bring in latest changes in main

Author: briantoby

.github/workflows/bilbao-test.yml

@@ -0,0 +1,34 @@
+name: Self-Test Bilbao access routines
+
+on:
+  schedule:
+    # Run weekly on Mondays at 5:00 AM UTC
+    - cron: '0 5 * * 1'
+  workflow_dispatch:
+
+# Default to bash
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: set up pixi
+      uses: prefix-dev/[email protected]
+      with:
+          manifest-path: pixi/pixi.toml
+
+    - name: Use pixi to install GSAS-II
+      run: |
+          cd pixi
+          pixi run install 
+
+    - name: run Bilbao self-test
+      run: |
+          cd pixi
+          pixi run python -m pytest ../tests/run_bilbao.py

GSASII/GSASIIctrlGUI.py

@@ -2915,7 +2915,7 @@ def __init__(self,parent,title,prompt,value,limits=[0.,1.],fmt='%.5g'):
         try:
             w = int(a)
         except:
-            w = 3+d
+            w = 5+d
         self.OKbtn = wx.Button(self,wx.ID_OK)
         CancelBtn = wx.Button(self,wx.ID_CANCEL)
         valItem = ValidatedTxtCtrl(self,self.buffer,0,nDig=(w,d,f),

GSASII/GSASIIpath.py

@@ -349,7 +349,8 @@ def getG2VersionInfo():
         elif len(rc) > 0:
             return f"  GSAS-II:    {gversion} posted {ctim} (\u2265{len(rc)} new updates) [{commit.hexsha[:8]}]{msg}"
         else:
-            return f"  GSAS-II:    {gversion} posted {ctim} (no new updates) [{commit.hexsha[:8]}]{msg}"
+#            return f"  GSAS-II:    {gversion} posted {ctim} (no new updates) [{commit.hexsha[:8]}]{msg}"
+            return f"  GSAS-II:    {gversion} posted {ctim} [{commit.hexsha[:8]}]{msg}"
     elif gv is not None:
         vt = ''
         cvt = ''

GSASII/GSASIIphsGUI2.py

@@ -355,11 +355,13 @@ def OnNewHarm(event):
     def OnDelHarm(event):
         Obj = event.GetEventObject()
         dId = Indx[Obj.GetId()]
+        minL = 1  #always an "Ne"
         for harm in data['Deformations'][dId]:
             if 'Sl' in harm[0]:
                 Harm = harm
+                minL = 2    # & 'kappa'
         Hkeys = list(Harm[1].keys())
-        if len(Hkeys) > 1:  #always an "Ne"
+        if len(Hkeys) > minL:
             maxord = max([int(item[2]) for item in Hkeys if 'D' in item])
             for item in Hkeys:
                 if 'D' in item and int(item[2]) == maxord:

GSASII/GSASIIplot.py

@@ -3523,7 +3523,6 @@ def PlotDeform(G2frame,general,atName,atType,deform,UVmat,radial,neigh):
     Y = 0.5*np.outer(npsind(PHI),npsind(PSI))
     Z = 0.5*np.outer(np.ones(np.size(PHI)),npcosd(PSI))
     XYZ = np.array([X.flatten(),Y.flatten(),Z.flatten()])
-#    XYZ = np.inner(UVmat,XYZ.T)
     RAP = G2mth.Cart2Polar(XYZ[0],XYZ[1],XYZ[2])
     P  = np.zeros((31,31))
     for shc in SHC:
@@ -7359,9 +7358,9 @@ def Draw(caller='',Fade=[],NPkey=False):
                             SGM = np.array(G2spc.GetOpFromCode(atom[cs-1],SGData)[0])
                             SHC = defParms[0][1]
                             SHC = {item.replace('D','C'):SHC[item] for item in SHC if item not in ['Ne','kappa']}
-                            SGC = G2lat.CrysM2CartM(Amat,Bmat,SGM)
-                            UVMat = np.inner(defCtrls['UVmat'],SGC)
-#                            print(atom[ct-1],atom[cs-1],'\n',UVMat,'\n',SGC)
+                            SGC = nl.inv(G2lat.CrysM2CartM(Amat,Bmat,SGM))
+                            UVMat = np.inner(defCtrls['UVmat'],SGC.T)
+        #                    print(nl.det(UVMat),atom[ct-1],atom[cs-1],'\n',UVMat,'\n',SGC)
                             Npsi,Ngam = 90,45 
                             PSI,GAM = np.mgrid[0:Npsi,0:Ngam]   #[azm,pol]
                             PSI = PSI.flatten()*360./Npsi  #azimuth 0-360 incl

