merge develop

3rdparty/getall

@@ -171,10 +171,10 @@ download('parmmg','https://github.com/prj-/ParMmg/archive/9cb2f7a22ef590d196d028
         'https://github.com/prj-',
         'parmmg.zip',
         '32035de70272121137c0869e8c49e4bd');
-download('PETSc','https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-3.20.2.tar.gz',
+download('PETSc','https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-3.20.3.tar.gz',
 	'https://web.cels.anl.gov/projects/petsc/download/release-snapshots/',
-	'petsc-3.20.2.tar.gz',
-	'1e170a5f096433ca21aa643c80c749eb');
+	'petsc-3.20.3.tar.gz',
+	'6308a8c0811f8bfaf4b6c71577d3f2d4');
 
 download('htool','https://github.com/htool-ddm/htool/archive/946875d79d0036afb4dc2c0c13c165a607d830df.zip',
 		'https://github.com/htool-ddm/',

3rdparty/mmg/Makefile

@@ -27,7 +27,7 @@ FAIT.done:tag-tar
 	cd build && cmake ../mmg-sources \
 	-DCMAKE_C_COMPILER=$(CC) \
 	-DCMAKE_C_FLAGS="$(CFLAGS) -fPIC" \
-	-DCMAKE_CXX_COMPILER=$(CXX) \
+	-DCMAKE_CXX_COMPILER="$(CXX)" \
 	-DCMAKE_CXX_FLAGS="$(CXXFLAGS) $(CXX11FLAGS) -fPIC" \
 	-DM_LIB="-lm" -DUSE_ELAS=OFF -DUSE_VTK=OFF \
 	-DSCOTCH_DIR=$(scotch_dir) \

CHANGELOG.md

@@ -27,7 +27,8 @@ All notable changes to this project will be documented in this file.
 
 ### Added
 
--
+- interface with functional interface with fgmres (Linear and affine) in real and complex case
+  see tutorial/algo.edp
 
 ### Changed
 
@@ -43,9 +44,11 @@ All notable changes to this project will be documented in this file.
 
 ### Fixed
 
-- ***
-
----
+- correct hidden faces on surface mesh (ffglut)
+- remove optimisation flag ppm2rnm.cpp in macos (load trap)
+- correct abcisse curviline on reparametrage function (setcurveabcisse) in load "Curvature"
+- correct compilation on ARM sonoma xcode 15.2
+- correct mpi essai.edp MPI_ANY_SOURCE Pb.
 
