Merge pull request #271 from phonopy/pmlp-cli-test

Add pypolymlp CLI test

.github/workflows/phono3py-pytest-conda-mkl-phphmtblas.yml

@@ -35,7 +35,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..

.github/workflows/phono3py-pytest-conda-mkl-v2.yml

@@ -35,7 +35,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..

.github/workflows/phono3py-pytest-conda-mkl.yml

@@ -35,7 +35,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..

.github/workflows/phono3py-pytest-conda-numpy2.yml

@@ -35,14 +35,14 @@ jobs:
     - name: Install symfc develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/symfc/symfc.git
+        git clone https://github.com/symfc/symfc.git
         cd symfc
         pip install -e . -vvv
         cd ..
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..

.github/workflows/phono3py-pytest-conda-phphmtblas.yml

@@ -28,14 +28,14 @@ jobs:
     - name: Install symfc develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/symfc/symfc.git
+        git clone https://github.com/symfc/symfc.git
         cd symfc
         pip install -e . -vvv
         cd ..
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..

.github/workflows/phono3py-pytest-conda.yml

@@ -28,7 +28,7 @@ jobs:
     - name: Install phonopy develop branch
       run: |
         conda activate test
-        git clone --depth 1 https://github.com/phonopy/phonopy.git
+        git clone https://github.com/phonopy/phonopy.git
         cd phonopy
         pip install -e . -vvv
         cd ..

phono3py/api_phono3py.py

@@ -2209,7 +2209,11 @@ def develop_mlp(
         else:
             _params = params
 
-        if _params.ntrain is not None and _params.ntest is not None:
+        if (
+            _params is not None
+            and _params.ntrain is not None
+            and _params.ntest is not None
+        ):
             ntrain = _params.ntrain
             ntest = _params.ntest
             disps = self._mlp_dataset["displacements"]
@@ -2248,7 +2252,7 @@ def develop_mlp(
             verbose=self._log_level - 1 > 0,
         )
 
-    def load_mlp(self, filename: str = "pypolymlp.mlp"):
+    def load_mlp(self, filename: str = "phono3py.pmlp"):
         """Load machine learning potential of pypolymlp."""
         self._mlp = load_polymlp(filename=filename)
 

phono3py/cui/create_force_constants.py

@@ -514,7 +514,7 @@ def run_pypolymlp_to_compute_forces(
     displacement_distance: Optional[float] = None,
     number_of_snapshots: Optional[int] = None,
     random_seed: Optional[int] = None,
-    mlp_filename: str = "pypolymlp.mlp",
+    mlp_filename: str = "phono3py.pmlp",
     log_level: int = 0,
 ):
     """Run pypolymlp to compute forces."""
@@ -533,6 +533,9 @@ def run_pypolymlp_to_compute_forces(
         if log_level:
             print("Developing MLPs by pypolymlp...", flush=True)
         ph3py.develop_mlp(params=mlp_params)
+        ph3py.mlp.save_mlp(filename=mlp_filename)
+        if log_level:
+            print(f'MLPs were written into "{mlp_filename}"', flush=True)
     else:
         if pathlib.Path(mlp_filename).exists():
             if log_level:
@@ -581,7 +584,6 @@ def run_pypolymlp_to_compute_forces(
         raise RuntimeError("Displacements are not set. Run generate_displacements.")
 
     ph3py.evaluate_mlp()
-    ph3py.save("phono3py_mlp_eval_dataset.yaml")
 
 
 def run_pypolymlp_to_compute_phonon_forces(

phono3py/cui/phono3py_script.py

@@ -163,6 +163,14 @@ def finalize_phono3py(
     else:
         yaml_filename = filename
 
