Merge pull request #3 from FEniCS/master

Update with upstream

.circleci/config.yml

@@ -3,7 +3,6 @@ install-python-components: &install-python-components
   command: |
             pip3 install git+https://bitbucket.org/fenics-project/fiat.git --upgrade
             pip3 install git+https://bitbucket.org/fenics-project/ufl.git --upgrade
-            pip3 install git+https://bitbucket.org/fenics-project/dijitso.git --upgrade
             pip3 install git+https://github.com/FEniCS/ffcx.git --upgrade
             rm -rf /usr/local/include/dolfin /usr/local/include/dolfin.h
 

Dockerfile

@@ -21,10 +21,10 @@
 #    docker run -p 8888:8888 -v "$(pwd)":/tmp quay.io/fenicsproject/dolfinx:notebook
 #
 
-ARG GMSH_VERSION=4.2.2
-ARG PYBIND11_VERSION=2.2.4
-ARG PETSC_VERSION=3.11.1
-ARG SLEPC_VERSION=3.11.0
+ARG GMSH_VERSION=4.3.0
+ARG PYBIND11_VERSION=2.3.0
+ARG PETSC_VERSION=3.11.2
+ARG SLEPC_VERSION=3.11.1
 ARG PETSC4PY_VERSION=3.11.0
 ARG SLEPC4PY_VERSION=3.11.0
 ARG TINI_VERSION=v0.18.0
@@ -48,10 +48,12 @@ ENV OPENBLAS_NUM_THREADS=1 \
     OPENBLAS_VERBOSE=0
 
 # Install dependencies available via apt-get.
-# First set of packages are required to build and run FEniCS.
-# Second set of packages are recommended and/or required to build documentation or tests.
-# Third set of packages are optional, but required to run gmsh pre-built binaries.
-# Fourth set of packages are optional, required for meshio.
+# - First set of packages are required to build and run FEniCS.
+# - Second set of packages are recommended and/or required to build
+#   documentation or tests.
+# - Third set of packages are optional, but required to run gmsh
+#   pre-built binaries.
+# - Fourth set of packages are optional, required for meshio.
 RUN export DEBIAN_FRONTEND=noninteractive && \
     apt-get -qq update && \
     apt-get -yq --with-new-pkgs -o Dpkg::Options::="--force-confold" upgrade && \
@@ -103,9 +105,11 @@ RUN cd /usr/local && \
 ENV PATH=/usr/local/gmsh-${GMSH_VERSION}-Linux64/bin:$PATH
 
 # Install Python packages (via pip)
-# First set of packages are required to build and run FEniCS.
-# Second set of packages are recommended and/or required to build documentation or run tests.
-# Third set of packages are optional but required for pygmsh/meshio/DOLFIN mesh pipeline.
+# - First set of packages are required to build and run FEniCS.
+# - Second set of packages are recommended and/or required to build
+#   documentation or run tests.
+# - Third set of packages are optional but required for
+#   pygmsh/meshio/DOLFIN mesh pipeline.
 RUN pip3 install --no-cache-dir mpi4py numba && \
     pip3 install --no-cache-dir cffi decorator flake8 pytest pytest-xdist sphinx sphinx_rtd_theme && \
     export HDF5_MPI="ON" && \
@@ -256,11 +260,11 @@ ARG MAKEFLAGS
 
 WORKDIR /tmp
 
-# Install ipython (optional), FIAT, UFL, dijitso and ffcX (development versions, master branch)
+# Install ipython (optional), FIAT, UFL and ffcX (development
+# versions, master branch)
 RUN pip3 install --no-cache-dir ipython && \
     pip3 install --no-cache-dir git+https://bitbucket.org/fenics-project/fiat.git && \
     pip3 install --no-cache-dir git+https://bitbucket.org/fenics-project/ufl.git && \
-    pip3 install --no-cache-dir git+https://bitbucket.org/fenics-project/dijitso.git && \
     pip3 install --no-cache-dir git+https://github.com/fenics/ffcX
 
 # Install dolfinx
@@ -285,11 +289,11 @@ ARG MAKEFLAGS
 
 WORKDIR /tmp
 
-# Install ipython (optional), FIAT, UFL, dijitso and ffcX (development versions, master branch)
+# Install ipython (optional), FIAT, UFL and ffcX (development versions,
+# master branch)
 RUN pip3 install --no-cache-dir ipython && \
     pip3 install --no-cache-dir git+https://bitbucket.org/fenics-project/fiat.git && \
     pip3 install --no-cache-dir git+https://bitbucket.org/fenics-project/ufl.git && \
-    pip3 install --no-cache-dir git+https://bitbucket.org/fenics-project/dijitso.git && \
     pip3 install --no-cache-dir git+https://github.com/fenics/ffcX
 
