Merge pull request #12 from rasmusthog/rasmus_refinements
Merge refinements into master
This commit is contained in:
Rasmus Vester Thøgersen
GitHub
commit
f0acae491f
6 changed files with 859 additions and 3 deletions
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@ -1,6 +1,10 @@
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import json
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import numpy as np
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import os
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import shutil
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import time
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from datetime import datetime
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def update_options(options, required_options, default_options):
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''' Takes a dictionary of options along with a list of required options and dictionary of default options, and sets all keyval-pairs of options that is not already defined to the default values'''
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@ -73,7 +77,7 @@ def floor(a, roundto=1):
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def write_log(message, options={}):
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from datetime import datetime
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required_options = ['logfile']
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default_options = {
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@ -111,4 +115,34 @@ def move_list_element_last(filenames,string):
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if string in file:
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del filenames[i]
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filenames.append(file)
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return filenames
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return filenames
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def backup_file(filename, backup_dir):
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# Creates backup-folder if it does not exist
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if not os.path.isdir(backup_dir):
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os.makedirs(backup_dir)
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# Get a list of all previous backup files with the same basename as well as the creation time for the
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prev_backup_files = [file for file in os.listdir(backup_dir) if os.path.basename(filename.split('.')[0]) in file]
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creation_time = datetime.strptime(time.ctime(os.path.getmtime(filename)), '%a %b %d %H:%M:%S %Y').strftime("%Y-%m-%d_%H-%M-%S")
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ext = '.' + filename.split('.')[-1]
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dst_basename = creation_time + '_' + filename.split('.')[0] + '_' + f'{len(prev_backup_files)}'.zfill(4) + ext
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dst = os.path.join(backup_dir, dst_basename)
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shutil.copy(filename, dst)
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def get_unique(full_list):
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unique_list = []
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for entry in full_list:
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if not entry in unique_list:
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unique_list.append(entry)
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return unique_list
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@ -1 +1 @@
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from . import io, plot
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from . import io, plot, refinement
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792
nafuma/xrd/refinement.py
Normal file
792
nafuma/xrd/refinement.py
Normal file
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@ -0,0 +1,792 @@
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import os
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import shutil
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import subprocess
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import re
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import numpy as np
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import time
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import datetime
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import warnings
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import json
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import pandas as pd
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import nafuma.auxillary as aux
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def make_initial_inp(data: dict, options={}):
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required_options = ['filename', 'overwrite', 'include', 'save_results', 'save_dir', 'topas_options', 'background', 'capillary', 'start', 'finish', 'exclude']
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default_options = {
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'filename': 'start.inp',
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'overwrite': False,
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'save_results': False,
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'save_dir': 'results/',
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'include': [], # Any files that should be included with #include
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'topas_options': {},
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'background': 7,
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'capillary': False,
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'interval': [None, None], # Start and finish values that TOPAS should refine on. Overrides 'start' and 'finish'
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'start': None, # Start value only. Overridden by 'interval' if this is set.
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'finish': None, # Finish value only. Overridden by 'interval' if this is set.
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'exlude': [] # Excluded regions. List of lists.
