Re: [SIESTA-L] Re: COOP Utility

Mon, 04 Oct 2010 08:14:04 -0700 

A lot of thaks for your replies.
Now, I have the file.mpr
I write:
./mprop  -s 0.01 -n 500 -m -15 -M 15 file.mpr
But the response is:
Image              PC                Routine            Line        Source
mprop              00000000004B9D9D  Unknown               Unknown  Unknown
mprop              00000000004B88A5  Unknown               Unknown  Unknown
mprop              0000000000467D49  Unknown               Unknown  Unknown
mprop              000000000042487D  Unknown               Unknown  Unknown
mprop              00000000004240CA  Unknown               Unknown  Unknown
mprop              000000000043395D  Unknown               Unknown  Unknown
mprop              0000000000416F2A  Unknown               Unknown  Unknown
mprop              000000000040C0DC  Unknown               Unknown  Unknown
libc.so.6          00002AFE61F67586  Unknown               Unknown  Unknown
mprop              000000000040BFD9  Unknown               Unknown  Unknown
And I don't obtain any ouput file.
It is a compilation problem?


El 30/09/2010 19:15, Marcos Veríssimo Alves escribió:

With mprop -h, one obtains, among other things:

(1)    /-[ If COOP selected; as many blocks as projections wanted ]
(2)    |    curve_name              # COOP curve name
(3)    |    Subset I of AO (*)      # Reference atoms or orbitals
(4)    |    d1 d2                   # Distance range
(5)    \-   Subset II of AO (*)     # Neighbour atoms or orbitals

(6) * SUBSET OF AO USING ATOM_SHELL NOTATION
(7)    List of atoms and shell groups of AO
(8)    General notation: ATOM_SHELL
(9) > ATOM:  Atomic symbol refers to all the atoms of that type
(10)              Integer number refers to the N-th atom in unit cell
(11) > SHELL: Integer1+Letter+Integer2
(12) > Integer1 refers to the n quantum number
(13) > Letter   refers to the l quantum number (s,p,d,f,g,h)
(14) > Integer2 refers to a single AO into the n-l shell
(15)                   Alternatively, alphanumerical strings can be used
(16)                     p-shells   1  y    d-shells   1  xy   4  xz
(17)                                2  z               2  yz   5  x2-y2
(18)                                3  x               3  z2
(19)    Particular cases:
(20) > Just ATOM is indicated: all the AO of the atom will be included
(21) > No value for Integer2:  all the AO of the shell will be included
(22)    Example: Ca_3p Al 4_4d3 5 O_2py

So, most likely, in Nguyen's example:

BaTiO3     # Name of the siesta output files (as in SystemLabel)
COOP      # calculation is a COOP analysis (could be DOS)
Ti-O # (line(2)) Name of the current curve: Coop/cohp for Ti-O which include Ti(3d, 4s,6p) and O(2s,2p) Ti # (lines(3,20)) Reference atom, for which you could have included a list of atomic orbitals. Since there's none, all the orbitals of the Ti will be included in the analysis. 
2.0  3.0    # (line(4)) Bond distance range in calculating COOP/COHP
O # (line(5)) Neighboring atoms, for which you could have included a list of atomic orbitals. Since there's none, all the orbitals of the O atoms in the range 2-3 Bohr will be included in the analysis. 
Ti3d-O2s  # Coop/Cohp for Ti(3d)-O(2s)
Ti_3d
2.0 3.0 # Bond distance range in calculating COOP/COHP
O_2s
Ti3d-O2p # Coop/Cohp for Ti(3d)-O(2p)
Ti_3d
2.0 3.0 # Bond distance range in calculating COOP/COHP
O_2p
The rest of the lines is pretty self-explanatory, I guess. Hope this helps. 

Marcos
2010/9/30 Gregorio García Moreno <[email protected] <mailto:[email protected]>> 

    Sorry, befere I write an erroneous sentence.
    Yes, I know that I can create mpr file with a text editor. But my
    doubt is that I can't understand each line of the mpr file in the
    Nguyen's mail. So I would need some specific about the meaning of
    the lines in mpr file.

    El 30/09/2010 18:51, Marcos Veríssimo Alves escribió:

        So that is the relevant question here - what the lines mean.

<<attachment: gjgarcia.vcf>>

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