 # Install dolfinx

cpp/demo/hyperelasticity/main.cpp

@@ -33,60 +33,6 @@ class Right : public mesh::SubDomain
   }
 };
 
-// Dirichlet boundary condition for clamp at left end
-class Clamp : public function::Expression
-{
-public:
-  Clamp() : function::Expression({3}) {}
-
-  void eval(Eigen::Ref<Eigen::Array<PetscScalar, Eigen::Dynamic, Eigen::Dynamic,
-                                    Eigen::RowMajor>>
-                values,
-            Eigen::Ref<const EigenRowArrayXXd> x) const
-  {
-    for (int i = 0; i < x.rows(); ++i)
-    {
-      values(i, 0) = 0.0;
-      values(i, 1) = 0.0;
-      values(i, 2) = 0.0;
-    }
-  }
-};
-
-// Dirichlet boundary condition for rotation at right end
-class Rotation : public function::Expression
-{
-public:
-  Rotation() : function::Expression({3}) {}
-
-  void eval(Eigen::Ref<Eigen::Array<PetscScalar, Eigen::Dynamic, Eigen::Dynamic,
-                                    Eigen::RowMajor>>
-                values,
-            Eigen::Ref<const EigenRowArrayXXd> x) const
-  {
-    const double scale = 0.005;
-
-    // Center of rotation
-    const double y0 = 0.5;
-    const double z0 = 0.5;
-
-    // Large angle of rotation (60 degrees)
-    double theta = 1.04719755;
-
-    for (int i = 0; i < x.rows(); ++i)
-    {
-      // New coordinates
-      double y = y0 + (x(1, 1) - y0) * cos(theta) - (x(i, 2) - z0) * sin(theta);
-      double z = z0 + (x(i, 1) - y0) * sin(theta) + (x(i, 2) - z0) * cos(theta);
-
-      // Rotate at right end
-      values(i, 0) = 0.0;
-      values(i, 1) = scale * (y - x(i, 1));
-      values(i, 2) = scale * (z - x(i, 2));
-    }
-  }
-};
-
 // Next:
 //
 // .. code-block:: cpp
@@ -207,13 +153,32 @@ int main(int argc, char* argv[])
   auto cmap = a->coordinate_mapping();
   mesh->geometry().coord_mapping = cmap;
 
-  Rotation rotation;
-  Clamp clamp;
-
   auto u_rotation = std::make_shared<function::Function>(V);
-  u_rotation->interpolate(rotation);
+  u_rotation->interpolate([](auto values, auto x) {
+    const double scale = 0.005;
+
+    // Center of rotation
+    const double y0 = 0.5;
+    const double z0 = 0.5;
+
+    // Large angle of rotation (60 degrees)
+    double theta = 1.04719755;
+
+    for (int i = 0; i < x.rows(); ++i)
+    {
+      // New coordinates
+      double y = y0 + (x(1, 1) - y0) * cos(theta) - (x(i, 2) - z0) * sin(theta);
+      double z = z0 + (x(i, 1) - y0) * sin(theta) + (x(i, 2) - z0) * cos(theta);
+
+      // Rotate at right end
+      values(i, 0) = 0.0;
+      values(i, 1) = scale * (y - x(i, 1));
+      values(i, 2) = scale * (z - x(i, 2));
+    }
+  });
+
   auto u_clamp = std::make_shared<function::Function>(V);
-  u_clamp->interpolate(clamp);
+  u_clamp->interpolate([](auto values, auto x) { values = 0.0; });
 
   L->set_coefficients({{"u", u}});
   a->set_coefficients({{"u", u}});

