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/
