Enabled cutoff-pair-distance with comapct fc

phono3py/cui/load.py

@@ -78,7 +78,7 @@ def load(
     store_dense_svecs=True,
     symprec=1e-5,
     log_level=0,
-):
+) -> Phono3py:
     """Create Phono3py instance from parameters and/or input files.
 
     "phono3py_yaml"-like file is parsed unless crystal structure information

phono3py/phonon3/fc3.py

@@ -84,7 +84,7 @@ def get_fc3(
         disp_dataset,
         fc2,
         symmetry,
-        is_compact_fc=is_compact_fc,
+        is_compact_fc=(is_compact_fc and "cutoff_distance" not in disp_dataset),
         verbose=verbose,
     )
     if verbose:
@@ -95,7 +95,7 @@ def get_fc3(
     lattice = supercell.cell.T
     permutations = symmetry.atomic_permutations
 
-    if is_compact_fc:
+    if is_compact_fc and "cutoff_distance" not in disp_dataset:
         s2p_map = primitive.s2p_map
         p2s_map = primitive.p2s_map
         p2p_map = primitive.p2p_map
@@ -124,9 +124,6 @@ def get_fc3(
                 "Cutting-off fc3 (cut-off distance: %f)"
                 % disp_dataset["cutoff_distance"]
             )
-        if is_compact_fc:
-            print("cutoff_fc3 doesn't support compact-fc3 yet.")
-            raise ValueError
         _cutoff_fc3_for_cutoff_pairs(
             fc3, supercell, disp_dataset, symmetry, verbose=verbose
         )
@@ -134,6 +131,11 @@ def get_fc3(
     if is_compact_fc:
         p2s_map = primitive.p2s_map
         fc2 = np.array(fc2[p2s_map], dtype="double", order="C")
+        if "cutoff_distance" in disp_dataset:
+            fc3_shape = (len(p2s_map), fc3.shape[1], fc3.shape[2])
+            fc3_cfc = np.zeros(fc3_shape, dtype="double", order="C")
+            fc3_cfc = fc3[p2s_map]
+            fc3 = fc3_cfc
 
     return fc2, fc3
 
@@ -278,7 +280,7 @@ def set_translational_invariance_fc3(fc3):
         _set_translational_invariance_fc3_per_index(fc3, index=i)
 
 
-def set_translational_invariance_compact_fc3(fc3, primitive):
+def set_translational_invariance_compact_fc3(fc3, primitive: Primitive):
     """Enforce translational symmetry to compact fc3."""
     try:
         import phono3py._phono3py as phono3c

test/conftest.py

@@ -227,7 +227,7 @@ def nacl_pbe_compact_fc(request):
 
 @pytest.fixture(scope="session")
 def nacl_pbe_cutoff_fc3(request):
-    """Return Phono3py instance of NaCl 2x2x2.
+    """Return Phono3py instance of NaCl 2x2x2 with cutoff-pair-distance.
 
     * cutoff pair with 5
 
@@ -253,7 +253,57 @@ def nacl_pbe_cutoff_fc3(request):
             second_atoms["forces"] = forces[count]
             count += 1
     ph3.dataset = dataset
-    ph3.produce_fc3(symmetrize_fc3r=True)
+    ph3.produce_fc3()
+    # ph3.produce_fc3(symmetrize_fc3r=True)
+    return ph3
+
+
+@pytest.fixture(scope="session")
+def nacl_pbe_cutoff_fc3_all_forces(request):
+    """Return Phono3py instance of NaCl 2x2x2 with cutoff-pair-distance.
+
+    * cutoff pair with 5
+    * All forces are set.
+
+    """
+    yaml_filename = os.path.join(current_dir, "phono3py_params_NaCl222.yaml.xz")
+    enable_v2 = request.config.getoption("--v1")
+    ph3 = phono3py.load(
+        yaml_filename,
+        store_dense_gp_map=enable_v2,
+        store_dense_svecs=enable_v2,
+        produce_fc=False,
+        log_level=1,
+    )
+    forces = ph3.forces
+    ph3.generate_displacements(cutoff_pair_distance=5)
+    ph3.forces = forces
+    ph3.produce_fc3()
+    return ph3
+
+
+@pytest.fixture(scope="session")
+def nacl_pbe_cutoff_fc3_compact_fc(request):
+    """Return Phono3py instance of NaCl 2x2x2 with cutoff-pair-distance.
+
+    * cutoff pair with 5
+    * All forces are set.
+    * Compact FC
+
+    """
+    yaml_filename = os.path.join(current_dir, "phono3py_params_NaCl222.yaml.xz")
+    enable_v2 = request.config.getoption("--v1")
+    ph3 = phono3py.load(
+        yaml_filename,
+        store_dense_gp_map=enable_v2,
+        store_dense_svecs=enable_v2,
+        produce_fc=False,
+        log_level=1,
+    )
+    forces = ph3.forces
+    ph3.generate_displacements(cutoff_pair_distance=5)
+    ph3.forces = forces
+    ph3.produce_fc3(is_compact_fc=True)
     return ph3
 
