parser for new type (aff) GPAW output files

parser/parser-gpaw/default_parameters.py

+import numpy as np
+
+parameters = {
+    'mode': 'fd',
+    'xc': 'LDA',
+    'occupations': None,
+    'poissonsolver': None,
+    'h': None,  # Angstrom
+    'gpts': None,
+    'kpts': [(0.0, 0.0, 0.0)],
+    'nbands': None,
+    'charge': 0,
+    'setups': {},
+    'basis': {},
+    'spinpol': None,
+    'fixdensity': False,
+    'filter': None,
+    'mixer': None,
+    'eigensolver': None,
+    'background_charge': None,
+    'external': None,
+    'random': False,
+    'hund': False,
+    'maxiter': 333,
+    'idiotproof': True,
+    'symmetry': {'point_group': True,
+                 'time_reversal': True,
+                 'symmorphic': True,
+                 'tolerance': 1e-7},
+    'convergence': {'energy': 0.0005,  # eV / electron
+                    'density': 1.0e-4,
+                    'eigenstates': 4.0e-8,  # eV^2
+                    'bands': 'occupied',
+                    'forces': np.inf},  # eV / Ang
+    'dtype': None,  # Deprecated
+    'width': None,  # Deprecated
+    'verbose': 0}
+
+

parser/parser-gpaw/parser2.py

+from __future__ import division
+import os
+from contextlib import contextmanager
+import numpy as np
+from ase import units
+from ase.data import chemical_symbols
+from ase.io.aff import affopen
+#from ase.io.trajectory import read_atoms
+from ase.data import atomic_masses
+from ase.units import Rydberg
+import setup_paths
+from nomadcore.unit_conversion.unit_conversion import convert_unit as cu
+from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
+from nomadcore.parser_backend import JsonParseEventsWriterBackend
+from libxc_names import get_libxc_name
+from default_parameters import parameters as parms
+
+
+@contextmanager
+def open_section(p, name):
+    gid = p.openSection(name)
+    yield gid
+    p.closeSection(name, gid)
+
+
+def c(value, unit=None):
+    """ Dummy function for unit conversion"""
+    return value
+    return cu(value, unit)
+
+
+parser_info = {"name": "parser2_gpaw", "version": "1.0"}
+path = '../../../../nomad-meta-info/meta_info/nomad_meta_info/' +\
+        'gpaw.nomadmetainfo.json'
+metaInfoPath = os.path.normpath(
+    os.path.join(os.path.dirname(os.path.abspath(__file__)), path))
+
+metaInfoEnv, warns = loadJsonFile(filePath=metaInfoPath,
+                                  dependencyLoader=None,
+                                  extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
+                                  uri=None)
+
+
+def parse(filename):
+    p = JsonParseEventsWriterBackend(metaInfoEnv)
+    o = open_section
+    r = affopen(filename) #  Reader(filename)
+    p.startedParsingSession(filename, parser_info)
+    parms.update(r.parameters.asdict())
+    with o(p, 'section_run'):
+        p.addValue('program_name', 'GPAW')
+        p.addValue('program_version', r.gpaw_version)
+        mode = parms['mode']
+        if isinstance(mode, basestring):
+            mode = {'name': mode}
+        if  mode['name'] == 'pw':
+            p.addValue('program_basis_set_type', 'plane waves')
+            with o(p, 'section_basis_set_cell_dependent'):
+                p.addValue('basis_set_cell_dependent_name',
+                           'PW_%.1f_Ry' % (mode['ecut'] / r.ha * 2))  # in Ry
+                p.addRealValue('basis_set_planewave_cutoff',
+                               c(mode['ecut'], 'eV'))
+        elif mode['name'] == 'fd':
+            p.addValue('program_basis_set_type', 'real space grid')
+            with o(p, 'section_basis_set_cell_dependent'):
+                cell = r.atoms.cell
+                ngpts = r.density.density.shape
+                h1 = np.linalg.norm(cell[0]) / ngpts[0]
+                h2 = np.linalg.norm(cell[1]) / ngpts[1]
+                h3 = np.linalg.norm(cell[2]) / ngpts[2]
+                h = (h1 + h2 + h3) / 3.0
+                p.addValue('basis_set_cell_dependent_name',
+                           'GR_%.1f' % (c(h, 'angstrom') * 1.0E15))  # in fm
+        elif mode['name'] == 'lcao':
+            p.addValue('program_basis_set_type', 'numeric AOs')
+            with o(p, 'section_basis_set_atom_centered'):
+                p.addValue('basis_set_atom_centered_short_name',
+                          parms['basis'])
+        with o(p, 'section_system') as system_gid:
+            p.addArrayValues('simulation_cell',
+                             c(r.atoms.cell, 'angstrom'))
