Merge branch 'materialsproject:master' into ele_band_color

materialsproject · Jan 15, 2023 · a0811e7 · a0811e7
2 parents 00dc5d3 + 00609e5
commit a0811e7
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diff --git a/README.md b/README.md
@@ -30,7 +30,7 @@ Pymatgen is free to use. However, we also welcome your help to improve this libr
 - Bug reports or feature requests: Please submit a [GitHub Issue](https://github.com/materialsproject/pymatgen/issues).
 - Code contributions via [pull requests](https://github.com/materialsproject/pymatgen/pulls) are welcome.
 - For help with usage that is unrelated to bugs or feature requests, please use the `pymatgen` [MatSci page](https://discuss.matsci.org/c/pymatgen).
-- [`matgenb`](https://matgenb.materialsvirtuallab.org) provides some Jupyter notebooks demonstrating functionality.
+- [`matgenb`](https://github.com/materialsvirtuallab/matgenb#introduction) provides some Jupyter notebooks demonstrating functionality.
 - Follow us on [Twitter](https://twitter.com/pymatgen) to get news and tips.
 
 ## Why use pymatgen?

diff --git a/docs_rst/introduction.rst b/docs_rst/introduction.rst
@@ -48,7 +48,7 @@ reports. The following are resources for pymatgen:
 * Code contributions via `pull requests <https://github.com/materialsproject/pymatgen/pulls>`_ welcome.
 * For help with usage that are unrelated to bugs or feature requests, please use the pymatgen `Discourse page
   <https://discuss.matsci.org/c/pymatgen>`_.
-* `matgenb <http://matgenb.materialsvirtuallab.org>`_ provides some Jupyter notebooks demonstrating functionality.
+* `matgenb <https://github.com/materialsvirtuallab/matgenb#introduction>`_ provides some Jupyter notebooks demonstrating functionality.
 * Follow us on `Twitter <http://twitter.com/pymatgen>`_ to get news and tips.
 
     *The code is mightier than the pen.*

diff --git a/pymatgen/core/composition.py b/pymatgen/core/composition.py
@@ -643,6 +643,23 @@ def from_dict(cls, d) -> Composition:
         """
         return cls(d)
 
+    @classmethod
+    def from_weight_dict(cls, weight_dict) -> Composition:
+        """
+        Creates a Composition based on a dict of atomic fractions calculated
+        from a dict of weight fractions. Allows for quick creation of the class
+        from weight-based notations commonly used in the industry, such as
+        Ti6V4Al and Ni60Ti40.
+
+        Args:
+            weight_dict (dict): {symbol: weight_fraction} dict.
+        """
+
+        weight_sum = sum([val / Element(el).atomic_mass for el, val in weight_dict.items()])
+        comp_dict = {el: val / Element(el).atomic_mass / weight_sum for el, val in weight_dict.items()}
+
+        return cls(comp_dict)
+
     def get_el_amt_dict(self) -> dict[str, float]:
         """
         Returns:
@@ -674,6 +691,15 @@ def to_reduced_dict(self) -> dict:
         """
         return self.get_reduced_composition_and_factor()[0].as_dict()
 
+    @property
+    def to_weight_dict(self) -> dict:
+        """
+        Returns:
+            Dict with weight fraction of each component
+            {"Ti": 0.90, "V": 0.06, "Al": 0.04}
+        """
+        return {str(el): self.get_wt_fraction(el) for el in self.elements}
+
     @property
     def to_data_dict(self) -> dict:
         """

diff --git a/pymatgen/core/tests/test_composition.py b/pymatgen/core/tests/test_composition.py
@@ -306,6 +306,22 @@ def test_from_dict(self):
         comp2 = Composition.from_dict(comp.as_dict())
         assert comp == comp2
 
