gnu: dealii: Update to 9.3.2.

* gnu/packages/maths.scm (dealii): Update to 9.3.2.
  [source]: Add dealii-fix-compiliation-with-boost-1.78.patch and
  dealii-fix-sundials.patch.
  [inputs]: Use simplified format.
  [native-inputs]: Use simplified format.
* gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch:
  New file.
* gnu/packages/patches/dealii-fix-sundials.patch: New file.
* gnu/local.mk: Add new patch files.

Signed-off-by: Nicolas Goaziou <mail@nicolasgoaziou.fr>

2 files changed, 100 insertions, 0 deletions

diff --git a/gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch b/gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch
new file mode 100644
index 0000000000..1937aa9afc
--- /dev/null
+++ b/gnu/packages/patches/dealii-fix-compiliation-with-boost-1.78.patch
@@ -0,0 +1,40 @@
+From cbef761731627cece2a6f0276b87dacabbdc8a72 Mon Sep 17 00:00:00 2001
+From: David Wells <drwells@email.unc.edu>
+Date: Tue, 4 Jan 2022 12:46:30 -0500
+Subject: [PATCH] Fix compilation with boost 1.78.
+
+I bisected (fortunately Boost.Geometry a header-only library so adding the
+include directory sufficed) and
+https://github.com/boostorg/geometry/commit/6eb9e238bcb37e26dc31d16acf826784a2ba30f4
+is where this problem starts for us. See also
+https://github.com/boostorg/geometry/issues/792 - the easiest fix for all such
+issues is to just include the project header `boost/geometry/geometry.hpp`.
+
+In this particular case, if you look at the commit which causes grid_tools.cc
+fails to compile, its because we were relying on some implicit includes. In
+particular, we need the distance header to find the distance between points and
+boxes, but that was previously included in another file.
+
+This patch has been adapted from
+e0e76835519d122fd12b5858e16d08641a641c6a to apply to dealii 9.3.2.
+
+See https://github.com/dealii/dealii/pull/13165.
+---
+ include/deal.II/numerics/rtree.h | 1 +
+ 1 file changed, 1 insertion(+)
+
+diff --git a/include/deal.II/numerics/rtree.h b/include/deal.II/numerics/rtree.h
+index 1b9d04dacd..1e1bfd2932 100644
+--- a/include/deal.II/numerics/rtree.h
++++ b/include/deal.II/numerics/rtree.h
+@@ -26,6 +26,7 @@
+ #include <deal.II/boost_adaptors/segment.h>
+ 
+ DEAL_II_DISABLE_EXTRA_DIAGNOSTICS
++#include <boost/geometry/algorithms/distance.hpp>
+ #include <boost/geometry/index/rtree.hpp>
+ #include <boost/geometry/strategies/strategies.hpp>
+ DEAL_II_ENABLE_EXTRA_DIAGNOSTICS
+-- 
+2.30.2
+
diff --git a/gnu/packages/patches/dealii-fix-sundials.patch b/gnu/packages/patches/dealii-fix-sundials.patch
new file mode 100644
index 0000000000..7dd5df45da
--- /dev/null
+++ b/gnu/packages/patches/dealii-fix-sundials.patch
@@ -0,0 +1,60 @@
+From af73f368f7f9d4a00df075d1a9f50fc495f8e87a Mon Sep 17 00:00:00 2001
+From: Timo Heister <timo.heister@gmail.com>
+Date: Sat, 25 Dec 2021 12:30:45 -0500
+Subject: [PATCH] fix sundials compilation
+
+---
+ include/deal.II/sundials/n_vector.templates.h | 11 ++++++-----
+ 1 file changed, 6 insertions(+), 5 deletions(-)
+
+diff --git a/include/deal.II/sundials/n_vector.templates.h b/include/deal.II/sundials/n_vector.templates.h
+index 2b49e3efc9..746f63a03b 100644
+--- a/include/deal.II/sundials/n_vector.templates.h
++++ b/include/deal.II/sundials/n_vector.templates.h
+@@ -253,13 +253,13 @@ namespace SUNDIALS
+       template <
+         typename VectorType,
+         typename std::enable_if_t<!IsBlockVector<VectorType>::value, int> = 0>
+-      MPI_Comm
++      const MPI_Comm &
+       get_communicator(N_Vector v);
+ 
+       template <
+         typename VectorType,
+         typename std::enable_if_t<IsBlockVector<VectorType>::value, int> = 0>
+-      MPI_Comm
++      const MPI_Comm &
+       get_communicator(N_Vector v);
+ 
+       /**
+@@ -481,7 +481,7 @@ SUNDIALS::internal::NVectorOperations::destroy(N_Vector v)
+ 
+ template <typename VectorType,
+           std::enable_if_t<IsBlockVector<VectorType>::value, int>>
+-MPI_Comm
++const MPI_Comm &
+ SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v)
+ {
+   return unwrap_nvector_const<VectorType>(v)->block(0).get_mpi_communicator();
+@@ -491,7 +491,7 @@ SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v)
+ 
+ template <typename VectorType,
+           std::enable_if_t<!IsBlockVector<VectorType>::value, int>>
+-MPI_Comm
++const MPI_Comm &
+ SUNDIALS::internal::NVectorOperations::get_communicator(N_Vector v)
+ {
+   return unwrap_nvector_const<VectorType>(v)->get_mpi_communicator();
+@@ -519,7 +519,8 @@ SUNDIALS::internal::NVectorOperations::get_communicator_as_void_ptr(N_Vector v)
+   (void)v;
+   return nullptr;
+ #  else
+-  return get_communicator<VectorType>(v);
++  // We need to cast away const here, as SUNDIALS demands a pure `void *`.
++  return &(const_cast<MPI_Comm &>(get_communicator<VectorType>(v)));
+ #  endif
+ }
+ 
+-- 
+2.30.2
+