Merge branch 'devel' into data_stat

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -21,10 +21,10 @@ body:
     validations:
       required: true
   - type: input
-    id: tf-version
+    id: backend-version
     attributes:
-      label: TensorFlow Version
-      description: "The version will be printed when running DeePMD-kit."
+      label: Backend and its version
+      description: "The backend and its version will be printed when running DeePMD-kit, e.g. TensorFlow v2.15.0."
     validations:
       required: true
   - type: dropdown

.github/ISSUE_TEMPLATE/generic-issue.yml

@@ -21,10 +21,10 @@ body:
     validations:
       required: true
   - type: input
-    id: tf-version
+    id: backend-version
     attributes:
-      label: TensorFlow Version
-      description: "The version will be printed when running DeePMD-kit."
+      label: Backend and its version
+      description: "The backend and its version will be printed when running DeePMD-kit, e.g. TensorFlow v2.15.0."
     validations:
       required: true
   - type: textarea

deepmd/dpmodel/fitting/invar_fitting.py

@@ -199,7 +199,11 @@ def output_def(self):
         return FittingOutputDef(
             [
                 OutputVariableDef(
-                    self.var_name, [self.dim_out], reduciable=True, differentiable=True
+                    self.var_name,
+                    [self.dim_out],
+                    reduciable=True,
+                    r_differentiable=True,
+                    c_differentiable=True,
                 ),
             ]
         )

deepmd/dpmodel/model/make_base_atomic_model.py

@@ -133,7 +133,10 @@ def do_grad_(
         ) -> bool:
             """Tell if the output variable `var_name` is differentiable."""
             assert var_name is not None
-            return self.fitting_output_def()[var_name].differentiable
+            return (
+                self.fitting_output_def()[var_name].r_differentiable
+                or self.fitting_output_def()[var_name].c_differentiable
+            )
 
     setattr(BAM, fwd_method_name, BAM.fwd)
     delattr(BAM, "fwd")

deepmd/dpmodel/model/pair_tab_model.py

@@ -70,7 +70,11 @@ def fitting_output_def(self) -> FittingOutputDef:
         return FittingOutputDef(
             [
                 OutputVariableDef(
-                    name="energy", shape=[1], reduciable=True, differentiable=True
+                    name="energy",
+                    shape=[1],
+                    reduciable=True,
+                    r_differentiable=True,
+                    c_differentiable=True,
                 )
             ]
         )

deepmd/dpmodel/model/transform_output.py

@@ -31,10 +31,13 @@ def fit_output_to_model_output(
         if vdef.reduciable:
             kk_redu = get_reduce_name(kk)
             model_ret[kk_redu] = np.sum(vv, axis=atom_axis)
-            if vdef.differentiable:
+            if vdef.r_differentiable:
                 kk_derv_r, kk_derv_c = get_deriv_name(kk)
                 # name-holders
                 model_ret[kk_derv_r] = None
+            if vdef.c_differentiable:
+                assert vdef.r_differentiable
+                kk_derv_r, kk_derv_c = get_deriv_name(kk)
                 model_ret[kk_derv_c] = None
     return model_ret
 
@@ -57,10 +60,13 @@ def communicate_extended_output(
         if vdef.reduciable:
             kk_redu = get_reduce_name(kk)
             new_ret[kk_redu] = model_ret[kk_redu]
-            if vdef.differentiable:
+            if vdef.r_differentiable:
                 kk_derv_r, kk_derv_c = get_deriv_name(kk)
                 # name holders
                 new_ret[kk_derv_r] = None
+            if vdef.c_differentiable:
+                assert vdef.r_differentiable
+                kk_derv_r, kk_derv_c = get_deriv_name(kk)
                 new_ret[kk_derv_c] = None
                 new_ret[kk_derv_c + "_redu"] = None
                 if not do_atomic_virial:

deepmd/dpmodel/output_def.py

@@ -68,9 +68,11 @@ def __call__(
                 if dd.reduciable:
                     rk = get_reduce_name(kk)
                     check_var(ret[rk], self.md[rk])
-                if dd.differentiable:
+                if dd.r_differentiable:
                     dnr, dnc = get_deriv_name(kk)
                     check_var(ret[dnr], self.md[dnr])
+                if dd.c_differentiable:
+                    assert dd.r_differentiable
                     check_var(ret[dnc], self.md[dnc])
             return ret
 