 ## [4.14]
 

Makefile.am

@@ -285,15 +285,16 @@ install-exec-local:: bin/script/PostInstall.sh FreeFEM-documentation.pdf
 	tar cvf - $(FF_EXAMPLES_FILES)| (cd "$(DESTDIR)$(pkgdatadir)/$(VERSION)"; tar xvf -)
 	$(INSTALL_SCRIPT) examples/CheckAll examples/CheckAllEdp "$(DESTDIR)$(pkgdatadir)/$(VERSION)"
 	$(mkinstalldirs) -m 755 "$(DESTDIR)${bindir}"
-	test ! -s FreeFEM-documentation.pdf || $(INSTALL_DATA) FreeFEM-documentation.pdf "$(DESTDIR)$(pkgdatadir)" 
-	test `uname` != Darwin || $(INSTALL_SCRIPT) FreeFem++-CoCoa "$(DESTDIR)${bindir}"
-	test `uname` != Darwin || echo "$(bindir)" > "$(DESTDIR)/etc/paths.d/FreeFem++"
-	test `uname` != Darwin || ( rm "$(DESTDIR)/usr/local/bin/FreeFem++-CoCoa"; $(INSTALL_SCRIPT) FreeFem++-CoCoa "$(DESTDIR)/usr/local/bin" )
-	test `uname` != Darwin || ( $(MAKE) FreeFem++.app.tgz; test -d "$(DESTDIR)/Applications" || mkdir -p "$(DESTDIR)/Applications"; tar zxf FreeFem++.app.tgz -C "$(DESTDIR)/Applications" )
-	test `uname` != Darwin || ( $(MAKE) bin/movefortranlib )
 	$(mkinstalldirs) -m 755 "$(DESTDIR)$(ff_prefix_dir)/idp"
 	cd idp; for i in *.idp; do \
 		if [ -f $$i ]; then $(INSTALL) -m 555 $$i "$(DESTDIR)$(ff_prefix_dir)/idp"; fi; done
+	test ! -s FreeFEM-documentation.pdf || $(INSTALL_DATA) FreeFEM-documentation.pdf "$(DESTDIR)$(pkgdatadir)" 	
+	test `uname` != Darwin || ( rm "$(DESTDIR)/usr/local/bin/FreeFem++-CoCoa"; $(INSTALL_SCRIPT) FreeFem++-CoCoa "$(DESTDIR)/usr/local/bin" )		
+	test `uname` != Darwin || $(INSTALL_SCRIPT) FreeFem++-CoCoa "$(DESTDIR)${bindir}"
+#    need sudo ...	
+#winDssSSs	test `uname` != Darwin || echo "$(bindir)" > "$(DESTDIR)/etc/paths.d/FreeFem++"
+#	test `uname` != Darwin || ( $(MAKE) FreeFem++.app.tgz; test -d "$(DESTDIR)/Applications" || mkdir -p "$(DESTDIR)/Applications"; tar zxf FreeFem++.app.tgz -C "$(DESTDIR)/Applications" )
+#	test `uname` != Darwin || ( $(MAKE) bin/movefortranlib )
 
 bin/script/PostInstall.sh:./Makefile bin/script/PostInstall.m4
 	m4 "-DFF__FVER=$(PACKAGE_VERSION)" "-DFF_BINDIR=$(bindir)" "-DFF__DATADIR=$(pkgdatadir)" bin/script/PostInstall.m4 > bin/script/PostInstall.sh

bin/Get-list-dylib-use

@@ -9,8 +9,8 @@
 #	  egrep '.dylib$'| sort -u \
 #|awk -F/ '{ if (f[$NF]!=1 ) print $0;  f[$NF]=1;}'
 (
-(echo export DYLD_PRINT_LIBRARIES=1;ls plugin/seq/*.dylib|grep -v fflapack| awk '{print "src/nw/FreeFem++ -check_plugin ",$0}' )|sh 2>&1|awk '$1 ~ /dyld\[[0-9]*\]/ {print $3}'| sort -u
-(echo export DYLD_PRINT_LIBRARIES=1;ls plugin/mpi/*.dylib|grep -v fflapack| awk '{print "src/mpi/FreeFem++-mpi -check_plugin ",$0}' )|sh 2>&1|awk '$1 ~ /dyld\[[0-9]*\]/  {print $3}'| sort -u
+(echo export DYLD_PRINT_LIBRARIES=1;ls plugin/seq/*.dylib|grep -v fflapack| awk '{print "src/nw/FreeFem++ -check_plugin ",$0}' )|sh 2>&1|awk '$1 ~ /dyld:/ {print $4}'| sort -u
+(echo export DYLD_PRINT_LIBRARIES=1;ls plugin/mpi/*.dylib|grep -v fflapack| awk '{print "src/mpi/FreeFem++-mpi -check_plugin ",$0}' )|sh 2>&1|awk '$1 ~ /dyld:/  {print $4}'| sort -u
 )| sort -u | grep .dylib > etc/list-dylib
 
 egrep -v '/usr/lib/|/System/|./plugin/' etc/list-dylib >etc/list-dylib-no-os

bin/compile-version-MacOS

@@ -7,7 +7,11 @@ nameopt=
 export dirdmgpkg=
 case $3 in
 *generic*) optionconf+=--enable-generic;;
+esac
+case $3 in
 *debug*) optionconf+=--enable-debug;nameopt+=-g;;
+esac
+case $3 in
 *optim*) optionconf+=--enable-optim;nameopt+=-O;;
 esac
 
