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module opt_orient
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!This module contains the orient option which allows for the reorientation
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!of simulation cells. This can be used to create arbitrarily oriented dislocation or loops.
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use parameters
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use subroutines
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use elements
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use box
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implicit none
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real(kind=dp), save :: new_orient(3,3)
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real(kind=dp), dimension(6) :: orig_box_bd
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real(kind=dp), allocatable :: orig_sub_box_ori(:,:,:)
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public
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contains
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subroutine orient(arg_pos)
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integer, intent(inout) :: arg_pos
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integer :: i, ibasis, inod
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real(kind=dp) :: inv_sub_box_ori(3,3,sub_box_num)
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!First parse the orient command
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call parse_orient(arg_pos)
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!Now rotate the basis. To do this we transform the basis to [100] [010] [001] and then
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!transform to user specified basis.
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!Find all inverse orientation matrices for all sub_boxes
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do i = 1, sub_box_num
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call matrix_inverse(sub_box_ori, 3, inv_sub_box_ori)
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end do
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!Now transform all atoms
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do i = 1, atom_num
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r_atom(:,i) = matmul(new_orient,matmul(inv_sub_box_ori(:,:,sbox_atom(i)),r_atom(:,i)))
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end do
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!Now transform all elements
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do i = 1, ele_num
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do inod =1, ng_node(lat_ele(i))
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do ibasis = 1, basisnum(lat_ele(i))
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r_node(:,ibasis,inod,i) = matmul(new_orient,matmul(inv_sub_box_ori(:,:,sbox_ele(i)),r_node(:,ibasis,inod,i)))
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end do
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end do
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end do
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!Now save the original sub_box_ori and overwrite them
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if(allocated(orig_sub_box_ori)) deallocate(orig_sub_box_ori)
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allocate(orig_sub_box_ori(3,3,sub_box_num))
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orig_sub_box_ori = sub_box_ori
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!Now overwrite the orientations
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do i = 1, sub_box_num
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sub_box_ori(:,:,i) = new_orient
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end do
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!Save original box boundaries
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orig_box_bd = box_bd
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!Now find new box boundaries
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call def_new_box
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end subroutine orient
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subroutine parse_orient(arg_pos)
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!This parses the orient option
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integer, intent(inout) :: arg_pos
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integer :: i, arg_len
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character(len=8) :: ori_string
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!Pull out the new user orientation
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do i = 1, 3
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arg_pos = arg_pos + 1
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call get_command_argument(arg_pos, ori_string, arg_len)
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if (arg_len == 0) print *, "Missing orientation vector in -orient option"
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call parse_ori_vec(ori_string, new_orient(i,:))
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end do
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!Normalize the orientation matrix
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new_orient = matrix_normal(new_orient,3)
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arg_pos = arg_pos + 1
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end subroutine parse_orient
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subroutine unorient
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integer :: i, ibasis, inod
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real(kind=dp) :: inv_ori(3,3)
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!Now rotate the basis. To do this we transform the basis to [100] [010] [001] and then
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!transform to the original sbox_ele
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!Find the inverse for the new orientation matrix
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call matrix_inverse(new_orient, 3, inv_ori)
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!Recover original sub_box_ori
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sub_box_ori = orig_sub_box_ori
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!Now transform all atoms
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do i = 1, atom_num
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r_atom(:,i) = matmul(sub_box_ori(:,:,sbox_atom(i)),matmul(inv_ori(:,:),r_atom(:,i)))
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end do
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!Now transform all elements
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do i = 1, ele_num
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do inod =1, ng_node(lat_ele(i))
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do ibasis = 1, basisnum(lat_ele(i))
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r_node(:,ibasis,inod,i) = matmul(sub_box_ori(:,:,sbox_ele(i)),matmul(inv_ori,r_node(:,ibasis,inod,i)))
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end do
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end do
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end do
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!Restore original box boundaries
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box_bd = orig_box_bd
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end subroutine unorient
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end module opt_orient
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