module io

    use elements
    use parameters
    use atoms
    use box

    implicit none

    integer :: outfilenum = 0, infilenum = 0
    character(len=100) :: outfiles(100), infiles(100)
    logical :: force_overwrite

   public 
   contains

    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Subroutines for writing out data files !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    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.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 
                    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', 'lmp', 'vtk', 'mb', 'restart')
                outfilenum=outfilenum+1
                outfiles(outfilenum) =  temp_outfile
                exit
            case('cac')
                lmpcac = .true. 
                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, lmp, vtk, cac."
                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 

        !Find max esize which will be needed later
        call set_max_esize

        do i = 1, outfilenum
        
            print *, "Writing data out to ", trim(adjustl(outfiles(i)))

            !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('vtk')
                call write_vtk(outfiles(i))
            case('mb')
                call write_mb(outfiles(i))
            case('restart')
                call write_pycac(outfiles(i))
            case('cac')
                call write_lmpcac(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 :: i, inod, ibasis

        open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')

        !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, '(i16, 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, '(i16, 3f23.15)') type_atom(i), r_atom(:,i) 
        end do

        !Finish writing 
        close(11)
    end subroutine write_xyz

    subroutine write_lmp(file)
        !This subroutine writes out a .lmp style dump file
        character(len=100), intent(in) :: file
        integer :: write_num, i, iatom, type_interp(max_basisnum*max_esize**3), interp_num
        real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3), mass

        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
        do i = 1,ele_num
            if(type_ele(i) == 'fcc') write_num = write_num + size_ele(i)**3
        end do
        !Write total number of atoms + elements
        write(11, '(i16, a)') write_num, ' atoms'
        !Write number of atom types 
        write(11, '(i16, a)') atom_types, ' 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)') ' '
        do i =1, atom_types
            call atommass(type_to_name(i),mass)
            write(11, '(i16, f23.15)') i, mass
        end do
        write(11, '(a)') ' '

        !Write atom positions
        write(11, '(a)') 'Atoms'
        write(11, '(a)') ' '
        do i = 1, atom_num
            write(11, '(2i16, 3f23.15)') i, type_atom(i), r_atom(:,i) 
        end do

        !Write refined element atomic positions
        interp_num = 0
        do i = 1, ele_num
            call interpolate_atoms(type_ele(i), size_ele(i), lat_ele(i), r_node(:,:,:,i), type_interp, r_interp)
            select case(trim(adjustl(type_ele(i))))
            case('fcc')
                do iatom = 1, basisnum(lat_ele(i))*size_ele(i)**3
                    interp_num = interp_num+1
                    call apply_periodic(r_interp(:,iatom))
                    write(11, '(2i16, 3f23.15)') atom_num+interp_num, type_interp(iatom), r_interp(:,iatom)
                end do
            end select
        end do
    end subroutine write_lmp

    subroutine write_lmpcac(file)
        !This subroutine writes out a .lmp style dump file
        character(len=100), intent(in) :: file
        integer :: write_num, i, inod, ibasis
        real(kind=dp) :: mass, fcc_adjust(3,8), local_adjust(3,8), rout(3)

1       format(i16, '   Eight_Node', 4i16)
2       format(i16, '   Atom', 4i16)
3       format(3i16,3f23.15)

        open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')

        !Comment line
        write(11, '(a)') '# CAC input file made with cacmb'
        write(11, '(a)')
        !Calculate total atom number
        write_num = atom_num + ele_num

        !Write total number of atoms + elements
        write(11, '(i16, a)') write_num, ' cac elements'
        !Write number of atom types 
        write(11, '(i16, a)') atom_types, ' 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)') ' '
        do i =1, atom_types
            call atommass(type_to_name(i),mass)
            write(11, '(i16, f23.15, 2a)') i, mass, ' # ', type_to_name(i)
        end do
        write(11, '(a)') ' '

        write(11, '(a)') 'CAC Elements'
        write(11, '(a)') ' '

        !Set up the nodal adjustment variables for all the different element types. This adjusts the node centers
        !from the center of the unit cell (as formulated in this code) to the corners of the unit cells
         do inod = 1, 8
            do i = 1,3
                if(is_equal(cubic_cell(i, inod),0.0_dp)) then 
                    fcc_adjust(i,inod) = -0.5_dp
                else 
                    fcc_adjust(i, inod) = 0.5_dp
                end if
            end do
        end do
        fcc_adjust = matmul(fcc_mat, fcc_adjust)