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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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options['topas_options'] = update_topas_options(options=options)
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if not os.path.exists(options['filename']) or options['overwrite']:
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with open(options['filename'], 'w') as fout:
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write_headers(fout=fout, options=options)
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\'START OF INP - XXXX')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('r_wp 0 r_exp 0 r_p 0 r_wp_dash 0 r_p_dash 0 r_exp_dash 0 weighted_Durbin_Watson 0 gof 0')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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write_xdd(fout=fout, data=data, options=options)
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\'PARAMETER DEFINITONS')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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for i, str in enumerate(data['str']):
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fout.write('\n\n')
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write_params(fout=fout, data=data, options=options, index=i)
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\'STR DEFINITIONS')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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for i, str in enumerate(data['str']):
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fout.write('\n\n')
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write_str(fout=fout, data=data, options=options, index=i)
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def write_xdd(fout, data, options):
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import nafuma.xrd as xrd
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basedir = os.path.dirname(xrd.__file__)
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with open (os.path.join(basedir, 'snippets.json'), 'r') as snip:
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snippets = json.load(snip)
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topas_options = options['topas_options']
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# Write initial parameters
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fout.write(f'xdd "{data["xdd"]}"\n')
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fout.write('\t'+snippets['calculation_step'].format(topas_options['convolution_step'])+'\n')
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for include in options['include']:
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if 'peak_width' in include:
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with open(include, 'r') as f:
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lines = f.readlines()
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peak_width_params = []
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for line in lines:
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param = line.split()[1][1:]
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peak_width_params.append(param)
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fout.write('\t'+snippets['gauss_fwhm'].format(peak_width_params[0], peak_width_params[1], peak_width_params[2])+'\n')
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# Write background
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fout.write('\tbkg @ ')
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for i in range(options['background']):
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fout.write('0 ')
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# Write wavelength and LP-factor
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fout.write('\n\n')
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fout.write('\t'+snippets['wavelength'].format(data['wavelength'])+'\n')
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fout.write('\t'+snippets['lp_factor'].format(topas_options['lp_factor'])+'\n')
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fout.write('\t'+snippets['zero_error']+'\n')
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if options['capillary']:
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fout.write('\n')
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for i, line in enumerate(snippets['capillary']):
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if i == 0:
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line = line.format(topas_options['packing_density'])
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if i == 1:
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line = line.format(topas_options['capdia'])
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fout.write('\t'+line+'\n')
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fout.write('\n')
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if options['interval'][0] or options['start']:
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options['start'] = options['interval'][0] if options['interval'][0] else options['start']
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fout.write(f'\tstart_X {options["start"]}\n')
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if options['interval'][1] or options['finish']:
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options['finish'] = options['interval'][1] if options['interval'][1] else options['finish']
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fout.write(f'\tfinish_X {options["finish"]}\n')
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if options['exclude']:
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for exclude in options['exclude']:
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fout.write(f'\texclude {exclude[0]} {exclude[1]}\n')
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def write_params(fout, data, options, index=0):
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atoms = read_cif(data['str'][index])
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if 'labels' in data.keys():
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label = data['labels'][index]
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else:
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label = index
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write(atoms['_chemical_name_common'] + f'({atoms["_space_group_name_H-M_alt"]}) - Parameters')
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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a = float(atoms['_cell_length_a'].split('(')[0])
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b = float(atoms['_cell_length_b'].split('(')[0])
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c = float(atoms['_cell_length_c'].split('(')[0])
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alpha = float(atoms['_cell_angle_alpha'].split('(')[0])
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beta = float(atoms['_cell_angle_beta'].split('(')[0])
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gamma = float(atoms['_cell_angle_gamma'].split('(')[0])
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# WRITE LATTICE PARAMETERS
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# If start_values is defined:
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fout.write(f'#ifdef start_values_{label}\n')
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lpa = f'local !lpa_{label} {a} ;: {a}'
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lpb = f'local !lpb_{label} {b} ;: {b}'
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lpc = f'local !lpc_{label} {c} ;: {c}'
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fout.write('{: <55} {: <55} {: <55}\n'.format(lpa, lpb, lpc))
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lpal = f'local !lpal_{label} {alpha} ;: {alpha}'
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lpbe = f'local !lpbe_{label} {beta} ;: {beta}'
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lpga = f'local !lpga_{label} {gamma} ;: {gamma}'
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fout.write('{: <55} {: <55} {: <55}\n'.format(lpal, lpbe, lpga))
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# Otherwise
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fout.write('\n')
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fout.write('#else\n')
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lpa = f'local !lpa_{label} {a}'
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lpb = f'local !lpb_{label} {b}'
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lpc = f'local !lpc_{label} {c}'
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fout.write('{: <55} {: <55} {: <55}\n'.format(lpa, lpb, lpc))
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lpal = f'local !lpal_{label} {alpha}'
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lpbe = f'local !lpbe_{label} {beta}'
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lpga = f'local !lpga_{label} {gamma}'
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fout.write('{: <55} {: <55} {: <55}\n'.format(lpal, lpbe, lpga))
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fout.write('#endif\n\n')
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sites = list(atoms['atoms'].keys())
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attrs = {
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'_atom_site_fract_x': 'x',
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'_atom_site_fract_y': 'y',
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'_atom_site_fract_z': 'z',
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'_atom_site_occupancy': 'occ',
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'_atom_site_B_iso_or_equiv': 'beq'
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}
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# WRITE SITE PARAMETERS
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for site in sites:
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params = []
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for attr in attrs:
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if attr in atoms["atoms"][site].keys():
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value = atoms["atoms"][site][attr].split("(")[0]
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value = value if value != '.' else 0.
