Merge pull request #35 from FreeFem/dev

Dev

Author: sgarnotel

source/introduction/index.rst

@@ -14,7 +14,7 @@
 
    <center>
     <t> FreeFEM </t> <br/>
-    Fourth edition, Version 4.8 </t>
+    Fourth edition, Version 4.11 </t>
    </center> 
 
 ===============
@@ -77,7 +77,7 @@ Problems involving partial differential equations from several branches of physi
     * `ARPACK <https://www.caam.rice.edu/software/ARPACK/>`_
     * `BLAS <http://www.netlib.org/blas/>`_
     * `OpenBLAS <http://www.openblas.net/>`_
-    * `FFTW 3.3.2 <http://www.fftw.org>`_
+    * `FFTW 3.3.8 <http://www.fftw.org>`_
     * `Ipopt 3.12.4 <https://github.com/coin-or/Ipopt>`_
     * `Gmm++ 4.2 <http://getfem.org/gmm.html>`_
     * `freeYams <https://www.ljll.math.upmc.fr/frey/software.html>`_
@@ -93,7 +93,6 @@ Problems involving partial differential equations from several branches of physi
     * `SuperLU <http://crd-legacy.lbl.gov/~xiaoye/SuperLU/>`_
     * `TetGen <http://www.tetgen.org/>`_
     * `PETSc <https://www.mcs.anl.gov/petsc/>`_
-    * `SLEPc <https://slepc.upv.es/>`_
     * `HTool <https://pierremarchand.netlify.com/project/htool/>`_
     * `HPDDM <https://github.com/hpddm/hpddm>`_
     * `BemTool <https://github.com/PierreMarchand20/BemTool>`_

source/introduction/installation.rst

@@ -177,7 +177,7 @@ Compilation on OSX (>=10.13)
    .. code-block:: bash
       :linenos:
 
-       brew cask install gfortran
+       brew --cask install gfortran
        
 .. note:: If you have installed gcc via brew, gfortran comes with it and you do not need this line       
 
@@ -191,25 +191,25 @@ Compilation on OSX (>=10.13)
        tar xf openmpi-4.0.1
        cd openmpi-4.0.1/
        # to install mpich
-       curl -L http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz --output mpich-3.3.2.tar.gz
-       tar xf mpich-3.3.2
-       cd mpich-3.3.2
+       curl -L https://www.mpich.org/static/downloads/4.0.2/mpich-4.0.2.tar.gz --output mpich-4.0.2.tar.gz
+       tar xf mpich-4.0.2.tar.gz
+       cd mpich-4.0.2
 	   
    .. code-block:: bash
       :lineno-start: 4
 	  
        # with brew gcc gfortran compilers
-       ./configure CC=clang CXX=clang++ FC=gfortran-9 F77=gfortran-9 --prefix=/where/you/want/to/have/files/installed
+       FFLAGS=-fallow-argument-mismatch FCFLAGS=-fallow-argument-mismatch ./configure CC=clang CXX=clang++ FC=gfortran-11 F77=gfortran-11 --prefix=/where/you/want/to/have/files/installed
     
        # with LLVM gcc and brew gfortran compilers
-       ./configure CC=gcc-9 CXX=g++-9 FC=gfortran-9 F77=gfortran-9 --prefix=/where/you/want/to/have/files/installed
+       FFLAGS=-fallow-argument-mismatch FCFLAGS=-fallow-argument-mismatch ./configure CC=gcc-11 CXX=g++-11 FC=gfortran-11 F77=gfortran-11 --prefix=/where/you/want/to/have/files/installed
    
 
    .. code-block:: bash
       :lineno-start: 5
 
        make -j<nbProcs>
-       make -j<nbProcs> install
+       make install
 
 4. Install the minimal libraries for **FreeFEM**
 
@@ -237,12 +237,12 @@ Compilation on OSX (>=10.13)
    .. code-block:: bash
       :linenos:
 
-      curl -O http://mirror.cyberbits.eu/gnu/gsl/gsl-2.5.tar.gz
-      tar zxvf gsl-2.5.tar.gz
-      cd gsl-2.5
+      curl -O https://mirror.ibcp.fr/pub/gnu/gsl/gsl-2.7.tar.gz
+      tar zxvf gsl-2.7.tar.gz
+      cd gsl-2.7
       ./configure
       make -j<nbProcs>
-      make -j<nbProcs> install --prefix=/where/you/want/to/have/files/installed
+      make install --prefix=/where/you/want/to/have/files/installed
 
 8. Download the latest Git for Mac installer `git <https://git-scm.com/download/mac>`__ and the **FreeFEM** source from the repository
 
