Merge branch 'development' into ft--random-position-selector

README.md

@@ -217,4 +217,12 @@ This command wraps atoms back into the simulation cell as though periodic bounda
 remesh esize 
 ```
 
-This command remeshes the atoms/elements within the group to the new element size `esize`. Currently only accepts an `esize` of 2 which refines it to full atomistics.
+This command remeshes the atoms/elements within the group to the new element size `esize`. Currently only accepts an `esize` of 2 which refines it to full atomistics.
+
+### Option overwrite 
+
+```
+-ow
+```
+
+If this option is passed then all files are automatically overwritten without asking the user.

src/call_option.f90

@@ -12,7 +12,11 @@ subroutine call_option(option, arg_pos)
         call dislocation(option, arg_pos)
     case('-group')
         call group(arg_pos)
+    case('-ow')
+        arg_pos = arg_pos + 1
+        continue
     case default
-        print *, 'Option ', trim(adjustl(option)), ' is not currently accepted.'
+        print *, 'Option ', trim(adjustl(option)), ' is not currently accepted. Skipping to next argument'
+        arg_pos = arg_pos + 1
     end select
 end subroutine call_option

src/io.f90

@@ -9,7 +9,7 @@ module io
 
     integer :: outfilenum = 0, infilenum = 0
     character(len=100) :: outfiles(10), infiles(10)
-    
+    logical :: force_overwrite
 
    public 
    contains
@@ -38,7 +38,7 @@ module io
 
             !Check to see if file exists, if it does then ask user if they would like to overwrite the file
             inquire(file=trim(temp_outfile), exist=file_exists)
-            if (file_exists) then 
+            if (file_exists.and.(.not.(force_overwrite))) then 
                 if (overwrite == 'r') print *, "File ", trim(temp_outfile), " already exists. Would you like to overwrite? (Y/N)"
                 read(*,*) overwrite
                 if((scan(overwrite, "n") > 0).or.(scan(overwrite, "N") > 0)) then 
@@ -627,6 +627,7 @@ module io
             temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
         end do 
         
+        call grow_box(temp_box_bd)
         !Read in the number of sub_boxes and allocate the variables
         read(11, *) n
 
@@ -707,6 +708,9 @@ module io
         call grow_ele_arrays(in_eles, in_atoms)
         allocate(r_innode(3,max_basisnum, max_ng_node))
 
+        print *, "Read in ", in_eles, " elements and ", in_atoms, " atoms from ", trim(adjustl(file))
+        print *, "New box dimensions are: ", box_bd
+
         !Read the atoms 
         do i = 1, in_atoms
             read(11,*) j, type, r(:)

src/main.f90

@@ -1,35 +1,60 @@
 program main
-    !**************************** CACmb  *******************************
+    !**************************** CACmb  ********************  
-    !*                 CAC model building toolkit                      *
+    !*                  CAC model building toolkit          *
-    !                        ____________                              *
+    !*                        ____________                  *
-    !                       /           /                              *    
+    !*                       /           /                  *    
-    !                      /           /                               *
+    !*                      /           /                   *
-    !                     /___________/                                *
+    !*                     /___________/                    *
-    !       _|_  _|_   _|____________                                  *
+    !*       _|_  _|_   _|____________                      *
-    !                   /           /                                  *
+    !*                   /           /                      *
-    !                  /           /                                   *
+    !*                  /           /                       *
-    !                 /___________/                                    *         
+    !*                 /___________/                        *         
-    !                                                                  *
+    !*                                                      *
-    !*******************************************************************
+    !********************************************************  
 
     use parameters
     use elements
     use io
     
-
+ 
     integer ::  i, end_mode_arg, arg_num, arg_pos
     character(len=100) ::  argument
 
+    !Print introduction text
+    print *, '*********************** CACmb  *********************'
+    print *, '*            CAC model building toolkit            *'
+    print *, '*                        _______                   *'
+    print *, '*                       /       /                  *'
+    print *, '*                      /       /                   *'
+    print *, '*                     /______ /                    *'
+    print *, '*       _|_  _|_   _|_______                       *'
+    print *, '*                   /       /                      *'
+    print *, '*                  /       /                       *'
+    print *, '*                 /______ /                        *'
+    print *, '*                                                  *'
+    print *, '****************************************************'
+
     !Call initialization functions
     call lattice_init
     call box_init
     call random_seed
-    
+    force_overwrite=.false.
+
     end_mode_arg = 0
     
     ! Command line parsing
     arg_num = command_argument_count()
 
+    !Check to see if overwrite flag is passed
+    do i = 1, arg_num
+        call get_command_argument(i,argument)
+        select case(trim(adjustl(argument)))
+
+        case('-ow')
+            force_overwrite = .true.
