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Kvieta1990Kvieta1990
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working on crystal systems
1 parent b0f8703 commit ada3a98

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+117
-66
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2 files changed

+117
-66
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‎GSASII/GSASIIpwdGUI.py

Lines changed: 115 additions & 64 deletions
Original file line numberDiff line numberDiff line change
@@ -4493,7 +4493,7 @@ def LoadUnitCell(event):
44934493

44944494
# TODO: I think this used to work, but this needs to be revisited due to
44954495
# AttributeError: 'G2DataWindow' object has no attribute 'ReImportMenuId'
4496-
# from:
4496+
# from:
44974497
# reqrdr = G2frame.dataWindow.ReImportMenuId.get(event.GetId())
44984498
#
44994499
# def ImportUnitCell(event):
@@ -5163,15 +5163,15 @@ def _showWebPage(event):
51635163
txt = event.GetEventObject().page
51645164
tmp = tempfile.NamedTemporaryFile(suffix='.html',delete=False)
51655165
with open(tmp.name,'w') as fp:
5166-
fp.write(txt.replace('<HEAD>','<head><base href="https://stokes.byu.edu/iso/">',))
5166+
fp.write(txt.replace('<HEAD>','<head><base href="https://stokes.byu.edu/">',))
51675167
fileList.append(tmp.name)
51685168
G2G.ShowWebPage('file://'+tmp.name,G2frame)
51695169

51705170
def showWebtext(txt):
51715171
import tempfile
51725172
tmp = tempfile.NamedTemporaryFile(suffix='.html',delete=False)
51735173
with open(tmp.name,'w') as fp:
5174-
fp.write(txt.replace('<HEAD>','<head><base href="https://stokes.byu.edu/iso/">',))
5174+
fp.write(txt.replace('<HEAD>','<head><base href="https://stokes.byu.edu/">',))
51755175
fileList.append(tmp.name)
51765176
G2G.ShowWebPage('file://'+tmp.name,G2frame)
51775177

@@ -5180,82 +5180,131 @@ def _get_opt_val(opt_name, out):
51805180
opt_match = re.search(opt_pattern, out)
51815181

