# -*- coding: utf-8 -*-
########### SVN repository information ###################
# $Date: 2023-05-11 23:37:57 -0500 (Thu, 11 May 2023) $
# $Author: toby $
# $Revision: 5578 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/ISODISTORT.py $
# $Id: ISODISTORT.py 5578 2023-05-12 04:37:57Z toby $
########### SVN repository information ###################
from __future__ import division, print_function
import subprocess as subp
import os
import os.path
try:
import requests
except:
print('Module requests not installed, access to ISODISTORT not possible')
import copy
import GSASIIscriptable as G2sc
import tempfile
isouploadsite = 'https://stokes.byu.edu/iso/isodistortuploadfile.php'
isoformsite = 'https://iso.byu.edu/iso/isodistortform.php'
def HandleError(out):
open('out.html','wb').write(out.encode("utf-8"))
url = os.path.realpath('out.html')
try:
os.startfile(url)
except AttributeError:
try: # should work on MacOS and most linux versions
subp.call(['open', url])
except:
print('Could not open URL')
def UploadCIF(cifname):
#upload cif file to BYU web site
ciffile = open(cifname,'rb')
up1 = {'toProcess':(cifname,ciffile),}
out1 = requests.post(isouploadsite,files=up1).text
ciffile.close()
#retrieve BYU temp file name for cif file
pos = out1.index('<INPUT')+7
pos1 = out1.index('VALUE=',pos)+7
filename = out1[pos1:out1.index('"',pos1)]
print('ciffile %s uploaded to ISODISTORT to make %s'%(cifname,filename))
return filename
def MakePhaseCif(data):
data['pId'] = data.get('pId',0) # needs a pId
proj = G2sc.G2Project(newgpx='tmp4cif.gpx')
ph = G2sc.G2Phase(data,data['General']['Name'],proj)
tempcif = 'ISOin.cif'
ph.export_CIF(tempcif)
return tempcif
[docs]
def GetISODISTORT(Phase):
'''Run Stokes & Campbell ISODISTORT.
This requires doing a post to the BYU upload site with a cif file, which returns a BYU local
copy. This is then sent to the BYU form site with various options, which returns all
subgroups of the entered space group as the text of a web page with a table containing the space
group symbol, the transformation matrix and index for each subgroup. Selection of one of these is
returned to the BYU form site which returns the text of a cif file to be used to create the new phase
which can apply the distortion mode constraints
:params dict Phase: GSAS-II phase data
:returns: radio: dict of possible distortion structures
:returns: data2: list of str input for next run of isositortform for extracting cif file
'''
print('''
For use of ISODISTORT, please cite:
H. T. Stokes, D. M. Hatch, and B. J. Campbell, ISODISTORT, ISOTROPY Software Suite, iso.byu.edu.
B. J. Campbell, H. T. Stokes, D. E. Tanner, and D. M. Hatch, "ISODISPLACE: An Internet Tool for Exploring Structural Distortions."
J. Appl. Cryst. 39, 607-614 (2006).
''')
ISOdata = Phase['ISODISTORT']
parentcif = ISOdata['ParentCIF']
childcif = None
if 'Use this phase' in parentcif:
parentcif = MakePhaseCif(Phase)
print(' Run ISODISTORT with %s as parent cif'%parentcif)
ISOparentcif = UploadCIF(parentcif)
#submit cif for processing by ISODISTORT
up2 = {'filename':ISOparentcif,'input':'uploadparentcif'}
out2 = requests.post(isoformsite,up2).text
#recover required info for the distortion search; includes info from cif file (no longer needed)
try:
pos = out2.index('<p><FORM')
except ValueError:
HandleError(out2)
return [],[]
data = {}
while True:
try:
posB = out2[pos:].index('INPUT TYPE')+pos
posF = out2[posB:].index('>')+posB
items = out2[posB:posF].split('=',3)
name = items[2].split()[0].replace('"','')
if 'isosystem' in name:
break
vals = items[3].replace('"','')
data[name] = vals
pos = posF
except ValueError:
break
#save copy for future use
data2 = copy.deepcopy(data)
#no limits on space group or lattice
if ISOdata['ISOmethod'] == 1:
data['isosubgroup'] = 'no choice'
data['isolattice'] = 'no choice'
data['isoplattice'] = 'no choice'
elif ISOdata['ISOmethod'] == 3:
print('method 3 TBD')
return [],[]
