modify r-factors in scriptref test; remove Bilbao pseudosym cmd -- removed from website

Author: briantoby

GSASII/GSASIIdataGUI.py

@@ -6867,7 +6867,8 @@ def _makemenu():     # routine to create menu when first used
         # PWDR / Unit Cells List
         G2G.Define_wxId('wxID_INDEXPEAKS', 'wxID_REFINECELL', 'wxID_COPYCELL', 'wxID_MAKENEWPHASE',
             'wxID_EXPORTCELLS','wxID_LOADCELL','wxID_IMPORTCELL','wxID_TRANSFORMCELL',
-            'wxID_RUNSUB','wxID_RUNSUBMAG','wxID_LATSYM')
+            'wxID_RUNSUB','wxID_RUNSUBMAG')
+        #G2G.Define_wxId('wxID_LATSYM')
         G2G.Define_wxId('wxID_NISTLATSYM')
         G2G.Define_wxId('wxID_SHOWGENHKLS')
         G2G.Define_wxId('wxID_CLEARCELLS')
@@ -6878,9 +6879,9 @@ def _makemenu():     # routine to create menu when first used
             self.IndexMenu.Append(menu=self.IndexEdit, title='Cell Index/Refine')
             self.IndexPeaks = self.IndexEdit.Append(G2G.wxID_INDEXPEAKS,'Index Cell',
                 'Find cells that index fitted peaks')
-            self.IndexEdit.Append(G2G.wxID_LATSYM,'Cell Symmetry Search-Bilbao',
-                'Run Bilbao "Lattice Symmetry" to find higher symmetry cells')
-            self.IndexEdit.Append(G2G.wxID_NISTLATSYM,'Cell Symmetry Search-NIST*LATTICE',
+            # self.IndexEdit.Append(G2G.wxID_LATSYM,'Cell Symmetry Search-Bilbao',
+            #     'Run Bilbao "Lattice Symmetry" to find higher symmetry cells')
+            self.IndexEdit.Append(G2G.wxID_NISTLATSYM,'Cell Symmetry Search',
                 'Run NIST*LATTICE to find higher symmetry cells')
             self.RunSubGroups = self.IndexEdit.Append(G2G.wxID_RUNSUB,'Run SUBGROUPS',
                 'If disabled, do Load Phase first')

GSASII/GSASIIpath.py

@@ -1923,6 +1923,7 @@ def postURL(URL,postdict,getcookie=None,usecookie=None,
         count += 1
         r = None
         repeat = False
+        if GetConfigValue('debug'): print('request to',URL)
         try:
             if timeout is not None:
                 r = reqopt(URL,params=postdict,cookies=usecookie,

GSASII/GSASIIpwdGUI.py

@@ -2044,7 +2044,7 @@ def OnCellChange(event):
             Types = [wg.GRID_VALUE_FLOAT+':10,2',wg.GRID_VALUE_BOOL,
             wg.GRID_VALUE_FLOAT+':12,5,g',wg.GRID_VALUE_BOOL,
             wg.GRID_VALUE_FLOAT+':12,3,g',wg.GRID_VALUE_BOOL,
-            wg.GRID_VALUE_FLOAT+':12,5,g',wg.GRID_VALUE_BOOL]
+            wg.GRID_VALUE_FLOAT+':12,3,g',wg.GRID_VALUE_BOOL]
             peaksTable = G2G.Table(data[1]['peaksList'],rowLabels=rowLabels,colLabels=colLabels,types=Types)
             peaksGrid = G2G.GSGrid(parent=G2frame.dataWindow)
             peaksGrid.SetRowLabelSize(45)
@@ -4825,45 +4825,45 @@ def TransformUnitCell(event):
         OnHklShow(None,indexFrom=' Indexing from transformed unit cell & symmetry settings')
         wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
 
