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

hillclimber/interfaces.py

@@ -69,13 +69,52 @@ class CollectiveVariable(Protocol):
         ...
 
 
-class MetadynamicsBiasCollectiveVariable(Protocol):
-    """Protocol for metadata associated with a bias in PLUMED."""
+class BiasProtocol(Protocol):
+    """Protocol for individual bias potentials that act on collective variables.
+
+    Individual bias potentials (restraints, walls) operate on collective variables
+    and generate their own PLUMED commands via to_plumed(). These biases are added
+    to MetaDynamicsModel via the `actions` parameter.
+
+    This is distinct from MetadynamicsBias, which is used for configuring the
+    collective METAD command itself (via the `bias_cvs` parameter).
+    """
+
+    cv: CollectiveVariable
+
+    def to_plumed(self, atoms: ase.Atoms) -> list[str]:
+        """Generate PLUMED input strings for this bias.
+
+        Parameters
+        ----------
+        atoms : ase.Atoms
+            The atomic structure to use for generating the PLUMED string.
+
+        Returns
+        -------
+        list[str]
+            List of PLUMED command strings.
+        """
+        ...
+
+
+class MetadynamicsBias(Protocol):
+    """Protocol for metadynamics bias configuration objects.
+
+    This protocol defines the configuration structure for per-CV metadynamics
+    parameters (sigma, grid settings, etc.). These configuration objects are
+    used in the `bias_cvs` parameter of MetaDynamicsModel to build the collective
+    METAD command.
+
+    This is distinct from BiasProtocol, which is for individual bias potentials
+    (restraints, walls) that generate their own PLUMED commands and are added
+    via the `actions` parameter.
+    """
 
     cv: CollectiveVariable
     sigma: float | None = None
-    grid_min: float | None = None
-    grid_max: float | None = None
+    grid_min: float | str | None = None
+    grid_max: float | str | None = None
     grid_bin: int | None = None
 
 
@@ -84,7 +123,8 @@ __all__ = [
     "AtomSelector",
     "PlumedGenerator",
     "CollectiveVariable",
-    "MetadynamicsBiasCollectiveVariable",
+    "BiasProtocol",
+    "MetadynamicsBias",
 ]
 
 def interfaces() -> dict[str, list[str]]:

hillclimber/metadynamics.py

@@ -1,4 +1,5 @@
 import dataclasses
+import typing as t
 from pathlib import Path
 
 import ase.units
@@ -7,26 +8,28 @@ import zntrack
 from hillclimber.calc import NonOverwritingPlumed
 from hillclimber.interfaces import (
     CollectiveVariable,
-    MetadynamicsBiasCollectiveVariable,
     NodeWithCalculator,
     PlumedGenerator,
 )
 
 
 @dataclasses.dataclass
-class MetaDBiasCV(MetadynamicsBiasCollectiveVariable):
-    """Metadynamics bias on a collective variable.
+class MetadBias:
+    """Metadynamics bias configuration for a collective variable.
 
     Parameters
     ----------
     cv : CollectiveVariable
         The collective variable to bias.
     sigma : float, optional
-        The width of the Gaussian potential, by default None.
+        The width of the Gaussian potential in the same units as the CV
+        (e.g., Å for distances, radians for angles), by default None.
     grid_min : float | str, optional
-        The minimum value of the grid, by default None.
+        The minimum value of the grid in CV units (or PLUMED expression like "-pi"),
+        by default None.
     grid_max : float | str, optional
-        The maximum value of the grid, by default None.
+        The maximum value of the grid in CV units (or PLUMED expression like "pi"),
+        by default None.
     grid_bin : int, optional
         The number of bins in the grid, by default None.
 
@@ -48,22 +51,32 @@ class MetaDynamicsConfig:
 
     This contains only the global parameters that apply to all CVs.
 
