nomad-faird infrastructure.

.gitignore

@@ -9,6 +9,7 @@ syntax: glob
 *.pyc
 *.bk
 *.swp
+*.egg-info
 .DS_Store
 
 # logging files

gpawparser/__init__.py

+from gpawparser.parser import GpawParserWrapper

gpawparser/libxc_names.py

+# Copyright 2015-2018 Mikkel Strange, Fawzi Mohamed, Ankit Kariryaa, Ask Hjorth Larsen, Jens Jørgen Mortensen
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+
+from __future__ import print_function
+import re
+#p = re.compile(r"(?P<x_name>.*_X.*)\+(?P<c_name>.*_C.*)")
+p = re.compile(
+  '((?P<x_name>(GGA|LDA|MGGA|HF|HYB_MGGA)_X.*)|(?P<c_name>(GGA|LDA|MGGA)_C.*))')
+
+short_names = {
+        'LDA': 'LDA_X+LDA_C_PW',
+        'PW91': 'GGA_X_PW91+GGA_C_PW91',
+        'PBE': 'GGA_X_PBE+GGA_C_PBE',
+        'PBEsol': 'GGA_X_PBE_SOL+GGA_C_PBE_SOL',
+        'revPBE': 'GGA_X_PBE_R+GGA_C_PBE',
+        'RPBE': 'GGA_X_RPBE+GGA_C_PBE',
+        'BLYP': 'GGA_X_B88+GGA_C_LYP',
+        'HCTH407': 'GGA_XC_HCTH_407',
+        'WC': 'GGA_X_WC+GGA_C_PBE',
+        'AM05': 'GGA_X_AM05+GGA_C_AM05',
+        # 'M06-L': 'MGGA_X_M06_L+MGGA_C_M06_L',
+        # 'TPSS': 'MGGA_X_TPSS+MGGA_C_TPSS',
+        # 'revTPSS': 'MGGA_X_REVTPSS+MGGA_C_REVTPSS',
+        'mBEEF': 'MGGA_X_MBEEF+GGA_C_PBE_SOL'}
+
+
+def get_libxc_name(name):
+    if name in short_names:
+        libxc_name = short_names[name]
+    else:
+        libxc_name = name
+    return libxc_name
+
+def get_libxc_xc_names(name):
+    name = get_libxc_name(name)
+    xc = {'xc_name': None,
+          'x_name' : None,
+          'c_name': None}
+
+    if '_XC_' in name:
+        xc['xc_name'] = name
+        return xc
+
+    if '+' in name:
+        s = name.split('+')
+        xc['x_name'] = s[0]
+        xc['c_name'] = s[1]
+        return xc
+
+    m = re.search(p, name)
+    if m is not None: # it is either a correlation or exchange functional
+        xc.update(m.groupdict())
+        return xc
+
+    xc['xc_name'] = name  # for something like BEEF-vdW
+    return xc
+
+if __name__ == '__main__':
+#    print(get_libxc_name('LDA'))
+#    print(get_libxc_name('GGA_X_PBE'))
+    names = ['GGA_X_B88+GGA_C_LYP',
+             'HF_X',
+             'HYB_GGA_XC_B1LYP',
+             'HYB_GGA_XC_HSE03',
+             'BEEF-vdW',
+             'LDA_K_TF']
+    for name in names:
+        print(get_libxc_xc_names(name))

gpawparser/parser-gpaw/default_parameters.py

+# Copyright 2015-2018 Mikkel Strange, Fawzi Mohamed, Ankit Kariryaa, Ask Hjorth Larsen, Jens Jørgen Mortensen
+# 
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+# 
+#     http://www.apache.org/licenses/LICENSE-2.0
+# 
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+
+"""
+used with parser2.py, the new file format (aff)
+"""
+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/parser.py → gpawparser/parser-gpaw/parser.py

 # Copyright 2015-2018 Mikkel Strange, Fawzi Mohamed, Ankit Kariryaa, Ask Hjorth Larsen, Jens Jørgen Mortensen
-# 
+#
 #   Licensed under the Apache License, Version 2.0 (the "License");
 #   you may not use this file except in compliance with the License.
 #   You may obtain a copy of the License at
-# 
+#
 #     http://www.apache.org/licenses/LICENSE-2.0
-# 
+#
 #   Unless required by applicable law or agreed to in writing, software
 #   distributed under the License is distributed on an "AS IS" BASIS,
 #   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -14,6 +14,7 @@
 
 from __future__ import division
 import os
+import logging
 from contextlib import contextmanager
 import numpy as np
 from ase.data import chemical_symbols
@@ -40,17 +41,38 @@ def c(value, unit=None):
 parser_info = {"name": "parser_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)
+
+import nomad_meta_info
 metaInfoPath = os.path.normpath(
-    os.path.join(os.path.dirname(os.path.abspath(__file__)), path))
+    os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)),
+    "gpaw.nomadmetainfo.json"))
+metaInfoEnv, warnings = loadJsonFile(
+    filePath = metaInfoPath, dependencyLoader = None,
+    extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
 
