def run(self) -> QMolecule:
psi4d_directory = os.path.dirname(os.path.realpath(__file__))
template_file = psi4d_directory + '/_template.txt'
qiskit_chemistry_directory = os.path.abspath(
os.path.join(psi4d_directory, '../..'))
molecule = QMolecule()
input_text = self._config + '\n'
input_text += 'import sys\n'
syspath = '[\'' + qiskit_chemistry_directory + '\',\'' + '\',\''.join(
sys.path) + '\']'
input_text += 'sys.path = ' + syspath + ' + sys.path\n'
input_text += 'from qmolecule import QMolecule\n'
input_text += '_q_molecule = QMolecule("{0}")\n'.format(
molecule.filename)
with open(template_file, 'r') as file:
input_text += file.read()
file_fd, input_file = tempfile.mkstemp(suffix='.inp')
os.close(file_fd)
with open(input_file, 'w') as stream:
stream.write(input_text)
file_fd, output_file = tempfile.mkstemp(suffix='.out')
os.close(file_fd)
try:
PSI4Driver._run_psi4(input_file, output_file)
if logger.isEnabledFor(logging.DEBUG):
with open(output_file, 'r') as file:
logger.debug('PSI4 output file:\n%s', file.read())
finally:
run_directory = os.getcwd()
for local_file in os.listdir(run_directory):
if local_file.endswith('.clean'):
os.remove(run_directory + '/' + local_file)
try:
os.remove('timer.dat')
except Exception: # pylint: disable=broad-except
pass
try:
os.remove(input_file)
except Exception: # pylint: disable=broad-except
pass
try:
os.remove(output_file)
except Exception: # pylint: disable=broad-except
pass
_q_molecule = QMolecule(molecule.filename)
_q_molecule.load()
# remove internal file
_q_molecule.remove_file()
_q_molecule.origin_driver_name = 'PSI4'
_q_molecule.origin_driver_config = self._config
return _q_molecule
def run(self) -> QMolecule:
hdf5_file = self._hdf5_input
if self.work_path is not None and not os.path.isabs(hdf5_file):
hdf5_file = os.path.abspath(os.path.join(self.work_path, hdf5_file))
if not os.path.isfile(hdf5_file):
raise LookupError('HDF5 file not found: {}'.format(hdf5_file))
molecule = QMolecule(hdf5_file)
molecule.load()
return molecule
def load_molecule(filename):
if os.path.exists(filename):
print(f"Found {filename}. Loading...")
molecule = QMolecule(filename)
molecule.load()
else:
# Regenerate
print(f"Couldn't find {filename}. Regenerating...")
molecule = self.driver.run()
molecule.save(filename)
return molecule
max_memory=1024 * 128,
basis='sto3g'
)
#driver = PySCFDriver(atom='H .0 .0 .0; H .0 .0 0.735',
# unit=UnitsType.ANGSTROM,
# basis='sto3g')
#FILENAME = "hdf5_files/femoco_sto3g_(-1,3).hdf5"
#FILENAME = "hdf5_files/femoco_nosulfer_sto3g_(-1,3).hdf5"
FILENAME = "hdf5_files/lih_sto3g_(0,0).hdf5"
#FILENAME = "hdf5_files/hydrogen.hdf5"
if os.path.exists(FILENAME):
print(f"Found {FILENAME}. Loading...")
molecule = QMolecule(FILENAME)
molecule.load()
else:
# Regenerate
print(f"Couldn't find {FILENAME}. Regenerating...")
molecule = driver.run()
molecule.save(FILENAME)
#print("Loading 1 body integrals...")
#one_body_integrals = molecule.one_body_integrals
##np.save("results/old/lih_1d.npy", one_body_integrals)
#np.save("results/new/lih_1d.npy", one_body_integrals)
#
#print("Loading 2 body integrals...")
#two_body_integrals = molecule.two_body_integrals
#np.save("results/new/lih_2d.npy", two_body_integrals)
