB
Plaintext
LAMMPS (30 Aug 2013)
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units metal
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variable s equal 100
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variable T equal 20
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variable n equal 0.000004
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variable tol equal 0.1
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variable W equal 1000
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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 FE block -8 8 -6 6 0 3
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region MD block -7 7 -6 0 0 3
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region FREE block -4 4 -6 0 0 3
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boundary f f p
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# create atoms
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create_box 1 FE
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Created orthogonal box = (-43.24 -32.43 0) to (43.24 32.43 16.215)
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2 by 2 by 1 MPI processor grid
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mass 1 39.95
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atom_modify sort 0 1
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timestep 0.002
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thermo $s
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thermo 100
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# ID group atc PhysicsType ParameterFile
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fix AtC all atc drift_diffusion Ar_ddm.mat
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ATC: constructing drift_diffusion coupling with parameter file Ar_ddm.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: WARNING: material units real do not match lammps
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ATC: WARNING: material units real do not match lammps
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ATC: 2 materials defined from Ar_ddm.mat
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ATC: creating drift_diffusion extrinsic model
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ATC: WARNING: material units real do not match lammps
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ATC: WARNING: material units real do not match lammps
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ATC: 2 materials defined from Ar_ddm.mat
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ATC: WARNING: material units real do not match lammps
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ATC: WARNING: material units real do not match lammps
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ATC: 2 materials defined from Ar_ddm.mat
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# ID part keywords nx ny nz region
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fix_modify AtC mesh create 4 4 1 FE f f p
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ATC: created uniform mesh with 50 nodes, 25 unique nodes, and 16 elements
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variable a equal $W+${tol}
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variable a equal 1000+${tol}
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variable a equal 1000+0.10000000000000000555
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fix_modify AtC mesh create_elementset wire -$a $a -INF ${tol} -INF INF
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fix_modify AtC mesh create_elementset wire -1000.1000000000000227 $a -INF ${tol} -INF INF
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fix_modify AtC mesh create_elementset wire -1000.1000000000000227 1000.1000000000000227 -INF ${tol} -INF INF
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fix_modify AtC mesh create_elementset wire -1000.1000000000000227 1000.1000000000000227 -INF 0.10000000000000000555 -INF INF
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ATC: created elementset wire with 8 elements
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fix_modify AtC mesh create_elementset gap -$a $a -${tol} INF -INF INF
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fix_modify AtC mesh create_elementset gap -1000.1000000000000227 $a -${tol} INF -INF INF
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fix_modify AtC mesh create_elementset gap -1000.1000000000000227 1000.1000000000000227 -${tol} INF -INF INF
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fix_modify AtC mesh create_elementset gap -1000.1000000000000227 1000.1000000000000227 -0.10000000000000000555 INF -INF INF
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ATC: created elementset gap with 8 elements
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# void is the complement of the wire nodeset
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variable a equal $W-${tol}
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variable a equal 1000-${tol}
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variable a equal 1000-0.10000000000000000555
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fix_modify AtC mesh create_nodeset void -$a $a ${tol} INF -INF INF
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fix_modify AtC mesh create_nodeset void -999.89999999999997726 $a ${tol} INF -INF INF
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fix_modify AtC mesh create_nodeset void -999.89999999999997726 999.89999999999997726 ${tol} INF -INF INF
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fix_modify AtC mesh create_nodeset void -999.89999999999997726 999.89999999999997726 0.10000000000000000555 INF -INF INF
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ATC: created nodeset void with 10 nodes
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fix_modify AtC mesh output null_material_ddmMESH binary
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fix_modify AtC control thermal none
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# fix a temperature
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fix_modify AtC initial temperature all $T
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fix_modify AtC initial temperature all 20
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fix_modify AtC initial electron_temperature all $T
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fix_modify AtC initial electron_temperature all 20
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fix_modify AtC initial electron_density all $n
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fix_modify AtC initial electron_density all 3.999999999999999819e-06
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fix_modify AtC initial electric_potential all 0.0
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fix_modify AtC initial temperature void 0.0
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fix_modify AtC initial electron_density void 0.0
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fix_modify AtC initial electric_potential void 0.0
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# create vacuum
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fix_modify AtC material gap Vacuum
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thermo_style custom step cpu f_AtC[1] f_AtC[2] f_AtC[3] f_AtC[4]
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fix_modify AtC output null_material_ddmFE $s full_text binary
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fix_modify AtC output null_material_ddmFE 100 full_text binary
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ATC: Warning : text output can create _LARGE_ files
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ATC: output custom names:
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fix_modify AtC extrinsic electron_integration implicit
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#
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fix_modify AtC mesh create_nodeset lbc -8.1 -7.9 -INF INF -INF INF
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ATC: created nodeset lbc with 5 nodes
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fix_modify AtC mesh create_nodeset rbc 7.9 8.1 -INF INF -INF INF
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ATC: created nodeset rbc with 5 nodes
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fix_modify AtC fix electron_temperature lbc $T
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fix_modify AtC fix electron_temperature lbc 20
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fix_modify AtC fix electron_temperature rbc $T
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fix_modify AtC fix electron_temperature rbc 20
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fix_modify AtC fix electron_density lbc $n
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fix_modify AtC fix electron_density lbc 3.999999999999999819e-06
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fix_modify AtC fix electric_potential lbc 0.0
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variable m equal $s*10
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variable m equal 100*10
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run $m
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run 1000
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Setting up run ...
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ATC: WARNING: material: [vacuum] cannot find heat_flux
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ATC: WARNING: physics model: [], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null
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ATC: WARNING: material: [vacuum] cannot find electron_phonon_exchange
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ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for <temperature> physics and will be treated as null
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ATC: WARNING: material: [vacuum] cannot find electron_flux
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ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for <electron_density> physics and will be treated as null
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ATC: WARNING: material: [vacuum] cannot find electron_heat_capacity
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ATC: WARNING: physics model: [drift-diffusion], material: [vacuum] does not provide all interfaces for <electron_temperature> physics and will be treated as null
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Memory usage per processor = 0.432121 Mbytes
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Step CPU AtC[1] AtC[2] AtC[3] AtC[4]
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0 0 94.264519 12 94.264519 20
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100 1.026444 94.267978 12.000392 94.299245 20.003477
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200 2.031791 94.276498 12.001352 94.329947 20.006513
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300 3.033854 94.289291 12.002784 94.363814 20.009841
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400 4.0406649 94.306379 12.004683 94.403041 20.013675
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500 5.0435619 94.328129 12.007084 94.449527 20.018196
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600 6.0397751 94.355216 12.010055 94.505534 20.023614
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700 7.0427639 94.388659 12.0137 94.573962 20.030199
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800 8.0464909 94.429901 12.01817 94.65867 20.03831
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900 9.0695961 94.480951 12.023673 94.764998 20.048448
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1000 10.076592 94.544631 12.030506 94.900724 20.061365
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Loop time of 10.0776 on 4 procs for 1000 steps with 0 atoms
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Pair time (%) = 0 (0)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00094372 (0.00936449)
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Outpt time (%) = 0.0274817 (0.272699)
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Other time (%) = 10.0492 (99.7179)
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Nlocal: 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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Nghost: 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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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: 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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Total # of neighbors = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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