@@ -74,6 +78,7 @@ rm -rf $fftmp
 )
 brewlibgfortran=`grep gfortran $prefix/gnu/list-dylib-gfortran` 
 brewlibquadmath=`grep libquadmath $prefix/gnu/list-dylib-gfortran` 
+brewlibgcc_s=`grep libgcc_s $prefix/gnu/list-dylib-gfortran` 
 ( 
 cd  $(dirname $brewlibgfortran)
 cp -f libgfortran.5.dylib libquadmath.0.dylib libgcc_s.1.1.dylib $prefix/gnu/
@@ -91,6 +96,8 @@ dirlibgfortranold=$(dirname $brewlibgfortran)
 dirlibgfortrannew=$prefix/gnu
 libgfortrandylib=$(basename $brewlibgfortran)
 libquadmathdylib=$(basename $brewlibquadmath)
+libgccsdylib=$(basename $brewlibgcc_s)
+echo2 dylibfort : $libgfortrandylib $libquadmathdylib $libgccsdylib
 cd - 
 test -d pkg || mkdir -v pkg 
 (
@@ -174,9 +181,10 @@ echo2 ================================
 tmpdylib=/tmp/dylib-ff-$$.txt
 tmplst=/tmp/otool-ff-$$.txt
 echo2 find $dirpkg/$prefix -name '*.dylib' 
-echo2 .. $changedylibgfortran $dirlibgfortranold $dirlibgfortrannew $libgfortrandylib $libquadmathdylib 
+echo2 ... $changedylibgfortran $dirlibgfortranold $dirlibgfortrannew $libgfortrandylib $libquadmathdylib $libgccsdylib
+echo2 ... $libgccsdylib
 find $dirpkg/$prefix -name '*.dylib' > $tmpdylib
- $changedylibgfortran $dirlibgfortranold $dirlibgfortrannew $libgfortrandylib $libquadmathdylib `cat $tmpdylib`
+ $changedylibgfortran $dirlibgfortranold $dirlibgfortrannew $libgfortrandylib $libquadmathdylib $libgccsdylib `cat $tmpdylib`
  ## verification 
  echo2 dylib to brew in installation for debug !!!! 
  cat $tmpdylib| xargs otool -L | egrep -i 'brew|/opt/' ||echo2 OK 
@@ -188,14 +196,13 @@ echo2 ================================
 
 
 test -d /tmp/$dirdmgpkg || ( 
-mkdir /tmp/$dirdmgpkg
+mkdir /tmp/$dirdmgpkg )
 cd /tmp/$dirdmgpkg
-mv $dirpkg/Applications/FreeFem++.app  /tmp/$dirdmgpkg
+rsync -av $dirpkg/Applications/FreeFem++.app  /tmp/$dirdmgpkg
 cp $dirscript/script/Install-app.sh /tmp/$dirdmgpkg
 fftestedp=`find . -name Laplace.edp`
 sed -e "s/@VV@/$ver/" -e "s%@APPFF@%$dirdmgpkg%" -e s%@FFTEST@%$fftestedp% <$dirscript/script/README.md.in  > README.md
 
