Changeset 102 for trunk

Timestamp:

Jul 5, 2010 4:19:33 PM (12 years ago)

Author:

toby

Message:

add space group list; fix minor bugs in GenHLaue & add unit test

Location:

trunk

Files:

• GSASIIlattice.py (modified) (6 diffs)
• GSASIIspc.py (modified) (1 diff)
• fsource/Makefile (moved) (moved from trunk/Makefile)
• testinp/genhkltest.py (added)
• testinp/sgtbxlattinp.py (added)
• unit_tests.py (modified) (2 diffs)

trunk/GSASIIlattice.py

@@ -383 +383 @@
                         HKL.append([h,k,l,1/math.sqrt(rdsq)])
     elif Laue == '2/m':                #monoclinic
-        Hmax = SwapIndx(Axis,Hmax)
+        axisnum = 1 + ['a','b','c'].index(Axis)
+        Hmax = SwapIndx(axisnum,Hmax)
         for h in range(Hmax[0]+1):
             for k in range(-Hmax[1],Hmax[1]+1):
@@ -389 +390 @@
                 if k < 0:lmin = 1
                 for l in range(lmin,Hmax[2]+1):
-                    [h,k,l] = SwapIndx(-Axis,[h,k,l])
+                    [h,k,l] = SwapIndx(-axisnum,[h,k,l])
                     H = []
                     if CentCheck(Cent,[h,k,l]): H=[h,k,l]
@@ -396 +397 @@
                         if 0 < rdsq <= dminsq:
                             HKL.append([h,k,l,1/math.sqrt(rdsq)])
-                    [h,k,l] = SwapIndx(Axis,[h,k,l])
+                    [h,k,l] = SwapIndx(axisnum,[h,k,l])
     elif Laue in ['mmm','4/m','6/m']:            #orthorhombic
         for l in range(Hmax[2]+1):
@@ -402 +403 @@
                 kmin = 1
                 if Laue == 'mmm' or h ==0: kmin = 0
-                for k in range(kmin,Hmax[2]+1):
+                for k in range(kmin,Hmax[1]+1):
                     H = []
                     if CentCheck(Cent,[h,k,l]): H=[h,k,l]
@@ -581 +582 @@
             assert np.allclose(frac,tf), msg
 
