Questions tagged [software-recommendations]
Questions of the form "Is there a software that can do...?" and similar.
44
questions
6
votes
2answers
78 views
Symmetry-preserving low-level structural relaxation
I would like some suggestions on how to do structural relaxation (while I'm at it, let me list some synonyms for search exposure - geometry optimization, structural refinement, energy minimization etc)...
4
votes
1answer
33 views
SiC surface reconstruction
I know how to cleave surfaces with integer Miller indices, however I wonder how I could cleave a $(\sqrt{3} \times \sqrt{3}) R30$ reconstruction of $(001)\,\, 4H-SiC$.
I have found a nice link to O-...
5
votes
0answers
17 views
Is it possible to calculate the variation of magnetization M(T) for a diluted magnetic semiconductor?
Please if you can help me with some resources and tutorials.
Is there any simulation program (for example a DFT package) to determine the variation of magnetization M(T) for diluted magnetic ...
14
votes
1answer
219 views
Software recommendations for passivating structures
I am looking for an open-source library that allows to passivate a structure, ideally starting from a xyz-file.
QuantumATK provides a function like this. However, this is not an option at the moment.
...
12
votes
1answer
88 views
What is the best program to manipulate numerical DFT wavefunctions to calculate custom matrix elements?
For pedagogical reasons, I am looking for ways to calculate quantum-mechanical quantities such as $\langle m | \dot{m}\rangle, \langle m | \dot{n}\rangle, \langle m | \ddot{n}\rangle$ using ...
11
votes
3answers
734 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. ?
7
votes
0answers
257 views
Is there any code for local-orbital ab initio tight binding molecular dynamics other than fireball?
I was searching for a local-orbital ab-initio tight binding implementation of molecular dynamics and Ive found a code called fireball. Ive tried to compile it but the code seems to be buggy and there ...
5
votes
0answers
23 views
Recommended code to do XAS/XES/RIXS calculations with?
I am a grad student looking to simulate several XAS/XES and potentially RIXS spectra for some strongly correlated metal-oxides. The materials in question will likely require solving the Bethe-Salpeter ...
10
votes
1answer
133 views
Calculating/Visualizing electronic density from orbital information written in the Molden format
I'm trying to obtain an electron density from orbital information written in the Molden format by the formula,
$$
\rho(\mathbf{r}) = \sum_{i}^{occ} |\phi_{i}(\mathbf{r})|^{2}. \tag{1}
$$
Is there any ...
13
votes
1answer
216 views
Software for Exact Diagonalization of quantum spin Hamiltonians in 1D and 2D
I'm looking for software (which can also run in parallel) for Exact Diagonalization of Quantum Spin Hamiltonians in 1D and 2D (e.g. Heisenberg Model) consisting of a large number of spin sites.
There ...
13
votes
1answer
148 views
Visualizing MD generated electron density cubes as trajectories
During an ab-inito MD simulation one can generate the electron density cube file which basically provides the electronic density data in a standard volumetric format as shown here. The file consists ...
8
votes
0answers
49 views
Periodic polarizable QM/MM embedding
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
90 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-...
12
votes
2answers
124 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 ...
11
votes
2answers
241 views
3D Visualization of Molecule / Surface by 3D Model (.stl)
I am looking for a software that is capable of converting some generic atomic format such as .xyz or POSCAR into a .stl format. Ideally it would support automatic generation of bonds so that the ...
7
votes
2answers
966 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 ...
11
votes
4answers
247 views
Create doped structures to POSCAR files for vasp
I have a perfect supercell structure Ni fcc. And I would like to dope another element O or N with a ratio of O:Ni=8:100 to the supercell of 3x3x3 and find the most stable ordering structure. The ...
11
votes
2answers
100 views
What are some available software packages for automated finding of local and absolute minima on PES?
I have never used any AI driven calculation package before and to be honest don't fully understand the ins and outs of it. To be more specific I'm looking for something that can find local minima for ...
7
votes
1answer
76 views
Software to generate compound library
I'm trying to perform a QSPR research and for it I need to generate a library of compounds.
Now I'm using a plugin for MarvinSkectch for enumerating Markush structures but it doesn't work properly (...
14
votes
1answer
77 views
Which modelling package currently implements an AI derived force field?
I would like to use an AI-derived force field as they seemed to have lesser computational cost.
Which simulation package (Gromacs, Amber, NAMD...) currently implement some of them?
8
votes
1answer
61 views
What software can perform block analysis on time sequence data?
I have a .xyz file for a trajectory and I want to perform block analysis on it, and to find the decorrelation time and to perform analysis on that as well.
What ...
13
votes
5answers
317 views
DFT software package for a beginner?
I would like to do start doing some basic calculations using DFT. I am interested in solid state physics of strongly correlated materials in 3D (for example high temperature superconductors) or 2D (...
11
votes
2answers
199 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 ...
