Refs #15068. More flexible atom strings

Framework/PythonInterface/plugins/algorithms/LoadCIF.py

-# pylint: disable=no-init,too-few-public-methods
+# pylint: disable=no-init,too-few-public-methods,wrong-import-position
 from mantid.kernel import *
 from mantid.simpleapi import *
 from mantid.api import *
 from mantid.geometry import SpaceGroupFactory, CrystalStructure
 
 import re
+import math
+
 
 # pylint: disable=invalid-name
 def removeErrorEstimateFromNumber(numberString):
@@ -16,6 +18,10 @@ def removeErrorEstimateFromNumber(numberString):
     return numberString[:errorBegin]
 
 
+def convertBisoToUiso(bIso):
+    return bIso / (8.0 * math.pi * math.pi)
+
+
 class CrystalStructureBuilder(object):
     '''
     Helper class that builds a CrystalStructure file from the result
@@ -46,8 +52,8 @@ class CrystalStructureBuilder(object):
             # pylint: disable=unused-variable,invalid-name
             except RuntimeError as e:
                 raise RuntimeError(
-                    'Can not create space group from supplied CIF-file. You could try to modify the HM-symbol'\
-                    'to contain spaces between the components.\n'\
+                    'Can not create space group from supplied CIF-file. You could try to modify the HM-symbol' \
+                    'to contain spaces between the components.\n' \
                     'Keys to look for: _space_group_name_H-M_alt, _symmetry_space_group_name_H-M')
 
     def _getSpaceGroupFromString(self, cifData):
@@ -109,12 +115,12 @@ class CrystalStructureBuilder(object):
         return ' '.join(unitCellValues)
 
     def _getAtoms(self, cifData):
-        atomFieldsRequirements = [(u'_atom_site_label', True),
-                                  (u'_atom_site_fract_x', True),
+        atomSymbols = self._getAtomSymbols(cifData)
+
+        atomFieldsRequirements = [(u'_atom_site_fract_x', True),
                                   (u'_atom_site_fract_y', True),
                                   (u'_atom_site_fract_z', True),
-                                  (u'_atom_site_occupancy', False),
-                                  (u'_atom_site_u_iso_or_equiv', False)]
+                                  (u'_atom_site_occupancy', False)]
 
         atomFields = []
 
@@ -127,7 +133,14 @@ class CrystalStructureBuilder(object):
                         'Mandatory field {0} not found in CIF-file.' \
                         'Please check the atomic position definitions.'.format(field))
 
-        atomLists = [cifData[x] for x in atomFields]
+        atomLists = [atomSymbols] + [cifData[x] for x in atomFields]
+
+        try:
+            isotropicUs = self._getIsotropicUs(cifData)
+            atomLists += [isotropicUs]
+        # pylint: disable=unused-variable,invalid-name
+        except RuntimeError as e:
+            pass
 
         atomLines = []
         for atomLine in zip(*atomLists):
@@ -139,6 +152,29 @@ class CrystalStructureBuilder(object):
 
         return ';'.join(atomLines)
 
+    def _getAtomSymbols(self, cifData):
+        rawAtomSymbols = [cifData[x] for x in [u'_atom_site_type_symbol', u'_atom_site_label'] if x in
+                          cifData.keys()]
+
+        if len(rawAtomSymbols) == 0:
+            raise RuntimeError('Cannot determine atom types, both _atom_site_type_symbol and _atom_site_label are '
+                               'missing.')
+
+        return [self._getCleanAtomSymbol(x) for x in rawAtomSymbols[0]]
+
+    def _getIsotropicUs(self, cifData):
+        keyUIso = u'_atom_site_u_iso_or_equiv'
+
+        if keyUIso in cifData.keys():
+            return cifData[keyUIso]
+
+        keyBIso = u'_atom_site_b_iso_or_equiv'
+
+        if keyBIso in cifData.keys():
+            return [convertBisoToUiso(float(x)) for x in cifData[keyBIso]]
+
+        raise RuntimeError('Neither U_iso nor B_iso are defined in the CIF-file.')
+
     def _getCleanAtomSymbol(self, atomSymbol):
         nonCharacterRe = re.compile('[^a-z]', re.IGNORECASE)
 

Framework/PythonInterface/test/python/plugins/algorithms/LoadCIFTest.py

@@ -96,10 +96,19 @@ class CrystalStructureBuilderTestUnitCell(unittest.TestCase):
         self.assertEqual(self.builder._getUnitCell(cell_errors), '5.6 5.6 2.3 90.0 90.0 120.0')
 
 
-
 class CrystalStructureBuilderTestAtoms(unittest.TestCase):
     def setUp(self):
         self.builder = CrystalStructureBuilder()
+        self._baseData = dict([
+            (u'_atom_site_fract_x', [u'1/8', u'0.34(1)']),
+            (u'_atom_site_fract_y', [u'1/8', u'0.56(2)']),
+            (u'_atom_site_fract_z', [u'1/8', u'0.23(2)'])])
+
+    def _getData(self, additionalData):
+        data = self._baseData.copy()
+        data.update(additionalData)
+
+        return data
 
     def test_getAtoms_required_keys(self):
         mandatoryKeys = dict([(u'_atom_site_label', [u'Si']),
@@ -113,15 +122,31 @@ class CrystalStructureBuilderTestAtoms(unittest.TestCase):
             self.assertRaises(RuntimeError, self.builder._getAtoms, cifData=tmp)
 
     def test_getAtoms_correct(self):
-        data = dict([(u'_atom_site_label', [u'Si', u'Al']),
-                     (u'_atom_site_fract_x', [u'1/8', u'0.34(1)']),
-                     (u'_atom_site_fract_y', [u'1/8', u'0.56(2)']),
-                     (u'_atom_site_fract_z', [u'1/8', u'0.23(2)']),
-                     (u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
-                     (u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])])
+        data = self._getData(dict([(u'_atom_site_label', [u'Si', u'Al']),
+                                   (u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
+                                   (u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
+
+        self.assertEqual(self.builder._getAtoms(data), 'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
+
+    def test_getAtoms_atom_type_symbol(self):
+        data = self._getData(dict([(u'_atom_site_label', [u'Fake1', u'Fake2']),
+                                   (u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
+                                   (u'_atom_site_u_iso_or_equiv', [u'0.01', u'0.02'])]))
+
+        self.assertEqual(self.builder._getAtoms(data), 'Fake 1/8 1/8 1/8 1.0 0.01;Fake 0.34 0.56 0.23 1.0 0.02')
+
+        data[u'_atom_site_type_symbol'] = [u'Si', u'Al']
 
         self.assertEqual(self.builder._getAtoms(data), 'Si 1/8 1/8 1/8 1.0 0.01;Al 0.34 0.56 0.23 1.0 0.02')
 
+    def test_getAtoms_B_iso(self):
+        data = self._getData(dict([(u'_atom_site_label', [u'Si', u'Al']),
+                                   (u'_atom_site_occupancy', [u'1.0', u'1.0(0)']),
+                                   (u'_atom_site_b_iso_or_equiv', [u'1.0', u'2.0'])]))
+
+        self.assertEqual(self.builder._getAtoms(data),
+                         'Si 1/8 1/8 1/8 1.0 0.0126651479553;Al 0.34 0.56 0.23 1.0 0.0253302959106')
+
 
 class UBMatrixBuilderTest(unittest.TestCase):
     def setUp(self):