From 6e06e823edace0956b8532bebde82058f0f3a14f Mon Sep 17 00:00:00 2001
From: Timo Koch <timo.koch@iws.uni-stuttgart.de>
Date: Wed, 15 Apr 2020 22:30:34 +0200
Subject: [PATCH] [python] Add first Python bindings for the TimeLoop and the
GridGeometry
---
CMakeLists.txt | 6 +
dumux/python/CMakeLists.txt | 2 +
dumux/python/common/CMakeLists.txt | 3 +
dumux/python/common/timeloop.hh | 48 ++++++++
dumux/python/discretization/gridgeometry.hh | 128 ++++++++++++++++++++
python/CMakeLists.txt | 2 +
python/dumux/CMakeLists.txt | 2 +
python/dumux/common/CMakeLists.txt | 5 +
python/dumux/common/__init__.py | 1 +
python/dumux/common/_common.cc | 27 +++++
python/dumux/discretization/CMakeLists.txt | 3 +
python/dumux/discretization/__init__.py | 21 ++++
python/setup.py.in | 11 ++
13 files changed, 259 insertions(+)
create mode 100644 dumux/python/CMakeLists.txt
create mode 100644 dumux/python/common/CMakeLists.txt
create mode 100644 dumux/python/common/timeloop.hh
create mode 100644 dumux/python/discretization/gridgeometry.hh
create mode 100644 python/CMakeLists.txt
create mode 100644 python/dumux/CMakeLists.txt
create mode 100644 python/dumux/common/CMakeLists.txt
create mode 100644 python/dumux/common/__init__.py
create mode 100644 python/dumux/common/_common.cc
create mode 100644 python/dumux/discretization/CMakeLists.txt
create mode 100644 python/dumux/discretization/__init__.py
create mode 100644 python/setup.py.in
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 8abf0ab4a7..ae7dcbcbef 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -33,5 +33,11 @@ add_subdirectory(dumux)
add_subdirectory(test EXCLUDE_FROM_ALL)
add_subdirectory(examples EXCLUDE_FROM_ALL)
+# if Python bindings are enabled, include necessary sub directories.
+if(DUNE_ENABLE_PYTHONBINDINGS)
+ add_subdirectory("python")
+ dune_python_install_package(PATH "python")
+endif()
+
# finalize the dune project, e.g. generating config.h etc.
finalize_dune_project(GENERATE_CONFIG_H_CMAKE)
diff --git a/dumux/python/CMakeLists.txt b/dumux/python/CMakeLists.txt
new file mode 100644
index 0000000000..4f95771a66
--- /dev/null
+++ b/dumux/python/CMakeLists.txt
@@ -0,0 +1,2 @@
+add_subdirectory(common)
+add_subdirectory(discretization)
diff --git a/dumux/python/common/CMakeLists.txt b/dumux/python/common/CMakeLists.txt
new file mode 100644
index 0000000000..b507d026f0
--- /dev/null
+++ b/dumux/python/common/CMakeLists.txt
@@ -0,0 +1,3 @@
+install(FILES
+timeloop.hh
+DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/dumux/python/common)
diff --git a/dumux/python/common/timeloop.hh b/dumux/python/common/timeloop.hh
new file mode 100644
index 0000000000..03a165a154
--- /dev/null
+++ b/dumux/python/common/timeloop.hh
@@ -0,0 +1,48 @@
+#ifndef DUMUX_PYTHON_COMMON_TIMELOOP_HH
+#define DUMUX_PYTHON_COMMON_TIMELOOP_HH
+
+#include <dumux/common/timeloop.hh>
+
+#include <dune/python/pybind11/pybind11.h>
+#include <dune/python/pybind11/stl.h>
+
+namespace Dumux::Python {
+
+template <class Scalar, class... options>
+void registerTimeLoop(pybind11::handle scope,
+ pybind11::class_<CheckPointTimeLoop<Scalar>, options...> cls)
+{
+ using pybind11::operator""_a;
+
+ using TimeLoop = CheckPointTimeLoop<Scalar>;