        !Write element nodal positions
        do i = 1, ele_num
            select case(trim(adjustl(type_ele(i))))
            case('fcc')
                !Now orient the current adjustment vector to the correct orientation
                local_adjust = matmul(sub_box_ori(:,:,sbox_ele(i)), fcc_adjust) * lapa(lat_ele(i))
                !The first entry is the element specifier 
                write(11,1) i, basisnum(lat_ele(i)), size_ele(i), size_ele(i), size_ele(i)
                do ibasis = 1, basisnum(lat_ele(i))
                    do inod = 1, 8
                        !Nodal information for every node
                        rout = r_node(:,ibasis,inod,i) + local_adjust(:,inod)
                        write(11,3) inod, ibasis, basis_type(ibasis,lat_ele(i)), rout
                    end do
                end do
            end select
        end do

        do i = 1, atom_num
            !Element specifier dictating that it is an atom
            write(11,2) ele_num+i, 1, 1, 1, 1
            !Write the atomic information
            write(11,3) 1, 1, type_atom(i), r_atom(:,i)
        end do
    end subroutine write_lmpcac

    subroutine write_vtk(file)
        !This subroutine writes out a vtk style dump file
        integer :: i, j, inod, ibasis
        character(len=100), intent(in) :: file

1       format('# vtk DataFile Version 4.0.1', / &
              'CAC output -- cg', / &
              'ASCII')
11      format('# vtk DataFile Version 4.0.1', / &
               'CACmb output -- atoms', / &
               'ASCII')
2       format('DATASET UNSTRUCTURED_GRID')
3       format('POINTS', i16, ' float')
4       format(/'CELLS', 2i16)
5       format(/'CELL_TYPES', i16)
12      format(/'CELL_DATA', i16)
16      format(/'POINT_DATA', i16)
17      format('SCALARS weight float', / &
               'LOOKUP_TABLE default')
18      format('SCALARS atom_type float', / &
               'LOOKUP_TABLE default')

20      format('SCALARS lattice_type float', /&
               'LOOKUP_TABLE default')

21      format('SCALARS esize float', /&
               'LOOKUP_TABLE default')

        !First we write the vtk file containing the atoms
        open(unit=11, file='atoms_'//trim(adjustl(file)), action='write', status='replace',position='rewind')

        write(11, 11)
        write(11, 2)
        write(11, 3) atom_num
        do i = 1, atom_num
            write(11, '(3f23.15)') r_atom(:,i)
        end do 
        write(11,4) atom_num, atom_num*2
        do i = 1, atom_num
            write(11, '(2i16)') 1, i-1
        end do
        write(11, 5) atom_num
        do i = 1, atom_num
            write(11, '(i16)') 1 
        end do
        write(11, 16) atom_num
        write(11, 18)
        do i = 1, atom_num
            write(11, '(i16)') type_atom(i)
        end do
        close(11)

        open(unit=11, file='cg_'//trim(adjustl(file)), action='write', status='replace',position='rewind')
        write(11,1)
        write(11,2)
        write(11,3) node_num
        do i = 1, ele_num
            do inod=1, ng_node(lat_ele(i))  
                do ibasis = 1, basisnum(lat_ele(i))
                    write(11, '(3f23.15)') sum(r_node(:,:,inod,i),2)/basisnum(lat_ele(i))
                end do 
            end do 
        end do
        write(11, 4) ele_num, ele_num + node_num
        do i =1, ele_num
            write(11, '(9i16)') ng_node(lat_ele(i)), (j, j = (i-1)*ng_node(lat_ele(i)), i*ng_node(lat_ele(i))-1)
        end do
        write(11,5) ele_num
        do i = 1, ele_num
            if(trim(adjustl(type_ele(i))) == 'fcc') write(11, '(i16)') 12
        end do
        write(11,12) ele_num
        write(11,20)
        do i = 1, ele_num
            write(11, '(i16)') lat_ele(i)
        end do
        write(11,21)
        do i = 1, ele_num
            write(11, '(i16)') size_ele(i)
        end do
        close(11)
    end subroutine

    subroutine write_pycac(file)
        !This subroutine writes restart files meant to be used with the McDowell Group CAC code.
        !NOTE: This code doesn't work for arbitrary number of basis atoms per node. It assumes that the 
        !each element has only 1 atom type at the node.
        character(len=100), intent(in) :: file
        integer :: interp_max, i, j, inod, ibasis, ip, unique_index(50), unique_size(50), unique_num, &
                   etype
        real(kind=dp) :: box_vec(3)

