Chimie Théorique » scripts_chimie4psmn » DockOnSurf

#!/usr/bin/env python

# -*- coding: utf-8 -*-

import ase

from ase import Atom

from ase import data

import numpy as np

# Chemical symbols of new types of atoms

data.chemical_symbols += ['Fe1', 'Fe2']

data.chemical_symbols += ['O1']

# Atomic numbers

Z_Fe = data.atomic_numbers['Fe']

Z_O = data.atomic_numbers['O']

data.atomic_numbers['Fe1'] = Z_Fe

data.atomic_numbers['Fe2'] = Z_Fe

data.atomic_numbers['O1'] = Z_O

# Atomic names

data.atomic_names += ['Iron', 'Iron']

data.atomic_names += ['Oxygen'] 

# Atomic masses

Fe_mass = data.atomic_masses_iupac2016[Z_Fe]

O_mass = data.atomic_masses_iupac2016[Z_O] 

data.atomic_masses_iupac2016 = np.concatenate((data.atomic_masses_iupac2016, np.array([Fe_mass,Fe_mass])))

data.atomic_masses_iupac2016 = np.concatenate((data.atomic_masses_iupac2016, np.array([O_mass])))

data.atomic_masses = data.atomic_masses_iupac2016

Fe_mass = data.atomic_masses_legacy[Z_Fe]

O_mass = data.atomic_masses_legacy[Z_O]

data.atomic_masses_legacy = np.concatenate((data.atomic_masses_legacy, np.array([Fe_mass,Fe_mass])))

data.atomic_masses_legacy = np.concatenate((data.atomic_masses_legacy, np.array([O_mass])))

# Atomic radius

Fe_radius = data.covalent_radii[Z_Fe]

O_radius = data.covalent_radii[Z_O]

data.covalent_radii = np.concatenate((data.covalent_radii, np.array([Fe_radius,Fe_radius])))

data.covalent_radii = np.concatenate((data.covalent_radii, np.array([O_radius])))

# Reference and ground state datas

data.reference_states += [data.reference_states[Z_Fe], data.reference_states[Z_Fe]]

data.reference_states += [data.reference_states[Z_O]]

Fe_gsmm = data.ground_state_magnetic_moments[Z_Fe]

O_gsmm = data.ground_state_magnetic_moments[Z_O]

data.ground_state_magnetic_moments = np.concatenate((data.ground_state_magnetic_moments, np.array([Fe_gsmm,Fe_gsmm])))

data.ground_state_magnetic_moments = np.concatenate((data.ground_state_magnetic_moments, np.array([O_gsmm])))

# VdW raduis

Fe_vdw_r = data.vdw_radii[Z_Fe]

O_vdw_r = data.vdw_radii[Z_O]

data.vdw_radii = np.concatenate((data.vdw_radii, np.array([Fe_vdw_r,Fe_vdw_r])))

data.vdw_radii = np.concatenate((data.vdw_radii, np.array([O_vdw_r])))