Merge branch 'ft--opt-dislloop' into development

README.md

@@ -112,3 +112,45 @@ This mode merges multiple data files and creates one big simulation cell. The pa
 `N` - The number of files which are being read
 
 `dim` - the dimension they are to be stacked along, can be either `x`, `y`, or `z`. If the argument `none` is passed then the cells are just overlaid. Future options will include a delete overlap command.
+
+## Options
+
+Options are additional portions of code which have additional functionality. Options are performed in the order that they appear in the argument list and can be added to any mode. If wanting to use strictly options use `--convert` to specify input and output files.
+
+### Option dislgen
+
+```
+-dislgen [ijk] [hkl] x y z char_angle poisson 
+```
+
+
+
+This options adds an arbitrarily oriented dislocation into your model based on user inputs using the volterra displacement fields. The options are below
+
+`[ijk]` - The vector for the line direction
+
+`[hkl]` - The vector for the slip plane 
+
+`x y z` - The position of the dislocation centroid
+
+`char_angle` - Character angle of the dislocation (0 is screw and 90 is edge)
+
+`poisson` - Poisson's ratio used for the displacement field.
+
+### Option disloop
+
+````
+-disloop loop_normal radius x y z bx by bz poisson
+````
+
+This option deletes vacancies on a plane which when minimized should result in a dislocation loop structure. The arguments are below:
+
+`dim` - The box dimension which defines the normal to the loop plane. As of now this dimension must be a closed back direction, meaning that for fcc a box dimension has to be of the (111) family of planes. Either `x`, `y`, or `z`.
+
+`n` - The number of atoms to delete on the loop plane
+
+`x y z` - The centroid of the loop. 
+
+`bx by bz` - The burgers vector for the dislocation
+
+`poisson` - Poisson ratio for continuum solution

src/Makefile

@@ -1,9 +1,9 @@
- 
 FC=ifort
 FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin
-#FFLAGS=-mcmodel=large -Ofast
+#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin
 MODES=mode_create.o mode_merge.o mode_convert.o
-OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o $(MODES)
+OPTIONS=opt_disl.o
+OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o call_option.o $(MODES) $(OPTIONS)
 
 .SUFFIXES:
 .SUFFIXES: .c .f .f90 .F90 .o
@@ -19,16 +19,25 @@ clean:
 	$(RM) cacmb  *.o 
 
 testfuncs: testfuncs.o functions.o subroutines.o
-	$(FC) testfuncs.o functions.o subroutines.o elements.o -o $@
+	$(FC) testfuncs.o functions.o subroutines.o box.o elements.o -o $@
 
 .PHONY: cleantest
 cleantest:
 	$(RM) testfuncs testfuncs.o
 
+.PHONY: test
+test: testfuncs
+	./testfuncs
+
+.PHONY: install
+install: cacmb
+	cp ./cacmb /usr/local/bin
+
 $(OBJECTS) : parameters.o
-atoms.o subroutines.o testfuncs.o : functions.o
+atoms.o subroutines.o testfuncs.o box.o : functions.o
-main.o io.o build_subroutines.o: elements.o 
+main.o io.o $(MODES) $(OPTIONS) : elements.o 
 call_mode.o : $(MODES)
+call_option.o : $(OPTIONS)
 $(MODES) io.o: atoms.o box.o
 $(MODES) main.o : io.o
-testfuncs.o elements.o mode_create.o: subroutines.o
+testfuncs.o elements.o mode_create.o opt_disl.o: subroutines.o

src/box.f90

@@ -1,7 +1,7 @@
 module box
     !This module contains information on the properties of the current box.
     use parameters
-
+    use functions
     implicit none 
 
     real(kind=dp) :: box_bd(6) !Global box boundaries
@@ -34,8 +34,14 @@ module box
 
         integer, intent(in) :: n
 
-        allocate(sub_box_ori(3,3,n), sub_box_bd(6,n), sub_box_array_bd(2,2,n))
+        integer :: i
 
+        allocate(sub_box_ori(3,3,n), sub_box_bd(6,n), sub_box_array_bd(2,2,n))
+        do i = 1, n
+            sub_box_ori(:,:,i) = identity_mat(3)
+            sub_box_bd(:,i) = 0.0_dp
+            sub_box_array_bd(:,:,i) = 1
+        end do
     end subroutine alloc_sub_box
 
     subroutine grow_sub_box(n)
@@ -58,7 +64,7 @@ module box
         call move_alloc(temp_bd, sub_box_bd)
 
         temp_array_bd(:,:,1:sub_box_num) = sub_box_array_bd
-        temp_array_bd(:,:,sub_box_num+1:) = 0.0_dp
+        temp_array_bd(:,:,sub_box_num+1:) = 1
         call move_alloc(temp_array_bd, sub_box_array_bd)
 
         return
@@ -79,4 +85,21 @@ module box
         return
     end subroutine grow_box
 
