Notch group shape

README.md

@@ -205,7 +205,8 @@ This selects a group residing in a block with edges perpendicular to the simulat
 
 `additional keywords`- Represents the various transformations which can be performed on a group. These additional keywords are given below.
 
-*Wedge*
+*Wedge:*
+
 `-group nodes wedge dim1 dim2 bx by bz bw` 
 This selects a group which are within a wedge shape. The options are given as follows:
 `dim1` - The dimension containing the plane normal of the wedge base.
@@ -213,7 +214,17 @@ This selects a group which are within a wedge shape. The options are given as fo
 `bx by bz` - Centroid of the center of the base
 `bw` - Base width
 
-**Displace**
+*Notch:*
+
+`-group nodes notch dim1 dim2 bx by bz bw tr`
+This shape is similar to a wedge shape except instead of becoming atomically sharp, it finishes in a rounded tip with tip radius `tr`. Options are as follows.
+`dim1` - The dimension containing the plane normal of the wedge base.
+`dim2` - The thickness dimension. Wedge groups are currently required to span the entire cell thickness in one dimensions which is normal to the triangular face. This through thickness dimension is dim2.
+`bx by bz` - Centroid of the center of the base
+`bw` - Base width
+`tr` - Tip radius
+
+**Displace:**
 
 ```
 displace x y z 

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 -heap-arrays
+#FFLAGS=-mcmodel=large -g -O0 -stand f08 -fpe0 -traceback -check bounds,uninit -warn all -implicitnone -no-wrap-margin -heap-arrays
-#FFLAGS=-mcmodel=large -Ofast -no-wrap-margin -heap-arrays
+FFLAGS=-mcmodel=large -Ofast -no-wrap-margin -heap-arrays
 MODES=mode_create.o mode_merge.o mode_convert.o
 OPTIONS=opt_disl.o opt_group.o opt_orient.o opt_delete.o 
-OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o  $(MODES) $(OPTIONS) call_option.o
+OBJECTS=main.o elements.o io.o subroutines.o functions.o atoms.o call_mode.o box.o  $(MODES) $(OPTIONS) call_option.o sorts.o
 
 .SUFFIXES:
 .SUFFIXES: .c .f .f90 .F90 .o
@@ -38,6 +38,7 @@ atoms.o subroutines.o testfuncs.o box.o : functions.o
 main.o io.o $(MODES) $(OPTIONS) : elements.o 
 call_mode.o : $(MODES)
 call_option.o : $(OPTIONS)
+elements.o : sorts.o
 $(MODES) $(OPTIONS) subroutines.o io.o : atoms.o box.o
 $(MODES) main.o : io.o
 testfuncs.o elements.o mode_create.o $(OPTIONS) $(MODES): subroutines.o

src/opt_group.f90

@@ -10,7 +10,7 @@ module opt_group
 
     integer :: group_ele_num, group_atom_num, remesh_size,normal, dim1, dim2
     character(len=15) :: type, shape !Type indicates what element type is selected and shape is the group shape
-    real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3) 
+    real(kind=dp) :: block_bd(6), centroid(3), vertices(3,3),disp_vec(3), tip_radius, bwidth
     logical :: displace, delete, max_remesh, refine
 
     integer, allocatable :: element_index(:), atom_index(:) 
@@ -56,7 +56,7 @@ module opt_group
 
         integer :: i, j, arglen, in_num
         character(len=100) :: textholder, type_spec
-        real(kind=dp) bwidth, wheight
+        real(kind=dp)  H
 
         !Parse type and shape command
         arg_pos = arg_pos + 1
@@ -131,6 +131,65 @@ module opt_group
                 end if
             end do 
 
+
+        case('notch')
+            arg_pos  = arg_pos + 1
+            call get_command_argument(arg_pos, textholder, arglen)
+            if (arglen==0) STOP "Missing normal dim in group notch command"
+            read(textholder,*) dim1
+            
+            arg_pos  = arg_pos + 1
+            call get_command_argument(arg_pos, textholder, arglen)
+            if (arglen==0) STOP "Missing normal dim in group notch command"
+            read(textholder,*) dim2
+
+            do i = 1, 3
+                arg_pos = arg_pos + 1
+                call get_command_argument(arg_pos, textholder, arglen)
+                if (arglen==0) STOP "Missing centroid in group notch 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 base width in group notch command"
+            read(textholder,*)  bwidth
+
+            arg_pos  = arg_pos + 1
