Merge pull request #53 from nomad-coe/merging_TB_and_TightBinding

Merging TB and TightBinding: DFTB+ and xTB parsers

atomisticparsers/bopfox/metainfo/bopfox.py

@@ -172,6 +172,17 @@ class Model(simulation.method.Model):
         ''')
 
 
+class xTB(simulation.method.xTB):
+
+    m_def = Section(validate=False, extends_base_section=True)
+
+    x_bopfox_parameters = Quantity(
+        type=JSON,
+        shape=[],
+        description='''
+        ''')
+
+
 class AtomParameters(simulation.method.AtomParameters):
 
     m_def = Section(validate=False, extends_base_section=True)

atomisticparsers/bopfox/parser.py

@@ -24,7 +24,7 @@
 from nomad.parsing.file_parser import TextParser, Quantity, DataTextParser
 from nomad.datamodel.metainfo.simulation.run import Run, Program
 from nomad.datamodel.metainfo.simulation.method import (
-    Method, TB, TBModel, ForceField, Model, Interaction
+    Method, TB, xTB, ForceField, Model, Interaction
 )
 from nomad.datamodel.metainfo.simulation.system import System, Atoms
 from nomad.datamodel.metainfo.simulation.calculation import (
@@ -345,7 +345,7 @@ def parse(self, filepath, archive, logger):
         self.init_parser()
 
         sec_run = archive.m_create(Run)
-        sec_run.program = Program(version=self.mainfile_parser.get('program_version'))
+        sec_run.program = Program(name='BOPfox', version=self.mainfile_parser.get('program_version'))
 
         sec_method = sec_run.m_create(Method)
         parameters = self.mainfile_parser.get_simulation_parameters()
@@ -358,11 +358,9 @@ def parse(self, filepath, archive, logger):
                 # bop uses a tight-binding model
                 tb = model.parameters.get('version', 'bop').lower() in ['bop', 'tight-binding']
                 if tb:
-                    sec_method_type = sec_method.m_create(TB)
-                    sec_model = sec_method_type.m_create(TBModel)
+                    sec_model = sec_method.m_create(TB).m_create(xTB)
                 else:
-                    sec_method_type = sec_method.m_create(ForceField)
-                    sec_model = sec_method_type.m_create(Model)
+                    sec_model = sec_method.m_create(ForceField).m_create(Model)
 
                 sec_model.name = model.name
                 sec_model.x_bopfox_parameters = model.parameters

atomisticparsers/dftbplus/metainfo/dftbplus.py

@@ -19,8 +19,7 @@
 import numpy as np            # pylint: disable=unused-import
 
 from nomad.metainfo import (  # pylint: disable=unused-import
-    MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
-    Reference, JSON
+    Package, Quantity, Section, SubSection, JSON
 )
 from nomad.datamodel.metainfo import simulation
 
@@ -153,7 +152,7 @@ class Energy(simulation.calculation.Energy):
     x_dftbp_force_related = SubSection(simulation.calculation.EnergyEntry.m_def)
 
 
-class Method(simulation.method.Method):
+class TB(simulation.method.TB):
 
     m_def = Section(validate=False, extends_base_section=True)
 
@@ -164,11 +163,6 @@ class Method(simulation.method.Method):
         -
         ''')
 
-
-class TB(simulation.method.TB):
-
-    m_def = Section(validate=False, extends_base_section=True)
-
     x_dftbp_n_sk_files = Quantity(
         type=np.dtype(np.int32),
         shape=[],

atomisticparsers/dftbplus/parser.py

@@ -353,8 +353,9 @@ def parse_system(source):
             setattr(sec_run, f'x_dftbp_{key}', self.out_parser.get(key))
 
         sec_method = sec_run.m_create(Method)
-        sec_method.x_dftbp_input_parameters = input_parameters
         sec_tb = sec_method.m_create(TB)
+        sec_tb.name = 'DFTB'
+        sec_tb.x_dftbp_input_parameters = input_parameters
         sec_tb.x_dftbp_sk_files = self.out_parser.sk_files
 
         for step in self.out_parser.get('step', []):

atomisticparsers/xtb/metainfo/xtb.py

@@ -19,8 +19,7 @@
 import numpy as np            # pylint: disable=unused-import
 
 from nomad.metainfo import (  # pylint: disable=unused-import
-    MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
-    Reference, JSON
+    Package, Quantity, Section, SubSection, JSON
 )
 from nomad.datamodel.metainfo import simulation
 
@@ -39,7 +38,7 @@ class Run(simulation.method.Method):
         ''')
 
 
-class Method(simulation.method.Method):
+class TB(simulation.method.TB):
 
     m_def = Section(validate=False, extends_base_section=True)
 

atomisticparsers/xtb/parser.py

@@ -26,7 +26,7 @@
 from nomad.units import ureg
 from nomad.parsing.file_parser import Quantity, TextParser
 from nomad.datamodel.metainfo.simulation.run import Run, Program, TimeRun
-from nomad.datamodel.metainfo.simulation.method import Method, TB, TBModel, Interaction
+from nomad.datamodel.metainfo.simulation.method import Method, TB, xTB, Interaction
 from nomad.datamodel.metainfo.simulation.system import System, Atoms
 from nomad.datamodel.metainfo.simulation.calculation import (
     Calculation, ScfIteration, Energy, EnergyEntry, BandEnergies, Multipoles, MultipolesEntry
@@ -584,27 +584,26 @@ def parse_method(self, section):
             return
 
