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Small bugfixes #579

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merged 6 commits into from
Oct 7, 2024
Merged

Small bugfixes #579

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28c7ceb
Renamed all scipy calls from simps to simpson and trpz to trapezoid
RandomDefaultUser Oct 7, 2024
d8ae8ad
Made path naming consistent.
RandomDefaultUser Oct 7, 2024
99f42b7
Updated test data repo
RandomDefaultUser Oct 7, 2024
c2c2b2d
Forgot to rename parameter in trainer class
RandomDefaultUser Oct 7, 2024
3fe785b
Forgot to rename a block in runner.py
RandomDefaultUser Oct 7, 2024
b6e6437
Formatting
RandomDefaultUser Oct 7, 2024
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2 changes: 1 addition & 1 deletion docs/source/install/installing_mala.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ itself is subject to ongoing development as well.

git clone https://github.com/mala-project/test-data ~/path/to/data/repo
cd ~/path/to/data/repo
git checkout v1.8.0
git checkout v1.8.1

* Export the path to that repo by ``export MALA_DATA_REPO=~/path/to/data/repo``

Expand Down
6 changes: 3 additions & 3 deletions mala/interfaces/ase_calculator.py
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Original file line number Diff line number Diff line change
Expand Up @@ -199,7 +199,7 @@ def calculate_properties(self, atoms, properties):
"e_ewald"
]

def save_calculator(self, filename, save_path="./"):
def save_calculator(self, filename, path="./"):
"""
Save parameters used for this calculator.

Expand All @@ -210,10 +210,10 @@ def save_calculator(self, filename, save_path="./"):
filename : string
Name of the file in which to store the calculator.

save_path : string
path : string
Path where the calculator should be saved.

"""
self.predictor.save_run(
filename, save_path=save_path, additional_calculation_data=True
filename, path=save_path, additional_calculation_data=True
)
110 changes: 53 additions & 57 deletions mala/network/runner.py
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Original file line number Diff line number Diff line change
Expand Up @@ -99,8 +99,7 @@ def _calculate_errors(
target_calculator, LDOS
) and not isinstance(target_calculator, Density):
raise Exception(
"Cannot calculate density from this "
"observable."
"Cannot calculate density from this " "observable."
)
target_calculator.read_additional_calculation_data(
self.data.get_snapshot_calculation_output(
Expand Down Expand Up @@ -145,8 +144,7 @@ def _calculate_errors(
target_calculator, LDOS
) and not isinstance(target_calculator, DOS):
raise Exception(
"Cannot calculate the DOS from this "
"observable."
"Cannot calculate the DOS from this " "observable."
)
target_calculator.read_additional_calculation_data(
self.data.get_snapshot_calculation_output(
Expand Down Expand Up @@ -299,10 +297,8 @@ def _calculate_energy_errors(
)
try:
target_calculator.read_from_array(predicted_outputs)
be_predicted_actual_fe = (
target_calculator.get_band_energy(
fermi_energy=fe_actual
)
be_predicted_actual_fe = target_calculator.get_band_energy(
fermi_energy=fe_actual
)
be_error_actual_fe = (
be_predicted_actual_fe - be_actual
Expand Down Expand Up @@ -386,9 +382,7 @@ def _calculate_energy_targets_and_predictions(
snapshot_number
)
if not output_file:
raise Exception(
"Output file needed for energy calculations."
)
raise Exception("Output file needed for energy calculations.")
target_calculator.read_additional_calculation_data(output_file)

