Merge pull request #283 from FreeFem/release-v4.13

Release v4.13
FreeFem · Jun 30, 2023 · cfb7acc · cfb7acc
2 parents bf4b5ac + 01b5db4
commit cfb7acc
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Showing 231 changed files with 16,115 additions and 4,980 deletions.
diff --git a/.gitignore b/.gitignore
@@ -318,6 +318,7 @@ src/mpi/ffapi.cpp
 src/mpi/lg.tab.cpp
 src/mpi/mymain.cpp
 src/mpi/sansrgraph.cpp
+src/mpi/compositeFESpace.cpp
 *stamp-h
 *stamp-h1
 *test-driver

diff --git a/3rdparty/ff-petsc/Makefile b/3rdparty/ff-petsc/Makefile
@@ -61,15 +61,15 @@ endif
 ifeq ($(FFCMAKE),no)
 PETSC_DOWNLOAD := $(PETSC_DOWNLOAD) --download-cmake
 endif
-PETSC_DOWNLOAD_C := $(PETSC_DOWNLOAD_C) --download-htool
+PETSC_DOWNLOAD_C := $(PETSC_DOWNLOAD_C) --download-htool --download-htool-commit=946875d79d0036afb4dc2c0c13c165a607d830df
 ifeq ($(FF_generic_petsc), yes)
 FLAGS_MTUNE := -mtune=generic
 else
 FLAGS_MTUNE := -mtune=native
 endif
 unexport MAKEFLAGS
-COMMON_FLAGS := --with-debugging=0 COPTFLAGS='-O3 $(FLAGS_MTUNE)' CXXOPTFLAGS='-O3 $(FLAGS_MTUNE)' FOPTFLAGS='-O3 $(FLAGS_MTUNE)' --with-cxx-dialect=11 --with-ssl=0 --with-x=0 --with-fortran-bindings=0 --with-cudac=0 \
-		--download-slepc --download-hpddm --download-slepc-commit=d9df183c341775ffc91510ec6827e13db44a25cd
+COMMON_FLAGS := --with-debugging=0 COPTFLAGS='-O3 $(FLAGS_MTUNE)' CXXOPTFLAGS='-O3 $(FLAGS_MTUNE)' FOPTFLAGS='-O3 $(FLAGS_MTUNE)' --with-ssl=0 --with-x=0 --with-fortran-bindings=0 --with-cudac=0 --with-tau-perfstubs=0 \
+		--download-slepc --download-hpddm
 
 ifneq ($(wildcard ~/.petsc_pkg),)
 COMMON_FLAGS += --with-packages-download-dir=~/.petsc_pkg
@@ -202,7 +202,7 @@ $(SRCDIR)/tag-make-real:$(SRCDIR)/tag-conf-real
 
 
 $(SRCDIR)/tag-install-real :$(SRCDIR)/tag-make-real
-	cd $(SRCDIR) && $(MAKE) PETSC_DIR=$(PETSC_DIR) PETSC_ARCH=fr install
+	cd $(SRCDIR) && $(MAKE) PETSC_DIR=$(PETSC_DIR) PETSC_ARCH=fr install-lib
 	cd $(SRCDIR) && $(MAKE) PETSC_DIR=$(PETSC_DIR) PETSC_ARCH=fr check
 	test -e $(DIR_INSTALL_REAL)/include/petsc.h
 	test -e $(DIR_INSTALL_REAL)/lib/petsc/conf/petscvariables
@@ -234,7 +234,7 @@ $(SRCDIR)/tag-make-complex:$(SRCDIR)/tag-conf-complex Make-petsc-download.mk
 	touch $@
 
 $(SRCDIR)/tag-install-complex :$(SRCDIR)/tag-make-complex
-	cd $(SRCDIR) && $(MAKE) PETSC_DIR=$(PETSC_DIR) PETSC_ARCH=fc install
+	cd $(SRCDIR) && $(MAKE) PETSC_DIR=$(PETSC_DIR) PETSC_ARCH=fc install-lib
 	test -e $(DIR_INSTALL_COMPLEX)/include/petsc.h
 	touch $@
 WHERE-complex:../lib/WHERE.PETSc-complex ../lib/WHERE.SLEPc-complex
@@ -332,8 +332,8 @@ echo:
 	@echo " # need sudo if '$(W_SUDO)' == 'sudo' .."
 
