Merge pull request #55 from mathLab/deal_v_9_6_modifications

implemented changes to move to deal.II version 9.6.0

Author: luca-heltai

.clang-format

@@ -1,5 +1,5 @@
 #
-# The clang-format (Clang 11) style file used by deal.II.
+# The clang-format (Clang 16) style file used by deal.II.
 #
 
 AccessModifierOffset: -2
@@ -160,6 +160,8 @@ PointerAlignment: Right
 ReflowComments: true
 CommentPragmas: '( \| |\*--|<li>|@ref | @p |@param |@name |@returns |@warning |@ingroup |@author |@date |@related |@relates |@relatesalso |@deprecated |@image |@return |@brief |@attention |@copydoc |@addtogroup |@todo |@tparam |@see |@note |@skip |@skipline |@until |@line |@dontinclude |@include)'
 
+QualifierAlignment: Left
+
 SortIncludes: true
 SortUsingDeclarations: true
 
@@ -175,7 +177,7 @@ SpacesInContainerLiterals: false
 SpacesInParentheses: false
 SpacesInSquareBrackets: false
 
-Standard: Cpp11
+Standard: c++20
 
 TabWidth: 2
 

.github/workflows/indentation.yml

@@ -11,7 +11,7 @@ jobs:
 
     runs-on: ubuntu-latest
     container:
-      image: dealii/dealii:v9.5.0-jammy
+      image: dealii/dealii:v9.6.0-jammy
       options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
     steps:

.github/workflows/tests.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
 
     container:
-      image: dealii/dealii:v9.5.0-jammy
+      image: dealii/dealii:v9.6.0-jammy
       options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
     steps:
@@ -32,7 +32,7 @@ jobs:
     runs-on: ubuntu-latest
 
     container:
-      image: dealii/dealii:v9.5.0-jammy
+      image: dealii/dealii:v9.6.0-jammy
       options: --user root --env OMPI_ALLOW_RUN_AS_ROOT=1 --env OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 
     steps:

CMakeLists.txt

@@ -1,7 +1,6 @@
 ##
 # CMake script for large project, with one executable
-# and a library of objects, optionally
-# depending on deal2lkit.
+# and a library of objects
 #
 # The structure of the directory is assumed to be:
 # ./source: containing implementations and one file with "int main()"
@@ -38,7 +37,7 @@ ENDIF()
 
 CMAKE_MINIMUM_REQUIRED(VERSION 3.13.4)
 
-FIND_PACKAGE(deal.II 9.5 REQUIRED
+FIND_PACKAGE(deal.II 9.5.0 REQUIRED
   HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
 )
 

README.md

@@ -4,19 +4,19 @@
   </a>
 </p>
 
-# pi-BEM: Parallel BEM Solver 
+# pi-BEM: Parallel BEM Solver
 
 [![Build Status](https://travis-ci.org/mathLab/pi-BEM.svg?branch=master)](https://travis-ci.org/mathLab/pi-BEM)
 
 Copyright (C) 2015 -- 2019 by Nicola Giuliani (1), Andrea Mola (2) and Luca Heltai (2)
 
-(1) Scuola Internazionale Superiore di Studi Avanzati E-mail: [email protected]
+(1) Scuola Internazionale Superiore di Studi Avanzati E-mail: <[email protected]>
 
-(2) Scuola Internazionale Superiore di Studi Avanzati E-mail: [email protected]
+(2) Scuola Internazionale Superiore di Studi Avanzati E-mail: <[email protected]>
 
-(3) Scuola Internazionale Superiore di Studi Avanzati E-mail: [email protected]
+(3) Scuola Internazionale Superiore di Studi Avanzati E-mail: <[email protected]>
 
-The library represents a parallel solver for the Laplace equation through Boundary Element Methods. We have developed the software in C++ on top of many high performance libraries, the [deal.II](https://github.com/dealii/dealii) library for Finite Element Handling, the [METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/download) project and [Trilinos](https://trilinos.org/) library for automatic Workload balance, [OpenCASCADE](https://www.opencascade.com/) for CAD integration, and [deal2lkit](https://github.com/luca-heltai/deal2lkit) for parameter handling. 
+The library represents a parallel solver for the Laplace equation through Boundary Element Methods. We have developed the software in C++ on top of many high performance libraries, the [deal.II](https://github.com/dealii/dealii) library for Finite Element Handling, the [METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/download) project and [Trilinos](https://trilinos.org/) library for automatic Workload balance, and [OpenCASCADE](https://www.opencascade.com/) for CAD integration.
 
