Merge branch 'use-sg-site-isotropy'

* set `Atom.anisotropy` per CIF spacegroup constraints
* test symmetry-derived site isotropy and its CIF overrides.

Resolves #30.

Author: pavoljuhas

src/diffpy/structure/parsers/p_cif.py

@@ -412,11 +412,8 @@ def _parse_atom_site_aniso_label(self, block):
         No return value.
         """
         if '_atom_site_aniso_label' not in block: return
-        # was anisotropy set in the _atom_site_label loop?
-        atom_site_loop = block.GetLoop('_atom_site_label')
-        anisotropy_already_set = (
-            '_atom_site_adp_type' in atom_site_loop or
-            '_atom_site_thermal_displace_type' in atom_site_loop)
+        # was anisotropy processed in the _atom_site_label loop?
+        isotropy_done = _hasAtomSiteADPType(block)
         # something to do here:
         adp_loop = block.GetLoop('_atom_site_aniso_label')
         # index of the _atom_site_label column
@@ -427,7 +424,7 @@ def _parse_atom_site_aniso_label(self, block):
         for values in sitedatalist:
             idx = self.labelindex[values[ilb]]
             a = self.stru[idx]
-            if not anisotropy_already_set:
+            if not isotropy_done:
                 a.anisotropy = True
             for fset, val in zip(prop_setters, values):
                 fset(a, val)
@@ -494,22 +491,32 @@ def _parse_space_group_symop_operation_xyz(self, block):
         if self.spacegroup is None:
             emsg = "CIF file has unknown space group identifier {!r}."
             raise StructureFormatError(emsg.format(sgid))
-        self._expandAsymmetricUnit()
+        self._expandAsymmetricUnit(block)
         return
 
 
-    def _expandAsymmetricUnit(self):
+    def _expandAsymmetricUnit(self, block):
         """Perform symmetry expansion of self.stru using self.spacegroup.
+
         This method updates data in stru and eau.
 
-        No return value.
+        Parameters
+        ----------
+        block : CifBlock
+            The top-level block containing crystal structure data.
         """
         from diffpy.structure.symmetryutilities import ExpandAsymmetricUnit
-        # get reverse-ordered unique indices
         corepos = [a.xyz for a in self.stru]
         coreUijs = [a.U for a in self.stru]
         self.eau = ExpandAsymmetricUnit(self.spacegroup, corepos, coreUijs,
                                         eps=self.eps)
+        # setup anisotropy according to symmetry requirements
+        # was isotropy flag already processed
+        isotropy_done = (_hasAtomSiteADPType(block) or
+                         '_atom_site_aniso_label' in block)
+        if not isotropy_done:
+            for ca, uisotropy in zip(self.stru, self.eau.Uisotropy):
+                ca.anisotropy = not uisotropy
         # build a nested list of new atoms:
         newatoms = []
         for i, ca in enumerate(self.stru):
@@ -727,3 +734,12 @@ def _suppressCifParserOutput():
     finally:
         yapps3_compiled_rt.print_error = print_error
     pass
+
+
+def _hasAtomSiteADPType(block):
+    """Return True if the CIF specifies _atom_site_adp_type.
+    """
+    atom_site_loop = block.GetLoop('_atom_site_label')
+    rv = ('_atom_site_adp_type' in atom_site_loop or
+          '_atom_site_thermal_displace_type' in atom_site_loop)
+    return rv

src/diffpy/structure/tests/testp_cif.py

@@ -66,7 +66,7 @@ def test_getSymOp(self):
 
 class TestP_cif(unittest.TestCase):
 
