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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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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8 votes
0 answers
60 views

What are some recent significant developments/studies in theoretical nonlinear chemical dynamics?

During my undergraduate studies, I was introduced to oscillatory and nonlinear reactions, which are essentially chemical reactions oscillating far away from equilibrium conditions - A very visual ...
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17 votes
4 answers
4k views

I am considering to purchase a GPU. What calculations would need FP32, and what would need FP64?

I would like to know how to choose the best GPU on the basis of its FP32 or FP64 efficiency, depending on different types of simulations. In brief I would like to know what types of simulations work ...
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  • 1,409
9 votes
2 answers
477 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 ...
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  • 5,544
8 votes
5 answers
276 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 ...
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7 votes
2 answers
136 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 ...
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  • 869
7 votes
3 answers
337 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? ...
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  • 14.2k
13 votes
1 answer
110 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 ...
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  • 5,544
13 votes
1 answer
236 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 ...
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  • 5,544
4 votes
1 answer
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.
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15 votes
2 answers
383 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. ...
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12 votes
3 answers
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 ...
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8 votes
1 answer
665 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 ...
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5 votes
1 answer
83 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.
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  • 3,074
8 votes
1 answer
383 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. ...
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  • 3,870
9 votes
1 answer
71 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 ...
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  • 99
9 votes
2 answers
114 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 ...
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  • 191
9 votes
0 answers
70 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 ...
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  • 641
12 votes
1 answer
175 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 ...
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  • 271
11 votes
2 answers
229 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?
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10 votes
3 answers
551 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 ...
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  • 589
8 votes
0 answers
85 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, ...
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  • 2,091
8 votes
1 answer
170 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, ...
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  • 367
4 votes
1 answer
61 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 ...
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  • 8,362
20 votes
4 answers
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 ...
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  • 371
13 votes
1 answer
130 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)...
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  • 6,852
9 votes
1 answer
96 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 ...
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13 votes
5 answers
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 ...
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9 votes
1 answer
75 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 ...
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21 votes
5 answers
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.
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  • 1,011
10 votes
2 answers
230 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)...
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  • 438
11 votes
3 answers
836 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. ?
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13 votes
0 answers
116 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) ...
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19 votes
0 answers
143 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 ...
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12 votes
1 answer
116 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 ...
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16 votes
2 answers
483 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? ...
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  • 433
12 votes
0 answers
112 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 ...
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  • 1,960
9 votes
1 answer
259 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-...
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  • 2,293
13 votes
3 answers
225 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 ...
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  • 4,258
10 votes
2 answers
121 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 ...
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  • 4,258
19 votes
2 answers
645 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 ...
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7 votes
2 answers
984 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 ...
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5 votes
1 answer
34 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 ...
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  • 1,192
16 votes
4 answers
3k 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 ...
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  • 1,029
13 votes
1 answer
403 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 ...
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10 votes
3 answers
2k 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, ...
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  • 7,764
12 votes
2 answers
806 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 ...
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7 votes
1 answer
75 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 ...
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  • 1,859
14 votes
1 answer
209 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 ...
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8 votes
1 answer
153 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 ...
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  • 3,870