hetero2d.io package

Submodules

hetero2d.io.VaspInterfaceSet module

This class instantiates the default VASP input set to simulate 2D-substrate slab hetero_interfaces.

class hetero2d.io.VaspInterfaceSet.CMDLRelaxSet(structure, **kwargs)

Bases: pymatgen.io.vasp.sets.DictSet

Implementation of VaspInputSet utilizing parameters in the public 2D Materials Synthesis Database.

CONFIG = {'INCAR': {'ALGO': 'FAST', 'EDIFF': 1e-06, 'EDIFFG': -0.02, 'ENCUT': 520, 'IBRION': 2, 'ICHARG': 1, 'ISIF': 3, 'ISMEAR': 0, 'ISPIN': 1, 'LORBIT': 11, 'LREAL': 'AUTO', 'LWAVE': False, 'MAGMOM': {'Ce': 5, 'Ce3+': 1, 'Co': 5, 'Co3+': 0.6, 'Co4+': 1, 'Cr': 5, 'Dy3+': 5, 'Er3+': 3, 'Eu': 10, 'Eu2+': 7, 'Eu3+': 6, 'Fe': 5, 'Gd3+': 7, 'Ho3+': 4, 'La3+': 0.6, 'Lu3+': 0.6, 'Mn': 5, 'Mn3+': 4, 'Mn4+': 3, 'Mo': 5, 'Nd3+': 3, 'Ni': 5, 'Pm3+': 4, 'Pr3+': 2, 'Sm3+': 5, 'Tb3+': 6, 'Tm3+': 2, 'V': 5, 'W': 5, 'Yb3+': 1}, 'NELM': 100, 'NSW': 99, 'POTIM': 0.15, 'PREC': 'Accurate', 'SIGMA': 0.05}, 'KPOINTS': {'reciprocal_density': 64}, 'POTCAR': {'Ac': 'Ac', 'Ag': 'Ag', 'Al': 'Al', 'Ar': 'Ar', 'As': 'As', 'Au': 'Au', 'B': 'B', 'Ba': 'Ba_sv', 'Be': 'Be_sv', 'Bi': 'Bi', 'Br': 'Br', 'C': 'C', 'Ca': 'Ca_sv', 'Cd': 'Cd', 'Ce': 'Ce', 'Cl': 'Cl', 'Co': 'Co', 'Cr': 'Cr_pv', 'Cs': 'Cs_sv', 'Cu': 'Cu_pv', 'Dy': 'Dy_3', 'Er': 'Er_3', 'Eu': 'Eu', 'F': 'F', 'Fe': 'Fe_pv', 'Ga': 'Ga_d', 'Gd': 'Gd', 'Ge': 'Ge_d', 'H': 'H', 'He': 'He', 'Hf': 'Hf_pv', 'Hg': 'Hg', 'Ho': 'Ho_3', 'I': 'I', 'In': 'In_d', 'Ir': 'Ir', 'K': 'K_sv', 'Kr': 'Kr', 'La': 'La', 'Li': 'Li_sv', 'Lu': 'Lu_3', 'Mg': 'Mg_pv', 'Mn': 'Mn_pv', 'Mo': 'Mo_pv', 'N': 'N', 'Na': 'Na_pv', 'Nb': 'Nb_pv', 'Nd': 'Nd_3', 'Ne': 'Ne', 'Ni': 'Ni_pv', 'Np': 'Np', 'O': 'O', 'Os': 'Os_pv', 'P': 'P', 'Pa': 'Pa', 'Pb': 'Pb_d', 'Pd': 'Pd', 'Pm': 'Pm_3', 'Pr': 'Pr_3', 'Pt': 'Pt', 'Pu': 'Pu', 'Rb': 'Rb_sv', 'Re': 'Re_pv', 'Rh': 'Rh_pv', 'Ru': 'Ru_pv', 'S': 'S', 'Sb': 'Sb', 'Sc': 'Sc_sv', 'Se': 'Se', 'Si': 'Si', 'Sm': 'Sm_3', 'Sn': 'Sn_d', 'Sr': 'Sr_sv', 'Ta': 'Ta_pv', 'Tb': 'Tb_3', 'Tc': 'Tc_pv', 'Te': 'Te', 'Th': 'Th', 'Ti': 'Ti_pv', 'Tl': 'Tl_d', 'Tm': 'Tm_3', 'U': 'U', 'V': 'V_pv', 'W': 'W_pv', 'Xe': 'Xe', 'Y': 'Y_sv', 'Yb': 'Yb_2', 'Zn': 'Zn', 'Zr': 'Zr_sv'}}
class hetero2d.io.VaspInterfaceSet.CMDLInterfaceSet(structure, k_product=20, iface=True, vdw='optB88', auto_dipole=False, set_mix=False, sort_structure=False, user_incar_settings=None, **kwargs)

Bases: hetero2d.io.VaspInterfaceSet.CMDLRelaxSet

Class for writing a set of interface vasp runs, including the 2D, substrate slabs, and hetero_interface (oriented along the c direction) as well as the bulk (3D) phase of the 2D material and the un-oriented unit cells, to ensure the same K_POINTS, POTCAR and INCAR criterion.

Parameters

structure (Structure) – The structure for the calculation

Other Parameters

  • k_product (int) – default to 20, k_point number x length for a & b directions, also for c direction in bulk calculations

  • iface (bool) – Set to False for initial structure calculations to fully relax the structures to calculate the adsorption energy of a 2D material on the substrate slab. Defaults to True.

  • vdw (str) – The string representation for the vdW correction functional that will be used for the simulations. Defaults to optB88.

  • auto_dipole (bool) – Whether to set dipole corrections. Defaults to False.

  • set_mix (bool) – Whether to set the mixing parameters. Defaults to False.

  • sort_structure (bool) – Whether to sort the structure. Defaults to False.

  • user_incar_settings (dict) – A way to override the default settings for the incar.

  • kwargs – Other kwargs supported by DictSet.

Returns

Vasp input set object

property kpoints

k_product (default to 20) is k_point number * length for a & b directions, also for c direction in bulk calculations. Automatic mesh & Gamma is the default setting.

as_dict(verbosity=2)

A JSON serializable dict representation of an object.

Module contents