+    Units
+    -----
+    hillclimber uses ASE units throughout. The UNITS line in the PLUMED input tells
+    PLUMED to interpret all values in ASE units:
+    - Distances: Ångström (Å)
+    - Energies: electronvolt (eV) - including HEIGHT, SIGMA for energy-based CVs, etc.
+    - Time: femtoseconds (fs)
+    - Temperature: Kelvin (K)
+
     Parameters
     ----------
     height : float, optional
-        The height of the Gaussian potential in kJ/mol, by default 1.0.
+        The height of the Gaussian potential in eV, by default 1.0.
     pace : int, optional
-        The frequency of Gaussian deposition, by default 500.
+        The frequency of Gaussian deposition in MD steps, by default 500.
     biasfactor : float, optional
         The bias factor for well-tempered metadynamics, by default None.
     temp : float, optional
         The temperature of the system in Kelvin, by default 300.0.
     file : str, optional
         The name of the hills file, by default "HILLS".
-    adaptive : str, optional
-        The adaptive scheme to use, by default "NONE".
+    adaptive : t.Literal["GEOM", "DIFF"] | None, optional
+        The adaptive scheme to use, by default None.
+        If None, no ADAPTIVE parameter is written to PLUMED.
     flush : int | None
-        The frequency of flushing the output files. 
+        The frequency of flushing the output files in MD steps.
         If None, uses the plumed default.
 
     Resources
@@ -77,7 +90,7 @@ class MetaDynamicsConfig:
     biasfactor: float | None = None
     temp: float = 300.0
     file: str = "HILLS"
-    adaptive: str = "NONE"  # NONE, DIFF, GEOM
+    adaptive: t.Literal["GEOM", "DIFF"] | None = None
     flush: int | None = None
 
 
@@ -115,7 +128,7 @@ class MetaDynamicsModel(zntrack.Node, NodeWithCalculator):
     ...     x2=pn.SMARTSSelector(pattern="CO[C:1]"),
     ...     prefix="d",
     ... )
-    >>> metad_cv1 = pn.MetaDBiasCV(
+    >>> metad_cv1 = pn.MetadBias(
     ...     cv=cv1, sigma=0.1, grid_min=0.0, grid_max=2.0, grid_bin=200
     ... )
     >>> model = pn.MetaDynamicsModel(
@@ -133,7 +146,7 @@ class MetaDynamicsModel(zntrack.Node, NodeWithCalculator):
     config: MetaDynamicsConfig = zntrack.deps()
     data: list[ase.Atoms] = zntrack.deps()
     data_idx: int = zntrack.params(-1)
-    bias_cvs: list[MetaDBiasCV] = zntrack.deps(default_factory=list)
+    bias_cvs: list[MetadBias] = zntrack.deps(default_factory=list)
     actions: list[PlumedGenerator] = zntrack.deps(default_factory=list)
     timestep: float = zntrack.params(1.0)  # in fs, default is 1 fs
     model: NodeWithCalculator = zntrack.deps()
@@ -188,8 +201,13 @@ class MetaDynamicsModel(zntrack.Node, NodeWithCalculator):
 
         sigmas, grid_mins, grid_maxs, grid_bins = [], [], [], []
 
+        # PLUMED UNITS line specifies conversion factors from ASE units to PLUMED's native units:
+        # - LENGTH=A: ASE uses Ångström (A), PLUMED native is nm → A is a valid PLUMED unit
+        # - TIME: ASE uses fs, PLUMED native is ps → 1 fs = 0.001 ps
+        # - ENERGY: ASE uses eV, PLUMED native is kJ/mol → 1 eV = 96.485 kJ/mol
+        # See: https://www.plumed.org/doc-master/user-doc/html/ (MD engine integration docs)
         plumed_lines.append(
-            f"UNITS LENGTH=A TIME={1 / (1000 * ase.units.fs)} ENERGY={ase.units.mol / ase.units.kJ}"
+            f"UNITS LENGTH=A TIME={1/1000} ENERGY={ase.units.mol / ase.units.kJ}"
         )
 
         for bias_cv in self.bias_cvs:
@@ -197,17 +215,20 @@ class MetaDynamicsModel(zntrack.Node, NodeWithCalculator):
             plumed_lines.extend(cv_str)
             all_labels.extend(labels)
 
