source: trunk/kSUBGROUPSMAG.py @ 3716

Last change on this file since 3716 was 3716, checked in by vondreele, 4 years ago

implement new version of SUBGROUPS & k-SUBGROUPDMAG that return conjugacy & super group lists
display the results from these
remove lattice parameter constraints (for now at least) - occasionally fail with bad consequences

File size: 9.5 KB
Line 
1# -*- coding: utf-8 -*-
2"""
3*kSUBGROUPSMAG: Interface to Bilbao k-SUBGROUPSMAG web page*
4-------------------------------
5
6Extraction of magnetic space groups for a given space group and a propagation vector
7from the k-SUBGROUPSMAG web page on the Bilbao Crystallographic server
8
9"""
10########### SVN repository information ###################
11# $Date: 2018-07-10 11:41:00 -0500 (Tue, 10 Jul 2018) $
12# $Author: vondreele $
13# $Revision: 3465 $
14# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/kSUBGROUPSMAG.py $
15# $Id: kSUBGROUPSMAG.py 3465 2018-07-10 16:41:00Z vondreele $
16########### SVN repository information ###################
17from __future__ import division, print_function
18import requests
19try:
20    import HTMLParser as HTML
21except ImportError: 
22    import html.parser as HTML # Python 3
23import GSASIIspc as G2spc
24import GSASIIpath
25GSASIIpath.SetBinaryPath()
26submagSite = 'http://www.cryst.ehu.es/cgi-bin/cryst/programs/subgrmag1_general.pl'
27
28class TableParser(HTML.HTMLParser):
29    def __init__(self):
30        HTML.HTMLParser.__init__(self)
31        self.spgp = ''
32        self.in_sp = False
33        self.in_pre = False
34        self.in_sub = False
35        self.MV = ''
36        self.BNS = ''
37        self.beg = False
38        self.SPGPs = []
39        self.MVs = []
40        self.BNSs = []
41   
42    def handle_starttag(self, tag, attrs):
43#        print('tag:',tag,self.beg,self.in_sp)
44        if tag == 'i' and self.beg:
45            if not self.in_sp:
46                self.in_sp = True
47                self.spgp = ''
48                self.BNS = ''
49        elif tag == 'pre':
50            self.in_pre = True
51            self.MV = ''
52        elif tag == 'sub':
53            self.in_sub = True
54   
55    def handle_data(self, data):
56#        print('*',data)
57        if self.in_sp:
58            if 'No.' in data:
59                self.spgp += data.split('(')[0]        #pick up trailing number!
60                self.in_sp = False
61                self.SPGPs.append(self.spgp)
62                self.BNSs.append(self.BNS)
63#                print('space group:',self.spgp,' BNS: ',self.BNS)
64            else:
65                if self.in_sub and len(self.spgp) == 1:
66                    self.spgp += '_'
67                self.spgp += data
68                if len(self.spgp) == 3 and '_' in self.spgp:
69                    self.spgp += ' '
70                    self.BNS = data
71                    if 'P_S' in self.spgp:      #fix ambiguous std. symbol for triclinics
72                        self.spgp.replace('_S','_c')
73                        self.BNS = 'c'
74#                print(self.spgp,self.BNS)
75        if self.in_pre:
76            self.MV = data
77   
78    def handle_endtag(self, tag):
79#        print ('    end tag: %s'%(tag))
80        if tag == 'script':
81            self.beg = True
82        elif tag == 'pre':
83            self.in_pre = False
84            MV = self.MV.split()
85            MV = ['[[%s,%s,%s],[%s,%s,%s],[%s,%s,%s]]'%(MV[0],MV[4],MV[8],MV[1],MV[5],MV[9],MV[2],MV[6],MV[10]),'[%s.,%s.,%s.]'%(MV[3],MV[7],MV[11])]
86            self.MVs.append(MV)
87#            print('MV:',self.MV)
88        elif tag == 'sub':
89            self.in_sub = False
90           
91def GetNonStdSubgroupsmag(SGData, kvec,star=False,landau=False,maximal=False):
92    '''Run Bilboa's k-Subgroupsmag for a non-standard space group.
93    This requires doing a post to the Bilboa site, which returns all
94    magnetic subgroups of the entered subgroup as the text of a web page
95    with a table containing the BNS magnetic space group symbol, the
96    transformation matrix and index for each subgroup.
97
98    :params list kvec: propogation vector as a list of three numbers
99    :params SGData: space group object (see :ref:`Space Group object<SGData_table>`)
100
101    :returns: (error,text) error: if True no error or False; where
102      text containts a possible web page text
103    '''
104    print('''
105    For use of k-SUBGROUPSMAG, please cite:
106      Symmetry-Based Computational Tools for Magnetic Crystallography,
107      J.M. Perez-Mato, S.V. Gallego, E.S. Tasci, L. Elcoro, G. de la Flor, and M.I. Aroyo
108      Annu. Rev. Mater. Res. 2015. 45,217-48.
109      doi: 10.1146/annurev-matsci-070214-021008
110    ''')
111    starmag = 'no'
112    if star:
113        starmag = 'yes'
114    land = 'no'
115    if landau:
116        land = 'yes'
117    celtodas = 'no'
118    limite = 'spgroup'
119    if maximal:
120        limite = 'maximal'
121    postdict = {'centrosymmetry':'0','crystalsystem':'0','landau':land,
122               'eleccion':'subgrmag1_k','inicio':'nostandard','celtodas':celtodas,
123               'limite':limite,'list':'Submit','listado':'lista','starmagnetica':starmag,
124               'pointgroup':'0','polarity':'0','sub':'1.1',