+ cls.def(pybind11::init([](Scalar startTime, Scalar dt, Scalar endTime, bool verbose){
+ return new TimeLoop(startTime, dt, endTime, verbose);
+ }), "startTime"_a, "dt"_a, "endTime"_a, "verbose"_a=true);
+
+ cls.def("time", &TimeLoop::time);
+ cls.def("timeStepSize", &TimeLoop::timeStepSize);
+ cls.def("start", &TimeLoop::start);
+ cls.def("reset", &TimeLoop::reset, "startTime"_a, "dt"_a, "endTime"_a, "verbose"_a=true);
+ cls.def("advanceTimeStep", &TimeLoop::advanceTimeStep);
+ cls.def("setTimeStepSize", &TimeLoop::setTimeStepSize, "dt"_a);
+ cls.def("setMaxTimeStepSize", &TimeLoop::setMaxTimeStepSize, "dt"_a);
+ cls.def("finished", &TimeLoop::finished);
+ cls.def("reportTimeStep", &TimeLoop::reportTimeStep);
+ cls.def("finalize", [](TimeLoop& self){ self.finalize(); });
+ cls.def("setPeriodicCheckPoint", &TimeLoop::setPeriodicCheckPoint, "interval"_a, "offset"_a=0.0);
+ cls.def("isCheckPoint", &TimeLoop::isCheckPoint);
+ cls.def("setCheckPoints", [](TimeLoop& self, const std::vector<double>& checkPoints) {
+ self.setCheckPoint(checkPoints);
+ });
+}
+
+template<class Scalar>
+void registerTimeLoop(pybind11::handle scope, const char *clsName = "TimeLoop")
+{
+ pybind11::class_<CheckPointTimeLoop<Scalar>> cls(scope, clsName);
+ registerTimeLoop(scope, cls);
+}
+
+} // namespace Dumux::Python
+
+#endif
diff --git a/dumux/python/discretization/gridgeometry.hh b/dumux/python/discretization/gridgeometry.hh
new file mode 100644
index 0000000000..619b1e468c
--- /dev/null
+++ b/dumux/python/discretization/gridgeometry.hh
@@ -0,0 +1,128 @@
+#ifndef DUMUX_PYTHON_DISCRETIZATION_GRIDGEOMETRY_HH
+#define DUMUX_PYTHON_DISCRETIZATION_GRIDGEOMETRY_HH
+
+#include <memory>
+#include <dune/python/pybind11/pybind11.h>
+#include <dune/python/common/typeregistry.hh>
+
+namespace Dumux::Python {
+
+namespace Impl {
+
+template<class SCV>
+void registerSubControlVolume(pybind11::handle scope)
+{
+ using namespace Dune::Python;
+
+ auto [cls, addedToRegistry] = insertClass<SCV>(
+ scope, "SubControlVolume",
+ GenerateTypeName("SubControlVolume"),
+ IncludeFiles{"dumux/python/discretization/gridgeometry.hh"}
+ );
+
+ if (addedToRegistry)
+ {
+ using pybind11::operator""_a;
+
+ cls.def("center", &SCV::center);
+ cls.def("volume", &SCV::volume);
+ cls.def("dofIndex", &SCV::dofIndex);
+ cls.def("localDofIndex", &SCV::localDofIndex);
+ cls.def("dofPosition", &SCV::dofPosition);
+ cls.def("elementIndex", &SCV::elementIndex);
+
+ }
+}
+
+template<class SCVF>
+void registerSubControlVolumeFace(pybind11::handle scope)
+{
+ using namespace Dune::Python;
+
+ auto [cls, addedToRegistry] = insertClass<SCVF>(
+ scope, "SubControlVolumeFace",
+ GenerateTypeName("SubControlVolumeFace"),
+ IncludeFiles{"dumux/python/discretization/gridgeometry.hh"}
+ );
+
+ if (addedToRegistry)
+ {
+ using pybind11::operator""_a;
+
+ cls.def("center", &SCVF::center);
+ cls.def("area", &SCVF::area);
+ cls.def("ipGlobal", &SCVF::ipGlobal);
+ cls.def("boundary", &SCVF::boundary);
+ cls.def("unitOuterNormal", &SCVF::unitOuterNormal);
+ cls.def("insideScvIdx", &SCVF::insideScvIdx);
+ cls.def("outsideScvIdx", [](SCVF& self){ return self.outsideScvIdx(); });
+ cls.def("index", &SCVF::index);
+ }
+}
+
+template<class FVEG>
