logger.warning("This output showed this calculation need to load xml file, so we need this xml file ('%s') to read geometry information"%os.path.normpath(xml_file))
...
...
@@ -99,8 +99,8 @@ class QboxParserContext(object):
logger.warning("Could not find xml file in directory '%s'. "%os.path.dirname(os.path.abspath(self.fName)))
SM (r"\s*\[qbox\]\s*\[qbox\]\s*<cmd>\s*set\s+e_field\s*(?P<qbox_efield_x>[-+0-9.]+)\s+(?P<qbox_efield_y>[-+0-9.]+)\s+(?P<qbox_efield_z>[-+0-9.]+)\s*</cmd>",repeats=True)
SM (r"\s*\[qbox\]\s*\[qbox\]\s*<cmd>\s*set\s+e_field\s*(?P<x_qbox_efield_x>[-+0-9.]+)\s+(?P<x_qbox_efield_y>[-+0-9.]+)\s+(?P<x_qbox_efield_z>[-+0-9.]+)\s*</cmd>",repeats=True)
#???both this version adn qbox_section_efield version could not give mather for efield, need to check.
SM (r"\s*[a-z]=\"\s*(?P<qbox_geometry_lattice_vector_x__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_lattice_vector_y__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_lattice_vector_z__bohr>[-+0-9.]+)\s*\"",repeats=True)
SM (r"\s*[a-z]=\"\s*(?P<x_qbox_geometry_lattice_vector_x__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_lattice_vector_y__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_lattice_vector_z__bohr>[-+0-9.]+)\s*\"",repeats=True)
]),
SM (startReStr=r"\s*<atom\s+name=\"(?P<qbox_geometry_atom_labels>[a-zA-Z0-9]+)\"",
SM (startReStr=r"\s*<atom\s+name=\"(?P<x_qbox_geometry_atom_labels>[a-zA-Z0-9]+)\"",
subMatchers=[
SM (r"\s*<position>\s+(?P<qbox_geometry_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_atom_positions_z__bohr>[-+0-9.]+)\s*</position>",repeats=True),
SM (r"\s*<force>\s+(?P<qbox_atom_force_x__hartree_bohr_1>[-+0-9.]+)\s+(?P<qbox_atom_force_y__hartree_bohr_1>[-+0-9.]+)\s+(?P<qbox_atom_force_z__hartree_bohr_1>[-+0-9.]+)\s*</force>",repeats=True)
SM (r"\s*<position>\s+(?P<x_qbox_geometry_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_atom_positions_z__bohr>[-+0-9.]+)\s*</position>",repeats=True),
SM (r"\s*<force>\s+(?P<x_qbox_atom_force_x__hartree_bohr_1>[-+0-9.]+)\s+(?P<x_qbox_atom_force_y__hartree_bohr_1>[-+0-9.]+)\s+(?P<x_qbox_atom_force_z__hartree_bohr_1>[-+0-9.]+)\s*</force>",repeats=True)
SM (r"\s*<mlwf center=\"\s*(?P<qbox_geometry_MLWF_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_MLWF_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_MLWF_atom_positions_z__bohr>[-+0-9.]+)\s*\"\s+spread=\"\s*(?P<qbox_geometry_MLWF_atom_spread__bohr>[-+0-9.]+)\s*\"",repeats=True)
SM (r"\s*<mlwf center=\"\s*(?P<x_qbox_geometry_MLWF_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_MLWF_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_MLWF_atom_positions_z__bohr>[-+0-9.]+)\s*\"\s+spread=\"\s*(?P<x_qbox_geometry_MLWF_atom_spread__bohr>[-+0-9.]+)\s*\"",repeats=True)
SM (r"\s*<dipole_total>\s+(?P<qbox_dipole_x>[-+0-9.]+)\s+(?P<qbox_dipole_y>[-+0-9.]+)\s+(?P<qbox_dipole_z>[-+0-9.]+)\s*</dipole_total>",repeats=True)
SM (r"\s*<dipole_total>\s+(?P<x_qbox_dipole_x>[-+0-9.]+)\s+(?P<x_qbox_dipole_y>[-+0-9.]+)\s+(?P<x_qbox_dipole_z>[-+0-9.]+)\s*</dipole_total>",repeats=True)
SM (r"\s*[a-z]=\"\s*(?P<qbox_geometry_lattice_vector_x__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_lattice_vector_y__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_lattice_vector_z__bohr>[-+0-9.]+)\s*\"",repeats=True)
SM (r"\s*[a-z]=\"\s*(?P<x_qbox_geometry_lattice_vector_x__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_lattice_vector_y__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_lattice_vector_z__bohr>[-+0-9.]+)\s*\"",repeats=True)
]),
SM (startReStr=r"\s*<atom\s+name=\"(?P<qbox_geometry_atom_labels>[a-zA-Z0-9]+)\"",
SM (startReStr=r"\s*<atom\s+name=\"(?P<x_qbox_geometry_atom_labels>[a-zA-Z0-9]+)\"",
subMatchers=[
SM (r"\s*<position>\s+(?P<qbox_geometry_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<qbox_geometry_atom_positions_z__bohr>[-+0-9.]+)\s*</position>",repeats=True),
SM (r"\s*<position>\s+(?P<x_qbox_geometry_atom_positions_x__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_atom_positions_y__bohr>[-+0-9.]+)\s+(?P<x_qbox_geometry_atom_positions_z__bohr>[-+0-9.]+)\s*</position>",repeats=True),