Random parser improvements

electronicparsers/openmx/parser.py

@@ -54,6 +54,7 @@
     Scf,
     BasisSetContainer,
     CoreHole,
+    KMesh,
 )
 from nomad.parsing.file_parser import TextParser, Quantity
 from simulationworkflowschema import (
@@ -257,6 +258,11 @@ def convert_eigenvalues(string):
             r'scf.ElectronicTemperature\s+(\S+)',
             repeats=False,
         ),
+        Quantity(
+            'scf.Kgrid',
+            r'scf.Kgrid\s+(\d+\s+\d+\s+\d+)',
+            repeats=False,
+        )
         Quantity('scf.dftD', r'scf.dftD\s+([a-z]+)', repeats=False),
         Quantity('version.dftD', r'version.dftD\s+([23])', repeats=False),
         Quantity(
@@ -726,18 +732,39 @@ def parse_method(self):
         else:
             sec_electronic.van_der_waals_method = ''
 
-    def parse_eigenvalues(self):
+    def parse_eigenvalues_and_kmesh(self):
         eigenvalues = BandEnergies()
+
+        sec_k_mesh = KMesh()
+        self.archive.run[-1].method[-1].k_mesh = sec_k_mesh
+
+        k_mesh_grid = mainfile_parser.get('scf.Kgrid')
+        if k_mesh_grid is not None:
+            sec_k_mesh.grid = k_mesh_grid
+
         self.archive.run[-1].calculation[-1].eigenvalues.append(eigenvalues)
         values = mainfile_parser.get('eigenvalues')
         if values is not None:
             kpoints = values.get('kpoints')
             if kpoints is not None:
                 eigenvalues.kpoints = kpoints
                 eigenvalues.n_kpoints = len(kpoints)
+                # OpenMX uses only inversion symmetry so every k-point except gamma-point has multiplicity of 2
+                kpoints_multiplicities = []
+                for kpoint in kpoints:
+                    if np.allclose(kpoint, [[0.0, 0.0, 0.0]], rtol=0.0):
+                        kpoints_multiplicities.append(1)
+                    else:
+                        kpoints_multiplicities.append(2)
+                sec_k_mesh.points = np.array(kpoints).astype(complex)
+                sec_k_mesh.multiplicities = kpoints_multiplicities
+                eigenvalues.kpoints_multiplicities = kpoints_multiplicities
             else:
                 eigenvalues.kpoints = [[0, 0, 0]]
                 eigenvalues.n_kpoints = 1
+                eigenvalues.kpoints_multiplicities = [1]
+                sec_k_mesh.points = [[0, 0, 0]]
+                sec_k_mesh.multiplicities = [1]
             values = values.get('eigenvalues')
             if values is not None:
                 if self.spinpolarized:
@@ -915,4 +942,4 @@ def parse(self, mainfile: str, archive: EntryArchive, logger):
         except (IndexError, AttributeError):
             pass
 
-        self.parse_eigenvalues()
+        self.parse_eigenvalues_and_kmesh()

electronicparsers/quantumespresso/parser.py

@@ -36,6 +36,7 @@
     BasisSetContainer,
     AtomParameters,
     KMesh,
+    Scf,
 )
 from runschema.system import System, Atoms
 from runschema.calculation import (
@@ -3248,6 +3249,8 @@ def parse_method(self, run):
         sec_method.dft = sec_dft
         sec_electronic = Electronic()
         sec_method.electronic = sec_electronic
+        sec_scf = Scf()
+        sec_method.scf = sec_scf
 
         starting_magnetization = run.get_header('starting_magnetization')
         spin_orbit_mode = run.get_header('spin_orbit_mode')
@@ -3260,6 +3263,8 @@ def parse_method(self, run):
         sec_kmesh.n_points = run.get_header('k_points', {}).get('nk', 1)
         sec_kmesh.points = run.get_header('k_points', {}).get('points', None)
 