 ## Provided features
 
@@ -32,131 +32,125 @@ We provide the following capabilities
 - Hybrid Distributed (MPI) - Shared (Intel Threaded Building Block) memory parallelisation for the BEM-FMM code
 - Recovery of both primal (potential) and dual (potential normal derivative) unknowns.
 - L2 projection of the full 3D potential gradient for post processing.
-- Extensive tuning via parameter file using the [deal2lkit](https://github.com/mathLab/deal2lkit) library 
-
+- Extensive tuning via parameter file using.
 
 ## Code Structure
+
 We have subdivided the code in main classes to handle the many different aspects of a complete BEM simulation.
 
 - Driver. This class is in charge of organising the overall BEM simulation. It has interfaces with all the other classes in order to perform a complete simulation.
 - ComputationalDomain. This class handles, and provides to the other classes, ONLY the geometry of the problem. In particular
- - it handles the domain decomposition using a graph partitioning tool (METIS);
- - it reads the domain from an external file.
+- it handles the domain decomposition using a graph partitioning tool (METIS);
+- it reads the domain from an external file.
 - BoundaryCondition. The class handles the boundary conditions. In particular
-	- it reads the boundary conditions for the potential and its normal derivative; 
-	- given the peculiarities of the BEM, the boundary conditions represent the actual unknowns, thus it creates the vectors containing the two variables and fills them with the proper data;
-	- it performs the error analysis on both unknowns.
+  - it reads the boundary conditions for the potential and its normal derivative;
+  - given the peculiarities of the BEM, the boundary conditions represent the actual unknowns, thus it creates the vectors containing the two variables and fills them with the proper data;
+  - it performs the error analysis on both unknowns.
 
 - BEMProblem. This class is the core of the BEM simulation
-	- it receives the variables vector filled in with the proper boundary condition;
-	- it creates the codimension 1 functional space setting up the BEM;
-	- it solves the system using a preconditioned parallel GMRES solver;
-	- it eventually interacts with the FMM accelerator.
+  - it receives the variables vector filled in with the proper boundary condition;
+  - it creates the codimension 1 functional space setting up the BEM;
+  - it solves the system using a preconditioned parallel GMRES solver;
+  - it eventually interacts with the FMM accelerator.
 - BEMFMA. This class handles the accelerator, in particular
-	- it sets up an hierarchical 3D space subdivision (octree);
-	- it receives two distributed vectors representing the unknowns and performs a full FMM matrix vector product.
+  - it sets up an hierarchical 3D space subdivision (octree);
+  - it receives two distributed vectors representing the unknowns and performs a full FMM matrix vector product.
 
 ## Install Procedure using CANDI
+
 To install from scratch all the needed library you can look to the automatic installation procedure provided by [CANDI](https://github.com/koecher/candi) developed Uwe Köcher.
 
 ## Install Procedure using spack
+
 Just follow the [instructions](https://github.com/dealii/dealii/wiki/deal.II-in-Spack) to install dealii@develop using spack.
 
 ## Install Procedure using Docker
-We provide the possibility of using Docker as a tool to provide a fully operational environment for our library. To use such tool you need to install Docker following the [instructions](https://docs.docker.com/engine/installation/) provided by its authors. Then you can execute the following command line instruction 
 
-	docker run -v `pwd`:/pwd_to_your_own_directory/ -i -t mathlab/deal2lkit:latest bash
+We provide the possibility of using Docker as a tool to provide a fully operational environment for our library. To use such tool you need to install Docker following the [instructions](https://docs.docker.com/engine/installation/) provided by its authors. Then you can execute the following command line instruction
+
+ docker run -v `pwd`:/pwd_to_your_own_directory/ -i -t dealii/dealii:v9.6.0-jammy bash
 
 to retrieve the environment. In such a shell you can easily compile the pi-BEM library following its own instructions.
 
 ## Install Procedure from scratch
-In order to successfully compile the code you need 
-
-- to install the Trilinos and Metis wrappers of the library, see the official [instructions](https://www.dealii.org/developer/readme.html) 
-- to install the [deal.II](https://github.com/dealii/dealii) library allowing both for multiprocessors and multithreaded environment.
-- to install the [deal2lkit](https://github.com/mathLab/deal2lkit) library allowing both for multiprocessors and multithreaded environment.
 
+In order to successfully compile the code you need
 
+- to install the Trilinos and Metis wrappers of the library, see the official [instructions](https://www.dealii.org/developer/readme.html)
+- to install the [deal.II](https://github.com/dealii/dealii) library allowing both for multiprocessors and multithreaded environment.
 
 ### deal.II Installation procedure
-Follow the detailed [instruction](https://www.dealii.org/developer/readme.html) to install deal with METIS and Trilinos wrappers. We highlight that in order to fully exploit pi-BEM you need to properly install the following additional packages: MPI, TBB, METIS, TRILINOS ans OPENCASCADE. For more detailed instruction you can look to the the deal.ii install procedures. In the following we provide an example of the installation of all the proper packages.
 
