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Updated dislocation analysis and fix to alloy opt_group option

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development
Alex Selimov 3 years ago
parent 612cea3891
commit 8fd2a7f65b
2 changed files with 103 additions and 19 deletions
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106
src/mode_da.f90
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@ -8,7 +8,9 @@ module mode_da
implicit none
integer :: num_d_points
integer, allocatable :: is_slipped(:,:,:)
real(kind=dp), allocatable :: disl_line(:,:), disl_data(:)
private :: write_xyz
public
@ -31,16 +33,28 @@ module mode_da
if(allocated(is_slipped)) deallocate(is_slipped)
allocate(is_slipped(max_basisnum, max_ng_node, ele_num))
if(allocated(disl_line)) deallocate(disl_line)
num_d_points=0
allocate(disl_line(3,1024))
allocate(disl_data(1024))
call cga_da
!Now create the output file num and write out to xyz format
ppos = scan(trim(infiles(1)),".", BACK= .true.)
if ( ppos > 0 ) then
outfile = 'da_'//infiles(1)(1:ppos)//'vtk'
else
outfile = 'da_'//infiles(1)//'.vtk'
end if
call write_da_vtk(outfile)
ppos = scan(trim(infiles(1)),".", BACK= .true.)
if ( ppos > 0 ) then
outfile = 'da_'//infiles(1)(1:ppos)//'xyz'
else
outfile = 'da_'//infiles(1)//'.xyz'
end if
call write_da_xyz(outfile)
return
@ -68,9 +82,10 @@ module mode_da
integer :: i, j, k, l, ibasis, nei, close_neighbors(2,4,6), far_neighbor(4,6), minindex, minindices(2), linevec(3)
integer :: face_types(ele_num*6), face_ele(6*ele_num), diff_pair(2,6)
real(kind = dp) :: face_centroids(3, ele_num*6), r(3), rc, vnode(3, max_basisnum, 4), vnorm(max_basisnum, 4), &
real(kind = dp) :: face_centroids(3, ele_num*6), r(3), rc, vnode(3, max_basisnum, 4), vnorm, &
max_node_dist, ndiff, rmax(3), rmin(3), rnorm, v1(3), v2(3), v1norm, v2norm, theta1, theta2, &
diff_mag(6)
diff_mag(6), diffvec(3)
real(kind=dp), allocatable :: disl_line_temp(:,:), disl_data_temp(:)
logical :: is_edge
!Initialize variables
@ -123,8 +138,6 @@ module mode_da
end do
!Calculate the largest difference between nodes for each face
end do
!Now set the cut off distance as half the distance from opposite nodes in the largest element
@ -153,22 +166,24 @@ module mode_da
end do
end do
do j = 1, 3
vnode(j,1:basisnum(lat_ele(face_ele(i))),:) = vnode(j,1:basisnum(lat_ele(face_ele(i))),:) - &
minval(vnode(j,1:basisnum(lat_ele(face_ele(i))),:))
end do
!Now calculate the maximum difference between nodes
vnorm = 0
do j = 1, 4
do ibasis = 1, basisnum(lat_ele(face_ele(i)))
vnorm(ibasis,j) = norm2(vnode(:, ibasis, j))
do k=j,4
v1=vnode(:,1,j) - vnode(:,1,k)
v1norm=norm2(v1)
if (vnorm < v1norm) then
vnorm = v1norm
diffvec= v1
end if
end do
end do
!Now calculate the difference between the largest norm and the smallest norm, if it's larger than 0.5 then mark it
!as slipped. This value probably can be converted to a variable value that depends on the current lattice parameter
!I think 0.5 works ok though.
if (any(vnorm > 1_dp)) then
if (vnorm>0.5_dp) then
print *, "Element number ", face_ele(i), " is dislocated along face ", face_types(i), &
" with neighbor ", face_ele(nei), " with max displacement of ", maxval(vnorm)
" with neighbor ", face_ele(nei), " with max displacement of ", vnorm
l=0
do j = 1, 4
is_slipped(:, cubic_faces(j,face_types(i)), face_ele(i)) = 1
@ -185,14 +200,15 @@ module mode_da
end do
end do
minindex = minloc(diff_mag,1)
!Now figure out if the min differnce between nodes is associated with a 112 direction
