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)