+void registerFVElementGeometry(pybind11::handle scope)
+{
+ using namespace Dune::Python;
+
+ auto [cls, addedToRegistry] = insertClass<FVEG>(
+ scope, "FVElementGeometry",
+ GenerateTypeName("FVElementGeometry"),
+ IncludeFiles{"dumux/python/discretization/gridgeometry.hh"}
+ );
+
+ if (addedToRegistry)
+ {
+ using pybind11::operator""_a;
+
+ cls.def("numScvf", &FVEG::numScv);
+ cls.def("numScv", &FVEG::numScv);
+ cls.def("bind", &FVEG::bind, "element"_a);
+ cls.def("hasBoundaryScvf", &FVEG::hasBoundaryScvf);
+ cls.def("scvs", [](FVEG& self){
+ const auto range = scvs(self);
+ return pybind11::make_iterator(range.begin(), range.end());
+ }, pybind11::keep_alive<0, 1>());
+ cls.def("scvfs", [](FVEG& self){
+ const auto range = scvfs(self);
+ return pybind11::make_iterator(range.begin(), range.end());
+ }, pybind11::keep_alive<0, 1>());
+ }
+}
+
+} // end namespace Impl
+
+// see python/dumux/discretization/__init__.py for how this is used for JIT compilation
+template <class GG, class... Options>
+void registerGridGeometry(pybind11::handle scope, pybind11::class_<GG, Options...> cls)
+{
+ using pybind11::operator""_a;
+ using namespace Dune::Python;
+
+ using GridView = typename GG::GridView;
+
+ cls.def(pybind11::init([](GridView gridView){
+ return std::make_unique<GG>(gridView);
+ }), "gridView"_a);
+
+ cls.def("update", &GG::update);
+ cls.def("numDofs", &GG::numDofs);
+ cls.def("numScv", &GG::numScv);
+ cls.def("numScvf", &GG::numScvf);
+
+ using SubControlVolume = typename GG::SubControlVolume;
+ Impl::registerSubControlVolume<SubControlVolume>(scope);
+
+ using SubControlVolumeFace = typename GG::SubControlVolumeFace;
+ Impl::registerSubControlVolumeFace<SubControlVolumeFace>(scope);
+
+ // also compile the corresponding local view
+ using LocalView = typename GG::LocalView;
+ Impl::registerFVElementGeometry<LocalView>(scope);
+ // and make it accessible
+ cls.def("localView", [](GG& self){ return localView(self); });
+}
+
+} // namespace Dumux::Python
+
+#endif
diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt
new file mode 100644
index 0000000000..0c4ddccf90
--- /dev/null
+++ b/python/CMakeLists.txt
@@ -0,0 +1,2 @@
+add_subdirectory(dumux)
+configure_file(setup.py.in setup.py)
diff --git a/python/dumux/CMakeLists.txt b/python/dumux/CMakeLists.txt
new file mode 100644
index 0000000000..4f95771a66
--- /dev/null
+++ b/python/dumux/CMakeLists.txt
@@ -0,0 +1,2 @@
+add_subdirectory(common)
+add_subdirectory(discretization)
diff --git a/python/dumux/common/CMakeLists.txt b/python/dumux/common/CMakeLists.txt
new file mode 100644
index 0000000000..38d491fa22
--- /dev/null
+++ b/python/dumux/common/CMakeLists.txt
@@ -0,0 +1,5 @@
+add_python_targets(common
+ __init__
+)
+dune_add_pybind11_module(NAME _common)
+set_property(TARGET _common PROPERTY LINK_LIBRARIES dunecommon dunegrid APPEND)
diff --git a/python/dumux/common/__init__.py b/python/dumux/common/__init__.py
new file mode 100644
index 0000000000..c897d03434
--- /dev/null
+++ b/python/dumux/common/__init__.py
@@ -0,0 +1 @@
+from ._common import *
diff --git a/python/dumux/common/_common.cc b/python/dumux/common/_common.cc
new file mode 100644
index 0000000000..49bca34533
--- /dev/null
