Refs #11510. Added system tests

Added system tests for different structures from different crystal systems.

Code/Mantid/Testing/SystemTests/tests/analysis/POLDICreatePeaksFromCellTest.py

@@ -0,0 +1,158 @@
+# pylint: disable=no-init,invalid-name,too-many-locals
+import stresstesting
+from mantid.simpleapi import *
+
+# These tests check the correctness of the structure factor calculation for some common crystal structures.
+# All structure factors for comparison have been calculated using VESTA 3.2.1, which is described in the following
+# publication:
+#
+# K. Momma and F. Izumi, "VESTA 3 for three-dimensional visualization of crystal,
+#           volumetric and morphology data," J. Appl. Crystallogr., 44, 1272-1276 (2011)
+#
+#           http://dx.doi.org/10.1107/S0021889811038970
+#
+# All crystal structure data have been acquired from http://www.crystallography.net/. DOIs of the original
+# papers with the published structures are given in the tests.
+#
+# Isotropic thermal parameters are rounded or arbitrary (the tests are meant for checking the calculations only).
+
+class ReflectionCheckingTest(stresstesting.MantidStressTest):
+    def runTest(self):
+        pass
+
+    def checkReflections(self, peakTable, data, structureFactorPrecision = 1e-5):
+        for idx in data.keys():
+            currentPeak = peakTable.row(idx)
+            reference = data[idx]
+
+            self.assertEquals([int(x) for x in currentPeak['HKL'].split()], reference[0])
+            self.assertDelta(float(currentPeak['d']), reference[1], 1e-4)
+
+            fSquaredReference = reference[2] ** 2 * reference[3]
+            self.assertDelta(float(currentPeak['Intensity']) / fSquaredReference, 1.0, structureFactorPrecision)
+
+
+class POLDICreatePeaksFromCellTestSiO2(ReflectionCheckingTest):
+    """Structure factor check for:
+            SiO2, 10.1107/S0108768105005240"""
+
+    data = {
+        0: ([1, 0, 0], 4.25588, 16.6297, 6),
+        1: ([1, 0, -1], 3.34393, 39.2576, 6),
+        14: ([0, 0, 3], 1.80193, 9.31225, 2),
+        40: ([2, 2, 0], 1.22857, 18.8765, 3),
+        117: ([3, 1, -4], 0.88902, 6.55526, 6)
+    }
+
+    def runTest(self):
+        peaks_SiO2 = PoldiCreatePeaksFromCell(
+            SpaceGroup="P 32 2 1",
+            Atoms="Si 0.4723 0.0 2/3 1.0 0.0075; O 0.416 0.2658 07881 1.0 0.0175",
+            a=4.91427, c=5.4058, LatticeSpacingMin=0.885)
+
+        peaks_SiO2 = SortTableWorkspace(InputWorkspace="peaks_SiO2", Columns=["d"], Ascending=[False])
+
+        self.assertEquals(peaks_SiO2.rowCount(), 118)
+
+
+class POLDICreatePeaksFromCellTestAl2O3(ReflectionCheckingTest):
+    """Structure factor check for:
+            Al2O3, 10.1107/S0021889890002382"""
+
+    data = {
+        0: ([1, 0, -2], 3.481144, 21.873, 6),
+        1: ([1, 0, 4], 2.551773, 23.6714, 6),
+        3: ([0, 0, 6], 2.165933, 68.8749, 2),
+        43: ([5, -2, -5], 0.88880, 23.6113, 12)
+    }
+
+
+    def runTest(self):
+        peaks_Al2O3 = PoldiCreatePeaksFromCell(
+            SpaceGroup="R -3 c",