+        sec_scf.threshold_energy_change = run.get_header('scf_threshold_energy_change')
+
         g_vector_sticks = run.get_header('g_vector_sticks', {}).get('Sum', None)
         if g_vector_sticks is not None:
             names = [
@@ -3330,7 +3335,6 @@ def parse_method(self, run):
 
         # other method variables
         names = [
-            'scf_threshold_energy_change',
             'x_qe_core_charge_realspace',
             'x_qe_exact_exchange_fraction',
             'x_qe_diagonalization_algorithm',

tests/test_openmxparser.py

@@ -79,6 +79,11 @@ def test_HfO2(parser):
     assert method.electronic.smearing.width == approx(K_to_J(300))
     assert method.dft.xc_functional.correlation[0].name == 'GGA_C_PBE'
     assert method.dft.xc_functional.exchange[0].name == 'GGA_X_PBE'
+    assert (method.k_mesh.grid == [10, 10, 10]).all()
+    assert np.allclose(method.k_mesh.points[0], np.array([-0.45000, -0.45000, -0.45000]).astype(complex), rtol=0.0)
+    assert np.allclose(method.k_mesh.points[499], np.array([-0.05000, 0.45000, 0.45000]).astype(complex), rtol=0.0)
+    assert method.k_mesh.multiplicities[0] == approx(2.0)
+    assert method.k_mesh.multiplicities[0] == approx(2.0)
 
     system = run.system[0]
     assert system.atoms.periodic == [True, True, True]
@@ -90,6 +95,9 @@ def test_HfO2(parser):
     assert len(system.atoms.labels) == 12
     assert system.atoms.labels[9] == 'O'
 
+    scc = run.calculation
+    assert scc[-1].eigenvalues[0].kpoints_multiplicities[0] == approx(2.0)
+
 
 def test_AlN(parser):
     """
@@ -121,6 +129,9 @@ def test_AlN(parser):
     scf = scc[3].scf_iteration
     assert len(scf) == 6
     scf[5].energy.sum_eigenvalues.value.magnitude == approx(-3.4038520917173614e-17)
+    assert len(scc[-1].eigenvalues[0].kpoints_multiplicities) == 74
+    assert scc[-1].eigenvalues[0].kpoints_multiplicities[-1] == approx(1.0)
+    assert scc[-1].eigenvalues[0].kpoints_multiplicities[0] == approx(2.0)
 
     method = run.method[0]
     assert method.electronic.n_spin_channels == 1
@@ -131,6 +142,11 @@ def test_AlN(parser):
     assert method.dft.xc_functional.exchange[0].name == 'GGA_X_PBE'
     assert method.scf.n_max_iteration == 100
     assert method.scf.threshold_energy_change.magnitude == approx(Ha_to_J(1e-7))
+    assert (method.k_mesh.grid == [7, 7, 3]).all()
+    assert np.allclose(method.k_mesh.points[0], np.array([ -0.42857, -0.42857, -0.33333]).astype(complex), rtol=0.0)
+    assert np.allclose(method.k_mesh.points[73], np.array([0.00000, -0.00000, 0.00000]).astype(complex), rtol=0.0)
+    assert np.allclose(method.k_mesh.multiplicities[0], np.array([2, 2, 2]).astype(complex), rtol=0.0)
+    assert method.k_mesh.multiplicities[73] == [1]
 
     workflow = archive.workflow2
     assert workflow.method.method == 'steepest_descent'
@@ -209,6 +225,7 @@ def test_C2N2(parser):
     assert np.shape(scc[0].forces.total.value) == (4, 3)
     assert scc[0].forces.total.value[0][0].magnitude == approx(HaB_to_N(0.10002))
     assert scc[99].forces.total.value[2][2].magnitude == approx(HaB_to_N(-0.00989))
+    assert scc[-1].eigenvalues[0].kpoints_multiplicities == approx(1.0)
 
