# All Questions

293 questions
Filter by
Sorted by
Tagged with
2 views

### What are the practical limitations of R12/F12 methods?

Electron correlation methods based on an expansion of the $N$-electron wavefunction in terms of Slater determinants have a slow basis set convergence. Moreover, explicitly correlated methods (such as ...
26 views

### How much does the initial geometry effect the final geometry in optimization calculations?

This might be a stupid question but to what extent will the initial configuration of a bulk phase geometry optimization calculation effect the final geometry? Most places say to start with ...
25 views

### Materials Modeling with Raspberry Pi?

Does anyone have any knowledge or direction for creating a homemade Beowolf cluster for materials modeling? I would like to be able to run my own "hobby" simulations at home, so a low energy, low ...
28 views

### Running quantum espresso calculations in google colab

So one big problem I experience in doing calculations with quantum espresso is that many calculations require a lot of computing power: you need large RAM capacities and powerful processors especially ...
179 views

### Difference between Van der Waals (DFT-D and DFT-D3) corrections in ab-initio calculations

In Kohn-Sham DFT calculations, Van der Waals corrections are often implemented in the structure optimization calculations because the typical functionals such as LDA and GGA are found to not treat ...
74 views

### What is the mathematical condition that ensure that the self-consistent field (SCF) procedure must converge?

We know that there is convergence issue of DFT method on study real molecular system. It would be conducive if people could pre-determine if the SCF procedure is converge analytically before starting ...
15 views

### Can you model Radiation Chemistry with existing MD software?

I'm wondering if it is possible to simulate the chemical changes materials undergo when exposed to ionizing radiation for a finite period of time with Molecular Dynamics (MD) software. In principal ...
265 views

### How does the Hartree-Fock method improve on Hartree after considering the wavefunction that takes the anti-symmetry property into account?

I am not able to understand the math of this. After taking the Slater determinant as a wavefunction in Hartree-Fock, does the procedure to find wavefunctions remain the same as in the Hartree method ...
40 views

### How the projected density of states is built

I'm new to DFT. I'm trying to figure out how projected density of states (PDOS) is built in solid state physics software package. I understand the basics of the density functional theory method: each ...
63 views

### What is the impact of the orientation of a molecule in cartesian coordinates to molecular properties?

According to my knowledge, each computational chemistry code optimizes a molecule keeping the input orientation of the molecule. The population and spectral analysis is performed on the optimized ...
110 views

### Predicting linear dependencies in a basis set in advance of calculating any integrals

I've been doing some calculations for a water molecule, with a big uncontracted basis set: For oxygen I am using aug-cc-pV9Z supplemented with the "tight" functions from cc-pCV7Z. The s-type exponents ...
18 views

### Can we do anything to reduce the number of displacements in a frozen phonon lattice dynamics study?

I realize that the more ordered the supercell is, the lower the number of displacements. Perhaps, we could say the same with respect to symmetry. Is there anything that can be done to reduce the ...
30 views

### Is there an example where TD-DFT fails to provide sufficient accuracy for a small system, where RI-CC2 is sufficient?

Time-dependent density functional theory (TD-DFT) is considered to be more efficient (in terms of its accuracy/speed ratio) than alternatives such as the approximate coupled-cluster singles and ...
102 views

### Since MKL is not optimized for AMD hardware, should I use a math library specific to AMD, or would an open-source one be just as good?

The codes for quantum mechanical calculations make heavy use of linear algebra, and it seems most of them delegate this task to time-tested and highly optimized libraries, instead of trying to deploy ...
40 views

### Discrete molecular models

It seems to be taken in Cheminformatics that molecules with similar physical structure tend to have similar chemical properties https://dl.acm.org/doi/pdf/10.1145/2366316.2366334 Based on this, our ...
53 views

### Is there any literature that systematically analyzes current quantum chemistry algorithms using Big O notation for time and memory cost?

Big O notation is commonly seen in the papers on novel computational methods. However, only a few of them include rigorous analysis of the algorithm. Is there any literature that summarizes current ...
26 views

### Avoiding charge-migration in electronic structure calculations with solvent like environments

When performing electronic structure calculations on a molecule one can surround it with point charges to mimic a solvent environment and lend polarization effects. There is a bit of caveat ...
22 views

### 2D Brillouin zone generator

There are several pages where you can find scripts/simulations to generate the first Brillouin zone for square and hexagonal 2D lattices. I wonder if there is a tool to generate the Brillouin for ...
229 views

### Labeling of high symmetry points in Brillouin zone

A Brillouin zone is defined as a Wigner~Secitz primitive cell in the reciprocal lattice [1,2]. The construction of the first Brillouin zone for two different 2D lattices are shown below: The ...
90 views

### Is it possible to use the Parrinello-Rahman barostat for NPT simulations in CP2K?

It is possible to use different types of thermostats in CP2K by specifying them in the corresponding section of the input as mentioned here. But there is no mention of specifying the barostat type in ...
59 views

### How to optimize zinc oxide bulk structure at certain pressure with LAMPPS

** edited ** I am trying to simulate the Zinc oxide bulk structure (periodic) with many different pressures to observe phase changing. Initially I would like to achieve constant pressure at 0.0 bars ...
60 views

### How accurately are magnetic effects treated in *ab initio* methods?

I am a condensed matter theorist and I mostly use quantum Monte Carlo methods. I use models like the Heisenberg model, an represent an extreme simplification of real materials to just localized spin ...
25 views

### Calculation of local dielectric constant from MD output?

Has anyone been able to successfully calculate a local dielectric constant profile from MD output positions and charges? All the papers I have found seem to focus on calculations for the entire system....
232 views