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params.append('{: <20} {: <20}'.format(f'local !{attrs[attr]}_{site}_{label}', f' = {value} ;: {value}'))
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#fout.write(f'local {attrs[attr]}_{site}_{label}\t\t =\t {value} \t ;= \t\t\t\t\t')
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fout.write('{: <55} {: <55} {: <55} {: <55} {: <55}\n'.format(*params))
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fout.write('\n')
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fout.write('{: <55} {: <55} {: <55} {: <55}\n'.format(
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f'local !csgc_{label}_XXXX = 200 ;: 200',
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f'local !cslc_{label}_XXXX = 200 ;: 200',
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f'local !sgc_{label}_XXXX = 0 ;: 0',
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f'local !slc_{label}_XXXX = 0 ;: 0',
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))
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# fout.write(f'local csgc_{label} ;:\t\t\t\t\t')
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# fout.write(f'local cslc_{label} ;:\t\t\t\t\t')
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# fout.write(f'local sgc_{label} ;:\t\t\t\t\t')
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# fout.write(f'local slc_{label} ;:\n')
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def write_str(fout, data, options, index=0):
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atoms = read_cif(data['str'][index])
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if 'labels' in data.keys():
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label = data['labels'][index]
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else:
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label = index
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\'' + atoms['_chemical_name_common'].strip('\'') + ' ' + f'({atoms["_space_group_name_H-M_alt"]})'.replace("\'", ""))
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fout.write('\n\'------------------------------------------------------------------------------------------------------------------------------------------\n')
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fout.write('\tstr\n')
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fout.write(f'\t\tphase_name "{atoms["_chemical_name_common"]} ({atoms["_space_group_name_H-M_alt"]})"\n'.replace('\'', ''))
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fout.write(f'\t\tspace_group {atoms["_space_group_IT_number"]}\n')
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fout.write(f'\t\ta = lpa_{label} ;\n')
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fout.write(f'\t\tb = lpb_{label} ;\n')
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fout.write(f'\t\tc = lpc_{label} ;\n')
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fout.write(f'\t\tal = lpal_{label} ;\n')
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fout.write(f'\t\tbe = lpbe_{label} ;\n')
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fout.write(f'\t\tga = lpga_{label} ;\n')
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fout.write('\n')
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fout.write(f'\t\tcell_volume\t vol_{label}_XXXX {atoms["_cell_volume"]}\n')
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fout.write(f'\t\tcell_mass\t mass_{label}_XXXX 1\n')
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fout.write(f'\t\tweight_percent\t wp_{label}_XXXX 100\n\n')
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fout.write('\n')
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fout.write('\t\tscale @ 1.0\n')
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fout.write('\t\tr_bragg 1.0\n\n')
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fout.write(f'\t\t#ifdef crystallite_size_gaussian_{label}\n')
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fout.write(f'\t\tCS_G(csgc_{label}_XXXX)\n')
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fout.write('\t\t#endif\n')
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fout.write(f'\t\t#ifdef crystallite_size_lorentzian_{label}\n')
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fout.write(f'\t\tCS_L(cslc_{label}_XXXX)\n')
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fout.write('\t\t#endif\n\n')
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fout.write(f'\t\t#ifdef strain_gaussian_{label}\n')
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fout.write(f'\t\tStrain_G(sgc_{label}_XXXX)\n')
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fout.write('\t\t#endif\n')
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fout.write(f'\t\t#ifdef strain_lorentzian_{label}\n')
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fout.write(f'\t\tStrain_L(slc_{label}_XXXX)\n')
