Feat: add zbl training

deepmd/dpmodel/atomic_model/__init__.py

@@ -22,8 +22,8 @@
     DPAtomicModel,
 )
 from .linear_atomic_model import (
-    DPZBLLinearAtomicModel,
-    LinearAtomicModel,
+    DPZBLLinearEnergyAtomicModel,
+    LinearEnergyAtomicModel,
 )
 from .make_base_atomic_model import (
     make_base_atomic_model,
@@ -37,6 +37,6 @@
     "BaseAtomicModel",
     "DPAtomicModel",
     "PairTabAtomicModel",
-    "LinearAtomicModel",
-    "DPZBLLinearAtomicModel",
+    "LinearEnergyAtomicModel",
+    "DPZBLLinearEnergyAtomicModel",
 ]

deepmd/dpmodel/atomic_model/linear_atomic_model.py

@@ -38,7 +38,7 @@
 )
 
 
-class LinearAtomicModel(BaseAtomicModel):
+class LinearEnergyAtomicModel(BaseAtomicModel):
     """Linear model make linear combinations of several existing models.
 
     Parameters
@@ -163,17 +163,21 @@ def forward_atomic(
                 self.mixed_types_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_)
-        ]
+        ener_list = []
+
+        for i, model in enumerate(self.models):
+            ori_map = model.get_type_map()
+            updated_atype = self.remap_atype(extended_atype, ori_map, self.type_map)
+            ener_list.append(
+                model.forward_atomic(
+                    extended_coord,
+                    updated_atype,
+                    nlists_[i],
+                    mapping,
+                    fparam,
+                    aparam,
+                )["energy"]
+            )
         self.weights = self._compute_weight(extended_coord, extended_atype, nlists_)
         self.atomic_bias = None
         if self.atomic_bias is not None:
@@ -184,6 +188,37 @@ def forward_atomic(
             }  # (nframes, nloc, 1)
         return fit_ret
 
+    @staticmethod
+    def remap_atype(
+        atype: np.ndarray, ori_map: List[str], new_map: List[str]
+    ) -> np.ndarray:
+        """
+        This method is used to map the atype from the common type_map to the original type_map of
+        indivial AtomicModels.
+
+        Parameters
+        ----------
+        atype : np.ndarray
+            The atom type tensor being updated, shape of (nframes, natoms)
+        ori_map : List[str]
+            The original type map of an AtomicModel.
+        new_map : List[str]
+            The common type map of the DPZBLLinearEnergyAtomicModel, created by the `get_type_map` method,
+            must be a subset of the ori_map.
+
+        Returns
+        -------
+        np.ndarray
+        """
+        assert np.max(atype) < len(
+            new_map
+        ), "The input `atype` cannot be handled by the type_map."
+        type_2_idx = {atp: idx for idx, atp in enumerate(ori_map)}
+        # this maps the atype in the new map to the original map
+        mapping = np.array([type_2_idx[new_map[idx]] for idx in range(len(new_map))])
+        updated_atype = mapping[atype]
+        return updated_atype
+
     def fitting_output_def(self) -> FittingOutputDef:
         return FittingOutputDef(
             [
@@ -261,7 +296,7 @@ def is_aparam_nall(self) -> bool:
         return False
 
 
-class DPZBLLinearAtomicModel(LinearAtomicModel):
+class DPZBLLinearEnergyAtomicModel(LinearEnergyAtomicModel):
     """Model linearly combine a list of AtomicModels.
 
     Parameters
@@ -308,7 +343,7 @@ def serialize(self) -> dict:
                 "@class": "Model",
                 "type": "zbl",
                 "@version": 1,
-                "models": LinearAtomicModel.serialize(
+                "models": LinearEnergyAtomicModel.serialize(
                     [self.dp_model, self.zbl_model], self.type_map
                 ),
                 "sw_rmin": self.sw_rmin,
@@ -319,7 +354,7 @@ def serialize(self) -> dict:
         return dd
 
     @classmethod
-    def deserialize(cls, data) -> "DPZBLLinearAtomicModel":
+    def deserialize(cls, data) -> "DPZBLLinearEnergyAtomicModel":
         data = copy.deepcopy(data)
         check_version_compatibility(data.pop("@version", 1), 1, 1)
         data.pop("@class")
@@ -328,7 +363,7 @@ def deserialize(cls, data) -> "DPZBLLinearAtomicModel":
         sw_rmax = data.pop("sw_rmax")
         smin_alpha = data.pop("smin_alpha")
 
