Examples
Contents
Examples#
Use aadhaar class#
import the aadhaar class
import esta.general.aadhaar as aadh aad = aadh.Aadhaar() aad.read_xyz(filename='x.xyz')
Use vaspBag class#
import the vasp class
import esta.vaspBag.inout.crystal_lattice as clatt xlatt = clatt.Crystal_Lattice("POSCAR", ''./) # or xlatt=clatt.CrystalLattice() xlatt.read_poscar() print('atomic positions: {}'.format(xlatt.tau_cartesian)) print('atomic positions in crystal coordinates: {}'.format(xlatt.tau_direct)) xlatt.get_cell_matrix #array([[7.35205746, 0. , 0. ], # [3.67602873, 6.36706853, 0. ], # [3.67602873, 2.12235618, 6.00292978]]) xlatt.get_cell_vectors #(array([7.35205746, 0. , 0. ]), # array([3.67602873, 6.36706853, 0. ]), # array([3.67602873, 2.12235618, 6.00292978])) xlatt.LV1 #array([7.35205746, 0. , 0. ]) xlatt.LV3 #array([3.67602873, 2.12235618, 6.00292978]) xlatt.real_volume #281.0034678144921 in A^3 # print each atom type xlatt.get_each_atm_type #[1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] # print no. of atoms of each type xlatt.get_natm_type #array([ 4, 4, 14]) *Similary other method of the xlatt object can be excessed; currently all available methods are:* # 'atm_type', 'each_atm_type', 'filename', 'get_all_atoms_labels', 'get_atm_type', 'get_cell_matrix', # 'get_cell_vectors', 'get_dispPOSCAR', 'get_each_atm_type', 'get_grouped_list', 'get_natm_type', # 'get_neach_type', 'get_poscar', 'get_rVolume', 'get_reciprocal_lattice', 'get_selectivePOSCAR', # 'get_unique_list', 'is_cartesian', 'is_crystal', 'is_selective_dynamics', 'l_SelectDynamics', # 'l_crystal', 'location', 'natm_type', 'natoms', 'read_poscar', 'real_volume', 'reciprocal_lattice', # 'tau_cartesian', 'tau_cartestain', 'tau_direct', 'to_cartesian', 'to_crystal'
Use qeBag class#
generate intermediate atomic structures between reactant and product structures:
import numpy as np from esta.vaspBag.inout.crystal_lattice import CrystalLattice import esta.general.get_configs as get_configs output = CrystalLattice(filename = 'ach3oh_00_POSCAR', location = "./") output.get_poscar() atompositions = output.tau_cartesian output2 = CrystalLattice(filename = 'cxyz_POSCAR', location = "./") output2.get_poscar() poscar_obj2 = output2 #.get_poscar() atompositions2 = output2.tau_cartesian N = 9 configurations = get_configs.get_atomic_configurations(N, atompositions, atompositions2) print(configurations[1]) get_configs.get_poscar_images(N, poscar_obj, poscar_obj2)
similarly other components of EStA canbe excessed.