+            print *, "Overwrite flag passed, output files will be overwritten"
+        end select 
+    end do 
     !Determine if a mode is being used and what it is. The first argument has to be the mode
     !if a mode is being used
     call get_command_argument(1, argument)
@@ -74,4 +99,4 @@ program main
     end if
     call write_out
 
-end program main
+end program main

src/mode_create.f90

@@ -30,6 +30,8 @@ module mode_create
         integer :: i, ibasis, inod
         real(kind=dp), allocatable :: r_node_temp(:,:,:)
 
+        print *, '-----------------------Mode Create---------------------------'
+
         !Initialize default parameters
         orient = reshape((/ 1.0_dp, 0.0_dp, 0.0_dp, 0.0_dp, 1.0_dp, 0.0_dp, 0.0_dp, 0.0_dp, 1.0_dp /), shape(orient))
         cell_mat(:,:)=0.0_dp
@@ -91,6 +93,8 @@ module mode_create
             end do 
         else
 
+            print *, "Creating 1 element"
+
             call cell_init(lattice_parameter, esize, element_type, orient, cell_mat) 
             !If the user doesn't pass any build instructions than we just put the cell mat into the element_array 
             call alloc_ele_arrays(1,0)
@@ -110,6 +114,7 @@ module mode_create
         
         !If we passed the dup_flag or dim_flag then we have to convert the lattice points and add them to the atom/element arrays
         if(dup_flag.or.dim_flag) then 
+
             !Call the build function with the correct transformation matrix
             select case(trim(adjustl(element_type)))
             case('fcc')
@@ -123,6 +128,8 @@ module mode_create
             !Now that it is built multiply by the lattice parameter
             box_bd = box_bd*lattice_parameter
 
+            print *, "Using mode create, ", lat_ele_num, " elements are created and ", lat_atom_num*basisnum(1), " atoms are created."
+
             !Allocate variables 
             call alloc_ele_arrays(lat_ele_num, lat_atom_num*basisnum(1))
             if(lat_atom_num > 0) then 

src/mode_merge.f90

@@ -20,6 +20,8 @@ module mode_merge
         integer :: i
         real(kind=dp) :: displace(3), temp_box_bd(6)
 
+        print *, '-----------------------Mode Merge---------------------------'
+        
         wrap = .false.
         shift_flag = .false.
 
@@ -34,6 +36,7 @@ module mode_merge
             !The new starts variable dictate where in the atom and element array each new 
             !file starts. This is used for additional options that can be applied to solely 
             !these new atoms/elements that are read in.
+
             new_starts(1) = atom_num + 1
             new_starts(2) = ele_num + 1
 
@@ -136,6 +139,8 @@ module mode_merge
         !Calculate the current shift which is the filenum-1 multiplied by the user specified shift
         current_shift = (filenum-1)*shift_vec
 
+        print *, "Atoms/elements from file ", trim(adjustl(infiles(filenum))), " are shifted by ", current_shift
+
         !First shift all the atoms
         do i = array_start(1), atom_num
             r_atom(:,i) = r_atom(:,i) + current_shift

src/opt_disl.f90

@@ -23,12 +23,12 @@ module opt_disl
     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 
 
+        print *, '--------------------Option Dislocation-----------------------'
 
         select case(trim(adjustl(option)))
         case('-dislgen')
@@ -97,6 +97,8 @@ module opt_disl
         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)
 
+        print *, "Dislocation with centroid ", centroid, " is inserted"
+
         !Calculate screw and edge burgers vectors
         be = sin(char_angle*pi/180.0_dp)*b
         bs = cos(char_angle*pi/180.0_dp)*b
@@ -254,6 +256,9 @@ module opt_disl
         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
 
+
+        print *, "Dislocation loop with centroid ", centroid, " is inserted"
+
         if(allocated(xLoop)) deallocate(xLoop)
 
         !Define new directions

src/opt_group.f90

@@ -22,6 +22,8 @@ module opt_group
         !Main calling function for the group option
         integer, intent(inout) :: arg_pos
 
+        print *, '-----------------------Option Group-------------------------'
+
         group_ele_num = 0
         group_atom_num = 0
         remesh_size=0
@@ -117,6 +119,9 @@ module opt_group
 
         select case(trim(adjustl(shape)))
         case('block')
+
+            print *, "Group has block shape with boundaries: ", block_bd
+
             !Allocate variables to arbitrary size
             allocate(element_index(1024), atom_index(1024))
             !Check the type to see whether we need to find the elements within the group
@@ -162,6 +167,8 @@ module opt_group
                 end do
             end select
         end select 
+
+        print *, 'Group contains ', group_ele_num, " elements and ", group_atom_num, " atoms."
     end subroutine get_group 
 
     subroutine displace_group
@@ -169,6 +176,8 @@ module opt_group
 
         integer :: i, inod, ibasis
 
+        print *, "Elements/atoms in group displaced by ", disp_vec
+
         !Displace atoms
         do i = 1, group_atom_num
             r_atom(:,atom_index(i)) = r_atom(:,atom_index(i)) + disp_vec
@@ -207,7 +216,7 @@ module opt_group
     subroutine remesh_group
         !This command is used to remesh the group to a desired element size
 
-        integer :: i, j, ie, type_interp(max_basisnum*max_esize**3), add_atom_num
+        integer :: i, j, ie, type_interp(max_basisnum*max_esize**3), add_atom_num, orig_atom_num
         real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3)
 
         !Refining to atoms and remeshing to elements are different processes so check which code we need to run
@@ -216,6 +225,7 @@ module opt_group
         !Refining to atoms
         case(2)
             if(group_ele_num > 0) then 
+                orig_atom_num = atom_num
                 !Estimate number of atoms we are adding, this doesn't have to be exact
                 add_atom_num = group_ele_num*basisnum(lat_ele(element_index(1)))*size_ele(element_index(1))**3
                 call grow_ele_arrays(0,add_atom_num)
@@ -236,6 +246,8 @@ module opt_group
                 !Once all atoms are added we delete all of the elements
                 call delete_elements(group_ele_num, element_index)
 
+                print *, group_ele_num, " elements of group are refined to ", atom_num -orig_atom_num, " atoms."
+
             end if                
         !Remeshing to elements, currently not available
         case default