+
+    subroutine in_sub_box(r, which_sub_box)
+        !This returns which sub_box a point is in. It returns the first sub_box with boundaries which 
+        !contain the point.
+        real(kind=dp), dimension(3), intent(in) :: r
+        integer, intent(out) :: which_sub_box
+
+        integer :: i 
+
+        do i = 1, sub_box_num
+            if( in_block_bd(r, sub_box_bd(:,i))) then 
+                which_sub_box = i
+                exit
+            end if
+        end do 
+    return 
+    end subroutine in_sub_box
 end module box

src/elements.f90

@@ -3,6 +3,7 @@ module elements
     !This module contains the elements data structures, structures needed for building regions
     !and operations that are done on elements
     use parameters
+    use functions
     use subroutines
     implicit none
 
@@ -373,4 +374,26 @@ module elements
         return
     end subroutine rhombshape
 
+    subroutine delete_atoms(num, index)
+        !This subroutine deletes atoms from the atom arrays 
+        integer, intent(in) :: num
+        integer, intent(inout), dimension(num) :: index
+
+        integer :: i, j
+
+        call heapsort(index)
+
+        !We go from largest index to smallest index just to make sure that we don't miss 
+        !accidentally overwrite values which need to be deleted
+        do i = num, 1, -1
+            if(index(i) == atom_num) then 
+                r_atom(:,index(i)) = 0.0_dp
+                type_atom(index(i)) = 0
+            else
+                r_atom(:,index(i)) = r_atom(:, atom_num)
+                type_atom(index(i)) = type_atom(atom_num)
+            end if            
+            atom_num = atom_num - 1
+        end do 
+    end subroutine
 end module elements

src/functions.f90

@@ -232,4 +232,22 @@ END FUNCTION StrDnCase
         end if
     return
     end function is_equal
+
+    pure function unitvec(n,vec)
+        integer, intent(in) :: n
+        real(kind=dp), intent(in) :: vec(n)
+        real(kind=dp) :: unitvec(n)
+
+        unitvec = vec/norm2(vec)
+        return
+    end function unitvec
+
+    pure function norm_dis(rl,rk)
+        !This just returns the magnitude of the vector between two points
+        real(kind=dp), dimension(3), intent(in) :: rl, rk
+        real(kind=dp) :: norm_dis(4)
+
+        norm_dis(1:3) = (rk - rl)
+        norm_dis(4) = norm2(rk-rl)
+    end function
 end module functions

src/io.f90

@@ -387,7 +387,7 @@ module io
         write(11,3) node_num
         write(11,19) max_ng_node
         write(11,4) lattice_types
-        write(11,2) atom_num
+        write(11,5) atom_num
         write(11,6) 1 !Grain_num is ignored 
         write(11,16) lattice_types, atom_types
         write(11,21)
@@ -481,7 +481,7 @@ module io
         end do
 
         !Write the number of atom types in the current model and all of their names
-        write(11,*) atom_types, (type_to_name(i), i=1, atom_types)
+        write(11,*) atom_types, (type_to_name(i)//' ', i=1, atom_types)
         !Write the number of lattice_types, basisnum and number of nodes for each lattice type
         write(11,*) lattice_types, (basisnum(i), i = 1, lattice_types), (ng_node(i), i = 1, lattice_types)
         !Now for every lattice type write the basis atom types
@@ -616,10 +616,14 @@ module io
             read(11,*) sub_box_bd(:,sub_box_num+i)
             sub_box_bd(:,sub_box_num+i) = sub_box_bd(:, sub_box_num+i) + displace(:)
             !Read in sub_box_array_bd
-            read(11,*) ((sub_box_ori(j, k, sub_box_num+i), j = 1, 2), k = 1, 2)
+            read(11,*) ((sub_box_array_bd(j, k, sub_box_num+i), j = 1, 2), k = 1, 2)
-
         end do
-            sub_box_num = sub_box_num + n
+
+        !Add the existing element boundaries
+        sub_box_array_bd(:,1,sub_box_num+1:) = sub_box_array_bd(:,1,sub_box_num+1:) + atom_num
+        sub_box_array_bd(:,2,sub_box_num+1:) = sub_box_array_bd(:,2,sub_box_num+1:) + ele_num
+
+        sub_box_num = sub_box_num + n
 
         !Read in the number of atom types and all their names
         read(11, *) new_atom_types, (new_type_to_name(i), i = 1, new_atom_types)

src/main.f90

@@ -17,12 +17,13 @@ program main
     use io
     
 
-    integer ::  i, end_mode_arg, arg_num
+    integer ::  i, end_mode_arg, arg_num, arg_pos
     character(len=100) ::  argument
 