 install-destdir:
-	cd $(SRCDIR) && $(MAKE) PETSC_DIR=$(PETSC_DIR) PETSC_ARCH=fr install DESTDIR=$(DESTDIR)
-	cd $(SRCDIR) && $(MAKE) PETSC_DIR=$(PETSC_DIR) PETSC_ARCH=fc install DESTDIR=$(DESTDIR)
+	cd $(SRCDIR) && $(MAKE) PETSC_DIR=$(PETSC_DIR) PETSC_ARCH=fr install-lib DESTDIR=$(DESTDIR)
+	cd $(SRCDIR) && $(MAKE) PETSC_DIR=$(PETSC_DIR) PETSC_ARCH=fc install-lib DESTDIR=$(DESTDIR)
 
 .NOTPARALLEL:
 # Local Variables:

diff --git a/3rdparty/ff-petsc/petsc-cmake-seq.patch b/3rdparty/ff-petsc/petsc-cmake-seq.patch
@@ -1,8 +1,7 @@
-diff --git a/config/BuildSystem/config/packages/SuperLU.py b/config/BuildSystem/config/packages/SuperLU.py
-index 217743097e..239ac7806d 100644
---- a/config/BuildSystem/config/packages/SuperLU.py
-+++ b/config/BuildSystem/config/packages/SuperLU.py
-@@ -52,5 +52,12 @@ class Configure(config.package.CMakePackage):
+diff --color -Naur petsc-3.19.0-p1/config/BuildSystem/config/packages/SuperLU.py petsc-3.19.0/config/BuildSystem/config/packages/SuperLU.py
+--- petsc-3.19.0-p1/config/BuildSystem/config/packages/SuperLU.py	2023-04-02 13:47:03
++++ petsc-3.19.0/config/BuildSystem/config/packages/SuperLU.py	2023-04-02 13:46:38
+@@ -52,5 +52,11 @@
        if item.find('CMAKE_C_FLAGS') >= 0 or item.find('CMAKE_CXX_FLAGS') >= 0:
          args[place]=item[:-1]+' '+mangledef+'"'
 
@@ -12,14 +11,12 @@ index 217743097e..239ac7806d 100644
 +        args = self.rmArgsStartsWith(args,['-DCMAKE_CXX_COMPILER','-DCMAKE_C_COMPILER'])
 +        args.append('-DCMAKE_C_COMPILER="'+mpicc.split(None, 1)[0]+'"')
 +        args.append('-DCMAKE_CXX_COMPILER="'+mpicxx.split(None, 1)[0]+'"')
-+
      return args
 
-diff --git a/config/BuildSystem/config/packages/metis.py b/config/BuildSystem/config/packages/metis.py
-index b2d66ab23f..08219fb317 100644
---- a/config/BuildSystem/config/packages/metis.py
-+++ b/config/BuildSystem/config/packages/metis.py
-@@ -41,6 +41,12 @@ class Configure(config.package.CMakePackage):
+diff --color -Naur petsc-3.19.0-p1/config/BuildSystem/config/packages/metis.py petsc-3.19.0/config/BuildSystem/config/packages/metis.py
+--- petsc-3.19.0-p1/config/BuildSystem/config/packages/metis.py	2023-04-02 13:47:03
++++ petsc-3.19.0/config/BuildSystem/config/packages/metis.py	2023-04-02 13:46:38
+@@ -44,6 +44,12 @@
      if self.framework.argDB['download-metis-use-doubleprecision']:
        args.append('-DMETIS_USE_DOUBLEPRECISION=1')
      args.append('-DMATH_LIB="'+self.libraries.toStringNoDupes(self.mathlib.lib)+'"')
@@ -32,26 +29,26 @@ index b2d66ab23f..08219fb317 100644
      return args
 
