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.
59
questions
5
votes
1answer
48 views
RDkit and PySmiles results differ on some SMILES strings
I recently started using both pysmiles and RDkit to parse SMILES strings into molecules. ...
4
votes
0answers
34 views
RDkit parse zero-order bonds (python)
I'm a computer scientist, helping with a chemistry project in python.
I have been working with the library pysmiles in order to parse ...
5
votes
1answer
49 views
Have I missed something? RDF (radial distribution) script cannot capture the correct .xyz
I am trying to learn how RDF is working. To learn how RDF is working in practice I am testing the script (below) by printing all of the variables using this .xyz file example:
I passed cartesian ...
7
votes
0answers
35 views
Bloch wave function extraction for the specific k points and specific band from QE calculation
I would like to use QE to obtain u_K(r), which is the Bloch wave function of spin-up maximum valance band at K point. If I define the K point in the input file and do a scf calculation by QE including ...
4
votes
0answers
59 views
Error while installing ShengBTE
I am trying to install the thirdorder script that is mean to work in tandem with ShengBTE on an Ubuntu OS, but I'm getting the following error:
...
7
votes
1answer
39 views
Thermo-Calc: how to suspend specific composition sets?
I am attempting to calculate the driving force of nucleation for several different precipitate phases using TC-Python. To this I want to suspend all phases, except for the matrix phase (e.g. FCC_L12). ...
13
votes
3answers
388 views
How to generate the high symmetry paths for band structure calculations?
Suppose I want to calculate the band structure of a material system along a specific high symmetry path in the Brillouin Zone. If the point group of the system is given, how can I easily compute the ...
10
votes
1answer
151 views
How should I generate a radial distribution function (RDF) for an MD trajectory with python?
I am attempting to analyse the radial distribution function (oxygen to oxygen) for a ~400ps simulation on a droplet of water (MD done with NAMD). I am using the python library MDAnalysis to do this. ...
8
votes
1answer
144 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. ...
5
votes
0answers
35 views
Error when using pycotem to index an electron diffraction pattern?
In the pycotem code, this error comes up when using the Diffraction GUI.
...
2
votes
0answers
44 views
How to plot a charge density from a CHGCAR file in Python?
I can convert a CHGCAR file on the NxNxN grid into a 3D array of shape (N,N,N) for better handling, if that helps. At the end of the day, I want plot/visualize the ...
4
votes
1answer
79 views
How to process electron-density data from a CHGCAR for better handling?
We all know that Vesta helps us visualize the electron clouds present in the CHGCAR data, but I am looking for a better way to process the electron-density data we get in a CHGCAR file for compact ...
11
votes
1answer
144 views
How to use wavefunctions/density to determine which orbitals lead to edge states?
I have a large matrix for a 1D zigzag edge model of an otherwise $3\times 3$ tight-binding Hamiltonian (3 basis functions, each corresponding to an atomic orbital), involving the variable $k_x$. The ...
8
votes
0answers
41 views
Is there a script that will suggest (hkl) indices based on distances in an electron diffraction pattern for a known crystal structure?
I am looking for a script (preferably in Python) that will suggest (hkl) indices based on distances in an electron diffraction pattern. The crystal structure is known,i.e. I have the CIF file and know ...
13
votes
1answer
132 views
Generating numpy-compatible electron density from Molden / QC calculation
I'd like to use a variety of Python tools (e.g., matplotlib and Mayavi) to analyze orbitals plot electron density contours, etc. ...
3
votes
1answer
56 views
How to make left and right handed material interface using python
I have a crystal structure, a B20 compound. I want to make an interface of that bulk compound with left and right-hand material. Is there any python code for writing such interfaces. or for writing ...
7
votes
1answer
77 views
Help with Definitions in Numerical Calculation of Multiband Berry Phase
In the third chapter of Vanderbilt's book, they discuss the so-called multiband parallel transport and provide a scheme for numerical calculations that is similar to the single band case (where the ...
7
votes
0answers
81 views
What are open source options to simulate kinematical electron diffraction patterns?
I tried using the python package diffsims. I get an image, but not a diffraction pattern I was expecting.
...
6
votes
0answers
44 views
Convert standard image file format to py4DSTEM datacube?
I want to analyze a diffraction pattern. Py4dSTEM is asking for a datacube to start with. I thought it might be able to convert an image to this format:
...
11
votes
0answers
83 views
What are good protocols for creating a database based on python?
