Merge pull request #1281 from glotzerlab/nanobind-order

Nanobind port: Order module

.github/workflows/release.yaml

@@ -125,7 +125,7 @@ jobs:
             gsd==${{ matrix.python.oldest_gsd }}
             matplotlib==${{ matrix.python.oldest_matplotlib }}
           # Test only the currently ported modules
-          CIBW_TEST_COMMAND: "cd {package}/tests && pytest test_box_box.py test_parallel.py test_locality_*.py test_data.py test_pmft.py test_util.py test_msd_msd.py test_interface.py test_cluster.py -v --log-level=DEBUG"
+          CIBW_TEST_COMMAND: "cd {package}/tests && pytest test_box_box.py test_parallel.py test_locality_*.py test_data.py test_pmft.py test_util.py test_msd_msd.py test_interface.py test_order_*.py test_cluster.py -v --log-level=DEBUG"
 
           # CIBW_TEST_COMMAND: "cd {package}/tests && pytest . -v --log-level=DEBUG"
 

.github/workflows/test.yaml

@@ -68,6 +68,7 @@ jobs:
           pytest tests/test_interface.py -v
           pytest tests/test_msd_msd.py -v
           pytest tests/test_cluster.py -v
+          pytest tests/test_order_*.py -v
           # pytest tests/ -v
 
   tests_complete:

.ruff.toml

@@ -26,6 +26,8 @@ lint.ignore = [
   "RUF012", # freud does not use typing hints
   "N802", # Allow names like Lx
   "NPY002", # TODO: Refactor benchmarks and tests to use numpy.random.Generator
+  "E741",
+  "E743"
 ]
 
 [lint.flake8-import-conventions]
@@ -34,7 +36,6 @@ aliases = {}
 
 [lint.per-file-ignores]
 "tests/*.py" = ["PLR6301", # methods defined this way are used by pytest.
-  "E741", # l is an appropriate variable name for Qlm order parameters.
   "PLW2901", # TODO: Enable this check and fix after tests can be executed.
   "B018", # TODO: Enable this check and fix after tests can be executed.
   "PT011", # TODO: Enable this check and fix after tests can be executed.

freud/CMakeLists.txt

@@ -89,23 +89,23 @@ add_library(
   ${VOROPP_SOURCE_DIR}/wall.cc
   ${VOROPP_SOURCE_DIR}/pre_container.cc
   ${VOROPP_SOURCE_DIR}/container_prd.cc
-  # order
-  # order/ContinuousCoordination.h
-  # order/ContinuousCoordination.cc
-  # order/Cubatic.cc
-  # order/Cubatic.h
-  # order/HexaticTranslational.cc
-  # order/HexaticTranslational.h
-  # order/Nematic.cc
-  # order/Nematic.h
-  # order/RotationalAutocorrelation.cc
-  # order/RotationalAutocorrelation.h
-  # order/SolidLiquid.cc
-  # order/SolidLiquid.h
-  # order/Steinhardt.cc
-  # order/Steinhardt.h
-  # order/Wigner3j.cc
-  # order/Wigner3j.h
+  order
+  order/ContinuousCoordination.h
+  order/ContinuousCoordination.cc
+  order/Cubatic.cc
+  order/Cubatic.h
+  order/HexaticTranslational.cc
+  order/HexaticTranslational.h
+  order/Nematic.cc
+  order/Nematic.h
+  order/RotationalAutocorrelation.cc
+  order/RotationalAutocorrelation.h
+  order/SolidLiquid.cc
+  order/SolidLiquid.h
+  order/Steinhardt.cc
+  order/Steinhardt.h
+  order/Wigner3j.cc
+  order/Wigner3j.h
   # parallel
   parallel/tbb_config.h
   parallel/tbb_config.cc
@@ -173,6 +173,20 @@ target_set_install_rpath(_locality)
 # order nanobind_add_module(_order order/...) target_link_libraries(_order
 # PUBLIC freud TBB::tbb) target_set_install_rpath(_order)
 
+# order
+nanobind_add_module(
+  _order
+  order/module-order.cc
+  order/export-Nematic.cc
+  order/export-RotationalAutocorrelation.cc
+  order/export-Steinhardt.cc
+  order/export-SolidLiquid.cc
+  order/export-ContinuousCoordination.cc
+  order/export-Cubatic.cc
+  order/export-HexaticTranslational.cc)
+target_link_libraries(_order PUBLIC freud)
+target_set_install_rpath(_order)
+
 # parallel
 nanobind_add_module(_parallel parallel/module-parallel.cc)
 target_link_libraries(_parallel PUBLIC freud TBB::tbb)
@@ -201,12 +215,13 @@ set(python_files
     errors.py
     locality.py
     msd.py
+    order.py
     parallel.py
     pmft.py
     interface.py
     plot.py
     util.py)
-# density.py diffraction.py environment.py order.py)
+# cluster.py density.py diffraction.py environment.py interface.py msd.py)
 
 copy_files_to_build("${python_files}" "freud" "*.py")
 
