Add POSCAR writer and str generator
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rasmusvt
parent
8aa8164a80
commit
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1 changed files with 213 additions and 0 deletions
213
nafuma/dft/io.py
213
nafuma/dft/io.py
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@ -2,6 +2,10 @@ import pandas as pd
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import matplotlib.pyplot as plt
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import numpy as np
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import warnings
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import os
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import linecache
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import nafuma.auxillary as aux
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@ -543,3 +547,212 @@ def get_doscar_information(path):
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#def get_bader_charges(poscar='POSCAR', acf='ACF.dat'):
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def write_poscar(data: dict, options={}):
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required_options = ['path', 'overwrite', 'scale']
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default_options = {
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'path': './POSCAR.vasp',
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'overwrite': False,
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'scale': 1.0
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}
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options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
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if os.path.isfile(options['path']) and not options['overwrite']:
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warnings.warn(f"File {options['path']} already exists, and overwrite disabled. Quitting.")
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return None
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atom_nums = count_atoms(data)
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with open(options['path'], 'w') as fout:
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# Write first line
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for atom in data['atoms']:
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if atom_nums[atom] > 1:
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fout.write(f'{atom}{atom_nums[atom]}')
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else:
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fout.write(f'{atom}')
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fout.write('\t - Automatically generated by the NAFUMA Python package.\n')
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# Write second line
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fout.write(str(options['scale'])+'\n')
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# Write lattice parameters
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# FIXME Now only writes cells without any angles
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fout.write('\t{:<09} \t {:<09} \t {:<09}\n'.format(
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str(data['lattice_parameters'][0]),
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str(0.0),
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str(0.0),
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)
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)
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fout.write('\t{:<09} \t {:<09} \t {:<09}\n'.format(
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str(0.0),
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str(data['lattice_parameters'][1]),
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str(0.0),
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)
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)
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fout.write('\t{:<09} \t {:<09} \t {:<09}\n'.format(
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str(0.0),
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str(0.0),
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str(data['lattice_parameters'][2]),
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)
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)
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# Write atoms
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for atom in data['atoms']:
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fout.write(f'\t{atom}')
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fout.write('\n')
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for atom in data['atoms']:
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fout.write(f'\t{atom_nums[atom]}')
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fout.write('\n')
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fout.write('Direct\n')
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for atom in data['atoms']:
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for label, coords in data['coordinates'].items():
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if atom in label:
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fout.write('\t{:<09} \t {:<09} \t {:<09}\n'.format(
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coords[0],
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coords[1],
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coords[2]
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)
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)
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def apply_transformation(data, rotation=[[1, 0, 0], [0, 1, 0], [0, 0, 1]], translation=[0,0,0]):
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if not isinstance(rotation, np.ndarray):
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rotation = np.array(rotation)
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if not rotation.shape == (3,3):
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print("NOOOO!!!!")
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for label in data['coordinates'].keys():
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data['coordinates'][label] = rotation.dot(data['coordinates'][label])
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data['coordinates'][label] = translate_back(data['coordinates'][label])
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data['coordinates'][label] = data['coordinates'][label] + translation
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return data
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def translate_back(coords):
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for i, coord in enumerate(coords):
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if coord < 0:
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while coords[i] < 0:
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coords[i] = coords[i]+1
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elif coord >= 1:
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while coords[i] >= 1:
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coords[i] = coords[i]-1
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return coords
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def count_atoms(data):
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atom_nums = {}
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for atom in data['atoms']:
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atom_nums[atom] = 0
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for label in data['coordinates'].keys():
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for atom in data['atoms']:
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if atom in label:
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atom_nums[atom] += 1
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return atom_nums
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def append_data(data, new_data):
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if not new_data:
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return data
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if not data:
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data = {
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'atoms': new_data['atoms'],
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'coordinates': {},
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'lattice_parameters': new_data['lattice_parameters']
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}
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atom_num = count_atoms(data)
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new_coords = {}
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for label, coords in data['coordinates'].items():
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new_coords[label] = coords
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extend_unit_cell = [0,0,0]
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for label, coords in new_data['coordinates'].items():
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atom = ''.join(filter(str.isalpha, label))
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number = int(''.join(filter(str.isnumeric, label)))
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new_number = number + atom_num[atom]
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new_label = atom+str(new_number)
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new_coords[new_label] = coords
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for i, coord in enumerate(coords):
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if coord > 1 and np.floor(coord) >= extend_unit_cell[i]:
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extend_unit_cell[i] = np.floor(coord)
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data['coordinates'] = new_coords
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return data
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def make_supercell(data, supercell):
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for i, param in enumerate(data['lattice_parameters']):
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data['lattice_parameters'][i] = supercell[i] * param
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if supercell[i] > 0:
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for label, coords in data['coordinates'].items():
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data['coordinates'][label][i] = (1/supercell[i])*data['coordinates'][label][i]
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def copy_data(data):
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new_data = {}
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new_data['atoms'] = list(data['atoms'])
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new_data['coordinates'] = data['coordinates'].copy()
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new_data['lattice_parameters'] = list(data['lattice_parameters'])
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return new_data
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def unit_vector(vector):
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""" Returns the unit vector of the vector. """
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return vector / np.linalg.norm(vector)
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def angle_between(v1, v2):
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""" Returns the angle in radians between vectors 'v1' and 'v2'::
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>>> angle_between((1, 0, 0), (0, 1, 0))
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1.5707963267948966
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>>> angle_between((1, 0, 0), (1, 0, 0))
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0.0
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>>> angle_between((1, 0, 0), (-1, 0, 0))
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3.141592653589793
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"""
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v1_u = unit_vector(v1)
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v2_u = unit_vector(v2)
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return np.arccos(np.clip(np.dot(v1_u, v2_u), -1.0, 1.0))
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