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Added disl option

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development
Alex Selimov 4 years ago
parent 0620a07847
commit 077574ea8d
4 changed files with 156 additions and 3 deletions
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2
src/call_option.f90
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@ -14,7 +14,7 @@ subroutine call_option(option, arg_pos)
character(len=100), intent(in) :: option
select case(trim(adjustl(option)))
case('-dislgen', '-disloop','-vacancydisloop')
case('-disl','-dislgen', '-disloop','-vacancydisloop')
call dislocation(option, arg_pos)
case('-group')
call group(arg_pos)

8
src/io.f90
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@ -119,7 +119,7 @@ module io
!This is the simplest visualization subroutine, it writes out all nodal positions and atom positions to an xyz file
character(len=100), intent(in) :: file
integer :: i, inod, ibasis
integer :: i, inod, ibasis, p_node, p_atom
open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
@ -128,21 +128,27 @@ module io
!Write comment line
write(11, '(a)') "#Node + atom file created using cacmb"
p_node=0
p_atom = 0
!Write nodal positions
do i = 1, ele_num
do inod = 1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i))
write(11, '(2i16, 3f23.15)') basis_type(ibasis,lat_ele(i)), 1, r_node(:,ibasis,inod,i)
p_node = p_node + 1
end do
end do
end do
if(p_node /= node_num) print *, "Error with node num"
!Write atom positions
do i = 1, atom_num
write(11, '(2i16, 3f23.15)') type_atom(i), 0, r_atom(:,i)
p_atom=p_atom +1
end do
if(p_atom /= atom_num) print *, "Error with atom num"
!Finish writing
close(11)
end subroutine write_xyz

146
src/opt_disl.f90
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@ -9,6 +9,7 @@ module opt_disl
implicit none
integer :: vloop_size ! Number of atoms to remove in planar vacancy cluster
integer :: iline, islip_plane
real(kind=dp), dimension(3) :: line, slip_plane, centroid!dislocation line, slip plane vectors, centroid,
real(kind=dp) :: burgers(3) !burgers vector of loop
real(kind=dp) :: poisson, char_angle, lattice_parameter!Poisson ratio and character angle, lattice_parameter for burgers vector
@ -31,6 +32,9 @@ module opt_disl
print *, '--------------------Option Dislocation-----------------------'
select case(trim(adjustl(option)))
case('-disl')
call parse_disl(arg_pos)
call disl
case('-dislgen')
call parse_dislgen(arg_pos)
call dislgen
@ -43,6 +47,148 @@ module opt_disl
end select
end subroutine dislocation
subroutine parse_disl(arg_pos)
!Parse disl command
integer, intent(inout) :: arg_pos
integer :: i,arglen
character(len=100) :: textholder
character(len=1) :: parse_dim
!Parse all of the commands
arg_pos = arg_pos + 1
line(:) = 0.0_dp
call get_command_argument(arg_pos, parse_dim, arglen)
if (arglen==0) STOP "Missing line dim in disl command"
select case(parse_dim)
case('x','X')
iline=1
case('y','Y')
iline=2
case('z','Z')
iline=3
end select
arg_pos=arg_pos + 1
call get_command_argument(arg_pos, parse_dim, arglen)
if (arglen==0) STOP "Missing plane dim in disl command"
select case(parse_dim)
case('x','X')
islip_plane=1
case('y','Y')
islip_plane=2
case('z','Z')
islip_plane=3
end select
do i = 1, 3
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing centroid in disl command"
call parse_pos(i, textholder, centroid(i))
end do
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing parameter in disl command"
read(textholder, *) b
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing character angle in disl command"
read(textholder, *) char_angle
arg_pos = arg_pos + 1
call get_command_argument(arg_pos, textholder, arglen)
if (arglen==0) STOP "Missing poisson in disl command"
read(textholder, *) poisson
arg_pos = arg_pos + 1
end subroutine parse_disl
subroutine disl
!This subroutine creates the actual dislocation
integer :: i, sub_box, inod, ibasis, ix, iy, iz
real(kind=dp) :: ss_ori(3,3), ss_inv(3,3), be, bs, slipx(3), disp_transform(3,3), inv_transform(3,3), &
actan, r(3), disp(3)
print *, "Dislocation with centroid ", centroid, " is inserted"
!Calculate screw and edge burgers vectors
be = sin(char_angle*pi/180.0_dp)*b
bs = cos(char_angle*pi/180.0_dp)*b
!Map box dimensions to dislocation dimensions, iz is along the dislocation line and iy is along the slip plane
iz = iline
iy = islip_plane
do i = 1, 3
if ((i /= iy).and.(i /=iz)) then
ix = i
exit
end if
end do
if(atom_num > 0) then
do i = 1, atom_num
r=r_atom(:,i) - centroid
if (r(ix) == 0) then
actan=pi/2
else
actan = datan2(r(iy),r(ix))
end if
if ((r(ix)**2 + r(iy)**2) == 0) cycle
!This is the elastic displacement field for dislocation according to Hirth and Lowe
disp(ix) = be/(2.0_dp*pi) * (actan + (r(ix)*r(iy))/(2.0_dp*(1.0_dp-poisson)*(r(ix)**2.0_dp + r(iy)**2.0_dp)))
disp(iy) = -be/(2.0_dp*pi)*((1.0_dp-2.0_dp*poisson)/(4.0_dp-4.0_dp*poisson) * &
log(r(ix)**2.0_dp + r(iy)**2.0_dp) &
+ (r(ix)**2.0_dp - r(iy)**2.0_dp)/(4.0_dp*(1.0_dp-poisson)&
*(r(ix)**2.0_dp+r(iy)**2.0_dp)))
disp(3) = bs/(2.0_dp*pi) * actan
r_atom(:,i) = r_atom(:,i) + disp
end do
end if
if(ele_num > 0) then
do i = 1, ele_num
do inod=1, ng_node(lat_ele(i))
do ibasis = 1, basisnum(lat_ele(i))
r = r_node(:,ibasis,inod,i)-centroid
if (r(ix) == 0) then
actan = pi/2
else
actan = datan2(r(iy),r(ix))
end if
if ((r(ix)**2 + r(iy)**2) == 0) cycle
!This is the elastic displacement field for dislocation according to Hirth and Lowe
disp(ix) = be/(2.0_dp*pi)*(actan + (r(ix)*r(iy))/(2.0_dp*(1.0_dp-poisson)*(r(ix)**2.0_dp + r(iy)**2.0_dp)))
disp(iy) = -be/(2.0_dp*pi)*((1.0_dp-2.0_dp*poisson)/(4.0_dp-4.0_dp*poisson) * &
log(r(ix)**2.0_dp + r(iy)**2.0_dp) &
+ (r(ix)**2.0_dp - r(iy)**2.0_dp)/(4.0_dp*(1.0_dp-poisson)&
*(r(ix)**2.0_dp+r(iy)**2.0_dp)))
disp(3) = bs/(2.0_dp*pi) * actan
r_node(:,ibasis,inod,i) = r_node(:,ibasis,inod,i) + disp
end do
end do
end do
end if
!Now make sure all atoms are wrapped back into the simulation cell
call wrap_atoms
end subroutine disl
subroutine parse_dislgen(arg_pos)
!Parse dislgen command

1
src/opt_redef_box.f90
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@ -68,6 +68,7 @@ module opt_redef_box
call delete_elements(delete_num, delete_list(1:delete_num))
print *, new_bd
box_bd=new_bd
box_bc = new_bc

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