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Thank you for your reply. I think I now understand that isovalues are different depending on the parameter being visualized. For Multiwfn, can you confirm:
When plotting wavefunction, the units of the isovalue are (effectively) sqrt(1/Bohr^3)
When plotting electron density, the units of the isovalue are 1/Bohr^3
Please, now, forgive me for asking this question: is there a way of visualizing the radial electron density function surfaces (4 x pi x r^2 x psi^2) for an atom or molecule?
Many thanks. Regards.
Many thanks for your reply. Once again, it has been very helpful. If I may, I have a few more questions relating to isovalue units.
Using Multiwfn, I have been visualizing wavefunction surfaces using an isovalue of 0.05. If I then switch to your electron density surface, I notice that the isovalue defaults to a much smaller value. Could you explain the change in isovalue? And please confirm the units of your isovalues in both cases.
In trying to understand wavefunction visualization, I have compared the visual outputs from Multiwfn and another software (IQMol). I guess this may be a difficult task since the output is very sensitive to the isovalue, and the computation methods may be different. I find that wavefunction visualizations from IQMol (at isovalue 0.05 / Angstrom^3) correspond very closely to visualizations from Multiwfn (at isovalue 0.03 / Bohr^3). I can't make sense of this, assuming your units are /Bohr^3. Perhaps IQMol is not the best?
In the past I have used different visualization software - Avogadro, IQMol, VMD, Molden, wxMacMolPlt, Gabedit - some with success, others not. I would be interested in your views on the subject of visualization - is it a science, or more of an art?
Thank you. Best regards.
Thank you for your reply. It has been very helpful. I would like to ask you to clarify some of the terminology you are using. I think it is important to get this right in my mind. From my understanding we have different parameters:
A Orbital (wavefunction) - a number, plus or minus
B electron density (wavefunction squared) - electrons per unit volume, e / Angstrom^3 ??
C electron probability density function (4 x pi x r^2 x psi^2 x dr) - a number, probability
Using Multiwfn, if I choose to calculate and visualize a "wavefunction" surface, what are the units of the isovalue I choose? Many visualization programs have the units as e / Angstrom^3 (electrons per cubic Angstrom). Is that true of Multiwfn?
Using Multiwfn, if I choose to calculate and visualize your "Density" surface, do you mean B or C? And what are the units of the isovalue in this case?
I hope my questions make sense. I look forward to your reply. Many thanks and regards.
I am studying chemical bonding in small molecules using localized orbitals. I use Multiwfn to calculate the localized data (.fchk file input, .fch file output). I use the output file with, for example, IQMol to calculate and visualize localized orbital surfaces (that is, the wavefunction surfaces).
I would now like to calculate and visualize the electron density (wavefunction squared) surfaces for each localized orbital. I do not know how to do this. I would be grateful for any assistance you could give. Thank you.
Hello again. I would like some advice please. I am successfully using Multiwfn to calculate localized orbitals and energies. However I am not sure if I am using the correct process for molecules that have an unpaired electron (unrestricted wavefunction) e.g. NO2. I have done localized energy calculations in such cases by combining the A Fock matrix with the B Fock matrix. Is this correct? The results show the A and B energies to be similar, but not the same. In some cases the A orbital is different from the corresponding B orbital. Can you give me any advice on the interpretation of the (different) A/B results? Thanks. Regards Donald.
Hi, this is my first post. I am quite new to ab initio electron calculations. I am using Psi4 with Multiwfn. I am interested in localized orbital calculations on small molecules, giving meaningful information on chemical bonding structures. I am first of all testing the programs on a methane molecule. The visual results using Psi4 / Multiwfn give 4 (beautiful) tetrahedral localized bonding orbitals, but I run into problems when I try to calculate the energy.
My question concerns the Fock matrix in lower triangular form. Examination shows the Fock matrix to be symmetric about the leading diagonal. Is "lower triangular form" the same matrix with just the upper triangular entries removed? Or is "lower triangular form" the matrix after a gaussian elimination to make the upper triangular entries equal to zero? I would value your help. Regards Donald.
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