-    goodciffile = datafile('PbTe.cif')
+    pbteciffile = datafile('PbTe.cif')
     badciffile = datafile('LiCl-bad.cif')
     graphiteciffile = datafile('graphite.cif')
     cdsebulkpdffitfile = datafile('CdSe_bulk.stru')
@@ -86,12 +86,12 @@ def tearDown(self):
     def test_parse(self):
         """check P_cif.parse()
         """
-        with open(self.goodciffile) as fp1:
+        with open(self.pbteciffile) as fp1:
             sgood = fp1.read()
         with open(self.badciffile) as fp2:
             sbad = fp2.read()
         pfile, ptest = self.pfile, self.ptest
-        stru_check = pfile.parseFile(self.goodciffile)
+        stru_check = pfile.parseFile(self.pbteciffile)
         stru = ptest.parse(sgood)
         self.assertEqual(str(stru_check), str(stru))
         self.assertEqual(str(stru_check.lattice), str(stru.lattice))
@@ -106,12 +106,12 @@ def test_parse(self):
     def test_parseLines(self):
         """check P_cif.parseLines()
         """
-        with open(self.goodciffile) as fp1:
+        with open(self.pbteciffile) as fp1:
             goodlines = fp1.readlines()
         with open(self.badciffile) as fp2:
             badlines = fp2.readlines()
         pfile, ptest = self.pfile, self.ptest
-        stru_check = pfile.parseFile(self.goodciffile)
+        stru_check = pfile.parseFile(self.pbteciffile)
         stru = ptest.parseLines(goodlines)
         self.assertEqual(str(stru_check), str(stru))
         self.assertEqual(str(stru_check.lattice), str(stru.lattice))
@@ -126,8 +126,8 @@ def test_parseLines(self):
     def test_parseFile(self):
         """check P_cif.parseFile()
         """
-        # goodciffile
-        stru = self.pfile.parseFile(self.goodciffile)
+        # pbteciffile
+        stru = self.pfile.parseFile(self.pbteciffile)
         self.assertEqual(8, len(stru))
         self.assertEqual(6.461, stru.lattice.a)
         self.assertEqual(6.461, stru.lattice.b)
@@ -289,6 +289,61 @@ def test_custom_spacegroup_cif(self):
         return
 
 
+    def test_spacegroup_isotropy(self):
+        "verify site isotropy due to site symmetry."
+        # remove the _atom_site_thermal_displace_type field
+        with open(self.pbteciffile) as fp:
+            lines = [line.replace(' Uiso ', ' ') for line in fp
+                     if '_atom_site_thermal_displace_type' not in line]
+        ciftxt = ''.join(lines)
+        ptest = self.ptest
+        stru = ptest.parse(ciftxt)
+        self.assertFalse(any(stru.anisotropy))
+        self.assertTrue(all(not a.anisotropy for a in ptest.asymmetric_unit))
+        return
+
+
+    def test_spacegroup_anisotropy(self):
+        "verify site anisotropy due to site symmetry."
+        stru = self.ptest.parseFile(self.graphiteciffile)
+        self.assertTrue(all(stru.anisotropy))
+        return
+
+
+    def test_adp_type_ani(self):
+        "verify adp type override to anisotropic"
+        with open(self.pbteciffile) as fp:
+            ciftxt = fp.read()
+            ciftxt = ciftxt.replace(' Uiso ', ' Uani ')
+        stru = self.ptest.parse(ciftxt)
+        self.assertTrue(all(stru.anisotropy))
+        return
+
+
+    def test_adp_type_iso(self):
+        "verify adp type override to isotropic"
+        with open(self.graphiteciffile) as fp:
+            lines = fp.readlines()
+        lines.insert(-2, '_atom_site_adp_type\n')
+        lines[-2] = lines[-2].rstrip() + '   Uiso\n'
+        lines[-1] = lines[-1].rstrip() + '   Uiso\n'
+        ciftxt = ''.join(lines)
+        stru = self.ptest.parse(ciftxt)
+        self.assertFalse(any(a.anisotropy for a in stru))
+        return
+
+
+    def test_adp_aniso_label(self):
+        "verify ADP type setting from _atom_site_aniso_label loop"
+        with open(self.teiciffile) as fp:
+            lines = [line.replace(' Uani ', ' ') for line in fp
+                     if not '_atom_site_adp_type' in line]
+        ciftxt = ''.join(lines)
+        stru = self.ptest.parse(ciftxt)
+        self.assertTrue(all(stru.anisotropy))
+        return
+
+
     def test_getParser(self):
         """Test passing of eps keyword argument by getParser function.
         """