Dataset Module
energy_gnome.dataset.CathodeDatabase
Bases: BaseDatabase
Source code in energy_gnome/dataset/cathodes.py
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__init__(data_dir=DATA_DIR, working_ion='Li', battery_type='insertion')
Initialize the CathodeDatabase with a root data directory and processing stage.
Sets up the directory structure for storing data across different processing stages (raw/
, processed/
, final/
) and initializes placeholders for database paths and data.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
data_dir | Path | Root directory path for storing data. Defaults to DATA_DIR from config. | DATA_DIR |
working_ion | str | The working ion used in the dataset (e.g., 'Li'). Defaults to "Li". | 'Li' |
battery_type | str | The type of battery type (e.g., 'insertion', 'conversion'). Defaults to "insertion". | 'insertion' |
Raises:
Type | Description |
---|---|
NotImplementedError | If the specified processing stage is not supported. |
ImmutableRawDataError | If attempting to set an unsupported processing stage. |
Source code in energy_gnome/dataset/cathodes.py
__repr__()
Text representation of the CathodeDatabase instance. Used for print() and str() calls.
Returns:
Name | Type | Description |
---|---|---|
str | str | ASCII table representation of the database |
Source code in energy_gnome/dataset/cathodes.py
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add_material_properties(stage, materials_mp_query, charge_state, mute_progress_bars=True)
Add material properties to the database from Material Project query results.
Saves CIF files for each material in the query and updates the database with file paths and properties.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
stage | str | Processing stage ('raw', 'processed', 'final'). | required |
materials_mp_query | List[Any] | List of material query results. | required |
charge_state | str | The state of the cathode ('charge' or 'discharge'). | required |
mute_progress_bars | bool | Disable progress bar if True. Defaults to True. | True |
Returns:
Type | Description |
---|---|
DataFrame | pd.DataFrame: Updated database with material properties. |
Raises:
Type | Description |
---|---|
ImmutableRawDataError | If attempting to modify immutable raw data. |
KeyError | If a material ID is not found in the database. |
Source code in energy_gnome/dataset/cathodes.py
Python | |
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backup_and_changelog(old_db, new_db, differences, stage)
Backup the old database and update the changelog with identified differences.
Creates a backup of the existing database and appends a changelog entry detailing the differences between the old and new databases. The changelog includes information such as entry identifiers, formulas, and last updated timestamps.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
old_db | DataFrame | The existing database before updates. | required |
new_db | DataFrame | The new database containing updates. | required |
differences | Series | Series of identifiers that are new or updated. | required |
stage | str | The processing stage ('raw', 'processed', 'final'). | required |
Source code in energy_gnome/dataset/cathodes.py
compare_and_update(new_db, stage)
Compare and update the database with new entries.
Identifies new entries and updates the database accordingly. Ensures that raw data remains immutable by preventing updates unless explicitly allowed.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
new_db | DataFrame | New database to compare. | required |
stage | str | Processing stage ("raw", "processed", "final"). | required |
Returns:
Type | Description |
---|---|
DataFrame | pd.DataFrame: Updated database containing new entries. |
Raises:
Type | Description |
---|---|
ImmutableRawDataError | If attempting to modify immutable raw data. |
Source code in energy_gnome/dataset/cathodes.py
compare_databases(new_db, stage)
Compare two databases and identify new entry IDs.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
new_db | DataFrame | New database to compare. | required |
stage | str | Processing stage ("raw", "processed", "final"). | required |
Returns:
Type | Description |
---|---|
DataFrame | pd.DataFrame: Subset of |
Source code in energy_gnome/dataset/cathodes.py
copy_cif_files(stage, charge_state, mute_progress_bars=True)
Copy CIF files from the raw stage to another processing stage.
