hillclimber 0.1.0a1__py3-none-any.whl

hillclimber/__init__.py

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+from hillclimber.actions import PrintCVAction
+from hillclimber.cvs import DistanceCV, CoordinationNumberCV, TorsionCV, RadiusOfGyrationCV
+from hillclimber.metadynamics import MetaDBiasCV, MetaDynamicsConfig, MetaDynamicsModel
+from hillclimber.selectors import IndexSelector, SMARTSSelector, SMILESSelector
+
+__all__ = [
+    "PrintCVAction",
+    "DistanceCV",
+    "CoordinationNumberCV",
+    "TorsionCV",
+    "RadiusOfGyrationCV",
+    "IndexSelector",
+    "SMILESSelector",
+    "SMARTSSelector",
+    "MetaDynamicsModel",
+    "MetaDBiasCV",
+    "MetaDynamicsConfig",
+]

hillclimber/actions.py

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+import dataclasses
+
+import ase
+
+from hillclimber.interfaces import CollectiveVariable
+
+
+@dataclasses.dataclass
+class PrintCVAction:
+    """Node for PRINT action."""
+
+    cvs: list[CollectiveVariable]
+    stride: int = 1
+    file: str = "COLVAR"
+
+    def to_plumed(self, atoms: ase.Atoms) -> list[str]:
+        """Convert the action node to a PLUMED input string."""
+        all_labels = set()
+        for cv in self.cvs:
+            labels, _ = cv.to_plumed(atoms)
+            all_labels.update(labels)
+
+        # Create the PRINT command with the unique labels
+        print_command = (
+            f"PRINT ARG={','.join(sorted(all_labels))} STRIDE={self.stride} FILE={self.file}"
+        )
+
+        # Return the command as a list
+        return [print_command]
+

hillclimber/calc.py

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+from ase.calculators.calculator import Calculator, all_changes
+from ase.calculators.plumed import Plumed
+
+
+class NonOverwritingPlumed(Plumed):
+    def calculate(self, atoms=None, properties=None, system_changes=all_changes):
+        if properties is None:
+            properties = ["energy", "forces"]
+        Calculator.calculate(self, atoms, properties, system_changes)
+        energy, forces = self.compute_energy_and_forces(
+            self.atoms.get_positions(), self.istep
+        )
+        self.istep += 1
+        self.results = {f"model_{k}": v for k, v in self.calc.results.items()}
+        self.results["energy"], self.results["forces"] = energy, forces