     assert len(run.system) == 100
 
@@ -218,6 +235,8 @@ def test_C2N2(parser):
     assert method.electronic.smearing.width == approx(K_to_J(500))
     assert method.dft.xc_functional.exchange[0].name == 'LDA_X'
     assert method.dft.xc_functional.correlation[0].name == 'LDA_C_PZ'
+    assert (method.k_mesh.grid == [1, 1, 1]).all()
+    assert method.k_mesh.multiplicities[0] == approx(1.0)
 
     workflow = archive.workflow2
     assert workflow.method.thermodynamic_ensemble == 'NVT'
@@ -284,6 +303,7 @@ def test_CrO2(parser):
     assert method.dft.xc_functional.correlation[0].name == 'LDA_C_PW'
     assert method.scf.n_max_iteration == 40
     assert method.scf.threshold_energy_change.magnitude == approx(Ha_to_J(1e-7))
+    assert (method.k_mesh.grid == [5, 5, 8]).all()
 
     eigenvalues = run.calculation[-1].eigenvalues[0]
     assert eigenvalues.n_kpoints == 100
@@ -316,6 +336,7 @@ def test_graphite(parser):
     assert method.electronic.van_der_waals_method == 'G10'
     assert method.scf.n_max_iteration == 100
     assert method.scf.threshold_energy_change.magnitude == approx(Ha_to_J(1e-8))
+    assert (method.k_mesh.grid == [12, 12, 4]).all()
 
     calculation_first = run.calculation[0]
     stress_tensor_first = calculation_first.stress.total.value

tests/test_quantumespressoparser.py

@@ -37,6 +37,10 @@ def RyB_to_N(value):
     return (value * ureg.rydberg / ureg.bohr).to_base_units().magnitude
 
 
+def Ry_to_eV(value):
+    return (value * ureg.rydberg).to_base_units().magnitude
+
+
 def test_scf(parser):
     archive = EntryArchive()
     parser.parse('tests/data/quantumespresso/HO_scf/benchmark2.out', archive, None)
@@ -73,6 +77,7 @@ def test_scf(parser):
     assert sec_method.dft.xc_functional.exchange[0].name == 'GGA_X_PBE'
     assert sec_method.electronic.n_electrons[0] == 8
     assert sec_method.electronic.n_spin_channels == 1
+    assert sec_method.scf.threshold_energy_change.magnitude == approx(Ry_to_eV(1e-6))
     sec_atoms = sec_method.atom_parameters
     assert len(sec_atoms) == 2
     assert sec_atoms[1].label == 'H'
@@ -157,6 +162,7 @@ def test_multirun(parser):
     assert sec_runs[2].calculation[0].scf_iteration[
         11
     ].time_physical.magnitude == approx(1189.6)
+    assert sec_method.scf.threshold_energy_change.magnitude == approx(Ry_to_eV(1e-5))
 
 
 def test_md(parser):
@@ -168,6 +174,7 @@ def test_md(parser):
     sec_method = sec_run.method[0]
     assert len(sec_method.k_mesh.points) == 1
     assert sec_method.electronic.n_spin_channels == 1
+    assert sec_method.scf.threshold_energy_change.magnitude == approx(Ry_to_eV(1e-8))
     sec_sccs = sec_run.calculation
     assert len(sec_sccs) == 50
     assert archive.run[0].system[6].atoms.positions[1][2].magnitude == approx(
@@ -217,6 +224,7 @@ def test_vcrelax(parser):
     assert sec_method.electronic.smearing.kind == 'tetrahedra'
     assert sec_method.electronic.smearing.width is None
     assert sec_method.electronic.n_spin_channels == 1
+    assert sec_method.scf.threshold_energy_change.magnitude == approx(Ry_to_eV(1e-8))
 
 
 def test_noncolmag(parser):
@@ -243,3 +251,4 @@ def test_noncolmag(parser):
         == (0.01 * ureg.rydberg).to_base_units().magnitude
     )
     assert sec_method.electronic.n_spin_channels is None
+    assert sec_method.scf.threshold_energy_change.magnitude == approx(Ry_to_eV(1e-8))