Questions tagged [software]
For questions about matter modeling software.
219
questions
4
votes
1
answer
65
views
How to make Pd(111) supercell (√3×√3)R30 via VESTA
How to make Pd(111) super-cell (√3×√3)R30 via VESTA or Avogadro software?
- 105
5
votes
0
answers
51
views
How do I install Quantum ESPRESSO on Windows 10?
Cross posted on LinkedIn
Struggling to install Quantum Espresso on Windows 10 for vital DFT calculations due to missing GitHub libraries. Seeking assistance from the LinkedIn community. If you have ...
-5
votes
1
answer
92
views
Are these simulator, visualizer, or force field? [closed]
I see that some "names" are available online in relation to MD simulation.
VMD
NAMD
LAMMPS
OpenMM
GROMACS
Amber
CHARMM
Are these "names" simulators, visualizers, force fields, or ...
- 2,352
4
votes
1
answer
359
views
Which MD software is preferable for protein simulation?
I see that some free MD simulation software are available online.
VMD
NAMD
LAMMPS
OpenMM
GROMACS
Amber
CHARMM
Which one above is the most appropriate for protein simulation?
- 2,352
9
votes
1
answer
3k
views
Software for quantum electrodynamics?
I've been reading some beginner books about quantum electrodynamics / quantum field theory (e.g. Feynman's QED book), and basically everything is done at the paper and pencil level.
I'm curious if ...
- 801
3
votes
1
answer
97
views
Transform Supercell to Unitcell
I’ve supercells of around 10,000 Metal–organic frameworks (MOF) structures in CIF format. I’m looking to convert them to unit cells. But I’m not able to find packages (or any other libraries like ...
- 83
8
votes
1
answer
388
views
How may I install the latest version of a software?
This is a follow-up of my previous question here: How to address 'saveGraphic: Method not found' error in automating the generation of figures in avogadro using Python?, at which I was told to ...
- 151
6
votes
2
answers
102
views
Is there any Python library for returning the atoms of a periodic material within a cube?
Is there any Python package that allows to cut defined by the points (0, 0, 0) and (x, y, z)?
That is, it should return all the atoms of the unit cell and periodic images inside the shaded region.
(...
- 211
5
votes
0
answers
141
views
Actual calculation of Coulomb energy in DFT softwares
I have a question about the actual calculation of classical Coulomb interaction term in density functional theory (DFT) softwares.
Of course I understand the form Coulomb energy as:
$\int\int \frac{\...
- 1,779
1
vote
0
answers
60
views
Is there a correct way for compiling and installing NWChem software with all modules from a source code on Linux Mint?
I have been trying to compile and install NWChem v6.8 from a source code on Linux Mint 21.2. According to instructions received from chatGPT, the following steps have to be done:
Install necessary ...
- 877
5
votes
1
answer
89
views
Calculating theoretical density from .cif files
I'm studying structure-property relations in MOFs and have a pool of hypothetical structures in .cif format generated using ToBaCCo code. I want to filter them based on theoretical density, but the &...
- 83
1
vote
0
answers
48
views
Resource recommendation for learning matter modeling for a novice [closed]
I am a starting researcher in condensed matter physics. Hence, i have all the necessary background regarding quantum physics, and condensed matter physics. But what i want to do is to learn different ...
- 11
4
votes
1
answer
57
views
Software for storing information of large number of atomic structures into database file
Say I have a MD trajectory that contains a million snapshots (i.e. a million atomic structures). Each snapshot contains some calculated information (either by DFT or some force field) such as energy, ...
- 1,550
4
votes
0
answers
46
views
Why, if the potential is different from the Coulomb one, but has spherical symmetry, the eigenvalues of the system are non-degenerate? [closed]
Question duplicated from here https://mathematica.stackexchange.com/questions/287433/why-if-the-potential-is-different-from-the-coulomb-one-but-has-spherical-symme and here https://physics....
- 233
3
votes
1
answer
44
views
Creating a beta cristobalite with 200 or fewer atoms
Can someone suggest me a method to generate a beta cristobalite structure with atoms less than 200.? I tried VMD's inorganic builder tool but so far unsuccessful.
