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Fix get_headers to read new formatting correctly

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rasmusvt 2022-07-15 11:26:57 +02:00
parent 7ea27abf3a
commit c987fc689f
1 changed files with 52 additions and 40 deletions
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92
nafuma/xrd/refinement.py
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@ -1,4 +1,3 @@
from email.policy import default
import os import os
import shutil import shutil
import subprocess import subprocess
@ -9,6 +8,8 @@ import datetime
import warnings import warnings
import json import json
import pandas as pd
import nafuma.auxillary as aux import nafuma.auxillary as aux
@ -160,25 +161,25 @@ def write_params(fout, data, options, index=0):
# WRITE LATTICE PARAMETERS # WRITE LATTICE PARAMETERS
# If start_values is defined: # If start_values is defined:
fout.write(f'#ifdef start_values_{label}\n') fout.write(f'#ifdef start_values_{label}\n')
lpa = f'local lpa_{label} {a} ;: {a}' lpa = f'local !lpa_{label} {a} ;: {a}'
lpb = f'local lpb_{label} {b} ;: {b}' lpb = f'local !lpb_{label} {b} ;: {b}'
lpc = f'local lpc_{label} {c} ;: {c}' lpc = f'local !lpc_{label} {c} ;: {c}'
fout.write('{: <55} {: <55} {: <55}\n'.format(lpa, lpb, lpc)) fout.write('{: <55} {: <55} {: <55}\n'.format(lpa, lpb, lpc))
lpal = f'local lpal_{label} {alpha} ;: {alpha}' lpal = f'local !lpal_{label} {alpha} ;: {alpha}'
lpbe = f'local lpbe_{label} {beta} ;: {beta}' lpbe = f'local !lpbe_{label} {beta} ;: {beta}'
lpga = f'local lpga_{label} {gamma} ;: {gamma}' lpga = f'local !lpga_{label} {gamma} ;: {gamma}'
fout.write('{: <55} {: <55} {: <55}\n'.format(lpal, lpbe, lpga)) fout.write('{: <55} {: <55} {: <55}\n'.format(lpal, lpbe, lpga))
# Otherwise # Otherwise
fout.write('\n') fout.write('\n')
fout.write('#else\n') fout.write('#else\n')
lpa = f'local lpa_{label} {a}' lpa = f'local !lpa_{label} {a}'
lpb = f'local lpb_{label} {b}' lpb = f'local !lpb_{label} {b}'
lpc = f'local lpc_{label} {c}' lpc = f'local !lpc_{label} {c}'
fout.write('{: <55} {: <55} {: <55}\n'.format(lpa, lpb, lpc)) fout.write('{: <55} {: <55} {: <55}\n'.format(lpa, lpb, lpc))
lpal = f'local lpal_{label} {alpha}' lpal = f'local !lpal_{label} {alpha}'
lpbe = f'local lpbe_{label} {beta}' lpbe = f'local !lpbe_{label} {beta}'
lpga = f'local lpga_{label} {gamma}' lpga = f'local !lpga_{label} {gamma}'
fout.write('{: <55} {: <55} {: <55}\n'.format(lpal, lpbe, lpga)) fout.write('{: <55} {: <55} {: <55}\n'.format(lpal, lpbe, lpga))
fout.write('#endif\n\n') fout.write('#endif\n\n')
@ -188,8 +189,8 @@ def write_params(fout, data, options, index=0):
'_atom_site_fract_x': 'x', '_atom_site_fract_x': 'x',
'_atom_site_fract_y': 'y', '_atom_site_fract_y': 'y',
'_atom_site_fract_z': 'z', '_atom_site_fract_z': 'z',
'_atom_site_occupancy': '!occ', '_atom_site_occupancy': 'occ',
'_atom_site_B_iso_or_equiv': '!beq' '_atom_site_B_iso_or_equiv': 'beq'
} }
@ -202,7 +203,7 @@ def write_params(fout, data, options, index=0):
value = atoms["atoms"][site][attr].split("(")[0] value = atoms["atoms"][site][attr].split("(")[0]
value = value if value != '.' else 0. value = value if value != '.' else 0.
params.append('{: <20} {: <20}'.format(f'local {attrs[attr]}_{site}_{label}', f' = {value} ;: {value}')) params.append('{: <20} {: <20}'.format(f'local !{attrs[attr]}_{site}_{label}', f' = {value} ;: {value}'))
#fout.write(f'local {attrs[attr]}_{site}_{label}\t\t =\t {value} \t ;= \t\t\t\t\t') #fout.write(f'local {attrs[attr]}_{site}_{label}\t\t =\t {value} \t ;= \t\t\t\t\t')
fout.write('{: <55} {: <55} {: <55} {: <55} {: <55}\n'.format(*params)) fout.write('{: <55} {: <55} {: <55} {: <55} {: <55}\n'.format(*params))
@ -210,10 +211,10 @@ def write_params(fout, data, options, index=0):
fout.write('\n') fout.write('\n')
fout.write('{: <55} {: <55} {: <55} {: <55}\n'.format( fout.write('{: <55} {: <55} {: <55} {: <55}\n'.format(
f'local csgc_{label}_XXXX = 200 ;: 200', f'local !csgc_{label}_XXXX = 200 ;: 200',
f'local cslc_{label}_XXXX = 200 ;: 200', f'local !cslc_{label}_XXXX = 200 ;: 200',
f'local sgc_{label}_XXXX = 0 ;: 0', f'local !sgc_{label}_XXXX = 0 ;: 0',
f'local slc_{label}_XXXX = 0 ;: 0', f'local !slc_{label}_XXXX = 0 ;: 0',
)) ))
@ -382,14 +383,13 @@ def write_output(fout, data, options, index=0):
) )
fout.write('\n') fout.write('\n')
fout.write('\t\tOut_String("\\n")\n')
fout.write('#endif')
fout.write('\n\n') fout.write('\n\n')
fout.write('#endif')
def read_cif(path): def read_cif(path):
@ -588,32 +588,40 @@ def write_headers(fout, options):
fout.write(f'{option} {value} \n') fout.write(f'{option} {value} \n')
def get_headers(inp): def get_headers(inp, path):
with open(inp, 'r') as inp: with open(inp, 'r') as inp:
headers = [] headers = ['index']
line = inp.readline() line = inp.readline()
while not all(keyword in line for keyword in ['out', 'append']): while not path in line:
line = inp.readline() line = inp.readline()
# Jump down to lines # Jump down to lines
line = inp.readline() line = inp.readline()
line = inp.readline() line = inp.readline()
while not 'Out_String' in line: while not '#endif' in line:
if line.split(): if line.split():
header = line.split()[1]
if all(keyword in header for keyword in ['Get', '(', ')']): regx = r"\([\S]*"
header = header[4:-1] headers_line = re.findall(regx, line)
headers.append(header) 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() line = inp.readline()
return headers return headers
@ -726,11 +734,14 @@ def refine(data: dict, options={}):
# 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 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 # 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 = get_paths(data['inp'])
headers = get_headers(data['inp']) paths = aux.get_unique(paths)
for path in paths: for path in paths:
headers = get_headers(data['inp'], path)
dirname = os.path.dirname(path) dirname = os.path.dirname(path)
if dirname and not os.path.isdir(dirname): if dirname and not os.path.isdir(dirname):
@ -763,9 +774,10 @@ def refine(data: dict, options={}):
def read_results(): def read_results(path):
# FIXME Write the function
return None results = pd.read_csv(path, delim_whitespace=True, index_col=0)
return results