Questions tagged [one-topic-per-answer]

Special tag for certain big-list questions. Answers should only go into detail about one specific topic related to the question. The original question will often present a template format for submitting answers.

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8
votes
2answers
211 views

Which methods are size-consistent / size-extensive, and why?

This is a follow up question from another question I posted here. I am looking for an explanation (or a mathematical proof, if possible) of the size extensivity and size consistency of the following ...
9
votes
5answers
250 views

Recommended software to open NetCDF files?

I found plenty of packages that open .nc files but all specifically catered to climate (meteorological) and geo-maps data. I would like to get suggestions of ...
7
votes
2answers
110 views

What software can be used for Crystal Surface Calculations?

I have been unable to find software for making surface calculations, so I currently perform surface calculations in LAMMPS by creating crystal structures in python, before rotating and cutting them ...
7
votes
3answers
303 views

Open source FCI solvers for exact diagonalization of the many-electron Hamiltonian

What open source solvers (according to the generally accepted Open Source Definition i.e. licensed under a valid open source license) are available for full configuration interaction calculations? ...
13
votes
1answer
99 views

How are structure descriptors used in regression or machine learning?

I am currently working on prediction of UV-vis spectra from structure of molecules. I have read multiple papers where structure descriptors were used as inputs for machine learning to find various ...
13
votes
1answer
233 views

Are there any benchmark test sets for UV-vis absorption maxima?

In computational chemistry, I have come across many test sets which are used to benchmark a new method. For example, the G2 test set for thermochemical calculations (heats of formation). There is the ...
4
votes
1answer
41 views

Is there a site to obtain or create membranes?

I am interested in creating an enterocyte intestinal basal membrane. So, I wonder if there is a database or site where the membrane could be downloaded or created.
15
votes
2answers
304 views

What's the best quantum chemistry output parser for the command line?

This question is about tools like Open Babel. Are there any good command-line parsers for quantum chemistry program outputs? A good Python library could come in as a close second. I am interested e.g. ...
13
votes
3answers
1k views

How can I submit jobs to an HPC scheduler?

It is my first time trying to use an HPC system and I am a bit overwhelmed. I have gone through a course on using HPC systems on Coursera and have a basic idea about using Linux. Could you guys tell ...
9
votes
1answer
316 views

How can we calculate the Gibbs free energy from first principles?

I am trying to calculate the Gibbs free energy for a bulk material. Since DFT ground state calculations give the energy at 0K, a temperature dependent part has to be added in this to obtain correct ...
5
votes
1answer
73 views

List of software for creating random multi-component alloy inputs for DFT or MD

I'm looking for a list of tools similar to ATAT which are available for creating random multi-component alloy inputs for DFT/MD.
8
votes
1answer
246 views

Functional group detection for group contribution methods

I would like to be able to parse a molecule into its functional groups, and, also, know the number of occurrences of each. A similar question was asked on matter modelling specifically for xyz files. ...
9
votes
1answer
65 views

Package for computing properties of excited vibrational states

We're starting to develop some calculations of the hyperfine parameters (electric field gradient, spin-rotation coupling, spin-spin coupling) with CFOUR, and we reached a limitation of the public ...
9
votes
2answers
98 views

Classes of Graphs used in Chemistry

I am looking for common categories of graphs used in chemistry, for math research I am doing in graph theory. When I write categories, the meaning is not for graphs design or types of design, but for ...
9
votes
0answers
66 views

Software for calculating the mirror Chern number of 2D systems? [closed]

Can anyone please explain to me how can I calculate the mirror Chern number of a 2D system? I will be very thankful if you can refer me to a package or software which can directly perform mirror Chern ...
12
votes
1answer
130 views

What are the databases of semiconductor properties?

Is there any database listing the experimentally-determined properties of semiconductor materials - things like Band Gap and Electron Mobility. These are easily found for common materials like ...
12
votes
2answers
162 views

Is there some free software to do Frank-Condon analysis?

I know Gaussian 16 can do it, but are there some free programs that can? For simple excited state calculations using TD-DFT, we can use NWChem and Octopus. Can these do Franck-Condon factors?
10
votes
3answers
549 views

Which DFT functional should I use to simulate spectra of pesticides?

I am mainly searching for functionals to calculate spectra of pesticides. I found the benchmark test from Goerigk and Grimme$^1$, but don't understand which of the functionals suits my purpose the ...
8
votes
0answers
79 views

What are some types of topologically-relevant band degeneracies in contemporary 2D condensed matter research?

Cross-posted on Physics.SE. In the study of 2D condensed matter systems, I have seen several kinds of band degeneracies. I call 'bands' the eigenvalues to the time-independent Schrodinger equation, ...
8
votes
1answer
141 views

Chimera or other software to perform protonation states of a protein

I want to perform a Molecular Docking between some ligands and a protein in different pH conditions. For this, I calculated the distance between atoms in different pH concentrations for the ligands, ...
4
votes
1answer
58 views

Optical anisotropy from first-principles

I am interested in the theoretical study of optical anisotropy (birefringence, dichroism etc.) of different materials. I have seen DFT works studying optical anisotropy from the calculation of ...
19
votes
3answers
3k views

Solving the Schrödinger equation as a service?

Does anyone know of a company with a cloud-based service which takes some representation of a molecule as an input, and then somehow solves the Schrödinger equation to some level of accuracy and ...
13
votes
1answer
121 views

GUI-based force field optimization with bond-typing

I am looking for a list of programs that support structure relaxations via molecular mechanics (e.g. via UFF) with the following conditions: The program is free (free with an academic license is okay)...
9
votes
1answer
87 views

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 ...
14
votes
5answers
1k views

What are some cloud services for computing?

