Merge branch 'devel' into data_stat

Signed-off-by: Duo <50307526+iProzd@users.noreply.github.com>

deepmd/dpmodel/model/linear_atomic_model.py

@@ -0,0 +1,300 @@
+# SPDX-License-Identifier: LGPL-3.0-or-later
+import sys
+from abc import (
+    abstractmethod,
+)
+from typing import (
+    Dict,
+    List,
+    Optional,
+    Tuple,
+    Union,
+)
+
+import numpy as np
+
+from deepmd.dpmodel import (
+    FittingOutputDef,
+    OutputVariableDef,
+)
+from deepmd.dpmodel.utils.nlist import (
+    build_multiple_neighbor_list,
+    get_multiple_nlist_key,
+    nlist_distinguish_types,
+)
+
+from .base_atomic_model import (
+    BaseAtomicModel,
+)
+from .dp_atomic_model import (
+    DPAtomicModel,
+)
+from .pairtab_atomic_model import (
+    PairTabModel,
+)
+
+
+class LinearAtomicModel(BaseAtomicModel):
+    """Linear model make linear combinations of several existing models.
+
+    Parameters
+    ----------
+    models : list[DPAtomicModel or PairTabModel]
+        A list of models to be combined. PairTabModel must be used together with a DPAtomicModel.
+    """
+
+    def __init__(
+        self,
+        models: List[BaseAtomicModel],
+        **kwargs,
+    ):
+        super().__init__()
+        self.models = models
+        self.distinguish_type_list = [
+            model.distinguish_types() for model in self.models
+        ]
+
+    def distinguish_types(self) -> bool:
+        """If distinguish different types by sorting."""
+        return False
+
+    def get_rcut(self) -> float:
+        """Get the cut-off radius."""
+        return max(self.get_model_rcuts())
+
+    def get_model_rcuts(self) -> List[float]:
+        """Get the cut-off radius for each individual models."""
+        return [model.get_rcut() for model in self.models]
+
+    def get_sel(self) -> List[int]:
+        return [max([model.get_nsel() for model in self.models])]
+
+    def get_model_nsels(self) -> List[int]:
+        """Get the processed sels for each individual models. Not distinguishing types."""
+        return [model.get_nsel() for model in self.models]
+
+    def get_model_sels(self) -> List[Union[int, List[int]]]:
+        """Get the sels for each individual models."""
+        return [model.get_sel() for model in self.models]
+
+    def _sort_rcuts_sels(self) -> Tuple[List[float], List[int]]:
+        # sort the pair of rcut and sels in ascending order, first based on sel, then on rcut.
+        zipped = sorted(
+            zip(self.get_model_rcuts(), self.get_model_nsels()),
+            key=lambda x: (x[1], x[0]),
+        )
+        return [p[0] for p in zipped], [p[1] for p in zipped]
+
+    def forward_atomic(
+        self,
+        extended_coord,
+        extended_atype,
+        nlist,
+        mapping: Optional[np.ndarray] = None,
+        fparam: Optional[np.ndarray] = None,
+        aparam: Optional[np.ndarray] = None,
+    ) -> Dict[str, np.ndarray]:
+        """Return atomic prediction.
+
+        Parameters
+        ----------
+        extended_coord
+            coodinates in extended region, (nframes, nall * 3)
+        extended_atype
+            atomic type in extended region, (nframes, nall)
+        nlist
+            neighbor list, (nframes, nloc, nsel).
+        mapping
+            mapps the extended indices to local indices.
+        fparam
+            frame parameter. (nframes, ndf)
+        aparam
+            atomic parameter. (nframes, nloc, nda)
+
+        Returns
+        -------
+        result_dict
+            the result dict, defined by the fitting net output def.
+        """
+        nframes, nloc, nnei = nlist.shape
+        extended_coord = extended_coord.reshape(nframes, -1, 3)
+        sorted_rcuts, sorted_sels = self._sort_rcuts_sels()
+        nlists = build_multiple_neighbor_list(
+            extended_coord,
+            nlist,
+            sorted_rcuts,
+            sorted_sels,
+        )
+        raw_nlists = [
+            nlists[get_multiple_nlist_key(rcut, sel)]
+            for rcut, sel in zip(self.get_model_rcuts(), self.get_model_nsels())
+        ]
+        nlists_ = [
+            nl if not dt else nlist_distinguish_types(nl, extended_atype, sel)
+            for dt, nl, sel in zip(
+                self.distinguish_type_list, raw_nlists, self.get_model_sels()
+            )
+        ]
+        ener_list = [
+            model.forward_atomic(
+                extended_coord,
+                extended_atype,
+                nl,
+                mapping,
+                fparam,
+                aparam,
+            )["energy"]
+            for model, nl in zip(self.models, nlists_)
+        ]
+        self.weights = self._compute_weight(extended_coord, extended_atype, nlists_)
+        self.atomic_bias = None
+        if self.atomic_bias is not None:
+            raise NotImplementedError("Need to add bias in a future PR.")
