36
votes
Accepted
Approximate equivalence table between Pople's basis sets and Jensen's DFT optimized polarization consistent basis sets (pcseg-n)
Disclaimer and warning: long and likely biased answer.
Background: The Pople style basis sets were defined almost 50 years ago. The 6-31G was designed for HF calculations, the 6-311G for MP2 ...
- 1,311
16
votes
Accepted
How to "get my feet wet" in Density Functional Theory by simulating a water molecule using Python
SlowQuant
In your question from 2015, you mentioned PyQuante and PySCF, but I saw no mention of SlowQuant in the question or in the multiple answers. I see that while writing this, someone else ...
- 33.5k
16
votes
How to "get my feet wet" in Density Functional Theory by simulating a water molecule using Python
If you're set on using Python here are some options. I haven't used these codes so I can't speak to their ease of use.
PyQyante
PyQuante is a suite of programs that can not only do DFT but also ...
- 3,081
16
votes
Solving the Schrödinger equation as a service?
SciCalQ
The company does more than solving the Schroedinger equation. From its site:
SciCalQ’s solid background in computational chemistry and quantum physics own extensive experiences in solving ...
- 22.3k
14
votes
Computational tool for identification of activity cliff
A 2015 paper [1] looked at the ability to predict activity cliffs structurally using docking models that could combine experimental and computational information about the conformation of the receptor ...
- 15.2k
13
votes
Solving the Schrödinger equation as a service?
Protheragen
Protheragen offers a Quantum Chemistry Service which includes:
ECD calculation service (absolute configuration determination)
Quantitative calculations (quantum chemical calculations)
QM, ...
- 33.5k
13
votes
Accepted
One-center two-electron integrals between 1s STO
Your Octave code is trying to do the integral by quadrature, which makes very little sense since it will have a huge problems with the cusp.
Since this is a one-center problem, the best approach is ...
- 17.9k
12
votes
Accepted
How to determine which levels correspond to each other in LS coupling and jj-coupling?
In the jj-representation, each electron from $i$ to $N$ will have:
$\vec{l}_i$ (orbital angular momentum),
$\vec{s}_i$ (spin angular momentum), and
$\vec{j}_i=\vec{l}_i + \vec{s}_i$ (total angular ...
- 33.5k
12
votes
Accepted
Understanding the GTH Pseudopotential
Great question, will allow me to advertize our newly-released DFT code :](https://github.com/JuliaMolSim/DFTK.jl/).
The rloc parameter is the characteristic distance at which the pseudopotential acts....
- 646
12
votes
How many spin states do Cu+ and Cu2+ have and why?
$\ce{Cu}^+$
This ion has 28 electrons. If all of them are up (i.e. aligned with the +z axis), then since each electron has a spin of magnitude 1/2, we would have a total spin of +14. If all of them ...
- 33.5k
11
votes
How many spin states do Cu+ and Cu2+ have and why?
Often when one is asked for the number of spin states, we are interested in determining the spin state of metal complexes containing these ions, rather than the lone ion itself. If you are interested ...
- 15.2k
10
votes
Accepted
Get fractional coordinates from special Wyckoff positions
From that reference, what we got is the bond length from the atomic positions.
One easy way is to look for a CIF file with the crystal information.
From the CIF49801 bellow, we get the following info:
...
- 22.3k
10
votes
Accepted
What does "Test job not archived" mean?
You are probably running a combined optimisation and frequency job in Gaussian. (I discourage that, but that's a different issue.)
The line means that the calculation preceding it has been run as a ...
- 1,571
9
votes
Accepted
What are the references in multi-reference methods?
I hope this basic example helps you to see the difference. I'll denote configurations by simple tuples where each number indicates the occupation of a spatial orbital, with increasing energy from left ...
- 829
9
votes
Accepted
Problem obtaining a Raman spectra of a graphene structure
Since you include the command cphf=RdFreq, Gaussian expects you to have entered a perturbation frequency after the rest of the input. You need to specify a ...
- 15.2k
9
votes
Accepted
Metropolis algorithm reduces energy in molecular simulation, but does not decrease euclidean distance
Most of the problem here appears to be because constraints in the test system default to app.HBonds, which means all bonds to hydrogen atoms are constrained. ...
- 2,027
9
votes
Accepted
Calculating/Visualizing electronic density from orbital information written in the Molden format
I highly recommend cclib which can read Molden and calculate the Density.
While I haven't used them as much, I'm pretty certain you can do this with:
Orbkit
Horton
There are undoubtedly other tools -...
- 9,045
9
votes
Accepted
Alternatives to VEDA 4 vibrational energy distribution analysis software?
LocVib (part of MoViPac)
I have never used VEDA before, but according to the paper, it decomposes the normal modes into vibrations of atomic groups, bond stretching, bending or something else. ...
- 1,124
9
votes
Accepted
Exchange-Correlation Two-Electron Integrals
I assume you're referring to eq 51 of the Hirata-Head-Gordon-Bartlett paper.
One should note that these are not two-electron integrals, since there is only one spatial position; these are rather ...
- 17.9k
9
votes
Software to draw 3d micelle configuration
I found some software that can do this kind of work:
Rhino3d
3ds Max
- 339
8
votes
One-center two-electron integrals between 1s STO
This can be solved analytically, a complete solution can be found here
To refrain from rewriting the entire derivation I will only say that you need to integrate over all 3 dimensional degrees of ...
- 7,957
8
votes
How to "get my feet wet" in Density Functional Theory by simulating a water molecule using Python
Psi4NumPy
First of all, thanks @uhoh for pointing me towards this question.
And as an answer (or rather different P.O.V), I want to suggest taking another look in the direction of PSI4 mainly ...
- 181
8
votes
Solving the Schrödinger equation as a service?
QSimulate
They advertise their ability to perform high throughput quantum mechanical simulations as well as large scale simulations on their web page. An e-mail address is provided for collaboration ...
- 766
8
votes
What are the references in multi-reference methods?
Rather than starting with a single-determinant (single-reference) such as the Hartree-Fock determinant which is obtained by an HF-SCF calculation, multi-reference methods such as MRCI, MR-ACPF, MR-...
- 33.5k
7
votes
Accepted
How do I create geometry files for carbon nanoribbons and molecular junctions for DFTB+?
Since you know how to use Avogadro to create XYZ files, a very simple solution to your problem is to simply create the XYZ file then use an xyz2gen script to ...
- 33.5k
6
votes
Accepted
What is the real reason behind the minimization of the system at the beginning of a Car-Parrinello MD calculation?
I explained Car-Parrinello MD here, and a key point is that it approximates BOMD (Born-Oppenheimer Molecular Dynamics) where the electronic state is minimized (i.e. the ground electronic state is ...
- 33.5k
6
votes
Exploiting 8-fold symmetry of ERI tensor for building Coulomb and Exchange matrices
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 ...
- 9,076
5
votes
How to build a simulation model for a molecular dynamics simulation
The question is how to build a simulation model rather than the choice of software. You can build a box and then put your four molecules into the box.
I have used the supported coordinates to build a ...
- 14.9k
5
votes
Accepted
Gaussian: Transition state convergence question
Are you doing an opt and freq calculation? In Gaussian, the opt keyword uses an approximate ...
- 15.2k
5
votes
What is the real reason behind the minimization of the system at the beginning of a Car-Parrinello MD calculation?
Yes your understanding is correct.
It helps to think about BOMD as classical dynamics. The electrons are the springs that hold the masses together and the nuclei are the masses.The two key terms are ...
- 7,957
Only top scored, non community-wiki answers of a minimum length are eligible