Merge branch 'develop' into rc

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,33 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+## Describe the bug
+
+<!-- A clear and concise description of what the bug is. -->
+
+## To Reproduce
+
+<!--
+If you use spglib's Python API, please do not use ASE or Pymatgen's wrapper to make it easier to identify your problem.
+The format for crystal structures is shown here: https://spglib.github.io/spglib/python-spglib.html#variables
+If spglib returns different results by changing `symprec`, `angle_tolerance`, or `mag_symprec`, please report it too.
+-->
+
+## Expected behavior
+
+<!-- A clear and concise description of what you expected to happen. -->
+
+## Environment
+
+- Python version:
+- Spglib's version:
+
+## Additional context
+
+<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,24 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+## Is your feature request related to a problem? Please describe.
+
+<!-- A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] -->
+
+## Describe the solution you'd like
+
+<!-- A clear and concise description of what you want to happen. -->
+
+## Describe alternatives you've considered
+
+<!-- A clear and concise description of any alternative solutions or features you've considered. -->
+
+## Additional context
+
+<!-- Add any other context or screenshots about the feature request here. -->

CMakeLists.txt

@@ -80,6 +80,17 @@ set(SOURCES ${PROJECT_SOURCE_DIR}/src/arithmetic.c
             ${PROJECT_SOURCE_DIR}/src/spin.c
             ${PROJECT_SOURCE_DIR}/src/symmetry.c)
 
+# avoid One Definition Rule problems
+# only available since 3.16.0
+# VERSION_GREATER_EQUAL only available since 3.7.0, so let's do it manually
+if (NOT CMAKE_MAJOR_VERSION LESS "3")
+  if (CMAKE_MAJOR_VERSION GREATER "3" OR NOT CMAKE_MINOR_VERSION LESS "16")
+    set_source_files_properties(
+        ${SOURCES} PROPERTIES SKIP_UNITY_BUILD_INCLUSION ON
+    )
+  endif()
+endif()
+
 # Shared library
 add_library(symspg SHARED ${SOURCES})
 

admin.md

@@ -0,0 +1,6 @@
+# Releasing a new Spglib version
+
+1. Update <doc/releases.md>
+2. Increment version at <src/version.h>
+3. Push the commit to `rc` branch (Github actions publishes the package to TestPyPI automatically)
+4. Push the commit to `master` branch (Github actions publishes the package to PyPI automatically)

doc/magnetic_symmetry_flags.md

@@ -30,10 +30,10 @@
 - `tensor_rank=1`
     - `with_time_reversal=true`: {math}`1' \circ \mathbf{m} = -\mathbf{m}`
         - `is_axial=true`: {math}`(\mathbf{R}, \mathbf{v}) \circ \mathbf{m} = (\mathrm{det} \mathbf{R}) \mathbf{R} \mathbf{m}`
-        - `is_axial=true`: {math}`(\mathbf{R}, \mathbf{v}) \circ \mathbf{m} = \mathbf{R} \mathbf{m}`
+        - `is_axial=false`: {math}`(\mathbf{R}, \mathbf{v}) \circ \mathbf{m} = \mathbf{R} \mathbf{m}`
     - `with_time_reversal=false`: {math}`1' \circ \mathbf{m} = \mathbf{m}`
         - `is_axial=true`: {math}`(\mathbf{R}, \mathbf{v}) \circ \mathbf{m} = (\mathrm{det} \mathbf{R}) \mathbf{R} \mathbf{m}`
-        - `is_axial=true`: {math}`(\mathbf{R}, \mathbf{v}) \circ \mathbf{m} = \mathbf{R} \mathbf{m}`
+        - `is_axial=false`: {math}`(\mathbf{R}, \mathbf{v}) \circ \mathbf{m} = \mathbf{R} \mathbf{m}`
 
