pt: support multitask finetune

deepmd/dpmodel/atomic_model/dp_atomic_model.py

@@ -83,6 +83,27 @@
         """
         return self.descriptor.mixed_types()
 
+    def set_out_bias(self, out_bias: np.ndarray, add=False) -> None:
+        """
+        Modify the output bias for the atomic model.
+
+        Parameters
+        ----------
+        out_bias : np.ndarray
+            The new bias to be applied.
+        add : bool, optional
+            Whether to add the new bias to the existing one.
+            If False, the output bias will be directly replaced by the new bias.
+            If True, the new bias will be added to the existing one.
+        """
+        self.fitting["bias_atom_e"] = (
+            out_bias + self.fitting["bias_atom_e"] if add else out_bias
+        )
+
+    def get_out_bias(self) -> np.ndarray:
+        """Return the output bias of the atomic model."""
+        return self.fitting["bias_atom_e"]
+
     def forward_atomic(
         self,
         extended_coord: np.ndarray,

deepmd/dpmodel/atomic_model/linear_atomic_model.py

@@ -275,6 +275,27 @@
         # join all the selected types
         return list(set().union(*[model.get_sel_type() for model in self.models]))
 
+    def set_out_bias(self, out_bias: np.ndarray, add=False) -> None:
+        """
+        Modify the output bias for all the models in the linear atomic model.
+
+        Parameters
+        ----------
+        out_bias : torch.Tensor
+            The new bias to be applied.
+        add : bool, optional
+            Whether to add the new bias to the existing one.
+            If False, the output bias will be directly replaced by the new bias.
+            If True, the new bias will be added to the existing one.
+        """
+        for model in self.models:
+            model.set_out_bias(out_bias, add=add)
+
+    def get_out_bias(self) -> np.ndarray:
+        """Return the weighted output bias of the linear atomic model."""
+        # TODO add get_out_bias for linear atomic model
+        raise NotImplementedError
+
     def is_aparam_nall(self) -> bool:
         """Check whether the shape of atomic parameters is (nframes, nall, ndim).
 

deepmd/dpmodel/atomic_model/make_base_atomic_model.py

@@ -95,6 +95,25 @@ def get_sel_type(self) -> List[int]:
             If returning an empty list, all atom types are selected.
             """
 
+        @abstractmethod
+        def set_out_bias(self, out_bias: t_tensor, add=False) -> None:
+            """
+            Modify the output bias for the atomic model.
+
+            Parameters
+            ----------
+            out_bias : t_tensor
+                The new bias to be applied.
+            add : bool, optional
+                Whether to add the new bias to the existing one.
+                If False, the output bias will be directly replaced by the new bias.
+                If True, the new bias will be added to the existing one.
+            """
+
+        @abstractmethod
+        def get_out_bias(self) -> t_tensor:
+            """Return the output bias of the atomic model."""
+
         @abstractmethod
         def is_aparam_nall(self) -> bool:
             """Check whether the shape of atomic parameters is (nframes, nall, ndim).

deepmd/dpmodel/atomic_model/pairtab_atomic_model.py

@@ -126,6 +126,25 @@
         # to match DPA1 and DPA2.
         return True
 
+    def set_out_bias(self, out_bias: np.ndarray, add=False) -> None:
+        """
+        Modify the output bias for the atomic model.
+
+        Parameters
+        ----------
+        out_bias : torch.Tensor
+            The new bias to be applied.
+        add : bool, optional
+            Whether to add the new bias to the existing one.
+            If False, the output bias will be directly replaced by the new bias.
+            If True, the new bias will be added to the existing one.
+        """
+        self.bias_atom_e = out_bias + self.bias_atom_e if add else out_bias
+
+    def get_out_bias(self) -> np.ndarray:
+        """Return the output bias of the atomic model."""
+        return self.bias_atom_e
+
     def serialize(self) -> dict:
         dd = BaseAtomicModel.serialize(self)
         dd.update(

deepmd/pt/entrypoints/main.py

@@ -90,13 +90,13 @@ def get_trainer(
         dist.init_process_group(backend="nccl")
 
     ckpt = init_model if init_model is not None else restart_model
-    config["model"] = change_finetune_model_params(
-        ckpt,
-        finetune_model,
-        config["model"],
-        multi_task=multi_task,
-        model_branch=model_branch,
-    )
+    finetune_links = None
+    if finetune_model is not None:
+        config["model"], finetune_links = change_finetune_model_params(
+            finetune_model,
+            config["model"],
+            model_branch=model_branch,
+        )
     config["model"]["resuming"] = (finetune_model is not None) or (ckpt is not None)
 