1  format('time' / i16, f23.15)
2  format('number of elements' / i16)
3  format('number of nodes' / i16)
4  format('element types' / i16)
5  format('number of atoms' / i16)
6  format('number of grains' / i16)
7  format('boundary ' / 3a1)
8  format('box bound' / 6f23.15)
9  format('box length' / 3f23.15)
10 format('box matrix')
11 format(3f23.15)
12 format('coarse-grained domain')
13 format('ie ele_type grain_ele lat_type_ele'/ 'ip ibasis x y z')
14 format('atomistic domain' / 'ia grain_atom type_atom x y z')
15 format('maximum lattice periodicity length' / 3f23.15)
16 format('Number of lattice types and atom types '/ 2i16)
17 format('lattice type IDs')
18 format('lattice types for grains')
19 format('max nodes per element' / i16)
20 format('max interpo per element' / i16)
21 format('atom types to elements')

        open(unit=11, file=trim(adjustl(file)), action='write', status='replace',position='rewind')

        write(11,1) timestep, total_time
        write(11,2) ele_num

        !Below writes the header information for the restart file


            !First figure out all of the unique element types
            unique_num = 0
            unique_index(:) = 0
            eleloop:do i = 1, ele_num
                do j =1 , unique_num
                    if ( ( size_ele(i) == size_ele( unique_index(j) ) ).and. &
                        ( lat_ele(i) == lat_ele(unique_index(j)) ) ) then
                        cycle eleloop
                    end if
                end do
                unique_num = unique_num + 1
                unique_index(unique_num) = i
                unique_size(unique_num) = size_ele(i)
            end do eleloop

        !Calculate the max number of atoms per element
        select case(max_ng_node)
        case(8)
            interp_max = (max_esize)**3
        case default
            interp_max = 0
        end select
        write(11,20) interp_max
        write(11,3) node_num
        write(11,19) max_ng_node
        write(11,4) unique_num
        write(11,5) atom_num
        write(11,6) 1 !Grain_num is ignored 
        write(11,16) lattice_types, atom_types
        write(11,21)
        do i = 1, atom_types
            write(11,*) i, type_to_name(i)
        end do
        write(11,7) box_bc(1:1), box_bc(2:2), box_bc(3:3)
        write(11,18)
        write(11,'(2i16)') 1,1 !This is another throwaway line that is meaningless
        write(11,17)
        !This may have to be updated in the future but currently the only 8 node element is fcc
        do i = 1, lattice_types
            select case(ng_node(i))
            case(8)
                write(11, *) i, 'fcc'
            end select
        end do
        write(11,15) 1.0_dp, 1.0_dp, 1.0_dp !Another throwaway line that isn't needed
        write(11,8) box_bd
        write(11,9) box_bd(2)-box_bd(1), box_bd(4) - box_bd(3), box_bd(6)-box_bd(5)
        write(11,10)
        !Current boxes are limited to being rectangular 
        do i = 1,3 
            box_vec(:) = 0.0_dp
            box_vec(i) = box_bd(2*i) - box_bd(2*i-1)
            write(11,11) box_vec
        end do
        !We write this as box_mat ori and box_mat current
        do i = 1,3 
            box_vec(:) = 0.0_dp
            box_vec(i) = box_bd(2*i) - box_bd(2*i-1)
            write(11,11) box_vec
        end do

        !write the element information
        if(ele_num > 0) then
            write(11,12)
           
            do i = 1, unique_num
                write(11,'(3i16)') i, size_ele(unique_index(i))-1, basis_type(1,lat_ele(unique_index(i)))
            end do
            ip = 0
            write(11,13)
            do i = 1, ele_num
                !Figure out the ele type
                do j = 1, unique_num
                    if ( unique_size(j) == size_ele(i)) then
                        etype = j
                        exit
                    endif
                end do
                write(11, '(4i16)') i, etype, 1, basis_type(1,lat_ele(i))
                do inod = 1, ng_node(lat_ele(i))
                    do ibasis = 1, basisnum(lat_ele(i))
                        ip = ip + 1
                        write(11, '(2i16, 3f23.15)') ip, ibasis, r_node(:, ibasis, inod, i)
                    end do
                end do
            end do 
        end if

