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LAMMPS (30 Aug 2013)
units real
atom_style atomic
# create domain
#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)
lattice fcc 5.2582305 origin 0.25 0.25 0.25
Lattice spacing in x,y,z = 5.25823 5.25823 5.25823
# NOTE following 3 lines added for restart
boundary f p p
pair_style lj/cut 13.
read_data temp.init
Reading data file ...
orthogonal box = (-47.3241 -15.7747 -15.7747) to (47.3241 15.7747 15.7747)
4 by 1 by 1 MPI processor grid
2304 atoms
2304 velocities
region simRegion block -12 12 -3 3 -3 3
# create atoms, NOTE commented out for restart
#region mdRegion block -8 8 -3 3 -3 3
#boundary f p p
#region mdBox block -9 9 -3 3 -3 3
#create_box 1 mdBox
#create_atoms 1 region mdRegion
#mass 1 39.95
# specify interal/ghost atoms
region mdInternal block -6 6 -3 3 -3 3
region leftghost block -8 -6 -3 3 -3 3
region rightghost block 6 8 -3 3 -3 3
group internal region mdInternal
1728 atoms in group internal
group Lghost region leftghost
288 atoms in group Lghost
group Rghost region rightghost
288 atoms in group Rghost
group ghosts union Lghost Rghost
576 atoms in group ghosts
# velocities have Vcm = 0, NOTE next for lines commented out for restart
#velocity internal create 40. 87287 mom yes loop geom
#pair_style lj/cut 13.
##pair_coeff 1 1 0.010323166 3.405 13.
#pair_coeff 1 1 .2381 3.405 13.
neighbor 5. bin
neigh_modify every 10 delay 0 check no
#write_restart tinit.dat
# zero initial momentum
fix AtC internal atc elastic Ar_thermo_elastic.mat
ATC: constructing elastic coupling with parameter file Ar_thermo_elastic.mat
ATC: version 2.0
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 1.09915
ATC: 1 materials defined from Ar_thermo_elastic.mat
# ID part keywords nx ny nz region
fix_modify AtC mesh create 12 1 1 simRegion f p p
ATC: created uniform mesh with 52 nodes, 13 unique nodes, and 12 elements
fix_modify AtC mesh create_faceset obndy box -6.0 6.0 -INF INF -INF INF outward
ATC: created faceset obndy with 2 faces
fix_modify AtC internal_quadrature off
fix_modify AtC fix displacement x all 0.
fix_modify AtC fix displacement y all 0.
fix_modify AtC fix displacement z all 0.
fix_modify AtC fix velocity x all 0.
fix_modify AtC fix velocity y all 0.
fix_modify AtC fix velocity z all 0.
fix_modify AtC control momentum glc_velocity
#fix_modify AtC output bar1d_thermo_elastic_initializeFE 1 text #binary
timestep 0
thermo 1
run 1
Setting up run ...
Memory usage per processor = 56.6533 Mbytes
Step Temp E_pair E_mol TotEng Press
0 29.995658 -4509.8851 0 -4303.9707 135.84496
1 29.920966 -4509.8851 0 -4304.4835 135.59617
Loop time of 0.0227802 on 4 procs for 1 steps with 2304 atoms
Pair time (%) = 0.00607026 (26.6471)
Neigh time (%) = 0 (0)
Comm time (%) = 0.00152951 (6.71423)
Outpt time (%) = 8.60691e-05 (0.377825)
Other time (%) = 0.0150943 (66.2608)
Nlocal: 576 ave 648 max 504 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5677 ave 7126 max 4228 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 218376 max 138456 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 436752 max 277776 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 0
Dangerous builds = 0
unfix AtC
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc thermo_elastic Ar_thermo_elastic.mat
ATC: constructing thermo-mechanical coupling with parameter file Ar_thermo_elastic.mat
ATC: version 2.0
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 1.09915
ATC: 1 materials defined from Ar_thermo_elastic.mat
fix_modify AtC boundary ghosts
ERROR: Illegal fix_modify command (../fix.cpp:104)
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