targets = {}
Expand All @@ -400,12 +394,8 @@ def _calculate_energy_targets_and_predictions(
actual_outputs
)
except ValueError:
targets = {
energy_type: np.nan for energy_type in energy_types
}
predictions = {
energy_type: np.nan for energy_type in energy_types
}
targets = {energy_type: np.nan for energy_type in energy_types}
predictions = {energy_type: np.nan for energy_type in energy_types}
printout(
"CAUTION! LDOS ground truth is so wrong that the "
"estimation of the self consistent Fermi energy fails."
Expand All @@ -416,12 +406,8 @@ def _calculate_energy_targets_and_predictions(
predicted_outputs
)
except ValueError:
targets = {
energy_type: np.nan for energy_type in energy_types
}
predictions = {
energy_type: np.nan for energy_type in energy_types
}
targets = {energy_type: np.nan for energy_type in energy_types}
predictions = {energy_type: np.nan for energy_type in energy_types}
printout(
"CAUTION! LDOS prediction is so wrong that the "
"estimation of the self consistent Fermi energy fails."
Expand All @@ -447,8 +433,12 @@ def _calculate_energy_targets_and_predictions(
be_predicted = target_calculator.get_band_energy(
fermi_energy=fe_predicted
)
targets[energy_type] = be_actual * 1000 / len(target_calculator.atoms)
predictions[energy_type] = be_predicted * 1000 / len(target_calculator.atoms)
targets[energy_type] = (
be_actual * 1000 / len(target_calculator.atoms)
)
predictions[energy_type] = (
be_predicted * 1000 / len(target_calculator.atoms)
)
except ValueError:
targets[energy_type] = np.nan
predictions[energy_type] = np.nan
Expand All @@ -461,13 +451,17 @@ def _calculate_energy_targets_and_predictions(
)
try:
target_calculator.read_from_array(predicted_outputs)
be_predicted_actual_fe = (
target_calculator.get_band_energy(
fermi_energy=fe_actual
)
be_predicted_actual_fe = target_calculator.get_band_energy(
fermi_energy=fe_actual
)
targets[energy_type] = (
be_actual * 1000 / len(target_calculator.atoms)
)
predictions[energy_type] = (
be_predicted_actual_fe
* 1000
/ len(target_calculator.atoms)
)
targets[energy_type] = be_actual * 1000 / len(target_calculator.atoms)
predictions[energy_type] = be_predicted_actual_fe * 1000 / len(target_calculator.atoms)
except ValueError:
targets[energy_type] = np.nan
predictions[energy_type] = np.nan
Expand All @@ -491,8 +485,12 @@ def _calculate_energy_targets_and_predictions(
te_predicted = target_calculator.get_total_energy(
fermi_energy=fe_predicted
)
targets[energy_type] = te_actual * 1000 / len(target_calculator.atoms)
predictions[energy_type] = te_predicted * 1000 / len(target_calculator.atoms)
targets[energy_type] = (
te_actual * 1000 / len(target_calculator.atoms)
)
predictions[energy_type] = (
te_predicted * 1000 / len(target_calculator.atoms)
)
except ValueError:
targets[energy_type] = np.nan
predictions[energy_type] = np.nan
Expand All @@ -509,9 +507,15 @@ def _calculate_energy_targets_and_predictions(
fermi_energy=fe_actual
)
)

targets[energy_type] = te_actual * 1000 / len(target_calculator.atoms)
predictions[energy_type] = te_predicted_actual_fe * 1000 / len(target_calculator.atoms)

targets[energy_type] = (
te_actual * 1000 / len(target_calculator.atoms)
)
predictions[energy_type] = (
te_predicted_actual_fe
* 1000
/ len(target_calculator.atoms)
)
except ValueError:
targets[energy_type] = np.nan
predictions[energy_type] = np.nan
Expand All @@ -524,7 +528,7 @@ def _calculate_energy_targets_and_predictions(
def save_run(
self,
run_name,
save_path="./",
path="./",
zip_run=True,
save_runner=False,
additional_calculation_data=None,
Expand All @@ -537,7 +541,7 @@ def save_run(
run_name : str
Name under which the run should be saved.

save_path : str
path : str
Path where to which the run.

