Hi Marcos [giac...@hadrianus pdosxml]$ head -n 4 anat.PDOS <pdos> <nspin>1</nspin> <norbitals>7376</norbitals> <energy_values units="eV">
....any idea? Best! G On Mon, 8 Nov 2010, Marcos Veríssimo Alves wrote:
Giacomo, What do you see when you issue the command head -n 4 file.PDOS replacing file by the appropriate filename? Marcos On Mon, Nov 8, 2010 at 2:33 PM, Giacomo Giorgi <[email protected]> wrote:Dear All, I am facing a problem with pdosxml utility that I am not able to solve. I have a system consisting of about 600 atoms. I would like to extract the PDOS due to the 456th atom according to this requirement I updated the m_orbital_chooser.f90 in the following way ! ! This file is part of the SIESTA package. ! ! Copyright (c) Fundacion General Universidad Autonoma de Madrid: ! E.Artacho, J.Gale, A.Garcia, J.Junquera, P.Ordejon, D.Sanchez-Portal ! and J.M.Soler, 1996-2006. ! ! Use of this software constitutes agreement with the full conditions ! given in the SIESTA license, as signed by all legitimate users. ! module m_orbital_chooser ! ! Determines which orbitals to consider when processing PDOS data ! type, public :: orbital_id_t integer :: n integer :: l integer :: m integer :: z integer :: index integer :: atom_index character(len=40) :: species end type orbital_id_t public :: want_orbital CONTAINS function want_orbital(orbid) result(wantit) type(orbital_id_t), intent(in) :: orbid logical :: wantit ! ! Examples ! ! 1. Want only s-orbitals ! ! wantit = ( orbid%l == 0 ) ! ! 2. Want only n=3 orbitals ! ! wantit = ( orbid%n == 3 ) ! ! 2. Want 3p orbitals ! ! wantit = ( ( orbid%n == 3 ) .and. (orbid%l == 0 ) ) ! ! 3. Want Oxygen orbitals ! ! wantit = ( orbid%species == "O" ) ! ! wantit = .true. ! wantit = ( orbid%atom_index == 456 ) end function want_orbital end module m_orbital_chooser and similarly I increased NMAX in pdos.f90 file up to 4000000 (!!!) I compiled successfully but when I read the .PDOS file I got this message: [giac...@hadrianus pdosxml]$ ./pdos anat.PDOS > 456.dat Found nspin element Too many numbers in nspin element. Taking first one. forrtl: severe (59): list-directed I/O syntax error, unit -5, file Internal List-Directed Read Image PC Routine Line Source pdos 000000000045D0FF Unknown Unknown Unknown pdos 000000000045B5DE Unknown Unknown Unknown pdos 0000000000440178 Unknown Unknown Unknown pdos 0000000000410B72 Unknown Unknown Unknown pdos 00000000004107D3 Unknown Unknown Unknown pdos 000000000042589A Unknown Unknown Unknown pdos 0000000000424E7D Unknown Unknown Unknown pdos 0000000000402B0E Unknown Unknown Unknown pdos 000000000040705C Unknown Unknown Unknown pdos 0000000000403F81 Unknown Unknown Unknown pdos 00000000004026AA Unknown Unknown Unknown libc.so.6 0000003ED1D1C40B Unknown Unknown Unknown pdos 00000000004025EA Unknown Unknown Unknown I think it is related to the size of the system since when I read the h2o_pdos.PDOS file in the example directory I do not find any problem in extracting the PDOS of each atomic species. Can anybody help me in fixing this doubt? Very best, Giacomo
-- * * * * * * * * * * * * * * * * * * * * * * * * * * Giacomo Giorgi * * Ph.D. * * Dipartimento di Chimica e Istituto di * * Scienze e Tecnologie Molecolari ISTM-CNR * * Universita' degli Studi di Perugia * * Via Elce di Sotto 8 06123 Perugia Italia * * Tel: +39 075-5855618 Fax: +39 075-5855606 * * E-mail: giac_at_thch.unipg.it * * * * * * * * * * * * * * * * * * * * * * * * * * "Oltre le illusioni di Timbuctu' e le gambe lunghe di Babalu' c'era questa strada... Questa strada zitta che vola via come una farfalla, una nostalgia, nostalgia al gusto di curacao... Forse un giorno meglio mi spieghero'..." (Paolo Conte, "Hemingway")
