114 lines
3.9 KiB
Plaintext
114 lines
3.9 KiB
Plaintext
LAMMPS (30 Aug 2013)
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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, where N=4 for fcc, s = 3.405 A (Wagner) and a = 5.25 A (Ashcroft & Mermin, p. 70)
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lattice fcc 5.2582305 origin 0.25 0.25 0.25
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Lattice spacing in x,y,z = 5.25823 5.25823 5.25823
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# NOTE following 3 lines added for restart
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boundary f p p
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pair_style lj/cut 13.
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read_data temp.init
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Reading data file ...
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orthogonal box = (-47.3241 -15.7747 -15.7747) to (47.3241 15.7747 15.7747)
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4 by 1 by 1 MPI processor grid
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2304 atoms
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2304 velocities
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region simRegion block -12 12 -3 3 -3 3
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# create atoms, NOTE commented out for restart
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#region mdRegion block -8 8 -3 3 -3 3
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#boundary f p p
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#region mdBox block -9 9 -3 3 -3 3
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#create_box 1 mdBox
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#create_atoms 1 region mdRegion
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#mass 1 39.95
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# specify interal/ghost atoms
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region mdInternal block -6 6 -3 3 -3 3
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region leftghost block -8 -6 -3 3 -3 3
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region rightghost block 6 8 -3 3 -3 3
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group internal region mdInternal
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1728 atoms in group internal
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group Lghost region leftghost
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288 atoms in group Lghost
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group Rghost region rightghost
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288 atoms in group Rghost
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group ghosts union Lghost Rghost
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576 atoms in group ghosts
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# velocities have Vcm = 0, NOTE next for lines commented out for restart
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#velocity internal create 40. 87287 mom yes loop geom
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#pair_style lj/cut 13.
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##pair_coeff 1 1 0.010323166 3.405 13.
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#pair_coeff 1 1 .2381 3.405 13.
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neighbor 5. bin
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neigh_modify every 10 delay 0 check no
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#write_restart tinit.dat
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# zero initial momentum
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fix AtC internal atc elastic Ar_thermo_elastic.mat
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ATC: constructing elastic coupling with parameter file Ar_thermo_elastic.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: computed mass density : 1.09915
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ATC: 1 materials defined from Ar_thermo_elastic.mat
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# ID part keywords nx ny nz region
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fix_modify AtC mesh create 12 1 1 simRegion f p p
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ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements
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fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
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ATC: created faceset obndy with 2 faces
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fix_modify AtC internal_quadrature off
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fix_modify AtC fix displacement x all 0.
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fix_modify AtC fix displacement y all 0.
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fix_modify AtC fix displacement z all 0.
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fix_modify AtC fix velocity x all 0.
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fix_modify AtC fix velocity y all 0.
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fix_modify AtC fix velocity z all 0.
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fix_modify AtC control momentum glc_velocity
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#fix_modify AtC output bar1d_thermo_elastic_initializeFE 1 text #binary
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timestep 0
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thermo 1
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run 1
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Setting up run ...
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Memory usage per processor = 56.6533 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 29.995658 -4509.8851 0 -4303.9707 135.84496
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1 29.920966 -4509.8851 0 -4304.4835 135.59617
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Loop time of 0.0227802 on 4 procs for 1 steps with 2304 atoms
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Pair time (%) = 0.00607026 (26.6471)
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Neigh time (%) = 0 (0)
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Comm time (%) = 0.00152951 (6.71423)
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Outpt time (%) = 8.60691e-05 (0.377825)
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Other time (%) = 0.0150943 (66.2608)
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Nlocal: 576 ave 648 max 504 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 5677 ave 7126 max 4228 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 178632 ave 218376 max 138456 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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FullNghs: 357264 ave 436752 max 277776 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 1429056
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Ave neighs/atom = 620.25
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Neighbor list builds = 0
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Dangerous builds = 0
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unfix AtC
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# define layer
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# ID group atc PhysicsType ParameterFile
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fix AtC internal atc thermo_elastic Ar_thermo_elastic.mat
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ATC: constructing thermo-mechanical coupling with parameter file Ar_thermo_elastic.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: computed mass density : 1.09915
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ATC: 1 materials defined from Ar_thermo_elastic.mat
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fix_modify AtC boundary ghosts
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ERROR: Illegal fix_modify command (../fix.cpp:104)
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