+++ b/python/dumux/common/_common.cc
@@ -0,0 +1,27 @@
+// -*- mode: C++; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*-
+// vi: set et ts=4 sw=4 sts=4:
+/*****************************************************************************
+ * See the file COPYING for full copying permissions. *
+ * *
+ * This program is free software: you can redistribute it and/or modify *
+ * it under the terms of the GNU General Public License as published by *
+ * the Free Software Foundation, either version 3 of the License, or *
+ * (at your option) any later version. *
+ * *
+ * This program is distributed in the hope that it will be useful, *
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of *
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
+ * GNU General Public License for more details. *
+ * *
+ * You should have received a copy of the GNU General Public License *
+ * along with this program. If not, see <http://www.gnu.org/licenses/>. *
+ *****************************************************************************/
+
+#include <dune/python/pybind11/pybind11.h>
+#include <dumux/python/common/timeloop.hh>
+
+PYBIND11_MODULE(_common, module)
+{
+ // export time loop
+ Dumux::Python::registerTimeLoop<double>(module);
+}
diff --git a/python/dumux/discretization/CMakeLists.txt b/python/dumux/discretization/CMakeLists.txt
new file mode 100644
index 0000000000..22b582c564
--- /dev/null
+++ b/python/dumux/discretization/CMakeLists.txt
@@ -0,0 +1,3 @@
+add_python_targets(discretization
+ __init__
+)
diff --git a/python/dumux/discretization/__init__.py b/python/dumux/discretization/__init__.py
new file mode 100644
index 0000000000..e4d73fb277
--- /dev/null
+++ b/python/dumux/discretization/__init__.py
@@ -0,0 +1,21 @@
+from dune.generator.generator import SimpleGenerator
+from dune.common.hashit import hashIt
+
+# construct a GridGeometry from a gridView
+# the grid geometry is JIT compiled
+def GridGeometry(gridView, discMethod="cctpfa"):
+ includes = gridView._includes + ["dumux/python/discretization/gridgeometry.hh"]
+
+ if discMethod == "cctpfa":
+ includes += ["dumux/discretization/cellcentered/tpfa/fvgridgeometry.hh"]
+ typeName = "Dumux::CCTpfaFVGridGeometry<" + gridView._typeName + ">"
+ elif discMethod == "box":
+ includes += ["dumux/discretization/box/fvgridgeometry.hh"]
+ typeName = "Dumux::BoxFVGridGeometry<double, " + gridView._typeName + ">"
+ else:
+ raise ValueError("Unknown discMethod {}".format(discMethod))
+
+ moduleName = "gridgeometry_" + hashIt(typeName)
+ generator = SimpleGenerator("GridGeometry", "Dumux::Python")
+ module = generator.load(includes, typeName, moduleName)
+ return module.GridGeometry(gridView)
diff --git a/python/setup.py.in b/python/setup.py.in
new file mode 100644
index 0000000000..8cb1413ea2
--- /dev/null
+++ b/python/setup.py.in
@@ -0,0 +1,11 @@
+from setuptools import setup, find_namespace_packages
+
+setup(name="dumux",
+ description="Python lib for dumux",
+ version="${DUMUX_VERSION}",
+ author="Timo Koch",
+ packages = find_namespace_packages(include=['dumux.*']),
+ zip_safe = 0,
+ package_data = {'': ['*.so']},
+ install_requires = ['portalocker'],
+)
--
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