From 0163596aa5b89e7f6b7ae007fdb5ede31013cd7c Mon Sep 17 00:00:00 2001
From: Michael Wedel <michael.wedel@esss.se>
Date: Mon, 25 Jan 2016 14:21:36 -0500
Subject: [PATCH] Refs #15068. More flexible atom strings
---
.../plugins/algorithms/LoadCIF.py | 52 ++++++++++++++++---
.../python/plugins/algorithms/LoadCIFTest.py | 39 +++++++++++---
2 files changed, 76 insertions(+), 15 deletions(-)
diff --git a/Framework/PythonInterface/plugins/algorithms/LoadCIF.py b/Framework/PythonInterface/plugins/algorithms/LoadCIF.py
index 3d47133ed57..4410076a8a8 100644
--- a/Framework/PythonInterface/plugins/algorithms/LoadCIF.py
+++ b/Framework/PythonInterface/plugins/algorithms/LoadCIF.py
@@ -1,10 +1,12 @@
-# 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)
diff --git a/Framework/PythonInterface/test/python/plugins/algorithms/LoadCIFTest.py b/Framework/PythonInterface/test/python/plugins/algorithms/LoadCIFTest.py
index 517a682c400..d7ec89b3da6 100644
--- a/Framework/PythonInterface/test/python/plugins/algorithms/LoadCIFTest.py
+++ b/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):
--
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