51825182
return opt_match.group(1)
5183-
5184-
def setup_kvec_input(k_vec):
5183+
5184+
def grab_all_kvecs(out_html):
5185+
"""Extract all k-vectors from the ISODISTORT output HTML."""
5186+
from fractions import Fraction
5187+
import re
5188+
5189+
kvec1_pattern = r'<SELECT NAME="kvec1">(.*?)</SELECT>'
5190+
kvec1_match = re.search(kvec1_pattern, out_html, re.DOTALL)
5191+
5192+
if kvec1_match:
5193+
select_content = kvec1_match.group(1)
5194+
5195+
# Extract option values
5196+
option_pattern = r'<OPTION VALUE="([^"]*)"[^>]*>([^<]*)</OPTION>'
5197+
options = re.findall(option_pattern, select_content)
5198+
5199+
final_kvec_keys = []
5200+
for value, _ in options:
5201+
final_kvec_keys.append(value)
5202+
5203+
all_kvecs = {}
5204+
for key in final_kvec_keys:
5205+
pattern_str = key.split("(")[1].split(")")[0]
5206+
a_val = pattern_str.split(",")[0]
5207+
b_val = pattern_str.split(",")[1]
5208+
c_val = pattern_str.split(",")[2]
5209+
if a_val == "1/2":
5210+
a_val = Fraction(1, 2)
5211+
elif a_val == "1/3":
5212+
a_val = Fraction(1, 3)
5213+
elif a_val == "1":
5214+
a_val = 1
5215+
elif a_val == "0":
5216+
a_val = 0
5217+
5218+
if b_val == "1/2":
5219+
b_val = Fraction(1, 2)
5220+
elif b_val == "1/3":
5221+
b_val = Fraction(1, 3)
5222+
elif b_val == "1":
5223+
b_val = 1
5224+
elif b_val == "0":
5225+
b_val = 0
5226+
5227+
if c_val == "1/2":
5228+
c_val = Fraction(1, 2)
5229+
elif c_val == "1/3":
5230+
c_val = Fraction(1, 3)
5231+
elif c_val == "1":
5232+
c_val = 1
5233+
elif c_val == "0":
5234+
c_val = 0
5235+
5236+
all_kvecs[key] = (a_val, b_val, c_val)
5237+
5238+
return all_kvecs
5239+
else:
5240+
return None
5241+
5242+
def setup_kvec_input(k_vec, k_vec_dict, symmetry=None):
51855243
"""Set up the input for isodistort post request
51865244
51875245
Args:
51885246
k_vec (str): The k-vector to use for the isodistort request.
5247+
k_vec_dict (dict): The dictionary containing the k-vector
5248+
form extracted from isodistort.
5249+
symmetry (str, optional): The crystal system.
51895250
51905251
Returns:
51915252
dict: New entries and those need to be corrected in the data
51925253
to be used in the post request.
51935254
"""
5194-
from fractions import Fraction
5195-
5196-
k_vec_dict = {
5197-
" 1 *GM, k16 (0,0,0)": (0, 0, 0),
5198-
" 2 *DT, k11 (0,0,g)": (0, 0, "a"),
5199-
" 3 *LD, k6 (a,a,0)": ("a", "a", 0),
5200-
" 4 *SM, k5 (a,0,0)": ("a", 0, 0),
5201-
" 5 *A, k17 (0,0,1/2)": (0, 0, Fraction(1, 2)),
5202-
" 6 *H, k15 (1/3,1/3,1/2)": (
5203-
Fraction(1, 3),
5204-
Fraction(1, 3),
5205-
Fraction(1, 2)
5206-
),
5207-
" 7 *K, k13 (1/3,1/3,0)": (Fraction(1, 3), Fraction(1, 3), 0),
5208-
" 8 *L, k14 (1/2,0,1/2)": (Fraction(1, 2), 0, Fraction(1, 2)),
5209-
" 9 *M, k12 (1/2,0,0)": (Fraction(1, 2), 0, 0),
5210-
"10 *P, k10 (1/3,1/3,g)": (
5211-
Fraction(1, 3),
5212-
Fraction(1, 3),
5213-
"g"
5214-
),
5215-
"11 *Q, k8 (a,a,1/2)": ("a", "a", Fraction(1, 2)),
5216-
"12 *R, k7 (a,0,1/2)": ("a", 0, Fraction(1, 2)),
5217-
"13 *U, k9 (1/2,0,g)": (Fraction(1, 2), 0, "g"),
5218-
"14 *B, k1 (a,b,0)": ("a", "b", 0),
5219-
"15 *C, k4 (a,a,g)": ("a", "a", "g"),
5220-
"16 *D, k3 (a,0,g)": ("a", 0, "g"),
5221-
"17 *E, k2 (a,b,1/2)": ("a", "b", Fraction(1, 2)),
5222-
"18 *GP, k0 (a,b,g)": ("a", "b", "g")
5223-
}
5224-
5225-
def match_vector_pattern(k_vec, k_vec_dict):
5255+
def match_vector_pattern(k_vec, k_vec_dict, symmetry=None):
52265256
"""Check the k-vector against the standard form in isodistort.
52275257
52285258
Args:
5229-
k_vec (str): The k-vector to use for the isodistort
5230-
request.
5231-
k_vec_dict (dict): The standard k-vector form in
5232-
isodistort.
5259+
k_vec (str): The k-vector to use for the isodistort request.
5260+
k_vec_dict (dict): The standard k-vector form in isodistort.
5261+
symmetry (str, optional): The crystal system.
52335262
52345263
Returns:
52355264
str: The standard k-vector form in isodistort.
52365265
"""
5266+
from itertools import permutations
5267+
52375268
all_matches = list()
5269+
52385270
for desc, pattern in k_vec_dict.items():
52395271
if len(pattern) != len(k_vec):
52405272
continue
5241-
placeholders = {}
5242-
match = True
5243-
for p_val, k_val in zip(pattern, k_vec):
5244-
if isinstance(p_val, str):
5245-
if p_val.isalpha():
5246-
if p_val not in placeholders:
5247-
placeholders[p_val] = k_val
5248-
elif placeholders[p_val] != k_val:
5273+
5274+
# Generate sequences to check based on symmetry
5275+
if symmetry == 'cubic':
5276+
# For cubic symmetry, check all permutations of k_vec
5277+
k_vec_sequences = list(permutations(k_vec))
5278+
else:
5279+
# For other symmetries, maintain original order
5280+
k_vec_sequences = [k_vec]
5281+
5282+
# Check if any permutation matches the pattern
5283+
pattern_matched = False
5284+
for k_vec_seq in k_vec_sequences:
5285+
placeholders = {}
5286+
match = True
5287+
for p_val, k_val in zip(pattern, k_vec_seq):
5288+
if isinstance(p_val, str):
5289+
if p_val.isalpha():
5290+
if p_val not in placeholders:
5291+
placeholders[p_val] = k_val
5292+
elif placeholders[p_val] != k_val:
5293+
match = False
5294+
break
5295+
else:
52495296
match = False
52505297
break
52515298
else:
5252-
match = False
5253-
break
5254-
else:
5255-
if p_val != k_val:
5256-
match = False
5257-
break
5258-
if match:
5299+
if p_val != k_val:
5300+
match = False
5301+
break
5302+
5303+
if match:
5304+
pattern_matched = True
5305+
break
5306+
5307+
if pattern_matched:
52595308
all_matches.append(desc)
52605309

