adapt missing from pybind11 interface

[Sa Wu]

adapt for adapting MeshFunction to refined meshes, formerly dolfin.cpp.fem.adapt is missing from new pybind11 interface. https://fenicsproject.org/docs/dolfin/dev/python/_autogenerated/dolfin.cpp.fem.html https://fenicsproject.org/docs/dolfin/2017.2.0/python/programmers-reference/cpp/fem/adapt.html

[Ivan Yashchuk]

A quick workaround for this omission:

cpp_code = """
    #include<pybind11/pybind11.h>
    #include<dolfin/adaptivity/adapt.h>
    #include<dolfin/mesh/Mesh.h>
    #include<dolfin/mesh/MeshFunction.h>

    namespace py = pybind11;

    PYBIND11_MODULE(SIGNATURE, m) {
       m.def("adapt", (std::shared_ptr<dolfin::MeshFunction<std::size_t>> (*)(const dolfin::MeshFunction<std::size_t>&,
          std::shared_ptr<const dolfin::Mesh>)) &dolfin::adapt,
          py::arg("mesh_function"), py::arg("adapted_mesh"));
    }
    """

adapt = compile_cpp_code(cpp_code).adapt

mesh = UnitSquareMesh.create(5, 5, CellType.Type.triangle)
rmesh = refine(mesh)
mf = MeshFunction("size_t", coarse_mesh, coarse_mesh.topology().dim(), 0)
# Now "adapt" is working
rmf = adapt(mf, rmesh)

[Sa Wu]

Thanks for the workaround.

[Jørgen Dokken]

I think what is needed in pybind is the following:

Add

#include <dolfin/adaptivity/adapt.h>

#include "casters.h"

namespace py = pybind11;

namespace dolfin_wrappers
{
  void fem(py::module& m)
  {
    // Adapt functions
    m.def("adapt", [](dolfin::Mesh mesh){return dolfin::adapt(mesh);});

for each adapt function. I will see if I can make a PR for several functions tomorrow. MWE of python demo:

from dolfin import *
import matplotlib.pyplot as plt

mesh = UnitSquareMesh(10,10)
rmesh = cpp.fem.adapt(mesh)
plot(mesh, color="b")
plt.figure()
plot(rmesh, color="r")
plt.show()

Which adapt functions from the c++ side is wanted, @sa_wu?