 <!-- ### Correspondence
 

doc/releases.md

@@ -1,6 +1,11 @@
 
 # Summary of releases
 
+## V2.0.2 (6 Nov. 2022)
+
+- Fix segmentation fault in `spgms_get_symmetry_with_site_tensors` with high symprec [[#195]](https://github.com/spglib/spglib/pull/195)
+- Fix possible segmentation fault in `get_magnetic_dataset` with high symprec [[#196]](https://github.com/spglib/spglib/pull/196)
+
 ## V2.0.1 (31 Aug. 2022)
 
 - Fix magnetic tolerance for judging type-II MSG (#187)

python/pyproject.toml

@@ -2,4 +2,6 @@
 requires = ["setuptools", "wheel", "numpy"]
 
 [tool.cibuildwheel]
-skip = ["pp*", "*-win32", "*-manylinux_i686"]
+skip = ["pp*", "*-win32", "*-manylinux_i686", "*-musllinux*"]
+manylinux-x86_64-image = "manylinux2014"
+manylinux-aarch64-image = "manylinux2014"

src/overlap.c

@@ -641,7 +641,7 @@ static int check_total_overlap_for_sorted(
     search_start = 0;
     for (i_orig = 0; i_orig < num_pos; i_orig++) {
         /* Permanently skip positions filled near the beginning. */
-        while (found[search_start]) {
+        while ((search_start < num_pos) && found[search_start]) {
             search_start++;
         }
 

src/spglib.c

@@ -1316,6 +1316,7 @@ static SpglibMagneticDataset *get_magnetic_dataset(
     if (spglib_error_code == SPGLIB_SUCCESS) {
         return dataset;
     } else {
+        spg_free_magnetic_dataset(dataset);
         return NULL;
     }
 }
@@ -1779,9 +1780,15 @@ static MagneticSymmetry *get_symmetry_with_site_tensors(
     spg_free_dataset(dataset);
     dataset = NULL;
 
-    magnetic_symmetry = spn_get_operations_with_site_tensors(
-        &equiv_atoms, permutations, primitive_lattice, sym_nonspin, cell,
-        with_time_reversal, is_axial, symprec, angle_tolerance, mag_symprec);
+    if ((magnetic_symmetry = spn_get_operations_with_site_tensors(
+             &equiv_atoms, permutations, primitive_lattice, sym_nonspin, cell,
+             with_time_reversal, is_axial, symprec, angle_tolerance,
+             mag_symprec)) == NULL) {
+        sym_free_symmetry(sym_nonspin);
+        sym_nonspin = NULL;
+        goto err;
+    }
+
     /* Set equivalent_atoms */
     for (i = 0; i < cell->size; i++) {
         equivalent_atoms[i] = equiv_atoms[i];

src/spin.c

@@ -408,8 +408,13 @@ static MagneticSymmetry *get_operations(
                 }
             }
             if (k == cell->size) {
-                /* Unreachable here! */
-                return NULL;
+                // Unreachable here in theory, but we rarely fail to overlap
+                // atoms possibly due to too high symprec. In that case, skip
+                // the symmetry operation.
+                debug_print("Failed to overlap atom-%d by operation-%d\n", j,
+                            i);
+                found = 0;
+                break;
             }
 
             // Skip if relevant tensors are zeros because they have nothing to
@@ -558,9 +563,9 @@ static MagneticSymmetry *get_operations(
     return NULL;
 }
 
-/* Return permutation tables `permutations` such that the p-th operation */
-/* in `magnetic_symmetry` maps site-`i` to site-`permutations[p * cell->size +
- * i]`. */
+// Return permutation tables `permutations` such that the p-th operation
+// in `magnetic_symmetry` maps site-`i` to site-`permutations[p * cell->size +
+// * i]`. If failed, return NULL.
 static int *get_symmetry_permutations(const MagneticSymmetry *magnetic_symmetry,
                                       const Cell *cell,
                                       const int with_time_reversal,
@@ -655,7 +660,7 @@ static int *get_symmetry_permutations(const MagneticSymmetry *magnetic_symmetry,
     return permutations;
 }
 