        !Now write the atomic information
        if(atom_num /= 0) then 
            write(11,14)
            do i = 1, atom_num
                write(11, '(3i16, 3f23.15)') i, 1, type_atom(i), r_atom(:,i)
            end do
        end if

        close(11)
    end subroutine write_pycac

    subroutine write_mb(file)

        !This subroutine writes the cacmb formatted file which provides necessary information for building models
        character(len=100), intent(in) :: file

        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')

        !First write the box boundary information
        !Write the global box boundaries
        write(11,*) box_bd(:)
        !Write the number of sub_boxes in the system
        write(11,*) sub_box_num
        !For every subbox write the orientation, sub box boundar
        do i = 1, sub_box_num
            write(11,*) sub_box_ori(:,:,i)
            write(11,*) sub_box_bd(:,i)
        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 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
        write(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = 1, lattice_types)
        !Now for every lattice type write the lattice parameters
        write(11,*) (lapa(i), i = 1, lattice_types)

        !Now write the numbers of elements and atoms
        write(11,*) atom_num, ele_num

        !Write out atoms first
        do i = 1, atom_num
            write(11,*) i, type_atom(i), sbox_atom(i), r_atom(:,i)
        end do

        !Write out the elements, this is written in two stages, one line for the element and then 1 line for 
        !every basis at every node
        do i = 1, ele_num
            write(11, *) i, lat_ele(i), size_ele(i), sbox_ele(i), type_ele(i)
            do inod = 1, ng_node(lat_ele(i))
                do ibasis =1, basisnum(lat_ele(i))
                    write(11,*) inod, ibasis, r_node(:, ibasis, inod, i)
                end do
            end do
        end do

        close(11)
    end subroutine write_mb


    !!!!!!!!!!!!! Below are subroutines for reading files !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

    subroutine get_in_file(filename)

        implicit none

        character(len=100), intent(in) :: filename
        character(len=100) :: temp_infile
        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_infile
        else
            temp_infile = filename
        end if

        !Infinite loop which only exists if user provides valid filetype
        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_infile), exist=file_exists)
            if (.not.file_exists) then 
                print *, "The file ", trim(adjustl(filename)), " does not exist. Please input a filename that exists"
                read(*,*) temp_infile
                cycle
            end if

            select case(temp_infile(scan(temp_infile,'.',.true.)+1:))
            case('restart', 'mb')
                infilenum=infilenum+1
                infiles(infilenum) =  temp_infile
                exit
            case default    
                print *, "File type: ", trim(temp_infile(scan(temp_infile,'.',.true.):)), "not currently accepted. ", &
                         "please input a filename with extension from following list: mb, restart."
                read(*,*) temp_infile

            end select
        end do

    end subroutine get_in_file 

    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, intent(in) :: i 
        real(kind=dp), dimension(3), intent(in) :: displace
        real(kind=dp), dimension(6), intent(out) :: temp_box_bd

        !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), displace, temp_box_bd)
        case('restart')
            call read_pycac(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 subroutine read_in

    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, l, n, inod, ibasis, type, size, in_atoms, in_eles, new_atom_types, &
                   new_type_to_type(10), new_lattice_types, sbox, new_lattice_map(10)
        character(len=100) :: etype
        real(kind=dp) ::  r(3), newdisplace(3)
        real(kind=dp), allocatable :: r_innode(:,:,:)
        character(len = 2) :: new_type_to_name(10)
        !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(:)

        do i = 1, 3
            if (abs(displace(i)) > lim_zero) then 
                newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
            else
                newdisplace(i)=displace(i)
            end if 
            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 
       
        call grow_box(temp_box_bd)
        !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,  n
            !Read in orientation with column major ordering
            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(:,sub_box_num+i)

            do j = 1, 3
                sub_box_bd(2*j-1,sub_box_num+i) = sub_box_bd(2*j-1, sub_box_num+i) + displace(j)
                sub_box_bd(2*j,sub_box_num+i) = sub_box_bd(2*j, sub_box_num+i) + displace(j)
            end do
        end do

