FArrayBox and BaseFab<Real> (#82)

Start to bind FArrayBox and BaseFab classes. Based on a question how to bind `FArrayBox::readFrom` to Python, e.g., can be done via * https://docs.python.org/3/library/io.html * https://gist.github.com/asford/544323a5da7dddad2c9174490eb5ed06#file-test_ostream_example-py
AMReX-Codes · Oct 17, 2022 · aa683b9 · aa683b9
1 parent 28e389d
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Showing 7 changed files with 216 additions and 2 deletions.
diff --git a/src/Base/BaseFab.cpp b/src/Base/BaseFab.cpp
@@ -0,0 +1,126 @@
+/* Copyright 2021-2022 The AMReX Community
+ *
+ * Authors: Axel Huebl
+ * License: BSD-3-Clause-LBNL
+ */
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+#include <AMReX_FArrayBox.H>
+
+#include <istream>
+
+namespace py = pybind11;
+using namespace amrex;
+
+namespace
+{
+    template< typename T >
+    void init_bf(py::module &m, std::string typestr) {
+        auto const bf_name = std::string("BaseFab_").append(typestr);
+        py::class_< BaseFab<T> >(m, bf_name.c_str())
+            .def("__repr__",
+                 [bf_name](BaseFab<Real> const & bf) {
+                     std::string r = "<amrex.";
+                     r.append(bf_name).append(" (n_comp=");
+                     r.append(std::to_string(bf.nComp())).append(")>");
+                     return r;
+                 }
+            )
+
+            .def(py::init< >())
+            //.def(py::init< Arena* >())
+            //.def(py::init< const Box&, int, Arena* >())
+            //.def(py::init< >( const Box&, int, bool, bool, Arena* ))
+            //.def(py::init< const BaseFab<T>&, MakeType, int, int >())
+            // non-owning
+            .def(py::init< const Box&, int, T* >())
+            .def(py::init< const Box&, int, T const* >())
+
+            .def(py::init< Array4<T> const& >())
+            .def(py::init< Array4<T> const&, IndexType >())
+            .def(py::init< Array4<T const> const& >())
+            .def(py::init< Array4<T const> const&, IndexType >())
+
+            //.def_static("initialize", &BaseFab<T>::Initialize )
+            //.def_static("finalize", &BaseFab<T>::Finalize )
+
+            .def("resize", &BaseFab<T>::resize )
+            .def("clear", &BaseFab<T>::clear )
+            //.def("release", &BaseFab<T>::release )
+
+            .def("n_bytes", py::overload_cast< >(&BaseFab<T>::nBytes, py::const_))
+            .def("n_bytes", py::overload_cast< Box const &, int >(&BaseFab<T>::nBytes, py::const_))
+            .def("n_bytes_owned", &BaseFab<T>::nBytesOwned )
+            .def("n_comp", &BaseFab<T>::nComp )
+            .def("num_pts", &BaseFab<T>::numPts )
+            .def("size", &BaseFab<T>::size )
+            .def("box", &BaseFab<T>::box )
+            .def("length", &BaseFab<T>::length )
+
+            .def("small_end", &BaseFab<T>::smallEnd )
+            .def("big_end", &BaseFab<T>::bigEnd )
+            .def("lo_vect", &BaseFab<T>::loVect )
+            .def("hi_vect", &BaseFab<T>::hiVect )
+
+            // contains
+            // prefetchToHost
+            // prefetchToDevice
+            .def("is_allocated", &BaseFab<T>::isAllocated )
+
+            //.def("array", &BaseFab<T>::array )
+            //.def("const_array", &BaseFab<T>::const_array )
+
+            // getVal
+            // setVal
+            // setValIf
+            // setValIfNot
+            // setComplement
+            // copy
+            // copyToMem
+            // copyFromMem
+            // addFromMem
+
+            // shift
+            // shiftHalf
+
+            // norminfmask
+            // norm
+            // abs
+            // min
+            // max
+            // minmax
+            // maxabs
+            // indexFromValue
+            // minIndex
+            // maxIndex
+            // maskLT
+            // maskLE
+            // maskEQ
+            // maskGT
+            // maskGE
+            // sum
+            // invert
+            // negate
+            // plus
+            // atomicAdd
+            // saxpy
+            // xpay
+            // addproduct
+            // minus
+            // mult
+            // divide
+            // protected_divide
+            // linInterp
+            // linComb
+            // dot
+            // dotmask
+
+            // SetBoxType
+        ;
+    }
+}
+
+void init_BaseFab(py::module &m) {
+    init_bf<Real>(m, "Real");
+}
diff --git a/src/Base/CMakeLists.txt b/src/Base/CMakeLists.txt
@@ -2,12 +2,14 @@ target_sources(pyAMReX
   PRIVATE
     AMReX.cpp
     Array4.cpp
+    BaseFab.cpp
     Box.cpp
     RealBox.cpp
     BoxArray.cpp
     CoordSys.cpp
     Dim3.cpp
     DistributionMapping.cpp
+    FArrayBox.cpp
     Geometry.cpp
     IntVect.cpp
     RealVect.cpp