cpp/demo/poisson/main.cpp

@@ -101,42 +101,6 @@ using namespace dolfin;
 //
 // .. code-block:: cpp
 
-// Source term (right-hand side)
-class Source : public function::Expression
-{
-public:
-  Source() : function::Expression({}) {}
-
-  void eval(Eigen::Ref<Eigen::Array<PetscScalar, Eigen::Dynamic, Eigen::Dynamic,
-                                    Eigen::RowMajor>>
-                values,
-            Eigen::Ref<const EigenRowArrayXXd> x) const
-  {
-    for (unsigned int i = 0; i != x.rows(); ++i)
-    {
-      double dx = x(i, 0) - 0.5;
-      double dy = x(i, 1) - 0.5;
-      values(i, 0) = 10 * exp(-(dx * dx + dy * dy) / 0.02);
-    }
-  }
-};
-
-// Normal derivative (Neumann boundary condition)
-class dUdN : public function::Expression
-{
-public:
-  dUdN() : function::Expression({}) {}
-
-  void eval(Eigen::Ref<Eigen::Array<PetscScalar, Eigen::Dynamic, Eigen::Dynamic,
-                                    Eigen::RowMajor>>
-                values,
-            Eigen::Ref<const EigenRowArrayXXd> x) const
-  {
-    for (unsigned int i = 0; i != x.rows(); ++i)
-      values(i, 0) = sin(5 * x(i, 0));
-  }
-};
-
 // The ``DirichletBoundary`` is derived from the :cpp:class:`SubDomain`
 // class and defines the part of the boundary to which the Dirichlet
 // boundary condition should be applied.
@@ -149,10 +113,7 @@ class DirichletBoundary : public mesh::SubDomain
   EigenArrayXb inside(Eigen::Ref<const EigenRowArrayXXd> x,
                       bool on_boundary) const
   {
-    EigenArrayXb result(x.rows());
-    for (unsigned int i = 0; i != x.rows(); ++i)
-      result[i] = (x(i, 0) < DBL_EPSILON or x(i, 0) > 1.0 - DBL_EPSILON);
-    return result;
+    return (x.col(0) < DBL_EPSILON or x.col(0) > 1.0 - DBL_EPSILON);
   }
 };
 
@@ -232,18 +193,21 @@ int main(int argc, char* argv[])
       std::initializer_list<std::shared_ptr<const function::FunctionSpace>>{V});
   std::free(linear_form);
 
-  auto f_expr = Source();
-  auto g_expr = dUdN();
-
   auto f = std::make_shared<function::Function>(V);
   auto g = std::make_shared<function::Function>(V);
 
   // Attach 'coordinate mapping' to mesh
   auto cmap = a->coordinate_mapping();
   mesh->geometry().coord_mapping = cmap;
 
-  f->interpolate(f_expr);
-  g->interpolate(g_expr);
+  // auto dx = Eigen::square(x - 0.5);
+  // values = 10.0 * Eigen::exp(-(dx.col(0) + dx.col(1)) / 0.02);
+  f->interpolate([](auto values, auto x) {
+    auto dx = Eigen::square(x - 0.5);
+    values = 10.0 * Eigen::exp(-(dx.col(0) + dx.col(1)) / 0.02);
+  });
+  g->interpolate(
+      [](auto values, auto x) { values = Eigen::sin(5 * x.col(0)); });
   L->set_coefficients({{"f", f}, {"g", g}});
 
   // Now, we have specified the variational forms and can consider the
@@ -290,7 +254,7 @@ int main(int argc, char* argv[])
   // .. code-block:: cpp
 
   // Save solution in VTK format
-  io::VTKFile file("poisson.pvd");
+  io::VTKFile file("u.pvd");
   file.write(u);
 
   return 0;

cpp/dolfin/common/CMakeLists.txt

@@ -17,7 +17,6 @@ set(HEADERS
   types.h
   UniqueIdGenerator.h
   utils.h
-  Variable.h
   PARENT_SCOPE)
 
 set(SOURCES
@@ -34,5 +33,4 @@ set(SOURCES
   timing.cpp
   UniqueIdGenerator.cpp
   utils.cpp
-  Variable.cpp
   PARENT_SCOPE)

cpp/dolfin/common/MPI.cpp

@@ -180,13 +180,13 @@ dolfin::Table dolfin::MPI::all_reduce(const MPI_Comm comm,
                                       const dolfin::Table& table,
                                       const MPI_Op op)
 {
-  const std::string new_title = "[" + operation_map[op] + "] " + table.name();
+  const std::string new_title = "[" + operation_map[op] + "] " + table.name;
 
   // Handle trivial reduction
   if (MPI::size(comm) == 1)
   {
     Table table_all(table);
-    table_all.rename(new_title);
+    table_all.name = new_title;
     return table_all;
   }
 

cpp/dolfin/common/SubSystemsManager.cpp

@@ -81,7 +81,7 @@ void SubSystemsManager::init_petsc()
 {
   // Dummy command-line arguments
   int argc = 0;
-  char** argv = NULL;
+  char** argv = nullptr;
 
   // Initialize PETSc
   init_petsc(argc, argv);
@@ -106,10 +106,10 @@ void SubSystemsManager::init_petsc(int argc, char* argv[])
   PetscBool is_initialized;
   PetscInitialized(&is_initialized);
   if (!is_initialized)
-    PetscInitialize(&argc, &argv, NULL, NULL);
+    PetscInitialize(&argc, &argv, nullptr, nullptr);
 
 #ifdef HAS_SLEPC
-  SlepcInitialize(&argc, &argv, NULL, NULL);
+  SlepcInitialize(&argc, &argv, nullptr, nullptr);
 #endif
 
   // Remember that PETSc has been initialized