    def configureLibrary(self):
-diff --git a/config/BuildSystem/config/packages/mmg.py b/config/BuildSystem/config/packages/mmg.py
-index dc8ce9817f..4ba1aec2f6 100644
---- a/config/BuildSystem/config/packages/mmg.py
-+++ b/config/BuildSystem/config/packages/mmg.py
-@@ -28,4 +28,10 @@ class Configure(config.package.CMakePackage):
+diff --color -Naur petsc-3.19.0-p1/config/BuildSystem/config/packages/mmg.py petsc-3.19.0/config/BuildSystem/config/packages/mmg.py
+--- petsc-3.19.0-p1/config/BuildSystem/config/packages/mmg.py	2023-04-02 13:47:03
++++ petsc-3.19.0/config/BuildSystem/config/packages/mmg.py	2023-04-02 13:46:38
+@@ -28,6 +28,12 @@
      args.append('-DUSE_VTK=OFF')
-     args.append('-DUSE_POINTMAP=ON')
+     args.append('-DMMG_INSTALL_PRIVATE_HEADERS=ON')
      args.append('-DSCOTCH_DIR:STRING="'+self.ptscotch.directory+'"')
 +    mpicc = self.framework.getMakeMacro('MPICC_SHOW')
 +    mpicxx = self.framework.getMakeMacro('MPICXX_SHOW')
 +    if mpicc and mpicxx:
 +        args = self.rmArgsStartsWith(args,['-DCMAKE_CXX_COMPILER','-DCMAKE_C_COMPILER'])
 +        args.append('-DCMAKE_C_COMPILER="'+mpicc.split(None, 1)[0]+'"')
 +        args.append('-DCMAKE_CXX_COMPILER="'+mpicxx.split(None, 1)[0]+'"')
-     return args
-diff --git a/src/mat/impls/aij/mpi/mumps/mumps.c b/src/mat/impls/aij/mpi/mumps/mumps.c
-index 01bbe45a39b..6b050057ccf 100644
---- a/src/mat/impls/aij/mpi/mumps/mumps.c
-+++ b/src/mat/impls/aij/mpi/mumps/mumps.c
-@@ -1860,11 +1860,7 @@ PetscErrorCode MatSetFromOptions_MUMPS(Mat F, Mat A) {
+     if self.getDefaultIndexSize() == 64:
+       int64_t = '''
+ #if !(defined(PETSC_HAVE_STDINT_H) && defined(PETSC_HAVE_INTTYPES_H) && defined(PETSC_HAVE_MPI_INT64_T))
+diff --color -Naur petsc-3.19.0-p1/src/mat/impls/aij/mpi/mumps/mumps.c petsc-3.19.0/src/mat/impls/aij/mpi/mumps/mumps.c
+--- petsc-3.19.0-p1/src/mat/impls/aij/mpi/mumps/mumps.c	2023-04-02 13:46:55
++++ petsc-3.19.0/src/mat/impls/aij/mpi/mumps/mumps.c	2023-04-02 13:46:45
+@@ -1889,11 +1889,7 @@
       see https://github.com/pmodels/mpich/issues/5589. This bug was fixed by https://github.com/pmodels/mpich/pull/5590.
       In short, we could not use distributed RHS with MPICH until v4.0b1.
     */
@@ -63,34 +60,50 @@ index 01bbe45a39b..6b050057ccf 100644
    PetscCall(PetscOptionsMUMPSInt("-mat_mumps_icntl_20", "ICNTL(20): give mumps centralized (0) or distributed (10) dense right-hand sides", "None", mumps->ICNTL20, &mumps->ICNTL20, &flg));
    PetscCheck(!flg || mumps->ICNTL20 == 10 || mumps->ICNTL20 == 0, PETSC_COMM_SELF, PETSC_ERR_SUP, "ICNTL(20)=%d is not supported by the PETSc/MUMPS interface. Allowed values are 0, 10", (int)mumps->ICNTL20);
  #if PETSC_PKG_MUMPS_VERSION_LT(5, 3, 0)
-diff --git a/config/BuildSystem/config/packages/PTScotch.py b/config/BuildSystem/config/packages/PTScotch.py
-index 5a46e581fd2..bc7535eb449 100644
---- a/config/BuildSystem/config/packages/PTScotch.py
-+++ b/config/BuildSystem/config/packages/PTScotch.py
-@@ -32,12 +32,16 @@ class Configure(config.package.Package):
+diff --color -Naur petsc-3.19.0-p1/config/BuildSystem/config/packages/PTScotch.py petsc-3.19.0/config/BuildSystem/config/packages/PTScotch.py
+--- petsc-3.19.0-p1/config/BuildSystem/config/packages/PTScotch.py	2023-04-02 13:47:03
++++ petsc-3.19.0/config/BuildSystem/config/packages/PTScotch.py	2023-04-02 13:46:38
+@@ -9,6 +9,8 @@
+     self.download         = ['git://https://gitlab.inria.fr/scotch/scotch.git',
+                              'https://gitlab.inria.fr/scotch/scotch/-/archive/'+self.gitcommit+'/scotch-'+self.gitcommit+'.tar.gz',
+                              'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/scotch-'+self.gitcommit+'.tar.gz']
++    self.download_macos   = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v6.1.2/scotch-v6.1.2.tar.gz',
++                             'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/scotch-v6.1.2.tar.gz']
+     self.downloaddirnames = ['scotch','petsc-pkg-scotch']
+     self.liblist          = [['libptesmumps.a','libptscotchparmetisv3.a','libptscotch.a','libptscotcherr.a','libesmumps.a','libscotch.a','libscotcherr.a'],['libptesmumps.a','libptscotchparmetis.a','libptscotch.a','libptscotcherr.a','libesmumps.a','libscotch.a','libscotcherr.a'],
+                              ['libptesmumps.a','libptscotchparmetis.a','libptscotch.a','libptscotcherr.a','libesmumps.a','libscotch.a','libscotcherr.a']]
+@@ -30,13 +32,18 @@
      self.odeps          = [self.pthread,self.zlib,self.bison]
      return
 