GSASII/GSASIIpwdGUI.py

@@ -5206,6 +5206,13 @@ def OnISODISTORT_kvec(event):
         '''Search for k-vector using the ISODISTORT web service.
         Developed by Yuanpeng Zhang with help from Branton Campbell.
         '''
+        if symbols is None:
+            G2G.G2MessageBox(G2frame,
+                    'Unable to perform ISODISTORT kvec search without the sympy module. Use Help/Add packages... to address','No sympy')
+            return
+        # symbolic "variables" needed below for routine to_fraction_strs()
+        a, b, g = symbols('a b g')
+
         def _showWebPage(event):
             'Show a web page when the user presses the "show" button'
             import tempfile
@@ -5259,8 +5266,6 @@ def grab_all_kvecs(out_html):
             else:
                 return None
 
-        a, b, g = symbols('a b g')
-
         def frac_str(value, max_den=1000):
             # Try to get a rational exactly; if huge, fall back to bounded approximation
             try:
@@ -5323,10 +5328,6 @@ def setup_kvec_input(k_vec, k_vec_dict, isocif_cif):
             return data_update
 
         # start of OnISODISTORT_kvec computations
-        if symbols is None:
-            G2G.G2MessageBox(G2frame,
-                    'Unable to perform ISODISTORT kvec search without the sympy module. Use Help/Add packages... to address','No sympy')
-            return
         try:
             import requests
         except:

GSASII/GSASIIstrMath.py

@@ -553,7 +553,8 @@ def MakePolar(Orient,QB):
             else:
                 orKeys = [item for item in orKeys if 'Sl' in item]
             orbs = SHCdict[iAt]
-            UVmat = np.inner(nl.inv(SHCdict[-iAt]['UVmat']),Bmat)
+            # UVmat = np.inner(nl.inv(SHCdict[-iAt]['UVmat']),Bmat)
+            UVmat = np.inner(SHCdict[-iAt]['UVmat'],Bmat)
             R,Th,Ph = G2lat.H2ThPh2(np.reshape(HKL,(-1,3)),UVmat)
             R = 1/R     # correct dspacings
             atFlg.append(1.0)

