# test external file ample preparation variable fname index Si_110_1-10_1225x245x10_s50.imdconf.lammps

# test external file
Step 1+2 : Sample preparation and quasi static loading
variable fname index
units
boundary
Si_110_1-10_1225x245x10_s50.imdconf.lammps
metal
s s p
atom_style atomic
read_data ${fname}
Define what style of
atoms to use in
asimulation (solids,
liquids, ect.).
Force field
coefficients
Set or change the
velocities of a
group of atoms in
one of several
styles.
http://lammps.sandi
a.gov/doc/velocity.
html
Sets the style of units used for a simulation. Metal :
eV, picoseconds, Angstros ect.
Set the style of boundaries for the global simulation
box in each dimension: p is periodic,
s is non-periodic and shrink-wrapped
#Dividing the sample into 6 areas
group test1 type 1
group test2 type 2
group test3 type 3
Identify a collection
group test4 type 4
of atoms as belonging
group test5 type 5
to a group.
group test6 type 6
group body type 1 2 3 4
group boundaryb type 5 6
#---------------------- LJ potentials--------------------------Set the formula(s)
pair_style sw
LAMMPS uses to
pair_coeff * * siMarder.sw Si Si Si Si Si Si
compute
pairwise
interactions.
Setting boundary conditions: top and lower layer with zero force
and zero velocity in x y directions, right end layer with zero
and force zero in x direction)
velocity
boundaryb set 0.0 0.0 NULL sum no units box
velocity
test2 set 0.0 NULL NULL sum no units box
fix zeromobile boundaryb setforce 0.0 0.0 NULL
fix zeromobile1 test2 setforce 0.0 NULL NULL
compute
compute
compute
temperature all temp
peratom all pe/atom
keatom all ke/atom
Define a computation
that will be performed
on a group of atoms.
minimization
algorithm to
use. cg:
conjugated
gradient
Set a fix that will be
applied to a group of
atoms. In LAMMPS, a
"fix" is any operation
that is applied to the
system during time
stepping or
minimization.
http://lammps.sandia.g
ov/doc/fix.html
#------------------- Minimize----------------------------------Achieving the minimum energy crack shape and atoms positions
#use cfg for atomeye
Energy minimization of the system. Iterations are
minimize
0.0 5.0e-6 10000 10000
terminated when one of the stopping criteria is
satisfied.
min_style
cg
dump
c_peratom
1 all cfg 1 relaxCG.*.cfg id type xs ys zs id type
c_keatom
http://lammps.sandia.go
dump_modify
1 element Si Si Si Si Si Si
v/doc/dump.html
run
undump
2
1
#-------------------NVE_1---------------------------------Step 3: Crack initiation modeled by MD.
velocity
all create 0.0001 4928459 dist gaussian
timestep
0.000383
fix
2 body nve
dump
2 all cfg 500 NVE_SS.*.cfg id type xs ys zs vx vy
vz id type c_peratom c_keatom
dump_modify
2 element Si Si Si Si Si Si
run
undump
unfix
10000
2
2
#-----------------Rescale--------------------------------------Step 4: homogenous rescaling
change_box
all
boundary p p p units box
Change the volume
and/or shape of the
simulation box during
a dynamics run.
dump
3 all cfg 1 deform.*.cfg id type xs ys zs vx vy vz
id type c_peratom c_keatom
dump_modify
3 element Si Si Si Si Si Si
Run or continue
dynamics for a
run
1
specified number of
unfix
strain
timesteps
undump
3
fix
Change the
volume and/or
shape and/or
boundary
conditions for the
simulation box.
Delete a fix that
was previously
defined.
strain
all deform 1 y
scale 1 units box
Delete a dump that
was previously
#---------------------NVE_2-Simulation-------------------------defined.
Step 5: crack propagation modeled by MD
change_box
fix
all
boundary s s p units box
1 body nve
#use cfg for atomeye
dump
4 all cfg 200 NVE.*.cfg id type xs ys zs c_peratom
c_keatom
dump_modify
4 element Si Si Si Si Si Si
#Display thermo
thermo
1
thermo_style custom step temp fnorm pe
thermo_modify temp temperature
run
undump
70000
4
ke