fix: manage testing models in a standard way (deepmodeling#4028)

Fix deepmodeling#2103. Migrate three models (se_e2_a, se_e2_r, and fparam_aparam)
for the Python unit tests. Fix several bugs. Old files are kept until
the C++ tests are also migrated.

Note that several models (for example, the dipole model due to deepmodeling#3672)
cannot be serialized yet.

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit


## Summary by CodeRabbit

- **New Features**
- Introduced a structured framework for managing and testing models with
YAML files.
- Added comprehensive configurations for energy calculations and
molecular simulations in YAML format.
- Implemented new test cases for the `DeepPot` and `DeepPotNeighborList`
classes.

- **Bug Fixes**
- Improved robustness in tensor reshaping, resolving potential dimension
mismatches.

- **Tests**
- Enhanced unit tests with a case-based approach for better adaptability
and maintainability.
- Consolidated tests by relocating obsolete classes to streamline the
test suite.

- **Chores**
- Updated deserialization functions for better type safety and input
handling.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>

deepmd/pt/infer/deep_eval.py

@@ -380,26 +380,28 @@ def _eval_model(
             natoms = len(atom_types[0])
 
         coord_input = torch.tensor(
-            coords.reshape([-1, natoms, 3]),
+            coords.reshape([nframes, natoms, 3]),
             dtype=GLOBAL_PT_FLOAT_PRECISION,
             device=DEVICE,
         )
         type_input = torch.tensor(atom_types, dtype=torch.long, device=DEVICE)
         if cells is not None:
             box_input = torch.tensor(
-                cells.reshape([-1, 3, 3]),
+                cells.reshape([nframes, 3, 3]),
                 dtype=GLOBAL_PT_FLOAT_PRECISION,
                 device=DEVICE,
             )
         else:
             box_input = None
         if fparam is not None:
-            fparam_input = to_torch_tensor(fparam.reshape(-1, self.get_dim_fparam()))
+            fparam_input = to_torch_tensor(
+                fparam.reshape(nframes, self.get_dim_fparam())
+            )
         else:
             fparam_input = None
         if aparam is not None:
             aparam_input = to_torch_tensor(
-                aparam.reshape(-1, natoms, self.get_dim_aparam())
+                aparam.reshape(nframes, natoms, self.get_dim_aparam())
             )
         else:
             aparam_input = None
@@ -451,31 +453,33 @@ def _eval_model_spin(
             natoms = len(atom_types[0])
 
         coord_input = torch.tensor(
-            coords.reshape([-1, natoms, 3]),
+            coords.reshape([nframes, natoms, 3]),
             dtype=GLOBAL_PT_FLOAT_PRECISION,
             device=DEVICE,
         )
         type_input = torch.tensor(atom_types, dtype=torch.long, device=DEVICE)
         spin_input = torch.tensor(
-            spins.reshape([-1, natoms, 3]),
+            spins.reshape([nframes, natoms, 3]),
             dtype=GLOBAL_PT_FLOAT_PRECISION,
             device=DEVICE,
         )
         if cells is not None:
             box_input = torch.tensor(
-                cells.reshape([-1, 3, 3]),
+                cells.reshape([nframes, 3, 3]),
                 dtype=GLOBAL_PT_FLOAT_PRECISION,
                 device=DEVICE,
             )
         else:
             box_input = None
         if fparam is not None:
-            fparam_input = to_torch_tensor(fparam.reshape(-1, self.get_dim_fparam()))
+            fparam_input = to_torch_tensor(
+                fparam.reshape(nframes, self.get_dim_fparam())
+            )
         else:
             fparam_input = None
         if aparam is not None:
             aparam_input = to_torch_tensor(
-                aparam.reshape(-1, natoms, self.get_dim_aparam())
+                aparam.reshape(nframes, natoms, self.get_dim_aparam())
             )
         else:
             aparam_input = None

deepmd/pt/utils/serialization.py

@@ -72,7 +72,7 @@ def deserialize_to_file(model_file: str, data: dict) -> None:
     model = BaseModel.deserialize(data["model"])
     # JIT will happy in this way...
     model.model_def_script = json.dumps(data["model_def_script"])
-    model = torch.jit.script(model)
     if "min_nbor_dist" in data.get("@variables", {}):
-        model.min_nbor_dist = data["@variables"]["min_nbor_dist"]
+        model.min_nbor_dist = float(data["@variables"]["min_nbor_dist"])
+    model = torch.jit.script(model)
     torch.jit.save(model, model_file)