+            call get_command_argument(arg_pos, textholder, arglen)
+            if (arglen==0) STOP "Missing tip radius in group notch command"
+            read(textholder,*)  tip_radius
+
+            !Calculate the vertex positions
+            vertices(:,1) = centroid
+            vertices(dim2,1) = 0.0_dp
+            do i = 1, 3
+                if (i == dim1) then 
+                    if (bwidth > 0) then 
+                        vertices(i,2) = box_bd(2*i)
+                        vertices(i,3) = box_bd(2*i)
+                        H= (box_bd(2*i) - centroid(i)) !Calculate the height of the wedge
+                    else if (bwidth < 0) then
+                        vertices(i,2) = box_bd(2*i-1)
+                        vertices(i,3) = box_bd(2*i-1)
+                        H = (centroid(i) - box_bd(2*i-1))
+                    else
+                        print *, "bwidth cannot be 0 in wedge shaped group"
+                        stop 3
+                    end if
+                else if (i == dim2) then 
+                    vertices(i,2) = 0.0_dp
+                    vertices(i,3) = 0.0_dp
+                else 
+                    vertices(i,2) = centroid(i) + 0.5_dp*bwidth
+                    vertices(i,3) = centroid(i) - 0.5_dp*bwidth
+                end if
+            end do 
+             
+            !Now update the centroid so that the desire tip diameter matches the wedge with
+            if (bwidth > 0) then 
+                centroid(dim1) = centroid(dim1) + 2*tip_radius*(H)/bwidth
+            end if
         !Read the ID type shape for group 
         case('id')
             arg_pos = arg_pos + 1
@@ -285,15 +344,15 @@ module opt_group
     subroutine get_group
         !This subroutine finds all elements and/or atoms within the group boundaries
         !specified by the user.
-        integer :: i, inod, ibasis
+        integer :: i, j, inod, ibasis
         integer, allocatable :: resize_array(:) 
         real(kind=dp) :: r_center(3)
 
         select case(trim(adjustl(shape)))
         case('block')
             print *, "Group has block shape with boundaries: ", block_bd
-        case ('crack')
+        case ('wedge')
-            print *, "Group has crack shape with dim1", dim1, "and dim2", dim2, "and vertices ", vertices
+            print *, "Group has wedge shape with dim1", dim1, "and dim2", dim2, "and vertices ", vertices
         case('id')
             print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms."
             return
@@ -343,6 +402,15 @@ module opt_group
                 end if
             end do
         end select
+        
+        j = 0
+        do i = 1, group_atom_num
+            if (atom_index(i) == 23318348) then
+                j = j + 1
+            end if
+        end do  
+
+        if (j > 1) stop "Code broken"
 
         print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms."
     end subroutine get_group 
@@ -691,12 +759,29 @@ module opt_group
     function in_group(r)
         !This subroutine determines if a point is within the group boundaries
         real(kind=dp), intent(in) :: r(3)
+        real(kind=dp) :: r_notch
+
+        integer :: dim3, i
         logical :: in_group
         select case(trim(adjustl(shape)))
         case('block')
             in_group=in_block_bd(r,block_bd)
         case('wedge')
             in_group = in_wedge_bd(r,vertices)
-        end select 
+        case('notch')
+            do i = 1, 3
+                if (.not.((dim1==i).or.(dim2==i))) dim3 = i
+            end do 
+
+            in_group = in_wedge_bd(r,vertices)
+            !Do a check to make sure the wedge isn't used if it should be the tip radius
+            if (bwidth>0) then 
+                if (r(dim1) < centroid(dim1)) in_group = .false.
+            end if
+
+            r_notch = sqrt((r(dim1) - centroid(dim1))**2 + (r(dim3)-centroid(dim3))**2)
+            in_group = in_group.or.(r_notch < tip_radius)
+
+                   end select 
     end function in_group
 end module opt_group