### Is there any software that is optimized specifically for QM/MM?

A lot of codes can do QM/MM, and I am not naively asking if there is a program that can do QM/MM. What I am interested in is a program that is purely QM/MM meaning that it is designed and optimized ...
166 views

### How to calculate energy of a molecule in an aligned electric field?

So I am aware that many quantum chemical codes are able to add external fields to molecular calculations (for example to calculate polarizabilities). I also know that in some (eg. Orca) you have some ...
2k views

### What are the “smart algorithms” applied in computational chemistry to solve the “curse of dimensionality” problem?

The "curse of dimensionality" is an ubiquitous issue arise in both electronic structure and quantum molecular dynamics in computational chemistry, which refers to the exponential scaling of the ...
618 views

### What exactly is the “Optimizer” in CP2K geometry optimization?

I'm just now starting to use the program CP2K, and I am having trouble understanding the difference between the optimizer options (CG, BFGS, LBFGS). I have seen ...
114 views

### CCSD(T) Transition State and Ground State Calculations in Gaussian09: “Unable to Determine Lambda”?

I’m doing CCSD(T) calculations (for both transition and ground state geometries) on a series of small molecules in Gaussian09. Several similar calculations terminated without any problems but one TS ...
404 views

### Is there a performance difference when using fractional coordinates instead of Cartesian coordinates?

In general, the CIF file with the crystal structure uses fractional coordinates for setting the atoms positions. In this type of coordinates, the atom positions are relative to the cell parameters. ...
57 views

### VASP Dielectric constants: What potential to use?

I've simulated the dielectric constants using the LEPSILON = .TRUE. tag and the PBE GPAW potentials. A collegue mentioned that for accurate results norm conserving pseudo-potentials are the way to go. ...
64 views

### Understanding the GTH Pseudopotential

I'm new to DFT. I want to make use of the GTH pseudopotential. I am trying to understand how this potential works. I read the article "Separable dual-space Gaussian pseudopotentials" by S. Goedecker, ...
580 views

### How to write my own density functional theory (DFT) code in Python?

I am a DFT user and at some point in the future, I would like to write my own DFT code in Python to help gain a deeper understanding of DFT. As mentioned in a previous answer people have written their ...
1k views

### How to “get my feet wet” in Density Functional Theory by simulating a water molecule using Python

I just saw I am a beginner in Density Functional Theory. What are some resources that could help me to learn the basics? and it reminded me that few years ago I'd asked How can I calculate the charge ...
46 views

### Hexagonal lattice volume EOS fit

I have a little problem concerning hexagonal volume fitting using VASP. I have followed these steps: Relax the structure from a given volume using ISIF =4 Copy ...
724 views

### I am a beginner in DFT. What are some resources that could help me to learn the basics?

I am a beginner in DFT. Please suggest me some good material to understand the basics.
73 views

### How to calculate homolytic bond dissociation energies?

An experimental colleague asked me how hard it would be to calculate homolytic bond-dissociation energies for different phosphonates which are involved in a Hydrophosphination. The compounds include ...
122 views

### Converting adsorption binding energy to absolute temperature

The binding interaction energy during the adsorption of system B on system A can give an idea if the interaction is favorable (negative value) or unfavorable (positive value). Also, the absolute value ...
31 views

### How to understand dynamical spin structure factor?

A newish area of interactions between quantum Monte Carlo (QMC) and experiments is in spin spectra. Recent improvements in stochastic analytic continuation have made it much easier to compare extract ...
48 views

### Cancellation of Errors in density functional approximations or any wavefunction based methods

I am curious to find references for when is it TRUE that the error cancellation in approximate methods like DFT/MP2/etc. are valid and when they fall apart. For example: My understanding is (please ...
40 views

### Parse linked frequency calculations with cclib

I have multiple Q-Chem output files for TS search starting and finishing with frequency calculations (two sets of calculated IR data in total). To parse and plot spectra I use cclib and a script ...
40 views

### Which basis set families were optimized to give the lowest possible variational energy for a given number of orbitals?

Dunning's basis set families (such as cc-pVXZ and aug-cc-pCVXZ) were not optimized to give the lowest variational energy for a given number of orbitals. For example the S-type orbitals are optimized, ...
36 views

### Developing skill in force matching of interatomic potentials?

I am building skills in using force matching from AIMD data (nonlinear least-squares minimization) to generate interatomic potentials for use in classical MD. I understand the concepts of selecting ...
148 views

### How is the material $\ce{\alpha-NaMnO2}$ pronounced? [closed]

I am a theoretical physicist, so I am not very familiar with chemical names. The material I am interested in is $\ce{\alpha-NaMnO2}$. Would that be pronounced alpha sodium manganese dioxide? Is it ...
280 views

### Is there any definitive evidence that implicit solvation methods are more accurate than explicit solvation methods for free energy calculations?

I am looking for real data that concludes that implicit solvent models are definitively better than explicit solvent models for solvation free energy calculations. The motivation is a lovely ...
46 views

### Discrepancy between numerical and transformed derivatives

This is related to a prior question of mine Derivatives with respect to user defined vibrational modes. While that one focuses on potential software to use for derivatives with respect to normal modes,...
100 views

### State of the art in computational materials design

With the advent of more computational power than ever in the recent years, interest in in silico design of interesting compounds has grown as well. I am wondering about the state of the art for the ...
368 views

### How to export a calculated Raman spectrum in Q-Chem, as a Gaussian profile?

Does anyone know how to export a calculated Raman spectrum (my calculation was performed in Q-Chem) as a data-file, which can be used to plot the profile of a Gaussian-shape spectrum (in origin, excel,...
36 views

### What is band inversion and how to recognize it in band structure?

Band inversion is a key ingredient of a topologically nontrivial material$^1$. What is band inversion? How to recognize it in a band structure? What conclusions can I infer if I observe band inversion ...