-)
 cp $dirscript/script/Install-app.sh /tmp/$dirdmgpkg
 
 exec 1>&3 # save log is closo $LOG

bin/script/Install-app.sh

@@ -95,5 +95,5 @@ vvv=`$dirff/FreeFem++ -nw| grep 'version'| wc -l`
 if [ $vvv -eq 0 ]; then
   echo Error missing install missing lib or quarantine ?
 else
-	echo FreeFem++ work
+	echo FreeFem++ seems to work!
 fi

configure.ac

@@ -194,9 +194,11 @@ AM_MAINTAINER_MODE
 echo >config_LIB_INFO
 
 # Necessary compilers
-
+#  remove the flag -sdt=gnu++11 in the compileur CXX (FH jan 2024)
+ac_cv_prog_cxx_cxx11=no
 AC_PROG_CC
 AC_PROG_CXX
+#  echo " #### $CXX"
 AC_LANG(C++)
 if test `uname` != Darwin; then
  ff_ldeg="-Wl,--end-group"

etc/config/m4/WindowsPackage.m4

@@ -43,6 +43,7 @@ Name: "{app}\examples\eigen"; Permissions: everyone-full
 Name: "{app}\idp"; Permissions: everyone-full
 IFMPI Name: "{app}\examples\mpi"; Permissions: everyone-full
 IFMPI Name: "{app}\examples\hpddm"; Permissions: everyone-full
+IFMPI Name: "{app}\examples\ffddm"; Permissions: everyone-full
 
 ; PETSc
 IFPETSC Name: "{app}\ff-petsc"; Permissions: everyone-full

examples/examples/stokes_periodic_composite.edp

@@ -18,6 +18,8 @@ fespace Ph(Th,P1);
 
 fespace Vh=UhPerio*Uh*Ph; // definition of the composite FE space
 
+cout << "ndof = " << Vh.ndof << endl;
+
 UhPerio u1;
 Uh u2;
 Ph p;

examples/mpi/essai.edp

@@ -100,6 +100,7 @@ else if (mpirank==0) Irecv(processor(1,mpiCommWorld,rr),B[3]);
 mpiWait(rr);
 if (mpirank==0)  cout << " B3= " << B[3] << endl;
 if (mpirank==1)  cout << " A= " << A << endl;
+
 }
 
 // asyncronous  send/recv  messages....
@@ -128,7 +129,7 @@ if(mpirank==0)
   {
     for (int i=0;i<mpisize;++i)
       {
-	processor(-1) >> ww;  
+	processor(mpiAnySource) >> ww;  // correction jan 2024  mpiAnySource==-2 in mpich 
 	cout << " case " << i << "   " <<  ww[0] << endl ;
       }
   }

examples/plugin/splitmesh6.edp

@@ -1,7 +1,9 @@
 load "splitmesh6"
 mesh Th=square(5,5);
 mesh Th6=splitmesh6(Th);
+mesh Th6b=splitmesh6PowellSabin(Th);// Add for François Bouchut  feb 2024 
 plot(Th6,wait=1);
+plot(Th6b,wait=1);
 
 fespace Vh(Th,P1);
 fespace Nh(Th,P0);

examples/tutorial/algo.edp

@@ -1,8 +1,10 @@
 //  cleanning version 07/2008  FH in Sevilla.
+// VERSION 2024  avec FGMRES test ...  FH
 int nerr =0; 
 int debugJ =0; 
 int debugdJ =0; 
 real umax=0;
+//load "fgmres"
 {
  func  bool stop(int iter,real[int] u,real[int] g)	
 {
@@ -12,6 +14,7 @@ real umax=0;
   // minimisation of $J(u) = \frac12\sum (i+1) u_i^2 - b_i $	
   // work array 
   real[int] b(10),u(10); 
+  complex[int] cb(10),cu(10); 
 
