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I tried to compute Voronoi charges on a platinum cluster consisting of 353 atoms. The total population ends up summing to ~ 176.5, which is roughly half the number of atoms.
Sum …
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![image](https://user-images.githubusercontent.com/1320252/58152555-6f45cb00-7c9f-11e9-89e4-a7cff8d2404b.png)
![image](https://user-images.githubusercontent.com/1320252/58152540-63f29f80-7c9f-11e9-91…
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This is a very interesting project and executes well something that many other projects have attempted in the past.
I have seen the sample contacts application, read the documentation, and I am curre…
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On Ubuntu 22.04.4 LTS, I tried to compile dftd4 `main` branch using intel oneapi/2024.2.0 and I noticed that the lapack package shipped with MKL cannot be used, so I must do the compilation as below:…
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Hi,
We are trying to follow the following description for loading large datasets
https://github.com/ACEsuit/mace?tab=readme-ov-file#on-line-data-loading-for-large-datasets
The script we ran i…
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I tried to validate the accuracy of Vina on the DUD-E dataset according to the AutoDock Vina v1.2.0 paper and the supporting information description.
After adding hydrogen to the receptor of the DU…
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I think we should go back to #112 and #124 and test density ovelap model (FDBM) properly, because I'm not sure it reproduce chemical intution and experimental data as it is now.
* Free-Electron pa…
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print(len(mol._atoms))
print(len(mol.bonds))
print(len(mol.atomic_charges))
bromines = [i for i in mol.yield_atoms_by_element('Br')]
…
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Complete input and outputs here:
[test.zip](https://github.com/shankar1729/jdftx/files/15471521/test.zip)
It seems like there is an issue with the MPI encoding/decoding leading to nan
```
# Ener…
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**Describe the bug**
When running part 4: Molecular Dynamics with MACE, will be IndexError: too many indices for tensor of dimension 1.
**To Reproduce**
Steps to reproduce the behavior:
1. Go to…