Hi Herbert, Siesta is also able (as of 3.2) to do Hirshfeld and Voronoi charge partitioning analyses.
Alberto On Thu, Jun 20, 2013 at 3:21 PM, Herbert Fruchtl < [email protected]> wrote: > Just to add to the discussion that started with the question about PDOS > projection radii: > > Any definition of atomic charge is necessarily arbitrary. There are no > atoms; there are only nuclei and a wavefunction and charge density of > electrons in the field of those nuclei. There are various different schemes > of partitioning this charge density into "atoms". The ones I know are > available for Siesta (two of them mentioned in earlier posts) with easily > accessible tools are: > > - Mulliken charges > Project the wavefunction onto atom centred basis functions and count them > towards the atom the function is centred on. > Advantages: Trivial and cheap if you have an atom centred basis. No double > counting. > Disadvantages: It's not really a spatial partitioning. The charge in one > point is split between multiple atoms, which may be far away. A diffuse > basis (which improves the description of the wavefunction and may be > otherwise desirable) makes things worse. > > - Atomic spheres > Draw a sphere around a nucleus and count all electron density within it > towards this nucleus. > Advantages: Relatively easy to implement. Intuitive (we all know that > atoms are little balls, right?). > Disadvantages: The radius is arbitrary. If the spheres are overlapping, > you count part of the charge twice. If they aren't, there are large parts > of space (and electron density) you don't count. In practice, you have a > mixture of both effects. If the sum of the volumes of spheres is the volume > of the enclosed space, it's called Wigner-Seitz radius. This is only > uniquely defined for monoatomic crystals, and even then the sum of atomic > charges will differ from the total charge. > > - Bader charges (Atoms in Molecules) > Perhaps the most chemically intuitive partitioning. Assuming that you > always have a local maximum of electron density at a nucleus, the boundary > between two atoms is the surface of lowest density between the nuclei. > Advantages: Intuitive. Unique. Not basis set dependent. > Disadvantages: If using pseudopotentials, you only see the valence > electrons. The density maximum at a nucleus may not exist or be so shallow > that it is not found. Particularly hydrogen atoms have a habit of > "disappearing", with their electron density lumped into the charge of a > neighbour. > > If somebody knows of other schemes (Hirshfeld, NBO, ...) available for > Siesta, I'd be interested to hear about them. > > Hope this helps, > > Herbert > > On 20/06/13 09:50, Emilio Artacho wrote: > >> And just to complete the story, some plane-wave codes >> do not do the muffin-tin analysis, but do a full projection >> onto atomic orbitals of the PW eigenstates, based on >> Sanchez-Portal et al; Solid St. Commun. 95, 685 (1995), and >> J. Phys. Condensed Matter 8, 3859 (1996). I think CASTEP and >> CPMD do this. In this case both the Mulliken charges and >> projected densities of states are conceptually the same as >> in Siesta. Mind you, the results will not be quantitatively >> comparable since in the case of PW they normally use >> a minimal (SZ) atomic basis set to project upon, while >> the original basis (PWs) is quite complete, while in Siesta >> the basis for the Mulliken analysis is the same as was used >> for the calculation. >> >> Emilio >> >> >> On Jun 20, 2013, at 10:13 AM, [email protected] >> <mailto:apostnik@uni-**osnabrueck.de <[email protected]>> wrote: >> >> Hi Benedikt, >>> Alberto is right, SIESTA does not need projections, >>> but YOU might need them; exactly for the sake of comparing >>> the charges with those from "muffin-tin"-type codes >>> I wrote some time ago a primitive tool >>> http://www.home.uni-**osnabrueck.de/apostnik/**Software/grdint.f<http://www.home.uni-osnabrueck.de/apostnik/Software/grdint.f> >>> which "integrates" grid properties, e.g. charge (spin) densities, >>> over given (atom-centered) spheres. >>> Some remarks: >>> 1. It integrates functions defined on the grid, which are not >>> (l,m) resolved. That means, you can produce spin-up and spin-down >>> charges, but not partial s,p,d-charges. Of course you can first >>> generate LDOS within some energy interval, if you find it useful, >>> and then integrate it over a sphere. >>> 2. The "integration" is in fact merely a counting of grid points >>> which either fall within, or not, of a given sphere. So the result >>> is not very accurate and prone to "noise". But it is usually OK >>> for the sake of comparison, and anyway becomes "better" >>> as the mesh density is increased. >>> 3. The tool as not fast as you may expect it to be, for the task >>> it performs, because the algorithm used is very straightforward; >>> please feel free to improve. >>> >>> Best regards >>> >>> Andrei Postnikov >>> >>> >>> >>> Hi Benedikt, >>>> >>>> SIESTA does not need projections, as the basis orbitals are localized on >>>> the atoms. You get naturally the "chemical" information one is used to. >>>> Plane-wave codes such as vasp do need projections to get some kind of >>>> "local" information from the delocalized basis. >>>> >>>> Alberto >>>> >>>> >>>> On Mon, Jun 17, 2013 at 4:28 PM, Benedikt Ziebarth < >>>> [email protected]> wrote: >>>> >>>> Hello, >>>>> >>>>> I have a question about PDOS calculations with siesta. Is there a way >>>>> to >>>>> specify the radius around the atoms in which the projection is carried >>>>> out? >>>>> This option exists in different other dft codes like vasp ( >>>>> http://cms.mpi.univie.ac.at/****vasp/vasp/RWIGS.html<http://cms.mpi.univie.ac.at/**vasp/vasp/RWIGS.html> >>>>> <http://**cms.mpi.univie.ac.at/vasp/**vasp/RWIGS.html<http://cms.mpi.univie.ac.at/vasp/vasp/RWIGS.html> >>>>> > >>>>> ). >>>>> Any help would be very welcome. >>>>> Thanks >>>>> >>>>> Benedikt Ziebarth >>>>> >>>>> >>>> >>> >> -- >> Emilio Artacho >> >> CIC nanoGUNE Consolider, and Cavendish Laboratory, University of Cambridge >> Tolosa Hiribidea 76, E-20018 Donostia - San Sebastián, Spain, >> [email protected] <mailto:[email protected]>**, +34 943 574039, >> http://theory.nanogune.eu >> >> > -- > Herbert Fruchtl > Senior Scientific Computing Officer > School of Chemistry, School of Mathematics and Statistics > University of St Andrews > -- > The University of St Andrews is a charity registered in Scotland: > No SC013532 >