     !Call initialization functions
     call lattice_init
     call box_init
+    end_mode_arg = 0
     
     ! Command line parsing
     arg_num = command_argument_count()
@@ -47,13 +48,30 @@ program main
         call call_mode(end_mode_arg, argument)
     end if
 
+    !Check to make sure a mode was called
+    if (end_mode_arg==0) then 
+        stop "Nothing to do, please run cacmb using an available mode"
+    end if
     !Now we loop through all of the arguments and check for passed options or for a filename to be written out
-    do i = end_mode_arg-1, arg_num
+    arg_pos = end_mode_arg
-        call get_command_argument(i, argument)
+    do while(.true.)
+        !Exit the loop if we are done reading
+        if(arg_pos > arg_num) exit
+
+        call get_command_argument(arg_pos, argument)
 
         !Check to see if a filename was passed
         if(scan(argument,'.',.true.) > 0) then 
             call get_out_file(argument)
+            arg_pos = arg_pos + 1
+
+        !Check to see if an option has been passed
+        else if(argument(1:1) == '-') then 
+            call call_option(argument, arg_pos)
+        !Otherwise print that the argument is not accepted and move on
+        else
+            print *, trim(adjustl(argument)), " is not accepted. Skipping to next argument"
+            arg_pos = arg_pos + 1
         end if
     end do
 

src/mode_create.f90

@@ -199,20 +199,7 @@ module mode_create
                     call get_command_argument(arg_pos, orient_string, arglen)
                     if (arglen==0) STOP "Missing orientation in orient command of mode create"
                     arg_pos = arg_pos+1
-                    ori_pos=2
+                    call parse_ori_vec(orient_string, orient(i,:))
-                    do j = 1,3
-                        if (orient_string(ori_pos:ori_pos) == '-') then 
-                            ori_pos = ori_pos + 1
-                            read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
-                            if (stat>0) STOP "Error reading orient value"
-                            orient(i,j) = -orient(i,j)
-                            ori_pos = ori_pos + 1
-                        else
-                            read(orient_string(ori_pos:ori_pos), *, iostat=stat) orient(i,j)
-                            if(stat>0) STOP "Error reading orient value"
-                            ori_pos=ori_pos + 1
-                        end if
-                    end do
                 end do
 
 
@@ -243,10 +230,10 @@ module mode_create
 
             case default
                 !If it isn't an option then you have to exit
+                arg_pos = arg_pos -1
                 exit
             end select
         end do
-
         !Calculate the lattice periodicity length in lattice units
         do i = 1, 3
             lattice_space(i) = norm2(orient(i,:))

