from pymatgen.core.operations import SymmOp from pymatgen.util.coord_utils import get_angle from mpinterfaces.transformations import reduced_supercell_vectors from mpinterfaces.utils import get_ase_slab from mpinterfaces.default_logger import get_default_logger __author__ = "Kiran Mathew, Joshua J. Gabriel" __copyright__ = "Copyright 2017, Henniggroup" __version__ = "1.6" __maintainer__ = "Joshua J. Gabriel" __email__ = "*****@*****.**" __status__ = "Production" __date__ = "March 3, 2017" logger = get_default_logger(__name__) class Interface(Slab): """ Interface = slab + ligand + environment(solvent) Creates a Slab - Ligand Interface of given coverage and given slab-ligand displacement Args: strt: Starting Structure Object for Slab of the Interface hkl: Miller Index of Slab min_thick: Minimum Slab Thickness in Angstroms desired min_vac: Minimum Vacuum Spacing (Padding top and bottom, each) in Angstroms supercell: Trial supercell to start with to enforce coverage,
from monty.json import MontyDecoder from fireworks.user_objects.queue_adapters.common_adapter import CommonAdapter from mpinterfaces.data_processor import MPINTVasprun from mpinterfaces.default_logger import get_default_logger __author__ = "Kiran Mathew, Joshua J. Gabriel" __copyright__ = "Copyright 2017, Henniggroup" __maintainer__ = "Joshua J. Gabriel" __email__ = "*****@*****.**" __status__ = "Production" __date__ = "March 3, 2017" logger = get_default_logger('Project') #get_default_logger(__name__) class MPINTVaspInputSet(DictSet): """ defines the set of input required for a vasp job i.e create INCAR, POSCAR, POTCAR & KPOINTS files """ def __init__(self, name, incar, poscar, kpoints, potcar=None, qadapter=None, script_name='submit_script',
from pymatgen.core.surface import Slab, SlabGenerator from pymatgen.core.operations import SymmOp from pymatgen.util.coord import get_angle from mpinterfaces.transformations import reduced_supercell_vectors from mpinterfaces.utils import get_ase_slab from mpinterfaces.default_logger import get_default_logger __author__ = "Kiran Mathew, Joshua J. Gabriel" __copyright__ = "Copyright 2017, Henniggroup" __maintainer__ = "Joshua J. Gabriel" __email__ = "*****@*****.**" __status__ = "Production" __date__ = "March 3, 2017" logger = get_default_logger(__name__) class Interface(Slab): """ Interface = slab + ligand + environment(solvent) Creates a Slab - Ligand Interface of given coverage and given slab-ligand displacement Args: strt: Starting Structure Object for Slab of the Interface hkl: Miller Index of Slab min_thick: Minimum Slab Thickness in Angstroms desired min_vac: Minimum Vacuum Spacing (Padding top and bottom, each) in Angstroms supercell: Trial supercell to start with to enforce coverage,
def setUp(self): self.mystdout = StringIO() self.logger = get_default_logger("Example_Module_name", self.mystdout)