source: trunk/SUBGROUPS.py @ 5036

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1# -*- coding: utf-8 -*-
2"""
3*SUBGROUPS: Interface to special GSAS Bilbao SUBGROUPS & k-SUBGROUPSMAG web pages*
4-------------------------------
5
6Extraction of  space subgroups for a given space group and a propagation vector
7from the GSAS version of SUBGROUPS & k-SUBGROUPSMAG web page on the Bilbao Crystallographic server
8
9"""
10########### SVN repository information ###################
11# $Date: 2020-03-19 15:51:52 +0000 (Thu, 19 Mar 2020) $
12# $Author: vondreele $
13# $Revision: 4374 $
14# $URL: trunk/SUBGROUPS.py $
15# $Id: SUBGROUPS.py 4374 2020-03-19 15:51:52Z vondreele $
16########### SVN repository information ###################
17from __future__ import division, print_function
18import numpy as np
19import numpy.linalg as nl
20import GSASIIspc as G2spc
21import GSASIIIO as G2IO
22import GSASIIpath
23GSASIIpath.SetBinaryPath()
24submagSite = 'https://www.cryst.ehu.es/cgi-bin/cryst/programs/subgrmag1_general_GSAS.pl?'
25
26def GetNonStdSubgroups(SGData, kvec,star=False,landau=False,maximal=False):
27    '''Run Bilboa's SUBGROUPS for a non-standard space group.
28    This requires doing a post to the Bilboa site, which returns all
29    subgroups of the entered space group as the text of a web page
30    with a table containing the space group symbol, the
31    transformation matrix and index for each subgroup.
32
33    :params list kvec: propogation vector as a list of nine string fractions or blank
34    :params SGData: space group object (see :ref:`Space Group object<SGData_table>`)
35
36    :returns: (error,text) error: if True no error or False; where
37      text containts a possible web page text
38    '''
39    print('''
40    For use of SUBGROUPS, please cite:
41      Symmetry-Based Computational Tools for Magnetic Crystallography,
42      J.M. Perez-Mato, S.V. Gallego, E.S. Tasci, L. Elcoro, G. de la Flor, and M.I. Aroyo
43      Annu. Rev. Mater. Res. 2015. 45,217-48.
44      doi: 10.1146/annurev-matsci-070214-021008
45    ''')
46       
47       
48    def getSpGrp(item):
49        return item.replace('<i>','').replace('</i>','').replace('<sub>','').replace('</sub>','')
50   
51    def getMatVec(item):
52        return item.replace('{','[').replace('}',']')
53               
54    starmag = 'no'
55    if star:
56        starmag = 'yes'
57    land = 'no'
58    if landau:
59        land = 'yes'
60    celtodas = 'no'
61    limite = 'spgroup'
62    if maximal:
63        limite = 'maximal'
64    postdict = {'centrosymmetry':'0','crystalsystem':'0','landau':land,
65               'eleccion':'subgrmag1_k','inicio':'nostandard','celtodas':celtodas,
66               'limite':limite,'list':'Submit','listado':'lista','starmagnetica':starmag,
67               'pointgroup':'0','polarity':'0','sub':'1',
68               'super':'','tipog':'gesp','wyckoffstrain':''}
69    text,table = G2spc.SGPrint(SGData)
70    OpList = G2spc.TextOps(text,table,reverse=True)
71#    GenList = G2spc.TextGen(SGData,reverse=True)
72    for item in OpList:
73        item += '\n'
74    sym = ""
75    for i in OpList:
76        if sym: sym += '\n'
77        #if sym: sym += ' ' # use this for testing to generate an error in place of previous
78        sym += i.lower()
79    postdict['generators'] = sym
80    for j in [1,2,3]:
81        if kvec[3*j-3] == ' ':
82            break
83        for i,k in zip(('x','y','z'),kvec[3*j-3:3*j]):
84            postdict['knm%d%s'%(j,i)] = k
85    page = G2IO.postURL(submagSite,postdict)
86    if not page:
87        print('connection error - not on internet?')
