diff --git a/README.md b/README.md index d3e677d..c37624d 100644 --- a/README.md +++ b/README.md @@ -111,8 +111,8 @@ cs_iso_uncertainty = np.std(cs_committee_iso, axis=1, ddof=1) cs_psa = np.linalg.eigvalsh(cs_tensor) ``` -This snippet will estimate the predicted chemical shieldings of diamond to be highly uncertain, -as expected and desired, given that diamond as an inorganic material is not well +This snippet will estimate the predicted chemical shieldings of diamond to be highly uncertain, +as expected and desired, given that diamond as an inorganic material is not well represented in the training data of the model. @@ -163,11 +163,11 @@ pip install shiftml==
ShiftML3 predictions aren’t identical for magnetically equivalent atoms. Why? -ShiftML3 is built on the **Point Edge Transformer (PET)** model, which is *not perfectly rotationally invariant*. -This can introduce tiny, random differences for atoms that are magnetically equivalent. +ShiftML3 is built on the **Point Edge Transformer (PET)** model, which is *not perfectly rotationally invariant*. +This can introduce tiny, random differences for atoms that are magnetically equivalent. We have verified that these fluctuations are minor and do **not** harm overall accuracy. -> **Tip – get identical shielding predictions** +> **Tip – get identical shielding predictions** > Average the predictions over all magnetically equivalent atoms.
@@ -177,10 +177,10 @@ We have verified that these fluctuations are minor and do **not** harm overall a
ShiftML3 shows large errors versus my GIPAW-DFT shieldings. What’s going on? -Chemical-shielding calculations are *very* sensitive to the **code and convergence parameters** used. +Chemical-shielding calculations are *very* sensitive to the **code and convergence parameters** used. Only compare ShiftML3 to GIPAW-DFT data generated with *exactly* the same settings as the training set. -*Reference inputs* for Quantum Espresso with the correct parameters are available in this +*Reference inputs* for Quantum Espresso with the correct parameters are available in this [Zenodo data repository](https://zenodo.org/records/7097427).
@@ -190,7 +190,7 @@ Only compare ShiftML3 to GIPAW-DFT data generated with *exactly* the same settin
I used identical GIPAW-DFT parameters but still see big errors. What now? -Check the model’s **uncertainty estimates** (committee variance; see “Advanced usage” above). +Check the model’s **uncertainty estimates** (committee variance; see “Advanced usage” above). If the uncertainty is **several ×** the element’s test-set RMSE, the prediction is probably unreliable for your structure. @@ -201,11 +201,11 @@ for your structure.
My calculated shieldings don’t correlate with experiment at all. Why? -1. **Validate the baseline.** - Make sure reliable **GIPAW/PBE** results exist (or recompute them) and confirm they correlate with experiment. +1. **Validate the baseline.** + Make sure reliable **GIPAW/PBE** results exist (or recompute them) and confirm they correlate with experiment. Inaccurate DFT—often the exchange–correlation functional—can be blamed. -2. **Check your structures.** +2. **Check your structures.** If candidate geometries don’t reflect experimental conditions *or* the inter-atomic potential used to generate structures is poor, both DFT and ML predictions will stray from reality. @@ -250,11 +250,13 @@ pytest ## Contributors -Matthias Kellner\ -Yuxuan Zhang\ -Ruben Rodriguez Madrid\ +Matthias Kellner +Yuxuan Zhang +Ruben Rodriguez Madrid Guillaume Fraux +This project is [maintained](https://github.com/lab-cosmo/.github/blob/main/Maintainers.md) by [@bananenpampe](https://github.com/bananenpampe), who will reply to issues and pull requests opened on this repository as soon as possible. You can mention them directly if you did not receive an answer after a couple of days. + ## References This package is based on the following papers: @@ -264,4 +266,3 @@ This package is based on the following papers: - A Machine Learning Model of Chemical Shifts for Chemically and\ Structurally Diverse Molecular Solids - Cordova et al. [[3](https://doi.org/10.1021/acs.jpcc.2c03854)] - A deep learning model for chemical shieldings in molecular organic solids including anisotropy - Kellner, Holmes, Rodriguez Madrid, Viscosi, Zhang, Emsley, Ceriotti [[4](https://doi.org/10.1021/acs.jpclett.5c01819)] -