Add tests for phono3py-load script

example/NaCl-alm/README.md

@@ -1,94 +1,32 @@
-This is the example of NaCl calculation. The supercell is 2x2x2 of the
-conventional unit cell. The VASP calculation was made for force calculations
-with 500 eV, 2x2x2 off-Gamma-centre k-point sampling mesh for the supercell, and
-PBE-sol. For dielectric constant and Born effective charges were calculated in a
-similar calculation settings with `LEPSILON = .TRUE.` and 4x4x4 off-Gamma-centre
-k-point sampling mesh.
+This is the example of NaCl calculation. Since all atoms are displaced, to
+obtain force constants, an external force constants calculator is necessary,
+i.e., build-in force constants calculator has no ability to compute force
+constants for such dataset. In this example, ALM is used. See
+https://phonopy.github.io/phonopy/setting-tags.html#alm. The easiest way to
+install ALM is to use conda.
+
+The supercell is 2x2x2 of the conventional unit cell. The VASP calculation was
+made for force calculations with 500 eV, 2x2x2 off-Gamma-centre k-point sampling
+mesh for the supercell, and PBE-sol. For dielectric constant and Born effective
+charges were calculated in a similar calculation settings with `LEPSILON =
+.TRUE.` and 4x4x4 off-Gamma-centre k-point sampling mesh.
 
 200 supercells were generated with random displacements of 0.03 A displacement
-distance.
+distance. The calculated forces, displacements, dielectric constant, and Born
+effective charges are all stored in `phono3py_params_NaCl222.yaml.xz`.
+
+Force constants are calculated by
 
 ```
-% phono3py -d --dim="2 2 2" -c POSCAR-unitcell --pa="F"
+% phono3py-load phono3py_params_NaCl222.yaml.xz -v --alm
 ```
 
-To create `fc3.hdf5` and `fc2.hdf5`,
+This calculation may require a few minutes depending on computer hardware and
+some amount of memory space. By this `fc2.hdf5` and `fc3.hdf5` are obtained. The
+lattice thermal conductivity at 300 K is calculated by
 
 ```
-% phono3py --sym-fc
+% phono3py-load phono3py_params_NaCl222.yaml.xz --mesh 50 --ts 300 --br
 ```
 
-Using 11x11x11 sampling mesh, lattice thermal conductivity is calculated by
-
-```
-% phono3py --mesh 11 11 11 --fc3 --fc2 --br
-```
-
-`kappa-m111111.hdf5` is written as the result. The lattice thermal conductivity
-is calculated as 109.0 W/m-K at 300 K. This becomes, with 19x19x19 sampling
-mesh, 123.2 W/m-K.
-
-Accumulated lattice thermal conductivity is calculated using `phono3py-kaccum`
-script.
-
-```
-% phono3py-kaccum kappa-m111111.hdf5 |tee kaccum.dat
-```
-
-`kaccum.dat` is plotted using gnuplot by
-
-```
-gnuplot> p 'kaccum.dat' i 30 u 1:2 w l, 'kaccum.dat' i 30 u 1:8 w l
-```
-
-![Si-kaccum.png](Si-kaccum.png)
-
-It is found that most of the lattice thermal conductivity owes the phonon modes
-below 6 THz.
-
-`fc2.hdf5` can be read by harmonic phonopy to rename it to force_constants.hdf5.
-The phonon band structure and DOS are plotted by
-
-```
-% ln -s fc2.hdf5 force_constants.hdf5
-% phonopy --mesh 19 19 19 --band 1/2 1/2 0 0 0 0 1/2 1/2 1/2 --hdf5 --readfc -p
-```
-
-![Si-band-DOS.png](Si-band-DOS.png)
-
-The shape of phonon DOS below 6 THz is similar to the derivative of the
-accumulated lattice thermal conductivity, i.e., the heat is conducted by the low
-frequency longitudinal-acoustic-like modes.
-
-The file `vasprun_xmls.tar.lzma` in this example contains VASP output files of
-`vasprun.xml`s that are used to generate `FORCES_FC3`. To test the `FORCES_FC3`
-generation, after decompressing this file, the following command is executed at
-current directory:
-
-```
-% phono3py --cf3 vasprun_xmls/disp-{00001..00111}/vasprun.xml
-```
-
-It is possible to combine different supercell sizes for fc2 and fc3, for which
-`FORCES_FC2` is required. Displacements for fc2 and its dataset
-(`phono3py_disp.yaml`) can be created by
-
-```
-% phono3py -d --dim 2 2 2 --dim-fc2 4 4 4 -c POSCAR-unitcell --pa auto
-```
-
-In this example directory, the dataset is renamed to
-`phono3py_disp_dimfc2.yaml`. The result of the VASP force calculation is found
-at `vasprun_xml_fc2/disp-fc2-00001/vasprun.xml`. `FORCES_FC2` is generated by
-
-```
-% phono3py phono3py_disp_dimfc2.yaml --cf2 vasprun_xml_fc2/disp-fc2-00001/vasprun.xml
-```
-
-A lattice thermal conductivity calculation is performed by, e.g.,
-
-```
-% phono3py-load phono3py_disp_dimfc2.yaml --mesh 11 11 11 --br --ts 300
-```
-
-The result is 108.0 W/m-K, and with the 19x19x19 mesh, 125.4 W/m-K.
+The result is ~7.2 W/m-K at 300 K.

