[Pw_forum] point charge-spin
david.grifith at gmail.com
Thu Dec 2 08:42:09 CET 2010
Many thanks for your kind attention and very detailed answer. It has
raised up our knowledge around the topic.
> As for point charges, here is a small recipe for isolated
> molecules (see below) for the ESP/RESP procedure [A].
> Reference is Bayly et al, J. Phys. Chem., 97, 10269 (1993).
> Final point charges for organo-metallic molecules compare
> fairly well with standard or published values.
> Another possibility is to compute charges by integrating
> over atomic basins built on the basis of QT-AIM (Bader) [B].
> 1) From PW or CP, write into the restart
> directory (I guess into the charge-density.dat file)
> the electrostatic potential in place of electron
> density. This requires a call before writefile
> in CPV/cpr.f90 (in case of CP). Paolo Giannozzi
> wrote the subroutine to do this in CP. It would be
> nice to have it in some contrib space.
> In the input, it is recommended to use
> explicit ion_radius(i), especially if you
> want to compare with other programs (like CPMD,
> for which the default radii are all 1.2 bohr).
> 2) Once the restart is generated, postprocess
> it with PP as to print the electron density
> into a friendly format, like a gaussian-cube file.
> This file will contain the electrostatic potential
> on a 3d-grid. PP can process restart produced also
> by CP, provided disk_io='high'.
> 3) Write your own program to map the 3d-grid on
> the molecular solvent-accessible surface. This will consist in reading
> the 3d-grid, reading the molecular surface produced
> with vdw radii and a rolling probe, and finally
> interpolate the potential at the surface point
> using neighbour points in the grid. For the molecular
> surface, I recommend an old program called NSC (numerical surface
> Eisenhaber et al, J. Comput. Chem., 16, 273 (1995)
> WARNING: this latter step for non-periodic systems!
> Non-periodicity is assumed in the ESP/RESP procedure,
> that consists in fitting the electrostatic surface
> potential with a LIMITED sum of Coulomb interactions.
> The interpolation can be very coarse, the entire method
> is plenty of error sources.
> The output of this procedure is a list with
> x y z U
> for each point of the molecular surface.
> In case step 4 is performed with the aresp code
> that was once part of Amber, the output for a water
> molecule is:
> 3 1072 0
> -0.9982123E-32 0.0000000E+00 0.2313846E+00
> -0.2610123E-32 0.1494187E+01 -0.9255383E+00
> -0.1829851E-15 -0.1494187E+01 -0.9255383E+00
> -6.5264638e-01 2.0485851e+00 1.0162867e+00 1.6945994e+00
> -7.2948945e-01 2.4209246e+00 6.0282018e-01 1.7305686e+00
> where 3 is the number of atoms, 1072 is the number of surface points,
> 0 is the net charge, the three following lines are the atomic coordinates
> in bohr, and the following lines are x,y,z,U (bohr,kcal/mol)
> for the 1072 surface points. This format was once produced
> by Gaussian.
> 4) Finally, one of the RESP codes available can be used.
> I used the original aresp code that was part of the Amber 4.1
> I think it is not worth to develop the RESP part in QE,
> but for sure steps 1-3 could be done relatively easily.
> And maybe with a minimum-image based periodicity.
> I really don't know how to do it, but I am available
> for testing.
> This is simpler, but for reasons that will be apparent to
> everybody in a few applications, it is rarely used.
> 1) Postprocess the restart with PP and write the electron density
> on a fine 3d-grid (cube-file). The size of 10 pm associated
> to a density energy-cutoff of 250 Ry is rather accurate.
> 2) Process this electron density cube-file with a real-space
> QT-AIM code. I used:
> Sanville et al., J. Comp. Chem., 28, 899 (2007).
> Charge are in ACF.dat.
> This works also for periodic systems (maybe only orthorhombic?).
> Problems occur with polar X-H bonds or in all cases
> where the zero-flux of density comes too close to atoms desribed
> with pseudo-potentials.
> Maybe, this will help,
> Giovanni La Penna - National research council (Cnr)
> Institute for chemistry of organo-metallic compounds (Iccom)
> via Madonna del Piano 10,
> I-50019 Sesto Fiorentino, Firenze, Italy
> tel.: +39 055 522-5264, fax: +39 055 522-5203
> e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna
> skype: giovannilapenna
> On Wed, 1 Dec 2010, David Grifith wrote:
> > Dear All
> > I am trying to calculate the point charge and the point spin density on
> > atom of a unit cell, certainly "WITHOUT" considering a 3D vector which is
> > ...
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