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fout.write('\t\t#endif\n\n')
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for atom in atoms['atoms'].keys():
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specie = '{}{}'.format(
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atoms["atoms"][atom]["_atom_site_type_symbol"],
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data['oxidation_states'][index][atoms["atoms"][atom]["_atom_site_type_symbol"]]
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)
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site = f'site {atom}'
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x = f'\t\tx = x_{atom}_{label}'
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y = f'\t\ty = y_{atom}_{label}'
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z = f'\t\tz = z_{atom}_{label}'
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occ = '\t\tocc {: <4} = occ_{}_{}'.format(specie, atom, label)
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#occ = f'\t\tocc {atoms["atoms"][atom]["_atom_site_type_symbol"]} occ_{atom}_{label}'
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beq = f'\t\tbeq = beq_{atom}_{label}'
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# FIXME Fix alignment here at some point
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#fout.write(f'\t\tsite {atom}\t x = x_{atom}_{label} ;\t y = y_{atom}_{label} ;\t z = z_{atom}_{label} ;\t occ {atoms["atoms"][atom]["_atom_site_type_symbol"]} occ_{atom}_{label} \t beq = beq_{atom}_{label} \t ;\n')
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fout.write('\t\t{: <9} {: <30}; {: <30}; {: <30}; {: <30}; {: <30};'.format(site, x, y, z, occ, beq))
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fout.write('\n')
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if options['save_results']:
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fout.write('\n\n')
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write_output(fout=fout, data=data, options=options, index=index)
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def write_output(fout, data, options, index=0):
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filename = os.path.basename(data['xdd']).split('.')[0]
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atoms = read_cif(data['str'][index])
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if 'labels' in data.keys():
|
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label = data['labels'][index]
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else:
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label = index
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fout.write('#ifdef output\n')
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fout.write(f'\t\tOut_Riet({options["save_dir"]}/{label}_XXXX_riet.xy)\n')
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fout.write(f'\t\tOut_CIF_STR({options["save_dir"]}/{label}_XXXX.cif)\n')
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fout.write(f'\t\tOut_CIF_ADPs({options["save_dir"]}/{label}_XXXX.cif)\n')
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fout.write(f'\t\tOut_CIF_Bonds_Angles({options["save_dir"]}/{label}_XXXX.cif)\n')
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fout.write(f'\t\tCreate_hklm_d_Th2_Ip_file({options["save_dir"]}/{label}_XXXX_hkl.dat)\n')
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fout.write('\n')
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fout.write(f'out {options["save_dir"]}/{filename}_{label}.dat append\n')
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fout.write(f'\t\tOut_String("XXXX")\n')
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# FIXME Does not write out weighted_Durbin_Watson, TOPAS complained about this
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fout.write('\t\t{: <40} {: <40} {: <40} {: <40} {: <40} {: <40}'.format(
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f'Out(Get(r_wp), "%11.5f")',
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f'Out(Get(r_exp), "%11.5f")',
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f'Out(Get(r_p), "%11.5f")',
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f'Out(Get(r_p_dash), "%11.5f")',
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f'Out(Get(r_exp_dash), "%11.5f")',
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f'Out(Get(gof), "%11.5f")',
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)
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)
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fout.write('\n')
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fout.write('\t\t{: <40} {: <40} {: <40}'.format(
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f'Out(vol_{label}_XXXX, "%11.5f")',
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f'Out(mass_{label}_XXXX, "%11.5f")',
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f'Out(wp_{label}_XXXX, "%11.5f")',