GSASII/SUBGROUPS.py

@@ -829,36 +829,37 @@ def createStdSetting(cifFile,rd):
     if not os.path.exists(cifFile):
         print(f'createStdSetting error: file {cifFile} not found')
         return False
-    files = {'cifile': open(cifFile,'rb')}
-    values = {'strtidy':''}
-    print(f'''Submitting structure to Bilbao "CIF to Standard Setting" (strtidy)
-web service. Please cite:
-{G2G.GetCite('Bilbao: PSEUDOLATTICE',wrap=70,indent=5)}''')
-    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]
-    #spgNam = G2spc.spgbyNum[int(spnum)]
-    cell = [float(i) for i in celllist.split()]
-    # replace cell, space group and atom info with info from Bilbao
-    # could try to xfer Uiso (Uij needs xform), but that would be too involved
-    rd.Phase['General']['SGData'] = SGData = G2spc.SpcGroup(G2spc.spgbyNum[int(spnum)])[1]
-    rd.Phase['General']['Cell'] = [False] + list(cell) + [G2lat.calc_V(G2lat.cell2A(cell))]
-    rd.Phase['Atoms'] = []
-    for i,line in enumerate(structure.split('\n')[3:]):
-        atomlist = ['','Xe','',0.,0.,0.,1.0,'',0.,'I',0.01, 0.,0.,0.,0.,0.,0.,]
-        elem,lbl,wyc,x,y,z = line.split()
-        elem = elem.rstrip('0123456789-+')
-        atomlist[0] = elem + lbl
-        if G2elem.CheckElement(elem):
-            atomlist[1] = elem
-        atomlist[3:6] = [float(i) for i in (x,y,z)]
-        atomlist[7],atomlist[8] = G2spc.SytSym(atomlist[3:6],SGData)[:2]
-        atomlist[1] = G2elem.FixValence(atomlist[1])
-
-        atomlist.append(ran.randint(0,sys.maxsize)) # add a random Id
-        rd.Phase['Atoms'].append(atomlist)
-        if i == int(natom)-1: break
-    del rd.SymOps['xyz'] # as-read sym ops now obsolete
+    with open(cifFile,'rb') as fil:
+        files = {'cifile': fil}
+        values = {'strtidy':''}
+        print(f'''Submitting structure to Bilbao "CIF to Standard Setting" (strtidy)
+    web service. Please cite:
+    {G2G.GetCite('Bilbao: PSEUDOLATTICE',wrap=70,indent=5)}''')
+        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]
+        #spgNam = G2spc.spgbyNum[int(spnum)]
+        cell = [float(i) for i in celllist.split()]
+        # replace cell, space group and atom info with info from Bilbao
+        # could try to xfer Uiso (Uij needs xform), but that would be too involved
+        rd.Phase['General']['SGData'] = SGData = G2spc.SpcGroup(G2spc.spgbyNum[int(spnum)])[1]
+        rd.Phase['General']['Cell'] = [False] + list(cell) + [G2lat.calc_V(G2lat.cell2A(cell))]
+        rd.Phase['Atoms'] = []
+        for i,line in enumerate(structure.split('\n')[3:]):
+            atomlist = ['','Xe','',0.,0.,0.,1.0,'',0.,'I',0.01, 0.,0.,0.,0.,0.,0.,]
+            elem,lbl,wyc,x,y,z = line.split()
+            elem = elem.rstrip('0123456789-+')
+            atomlist[0] = elem + lbl
+            if G2elem.CheckElement(elem):
+                atomlist[1] = elem
+            atomlist[3:6] = [float(i) for i in (x,y,z)]
+            atomlist[7],atomlist[8] = G2spc.SytSym(atomlist[3:6],SGData)[:2]
+            atomlist[1] = G2elem.FixValence(atomlist[1])
+
+            atomlist.append(ran.randint(0,sys.maxsize)) # add a random Id
+            rd.Phase['Atoms'].append(atomlist)
+            if i == int(natom)-1: break
+        del rd.SymOps['xyz'] # as-read sym ops now obsolete
 
 #if __name__ == '__main__':
     # Note that self-tests have been moved to file ``tests/run_bilbao.py``.

GSASII/tutorialIndex.py

@@ -95,11 +95,14 @@
     ['Magnetic-V', 'Magnetic-V.htm',"Magnetic Structure Analysis-V",
      '''Analysis of a complex Type IV antiferromagnet with two propagation vectorse using Bilbao k-SUBGROUPSMAG from TOF neutron powder data'''],
 
-    ['k_vec_tutorial', 'k_vec_tutorial.html', 'k-vector searching in GSAS-II #1',
+    ['k_vec_tutorial', 'k_vec_tutorial.html', 'k-vector searching in GSAS-II #1 (all-zero vector)',
     '''Search neutron diffraction data of Er2Ge2O7 for a all-zero magnetic k-vector'''],
 
-    ['k_vec_tutorial_non_zero', 'k_vec_tutorial_non_zero.html', 'k-vector searching in GSAS-II #2',
+    ['k_vec_tutorial_non_zero', 'k_vec_tutorial_non_zero.html', 'k-vector searching in GSAS-II #2 (non-zero vector)',
     '''Search neutron diffraction data used in Magnetic Structure Analysis-III for a non-zero magnetic k-vector'''],
+    
+    ['k_vec_isodistort', 'k_vec_isodistort.html', 'Use of  ISODISTORT with a k-vector found by GSAS-II',
+    '''Use ISODISTORT to find isotropic subgroups that are compatible with a magnetic k-vector'''],
 
     #['ExampleDir', 'ExamplePage.html', 'Example Tutorial Title', '''Example descriptive text'''],