Questions tagged [python]

For questions about materials modeling scripts written in the Python programming language. Questions should focus on interfacing with existing packages and aspects related to modeling, not general debugging.

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4
votes
0answers
33 views

Cannot import both numpy and LAMMPS to python after installing with conda

I installed the module LAMMPS by using this command conda install -c conda-forge lammps I want to import LAMMPS to python code, but it says: ...
7
votes
1answer
66 views

How to understand the wavefunction outputed by QE with HDF5 format?

Following the answer to my question: What is the best program to manipulate numerical DFT wavefunctions to calculate custom matrix elements?, I compiled Quantum ESPRESSO with the hdf5 flag on, and now ...
7
votes
1answer
37 views

Fractal dimension (SEM image) using the box-counting method

I am trying to discover the fractal dimension of the image of the following dendrite that was obtained by SEM (scanning electron microscope) by the box-counting method (Python). I found this code on ...
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 ...
8
votes
1answer
61 views

Using OpenBabel or RDKIT Python API to generate conformers from a SMILES string

I have a bunch of monomers in the form of SMILES string and I want to generate conformers from them. At the moment, I am using RDKit to convert these SMILES strings to .sdf files, then using ...
7
votes
1answer
84 views

How to build the [111] slab model of NiSe2 with different terminations with ASE tool?

The following figure is the bulk structure of NiSe$_2$ downloaded from the materials project database. Now I want to study the properties of its [111] plane. In detial, I cut the slab with atomic ...
11
votes
1answer
57 views

Interpret 2D and 3D data from a PubChem summary of organometallic molecule? Can I “flatten” it when showing on a surface?

I need to "build" an organometallic molecule in Blender/Python then represent it resting on a crystal surface. I'm looking at a PubChem summary for Chloroaluminum phthalocyanine and I can ...
12
votes
1answer
152 views

Is there a more efficient hard sphere packing algorithm?

I am trying to pack hard-spheres in a unit cubical box, such that these spheres cannot overlap on each other. This is being done in Python. I am given some packing fraction ...
7
votes
1answer
65 views

Normalization condition in evaluating the radial distribution function for a hard-spheres system

I am trying to simulate a 3D hard-spheres in a box system in python. The idea behind this is that I have to create a system in a 1-by-1-by-1 box with periodic boundary conditions and with $N = 500$ ...
8
votes
0answers
51 views

How to get order constitution data for single equilibrium calculation in Thermo-Calc's TC Python module?

I know that it is possible to get order constitution data for phases when using Thermo-Calc's GUI (e.g. to get "BCC_B2 DISORD" instead of just "BCC_B2") for a single equilibrium ...
10
votes
1answer
100 views

Generating SOAP descriptors in python

What is the best python package to construct Smooth Overlap of Atomic Positions (SOAP) descriptors given SMILES representation of a molecule? Is this even possible without providing 3D geometry? An ...
15
votes
2answers
590 views

Open Source PyMol Conda Package: UnsatisfiableError

I'm having an issue installing the open-source version of Pymol using Anaconda on Windows. I have Python3.8.3 installed and when I try add the package with Conda using ...
9
votes
3answers
409 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, ...
9
votes
2answers
56 views

Evaluating the MSD of my simulation

I am running a molecular dynamics simulation of water in TIP3P, and I am storing the positions of my particles in a 2D array called relevant_positions. The number ...
10
votes
2answers
434 views

RDkit: While converting a *.sdf file to fingerprint, I'm facing several errors

suppl = Chem.SDMolSupplier('1.sdf') for mol in suppl: if mol is None: continue # print(mol.GetNumAtoms()) fps = [Chem.RDKFingerprint(x) for x in supply] I am ...
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 ...
10
votes
3answers
129 views

Is python sufficient for serious tensor network or DMRG calculations?

There are enough tensor-network/DMRG packages that support python (ALPS, OpenMPS, pyUni10) that it would seem (to an outsider) that it's possible to do some substantial work with DMRG without messing ...
9
votes
0answers
142 views

I wrote a Python code to do MD for a Lennard-Jones fluid but the VACF is wrong: What might be the problem? [closed]

I am trying to write a molecular dynamics simulation for a Lennard-Jones fluid in a box with periodic boundary conditions. The box has no net momentum. I am writing this in python. I have written a ...
17
votes
2answers
579 views

How to find Young's Modulus using stress strain curve using Python?

I am trying to find the The Young's Modulus of an aluminum alloy The yield stress Below is the data for the stress-strain curve. I tried finding the region where the slope is constant and to my ...
21
votes
4answers
2k views

How to write my own density functional theory (DFT) code in Python?

I am a DFT user and at some point in the future, I would like to write my own DFT code in Python to help gain a deeper understanding of DFT. As mentioned in a previous answer people have written their ...
25
votes
3answers
2k views

How to “get my feet wet” in Density Functional Theory by simulating a water molecule using Python

I just saw I am a beginner in Density Functional Theory. What are some resources that could help me to learn the basics? and it reminded me that few years ago I'd asked How can I calculate the charge ...
23
votes
2answers
311 views

How is Julia used in Materials Modeling?

What are the main uses and applications of Julia in Materials Modeling? Python for example is used in codes such as kwant, ...
16
votes
1answer
165 views

How to calculate t-zero temperature using Thermo-Calc- Python (TCPython) for multiple alloys?

T-zero temperature is the temperature at which the Gibbs energies of two phases are equal. Here, I wish to find the temperature at which FCC and BCC have same Gibbs energy. Thermo-Calc console mode ...
33
votes
13answers
2k views

What is a good programming language for matter modeling?

What is a good programming language for matter (e.g. molecular or materials) modeling? Since this is a broad field, I don't expect there to be only one answer.