module opt_slip_plane
    use parameters 
    use elements
    use functions 
    use subroutines

    implicit none

    integer :: sdim
    real(kind=dp) :: spos
    logical :: efill
    
    public 
    contains

    subroutine run_slip_plane(arg_pos)
        !Main calling function for the slip_plane option
        integer, intent(inout) :: arg_pos 

        integer :: ie, ia, slip_enum, old_atom_num, esize, new_ele_num, n, m, o, ele(3,8), nump_ele, inod, vlat(3), &
        rfill(3,max_basisnum, max_ng_node)
        
        integer, allocatable :: slip_eles(:), temp_int(:)
        real(kind=dp) :: r_interp(3, max_basisnum*max_esize**3)
        integer :: type_interp(max_basisnum*max_esize**3)
        logical :: lat_points(max_esize,max_esize, max_esize)
    

        print *, '---------------------Option Slip_Plane----------------------'

        !Initialize variables
        efill = .false.
        slip_enum = 0
        old_atom_num = atom_num

        !!Parse the argument
        call parse(arg_pos)


        !If we are running the efill code then we have to initiate some variables
        if(efill) then 
            new_ele_num = 0
        end if
        allocate(slip_eles(1024))
        !Now loop over all elements, find which ones intersect 
        do ie = 1, ele_num
            if( (spos < maxval(r_node(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie)),ie))).and. &
                (spos > minval(r_node(sdim,1:basisnum(lat_ele(ie),1:ng_node(lat_ele(ie)),ie)))) then 
                slip_enum = slip_enum + 1
                if (slip_enum > size(slip_eles)) then 
                    allocate(temp_int(size(slip_eles)+1024))
                    temp_int(1:size(slip_eles)) = slip_eles
                    temp_int(size(slip_eles)+1:)  = 0
                    call move_alloc(temp_int, slip_eles)
                end if
                slip_eles(slip_enum) = ie
                
                !If we aren't efilling then just refine the element
                if(.not.efill) then 
                    call interpolate_atoms(type_ele(ie), size_ele(ie), lat_ele(ie), r_node(:,:,:,ie), type_interp, r_interp)
                    do ia = 1, basisnum(lat_ele(ie)) * size_ele(ie)**3           
                        call apply_periodic(r_interp(:,ia))
                        call add_atom(0, type_interp(ia), sbox_ele(ie), r_interp(:,ia))
                    end do
                !If we are efilling then the code is slightly more complex
                else
                !First populate the lat points array 
                lat_points(1:size_ele(ie),1:size_ele(ie), 1:size_ele(ie)) = .true.

                !Now start trying to remesh the region, leaving the slip plane as a discontinuity
                esize = size_ele(ie) - 2
                nump_ele = size_ele(ie)**3
                do while(esize > min_efillsize
                    if(nump_ele < esize**3) then 
                        esize = esize - 2
                    else
                        ele = cubic_cell*(esize -1) 
                        do o = 1, size_ele(ie) - esize
                            do n = 1, size_ele(ie) - esize
                                do m = 1, size_ele(ie) - esize
                                    do inod = 1, ng_node(lat_ele(ie)
                                        vlat = ele(:,inod) + (/ m, n, o /)
                                        call get_interp_pos(vlat(1), vlat(2), vlat(3), ie, rfill(:,:,inod))
                                        
                                    end do
                                    !Check to see if the plane intersects this element if not then add it 
                                    if((spos < maxval(rfill(sdim,1:basisnum(lat_ele(ie)),1:ng_node(lat_ele(ie)),ie))).and. &
                                        (spos > minval(rfill(sdim,1:basisnum(lat_ele(ie),1:ng_node(lat_ele(ie)),ie)))) then 
                                        nump_ele = nump_ele - esize**3 

                                    end if
                                end do
                            end do
                        end do
                    end if
                end if
            end if
        end do 

        !Once we finish adding elements delete the old ones
        call delete_elements(slip_enum, slip_eles(1:slip_enum))

        !Output data
        if(.not.efill) then 
            print *, "We refine ", slip_enum, " elements into ", atom_num - old_atom_num , " atoms"
        end if

    end subroutine run_slip_plane 

    subroutine parse(arg_pos)
        !This subroutine parses the input arguments to the mode
        integer, intent(inout) :: arg_pos 

        integer :: arglen
        character(len = 100) :: textholder

        !First read the dimension
        arg_pos = arg_pos +1
        call get_command_argument(arg_pos,textholder, arglen) 
        if(arglen == 0) stop "Incorrect slip_plane command. Please check documentation for correct format"
        
        !Check to make sure that the dimension is correct
        select case(trim(adjustl(textholder))) 
        case('x','X')
            sdim = 1
        case('y','Y')
            sdim = 2
        case('z','Z')
            sdim = 3
        case default
            print *, "Error: dimension ", trim(adjustl(textholder)), " is not accepted. Please select from x, y, or z"
        end select 

        !Now parse the position of the slip plane
        arg_pos = arg_pos + 1
        call get_command_argument(arg_pos, textholder, arglen)
        if(arglen == 0) stop "Incorrect slip_plane command. Please check documentation for correct format"
        call parse_pos(sdim, textholder, spos)

        !Now check to see if efill was passed 
        arg_pos = arg_pos + 1
        if(.not.(arg_pos > command_argument_count())) then 
            call get_command_argument(arg_pos, textholder, arglen)
            if(arglen == 0) stop "Incorrect slip_plane command. Please check documentation for correct format"
            if(trim(adjustl(textholder)) == "efill") then 
                arg_pos = arg_pos +1 
                efill = .true.
            end if
        end if
    end subroutine parse
end module opt_slip_plane