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Merge pull request #1256 from glotzerlab/pybind11-box
Convert Box Module to Use nanobind
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,22 @@ | ||
| # create the target and add the needed properties | ||
| nanobind_add_module(_box SHARED module-box.cc export_Box.cc) | ||
| target_link_libraries(_box PUBLIC TBB::tbb) | ||
| # this probably isn't needed for box, but may be needed by other modules | ||
| # target_compile_definitions( box # Avoid deprecation warnings for unsupported | ||
| # NumPy API versions. See # | ||
| # https://numpy.org/doc/1.19/reference/c-api/deprecations.html PRIVATE | ||
| # "NPY_NO_DEPRECATED_API=NPY_1_10_API_VERSION" # Default voro++ verbosity is | ||
| # high. PRIVATE "VOROPP_VERBOSE=1") | ||
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| if(APPLE) | ||
| set_target_properties(_box PROPERTIES INSTALL_RPATH "@loader_path") | ||
| else() | ||
| set_target_properties(_box PROPERTIES INSTALL_RPATH "\$ORIGIN") | ||
| endif() | ||
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| if(_using_conda OR DEFINED ENV{CIBUILDWHEEL}) | ||
| set_target_properties(_box PROPERTIES INSTALL_RPATH_USE_LINK_PATH True) | ||
| endif() | ||
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| # install | ||
| install(TARGETS _box DESTINATION freud) |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,107 @@ | ||
| // 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. | ||
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| #include "export_Box.h" | ||
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| namespace nb = nanobind; | ||
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| namespace freud { namespace box { namespace wrap { | ||
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| void makeAbsolute(std::shared_ptr<Box> box, nb_array<float, nb::shape<-1, 3>> vecs, | ||
| nb_array<float, nb::shape<-1, 3>> out) | ||
| { | ||
| unsigned int Nvecs = vecs.shape(0); | ||
| vec3<float>* vecs_data = (vec3<float>*) (vecs.data()); | ||
| vec3<float>* out_data = (vec3<float>*) (out.data()); | ||
| box->makeAbsolute(vecs_data, Nvecs, out_data); | ||
| } | ||
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| void makeFractional(std::shared_ptr<Box> box, nb_array<float, nb::shape<-1, 3>> vecs, | ||
| nb_array<float, nb::shape<-1, 3>> out) | ||
| { | ||
| unsigned int Nvecs = vecs.shape(0); | ||
| vec3<float>* vecs_data = (vec3<float>*) (vecs.data()); | ||
| vec3<float>* out_data = (vec3<float>*) (out.data()); | ||
| box->makeFractional(vecs_data, Nvecs, out_data); | ||
| } | ||
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| void getImages(std::shared_ptr<Box> box, nb_array<float, nb::shape<-1, 3>> vecs, | ||
| nb_array<int, nb::shape<-1, 3>> images) | ||
| { | ||
| const unsigned int Nvecs = vecs.shape(0); | ||
| vec3<float>* vecs_data = (vec3<float>*) (vecs.data()); | ||
| vec3<int>* images_data = (vec3<int>*) (images.data()); | ||
| box->getImages(vecs_data, Nvecs, images_data); | ||
| } | ||
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| void wrap(std::shared_ptr<Box> box, nb_array<float, nb::shape<-1, 3>> vecs, | ||
| nb_array<float, nb::shape<-1, 3>> out) | ||
| { | ||
| const unsigned int Nvecs = vecs.shape(0); | ||
| vec3<float>* vecs_data = (vec3<float>*) (vecs.data()); | ||
| vec3<float>* out_data = (vec3<float>*) (out.data()); | ||
| box->wrap(vecs_data, Nvecs, out_data); | ||
| } | ||
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| void unwrap(std::shared_ptr<Box> box, nb_array<float> vecs, nb_array<int> images, nb_array<float> out) | ||
| { | ||
| const unsigned int Nvecs = vecs.shape(0); | ||
| vec3<float>* vecs_data = (vec3<float>*) (vecs.data()); | ||
| vec3<int>* images_data = (vec3<int>*) (images.data()); | ||
| vec3<float>* out_data = (vec3<float>*) (out.data()); | ||
| box->unwrap(vecs_data, images_data, Nvecs, out_data); | ||
| } | ||
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| std::vector<float> centerOfMass(std::shared_ptr<Box> box, nb_array<float> vecs, | ||
| nb_array<float, nb::shape<-1>> masses) | ||
| { | ||
| const unsigned int Nvecs = vecs.shape(0); | ||
| vec3<float>* vecs_data = (vec3<float>*) (vecs.data()); | ||
| float* masses_data = (float*) (masses.data()); | ||
| auto com = box->centerOfMass(vecs_data, Nvecs, masses_data); | ||
| return {com.x, com.y, com.z}; | ||
| } | ||
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| void center(std::shared_ptr<Box> box, nb_array<float> vecs, nb_array<float, nb::ndim<1>> masses) | ||
| { | ||
| const unsigned int Nvecs = vecs.shape(0); | ||
| vec3<float>* vecs_data = (vec3<float>*) (vecs.data()); | ||
| float* masses_data = (float*) (masses.data()); | ||
| box->center(vecs_data, Nvecs, masses_data); | ||
| } | ||
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| void computeDistances(std::shared_ptr<Box> box, nb_array<float> query_points, nb_array<float> points, | ||
| nb_array<float, nb::ndim<1>> distances) | ||
| { | ||
| const unsigned int n_query_points = query_points.shape(0); | ||
| vec3<float>* query_points_data = (vec3<float>*) (query_points.data()); | ||
| const unsigned int n_points = points.shape(0); | ||
| vec3<float>* points_data = (vec3<float>*) (points.data()); | ||
| float* distances_data = (float*) (distances.data()); | ||
| if (n_query_points != n_points) | ||
| { | ||
| throw std::invalid_argument("The number of query points and points must match."); | ||
| } | ||
| box->computeDistances(query_points_data, n_query_points, points_data, n_points, distances_data); | ||
| } | ||
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| void computeAllDistances(std::shared_ptr<Box> box, nb_array<float> query_points, nb_array<float> points, | ||
| nb_array<float, nb::ndim<2>> distances) | ||
| { | ||
| const unsigned int n_query_points = query_points.shape(0); | ||
| vec3<float>* query_points_data = (vec3<float>*) (query_points.data()); | ||
| const unsigned int n_points = points.shape(0); | ||
| vec3<float>* points_data = (vec3<float>*) (points.data()); | ||
| float* distances_data = (float*) (distances.data()); | ||
| box->computeAllDistances(query_points_data, n_query_points, points_data, n_points, distances_data); | ||
| } | ||
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| void contains(std::shared_ptr<Box> box, nb_array<float> points, nb_array<bool, nb::ndim<1>> contains_mask) | ||
| { | ||
| const unsigned int n_points = points.shape(0); | ||
| vec3<float>* points_data = (vec3<float>*) (points.data()); | ||
| bool* contains_mask_data = (bool*) (contains_mask.data()); | ||
| box->contains(points_data, n_points, contains_mask_data); | ||
| } | ||
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| }; }; }; // namespace freud::box::wrap |
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