+Follow the detailed [instruction](https://www.dealii.org/developer/readme.html) to install deal with METIS and Trilinos wrappers. We highlight that in order to fully exploit pi-BEM you need to properly install the following additional packages: MPI, TBB, METIS, TRILINOS ans OPENCASCADE. For more detailed instruction you can look to the the deal.ii install procedures. In the following we provide an example of the installation of all the proper packages.
 
 ### OpenCASCADE Installation procedure
-- Download the latest version at [OpenCASCADE](https://github.com/tpaviot/oce) 
-- Follow the instructions
 
+- Download the latest version at [OpenCASCADE](https://github.com/tpaviot/oce)
+- Follow the instructions
 
 ### METIS-PARMETIS Installation procedure
+
 - Download the latest version at [METIS](http://glaros.dtc.umn.edu/gkhome/metis/metis/download)
 - Follow the [instructions](http://glaros.dtc.umn.edu/gkhome/metis/metis/download) for the correct installation of the package
 
-
 ### Trilinos Installation procedure
+
 - Download the latest version at [Trilinos](https://trilinos.org/download/)
 - This is a possible configuration file
 
-		cmake -D Trilinos_ENABLE_OPTIONAL_PACKAGES:BOOL=ON \
-		-D Trilinos_ENABLE_ALL_PACKAGES:BOOL=ON \
-		-D CMAKE_CXX_FLAGS:STRING="-O3" \
-		-D CMAKE_C_FLAGS:STRING="-O3" \
-		-D CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE \
-		-D Trilinos_VERBOSE_CONFIGURE:BOOL=FALSE \
-		-D TPL_ENABLE_MPI:BOOL=ON \
-		-D CMAKE_BUILD_TYPE:STRING=RELEASE \
-		-D Trilinos_ENABLE_Fortran:BOOL=ON \
-		-D BLAS_LIBRARY_NAMES:STRING="blas" \
-		-D BLAS_LIBRARY_DIRS:PATH=/usr/lib/libblas/ \
-		-D TPL_BLAS_LIBRARIES:PATH=/usr/lib/libblas/ \
-		-D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING="" \
-		-D CMAKE_INSTALL_PREFIX:PATH=/usr/local/ \
-		-D BUILD_SHARED_LIBS:BOOL=ON ../
-		
-		make install
+  cmake -D Trilinos_ENABLE_OPTIONAL_PACKAGES:BOOL=ON \
+  -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=ON \
+  -D CMAKE_CXX_FLAGS:STRING="-O3" \
+  -D CMAKE_C_FLAGS:STRING="-O3" \
+  -D CMAKE_VERBOSE_MAKEFILE:BOOL=FALSE \
+  -D Trilinos_VERBOSE_CONFIGURE:BOOL=FALSE \
+  -D TPL_ENABLE_MPI:BOOL=ON \
+  -D CMAKE_BUILD_TYPE:STRING=RELEASE \
+  -D Trilinos_ENABLE_Fortran:BOOL=ON \
+  -D BLAS_LIBRARY_NAMES:STRING="blas" \
+  -D BLAS_LIBRARY_DIRS:PATH=/usr/lib/libblas/ \
+  -D TPL_BLAS_LIBRARIES:PATH=/usr/lib/libblas/ \
+  -D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING="" \
+  -D CMAKE_INSTALL_PREFIX:PATH=/usr/local/ \
+  -D BUILD_SHARED_LIBS:BOOL=ON ../
+  
+  make install
 
 - if some packages create conflicts they can be disabled as seen on the Trilinos webpage
 
-
-
-
-
-### deal2lkit Installation procedure
-Follow the detailed [instruction](https://https://github.com/mathLab/deal2lkit) to install deal2lkit.
-
-
 ### pi-BEM Installation procedure
 
 Then you can clone the repository and compile it
 
-	git clone https://github.com/mathLab/pi-BEM.git
-	cd pi-BEM
-	mkdir build
-	cd build
-	cmake ../
-	make -j4
+ git clone <https://github.com/mathLab/pi-BEM.git>
+ cd pi-BEM
+ mkdir build
+ cd build
+ cmake ../
+ make -j4
 
-After you have compiled your application, you can run 
+After you have compiled your application, you can run
 
-	make test
+ make test
 
 or
-	
-	ctest 
+
+ ctest
 
 to start the testsuite.
 
 Take a look at
-https://www.dealii.org/developer/developers/testsuite.html for more
+<https://www.dealii.org/developer/developers/testsuite.html> for more
 information on how to create tests and add categories of tests.
 