+            symbols = np.array([chemical_symbols[z] for z in r.atoms.numbers])
+            p.addArrayValues('atom_labels', symbols)
+            p.addArrayValues('atom_positions', c(r.atoms.positions, 'angstrom'))
+            p.addArrayValues('configuration_periodic_dimensions',
+                             np.array(r.atoms.pbc, bool))
+            if hasattr(r.atoms, 'momenta'):
+                masses = atomic_masses[r.atoms.numbers]
+                velocities = r.atoms.momenta / masses.reshape(-1, 1)
+                p.addArrayValues('atom_velocities',
+                                c(velocities * units.fs / units.Angstrom,
+                                  'angstrom/femtosecond'))
+        with o(p, 'section_sampling_method'):
+            p.addValue('ensemble_type', 'NVE')
+        with o(p, 'section_frame_sequence'):
+            pass
+        with o(p, 'section_method') as method_gid:
+            p.addValue('relativity_method', 'pseudo_scalar_relativistic')
+            p.addValue('electronic_structure_method', 'DFT')
+            p.addValue('scf_threshold_energy_change',
+                       c(parms['convergence']['energy'], 'eV')) # eV / electron
+            #if r.FixMagneticMoment:
+            #    p.addValue('x_gpaw_fixed_spin_Sz',
+            #               r.MagneticMoments.sum() / 2.)
+            if parms['occupations'] is None:  # use default values
+                if tuple(parms['kpts']) == (1, 1, 1):
+                    width = 0.0
+                else:
+                    width = 0.1
+                parms['occupations'] = {'width': width, 'name': 'fermi-dirac'}
+
+            p.addValue('smearing_kind', parms['occupations']['name'])
+            p.addRealValue('smearing_width',
+                               c(parms['occupations']['width'], 'eV'))
+            p.addRealValue('total_charge', parms['charge'])
+            with o(p, 'section_XC_functionals'):
+                p.addValue('XC_functional_name',
+                           get_libxc_name(parms['xc']))
+        with o(p, 'section_single_configuration_calculation'):
+            p.addValue('single_configuration_calculation_to_system_ref',
+                       system_gid)
+            p.addValue('single_configuration_to_calculation_method_ref',
+                       method_gid)
+            p.addValue('single_configuration_calculation_converged',
+                      r.scf.converged)
+            p.addRealValue('energy_total',
+                           c(r.hamiltonian.e_total_extrapolated, 'eV'))
+            p.addRealValue('energy_free',
+                           c(r.hamiltonian.e_total_free, 'eV'))
+            p.addRealValue('energy_XC', c(r.hamiltonian.e_xc, 'eV'))
+            p.addRealValue('electronic_kinetic_energy',
+                           c(r.hamiltonian.e_kinetic, 'eV'))
+            p.addRealValue('energy_correction_entropy',
+                           c(r.hamiltonian.e_entropy, 'eV'))
+            p.addRealValue('energy_reference_fermi',
+                          c(r.occupations.fermilevel, 'eV'))
+            p.addRealValue('energy_reference_fermi',
+                          c(r.occupations.fermilevel, 'eV'))
+            if hasattr(r.results, 'forces'):
+                p.addArrayValues('atom_forces_free',
+                                 c(r.results.forces, 'eV/angstrom'))
+            if hasattr(r.results, 'magmoms'):
+                p.addArrayValues('x_gpaw_magnetic_moments',
+                                 r.results.magmoms)
+                p.addRealValue('x_gpaw_spin_Sz', r.results.magmoms.sum() / 2.0)
+            #p.addArrayValues('x_gpaw_atomic_density_matrices',
+            #                 r.AtomicDensityMatrices)
+            #p.addArrayValues('x_gpaw_projections_real', r.Projections.real)
+            #p.addArrayValues('x_gpaw_projections_imag', r.Projections.imag)
+            with o(p, 'section_eigenvalues'):
+                p.addValue('eigenvalues_kind', 'normal')
+                p.addArrayValues('eigenvalues_values',
+                                 c(r.wave_functions.eigenvalues, 'eV'))
+                p.addArrayValues('eigenvalues_occupation',
+                                 r.wave_functions.occupations)
+                #p.addArrayValues('eigenvalues_kpoints', r.IBZKPoints)
+    p.finishedParsingSession("ParseSuccess", None)
+
+if __name__ == '__main__':
+    import sys
+    filename = sys.argv[1]
+    parse(filename)