-    def OnLatSym(event):
-        'Run Bilbao PseudoLattice cell search'
-        # look up a space group matching Bravais lattice (should not matter which one)
-        bravaisSPG = {'Fm3m':225,'Im3m':229,'Pm3m':221,'R3-H':146,'P6/mmm':191,
-                       'I4/mmm':139,'P4/mmm':123,'Fmmm':69,'Immm':71,
-                       'Cmmm':65,'Pmmm':47,'C2/m':12,'P2/m':10,'P1':2}
-        pUCid = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Unit Cells List')
-        controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(pUCid)
-        sgNum = bravaisSPG.get(controls[5],0)
-        if sgNum < 1:
-            wx.MessageBox('Sorry, only standard cell settings are allowed, please transform axes',caption='Bilbao requires standard settings',style=wx.ICON_EXCLAMATION)
-            return
-        cell = controls[6:12]
-        tolerance = 5.
-        dlg = G2G.SingleFloatDialog(G2frame,'Tolerance',
-                'Enter angular tolerance for search',5.0,[.1,30.],"%.1f")
-        if dlg.ShowModal() == wx.ID_OK:
-            tolerance = dlg.GetValue()
-            dlg.Destroy()
-        else:
-            dlg.Destroy()
-            return
-        wx.MessageBox(' For use of PSEUDOLATTICE, please cite:\n\n'+
-                          G2G.GetCite('Bilbao: PSEUDOLATTICE'),
-                          caption='Bilbao PSEUDOLATTICE',
-                          style=wx.ICON_INFORMATION)
-        wx.BeginBusyCursor()
-        page = kSUB.subBilbaoCheckLattice(sgNum,cell,tolerance)
-        wx.EndBusyCursor()
-        if not page: return
-        cells.clear()
-        for i,(cell,mat) in enumerate(kSUB.parseBilbaoCheckLattice(page)):
-            cells.append([])
-            cells[-1] += [mat,0,16]
-            cells[-1] += cell
-            cells[-1] += [G2lat.calc_V(G2lat.cell2A(cell)),False,False]
-        G2frame.GPXtree.SetItemPyData(pUCid,data)
-        G2frame.OnFileSave(event)
-        wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
+    # def OnLatSym(event):
+    #     'Run Bilbao PseudoLattice cell search'
+    #     # look up a space group matching Bravais lattice (should not matter which one)
+    #     bravaisSPG = {'Fm3m':225,'Im3m':229,'Pm3m':221,'R3-H':146,'P6/mmm':191,
+    #                    'I4/mmm':139,'P4/mmm':123,'Fmmm':69,'Immm':71,
+    #                    'Cmmm':65,'Pmmm':47,'C2/m':12,'P2/m':10,'P1':2}
+    #     pUCid = G2gd.GetGPXtreeItemId(G2frame,G2frame.PatternId, 'Unit Cells List')
+    #     controls,bravais,cells,dminx,ssopt,magcells = G2frame.GPXtree.GetItemPyData(pUCid)
+    #     sgNum = bravaisSPG.get(controls[5],0)
+    #     if sgNum < 1:
+    #         wx.MessageBox('Sorry, only standard cell settings are allowed, please transform axes',caption='Bilbao requires standard settings',style=wx.ICON_EXCLAMATION)
+    #         return
+    #     cell = controls[6:12]
+    #     tolerance = 5.
+    #     dlg = G2G.SingleFloatDialog(G2frame,'Tolerance',
+    #             'Enter angular tolerance for search',5.0,[.1,30.],"%.1f")
+    #     if dlg.ShowModal() == wx.ID_OK:
+    #         tolerance = dlg.GetValue()
+    #         dlg.Destroy()
+    #     else:
+    #         dlg.Destroy()
+    #         return
+    #     wx.MessageBox(' For use of PSEUDOLATTICE, please cite:\n\n'+
+    #                       G2G.GetCite('Bilbao: PSEUDOLATTICE'),
+    #                       caption='Bilbao PSEUDOLATTICE',
+    #                       style=wx.ICON_INFORMATION)
+    #     wx.BeginBusyCursor()
+    #     page = kSUB.subBilbaoCheckLattice(sgNum,cell,tolerance)
+    #     wx.EndBusyCursor()
+    #     if not page: return
+    #     cells.clear()
+    #     for i,(cell,mat) in enumerate(kSUB.parseBilbaoCheckLattice(page)):
+    #         cells.append([])
+    #         cells[-1] += [mat,0,16]
+    #         cells[-1] += cell
+    #         cells[-1] += [G2lat.calc_V(G2lat.cell2A(cell)),False,False]
+    #     G2frame.GPXtree.SetItemPyData(pUCid,data)
+    #     G2frame.OnFileSave(event)
+    #     wx.CallAfter(UpdateUnitCellsGrid,G2frame,data)
 
