On May 24, 2013, at 8:15 AM, David A Case wrote:
> On Thu, May 23, 2013, Franz Symalla wrote:
>>
>> does anyone know how to extract a charge density from a pm3 (or other
>> mndo based run) calculation?
>> I figured that the density matrix is in qm2_struct%den_matrix() of the
>> qmmm_module, but i dont know
>> a) where to get the related ao-basis, and b) how to access the basis
>> explicitly ( i.e. its real space values).
>
> I don't think there is any real basis set in pm3 calculations: the method
> just prescribes how to get integrals needed to construct the Fock matrix from
> the geometry of the molecule.
The Fock matrix elements are parameterized or obtained from semiempirical multipole expansions, but NDDO methods do use a minimal basis set of Slater type functions for valence electrons (and a set of d-type polarization functions for some elements with MNDO/d, AM1/d and PM6).
There is no code in sqm to assist with the visualization of the electron density. With regard to Franz' questions:
a)
All parameters are in $AMBERHOME/AmberTools/src/sqm/qm2_parameters.F90 from which you can get the exponents of the basis functions (s_orb_exp, p_orb_exp, d_orb_exp). The exponents get loaded by atom type into qm2_params%s_orb_exp_by_type etc. The principal quantum numbers are in $AMBERHOME/AmberTools/src/sqm/elementOrbitalIndex.F90 and get loaded by atom type into qm2_params%sp_quantum_number and qm2_params%d_quantum_number
b)
The information from a) together with the atomic coordinates and density matrix is all you need to compute the electron density in space, for example on grid points for visualization. Off the top of my head I don't know which parts of the code you could hijack to assist here. If you write code for calculating the electron density, please share it for inclusion into sqm :-)
All the best,
Andy
> I'm not sure what other programs do (if anything), here. You could just use a
> minimal basis (e.g. sto-3g) for visualization or similar purposes. But as far
> as I know, this is not in the sqm code.
> ...dac
>
>
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--
Dr. Andreas W. Goetz
Assistant Project Scientist
San Diego Supercomputer Center
Tel : +1-858-822-4771
Email: agoetz.sdsc.edu
Web : www.awgoetz.de
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Received on Fri May 24 2013 - 16:30:02 PDT
