def test_missing_potfile(self):
"""
Parse output where output.pot is missing and compare error messages/rest of out_dict
"""
out_dict = {'parser_version': 'some_version_number'}
success, msg_list, out_dict = parse_voronoi_output(out_dict, outfile, 'wrong_name', atominfo, radii, inputfile)
out_dict['parser_warnings'] = msg_list
dref2 = {'volumes_group': {'volume_total': 3.00000186, 'volume_unit': 'alat^3', 'volume_atoms': [{'iatom': 1, 'v_atom': 0.50000031}, {'iatom': 2, 'v_atom': 0.50000031}, {'iatom': 3, 'v_atom': 0.50000031}, {'iatom': 4, 'v_atom': 0.50000031}, {'iatom': 5, 'v_atom': 0.50000031}, {'iatom': 6, 'v_atom': 0.50000031}]}, 'parser_version': 'some_version_number', 'fpradius_atoms': [0.4696902, 0.4696902, 0.4696902, 0.4696902, 0.4696902, 0.4696902], 'alat_unit': 'a_Bohr', 'shapes': [1, 1, 1, 1, 1, 1], 'code_info_group': {'code_version': 'v1.0-6-gf0c2ac3', 'calculation_serial_number': 'voro_v1.0-6-gf0c2ac3_serial_20171207092915', 'compile_options': 'serial-O2 -r8 -traceback -i8-mkl -Wl,-stack_size,0x40000000,-stack_addr,0xf0000000'}, 'fpradius_atoms_unit': 'alat', 'alat': 5.423514, 'parser_warnings': ["Error parsing output of voronoi: 'EMIN'", 'Error parsing output of voronoi: core_states', 'Error parsing output of voronoi: radial meshpoints'], 'start_from_jellium_potentials': True, 'radii_atoms_group': [{'rout': 0.5590171328, 'iatom': 1, 'dist_nn': 0.8660255824, 'rout_over_dist_nn': 64.55, 'rmt0_over_rout': 77.46, 'rmt0': 0.4330127912}, {'rout': 0.5590171328, 'iatom': 2, 'dist_nn': 0.8660255824, 'rout_over_dist_nn': 64.55, 'rmt0_over_rout': 77.46, 'rmt0': 0.4330127912}, {'rout': 0.5590171328, 'iatom': 3, 'dist_nn': 0.8660247659, 'rout_over_dist_nn': 64.55, 'rmt0_over_rout': 77.46, 'rmt0': 0.4330127912}, {'rout': 0.5590171328, 'iatom': 4, 'dist_nn': 0.8660247659, 'rout_over_dist_nn': 64.55, 'rmt0_over_rout': 77.46, 'rmt0': 0.4330127912}, {'rout': 0.5590171328, 'iatom': 5, 'dist_nn': 0.8660255824, 'rout_over_dist_nn': 64.55, 'rmt0_over_rout': 77.46, 'rmt0': 0.4330127912}, {'rout': 0.5590171328, 'iatom': 6, 'dist_nn': 0.8660255824, 'rout_over_dist_nn': 64.55, 'rmt0_over_rout': 77.46, 'rmt0': 0.4330127912}, {'radii_units': 'alat'}], 'cluster_info_group': {'cluster_info_atoms': [{'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 1, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 2, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 3, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 4, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 5, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 6, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 7, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 8, 'tb_cluster_id': 1, 'sites': 27}], 'number_of_clusters': 1}}
assert not success
assert out_dict == dref2
assert msg_list == ["Error parsing output of voronoi: 'EMIN'", 'Error parsing output of voronoi: core_states', 'Error parsing output of voronoi: radial meshpoints']
return out_dict
def test_complete_voro_output(self):
"""
Parse complete output of voronoi calculation and compare out_dict, grouping, warnings
"""
out_dict = {'parser_version': 'some_version_number'}
success, msg_list, out_dict = parse_voronoi_output(out_dict, outfile, potfile, atominfo, radii, inputfile)
out_dict['parser_warnings'] = msg_list
assert success
return out_dict
assert out_dict == dref
assert msg_list == []
groups = [i for i in out_dict.keys() if 'group' in i]
assert set(groups) == set(grouping_ref)
def test_missing_outfile(self):
"""
Parse output where out_voronoi is missing and compare error messages/rest of out_dict
"""
out_dict = {'parser_version': 'some_version_number'}
success, msg_list, out_dict = parse_voronoi_output(out_dict, '', potfile, atominfo, radii, inputfile)
out_dict['parser_warnings'] = msg_list
