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(arg_pos)
        
        integer, intent(out) :: arg_pos 
        integer :: i
        real(kind=dp) :: displace(3), temp_box_bd(6)

        !First we parse the merge command
        call parse_command(arg_pos)

        !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(arg_pos)

        integer, intent(out) :: arg_pos

        character(len=100) :: textholder
        integer :: i, stat, arglen

        !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
                !If it isn't an available option to mode merge then we just exit
                exit 
            end select
        end do

    end subroutine parse_command
end module mode_merge