elif ISOdata['ISOmethod'] == 4:
childcif = ISOdata['ChildCIF']
if 'Use this phase' in childcif:
childcif = MakePhaseCif(Phase)
print(' Run ISODISTORT with %s as child cif'%childcif)
ISOchildcif = UploadCIF(childcif)
data['input'] = 'uploadsubgroupcif'
data['filename'] = ISOchildcif
out24 = requests.post(isoformsite,data=data).text
posB = out24.index('OPTION VALUE=')
posF = out24[posB:].index('>')+posB
value = out24[posB+13:posF]
data['input'] = 'distort'
data['origintype'] = 'method4'
data['inputbasis'] = 'list'
data['basisselect'] = value[1:-1]
data['chooseorigin'] = False
data['trynearest'] = True
data['dmax'] = '1'
out25 = requests.post(isoformsite,data=data).text
cifout = GetISOcif(out25,4)
if cifout is None:
return None,None
cifFile = '%s_%s.cif'%(Phase['General']['Name'],'child')
fl = open(cifFile,'wb')
fl.write(cifout.encode("utf-8"))
fl.close()
return [],cifFile
#do the distortion search - result is radio button list of choices
out3 = requests.post(isoformsite,data=data).text
#extract the radio button collection
radio = {}
num = 0
try:
pos = out3.index('RADIO')
except ValueError:
HandleError(out3)
return [],[]
while True:
try:
posF = out3[pos:].index('<BR>')+pos
num += 1
items = out3[pos:posF].split('=',2)[2].split('>')[0]
radio['orderparam%d'%num] = items.replace('"','').replace('CHECKED','')
pos = out3[posF:].index('RADIO')+posF
except ValueError:
break
if parentcif == 'ISOin.cif' or childcif == 'ISOin.cif':
os.remove('ISOin.cif')
return radio,data2
def GetISOcif(out4,method):
try:
pos = out4.index('<FORM ACTION')
except ValueError:
HandleError(out4)
return None
data3 = {}
while True:
try:
posB = out4[pos:].index('INPUT TYPE')+pos
posF = out4[posB:].index('>')+posB
items = out4[posB:posF].split('=',3)
name = items[2].split()[0].replace('"','')
if 'subsetting' in name:
data3[name] = ''
pos = posF
continue
elif 'atomsfile' in name:
data3[name] = ' '
pos = posF
continue
vals = items[3].replace('"','')
data3[name] = vals
pos = posF
if 'origintype' in name:
break
except ValueError:
break
if method == 4:
try:
pos = out4[posF:].index('Enter mode')+posF
pos = out4[pos:].index('<p>')+pos
except ValueError:
HandleError(out4)
while True:
try:
posB = out4[pos:].index('name')+pos
posF = out4[posB:].index('>')+posB
items = out4[posB:posF].split('=')
name = items[1].split()[0].replace('"','')
if name == 'atomicradius':
break
vals = items[2].split()[0].replace('"','')
data3[name] = vals
pos = posF
except ValueError:
break
data3['zeromodes'] = False
#request a cif file
data3['origintype'] = 'structurefile'
data3['inputvalues'] = 'false'
data3['atomicradius'] = '0.4'
data3['bondlength'] = '2.50'
data3['modeamplitude'] = '1.0'
data3['strainamplitude'] = '0.1'
# for item in data3:
# print(item,data3[item])
k = requests.post(isoformsite,data=data3)
out5 = k.text #this is output cif!
#print(out5)
return out5
[docs]
def GetISODISTORTcif(Phase):
'''Run Stokes & Campbell ISODISTORT.
Selection of one of the order parameter disrections is returned to the BYU
form site which returns the text of a cif file to be used to create the new phase
which can apply the distortion mode constraints
:params dict Phase: GSAS-II phase data; contains result of GetISODISTORT above & selection
:returns: CIFfile str: name of cif file created by this in local directory
'''
ISOdata = Phase['ISODISTORT']
data2 = ISOdata['rundata']
#choose one & resubmit
data2['origintype'] = 'method1'
data2['orderparam'] = ISOdata['selection'][1]
data2['input'] = 'distort'
# for item in data2:
# print(item,data2[item])
out4 = requests.post(isoformsite,data=data2).text
#print(out4)
#open('pyout4.html','wb').write(out4.encode("utf-8"))
#retrieve data needed for next(last) step
out5 = GetISOcif(out4,1)
names = ISOdata['selection'][1].split()
cifFile = '%s_%s%s%s.cif'%(Phase['General']['Name'],names[1],names[2].replace('*','_'),names[3])
fl = open(cifFile,'wb')
fl.write(out5.encode("utf-8"))
fl.close()
return cifFile