Copies CIF files corresponding to the specified cathode state from the 'raw' processing stage to the target stage. Updates the database with the new file paths.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
stage | str | Target processing stage ('processed', 'final'). | required |
charge_state | str | The charge state of the cathode ('charge' or 'discharge'). | required |
mute_progress_bars | bool | Disable progress bar if True. Defaults to True. | True |
Raises:
Type | Description |
---|---|
ValueError | If the target stage is 'raw'. |
MissingData | If the source CIF directory does not exist or is empty. |
Source code in energy_gnome/dataset/cathodes.py
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retrieve_materials(stage, charge_state, mute_progress_bars=True)
Retrieve material structures from the Material Project API.
Fetches material structures based on the processing stage and charge state.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
stage | str | Processing stage ('raw', 'processed', 'final'). | required |
charge_state | str | Cathode charge state ('charge', 'discharge'). | required |
mute_progress_bars | bool | Disable progress bar if True. Defaults to True. | True |
Returns:
Type | Description |
---|---|
list[Any] | List[Any]: List of retrieved material objects. |
Raises:
Type | Description |
---|---|
ValueError | If the charge_state is invalid. |
MissingData | If the required data is missing in the database. |
Source code in energy_gnome/dataset/cathodes.py
retrieve_models(mute_progress_bars=True)
Retrieve battery models from the Materials Project API.
Connects to the Material Project API using MPRester, queries for materials based on the working ion and processing stage, and retrieves the specified fields. Cleans the data by removing entries with missing critical identifiers.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
mute_progress_bars | bool | If | True |
Returns:
Type | Description |
---|---|
DataFrame | pd.DataFrame: DataFrame containing the retrieved and cleaned models. |
Raises:
Type | Description |
---|---|
Exception | If the API query fails. |
Source code in energy_gnome/dataset/cathodes.py
retrieve_remote(mute_progress_bars=True)
Retrieve models from the Material Project API.
Wrapper method to call retrieve_models
.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
mute_progress_bars | bool | If | True |
Returns:
Type | Description |
---|---|
DataFrame | pd.DataFrame: DataFrame containing the retrieved models. |
Source code in energy_gnome/dataset/cathodes.py
save_cif_files(stage, materials_mp_query, charge_state, mute_progress_bars=True)
Save CIF files for materials and update the database accordingly.
Manages the saving of CIF files for each material and updates the database with the file paths and relevant properties. Ensures that raw data remains immutable.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
stage | str | Processing stage ('raw', 'processed', 'final'). | required |
materials_mp_query | List[Any] | List of material query results. | required |
charge_state | str | The charge state of the cathode ('charge' or 'discharge'). | required |
mute_progress_bars | bool | Disable progress bar if True. Defaults to True. | True |
Raises:
Type | Description |
---|---|
ImmutableRawDataError | If attempting to modify immutable raw data. |
Source code in energy_gnome/dataset/cathodes.py
Python | |
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energy_gnome.dataset.PerovskiteDatabase
Bases: BaseDatabase
Source code in energy_gnome/dataset/perovskites.py
Python | |
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__init__(data_dir=DATA_DIR, external_perovproj_path=EXTERNAL_DATA_DIR / Path('perovskites') / Path('perovproject_db.json'))
Initialize the PerovskiteDatabase with a root data directory and processing stage.
Sets up the directory structure for storing data across different processing stages (raw/
, processed/
, final/
) and initializes placeholders for database paths and data.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
data_dir | Path | Root directory path for storing data. Defaults to DATA_DIR from config. | DATA_DIR |
Raises:
Type | Description |
---|---|
NotImplementedError | If the specified processing stage is not supported. |
ImmutableRawDataError | If attempting to set an unsupported processing stage. |
Source code in energy_gnome/dataset/perovskites.py
__repr__()
Text representation of the PerovskiteDatabase instance. Used for print() and str() calls.
Returns:
Name | Type | Description |
---|---|---|
str | str | ASCII table representation of the database |
Source code in energy_gnome/dataset/perovskites.py
Python | |
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add_material_properties(stage, materials_mp_query, mute_progress_bars=True)
Add material properties to the database from Material Project query results.