src/opt_disl.f90

@@ -0,0 +1,520 @@
+module opt_disl
+
+    !This module contains all code associated with dislocations
+
+    use parameters
+    use elements
+    use subroutines
+    use box 
+    implicit none
+
+
+    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
+    character(len=10) :: lattice
+    character(len=1) :: loop_normal
+    real(kind=dp) :: loop_radius !Dislocation loop radius
+    
+    real(kind=dp) :: b !burgers vector
+
+
+    public 
+    contains 
+
+    subroutine dislocation(option, arg_pos)
+
+        !Main calling function for all codes related to dislocations
+
+        character(len=100), intent(in) :: option
+        integer, intent(inout) :: arg_pos 
+
+
+        select case(trim(adjustl(option)))
+        case('-dislgen')
+            call parse_dislgen(arg_pos)
+            call dislgen
+        case('-disloop')
+            call parse_disloop(arg_pos)
+            call disloop
+        end select
+    end subroutine dislocation
+
+    subroutine parse_dislgen(arg_pos)
+
+        !Parse dislgen command
+
+        integer, intent(inout) :: arg_pos
+
+        integer :: i,arglen
+        character(len=8) :: ori_string
+        character(len=100) :: textholder
+
+        !Parse all of the commands
+        arg_pos = arg_pos + 1
+        line(:) = 0.0_dp
+        call get_command_argument(arg_pos, ori_string, arglen)
+        if (arglen==0) STOP "Missing line vector in dislgen command"
+        call parse_ori_vec(ori_string, line)
+
+        arg_pos=arg_pos + 1
+        slip_plane(:) = 0.0_dp
+        call get_command_argument(arg_pos, ori_string, arglen)
+        if (arglen==0) STOP "Missing plane vector in dislgen command"
+        call parse_ori_vec(ori_string, slip_plane)
+
+        do i = 1, 3
+            arg_pos = arg_pos + 1
+            call get_command_argument(arg_pos, textholder, arglen)
+            if (arglen==0) STOP "Missing centroid in dislgen command"
+            call parse_pos(i, textholder, centroid(i))           
+        end do
+
+        print *, centroid
+
+        arg_pos = arg_pos + 1
+        call get_command_argument(arg_pos, textholder, arglen)
+        if (arglen==0) STOP "Missing character angle in dislgen 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 dislgen command"
+        read(textholder, *) poisson
+
+        arg_pos = arg_pos + 1
+        call get_command_argument(arg_pos, lattice, arglen)
+        if (arglen==0) STOP "Missing lattice in dislgen command"
+
+        arg_pos = arg_pos + 1
+        call get_command_argument(arg_pos, textholder, arglen)
+        if (arglen==0) STOP "Missing lattice parameter in dislgen command"
+        read(textholder, *) lattice_parameter
+
+        arg_pos = arg_pos + 1
+        !Now set the vurgers vector based on the lattice paarameter and lattice type
+        select case(lattice)
+            case('fcc')
+                b = lattice_parameter / sqrt(2.0_dp)
+            ! case('bcc')
+            !     b = lattice_parameter * sqrt(3.0_dp) / 2.0_dp
+            case default
+                print *, 'Error: Lattice structure', lattice, ' is not accepted for dislgen option'
+                STOP
+       end select
+
+    end subroutine parse_dislgen
+
+    subroutine dislgen
+        !This subroutine creates the actual dislocation
+
+        integer :: i, sub_box, inod, ibasis
+        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)
+
+        !Calculate screw and edge burgers vectors
+        be = sin(char_angle*pi/180.0_dp)*b
+        bs = cos(char_angle*pi/180.0_dp)*b
+
+        !Figure out which sub box you are in so you can access it's orientation, this code will not work
+        !with overlapping sub_boxes
+        do i = 1, sub_box_num
+            if(in_block_bd(centroid, sub_box_bd(:,i))) then 
+                sub_box = i
+                exit
+            end if
+        end do
+
+        !Construct the slip system orientation matrix in an unrotated system 
+        slipx = cross_product(slip_plane, line)
+        ss_ori(1,:) = unitvec(3,slipx)
+        ss_ori(2,:) = unitvec(3,slip_plane)
+        ss_ori(3,:) = unitvec(3,line)
+        call matrix_inverse(ss_ori, 3, ss_inv)
+
+        !Apply the rotation
+        disp_transform = matmul(sub_box_ori(:,:,i), ss_inv)
+        call matrix_inverse(disp_transform,3,inv_transform)
+
+        if(atom_num > 0) then 
+            do i = 1, atom_num
+                r=r_atom(:,i) - centroid
+                r=matmul(inv_transform, r)
+                if (r(1) == 0) then 
+                    actan=pi/2
+                else
+                    actan = datan2(r(2),r(1))
+                end if
+
+                if ((r(1)**2 + r(2)**2) == 0) cycle
+
+                !This is the elastic displacement field for dislocation according to Hirth and Lowe
