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

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This commit is contained in:
halvorhv 2022-07-15 11:35:09 +02:00
commit dec40c217c
2 changed files with 64 additions and 41 deletions
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13
nafuma/auxillary.py
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@ -134,4 +134,15 @@ def backup_file(filename, backup_dir):
dst = os.path.join(backup_dir, dst_basename)
shutil.copy(filename, dst)
shutil.copy(filename, dst)
def get_unique(full_list):
unique_list = []
for entry in full_list:
if not entry in unique_list:
unique_list.append(entry)
return unique_list

92
nafuma/xrd/refinement.py
View file

@ -1,4 +1,3 @@
from email.policy import default
import os
import shutil
import subprocess
@ -9,6 +8,8 @@ import datetime
import warnings
import json
import pandas as pd
import nafuma.auxillary as aux
@ -160,25 +161,25 @@ def write_params(fout, data, options, index=0):
# WRITE LATTICE PARAMETERS
# If start_values is defined:
fout.write(f'#ifdef start_values_{label}\n')
lpa = f'local lpa_{label} {a} ;: {a}'
lpb = f'local lpb_{label} {b} ;: {b}'
lpc = f'local lpc_{label} {c} ;: {c}'
lpa = f'local !lpa_{label} {a} ;: {a}'
lpb = f'local !lpb_{label} {b} ;: {b}'
lpc = f'local !lpc_{label} {c} ;: {c}'
fout.write('{: <55} {: <55} {: <55}\n'.format(lpa, lpb, lpc))
lpal = f'local lpal_{label} {alpha} ;: {alpha}'
lpbe = f'local lpbe_{label} {beta} ;: {beta}'
lpga = f'local lpga_{label} {gamma} ;: {gamma}'
lpal = f'local !lpal_{label} {alpha} ;: {alpha}'
lpbe = f'local !lpbe_{label} {beta} ;: {beta}'
lpga = f'local !lpga_{label} {gamma} ;: {gamma}'
fout.write('{: <55} {: <55} {: <55}\n'.format(lpal, lpbe, lpga))
# Otherwise
fout.write('\n')
fout.write('#else\n')
lpa = f'local lpa_{label} {a}'
lpb = f'local lpb_{label} {b}'
lpc = f'local lpc_{label} {c}'
lpa = f'local !lpa_{label} {a}'
lpb = f'local !lpb_{label} {b}'
lpc = f'local !lpc_{label} {c}'
fout.write('{: <55} {: <55} {: <55}\n'.format(lpa, lpb, lpc))
lpal = f'local lpal_{label} {alpha}'
lpbe = f'local lpbe_{label} {beta}'
lpga = f'local lpga_{label} {gamma}'
lpal = f'local !lpal_{label} {alpha}'
lpbe = f'local !lpbe_{label} {beta}'
lpga = f'local !lpga_{label} {gamma}'
fout.write('{: <55} {: <55} {: <55}\n'.format(lpal, lpbe, lpga))
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_y': 'y',
'_atom_site_fract_z': 'z',
'_atom_site_occupancy': '!occ',
'_atom_site_B_iso_or_equiv': '!beq'
'_atom_site_occupancy': 'occ',
'_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 = 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('{: <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('{: <55} {: <55} {: <55} {: <55}\n'.format(
f'local csgc_{label}_XXXX = 200 ;: 200',
f'local cslc_{label}_XXXX = 200 ;: 200',
f'local sgc_{label}_XXXX = 0 ;: 0',
f'local slc_{label}_XXXX = 0 ;: 0',
f'local !csgc_{label}_XXXX = 200 ;: 200',
f'local !cslc_{label}_XXXX = 200 ;: 200',
f'local !sgc_{label}_XXXX = 0 ;: 0',
f'local !slc_{label}_XXXX = 0 ;: 0',
))
@ -378,14 +379,13 @@ def write_output(fout, data, options, index=0):
)
fout.write('\n')
fout.write('\t\tOut_String("\\n")\n')
fout.write('#endif')
fout.write('\n\n')
fout.write('#endif')
def read_cif(path):
@ -591,32 +591,40 @@ def write_headers(fout, options):
fout.write(f'{option} {value} \n')
def get_headers(inp):
def get_headers(inp, path):
with open(inp, 'r') as inp:
headers = []
headers = ['index']
line = inp.readline()
while not all(keyword in line for keyword in ['out', 'append']):
while not path in line:
line = inp.readline()
# Jump down to lines
line = inp.readline()
line = inp.readline()
while not 'Out_String' in line:
while not '#endif' in line:
if line.split():
header = line.split()[1]
if all(keyword in header for keyword in ['Get', '(', ')']):
header = header[4:-1]
regx = r"\([\S]*"
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()
return headers
@ -729,11 +737,14 @@ 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 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'])
headers = get_headers(data['inp'])
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):
@ -766,9 +777,10 @@ def refine(data: dict, options={}):
def read_results():
# FIXME Write the function
def read_results(path):
return None
results = pd.read_csv(path, delim_whitespace=True, index_col=0)
return results