     def OnNISTLatSym(event):
         'Run NIST*LATTICE cell search'
@@ -6990,7 +6990,7 @@ def OnRefreshKeep(event):
     G2frame.Bind(wx.EVT_MENU, OnIndexPeaks, id=G2G.wxID_INDEXPEAKS)
     G2frame.Bind(wx.EVT_MENU, OnRunSubs, id=G2G.wxID_RUNSUB)
     G2frame.Bind(wx.EVT_MENU, OnRunSubsMag, id=G2G.wxID_RUNSUBMAG)
-    G2frame.Bind(wx.EVT_MENU, OnLatSym, id=G2G.wxID_LATSYM)
+    #G2frame.Bind(wx.EVT_MENU, OnLatSym, id=G2G.wxID_LATSYM) # removed from site
     G2frame.Bind(wx.EVT_MENU, OnNISTLatSym, id=G2G.wxID_NISTLATSYM)
     G2frame.Bind(wx.EVT_MENU, CopyUnitCell, id=G2G.wxID_COPYCELL)
     G2frame.Bind(wx.EVT_MENU, LoadUnitCell, id=G2G.wxID_LOADCELL)

GSASII/SUBGROUPS.py

@@ -24,9 +24,15 @@
 from . import GSASIIlattice as G2lat
 from . import GSASIIElem as G2elem
 from . import GSASIIctrlGUI as G2G
-bilbaoURL = "http://webbdcrista2.ehu.es"
+bilbaoURL = "http://cryst.ehu.es"
 bilbaoSite = f'{bilbaoURL}/cgi-bin/cryst/programs/'
+# routines used here:
 pseudosym = 'pseudosym/nph-pseudosym'
+#pseudolattice = "pseudosym/nph-pseudolattice"
+cif2std = 'nph-cif2std'
+subgrmag1 = 'subgrmag1_general_GSAS.pl?'
+checkgr = 'checkgr_gsas.pl'
+minsup = 'nph-minsup' # coded but not used
 timeout=150  # time to wait for Bilbao to respond; 2.5 minutes
 
 def postpostURL(page):
@@ -38,7 +44,7 @@ def postpostURL(page):
         import re
         print(f"Website down? See message below:\n\n{re.sub('<.+>','',page)}")
         try:
-            dlg = G2G.viewWebPage(wx.GetApp().GetMainTopWindow(),URL,HTML=page)
+            G2G.viewWebPage(wx.GetApp().GetMainTopWindow(),HTML=page)
         except:
             pass
         return True
@@ -98,7 +104,7 @@ def getMatVec(item):
             break
         for i,k in zip(('x','y','z'),kvec[3*j-3:3*j]):
             postdict['knm%d%s'%(j,i)] = k
-    page = GSASIIpath.postURL(bilbaoSite+'subgrmag1_general_GSAS.pl?',postdict)
+    page = GSASIIpath.postURL(bilbaoSite+subgrmag1,postdict)
     if postpostURL(page): return None,None
     if not page:
         print('connection error - not on internet?')
@@ -212,7 +218,7 @@ def getMatVec(item):
             break
         for i,k in zip(('x','y','z'),kvec[3*j-3:3*j]):
             postdict['km%d%s'%(j,i)] = k
-    page = GSASIIpath.postURL(bilbaoSite+'subgrmag1_general_GSAS.pl?',postdict)
+    page = GSASIIpath.postURL(bilbaoSite+subgrmag1,postdict)
     if postpostURL(page): return None,None
     if not page:
         print('connection error - not on internet?')
@@ -267,20 +273,20 @@ def getMatVec(item):
     result = list(zip(SPGPs,BNSs,MVs,itemList,altList,superList))
     return result,baseList
 