     def prepare_trainer_input_single(
@@ -194,6 +194,7 @@ def prepare_trainer_input_single(
         finetune_model=finetune_model,
         force_load=force_load,
         shared_links=shared_links,
+        finetune_links=finetune_links,
         init_frz_model=init_frz_model,
     )
     return trainer

deepmd/pt/model/atomic_model/base_atomic_model.py

@@ -1,13 +1,16 @@
 # SPDX-License-Identifier: LGPL-3.0-or-later
 
 
+import logging
 from typing import (
+    Callable,
     Dict,
     List,
     Optional,
     Tuple,
 )
 
+import numpy as np
 import torch
 
 from deepmd.dpmodel.atomic_model import (
@@ -21,10 +24,21 @@
     AtomExcludeMask,
     PairExcludeMask,
 )
+from deepmd.pt.utils.nlist import (
+    extend_input_and_build_neighbor_list,
+)
+from deepmd.pt.utils.stat import (
+    compute_output_stats,
+)
+from deepmd.pt.utils.utils import (
+    to_numpy_array,
+)
 from deepmd.utils.path import (
     DPPath,
 )
 
+log = logging.getLogger(__name__)
+
 BaseAtomicModel_ = make_base_atomic_model(torch.Tensor)
 
 
@@ -176,6 +190,40 @@
             "pair_exclude_types": self.pair_exclude_types,
         }
 
+    def get_forward_wrapper_func(self) -> Callable[..., torch.Tensor]:
+        """Get a forward wrapper of the atomic model for output bias calculation."""
+        model_output_type = list(self.atomic_output_def().keys())
+        if "mask" in model_output_type:
+            model_output_type.pop(model_output_type.index("mask"))
+        out_name = model_output_type[0]
+
+        def model_forward(coord, atype, box, fparam=None, aparam=None):
+            with torch.no_grad():  # it's essential for pure torch forward function to use auto_batchsize
+                (
+                    extended_coord,
+                    extended_atype,
+                    mapping,
+                    nlist,
+                ) = extend_input_and_build_neighbor_list(
+                    coord,
+                    atype,
+                    self.get_rcut(),
+                    self.get_sel(),
+                    mixed_types=self.mixed_types(),
+                    box=box,
+                )
+                atomic_ret = self.forward_common_atomic(
+                    extended_coord,
+                    extended_atype,
+                    nlist,
+                    mapping=mapping,
+                    fparam=fparam,
+                    aparam=aparam,
+                )
+                return atomic_ret[out_name].detach()
+
+        return model_forward
+
     def compute_or_load_stat(
         self,
         sampled_func,
@@ -197,3 +245,62 @@
             The path to the statistics files.
         """
         raise NotImplementedError
+
+    def change_out_bias(
+        self,
+        merged,
+        origin_type_map,
+        full_type_map,
+        bias_adjust_mode="change-by-statistic",
+    ) -> None:
+        """Change the output bias according to the input data and the pretrained model.
+
+        Parameters
+        ----------
+        merged : Union[Callable[[], List[dict]], List[dict]]
+            - List[dict]: A list of data samples from various data systems.
+                Each element, `merged[i]`, is a data dictionary containing `keys`: `torch.Tensor`
+                originating from the `i`-th data system.
+            - Callable[[], List[dict]]: A lazy function that returns data samples in the above format
+                only when needed. Since the sampling process can be slow and memory-intensive,
+                the lazy function helps by only sampling once.
+        origin_type_map : List[str]
+            The original type_map in dataset, they are targets to change the output bias.
+        full_type_map : List[str]
+            The full type_map in pre-trained model
+        bias_adjust_mode : str
+            The mode for changing output bias : ['change-by-statistic', 'set-by-statistic']
+            'change-by-statistic' : perform predictions on labels of target dataset,
+                    and do least square on the errors to obtain the target shift as bias.
+            'set-by-statistic' : directly use the statistic output bias in the target dataset.
+        """
+        sorter = np.argsort(full_type_map)
+        missing_types = [t for t in origin_type_map if t not in full_type_map]
+        assert (
+            not missing_types
+        ), f"Some types are not in the pre-trained model: {list(missing_types)} !"
+        idx_type_map = sorter[
+            np.searchsorted(full_type_map, origin_type_map, sorter=sorter)
+        ]
+        original_bias = self.get_out_bias()
+        if bias_adjust_mode == "change-by-statistic":
+            delta_bias = compute_output_stats(
+                merged,
+                self.get_ntypes(),
+                model_forward=self.get_forward_wrapper_func(),
+            )
+            self.set_out_bias(delta_bias, add=True)
+        elif bias_adjust_mode == "set-by-statistic":
+            bias_atom = compute_output_stats(
+                merged,
+                self.get_ntypes(),
+            )
+            self.set_out_bias(bias_atom)
+        else:
+            raise RuntimeError("Unknown bias_adjust_mode mode: " + bias_adjust_mode)
+        bias_atom = self.get_out_bias()
+        log.info(
+            f"Change output bias of {origin_type_map!s} "
+            f"from {to_numpy_array(original_bias[idx_type_map]).reshape(-1)!s} "
+            f"to {to_numpy_array(bias_atom[idx_type_map]).reshape(-1)!s}."
+        )