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)
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)
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|
||||
fout.write('\n')
|
||||
|
||||
|
||||
fout.write('\t\t{: <40} {: <40} {: <40} {: <40} {: <40} {: <40}'.format(
|
||||
f'Out(lpa_{label}, "%11.5f")',
|
||||
f'Out(lpb_{label}, "%11.5f")',
|
||||
f'Out(lpc_{label}, "%11.5f")',
|
||||
f'Out(lpal_{label}, "%11.5f")',
|
||||
f'Out(lpbe_{label}, "%11.5f")',
|
||||
f'Out(lpga_{label}, "%11.5f")',
|
||||
|
||||
)
|
||||
)
|
||||
|
||||
fout.write('\n\n')
|
||||
|
||||
for atom in atoms['atoms']:
|
||||
fout.write('\t\t{: <40} {: <40} {: <40} {: <40} {: <40}'.format(
|
||||
f'Out(x_{atom}_{label}, "%11.5f")',
|
||||
f'Out(y_{atom}_{label}, "%11.5f")',
|
||||
f'Out(z_{atom}_{label}, "%11.5f")',
|
||||
f'Out(occ_{atom}_{label}, "%11.5f")',
|
||||
f'Out(beq_{atom}_{label}, "%11.5f")',
|
||||
)
|
||||
)
|
||||
|
||||
fout.write('\n')
|
||||
|
||||
fout.write('\t\tOut_String("\\n")\n')
|
||||
fout.write('#endif')
|
||||
fout.write('\n\n')
|
||||
|
||||
|
||||
|
||||
|
||||
def read_cif(path):
|
||||
|
||||
atoms = {'atoms': {}} # Initialise dictionary
|
||||
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
|
||||
attrs = ['_chemical_name_common', '_cell', '_space_group_name_H-M_alt', '_space_group_IT_number']
|
||||
|
||||
# Open file
|
||||
with open(path, 'r') as cif:
|
||||
line = cif.readline()
|
||||
|
||||
# Read until encountering #End
|
||||
while read:
|
||||
|
||||
# Break loop if #End is reached
|
||||
if not line or line.startswith('#End'):
|
||||
read = False
|
||||
break
|
||||
|
||||
# Handle loops
|
||||
if line.lstrip().startswith('loop_'):
|
||||
loop = []
|
||||
line = cif.readline()
|
||||
|
||||
# Only handle loops with attributes that starts with _atom. Other loops are incompatible with below code due to slight differences in formatting (e.g. lineshifts)
|
||||
while line.lstrip().startswith('_atom'):
|
||||
loop.append(line) # add the attributes of the loop to a list (every keywords starting with _atom)
|
||||
line = cif.readline() # Read next line
|
||||
|
||||
|
||||
# If there were any attributes that started with _atom - if this is empty is just means there were other attributes in this loop
|
||||
if loop:
|
||||
# Read every line after the attribute listing has ended - until it encounters a new attribute, loop or #End tag
|
||||
# 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':
|
||||
# Initialise empty dictionary for a given atom if it has not already been created in another loop
|
||||
if line.split()[0] not in atoms['atoms'].keys():
|
||||
atoms["atoms"][line.split()[0]] = {}
|
||||
|
||||
# Add all the attribute / value pairs for the current loop
|
||||
for i, attr in enumerate(loop):
|
||||
atoms["atoms"][line.split()[0]][attr[:-1].lstrip()] = line.split()[i]
|
||||
|
||||
# Read new line
|
||||
line = cif.readline()
|
||||
|
||||
# If loop list was empty, keep going to the next line
|
||||
else:
|
||||
line = cif.readline()
|
||||
|
||||
|
||||
|
||||
# Handle free-standing attributes
|
||||
elif any([line.lstrip().startswith(i) for i in attrs]):
|
||||
#line.startswith() or line.startswith('_symmetry_space_group_name') or line.startswith('_symmetry_Int_Tables'):
|
||||
#
|
||||
#
|
||||
attr, *value = line.split()
|
||||
|
||||
value = ' '.join([str(i) for i in value])
|
||||
|
||||
atoms[attr] = value
|
||||
line = cif.readline()
|
||||
|
||||
else:
|
||||
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])
|
||||
|
||||
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 atoms
|
||||
|
||||
|
||||
|
||||
|
||||
def update_topas_options(options):
|
||||
import nafuma.xrd as xrd
|
||||
basedir = os.path.dirname(xrd.__file__)
|
||||
|
||||
with open(os.path.join(basedir, 'topas_default.json'), 'r') as default:
|
||||
topas_defaults = json.load(default)
|
||||
|
||||
options['topas_options'] = aux.update_options(options=options['topas_options'], required_options=topas_defaults.keys(), default_options=topas_defaults)
|
||||
|
||||
return options['topas_options']
|
||||
|
||||
def make_big_inp(data: dict, options={}):
|
||||
''' Generates a big .INP-file with all filenames found in data["path"]. Uses a template .INP-file (which has to be generated manually from an initial refinement in TOPAS) and appends this to a large .INP-file
|
||||
while changing the filenames. '''
|
||||
|
||||
|
||||
# FIXME Strip headers from initial INP file before copying it.
|
||||
|
||||
required_options = ['template', 'output', 'overwrite', 'backup', 'backup_dir', 'include', 'topas_options', 'save_results', 'save_dir', 'log', 'logfile']
|
||||
|
||||
default_options = {
|
||||
'template': 'start.inp', # Name of the template .INP-file
|
||||
'output': 'big.inp', # Name of the output .INP-file
|
||||
'overwrite': False, # Toggles overwrite on / off
|
||||
'backup': True, # Toggles backup on / off. Makes a backup of the file if it already exists. Only runs if overwrite is enabled.