+            Atoms="Al 0 0 0.35216 1.0 0.009; O 0.30668 0 1/4 1.0 0.0125",
+            a=4.7605, c=12.9956, LatticeSpacingMin=0.885)
+
+        peaks_Al2O3 = SortTableWorkspace(InputWorkspace="peaks_Al2O3", Columns=["d"], Ascending=[False])
+
+        self.assertEquals(peaks_Al2O3.rowCount(), 44)
+
+        self.checkReflections(peaks_Al2O3, self.data)
+
+class POLDICreatePeaksFromCellTestFeTiO3(ReflectionCheckingTest):
+    """Structure factor check for:
+            FeTiO3, 10.1007/s00269-007-0149-7
+
+        Note: Ti replaced by Zr"""
+
+    data = {
+        0: ([0, 0, 3], 4.6970, 2.0748, 2),
+        1: ([1, 0, 1], 4.20559, 1.60512, 6),
+        3: ([1, 0, 4], 2.75153, 76.1855, 6),
+        107: ([5, -4, 6], 0.88986, 100.244, 6)
+    }
+
+
+    def runTest(self):
+        peaks_FeTiO3 = PoldiCreatePeaksFromCell(
+            SpaceGroup="R -3",
+            Atoms="Fe 0 0 0.35543 1.0 0.005; Zr 0 0 0.14643 1.0 0.004; O 0.31717 0.02351 0.24498 1.0 0.006",
+            a=5.0881, c=14.091, LatticeSpacingMin=0.885)
+
+        peaks_FeTiO3 = SortTableWorkspace(InputWorkspace="peaks_FeTiO3", Columns=["d", "HKL"], Ascending=[False, True])
+
+        self.assertEquals(peaks_FeTiO3.rowCount(), 108)
+
+        self.checkReflections(peaks_FeTiO3, self.data, 6e-5)
+
+class POLDICreatePeaksFromCellTestCO(ReflectionCheckingTest):
+    """Structure factor check for:
+            CO, 10.1007/BF01339658
+
+        Notes: Non-centrosymmetric, cubic, negative coordinates"""
+
+    data = {
+        0: ([1, 1, 0], 3.98101, 1.93291, 12),
+        1: ([1, 1, -1], 3.25048, 40.6203, 4),
+        3: ([2, 0, 0], 2.815, 37.248, 6),
+        90: ([6, 2, 0], 0.89018, 9.45489, 12)
+    }
+
+
+    def runTest(self):
+        peaks_CO = PoldiCreatePeaksFromCell(
+            SpaceGroup="P 21 3",
+            Atoms="C -0.042 -0.042 -0.042 1.0 0.0125; O 0.067 0.067 0.067 1.0 0.0125",
+            a=5.63, LatticeSpacingMin=0.885)
+
+        peaks_CO = SortTableWorkspace(InputWorkspace="peaks_CO", Columns=["d"], Ascending=[False])
+
+        self.assertEquals(peaks_CO.rowCount(), 91)
+
+        self.checkReflections(peaks_CO, self.data, 1e-5)
+
+class POLDICreatePeaksFromCellTestBetaQuartz(ReflectionCheckingTest):
+    """Structure factor check for:
+            SiO2 (beta-quartz, high temperature), 10.1127/ejm/2/1/0063
+
+        Notes: Non-centrosymmetric, hexagonal, with coordinate 1/6"""
+
+    data = {
+        0: ([1, 0, 0], 4.32710, 7.74737, 6),
+        1: ([1, 0, 1], 3.38996, 19.7652, 12),
+        3: ([1, 0, 2], 2.30725, 2.96401, 12),
+        64: ([1, 0, 6], 0.88968, 3.15179, 12)
+    }
+
+
+    def runTest(self):
+        peaks_betaSiO2 = PoldiCreatePeaksFromCell(
+            SpaceGroup="P 62 2 2",
+            Atoms="Si 1/2 0 0 1.0 0.025; O 0.41570 0.20785 1/6 1.0 0.058",
+            a=4.9965, c=5.4546, LatticeSpacingMin=0.885)
+
+        peaks_betaSiO2 = SortTableWorkspace(InputWorkspace="peaks_betaSiO2", Columns=["d"], Ascending=[False])
+
+        self.assertEquals(peaks_betaSiO2.rowCount(), 65)
+
+        self.checkReflections(peaks_betaSiO2, self.data, 1e-5)