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Plotting robustness; allow unrecognised distortion names (in case use…
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…r renames), and add tests
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@kavanase
kavanase committed May 20, 2024
1 parent c30b3bc commit 2115ac2
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Showing 19 changed files with 2,624 additions and 123 deletions.
33 changes: 21 additions & 12 deletions shakenbreak/plotting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -213,7 +213,7 @@ def _purge_data_dicts(
"""
Purges dictionaries of displacements and energies so that they are consistent
(i.e. contain data for same distortions).
To achieve this, it removes any data point from disp_dict if its energy is not
To achieve this, it removes any data point from ``disp_dict`` if its energy is not
in the energy dict (this may be due to relaxation not converged).
Args:
Expand Down Expand Up @@ -334,8 +334,8 @@ def _get_displacement_dict(
disp_dict, energies_dict = _purge_data_dicts(
disp_dict=disp_dict,
energies_dict=energies_dict,
) # make disp and energies dict consistent by removing any data point
# if its energy is not in the energy dict and viceversa
) # make disp and energies dict consistent by removing any data point from disp_dict
# if its energy is not in the energy dict (this may be due to relaxation not converged etc)
else:
warnings.warn(
"Structure comparison algorithm struggled matching lattices. "
Expand Down Expand Up @@ -389,7 +389,7 @@ def _format_datapoints_from_other_chargestates(
keys.append(float(entry.split("%")[0]) / 100)
elif isinstance(entry, str) and ("Rattled_from_" in entry or "Dimer_from_" in entry):
keys.append(0.0) # Rattled and Dimer will be plotted at x = 0.0
elif entry == "Rattled" or entry == "Dimer": # add 0.0 for Rattled
elif entry in ["Rattled", "Dimer"]: # add 0.0 for Rattled
# (to avoid problems when sorting distortions)
keys.append(0.0)
else:
Expand All @@ -398,7 +398,7 @@ def _format_datapoints_from_other_chargestates(
if disp_dict:
# Sort displacements in same order as distortions and energies,
# for proper color mapping
sorted_disp = [disp_dict[k] for k in energies_dict["distortions"] if k in disp_dict]
sorted_disp = [disp_dict.get(k, None) for k in energies_dict["distortions"]]
# Save the values of the displacements from *other charge states*
# As the displacements will be re-sorted -> we'll need to
# find the index of t
Expand Down Expand Up @@ -720,6 +720,17 @@ def _format_colorbar(
return cbar


def _parse_other_charge_state_label(distortion_key: str) -> tuple:
try:
other_charge_state = int(distortion_key.split("_")[-1])
label = f"From {'+' if other_charge_state > 0 else ''}{other_charge_state} charge state"
except ValueError:
other_charge_state = distortion_key.split("_")[-1]
label = f"From {other_charge_state}"

return label


# Main plotting functions:
def plot_all_defects(
defect_charges_dict: dict,
Expand Down Expand Up @@ -1364,7 +1375,6 @@ def plot_colorbar(
]
)
for i, j in zip(imported_indices.keys(), range(other_charges)):
other_charge_state = int(list(energies_dict["distortions"].keys())[i].split("_")[-1])
sorted_i = imported_indices[i] # index for the sorted dicts
ax.scatter( # plot any datapoints where disp could not be determined as black
np.array(keys)[i],
Expand All @@ -1382,8 +1392,9 @@ def plot_colorbar(
cmap=(colormap if isinstance(sorted_disp[sorted_i], float) else None),
norm=norm if isinstance(sorted_disp[sorted_i], float) else None,
alpha=1,
label=f"From {'+' if other_charge_state > 0 else ''}{other_charge_state} "
f"charge state",
label=_parse_other_charge_state_label(
list(energies_dict["distortions"].keys())[i]
),
)

# Plot reference energy
Expand Down Expand Up @@ -1668,7 +1679,7 @@ def plot_datasets(
)

if len(sorted_distortions) > 0 and [
key for key in dataset["distortions"] if (key != "Rattled" and key != "Dimer")
key for key in dataset["distortions"] if key not in ["Rattled", "Dimer"]
]: # more than just Rattled
if imported_indices: # Exclude datapoints from other charge states
non_imported_sorted_indices = [
Expand Down Expand Up @@ -1697,7 +1708,6 @@ def plot_datasets(
] # number of other charge states whose distortions have been imported
)
for i, j in zip(imported_indices, range(other_charges)):
other_charge_state = int(list(dataset["distortions"].keys())[i].split("_")[-1])
ax.scatter( # distortions from other charge states
np.array(keys)[i],
list(dataset["distortions"].values())[i],
Expand All @@ -1712,8 +1722,7 @@ def plot_datasets(
j
], # different markers for different charge states
alpha=1,
label=f"From {'+' if other_charge_state > 0 else ''}{other_charge_state} "
f"charge state",
label=_parse_other_charge_state_label(list(dataset["distortions"].keys())[i]),
)

datasets[0]["Unperturbed"] = 0.0 # unperturbed energy of first dataset (our reference energy)
Expand Down
Binary file added ...data/remote_baseline_plots/Va_O1_1_plot_defect_with_unrecognised_distortion.png
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167 changes: 167 additions & 0 deletions tests/data/vasp/Va_O1_1/Bond_Distortion_-10.0%/CONTCAR
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