phono3py/cui/phono3py_script.py

@@ -1099,7 +1099,11 @@ def main(**argparse_control):
     # warnings.simplefilter("error")
     load_phono3py_yaml = argparse_control.get("load_phono3py_yaml", False)
 
-    args, log_level = start_phono3py(**argparse_control)
+    if "args" in argparse_control:  # For pytest
+        args = argparse_control["args"]
+        log_level = args.log_level
+    else:
+        args, log_level = start_phono3py(**argparse_control)
 
     if load_phono3py_yaml:
         input_filename = None

test/cui/test_phono3py_load_script.py

@@ -0,0 +1,87 @@
+"""Tests of Phono3py API."""
+import os
+import pathlib
+from collections.abc import Sequence
+from dataclasses import dataclass, fields
+from typing import Optional
+
+import pytest
+
+from phono3py.cui.phono3py_script import main
+
+cwd = pathlib.Path(__file__).parent
+cwd_called = pathlib.Path.cwd()
+
+
+@dataclass
+class MockArgs:
+    """Mock args of ArgumentParser."""
+
+    filename: Sequence[os.PathLike]
+    conf_filename: Optional[os.PathLike] = None
+    fc_calculator: Optional[str] = None
+    force_sets_mode: bool = False
+    force_sets_to_forces_fc2_mode: bool = False
+    log_level: Optional[int] = None
+    output_yaml_filename: Optional[os.PathLike] = None
+    show_num_triplets: bool = False
+    write_grid_points: bool = False
+
+    def __iter__(self):
+        """Make self iterable to support in."""
+        return (getattr(self, field.name) for field in fields(self))
+
+
+def test_phono3py_load():
+    """Test phono3py-load script."""
+    # Check sys.exit(0)
+    argparse_control = _get_phono3py_load_args(
+        cwd / ".." / "phono3py_params_Si-111-222.yaml"
+    )
+    with pytest.raises(SystemExit) as excinfo:
+        main(**argparse_control)
+    assert excinfo.value.code == 0
+
+    # Clean files created by phono3py-load script.
+    for created_filename in ("phono3py.yaml", "fc2.hdf5", "fc3.hdf5"):
+        file_path = pathlib.Path(cwd_called / created_filename)
+        if file_path.exists():
+            file_path.unlink()
+
+
+@pytest.mark.parametrize("fc_calculator,exit_code", [(None, 1), ("alm", 0)])
+def test_phono3py_load_with_typeII_dataset(fc_calculator, exit_code):
+    """Test phono3py-load script with typeII dataset."""
+    # Check sys.exit(0)
+    if fc_calculator == "alm":
+        pytest.importorskip("alm")
+    argparse_control = _get_phono3py_load_args(
+        cwd / ".." / "phono3py_params-Si111-rd.yaml.xz", fc_calculator=fc_calculator
+    )
+    with pytest.raises(SystemExit) as excinfo:
+        main(**argparse_control)
+    assert excinfo.value.code == exit_code
+
+    # Clean files created by phono3py-load script.
+    for created_filename in ("phono3py.yaml", "fc2.hdf5", "fc3.hdf5"):
+        file_path = pathlib.Path(cwd_called / created_filename)
+        if file_path.exists():
+            file_path.unlink()
+
+
+def _get_phono3py_load_args(phono3py_yaml_filepath, fc_calculator=None):
+    # Mock of ArgumentParser.args.
+    mockargs = MockArgs(
+        filename=[phono3py_yaml_filepath],
+        fc_calculator=fc_calculator,
+        log_level=1,
+    )
+
+    # See phono3py-load script.
+    argparse_control = {
+        "fc_symmetry": True,
+        "is_nac": True,
+        "load_phono3py_yaml": True,
+        "args": mockargs,
+    }
+    return argparse_control