def test_nwcpymatgen_translation(self):
from aiida.tools.dbexporters.tcod \
import translate_calculation_specific_values
# from aiida.tools.dbexporters.tcod_plugins.nwcpymatgen \
# import NwcpymatgenTcodtranslator as NPT
from aiida.orm.data.parameter import ParameterData
from tcodexporter import FakeObject
from aiida.common.pluginloader import get_plugin
NPT = get_plugin('tools.dbexporters.tcod_plugins',
'nwchem.nwcpymatgen')
calc = FakeObject({
"out": {
"output":
ParameterData(
dict={
"basis_set": {
"H": {
"description": "6-31g",
"functions": "2",
"shells": "2",
"types": "2s"
},
"O": {
"description": "6-31g",
"functions": "9",
"shells": "5",
"types": "3s2p"
}
},
"corrections": {},
"energies": [-2057.99011937535],
"errors": [],
"frequencies": None,
"has_error": False,
"job_type": "NWChem SCF Module"
}),
"job_info":
ParameterData(
dict={
"0 permanent": ".",
"0 scratch": ".",
"argument 1": "aiida.in",
"compiled": "Sun_Dec_22_04:02:59_2013",
"data base": "./aiida.db",
"date": "Mon May 11 17:10:07 2015",
"ga revision": "10379",
"global": "200.0 Mbytes (distinct from heap & stack)",
"hardfail": "no",
"heap": "100.0 Mbytes",
"hostname": "theospc11",
"input": "aiida.in",
"nproc": "6",
"nwchem branch": "6.3",
"nwchem revision": "24277",
"prefix": "aiida.",
"program": "/usr/bin/nwchem",
"source": "/build/buildd/nwchem-6.3+r1",
"stack": "100.0 Mbytes",
"status": "startup",
"time left": "-1s",
"total": "400.0 Mbytes",
"verify": "yes",
})
}
})
res = translate_calculation_specific_values(calc, NPT)
self.assertEquals(
res, {
'_tcod_software_package': 'NWChem',
'_tcod_software_package_version': '6.3',
'_tcod_software_package_compilation_date':
'2013-12-22T04:02:59',
'_atom_type_symbol': ['H', 'O'],
'_dft_atom_basisset': ['6-31g', '6-31g'],
'_dft_atom_type_valence_configuration': ['2s', '3s2p'],
})
def test_pw_translation(self):
from aiida.tools.dbexporters.tcod \
import translate_calculation_specific_values
# from aiida.tools.dbexporters.tcod_plugins.pw \
# import PwTcodtranslator as PWT
# from aiida.tools.dbexporters.tcod_plugins.cp \
# import CpTcodtranslator as CPT
from aiida.orm.code import Code
from aiida.orm.data.array import ArrayData
from aiida.orm.data.array.kpoints import KpointsData
from aiida.orm.data.parameter import ParameterData
import numpy
from aiida.common.pluginloader import get_plugin
PWT = get_plugin('tools.dbexporters.tcod_plugins',
'quantumespresso.pw')
CPT = get_plugin('tools.dbexporters.tcod_plugins',
'quantumespresso.cp')
code = Code()
code._set_attr('remote_exec_path', '/test')
kpoints = KpointsData()
kpoints.set_kpoints_mesh([2, 3, 4], offset=[0.25, 0.5, 0.75])
def empty_list():
return []
calc = FakeObject({
"inp": {
"parameters": ParameterData(dict={}),
"kpoints": kpoints,
"code": code
},
"out": {
"output_parameters": ParameterData(dict={})
},
"get_inputs": empty_list
})
res = translate_calculation_specific_values(calc, PWT)
self.assertEquals(
res, {
'_dft_BZ_integration_grid_X': 2,
'_dft_BZ_integration_grid_Y': 3,
'_dft_BZ_integration_grid_Z': 4,
'_dft_BZ_integration_grid_shift_X': 0.25,
'_dft_BZ_integration_grid_shift_Y': 0.5,
'_dft_BZ_integration_grid_shift_Z': 0.75,
'_dft_pseudopotential_atom_type': [],
'_dft_pseudopotential_type': [],
'_dft_pseudopotential_type_other_name': [],
'_tcod_software_package': 'Quantum ESPRESSO',
'_tcod_software_executable_path': '/test',
})
calc = FakeObject({
"inp": {
"parameters":
ParameterData(dict={
'SYSTEM': {
'ecutwfc': 40,
'occupations': 'smearing'
}
})
},
"out": {
"output_parameters":
ParameterData(dict={
'number_of_electrons': 10,
})
},
"get_inputs": empty_list