dref2 = {'parser_warnings': ['Error parsing output of voronoi: Version Info', "Error parsing output of voronoi: 'EMIN'", 'Error parsing output of voronoi: Cluster Info', 'Error parsing output of voronoi: Jellium startpot', 'Error parsing output of voronoi: SHAPE Info', 'Error parsing output of voronoi: Volume Info', 'Error parsing output of voronoi: radii.dat Info', 'Error parsing output of voronoi: full potential radius'], 'alat_unit': 'a_Bohr', 'parser_version': 'some_version_number', 'alat': 5.423514,
'core_states_group': {'descr_highest_lying_core_state_per_atom': ['no core states','no core states','no core states','no core states','3p','3p','3p','3p','no core states','no core states','no core states','no core states'],
'energy_highest_lying_core_state_per_atom': [None,None,None,None,-3.3287908000000002,-3.3287908000000002,-3.3287908000000002,-3.3287908000000002,None,None,None,None],
'energy_highest_lying_core_state_per_atom_unit': 'Rydberg',
'number_of_core_states_per_atom': [0,0,0,0,5,5,5,5,0,0,0,0]},
'radial_meshpoints': [484.0 for i in range(12)]}
assert not success
assert out_dict == dref2
assert msg_list == ['Error parsing output of voronoi: Version Info', "Error parsing output of voronoi: 'EMIN'", 'Error parsing output of voronoi: Cluster Info', 'Error parsing output of voronoi: Jellium startpot', 'Error parsing output of voronoi: SHAPE Info', 'Error parsing output of voronoi: Volume Info', 'Error parsing output of voronoi: radii.dat Info', 'Error parsing output of voronoi: full potential radius']
def test_missing_inputfile(self):
"""
Parse output where inputcard is missing and compare error messages/rest of out_dict
"""
out_dict = {'parser_version': 'some_version_number'}
success, msg_list, out_dict = parse_voronoi_output(out_dict, outfile, potfile, atominfo, radii, 'wrong_name')
out_dict['parser_warnings'] = msg_list
dref2 = {'volumes_group': {'volume_total': 3.00000186, 'volume_unit': 'alat^3', 'volume_atoms': [{'iatom': 1, 'v_atom': 0.50000031}, {'iatom': 2, 'v_atom': 0.50000031}, {'iatom': 3, 'v_atom': 0.50000031}, {'iatom': 4, 'v_atom': 0.50000031}, {'iatom': 5, 'v_atom': 0.50000031}, {'iatom': 6, 'v_atom': 0.50000031}]}, 'parser_version': 'some_version_number', 'emin': -0.5, 'radii_atoms_group': [{'rout': 0.5590171328, 'iatom': 1, 'dist_nn': 0.8660255824, 'rout_over_dist_nn': 64.55, 'rmt0_over_rout': 77.46, 'rmt0': 0.4330127912}, {'rout': 0.5590171328, 'iatom': 2, 'dist_nn': 0.8660255824, 'rout_over_dist_nn': 64.55, 'rmt0_over_rout': 77.46, 'rmt0': 0.4330127912}, {'rout': 0.5590171328, 'iatom': 3, 'dist_nn': 0.8660247659, 'rout_over_dist_nn': 64.55, 'rmt0_over_rout': 77.46, 'rmt0': 0.4330127912}, {'rout': 0.5590171328, 'iatom': 4, 'dist_nn': 0.8660247659, 'rout_over_dist_nn': 64.55, 'rmt0_over_rout': 77.46, 'rmt0': 0.4330127912}, {'rout': 0.5590171328, 'iatom': 5, 'dist_nn': 0.8660255824, 'rout_over_dist_nn': 64.55, 'rmt0_over_rout': 77.46, 'rmt0': 0.4330127912}, {'rout': 0.5590171328, 'iatom': 6, 'dist_nn': 0.8660255824, 'rout_over_dist_nn': 64.55, 'rmt0_over_rout': 77.46, 'rmt0': 0.4330127912}, {'radii_units': 'alat'}], 'shapes': [1, 1, 1, 1, 1, 1], 'code_info_group': {'code_version': 'v1.0-6-gf0c2ac3', 'calculation_serial_number': 'voro_v1.0-6-gf0c2ac3_serial_20171207092915', 'compile_options': 'serial-O2 -r8 -traceback -i8-mkl -Wl,-stack_size,0x40000000,-stack_addr,0xf0000000'}, 'fpradius_atoms_unit': 'alat', 'parser_warnings': ['Error parsing output of voronoi: alat'], 'start_from_jellium_potentials': True, 'emin_units': 'Ry', 'fpradius_atoms': [0.4696902, 0.4696902, 0.4696902, 0.4696902, 0.4696902, 0.4696902], 'cluster_info_group': {'cluster_info_atoms': [{'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 1, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 2, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 3, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 4, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 5, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 6, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 7, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 8, 'tb_cluster_id': 1, 'sites': 27}], 'number_of_clusters': 1},
