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@killiansheriff
killiansheriff committed Nov 23, 2023
1 parent 24d8814 commit 8827439
Showing 1 changed file with 84 additions and 81 deletions.
165 changes: 84 additions & 81 deletions src/WarrenCowleyParameters/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,54 @@
from traits.api import Bool, Int, List


class WarrenCowleyParameters(ModifierInterface):
"""Compute the Warren-Cowley parameters.
```python
from ovito.io import import_file
import WarrenCowleyParameters as WarrenCowleyParameters
pipeline = import_file("fcc.dump")
mod = WarrenCowleyParameters(nneigh=[0, 12, 18])
pipeline.modifiers.append(mod)
data = pipeline.compute()
wc_for_shells = data.attributes["Warren-Cowley parameters"]
print(f"1NN Warren-Cowley parameters: \n {wc_for_shells[0]}")
print(f"2NN Warren-Cowley parameters: \n {wc_for_shells[1]}")
```
"""

# List of integers representing the maximum number of atoms in shells
nneigh = List(Int, value=[0, 12], label="Max atoms in shells", minlen=2)

# Wheather or not to apply it on only selected particles
only_selected = Bool(False, label="Only selected")

def modify(self, data: DataCollection, frame: int, **kwargs):
# Validate input arguments
validator = InputValidator(data, self.nneigh, self.only_selected)
validator.validate()

# Compute Warren-Cowley parameters for each NN shell
calculator = WarrenCowleyCalculator(data, self.nneigh, self.only_selected)
wc_for_shells = calculator.calculate_warren_cowley_parameters()

# Storing the Warren-Cowley parameters as a data attributes
data.attributes["Warren-Cowley parameters"] = wc_for_shells

# Ovito DataTables visualization
visualizer = WarrenCowleyVisualization(data)
visualizer.create_visualization_tables(
unique_types=calculator.unique_types,
nshells=len(self.nneigh) - 1,
wc_for_shells=wc_for_shells,
)


###########################################################


class InputValidator:
def __init__(self, data, nneigh, only_selected):
self.data = data
Expand All @@ -25,52 +73,6 @@ def _validate_selection_existence(self):
raise KeyError("No selection defined in the data")


class WarrenCowleyVisualization:
def __init__(self, data: DataCollection) -> None:
self.data = data

def get_type_name(self, id: int) -> str:
"""Get the name of a particle type by its ID"""
particle_type = self.data.particles["Particle Type"].type_by_id(id)
return particle_type.name or f"Type {id}"

def create_visualization_tables(self, unique_types, nshells, wc_for_shells):
for m in range(nshells):
labels, values = self._get_labels_and_values(unique_types, wc_for_shells, m)
self._create_data_table(m, labels, values)

def _get_labels_and_values(self, unique_types, wc_for_shells, shell_index):
labels, values = [], []
idx = range(len(unique_types))

for i, j in itertools.combinations_with_replacement(idx, 2):
namei = self.get_type_name(unique_types[i])
namej = self.get_type_name(unique_types[j])
labels.append(f"{namei}-{namej}")
values.append(wc_for_shells[shell_index, i, j])

return labels, values

def _create_data_table(self, shell_index, labels, values):
table = self._create_table(shell_index, labels, values)
self.data.objects.append(table)

def _create_table(self, shell_index, labels, values):
"""Creates and configures a data table."""
table = DataTable(
title=f"Warren-Cowley parameter (shell={shell_index + 1})",
plot_mode=DataTable.PlotMode.BarChart,
)
table.x = table.create_property("i-j pair", data=range(len(labels)))
table.x.types = [
ElementType(id=idx, name=label) for idx, label in enumerate(labels)
]
table.y = table.create_property(
f"Warren-Cowley parameter (shell={shell_index + 1})", data=values
)
return table


class WarrenCowleyCalculator:
def __init__(self, data, nneigh, only_selected):
self.data = data
Expand Down Expand Up @@ -176,46 +178,47 @@ def verify_symmetry(parameters):
print("WARNING: The parameters are not symmetric.")


class WarrenCowleyParameters(ModifierInterface):
"""Compute the Warren-Cowley parameters.
```python
from ovito.io import import_file
import WarrenCowleyParameters as WarrenCowleyParameters
pipeline = import_file("fcc.dump")
mod = WarrenCowleyParameters(nneigh=[0, 12, 18])
pipeline.modifiers.append(mod)
data = pipeline.compute()
class WarrenCowleyVisualization:
def __init__(self, data: DataCollection) -> None:
self.data = data

wc_for_shells = data.attributes["Warren-Cowley parameters"]
print(f"1NN Warren-Cowley parameters: \n {wc_for_shells[0]}")
print(f"2NN Warren-Cowley parameters: \n {wc_for_shells[1]}")
```
"""
def get_type_name(self, id: int) -> str:
"""Get the name of a particle type by its ID"""
particle_type = self.data.particles["Particle Type"].type_by_id(id)
return particle_type.name or f"Type {id}"

# List of integers representing the maximum number of atoms in shells
nneigh = List(Int, value=[0, 12], label="Max atoms in shells", minlen=2)
def create_visualization_tables(self, unique_types, nshells, wc_for_shells):
for m in range(nshells):
labels, values = self._get_labels_and_values(unique_types, wc_for_shells, m)
self._create_data_table(m, labels, values)

# Wheather or not to apply it on only selected particles
only_selected = Bool(False, label="Only selected")
def _get_labels_and_values(self, unique_types, wc_for_shells, shell_index):
labels, values = [], []
idx = range(len(unique_types))

def modify(self, data: DataCollection, frame: int, **kwargs):
# Validate input arguments
validator = InputValidator(data, self.nneigh, self.only_selected)
validator.validate()
for i, j in itertools.combinations_with_replacement(idx, 2):
namei = self.get_type_name(unique_types[i])
namej = self.get_type_name(unique_types[j])
labels.append(f"{namei}-{namej}")
values.append(wc_for_shells[shell_index, i, j])

# Compute Warren-Cowley parameters for each NN shell
calculator = WarrenCowleyCalculator(data, self.nneigh, self.only_selected)
wc_for_shells = calculator.calculate_warren_cowley_parameters()
return labels, values

# Storing the Warren-Cowley parameters as a data attributes
data.attributes["Warren-Cowley parameters"] = wc_for_shells
def _create_data_table(self, shell_index, labels, values):
table = self._create_table(shell_index, labels, values)
self.data.objects.append(table)

# Ovito DataTables visualization
visualizer = WarrenCowleyVisualization(data)
visualizer.create_visualization_tables(
unique_types=calculator.unique_types,
nshells=len(self.nneigh) - 1,
wc_for_shells=wc_for_shells,
def _create_table(self, shell_index, labels, values):
"""Creates and configures a data table."""
table = DataTable(
title=f"Warren-Cowley parameter (shell={shell_index + 1})",
plot_mode=DataTable.PlotMode.BarChart,
)
table.x = table.create_property("i-j pair", data=range(len(labels)))
table.x.types = [
ElementType(id=idx, name=label) for idx, label in enumerate(labels)
]
table.y = table.create_property(
f"Warren-Cowley parameter (shell={shell_index + 1})", data=values
)
return table

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