-            # Collect per-CV parameters for later
-            sigmas.append(str(bias_cv.sigma) if bias_cv.sigma is not None else None)
-            grid_mins.append(
-                str(bias_cv.grid_min) if bias_cv.grid_min is not None else None
-            )
-            grid_maxs.append(
-                str(bias_cv.grid_max) if bias_cv.grid_max is not None else None
-            )
-            grid_bins.append(
-                str(bias_cv.grid_bin) if bias_cv.grid_bin is not None else None
-            )
+            # Collect per-CV parameters for later - repeat for each label
+            # PLUMED requires one parameter value per ARG, so if a CV generates
+            # multiple labels, we need to repeat the parameter values
+            for _ in labels:
+                sigmas.append(str(bias_cv.sigma) if bias_cv.sigma is not None else None)
+                grid_mins.append(
+                    str(bias_cv.grid_min) if bias_cv.grid_min is not None else None
+                )
+                grid_maxs.append(
+                    str(bias_cv.grid_max) if bias_cv.grid_max is not None else None
+                )
+                grid_bins.append(
+                    str(bias_cv.grid_bin) if bias_cv.grid_bin is not None else None
+                )
 
         metad_parts = [
             "METAD",
@@ -216,16 +237,31 @@ class MetaDynamicsModel(zntrack.Node, NodeWithCalculator):
             f"PACE={self.config.pace}",
             f"TEMP={self.config.temp}",
             f"FILE={self.config.file}",
-            f"ADAPTIVE={self.config.adaptive}",
         ]
+        if self.config.adaptive is not None:
+            metad_parts.append(f"ADAPTIVE={self.config.adaptive}")
         if self.config.biasfactor is not None:
             metad_parts.append(f"BIASFACTOR={self.config.biasfactor}")
 
         # Add SIGMA, GRID_MIN, GRID_MAX, GRID_BIN only if any value is set
         if any(v is not None for v in sigmas):
-            metad_parts.append(
-                f"SIGMA={','.join(v if v is not None else '0.0' for v in sigmas)}"
-            )
+            # When using ADAPTIVE, PLUMED requires only one sigma value
+            if self.config.adaptive is not None:
+                # Validate that all sigma values are the same when adaptive is set
+                unique_sigmas = set(v for v in sigmas if v is not None)
+                if len(unique_sigmas) > 1:
+                    raise ValueError(
+                        f"When using ADAPTIVE={self.config.adaptive}, all CVs must have the same sigma value. "
+                        f"Found different sigma values: {unique_sigmas}"
+                    )
+                # Use the first non-None sigma value
+                sigma_value = next(v for v in sigmas if v is not None)
+                metad_parts.append(f"SIGMA={sigma_value}")
+            else:
+                # Standard mode: one sigma per CV
+                metad_parts.append(
+                    f"SIGMA={','.join(v if v is not None else '0.0' for v in sigmas)}"
+                )
         if any(v is not None for v in grid_mins):
             metad_parts.append(
                 f"GRID_MIN={','.join(v if v is not None else '0.0' for v in grid_mins)}"
@@ -240,10 +276,50 @@ class MetaDynamicsModel(zntrack.Node, NodeWithCalculator):
             )
 
