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## Structure of LMDB
### Notes
- The coordinates at the last step of one stage match the first step coordinates of the next stage
- In some cases, the Hartree Fork results were copied to the raw DFT first substage files and in this case the value of `DFT_1st` is None
### Key-Value Structure
- **Keys**:
- CIDs as strings, e.g., `b'000015111'`
- Note: These are byte-encoded using `string.encode()` or `b'string'`
- **Values**:
- A nested dictionary containing multiple calculation methods:
- Uncompress values with:
```python
pickle.loads(gzip.decompress(val))
```
- Structure example:
```python
b'000015111' : {
'pm3' : [{step1}, {step2}, ..., {step_n}],
'hf' : [{step1}, {step2}, ..., {step_m}],
'DFT_1st' : [{step1}, {step2}, ..., {step_z}],
'DFT_2nd' : [{step1}, {step2}, ..., {step_k}]
}
```
- Each step is a nested dictionary with the following structure:
```python
{
'coordinates': {'atom': f'{element_letter}', 'charge': float(charge_val), 'x': float(x_val), 'y': float(y_val), 'z': float(z_val)}, ...
'energy': float(energy_val),
'gradient': {'atom': f'{element_letter}', 'charge': float(charge_val), 'dx': float(dx_val), 'dy': float(dy_val), 'dz': float(dz_val)}, ...
}
```
Note: `DFT_1st` stage for each molecule is calculated with either FireFly or SMASH. For SMASH method, it does not contain a charge value associated with each atom.
### Accessing LMDB Example
```python
import lmdb
import pickle
import gzip
lmdb_file = '/path/to/lmdb/dir/hokusai2017.lmdb'
with lmdb.open(lmdb_file, readonly=True, subdir=False) as env:
with env.begin() as txn:
val = pickle.loads(gzip.decompress((txn.get(b'000000984'))))
pm3_val = val['pm3']
hf_val = val['hf']
dft1st_val = val['DFT_1st']
dft2nd_val = val['DFT_2nd']
for step in dft1st_val:
# coords & grad is a list of dictionaries that stores the relevant information of each atom
# energy is a scalar representing the energy for that conformer
coords = step['coordinates']
energy = step['energy']
grad = step['gradient']
for atom in coords:
# access atom's attributes
element = atom['atom']
x = atom['x']
y = atom['y']
z = atom['z']
for atom in grad:
# access atom's attributes
element = atom['atom']
dx = atom['dx']
dy = atom['dy']
dz = atom['dz']
```
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