def test_psi4_qmefp_6d():
subject = subject6
fullans = copy.deepcopy(fullans6)
fullans['efp']['geom'] = np.array([-2.22978429, 1.19270015, -0.99721732, -1.85344873, 1.5734809 ,
0.69660583, -0.71881655, 1.40649303, -1.90657336, 0.98792 ,
1.87681 , 2.85174 , 2.31084386, 0.57620385, 3.31175679,
1.87761143, 3.16604791, 1.75667803, 0.55253064, 2.78087794,
4.47837555])
fullans['efp']['elea'] = np.array([16, 1, 1, 14, 1, 1, 1])
fullans['efp']['elez'] = np.array([8, 1, 1, 7, 1, 1, 1])
fullans['efp']['elem'] = np.array(['O', 'H', 'H', 'N', 'H', 'H', 'H'])
fullans['efp']['mass'] = np.array([15.99491462, 1.00782503, 1.00782503, 14.00307400478, 1.00782503, 1.00782503, 1.00782503])
fullans['efp']['real'] = np.array([True, True, True, True, True, True, True])
fullans['efp']['elbl'] = np.array(['_a01o1', '_a02h2', '_a03h3', '_a01n1', '_a02h2', '_a03h3', '_a04h4'])
fullans['efp']['fragment_separators'] = [3]
fullans['efp']['fragment_charges'] = [0., 0.]
fullans['efp']['fragment_multiplicities'] = [1, 1]
fullans['efp']['molecular_charge'] = 0.
fullans['efp']['molecular_multiplicity'] = 1
fullans['efp']['hint_types'] = ['xyzabc', 'xyzabc']
fullans['efp']['geom_hints'][1] = [1.093116487139866, 1.9296501432128303, 2.9104336205167156, -1.1053108079381473, 2.0333070957565544, -1.488586877218809]
final, intermed = qcdb.molparse.from_string(subject, return_processed=True)
import pylibefp
efpobj = pylibefp.from_dict(final['efp'])
efpfinal = efpobj.to_dict()
efpfinal = qcdb.molparse.from_arrays(speclabel=False, domain='efp', **efpfinal)
assert compare_molrecs(fullans['qm'], final['qm'], 4, sys._getframe().f_code.co_name + ': full qm')
assert compare_molrecs(fullans['efp'], efpfinal, 4, sys._getframe().f_code.co_name + ': full efp')
def test_psi4_qmefp_6d():
subject = subject6
fullans = copy.deepcopy(fullans6)
fullans['efp']['geom'] = np.array([-2.22978429, 1.19270015, -0.99721732, -1.85344873, 1.5734809 ,
0.69660583, -0.71881655, 1.40649303, -1.90657336, 0.98792 ,
1.87681 , 2.85174 , 2.31084386, 0.57620385, 3.31175679,
1.87761143, 3.16604791, 1.75667803, 0.55253064, 2.78087794,
4.47837555])
fullans['efp']['elea'] = np.array([16, 1, 1, 14, 1, 1, 1])
fullans['efp']['elez'] = np.array([8, 1, 1, 7, 1, 1, 1])
fullans['efp']['elem'] = np.array(['O', 'H', 'H', 'N', 'H', 'H', 'H'])
fullans['efp']['mass'] = np.array([15.99491462, 1.00782503, 1.00782503, 14.00307400478, 1.00782503, 1.00782503, 1.00782503])
fullans['efp']['real'] = np.array([True, True, True, True, True, True, True])
fullans['efp']['elbl'] = np.array(['_a01o1', '_a02h2', '_a03h3', '_a01n1', '_a02h2', '_a03h3', '_a04h4'])
fullans['efp']['fragment_separators'] = [3]
fullans['efp']['fragment_charges'] = [0., 0.]
fullans['efp']['fragment_multiplicities'] = [1, 1]
fullans['efp']['molecular_charge'] = 0.
fullans['efp']['molecular_multiplicity'] = 1
fullans['efp']['hint_types'] = ['xyzabc', 'xyzabc']
fullans['efp']['geom_hints'][1] = [1.093116487139866, 1.9296501432128303, 2.9104336205167156, -1.1053108079381473, 2.0333070957565544, -1.488586877218809]
final, intermed = qcel.molparse.from_string(subject, return_processed=True)
import pylibefp
efpobj = pylibefp.from_dict(final['efp'])
efpfinal = efpobj.to_dict()
efpfinal = qcel.molparse.from_arrays(speclabel=False, domain='efp', **efpfinal)
assert compare_molrecs(fullans['qm'], final['qm'], 4, sys._getframe().f_code.co_name + ': full qm')
assert compare_molrecs(fullans['efp'], efpfinal, 4, sys._getframe().f_code.co_name + ': full efp')
def geometry(geom, name="default"):
"""Function to create a molecule object of name *name* from the
geometry in string *geom*. Permitted for user use but deprecated
in driver in favor of explicit molecule-passing. Comments within
the string are filtered.
"""
molrec = qcel.molparse.from_string(
geom, enable_qm=True, missing_enabled_return_qm='minimal', enable_efp=True, missing_enabled_return_efp='none')
molecule = core.Molecule.from_dict(molrec['qm'])
molecule.set_name(name)
if 'efp' in molrec:
try:
import pylibefp
except ImportError as e: # py36 ModuleNotFoundError
raise ImportError("""Install pylibefp to use EFP functionality. `conda install pylibefp -c psi4` Or build with `-DENABLE_libefp=ON`""") from e
#print('Using pylibefp: {} (version {})'.format(pylibefp.__file__, pylibefp.__version__))
efpobj = pylibefp.from_dict(molrec['efp'])
# pylibefp.core.efp rides along on molecule
molecule.EFP = efpobj
# Attempt to go ahead and construct the molecule
try:
molecule.update_geometry()
except:
core.print_out("Molecule: geometry: Molecule is not complete, please use 'update_geometry'\n"
" once all variables are set.\n")
activate(molecule)
return molecule
def geometry(geom, name="default"):
"""Function to create a molecule object of name *name* from the
geometry in string *geom*. Permitted for user use but deprecated
in driver in favor of explicit molecule-passing. Comments within
the string are filtered.
"""
molrec = qcel.molparse.from_string(
geom, enable_qm=True, missing_enabled_return_qm='minimal', enable_efp=True, missing_enabled_return_efp='none')
molecule = core.Molecule.from_dict(molrec['qm'])
molecule.set_name(name)
if 'efp' in molrec:
try:
import pylibefp
except ImportError as e: # py36 ModuleNotFoundError
raise ImportError("""Install pylibefp to use EFP functionality. `conda install pylibefp -c psi4` Or build with `-DENABLE_libefp=ON`""") from e
#print('Using pylibefp: {} (version {})'.format(pylibefp.__file__, pylibefp.__version__))
efpobj = pylibefp.from_dict(molrec['efp'])
# pylibefp.core.efp rides along on molecule
molecule.EFP = efpobj
# Attempt to go ahead and construct the molecule
try:
molecule.update_geometry()
except:
core.print_out("Molecule: geometry: Molecule is not complete, please use 'update_geometry'\n"
" once all variables are set.\n")
activate(molecule)
return molecule
