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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
region simRegion block -12 12 -3 3 -3 3
region mdRegion block -8 8 -3 3 -3 3
boundary f p p
create_box 1 simRegion
Created orthogonal box = (-63.0988 -15.7747 -15.7747) to (63.0988 15.7747 15.7747)
4 by 1 by 1 MPI processor grid
create_atoms 1 region mdRegion
Created 2304 atoms
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
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
# define layer
# ID group atc PhysicsType ParameterFile
fix AtC internal atc elastic Ar_elastic.mat
ATC: constructing elastic coupling with parameter file Ar_elastic.mat
ATC: version 2.0
ATC: peratom PE compute created with ID: 3
ATC: computed mass density : 1.09915
ATC: computed mass density : 1.09915
ATC: computed mass density : 1.09915
ATC: 3 materials defined from Ar_elastic.mat
fix_modify AtC boundary ghosts
# 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 internal_atom_integrate off
fix iNVE internal nve
# initial conditions
fix_modify AtC initial displacement x all 0.0
fix_modify AtC fix displacement y all 0.0
fix_modify AtC fix displacement z all 0.0
fix_modify AtC initial velocity x all 0.0
fix_modify AtC fix velocity y all 0.0
fix_modify AtC fix velocity z all 0.0
# set node sets and bcs
# ID mesh create_nodeset tag xmin xmax ymin ymax zmin zmax
fix_modify AtC mesh create_nodeset lbc -12.1 -11.9 -INF INF -INF INF
ATC: created nodeset lbc with 1 nodes
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
ATC: created nodeset rbc with 1 nodes
#fix_modify AtC fix velocity x rbc 0.
#fix_modify AtC fix displacement x rbc 0.
fix_modify AtC fix displacement x lbc 0.
fix_modify AtC fix velocity x lbc 0.
# turn on multiscale
fix_modify AtC control momentum ghost_flux
# new boundary conditions
fix_modify AtC fix velocity x rbc 0.00000004
#fix_modify AtC output follow_ex.fe 50
#fix_modify AtC localized_lambda on
#fix_modify AtC momentum control glc_velocity
#fix_modify AtC momentum control flux faceset obndy
#fix_modify AtC control momentum flux
#fix_modify AtC control momentum ghost_flux
#fix_modify AtC filter scale 1000.0
# run to extension
compute myTemp internal temp
compute atomStress internal stress/atom
compute avgStress internal reduce sum c_atomStress[1] c_atomStress[2] c_atomStress[3]
variable myPres equal -(c_avgStress[1]+c_avgStress[2]+c_avgStress[3])/(3*vol)
thermo_style custom step c_myTemp v_myPres pe
fix_modify AtC output bar1d_ghost_fluxFE 500 text
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
#dump D1 all atom 100 bar1d_ghost_flux.dmp
timestep 5
thermo 100
run 1000
Setting up run ...
Memory usage per processor = 65.6268 Mbytes
Step myTemp myPres PotEng
0 0 -0.00072339042 -4509.8851
100 7.1225566e-14 -0.00069609188 -4509.8851
200 3.7853133e-13 -0.00065829543 -4509.8851
300 1.6363911e-11 -0.00093014878 -4509.8851
400 2.6679578e-10 -0.0022162027 -4509.8852
500 1.616056e-09 -0.0053039586 -4509.8852
600 5.0333459e-09 -0.010270696 -4509.8852
700 9.7370581e-09 -0.016093983 -4509.8852
800 1.3809125e-08 -0.021486202 -4509.8852
900 1.6783957e-08 -0.026147268 -4509.8852
1000 1.9615527e-08 -0.030744945 -4509.8852
Loop time of 18.3775 on 4 procs for 1000 steps with 2304 atoms
Pair time (%) = 5.94283 (32.3375)
Neigh time (%) = 2.46573 (13.4171)
Comm time (%) = 6.00265 (32.663)
Outpt time (%) = 0.00820392 (0.044641)
Other time (%) = 3.95812 (21.5378)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288581 max 68542 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 100
Dangerous builds = 0
# change nodes to fixed
fix_modify AtC unfix velocity x rbc
#fix_modify AtC fix displacement x rbc 0.0002
#fix_modify AtC output bar1d_fluxFE 500 text binary
# run to equilibrium
timestep 5
thermo 100
run 3000
Setting up run ...
Memory usage per processor = 66.0846 Mbytes
Step myTemp myPres PotEng
1000 1.9615527e-08 -0.030744945 -4509.8852
1100 2.3080841e-08 -0.035570103 -4509.8852
1200 2.6803382e-08 -0.039749355 -4509.8852
1300 2.8836885e-08 -0.041881649 -4509.8852
1400 2.7038886e-08 -0.04118176 -4509.8852
1500 2.247439e-08 -0.037776265 -4509.8852
1600 1.8021787e-08 -0.032491325 -4509.8852
1700 1.4774855e-08 -0.026754505 -4509.8852
1800 1.2061023e-08 -0.022034601 -4509.8852
1900 8.5768539e-09 -0.018709001 -4509.8852
2000 3.6373058e-09 -0.016114748 -4509.8852
2100 5.3669536e-10 -0.014163462 -4509.8853
2200 3.2454928e-09 -0.014205399 -4509.8853
2300 1.030702e-08 -0.017492992 -4509.8853
2400 1.6038797e-08 -0.023210717 -4509.8852
2500 1.7061988e-08 -0.029013462 -4509.8851
2600 1.9296258e-08 -0.03339452 -4509.8852
2700 2.2816944e-08 -0.036626152 -4509.8852
2800 2.6944075e-08 -0.039307649 -4509.8852
2900 2.8170813e-08 -0.040972921 -4509.8852
3000 2.7256286e-08 -0.040327211 -4509.8852
3100 2.445985e-08 -0.036617618 -4509.8852
3200 1.8787648e-08 -0.03049195 -4509.8852
3300 1.4750104e-08 -0.023629006 -4509.8852
3400 1.3515772e-08 -0.017473229 -4509.8852
3500 1.157919e-08 -0.012114855 -4509.8851
3600 9.6213234e-09 -0.0064144434 -4509.8851
3700 9.1781574e-09 0.00062376196 -4509.8851
3800 9.0938842e-09 0.0087100206 -4509.885
3900 7.7454581e-09 0.016669158 -4509.885
4000 9.3314606e-09 0.023405906 -4509.885
Loop time of 54.728 on 4 procs for 3000 steps with 2304 atoms
Pair time (%) = 17.812 (32.5465)
Neigh time (%) = 7.39237 (13.5075)
Comm time (%) = 17.7536 (32.4397)
Outpt time (%) = 0.0253569 (0.0463326)
Other time (%) = 11.7446 (21.46)
Nlocal: 576 ave 864 max 288 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 5170 ave 6910 max 3430 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 178632 ave 288933 max 68141 min
Histogram: 2 0 0 0 0 0 0 0 0 2
FullNghs: 357264 ave 577008 max 137520 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 1429056
Ave neighs/atom = 620.25
Neighbor list builds = 300
Dangerous builds = 0
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