deepmd/pt/model/atomic_model/dp_atomic_model.py

@@ -223,6 +223,27 @@ def wrapped_sampler():
         if self.fitting_net is not None:
             self.fitting_net.compute_output_stats(wrapped_sampler, stat_file_path)
 
+    def set_out_bias(self, out_bias: torch.Tensor, add=False) -> None:
+        """
+        Modify the output bias for the atomic model.
+
+        Parameters
+        ----------
+        out_bias : torch.Tensor
+            The new bias to be applied.
+        add : bool, optional
+            Whether to add the new bias to the existing one.
+            If False, the output bias will be directly replaced by the new bias.
+            If True, the new bias will be added to the existing one.
+        """
+        self.fitting_net["bias_atom_e"] = (
+            out_bias + self.fitting_net["bias_atom_e"] if add else out_bias
+        )
+
+    def get_out_bias(self) -> torch.Tensor:
+        """Return the output bias of the atomic model."""
+        return self.fitting_net["bias_atom_e"]
+
     def get_dim_fparam(self) -> int:
         """Get the number (dimension) of frame parameters of this atomic model."""
         return self.fitting_net.get_dim_fparam()

deepmd/pt/model/atomic_model/linear_atomic_model.py

@@ -289,6 +289,27 @@
             for _ in range(nmodels)
         ]
 
+    def set_out_bias(self, out_bias: torch.Tensor, add=False) -> None:
+        """
+        Modify the output bias for all the models in the linear atomic model.
+
+        Parameters
+        ----------
+        out_bias : torch.Tensor
+            The new bias to be applied.
+        add : bool, optional
+            Whether to add the new bias to the existing one.
+            If False, the output bias will be directly replaced by the new bias.
+            If True, the new bias will be added to the existing one.
+        """
+        for model in self.models:
+            model.set_out_bias(out_bias, add=add)
+
+    def get_out_bias(self) -> torch.Tensor:
+        """Return the weighted output bias of the linear atomic model."""
+        # TODO add get_out_bias for linear atomic model
+        raise NotImplementedError
+
     def get_dim_fparam(self) -> int:
         """Get the number (dimension) of frame parameters of this atomic model."""
         # tricky...
@@ -390,10 +411,6 @@
         self.models[0].compute_or_load_stat(sampled_func, stat_file_path)
         self.models[1].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(

deepmd/pt/model/atomic_model/pairtab_atomic_model.py

@@ -234,9 +234,24 @@
             torch.tensor(bias_atom_e, device=env.DEVICE).view([self.ntypes, 1])
         )
 
-    def change_energy_bias(self) -> None:
-        # need to implement
-        pass
+    def set_out_bias(self, out_bias: torch.Tensor, add=False) -> None:
+        """
+        Modify the output bias for the atomic model.
+
+        Parameters
+        ----------
+        out_bias : torch.Tensor
+            The new bias to be applied.
+        add : bool, optional
+            Whether to add the new bias to the existing one.
+            If False, the output bias will be directly replaced by the new bias.
+            If True, the new bias will be added to the existing one.
+        """
+        self.bias_atom_e = out_bias + self.bias_atom_e if add else out_bias
+
+    def get_out_bias(self) -> torch.Tensor:
+        """Return the output bias of the atomic model."""
+        return self.bias_atom_e
 
     def forward_atomic(
         self,