'emin_minus_efermi': -12.370853917196168, 'emin_minus_efermi_Ry': -0.90924099999999997, 'emin_minus_efermi_Ry_units': 'Ry', 'emin_minus_efermi_units': 'eV',
'core_states_group': {'descr_highest_lying_core_state_per_atom': ['no core states','no core states','no core states','no core states','3p','3p','3p','3p','no core states','no core states','no core states','no core states'],
'energy_highest_lying_core_state_per_atom': [None,None,None,None,-3.3287908000000002,-3.3287908000000002,-3.3287908000000002,-3.3287908000000002,None,None,None,None],
'energy_highest_lying_core_state_per_atom_unit': 'Rydberg',
'number_of_core_states_per_atom': [0,0,0,0,5,5,5,5,0,0,0,0]},
'radial_meshpoints': [484.0 for i in range(12)]}
assert not success
assert out_dict == dref2
assert msg_list == ['Error parsing output of voronoi: alat']
return out_dict
def test_missing_atominfo(self):
"""
Parse output where atominfo.txt is missing and compare error messages/rest of out_dict
"""
out_dict = {'parser_version': 'some_version_number'}
success, msg_list, out_dict = parse_voronoi_output(out_dict, outfile, potfile, 'wrong_name', radii, inputfile)
out_dict['parser_warnings'] = msg_list
dref2 = {'parser_version': 'some_version_number', 'emin': -0.5, 'alat_unit': 'a_Bohr', 'code_info_group': {'code_version': 'v1.0-6-gf0c2ac3', 'calculation_serial_number': 'voro_v1.0-6-gf0c2ac3_serial_20171207092915', 'compile_options': 'serial-O2 -r8 -traceback -i8-mkl -Wl,-stack_size,0x40000000,-stack_addr,0xf0000000'}, 'alat': 5.423514, 'parser_warnings': ['Error parsing output of voronoi: SHAPE Info', 'Error parsing output of voronoi: Volume Info', 'Error parsing output of voronoi: radii.dat Info', 'Error parsing output of voronoi: full potential radius'], 'start_from_jellium_potentials': True, 'emin_units': 'Ry', 'cluster_info_group': {'cluster_info_atoms': [{'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 1, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 2, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 3, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 4, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 5, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 6, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 7, 'tb_cluster_id': 1, 'sites': 27}, {'rmt_ref': 2.3166, 'refpot': 1, 'iatom': 8, 'tb_cluster_id': 1, 'sites': 27}], 'number_of_clusters': 1},
'emin_minus_efermi': -12.370853917196168, 'emin_minus_efermi_Ry': -0.90924099999999997, 'emin_minus_efermi_Ry_units': 'Ry', 'emin_minus_efermi_units': 'eV',
'core_states_group': {'descr_highest_lying_core_state_per_atom': ['no core states','no core states','no core states','no core states','3p','3p','3p','3p','no core states','no core states','no core states','no core states'],
'energy_highest_lying_core_state_per_atom': [None,None,None,None,-3.3287908000000002,-3.3287908000000002,-3.3287908000000002,-3.3287908000000002,None,None,None,None],
'energy_highest_lying_core_state_per_atom_unit': 'Rydberg',
'number_of_core_states_per_atom': [0,0,0,0,5,5,5,5,0,0,0,0]},
'radial_meshpoints': [484.0 for i in range(12)]}
assert not success
assert out_dict == dref2
assert msg_list == ['Error parsing output of voronoi: SHAPE Info', 'Error parsing output of voronoi: Volume Info', 'Error parsing output of voronoi: radii.dat Info', 'Error parsing output of voronoi: full potential radius']
return out_dict
def parse_with_retrieved(self, retrieved):
"""
Parse output data folder, store results in database.