+                disp(1) = be/(2.0_dp*pi) * (actan + (r(1)*r(2))/(2.0_dp*(1.0_dp-poisson)*(r(1)**2.0_dp + r(2)**2.0_dp)))
+                disp(2) = -be/(2.0_dp*pi)*((1.0_dp-2.0_dp*poisson)/(4.0_dp-4.0_dp*poisson) * &
+                                            log(r(1)**2.0_dp + r(2)**2.0_dp) &
+                                            + (r(1)**2.0_dp - r(2)**2.0_dp)/(4.0_dp*(1.0_dp-poisson)&
+                                            *(r(1)**2.0_dp+r(2)**2.0_dp)))
+                disp(3) = bs/(2.0_dp*pi) * actan
+
+                !This transforms the displacement to the correct orientation
+                disp = matmul(disp_transform, disp)
+
+                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)
+                        r = matmul(inv_transform, r)
+                        if (r(1) == 0) then 
+                            actan = pi/2
+                        else
+                            actan = datan2(r(2),r(1))
+                        end if
+
+                        if ((r(1)**2 + r(2)**2) == 0) cycle
+                
+                        !This is the elastic displacement field for dislocation according to Hirth and Lowe
+                        disp(1) = be/(2.0_dp*pi) * (actan + (r(1)*r(2))/(2.0_dp*(1.0_dp-poisson)*(r(1)**2.0_dp + r(2)**2.0_dp)))
+                        disp(2) = -be/(2.0_dp*pi)*((1.0_dp-2.0_dp*poisson)/(4.0_dp-4.0_dp*poisson) * &
+                                                    log(r(1)**2.0_dp + r(2)**2.0_dp) &
+                                                    + (r(1)**2.0_dp - r(2)**2.0_dp)/(4.0_dp*(1.0_dp-poisson)&
+                                                    *(r(1)**2.0_dp+r(2)**2.0_dp)))
+                        disp(3) = bs/(2.0_dp*pi) * actan
+
+
+                        disp = matmul(disp_transform, disp)
+                        r_node(:,ibasis,inod,i) = r_node(:,ibasis,inod,i) + disp
+                    end do
+                end do
+            end do
+        end if
+
+    end subroutine dislgen
+
+    subroutine parse_disloop(arg_pos)
+        !This subroutine parses the disloop command
+
+        integer, intent(inout) :: arg_pos
+
+        integer :: i,arglen, sbox
+        character(len=8) :: ori_string
+        character(len=100) :: textholder
+
+        !Parse all of the commands
+        arg_pos = arg_pos + 1
+        loop_normal = ' '
+        call get_command_argument(arg_pos, loop_normal, arglen)
+        if (arglen==0) STOP "Missing loop_normal in disloop command"
+        !Convert the loop_normal to the dimension
+        select case(loop_normal)
+            case('x','X', 'y', 'Y', 'z', 'Z')
+               continue
+            case default
+                print *, "Dimension argument must either be x, y, or z not", loop_normal
+                stop 3
+        end select
+
+        arg_pos = arg_pos + 1
+        loop_radius = 0
+        call get_command_argument(arg_pos, textholder, arglen)
+        if (arglen==0) STOP "Missing loop_size in disloop command"
+        read(textholder, *) loop_radius
+
+        do i = 1, 3
+            arg_pos = arg_pos + 1
+            call get_command_argument(arg_pos, textholder, arglen)
+            if (arglen==0) STOP "Missing centroid in disloop command"
+            call parse_pos(i, textholder, centroid(i))           
+        end do
+
+        burgers(:) = 0.0_dp
+        do i = 1, 3
+            arg_pos = arg_pos + 1
+            call get_command_argument(arg_pos, textholder, arglen)
+            if (arglen==0) STOP "Missing burgers vector in disloop command"
+            read(textholder, *) burgers(i)
+        end do
+
+        arg_pos = arg_pos + 1
+        call get_command_argument(arg_pos, textholder, arglen)
+        if (arglen==0) STOP "Missing poisson ratio in disloop command"
+        read(textholder, *) poisson
+
+        arg_pos = arg_pos + 1
+
+        !Now check to make sure that the dimension selected is actually a 1 1 1 direction.
+        ! call in_sub_box(centroid, sbox)
+        ! if(.not.((abs(sub_box_ori(loop_normal,1,sbox)) == abs(sub_box_ori(loop_normal,2,sbox))).and. &
+        !          (abs(sub_box_ori(loop_normal,2,sbox)) == abs(sub_box_ori(loop_normal,3,sbox))).and. &
+        !          (abs(sub_box_ori(loop_normal,3,sbox)) == abs(sub_box_ori(loop_normal,1,sbox))))) then 
+
+        !     print *, "The selected dimension ", loop_normal, " for sub_box ", sbox, " is ", &
+        !              sub_box_ori(loop_normal,:,sbox), " which is not in the (111) family of planes"
+        !     STOP 3 
+        ! end if
+
+
+    end subroutine
+
+    !Code for the creation of dislocation loops is based on functions from atomsk
+    !which is available from https://atomsk.univ-lille.fr/. They have been adapted to fit cacmb.
+    subroutine disloop