A group of researchers in my university (including me), started to study the possibility to move to cloud computing services in order to run our simulations. The simulation areas include condensed ...
9
votes
1answer
70 views

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 ...
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.
10
votes
2answers
176 views

Programs/Libraries for calculating solvent excluded surface and excluded volume

Given the 3D structure of a molecule (e.g. as *.mol) and a probe radius r, I want to calculate the solvent excluded surface (SES)...
11
votes
3answers
791 views

How to build a nanocluster?

What are the software tools (if possible open source) or methods we can use for constructing a nanocluster, most preferably with high symmetry such as icosahedron, octahedron, cuboctahedron etc. ?
12
votes
0answers
106 views

What are the recent developments of GW@BSE to simulate the excited properties of materials?

A twin question related to the TDDFT method is asked in another post. But any comparisons between both methods in recent developments are welcome. The time-dependent density functional theory (TDDFT) ...
18
votes
0answers
132 views

What are the recent developments of TDDFT to simulate the excited properties of materials?

The time-dependent density functional theory (TDDFT) and the many-body perturbation method (GW@BSE) are considered as the two most popular and successful methods to describe the excited-stated ...
12
votes
1answer
106 views

Recent developments in QM/MM for Molecular Dynamics

I am looking for new QM/MM methodologies which have recently developed and implemented into MD packages. Any applications or molecular systems studies with these methods can be used as an example as ...
16
votes
2answers
440 views

Software for solving quantum systems in 1D and 2D

I'm looking to solve quantum system in 1D and 2D consisting of a large number of sites. What are the pros and cons of each package, and which package is more suitable for what type of calculations? ...
12
votes
0answers
102 views

Periodic polarizable QM/MM embedding [closed]

Are there any standalone open source software codes available for periodic polarizable QM/MM embedding MD simulations? In my knowledge, CP2K only has the option for electrostatic embedding and other ...
9
votes
1answer
185 views

A good software for DFT optimization and nonlinear optical properties

I'm running a series of calculation for nonlinear chromophores. The general pipeline is geometry optimization (B3LYP/def2-TZVP) -> Frequencies -> Hyperpolarizability calculation (M06-2X (or CAM-...
13
votes
3answers
203 views

Are there any codes to study magnetic materials?

I have used a few codes for studying magnetic materials (specifically core-shell nanoparticles with an AFM shell and an FM core). These are: Vampire: For the calculation of curie temperature via ...
10
votes
2answers
110 views

Can you list some useful code snippets for processing quantum ESPRESSO output files?

I know that this is quite general. But we have all written code for processing output files from various dft codes. The functionality of which, may range from analysing time traces to finding ...
19
votes
2answers
466 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 ...
7
votes
2answers
978 views

Computer simulation of squeezing flexible objects with force

I am looking for any software, or scientific works, or search phrase in the field of simulating graphic modeling of squeezing objects. I would like to simulate packing very oddly shaped soft elastic ...
5
votes
1answer
32 views

What are some ways to model disequilibrium processes with current software?

Its normally that case that most material modeling techniques rely on energy minimizations, which result in the equilibrium solutions for most chemical of physical processes. While this is great for ...
15
votes
4answers
2k views

How can I visualize the trajectory of a VASP simulation?

Which software package(s) can be used to visualize the trajectory of VASP MD simulation? VMD claims that there is a plugin to read the VASP output, while in the last version for Linux, I did not find ...
13
votes
1answer
356 views

Suggestions for a good crystal structure visualization workflow

Following up on this question about freely available crystal structure visualization codes, I wish to know what procedures people follow from start to finish in preparing images of their materials for ...
9
votes
3answers
1k views

Molecular visualization software in Jupyter (IPython) Notebooks

Jupyter notebooks have always been a great way for me to create high-quality graphs, and write code. The features also continue to improve with packages such as Jupyter Lab, and now Jupyter Books, ...
12
votes
2answers
615 views

What software can be used to do QTAIM analysis?

I have a rather general question of what software packages exist to do Quantum Theory Atom in Molecule (QTAIM) analysis of periodic and non-periodic systems. Working with Gaussian I have previously ...
7
votes
1answer
71 views

What are the methods for calculating interaction energies of layered materials, and where are they implemented?

What are the available methods for the calculation of reference interaction energies of layered materials and in which codes they are implemented? For example, I know RPA-ACFDT in the DFT concept. But ...
14
votes
1answer
188 views

Is there a software that has implemented forces of TDDFT calculations for solids?

I'd like to investigate the structural relaxations of the excited state for periodic systems. BSE and TDDFT are two promising methods for this purpose. While there is a discussion on forces with BSE ...
8
votes
1answer
140 views

Are there other custom chemistry programming languages besides SVL?

I must confess some ignorance... I just became aware of the Scientific Vector Language (SVL) which has been around since 1994 and was created solely for computational chemistry. It has a large ...
15
votes
3answers
151 views

Candidate structures for global minimum determination

What are the best packages that can generate candidate structures for quantum chemical optimization (DFT or CCSD) to find the global minimum? I am working on the gas-phase small inorganic clusters (...
23
votes
0answers
310 views

What are the tools available for point defects calculations? [closed]

It would be appreciated if you could explain one of the tools below (or another tool not listed), in the format used here (for example): What software will allow me to combine two images? What ...
10
votes
4answers
885 views

Codes for post-processing Gaussian cube files?

I have generated MOs of a molecular system and I need to recreate its electronic density via $\rho(r)=\sum_{A_i}|\psi_i(\mathbf{r})|^2$ where $A$ is a set of occupied MOs. I am trying to do this via ...