@@ -160,10 +162,16 @@ class OutputVariableDef:
           dipole should be [3], polarizabilty should be [3,3].
     reduciable
           If the variable is reduced.
-    differentiable
+    r_differentiable
           If the variable is differentiated with respect to coordinates
-          of atoms and cell tensor (pbc case). Only reduciable variable
+          of atoms. Only reduciable variable are differentiable.
+          Negative derivative w.r.t. coordinates will be calcualted. (e.g. force)
+    c_differentiable
+          If the variable is differentiated with respect to the
+          cell tensor (pbc case). Only reduciable variable
           are differentiable.
+          Virial, the transposed negative gradient with cell tensor times
+          cell tensor, will be calculated, see eq 40 JCP 159, 054801 (2023).
     category : int
           The category of the output variable.
     """
@@ -173,19 +181,25 @@ def __init__(
         name: str,
         shape: List[int],
         reduciable: bool = False,
-        differentiable: bool = False,
+        r_differentiable: bool = False,
+        c_differentiable: bool = False,
         atomic: bool = True,
         category: int = OutputVariableCategory.OUT.value,
     ):
         self.name = name
         self.shape = list(shape)
         self.atomic = atomic
         self.reduciable = reduciable
-        self.differentiable = differentiable
-        if not self.reduciable and self.differentiable:
-            raise ValueError("only reduciable variable are differentiable")
+        self.r_differentiable = r_differentiable
+        self.c_differentiable = c_differentiable
+        if self.c_differentiable and not self.r_differentiable:
+            raise ValueError("c differentiable requires r_differentiable")
+        if not self.reduciable and self.r_differentiable:
+            raise ValueError("only reduciable variable are r differentiable")
+        if not self.reduciable and self.c_differentiable:
+            raise ValueError("only reduciable variable are c differentiable")
         if self.reduciable and not self.atomic:
-            raise ValueError("only reduciable variable should be atomic")
+            raise ValueError("a reduciable variable should be atomic")
         self.category = category
 
 
@@ -358,7 +372,8 @@ def do_reduce(
                 rk,
                 vv.shape,
                 reduciable=False,
-                differentiable=False,
+                r_differentiable=False,
+                c_differentiable=False,
                 atomic=False,
                 category=apply_operation(vv, OutputVariableOperation.REDU),
             )
@@ -371,21 +386,26 @@ def do_derivative(
     def_derv_r: Dict[str, OutputVariableDef] = {}
     def_derv_c: Dict[str, OutputVariableDef] = {}
     for kk, vv in def_outp_data.items():
-        if vv.differentiable:
-            rkr, rkc = get_deriv_name(kk)
+        rkr, rkc = get_deriv_name(kk)
+        if vv.r_differentiable:
             def_derv_r[rkr] = OutputVariableDef(
                 rkr,
                 vv.shape + [3],  # noqa: RUF005
                 reduciable=False,
-                differentiable=False,
+                r_differentiable=False,
+                c_differentiable=False,
                 atomic=True,
                 category=apply_operation(vv, OutputVariableOperation.DERV_R),
             )
+        if vv.c_differentiable:
+            assert vv.r_differentiable
+            rkr, rkc = get_deriv_name(kk)
             def_derv_c[rkc] = OutputVariableDef(
                 rkc,
-                vv.shape + [3, 3],  # noqa: RUF005
+                vv.shape + [9],  # noqa: RUF005
                 reduciable=True,
-                differentiable=False,
+                r_differentiable=False,
+                c_differentiable=False,
                 atomic=True,
                 category=apply_operation(vv, OutputVariableOperation.DERV_C),
             )

deepmd/pt/model/model/pair_tab_model.py

@@ -82,7 +82,11 @@ def fitting_output_def(self) -> FittingOutputDef:
         return FittingOutputDef(
             [
                 OutputVariableDef(
-                    name="energy", shape=[1], reduciable=True, differentiable=True
+                    name="energy",
+                    shape=[1],
+                    reduciable=True,
+                    r_differentiable=True,
+                    c_differentiable=True,
                 )
             ]
         )

deepmd/pt/model/model/transform_output.py

@@ -56,6 +56,7 @@ def task_deriv_one(
     atom_energy: torch.Tensor,
     energy: torch.Tensor,
     extended_coord: torch.Tensor,
+    do_virial: bool = True,
     do_atomic_virial: bool = False,
 ):
     faked_grad = torch.ones_like(energy)
@@ -65,13 +66,16 @@ def task_deriv_one(
     )[0]
     assert extended_force is not None
     extended_force = -extended_force
-    extended_virial = extended_force.unsqueeze(-1) @ extended_coord.unsqueeze(-2)
-    # the correction sums to zero, which does not contribute to global virial
-    if do_atomic_virial:
-        extended_virial_corr = atomic_virial_corr(extended_coord, atom_energy)
-        extended_virial = extended_virial + extended_virial_corr
-    # to [...,3,3] -> [...,9]
-    extended_virial = extended_virial.view(list(extended_virial.shape[:-2]) + [9])  # noqa:RUF005
+    if do_virial:
+        extended_virial = extended_force.unsqueeze(-1) @ extended_coord.unsqueeze(-2)
+        # the correction sums to zero, which does not contribute to global virial
+        if do_atomic_virial:
+            extended_virial_corr = atomic_virial_corr(extended_coord, atom_energy)
+            extended_virial = extended_virial + extended_virial_corr
+        # to [...,3,3] -> [...,9]
+        extended_virial = extended_virial.view(list(extended_virial.shape[:-2]) + [9])  # noqa:RUF005
+    else:
+        extended_virial = None
     return extended_force, extended_virial
 
