minor adjustments to Mesh and NumericalIntegration

nomad-coe · Nov 19, 2024 · cca109f · cca109f · github-actions · Nov 19, 2024
1 parent 646430c
commit cca109f
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Showing 2 changed files with 19 additions and 11 deletions.
diff --git a/src/nomad_simulations/schema_packages/model_method.py b/src/nomad_simulations/schema_packages/model_method.py
@@ -1224,7 +1224,7 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
 
 
 class MolecularHamiltonianSubTerms(BaseModelMethod):
-    type=Quantity(
+    type = Quantity(
         type=MEnum('coulomb', 'exchange'),
         description="""
         Typical sub-terms of the molecular hamiltonian.
@@ -1233,4 +1233,4 @@ class MolecularHamiltonianSubTerms(BaseModelMethod):
     )
 
     def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
-        super().normalize(archive, logger)
+        super().normalize(archive, logger)
diff --git a/src/nomad_simulations/schema_packages/numerical_settings.py b/src/nomad_simulations/schema_packages/numerical_settings.py
@@ -92,6 +92,12 @@ class Mesh(ArchiveSection):
         """,
     )
 
+    spacing = Quantity(
+        type=np.float64,
+        shape=['dimensionality'],
+        description='Grid spacing for equidistant meshes. Ignored for other kinds.',
+    )
+
     points = Quantity(
         type=np.complex128,
         shape=['n_points', 'dimensionality'],
@@ -117,14 +123,16 @@ class Mesh(ArchiveSection):
         In the fixed grid methods, the number of angular grid points is predetermined for
         ranges of radial grid points, while in the adaptive methods, the angular grid is adjusted
         on-the-fly for each radial point according to some accuracy criterion.
-        """
+        """,
     )
 
     def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
         super().normalize(archive, logger)
 
         if self.dimensionality not in [1, 2, 3]:
-            logger.error('`dimensionality` meshes different than 1, 2, or 3 are not supported.')
+            logger.error(
+                '`dimensionality` meshes different than 1, 2, or 3 are not supported.'
+            )
 
 
 class NumericalIntegration(NumericalSettings):
@@ -145,10 +153,10 @@ class NumericalIntegration(NumericalSettings):
     """
 
     coordinate = Quantity(
-        type=MEnum('all', 'radial', 'angular'),
+        type=MEnum('full', 'radial', 'angular'),
         description="""
-        Coordinate over which the integration is performed. `all` means the integration is performed in
-        all the space. `radial` and `angular` describe cases where the integration is performed for
+        Coordinate over which the integration is performed. `full` means the integration is performed in
+        entire space. `radial` and `angular` describe cases where the integration is performed for
         functions which can be splitted into radial and angular distributions (e.g., orbital wavefunctions).
         """,
     )
@@ -158,16 +166,16 @@ class NumericalIntegration(NumericalSettings):
         description="""
         Integration rule used. This can be any 1D Gaussian quadrature rule or multi-dimensional `angular` rules,
         e.g., Lebedev quadrature rule (see e.g., Becke, Chem. Phys. 88, 2547 (1988)).
-        """
+        """,
     )
 
-    weight_partitioning = Quantity(
+    weight_approximtion = Quantity(
         type=str,
         description="""
         Approximation applied to the weight when doing the numerical integration.
         See e.g., C. W. Murray, N. C. Handy
         and G. J. Laming, Mol. Phys. 78, 997 (1993).
-        """
+        """,
     )
 
     mesh = SubSection(sub_section=Mesh.m_def)
@@ -937,4 +945,4 @@ class GTOIntegralDecomposition(NumericalSettings):
     )
 
     def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger') -> None:
-        super().normalize(archive, logger)
+        super().normalize(archive, logger)
File	Stmts	Miss	Cover	Missing
src/nomad_simulations
__init__.py	4	2	50%	3–4
_version.py	11	2	82%	5–6
src/nomad_simulations/schema_packages
__init__.py	15	2	87%	39–41
atoms_state.py	190	21	89%	13–15, 201–204, 228, 283–284, 352–353, 355, 537, 549–550, 611–615, 630–634, 641
basis_set.py	250	29	88%	8–9, 122–133, 172–185, 244, 290, 471–475, 497–498, 542–545, 664, 695, 697
general.py	89	8	91%	4–7, 121, 185, 295–296, 306
model_method.py	273	79	71%	10–12, 171–174, 177–184, 276–277, 297, 318–339, 355–381, 384–401, 587, 780, 791, 833–840, 878, 897, 977, 1034, 1109, 1223, 1236
model_system.py	348	37	89%	45–51, 235, 254, 258, 261, 264, 290, 376–377, 454–455, 472–473, 686–689, 736–743, 917–918, 1140–1144, 1150–1151, 1159–1160, 1165, 1188
numerical_settings.py	272	64	76%	12–14, 133, 184, 254, 256–257, 260–263, 267–268, 275–278, 287–290, 294–297, 299–302, 307–310, 316–319, 506–533, 608, 643–646, 670, 673, 718, 720–723, 727, 731, 778, 782–803, 858–859, 926, 948
outputs.py	120	10	92%	9–10, 252–255, 295–298, 323, 325, 362, 381
physical_property.py	102	7	93%	20–22, 202, 331–333
variables.py	86	12	86%	8–10, 98, 121, 145, 167, 189, 211, 233, 256, 276
src/nomad_simulations/schema_packages/properties
band_gap.py	51	5	90%	8–10, 135–136
band_structure.py	123	25	80%	9–11, 232–265, 278, 285, 321–322, 325, 372–373, 378
energies.py	42	9	79%	7–9, 36, 57, 82, 103, 119, 134
fermi_surface.py	17	4	76%	7–9, 40
forces.py	22	6	73%	7–9, 36, 56, 79
greens_function.py	99	13	87%	7–9, 210–211, 214, 235–236, 239, 260–261, 264, 400
hopping_matrix.py	29	5	83%	7–9, 58, 94
permittivity.py	48	8	83%	7–9, 97–105
spectral_profile.py	260	128	51%	9–11, 57–60, 95–98, 199–300, 356–368, 393–396, 416, 421–424, 466–502, 526, 573–576, 592–593, 598–604
thermodynamics.py	75	27	64%	7–9, 35, 56, 72, 81, 90, 101, 110, 137, 147, 157, 172–174, 177, 193, 213–215, 218, 234, 254–256, 259
src/nomad_simulations/schema_packages/utils
utils.py	79	16	80%	8–11, 65–74, 83–84, 89, 92, 169–170
TOTAL	2616	519	80%