         plumed_lines.append(f"metad: {' '.join(metad_parts)}")
-        # Temporary until https://github.com/zincware/ZnTrack/issues/936
-        from hillclimber.actions import PrintCVAction
-        lines = PrintCVAction(cvs=[x.cv for x in self.bias_cvs], stride=100).to_plumed(atoms)
-        plumed_lines.extend(lines)
+
+        # Track defined commands to detect duplicates and conflicts
+        # Map label -> full command for labeled commands (e.g., "d: DISTANCE ...")
+        defined_commands = {}
+        for line in plumed_lines:
+            # Check if this is a labeled command (format: "label: ACTION ...")
+            if ": " in line:
+                label = line.split(": ", 1)[0]
+                defined_commands[label] = line
+
+        # Add any additional actions (restraints, walls, print actions, etc.)
+        for action in self.actions:
+            action_lines = action.to_plumed(atoms)
+
+            # Filter out duplicate CV definitions, but detect conflicts
+            filtered_lines = []
+            for line in action_lines:
+                # Check if this is a labeled command
+                if ": " in line:
+                    label = line.split(": ", 1)[0]
+
+                    # Check if this label was already defined
+                    if label in defined_commands:
+                        # If the command is identical, skip (deduplication)
+                        if defined_commands[label] == line:
+                            continue
+                        # If the command is different, raise error (conflict)
+                        else:
+                            raise ValueError(
+                                f"Conflicting definitions for label '{label}':\n"
+                                f"  Already defined: {defined_commands[label]}\n"
+                                f"  New definition:  {line}"
+                            )
+                    else:
+                        # New labeled command, track it
+                        defined_commands[label] = line
+                        filtered_lines.append(line)
+                else:
+                    # Unlabeled command, always add
+                    filtered_lines.append(line)
+
+            plumed_lines.extend(filtered_lines)
+
+        # Add FLUSH if configured
         if self.config.flush is not None:
             plumed_lines.append(f"FLUSH STRIDE={self.config.flush}")
         return plumed_lines