 
@@ -97,6 +101,7 @@ def take_deriv(
     svv: torch.Tensor,
     vdef: OutputVariableDef,
     coord_ext: torch.Tensor,
+    do_virial: bool = False,
     do_atomic_virial: bool = False,
 ):
     size = 1
@@ -110,16 +115,25 @@ def take_deriv(
     for vvi, svvi in zip(split_vv1, split_svv1):
         # nf x nloc x 3, nf x nloc x 9
         ffi, aviri = task_deriv_one(
-            vvi, svvi, coord_ext, do_atomic_virial=do_atomic_virial
+            vvi,
+            svvi,
+            coord_ext,
+            do_virial=do_virial,
+            do_atomic_virial=do_atomic_virial,
         )
         # nf x nloc x 1 x 3, nf x nloc x 1 x 9
         ffi = ffi.unsqueeze(-2)
-        aviri = aviri.unsqueeze(-2)
         split_ff.append(ffi)
-        split_avir.append(aviri)
+        if do_virial:
+            assert aviri is not None
+            aviri = aviri.unsqueeze(-2)
+            split_avir.append(aviri)
     # nf x nloc x v_dim x 3, nf x nloc x v_dim x 9
     ff = torch.concat(split_ff, dim=-2)
-    avir = torch.concat(split_avir, dim=-2)
+    if do_virial:
+        avir = torch.concat(split_avir, dim=-2)
+    else:
+        avir = None
     return ff, avir
 
 
@@ -141,18 +155,23 @@ def fit_output_to_model_output(
         if vdef.reduciable:
             kk_redu = get_reduce_name(kk)
             model_ret[kk_redu] = torch.sum(vv, dim=atom_axis)
-            if vdef.differentiable:
+            if vdef.r_differentiable:
                 kk_derv_r, kk_derv_c = get_deriv_name(kk)
                 dr, dc = take_deriv(
                     vv,
                     model_ret[kk_redu],
                     vdef,
                     coord_ext,
+                    do_virial=vdef.c_differentiable,
                     do_atomic_virial=do_atomic_virial,
                 )
                 model_ret[kk_derv_r] = dr
-                model_ret[kk_derv_c] = dc
-                model_ret[kk_derv_c + "_redu"] = torch.sum(model_ret[kk_derv_c], dim=1)
+                if vdef.c_differentiable:
+                    assert dc is not None
+                    model_ret[kk_derv_c] = dc
+                    model_ret[kk_derv_c + "_redu"] = torch.sum(
+                        model_ret[kk_derv_c], dim=1
+                    )
     return model_ret
 
 
@@ -174,12 +193,12 @@ def communicate_extended_output(
         if vdef.reduciable:
             kk_redu = get_reduce_name(kk)
             new_ret[kk_redu] = model_ret[kk_redu]
-            if vdef.differentiable:
-                # nf x nloc
-                vldims = get_leading_dims(vv, vdef)
-                # nf x nall
-                mldims = list(mapping.shape)
-                kk_derv_r, kk_derv_c = get_deriv_name(kk)
+            # nf x nloc
+            vldims = get_leading_dims(vv, vdef)
+            # nf x nall
+            mldims = list(mapping.shape)
+            kk_derv_r, kk_derv_c = get_deriv_name(kk)
+            if vdef.r_differentiable:
                 # vdim x 3
                 derv_r_ext_dims = list(vdef.shape) + [3]  # noqa:RUF005
                 mapping = mapping.view(mldims + [1] * len(derv_r_ext_dims)).expand(
@@ -196,10 +215,13 @@ def communicate_extended_output(
                     src=model_ret[kk_derv_r],
                     reduce="sum",
                 )
+            if vdef.c_differentiable:
+                assert vdef.r_differentiable
                 derv_c_ext_dims = list(vdef.shape) + [9]  # noqa:RUF005
                 # nf x nloc x nvar x 3 -> nf x nloc x nvar x 9
                 mapping = torch.tile(
-                    mapping, [1] * (len(mldims) + len(vdef.shape)) + [3]
+                    mapping,
+                    [1] * (len(mldims) + len(vdef.shape)) + [3],
                 )
                 virial = torch.zeros(
                     vldims + derv_c_ext_dims, dtype=vv.dtype, device=vv.device

deepmd/pt/model/task/denoise.py

@@ -75,10 +75,18 @@ def output_def(self):
         return FittingOutputDef(
             [
                 OutputVariableDef(
-                    "updated_coord", [3], reduciable=False, differentiable=False
+                    "updated_coord",
+                    [3],
+                    reduciable=False,
+                    r_differentiable=False,
+                    c_differentiable=False,
                 ),
                 OutputVariableDef(
-                    "logits", [-1], reduciable=False, differentiable=False
+                    "logits",
+                    [-1],
+                    reduciable=False,
+                    r_differentiable=False,
+                    c_differentiable=False,
                 ),
             ]
         )