 +  def configureLibrary(self):
 +    if not self.bison.haveBison3plus:
-+      self.download = self.download_mingw
++      self.download = self.download_macos
 +    config.package.Package.configureLibrary(self)
 +
    def Install(self):
      import os
 
-     self.programs.getExecutable('flex', getFullPath = 1)
+     if not hasattr(self.programs, 'flex'):
+       self.programs.getExecutable('flex', getFullPath = 1)
      if not hasattr(self.programs, 'flex'): raise RuntimeError('PTScotch needs flex installed')
 -    if not self.bison.found or not self.bison.haveBison3plus: raise RuntimeError('PTScotch needs Bison version 3.0 or above, use --download-bison')
++    if not self.bison.found: raise RuntimeError('PTScotch needs Bison, use --download-bison')
 
      self.log.write('Creating PTScotch '+os.path.join(os.path.join(self.packageDir,'src'),'Makefile.inc')+'\n')
 
-@@ -94,7 +98,7 @@ class Configure(config.package.Package):
+@@ -93,8 +100,12 @@
      g.write('MKDIR    = '+self.programs.mkdir+'\n')
      g.write('MV       = '+self.programs.mv+'\n')
      g.write('RANLIB   = '+self.setCompilers.RANLIB+'\n')
--    if self.setCompilers.isMINGW(self.framework.getCompiler(), self.log):
-+    if self.setCompilers.isMINGW(self.framework.getCompiler(), self.log) or not self.bison.haveBison3plus:
-       g.write('LEX      = '+self.programs.flex+'\n')
-       g.write('YACC     = '+getattr(self.bison,self.bison.executablename)+' -y\n')
-     else:
+-    g.write('FLEX     = '+self.programs.flex+'\n')
+-    g.write('BISON    = '+getattr(self.bison,self.bison.executablename)+' -y\n')
++    if not self.bison.haveBison3plus:
++      g.write('LEX      = '+self.programs.flex+'\n')
++      g.write('YACC     = '+getattr(self.bison,self.bison.executablename)+' -y\n')
++    else:
++      g.write('FLEX     = '+self.programs.flex+'\n')
++      g.write('BISON    = '+getattr(self.bison,self.bison.executablename)+' -y\n')
+     g.close()
+
+     self.popLanguage()
diff --git a/3rdparty/getall b/3rdparty/getall
@@ -171,26 +171,26 @@ download('parmmg','https://github.com/prj-/ParMmg/archive/9cb2f7a22ef590d196d028
         'https://github.com/prj-',
         'parmmg.zip',
         '32035de70272121137c0869e8c49e4bd');
-download('PETSc','https://www.mcs.anl.gov/petsc/mirror/release-snapshots/petsc-3.18.2.tar.gz',
+download('PETSc','https://www.mcs.anl.gov/petsc/mirror/release-snapshots/petsc-3.19.2.tar.gz',
 	'https://www.mcs.anl.gov/petsc/mirror/release-snapshots/',
-	'petsc-3.18.2.tar.gz',
-	'6562062a0666ccb3f07a5db3dedcb9e4');
+	'petsc-3.19.2.tar.gz',
+	'9d53f784ca2ab37bf25b7991ceefa1d9');
 
