Questions tagged [python]
Questions about or related to Matter Modeling with Python or Python's relationship to Matter Modeling.
236
questions
0
votes
0
answers
36
views
2
votes
0
answers
72
views
How can I call LAMMPS from a Python script multiple times in paralllel?
I'm working on a Python program that needs to call multiple LAMMPS runs and extract some computes. The code looks something like this:
...
1
vote
0
answers
26
views
Problem with finding band structures, formation energy and bandgap of the crystal using Vasp
so I have a crystal now I want to perform dft on that crystal and find the energy, formation energy, bandgap and band structures. idea is to validate the generated crystals
so the cif I am using is
<...
- 241
1
vote
0
answers
12
views
From Monolayer POSCAR to Multilayer POSCAR in Python
I have monolayer POSCAR file and I want to convert it to Multilayer. For example, for 20 layers. Can anyone suggest me how to do it in Python? or if you have already written code, please share.
- 11
1
vote
0
answers
21
views
How would someone go about calculating the temperature change of a reaction using the enthalpies of reactants an products?
Cross-posted on Chemistry.SE.
I am designing software which calculates the stoichiometric combustion temperatures of different rocket fuel and oxidizer combinations. I've been using a specific method ...
- 11
3
votes
1
answer
32
views
RDKit PandasTools WriteSDF: RuntimeError: Bad pickle format: unexpected End-of-File while reading
I face the error:
...
- 131
3
votes
0
answers
28
views
martinize issue
PS C:\Users\MALINE\Desktop\martini> python martinize.py -f polypropylene.pdb -o output.pdb
...
- 31
4
votes
1
answer
37
views
ASE EquationOfState error
I am running QE with ASE using Ubuntu WSL and trying to recreate simple case of calculating lattice constant (https://wiki.fysik.dtu.dk/ase/tutorials/eos/eos.html). Here is part of the code that is ...
- 121
4
votes
2
answers
144
views
Running Quantum Espresso from ASE
On my Windows Subsystem for Linux I compiled QE and I can execute simple test script from terminal. However, if I try to run QE using ASE I get the following error:
...
- 121
3
votes
1
answer
53
views
What are the specific differences between these two notations of supercell denoted by (√3×√3)R30∘ and (√3×√3)?
I am studying the super-cell structures in crystallography and came across two different notations:
(√3×√3)R30∘ and (√3×√3). I would like to understand whether these two notations represent the same ...
- 587
3
votes
0
answers
65
views
How to choose a proper rotation matrix and apply it to rotate unit cell about Cartesian axis to align I-Cr-I bonds parallel to Cartesian axis
I was surveying this paper Remarkably enhanced Curie temperature in monolayer CrI3 by hydrogen and oxygen adsorption: A first-principles calculations, where they have rotated the unit cell (without ...
- 470
1
vote
0
answers
39
views
How to align O-TM-O along z axis of unit cell of P2 like structure
I was surveying this article https://www.nature.com/articles/s41524-018-0117-4, here the P2 like layered oxide structure where he O-TM-O bonds are not aligned along the z-axis. As a result, VASP ...
- 470
3
votes
1
answer
57
views
How to calculate height of the center of the H2 molecule from surface via ASE?
I have XDATCAR file, i want to calculate graph of time vs height of the H2 molecule(center of the H2 molecule) from surface.
...
- 587
5
votes
1
answer
198
views
problem calculating formation energy per atom using vasp
Using the below code I am trying to calculate the formation energy per atom and bandgap given the cif file. the values that are present in the material project.
but I got these values which are wrong ...
- 241
3
votes
0
answers
66
views
Electronic density of states from not the usual VASP outputs
In a very frustrating development, my VASP has decided to hang at the writing of outputs stage. While I troubleshoot that separately, for the moment I need to get an electronic density of states from ...
- 1,658
5
votes
0
answers
122
views
Problem with using VASP with ase on a GPU
I am a newbie using VASP, currently I am trying to calculate the formation energy per atom and pre bandgap using DFT with VASP on a GPU machine.
I wrote the following script for calculating the ...
- 241
6
votes
0
answers
126
views
Normalization of the Smooth Overlap of Atomic Positions (SOAP) Kernel
I am using the DScribe implementation (https://singroup.github.io/dscribe/latest/tutorials/descriptors/soap.html) of the Smooth overlap of atomic positions (SOAP) ...