-def subBilbaoCheckLattice(spgNum,cell,tol=5):
-    '''submit a unit cell to  Bilbao PseudoLattice
-    '''
-    psSite = bilbaoSite + "pseudosym/nph-pseudolattice"
-    cellstr = '+'.join(['{:.5f}'.format(i) for i in cell])
-    datastr = "sgr={:}&cell={:}&tol={:}&submit=Show".format(
-        str(int(spgNum)),cellstr,str(int(tol)))
-    page = GSASIIpath.postURL(psSite,datastr,timeout=timeout)
-    if postpostURL(page): return None
-    if not page:
-        print('connection error - not on internet?')
-        return None
-    page = page.replace('<font style= "text-decoration: overline;">','<font>-')
-    return page
+# def subBilbaoCheckLattice(spgNum,cell,tol=5):
+#     '''submit a unit cell to  Bilbao PseudoLattice
+#     '''
+#     psSite = bilbaoSite + pseudolattice
+#     cellstr = '+'.join(['{:.5f}'.format(i) for i in cell])
+#     datastr = "sgr={:}&cell={:}&tol={:}&submit=Show".format(
+#         str(int(spgNum)),cellstr,str(int(tol)))
+#     page = GSASIIpath.postURL(psSite,datastr,timeout=timeout)
+#     if postpostURL(page): return None
+#     if not page:
+#         print('connection error - not on internet?')
+#         return None
+#     page = page.replace('<font style= "text-decoration: overline;">','<font>-')
+#     return page
 
 def parseBilbaoCheckLattice(page):
     '''find the cell options from the web page returned by Bilbao PseudoLattice
@@ -320,7 +326,7 @@ def GetStdSGset(SGData=None, oprList=[]):
       Note that the new cell is given by G2lat.TransformCell([a,b,...],xformM)
     '''
     import re
-    Site = bilbaoSite + 'checkgr.pl'
+    Site = bilbaoSite + checkgr
 
     if not bool(oprList) ^ bool(SGData):
         raise ValueError('GetStdSGset: Must specify oprList or SGData and not both')
@@ -376,7 +382,7 @@ def GetSupergroup(SGnum,dlg=None):
         Note that the new cell is given by G2lat.TransformCell([a,b,...],M)
     '''
     import re
-    Site = bilbaoSite + 'nph-minsup'
+    Site = bilbaoSite + minsup
     if dlg: dlg.Update(0,newmsg='Waiting for initial web response')
     out = GSASIIpath.postURL(Site,{'gnum':f'{SGnum:}'},timeout=timeout)
     if postpostURL(out): return None
@@ -825,7 +831,6 @@ def createStdSetting(cifFile,rd):
         # macs; it should not!
         print('Warning: failed to import requests. Python config error')
         return None
-    cif2std = 'nph-cif2std'
     if not os.path.exists(cifFile):
         print(f'createStdSetting error: file {cifFile} not found')
         return False
@@ -835,6 +840,8 @@ def createStdSetting(cifFile,rd):
         print(f'''Submitting structure to Bilbao "CIF to Standard Setting" (strtidy)
     web service. Please cite:
     {G2G.GetCite('Bilbao: PSEUDOLATTICE',wrap=70,indent=5)}''')
+        if GSASIIpath.GetConfigValue('debug'): print('request to',bilbaoSite+cif2std)
+
         r0 = requests.post(bilbaoSite+cif2std, files=files, data=values)
         structure = r0.text[r0.text.lower().find('<pre>')+5:r0.text.lower().find('</pre>')].strip()
         spnum,celllist,natom = structure.split('\n')[:3]

docs/source/packages.rst

@@ -485,7 +485,7 @@ The following web services can also be accessed from computers that
 have internet access. All software needed for this access is included
 with GSAS-II.
 
-  **Bilbao Crystallographic Server** (http://webbdcrista2.ehu.es/):
+  **Bilbao Crystallographic Server** (http://cryst.ehu.es/):
     GSAS-II can directly access the Bilbao Crystallographic Server to
     utilize the k-SUBGROUPSMAG, k-SUBGROUPS and PseudoLattice web utilities for
     computation of space group subgroups, color (magnetic) subgroups &

tests/run_bilbao.py

@@ -107,10 +107,10 @@ def test_GetStdSGset():
 
