Refactor flow fields (#78)

* Update to flow fields

* Formatting changes

* Add cpp files for Parabolic and Constant flow class

* Revise parabolic flow coordinate system

* Fix pybind11 visbility

---------

Co-authored-by: Michael Howard <[email protected]>

.ruff.toml

@@ -32,6 +32,8 @@ ignore = [
 
 "__init__.py" = ["F401", # __init__.py import submodules for use by the package importer.
 ]
+"*/pytest/*.py" = ["PLR2004", # allow "magic numbers" in tests
+]
 
 [lint.pydocstyle]
 convention = "google"

src/CMakeLists.txt

@@ -3,8 +3,10 @@ set(COMPONENT_NAME azplugins)
 
 # TODO: List all host C++ source code files in _${COMPONENT_NAME}_sources.
 set(_${COMPONENT_NAME}_sources
+    ConstantFlow.cc
     GroupVelocityCompute.cc
     module.cc
+    ParabolicFlow.cc
     )
 
 # TODO: List all GPU C++ source code files in _${COMPONENT_NAME}_cu_sources.
@@ -16,6 +18,7 @@ set(python_files
     __init__.py
     conftest.py
     bond.py
+    flow.py
     pair.py
     )
 

src/ConstantFlow.cc

@@ -0,0 +1,34 @@
+// Copyright (c) 2018-2020, Michael P. Howard
+// Copyright (c) 2021-2024, Auburn University
+// Part of azplugins, released under the BSD 3-Clause License.
+
+#include "ConstantFlow.h"
+
+namespace hoomd
+    {
+namespace azplugins
+    {
+namespace detail
+    {
+void export_ConstantFlow(pybind11::module& m)
+    {
+    namespace py = pybind11;
+    py::class_<ConstantFlow, std::shared_ptr<ConstantFlow>>(m, "ConstantFlow")
+        .def(py::init<Scalar3>())
+        .def_property(
+            "velocity",
+            [](const ConstantFlow& U)
+            {
+                const auto field = U.getVelocity();
+                return pybind11::make_tuple(field.x, field.y, field.z);
+            },
+            [](ConstantFlow& U, const pybind11::tuple& field)
+            {
+                U.setVelocity(make_scalar3(pybind11::cast<Scalar>(field[0]),
+                                           pybind11::cast<Scalar>(field[1]),
+                                           pybind11::cast<Scalar>(field[2])));
+            });
+    }
+    } // end namespace detail
+    } // end namespace azplugins
+    } // end namespace hoomd

src/ConstantFlow.h

@@ -0,0 +1,73 @@
+// Copyright (c) 2018-2020, Michael P. Howard
+// Copyright (c) 2021-2024, Auburn University
+// Part of azplugins, released under the BSD 3-Clause License.
+
+#ifndef AZPLUGINS_CONSTANT_FLOW_H_
+#define AZPLUGINS_CONSTANT_FLOW_H_
+
+#ifndef __HIPCC__
+#include <pybind11/pybind11.h>
+#endif
+
+#include "hoomd/HOOMDMath.h"
+
+#ifndef __HIPCC__
+#define HOSTDEVICE __host__ __device__
+#else
+#define HOSTDEVICE
+#endif // __HIPCC__
+
+#ifndef PYBIND11_EXPORT
+#define PYBIND11_EXPORT __attribute__((visibility("default")))
+#endif
+
+namespace hoomd
+    {
+namespace azplugins
+    {
+
+//! Position-independent flow along a vector
+class PYBIND11_EXPORT ConstantFlow
+    {
+    public:
+    //! Constructor
+    /*!
+     *\param U_ Flow field
+     */
+    ConstantFlow(Scalar3 velocity)
+        {
+        setVelocity(velocity);
+        }
+
+    //! Evaluate the flow field
+    /*!
+     * \param r position to evaluate flow
+     *
+     * This is just a constant, independent of \a r.
+     */
+    HOSTDEVICE Scalar3 operator()(const Scalar3& r) const
+        {
+        return U;
+        }
+
+    HOSTDEVICE Scalar3 getVelocity() const
+        {
+        return U;
+        }
+
+    HOSTDEVICE void setVelocity(const Scalar3& U_)
+        {
+        U = U_;
+        }
+
+    private:
+    Scalar3 U; //!< Flow field
+    };
+
+    } // namespace azplugins
+    } // namespace hoomd
+
+#undef HOSTDEVICE
+#undef PYBIND11_EXPORT
+
+#endif // AZPLUGINS_CONSTANT_FLOW_H_

src/ParabolicFlow.cc

@@ -0,0 +1,25 @@
+// Copyright (c) 2018-2020, Michael P. Howard
+// Copyright (c) 2021-2024, Auburn University
+// Part of azplugins, released under the BSD 3-Clause License.
+
+#include "ParabolicFlow.h"
+
+namespace hoomd
+    {
+namespace azplugins
+    {
+namespace detail
+    {
+void export_ParabolicFlow(pybind11::module& m)
+    {
+    namespace py = pybind11;
+    py::class_<ParabolicFlow, std::shared_ptr<ParabolicFlow>>(m, "ParabolicFlow")
+        .def(py::init<Scalar, Scalar>())
+        .def_property("mean_velocity",
+                      &ParabolicFlow::getMeanVelocity,
+                      &ParabolicFlow::setMeanVelocity)
+        .def_property("separation", &ParabolicFlow::getSeparation, &ParabolicFlow::setSeparation);
+    }
+    } // namespace detail
+    } // namespace azplugins
+    } // namespace hoomd