        !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)
        !Now fit these into the global list of atom types, after this new_type_to_type is the actual global 
        !type of the atoms within this file
        do i = 1, new_atom_types
            call add_atom_type(new_type_to_name(i), new_type_to_type(i))
        end do
        !Read the number of lattice types, basisnum, and number of nodes for each lattice type
        read(11,*) new_lattice_types, (basisnum(i), i = lattice_types+1, lattice_types+new_lattice_types), &
                   (ng_node(i), i = lattice_types+1, lattice_types+new_lattice_types)
        !Define max_ng_node and max_basis_num
        max_basisnum = maxval(basisnum)
        max_ng_node = maxval(ng_node)
        !Read the basis atom types for every lattice
        read(11,*) ((basis_type(i,j), i = 1, basisnum(j)), j = lattice_types+1, lattice_types+new_lattice_types)
        !Convert the basis_atom types
        do j  = lattice_types+1, lattice_types+new_lattice_types
            do i = 1, basisnum(j)
                basis_type(i,j) = new_type_to_type(basis_type(i,j))
            end do 
        end do
        !Read the lattice parameters for every lattice type
        read(11,*) (lapa(i), i = lattice_types+1, lattice_types+new_lattice_types)

        !Now we loop over all new lattice types and check to see if they are exactly the same as any old lattice types
        !If they are then we map the new type to the old type.
        k = lattice_types + 1
        new_lattice_map(:) = 0
        new_loop:do i = 1, new_lattice_types
            old_loop:do j = 1, lattice_types
                !First check all the lattice level variables
                if ((basisnum(lattice_types + i) == basisnum(j)).and. &
                    (ng_node(lattice_types + i) == ng_node(j))) then 
                    !Now check the basis  level variables
                    do ibasis =1, basisnum(i)
                        if(basis_type(ibasis,lattice_types+i) /= basis_type(ibasis,j)) then 
                            cycle old_loop
                        end if
                    end do
                    new_lattice_map(i) = j
                    cycle new_loop
                end if
            end do old_loop
            new_lattice_map(i) = k 
            k = k+1
        end do new_loop

        !Read number of elements and atoms and allocate arrays
        read(11, *) in_atoms, in_eles
        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, sbox, r(:)
            r = r+newdisplace
            call add_atom(new_type_to_type(type), sbox+sub_box_num, r)
        end do

        !Read the elements
        do i = 1, in_eles
            read(11, *) l, type, size, sbox, etype
            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, new_lattice_map(type), sbox+sub_box_num, r_innode)
        end do

        !Close the file being read
        close(11)

        !Only increment the lattice types if there are elements, if there are no elements then we 
        !just overwrite the arrays
        lattice_types =  maxval(new_lattice_map)


        sub_box_num = sub_box_num + n
    
        call set_max_esize
    end subroutine read_mb

    subroutine read_pycac(file, displace, temp_box_bd)
        !Add subroutine for reading in restart files from PyCAC. This code currently only 
        !works for 8 node elements.
        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, inod, ibasis, j, k, in_eles, in_atoms, ele_types, in_lat_num, in_atom_types, &
                   atom_type_map(10), etype_map(10), etype, lat_type, new_lattice_map(10), &
                   atom_type
        real(kind=dp) :: newdisplace(3), r_in(3,1,8), r_in_atom(3), new_displace(3)
        character(len=100) :: textholder, in_lattype_map(10) 
        character(len=2) :: atomic_element
        !First open the file
        open(unit=11, file=trim(adjustl(file)), action='read',position='rewind') 

        !Disregard unneeded information
        do i = 1, 3
            read(11,*) textholder
        end do 

        !Read element number
        read(11,*) in_eles 

        !Discard info and read ng_max_node
        do i = 1, 5 
            read(11,*) textholder
        end do 
        read(11,*) max_ng_node

        !Read element types (only needed inside this subroutine)
        read(11,*) textholder
        read(11,*) ele_types

        !Read in atom num
        read(11,*) textholder
        read(11,*) in_atoms

        !read in lattice_types and atom types
        do i = 1,3 
            read(11,*) textholder
        end do
        read(11,*) in_lat_num, in_atom_types