+        !This subroutine applies the displacement field for a dislocation loop to all atoms and elements.
+        integer :: a1, a2, a3 !New directions
+        integer :: i, j, inod, ibasis, Npoints 
+        real(kind = dp) :: perimeter, angle, theta, omega, xA(3), xB(3), xC(3), u(3)
+        real(kind=dp), dimension(:,:), allocatable :: xloop !coordinate of points forming loop
+
+        if(allocated(xLoop)) deallocate(xLoop)
+
+        !Define new directions
+        select case(loop_normal)
+        case('x','X')
+            !Loop in (y,z) plane
+            a1 = 2
+            a2 = 3
+            a3 = 1
+        case('y','Y')
+            !Loop in (x,z) plane
+            a1 = 3
+            a2 = 1
+            a3 = 2
+        case default
+            !Loop in (x,y) plane
+            a1 = 1
+            a2 = 2
+            a3 = 3
+        end select
+
+        !Calculate loop perimeter
+        perimeter = 2.0_dp*pi*loop_radius
+
+        !Define the number of points forming the loop 
+        ! The following criteria are used as a trade-off between
+        ! good accuracy and computational efficiency:
+        ! - each dislocation segment should have a length of 5 angströms;
+        ! - the loop should contain at least 3 points
+        !    (for very small loops, this will result in segments shorter than 5 A);
+        ! - there should not be more than 100 points
+        !    (for very large loops, this will result in segments longer than 5 A).
+        Npoints = MAX( 3 , MIN( NINT(perimeter/5.d0) , 100 ) )
+
+        !angle between two consecutive points
+        theta = 2.0_dp*pi / dble(Npoints)
+
+        !allocate xLoop
+        allocate(xLoop(Npoints,3))
+        xLoop(:,:) = 0.0_dp
+
+        !Calculate the position of each point in the loop
+        angle = 0.0_dp
+        do i = 1, size(xLoop,1)
+            xLoop(i,a1) = centroid(a1) + loop_radius*dcos(angle)
+            xLoop(i,a2) = centroid(a2) + loop_radius*dsin(angle)
+            xLoop(i,a3) = centroid(a3)
+            ! Increment angle for next point
+            angle = angle + theta
+        end do
+
+        !Now actually calculate the displacement created by a loop for every atom
+        do i = 1, atom_num
+            u = 0.0_dp
+            omega = 0.0_dp
+            xC(:) = centroid - r_atom(:,i)
+
+            !Loop over all dislocation segments
+            do j = 1, size(xLoop,1)
+                !Coordinates of point A
+                if (j ==1) then
+                    xA(:) = xLoop(size(xLoop,1),:) - r_atom(:,i)
+                else
+                    xA(:) = xLoop(j-1, :) - r_atom(:,i)
+                end if
+
+                !Coordinates of point B
+                xB(:) = xLoop(j,:) - r_atom(:,i)
+
+                !Displacement due to solid angle
+                omega = omega + SolidAngle(xA, xB, xC)
+                !Displacement due to elasticity
+                u(:) = u(:) + DisloSeg_displacement_iso(xA, xB, burgers(:), poisson)
+            end do
+
+            !Total displacement
+            u=u(:) + burgers(:) * omega
+
+            !Apply displacement to atom
+            r_atom(:,i) = r_atom(:,i) + u(:)
+        end do
+
+        !Repeat for element nodes
+        do i = 1, ele_num
+            do inod =1, ng_node(lat_ele(i))
+                do ibasis = 1, basisnum(lat_ele(i))
+                    u = 0.0_dp
+                    omega = 0.0_dp
+                    xC(:) = centroid - r_node(:,ibasis,inod,i)
+
+                    !Loop over all dislocation segments
+                    do j = 1, size(xLoop,1)
+                        !Coordinates of point A
+                        if (j ==1) then
+                            xA(:) = xLoop(size(xLoop,1),:) - r_node(:,ibasis,inod,i)
+                        else
+                            xA(:) = xLoop(j-1, :) - r_node(:,ibasis,inod,i)
+                        end if
+
+                        !Coordinates of point B
+                        xB(:) = xLoop(j,:) - r_node(:,ibasis,inod,i)
+
+                        !Displacement due to solid angle
+                        omega = omega + SolidAngle(xA, xB, xC)
+                        !Displacement due to elasticity
+                        u(:) = u(:) + DisloSeg_displacement_iso(xA, xB, burgers(:), poisson)
+                    end do
+
+                    !Total displacement
+                    u=u(:) + burgers(:) * omega
+
+                    !Apply displacement to atom
+                    r_node(:,ibasis,inod,i) = r_node(:,ibasis,inod,i) + u(:)
+                end do
+            end do 
+        end do
+        return
+    end subroutine
+
+    !********************************************************
+    ! SOLIDANGLE
+    ! Calculate solid angle (normalized by 4*pi) used to obtain the 
+    ! displacement created by a dislocation triangle loop ABC at the origin