|
||||
'backup_dir': 'backup', # Specifies the path where the backup files should be located
|
||||
'include': [],
|
||||
'topas_options': None,
|
||||
'save_results': True,
|
||||
'save_dir': 'results',
|
||||
'log': False,
|
||||
'logfile': f'{datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")}_generate_big_inp.log',
|
||||
}
|
||||
|
||||
options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
|
||||
|
||||
required_topas_options = ['iters', 'chi2_convergence_criteria', 'bootstrap_errors', 'A_matrix_memory_allowed_in_Mbytes', 'approximate_A', 'conserve_memory', 'do_errors', 'continue_after_convergence', 'num_runs']
|
||||
default_topas_options = {
|
||||
'iters': 100000,
|
||||
'chi2_convergence_criteria': 0.001,
|
||||
'bootstrap_errors': None,
|
||||
'A_matrix_memory_allowed_in_Mbytes': None,
|
||||
'approximate_A': False,
|
||||
'conserve_memory': False,
|
||||
'do_errors': False,
|
||||
'continue_after_convergence': False,
|
||||
'num_runs': None,
|
||||
}
|
||||
|
||||
options['topas_options'] = aux.update_options(options=options['topas_options'], required_options=required_topas_options, default_options=default_topas_options)
|
||||
|
||||
|
||||
if not os.path.exists(options['template']):
|
||||
raise Exception(f'Template file not found: {options["template"]}')
|
||||
|
||||
# Raises exception if files exists and overwrite is not enabled
|
||||
if not options['overwrite']:
|
||||
if os.path.exists(options['output']):
|
||||
raise Exception(f'Overwrite disabled and file already exists: {options["output"]}')
|
||||
|
||||
|
||||
# Makes a backup of file
|
||||
elif options['backup'] and os.path.exists(options['output']):
|
||||
|
||||
if options['log']:
|
||||
aux.write_log(message=f'File {options["output"]} already exists. Creating backup in {options["backup_dir"]}.')
|
||||
|
||||
aux.backup_file(filename=options['output'], backup_dir=options['backup_dir'])
|
||||
|
||||
|
||||
runlist = os.path.join(os.path.dirname(options['output']), 'runlist.txt')
|
||||
options['include'].append(runlist)
|
||||
|
||||
with open(options['template'], 'r') as template:
|
||||
strip_headers(template)
|
||||
|
||||
|
||||
with open('tmp_template.inp', 'r') as template, open(options['output'], 'w', newline='\n') as output, open(runlist, 'w', newline='\n') as runlist:
|
||||
|
||||
write_headers(output, options)
|
||||
|
||||
template = template.read()
|
||||
|
||||
for i, path in enumerate(data['path']):
|
||||
|
||||
s = make_inp_entry(template=template, xdd=path, num=i, options=options)
|
||||
output.write(s)
|
||||
output.write('\n\n')
|
||||
|
||||
runlist.write('#define \tUSE_'+f'{i}'.zfill(4) + '\n')
|
||||
|
||||
os.remove('tmp_template.inp')
|
||||
|
||||
|
||||
def strip_headers(fin):
|
||||
|
||||
line = fin.readline()
|
||||
newlines = []
|
||||
|
||||
while 'r_wp' not in line:
|
||||
if line[0] != '\'':
|
||||
line = fin.readline()
|
||||
else:
|
||||
newlines.append(line)
|
||||
line = fin.readline()
|
||||
|
||||
newlines.append(line)
|
||||
newlines = newlines + fin.readlines()
|
||||
|
||||
with open('tmp_template.inp', 'w') as fout:
|
||||
for line in newlines:
|
||||
fout.write(line)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
def write_headers(fout, options):
|
||||
# FIXME Could modify this to make sure that certain combinations of options is not written, such as both do_errors and bootstrap_errors.