deepmd/tf/descriptor/se_a.py

@@ -720,10 +720,11 @@ def prod_force_virial(
         """
         [net_deriv] = tf.gradients(atom_ener, self.descrpt_reshape)
         tf.summary.histogram("net_derivative", net_deriv)
+        nf = tf.shape(self.nlist)[0]
         net_deriv_reshape = tf.reshape(
             net_deriv,
             [
-                np.asarray(-1, dtype=np.int64),
+                nf,
                 natoms[0] * np.asarray(self.ndescrpt, dtype=np.int64),
             ],
         )

deepmd/tf/descriptor/se_r.py

@@ -512,10 +512,11 @@ def prod_force_virial(
         """
         [net_deriv] = tf.gradients(atom_ener, self.descrpt_reshape)
         tf.summary.histogram("net_derivative", net_deriv)
+        nf = tf.shape(self.nlist)[0]
         net_deriv_reshape = tf.reshape(
             net_deriv,
             [
-                np.asarray(-1, dtype=np.int64),
+                nf,
                 natoms[0] * np.asarray(self.ndescrpt, dtype=np.int64),
             ],
         )

deepmd/tf/utils/serialization.py

@@ -91,13 +91,13 @@ def deserialize_to_file(model_file: str, data: dict) -> None:
         if model.get_numb_fparam() > 0:
             inputs["fparam"] = tf.placeholder(
                 GLOBAL_TF_FLOAT_PRECISION,
-                [None, model.get_numb_fparam()],
+                [None],
                 name="t_fparam",
             )
         if model.get_numb_aparam() > 0:
             inputs["aparam"] = tf.placeholder(
                 GLOBAL_TF_FLOAT_PRECISION,
-                [None, model.get_numb_aparam()],
+                [None],
                 name="t_aparam",
             )
         model.build(

source/tests/consistent/model/test_frozen.py

@@ -31,36 +31,29 @@
     from deepmd.tf.model.model import Model as FrozenModelTF
 else:
     FrozenModelTF = None
-from pathlib import (
-    Path,
-)
 
-from deepmd.entrypoints.convert_backend import (
-    convert_backend,
-)
 from deepmd.utils.argcheck import (
     model_args,
 )
 
-original_model = str(Path(__file__).parent.parent.parent / "infer" / "deeppot.dp")
+from ...infer.case import (
+    get_cases,
+)
+
 pt_model = "deeppot_for_consistent_frozen.pth"
 tf_model = "deeppot_for_consistent_frozen.pb"
-dp_model = original_model
+dp_model = "deeppot_for_consistent_frozen.dp"
 
 
 def setUpModule():
-    convert_backend(
-        INPUT=dp_model,
-        OUTPUT=tf_model,
-    )
-    convert_backend(
-        INPUT=dp_model,
-        OUTPUT=pt_model,
-    )
+    case = get_cases()["se_e2_a"]
+    case.get_model(".dp", dp_model)
+    case.get_model(".pb", tf_model)
+    case.get_model(".pth", pt_model)
 
 
 def tearDownModule():
-    for model_file in (pt_model, tf_model):
+    for model_file in (dp_model, pt_model, tf_model):
         try:
             os.remove(model_file)
         except FileNotFoundError:

