Update README.md

README.md

@@ -1,3 +1,225 @@
----
-license: mit
----
+---
+license: mit
+language:
+- en
+tags:
+- chemistry
+pretty_name: Minimal QM9 and QMugs dataset
+size_categories:
+- 1K<n<10K
+---
+# `minimal_data_QM9_QMUGS` dataset
+
+This dataset is used to enable simple experiments with our orbital-free density functional theory code from https://github.com/sciai-lab/structures25.
+
+## Dataset 1: QM9_perturbed_fock
+This dataset contains a small subset of [QM9](https://www.nature.com/articles/sdata201422) molecules.
+
+```text
+minimal_data_QM9_QMugs/
+├── QM9_perturbed_fock/
+│   ├── dataset_statistics/
+│   │   ├── dataset_statistics_labels_local_frames_global_symmetric_natrep_e_kin_plus_xc.zarr
+│   │   └── dataset_statistics_labels_no_basis_transforms_e_kin_plus_xc.zarr
+│   ├── labels/
+│   │   ├── 0000825.zarr.zip
+│   │   └── ...
+│   ├── labels_local_frames_global_symmetric_natrep/
+│   │   ├── 0000825.zarr.zip
+│   │   └── ...
+│   ├── split.pkl
+│   └── split.yaml    
+└── QMUGS_perturbed_fock/
+    ├── dataset_statistics/
+    │   ├── dataset_statistics_labels_local_frames_global_symmetric_natrep_e_kin_plus_xc.zarr
+    │   └── dataset_statistics_labels_no_basis_transforms_e_kin_plus_xc.zarr
+    ├── labels/
+    │   ├── 0342979.zarr.zip
+    │   └── ...
+    ├── labels_local_frames_global_symmetric_natrep/
+    │   ├── 0342979.zarr.zip
+    │   └── ...
+    ├── split.pkl
+    └── split.yaml  
+```
+
+### Description folder:
+- `dataset_statistics`: The dataset statistics contain information about the statistics of the energies, coefficients and gradients of the data. These are used for normalization techniques inside the model, and intial guesses of the density. They are loaded once at model or `SADGuesser` initialization. For each basis transform, the statistics will vary which is why each basis transformations gets its own directory. The `dataset_statistics_labels_local_frames_global_symmetric_natrep_e_kin_plus_xc.zarr` statistics used for the model, while the `dataset_statistics_labels_no_basis_transforms_e_kin_plus_xc.zarr` statistics are used for the `SADGuesser`.
+- `labels`: The untransformed label zarr files. These contain all data necessary for model training as well as OFDFT evaluations.
+- `labels_local_frames_global_symmetric_natrep`: The transformed label zarr files. The transformation is applied to all values in the `spatial` group according to their representation. 
+- `split.pkl`: The split file, defining which label files belong to `train`, `val` and `test` split.
+- `split.yaml`: The same split file in `yaml` format, not used by the code but for humans to parse quickly.
+
+#### Internal structure .zarr file (e.g., `0000825.zarr.zip`)
+`geometry` and `of_labels` are used during training and density optimization, while `ks_labels` is there to easily compare against Kohn-Sham energies but is not used in the usual workflows.
+```bash
+>>> print(zarr_store.tree())
+/
+├── geometry
+│   ├── atom_pos (13, 3) float64
+│   ├── atomic_numbers (13,) uint8
+│   └── mol_id () <U11
+├── ks_labels
+│   ├── basis () <U12
+│   └── energies
+│       ├── e_electron (35,) float64
+│       ├── e_ext (35,) float64
+│       ├── e_hartree (35,) float64
+│       ├── e_kin (35,) float64
+│       ├── e_nuc_nuc (35,) float64
+│       ├── e_tot (35,) float64
+│       ├── e_xc (35,) float64
+│       └── has_energy_label (35,) bool
+└── of_labels
+    ├── basis () <U96
+    ├── energies
+    │   ├── e_electron (35,) float64
+    │   ├── e_ext (35,) float64
+    │   ├── e_ext_mod (35,) float64
+    │   ├── e_hartree (35,) float64
+    │   ├── e_kin (35,) float64
+    │   ├── e_kin_minus_apbe (35,) float64
+    │   ├── e_kin_plus_xc (35,) float64
+    │   ├── e_kinapbe (35,) float64
+    │   ├── e_tot (35,) float64
+    │   └── e_xc (35,) float64
+    ├── n_scf_steps () int64
+    └── spatial
+        ├── basis_integrals (35, 904) float64
+        ├── coeffs (35, 904) float64
+        ├── dual_basis_integrals (35, 904) float64
+        ├── grad_ext (35, 904) float64
+        ├── grad_hartree (35, 904) float64
+        ├── grad_kin (35, 904) float64
+        ├── grad_kin_minus_apbe (35, 904) float64
+        ├── grad_kin_plus_xc (35, 904) float64
+        ├── grad_kinapbe (35, 904) float64
+        ├── grad_tot (35, 904) float64
+        └── grad_xc (35, 904) float64
+
+```
+#### Internal structure `dataset_statistics_labels_local_frames_global_symmetric_natrep_e_kin_plus_xc.zarr`
+The dataset statistcs are split into multiple `weigher_keys` like `constant` or `ground_state_only`. This is because for some applications we want to filter, mainly which SCF iterations of our data we want to include. For example, for a good ground state prediction, only the ground state coefficients matter.