hillclimber/opes.py

@@ -0,0 +1,357 @@
+"""OPES (On-the-fly Probability Enhanced Sampling) methods.
+
+This module provides classes for OPES enhanced sampling, a modern alternative
+to traditional metadynamics with improved convergence properties.
+"""
+
+import dataclasses
+from pathlib import Path
+
+import ase.units
+import zntrack
+
+from hillclimber.calc import NonOverwritingPlumed
+from hillclimber.interfaces import (
+    CollectiveVariable,
+    NodeWithCalculator,
+    PlumedGenerator,
+)
+
+
+@dataclasses.dataclass
+class OPESBias:
+    """OPES bias configuration for a collective variable.
+
+    Parameters
+    ----------
+    cv : CollectiveVariable
+        The collective variable to bias.
+    sigma : float | str, optional
+        Initial kernel width in CV units (e.g., Å for distances, radians for angles).
+        Use "ADAPTIVE" for automatic adaptation (recommended).
+        If numeric, specifies the initial width.
+        Default: "ADAPTIVE".
+
+    Resources
+    ---------
+    - https://www.plumed.org/doc-master/user-doc/html/OPES_METAD/
+
+    Notes
+    -----
+    The ADAPTIVE sigma option automatically adjusts kernel widths based on
+    CV fluctuations, which is usually the best choice. The automatic width
+    is measured every ADAPTIVE_SIGMA_STRIDE steps (default: 10×PACE).
+    """
+
+    cv: CollectiveVariable
+    sigma: float | str = "ADAPTIVE"
+
+
+@dataclasses.dataclass
+class OPESConfig:
+    """Configuration for OPES_METAD and OPES_METAD_EXPLORE.
+
+    OPES (On-the-fly Probability Enhanced Sampling) is a modern enhanced
+    sampling method that samples well-tempered target distributions.
+
+    Units
+    -----
+    hillclimber uses ASE units throughout. The UNITS line in the PLUMED input tells
+    PLUMED to interpret all values in ASE units:
+    - Distances: Ångström (Å)
+    - Energies: electronvolt (eV) - including BARRIER, SIGMA_MIN, etc.
+    - Time: femtoseconds (fs)
+    - Temperature: Kelvin (K)
+
+    Parameters
+    ----------
+    barrier : float
+        Highest free energy barrier to overcome (eV). This is the key
+        parameter that determines sampling efficiency.
+    pace : int, optional
+        Frequency of kernel deposition in MD steps (default: 500).
+    temp : float, optional
+        Temperature in Kelvin (default: 300.0). If -1, retrieved from MD engine.
+    explore_mode : bool, optional
+        If True, uses OPES_METAD_EXPLORE which estimates target distribution
+        directly (better exploration, slower reweighting convergence).
+        If False, uses OPES_METAD which estimates unbiased distribution
+        (faster convergence, less exploration). Default: False.
+    biasfactor : float, optional
+        Well-tempered gamma factor. If not specified, uses default behavior.
+        Set to inf for custom target distributions.
+    compression_threshold : float, optional
+        Merge kernels if closer than this threshold in sigma units (default: 1.0).
+    file : str, optional
+        File to store deposited kernels (default: "KERNELS").
+    adaptive_sigma_stride : int, optional
+        MD steps between adaptive sigma measurements. If not set, uses 10×PACE.
+    sigma_min : float, optional
+        Minimum allowable sigma value for adaptive sigma in CV units.
+    state_wfile : str, optional
+        State file for writing exact restart information.
+    state_rfile : str, optional
+        State file for reading restart information.
+    state_wstride : int, optional
+        Frequency of STATE file writing in number of kernel depositions.
+    walkers_mpi : bool, optional
+        Enable multiple walker mode with MPI communication (default: False).
+    calc_work : bool, optional
+        Calculate and output accumulated work (default: False).
+    flush : int, optional
+        Frequency of flushing output files in MD steps.
+
+    Resources
+    ---------
+    - https://www.plumed.org/doc-master/user-doc/html/OPES_METAD/
+    - https://www.plumed.org/doc-master/user-doc/html/OPES_METAD_EXPLORE/
+    - Invernizzi & Parrinello, J. Phys. Chem. Lett. 2020
+
+    Notes
+    -----
+    **When to use OPES_METAD vs OPES_METAD_EXPLORE:**
+
+    - OPES_METAD: Use when you want quick convergence of reweighted free energy.
+      Estimates unbiased distribution P(s).
+
+    - OPES_METAD_EXPLORE: Use for systems with unknown barriers or when testing
+      new CVs. Allows more exploration but slower reweighting convergence.
+      Estimates target distribution p^WT(s) directly.
+