-download('htool','https://github.com/htool-ddm/htool/archive/b6e91690f8d7c20d67dfb3b8db2e7ea674405a37.zip',
+download('htool','https://github.com/htool-ddm/htool/archive/946875d79d0036afb4dc2c0c13c165a607d830df.zip',
 		'https://github.com/htool-ddm/',
 		'htool.zip',
-		'ca726483c442a3eca6522c1c69cee76f');
+		'1403db4800a2d4b69f3da7eb3f6687a2');
 
 
 download('hpddm','https://codeload.github.com/hpddm/hpddm/zip/7113b9a6b77fceee3f52490cb27941a87b96542f',
 	'https://codeload.github.com/hpddm',
 	'hpddm.zip',
 	'6910b7b974f0b60d9c247c666e7f3862');
 
-download('bemtool','https://github.com/PierreMarchand20/BemTool/archive/6042818bd7585a1ba01c1fc8889dc27f9e608a3f.zip',
+download('bemtool','https://github.com/PierreMarchand20/BemTool/archive/435b9d8ea86228b9ec4b526fc915aa35a7a8bec6.zip',
 	'https://github.com/PierreMarchand20/BemTool',
 	'bemtool.zip',
-	'1ee3a9eea2451314dcbb0a3ebd6c6be3');
+	'3f9c95580efeb4d2b8f1fa977f7fd395');
 
 download('Boost','https://www.ljll.math.upmc.fr/~tournier/boost_for_bemtool.tar.gz',
 	'https://www.boost.org',

diff --git a/AutoGeneratedFile.tar.gz b/AutoGeneratedFile.tar.gz
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,70 @@
 # Changelog
 All notable changes to this project will be documented in this file.
 