+
+```bash
+>>> print(dataset.tree())
+/
+├── constant
+│   └── initial_guess_delta
+│       ├── abs_max (477,) float64
+│       ├── mean (477,) float64
+│       └── std (477,) float64
+├── ground_state_only
+│   ├── atom_ref_atom_type_bias (5,) float64
+│   ├── atom_ref_energy_only_atom_type_bias (5,) float64
+│   ├── atom_ref_energy_only_global_bias () float64
+│   ├── atom_ref_global_bias () float64
+│   ├── coeffs
+│   │   ├── abs_max (477,) float64
+│   │   ├── mean (477,) float64
+│   │   └── std (477,) float64
+│   ├── energy_minus_atom_ref
+│   │   ├── abs_max () float64
+│   │   ├── mean () float64
+│   │   └── std () float64
+│   ├── energy_minus_scalar_atom_ref
+│   │   ├── abs_max () float64
+│   │   ├── mean () float64
+│   │   └── std () float64
+│   ├── gradient_label
+│   │   ├── abs_max (477,) float64
+│   │   ├── mean (477,) float64
+│   │   └── std (477,) float64
+│   ├── gradient_max_after_atom_ref (477,) float64
+│   ├── gradient_max_after_scalar_atom_ref (477,) float64
+│   ├── scalar_atom_ref_atom_type_bias (5,) float64
+│   └── scalar_atom_ref_global_bias () float64
+├── has_energy_label
+│   ├── atom_ref_atom_type_bias (5,) float64
+│   ├── atom_ref_energy_only_atom_type_bias (5,) float64
+│   ├── atom_ref_energy_only_global_bias () float64
+│   ├── atom_ref_global_bias () float64
+│   ├── coeffs
+│   │   ├── abs_max (477,) float64
+│   │   ├── mean (477,) float64
+│   │   └── std (477,) float64
+│   ├── energy_minus_atom_ref
+│   │   ├── abs_max () float64
+│   │   ├── mean () float64
+│   │   └── std () float64
+│   ├── energy_minus_scalar_atom_ref
+│   │   ├── abs_max () float64
+│   │   ├── mean () float64
+│   │   └── std () float64
+│   ├── gradient_label
+│   │   ├── abs_max (477,) float64
+│   │   ├── mean (477,) float64
+│   │   └── std (477,) float64
+│   ├── gradient_max_after_atom_ref (477,) float64
+│   ├── gradient_max_after_scalar_atom_ref (477,) float64
+│   ├── scalar_atom_ref_atom_type_bias (5,) float64
+│   └── scalar_atom_ref_global_bias () float64
+├── initial_guess_only
+│   └── initial_guess_delta
+│       ├── abs_max (477,) float64
+│       ├── mean (477,) float64
+│       └── std (477,) float64
+├── min_scf_iteration_3
+│   ├── atom_ref_atom_type_bias (5,) float64
+│   ├── atom_ref_energy_only_atom_type_bias (5,) float64
+│   ├── atom_ref_energy_only_global_bias () float64
+│   ├── atom_ref_global_bias () float64
+│   ├── coeffs
+│   │   ├── abs_max (477,) float64
+│   │   ├── mean (477,) float64
+│   │   └── std (477,) float64
+│   ├── energy_minus_atom_ref
+│   │   ├── abs_max () float64
+│   │   ├── mean () float64
+│   │   └── std () float64
+│   ├── energy_minus_scalar_atom_ref
+│   │   ├── abs_max () float64
+│   │   ├── mean () float64
+│   │   └── std () float64
+│   ├── gradient_label
+│   │   ├── abs_max (477,) float64
+│   │   ├── mean (477,) float64
+│   │   └── std (477,) float64
+│   ├── gradient_max_after_atom_ref (477,) float64
+│   ├── gradient_max_after_scalar_atom_ref (477,) float64
+│   ├── initial_guess_delta
+│   │   ├── abs_max (477,) float64
+│   │   ├── mean (477,) float64
+│   │   └── std (477,) float64
+│   ├── scalar_atom_ref_atom_type_bias (5,) float64
+│   └── scalar_atom_ref_global_bias () float64
+└── min_scf_iteration_5
+    ├── atom_ref_atom_type_bias (5,) float64
+    ├── atom_ref_energy_only_atom_type_bias (5,) float64
+    ├── atom_ref_energy_only_global_bias () float64
+    ├── atom_ref_global_bias () float64
+    ├── coeffs
+    │   ├── abs_max (477,) float64
+    │   ├── mean (477,) float64
+    │   └── std (477,) float64
+    ├── energy_minus_atom_ref
+    │   ├── abs_max () float64
+    │   ├── mean () float64
+    │   └── std () float64
+    ├── energy_minus_scalar_atom_ref
+    │   ├── abs_max () float64
+    │   ├── mean () float64
+    │   └── std () float64
+    ├── gradient_label
+    │   ├── abs_max (477,) float64
+    │   ├── mean (477,) float64
+    │   └── std (477,) float64
+    ├── gradient_max_after_atom_ref (477,) float64
+    ├── gradient_max_after_scalar_atom_ref (477,) float64
+    ├── scalar_atom_ref_atom_type_bias (5,) float64
+    └── scalar_atom_ref_global_bias () float64
+
+```
+
+## Dataset 2: QMUGS_perturbed_fock
+This dataset contains a small subset of [QMugs](https://www.nature.com/articles/s41597-022-01390-7) molecules, which we use to test generalization to larger molecules. The structure of the data is exactly the same as for QM9.