88        return None,None
89    page = page.replace('<font style= "text-decoration: overline;">','<font>-')
90    result = page.replace('&','\n')
91    result = result.split('\n')
92    SPGPs = []
93    MVs = []
94    baseList = []
95    itemList = []
96    superList = []
97    altList = []
98    start = 0
99    for line in result:    #work around bug report from Bilbao
100        start += 1
101        if 'yesz' in line:
102            break
103    for line in result[start:]:
104        if 'GGG' in line:
105            lines = line.split('GGG')
106            line = lines[0]
107            alts = []
108            beg = True
109            for sline in lines:
110                items = sline.split('z')
111                gid = int(items[0])
112                if beg:
113                    baseList.append(gid)
114                    beg = False
115                alts.append(gid)
116                itemList.append(gid)
117                superList.append(getMatVec(items[7]))
118                SPGPs.append(getSpGrp(items[4]))
119                MVs.append([getMatVec(items[5]),getMatVec(items[6])])
120            altList.append(alts)
121            for sline in lines[1:]:
122                altList.append([])
123        else:
124            items = line.split('z')
125            gid = int(items[0])
126            altList.append([gid,])
127            baseList.append(gid)
128            itemList.append(gid)
129            superList.append(getMatVec(items[7]))
130            SPGPs.append(getSpGrp(items[4]))
131            MVs.append([getMatVec(items[5]),getMatVec(items[6])])
132    result = list(zip(SPGPs,MVs,itemList,altList,superList))
133    return result,baseList
134
135def GetNonStdSubgroupsmag(SGData, kvec,star=False,landau=False,maximal=False):
136    '''Run Bilboa's k-Subgroupsmag for a non-standard space group.
137    This requires doing a post to the Bilboa site, which returns all
138    magnetic subgroups of the entered subgroup as the text of a web page
139    with a table containing the BNS magnetic space group symbol, the
140    transformation matrix and index for each subgroup.
141
142    :params list kvec: propogation vector as a list of three numbers
143    :params SGData: space group object (see :ref:`Space Group object<SGData_table>`)
144
145    :returns: (error,text) error: if True no error or False; where
146      text containts a possible web page text
147    '''
148    print('''
149    For use of k-SUBGROUPSMAG, please cite:
150      Symmetry-Based Computational Tools for Magnetic Crystallography,
151      J.M. Perez-Mato, S.V. Gallego, E.S. Tasci, L. Elcoro, G. de la Flor, and M.I. Aroyo
152      Annu. Rev. Mater. Res. 2015. 45,217-48.
153      doi: 10.1146/annurev-matsci-070214-021008
154    ''')
155
156    def getSpGrp(item):
157        return item.replace('<i>','').replace('</i>','').replace('<sub>','').replace('</sub>','')
158   
159    def getBNS(item):
160        spgrp = getSpGrp(item)
161        bns = ''
162        sid = item.find('<sub>')
163        if sid == 8:
164            bns = spgrp[1]
165            spgrp = '%s_%s %s'%(spgrp[0],bns,spgrp[2:])
166        return spgrp,bns
167   
168    def getMatVec(item):
169        return item.replace('{','[').replace('}',']')
170               
171    starmag = 'no'
172    if star:
173        starmag = 'yes'
174    land = 'no'
175    if landau:
176        land = 'yes'
177    celtodas = 'no'
178    limite = 'spgroup'
179    if maximal:
180        limite = 'maximal'
181    postdict = {'centrosymmetry':'0','crystalsystem':'0','landau':land,
182               'eleccion':'subgrmag1_k','inicio':'nostandard','celtodas':celtodas,
183               'limite':limite,'list':'Submit','listado':'lista','starmagnetica':starmag,
184               'pointgroup':'0','polarity':'0','sub':'1.1',
185               'super':'','tipog':'gmag','wyckoffstrain':''}
186    text,table = G2spc.SGPrint(SGData)
187    OpList = G2spc.TextOps(text,table,reverse=True)
188#    OpList = G2spc.TextGen(SGData,reverse=True)
189    for item in OpList:
190        item += '\n'
191    sym = ""
192    for i in OpList:
193        if sym: sym += '\n'
194        #if sym: sym += ' ' # use this for testing to generate an error in place of previous
195        sym += i.lower()
196    postdict['generators'] = sym
197    for j in [1,2,3]:
198        if kvec[3*j-3] == ' ':
199            break
200        for i,k in zip(('x','y','z'),kvec[3*j-3:3*j]):
201            postdict['km%d%s'%(j,i)] = k
202    page = G2IO.postURL(submagSite,postdict)
203    if not page:
204        print('connection error - not on internet?')
