forked from lijiext/lammps
100 lines
3.0 KiB
Plaintext
100 lines
3.0 KiB
Plaintext
# needs description
|
|
#AtC Elastic Coupling
|
|
echo both
|
|
|
|
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
|
|
|
|
# create atoms
|
|
region simRegion block -12 12 -3 3 -3 3
|
|
region atomRegion block -8 8 -3 3 -3 3
|
|
region mdRegion block -6 6 -3 3 -3 3
|
|
boundary f p p
|
|
create_box 1 simRegion
|
|
create_atoms 1 region atomRegion
|
|
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
|
|
group Lghost region leftghost
|
|
group Rghost region rightghost
|
|
group ghosts union Lghost Rghost
|
|
|
|
pair_style lj/cut 13.
|
|
#pair_coeff 1 1 0.010323166 3.405 13.5
|
|
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
|
|
|
|
# ID part keywords nx ny nz region
|
|
fix_modify AtC mesh create 12 1 1 simRegion f p p
|
|
|
|
# initial conditions
|
|
fix_modify AtC initial displacement x all 0.0
|
|
fix_modify AtC initial displacement y all 0.0
|
|
fix_modify AtC initial displacement z all 0.0
|
|
fix_modify AtC initial velocity x all 0.0
|
|
fix_modify AtC initial velocity y all 0.0
|
|
fix_modify AtC initial velocity z all 0.0
|
|
fix_modify AtC time_integration fractional_step
|
|
fix_modify AtC internal_atom_integrate off
|
|
fix iNVE internal nve
|
|
|
|
# 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
|
|
fix_modify AtC mesh create_nodeset rbc 11.9 12.1 -INF INF -INF INF
|
|
fix_modify AtC fix velocity x rbc 0.00000004
|
|
fix_modify AtC fix displacement x lbc 0.
|
|
fix_modify AtC fix velocity x lbc 0.
|
|
|
|
# specify atom types
|
|
#fix_modify AtC boundary Lghost
|
|
#fix_modify AtC boundary Rghost
|
|
fix_modify AtC boundary ghosts
|
|
|
|
fix_modify AtC internal_quadrature off
|
|
fix_modify AtC control localized_lambda on
|
|
fix_modify AtC control momentum flux interpolate
|
|
#fix_modify AtC control momentum hoover # tested in this mode
|
|
#fix_modify AtC filter type exponential
|
|
#fix_modify AtC filter scale 1000.0
|
|
#fix_modify AtC filter on
|
|
|
|
# run to extension
|
|
#fix_modify AtC output bar1d_frac_step_initFE 50 text binary
|
|
#dump D1 all atom 50 bar1d_frac_step_init.dmp
|
|
timestep 5
|
|
thermo 100
|
|
run 1000
|
|
|
|
# reset time
|
|
fix_modify AtC reset_time 0.
|
|
reset_timestep 0
|
|
|
|
# change nodes to fixed
|
|
fix_modify AtC fix velocity x rbc 0.
|
|
fix_modify AtC fix displacement x rbc 0.0002
|
|
|
|
fix_modify AtC output bar1d_frac_stepFE 500 text #binary
|
|
#fix_modify AtC output index step
|
|
#undump D1
|
|
#dump D1 all atom 500 bar1d_frac_step.dmp
|
|
|
|
# run to equilibrium
|
|
timestep 5
|
|
thermo 100
|
|
run 5000
|