@@ -266,14 +266,12 @@ Compilation on OSX (>=10.13)
       :lineno-start: 3
       
       // with brew gcc gfortran compilers 
-      ./configure --enable-download CC=clang CXX=clang++ F77=gfortran-9 
-	  FC=gfortran-9 --prefix=/where/you/want/to/have/files/installed
+      ./configure --enable-download -enable-optim CC=clang CXX=clang++ F77=gfortran-11 
+	  FC=gfortran-11 --prefix=/where/you/want/to/have/files/installed
 
       // with LLVM gcc and brew gfortran compilers 
-      ./configure --enable-download CC=clang CXX=clang++ F77=gfortran-9 
-	  FC=gfortran-9 --prefix=/where/you/want/to/have/files/installed
-
-   
+      ./configure --enable-download -enable-optim CC=gcc CXX=g++ F77=gfortran-11 
+	  FC=gfortran-11 --prefix=/where/you/want/to/have/files/installed
 
 10. Download the 3rd party packages to use FreeFEM plugins
 

source/introduction/new-features.rst

@@ -63,3 +63,268 @@ Boundary Element Method
 
 Allows to define and solve a 2d/3d BEM formulation and rebuild the associated potential.
 The document is in construction.
+
+Version 4.6: new features
+=========================
+
+* Added
+  - new search algorithm for the element containing a point (more safe) in mesh of type mesh3, meshS, or meshL.
+  - new function `hasType` to know if a PETSc component has been installed, e.g., `hasType("PC", "hypre")`
+  - eigenvalue problems on linear elements, cf. `examples/eigen/LapEigen1DBeltrami.edp` or `examples/hpddm/laplace-beltrami-3d-line-SLEPc.edp`
+  - `--download-cmake` in PETSc configure if there is no CMake available
+  - flags `--with-[slepc|slepccomplex]-include` and `--with-[slepc|slepccomplex]-ldflags` for when SLEPc has been built outside of FreeFEM or PETSc
+  - interface to `KSPSetResidualHistory` and `KSPGetIterationNumber`
+  - interface to `mpiWaitAll`
+  - new function extract, allows to build a curve mesh from a 2d mesh (can extract a labeled boundary, apply a geometric transformation)
+  - ffglut can plot a vectorial FE function in surface 3d
+  - distributed ParMmg interface, cf. `examples/hpddm/distributed-parmmg.edp` or `examples/hpddm/laplace-adapt-dist-3d-PETSc.edp`
+  - new parallel interpolator on non-matching meshes, cf. `examples/hpddm/transfer.edp`
+  - ability to solve problems in single precision or with 64 bit integers
+  - tool to read data form vtk file only in 3d (cf. plugin iovtk a first example `examples/plugin/iovtk.edp`)
+  - tool to read/wrile ply file of meshL, mesh3, MeshS : Polygon File Format / Stanford Triangle Format do  `load "ioply"`
+     see `examples//3dSurf/operatorsOnMeshS.edp`
+
+* Changed
+  - new `tgv` values: -10 => zero row, -20 => zero row/column
+  - Windows binary now shipped with PETSc/SLEPc
+  - BEM examples are now in `examples/mpi`
+  - plot border type is now in 3d (border 2d and 3d)
+  - PETSc version 3.13.0
+
+* Fixed
+  - `--enable-download_package` may now be used to download a single package, e.g., `--enable-download_metis`
+  - compilation of PETSc under Windows
+  - compilation of plugins when using static libraries
+  - correct detection problem in FE type when use a vectorial FE
+  - macro concatenation with spaces in arguments
+  - correct bug in `plugin/seq/Schur-Complement.cpp`
+  - correct ambiguity bug in `plugin/seq/bfstream.cpp` (reading real or integer)
+  - compilation of plugin libff-mmap-semaphore.c under windows
+
+Version 4.7: new features
+=========================
+
+* Added
+
+  - new way to build matrix between 2d Finite element 2d and Curve finite element to do mortar (Thank to Axel ) , see first example `examples/tutorial/mortar-DN-4-v4.5.edp`
+  - add `Ns` normal vector  in R^3 on meshS (normal of the surface) of current point (to day Ns of [x,y,0] plan  is [0,0,-1])  no be compatible to exterior normal.
+  - add `Tl` tangent vector in R^3 on meshL (tangent vector of the line/curve) of current point
+  - compile ffmaster / ffslave example under windows (thanks to johann@ifado.de)