 

test/phonon3/test_fc3.py

@@ -1,18 +1,55 @@
 """Tests for fc3."""
 import numpy as np
 
+from phono3py import Phono3py
 from phono3py.phonon3.fc3 import cutoff_fc3_by_zero
 
 
-def test_cutoff_fc3(nacl_pbe_cutoff_fc3, nacl_pbe):
-    """Test for cutoff pair option."""
+def test_cutoff_fc3(nacl_pbe_cutoff_fc3: Phono3py, nacl_pbe: Phono3py):
+    """Test for cutoff-pair-distance option.
+
+    Only supercell forces that satisfy specified cutoff pairs are set in
+    dataset preparation.
+
+    """
     fc3_cut = nacl_pbe_cutoff_fc3.fc3
     fc3 = nacl_pbe.fc3
     abs_delta = np.abs(fc3_cut - fc3).sum()
-    assert np.abs(1894.2058837 - abs_delta) < 1e-3
+
+    assert fc3.shape == (64, 64, 64, 3, 3, 3)
+    assert np.abs(1901.0248613 - abs_delta) < 1e-3
 
 
-def test_cutoff_fc3_zero(nacl_pbe):
+def test_cutoff_fc3_all_forces(
+    nacl_pbe_cutoff_fc3: Phono3py, nacl_pbe_cutoff_fc3_all_forces: Phono3py
+):
+    """Test for cutoff-pair-distance option with all forces are set.
+
+    By definition, displacement datasets are kept unchanged when
+    cutoff-pair-distance is specified.
+
+    This test checkes only supercell forces that satisfy specified cutoff pairs
+    are chosen properly.
+
+    """
+    fc3_cut = nacl_pbe_cutoff_fc3.fc3
+    fc3_cut_all_forces = nacl_pbe_cutoff_fc3_all_forces.fc3
+    np.testing.assert_allclose(fc3_cut, fc3_cut_all_forces, atol=1e-8)
+
+
+def test_cutoff_fc3_compact_fc(
+    nacl_pbe_cutoff_fc3_compact_fc: Phono3py, nacl_pbe_cutoff_fc3: Phono3py
+):
+    """Test for cutoff-pair-distance option with compact-fc."""
+    fc3_cfc = nacl_pbe_cutoff_fc3_compact_fc.fc3
+    fc3_full = nacl_pbe_cutoff_fc3.fc3
+    p2s_map = nacl_pbe_cutoff_fc3.primitive.p2s_map
+    assert fc3_cfc.shape == (2, 64, 64, 3, 3, 3)
+    assert fc3_full.shape == (64, 64, 64, 3, 3, 3)
+    np.testing.assert_allclose(fc3_cfc, fc3_full[p2s_map], atol=1e-8)
+
+
+def test_cutoff_fc3_zero(nacl_pbe: Phono3py):
     """Test for abrupt cut of fc3 by distance."""
     ph = nacl_pbe
     fc3 = ph.fc3.copy()
@@ -21,7 +58,7 @@ def test_cutoff_fc3_zero(nacl_pbe):
     assert np.abs(5259.2234163 - abs_delta) < 1e-3
 
 
-def test_cutoff_fc3_zero_compact_fc(nacl_pbe_compact_fc):
+def test_cutoff_fc3_zero_compact_fc(nacl_pbe_compact_fc: Phono3py):
     """Test for abrupt cut of fc3 by distance."""
     ph = nacl_pbe_compact_fc
     fc3 = ph.fc3.copy()
@@ -30,7 +67,7 @@ def test_cutoff_fc3_zero_compact_fc(nacl_pbe_compact_fc):
     assert np.abs(164.359250 - abs_delta) < 1e-3
 
 
-def test_fc3(si_pbesol_111):
+def test_fc3(si_pbesol_111: Phono3py):
     """Test fc3 with Si PBEsol 1x1x1."""
     ph = si_pbesol_111
     fc3_ref = [
@@ -54,7 +91,7 @@ def test_fc3(si_pbesol_111):
 
 
 # @pytest.mark.skipif(not FC_CALCULATOR_ALM_AVAILABLE, reason="not found ALM package")
-def test_fc3_alm(si_pbesol_111_alm):
+def test_fc3_alm(si_pbesol_111_alm: Phono3py):
     """Test fc3 with Si PBEsol 1x1x1 calcualted using ALM."""
     ph = si_pbesol_111_alm
     fc3_ref = [