diff --git a/src/Base/FArrayBox.cpp b/src/Base/FArrayBox.cpp
@@ -0,0 +1,57 @@
+/* Copyright 2021-2022 The AMReX Community
+ *
+ * Authors: Axel Huebl
+ * License: BSD-3-Clause-LBNL
+ */
+#include <pybind11/pybind11.h>
+#include <pybind11/stl.h>
+
+#include <AMReX_FArrayBox.H>
+
+#include <istream>
+#include <ostream>
+#include <string>
+
+namespace py = pybind11;
+using namespace amrex;
+
+
+void init_FArrayBox(py::module &m) {
+    py::class_< FArrayBox, BaseFab<Real> >(m, "FArrayBox")
+        .def("__repr__",
+             [](FArrayBox const & /* fab */) {
+                 std::string r = "<amrex.FArrayBox>";
+                 return r;
+             }
+        )
+
+        .def(py::init< >())
+        //.def(py::init< Arena* >())
+        //.def(py::init< Box const &, int, Arena* >())
+        //.def(py::init< const Box&, int, bool, bool, Arena* >())
+        //.def(py::init< const FArrayBox&, MakeType, int, int >())
+        .def(py::init< const Box&, int, Real const* >())
+        .def(py::init< const Box&, int, Real* >())
+        .def(py::init< Array4<Real> const& >())
+        .def(py::init< Array4<Real> const&, IndexType >())
+        .def(py::init< Array4<Real const> const& >())
+        .def(py::init< Array4<Real const> const&, IndexType >())
+
+        .def("read_from",
+             py::overload_cast<std::istream&>(&FArrayBox::readFrom),
+             py::arg("is")
+        )
+        .def("read_from",
+             py::overload_cast<std::istream&, int>(&FArrayBox::readFrom),
+             py::arg("is"), py::arg("compIndex")
+        )
+        .def("write_on",
+             py::overload_cast<std::ostream&>(&FArrayBox::writeOn, py::const_),
+             py::arg("of")
+        )
+        .def("write_on",
+             py::overload_cast<std::ostream&, int, int>(&FArrayBox::writeOn, py::const_),
+             py::arg("of"), py::arg("comp"), py::arg("num_comp")
+        )
+    ;
+}
diff --git a/src/Base/MultiFab.cpp b/src/Base/MultiFab.cpp
@@ -9,6 +9,7 @@
 #include <AMReX_Config.H>
 #include <AMReX_BoxArray.H>
 #include <AMReX_DistributionMapping.H>
+#include <AMReX_FArrayBox.H>
 #include <AMReX_FabArray.H>
 #include <AMReX_FabArrayBase.H>
 #include <AMReX_MultiFab.H>
@@ -45,8 +46,6 @@ void init_MultiFab(py::module &m) {
         )
     ;
 
-    py::class_< FArrayBox >(m, "FArrayBox");
-
     py::class_< MFIter >(m, "MFIter", py::dynamic_attr())
         .def("__repr__",
              [](MFIter const & mfi) {

diff --git a/src/pyAMReX.cpp b/src/pyAMReX.cpp
@@ -18,12 +18,14 @@ namespace py = pybind11;
 // forward declarations of exposed classes
 void init_AMReX(py::module&);
 void init_Array4(py::module&);
+void init_BaseFab(py::module&);
 void init_Box(py::module &);
 void init_RealBox(py::module &);
 void init_BoxArray(py::module &);
 void init_CoordSys(py::module&);
 void init_Dim3(py::module&);
 void init_DistributionMapping(py::module&);
+void init_FArrayBox(py::module&);
 void init_Geometry(py::module&);
 void init_IntVect(py::module &);
 void init_RealVect(py::module &);
@@ -57,6 +59,7 @@ PYBIND11_MODULE(amrex_pybind, m) {
                RealBox
                BoxArray
                Dim3
+               FArrayBox
                IntVect
                RealVect
                MultiFab
@@ -81,6 +84,8 @@ PYBIND11_MODULE(amrex_pybind, m) {
     init_Box(m);
     init_BoxArray(m);
     init_ParmParse(m);
+    init_BaseFab(m);
+    init_FArrayBox(m);
     init_MultiFab(m);
     init_DistributionMapping(m);
     init_RealBox(m);

diff --git a/tests/test_basefab.py b/tests/test_basefab.py
@@ -0,0 +1,7 @@
+# -*- coding: utf-8 -*-
+
+import amrex
+
+
+def test_basefab():
+    bf = amrex.BaseFab_Real()
diff --git a/tests/test_farraybox.py b/tests/test_farraybox.py
@@ -0,0 +1,18 @@
+# -*- coding: utf-8 -*-
+
+import amrex
+
+
+def test_farraybox():
+    fab = amrex.FArrayBox()
+
+
+def test_farraybox_io():
+    fab = amrex.FArrayBox()
+
+    # https://docs.python.org/3/library/io.html
+    # https://gist.github.com/asford/544323a5da7dddad2c9174490eb5ed06#file-test_ostream_example-py
+    # import io
+    # iob = io.BytesIO()
+    # assert iob.getvalue() == b"..."
+    # fab.read_from(iob)