Remove symmetry elements for SaveINS

Framework/PythonInterface/plugins/algorithms/SaveINS.py

@@ -5,14 +5,41 @@
 #   Institut Laue - Langevin & CSNS, Institute of High Energy Physics, CAS
 # SPDX - License - Identifier: GPL - 3.0 +
 from mantid.api import AlgorithmFactory, FileProperty, FileAction, WorkspaceProperty, PythonAlgorithm
-from mantid.kernel import Direction
+from mantid.kernel import Direction, V3D
 from mantid.geometry import SymmetryOperationFactory, SpaceGroupFactory
 from os import path, makedirs
+import numpy as np
 
 
 class SaveINS(PythonAlgorithm):
     LATT_TYPE_MAP = {type: itype + 1 for itype, type in enumerate(["P", "I", "R", "F", "A", "B", "C"])}
+    IDENTIY_OP = SymmetryOperationFactory.createSymOp("x,y,z")
     INVERSION_OP = SymmetryOperationFactory.createSymOp("-x,-y,-z")
+    ROTATION_OPS = {1: [IDENTIY_OP, INVERSION_OP], -1: [IDENTIY_OP]}
+    CENTERING_OPS = {
+        1: [IDENTIY_OP],
+        2: [
+            SymmetryOperationFactory.createSymOp("x+1/2,y+1/2,z+1/2"),
+        ],
+        3: [
+            SymmetryOperationFactory.createSymOp("x+1/3,y+2/3,z+2/3"),
+            SymmetryOperationFactory.createSymOp("x+2/3,y+1/3,z+1/3"),
+        ],
+        4: [
+            SymmetryOperationFactory.createSymOp("x,y+1/2,z+1/2"),
+            SymmetryOperationFactory.createSymOp("x+1/2,y,z+1/2"),
+            SymmetryOperationFactory.createSymOp("x+1/2,y+1/2,z"),
+        ],
+        5: [
+            SymmetryOperationFactory.createSymOp("x,y+1/2,z+1/2"),
+        ],
+        6: [
+            SymmetryOperationFactory.createSymOp("x+1/2,y,z+1/2"),
+        ],
+        7: [
+            SymmetryOperationFactory.createSymOp("x+1/2,y+1/2,z"),
+        ],
+    }
     DUMMY_WAVELENGTH = 1.0
 
     def category(self):
@@ -113,7 +140,7 @@ def PyExec(self):
             f_handle.write(f"LATT {latt_type}\n")
 
             # print sym operations
-            for sym_str in spgr.getSymmetryOperationStrings():
+            for sym_str in self._get_shelx_symmetry_operators(spgr, latt_type):
                 f_handle.write(f"SYMM {sym_str}\n")
 
             # print atom info
@@ -140,5 +167,47 @@ def PyExec(self):
             f_handle.write("HKLF 2\n")  # tells SHELX the columns saved in the reflection file
             f_handle.write("END")
 
+    def _symmetry_operation_key(self, W1, w1, W2=np.eye(3), w2=np.zeros(3)):
+        """Symmetry element key (9 element tuple) for comparison"""
+        W = W1 @ W2
+        w = W1 @ w2 + w1
+        w[w < 0] += 1
+        w[w > 1] -= 1
+        return tuple(np.round(W, 0).astype(int).flatten().tolist() + np.round(w, 3).tolist())
+
+    def _symmetry_matrix_vector(self, symop):
+        """Symmetry rotation matrix and translation vector"""
+        W = np.linalg.inv(np.column_stack([symop.transformHKL(V3D(*vec)) for vec in np.eye(3)]))
+        w = np.array(symop.transformCoordinates(V3D(0, 0, 0)))
+        return W, w
+
+    def _get_shelx_symmetry_operators(self, spgr, latt_type):
+        """Get SHELX SYMM records https://cci.lbl.gov/cctbx/shelx.html"""
+        indentity = self.IDENTIY_OP.getIdentifier()
+        inversion = self.INVERSION_OP.getIdentifier()
+        latt_numb = abs(latt_type)
+        latt_sign = 1 if latt_type > 0 else -1
+        sym_ops = spgr.getSymmetryOperations()
+        sym_ops_list = []
+        sym_ops_set = set()
+        for sym_op in sym_ops:
+            # space group symmetry operator
+            W1, w1 = self._symmetry_matrix_vector(sym_op)
+            sym_key = sym_op.getIdentifier()
+            if sym_key != indentity and sym_key != inversion:
+                S1 = self._symmetry_operation_key(W1, w1)
+                if S1 not in sym_ops_set:
+                    sym_ops_list.append(sym_key)
+                # identity(/inversion) rotation symmetry operator
+                for rot in self.ROTATION_OPS[latt_sign]:
+                    W2, _ = self._symmetry_matrix_vector(rot)
+                    # lattice centering translation symmetry operator
+                    for cent in self.CENTERING_OPS[latt_numb]:
+                        _, w2 = self._symmetry_matrix_vector(cent)
+                        # equivalent symmetry operator generated from rotation and translation
+                        S3 = self._symmetry_operation_key(W1, w1, W2, w2)
+                        sym_ops_set.add(S3)
+        return sym_ops_list
+
 
 AlgorithmFactory.subscribe(SaveINS)

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

@@ -25,9 +25,6 @@ def setUpClass(cls):
             "ZERR 4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000\n",
             "LATT 1\n",
             "SYMM -x+1/2,y+1/2,-z+1/2\n",
-            "SYMM -x,-y,-z\n",
-            "SYMM x+1/2,-y+1/2,z+1/2\n",
-            "SYMM x,y,z\n",
             "NEUT\n",
         ]
         cls.file_end = ["UNIT 48 36 12 8 4\n", "MERG 0\n", "HKLF 2\n", "END"]

docs/source/release/6.12.0/Diffraction/Single_Crystal/38605.rst

@@ -0,0 +1 @@
+- Fix :ref:`SaveINS<algm-SaveINS-v1>` that saved all symmetry records to file. Only the minimum are needed that can be generated by translation/rotation corresponding to the lattice type.