zip_run : bool
Expand Down Expand Up @@ -567,20 +571,16 @@ def save_run(
params_file = run_name + ".params.json"
if save_runner:
optimizer_file = run_name + ".optimizer.pth"
os.makedirs(save_path, exist_ok=True)
self.parameters_full.save(os.path.join(save_path, params_file))
os.makedirs(path, exist_ok=True)
self.parameters_full.save(os.path.join(path, params_file))
if self.parameters_full.use_ddp:
self.network.module.save_network(
os.path.join(save_path, model_file)
os.path.join(path, model_file)
)
else:
self.network.save_network(os.path.join(save_path, model_file))
self.data.input_data_scaler.save(
os.path.join(save_path, iscaler_file)
)
self.data.output_data_scaler.save(
os.path.join(save_path, oscaler_file)
)
self.network.save_network(os.path.join(path, model_file))
self.data.input_data_scaler.save(os.path.join(path, iscaler_file))
self.data.output_data_scaler.save(os.path.join(path, oscaler_file))

files = [model_file, iscaler_file, oscaler_file, params_file]
if save_runner:
Expand All @@ -593,27 +593,23 @@ def save_run(
additional_calculation_data
)
self.data.target_calculator.write_additional_calculation_data(
os.path.join(
save_path, additional_calculation_file
)
os.path.join(path, additional_calculation_file)
)
elif isinstance(additional_calculation_data, bool):
if additional_calculation_data:
self.data.target_calculator.write_additional_calculation_data(
os.path.join(
save_path, additional_calculation_file
)
os.path.join(path, additional_calculation_file)
)

files.append(additional_calculation_file)
with ZipFile(
os.path.join(save_path, run_name + ".zip"),
os.path.join(path, run_name + ".zip"),
"w",
compression=ZIP_STORED,
) as zip_obj:
for file in files:
zip_obj.write(os.path.join(save_path, file), file)
os.remove(os.path.join(save_path, file))
zip_obj.write(os.path.join(path, file), file)
os.remove(os.path.join(path, file))

@classmethod
def load_run(
Expand Down
2 changes: 1 addition & 1 deletion mala/network/trainer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1046,7 +1046,7 @@ def __create_training_checkpoint(self):
self.save_run(
self.parameters.checkpoint_name,
save_runner=True,
save_path=self.parameters.run_name,
path=self.parameters.run_name,
)
else:
self.save_run(self.parameters.checkpoint_name, save_runner=True)
Expand Down
12 changes: 6 additions & 6 deletions mala/targets/calculation_helpers.py
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Expand Up @@ -21,8 +21,8 @@ def integrate_values_on_spacing(values, spacing, method, axis=0):
method : string
Integration method to be used. Currently supported:

- "trapz" for trapezoid method
- "simps" for Simpson method.
- "trapezoid" for trapezoid method
- "simpson" for Simpson method.
axis : int
Axis along which the integration is performed.

Expand All @@ -31,10 +31,10 @@ def integrate_values_on_spacing(values, spacing, method, axis=0):
integral_values : float
The value of the integral.
"""
if method == "trapz":
return integrate.trapz(values, dx=spacing, axis=axis)
elif method == "simps":
return integrate.simps(values, dx=spacing, axis=axis)
if method == "trapezoid":
return integrate.trapezoid(values, dx=spacing, axis=axis)
elif method == "simpson":
return integrate.simpson(values, dx=spacing, axis=axis)
else:
raise Exception("Unknown integration method.")

Expand Down
4 changes: 2 additions & 2 deletions mala/targets/density.py
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Expand Up @@ -575,8 +575,8 @@ def get_number_of_electrons(
Integration method used to integrate density on the grid.
Currently supported:

- "trapz" for trapezoid method (only for cubic grids).
- "simps" for Simpson method (only for cubic grids).
- "trapezoid" for trapezoid method (only for cubic grids).
- "simpson" for Simpson method (only for cubic grids).
- "summation" for summation and scaling of the values (recommended)
"""
if density_data is None:
Expand Down
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