- 491
4
votes
1
answer
103
views
LAMMPS error "Two fix ave commands using same compute chunk/atom command in incompatible ways"
I am very new to using LAMMPS. I am trying to obtain some simulations. I was using an older code which had ave/spatial fix style. In the new LAMMPS version it doesn't work so I am switching to ave/...
6
votes
2
answers
332
views
What are some pros/cons of Quantum ESPRESSO and FLEUR?
I want to know the pros/cons of plane wave (PW) pseudopotential (PP) based DFT codes and all-electron full-potential linearised augmented-plane wave (FLAPW) DFT codes. In the title, I mentioned ...
- 2,091
2
votes
0
answers
29
views
How to generate pole figures from limited amounts of area detector X-ray diffraction from thin films (explain it like I'm five years old)
Historically powder X-ray diffraction was the go-to method for reconstructing crystal structure. X-ray sources were limited in intensity and emittance and so to collect data in a reasonable amount of ...
- 1,894
2
votes
1
answer
38
views
Encode a spectrum to be uniquely identifiable (binary, colour,...)?
Context
The picture you see below is what I obtain from an experiment where I measure the absorption change of circularly polarized (y-axis, milli-degrees) light against the wavelength (x-axis, nm). ...
TheChemist
3
votes
1
answer
786
views
Why Windows is not showing in the Dual-Boot menu and boot into Ubuntu directly? [closed]
It's been more than a month that I installed Ubuntu 20.04 on a desktop along side with windows (Probably 10 or 11) that was already on the desktop. Now I noticed that the computer boot directly into ...
- 1,957
7
votes
3
answers
187
views
What would be the preferred format for a geometry database?
Introduction (analogy to basis set database files)
Many programs have a database of basis sets stored in a file such as the following (so that users can just specify in their input file something like ...
- 33.6k
6
votes
1
answer
429
views
How can I predict the time of a simulation using Quantum ESPRESSO?
I performed a vc-relax calculation with hybrid functional on a 2 atoms material using the command ...
- 1,957
6
votes
1
answer
502
views
How do I install Quantum ESPRESSO on Linux?
People, can someone please help me how to solve this problem with QE 7.0 installation:
- 575
5
votes
0
answers
58
views
Is there a free software to build a crystal shape that is cut with a specific angle plane (like 40 degrees), which is not implemented in Vesta? [closed]
I would like to cut $\ce{SrTiO3}$ with a specific angle of 40 degrees, or to choose an angle plane which is not implemented in the Vesta software.
Could you please recommend a free software to build ...
- 51
3
votes
0
answers
194
views
How can we build a polymer from a monomer in Avogadro? [closed]
I have been trying to reproduce a geometry optimization from a research paper, where it was done by Avogadro.
However, I cannot find the option for building a polymer from a monomer. I am using ...
4
votes
1
answer
366
views
Does anyone know where and how I can download and install Spartan (the Molecular Modeling software)?
I've been given the task to calculate the energy of the lowest unoccupied molecular orbital (eLUMO) using Spartan but I'm not really familiar with the said software, can anyone tell me a bit of an ...
- 41
7
votes
3
answers
1k
views
Print chemical formula from list of atoms in Python?
Lets consider the following code which uses the Mole object:
...
- 33.6k
5
votes
1
answer
159
views
MOLPRO: is there an analogue of the Gaussian FCHK file?
With the Gaussian quantum chemistry program, I usually generate formatted checkpoint files (.fchk) that I then use to perform different atom-in-molecule analyses. I am currently facing the need of ...
- 151
5
votes
1
answer
233
views
What is a good software for computational electrochemistry?
I am thinking about working on computational electrochemistry for a limited subject and don't have a huge amount of time I can invest to explore different software. The JDFTx software seems like a ...
- 1,377
3
votes
0
answers
38
views
Prevent Avogadro from clipping wavefunction plots [closed]
When I try to plot wavefunctions in the Avogadro software I find that the orbitals are often clipped by a rectangular box. Does anyone know how to increase the size of this box so that I can plot ...
pQ12branch
4
votes
1
answer
150
views
How to simulate on a computer dissolution of one substance by another?
