Questions tagged [software]

For questions about matter modeling software. Questions can be about usage or recommendations.

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Benchmarks for optimised Math Libraries across platforms

Are there any benchmarks of low-level and high-level math operations from different Math libraries on corresponding architectures? Here are a few packages: LAPACK / BLAS + ATLAS (stock version from ...
132 views

Raman Spectra in Quantum Espresso

Does anyone have any experience simulating Raman spectra in Quantum ESPRESSO? Following the example 15 that comes with QE, I have attempted to simulate the Raman spectrum of MgO. I know the lraman ...
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1k views

DFT code for simulating thousands of atoms in a supercell

I'm trying to simulate a supercell that contains thousands of atoms with the DFT method, but it seems VASP couldn't handle such a large system, its parallel efficiency is relatively low, when I try to ...
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How to run SCRF in Gaussian with extra basis?

I want to run a SCRF calculation in Gaussian for a molecule. This has been done as standard with several geometries without issue using the aug-cc-pvtz basis and ...
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List of programs for post-CCSD(T) calculations

Implementations of CCSD(T) are almost too numerous to list, but CCSDT and CCSDT(Q) are much more rare. I have compiled a list of such programs below, and I would be interested to hear if anyone is ...
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Repeated error in Quantum Espresso "Error in routine potinit (1)"

I have been trying to perform some calculations in Quantum espresso on mono-layer Borophene. Initially, I have optimized the structure which succeeds. Subsequently, I am trying to use this optimized ...
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Extracting bond information from the xyz positions of atoms?

I have xyz positions of my atoms in a .txt file, how can I extract information about bonding using VMD? I want to create a LAMMPS input file that contains not only ...
64 views

RPA calculations with Hybrid Functionals

When doing RPA calculations as explained here, if I want to calculate it with hybrid PBE0 should I put LHFCALC = .TRUE. for just step 1 or step 1, step 3 and step 4?...
48 views

How to export .xyz files from VESTA of crystal viewed along different crystallographic axes

I've only been able to export atomic coordinates for a crystal when looking down the c axis, but I need to do so along the a and b axis as well. I've tried changing the Projection Vector in the ...
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Functional group detection from geometry

I am currently looking for an efficient way to detect common functional groups - that is, characterize whether a molecule is an alcohol, an aromatic compound, etc. - in a larger database consisting of ...
1k views

Converting SDF to PDBQT using OpenBabel

I want to convert several molecules from sdf format to pdbqt using OpenBabel. However, I can't find ...
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108 views

Excited determinants, electronic partition function and thermochemistry calculation

While studying statistical thermodynamics I came across the partition functions, which connect the quantum world to the macroscopic world. I understand that partition functions are used to calculate ...
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What do the parameters at the top of an FCIDUMP file mean?

A while ago I wrote a simple program that takes in an FCIDUMP file (generated by MOLRPO) and can determine matrix elements (or ...
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What software can do RNA secondary structure prediction?

This question is a follow-up to this previous question. I have learnt there that there are reasonable ways to predict RNA tertiary structure. Here I inquire about how to predict RNA secondary ...
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What software is a software for RNA tertiary structure prediction?

It seems that the prediction of protein folding is a pretty advanced area. Are there options based on some GDT-like measure? For me, it has relevance in connection with the origin of life (cf. RNA ...
4k views

What is a good replacement for Gaussian?

When I started studying computational chemistry (circa 2007), my supervisor used to tell me about the controversy surrounding Gaussian, Inc. regarding the banning of researchers involved in the ...
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