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Add intial version of refinement function

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rasmusvt 2022-07-12 17:51:08 +02:00
parent 71f3940c12
commit d32b40409c
2 changed files with 156 additions and 21 deletions
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176
nafuma/xrd/refinement.py
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@ -1,17 +1,22 @@
from email.policy import default
import os
import shutil
import time
import subprocess
import re
import time
import datetime
import warnings
import nafuma.auxillary as aux
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. '''
required_options = ['template', 'output', 'overwrite', 'backup', 'backup_dir', 'include', 'topas_options', 'save_dir', 'log', 'logfile']
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
@ -20,7 +25,19 @@ def make_big_inp(data: dict, options={}):
'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': {
'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,
@ -28,13 +45,9 @@ def make_big_inp(data: dict, options={}):
'do_errors': False,
'continue_after_convergence': False,
'num_runs': None,
},
'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)
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']):
@ -55,45 +68,101 @@ def make_big_inp(data: dict, options={}):
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, 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 = change_labels_and_paths(template, path, i, options)
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')
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.
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:
fout.write(f'{option} {value} \n')
if isinstance(value, bool):
fout.write(f'{option} \n')
else:
fout.write(f'{option} {value} \n')
def get_headers(inp):
def change_labels_and_paths(template, path, i, options):
with open(inp, 'r') as inp:
headers = []
line = inp.readline()
while not all(keyword in line for keyword in ['out', 'append']):
line = inp.readline()
# Jump down to lines
line = inp.readline()
line = inp.readline()
while not 'Out_String' in line:
if line.split():
header = line.split()[1]
if all(keyword in header for keyword in ['Get', '(', ')']):
header = header[4:-1]
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, path).replace('XXXX', f'{i}'.zfill(4))
s = template.replace(temp_xdd, xdd).replace('XXXX', num_str)
basename = os.path.basename(path).split(".")[0]
basename = os.path.basename(xdd).split(".")[0]
# Define regular expressions for output lines
regs = [r'Out_Riet\([\S]*\)',
@ -106,23 +175,24 @@ def change_labels_and_paths(template, path, i, options):
# Define substitute strings for output lines
subs = [f'Out_Riet({options["save_dir"]}/{basename}_riet.xy)',
f'Out_CIF_STR({options["save_dir"]}/{basename}.cif))',
f'Out_CIF_ADPs({options["save_dir"]}/{basename}.cif))',
f'Out_CIF_Bonds_Angles({options["save_dir"]}/{basename}.cif))',
f'Out_CIF_STR({options["save_dir"]}/{basename}.cif)',
f'Out_CIF_ADPs({options["save_dir"]}/{basename}.cif)',
f'Out_CIF_Bonds_Angles({options["save_dir"]}/{basename}.cif)',
f'Out_FCF({options["save_dir"]}/{basename}.fcf)',
f'Create_hklm_d_Th2_Ip_file({options["save_dir"]}/{basename}_hkl.dat)',
f'out \t {options["save_dir"]}/{basename}_refined_params.dat']
f'out \t {options["save_dir"]}/{basename}_refined_params.dat \t append']
# Substitute strings in output lines
for reg, sub in zip(regs, subs):
s = re.sub(reg, sub, s)
return s
def find_xdd_in_inp(path):
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:
@ -139,3 +209,67 @@ def find_xdd_in_inp(path):
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
paths, headers = get_paths(data['inp']), get_headers(data['inp'])
for path in paths:
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)

1
nafuma/xrd/topas.conf Normal file
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@ -0,0 +1 @@
C:/TOPAS6/