@@ -218,7 +233,7 @@ if(SKBUILD)
   # install(TARGETS _density DESTINATION freud) install(TARGETS _diffraction
   # DESTINATION freud) install(TARGETS _environment DESTINATION freud)
   install(TARGETS _locality DESTINATION freud)
-  # install(TARGETS _order DESTINATION freud)
+  install(TARGETS _order DESTINATION freud)
   install(TARGETS _parallel DESTINATION freud)
   install(TARGETS _pmft DESTINATION freud)
   install(TARGETS _util DESTINATION freud)

freud/__init__.py

@@ -1,8 +1,8 @@
 # Copyright (c) 2010-2024 The Regents of the University of Michigan
 # This file is from the freud project, released under the BSD 3-Clause License.
 
-# density,; diffraction,; environment,; order,
-from . import box, cluster, data, interface, locality, msd, parallel, pmft
+# cluster,; density,; diffraction,; environment,; interface,; msd,;
+from . import box, cluster, data, interface, locality, msd, order, parallel, pmft
 from .box import Box
 from .locality import AABBQuery, LinkCell, NeighborList
 from .parallel import NumThreads, get_num_threads, set_num_threads
@@ -24,7 +24,7 @@
     "interface",
     "locality",
     "msd",
-    # "order",
+    "order",
     "parallel",
     "pmft",
     "Box",

freud/locality/NeighborComputeFunctional.h

@@ -40,7 +40,7 @@ std::shared_ptr<NeighborList> makeDefaultNlist(const std::shared_ptr<NeighborQue
 class NeighborListPerPointIterator : public NeighborPerPointIterator
 {
 public:
-    NeighborListPerPointIterator(const NeighborList* nlist, size_t point_index)
+    NeighborListPerPointIterator(const std::shared_ptr<NeighborList>& nlist, size_t point_index)
         : NeighborPerPointIterator(point_index), m_nlist(nlist)
     {
         m_current_index = m_nlist->find_first_index(point_index);
@@ -76,8 +76,8 @@ class NeighborListPerPointIterator : public NeighborPerPointIterator
     }
 
 private:
-    const NeighborList* m_nlist; //! The NeighborList being iterated over.
-    size_t m_current_index;      //! The row of m_nlist where the iterator is currently located.
+    const std::shared_ptr<NeighborList> m_nlist; //! The NeighborList being iterated over.
+    size_t m_current_index; //! The row of m_nlist where the iterator is currently located.
     size_t m_returned_point_index {
         0xffffffff}; //! The index of the last returned point (i.e. the value of
                      //! m_nlist.getNeighbors()(m_current_index, 0)). Initialized to an arbitrary sentinel in
@@ -110,9 +110,10 @@ class NeighborListPerPointIterator : public NeighborPerPointIterator
  * input. It should implement iteration logic over the iterator.
  */
 template<typename ComputePairType>
-void loopOverNeighborsIterator(const NeighborQuery* neighbor_query, const vec3<float>* query_points,
-                               unsigned int n_query_points, QueryArgs qargs, const NeighborList* nlist,
-                               const ComputePairType& cf, bool parallel = true)
+void loopOverNeighborsIterator(const std::shared_ptr<NeighborQuery>& neighbor_query,
+                               const vec3<float>* query_points, unsigned int n_query_points, QueryArgs qargs,
+                               const std::shared_ptr<NeighborList>& nlist, const ComputePairType& cf,
+                               bool parallel = true)
 {
     // check if nlist exists
     if (nlist != nullptr)
@@ -235,7 +236,8 @@ void loopOverNeighbors(const std::shared_ptr<NeighborQuery>& neighbor_query, con
  * input. It should implement iteration logic over the iterator.
  */
 template<typename ComputePairType>
-void loopOverNeighborListIterator(const NeighborList* nlist, const ComputePairType& cf, bool parallel = true)
+void loopOverNeighborListIterator(const std::shared_ptr<NeighborList>& nlist, const ComputePairType& cf,
+                                  bool parallel = true)
 {
     util::forLoopWrapper(
         0, nlist->getNumQueryPoints(),