-/* Return equivalent_atoms */
+// Return equivalent_atoms. If failed, return NULL.
 static int *get_orbits(const int *permutations, const int num_sym,
                        const int num_atoms) {
     int s, i;

src/version.h

@@ -37,6 +37,6 @@
 
 #define SPGLIB_MAJOR_VERSION 2
 #define SPGLIB_MINOR_VERSION 0
-#define SPGLIB_MICRO_VERSION 1
+#define SPGLIB_MICRO_VERSION 2
 
 #endif

test/test_magnetic_symmetry.cpp

@@ -360,6 +360,79 @@ TEST(
     free(time_reversals);
 }
 
+TEST(
+    test_magnetic_symmetry,
+    test_with_broken_symmetry) {
+    // https://github.com/spglib/spglib/issues/194
+    // Part of "mp-806965" in the Materials Project database
+    double lattice[][3] = {  // column-wise!
+        {5.24191, -0.003459, -2.618402},
+        {0, 5.600534, -1.87898},
+        {0, 0, 11.148141},
+    };
+    double positions[][3] = {
+        {0.829407, 0.834674, 0.662821},
+        {0.665078, 0.665214, 0.316142},
+        {0.001174, 0.996383, 0.002809},
+        {0.181127, 0.169218, 0.349259},
+    };
+    int types[] = {0, 0, 0, 0};
+    double tensors[] = {1.927, 1.947, 1.928, 1.949};
+    int num_atoms = 4;
+    int max_size = num_atoms * 96;
+
+    double symprec = 0.1;  // with very high symprec
+    double mag_symprec = symprec;
+
+    int i, size;
+    int equivalent_atoms[4];
+    double primitive_lattice[3][3];
+    int(*rotations)[3][3];
+    double(*translations)[3];
+    int *spin_flips;
+    int *time_reversals;
+
+    rotations = (int(*)[3][3])malloc(sizeof(int[3][3]) * max_size);
+    translations = (double(*)[3])malloc(sizeof(double[3]) * max_size);
+    spin_flips = (int *)malloc(sizeof(int *) * max_size);
+    time_reversals = (int *)malloc(sizeof(int *) * max_size);
+
+    // Check magnetic symmetry search
+    // spg_get_symmetry returns four operations, but spgms_get_symmetry_with_site_tensors
+    // only returns three of them. This is due to too high symprec: detected operations
+    // in `sym_get_operation` follow `symprec`, but refined operations in
+    // `ref_get_exact_structure_and_symmetry` does not.
+    size = spgms_get_symmetry_with_site_tensors(
+        rotations, translations, equivalent_atoms, primitive_lattice, spin_flips,
+        max_size, lattice, positions, types, tensors,
+        0 /* tensor_rank */ , num_atoms,
+        1 /* with_time_reversal */,
+        0 /* is_axial */,
+        symprec, -1 /* angle_tolerance */, mag_symprec);
+
+    for (i = 0; i < size; i++) {
+        time_reversals[i] = (1 - spin_flips[i]) / 2;
+    }
+    show_magnetic_symmetry_operations(rotations, translations, time_reversals, size);
+    ASSERT_TRUE(size >= 1);
+
+    // Check magnetic dataset construction
+    // Since detected magnetic symmetry operations do not form a group due to high symprec,
+    // we fail to get magnetic dataset for now.
+    SpglibMagneticDataset *dataset;
+    dataset = spg_get_magnetic_dataset(lattice, positions, types, tensors,
+                                        0 /* tensor_rank */, num_atoms,
+                                        0 /* is_axial */, symprec);
+    ASSERT_TRUE(dataset == NULL);
+
+    free(rotations);
+    free(translations);
+    free(spin_flips);
+    free(time_reversals);
+    if (dataset != NULL) spg_free_magnetic_dataset(dataset);
+    free(dataset);
+}
+
 // TODO: test get_magnetic_dataset with distorted positions
 
 // ****************************************************************************