+    Both methods converge to the same bias given enough time, but approach it
+    differently. OPES is more sensitive to degenerate CVs than standard METAD.
+    """
+
+    barrier: float  # kJ/mol
+    pace: int = 500
+    temp: float = 300.0
+    explore_mode: bool = False  # False=OPES_METAD, True=OPES_METAD_EXPLORE
+    biasfactor: float | None = None
+    compression_threshold: float = 1.0
+    file: str = "KERNELS"
+    adaptive_sigma_stride: int | None = None
+    sigma_min: float | None = None
+    state_wfile: str | None = None
+    state_rfile: str | None = None
+    state_wstride: int | None = None
+    walkers_mpi: bool = False
+    calc_work: bool = False
+    flush: int | None = None
+
+
+class OPESModel(zntrack.Node, NodeWithCalculator):
+    """OPES (On-the-fly Probability Enhanced Sampling) model.
+
+    Implements OPES_METAD and OPES_METAD_EXPLORE enhanced sampling methods.
+    OPES samples well-tempered target distributions and provides better
+    convergence properties than traditional metadynamics.
+
+    Parameters
+    ----------
+    config : OPESConfig
+        Configuration for the OPES simulation.
+    data : list[ase.Atoms]
+        Input data for simulation.
+    data_idx : int, optional
+        Index of data to use (default: -1).
+    bias_cvs : list[OPESBias], optional
+        Collective variables to bias (default: []).
+    actions : list[PlumedGenerator], optional
+        Additional actions like restraints, walls, print (default: []).
+    timestep : float, optional
+        Timestep in fs (default: 1.0).
+    model : NodeWithCalculator
+        Underlying force field model.
+
+    Examples
+    --------
+    >>> import hillclimber as hc
+    >>>
+    >>> # Define collective variables
+    >>> phi = hc.TorsionCV(...)
+    >>> psi = hc.TorsionCV(...)
+    >>>
+    >>> # OPES configuration (standard mode)
+    >>> config = hc.OPESConfig(
+    ...     barrier=40.0,  # kJ/mol
+    ...     pace=500,
+    ...     temp=300.0,
+    ...     explore_mode=False  # Use OPES_METAD
+    ... )
+    >>>
+    >>> # Bias configuration with adaptive sigma
+    >>> bias1 = hc.OPESBias(cv=phi, sigma="ADAPTIVE")
+    >>> bias2 = hc.OPESBias(cv=psi, sigma="ADAPTIVE")
+    >>>
+    >>> # Create OPES model
+    >>> opes = hc.OPESModel(
+    ...     config=config,
+    ...     bias_cvs=[bias1, bias2],
+    ...     data=data.frames,
+    ...     model=force_field,
+    ...     timestep=0.5
+    ... )
+    >>>
+    >>> # For exploration mode, set explore_mode=True
+    >>> explore_config = hc.OPESConfig(
+    ...     barrier=40.0,
+    ...     pace=500,
+    ...     explore_mode=True  # Use OPES_METAD_EXPLORE
+    ... )
+
+    Resources
+    ---------
+    - https://www.plumed.org/doc-master/user-doc/html/OPES_METAD/
+    - https://www.plumed.org/doc-master/user-doc/html/OPES_METAD_EXPLORE/
+    - https://www.plumed.org/doc-master/user-doc/html/masterclass-22-03.html
+    - Invernizzi & Parrinello, J. Phys. Chem. Lett. 2020
+
+    Notes
+    -----
+    **Output Components:**
+    OPES provides several diagnostic outputs (accessible via PrintAction):
+    - opes.bias: Instantaneous bias potential value
+    - opes.rct: Convergence indicator (should flatten at convergence)
+    - opes.zed: Normalization estimate (should stabilize)
+    - opes.neff: Effective sample size
+    - opes.nker: Number of compressed kernels
+    - opes.work: Accumulated work (if calc_work=True)
+
+    **Advantages over Metadynamics:**
+    - Better convergence properties
+    - Automatic variance adaptation
+    - Lower systematic error
+    - More sensitive to degenerate CVs (helps identify CV problems)
+    """
+
+    config: OPESConfig = zntrack.deps()
+    data: list[ase.Atoms] = zntrack.deps()
+    data_idx: int = zntrack.params(-1)
+    bias_cvs: list[OPESBias] = zntrack.deps(default_factory=list)
+    actions: list[PlumedGenerator] = zntrack.deps(default_factory=list)
+    timestep: float = zntrack.params(1.0)
+    model: NodeWithCalculator = zntrack.deps()
+
+    figures: Path = zntrack.outs_path(zntrack.nwd / "figures", independent=True)
+
+    def run(self):
+        self.figures.mkdir(parents=True, exist_ok=True)
+        for cv in self.bias_cvs:
+            img = cv.cv.get_img(self.data[self.data_idx])
+            img.save(self.figures / f"{cv.cv.prefix}.png")
+
+    def get_calculator(
+        self, *, directory: str | Path | None = None, **kwargs
+    ) -> NonOverwritingPlumed:
+        if directory is None:
+            raise ValueError("Directory must be specified for PLUMED input files.")