   func real J(real[int] & u)
     {
@@ -21,8 +24,16 @@ real umax=0;
       if(debugJ) cout << "J ="<< s << " u =" <<  u[0] << " " << u[1] << "...\n" ;
       return s;
     }
-
-//  the grad of J (this is a affine version (the RHS is in  )
+    func complex cJ(complex[int] & u)
+      {
+        complex s=0;
+        for (int i=0;i<u.n;i++)
+  	s +=(i+1)*u[i]*u[i]*0.5 - b[i]*u[i];
+        if(debugJ) cout << "J ="<< s << " u =" <<  u[0] << " " << u[1] << "...\n" ;
+        return s;
+      }
+
+//  the grad of J (this	 is a affine version (the RHS is in  )
   func real[int] DJ(real[int] &u)
     { 
       for (int i=0;i<u.n;i++)
@@ -32,6 +43,15 @@ real umax=0;
       if(debugdJ) cout << "dJ-b ="<< " u =" <<  u[0] << " " << u[1] << " " << u[2]  << "...\n" ;	
       return u;  // return of global variable ok 
     };
+    func complex[int] cDJ(complex[int] &u)
+      { 
+        for (int i=0;i<u.n;i++)
+  	u[i]=(i+1)*u[i];
+        if(debugdJ) cout << "dJ0  ="<< " u =" <<  u[0] << " " << u[1] << " " << u[2]  << "...\n" ;	
+        u -= cb; 
+        if(debugdJ) cout << "dJ-b ="<< " u =" <<  u[0] << " " << u[1] << " " << u[2]  << "...\n" ;	
+        return u;  // return of global variable ok 
+      };
 
 // the grad of the bilinear part of J (the RHS in remove)
   func real[int] DJ0(real[int] &u)
@@ -50,7 +70,15 @@ real umax=0;
 	s += abs((i+1)*u[i] - b[i]);
    return s;    
    }
+   func real error(complex[int] & u,complex[int] & b)
+    {
+    real s=0;
+      for (int i=0;i<u.n;i++)
+ 	s += abs((i+1)*u[i] - b[i]);
+    return s;    
+    }
   func real[int] matId(real[int] &u) { return u;};
+  func complex[int] cmatId(complex[int] &u) { return u;};
   int verb=5; // verbosity of algo ..
   b=1. ; u=0.; // set  right hand side and initial gest
   LinearCG(DJ,u,eps=1.e-6,nbiter=20,precon=matId,verbosity=verb);
@@ -70,13 +98,25 @@ real umax=0;
   nerr += !(error(u,b) < 1e-5);
   if(nerr) cout << "    sol: "<< " u =" <<  u[0] << " " << u[1] << " " << u[2]  << "...\n" ;		
 
-
   b=1; u=0; // set  right hand side and initial gest
   AffineGMRES(DJ,u,eps=1.e-6,nbiter=20,precon=matId,verbosity=verb); // correct in version 3.11 
   cout << "LinearGMRES (Affine) : J(u) = " << J(u) << " err=" << error(u,b) << endl;
   nerr += !(error(u,b) < 1e-5);
   if(nerr) cout << "    sol: "<< " u =" <<  u[0] << " " << u[1] << " " << u[2]  << "...\n" ;		
 
+
+  b=1; u=0; // set  right hand side and initial gest
+  AffineFGMRES(DJ,u,eps=1.e-6,nbiter=20,precon=matId,verbosity=verb); // correct in version 3.11 
+  cout << "LinearFGMRES (Affine) : J(u) = " << J(u) << " err=" << error(u,b) << endl;
+  nerr += !(error(u,b) < 1e-5);
+  if(nerr) cout << "    sol: "<< " u =" <<  u[0] << " " << u[1] << " " << u[2]  << "...\n" ;		
+
+  cb=1; cu=0; // set  right hand side and initial gest
+  AffineFGMRES(cDJ,cu,eps=1.e-6,nbiter=20,verbosity=verb); // correct in version 3.11 
+  cout << "complex LinearFGMRES (Affine) : " << " err=" << error(cu,cb) << endl;
+  nerr += !(error(cu,cb) < 1e-5);
+  if(nerr) cout << "    sol: "<< " cu =" <<  cu[0] << " " << cu[1] << " " << cu[2]  << "...\n" ;		
+
   b=1; u=0; // set  right hand side and initial gest
   LinearGMRES(DJ0,u,b,eps=1.e-6,nbiter=20,precon=matId,verbosity=verb);
   cout << "LinearGMRES (Linear) : J(u) = " << J(u) << " err=" << error(u,b) << endl;

plugin/mpi/bem.cpp

@@ -795,8 +795,8 @@ AnyType SetOpHMatrixUser(Stack stack,Expression emat, Expression eop)
     ffassert(Vh);
     ffassert(Uh);
 