+    def test_from_weight_dict(self):
+        weight_dict_list = [{"Ti": 90, "V": 6, "Al": 4}, {"Ni": 60, "Ti": 40}, {"H": 0.1119, "O": 0.8881}]
+        formula_list = ["Ti87.6 V5.5 Al6.9", "Ti44.98 Ni55.02", "H2O"]
+
+        for weight_dict, formula in zip(weight_dict_list, formula_list):
+            c1 = Composition(formula).fractional_composition
+            c2 = Composition.from_weight_dict(weight_dict).fractional_composition
+            assert set(c1.elements) == set(c2.elements)
+            for el in c1.elements:
+                assert c1[el] == pytest.approx(c2[el], abs=1e-3)
+
+    def test_tofrom_weight_dict(self):
+        for c in self.comp:
+            c2 = Composition().from_weight_dict(c.to_weight_dict)
+            c.almost_equals(c2)
+
     def test_as_dict(self):
         c = Composition.from_dict({"Fe": 4, "O": 6})
         d = c.as_dict()

diff --git a/pymatgen/electronic_structure/tests/test_bandstructure.py b/pymatgen/electronic_structure/tests/test_bandstructure.py
@@ -70,7 +70,7 @@ def test_from_dict(self):
         self.assertEqual(kpoint.label, "X")
 
 
-class BandStructureSymmLine_test(PymatgenTest):
+class BandStructureSymmLineTest(PymatgenTest):
     def setUp(self):
         self.bs = loadfn(os.path.join(PymatgenTest.TEST_FILES_DIR, "Cu2O_361_bandstructure.json"))
         self.bs2 = loadfn(os.path.join(PymatgenTest.TEST_FILES_DIR, "CaO_2605_bandstructure.json"))
@@ -213,12 +213,29 @@ def test_get_sym_eq_kpoints_and_degeneracy(self):
         self.assertTrue([0.0, 0.0, 0.0] in vbm_eqs)
 
     def test_as_dict(self):
-        s = json.dumps(self.bs.as_dict())
-        self.assertIsNotNone(s)
-        s = json.dumps(self.bs2.as_dict())
-        self.assertIsNotNone(s)
-        s = json.dumps(self.bs_spin.as_dict())
-        self.assertIsNotNone(s)
+        expected_keys = {
+            "@module",
+            "@class",
+            "lattice_rec",
+            "efermi",
+            "kpoints",
+            "bands",
+            "is_metal",
+            "vbm",
+            "cbm",
+            "band_gap",
+            "labels_dict",
+            "is_spin_polarized",
+            "projections",
+            # "structure",  # not always present
+            "branches",
+        }
+        d1 = self.bs.as_dict()
+        assert set(d1) >= expected_keys, f"{expected_keys - set(d1)=}"
+        d2 = self.bs2.as_dict()
+        assert set(d2) >= expected_keys, f"{expected_keys - set(d2)=}"
+        d3 = self.bs_spin.as_dict()
+        assert set(d3) >= expected_keys, f"{expected_keys - set(d3)=}"
 
     def test_old_format_load(self):
         with open(os.path.join(PymatgenTest.TEST_FILES_DIR, "bs_ZnS_old.json")) as f:
@@ -252,7 +269,7 @@ def test_vasprun_bs(self):
         bs.get_projection_on_elements()
 
 
-class LobsterBandStructureSymmLine_test(PymatgenTest):
+class LobsterBandStructureSymmLineTest(PymatgenTest):
     def setUp(self):
         warnings.simplefilter("ignore")
         with open(

