Questions tagged [python]
Questions about or related to Matter Modeling with Python or Python's relationship to Matter Modeling.
265 questions
9 votes
2 answers
193 views
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, $...
- 1,083
3 votes
0 answers
21 views
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 ...
4 votes
1 answer
77 views
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 ...
- 5,316
1 vote
0 answers
43 views
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
6 votes
2 answers
191 views
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
5 votes
1 answer
85 views
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
5 votes
2 answers
191 views
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 ...
3 votes
0 answers
110 views
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