-        ([dp_model, zbl_model], type_map) = LinearAtomicModel.deserialize(
+        ([dp_model, zbl_model], type_map) = LinearEnergyAtomicModel.deserialize(
             data.pop("models")
         )
 

deepmd/dpmodel/atomic_model/make_base_atomic_model.py

@@ -54,18 +54,13 @@ def get_rcut(self) -> float:
             pass
 
         @abstractmethod
-        def get_type_map(self) -> Optional[List[str]]:
+        def get_type_map(self) -> List[str]:
             """Get the type map."""
+            pass
 
         def get_ntypes(self) -> int:
             """Get the number of atom types."""
-            tmap = self.get_type_map()
-            if tmap is not None:
-                return len(tmap)
-            else:
-                raise ValueError(
-                    "cannot infer the number of types from a None type map"
-                )
+            return len(self.get_type_map())
 
         @abstractmethod
         def get_sel(self) -> List[int]:

deepmd/dpmodel/atomic_model/pairtab_atomic_model.py

@@ -66,9 +66,17 @@ def __init__(
         self.type_map = type_map
 
         self.tab = PairTab(self.tab_file, rcut=rcut)
+        self.type_map = type_map
+        self.ntypes = len(type_map)
 
         if self.tab_file is not None:
             self.tab_info, self.tab_data = self.tab.get()
+            nspline, ntypes_tab = self.tab_info[-2:].astype(int)
+            self.tab_data = self.tab_data.reshape(ntypes_tab, ntypes_tab, nspline, 4)
+            if self.ntypes != ntypes_tab:
+                raise ValueError(
+                    "The `type_map` provided does not match the number of columns in the table."
+                )
         else:
             self.tab_info, self.tab_data = None, None
 
@@ -145,7 +153,8 @@ def deserialize(cls, data) -> "PairTabAtomicModel":
         tab_model = cls(None, rcut, sel, type_map, **data)
         tab_model.tab = tab
         tab_model.tab_info = tab_model.tab.tab_info
-        tab_model.tab_data = tab_model.tab.tab_data
+        nspline, ntypes = tab_model.tab_info[-2:].astype(int)
+        tab_model.tab_data = tab_model.tab.tab_data.reshape(ntypes, ntypes, nspline, 4)
         return tab_model
 
     def forward_atomic(

deepmd/pt/model/atomic_model/__init__.py

@@ -21,8 +21,8 @@
     DPAtomicModel,
 )
 from .linear_atomic_model import (
-    DPZBLLinearAtomicModel,
-    LinearAtomicModel,
+    DPZBLLinearEnergyAtomicModel,
+    LinearEnergyAtomicModel,
 )
 from .pairtab_atomic_model import (
     PairTabAtomicModel,
@@ -32,6 +32,6 @@
     "BaseAtomicModel",
     "DPAtomicModel",
     "PairTabAtomicModel",
-    "LinearAtomicModel",
-    "DPZBLLinearAtomicModel",
+    "LinearEnergyAtomicModel",
+    "DPZBLLinearEnergyAtomicModel",
 ]

deepmd/pt/model/atomic_model/linear_atomic_model.py

@@ -25,6 +25,9 @@
     get_multiple_nlist_key,
     nlist_distinguish_types,
 )
+from deepmd.utils.path import (
+    DPPath,
+)
 from deepmd.utils.version import (
     check_version_compatibility,
 )
@@ -40,7 +43,7 @@
 )
 
 
-class LinearAtomicModel(torch.nn.Module, BaseAtomicModel):
+class LinearEnergyAtomicModel(torch.nn.Module, BaseAtomicModel):
     """Linear model make linear combinations of several existing models.
 
     Parameters
@@ -93,7 +96,6 @@ def get_rcut(self) -> float:
 
     @torch.jit.export
     def get_type_map(self) -> List[str]:
-        """Get the type map."""
         return self.type_map
 
     def get_model_rcuts(self) -> List[float]:
@@ -117,8 +119,8 @@ def _sort_rcuts_sels(self, device: torch.device) -> Tuple[List[float], List[int]
         nsels = torch.tensor(self.get_model_nsels(), device=device)
         zipped = torch.stack(
             [
-                torch.tensor(rcuts, device=device),
-                torch.tensor(nsels, device=device),
+                rcuts,
+                nsels,
             ],
             dim=0,
         ).T
@@ -185,10 +187,12 @@ def forward_atomic(
         ener_list = []
 
         for i, model in enumerate(self.models):
+            ori_map = model.get_type_map()
+            updated_atype = self.remap_atype(extended_atype, ori_map, self.type_map)
             ener_list.append(
                 model.forward_atomic(
                     extended_coord,
-                    extended_atype,
+                    updated_atype,
                     nlists_[i],
                     mapping,
                     fparam,
@@ -198,16 +202,56 @@ def forward_atomic(
 
         weights = self._compute_weight(extended_coord, extended_atype, nlists_)
 