        !Read define atom_types by name
        read(11,*) textholder
        do i = 1, in_atom_types
            read(11,*) j, atomic_element
            call add_atom_type(atomic_element, atom_type_map(i))
        end do 

        !Read in the boundary
        read(11,*) textholder
        read(11,*) box_bc

        !Disregard useless info
        do i = 1, 3
            read(11,*) textholder
        end do 

        !Read in lat_type map
        do i = 1, in_lat_num
            read(11,*) j, in_lattype_map(i)
            ng_node(lattice_types+i) = 8 !Only cubic elements are currently supported in pyCAC
        end do 

        !Disregard useless info
        do i =1 , 3 
            read(11,*) textholder
        end do 

        !Read box boundaries and displace them if necessary 
        read(11,*) temp_box_bd(:)
        do i = 1, 3
            if (abs(displace(i)) > lim_zero) then 
                newdisplace(i) = displace(i) - temp_box_bd(2*i-1)
            else
                newdisplace(i)=displace(i)
            end if 
            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 

        call grow_box(temp_box_bd)

        !Allocate sub_box 
        if (sub_box_num == 0) then 
            call alloc_sub_box(1)
        else
            call grow_sub_box(1)
        end if

        !Because orientations and other needed sub_box information isn't really 
        !present within the restart file we just default a lot of it.
        sub_box_ori(:,:,sub_box_num+1) = identity_mat(3)
        sub_box_bd(:, sub_box_num+1) = temp_box_bd

        !Read in more useless info
        do i = 1, 10
            read(11,*) textholder
        end do  

        !Now read the ele_type to size and lat map
        do i = 1, ele_types
            read(11,*) j, etype_map(i)
            etype_map(i) = etype_map(i) + 1
        end do 


        !Now set up the lattice types. In this code it assumes that lattice_type 1 maps to 
        !atom type 1 because it only allows 1 atom per basis in pyCAC at the moment.
        do i = 1, in_lat_num
            basisnum(lattice_types+i) = 1
            basis_type(1,lattice_types+i) = atom_type_map(i)
        end do 

        !Figure out the lattice type maps in case we have repeated lattice_types
        k = lattice_types + 1
        new_lattice_map(:) = 0
        new_loop:do i = 1, in_lat_num
            old_loop:do j = 1, lattice_types
                !First check all the lattice level variables
                if ((basisnum(lattice_types+i) == basisnum(j)).and. &
                    (ng_node(lattice_types+i) == ng_node(j))) then 
                    !Now check the basis  level variables
                    do ibasis =1, basisnum(i)
                        if(basis_type(ibasis,lattice_types+i) /= basis_type(ibasis,j)) then 
                            cycle old_loop
                        end if
                    end do
                    new_lattice_map(i) = j
                    cycle new_loop
                end if
            end do old_loop
            new_lattice_map(i) = k 
            k = k+1
        end do new_loop

        !Read more useless data
        read(11,*) textholder

        !set max values and allocate variables 
        max_basisnum = maxval(basisnum)
        max_ng_node = maxval(ng_node)
        call grow_ele_arrays(in_eles, in_atoms)

        !Now start reading the elements 
        if(in_eles > 0) then
            read(11,*) textholder
            do i = 1, in_eles 
                read(11,*) j, etype, k, lat_type 
                do inod = 1, 8
                    read(11, *) j, k, r_in(:,1,inod)
                    r_in(:,1,inod) = r_in(:,1,inod) + newdisplace
                end do 
                call add_element(in_lattype_map(lat_type), etype_map(etype), new_lattice_map(lat_type), sub_box_num + 1, r_in)
            end do
        end if

        if(in_atoms > 0) then 

            if (in_eles > 0) then 
                !Read useless data 
                read(11,*)  textholder
                read(11,*) textholder
            end if

            do i = 1, in_atoms
                read(11,*) j, k, atom_type, r_in_atom(:)
                r_in_atom = r_in_atom + newdisplace
                call add_atom(atom_type_map(atom_type), sub_box_num + 1, r_in_atom)
            end do 
            !Close file
            close(11)

            lattice_types = maxval(new_lattice_map)

            sub_box_num = sub_box_num + 1

            call set_max_esize
        end if
    end subroutine read_pycac
end module io