# Matter Modeling Stack Exchange Community Digest

## Top new questions this week:

### Using OpenBabel's gen3d in a Python notebook

I want to preface this by saying I am really new to computational chemistry and this kind of programming in general, but I am having real trouble figuring out how to use OpenBabel's ...

computational-chemistry python smiles openbabel
 asked by Meheret Score of 6
 answered by Ivan Chernyshov Score of 3

### gyration radius of short freely jointed chain with excluded volume

The freely jointed chain model without excluded volume has the following gyration radius, $$\langle R_g^2 \rangle=\frac{1}{6}\frac{N+2}{N+1}Na^2$$ where $N$ is the number of bonds and $a$ their ...

molecular-dynamics statistical-thermodynamics polymers
 asked by Marco Mendívil Carboni Score of 5
 answered by Shern Ren Tee Score of 5

### Extracting band structure data using Boltztrap for Quantum ESPRESSO

I used PBE0 in my calculations using Quantum ESPRESSO . I have ran a scf calculation then I used Boltztrap by running the command btp2 -vv interpolate -m 3 ./ then <...

density-functional-theory quantum-espresso band-structure bandgap boltztrap
 asked by Camilla Score of 5
 answered by Phil Hasnip Score of 4

### Constrained optimisation on a hypersphere

I am currently trying to implement a GS2 (Gonzalez-Schlegel second order) IRC algorithm in a python code. I am following the original paper ref(1). The main problem is in the constrained optimisation ...

python geometry-optimization mathematical-modeling derivations
 asked by S R Maiti Score of 5
 answered by Shern Ren Tee Score of 6

### What's the meaning of k-points with weight zero?

In a post from the Quantum Espresso mailing list, a user suggests adding k-points with weight zero to an SCF calculation as a workaround to allow bandstructure to be computed using a hybrid functional....

density-functional-theory quantum-espresso physical-properties-of-materials k-points
 asked by Camilla Score of 4
 answered by Laura Score of 5

### How do I get openMPI to run with gromacs?

When I run the command mpirun -np 48 mdrun_mpi -deffnm md -v, the software works with no error, but it only runs as fast as when I'm using 1 CPU (the computer I'm ...

gromacs
 asked by hbc8 Score of 4

### Absorption spectra with Gaussian

I want to calculate the absorption spectra of molecules (and possibly ions) with TD-DFT. I have used Gaussian in the past and, to my knowledge, the application of TD-DFT is implemented in this code. ...

gaussian td-dft optical-properties
 asked by Laura Score of 4

## Greatest hits from previous weeks:

### When should spin polarized calculations be done?

Should the presence of a d block element in the unit cell mandate the need for performing spin-polarized calculations? I wanted to find out the DOS, PDOS, and the band structure. I'm new to DFT and I'...

density-functional-theory vasp quantum-espresso magnetism spin
 asked by Anoop A Nair Score of 13
 answered by Thomas Score of 9

### Is the number of possible Bravais lattices a mathematical fact?

Almost anyone that has taken a Solid State Physics course will know, that any 3D crystal must be in one of the 14 Bravais lattices due to symmetry operations and space filling. In 2015, a paper was ...

crystal-structure crystallography symmetry
 asked by Camps Score of 20
 answered by Anyon Score of 22

### How to understand the time-reversal symmetry in graphene?

A lot of references say that the Dirac cone in graphene is protected by inversion and time-reversal symmetries. How can one understand this statement? How can one show explicitly that the gapless ...

condensed-matter band-structure tight-binding symmetry graphene
 asked by JensenPang Score of 17
 answered by ProfM Score of 19

### Classical Monte Carlo vs. Molecular Dynamics

Both Classical Monte Carlo (MC) and Classical Molecular Dynamics (MD) simulations are used to perform simulations of ensembles of molecules. These MC calculations are calculating thermodynamic ...

molecular-dynamics monte-carlo ergodicity
 asked by 2ndQuantized Score of 15
 answered by ProfM Score of 14

### What software will allow me to combine two images?

I have seen in many presentations and publications, things like a human on a molecule (for example). What software can do this? It's for a presentation I'm doing.

 asked by Savir Score of 21
 answered by Alessio Valentini Score of 21

### GUIs for Quantum Chemistry... Where are they?

I have a general and maybe a little silly / funny question. Why don't most CompChem or QuantumChem software have a GUI? SIESTA is trying with Simune as far as I know, but even proprietary software ...

software computational-chemistry high-performance-computing graphical-user-interface matlab
 asked by Elie H Score of 20
 answered by Tyberius Score of 15

### What are the freely available crystal-structure visualization softwares?

I use VESTA mostly for crystal structure visualizations. What other options are available?

software crystal-structure vesta atomic-simulation-environment
 asked by Thomas Score of 31
 answered by Fabian Score of 29

## Can you answer this question?

### How to determine high-symmetry points in case of PBE0 using Quantum ESPRESSO?

Normally when we use PBE-GGA as an approximation we can determine the high symmetry points in x coordinate from the output file of bands.x calculation . But in the ...

density-functional-theory quantum-espresso band-structure symmetry bandgap
 asked by Camilla Score of 1
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