Initial commit with file writing and create mode working for atoms

src/io.f90

@@ -0,0 +1,177 @@
+module io
+
+    use elements
+    use parameters
+    use atoms
+
+    implicit none
+
+    integer :: outfilenum = 0
+    character(len=100) :: outfiles(10)
+
+   public 
+   contains
+
+    subroutine get_out_file(filename)
+
+        implicit none
+
+        character(len=100), intent(in) :: filename
+        character(len=100) :: temp_outfile
+        character(len=1) :: overwrite
+        logical :: file_exists
+
+        !If no filename is provided then this function is called with none and prompts user input
+        if (filename=='none') then 
+            print *, "Please specify a filename or extension to output to:"
+            read(*,*) temp_outfile
+        else
+            temp_outfile = filename
+        end if
+
+        !Infinite loop which only exists if user provides valid filetype
+        overwrite = 'r'
+        do while(.true.)
+
+            !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 (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 
+                    print *, "Please specify a new filename with extension:"
+                    read(*,*) temp_outfile
+                else if((scan(overwrite, "y") > 0).or.(scan(overwrite, "Y") > 0)) then 
+                    continue
+                else
+                    print *, "Please pick either y or n"
+                    read(*,*) overwrite
+                end if
+
+            end if
+
+            if (scan(temp_outfile,'.',.true.) == 0) then 
+                print *, "No extension included on filename, please type a full filename that includes an extension."
+                read(*,*) temp_outfile
+                cycle
+            end if
+            select case(temp_outfile(scan(temp_outfile,'.',.true.)+1:))
+            case('xyz')
+                outfilenum=outfilenum+1
+                outfiles(outfilenum) =  temp_outfile
+                exit
+            case('lmp')
+                outfilenum=outfilenum+1
+                outfiles(outfilenum) = temp_outfile
+                exit
+
+            case default    
+                print *, "File type: ", trim(temp_outfile(scan(temp_outfile,'.',.true.):)), "not currently accepted. ", &
+                         "please input a filename with extension from following list: xyz."
+                read(*,*) temp_outfile
+
+            end select
+        end do
+
+    end subroutine get_out_file 
+
+
+    subroutine write_out
+        !This subroutine loops over alll of the outfile types defined and calls the correct writing subroutine
+
+        integer :: i 
+
+        do i = 1, outfilenum
+            !Pull out the extension of the file and call the correct write subroutine
+            select case(trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))))
+            case('xyz')
+                call write_xyz(outfiles(i))
+            case('lmp')
+                call write_lmp(outfiles(i))
+            case default
+                print *, "The extension ", trim(adjustl(outfiles(i)(scan(outfiles(i),'.',.true.)+1:))), &
+                         " is not accepted for writing. Please select from: xyz and try again"
+                stop 
+
+            end select
+        end do 
+    end subroutine write_out
+
+
+
+    subroutine write_xyz(file)
+        !This is the simplest visualization subroutine, it writes out all nodal positions and atom positions to an xyz file
+        character(len=100), intent(in) :: file 
+
+        integer :: node_num, i, inod, ibasis
+
+        open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
+
+        !Calculate total node number
+        node_num=0
+        do i = 1, ele_num
+            node_num = node_num + basisnum(lat_ele(i))*ng_node(lat_ele(i))
+        end do
+
+        !Write total number of atoms + elements
+        write(11, '(i16)') node_num+atom_num
+         
+        !Write comment line
+        write(11, '(a)') "#Node + atom file created using cacmb"
+
+        !Write nodal positions
+        do i = 1, ele_num
+            do inod = 1, ng_node(lat_ele(i))
+                do ibasis = 1, basisnum(lat_ele(i))
+                        write(11, '(a, 3f23.15)') basis_type(ibasis,lat_ele(i)), r_node(:,ibasis,inod,i)
+                end do 
+            end do 
+        end do 
+
+        !Write atom positions
+        do i = 1, atom_num
+            write(11, '(a, 3f23.15)') type_atom(i), r_atom(:,i) 
+        end do
+
+        !Finish writing 
+        close(11)
+    end subroutine write_xyz
+
+    subroutine write_lmp(file)
+
+        integer :: write_num, i
+        character(len=100), intent(in) :: file
+        !This subroutine writes out a .lmp style dump file
+
+        open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')
+
+        !Comment line
+        write(11, '(a)') '# lmp file made with cacmb'
+        write(11, '(a)')
+        !Calculate total atom number
+        write_num = atom_num
+        !Write total number of atoms + elements
+        write(11, '(i16, a)') write_num, ' atoms'
+        !Write number of atom types 
+        write(11, '(i16, a)') 1, ' atom types'
+
+        write(11,'(a)') ' '
+        !Write box bd
+        write(11, '(2f23.15, a)') box_bd(1:2), ' xlo xhi'
+        write(11, '(2f23.15, a)') box_bd(3:4), ' ylo yhi'
+        write(11, '(2f23.15, a)') box_bd(5:6), ' zlo zhi'
+
+        !Masses
+        write(11, '(a)') 'Masses'
+        write(11, '(a)') ' '
+        write(11, '(i16, f23.15)') 1, 63.546
+        write(11, '(a)') ' '
+
+        !Write atom positions
+        write(11, '(a)') 'Atoms'
+        write(11, '(a)') ' '
+        do i = 1, atom_num
+            write(11, '(2i16, 3f23.15)') i, 1, r_atom(:,i) 
+        end do
+    end subroutine write_lmp
+end module io