})
res = translate_calculation_specific_values(calc, PWT)
self.assertEquals(
res, {
'_dft_cell_valence_electrons': 10,
'_tcod_software_package': 'Quantum ESPRESSO',
'_dft_BZ_integration_smearing_method': 'Gaussian',
'_dft_pseudopotential_atom_type': [],
'_dft_pseudopotential_type': [],
'_dft_pseudopotential_type_other_name': [],
'_dft_kinetic_energy_cutoff_EEX': 2176.910676048,
'_dft_kinetic_energy_cutoff_charge_density': 2176.910676048,
'_dft_kinetic_energy_cutoff_wavefunctions': 544.227669012,
})
calc = FakeObject({
"inp": {
"parameters": ParameterData(dict={})
},
"out": {
"output_parameters": ParameterData(dict={
'energy_xc': 5,
})
},
"get_inputs": empty_list
})
with self.assertRaises(ValueError):
translate_calculation_specific_values(calc, PWT)
calc = FakeObject({
"inp": {
"parameters": ParameterData(dict={})
},
"out": {
"output_parameters":
ParameterData(dict={
'energy_xc': 5,
'energy_xc_units': 'meV'
})
},
"get_inputs": empty_list
})
with self.assertRaises(ValueError):
translate_calculation_specific_values(calc, PWT)
energies = {
'energy': -3701.7004199449257,
'energy_one_electron': -984.0078459766,
'energy_xc': -706.6986753641559,
'energy_ewald': -2822.6335103043157,
'energy_hartree': 811.6396117001462,
'fermi_energy': 10.25208617898623,
}
dct = energies
for key in energies.keys():
dct["{}_units".format(key)] = 'eV'
calc = FakeObject({
"inp": {
"parameters":
ParameterData(dict={'SYSTEM': {
'smearing': 'mp'
}})
},
"out": {
"output_parameters": ParameterData(dict=dct)
},
"get_inputs": empty_list
})
res = translate_calculation_specific_values(calc, PWT)
self.assertEquals(
res, {
'_tcod_total_energy': energies['energy'],
'_dft_1e_energy': energies['energy_one_electron'],
'_dft_correlation_energy': energies['energy_xc'],
'_dft_ewald_energy': energies['energy_ewald'],
'_dft_hartree_energy': energies['energy_hartree'],
'_dft_fermi_energy': energies['fermi_energy'],
'_tcod_software_package': 'Quantum ESPRESSO',
'_dft_BZ_integration_smearing_method': 'Methfessel-Paxton',
'_dft_BZ_integration_MP_order': 1,
'_dft_pseudopotential_atom_type': [],
'_dft_pseudopotential_type': [],
'_dft_pseudopotential_type_other_name': [],
})
dct = energies
dct['number_of_electrons'] = 10
for key in energies.keys():
dct["{}_units".format(key)] = 'eV'
calc = FakeObject({
"inp": {
"parameters":
ParameterData(dict={'SYSTEM': {
'smearing': 'unknown-method'
}})
},
"out": {
"output_parameters": ParameterData(dict=dct)
},
"get_inputs": empty_list
})
res = translate_calculation_specific_values(calc, CPT)
self.assertEquals(
res, {
'_dft_cell_valence_electrons': 10,
'_tcod_software_package': 'Quantum ESPRESSO'
})
ad = ArrayData()
ad.set_array("forces", numpy.array([[[1, 2, 3], [4, 5, 6]]]))
calc = FakeObject({
"inp": {
"parameters":
ParameterData(dict={'SYSTEM': {
'smearing': 'unknown-method'
}})
},
"out": {
"output_parameters": ParameterData(dict={}),
"output_array": ad
},
"get_inputs": empty_list
})
res = translate_calculation_specific_values(calc, PWT)
self.assertEquals(
res,
{
'_tcod_software_package': 'Quantum ESPRESSO',
'_dft_BZ_integration_smearing_method': 'other',
'_dft_BZ_integration_smearing_method_other': 'unknown-method',
'_dft_pseudopotential_atom_type': [],
'_dft_pseudopotential_type': [],
'_dft_pseudopotential_type_other_name': [],
## Residual forces are no longer produced, as they should
## be in the same CIF loop with coordinates -- to be
## implemented later, since it's not yet clear how.
# '_tcod_atom_site_resid_force_Cartn_x': [1,4],
# '_tcod_atom_site_resid_force_Cartn_y': [2,5],
# '_tcod_atom_site_resid_force_Cartn_z': [3,6],
})