125               'super':'','tipog':'gmag','wyckoffstrain':''}
126    text,table = G2spc.SGPrint(SGData)
127    OpList = G2spc.TextOps(text,table,reverse=True)
128#    GenList = G2spc.TextGen(SGData,reverse=True)
129    for item in OpList:
130        item += '\n'
131    sym = ""
132    for i in OpList:
133        if sym: sym += '\n'
134        #if sym: sym += ' ' # use this for testing to generate an error in place of previous
135        sym += i.lower()
136    postdict['generators'] = sym
137    for j in [1,2,3]:
138        if kvec[3*j-3] == ' ':
139            break
140        for i,k in zip(('x','y','z'),kvec[3*j-3:3*j]):
141            postdict['km%d%s'%(j,i)] = k
142    try:
143        r = requests.post(submagSite,postdict)
144    except:     #ConnectionError?
145        page = ''
146        print('connection error - not on internet')
147        return None,None
148    if r.status_code == 200:
149        print('request OK')
150        page = r.text
151        page = page.replace('<font style= "text-decoration: overline;">','<font>-')
152    else:
153        page = ''
154        print('request failed. Reason=',r.reason)
155        return None,None
156    r.close()
157
158    p = TableParser()
159    p.feed(page)
160    nItms = len(p.MVs)
161    result = list(zip(p.SPGPs,p.BNSs,p.MVs,range(nItms),nItms*[[],],nItms*['[]',]))
162    return result,range(nItms)
163
164def GetNonStdSubgroups(SGData, kvec,star=False,landau=False,maximal=False):
165    '''Run Bilboa's SUBGROUPS for a non-standard space group.
166    This requires doing a post to the Bilboa site, which returns all
167    subgroups of the entered space group as the text of a web page
168    with a table containing the space group symbol, the
169    transformation matrix and index for each subgroup.
170
171    :params list kvec: propogation vector as a list of nine string fractions or blank
172    :params SGData: space group object (see :ref:`Space Group object<SGData_table>`)
173
174    :returns: (error,text) error: if True no error or False; where
175      text containts a possible web page text
176    '''
177    print('''
178    For use of SUBGROUPS, please cite:
179      Symmetry-Based Computational Tools for Magnetic Crystallography,
180      J.M. Perez-Mato, S.V. Gallego, E.S. Tasci, L. Elcoro, G. de la Flor, and M.I. Aroyo
181      Annu. Rev. Mater. Res. 2015. 45,217-48.
182      doi: 10.1146/annurev-matsci-070214-021008
183    ''')
184    starmag = 'no'
185    if star:
186        starmag = 'yes'
187    land = 'no'
188    if landau:
189        land = 'yes'
190    celtodas = 'no'
191    limite = 'spgroup'
192    if maximal:
193        limite = 'maximal'
194    postdict = {'centrosymmetry':'0','crystalsystem':'0','landau':land,
195               'eleccion':'subgrmag1_k','inicio':'nostandard','celtodas':celtodas,
196               'limite':limite,'list':'Submit','listado':'lista','starmagnetica':starmag,
197               'pointgroup':'0','polarity':'0','sub':'1',
198               'super':'','tipog':'gesp','wyckoffstrain':''}
199    text,table = G2spc.SGPrint(SGData)
200    OpList = G2spc.TextOps(text,table,reverse=True)
201#    GenList = G2spc.TextGen(SGData,reverse=True)
202    for item in OpList:
203        item += '\n'
204    sym = ""
205    for i in OpList:
206        if sym: sym += '\n'
207        #if sym: sym += ' ' # use this for testing to generate an error in place of previous
208        sym += i.lower()
209    postdict['generators'] = sym
210    for j in [1,2,3]:
211        if kvec[3*j-3] == ' ':
212            break
213        for i,k in zip(('x','y','z'),kvec[3*j-3:3*j]):
214            postdict['knm%d%s'%(j,i)] = k
215    try:
216        r = requests.post(submagSite,postdict)
217    except:     #ConnectionError?
218        page = ''
219        print('connection error - not on internet')
220        return None
221    if r.status_code == 200:
222        print('request OK')
223        page = r.text
224        page = page.replace('<font style= "text-decoration: overline;">','<font>-')
225    else:
226        page = ''
227        print('request failed. Reason=',r.reason)
228        return None
229    r.close()
230
231    p = TableParser()
232    p.feed(page)
233    nItms = len(p.MVs)
234    result = list(zip(p.SPGPs,p.MVs,range(nItms),range(nItms),nItms*[0,]))
235    return result,range(nItms)
236
237def test():
238    SGData = G2spc.SpcGroup('p -3 m 1')[1]
239    results,baseList = GetNonStdSubgroupsmag(SGData,('1/3','1/3','1/2',' ',' ',' ',' ',' ',' ',' '))
240    if results:
241        for [spgp,mv,bns,gid,altList,supList] in results:
242            if gid in baseList:
243                print('Space group:',spgp, 'BNS:',bns)
244                print('MV')
245                print(mv)
246    results,baseList = GetNonStdSubgroups(SGData,('1/3','1/3','1/2',' ',' ',' ',' ',' ',' ',' '))
247    if results:
248        for [spgp,mv,gid,altList,supList] in results:
249            if gid in baseList:
250                print('Space group:',spgp)
251                print('MV')
252                print(mv)
253       
254
255if __name__ == '__main__':
256    # run self-tests
257    selftestquiet = False
258    test()
259    print ("OK")
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