 If you want you can run a preliminary execution in the build library typing
-	
-	mpirun -np 1 bem_fma_2d
-	
-this will automatically generate the parameter file for the bi-dimensional run while 
 
-	mpirun -np 1 bem_fma_3d
-	
+ mpirun -np 1 bem_fma_2d
+
+this will automatically generate the parameter file for the bi-dimensional run while
+
+ mpirun -np 1 bem_fma_3d
+
 will create a proper parameter file for a 3 dimensional simulation.
 
 # Notice to developers
@@ -165,34 +159,28 @@ Before making a pull request, please make sure you run the script
 
     ./scripts/indent
 
-from the base directory of this project, to ensure that no random 
+from the base directory of this project, to ensure that no random
 white space changes are inserted in the repository.
 
-The script requires Artistic Style Version 2.04 (astyle) to work 
-properly.
+The script requires `clang-format` version 16.0.6 to work properly.
 
 # Cite this work
 
 If you use this software, please consider citing the following work:
 
-	@article{GiulianiMolaHeltai2018,
-	 doi = {10.1016/j.advengsoft.2018.03.008},
-	 url = {https://doi.org/10.1016/j.advengsoft.2018.03.008},
-	 year  = {2018},
-	 month = {jul},
-	 publisher = {Elsevier {BV}},
-	 volume = {121},
-	 pages = {39--58},
-	 author = {Nicola Giuliani and Andrea Mola and Luca Heltai},
-	 title = {$\uppi$ - {BEM} : A flexible parallel implementation for adaptive,  geometry aware,  and high order boundary element methods},
-	 journal = {Advances in Engineering Software}
-	 }
-
-
-
-#Licence
+ @article{GiulianiMolaHeltai2018,
+  doi = {10.1016/j.advengsoft.2018.03.008},
+  url = {<https://doi.org/10.1016/j.advengsoft.2018.03.008}>,
+  year  = {2018},
+  month = {jul},
+  publisher = {Elsevier {BV}},
+  volume = {121},
+  pages = {39--58},
+  author = {Nicola Giuliani and Andrea Mola and Luca Heltai},
+  title = {$\uppi$ - {BEM} : A flexible parallel implementation for adaptive,  geometry aware,  and high order boundary element methods},
+  journal = {Advances in Engineering Software}
+  }
+
+# Licence
 
 Please see the file [LICENSE](https://github.com/mathLab/pi-BEM/blob/master/LICENSE) for details
-
-
-

VERSION

@@ -1 +1 @@
-9.5.0
+9.6.0

docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM dealii/dealii:v9.5.0-jammy
+FROM dealii/dealii:v9.6.0-jammy
 
 # pi-BEM master image
 RUN git clone https://github.com/mathLab/pi-BEM/ &&\

include/bem_fma.h

@@ -98,10 +98,10 @@ class BEMFMA : public ParameterAcceptor
   /// Mapping in the BEMFMA class. It also sets up some useful vector for,
   /// mixed boundary conditions and double nodes handling.
   void
-  init_fma(const DoFHandler<dim - 1, dim> &                      input_dh,
+  init_fma(const DoFHandler<dim - 1, dim>                       &input_dh,
            const std::vector<std::set<types::global_dof_index>> &db_in,
-           const TrilinosWrappers::MPI::Vector &                 input_sn,
-           const Mapping<dim - 1, dim> &                         input_mapping =
+           const TrilinosWrappers::MPI::Vector                  &input_sn,
+           const Mapping<dim - 1, dim>                          &input_mapping =
              StaticMappingQ1<dim - 1, dim>::mapping,
            unsigned int quad_order      = 4,
            unsigned int sing_quad_order = 5);
@@ -173,8 +173,8 @@ class BEMFMA : public ParameterAcceptor
   multipole_matr_vect_products(
     const TrilinosWrappers::MPI::Vector &phi_values,
     const TrilinosWrappers::MPI::Vector &dphi_dn_values,
-    TrilinosWrappers::MPI::Vector &      matrVectProdN,
-    TrilinosWrappers::MPI::Vector &      matrVectProdD) const;
+    TrilinosWrappers::MPI::Vector       &matrVectProdN,
+    TrilinosWrappers::MPI::Vector       &matrVectProdD) const;
 
 
   // void compute_m2l_flags();
@@ -209,7 +209,7 @@ class BEMFMA : public ParameterAcceptor
   /// architectures.
   TrilinosWrappers::PreconditionILU &
   FMA_preconditioner(const TrilinosWrappers::MPI::Vector &alpha,
-                     AffineConstraints<double> &          c);
+                     AffineConstraints<double>           &c);
 
 protected:
   /// Three pointers to the problem parameters to be set equal to