|
||||
|
||||
headers = [
|
||||
"A_matrix_memory_allowed_in_Mbytes",
|
||||
"approximate_A",
|
||||
"bootstrap_errors",
|
||||
"conserve_memory",
|
||||
"continue_after_convergence",
|
||||
"do_errors",
|
||||
"chi2_convergence_criteria",
|
||||
"iters",
|
||||
"num_runs" ]
|
||||
|
||||
|
||||
for file in options['include']:
|
||||
fout.write(f'#include {file} \n')
|
||||
|
||||
fout.write('\n')
|
||||
|
||||
if options['save_results']:
|
||||
fout.write('#define output \n')
|
||||
|
||||
fout.write('\n')
|
||||
|
||||
for option, value in options['topas_options'].items():
|
||||
if value and option in headers:
|
||||
if isinstance(value, bool):
|
||||
fout.write(f'{option} \n')
|
||||
else:
|
||||
fout.write(f'{option} {value} \n')
|
||||
|
||||
|
||||
def get_headers(inp, path):
|
||||
|
||||
with open(inp, 'r') as inp:
|
||||
headers = ['index']
|
||||
|
||||
line = inp.readline()
|
||||
|
||||
while not path in line:
|
||||
line = inp.readline()
|
||||
|
||||
# Jump down to lines
|
||||
line = inp.readline()
|
||||
line = inp.readline()
|
||||
|
||||
while not '#endif' in line:
|
||||
if line.split():
|
||||
|
||||
regx = r"\([\S]*"
|
||||
headers_line = re.findall(regx, line)
|
||||
|
||||
for i, header in enumerate(headers_line):
|
||||
header = header[1:-1]
|
||||
|
||||
if all(keyword in header for keyword in ['Get', '(', ')']):
|
||||
header = header[4:-1]
|
||||
|
||||
headers_line[i] = header
|
||||
|
||||
for header in headers_line:
|
||||
if header != '"\\n"':
|
||||
headers.append(header)
|
||||
|
||||
line = inp.readline()
|
||||
|
||||
return headers
|
||||
|
||||
|
||||
def get_paths(inp):
|
||||
|
||||
paths = []
|
||||
|
||||
with open(inp, 'r') as inp:
|
||||
lines = inp.readlines()
|
||||
|
||||
for line in lines:
|
||||
if all(keyword in line for keyword in ['out', 'append']):
|
||||
paths.append(line.split()[1])
|
||||
|
||||
|
||||
return paths
|
||||
|
||||
def make_inp_entry(template: str, xdd: str, num: int, options: dict) -> str:
|
||||
''' Takes a template and creates an entry with xdd as path to file and with number num.'''
|
||||
|
||||
temp_xdd = find_xdd_in_inp(options['template'])
|
||||
|
||||
|
||||
num_str = f'{num}'.zfill(4)
|
||||
|
||||
# Replace diffractogram-path
|
||||
s = template.replace(temp_xdd, xdd).replace('XXXX', num_str)
|
||||
|
||||
return s
|
||||
|
||||
|
||||
|
||||
def find_xdd_in_inp(path: str) -> str:
|
||||
''' Finds the path to the .xy / .xye scan in a given .INP-file. Assumes only one occurence of xdd and will return the last one no matter what, but outputs a UserWarning if more than one xdd is found.'''
|
||||
|
||||
with open(path, 'r') as f:
|
||||
lines = f.readlines()
|
||||
|
||||
|
||||
xdds = 0
|
||||
for line in lines:
|
||||
if 'xdd' in line:
|
||||
xdd = line.split()[-1].strip('"')
|
||||
xdds += 1
|
||||
|
||||
if xdds > 1:
|
||||
warnings.warn(f'More than one path was found in {path}. Returning last occurence - please make sure this is what you want!')
|
||||
|
||||
return xdd
|
||||
|
||||
|
||||
def refine(data: dict, options={}):
|
||||
''' Calls TOPAS from options['topas_path'], which should point to tc.exe in the TOPAS-folder. If not explicitly passed, will try to use what is in topas.conf.'''
|
||||
|
||||
required_options = ['topas_path', 'topas_log', 'topas_logfile', 'log', 'logfile', 'overwrite']
|
||||
|
||||
default_options = {
|
||||
'topas_path': None,
|
||||
'topas_log': False,
|
||||
'topas_logfile': f'{datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")}_topas.out',
|
||||
'log': False,
|
||||
'logfile': f'{datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")}_generate_big_inp.log',
|
||||
'overwrite': False
|
||||
}
|
||||
|
||||
options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
|
||||
|
||||
if not options['topas_path']:
|
||||
import nafuma.xrd as xrd
|
||||
|
||||
# Open topas.conf in the nafuma/xrd
|
||||
with open(os.path.join(os.path.dirname(xrd.__file__), 'topas.conf'), 'r') as f:
|
||||
topas_base = f.read()
|
||||
|
||||
options['topas_path'] = os.path.join(topas_base, 'tc.exe')
|
||||
|
||||
|
||||
# Check to see if the executable exists
|
||||
if not os.path.exists(options['topas_path']):
|
||||
raise Exception('TOPAS executable not found! Please explicitly pass path to tc.exe directly in options["topas_path"] or change base folder in topas.conf to the correct one.')
