Questions tagged [software]

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

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70
votes
6answers
8k views

Did the 2019 discovery of O(N log(N)) multiplication have a practical outcome?

Some time ago I've read this news article, Mathematicians Discover the Perfect Way to Multiply, reporting a discovery published in 2019, where Harvey and Hoeven[1] found a algorithm able to execute ...
34
votes
13answers
2k views

What is a good programming language for matter modeling?

What is a good programming language for matter (e.g. molecular or materials) modeling? Since this is a broad field, I don't expect there to be only one answer.
34
votes
5answers
767 views

Why do we have so many DFT codes (softwares)? Are they redundant?

Lejaeghere et. al studied reproducibility of DFT codes (softwares) by comparing 15 different codes employing 40 different potentials. The study concluded that most codes agree very well, with ...
30
votes
5answers
2k 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 ...
29
votes
3answers
388 views

What are the positives and negatives of periodic DFT codes that don't use plane-wave basis sets?

Most periodic density functional theory (DFT) codes use plane-wave basis sets in conjunction with three-dimensional periodic boundary conditions. In contrast, for molecular systems of finite size, ...
28
votes
9answers
637 views

Is there a free package with robust CASSCF functionality?

Among free software packages, which one has robust CASSCF functionality? The FCI solver can be implemented in either way, e.g., direct solver, DMRG, etc.
27
votes
9answers
4k views

Which Linux distribution is best for Matter Modeling?

In some science fields there are efforts to provide customized distributions, so you can get a productive environment with minimum set-up overhead. For example, in high energy particle physics, we ...
27
votes
2answers
439 views

How is Julia used in Materials Modeling?

What are the main uses and applications of Julia in Materials Modeling? Python for example is used in codes such as kwant, ...
26
votes
12answers
691 views

What are the freely available crystal-structure visualization softwares?

I use VESTA mostly for crystal structure visualizations. What other options are available?
25
votes
4answers
3k 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 ...
24
votes
4answers
300 views

What are the main computational frameworks used in materials modeling?

What are the main computational frameworks used in materials modeling? Software packages can include those designed to run on both classical and quantum devices.
22
votes
3answers
169 views

Enforce a space group on a given crystal structure

If I have a CIF that is P1, is there a (preferably free) code that can map the structure to some user-specified space group? I know that there are ways to do similar things with molecular systems. For ...
21
votes
5answers
4k views

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.
21
votes
3answers
1k 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 ...
21
votes
2answers
280 views

How to calculate diffraction pattern from a model of unit cell?

I remember that 20+ years ago we used a program called Powder Cell to calculate diffraction patterns from models of materials (for example, to compare it with experimental data from powder diffraction)...
20
votes
2answers
183 views

What software are used to model the optical behavior of metallic nanoparticles?

It's fairly routine to calculate absorption of single molecules, essentially this can be done by calculating the excited-state wavefunctions and the oscillator strengths between the states. For ...
19
votes
5answers
2k views

What software is available to do molecular dynamics on Windows?

Is there a Windows-based molecular dynamics simulation software which is easy to use?
19
votes
3answers
254 views

What software is needed in chemoinformatics or materials modeling, that a solo programmer could work on?

I want to make a pet project in cheminformatics and I need to hear from the community about the actual challenges in chemistry that might be resolved with a digital solution. I've been working in ...
19
votes
2answers
329 views

What significant matter modelling methods are implemented in commercial software, for which there is no freeware alternative?

There is an ever-growing list of freeware and open-source software for solid-state physics and quantum chemistry. But many commercial programs still thrive, even in 2020, and their cost can be in ...
19
votes
3answers
226 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 ...
18
votes
3answers
161 views

What tools are used for the preparation of grain boundary models?

What methods and tools are used for building models of grain boundaries? I mean initial models that are then optimized using molecular dynamics potentials or a different methods. When I was involved ...
18
votes
2answers
377 views

What is a chemputer?

I first saw the term "chemputer" when reading about the work of Neil Ostlund (who you may know as one of the authors of the famous book "Modern Quantum Chemistry"). Based on the ...
18
votes
1answer
257 views

How to set up a local server for iQmol on macOS?

I'm trying to set up iQmol as a tool to submit calculations to Q-Chem on our lab machines to make access to it easier for OChem students. Unfortunately, it is not working properly "from the box&...
17
votes
2answers
2k views

Calculating HSE06 band structures on Quantum ESPRESSO

I am currently trying to figure out how to compute band structures for my system, using the hybrid functional HSE06. I'm doing this on Quantum Espresso. As I understand, there are a handful of ways to ...
17
votes
1answer
302 views

Alternatives to VEDA 4 vibrational energy distribution analysis software?

Said software is useful when you need to assign the peaks in vibrational spectra to different vibrational modes found in a hessian calculation for a given molecule, as described in Jamróz, Michał H. “...
17
votes
1answer
407 views

Are there problems with the Tran-Blaha modified Becke-Johnson potential (mBJ, a.k.a. TB09) in Quantum ESPRESSO?

I have used the modified Becke-Johnson (mBJ) exchange potential before, as it was developed and implemented in Wien2K by Fabien Tran and Peter Blaha (1). In 2013, Éric Germaneau et al. implemented mBJ ...
17
votes
1answer
86 views

Converging the potential of a dilute binary alloy system using the Coherent Potential Approximation. What troubleshooting options could I take?