- 543
2
votes
2
answers
115
views
Tool for plotting spin texture
Is there a tool that can plot a spin texture graph like these two examples below:
Or does anyone know an example using matplotlib?
- 481
3
votes
0
answers
57
views
Hydrogen bonding rate of relaxation on molecular dynamics
I am studying the works of Alenka Luzar on the hydrogen bonding kinetics in liquid water. Luzar defines an autocorrelation function c(t) that gives the probability that an hydrogen bond is intact at ...
- 303
5
votes
0
answers
36
views
How can calculate length or coordinate of any molecule in different quantum state [like (rotational quantum state)j=2] with any software or code?
How can one determine the bond length of a diatomic or tri-atomic molecule(rot. state J=3 and vib. state v=2) from its ground state bond length (x angstrom) using computational tools or programming ...
- 587
5
votes
1
answer
79
views
How to convert all structure coordinates in .traj file to separate .txt files (e.g. POSCAR format files)?
I am using the ACAT code for generating the structures.
...
- 587
7
votes
1
answer
258
views
Is there any software or Python library for visualizing higher-order Brillouin Zones of standard lattices?
I am looking for a software or Python library to help me visualize higher-order Brillouin Zones (BZs) of standard lattices like FCC, BCC, etc. I have already plotted the first BZ of an FCC lattice ...
5
votes
0
answers
17
views
Compound Bioactivity classification
I am trying to train a model to classify whether a compound is active or inactive looking at its SMILES. I have a table with 3 columns-InchiKey, SMILES, and activity-5300 rows in total -35 % of which ...
- 51
8
votes
3
answers
393
views
Hydrogen bonding autocorrelations
I am currently analyzing hydrogen bonding behaviour and kinetics with molecular dynamics simulations. I've been trying to compute autocorrelation functions for hydrogen bonds in a water system. Some ...
- 303
8
votes
5
answers
783
views
How to identify small molecules in a structure without bonds
If I have an XYZ file with a cluster of a dozen of molecules: water, $\ce{O2}$, $\ce{H2}$, $\ce{H2O2}$. A human may easily identify these molecules. But how to do it automatically? I need to identify ...
- 730
3
votes
0
answers
44
views
Unexpected behavior when running LAMMPS from Python
I am trying to run a series of LAMMPS input files to parameterize a system, and then using the residuals to optimize the Force Field parameters. I am able to generate the input files and run them ...
- 4,036
2
votes
1
answer
76
views
Building Fullerenes using scikit-nano package
I am trying to use scikit-nano package to build the various isomers of fullerenes. However, none of the methods that is presented in the manual seem to work for installing the package.
These are the ...
- 4,036
5
votes
1
answer
132
views
Neural Network to predict atomic forces using SOAP descriptors
I am working on neural network in tensorflow to train a model to predict atomic forces from SOAP descriptors (regression problem).
I have 64 020 data points (chemical structures), each structure has ...
- 73
5
votes
1
answer
84
views
How can one create various arrangements of two or more types of atoms (like O, N etc.) with distinct coverages on a metal surface?
How can I modify the procedure described in this answer to achieve adsorption of two or more types of atoms on a surface, each with distinct coverages?
Is there an extension to the described method ...
- 587
4
votes
0
answers
73
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 ...
- 233
3
votes
0
answers
56
views
Obtaining RDF from provided structure factor
I have a test structure factor dataset from water O-O pairs and I am trying to get the $g_{OO}(r)$.
...
- 2,352
2
votes
1
answer
245
views
Velocity autocorrelation function for molecular dynamics trajectory
I have a 1 ns long molecular dynamics trajectory of 884 molecules of water, and I am trying to compute the velocity autocorrelation function using MDAnalysis to analyze the GROMACS output files.
I ...
- 303
4
votes
1
answer
187
views
How to resolve ModuleNotFoundError: No module named 'pymatgen.analysis.defects'?
Background
My goal is to use PyCDT: Python Charged Defect Toolkit (paper, github, pypi). I installed the code by doing:
pip3 install pycdt
I am not using any ...
6
votes
1
answer
218
views
Speed of atom from kinetic energy of molecule
What is the velocity of each hydrogen atom in an H2 molecule, given a kinetic energy of hydrogen molecule is 0.12 eV, when expressed in angstroms per femtosecond and assuming equal velocities for both ...