+# test GetBraviasNum(...) and GenHBravais(...)
+def test7():
+    import os.path
+    import sys
+    import GSASIIspc as spc
+    testdir = os.path.join(os.path.split(os.path.abspath( __file__ ))[0],'testinp')
+    if os.path.exists(testdir):
+        if testdir not in sys.path: sys.path.insert(0,testdir)
+    import sgtbxlattinp
+    derror = 1e-4
+    def indexmatch(hklin, hkllist, system):
+        for hklref in hkllist:
+            hklref = list(hklref)
+            # these permutations are far from complete, but are sufficient to 
+            # allow the test to complete
+            if system == 'cubic':
+                permlist = [(1,2,3),(1,3,2),(2,1,3),(2,3,1),(3,1,2),(3,2,1),]
+            elif system == 'monoclinic':
+                permlist = [(1,2,3),(-1,2,-3)]
+            else:
+                permlist = [(1,2,3)]
+
+            for perm in permlist:
+                hkl = [abs(i) * hklin[abs(i)-1] / i for i in perm]
+                if hkl == hklref: return True
+                if [-i for i in hkl] == hklref: return True
+        else:
+            return False
+
+    for key in sgtbxlattinp.sgtbx7:
+        spdict = spc.SpcGroup(key)
+        cell = sgtbxlattinp.sgtbx7[key][0]
+        system = spdict[1]['SGSys']
+        center = spdict[1]['SGLatt']
+
+        bravcode = GetBraviasNum(center, system)
+
+        g2list = GenHBravais(sgtbxlattinp.dmin, bravcode, cell2A(cell))
+
+        assert len(sgtbxlattinp.sgtbx7[key][1]) == len(g2list), 'Reflection lists differ for %s' % key
+        for h,k,l,d,num in g2list:
+            for hkllist,dref in sgtbxlattinp.sgtbx7[key][1]: 
+                if abs(d-dref) < derror:
+                    if indexmatch((h,k,l,), hkllist, system):
+                        break
+            else:
+                assert 0,'No match for %s at %s (%s)' % ((h,k,l),d,key)
+
+def test8():
+    import GSASIIspc as spc
+    import sgtbxlattinp
+    derror = 1e-4
+    dmin = sgtbxlattinp.dmin
+
+    def indexmatch(hklin, hklref, system, axis):
+        # these permutations are far from complete, but are sufficient to 
+        # allow the test to complete
+        if system == 'cubic':
+            permlist = [(1,2,3),(1,3,2),(2,1,3),(2,3,1),(3,1,2),(3,2,1),]
+        elif system == 'monoclinic' and axis=='b':
+            permlist = [(1,2,3),(-1,2,-3)]
+        elif system == 'monoclinic' and axis=='a':
+            permlist = [(1,2,3),(1,-2,-3)]
+        elif system == 'monoclinic' and axis=='c':
+            permlist = [(1,2,3),(-1,-2,3)]
+        elif system == 'trigonal':
+            permlist = [(1,2,3),(2,1,3),(-1,-2,3),(-2,-1,3)]
+        else:
+            permlist = [(1,2,3)]
+
+        hklref = list(hklref)
+        for perm in permlist:
+            hkl = [abs(i) * hklin[abs(i)-1] / i for i in perm]
+            if hkl == hklref: return True
+            if [-i for i in hkl] == hklref: return True
+        return False
+
+    for key in sgtbxlattinp.sgtbx8:
+        spdict = spc.SpcGroup(key)[1]
+        cell = sgtbxlattinp.sgtbx8[key][0]
+        center = spdict['SGLatt']
+        Laue = spdict['SGLaue']
+        Axis = spdict['SGUniq']
+        system = spdict['SGSys']
+
+        g2list = GenHLaue(dmin,Laue,center,Axis,cell2A(cell))
+        #if len(g2list) != len(sgtbxlattinp.sgtbx8[key][1]):
+        #    print 'failed',key,':' ,len(g2list),'vs',len(sgtbxlattinp.sgtbx8[key][1])
+        #    print 'GSAS-II:'
+        #    for h,k,l,d in g2list: print '  ',(h,k,l),d
+        #    print 'SGTBX:'
+        #    for hkllist,dref in sgtbxlattinp.sgtbx8[key][1]: print '  ',hkllist,dref
+        assert len(g2list) == len(sgtbxlattinp.sgtbx8[key][1]), (
+            'Reflection lists differ for %s' % key
+            )
+        #match = True
+        for h,k,l,d in g2list:
+            for hkllist,dref in sgtbxlattinp.sgtbx8[key][1]: 
+                if abs(d-dref) < derror:
+                    if indexmatch((h,k,l,), hkllist, system, Axis): break
+            else:
+                assert 0,'No match for %s at %s (%s)' % ((h,k,l),d,key)
+                #match = False
+        #if not match: 
+            #for hkllist,dref in sgtbxlattinp.sgtbx8[key][1]: print '  ',hkllist,dref
+            #print center, Laue, Axis, system
+
 if __name__ == '__main__':
     test0()
@@ -589 +697 @@
     test5()
     test6()
+    test7()
+    test8()
     print "OK"

