hillclimber 0.1.0a1__py3-none-any.whl → 0.1.0a3__py3-none-any.whl

hillclimber/__init__.py

@@ -1,18 +1,33 @@
-from hillclimber.actions import PrintCVAction
-from hillclimber.cvs import DistanceCV, CoordinationNumberCV, TorsionCV, RadiusOfGyrationCV
-from hillclimber.metadynamics import MetaDBiasCV, MetaDynamicsConfig, MetaDynamicsModel
+from hillclimber.actions import PrintAction
+from hillclimber.analysis import sum_hills, read_colvar, plot_cv_time_series
+from hillclimber.biases import RestraintBias, UpperWallBias, LowerWallBias
+from hillclimber.cvs import DistanceCV, AngleCV, CoordinationNumberCV, TorsionCV, RadiusOfGyrationCV
+from hillclimber.metadynamics import MetadBias, MetaDynamicsConfig, MetaDynamicsModel
+from hillclimber.opes import OPESBias, OPESConfig, OPESModel
 from hillclimber.selectors import IndexSelector, SMARTSSelector, SMILESSelector
+from hillclimber.virtual_atoms import VirtualAtom
 
 __all__ = [
-    "PrintCVAction",
+    "PrintAction",
     "DistanceCV",
+    "AngleCV",
     "CoordinationNumberCV",
     "TorsionCV",
     "RadiusOfGyrationCV",
     "IndexSelector",
     "SMILESSelector",
     "SMARTSSelector",
+    "VirtualAtom",
     "MetaDynamicsModel",
-    "MetaDBiasCV",
+    "MetadBias",
     "MetaDynamicsConfig",
+    "OPESModel",
+    "OPESBias",
+    "OPESConfig",
+    "RestraintBias",
+    "UpperWallBias",
+    "LowerWallBias",
+    "sum_hills",
+    "read_colvar",
+    "plot_cv_time_series",
 ]

hillclimber/actions.py

@@ -2,12 +2,38 @@ import dataclasses
 
 import ase
 
-from hillclimber.interfaces import CollectiveVariable
+from hillclimber.interfaces import CollectiveVariable, PlumedGenerator
 
 
 @dataclasses.dataclass
-class PrintCVAction:
-    """Node for PRINT action."""
+class PrintAction(PlumedGenerator):
+    """PLUMED PRINT action for outputting collective variables.
+
+    This action prints the values of collective variables to a file during
+    the simulation. Multiple CVs can be printed to the same file.
+
+    Parameters
+    ----------
+    cvs : list[CollectiveVariable]
+        List of collective variables to print.
+    stride : int, optional
+        Print every N steps, by default 1.
+    file : str, optional
+        Output file name, by default "COLVAR".
+
+    Examples
+    --------
+    >>> import hillclimber as hc
+    >>> print_action = hc.PrintAction(
+    ...     cvs=[cv1, cv2, cv3],
+    ...     stride=100,
+    ...     file="COLVAR"
+    ... )
+
+    Resources
+    ---------
+    - https://www.plumed.org/doc-master/user-doc/html/PRINT/
+    """
 
     cvs: list[CollectiveVariable]
     stride: int = 1