- 587
2
votes
1
answer
51
views
How to make initial trajectory for incident A2 molecule on any surface?
I want to write code to simulate the impingement of any molecule on a surface at different (r, theta, and phi) angles in XYZ format.
- 587
3
votes
1
answer
115
views
How may I verify that my A matrix for TDA (Tamm-Dancoff Approximation of TD-DFT) from PySCF is correct?
This is a follow-up to a series of questions that I have asked here:
Is a D-Wave quantum computer able to do TD-DFT calculations? (answer was "yes, but it might not be efficient")
Inquiry ...
- 151
6
votes
1
answer
203
views
How to convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA software?
Convert MoO3 bulk structure to MoO3 (010) plane surface via VESTA
- 587
5
votes
1
answer
65
views
A matrix form used in the Quantum Annealer Eigensolver (QAE)
In the paper "Computing molecular excited states on a D‑Wave quantum annealer", PySCF is employed to compute the TDA matrix. Then a few of the lowest eigenvalues and eigenvectors of a TDA ...
- 151
5
votes
2
answers
190
views
ASE: How to plot the irreducible Brillouin zone and this bandpath from a bandpath object
I am using ASE (Atomic Simulation Environment) for theoretical chemistry and I see an option to plot the irreducible Brillouin zone and this bandpath but I can't figure out how. I'm not a programmer.
...
- 61
4
votes
1
answer
252
views
Random velocity generation
How to generate random velocities in the geometry coordinates of a surface (POSCAR file) using the Boltzmann distribution law with Atomic Simulation Environment (ASE) or other codes for Molecular ...
- 587
2
votes
1
answer
50
views
Non-Equivalent T-Sites from a cif file
I am trying to find symmetrically inequivalent T-atoms in a crystal structure (zeolite).
Does anyone happen to know any package that can help with that? I see that pymatgen does have options for ...
- 989
5
votes
1
answer
208
views
Plot MSD (mean square displacement) versus time for a polymer chain
Cross-posted on Computational Science SE.
The following are the movements of the center of mass of a polymer chain over time in a monte carlo simulation.
...
- 2,566
3
votes
1
answer
197
views
Print full stress tensor in ASE to calculate Green Kubo viscosity
I would like to print out the off diagonal components of the full stress tensor in ASE. The goal is then to calculate the Green Kubo viscosity. One should use the ensemble average of the off diagonal ...
- 699
3
votes
0
answers
341
views
Read and run lammps water model in ASE
I want to read a lammps data file in ASE, for instance the TIP3P or the SPC model. The lammps examples provide the input script and the data file, which work perfectly.
ASE is not able to read the <...
- 699
3
votes
0
answers
84
views
Using GPyTorch for GPR together with the SOAP-Kernel
My goal is to use a Gaussian Process Regression (GPR) model with the GPyTorch library with the SOAP (smooth overlap of atomic positions) descriptor that can be obtained with the DScribe library.
I ...
- 543
4
votes
1
answer
209
views
What is the best way to save a psi4 molecule object in Python?
what is the best way to save and load a psi4 molecule? I tried pickle/dill but they both failed. I see a feature to save as xyz, but I'm not seeing a function to load as xyz and I'm not sure if save ...
- 195
5
votes
1
answer
145
views
Evaluating analytic gradients for overlap integrals
I have been working on a toy HF code for some time. From this reference I am trying to work out an analytic expression for the first derivatives of overlap integrals.
The original expression for ...
- 4,036
9
votes
0
answers
117
views
How does the line search in geometry optimisations work?
I am trying to write a Newton-Raphson geometry optimisation script in python (Current version of my code) using the energy, gradient and Hessian from Gaussian 16. In order to reach a minimum, I would ...
- 91
5
votes
1
answer
387
views
Contents of a CHGCAR file and how to read it appropriately in Python? [duplicate]
Rephrasing the above, what is the content of the data in the CHGCAR file?
Is the data part shown below representative of the electron-charge density or is it the actual charge in the system and I have ...
- 1,637
4
votes
1
answer
120
views
How to get displacements along VASP NEB trajectory?
I am performing an NEB calculation with VASP and VTST. I would like to visualize the atoms along the path and to calculate their displacements. When I have a single relaxation's XDATCAR, I can unwrap ...
- 159