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Merge branch 'rasmus_refinements' of github.com:rasmusthog/nafuma into rasmus_refinements

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rasmusvt 2022-07-15 11:51:47 +02:00
commit 772bd25019
1 changed files with 16 additions and 13 deletions
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27
nafuma/xrd/refinement.py
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@ -2,7 +2,7 @@ import os
import shutil import shutil
import subprocess import subprocess
import re import re
import numpy as np
import time import time
import datetime import datetime
import warnings import warnings
@ -250,10 +250,6 @@ def write_str(fout, data, options, index=0):
fout.write(f'\t\tbe = lpbe_{label} ;\n') fout.write(f'\t\tbe = lpbe_{label} ;\n')
fout.write(f'\t\tga = lpga_{label} ;\n') fout.write(f'\t\tga = lpga_{label} ;\n')
fout.write('\n') fout.write('\n')
#FIXME fix the if-statement below, so that cell-volume is the correct formula, based on lattice params and angles.
if '_cell_volume' not in atoms.keys():
atoms['_cell_volume'] = 0
else:
fout.write(f'\t\tcell_volume\t vol_{label}_XXXX {atoms["_cell_volume"]}\n') fout.write(f'\t\tcell_volume\t vol_{label}_XXXX {atoms["_cell_volume"]}\n')
fout.write(f'\t\tcell_mass\t mass_{label}_XXXX 1\n') fout.write(f'\t\tcell_mass\t mass_{label}_XXXX 1\n')
fout.write(f'\t\tweight_percent\t wp_{label}_XXXX 100\n\n') fout.write(f'\t\tweight_percent\t wp_{label}_XXXX 100\n\n')
@ -393,7 +389,7 @@ def write_output(fout, data, options, index=0):
def read_cif(path): def read_cif(path):
data = {'atoms': {}} # Initialise dictionary atoms = {'atoms': {}} # Initialise dictionary
read = True # Initialise read toggle read = True # Initialise read toggle
# Lists attributes to get out of the .CIF-file. This will correspond to what VESTA writes out, not necessarily what you will find in ICSD # Lists attributes to get out of the .CIF-file. This will correspond to what VESTA writes out, not necessarily what you will find in ICSD
@ -428,12 +424,12 @@ def read_cif(path):
# FIXME WHat a horrible condition statement - need to fix this! # FIXME WHat a horrible condition statement - need to fix this!
while line and not line.lstrip().startswith('_') and not line.lstrip().startswith('loop_') and not line.lstrip().startswith('#End') and not line=='\n': while line and not line.lstrip().startswith('_') and not line.lstrip().startswith('loop_') and not line.lstrip().startswith('#End') and not line=='\n':
# Initialise empty dictionary for a given atom if it has not already been created in another loop # Initialise empty dictionary for a given atom if it has not already been created in another loop
if line.split()[0] not in data['atoms'].keys(): if line.split()[0] not in atoms['atoms'].keys():
data["atoms"][line.split()[0]] = {} atoms["atoms"][line.split()[0]] = {}
# Add all the attribute / value pairs for the current loop # Add all the attribute / value pairs for the current loop
for i, attr in enumerate(loop): for i, attr in enumerate(loop):
data["atoms"][line.split()[0]][attr[:-1].lstrip()] = line.split()[i] atoms["atoms"][line.split()[0]][attr[:-1].lstrip()] = line.split()[i]
# Read new line # Read new line
line = cif.readline() line = cif.readline()
@ -453,15 +449,22 @@ def read_cif(path):
value = ' '.join([str(i) for i in value]) value = ' '.join([str(i) for i in value])
data[attr] = value atoms[attr] = value
line = cif.readline() line = cif.readline()
else: else:
line = cif.readline() line = cif.readline()
if '_cell_volume' not in atoms.keys():
a = float(atoms['_cell_length_a'].split('(')[0])
b = float(atoms['_cell_length_b'].split('(')[0])
c = float(atoms['_cell_length_c'].split('(')[0])
alpha = float(atoms['_cell_angle_alpha'].split('(')[0])
beta = float(atoms['_cell_angle_beta'].split('(')[0])
gamma = float(atoms['_cell_angle_gamma'].split('(')[0])
print(data.keys()) atoms['_cell_volume'] = a * b * c * np.sqrt(1-np.cos(alpha)**2 - np.cos(beta)**2 - np.cos(gamma)**2 + 2 * np.cos(alpha) * np.cos(beta) * np. cos(gamma))
return data return atoms