Implemented phonon workflow

phonopy @ 6af93535

-Subproject commit 99f576323efc2aa8ede5b63b108d9fe6901a8795
+Subproject commit 6af93535078cb43d11b3d5b950525e76b78acb74

nomad/datamodel/metainfo/public.py

@@ -1221,7 +1221,7 @@ class section_dos_fingerprint(MSection):
 
     indices = Quantity(
         type=np.dtype(np.int16),
-        shape=[2],
+        shape=['first_index_of_DOS_grid', 'last_index_of_DOS_grid'],
         description='''
         Indices used to compare DOS fingerprints of different energy ranges.
         ''',
@@ -5639,6 +5639,67 @@ class Relaxation(MSection):
         a_legacy=LegacyDefinition(name='final_calculation_ref'))
 
 
+class Phonon(MSection):
+    '''
+    Section containing the results of a phonon workflow.
+    '''
+
+    m_def = Section(validate=False, a_legacy=LegacyDefinition(name='section_phonon'))
+
+    force_calculator = Quantity(
+        type=str,
+        shape=[],
+        description='''
+        Name of the program used to calculate the forces.
+        ''',
+        a_legacy=LegacyDefinition(name='force_calculator'))
+
+    mesh_density = Quantity(
+        type=np.dtype(np.float64),
+        shape=[],
+        unit='1 / m ** 3',
+        description='''
+        Density of the k-mesh for sampling.
+        ''',
+        a_legacy=LegacyDefinition(name='mesh_density'),
+        a_search=Search())
+
+    n_imaginary_frequencies = Quantity(
+        type=int,
+        shape=[],
+        description='''
+        Number of modes with imaginary frequencies.
+        ''',
+        a_legacy=LegacyDefinition(name='n_imaginary_frequencies'),
+        a_search=Search())
+
+    random_displacements = Quantity(
+        type=bool,
+        shape=[],
+        description='''
+        Identifies if displacements are made randomly.
+        ''',
+        a_legacy=LegacyDefinition(name='random_displacements'))
+
+    with_non_analytic_correction = Quantity(
+        type=bool,
+        shape=[],
+        description='''
+        Identifies if non-analytical term corrections are applied to dynamical matrix.
+        ''',
+        a_legacy=LegacyDefinition(name='with_non_analytic_correction'),
+        a_search=Search())
+
+    with_grueneisen_parameters = Quantity(
+        type=bool,
+        shape=[],
+        description='''
+        Identifies if Grueneisen parameters are calculated.
+        ''',
+        a_legacy=LegacyDefinition(name='with_grueneisen_parameters'),
+        a_search=Search())
+
+
 class Workflow(MSection):
     '''
     Section containing the  results of a workflow.
@@ -5660,5 +5721,9 @@ class Workflow(MSection):
         sub_section=SectionProxy('Relaxation'),
         a_legacy=LegacyDefinition(name='section_relaxation'))
 
+    section_phonon = SubSection(
+        sub_section=SectionProxy('Phonon'),
+        a_legacy=LegacyDefinition(name='section_phonon'))
+
 
 m_package.__init_metainfo__()

nomad/normalizing/workflow.py

@@ -15,14 +15,13 @@
 import numpy as np
 
 from nomad.normalizing.normalizer import Normalizer
-from nomad.datamodel.metainfo.public import Workflow, Relaxation
+from nomad.datamodel.metainfo.public import Workflow, Relaxation, Phonon
 
 
-class WorkflowNormalizer(Normalizer):
-    '''
-    This normalizer performs all produces a section all data necessary for the Optimade API.
-    It assumes that the :class:`SystemNormalizer` was run before.
-    '''
+class RelaxationNormalizer(Normalizer):
+    def __init__(self, entry_archive):
+        super().__init__(entry_archive)
+
     def _get_relaxation_type(self):
         sec_system = self.section_run.section_system
         if not sec_system:
@@ -59,20 +58,20 @@ class WorkflowNormalizer(Normalizer):
 
             return 'ionic'
 
-    def normalize_relaxation(self):
-        sec_relaxation = self.entry_archive.section_workflow.section_relaxation
-        if not sec_relaxation:
-            sec_relaxation = self.entry_archive.section_workflow.m_create(Relaxation)
+    def normalize(self):
+        self.section = self.entry_archive.section_workflow.section_relaxation
+        if not self.section:
+            self.section = self.entry_archive.section_workflow.m_create(Relaxation)
 
