From f37f19cbcf427c87b155308fa381c33a138649d0 Mon Sep 17 00:00:00 2001
From: Alex Selimov <alsel@tuta.io>
Date: Mon, 3 Feb 2020 17:35:22 -0500
Subject: [PATCH] Forgot to add the option file

---
 src/opt_orient.f90 | 121 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 121 insertions(+)
 create mode 100644 src/opt_orient.f90

diff --git a/src/opt_orient.f90 b/src/opt_orient.f90
new file mode 100644
index 0000000..21d9d3f
--- /dev/null
+++ b/src/opt_orient.f90
@@ -0,0 +1,121 @@
+module opt_orient
+    !This module contains the orient option which allows for the reorientation 
+    !of simulation cells. This can be used to create arbitrarily oriented dislocation or loops.
+    use parameters
+    use subroutines
+    use elements
+    use box
+    implicit none
+
+
+    real(kind=dp), save :: new_orient(3,3)
+    real(kind=dp), dimension(6) :: orig_box_bd
+    real(kind=dp), allocatable :: orig_sub_box_ori(:,:,:)
+
+    public 
+    contains
+
+    subroutine orient(arg_pos)
+
+        integer, intent(inout) :: arg_pos
+
+        integer :: i, ibasis, inod
+        real(kind=dp) :: inv_sub_box_ori(3,3,sub_box_num)
+
+        !First parse the orient command
+        call parse_orient(arg_pos)
+
+        !Now rotate the basis. To do this we transform the basis to [100] [010] [001] and then 
+        !transform to user specified basis.
+
+        !Find all inverse orientation matrices for all sub_boxes
+        do i = 1, sub_box_num
+            call matrix_inverse(sub_box_ori, 3, inv_sub_box_ori)
+        end do
+
+        !Now transform all atoms
+        do i = 1, atom_num
+            r_atom(:,i) = matmul(new_orient,matmul(inv_sub_box_ori(:,:,sbox_atom(i)),r_atom(:,i)))
+        end do 
+
+        !Now transform all elements
+        do i = 1, ele_num
+            do inod =1, ng_node(lat_ele(i))
+                do ibasis = 1, basisnum(lat_ele(i))
+                    r_node(:,ibasis,inod,i) = matmul(new_orient,matmul(inv_sub_box_ori(:,:,sbox_ele(i)),r_node(:,ibasis,inod,i)))
+                end do
+            end do  
+        end do
+
+        !Now save the original sub_box_ori and overwrite them
+        if(allocated(orig_sub_box_ori)) deallocate(orig_sub_box_ori)
+
+        allocate(orig_sub_box_ori(3,3,sub_box_num))
+        orig_sub_box_ori = sub_box_ori
+
+        !Now overwrite the orientations
+        do i = 1, sub_box_num
+            sub_box_ori(:,:,i) = new_orient
+        end do 
+
+        !Save original box boundaries
+        orig_box_bd = box_bd
+
+        !Now find new box boundaries
+        call def_new_box
+    end subroutine orient
+
+    subroutine parse_orient(arg_pos)
+        !This parses the orient option 
+        integer, intent(inout) :: arg_pos
+
+        integer :: i, arg_len
+        character(len=8) :: ori_string
+
+        !Pull out the new user orientation
+        do i = 1, 3
+            arg_pos = arg_pos + 1
+            call get_command_argument(arg_pos, ori_string, arg_len)
+            if (arg_len == 0) print *, "Missing orientation vector in -orient option"
+            call parse_ori_vec(ori_string, new_orient(i,:))
+        end do
+
+        !Normalize the orientation matrix
+        new_orient = matrix_normal(new_orient,3)
+        arg_pos = arg_pos + 1
+
+    end subroutine parse_orient
+
+    subroutine unorient
+
+        integer :: i, ibasis, inod
+        real(kind=dp) :: inv_ori(3,3)
+
+        !Now rotate the basis. To do this we transform the basis to [100] [010] [001] and then 
+        !transform to the original sbox_ele
+
+        !Find the inverse for the new orientation matrix
+        call matrix_inverse(new_orient, 3, inv_ori)
+
+        !Recover original sub_box_ori
+        sub_box_ori = orig_sub_box_ori 
+
+        !Now transform all atoms
+        do i = 1, atom_num
+            r_atom(:,i) = matmul(sub_box_ori(:,:,sbox_atom(i)),matmul(inv_ori(:,:),r_atom(:,i)))
+        end do 
+
+        !Now transform all elements
+        do i = 1, ele_num
+            do inod =1, ng_node(lat_ele(i))
+                do ibasis = 1, basisnum(lat_ele(i))
+                    r_node(:,ibasis,inod,i) = matmul(sub_box_ori(:,:,sbox_ele(i)),matmul(inv_ori,r_node(:,ibasis,inod,i)))
+                end do
+            end do  
+        end do
+
+        !Restore original box boundaries
+        box_bd = orig_box_bd
+    end subroutine unorient
+
+end module opt_orient
\ No newline at end of file