         sec_method = self.archive.run[-1].m_create(Method)
-        # calculation paraeters
         parameters = {p[0]: p[1] for p in self.out_parser.get(section, {}).get('setup', {}).get('parameter', [])}
-        sec_method.x_xtb_setup = parameters
-        # tight-binding model
-        sec_method.tb = TB()
-        sec_tb_model = sec_method.tb.m_create(TBModel)
-        sec_tb_model.name = section
+        sec_tb = sec_method.m_create(TB)
+        sec_tb.name = 'xTB'
+        sec_tb.x_xtb_setup = parameters
+        sec_xtb = sec_tb.m_create(xTB)
+        sec_xtb.name = section
 
         if model.get('reference') is not None:
-            sec_tb_model.reference = model.reference
+            sec_xtb.reference = model.reference
 
         for contribution in model.get('contribution', []):
             name = contribution.name.lower()
             if name == 'hamiltonian':
-                sec_interaction = sec_tb_model.m_create(Interaction, TBModel.hamiltonian)
+                sec_interaction = sec_xtb.m_create(Interaction, xTB.hamiltonian)
             elif name == 'coulomb':
-                sec_interaction = sec_tb_model.m_create(Interaction, TBModel.coulomb)
+                sec_interaction = sec_xtb.m_create(Interaction, xTB.coulomb)
             elif name == 'repulsion':
-                sec_interaction = sec_tb_model.m_create(Interaction, TBModel.repulsion)
+                sec_interaction = sec_xtb.m_create(Interaction, xTB.repulsion)
             else:
-                sec_interaction = sec_tb_model.m_create(Interaction, TBModel.contributions)
+                sec_interaction = sec_xtb.m_create(Interaction, xTB.contributions)
                 sec_interaction.type = name
             sec_interaction.parameters = {
                 p[0]: p[1].tolist() if isinstance(p[1], np.ndarray) else p[1] for p in contribution.parameters}

tests/test_bopfoxparser.py

@@ -17,6 +17,7 @@
 #
 
 import pytest
+import numpy as np
 
 from nomad.datamodel import EntryArchive
 from atomisticparsers.bopfox import BOPfoxParser
@@ -41,7 +42,7 @@ def test_energy(parser):
     sec_method = sec_run.method[0]
     assert sec_method.x_bopfox_simulation_parameters['bopkernel'] == 'jackson'
     assert sec_method.x_bopfox_simulation_parameters['scftol'] == approx(0.001)
-    sec_model = sec_method.tb.model[0]
+    sec_model = sec_method.tb.xtb
     assert sec_model.name == 'test'
     assert sec_model.hamiltonian[0].name == 'ddsigma'
     assert (sec_model.hamiltonian[1].atom_labels == ['W', 'W']).all()

tests/test_dftbplusparser.py

@@ -41,8 +41,9 @@ def test_static(parser):
     assert sec_run[0].x_dftbp_parser_version == '8'
 
     sec_method = archive.run[0].method
-    assert sec_method[0].x_dftbp_input_parameters['Hamiltonian']['Mixer']['InverseJacobiWeight'] == 0.01
-    assert sec_method[0].x_dftbp_input_parameters['Analysis']['ElectronDynamics']['Perturbation']['SpinType'] == 'Singlet'
+    assert sec_method[0].tb.name == 'DFTB'
+    assert sec_method[0].tb.x_dftbp_input_parameters['Hamiltonian']['Mixer']['InverseJacobiWeight'] == 0.01
+    assert sec_method[0].tb.x_dftbp_input_parameters['Analysis']['ElectronDynamics']['Perturbation']['SpinType'] == 'Singlet'
 
     sec_system = archive.run[0].system
     assert len(sec_system[0].atoms.labels) == 1415

tests/test_xtbparser.py

@@ -43,16 +43,17 @@ def test_scf(parser):
     assert sec_run.time_run.date_end > 0
 
     sec_method = sec_run.method
-    assert sec_method[0].x_xtb_setup['# basis functions'] == 6
-    assert sec_method[0].x_xtb_setup['Broyden damping'] == approx(0.4)
-
-    sec_model = sec_method[0].tb.model
-    assert sec_model[0].hamiltonian[0].parameters['H0-scaling (s, p, d)'][1] == approx(2.23)
-    assert sec_model[0].contributions[0].type == 'dispersion'
-    assert sec_model[0].contributions[0].parameters['a1'][0] == approx(0.52)
-    assert sec_model[0].repulsion[0].parameters['rExp'][0] == approx(1.0)
-    assert sec_model[0].coulomb[0].parameters['third order'][0] == 'shell-resolved'
-    assert sec_model[0].coulomb[0].parameters['cn-shift'][0] == approx(1.2)
+    assert sec_method[0].tb.name == 'xTB'
+    assert sec_method[0].tb.x_xtb_setup['# basis functions'] == 6
+    assert sec_method[0].tb.x_xtb_setup['Broyden damping'] == approx(0.4)
+
+    sec_model = sec_method[0].tb.xtb
+    assert sec_model.hamiltonian[0].parameters['H0-scaling (s, p, d)'][1] == approx(2.23)
+    assert sec_model.contributions[0].type == 'dispersion'
+    assert sec_model.contributions[0].parameters['a1'][0] == approx(0.52)
+    assert sec_model.repulsion[0].parameters['rExp'][0] == approx(1.0)
+    assert sec_model.coulomb[0].parameters['third order'][0] == 'shell-resolved'
+    assert sec_model.coulomb[0].parameters['cn-shift'][0] == approx(1.2)
 
     sec_system = sec_run.system
     assert len(sec_system) == 1