Questions tagged [python]
Questions about or related to Matter Modeling with Python or Python's relationship to Matter Modeling.
265 questions
9
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How to compute the Green function with the non-orthogonal basis?
I want to implement the numerical code to do the calculation, based on equation (1).
$$Tr\left[ v\left( G^{R}-G^{A}\right) s \left( G^{R}\times G^{R}-G^{A}\times G^{A}\right) \right]\tag{1}$$
where, $...
- 1,113
4
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0
answers
71
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Exporting images (PDF) using the Python CSD API
I would like to export a visual representation (e.g. ORTEP) of a crystal structure from a .cif file to an image (preferably PDF) using the Python CSD API through Mercury, since I want to use that ...
- 41
3
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41
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Quantum Capacitance and surface charge calculation using QE
i want to calculate quantum capacitance and surface charge density. i have already calculated density of states with dense grid using quantum espresso . can anyone please help me with the post ...
2
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1
answer
120
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Running Particle Swarm Optimizations in Python for Modeling
This question is in continuation to my previous question here. I now have a code that works both in serial and in parallel (with MPI). However, I am now trying to implement a load-balancing system to ...
- 5,361
4
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1
answer
106
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Running LAMMPS from Python
Cross-posted (not exactly) on the LAMMPS forum.
I am trying to develop a Python workflow that can perform multiple-walker simulations to optimize a set of parameters. I am using LAMMPS to perform my ...
- 5,361
2
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0
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63
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Please suggest some training/tutorial for ML and AI
Could you please suggest a beginner friendly course type tutorial or training for latest ML and AI?
Provided that the learner has basic concepts of Python and has around one month time (or so) for the ...
- 931
1
vote
0
answers
95
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MAGMOM error during the SOC calculation
Can you please help me solve this problem? I have optimised my structure without SOC. After doing the single point by turn on the soc, I am getting the following error.
ERROR:You have set 162 value(s) ...
- 99
5
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0
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124
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Tight Binding and Non hermitian hamiltonians
I'm seeking help and advice because I'm trying to construct a tight-binding model for a finite system (i.e., without periodic boundary conditions), including two spin components and a non-Hermitian ...
- 123
6
votes
2
answers
411
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How to convert chemical formula to SMILES?
I have several chemical formulas along with their names. I want to convert them (or retrieve from public databases if available) into SMILES by using Python code.
I've done several searches on Google, ...
- 243
2
votes
0
answers
76
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Computing carrier concentrations for a given chemical potential range
I want to know how carrier concentrations for a given chemical potential range is computed using DOS and Fermi-Dirac distribution function from quantum ESPRESSO output. Can anyone kindly help me with ...
- 1,101
5
votes
1
answer
111
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Can I capture warning messages into a log file during executing pybel?
Context
I need to convert thousands of SMILES into SDF file using pybel via python scripts (several code lines below).
...
- 243
2
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0
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73
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Correct dislocation insertion in OVITO using python script
When writing a Python script for ovito, to insert screw and edge dislocations, how to make sure that when changing the Burgers vector and dislocation line, the overall picture does not change, that is,...
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5
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2
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283
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Is there have any quick way to find overall charge from xyz of a ligand?
I use xyz2mol.py to convert an XYZ file to an RDKit mol object. But the problem is my sets of ligands with variable charge, which are not listed in the XYZ file. Is there any way I can determine the ...
6
votes
1
answer
277
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How to write a LAMMPS dump command compatible with ASE that includes forces and energy?
I am using LAMMPS and want to write a dump command that outputs atomic positions, forces, and total energy in a format that ASE (Atomic Simulation Environment) can read and attach a ...
- 181
3
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0
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165
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Is there a tool to import Pyscf output into Psi4?
I want to predict NIR spectra from SMILES
With little to no background in computational chemistry I have been exploring open source tools for predicting NIR spectra of some molecules whose SMILES ...
- 203