-metaInfoEnv, warns = loadJsonFile(filePath=metaInfoPath,
-                                  dependencyLoader=None,
-                                  extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
-                                  uri=None)
+class LibAtomsParserWrapper():
+    """ A proper class envolop for running this parser using Noamd-FAIRD infra. """
+    def __init__(self, backend, **kwargs):
+        self.backend_factory = backend
 
+    def parse(self, mainfile):
+        from unittest.mock import patch
+        logging.info('lib-atoms parser started')
+        logging.getLogger('nomadcore').setLevel(logging.WARNING)
+        backend = self.backend_factory(metaInfoEnv)
+        backend = parse_without_class(mainfile, backend)
+        return backend
 
-def parse(filename):
-    p = JsonParseEventsWriterBackend(metaInfoEnv)
+def parse_without_class(filename, backend):
+    # p = JsonParseEventsWriterBackend(metaInfoEnv)
+    p = backend
     o = open_section
     r = Reader(filename)
     p.startedParsingSession(filename, parser_info)

gpawparser/parser.py

+# Copyright 2015-2018 Mikkel Strange, Fawzi Mohamed, Ankit Kariryaa, Ask Hjorth Larsen, Jens Jørgen Mortensen
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+
+from __future__ import division
+import os
+import logging
+from contextlib import contextmanager
+import numpy as np
+from ase.data import chemical_symbols
+# 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 gpawparser.tar import Reader
+from gpawparser.libxc_names import get_libxc_xc_names
+from gpawparser.versions import get_prog_version
+
+@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 cu(value, unit)
+
+
+parser_info = {"name": "parser_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)
+
+import nomad_meta_info
+metaInfoPath = os.path.normpath(
+    os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)),
+    "gpaw.nomadmetainfo.json"))
+metaInfoEnv, warnings = loadJsonFile(
+    filePath = metaInfoPath, dependencyLoader = None,
+    extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
+
+class GpawParserWrapper():
+    """ A proper class envolop for running this parser using Noamd-FAIRD infra. """
+    def __init__(self, backend, **kwargs):
+        self.backend_factory = backend
+
+    def parse(self, mainfile):
+        from unittest.mock import patch
+        logging.info('lib-atoms parser started')
+        logging.getLogger('nomadcore').setLevel(logging.WARNING)
+        backend = self.backend_factory(metaInfoEnv)
+        backend = parse_without_class(mainfile, backend)
+        return backend
+
+def parse_without_class(filename, backend):
+    # p = JsonParseEventsWriterBackend(metaInfoEnv)
+    p = backend
+    o = open_section
+    r = Reader(filename)
+    p.startedParsingSession(filename, parser_info)
+
+    with o(p, 'section_run'):
+        p.addValue('program_name', 'GPAW')
+        p.addValue('program_version', get_prog_version(r.version))
+        if r.Mode == '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' % (r.PlaneWaveCutoff * 2.0))  # in Ry
+                p.addRealValue('basis_set_planewave_cutoff',
+                               c(r.PlaneWaveCutoff, 'hartree'))
+        elif r.Mode == 'fd':
+            with o(p, 'section_basis_set_cell_dependent'):
+                h1 = np.linalg.norm(r.UnitCell[0]) / r.dims['ngptsx']
+                h2 = np.linalg.norm(r.UnitCell[1]) / r.dims['ngptsy']
+                h3 = np.linalg.norm(r.UnitCell[2]) / r.dims['ngptsz']
+                h = (h1 + h2 + h3) / 3.0
+                p.addValue('basis_set_cell_dependent_name',
+                           'GR_%.1f' % (c(h, 'bohr') * 1.0E15))  # in fm
+        elif r.Mode == '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', r.BasisSet)
+        with o(p, 'section_system') as system_gid:
+            p.addArrayValues('simulation_cell', c(r.UnitCell, 'bohr'))
+            symbols = np.array([chemical_symbols[z] for z in r.AtomicNumbers])
+            p.addArrayValues('atom_labels', symbols)
+            p.addArrayValues('atom_positions', c(r.CartesianPositions, 'bohr'))
+            if r.Mode == 'pw':
+                pbc = np.array((1, 1, 1), bool)
+            else:
+                pbc = np.array(r.BoundaryConditions, bool)
+            p.addArrayValues('configuration_periodic_dimensions', pbc)
+        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(r.EnergyError,
+                                                        'hartree'))
+            if 'FixMagneticMoment' in r:
+                p.addValue('x_gpaw_fix_magnetic_moment',
+                           r.FixMagneticMoment)
+                if r.FixMagneticMoment:
+                    p.addValue('x_gpaw_fixed_spin_Sz',
+                               r.MagneticMoments.sum() / 2.)
+            if 'FermiWidth' in r:
+                p.addValue('smearing_kind', 'fermi')
+                p.addRealValue('smearing_width',
+                               c(r.FermiWidth, 'hartree'))
+            if 'FixDensity' in r:
+                p.addValue('x_gpaw_fix_density', r.FixDensity)
+            if 'DensityConvergenceCriterion' in r:
+                p.addRealValue('x_gpaw_density_convergence_criterion',
+                               r.DensityConvergenceCriterion)
+            if 'MixClass' in r:
+                p.addValue('x_gpaw_mix_class', r.MixClass)
+            if 'MixBeta' in r:
+                p.addValue('x_gpaw_mix_beta', r.MixBeta)
+            if 'MixWeight' in r:
+                p.addValue('x_gpaw_mix_weight', r.MixWeight)
+            if 'MixOld' in r:
+                p.addValue('x_gpaw_mix_old', r.MixOld)
+            if 'MaximumAngularMomentum' in r:
+                p.addValue('x_gpaw_maximum_angular_momentum',
+                           r.MaximumAngularMomentum)
+            if 'SymmetryTimeReversalSwitch' in r:
+                p.addValue('x_gpaw_symmetry_time_reversal_switch',
+                           r.SymmetryTimeReversalSwitch)
+            p.addValue('x_gpaw_xc_functional', r.XCFunctional)
+            xc_names = get_libxc_xc_names(r.XCFunctional)
+            for name in xc_names.values():
+                if name is not None:
+                    with o(p, 'section_XC_functionals'):
+                        p.addValue('XC_functional_name', name)
+        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.addRealValue('energy_total', c(r.Epot, 'hartree'))
+            p.addRealValue('energy_XC', c(r.Exc, 'hartree'))
+            p.addRealValue('electronic_kinetic_energy', c(r.Ekin, 'hartree'))
+            p.addRealValue('energy_correction_entropy', c(r.S, 'hartree'))
+            if 'CartesianForces' in r:
+                p.addArrayValues('atom_forces_free',
+                                 c(r.CartesianForces, 'bohr/hartree'))
+            p.addArrayValues('x_gpaw_magnetic_moments', r.MagneticMoments)
+            p.addRealValue('x_gpaw_spin_Sz', r.MagneticMoments.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.Eigenvalues, 'hartree'))
+                p.addArrayValues('eigenvalues_occupation', r.OccupationNumbers)
+                p.addArrayValues('eigenvalues_kpoints', r.IBZKPoints)
+    p.finishedParsingSession("ParseSuccess", None)
+    return p  # Return the backend
+
+if __name__ == '__main__':
+    import sys
+    filename = sys.argv[1]
+    parse(filename)