I'm trying to converge a dilute fcc alloy consisting of Cu and U, with the Uranium concentration at 0.01% and the lattice parameter of Cu, using Hubert Ebert's Spin Polarized Relativistic Korringa-...
16
votes
4answers
414 views

Is there a set of updated, comprehensive benchmarks for speed comparison between different quantum chemistry packages?

I've found a page dedicated to quantum chemistry packages benchmarks, on GitHub, qmspeedtest. But most results there are several years old, and so probably outdated. Is there some place where we can ...
16
votes
2answers
389 views

How should I organize and keep track of a huge number of calculations systematically?

Doing matter modeling generates vast amounts of data. We might most probably be working on different projects simultaneously. We definitely will have to revisit old data for revisions, post-processing,...
16
votes
3answers
371 views

Computational tools for automatic creation of surface slab models of complex systems

I am looking for computational tools that can be used to automatize the generation surface slab models of latices of oxides, layered oxides, perovskites etc. I have found a promising Python package, ...
16
votes
2answers
105 views

Methods for visualising aromaticity

I was wondering what tools there are for visualising aromaticity and anti-aromaticity in molecules, to what quantum chemistry programs they are interfaced, and what other relevant features they have. ...
16
votes
2answers
406 views

What's the best way to compare two DFT codes?

What's the most efficient way to compare the two DFT codes in terms of computation time, basis sets (for example, one plane wave vs one atomic orbitals), functional performance, etc.?
16
votes
1answer
368 views

How to map the electrostatic potential from GAUSSIAN, on a solvent accessible surface?

Gaussian cubegen and surface generators in Gaussview seem to only allow to map the ESP on SCF densities. I used G16 for the ESP generation. I would like to plot it on the solvent accessible surface. ...
16
votes
1answer
109 views

What are typical RPA capabilities of plane-wave codes?

Plenty of standard plane-wave codes are able to compute correlation energies on top of DFT solutions using the random-phase approximation (RPA). I was wondering what the typical capabilities are in ...
16
votes
1answer
155 views

How are one-/two- particle reduced density matrices printed in mainstream programs?

The FCIDUMP format is widely used for the communication of one- and two- body integrals. I wonder what formats are used for 1-/2-RDMs, which are important in many basis rotation or compression tasks. ...
16
votes
1answer
194 views

How to calculate t-zero temperature using Thermo-Calc- Python (TCPython) for multiple alloys?

T-zero temperature is the temperature at which the Gibbs energies of two phases are equal. Here, I wish to find the temperature at which FCC and BCC have same Gibbs energy. Thermo-Calc console mode ...
15
votes
4answers
236 views

Are there any open source software for calculating the rotational and translational entropy of molecules?

What is a good open source software for calculating the rotational and translational entropy of molecules? The National Institute of Standards and Technology does not provide standard molar entropy ...
15
votes
3answers
267 views

What are some codes available for Dynamical Mean Field Theory (DMFT)?

One particularly field of matter modeling is that of strongly correlated materials, heavy-fermion compounds with partially filled 4f or 5f orbitals. In brief, these are materials whose complex ...
15
votes
3answers
412 views

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

A lot of codes can do Quantum Mechanics/ Molecular Mechanics (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 ...
15
votes
3answers
167 views

Does anyone know any software for MD simulation which include the effect of magnetic field?

I am interested to generate some configurations from MD simulations which include the presence of strong magnetic field. Does anyone know any software that has some functionality to do this?
15
votes
1answer
122 views

Where can I find a tool or server to generate tiles nodes cordinates?

Does anyone know a tool or a server that can generate the node coordinates for different tiles? I would like to create 2D materials based in some periodic tiles like the ones in the image below: ...
15
votes
0answers
128 views

Is there a software that can do derivatives with respect to user defined vibrational modes? [closed]

I'm doing some property calculations that depend on a sum of derivatives of some quantity with respect to normal vibrational modes. I was hoping to find some physical intuition relating the type of ...
14
votes
8answers
2k views

What are some free programs to do docking?

I'm interested in doing molecular docking. What are some free programs for it and what are their pros and cons?
14
votes
3answers
542 views

Is the DYNAMO code developed by LAMMPS still available?

In 2013 it was stated that v8.8 of DYNAMO was the version mostly used for the last 10-12 years. However I am struggling to find the code repository. It was developed by the LAMMPS developers and is ...
14
votes
2answers
764 views

What is the most user friendly software for frequency visualization rendering?

I perform my calculations in Q-Chem and would like to make short movies of IR modes. As of now, I render them with IQmol, but I believe graphics properties (colors and resolution) can be much better. ...
14
votes
1answer
163 views

Software to draw 3d micelle configuration

I am looking for a free software able to draw 3d micelle configuration like the figure attached. Any suggestion?
14
votes
1answer
201 views

Great computer graphics for matter modelling

I am trying to write some code to automatically generate a judicious set of graphics from DFT/fn-DMC calculations so that users can sanity check their results quickly. My literature review has found ...
13
votes
4answers
265 views

Is python sufficient for serious tensor network or DMRG calculations?

There are enough tensor-network/DMRG packages that support python (ALPS, OpenMPS, pyUni10) that it would seem (to an outsider) that it's possible to do some substantial work with DMRG without messing ...
13
votes
5answers
2k views

Can I use two different codes?

Can I use one code for geometry optimization and another code for a single point calculation on that optimized geometry? Can one publish results like that?
13
votes
4answers
267 views

What are some open-source all-electron DFT alternatives to Wien2K?

Since the beginning of the century, Wien2K has proven to be a very powerful player in computational condensed matter and materials physics. Wien2K is an all-electron periodic DFT code based on the ...