-    int n=Uh->NbOfDF;
-    int m=Vh->NbOfDF;
+    int m=Uh->NbOfDF;
+    int n=Vh->NbOfDF;
 
     HMatrixVirt<R>** Hmat =GetAny<HMatrixVirt<R>** >((*emat)(stack));
 
@@ -826,8 +826,8 @@ AnyType SetOpHMatrixUser(Stack stack,Expression emat, Expression eop)
 
     *Hmat =0;
 
-    vector<double> p1(3*n);
-    vector<double> p2(3*m);
+    vector<double> pt(3*n);
+    vector<double> ps(3*m);
     Fem2D::R3 pp;
     bemtool::R3 p;
     SRdHat pbs;
@@ -851,7 +851,7 @@ AnyType SetOpHMatrixUser(Stack stack,Expression emat, Expression eop)
     bool TP0 = TRdHat::d == 1 ? (Tnbv == 0) && (Tnbe == 1) && (Tnbt == 0) : (Tnbv == 0) && (Tnbe == 0) && (Tnbt == 1);
     bool TP1 = (Tnbv == 1) && (Tnbe == 0) && (Tnbt == 0);
 
-    for (int i=0; i<n; i++) {
+    for (int i=0; i<m; i++) {
         if (SP1)
             pp = ThU.vertices[i];
         else if (SP0)
@@ -860,13 +860,13 @@ AnyType SetOpHMatrixUser(Stack stack,Expression emat, Expression eop)
             if (mpirank == 0) std::cerr << "ff-Htool error: only P0 and P1 discretizations are available for now." << std::endl;
             ffassert(0);
         }
-        p1[3*i+0] = pp.x;
-        p1[3*i+1] = pp.y;
-        p1[3*i+2] = pp.z;
+        ps[3*i+0] = pp.x;
+        ps[3*i+1] = pp.y;
+        ps[3*i+2] = pp.z;
     }
 
     if(!samemesh) {
-        for (int i=0; i<m; i++) {
+        for (int i=0; i<n; i++) {
             if (TP1)
                 pp = ThV.vertices[i];
             else if (TP0)
@@ -875,22 +875,22 @@ AnyType SetOpHMatrixUser(Stack stack,Expression emat, Expression eop)
                 if (mpirank == 0) std::cerr << "ff-Htool error: only P0 and P1 discretizations are available for now." << std::endl;
                 ffassert(0);
             }
-            p2[3*i+0] = pp.x;
-            p2[3*i+1] = pp.y;
-            p2[3*i+2] = pp.z;
+            pt[3*i+0] = pp.x;
+            pt[3*i+1] = pp.y;
+            pt[3*i+2] = pp.z;
         }
     }
     else{
-        p2=p1;
+        pt=ps;
     }
 
     VirtualGenerator<R>** generator = GetAny<VirtualGenerator<R>**>((*op->g)(stack));
 
     MPI_Comm comm = ds.commworld ? *(MPI_Comm*)ds.commworld : MPI_COMM_WORLD;
     std::shared_ptr<VirtualCluster> t, s;
-    t = build_clustering(n, Uh, p1, ds, comm);
-    s = build_clustering(m, Vh, p2, ds, comm);
-    buildHmat(Hmat, *generator, ds, t, s, p1, p2, comm);
+    s = build_clustering(m, Uh, ps, ds, comm);
+    t = build_clustering(n, Vh, pt, ds, comm);
+    buildHmat(Hmat, *generator, ds, t, s, pt, ps, comm);
 
     return Hmat;
 }