+    ! (field point = origin)
+    ! Ref.: Van Oosterom, A. and Strackee, J., 
+    !       The Solid Angle of a Plane Triangle, 
+    !       IEEE Transactions on Biomedical Engineering BME-30, 125 (1983).
+    !********************************************************
+    FUNCTION SolidAngle(xA, xB, xC) RESULT(Omega)
+    !
+    IMPLICIT NONE
+    !
+    ! Extremities of the triangle loop
+    REAL(dp),DIMENSION(3),INTENT(IN) :: xA, xB, xC
+    !
+    ! Solid angle (normalized by 4*pi)
+    REAL(dp):: omega
+    REAL(dp),PARAMETER:: factor=1.d0/(2.d0*pi)
+    !
+    REAL(dp) :: rA, rB, rC, numerator, denominator
+    !
+    rA = norm2(xA)
+    rB = norm2(xB)
+    rC = norm2(xC)
+    !
+    numerator = TRIPLE_PRODUCT( xA, xB, xC )
+    denominator = rA*rB*rC + DOT_PRODUCT( xA, xB )*rC &
+                & + DOT_PRODUCT( xB, xC )*rA + DOT_PRODUCT( xC, xA )*rB
+    !
+    omega = factor*ATAN2( numerator, denominator )
+    !
+    END FUNCTION SolidAngle
+
+    !********************************************************
+    ! DISLOSEG_DISPLACEMENT_ISO
+    ! Calculate displacement created by dislocation segment AB
+    ! once the solid angle part has been removed
+    ! Isotropic elastic calculation with nu Poisson coef.
+    ! Ref.: Eq. (1) in Barnett, D. M. 
+    !       The Displacement Field of a Triangular Dislocation Loop
+    !       Philos. Mag. A, 1985, 51, 383-387 
+    !********************************************************
+    FUNCTION DisloSeg_displacement_iso(xA, xB, b, nu) RESULT(u)
+    !
+    IMPLICIT NONE
+    REAL(dp),DIMENSION(3),INTENT(IN):: xA, xB ! Extremities of the segment
+    REAL(dp),DIMENSION(3),INTENT(IN):: b  ! Burgers vector
+    REAL(dp),INTENT(IN):: nu    ! Poisson coefficient
+    REAL(dp),DIMENSION(3):: u ! Displacement
+    REAL(dp):: rA, rB
+    REAL(dp),DIMENSION(1:3)::  tAB, nAB 
+    !
+    rA = norm2(xA)
+    rB = norm2(xB)
+    !
+    ! Tangent vector
+    tAB(:) = xB(:) - xA(:)
+    tAB(:) = tAB(:)/norm2(tAB)
+    !
+    ! Normal vector
+    nAB(:) = CROSS_PRODUCT(xA,xB)
+    nAB(:) = nAB(:)/norm2(nAB)
+    !
+    u(:) = ( -(1.d0-2.d0*nu)*CROSS_PRODUCT(b, tAB)* &
+         &  LOG( (rB + DOT_PRODUCT(xB,tAB))/(rA + DOT_PRODUCT(xA,tAB)) ) &
+         &  + DOT_PRODUCT(b,nAB)*CROSS_PRODUCT(xB/rB-xA/rA,nAB) ) &
+         &  /(8.d0*pi*(1.d0-nu))
+    !
+    END FUNCTION DisloSeg_displacement_iso
+!
+    !This code simply creates a planar vacancy cluster and does not apply the dislocation loop displacement field.
+    ! subroutine disloop
+    !     !This subroutine actually creates the dislocation loop.
+
+    !     real(kind=dp) :: neighbor_dis(loop_size), temp_box(6), dis
+    !     integer :: i, j, index(loop_size)
+
+    !     neighbor_dis(:) = HUGE(1.0_dp)
+    !     index(:) = 0
+
+    !     !First find the nearest atom to the centroid 
+    !     do i = 1, atom_num
+    !         if(norm2(r_atom(:,i) - centroid) < neighbor_dis(1)) then 
+    !             neighbor_dis(1) = norm2(r_atom(:,i) - centroid)
+    !             index(1) = i
+    !         end if
+    !     end do 
+
+    !     !Define a new box, this box tries to isolate all atoms on the plane of the atom 
+    !     !closest to the user defined centroid.
+    !     temp_box(:) = box_bd(:) 
+    !     temp_box(2*loop_normal) = r_atom(loop_normal,index(1)) + 10.0_dp**(-2.0_dp)
+    !     temp_box(2*loop_normal-1) = r_atom(loop_normal,index(1)) - 10.0_dp**(-2.0_dp)
+
+    !     !Now reset the list for the scanning algorithm
+    !     index(1) = 0
+    !     neighbor_dis(1) = HUGE(1.0_dp)
+
+    !     !Now scan over all atoms again and find the closest loop_size number of atoms to the initial atom 
+    !     !that reside on the same plane.
+
+    !     do i = 1, atom_num
+    !         !Check to see if it is on the same plane
+    !         if (in_block_bd(r_atom(:,i), temp_box)) then 
+    !             dis = norm2(r_atom(:,i) - centroid)
+    !             do j = 1, loop_size
+    !                 !Check to see if it is closer than other atoms
+    !                 if (dis < neighbor_dis(j)) then 
+    !                     !Move values in the neighbor array and add the new neighbor
+    !                     if(j < loop_size) then 
+    !                         neighbor_dis(j+1:loop_size) = neighbor_dis(j:loop_size-1)
+    !                         index(j+1:loop_size) = index(j:loop_size-1)
+    !                     end if
+    !                     neighbor_dis(j) = dis
+    !                     index(j) = i
+    !                     exit
+    !                 end if
+    !             end do 
+    !         end if
+    !     end do 
+
+    !     !Now delete the atoms
+    !     call delete_atoms(loop_size, index)
+
+    !     return
+    ! end subroutine disloop
+
+end module opt_disl