 if __name__ == '__main__':
     # run self-tests
-    test_GetStdSGset()
-    test_SUBGROUPSMAG()
-    test_SUBGROUPS()
-    test_pseudosym()
-    test_CheckLattice()
-    test_createStdSetting()
+    test_GetStdSGset()      # checkgr_gsas.pl
+    test_SUBGROUPSMAG()     # subgrmag1_general_GSAS.pl 
+    test_SUBGROUPS()        # subgrmag1_general_GSAS.pl 
+    test_pseudosym()        # nph-pseudosym
+    #test_CheckLattice()     # nph-pseudolattice (removed from Bilbao)
+    test_createStdSetting() # nph-cif2std
     print ("OK")

tests/test_scriptref.py

@@ -46,7 +46,7 @@ def testR(msg,w1,w2):
     phase0 = gpx.add_phase(dataloc("PbSO4-Wyckoff.cif"),
                                phasename="PbSO4", histograms=[h1,h2])
     gpx.set_Controls('cycles', 0)
-    gpx.refine()
+    gpx.refine(makeBack=True)
     testR('Before fitting',96.681098,99.748994)
     # 
     #h1.set_refinements({'Limits': [16.,158.4]})
@@ -57,22 +57,31 @@ def testR(msg,w1,w2):
     gpx.set_Controls('cycles', 3)  # also gains ~x1.5 in speed
     h1.set_refinements({"Background": { "no. coeffs": 6, "refine": True }})
     h2.set_refinements({"Background": { "no. coeffs": 3, "refine": True }})
-    gpx.refine()
+    gpx.refine(makeBack=True)
     testR('Fit scale & bkg',45.811562,17.864834)
     #
     phase0.set_refinements({'Cell':True})
     phase0.set_HAP_refinements({'HStrain':True},[h2])
-    gpx.refine()
+    gpx.refine(makeBack=True)
     testR('Fit cells',32.475886, 15.02412)
     #
     phase0.set_HAP_refinements({'Mustrain':{'refine':True}},[h1])
+    #gpx.refine(makeBack=True)
+    #msg = '?'
+    #print(f"*** {msg}: Rwp(h1)={h1.residuals['wR']:.5f}, Rwp(h2)={h2.residuals['wR']:.5f}")
     #phase0.set_HAP_refinements({'Size':{'refine':True}},[h1])
     h1.set_refinements({"Sample Parameters": {"Shift": True}})
+    #gpx.refine(makeBack=True)
+    #print(f"*** {msg}: Rwp(h1)={h1.residuals['wR']:.5f}, Rwp(h2)={h2.residuals['wR']:.5f}")
     h2.set_refinements({"Sample Parameters":["DisplaceX","DisplaceY"]})
+    #gpx.refine(makeBack=True)
+    #print(f"*** {msg}: Rwp(h1)={h1.residuals['wR']:.5f}, Rwp(h2)={h2.residuals['wR']:.5f}")
     phase0.set_refinements({"Atoms":{"all":"XU"}})
-    gpx.refine()
+    #gpx.refine(makeBack=True)
+    #print(f"*** {msg}: Rwp(h1)={h1.residuals['wR']:.5f}, Rwp(h2)={h2.residuals['wR']:.5f}")
+    gpx.refine(makeBack=True)
     testR('add Mustrain, Shift, Displace[XY], atomic X & Uiso',
-              13.407161,  6.360408)
+              13.40599,  6.36131)
     #
     #h1.set_refinements({'Instrument Parameters': ['U', 'V', 'W']})
     #h2.set_refinements({'Instrument Parameters': ['U', 'V', 'W']})
@@ -81,12 +90,12 @@ def testR(msg,w1,w2):
     # change to Spherical Harmonics, order=2 for the 1st histogram & refine
     phase0.HAPvalue('PO',2,[h1])
     phase0.set_HAP_refinements({"Pref.Ori.":True})
-    gpx.refine()
+    gpx.refine(makeBack=True)
     POdict = phase0.HAPvalue('PO',targethistlist=[h1])[5]
     print('Spherical harmonics values:',POdict)
     npt.assert_allclose((POdict['C(2,0)'],POdict['C(2,2)']),
                             [0.127404, 0.09406], rtol=0.001)
-    testR('add PO',13.166705,  6.381183)
+    testR('add PO',13.16483,  6.38230)
     #
     print('OK')