|
||||
|
||||
|
||||
# Create folders if they don't exist
|
||||
|
||||
# FIXME Since the big INP files now have the same filename for all iterations, we need to adjust the code to only get unique values from the get_paths function
|
||||
# FIXME get_headers() is also not working now. Needs to be adjusted to the new way of writing the Out-parameters
|
||||
paths = get_paths(data['inp'])
|
||||
paths = aux.get_unique(paths)
|
||||
|
||||
|
||||
|
||||
for path in paths:
|
||||
headers = get_headers(data['inp'], path)
|
||||
|
||||
dirname = os.path.dirname(path)
|
||||
|
||||
if dirname and not os.path.isdir(dirname):
|
||||
os.makedirs(dirname)
|
||||
|
||||
if not os.path.exists(path) or options['overwrite']:
|
||||
with open(path, 'w') as results:
|
||||
for header in headers:
|
||||
results.write(header+'\t')
|
||||
|
||||
results.write('\n')
|
||||
else:
|
||||
raise Exception(f'Results file already exists: {path}')
|
||||
|
||||
|
||||
# Create shell command
|
||||
command = ' '.join([options['topas_path'], data['inp']])
|
||||
|
||||
# Append output if logging is enabled
|
||||
if options['topas_log']:
|
||||
command = ' '.join([command, f'>{options["topas_logfile"]}'])
|
||||
|
||||
if os.path.dirname(options['topas_logfile']) and not os.path.isdir(os.path.dirname(options['topas_logfile'])):
|
||||
os.makedirs(os.path.dirname(options['topas_logfile']))
|
||||
|
||||
|
||||
subprocess.call(command, shell=True)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
def read_results(path):
|
||||
|
||||
results = pd.read_csv(path, delim_whitespace=True, index_col=0)
|
||||
|
||||
return results
|
||||
|
||||
|
||||
14
nafuma/xrd/snippets.json
Normal file
14
nafuma/xrd/snippets.json
Normal file
|
|
@ -0,0 +1,14 @@
|
|||
{
|
||||
"calculation_step": "x_calculation_step = Yobs_dx_at(Xo); convolution_step {}",
|
||||
"capillary": [
|
||||
"local !packing_density {} min 0.1 max 1.0 'typically 0.2 to 0.5",
|
||||
"local !capdia {} 'capillary diameter in mm",
|
||||
"local !linab = Get(mixture_MAC) Get(mixture_density_g_on_cm3);: 'in cm-1",
|
||||
"local muR = (capdia/20)*linab*packing_density;",
|
||||
"Cylindrical_I_Correction(muR)"
|
||||
],
|
||||
"gauss_fwhm": "gauss_fwhm = Sqrt({} Cos(2 * Th)^4 + {} Cos(2 * Th)^2 + {});",
|
||||
"lp_factor": "LP_Factor({}) 'change the LP correction or lh value if required",
|
||||
"wavelength": "lam ymin_on_ymax 0.0001 la 1.0 lo {} lh 0.1",
|
||||
"zero_error": "Zero_Error(zero, 0)"
|
||||
}
|
||||
1
nafuma/xrd/topas.conf
Normal file
1
nafuma/xrd/topas.conf
Normal file
|
|
@ -0,0 +1 @@
|
|||
C:/TOPAS6/
|
||||
15
nafuma/xrd/topas_default.json
Normal file
15
nafuma/xrd/topas_default.json
Normal file
|
|
@ -0,0 +1,15 @@
|
|||
{
|
||||
"A_matrix_memory_allowed_in_Mbytes": null,
|
||||
"approximate_A": false,
|
||||
"bootstrap_errors": null,
|
||||
"capdia": 0.5,
|
||||
"chi2_convergence_criteria": 0.001,
|
||||
"conserve_memory": false,
|
||||
"continue_after_convergence": false,
|
||||
"convolution_step": 1,
|
||||
"do_errors": false,
|
||||
"iters": 100000,
|
||||
"lp_factor": 90,
|
||||
"num_runs": null,
|
||||
"packing_density": 0.5
|
||||
}
|
||||
Loading…
Add table
Add a link
Reference in a new issue