I am aware of software tools such as atomate, but that is quite specific to crystals. There are other equally specific workflows - I think we all have our own...
What I am interested in is making my ...
10
votes
1answer
61 views
Pycalphad most efficient way to gather equilibirum phase data for set of alloy compositions?
What's the most efficient way to get the equilibrium phases and phase fractions for a set of alloy compositions? For context, I'm coming from Thermo-Calc/TC-Python where I would just loop through the ...
6
votes
1answer
135 views
Pycalphad “Failed while parsing” Yttrium from light alloys database
The code in question is just 2 lines used to import the "COST507 database for light alloys" (downloaded from the opencalphad homepage http://www.opencalphad.com/).
...
13
votes
3answers
1k views
Python script for convergence test
I want to do a convergence test of Ni using a Python script in Pyiron. Can someone please suggest how to write a script to test energy and k-mesh convergence?
6
votes
1answer
55 views
Downloading ASE (Atomic Simulation Environment) on older versions of Python
I'm trying to install something called ASE that models atomic structures. I have ASE currently installed on python 3.7, however I need to run scripts that can import and recognize ASE in an older ...
12
votes
1answer
112 views
How to numerically solve real-space 1D time-independent Schrodinger equation using 2D momentum-space Hamiltonian?
Consider the usual simple 2-level graphene Hamiltonian with mass in momentum-space where:
$$
H(k,V)=-t \sum_{\delta} [\cos(k\cdot\delta)\sigma_x-\sin(k\cdot\delta)\sigma_y+V\sigma_z],
$$
where $t$ is ...
12
votes
3answers
369 views
How to create a 3D band structure from DFT band structure calculation?
How can I create such a 3D plot using matplotlib? Like the one in Figure (a) below:
I want to create it using DFT bandstructure calculation result
10
votes
1answer
204 views
What is the right way to calculate <A><A>?
We asked a similar question somewhere else and someone advised trying here instead.
How should we calculate $\langle A\rangle \langle A\rangle$ from data on dipole moments? It is a term in an ...
11
votes
3answers
2k views
How to make a python code that can read a .xyz file and find the distance between atoms?
I want to make a python script that will load an xyz file. From the xyz parameters, I need to find the distance between atoms, angle and dihedral between atoms.
The file xyz have this structure:
...
9
votes
2answers
547 views
Python program that returns elements from a SMILE string
Given a SMILES string for a molecule, I want to know the elements in the molecule, I then send this to basis_set_exchange to get a "custom" basis set for use in Gaussian.
This seems like ...
10
votes
1answer
114 views
Computing optimized 3D structures in python that take solvent into account
I have been using RDKit to generate 3D coordinates, cleaning-up the structures using a general-purpose force field as follows:
...
10
votes
2answers
127 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)...
6
votes
0answers
57 views
How to interpret WannierTools Python code that generates tight-binding model in the wannier90_hr.dat format?
I am getting myself acquainted with Wannier Tools. Wannier Tools requires two inputs, a wt.in file, and a .dat file. This .dat file should have the structure explained in the manual here. This file ...
6
votes
1answer
58 views
How to obtain electron charge density per unit volume about a water molecule using SlowQuant?
@Nike Dattani's answer to How to “get my feet wet” in Density Functional Theory by simulating a water molecule using Python recommends SlowQuant. I've used the install instructions for Linux on my ...
12
votes
1answer
91 views
Metropolis algorithm reduces energy in molecular simulation, but does not decrease euclidean distance
I am using an open source python package openmmtools to run a simple molecular simulation problem using the metropolis algorithm.
I first load a default system of particles (alanine-dipeptide in ...
5
votes
0answers
73 views
Cannot import both numpy and LAMMPS to python after installing with conda [closed]
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:
...
9
votes
4answers
733 views
How to make a python code that can read a .xyz file and find distance, angle and dihedral angle between atoms?
I want to make a python script that will load an xyz file. From the xyz parameters, I need to find the distance between atoms, angle and dihedral between atoms.
If I have a xyz coordinate in this ...
7
votes
1answer
152 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
50 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
120 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 ...
9
votes
1answer
222 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
121 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
73 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
320 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
78 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 $N = 500$ ...
11
votes
1answer
121 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
188 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 ...
16
votes
2answers
809 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 Python 3.8.3 installed and when I try to add the package with Conda using ...
9
votes
3answers
691 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
64 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
631 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 ...