+        else:
+            fit_ret = {
+                "energy": np.sum(np.stack(ener_list) * np.stack(self.weights), axis=0),
+            }  # (nframes, nloc, 1)
+        return fit_ret
+
+    def fitting_output_def(self) -> FittingOutputDef:
+        return FittingOutputDef(
+            [
+                OutputVariableDef(
+                    name="energy",
+                    shape=[1],
+                    reduciable=True,
+                    r_differentiable=True,
+                    c_differentiable=True,
+                )
+            ]
+        )
+
+    @staticmethod
+    def serialize(models) -> dict:
+        return {
+            "models": [model.serialize() for model in models],
+            "model_name": [model.__class__.__name__ for model in models],
+        }
+
+    @staticmethod
+    def deserialize(data) -> List[BaseAtomicModel]:
+        model_names = data["model_name"]
+        models = [
+            getattr(sys.modules[__name__], name).deserialize(model)
+            for name, model in zip(model_names, data["models"])
+        ]
+        return models
+
+    @abstractmethod
+    def _compute_weight(
+        self,
+        extended_coord: np.ndarray,
+        extended_atype: np.ndarray,
+        nlists_: List[np.ndarray],
+    ) -> np.ndarray:
+        """This should be a list of user defined weights that matches the number of models to be combined."""
+        raise NotImplementedError
+
+
+class DPZBLLinearAtomicModel(LinearAtomicModel):
+    """Model linearly combine a list of AtomicModels.
+
+    Parameters
+    ----------
+    models
+            This linear model should take a DPAtomicModel and a PairTable model.
+    """
+
+    def __init__(
+        self,
+        dp_model: DPAtomicModel,
+        zbl_model: PairTabModel,
+        sw_rmin: float,
+        sw_rmax: float,
+        smin_alpha: Optional[float] = 0.1,
+        **kwargs,
+    ):
+        models = [dp_model, zbl_model]
+        super().__init__(models, **kwargs)
+        self.dp_model = dp_model
+        self.zbl_model = zbl_model
+
+        self.sw_rmin = sw_rmin
+        self.sw_rmax = sw_rmax
+        self.smin_alpha = smin_alpha
+
+    def serialize(self) -> dict:
+        return {
+            "models": LinearAtomicModel.serialize([self.dp_model, self.zbl_model]),
+            "sw_rmin": self.sw_rmin,
+            "sw_rmax": self.sw_rmax,
+            "smin_alpha": self.smin_alpha,
+        }
+
+    @classmethod
+    def deserialize(cls, data) -> "DPZBLLinearAtomicModel":
+        sw_rmin = data["sw_rmin"]
+        sw_rmax = data["sw_rmax"]
+        smin_alpha = data["smin_alpha"]
+
+        dp_model, zbl_model = LinearAtomicModel.deserialize(data["models"])
+
+        return cls(
+            dp_model=dp_model,
+            zbl_model=zbl_model,
+            sw_rmin=sw_rmin,
+            sw_rmax=sw_rmax,
+            smin_alpha=smin_alpha,
+        )
+
+    def _compute_weight(
+        self,
+        extended_coord: np.ndarray,
+        extended_atype: np.ndarray,
+        nlists_: List[np.ndarray],
+    ) -> List[np.ndarray]:
+        """ZBL weight.
+
+        Returns
+        -------
+        List[np.ndarray]
+            the atomic ZBL weight for interpolation. (nframes, nloc, 1)
+        """
+        assert (
+            self.sw_rmax > self.sw_rmin
+        ), "The upper boundary `sw_rmax` must be greater than the lower boundary `sw_rmin`."
+
+        dp_nlist = nlists_[0]
+        zbl_nlist = nlists_[1]
+
+        zbl_nnei = zbl_nlist.shape[-1]
+        dp_nnei = dp_nlist.shape[-1]
+
+        # use the larger rr based on nlist
+        nlist_larger = zbl_nlist if zbl_nnei >= dp_nnei else dp_nlist
+        masked_nlist = np.clip(nlist_larger, 0, None)
+        pairwise_rr = PairTabModel._get_pairwise_dist(extended_coord, masked_nlist)
+
+        numerator = np.sum(
+            pairwise_rr * np.exp(-pairwise_rr / self.smin_alpha), axis=-1
+        )  # masked nnei will be zero, no need to handle
+        denominator = np.sum(
+            np.where(
+                nlist_larger != -1,
+                np.exp(-pairwise_rr / self.smin_alpha),
+                np.zeros_like(nlist_larger),
+            ),
+            axis=-1,
+        )  # handle masked nnei.
+        sigma = numerator / denominator
+        u = (sigma - self.sw_rmin) / (self.sw_rmax - self.sw_rmin)
+        coef = np.zeros_like(u)
+        left_mask = sigma < self.sw_rmin
+        mid_mask = (self.sw_rmin <= sigma) & (sigma < self.sw_rmax)
+        right_mask = sigma >= self.sw_rmax
+        coef[left_mask] = 1
+        smooth = -6 * u**5 + 15 * u**4 - 10 * u**3 + 1
+        coef[mid_mask] = smooth[mid_mask]
+        coef[right_mask] = 0
+        self.zbl_weight = coef
+        return [1 - np.expand_dims(coef, -1), np.expand_dims(coef, -1)]