Added mode merge, adjusted how file reading works to accomodate model merge

src/call_mode.f90

@@ -4,6 +4,7 @@ subroutine call_mode(arg_num,mode)
 
     use mode_create
     use mode_convert
+    use mode_merge
     use parameters
 
     implicit none    
@@ -16,8 +17,10 @@ subroutine call_mode(arg_num,mode)
         call create
     case('--convert')
         call convert   
+    case('--merge')
+        call merge 
     case default
-        print *, "Mode ", mode, " currently not accepted. Please check documentation for ", &
+        print *, "Mode ", trim(adjustl(mode)), " currently not accepted. Please check documentation for ", &
                  "accepted modes and rerun."
 
         stop 3

src/io.f90

@@ -278,7 +278,7 @@ module io
         !This subroutine writes the cacmb formatted file which provides necessary information for building models
         character(len=100), intent(in) :: file
 
-        integer :: i, j, inod, ibasis
+        integer :: i, j, k, inod, ibasis
 
         !Open the .mb file for writing
         open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
@@ -288,10 +288,11 @@ module io
         write(11,*) box_bd(:)
         !Write the number of sub_boxes in the system
         write(11,*) sub_box_num
-        !For every subbox write the orientation and sub box boundary
+        !For every subbox write the orientation, sub box boundary, and sub_box_array_bds
         do i = 1, sub_box_num
             write(11,*) sub_box_ori(:,:,i)
             write(11,*) sub_box_bd(:,i)
+            write(11,*) ((sub_box_array_bd(j,k,i), j = 1, 2), k = 1, 2)
         end do
 
         !Write the number of atom types in the current model and all of their names
@@ -346,7 +347,7 @@ 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_infile), exist=file_exists)
             if (.not.file_exists) then 
-                print *, "The file ", filename, " does not exist. Please input a filename that exists"
+                print *, "The file ", trim(adjustl(filename)), " does not exist. Please input a filename that exists"
                 read(*,*) temp_infile
                 cycle
             end if
@@ -366,52 +367,70 @@ module io
 
     end subroutine get_in_file 
 
-    subroutine read_in
+    subroutine read_in(i, displace, temp_box_bd)
         !This subroutine loops over alll of the outfile types defined and calls the correct writing subroutine
 
-        integer :: i 
+        integer, intent(in) :: i 
+        real(kind=dp), dimension(3), intent(in) :: displace
+        real(kind=dp), dimension(6), intent(out) :: temp_box_bd
 
-        do i = 1, infilenum
         !Pull out the extension of the file and call the correct write subroutine
         select case(trim(adjustl(infiles(i)(scan(infiles(i),'.',.true.)+1:))))
         case('mb')
-                call read_mb(infiles(i))
+            call read_mb(infiles(i), displace, temp_box_bd)
         case default
             print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
                      " is not accepted for writing. Please select from: mb and try again"
             stop 
 
         end select
-        end do 
+
     end subroutine read_in
 
-    subroutine read_mb(file)
+    subroutine read_mb(file, displace, temp_box_bd)
         !This subroutine reads in an mb file for operation
 
         character(len=100), intent(in) :: file
+        real(kind=dp), dimension(3), intent(in) :: displace
+        real(kind = dp), dimension(6), intent(out) :: temp_box_bd
 
         integer :: i, j, k, n, inod, ibasis, type, size, in_atoms, in_eles
         character(len=100) :: etype
-        real(kind=dp) :: temp_box_bd(6), r(3)
+        real(kind=dp) ::  r(3), newdisplace(3)
         real(kind=dp), allocatable :: r_innode(:,:,:)
         !First open the file
         open(unit=11, file=trim(adjustl(file)), action='read',position='rewind')
 
         !Read in the box boundary and grow the current active box bd 
         read(11, *) temp_box_bd(:)
-        call grow_box(temp_box_bd)
+
+        do i = 1, 3
+            newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
+            temp_box_bd(2*i-1) = temp_box_bd(2*i-1) + newdisplace(i)
+            temp_box_bd(2*i) = temp_box_bd(2*i) + newdisplace(i)
+        end do 
         
         !Read in the number of sub_boxes and allocate the variables
         read(11, *) n
+
+        if (sub_box_num == 0) then 
             call alloc_sub_box(n)
+        else
+            call grow_sub_box(n)
+        end if
 
         !Read in subbox orientations and boundaries
-        do i = 1,  sub_box_num
+        do i = 1,  n
             !Read in orientation with column major ordering
-            read(11,*) ((sub_box_ori(j, k, i), j = 1, 3), k = 1, 3)
+            read(11,*) ((sub_box_ori(j, k, sub_box_num+i), j = 1, 3), k = 1, 3)
             !Read in subbox boundaries
-            read(11,*) sub_box_bd(:,i)
+            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)
+
         end do
+            sub_box_num = sub_box_num + n
 