gpawparser/parser2.py

+# Copyright 2015-2018 Mikkel Strange, Fawzi Mohamed, Ankit Kariryaa, Ask Hjorth Larsen, Jens Jørgen Mortensen
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+
+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.ulm import ulmopen
+from ase.utils import basestring
+#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 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)
+import nomad_meta_info
+metaInfoPath = os.path.normpath(
+    os.path.join(os.path.dirname(os.path.abspath(nomad_meta_info.__file__)),
+    "gpaw.nomadmetainfo.json"))
+metaInfoEnv, warnings = loadJsonFile(
+    filePath = metaInfoPath, dependencyLoader = None,
+    extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
+
+def parse(filename):
+    p = JsonParseEventsWriterBackend(metaInfoEnv)
+    o = open_section
+    r = ulmopen(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 'momenta' in r.atoms:
+                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'))
+            nspin = r.density.density.shape[0]
+            ef = r.occupations.fermilevel
+            fermilevels = np.zeros(nspin)
+            if nspin == 1:
+                fermilevels[:] = ef
+            elif nspin == 2:
+                split = r.occupations.split
+                fermilevels[0] = ef + 0.5 * split
+                fermilevels[1] = ef - 0.5 * split
+            p.addArrayValues('energy_reference_fermi',
+                             c(fermilevels, 'eV'))
+
+            # Load 3D arrays ("volumetric data")
+            origin = -0.5 * r.atoms.cell.sum(axis=0)
+            npoints = np.array(r.density.density.shape[1:])
+            npoints[~r.atoms.pbc] += 1
+            displacements = r.atoms.cell / npoints
+
+            def add_3d_array(values, kind, unit):
+                with o(p, 'section_volumetric_data'):
+                    p.addArrayValues('volumetric_data_origin',
+                                     c(origin, 'angstrom'))
+                    p.addArrayValues('volumetric_data_displacements',
+                                     c(displacements, 'angstrom'))
+                    p.addArrayValues('volumetric_data_values',
+                                     c(values, unit))
+                    p.addValue('volumetric_data_kind', kind)
+
+            # H.atom.ulm.gpw test can be used to verify that pseudodensity
+            # integrates to 0.98, corresponding closely to the norm of the
+            # H 1s pseudowavefunction (see output of "gpaw-setup H").
+            # It has mixed BCs so this should show that npoints is taken
+            # care of correctly, hopefully.
+            add_3d_array(r.density.density, kind='density',
+                         unit='angstrom**(-3)')
+            add_3d_array(r.hamiltonian.potential, kind='potential_effective',
+                         unit='eV*angstrom**(-3)