Saves CIF files for each material in the query and updates the database with file paths and properties.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
stage | str | Processing stage ('raw', 'processed', 'final'). | required |
materials_mp_query | List[Any] | List of material query results. | required |
mute_progress_bars | bool | Disable progress bar if True. Defaults to True. | True |
Returns:
Type | Description |
---|---|
DataFrame | pd.DataFrame: Updated database with material properties. |
Raises:
Type | Description |
---|---|
ImmutableRawDataError | If attempting to modify immutable raw data. |
KeyError | If a material ID is not found in the database. |
Source code in energy_gnome/dataset/perovskites.py
backup_and_changelog(old_db, new_db, differences, stage)
Backup the old database and update the changelog with identified differences.
Creates a backup of the existing database and appends a changelog entry detailing the differences between the old and new databases. The changelog includes information such as entry identifiers, formulas, and last updated timestamps.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
old_db | DataFrame | The existing database before updates. | required |
new_db | DataFrame | The new database containing updates. | required |
differences | Series | Series of identifiers that are new or updated. | required |
stage | str | The processing stage ('raw', 'processed', 'final'). | required |
Source code in energy_gnome/dataset/perovskites.py
compare_and_update(new_db, stage)
Compare and update the database with new entries.
Identifies new entries and updates the database accordingly. Ensures that raw data remains immutable by preventing updates unless explicitly allowed.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
new_db | DataFrame | New database to compare. | required |
stage | str | Processing stage ("raw", "processed", "final"). | required |
Returns:
Type | Description |
---|---|
DataFrame | pd.DataFrame: Updated database containing new entries. |
Raises:
Type | Description |
---|---|
ImmutableRawDataError | If attempting to modify immutable raw data. |
Source code in energy_gnome/dataset/perovskites.py
compare_databases(new_db, stage)
Compare two databases and identify new entry IDs.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
new_db | DataFrame | New database to compare. | required |
stage | str | Processing stage ("raw", "processed", "final"). | required |
Returns:
Type | Description |
---|---|
DataFrame | pd.DataFrame: Subset of |
Source code in energy_gnome/dataset/perovskites.py
copy_cif_files(stage, mute_progress_bars=True)
Copy CIF files from the raw stage to another processing stage.
Copies CIF files corresponding to the specified cathode state from the 'raw' processing stage to the target stage. Updates the database with the new file paths.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
stage | str | Target processing stage ('processed', 'final'). | required |
mute_progress_bars | bool | Disable progress bar if True. Defaults to True. | True |
Raises:
Type | Description |
---|---|
ValueError | If the target stage is 'raw'. |
MissingData | If the source CIF directory does not exist or is empty. |
Source code in energy_gnome/dataset/perovskites.py
Python | |
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retrieve_materials(mute_progress_bars=True)
Retrieve perovskites from the Materials Project API.
Connects to the Material Project API using MPRester, queries for materials, and retrieves the specified fields. Cleans the data by removing entries with missing critical identifiers.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
mute_progress_bars | bool | If | True |
Returns:
Type | Description |
---|---|
DataFrame | pd.DataFrame: DataFrame containing the retrieved and cleaned models. |
Raises:
Type | Description |
---|---|
Exception | If the API query fails. |
Source code in energy_gnome/dataset/perovskites.py
Python | |
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retrieve_remote(mute_progress_bars=True)
Retrieve materials from the Material Project API.
Wrapper method to call retrieve_materials
.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
mute_progress_bars | bool | If | True |
Returns:
Type | Description |
---|---|
DataFrame | pd.DataFrame: DataFrame containing the retrieved materials. |
Source code in energy_gnome/dataset/perovskites.py
save_cif_files(stage, materials_mp_query, mute_progress_bars=True)
Save CIF files for materials and update the database accordingly.
Manages the saving of CIF files for each material and updates the database with the file paths and relevant properties. Ensures that raw data remains immutable.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
stage | str | Processing stage ('raw', 'processed', 'final'). | required |
materials_mp_query | List[Any] | List of material query results. | required |
mute_progress_bars | bool | Disable progress bar if True. Defaults to True. | True |
Raises:
Type | Description |
---|---|
ImmutableRawDataError | If attempting to modify immutable raw data. |
Source code in energy_gnome/dataset/perovskites.py
Python | |
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