File size: 2,720 Bytes
81d6afe | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 | # Training Data (Unit-Corrected)
This directory contains molecular data with **corrected units** ready for DCMnet/PhysnetJax training.
## Data Corrections Applied
### 1. Atomic Coordinates (R)
- **Original**: Angstroms (verified)
- **Status**: ✓ Correct
- **Units**: Angstrom (ASE standard)
### 2. Energies (E)
- **Original**: Hartree
- **Converted**: eV (ASE standard)
- **Factor**: ×27.211386
### 3. Forces (F)
- **Original**: Hartree/Bohr
- **Converted**: eV/Angstrom (ASE standard)
- **Factor**: ×51.42208
### 4. ESP Grid Coordinates (vdw_surface)
- **Original**: Grid index space
- **Fixed**: Physical Angstroms
- **Conversion**: Applied proper grid spacing (0.25 Bohr = 0.132294 Å)
## Data Splits
- **Train**: 800 samples (80%)
- **Valid**: 100 samples (10%)
- **Test**: 101 samples (10%)
- **Seed**: 42 (reproducible)
## Files
### Energy, Forces, and Dipoles
- `energies_forces_dipoles_train.npz`
- `energies_forces_dipoles_valid.npz`
- `energies_forces_dipoles_test.npz`
Each contains:
- `R`: Atomic coordinates [Angstrom]
- `Z`: Atomic numbers [int]
- `N`: Number of atoms [int]
- `E`: Energies [eV] ← CONVERTED from Hartree
- `F`: Forces [eV/Angstrom] ← CONVERTED from Hartree/Bohr
- `Dxyz`: Dipole moments [e·Å] ← CONVERTED from Debye
### ESP Grids
- `grids_esp_train.npz`
- `grids_esp_valid.npz`
- `grids_esp_test.npz`
Each contains:
- `R`: Atomic coordinates [Angstrom]
- `Z`: Atomic numbers [int]
- `N`: Number of atoms [int]
- `esp`: ESP values [Hartree/e]
- `vdw_surface`: Grid coordinates [Angstrom] ← FIXED
- `vdw_grid`: Same as vdw_surface (backward compatibility)
- `grid_dims`: Original cube dimensions (if available)
- `grid_origin`: Original cube origins [Bohr] (if available)
- `grid_axes`: Original cube axes (if available)
- `Dxyz`: Dipole moments [e·Å] ← CONVERTED from Debye
## Units Summary (ASE Standard)
| Property | Unit | Status |
|----------|------|--------|
| R (coordinates) | Angstrom | ✓ Correct |
| E (energy) | eV | ✓ Converted |
| F (forces) | eV/Angstrom | ✓ Converted |
| Dxyz (dipoles) | e·Å | ✓ Converted from Debye |
| esp (values) | Hartree/e | ✓ Correct |
| vdw_surface | Angstrom | ✓ Fixed |
## Usage
```python
import numpy as np
# Load training data
train_props = np.load('energies_forces_dipoles_train.npz')
# All units are ASE-standard - ready to use!
R = train_props['R'] # Angstroms
E = train_props['E'] # eV
F = train_props['F'] # eV/Angstrom
Dxyz = train_props['Dxyz'] # e·Å (converted from Debye)
# Load grid data (if available)
train_grids = np.load('grids_esp_train.npz')
esp = train_grids['esp'] # Hartree/e
vdw_surface = train_grids['vdw_surface'] # Angstroms
Generated by: mmml.cli.fix_and_split
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