Fix get_headers to read new formatting correctly
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rasmusvt
parent
7ea27abf3a
commit
c987fc689f
1 changed files with 52 additions and 40 deletions
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@ -1,4 +1,3 @@
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from email.policy import default
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import os
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import shutil
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import subprocess
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@ -9,6 +8,8 @@ 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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@ -160,25 +161,25 @@ def write_params(fout, data, options, index=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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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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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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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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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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@ -188,8 +189,8 @@ def write_params(fout, data, options, index=0):
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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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'_atom_site_occupancy': 'occ',
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'_atom_site_B_iso_or_equiv': 'beq'
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}
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@ -202,7 +203,7 @@ def write_params(fout, data, options, index=0):
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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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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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@ -210,10 +211,10 @@ def write_params(fout, data, options, index=0):
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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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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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@ -383,13 +384,12 @@ def write_output(fout, data, options, index=0):
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fout.write('\n')
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fout.write('\t\tOut_String("\\n")\n')
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fout.write('#endif')
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fout.write('\n\n')
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fout.write('#endif')
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def read_cif(path):
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@ -588,32 +588,40 @@ def write_headers(fout, options):
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fout.write(f'{option} {value} \n')
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def get_headers(inp):
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def get_headers(inp, path):
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with open(inp, 'r') as inp:
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headers = []
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headers = ['index']
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line = inp.readline()
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while not all(keyword in line for keyword in ['out', 'append']):
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while not path in line:
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line = inp.readline()
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# Jump down to lines
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line = inp.readline()
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line = inp.readline()
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while not 'Out_String' in line:
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while not '#endif' in line:
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if line.split():
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header = line.split()[1]
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regx = r"\([\S]*"
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headers_line = re.findall(regx, line)
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for i, header in enumerate(headers_line):
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header = header[1:-1]
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if all(keyword in header for keyword in ['Get', '(', ')']):
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header = header[4:-1]
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headers_line[i] = header
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for header in headers_line:
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if header != '"\\n"':
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headers.append(header)
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line = inp.readline()
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return headers
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@ -727,10 +735,13 @@ def refine(data: dict, options={}):
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# 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
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# FIXME get_headers() is also not working now. Needs to be adjusted to the new way of writing the Out-parameters
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paths = get_paths(data['inp'])
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headers = get_headers(data['inp'])
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paths = aux.get_unique(paths)
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for path in paths:
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headers = get_headers(data['inp'], path)
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dirname = os.path.dirname(path)
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if dirname and not os.path.isdir(dirname):
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@ -763,9 +774,10 @@ def refine(data: dict, options={}):
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def read_results():
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# FIXME Write the function
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def read_results(path):
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return None
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results = pd.read_csv(path, delim_whitespace=True, index_col=0)
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return results
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