+    if phono3py.mlp_dataset is not None:
+        mlp_eval_filename = "phono3py_mlp_eval_dataset.yaml"
+        if log_level:
+            print(
+                f'Dataset generated using MMLPs was written in "{mlp_eval_filename}".'
+            )
+        phono3py.save(mlp_eval_filename)
+
     _physical_units = get_default_physical_units(phono3py.calculator)
 
     ph3py_yaml = Phono3pyYaml(

test/api/test_api_phono3py.py

@@ -173,6 +173,7 @@ def test_type2_forces_energies_setter_Si(si_111_222_rd: Phono3py):
 def test_use_pypolymlp_mgo(mgo_222rd_444rd: Phono3py):
     """Test use_pypolymlp in produce_fc3."""
     pytest.importorskip("pypolymlp")
+    pytest.importorskip("symfc")
 
     ph3_in = mgo_222rd_444rd
     ph3 = Phono3py(

test/cui/test_phono3py_load_script.py

@@ -36,6 +36,7 @@ class MockArgs:
     is_bterta: Optional[bool] = None
     mesh_numbers: Optional[Sequence] = None
     temperatures: Optional[Sequence] = None
+    use_pypolymlp: bool = False
     input_filename = None
     output_filename = None
     input_output_filename = None
@@ -114,13 +115,62 @@ def test_phono3py_with_QE_calculator(load_phono3py_yaml):
             file_path.unlink()
 
 
+def test_phono3py_load_with_pypolymlp_si():
+    """Test phono3py-load script with pypolymlp.
+
+    First run generates phono3py.pmlp.
+    Second run uses phono3py.pmlp.
+
+    """
+    pytest.importorskip("pypolymlp")
+    pytest.importorskip("symfc")
+
+    argparse_control = _get_phono3py_load_args(
+        cwd / ".." / "phono3py_params_Si-111-222-rd.yaml.xz",
+        fc_calculator="symfc",
+        use_pypolymlp=True,
+    )
+
+    with pytest.raises(SystemExit) as excinfo:
+        main(**argparse_control)
+    assert excinfo.value.code == 0
+
+    # phono3py.yaml and fc2.hd5 are used in the next run. So they are not deleted.
+    for created_filename in ("fc3.hdf5", "phono3py_mlp_eval_dataset.yaml"):
+        file_path = pathlib.Path(cwd_called / created_filename)
+        if file_path.exists():
+            file_path.unlink()
+
+    argparse_control = _get_phono3py_load_args(
+        cwd_called / "phono3py.yaml",
+        fc_calculator="symfc",
+        use_pypolymlp=True,
+    )
+
+    with pytest.raises(SystemExit) as excinfo:
+        main(**argparse_control)
+    assert excinfo.value.code == 0
+
+    for created_filename in (
+        "phono3py.yaml",
+        "fc2.hdf5",
+        "fc3.hdf5",
+        "phono3py.pmlp",
+        "phono3py_mlp_eval_dataset.yaml",
+    ):
+        file_path = pathlib.Path(cwd_called / created_filename)
+        if file_path.exists():
+            file_path.unlink()
+
+
 def _get_phono3py_load_args(
     phono3py_yaml_filepath: Union[str, pathlib.Path],
     fc_calculator: Optional[str] = None,
     load_phono3py_yaml: bool = True,
     is_bterta: bool = False,
     temperatures: Optional[Sequence] = None,
     mesh_numbers: Optional[Sequence] = None,
+    use_pypolymlp: bool = False,
 ):
     # Mock of ArgumentParser.args.
     if load_phono3py_yaml:
@@ -130,6 +180,7 @@ def _get_phono3py_load_args(
             is_bterta=is_bterta,
             temperatures=temperatures,
             mesh_numbers=mesh_numbers,
+            use_pypolymlp=use_pypolymlp,
             log_level=1,
         )
     else:
@@ -141,6 +192,7 @@ def _get_phono3py_load_args(
             is_bterta=is_bterta,
             temperatures=temperatures,
             mesh_numbers=mesh_numbers,
+            use_pypolymlp=use_pypolymlp,
         )
 
     # See phono3py-load script.