-        if self.atomic_bias is not None:
-            raise NotImplementedError("Need to add bias in a future PR.")
-        else:
-            fit_ret = {
-                "energy": torch.sum(
-                    torch.stack(ener_list) * torch.stack(weights), dim=0
-                ),
-            }  # (nframes, nloc, 1)
+        atype = extended_atype[:, :nloc]
+        for idx, model in enumerate(self.models):
+            if isinstance(model, DPAtomicModel):
+                bias_atom_e = model.fitting_net.bias_atom_e
+            elif isinstance(model, PairTabAtomicModel):
+                bias_atom_e = model.bias_atom_e
+            else:
+                bias_atom_e = None
+            if bias_atom_e is not None:
+                ener_list[idx] += bias_atom_e[atype]
+
+        fit_ret = {
+            "energy": torch.sum(torch.stack(ener_list) * torch.stack(weights), dim=0),
+        }  # (nframes, nloc, 1)
         return fit_ret
 
+    @staticmethod
+    def remap_atype(
+        atype: torch.Tensor, ori_map: List[str], new_map: List[str]
+    ) -> torch.Tensor:
+        """
+        This method is used to map the atype from the common type_map to the original type_map of
+        indivial AtomicModels.
+
+        Parameters
+        ----------
+        atype : torch.Tensor
+            The atom type tensor being updated, shape of (nframes, natoms)
+        ori_map : List[str]
+            The original type map of an AtomicModel.
+        new_map : List[str]
+            The common type map of the DPZBLLinearEnergyAtomicModel, created by the `get_type_map` method,
+            must be a subset of the ori_map.
+
+        Returns
+        -------
+        torch.Tensor
+        """
+        assert torch.max(atype) < len(
+            new_map
+        ), "The input `atype` cannot be handled by the type_map."
+        type_2_idx = {atp: idx for idx, atp in enumerate(ori_map)}
+        # this maps the atype in the new map to the original map
+        mapping = torch.tensor(
+            [type_2_idx[new_map[idx]] for idx in range(len(new_map))],
+            device=atype.device,
+        )
+        updated_atype = mapping[atype.long()]
+        return updated_atype
+
     def fitting_output_def(self) -> FittingOutputDef:
         return FittingOutputDef(
             [
@@ -292,7 +336,7 @@ def is_aparam_nall(self) -> bool:
         return False
 
 
-class DPZBLLinearAtomicModel(LinearAtomicModel):
+class DPZBLLinearEnergyAtomicModel(LinearEnergyAtomicModel):
     """Model linearly combine a list of AtomicModels.
 
     Parameters
@@ -336,14 +380,41 @@ def __init__(
         # this is a placeholder being updated in _compute_weight, to handle Jit attribute init error.
         self.zbl_weight = torch.empty(0, dtype=torch.float64, device=env.DEVICE)
 
+    def compute_or_load_stat(
+        self,
+        sampled_func,
+        stat_file_path: Optional[DPPath] = None,
+    ):
+        """
+        Compute or load the statistics parameters of the model,
+        such as mean and standard deviation of descriptors or the energy bias of the fitting net.
+        When `sampled` is provided, all the statistics parameters will be calculated (or re-calculated for update),
+        and saved in the `stat_file_path`(s).
+        When `sampled` is not provided, it will check the existence of `stat_file_path`(s)
+        and load the calculated statistics parameters.
+
+        Parameters
+        ----------
+        sampled_func
+            The lazy sampled function to get data frames from different data systems.
+        stat_file_path
+            The dictionary of paths to the statistics files.
+        """
+        self.dp_model.compute_or_load_stat(sampled_func, stat_file_path)
+        self.zbl_model.compute_or_load_stat(sampled_func, stat_file_path)
+
+    def change_energy_bias(self):
+        # need to implement
+        pass
+
     def serialize(self) -> dict:
         dd = BaseAtomicModel.serialize(self)
         dd.update(
             {
                 "@class": "Model",
                 "@version": 1,
                 "type": "zbl",
-                "models": LinearAtomicModel.serialize(
+                "models": LinearEnergyAtomicModel.serialize(
                     [self.dp_model, self.zbl_model], self.type_map
                 ),
                 "sw_rmin": self.sw_rmin,
@@ -354,14 +425,14 @@ def serialize(self) -> dict:
         return dd
 
     @classmethod
-    def deserialize(cls, data) -> "DPZBLLinearAtomicModel":
+    def deserialize(cls, data) -> "DPZBLLinearEnergyAtomicModel":
         data = copy.deepcopy(data)
         check_version_compatibility(data.pop("@version", 1), 1, 1)
         sw_rmin = data.pop("sw_rmin")
         sw_rmax = data.pop("sw_rmax")
         smin_alpha = data.pop("smin_alpha")
 
-        [dp_model, zbl_model], type_map = LinearAtomicModel.deserialize(
+        [dp_model, zbl_model], type_map = LinearEnergyAtomicModel.deserialize(
             data.pop("models")
         )