:param retrieved: a dictionary of retrieved nodes, where
the key is the link name
:returns: a tuple with two values ``(bool, node_list)``,
where:
* ``bool``: variable to tell if the parsing succeeded
* ``node_list``: list of new nodes to be stored in the db
(as a list of tuples ``(link_name, node)``)
"""
success = False
node_list = ()
# Check that the retrieved folder is there
try:
out_folder = retrieved[self._calc._get_linkname_retrieved()]
except KeyError:
self.logger.error("No retrieved folder found")
return success, node_list
# check what is inside the folder
list_of_files = out_folder.get_folder_list()
# we need at least the output file name as defined in calcs.py
if self._calc._OUTPUT_FILE_NAME not in list_of_files:
self.logger.error("Output file '{}' not found".format(self._calc._OUTPUT_FILE_NAME))
return success, node_list
#Parse voronoi output, results that are stored in database are in out_dict
# get path to files and catch errors if files are not present
file_errors = []
try:
potfile = out_folder.get_abs_path(self._calc._OUT_POTENTIAL_voronoi)
except OSError:
# cover case where potfile is overwritten from input to voronoi calculation
try:
potfile = out_folder.get_abs_path(self._calc._POTENTIAL_IN_OVERWRITE)
except OSError:
file_errors.append("Critical error! Neither potfile {} not {} "
"was found".format(self._calc._OUT_POTENTIAL_voronoi,
self._calc._POTENTIAL_IN_OVERWRITE))
potfile = 'file_not_found'
try:
outfile = out_folder.get_abs_path(self._calc._OUTPUT_FILE_NAME)
except OSError:
file_errors.append("Critical error! outfile not found {}".format(self._calc._OUTPUT_FILE_NAME))
outfile = 'file_not_found'
try:
atominfo = out_folder.get_abs_path(self._calc._ATOMINFO)
except OSError:
file_errors.append("Critical error! atominfo not found {}".format(self._calc._ATOMINFO))
atominfo = 'file_not_found'
try:
radii = out_folder.get_abs_path(self._calc._RADII)
except OSError:
file_errors.append("Critical error! radii not found {}".format(self._calc._RADII))
radii = 'file_not_found'
try:
inputfile = out_folder.get_abs_path(self._calc._INPUT_FILE_NAME)
except OSError:
file_errors.append("Critical error! inputfile not found {}".format(self._calc._INPUT_FILE_NAME))
inputfile = 'file_not_found'
# initialize out_dict and parse output files
out_dict = {'parser_version': self._ParserVersion}
out_dict['calculation_plugin_version'] = self._calc._CALCULATION_PLUGIN_VERSION
#TODO add job description, compound name, calculation title
success, msg_list, out_dict = parse_voronoi_output(out_dict, outfile,
potfile, atominfo,
radii, inputfile)
# add file open errors to parser output of error messages
for f_err in file_errors:
msg_list.append(f_err)
out_dict['parser_errors'] = msg_list
#create output node and link
output_data = ParameterData(dict=out_dict)
link_name = self.get_linkname_outparams()
node_list = [(link_name, output_data)]
return success, node_list