trunk/GSASIIspc.py

@@ -489 +489 @@
     return GetKNsym(str(Isym)),Mult
     
+'''A list of space groups as ordered and named in the pre-2002 International 
+Tables Volume A, except that spaces are used following the GSAS convention to 
+separate the different crystallographic directions.
+Note that the symmetry codes here will recognize many non-standard space group 
+symbols with different settings.
+'''
+spglist = {
+    'triclinic' : ('P 1','P -1',), # 1-2
+    'monoclinic': ('P 2','P 21','C 2','P m','P c','C m','C c','P 2/m','P 21/m',
+                   'C 2/m','P 2/c','P 21/c','C 2/c',), #3-15
+    'orthorhombic': ('P 2 2 2','P 2 2 21','P 21 21 2','P 21 21 21','C 2 2 21',
+                     'C 2 2 2','F 2 2 2','I 2 2 2','I 21 21 21',
+                     'P m m 2','P m c 21','P c c 2','P m a 2','P c a 21',
+                     'P n c 2','P m n 21','P b a 2','P n a 21','P n n 2',
+                     'C m m 2','C m c 21','C c c 2','A m m 2','A b m 2',
+                     'A m a 2','A b a 2','F m m 2','F d d 2','I m m 2',
+                     'I b a 2','I m a 2','P m m m','P n n n','P c c m',
+                     'P b a n','P m m a','P n n a','P m n a','P c c a',
+                     'P b a m','P c c n','P b c m','P n n m','P m m n',
+                     'P b c n','P b c a','P n m a','C m c m','C m c a',
+                     'C m m m','C c c m','C m m a','C c c a','F m m m',
+                     'F d d d','I m m m','I b a m','I b c a','I m m a',), #16-74
+    'tetragonal': ('P 4','P 41','P 42','P 43','I 4','I 41','P -4','I -4',
+                   'P 4/m','P 42/m','P 4/n','P 42/n','I 4/m','I 41/a',
+                   'P 4 2 2','P 4 21 2','P 41 2 2','P 41 21 2','P 42 2 2',
+                   'P 42 21 2','P 43 2 2','P 43 21 2','I 4 2 2','I 41 2 2',
+                   'P 4 m m','P 4 b m','P 42 c m','P 42 n m','P 4 c c',
+                   'P 4 n c','P 42 m c','P 42 b c','I 4 m m','I 4 c m',
+                   'I 41 m d','I 41 c d','P -4 2 m','P -4 2 c','P -4 21 m',
+                   'P -4 21 c','P -4 m 2','P -4 c 2','P -4 b 2','P -4 n 2',
+                   'I -4 m 2','I -4 c 2','I -4 2 m','I -4 2 d','P 4/m m m',
+                   'P 4/m c c','P 4/n b m','P 4/n n c','P 4/m b m','P 4/m n c',
+                   'P 4/n m m','P 4/n c c','P 42/m m c','P 42/m c m',
+                   'P 42/n b c','P 42/n n m','P 42/m b c','P 42/m n m',
+                   'P 42/n m c','P 42/n c m','I 4/m m m','I 4/m c m',
+                   'I 41/a m d','I 41/a c d',), # 75-142
+    'trigonal': ('P 3','P 31','P 32','R 3','P -3','R -3','P 3 1 2','P 3 2 1',
+                 'P 31 1 2','P 31 2 1','P 32 1 2','P 32 2 1','R 3 2', 'P 3 m 1',
+                 'P 3 1 m','P 3 c 1','P 3 1 c','R 3 m','R 3 c','P -3 1 m',
+                 'P -3 1 c','P -3 m 1','P -3 c 1','R -3 m','R -3 c',), #143-167
+    'hexagonal': ('P 6','P 61','P 65','P 62','P 64','P 63','P -6','P 6/m',
+                  'P 63/m','P 6 2 2','P 61 2 2','P 65 2 2','P 62 2 2',
+                  'P 64 2 2','P 63 2 2','P 6 m m','P 6 c c','P 63 c m',
+                  'P 63 m c','P -6 m 2','P -6 c 2','P -6 2 m','P -6 2 c',
+                  'P 6/m m m','P 6/m c c','P 63/m c m','P 63/m m c',), #144-194
+    'cubic': ('P 2 3','F 2 3','I 2 3','P 21 3','I 21 3','P m -3','P n -3',
+              'F m -3','F d -3','I m -3','P a -3','I a -3','P 4 3 2','P 42 3 2',
+              'F 4 3 2','F 41 3 2','I 4 3 2','P 43 3 2','P 41 3 2','I 41 3 2',
+              'P -4 3 m','F -4 3 m','I -4 3 m','P -4 3 n','F -4 3 c','I -4 3 d',
+              'P m -3 m','P n -3 n','P m -3 n','P n -3 m','F m -3 m','F m -3 c',
+              'F d -3 m','F d -3 c','I m -3 m','I a -3 d',), #195-230
+}
+'A few non-standard space groups for test use'
+nonstandard_sglist = ('P 21 1 1','P 1 21 1','P 1 1 21','R 3 r','R 3 2 h', 
+                      'R -3 r', 'R 3 2 r','R 3 m h', 'R 3 m r',
+                      'R 3 c r','R -3 c r','R -3 m r',),
+'''A list of orthorhombic space groups that were renamed in the 2002 Volume A,
+along with the pre-2002 name. The e designates a double glide-plane'''
+sgequiv_2002_orthorhombic= (('A e m 2', 'A b m 2',),
+                            ('A e a 2', 'A b a 2',),
+                            ('C m c e', 'C m c a',),
+                            ('C m m e', 'C m m a',),
+                            ('C c c e', 'C c c a'),)
+'''Use the space groups types in this order to list the symbols in the 
+order they are listed in the International Tables, vol. A'''
+symtypelist = ('triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 
+               'trigonal', 'hexagonal', 'cubic')
+
 # self-test materials follow. Requires files in directory testinp
 def test0():

trunk/unit_tests.py

@@ -23 +23 @@
 def test_GSASIIlattice6():
     G2l.test6()
+def test_GSASIIlattice7():
+    G2l.test7()
+def test_GSASIIlattice8():
+    G2l.test8()
 
 if __name__ == '__main__':
@@ -36 +40 @@
     G2l.test5()
     G2l.test6()
+    G2l.test7()
+    G2l.test8()
     print "OK"