33

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 calculations. For computational efficiency reasons, the s- and p-exponents were constrained to be identical. Polarization functions were defined for 1d, 2d, 3d and 1f. ...


15

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 answered, with mentions of PyQuante, PySCF, and Psi4 again. Still no mention of SlowQuant. The author of SlowQuant has described the program this way (emphasis mine)...


15

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 Hartree-Fock, MP2, and more. Certain parts of the code are written in C for speed. A package can be downloaded and then installed with Python, but a newer version, ...


15

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 practical and academic problems with scientific computing. They do: Density Functional Theory (DFT) Computation Geometric Configuration: Bond length, bond angle, ...


14

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 and/or binding molecule. They found that they could achieve reasonable prediction accuracy and planned to implement further improvements to make a more robust ...


13

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 momentum). In your example we have $N=2$ and both electrons are $p$-type so we have: $$\tag{1} {l}_1=1,~~~~~~~{l}_2=1. $$ Let's also assign the spins for each ...


12

Protheragen Protheragen offers a Quantum Chemistry Service which includes: ECD calculation service (absolute configuration determination) Quantitative calculations (quantum chemical calculations) QM, QM/MM, QM/MD Catalytic reaction mechanism calculation Transition state search and energy calculation Chemical reaction pathway and potential energy surface ...


12

Constraint #13: Size-Extensivity While the Wikipedia page for size-consistency and size-extensivity gives a clear formula for the definition of size-consistency, unfortunately they did not give a definition of size-extensivity, so I had to look deeper into the reference that they provided. They say that size-extensivity was introduced by Bartlett, and they ...


11

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 to use the Legendre expansion for $|r_1-r_2|^{-1}$, which decomposes the interaction into a radial part and an angular part: $r_{12}^{-1} = \frac {4\pi} {r_>} ...


11

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. At distances bigger than rloc, the potential starts to behave like a Coulomb potential. Note that the nonlocal potential also has a characteristic size, ...


11

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 in just the lone ion itself, Nike Dattani's answer goes into depth about that. My answer will focus on the determination of spin states of ions within metal ...


11

$\ce{Cu}^+$ 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 are down we would have a total spin of -14. We could also have 1 up and 27 down, meaning $+\frac{1}{2} - \frac{27}{2} = -\frac{26}{2} = -13$. The number of total ...


10

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 test calculation, see https://gaussian.com/test. An archive entry has not been created. The reasons may be multiple and depend on the actual input file. That's ...


9

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. Something goes very weird when you force a large, unphysical change on the system, and then try to apply HBond constraints (it looks to me like it isn't even constraining HBonds to the unphysical ...


9

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 - Molden is a pretty standard format for quantum chemical interchange.


9

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: (label type_symbol symmetry_multiplicity Wyckoff_symbol fract_x fract_y fract_z B_iso_or_equiv occupancy) Mo1 Mo4+ 2 c 0.3333 0.6667 0.25 . 1. S1 ...


9

I found some software that can do this kind of work: Rhino3d 3ds Max


8

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 frequency in order to compute dynamic properties. Here is how it would look for your case. Note you can specify the perturbation in a couple different units (nm, au,etc). --Link1-- %chk=go40r.chk %nproc=...


8

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 to right. Let's take only the ground state determinant as reference and do CIS within a space of 4 spatial orbitals (yielding 8 spin orbitals in total) and ...


8

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-AQCC, and even MR-CC will start with a multi-configurational SCF (MCSCF) calcualtion. There's many types of these, and many can be found here: What are the types ...


8

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. Something similar is LocVib, which localizes normal modes to localized vibrational modes by maximizing the "distances" between vibrational modes and "...


8

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 weighted four-center one-electron integrals. As always, the problem when you have four indices is that there is a huge number of integrals that come out, and you ...


8

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 freedom for both electrons, so TAR86 is correct. In the derivation at the link, the distance between the electrons ($\mid r_1 - r_2 \mid \equiv r_{12}$) is better ...


7

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 PSI4NUMPY. LINK: https://github.com/psi4/psi4numpy I was recently suggested to this amazing git on my Reddit post. PSI4NUMPY contains literally a lot of python codes ...


6

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 found and used) at each step. The reason for the minimization in CPMD at the first step, is the same as the reason in the earlier BOMD method that it approximates. ...


6

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 convert fron XYZ format to the GEN format you seek. This is an example of a script that converts from XYZ to DFTB+ format. The beauty of the GEN format of DFTB+ is that with only a few lines, you can &...


6

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 inquiries and other questions. https://qsimulate.com/technology.html An exemplary application is reported here: https://arxiv.org/abs/2004.08725


5

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 the internal energy (U) and the kinetic energy of the masses (K). We seek to calculate the positions of the system as a function of time, which we can do ...


4

I am assuming you mean just the electron density (as its typically referred to in my experience). In that case, if using VASP, you just set LCHARG = .TRUE. and you can load the CHGCAR file in a program such as VESTA. You can also view the charge density of a specific band / kpoint. This page on the VASP wiki will help you set up your desired calculation. ...


4

Are you doing an opt and freq calculation? In Gaussian, the opt keyword uses an approximate Hessian to determine the displacement at each step. The freq keyword will recalculate these displacements using the actual Hessian for that level of theory and sometimes you will find that they are no longer below the threshold. This can mean that your structure is ...


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