+  - Boolean parameter `spiltpbedge` in `buildmesh` to split in to edge with two boundary vertices
+  - interface to PETSc DMPlex, see `examples/hpddm/DMPlex-PETSc.edp`
+  - function `MatDestroy`
+  - function `MatPtAP` and `transferMat` for parallel interpolation between non-matching grids, see `examples/hpddm/PtAP-2d-PETSc.edp` or `examples/hpddm/diffusion-mg-2d-PETSc.edp`
+  - preliminary interface to `SVDSolve` from SLEPc to compute singular value decompositions, see `examples/hpddm/mf-2d-SLEPc.edp` or `examples/hpddm/helmholtz-2d-SLEPc-complex.edp`
+  - preliminary interface to `NEPSolve` from SLEPc to solve nonlinear eigenvalue problems, see `examples/hpddm/nonlinear-2d-SLEPc-complex.edp`
+  - `transpose` parameter when constructing a `Mat` for defining a matrix-free transposed operation
+  - interface to `PetscMemoryGetCurrentUsage`
+  - add P2b, RT0, RT1 surface FE (P2bS, RT0S, RT1S))
+  - add operator interpolate (2d->3d surface)
+  - add operator x = A'\*b; where x, b are array and A 2 dim array (full matrix) and generate an error in case of b'\*A or b'\*A expression
+  - function `MatLoad` to load a PETSc `Mat` from disk, see `examples/hpddm/MatLoad-PETSc.edp`
+  - possibility to assemble a symmetric `HMatrix<complex>` and to densify a `HMatrix<complex>` into a `Mat<complex>`
+
+* Changed
+  - moved Htool to its new GitHub location
+  - ScaLAPACK and MUMPS are not compiled by PETSc anymore if there is no Fortran compiler
+  - MPICH is compiled by PETSc if no MPI is detected during configure, see https://community.freefem.org/t/feature-request-use-download-mpich-on-ubuntu/407
+  - PETSc version 3.13.5
+  - force `--with-cudac=0` in `make petsc-slepc`, see https://github.com/FreeFem/FreeFem-sources/issues/141
+  - change DSL keyword P1dc3dL->P1dcL and P1dc3dS->P1dcS
+  - rename `view`, `hasType`, `changeSchur` to respectively `ObjectView`, `HasType`, and `ChangeSchur`
+
+* Deprecated
+  - rename `changeNumbering`, `globalNumbering`, `originalNumbering`, `changeOperator`, `destroyRecycling`, and `attachCoarseOperator` to respectively `ChangeNumbering`, `GlobalNumbering`, `OriginalNumbering`, `ChangeOperator`, `DestroyRecycling`, and `AttachCoarseOperator`
+  - `Nt` the normal vector of the current (wrong on meshL) use `Ns` or `Tl`
+* Removed 
+  - `augmentation` routine from the PETSc plugin
+  - `MPIF77` variable
+
+* Fixed
+  - lot of mistake in MeshL element add a example o check lot of thing `tutomesh1d.edp`
+  - fixed problem of change of mesh when rebuild 2d mesh with buildmesh, .... (Thank to P. Jovilet to points this problem)
+  - missing METIS library when using SuiteSparse compiled by PETSc
+  - missing `-fno-stack-protector` when building PETSc on Windows, see https://community.freefem.org/t/error-loading-complex-petsc-slepc-library/370
+  - fixed ffglut for the plotting of FE array solution
+  - fixed  ffglut bug on MacOS Catalina , draw inn only half windows screen (Apple Bug ???)
+  - correct P0VF  finite element
+  - `abs` function of array
+
+Version [4.7-1]: new features
+=========================
+
+* Changed
+  - change the language definition to use type as a construction function with named arguments for bem plugin
+  - PETSc version 3.14.0
+  - ARPACK compiled by SLEPc
+  - Mmg version 5.5.0
+  - -std=c++14 instead of -std=c++11 when possible
+
+* Removed
+  - plugins thresholdings, symmetrizeCSR, and fflapack and associed example
+
+* Fixed
+  - problem compilation with gfortran-10 of arpack and mumps (add -fallow-argument-mismatch flags)
+
+
+Version 4.8: new features
+=========================
+
+* Added
+  - Bilaplacian example using Morley FE with PETSc, see `examples/hpddm/bilaplacian-2d-PETSc.edp`
+  - Oseen problem preconditioned by PCD, see `examples/hpddm/oseen-2d-PETSc.edp`
+  - SLEPc polynomial eigenvalue solver `PEPSolve()`
+  - add trivial example to check periodic boundary condition on meshS , meshL  , mesh3