-        if not sec_relaxation.relaxation_type:
-            sec_relaxation.relaxation_type = self._get_relaxation_type()
+        if not self.section.relaxation_type:
+            self.section.relaxation_type = self._get_relaxation_type()
 
-        if not sec_relaxation.final_calculation_ref:
+        if not self.section.final_calculation_ref:
             scc = self.section_run.section_single_configuration_calculation
             if scc:
-                sec_relaxation.final_calculation_ref = scc[-1]
+                self.section.final_calculation_ref = scc[-1]
 
-        if not sec_relaxation.final_energy_difference:
+        if not self.section.final_energy_difference:
             energies = []
             for scc in self.section_run.section_single_configuration_calculation:
                 if scc.energy_total_T0:
@@ -89,9 +88,9 @@ class WorkflowNormalizer(Normalizer):
                     pass
 
             if delta_energy:
-                sec_relaxation.final_energy_difference = delta_energy
+                self.section.final_energy_difference = delta_energy
 
-        if not sec_relaxation.final_force_maximum:
+        if not self.section.final_force_maximum:
             scc = self.section_run.section_single_configuration_calculation
             max_force = None
             if scc:
@@ -99,7 +98,39 @@ class WorkflowNormalizer(Normalizer):
                     forces = np.array(scc[-1].atom_forces)
                     max_force = np.max(np.linalg.norm(forces, axis=1))
             if max_force is not None:
-                sec_relaxation.final_force_maximum = max_force
+                self.section.final_force_maximum = max_force
+
+
+class PhononNormalizer(Normalizer):
+    def __init__(self, entry_archive):
+        super().__init__(entry_archive)
+
+    def _get_n_imaginary_frequencies(self):
+        scc = self.entry_archive.section_run[0].section_single_configuration_calculation
+        sec_band = scc[0].section_k_band
+        result = 0
+        for band_segment in sec_band[0].section_k_band_segment:
+            freq = band_segment.band_energies
+            result += np.count_nonzero(np.array(freq) < 0)
+        return result
+
+    def normalize(self):
+        self.section = self.entry_archive.section_workflow.section_phonon
+        if not self.section:
+            self.entry_archive.section_workflow.m_create(Phonon)
+
+        if not self.section.n_imaginary_frequencies:
+            # get number from bands (not complete as this is not the whole mesh)
+            self.section.n_imaginary_frequencies = self._get_n_imaginary_frequencies()
+
+
+class WorkflowNormalizer(Normalizer):
+    '''
+    This normalizer performs all produces a section all data necessary for the Optimade API.
+    It assumes that the :class:`SystemNormalizer` was run before.
+    '''
+    def __init__(self, entry_archive):
+        super().__init__(entry_archive)
 
     def normalize(self, logger=None) -> None:
         # Setup logger
@@ -124,4 +155,7 @@ class WorkflowNormalizer(Normalizer):
                 sec_workflow.workflow_type = workflow_type
 
         if sec_workflow.workflow_type in ['geometry_optimization', 'relaxation']:
-            self.normalize_relaxation()
+            RelaxationNormalizer(self.entry_archive).normalize()
+
+        elif sec_workflow.workflow_type == 'phonon':
+            PhononNormalizer(self.entry_archive).normalize()

nomad/parsing/parsers.py

@@ -25,6 +25,7 @@ from eelsparser import EelsParser
 from mpesparser import MPESParser
 from aptfimparser import APTFIMParser
 from vaspparser import VASPParser
+from phonopyparser import PhonopyParser
 
 try:
     # these packages are not available without parsing extra, which is ok, if the
@@ -116,12 +117,7 @@ parsers = [
     GenerateRandomParser(),
     TemplateParser(),
     ChaosParser(),
-    LegacyParser(
-        name='parsers/phonopy', code_name='Phonopy', code_homepage='https://phonopy.github.io/phonopy/',
-        parser_class_name='phonopyparser.PhonopyParserWrapper',
-        # mainfile_contents_re=r'',  # Empty regex since this code calls other DFT codes.
-        mainfile_name_re=(r'.*/phonopy-FHI-aims-displacement-0*1/control.in$')
-    ),
+    PhonopyParser(),
     VASPParser(),
     VaspOutcarParser(
         name='parsers/vasp-outcar', code_name='VASP', code_homepage='https://www.vasp.at/',