diff --git a/test_files/.pytest-split-durations b/test_files/.pytest-split-durations
@@ -1127,33 +1127,33 @@
     "pymatgen/core/tests/test_units.py::FloatWithUnitTest::test_unitized": 0.0010557089990470558,
     "pymatgen/core/tests/test_units.py::UnitTest::test_init": 0.00048183402395807207,
     "pymatgen/core/tests/test_xcfunc.py::LibxcFuncTest::test_xcfunc_api": 0.000498748995596543,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLine_test::test_as_dict": 0.10654545793659054,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLine_test::test_basic": 0.41333766595926136,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLine_test::test_get_band_gap": 0.3354746660334058,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLine_test::test_get_branch": 0.047333666996564716,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLine_test::test_get_cbm": 0.048969583003781736,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLine_test::test_get_direct_band_gap": 0.04812708401004784,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLine_test::test_get_direct_band_gap_dict": 0.048522499011596665,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLine_test::test_get_sym_eq_kpoints_and_degeneracy": 0.16099829101585783,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLine_test::test_get_vbm": 0.048561333009274676,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLine_test::test_is_metal": 0.048073498968733475,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLine_test::test_old_format_load": 0.40718304202891886,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLine_test::test_properties": 0.04850958302267827,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLineTest::test_as_dict": 0.10654545793659054,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLineTest::test_basic": 0.41333766595926136,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLineTest::test_get_band_gap": 0.3354746660334058,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLineTest::test_get_branch": 0.047333666996564716,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLineTest::test_get_cbm": 0.048969583003781736,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLineTest::test_get_direct_band_gap": 0.04812708401004784,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLineTest::test_get_direct_band_gap_dict": 0.048522499011596665,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLineTest::test_get_sym_eq_kpoints_and_degeneracy": 0.16099829101585783,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLineTest::test_get_vbm": 0.048561333009274676,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLineTest::test_is_metal": 0.048073498968733475,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLineTest::test_old_format_load": 0.40718304202891886,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::BandStructureSymmLineTest::test_properties": 0.04850958302267827,
     "pymatgen/electronic_structure/tests/test_bandstructure.py::KpointTest::test_as_dict": 0.0004644579894375056,
     "pymatgen/electronic_structure/tests/test_bandstructure.py::KpointTest::test_from_dict": 0.0003553740098141134,
     "pymatgen/electronic_structure/tests/test_bandstructure.py::KpointTest::test_properties": 0.00022700100089423358,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLine_test::test_as_dict": 0.07780262498999946,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLine_test::test_basic": 2.6535320830298588,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLine_test::test_get_band_gap": 0.03351566698984243,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLine_test::test_get_branch": 0.029398249986115843,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLine_test::test_get_cbm": 0.029687250062124804,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLine_test::test_get_direct_band_gap": 0.02957983303349465,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLine_test::test_get_direct_band_gap_dict": 0.028597293014172465,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLine_test::test_get_sym_eq_kpoints_and_degeneracy": 0.030959791998611763,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLine_test::test_get_vbm": 0.02978300000540912,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLine_test::test_is_metal": 0.028640333970542997,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLine_test::test_old_format_load": 0.038196709007024765,
-    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLine_test::test_proj_bandstructure_plot": 4.267984291975154,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLineTest::test_as_dict": 0.07780262498999946,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLineTest::test_basic": 2.6535320830298588,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLineTest::test_get_band_gap": 0.03351566698984243,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLineTest::test_get_branch": 0.029398249986115843,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLineTest::test_get_cbm": 0.029687250062124804,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLineTest::test_get_direct_band_gap": 0.02957983303349465,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLineTest::test_get_direct_band_gap_dict": 0.028597293014172465,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLineTest::test_get_sym_eq_kpoints_and_degeneracy": 0.030959791998611763,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLineTest::test_get_vbm": 0.02978300000540912,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLineTest::test_is_metal": 0.028640333970542997,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLineTest::test_old_format_load": 0.038196709007024765,
+    "pymatgen/electronic_structure/tests/test_bandstructure.py::LobsterBandStructureSymmLineTest::test_proj_bandstructure_plot": 4.267984291975154,
     "pymatgen/electronic_structure/tests/test_bandstructure.py::ReconstructBandStructureTest::test_reconstruct_band_structure": 0.025210416002664715,
     "pymatgen/electronic_structure/tests/test_bandstructure.py::ReconstructBandStructureTest::test_vasprun_bs": 1.0287437920051161,
     "pymatgen/electronic_structure/tests/test_boltztrap.py::BoltztrapAnalyzerTest::test_extreme": 0.00022050002007745206,
@@ -2375,4 +2375,4 @@
     "pymatgen/util/tests/test_typing.py::test_vector_like": 0.00013479203335009515,
     "pymatgen/vis/tests/test_plotters.py::SpectrumPlotterTest::test_get_plot": 0.07970808498794213,
     "pymatgen/vis/tests/test_plotters.py::SpectrumPlotterTest::test_get_stacked_plot": 0.02657462502247654
-}
+}