!Now figure out if the min difference between nodes is associated with a 112 direction
is_edge = .false.
do j = 1,6
if((diff_pair(1,minindex) == oneonetwopairs(1,j)).and.(diff_pair(2,minindex)==oneonetwopairs(2,j))) then
is_edge=.true.
exit
else if((diff_pair(2,minindex)==oneonetwopairs(1,j)).and.(diff_pair(1,minindex)==oneonetwopairs(2,j)))then
is_edge=.true.
exit
end if
end do
@ -201,12 +217,70 @@ module mode_da
else
print *, 'Dislocation has primarily screw character'
end if
if( i < nei) then
num_d_points=num_d_points+2
if(num_d_points > size(disl_line,2)) then
allocate(disl_line_temp(3,size(disl_line,2)+1024))
disl_line_temp=0.0_dp
disl_line_temp(:, 1:size(disl_line,2))=disl_line
call move_alloc(disl_line_temp, disl_line)
end if
if(num_d_points/2 > size(disl_data)) then
allocate(disl_data_temp(size(disl_data)+1024))
disl_data_temp=0
disl_data_temp(1:size(disl_data)) = disl_data
call move_alloc(disl_data_temp, disl_data)
end if
print *, num_d_points/2, vnorm
disl_data(num_d_points/2)=vnorm
disl_line(:,num_d_points-1) =r_node(:, 1, diff_pair(1,minindex), face_ele(i))
disl_line(:,num_d_points) =r_node(:, 1, diff_pair(2,minindex), face_ele(i))
end if
end if
end if
end do
end subroutine cga_da
subroutine write_da_vtk(outfile)
character (len=*), intent(in) :: outfile
integer :: i
open(unit=11, file=outfile, action='write', status='replace', position='rewind')
write(11, '(a)') '# vtk DataFile Version 4.0.1'
write(11, '(a)') 'Dislocation line analyzed via cacmb dislocation analysis'
write(11, '(a)') 'ASCII'
write(11, '(a)') 'DATASET UNSTRUCTURED_GRID'
write(11, *) 'POINTS', num_d_points, 'float'
!Write the points to the file
do i = 1, num_d_points
write(11, '(3f23.15)') disl_line(:, i)
end do
write(11,*) 'CELLS', num_d_points/2, num_d_points/2*3
do i=1, num_d_points, 2
write(11,'(3i16)') 2, i-1, i
end do
write(11,*) 'CELL_TYPES', num_d_points/2
do i=1, num_d_points, 2
write(11,'(i16)') 3
end do
write(11,*) 'CELL_DATA', num_d_points/2
write(11, '(a)') 'SCALARS burgers_vec, float'
write(11, '(a)') 'LOOKUP_TABLE default'
do i=1, num_d_points, 2
write(11, '(f23.15)') disl_data((i+1)/2)
end do
close(11)
end subroutine write_da_vtk
subroutine write_da_xyz(outfile)
!This subroutine write the element positions to a .xyz file and marks whether they are slipped or not
character(len=*), intent(in) :: outfile

14
src/opt_group.f90
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@ -1187,17 +1187,27 @@ module opt_group
subroutine alloy_group
!This subroutine randomizes the atom types to reach desired concentrations, this only operates on atoms
integer :: i, j, ia, type_map(10), added_types(num_species)
real(kind=dp) :: rand, mass
real(kind=dp) :: rand, mass, old_fractions(num_species)
character(len=2) :: sorted_species_type(10)
print *, "Alloying group with desired fractions", s_fractions(1:num_species)
old_fractions=s_fractions(1:num_species)
!First we sort the fractions
call quicksort(s_fractions(1:num_species))
do i = 1,num_species
do j=1, num_species
if (is_equal(s_fractions(i), old_fractions(j))) then
sorted_species_type(i)=species_type(j)
end if
end do
end do
!Now get the atom type maps for all the atoms and make the fractions a running sum
do i = 1, num_species
call atommass(species_type(i), mass)
call atommass(sorted_species_type(i), mass)
call add_atom_type(mass, type_map(i))
if(i > 1) s_fractions(i) = s_fractions(i) + s_fractions(i-1)
end do

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