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Questions tagged [software]

For questions about matter modeling software.

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9 votes
0 answers
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Software recommendation for drawing atomic structures

Anyone familiar what kind of software is used for drawing the atomic strucutres shown in the attached figure?
Jaafar Mehrez's user avatar
5 votes
1 answer
104 views

How are z-matrices represented in the various matter modeling packages?

Is there a standardized format that is commonly used across molecular simulation (or QM) software packages to store z-matrix information about a molecule? For instance, in CHARMM, which is a Molecular ...
Hemanth Haridas's user avatar
1 vote
0 answers
35 views

Free Cloud Computing for VASP Simulation

I am looking for suggestions for a free cloud-computing platform for running the VASP simulations. I do have the VASP license. I am also ok, if I am allowed to use for a week or so. I can also install ...
Schrodinger's user avatar
6 votes
1 answer
182 views

Is there a dictionary for VASP tags to know what they stand for?

I find the short form of the vasp tag are hard to remember. Is there a dictionary what these short form are stand for. For example USA stand for ...
an offer can't refuse's user avatar
2 votes
1 answer
36 views

How to call VASP input files from parent directory

Let's suppose I want to run the same calculation but for different configurations (= different POSCAR). For all calculations I have the same INCAR, POTCAR and KPOINTS. Those could be stored in a ...
Lukas's user avatar
  • 151
7 votes
1 answer
322 views

Why use PySCF/OpenMolcas instead of VASP/QuantumESPRESSO

While I am aware that VASP and QE are widely used for solid-state materials and PySCF/OpenMolcas are primarily designed for molecular systems. I want to know why should I use PySCF/OpenMolcas for ...
Jaafar Mehrez's user avatar
4 votes
0 answers
72 views

Solvation_analysis subpackage for MDAnalysis multi-atom solute

I have a simulation trajectory from DFTB+ for 1 NaNO3 in 32 H2O molecules. The trajectory is in xyz format and I converted a frame of xyz to pdb using openbabel to serve as topology input. I am ...
bhopshang's user avatar
  • 233
4 votes
0 answers
37 views

Which one of the following showing the correct structure Jsmol or Vesta? Or they are just same

Let me explain. I found that the structure for TiFeSi given in the ICSD database using Jsmol software is a little different from what can be obtained using Vesta software using the same cif file ...
Nilabja Kanti Sarkar's user avatar
2 votes
0 answers
22 views

Are there any good tutorials on SHARC-Gaussian interface?

I am an aspiring quantum chemist planning on trying out the SHARC approach to study excited state proton transfer dynamics of organic molecules. I am comfortable with Gaussian 16 as that is the ...
Uranium238's user avatar
4 votes
1 answer
149 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?
Rubi Agrawal's user avatar
5 votes
0 answers
160 views

How do I install Quantum ESPRESSO on Windows 10? [closed]

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 ...
86_ Kamran Elyas's user avatar
-4 votes
1 answer
101 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 ...
user366312's user avatar
  • 2,516
6 votes
3 answers
805 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?
user366312's user avatar
  • 2,516
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 ...
Alex I's user avatar
  • 1,038
3 votes
1 answer
209 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 ...
hari's user avatar
  • 83
8 votes
1 answer
405 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 ...
Aimun Jawed's user avatar
6 votes
2 answers
124 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. (...
ado sar's user avatar
  • 211
5 votes
0 answers
149 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{\...
neco's user avatar
  • 1,789
1 vote
0 answers
82 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 ...
SFriendly's user avatar
  • 897
5 votes
1 answer
155 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 &...
hari's user avatar
  • 83
1 vote
0 answers
53 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 ...
kal92's user avatar
  • 11
4 votes
1 answer
60 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, ...
Shaun Han's user avatar
  • 1,855
4 votes
0 answers
47 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....
Mam Mam's user avatar
  • 253
3 votes
1 answer
45 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.
Xdrake's user avatar
  • 541
5 votes
1 answer
144 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/...
Gaurav Maurya's user avatar
6 votes
2 answers
482 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 ...
Abdul Muhaymin's user avatar
2 votes
0 answers
43 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 ...
uhoh's user avatar
  • 1,974
3 votes
1 answer
932 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 ...
Camilla's user avatar
  • 2,129
7 votes
3 answers
198 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 ...
Nike Dattani - No Free Time's user avatar
6 votes
1 answer
591 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 ...
Camilla's user avatar
  • 2,129
7 votes
1 answer
1k 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:
Everson Gomes's user avatar
3 votes
0 answers
279 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 ...
Unni Krishnan's user avatar
4 votes
1 answer
605 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 ...
Ellie's user avatar
  • 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: ...
Nike Dattani - No Free Time's user avatar
5 votes
1 answer
191 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 ...
wolfram's user avatar
  • 151
5 votes
1 answer
274 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 ...
Elie H's user avatar
  • 1,412
3 votes
0 answers
41 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 ...
user avatar
4 votes
1 answer
152 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)?
user avatar
1 vote
1 answer
74 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 ...
Kanghun Kim's user avatar
13 votes
3 answers
239 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 ...
Fracton's user avatar
  • 271
2 votes
0 answers
163 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
diamond999's user avatar
3 votes
1 answer
770 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 ...
diamond999's user avatar
3 votes
0 answers
33 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.) &...
Andrea's user avatar
  • 856
2 votes
1 answer
395 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.
Davron Kurbanov's user avatar
5 votes
1 answer
598 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?
Davron Kurbanov's user avatar
7 votes
2 answers
190 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 ...
SFriendly's user avatar
  • 897
6 votes
1 answer
433 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 ...
Camps's user avatar
  • 23.3k
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 ...
Derive D1's user avatar
  • 135
3 votes
1 answer
74 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 ...
rmza7's user avatar
  • 329
5 votes
0 answers
108 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 ...
ZHIBO LIU's user avatar

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