src/parameters.f90

@@ -2,9 +2,14 @@ module parameters
 
     implicit none
 
+    !Default precision
     integer, parameter :: dp= selected_real_kind(15,307)
+    !Parameters for floating point tolerance
     real(kind=dp), parameter :: lim_zero = epsilon(1.0_dp), &
                                 lim_large = huge(1.0_dp)
     logical, save :: lmpcac
     
+    !Numeric constants
+    real(kind=dp), parameter :: pi = 3.14159265358979323846_dp
+
 end module parameters

src/subroutines.f90

@@ -1,6 +1,7 @@
 module subroutines
     use parameters
     use functions
+    use box
     implicit none
 
     integer :: allostat, deallostat
@@ -145,4 +146,107 @@ module subroutines
     return
     end subroutine matrix_inverse
 
+    subroutine parse_ori_vec(ori_string, ori_vec)
+        !This subroutine parses a string to vector in the format [ijk]
+        character(len=8), intent(in) :: ori_string
+        real(kind=dp), dimension(3), intent(out) :: ori_vec
+
+        integer :: i, ori_pos, stat
+
+        ori_pos=2
+        do i = 1,3
+            if (ori_string(ori_pos:ori_pos) == '-') then 
+                ori_pos = ori_pos + 1
+                read(ori_string(ori_pos:ori_pos), *, iostat=stat) ori_vec(i)
+                if (stat>0) STOP "Error reading orientation value"
+                ori_vec(i) = -ori_vec(i)
+                ori_pos = ori_pos + 1
+            else
+                read(ori_string(ori_pos:ori_pos), *, iostat=stat) ori_vec(i)
+                if(stat>0) STOP "Error reading orientation value"
+                ori_pos=ori_pos + 1
+            end if
+        end do
+
+        return
+    end subroutine parse_ori_vec
+
+    subroutine parse_pos(i, pos_string, pos)
+        !This subroutine parses the pos command allowing for command which include inf
+        integer, intent(in) ::  i !The dimension of the position
+        character(len=100), intent(in) :: pos_string !The position string
+        real(kind=dp), intent(out) :: pos !The output parsed position value
+
+        integer :: iospara
+        if(trim(adjustl(pos_string)) == 'inf') then 
+            pos=box_bd(2*i)
+        else if(trim(adjustl(pos_string)) == '-inf') then
+            pos=box_bd(2*i-1)
+        else if ((index(pos_string,'-') > 0).and.(index(pos_string,'inf')>0)) then 
+            !Now extract the number we are reducing from infinity
+            read(pos_string(index(pos_string,'-')+1:), *, iostat=iospara) pos
+            pos = box_bd(2*i) - pos
+        else if ((index(pos_string,'+') > 0).and.(index(pos_string,'inf')>0)) then 
+            !Now extract the number we are reducing from infinity
+            read(pos_string(index(pos_string,'+')+1:), *, iostat=iospara) pos
+            pos = box_bd(2*i-1) + pos
+        else if ((index(pos_string,'*') > 0).and.(index(pos_string,'inf')>0)) then 
+            !Now extract the number we are reducing from infinity
+            read(pos_string(index(pos_string,'*')+1:), *, iostat=iospara) pos
+            pos = (box_bd(2*i)-box_bd(2*i-1))*pos
+        else
+            read(pos_string, *, iostat=iospara) pos
+        end if
+
+        if (iospara > 0) then 
+            print *, "Error reading position argument ", trim(adjustl(pos_string)), ". Please reformat and try again."
+        end if
+    end subroutine parse_pos
+
+    subroutine heapsort(a)
+     
+       integer, intent(in out) :: a(0:)
+       integer :: start, n, bottom
+       real :: temp
+     
+       n = size(a)
+       do start = (n - 2) / 2, 0, -1
+         call siftdown(a, start, n);
+       end do
+     
+       do bottom = n - 1, 1, -1
+         temp = a(0)
+         a(0) = a(bottom)
+         a(bottom) = temp;
+         call siftdown(a, 0, bottom)
+       end do
+     
+    end subroutine heapsort
+     
+    subroutine siftdown(a, start, bottom)
+     
+      integer, intent(in out) :: a(0:)
+      integer, intent(in) :: start, bottom
+      integer :: child, root
+      real :: temp
+     
+      root = start
+      do while(root*2 + 1 < bottom)
+        child = root * 2 + 1
+     
+        if (child + 1 < bottom) then
+          if (a(child) < a(child+1)) child = child + 1
+        end if
+     
+        if (a(root) < a(child)) then
+          temp = a(child)
+          a(child) = a (root)
+          a(root) = temp
+          root = child
+        else
+          return
+        end if  
+      end do      
+     
+    end subroutine siftdown
 end module subroutines