205        return None,None
206    page = page.replace('<font style= "text-decoration: overline;">','<font>-')
207    result = page.replace('&','\n')
208    result = result.split('\n')
209    start = 0
210    for line in result:    #work around bug report from Bilbao
211        start += 1
212        if 'yesz' in line:
213            break
214    SPGPs = []
215    BNSs = []
216    MVs = []
217    baseList = []
218    itemList = []
219    superList = []
220    altList = []
221    for line in result[start:]:
222        if 'GGG' in line:
223            lines = line.split('GGG')
224            alts = []
225            beg = True
226            for sline in lines:
227                items = sline.split('z')
228                gid = int(items[0])
229                if beg:
230                    baseList.append(gid)
231                    beg = False
232                alts.append(gid)
233                itemList.append(gid)
234                superList.append(getMatVec(items[7]))
235                spgrp,bns = getBNS(items[4])
236                SPGPs.append(spgrp)
237                BNSs.append(bns)
238                MVs.append([getMatVec(items[5]),getMatVec(items[6])])
239            altList.append(alts)
240            for sline in lines[1:]:
241                altList.append([])
242        else:
243            items = line.split('z')
244            gid = int(items[0])
245            altList.append([gid,])
246            baseList.append(gid)
247            itemList.append(gid)
248            superList.append(getMatVec(items[7]))
249            spgrp,bns = getBNS(items[4])
250            SPGPs.append(spgrp)
251            BNSs.append(bns)
252            MVs.append([getMatVec(items[5]),getMatVec(items[6])])
253    result = list(zip(SPGPs,BNSs,MVs,itemList,altList,superList))
254    return result,baseList
255
256def subBilbaoCheckLattice(spgNum,cell,tol=5):
257    '''submit a unit cell to  Bilbao PseudoLattice
258    '''
259    psSite = "http://www.cryst.ehu.es/cgi-bin/cryst/programs/pseudosym/nph-pseudolattice"
260    cellstr = '+'.join(['{:.5f}'.format(i) for i in cell])
261    datastr = "sgr={:}&cell={:}&tol={:}&submit=Show".format(
262        str(int(spgNum)),cellstr,str(int(tol)))
263    page = G2IO.postURL(psSite,datastr)
264    if not page:
265        print('connection error - not on internet?')
266        return None
267    page = page.replace('<font style= "text-decoration: overline;">','<font>-')
268    return page
269
270def parseBilbaoCheckLattice(page):
271    '''find the cell options from the web page returned by Bilbao PseudoLattice
272    '''
273    cellopts = [i for i in page.split('<tr>') if '<td><pre>' in i]
274    found = []
275    for c in cellopts:
276        cells = c.split("pre")[1].split('<')[0].replace('>','').split('\n') # list of cells, 1st is approx
277        try:
278            acell = [float(i) for i in cells[0].split()]
279            xmatA = [c.split('[')[i].split(']')[0].split() for i in (1,2,3)]
280            xmat =  np.array([[eval(i) for i in j] for j in xmatA])
281            cellmat = nl.inv(xmat).T
282        except:
283            print('Error processing cell in',c)
284            continue
285        found.append((acell,cellmat))
286    return found
287
288
289def test():
290    SGData = G2spc.SpcGroup('f d -3 m')[1]
291   
292    print('test SUBGROUPSMAG')           
293    results,baseList = GetNonStdSubgroupsmag(SGData,('0','0','0',' ',' ',' ',' ',' ',' ',' '))
294    print(results)
295    if results:
296        for [spgp,bns,mv,gid,altList,supList] in results:
297            if gid in baseList:
298                print('Space group: %d %s BNS: %s'%(gid,spgp,bns))
299                print('MV',mv)
300                print('altList:',altList)
301                print('superList: ',supList)
302               
303    print('test SUBGROUPS')
304    results,baseList = GetNonStdSubgroups(SGData,('1/3','1/3','1/2',' ',' ',' ',' ',' ',' ',' '))
305    print(results)
306    if results:
307        for [spgp,mv,gid,altList,supList] in results:
308            if gid in baseList:
309                print('Space group: %d %s'%(gid,spgp))
310                print('MV',mv)
311                print('altList:',altList)
312                print('superList: ',supList)
313               
314       
315
316if __name__ == '__main__':
317    # run self-tests
318    selftestquiet = False
319    test()
320    print ("OK")
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