wzkchem5
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How do we know how much computational power is required for a particular calculation?
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15 votes

Computational power is a relatively vague term, and can include at least three dimensions: computational time, memory consumption, and disk usage. Under this definition, it's trivial to find out how ...

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How do you incorporate hydrogen bonding into molecular simulations?
14 votes

The short answer is that, while hydrogen bonds do have some covalent character, you can mimic that covalent character by increasing the electrostatic term. For example you can specify point charges to ...

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What is the minimum basis set one should use?
14 votes

Different people will have slightly different opinions, so take my answer with a grain of salt. I'll try to give the minimum publishable basis sets, i.e. if you use worse basis sets than these, you'll ...

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How reactivity of a organic molecule depends upon HOMO and LUMO
13 votes

The HOMO-LUMO gap is only weakly correlated with the reactivity of the molecule. Many sources, however, only point out the correlation between the HOMO-LUMO gap and reactivity, but fail to point out ...

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How can I learn LaTeX?
13 votes

I personally started with "The Not So Short Introduction to LaTeX", a PDF file that should come with most LaTeX distributions under the name "lshort.pdf". The document claims that ...

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Why is my ORCA calculation of nitrogen iodide failing?
13 votes

There was a bug with the PModel guess of iodine, which leads to a very poor initial guess for molecules containing iodine, and consequently divergent SCF calculation. This bug has been fixed in ORCA 5....

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Choice of coordinate system for geometry optimization
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13 votes

You may want to have a look at this paper: "Geometry optimization made simple with translation and rotation coordinates" https://aip.scitation.org/doi/10.1063/1.4952956 This is not a ...

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Are there any benchmark test sets for UV-vis absorption maxima?
12 votes

There is a program called PhotochemCAD by Tanuchi and Lindsey which contains a database of experimental absorption and emission spectra of more than 300 organic and organometallic compounds. The ...

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Why is uncertainty not a big problem in computational chemistry?
12 votes

Indeed, due to the uncertainty relation, the electrons in a molecule do not have a definite potential energy, nor do they have a definite kinetic energy (yet they have well-defined expectation values ...

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Do we know for sure that all atomic and molecular wavefunctions decay exponentially as $r \to \infty$?
10 votes

I'll answer this question from the theoretical side. The exponential behavior follows simply from the Schrödinger equation. Consider the one-electron Schrödinger equation: $$ (-\frac{1}{2}\nabla^2 + V(...

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Can the dehydrogenation energy be negative?
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10 votes

Because the hydrogenation release has a barrier (activation energy) that is not too low. The fact that the dehydrogenation energy of $\ce{H3N-BH3}$ is negative does prove that it will eventually ...

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Does the spin polarised DFT calculation mean broken time reversal symmetry?
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10 votes

Yes, broken symmetry solutions do break time-reversal symmetry, and that's one of the reasons why they are unphysical when the total magnetic moment of the system is 0 (although they are physical when ...

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MD: How to estimate number of timesteps to converge a property
10 votes

On the mathematical side, there exists no algorithm that estimates the time required to converge a property within any predefined accuracy, however low the accuracy is. The reason is simple. Suppose ...

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Accuracy trade-off between energy and density in DFT calculations
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9 votes

If a functional always gives the exact energy for arbitrary external potentials, then it is easy to see that the functional must always give the exact density. Consider two DFT calculations, one with ...

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Soil Modelling: Getting accurate Thermal Conductivity values
9 votes

I don't think this is something that you can model accurately in an ab initio manner, as there is no good method for predicting the thermal conductivity of amorphous materials yet, let alone materials ...

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Replacement from minimizing the energy to solving the KS equation (or eigenvalue problem)
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9 votes

The trick is that, instead of solving $\frac{\delta E}{\delta \rho}=0$, we solve the equivalent set of equations $\frac{\delta E}{\delta \psi^*_n}=0, \forall n$ (plus the Lagrange multipliers required ...

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What are the advantages of the Davidson diagonalization method over other sparse matrix diagonalization methods?
9 votes

Following Nike Dattani's suggestion, I now add some comparisons of the Davidson method with methods that are more "modern" than it, to supplement the existing answers which compared the ...

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Convert reduced density matrix from M.O. to A.O. basis
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9 votes

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. ...

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External potential in the Hohenberg-Kohn map
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9 votes

The actual external potential of molecules is indeed a sum of the Coulomb potentials of the nuclei (except when one uses a pseudopotential, where the potential will be Gaussian-like near the nuclei; ...

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Keesom and Debye forces in DFT
9 votes

In computational chemistry, the term "van der Waals interaction" tend to refer to the London term only; the Keesom term (electrostatic interactions between two freely-rotating permanent ...

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How to address the errors on Automated Topology Builder?
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9 votes

Did you want to draw Si instead of S? Sulfur atoms bonded to two oxygens and two carbons, like the ones you have drawn here, are at least very rare, if not non-existent. It makes much better sense if ...

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Kramer's Degeneracy and Antiferromagnetism
8 votes

You may want to have a look at my answer to a related question. Basically, in the usual single-particle-model picture of an antiferromagnetic system, the total wavefunction is like $\Psi=|\uparrow\...

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How can I quantify the uncertainty of thermal molecule properties in molecular dynamics simulations?
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8 votes

The error of a MD simulation can be roughly partitioned into four contributions: Error due to short-period statistical fluctuations; Error due to poor- or non-ergodicity (in other words, extremely ...

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Calculate number of electrons per shell for an atom
8 votes

Yes - you can just pre-calculate them and hard-code them into your code, so that the script is simply a conditional switch that returns the required array when given the atomic number, without any ...

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Understanding emission spectra using TDDFT calculation
7 votes

In general, you should use the $S_1$ state by default, unless you have reasons to suspect that your molecule is anti-Kasha. IMHO satisfying one of the following criteria guarantees that your molecule ...

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How can I calculate the energy gap between the singlet and triplet state using ORCA?
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7 votes

First of all, if you are only interested in molecules with about the same size as the ones in the article you cited, then TDDFT is probably not the best method for this purpose. ORCA supports many ...

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Emission and absorption UV-Visible spectrum using GAUSSIAN-09
7 votes

Roughly speaking, absorption spectra are obtained by TDDFT calculations on optimized ground-state geometries, while emission spectra are obtained by TDDFT calculations on optimized excited state ...

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Which DFT functional should I use to simulate spectra of pesticides?
7 votes

If you are talking about IR or Raman spectra, then B3LYP is essentially the best choice possible. But if you are talking about UV-Vis, and if the excited states of the pesticide contain significant ...

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Exploiting 8-fold symmetry of ERI tensor for building Coulomb and Exchange matrices
6 votes

AFAIK the standard way is to obtain the memory efficiency at the expense of some code repetition in the innermost loop. A preliminary example goes like: Construct a nested loop that only loops over ...

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Numerical Frequency Parallelization in ORCA
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6 votes

This is exactly what ORCA actually does. For example if you have 48 cores, then ORCA does 48 displacements at once, each using only a single core. This is trivial to implement and is one of the major ...

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