13
votes
0answers
122 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 BSE Is there a ...
10
votes
1answer
149 views
Is there a software that has implemented forces of BSE calculations for solids?
I'd like to investigate the structural relaxations of the excited state for periodic systems. It seems BSE is a practical method that has already been implemented in many codes for static calculations....
11
votes
1answer
78 views
adaptive k-mesh
Are there any known codes or scripts to generate an adaptive k-mesh for DFT calculations? For example, I'd like to make the k-mesh near the $\Gamma$ point (e.g., half the zone) more denser ($20\...
7
votes
2answers
90 views
Software recommendations for peptide conformation
I have a series of alanine dipeptide trajectories and would like to get the conformation type ($\alpha$, $\beta$, etc.) from the atom coordinates or dihedral angles. Does any package (like RDKit for ...
9
votes
1answer
56 views
Finding conformations of peptide based on dihedral angles
I was trying to look at the alanine dipeptide trajectories from this link and track the trajectories in a Ramachandran plot. Below is a plot based on dihedral angles at each timestep for all ...
8
votes
2answers
143 views
Tools for structural analysis on LAMMPS trajectories
I have a very general question but still quite important since I didn't find convincing tools to get the structural analysis done for LAMMPS dump file (trajectories). I am looking for post processing ...
21
votes
6answers
4k views
Is ARM64 the next big thing?
Considering how GPUs in matter modeling was first recognized in gaming devices like PlayStation, it is also interesting to consider whether ARM64 chips, which are the type of chips in modern smart ...
12
votes
2answers
105 views
How to classify structures and identify duplicates from a set of .xyz files?
Does there exist a program that can compare a series of (ideally.xyz) files to each other to identify duplicate structures, and then identify the structures in some ...
9
votes
3answers
83 views
Which non-commercial softwares can be used to model amorphous carbon?
I have a fair idea of generating and modeling crystalline materials but what non commercial software programs can be used to model amorphous carbon of a specific dimension, say a $6\times6\times6$ Å ...
12
votes
1answer
152 views
Is there a software that can calculate collision cross-sections involving molecules with several atoms?
What software currently can be accessibly used to calculate collision cross section using the geometries obtained from DFT? In my case, Q-Chem is used for geometry optimization.
The goal is to compute ...
9
votes
2answers
200 views
How to calculate the nuclear energy derivatives in molecular mechanics?
In molecular mechanics, the energy is often written as a sum of bonds, angles and torsion energies, and an electrostatic term, e.g.
$V = \sum_{bonds} K_r (r-r_{eq})^2 +\sum_{angles}K_{\theta}(\theta -\...
9
votes
2answers
127 views
How to build a simulation model for a molecular dynamics simulation
I have got aggregate of 4 non-protein compounds I would submit for molecular dynamics simulation. The problem is I can't find software capable to do that. Amber, GROMACS, LAMMPS, all of them require ...
10
votes
1answer
188 views
How do I predict the structure of a nanoparticle with Calypso and Quantum ESPRESSO?
I want to create a nanoparticle of CuO and predict it's structure. I've done unit cell relaxation with Quantum ESPRESSO. One tool to predict nanocluster structure is Calypso which is PSO-based. I'm ...
9
votes
1answer
64 views
Docking proteins with glycans
Do you know of a good software or web server tool that helps doing docking of proteins with rather large glycans? An example I'm interested in is tens of dimers of sugars (or similar), docked to ...
9
votes
0answers
70 views
Is there any code that runs WHAM starting from histograms rather than time series?
I'm looking for a way to run the Weighted Histogram Analsys Method, but I don't have a time series to feed to the code as usually happens, but rather I have histograms coming from the debiasing of a ...
14
votes
0answers
95 views
What are the advantages of different point defects calculation tools?
As far as I know, there are mainly PyCDT, PyDEF, pylada and some part of pymatgen. As a new user to those tools, which one would be a good choice?
pycdt: Python Charge Defects Toolkit (PyCDT) is a ...
9
votes
1answer
133 views
Freely available constrained DFT implementations
What free quantum chemistry packages that have constrained DFT (CDFT) implemented? A google search does not reveal anything, perhaps there may exist a better resource to find the packages.
8
votes
4answers
186 views
Tools for electronic transport calculations
Electronic transport calculations play an important role in device simulation.
What tools can do electronic transport calculation?
I am familiar with TranSIESTA (a module of SIESTA program) and ...
6
votes
0answers
115 views
Which DMRG package has the easiest learning curve?
I've been meaning to learn how to use DMRG (density matrix renormalization group) for a long time. Which package has the easiest learning curve? I specifically mean it should be easy to actually learn ...
19
votes
5answers
2k views
Molecular Dynamics simulation software for Windows
Is there a Windows-based Molecular Dynamics simulation software which is easy to use?
15
votes
0answers
126 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 ...