source/tests/infer/.gitignore

@@ -0,0 +1 @@
+deepmd_test_models*/

source/tests/infer/__init__.py

@@ -0,0 +1 @@
+# SPDX-License-Identifier: LGPL-3.0-or-later

source/tests/infer/case.py

@@ -0,0 +1,195 @@
+# SPDX-License-Identifier: LGPL-3.0-or-later
+"""Manage testing models in a standard way.
+
+For each model, a YAML file ending with `-testcase.yaml` must be given. It should contains the following keys:
+
+- `key`: The key of the model.
+- `filename`: The path to the model file.
+- `ntypes`: The number of atomic types.
+- `rcut`: The cutoff radius.
+- `type_map`: The mapping between atomic types and atomic names.
+- `dim_fparam`: The number of frame parameters.
+- `dim_aparam`: The number of atomic parameters.
+- `results`: A list of results. Each result should contain the following keys:
+    - `atype`: The atomic types.
+    - `coord`: The atomic coordinates.
+    - `box`: The simulation box.
+    - `atomic_energy` or `energy` (optional): The atomic energies or the total energy.
+    - `force` (optional): The atomic forces.
+    - `atomic_virial` or `virial` (optional): The atomic virials or the total virial.
+"""
+
+import tempfile
+from functools import (
+    lru_cache,
+)
+from pathlib import (
+    Path,
+)
+from typing import (
+    Dict,
+    Optional,
+)
+
+import numpy as np
+import yaml
+
+from deepmd.entrypoints.convert_backend import (
+    convert_backend,
+)
+
+this_directory = Path(__file__).parent.resolve()
+# create a temporary directory under this directory
+# to store the temporary model files
+# it will be deleted when the program exits
+tempdir = tempfile.TemporaryDirectory(dir=this_directory, prefix="deepmd_test_models_")
+
+
+class Result:
+    """Test results.
+
+    Parameters
+    ----------
+    data : dict
+        Dictionary containing the results.
+
+    Attributes
+    ----------
+    atype : np.ndarray
+        The atomic types.
+    nloc : int
+        The number of atoms.
+    coord : np.ndarray
+        The atomic coordinates.
+    box : np.ndarray
+        The simulation box.
+    atomic_energy : np.ndarray
+        The atomic energies.
+    energy : np.ndarray
+        The total energy.
+    force : np.ndarray
+        The atomic forces.
+    atomic_virial : np.ndarray
+        The atomic virials.
+    virial : np.ndarray
+        The total virial.
+    """
+
+    def __init__(self, data: dict) -> None:
+        self.atype = np.array(data["atype"], dtype=np.int64)
+        self.nloc = self.atype.size
+        self.coord = np.array(data["coord"], dtype=np.float64).reshape(self.nloc, 3)
+        if data["box"] is not None:
+            self.box = np.array(data["box"], dtype=np.float64).reshape(3, 3)
+        else:
+            self.box = None
+        if "fparam" in data:
+            self.fparam = np.array(data["fparam"], dtype=np.float64).ravel()
+        else:
+            self.fparam = None
+        if "aparam" in data:
+            self.aparam = np.array(data["aparam"], dtype=np.float64).reshape(
+                self.nloc, -1
+            )
+        else:
+            self.aparam = None
+        if "atomic_energy" in data:
+            self.atomic_energy = np.array(
+                data["atomic_energy"], dtype=np.float64
+            ).reshape(self.nloc, 1)
+            self.energy = np.sum(self.atomic_energy, axis=0)
+        elif "energy" in data:
+            self.atomic_energy = None
+            self.energy = np.array(data["energy"], dtype=np.float64).reshape(1)
+        else:
+            self.atomic_energy = None
+            self.energy = None
+        if "force" in data:
+            self.force = np.array(data["force"], dtype=np.float64).reshape(self.nloc, 3)
+        else:
+            self.force = None
+        if "atomic_virial" in data:
+            self.atomic_virial = np.array(
+                data["atomic_virial"], dtype=np.float64
+            ).reshape(self.nloc, 9)
+            self.virial = np.sum(self.atomic_virial, axis=0)
+        elif "virial" in data:
+            self.atomic_virial = None
+            self.virial = np.array(data["virial"], dtype=np.float64).reshape(9)
+        else:
+            self.atomic_virial = None
+            self.virial = None
+        if "descriptor" in data:
+            self.descriptor = np.array(data["descriptor"], dtype=np.float64).reshape(
+                self.nloc, -1
+            )
+        else:
+            self.descriptor = None
+
+
+class Case:
+    """Test case.
+
+    Parameters
+    ----------
+    filename : str
+        The path to the test case file.
+    """
+
+    def __init__(self, filename: str):
+        with open(filename) as file:
+            config = yaml.safe_load(file)
+        self.key = config["key"]
+        self.filename = str(Path(filename).parent / config["filename"])
+        self.results = [Result(data) for data in config["results"]]
+        self.ntypes = config["ntypes"]
+        self.rcut = config["rcut"]
+        self.type_map = config["type_map"]
+        self.dim_fparam = config["dim_fparam"]
+        self.dim_aparam = config["dim_aparam"]
+
+    @lru_cache
+    def get_model(self, suffix: str, out_file: Optional[str] = None) -> str:
+        """Get the model file with the specified suffix.
+
+        Parameters
+        ----------
+        suffix : str
+            The suffix of the model file.
+        out_file : str, optional
+            The path to the output model file. If not given, a temporary file will be created.
+
+        Returns
+        -------
+        str
+            The path to the model file.
+        """
+        # generate a temporary model file
+        if out_file is None:
+            out_file = tempfile.NamedTemporaryFile(
+                suffix=suffix, dir=tempdir.name, delete=False, prefix=self.key + "_"
+            ).name
+        convert_backend(INPUT=self.filename, OUTPUT=out_file)
+        return out_file
+
+
+@lru_cache
+def get_cases() -> Dict[str, Case]:
+    """Get all test cases.
+
+    Returns
+    -------
+    Dict[str, Case]
+        A dictionary containing all test cases.
+
+    Examples
+    --------
+    To get a specific case:
+
+    >>> get_cases()["se_e2_a"]
+    """
+    cases = {}
+    for ff in this_directory.glob("*-testcase.yaml"):
+        case = Case(ff)
+        cases[case.key] = case
+    return cases