Hi Peter,
When I tried to compile your code using fortran compiler
following error appeared:
*HSX.f95:6.15:
use modul_log
1
Fatal Error: Can't open module file 'modul_log.mod' for reading at (1): No
such file or directory
*
I can't find in siesta code such a module.
I also thought that maybe the name was changed, but I can't find any similar
one.
Can you help me with that?
Best Regards,
Magda
2010/3/13 Peter Koval <koval.pe...@googlemail.com>
> Hello Doron!
>
> I think you can use my program for this, although it is not perfect. The
> program reads the .HSX file. At least one thing must be obviously corrected
> in the program: the row and columns are interchanged, therefore it might be
> necessary to interchange them in periodic systems.
>
> Best regards,
>
> Peter
>
> !!
> !!
> !!
> subroutine import_hsx(fname, haux, saux, iv)
> use modul_log
> use modul_precision
> use modul_orbital_vars, only : norbitals, nspin, orb_occ, Temp,
> total_electronic_charge
> !! external
> character(len=*), intent(in) :: fname
> real(dp) :: haux(norbitals, norbitals, nspin), saux(norbitals,
> norbitals);
> integer, intent(in) :: iv
>
> !! internal
> integer, allocatable :: int_buff(:) !! buffer for pointers (to
> nonzero elements) within a column
> real(sp), allocatable :: sp_buff(:) !! buffer for vector values (of
> nonzero elements) within a column
> integer :: ifile, iostat, icol, i, ispin, sum_col2nnzero, maxnnzero
> integer(4) :: norbitals_in, norbitals_in_supercell, nspin_in
> logical(4) :: gamma ! Gamma point or not
>
> ifile = get_free_handle();
>
> open(ifile,file=trim(fname),form='unformatted',action='read',status='old',iostat=iostat);
> if(iostat/=0) then; write(ilog,*)'import_hsx: error: file ', trim(fname),
> " ?"; stop; endif;
> rewind(ifile)
> read(ifile,iostat=iostat) norbitals_in, norbitals_in_supercell, nspin_in,
> nnonzero
> if (norbitals /= norbitals_in) then
> write(ilog,*)norbitals_in, norbitals_in_supercell, nspin_in, nnonzero
> write(ilog,*)"import_hsx: norbitals, norbitals_in:", norbitals,
> norbitals_in
> stop "import_hsx: (norbitals /= norbitals_in)"
> endif
> if (nspin_in /= nspin) then
> write(ilog,*) "import_hsx: nspin, nspin_in:", nspin, nspin_in
> stop "import_hsx: (nspin /= nspin_in)"
> endif
> if (nspin==1) then; orb_occ=2;
> else if (nspin==2) then; orb_occ=1;
> else; write(ilog,*)'import_hsx: nspin', nspin; stop '(nspin/=1 .and.
> nspin/=2)'; endif
>
> if(iv>1) write(ilog,*) "import_hsx: norbitals_in, norbitals_in_supercell,
> nspin_in, nnonzero"
> if(iv>1) write(ilog,*) norbitals_in, norbitals_in_supercell, nspin_in,
> nnonzero
>
> read(ifile,iostat=iostat) gamma
> if (.not. gamma)stop "import_hsx: .not. gamma";
>
> !! allocate the buffers
> allocate(col2nnzero(norbitals), col2displ(norbitals),
> sparse_ind2row(nnonzero))
> allocate(H_sparse(nnonzero,nspin), stat=iostat); ! Hamiltonian matrix in
> packed form
> allocate(S_sparse(nnonzero), stat=iostat); ! Overlap matrix in
> packed form
>
> read(ifile,iostat=iostat)col2nnzero
> sum_col2nnzero = sum(col2nnzero)
> if (sum_col2nnzero > nnonzero) then
> write(ilog,*) 'import_hsx: sum_col2nnzero > nnonzero ', sum_col2nnzero,
> nnonzero;
> write(ilog,*) col2nnzero;
> stop 'import_hsx:';
> endif
>
> maxnnzero = maxval(col2nnzero)
> allocate(int_buff(maxnnzero), sp_buff(maxnnzero));
>
> !! Fill the displacements (according to col2nnzero) col2displ
> col2displ(1)=0
> do icol=2, norbitals
> col2displ(icol) = col2displ(icol-1) + col2nnzero(icol-1)
> enddo
>
> !! Fill the rows for each index in *_sparse arrays
> do icol=1, norbitals
> read(ifile,iostat=iostat)int_buff(1:col2nnzero(icol)) ! read set of
> rows where nonzero elements reside
> if (iostat/=0) stop "import_hsx: (iostat/=0) int_buff"
>
> do i=1, col2nnzero(icol)
> sparse_ind2row(col2displ(icol)+i) = int_buff(i)
> enddo
> enddo
>
> !! Read the data to H_sparse array
> do ispin=1,nspin
> do icol=1,norbitals
> read(ifile,iostat=iostat)sp_buff(1:col2nnzero(icol))
> if (iostat /= 0) stop "import_hsx: (iostat/=0) Hamiltonian matrix"
> do i=1,col2nnzero(icol); H_sparse(col2displ(icol)+i, ispin) =
> sp_buff(i); enddo;
> enddo
> enddo
>
> !! Read the data to S_sparse array
> do icol=1,norbitals
> read(ifile,iostat=iostat)sp_buff(1:col2nnzero(icol))
> if (iostat /= 0) stop "import_hsx: (iostat/=0) overlap matrix"
> do i=1,col2nnzero(icol); S_sparse(col2displ(icol)+i) = sp_buff(i);
> enddo
> enddo
>
> do ispin=1, nspin
> call sparse2full(norbitals, Haux(:,:,ispin), H_sparse(:,ispin),
> col2nnzero, col2displ, sparse_ind2row);
> if(ispin==1) &
> call sparse2full(norbitals, Saux, S_sparse(:), col2nnzero, col2displ,
> sparse_ind2row);
> enddo
>
> read(ifile,iostat=iostat) total_electronic_charge, Temp ! Total
> electronic charge and Temperature
> if(iv>0)write(ilog,*) "import_hsx: total_electronic_charge, Temp (Ry):",
> real(total_electronic_charge,4), real(Temp,4)
> deallocate(int_buff, sp_buff);
> close(ifile);
>
> end subroutine !import_hsx
>
> !!
> !!
> !!
> subroutine sparse2full(ndim, M_full, M_sparse, col2nnzero, col2displ,
> sparse_ind2row)
> use modul_precision
> !! external
> integer(4), intent(in) :: ndim
> real(dp), intent(out) :: M_full(ndim,ndim)
> real(dp), intent(in) :: M_sparse(:)
> integer(4), intent(in) :: col2nnzero(ndim), col2displ(ndim),
> sparse_ind2row(:)
>
> !! internal
> integer :: icol, i, irow, sparse_ind
>
> do icol=1,ndim
> do i=1,col2nnzero(icol);
> sparse_ind = col2displ(icol)+i;
> irow = sparse_ind2row(sparse_ind);
> M_full(irow, icol) = M_sparse(sparse_ind)
> enddo
> enddo
>
> end subroutine !sparse2full
>
>
>
> On Fri, Mar 12, 2010 at 7:41 PM, Doron Naveh <na...@cmu.edu> wrote:
>
>> Hi,
>> I'm trying to obtain the overlap matrix of basis set functions,
>> does anyone know how?
>> Thanks,
>> Doron.
>>
>>
>
>
> --
> Dr. Peter Koval
> email: koval.pe...@gmail.com
> inet: http://sites.google.com/site/kovalpeter/
>