         !Read in the number of atom types and all their names
         read(11, *) atom_types, (type_to_name(i), i = 1, atom_types)
@@ -424,14 +443,14 @@ module io
         read(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = 1, lattice_types)
 
         !Read number of elements and atoms and allocate arrays
-        read(11, *) in_atoms,in_eles
+        read(11, *) in_atoms, in_eles
         call grow_ele_arrays(in_eles, in_atoms)
         allocate(r_innode(3,max_basisnum, max_ng_node))
 
         !Read the atoms 
         do i = 1, in_atoms
             read(11,*) j, type, r(:)
-            call add_atom(type, r)
+            call add_atom(type, r+newdisplace)
         end do
 
         !Read the elements
@@ -440,11 +459,14 @@ module io
             do inod = 1, ng_node(type)
                 do ibasis =1, basisnum(type)
                     read(11,*) j, k, r_innode(:, ibasis, inod)
+                    r_innode(:,ibasis,inod) = r_innode(:, ibasis, inod) + newdisplace
                 end do
             end do
 
             call add_element(etype, size, type, r_innode)
         end do
 
+        !Close the file being read
+        close(11)
     end subroutine read_mb
 end module io

src/mode_merge.f90

@@ -0,0 +1,102 @@
+module mode_merge
+    !This module contains the code needed for merging several .mb files together
+
+    use parameters
+    use atoms   
+    use io
+    use subroutines
+    use elements
+
+    character(len=4) :: dim
+    integer :: in_num
+
+    public 
+    contains
+    subroutine merge
+        
+        integer :: i
+        real(kind=dp) :: displace(3), temp_box_bd(6)
+
+        !First we parse the merge command
+        call parse_command
+
+        !Now loop over all files and stack them 
+        do i = 1, in_num
+            displace(:) = 0.0_dp
+            if ((i==1).or.(trim(adjustl(dim)) == 'none')) then 
+                call read_in(i, displace, temp_box_bd)
+                call grow_box(temp_box_bd)
+            else
+                select case(trim(adjustl(dim)))
+                case('x')
+                    displace(1) = box_bd(2)
+                case('y')
+                    displace(2) = box_bd(4)
+                case('z')
+                    displace(3) = box_bd(6)
+                end select
+
+                call read_in(i, displace, temp_box_bd)
+                call grow_box(temp_box_bd)
+            end if 
+        end do
+
+        return
+    end subroutine merge
+
+    subroutine parse_command
+
+        character(len=100) :: textholder
+        integer :: i, stat, arglen, arg_pos
+
+        !Get dimension to concatenate along
+        call get_command_argument(2, dim, arglen)
+        if (arglen == 0) STOP "Missing dim in mode_merge command"
+        select case(trim(adjustl(dim)))
+        case('x','y','z','none')
+            continue
+        case default
+            print *, dim, " not accepted as a dimension in mode_merge"
+            stop 3
+        end select
+        !Get number of files to read in 
+        call get_command_argument(3, textholder, arglen)
+        if (arglen == 0) STOP "Number of files to read missing in mode_merge command"
+        read(textholder, *, iostat = stat) in_num
+        if (stat > 0) STOP "Error reading number of files in, must be integer"
+
+        !Now loop and pull out all files 
+        do i = 1, in_num
+            call get_command_argument(3+i, textholder, arglen)
+            if (arglen == 0) STOP "Fewer files to read in then specified"
+            !Make sure this file is readable
+            call get_in_file(textholder)
+        end do
+
+        !Set argpos accordingly
+        arg_pos = 3+in_num+1
+        !Now options loop
+        !Check for optional keywords
+        do while(.true.)
+            if(arg_pos > command_argument_count()) exit
+            !Pull out the next argument which should either be a keyword or an option
+            call get_command_argument(arg_pos, textholder)
+            textholder=adjustl(textholder)
+            arg_pos=arg_pos+1
+
+            !Choose what to based on what the option string is 
+            select case(trim(textholder))
+
+            case default
+                !Check to see if it is an option command, if so then mode_create must be finished
+                if(textholder(1:1) == '-') then 
+                    exit
+                !Check to see if a filename was passed
+                elseif(scan(textholder,'.',.true.) > 0) then 
+                    call get_out_file(textholder)
+                end if
+            end select
+        end do
+
+    end subroutine parse_command
+end module mode_merge