Merge pull request #24 from bpuchala/2.X_array_order

2.X array order

.github/workflows/build_wheels.yml

@@ -45,7 +45,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.x'
+          python-version: '3.11'
 
       - name: Set up requirements and configuration variables
         run: |

.github/workflows/test-linux-build.yml

@@ -17,7 +17,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.x'
+          python-version: '3.11'
 
       - name: Set up requirements & configuration variables
         run: |

.github/workflows/test-linux-cxx-only.yml

@@ -10,13 +10,14 @@ jobs:
     uses: ./.github/workflows/test-linux-dependencies.yml
 
   build:
+    needs: build-depends
     runs-on: ubuntu-latest
     timeout-minutes: 60
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.x'
+          python-version: '3.11'
 
       - name: Set up requirements & configuration variables
         run: |

.github/workflows/test-linux-dependencies.yml

@@ -10,7 +10,7 @@ jobs:
     steps:
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.x'
+          python-version: '3.11'
 
       - name: Set up requirements & configuration variables
         run: |

.github/workflows/test-linux.yml

@@ -17,7 +17,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.x'
+          python-version: '3.11'
 
       - name: Set up requirements & configuration variables
         run: |

.github/workflows/test-macos-build.yml

@@ -10,7 +10,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.x'
+          python-version: '3.11'
 
       - name: Set up requirements & configuration variables
         run: |

.github/workflows/test-macos.yml

@@ -10,7 +10,7 @@ jobs:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.x'
+          python-version: '3.11'
 
       - name: Set up requirements & configuration variables
         run: |

include/casm/crystallography/SymInfo.hh

@@ -23,6 +23,9 @@ enum class symmetry_type {
 struct SymInfo {
   SymInfo(SymOp const &op, xtal::Lattice const &lat);
 
+  /// The lattice used for coordinates
+  xtal::Lattice lattice;
+
   /// One of: identity_op, mirror_op, glide_op, rotation_op, screw_op,
   ///         inversion_op, rotoinversion_op, or invalid_op
   symmetry_type op_type;

python/tests/test_structure.py

@@ -414,9 +414,32 @@ def test_make_superstructure_1():
 
 def test_make_superstructure_2():
     struc = xtal_structures.BCC(r=1)
-    transformation_matrix = np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]], dtype=int).T
+    transformation_matrix = np.array([[0, 1, 1], [2, 0, 1], [1, 1, 0]], dtype=int).T
+    assert transformation_matrix.flags.f_contiguous
     assert transformation_matrix.dtype is np.dtype(np.int64)
-    xtal.make_superstructure(transformation_matrix, struc)
+    superstruc = xtal.make_superstructure(transformation_matrix, struc)
+    assert np.allclose(
+        superstruc.lattice().column_vector_matrix(),
+        struc.lattice().column_vector_matrix() @ transformation_matrix,
+    )
+
+    transformation_matrix_b = np.array([[0, 2, 1], [1, 0, 1], [1, 1, 0]], dtype=int)
+    assert transformation_matrix_b.flags.c_contiguous
+    assert transformation_matrix.dtype is np.dtype(np.int64)
+    superstruc_b = xtal.make_superstructure(transformation_matrix_b, struc)
+    assert np.allclose(
+        superstruc_b.lattice().column_vector_matrix(),
+        struc.lattice().column_vector_matrix() @ transformation_matrix_b,
+    )
+
+    assert np.allclose(
+        transformation_matrix,
+        transformation_matrix_b,
+    )
+    assert np.allclose(
+        superstruc.lattice().column_vector_matrix(),
+        superstruc_b.lattice().column_vector_matrix(),
+    )
 
 
 def test_make_superstructure_and_rotate():

python/tests/test_syminfo.py

@@ -1,10 +1,26 @@
 import numpy as np
 
 import libcasm.xtal as xtal
+import libcasm.xtal.prims as xtal_prims
 
 
 def test_SymInfo_constructor():
     lattice = xtal.Lattice(np.eye(3))
     op = xtal.SymOp(np.eye(3), np.zeros((3, 1)), False)
     syminfo = xtal.SymInfo(op, lattice)
     assert syminfo.op_type() == "identity"
+
+
+def test_SymInfo_to_dict():
+    xtal_prim = xtal_prims.BCC(r=1.0, occ_dof=["A"])
+    factor_group = xtal.make_factor_group(xtal_prim)
+    symgroup_info = []
+    for op in factor_group:
+        syminfo = xtal.SymInfo(op, xtal_prim.lattice())
+        symgroup_info.append(
+            {
+                "info": syminfo.to_dict(),
+                "op": op.to_dict(),
+            }
+        )
+    assert len(symgroup_info) == 48

src/casm/crystallography/SymInfo.cc

@@ -6,9 +6,10 @@ namespace CASM {
 namespace xtal {
 
 SymInfo::SymInfo(SymOp const &op, xtal::Lattice const &lat)
-    : axis(lat),
-      screw_glide_shift(lat),
-      location(lat),
+    : lattice(lat),
+      axis(lattice),
+      screw_glide_shift(lattice),
+      location(lattice),
       time_reversal(op.is_time_reversal_active) {
   auto matrix = op.matrix;
   auto tau = op.translation;
@@ -23,7 +24,7 @@ SymInfo::SymInfo(SymOp const &op, xtal::Lattice const &lat)
     op_type = symmetry_type::identity_op;
     _axis = Eigen::Vector3d::Zero();
     _location = Eigen::Vector3d::Zero();
-    _set(_axis, _screw_glide_shift, _location, lat);
+    _set(_axis, _screw_glide_shift, _location, lattice);
     return;
   }
 
@@ -33,7 +34,7 @@ SymInfo::SymInfo(SymOp const &op, xtal::Lattice const &lat)
     op_type = symmetry_type::inversion_op;
     _axis = Eigen::Vector3d::Zero();
     _location = tau / 2.;
-    _set(_axis, _screw_glide_shift, _location, lat);
+    _set(_axis, _screw_glide_shift, _location, lattice);
     return;
   }
 
@@ -81,7 +82,7 @@ SymInfo::SymInfo(SymOp const &op, xtal::Lattice const &lat)
   if (det < 0) {
     if (almost_equal(angle, 180.)) {
       // shift is component of tau perpendicular to axis
-      xtal::Coordinate coord(tau - tau.dot(_axis) * _axis, lat, CART);
+      xtal::Coordinate coord(tau - tau.dot(_axis) * _axis, lattice, CART);
       _screw_glide_shift = coord.cart();
 
       // location is 1/2 of component of tau parallel to axis:
@@ -102,7 +103,7 @@ SymInfo::SymInfo(SymOp const &op, xtal::Lattice const &lat)
     }
   } else {
     // shift is component of tau parallel to axis
-    xtal::Coordinate coord(tau.dot(_axis) * _axis, lat, CART);
+    xtal::Coordinate coord(tau.dot(_axis) * _axis, lattice, CART);
     _screw_glide_shift = coord.cart();
 
     // Can only solve 2d location problem
@@ -121,7 +122,7 @@ SymInfo::SymInfo(SymOp const &op, xtal::Lattice const &lat)
     op_type = coord.is_lattice_shift() ? symmetry_type::rotation_op
                                        : symmetry_type::screw_op;
   }
-  _set(_axis, _screw_glide_shift, _location, lat);
+  _set(_axis, _screw_glide_shift, _location, lattice);
   return;
 }