New answers tagged quantum-chemistry
8
Only the first line is correct, as long as the AO basis is not orthogonal.
The point is: the AO $\leftrightarrow$ MO transformations of density matrices and Fock matrices require different formulas. For the Fock matrix the formulas are
\begin{align}
F_{MO} &= C^T F_{AO} C \tag{1}\\
F_{AO} &= SC F_{MO} C^TS \tag{2}
\end{align}
While for the density ...
6
The open-source program Multiwfn (http://sobereva.com/multiwfn/) contains a module that calculates the electrostatic potentials. According to Tian Lu, it has been quite thoroughly optimized for speed. Depending on your workflow, you may even be able to obtain the electrostatic potentials by calling Multiwfn in a black-box manner through command line, without ...
5
If you know the Gaussian basis set and the density matrix, the task simplifies to the calculation of nuclear attraction integrals.
The electron density is expanded in the basis set as
$$ n({\bf r}) = \sum_{\mu \nu} P_{\mu \nu} \chi_\mu({\bf r}) \chi_\nu({\bf r}).$$
When you substitute this into your equation, you get
$$ V({\bf r}) = \sum_{A=1}^{N_{\rm atoms}}...
7
This is just the Gaussian cube format. It's essentially a voxel dump of the wave function evaluated on a grid. You can find some documentation at http://paulbourke.net/dataformats/cube/ and https://h5cube-spec.readthedocs.io/en/latest/cubeformat.html .
Most electronic structure programs are able to generate Gaussian cube files. Several molecular viewers can ...
5
PySCF and Psi4 both implement analytical geometric Hessians for Hartree-Fock calculations. The computation of the geometric Hessian indeed requires solving the coupled perturbed Hartree-Fock equations: while one can evaluate the force acting on the nuclei just with the SCF wave function and the integral derivatives, the second derivative also contains a ...
4
I disagree with the statement by Tyberius that: "Bond order isn't terribly useful to a computationalist directly; however, it can be invaluable for translating Quantum Mechanical results into a framework thats readily understood by experimentalists.".
Bond order quantifies the number of electrons that are shared (technically, 'dressed exchanged') ...
6
ORBKIT
This uses the ORBKIT package.
Gunter Hermann, Vincent Pohl, Jean Christophe Tremblay, Beate Paulus, Hans-Christian Hege, and Axel Schild, "ORBKIT: A Modular Python Toolbox for Cross-Platform Postprocessing of Quantum Chemical Wavefunction Data", J. Comput. Chem. 2016, 37, 1511-1520.
import orbkit as ok
ok.options.filename = '/path/to/86....
3
As specified in the GAMESS Documentation:
nspace=n means the active space will be split into $n$ groups.
mstart sets the starting orbital for each of the $n$ groups. In your case, the first group extends from orbital 3 to orbital 9, while the second is from orbital 10 to NCORE+NACT (the number of core and active space orbitals). They mention that in this ...
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