+## [4.13]
+
+### Added
+
+- Composite FE spaces and variational forms for coupled problems:
+  - can now define composite FE spaces with different meshes/mesh types as
+    ```
+    fespace Uh(Th1,[P2,P2]);
+    fespace Ph(Th2,P1);
+    fespace Vh=Uh*Ph;
+    ```
+  - can define coupled problems using composite FE spaces, or directly with `<` `>` syntax:
+    ```
+    fespace Uh(Th1,[P2,P2]);
+    fespace Ph(Th2,P1);
+    Uh [u1,u2],[v1,v2];
+    Ph p,q;
+
+    solve Pb (<[u1,u2],[p]>, <[v1,v2],[q]>) = ...
+    ```
+    see `examples/examples/stokes_composite.edp` and `examples/examples/stokes_periodic_composite.edp`
+  - this new type of composite problem can be used for FEM-BEM coupling and also benefits from automatic parallel assembly (in test) and can be easily solved using the distributed solver MUMPS, see `examples/bem/Helmholtz-2d-FEM-BEM-coupling-MUMPS-composite.edp`
+  - composite problems can also be solved using PETSc (in test), see `examples/hpddm/Helmholtz-2d-FEM-BEM-coupling-PETSc-composite.edp`
+
+- remove spurious cout in Curve/Line DG definition.
+
+- add New Finite element 2d on mesh :  RT0dc (discontinios RT0 ) in plugin Element_Mixte
+      	see example plugin/RT0dc.edp 
+  and P1nc (Crouziex-Raviat) + bulle : name P1bnc in plugin Element_P1ncdc
+  and P1nc totaly discontinous + bulle  ; name P1bdcnc in plugin Element_P1ncdc
+      	see example plugin/example testp1dcnc.edp
+	for akram.beni-hamad@inria.fr 
+- add New finite element:  P4S P^4 on meshS , P3pnc3d in Element_P3pnc_3d (Couziex-Raviart with P3 )
+   see loic.balaziatchynillama@cea.fr for more information. 
+- add new interface for metis (see examples/plugin/metis.edp)
+- Correct jump, mean, otherside of finite element function on mesh3, meshS, meshL 
+   (add missing code in method: MeshPoint::SetAdj()  thanks to zuqi.tang@univ-lille.fr)  
+-  try to build dmg install mac version 
+-  add  file script to build meshS from boundary meshL TL if the boundary is
+    the graph of function from  mean plane. see example in examples/3dSurf/buildmeshS.edp
+    meshS Ts=buildmeshSminsurf(TL,1);// minimal surface
+    meshS Tsl=buildmeshSLap(TL,1);//  Laplace Surface ..
+    meshS Tsl=buildmesh(TL,1,op);// op = 0 Lap and op =1 => minsurf. 
+- add sparse block to sparse  matrix 
+  matrix A = va(Vh,Vh);
+  matrix B(A.n*5,A.n*5);
+  int i=2;
+  B.add(1.+10*i,A,i*ndof,i*ndof); 
+### Changed
+-  change  isoline to do the job for meshS, see example plugin/isoline.edp
+-  change  Curve function to be with 3 components to use the isoline data.
+-  change  Curvature plugin to compatible with new isoline data for 3 d case.
+-  change some sprintf in snprint to remove warning 
+
+### Deprecated
+
+### Removed
+
+### Fixed
+- bug in all P0face, P0edge, P0VF on mesh3,meshS, MeshL  and also discontinous  version (missing  initialisation)
+- bug in  plot function and ffglut with parameter pdf="file.pdf" , because shift in plot named parameter not change in ffglut.
+- genere a bug if zero size element in read MeshL from file. 
+- remove  mistake when the border is badly defined , remove empty element in buildmeshL function. 
+- bug in array quadrature FE.
 ## [4.12]
 ### Added
 - add new finite Element P2pnc3d of Stokes problem like Crouzeix-Raviard in 3d of P2 pylynome (see G. Allaire or loic.balaziatchynillama@cea.fr
@@ -39,7 +103,7 @@ All notable changes to this project will be documented in this file.
 
 - New 1d finite element P3 hermite (C1) finite element in plugin `Element_P3` 
 	meshL Th=segment(1,[x*L,0,0]); fespace Vh(Th,P3HL);
-	see exemple end of exemple plugin/testFE-P3
+	see example end of example plugin/testFE-P3
 - missing new 1d finite element P4 in plugin `Elemnt_P4`
 - plugin `plugin/seq/MatrixMarket.cpp`  to read and save matrix in MatrixMarket and add also a binary form 
      (see examples/plugin/MatrixMarket.edp test)
@@ -71,7 +135,7 @@ All notable changes to this project will be documented in this file.
 - add R3 Th.be(k)[i].P  to  get the point (R3)  of boundary vertices
 - add R3 Th.be(k).measure to  get the measure of the boundary elment 
 - add projection  function to a mesh , meshL, MeshS or  mesh3 with return a R3 point 
-- see new example dist-projection.edp example in exemples 
+- see new example dist-projection.edp example in examples 
 - add dxx, dyy, dzz, dxy,  .. on P2L finite element 
 - add tools to compute solid angle :  let R3 O; a given point, Th3 a mesh3 and ThS a meshS. 
      solidangle(O,Th3.be(ke)) // triangular face is the boundary face 
@@ -541,6 +605,7 @@ All notable changes to this project will be documented in this file.
 - The main distribution is now on Github
 
 [Unreleased]: https://github.com/FreeFem/FreeFem-sources/compare/v4.12..develop
+[4.13]: https://github.com/FreeFem/FreeFem-sources/compare/v4.12..v4.13
 [4.12]: https://github.com/FreeFem/FreeFem-sources/compare/v4.11..v4.12
 [4.11]: https://github.com/FreeFem/FreeFem-sources/compare/v4.10..v4.11
 [4.10]: https://github.com/FreeFem/FreeFem-sources/compare/v4.9..v4.10