Is there any publicly available software to simulate this or some other method to see if one substance can be dissolved by the other (and preferably to see how fast)?
Ya Y
1
vote
1
answer
67
views
How do I install the beta5 version of PSI4 on my WebMO Basic server?
Installing the basic version of PSI4 on my personal LG Gram 360 (with a Windows OS), used as a my-own WebMO Basic server, was done according to the WebMO tutorial. I then tried to compute the energy ...
- 870
13
votes
3
answers
226
views
Improving my programming for computational chemistry/physics
What are some good textbooks or online resources to improve my skills in C++, C and Fortran, specifically for computational chemistry.
For example, I am interested in learning about parallelisation ...
- 231
2
votes
0
answers
141
views
"Gview.exe" in Linux is not responding [closed]
I successfuly installed g16 and gview6 under fedora linux , the issue that I have is when I open gview after few seconds it stopped and a message is displayed on my screen
- 835
3
votes
1
answer
584
views
problem with the installation of g16 with gaussview under Linux
I don't know how to install the g16 with gv under Linux. According to the internet the installation seems to require a file called a tar.gz which I don't find in the g16 folder. I have a lot of files ...
- 835
3
votes
0
answers
32
views
Problem with installation of Multiwell Software package and open mpi [closed]
I'm trying to install Multiwell including Thermo. The manual says under 1.4. that I have to install openmpi before. So I followed the instructions from the multiwell manual but get an error at 8.) &...
- 816
2
votes
1
answer
286
views
Studying computing on HSE06 in VASP
I optimized the structure in PBE. Can anyone help me with HSE06 to calculate the optics and DOS of the material from this step? I would be grateful if you could write step by step.
4
votes
1
answer
498
views
Calculation of DOS in HSE06
Do I do rest, scf, dos steps when calculating DOS like PBE in HSE06? Can anyone help me with this?
7
votes
2
answers
177
views
Which equation makes it possible to calculate the forces of attraction between a surface and molecules?
Which equation makes it possible to calculate the forces of attraction between a surface and molecules? Is there any free software that implements such a calculation?
[Clarification 1] Between a ...
- 877
6
votes
1
answer
370
views
Alternatives to OpenBabel for converting *large* files?
I have been using OpenBabel as a handy-tool for converting small files without any issues.
Now, I am working with graphene-like systems with hundreds or even ...
- 22.3k
5
votes
3
answers
1k
views
Is there a pre-compiled Quantum ESPRESSO?
As is well known, the compilation and ./configure stage is the most tricky part in installing QE. As it depends on the environment of the operating system and the ...
- 135
3
votes
1
answer
62
views
How to determine defect charge state degeneracies?
I am doing defect calculations using the SC-FERMI package. However, one of the inputs is the degeneracy of the charge states of each defect. I know degeneracy is the number of states with the same ...
- 319
5
votes
0
answers
91
views
Compute the energy of carbon atom with Molpro [closed]
I have been learning some basics of molpro and quantum chemistry, however I am deeply confused now.
As a very simple example, I want to compute the energy of a carbon atom using D2h group
For its ...
- 81
9
votes
1
answer
186
views
Can energies obtained with different pseudopotentials be compared?
I calculated energies per atom of bulk configurations of transition metals in VASP in order to use them as reference energies for adsorption on surfaces, etc. I downloaded POSCAR files from the ...
5
votes
0
answers
62
views
Ask tips: For merging small figures into a big one with high resolution
my question is not related to material or modeling, but I guess many people in this community face it. I took a figure of a crystal structure by cropping the VESTA app on my laptop screen; band and ...
- 2,025
4
votes
0
answers
71
views
Benchmarks for optimised Math Libraries across platforms [closed]
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 ...
user784
7
votes
1
answer
2k
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 ...
- 231
5
votes
1
answer
181
views
How to download METADISE code?
I have a (possibly trivial) question regarding the METADISE code. I can find the documentation related to this code, but I cannot find the download page or tarball anywhere.
Can someone kindly share ...
- 911
8
votes
4
answers
2k
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 ...
- 1,977
5
votes
1
answer
133
views
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 ...
- 51