+        directory = Path(directory)
+        directory.mkdir(parents=True, exist_ok=True)
+
+        lines = self.to_plumed(self.data[self.data_idx])
+        # replace FILE= with f"FILE={directory}/" inside config
+        lines = [line.replace("FILE=", f"FILE={directory}/") for line in lines]
+
+        # Write plumed input file
+        with (directory / "plumed.dat").open("w") as file:
+            for line in lines:
+                file.write(line + "\n")
+
+        kT = ase.units.kB * self.config.temp
+
+        return NonOverwritingPlumed(
+            calc=self.model.get_calculator(directory=directory),
+            atoms=self.data[self.data_idx],
+            input=lines,
+            timestep=float(self.timestep * ase.units.fs),
+            kT=float(kT),
+            log=(directory / "plumed.log").as_posix(),
+        )
+
+    def to_plumed(self, atoms: ase.Atoms) -> list[str]:
+        """Generate PLUMED input string for the OPES model."""
+        # check for duplicate CV prefixes
+        cv_labels = set()
+        for bias_cv in self.bias_cvs:
+            if bias_cv.cv.prefix in cv_labels:
+                raise ValueError(f"Duplicate CV prefix found: {bias_cv.cv.prefix}")
+            cv_labels.add(bias_cv.cv.prefix)
+
+        plumed_lines = []
+        all_labels = []
+
+        sigmas = []
+
+        # PLUMED UNITS line specifies conversion factors from ASE units to PLUMED's native units:
+        # - LENGTH=A: ASE uses Ångström (A), PLUMED native is nm → A is a valid PLUMED unit
+        # - TIME: ASE uses fs, PLUMED native is ps → 1 fs = 0.001 ps
+        # - ENERGY: ASE uses eV, PLUMED native is kJ/mol → 1 eV = 96.485 kJ/mol
+        # See: https://www.plumed.org/doc-master/user-doc/html/ (MD engine integration docs)
+        plumed_lines.append(
+            f"UNITS LENGTH=A TIME={1/1000} ENERGY={ase.units.mol / ase.units.kJ}"
+        )
+
+        for bias_cv in self.bias_cvs:
+            labels, cv_str = bias_cv.cv.to_plumed(atoms)
+            plumed_lines.extend(cv_str)
+            all_labels.extend(labels)
+
+            # Collect sigma values
+            if isinstance(bias_cv.sigma, str):
+                sigmas.append(bias_cv.sigma)
+            else:
+                sigmas.append(str(bias_cv.sigma))
+
+        # Determine which OPES method to use
+        method_name = "OPES_METAD_EXPLORE" if self.config.explore_mode else "OPES_METAD"
+
+        # Build OPES command
+        opes_parts = [
+            f"opes: {method_name}",
+            f"ARG={','.join(all_labels)}",
+            f"PACE={self.config.pace}",
+            f"BARRIER={self.config.barrier}",
+            f"TEMP={self.config.temp}",
+        ]
+
+        # Add SIGMA (required parameter)
+        # If all sigmas are the same, use single value; otherwise comma-separated
+        if len(set(sigmas)) == 1:
+            opes_parts.append(f"SIGMA={sigmas[0]}")
+        else:
+            opes_parts.append(f"SIGMA={','.join(sigmas)}")
+
+        # Add FILE and COMPRESSION_THRESHOLD
+        opes_parts.append(f"FILE={self.config.file}")
+        opes_parts.append(f"COMPRESSION_THRESHOLD={self.config.compression_threshold}")
+
+        # Optional parameters
+        if self.config.biasfactor is not None:
+            opes_parts.append(f"BIASFACTOR={self.config.biasfactor}")
+        if self.config.adaptive_sigma_stride is not None:
+            opes_parts.append(f"ADAPTIVE_SIGMA_STRIDE={self.config.adaptive_sigma_stride}")
+        if self.config.sigma_min is not None:
+            opes_parts.append(f"SIGMA_MIN={self.config.sigma_min}")
+        if self.config.state_wfile is not None:
+            opes_parts.append(f"STATE_WFILE={self.config.state_wfile}")
+        if self.config.state_rfile is not None:
+            opes_parts.append(f"STATE_RFILE={self.config.state_rfile}")
+        if self.config.state_wstride is not None:
+            opes_parts.append(f"STATE_WSTRIDE={self.config.state_wstride}")
+        if self.config.walkers_mpi:
+            opes_parts.append("WALKERS_MPI")
+        if self.config.calc_work:
+            opes_parts.append("CALC_WORK")
+
+        plumed_lines.append(" ".join(opes_parts))
+
+        # Add any additional actions (restraints, walls, print actions, etc.)
+        for action in self.actions:
+            action_lines = action.to_plumed(atoms)
+            plumed_lines.extend(action_lines)
+
+        # Add FLUSH if configured
+        if self.config.flush is not None:
+            plumed_lines.append(f"FLUSH STRIDE={self.config.flush}")
+
+        return plumed_lines