52615310
idp_params_num = 3
@@ -5271,7 +5320,7 @@ def match_vector_pattern(k_vec, k_vec_dict):
52715320

52725321
return final_match
52735322

5274-
k_vec_form = match_vector_pattern(k_vec, k_vec_dict)
5323+
k_vec_form = match_vector_pattern(k_vec, k_vec_dict, symmetry="cubic")
52755324

52765325
data_update = dict()
52775326
data_update['kvec1'] = k_vec_form
@@ -5298,7 +5347,7 @@ def match_vector_pattern(k_vec, k_vec_dict):
52985347
from fractions import Fraction
52995348
from GSASII.exports import G2export_CIF
53005349
from . import ISODISTORT as ISO
5301-
isoformsite = 'https://iso.byu.edu/iso/isodistortform.php'
5350+
isoformsite = 'https://iso.byu.edu/isodistortform.php'
53025351

53035352
if not G2frame.kvecSearch['mode']:
53045353
return
@@ -5313,7 +5362,7 @@ def match_vector_pattern(k_vec, k_vec_dict):
53135362

53145363
if kpoint is None:
53155364
wx.MessageBox(
5316-
"Please select a k-vector from the table.",
5365+
"Please select a k-vector from the table.",
53175366
style=wx.ICON_INFORMATION,
53185367
caption='Isotropic Subgroup Generation'
53195368
)
@@ -5329,7 +5378,7 @@ def match_vector_pattern(k_vec, k_vec_dict):
53295378
This can take up to a few minutes. Check the terminal for progress.
53305379
'''
53315380
wx.MessageBox(
5332-
f"{isoCite}\n\n{info_str}",
5381+
f"{isoCite}\n\n{info_str}",
53335382
style=wx.ICON_INFORMATION,
53345383
caption='Isotropic Subgroup Generation'
53355384
)
@@ -5438,7 +5487,9 @@ def match_vector_pattern(k_vec, k_vec_dict):
54385487
data['input'] = 'kvector'
54395488
data['irrepcount'] = '1'
54405489

5441-
data_update = setup_kvec_input(kpoint_frac)
5490+
kvec_dict = grab_all_kvecs(out2)
5491+
5492+
data_update = setup_kvec_input(kpoint_frac, kvec_dict)
54425493
for key, value in data_update.items():
54435494
data[key] = value
54445495

@@ -5552,7 +5603,7 @@ def match_vector_pattern(k_vec, k_vec_dict):
55525603
# reopen tree to the original phase
55535604
def _ShowPhase():
55545605
phId = G2gd.GetGPXtreeItemId(G2frame, G2frame.root, 'Phases')
5555-
G2frame.GPXtree.Expand(phId)
5606+
G2frame.GPXtree.Expand(phId)
55565607
phId = G2gd.GetGPXtreeItemId(G2frame, phId, phsnam)
55575608
G2frame.GPXtree.SelectItem(phId)
55585609

@@ -5563,7 +5614,7 @@ def _ShowPhase():
55635614
{os.getcwd()}
55645615
'''
55655616
wx.MessageBox(
5566-
info_msg,
5617+
info_msg,
55675618
style=wx.ICON_INFORMATION,
55685619
caption='Isotropic Subgroup Generation'
55695620
)
@@ -7470,7 +7521,7 @@ def setBackgroundColors(im,it):
74707521
def OnToggleExt(event):
74717522
G2frame.Hide = not G2frame.Hide
74727523
UpdateReflectionGrid(G2frame,data,HKLF=True,Name=Name)
7473-
7524+
74747525
def OnPageChanged(event):
74757526
'''Respond to a press on a phase tab by displaying the reflections. This
74767527
routine is needed because the reflection table may not have been created yet.

‎GSASII/ISODISTORT.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -11,8 +11,8 @@
1111
from . import GSASIIscriptable as G2sc
1212
from . import GSASIIctrlGUI as G2G
1313
#import tempfile
14-
isouploadsite = 'https://stokes.byu.edu/iso/isodistortuploadfile.php'
15-
isoformsite = 'https://iso.byu.edu/iso/isodistortform.php'
14+
isouploadsite = 'https://iso.byu.edu/isodistortuploadfile.php'
15+
isoformsite = 'https://iso.byu.edu/isodistortform.php'
1616

1717
def HandleError(out):
1818
with open('out.html','wb') as fp:

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