+    examples/3d/periodic3.edp	examples/3dSurf/periodicS.edp
+    examples/3dCurve/periodicL.edp
+
+* Changed
+  - PETSc version 3.14.2
+  - Mmg version 5.5.2
+  - link of ffglut so change in configure.ac and Makefile.am  LIBS -> FF_LIBS and LIBS become empty
+    to remove default libs
+  - change number of save plot in ffglut from 10 to 20 for O. Pironneau
+
+* Fixed
+  - some memory leaks
+  - the periodic boundary condition have wrong before first a sementic level of MeshS and MeshL case.
+     the new syntexe is for example:
+     meshL Tl=segment(10);   fespace Vl(Tl,P1,periodic=[[1],[2]]);
+     meshS Th=square3(10,10,[x*2*pi,y*2*pi]); fespace Vh2(Th,P1,periodic=[[1,x],[3,x],[2,y],[4,y]]);
+  - fixed '*' keyboard trick,  to keep  the viewpoint in ffglut or not.
+
+Version 4.9: new features
+=========================
+
+* Added
+  - add P3 lagrange finite element on meshS and meshS
+  - add new plugin `meshtool`to add tool to compute the number of connected components of a all kind of mesh
+    (mesh,mesh3,meshS,meshL) with 2 kind of connected components ones on interior part of the mesh (default) ans
+    secondly on the closure of the mesh (see `examples/hpddm/bConnectedComponents.edp` )
+    add functions  int[int] In=iminP1K(Th,u) or int[int] Ix=imaxP1K(Th,u)  get the array min/max of value u[i]  
+    where i is vertex number on  each element k, so we have  u[Im[k]] = min u[i]/ i in k;
+  - add in plugin `bfstream` to to read binary int (4 bytes) to read fortran file and try to pull tools to share the endiannes
+    in progress
+  - add gluemesh of array of MeshL and MeshS type
+  - interface to `PC_MG_GALERKIN_BOTH`
+  - Kronecker product of two sparse matrices `matrix C = kron(A, B)`
+  - add lot of finite element on Mesh3, MeshS, MeshL of Discontinous Galerling Element
+    in 3d       : P1dc3d, P2dc3d, P3dc3d, P4dc3d , P0edge3d ,P0edgedc3d ,  P0face3d ,P0facedc3d , P0VF3d ,P0VFdc3d ,
+    on Surface  : P1dcS, P2dcS, P3dcS, P4dcS , P0edgeS ,P0edgedcS , P0VFS ,P0VFdcS,
+    on Curve   : P1dcL, P2dcL, P3dcL, P4dcL ,  P0VFL ,P0VFdcL
+    remark; the associated generic name existe of P1dc, P2dc, P0edge, P0VF and all  dc finite element corresponding to
+    no continuity across element.
+  - add code of intallfaces to  do Discontinous Galerkin  formulation in 3d (in test FH.)
+  - add dist function to a mesh , meshL, MeshS or  mesh3 
+  - signeddistfunction to a meshL or  meshS 
+  - add buildmesh functon to build a 2d mesh from a meshL (same as buildmesh see examples/3dCurve/border.edp)
+ 
+* Changed
+  - Now the order to find MPI in configure is first if you have PETSC then take MPI from PETSc
+    otherwise use previous method
+  - on MeshL defined with buildmeshL now the default label are 2*k-1  (resp. 2*k)  for the begin (resp. end) of curve
+    where k is the order of curve use in buildmeshL. So if you have one curve the  labels are 1  and 2.
+    And new  the element label are te region number not the label.
+    This element are not really test so be carfull.
+  - PETSc 3.15.0
+
+
+* Fixed
+  - bug in Find triangle contening point in 2d (border case),
+    `int Mesh::DataFindBoundary::Find(R2 PP,R *l,int & outside) const`
+    the parameter l not correclty return due to local variable.
+  - set CFLAGS=-Wno-implicit-function-declaration to complie with Apple clang version 12.0.0 (clang-1200.0.32.29)
+    to remove following error: implicit declaration of function
+    correct `3dCurve/basicGlue.edp`and add missing test
+  - bugs in SLEPc `SVDSolve()` with a rectangular `Mat`
+  - bugs in nElementonB for DG 3d formulation.
+
+Version 4.10: new features
+=========================
+
+* Added
+  - ridgeangle named parameter in ExtractMeshL in msh3 plugin
+  - DG formulation in 1d :
+    add integral of all border of element : `intallBE(ThL)` and unified the notation by adding
+    `intallBE(ThS)` , `intallBE(Th2)`, `intallBE(Th3)`
+    `nuVertex` of now the vertex number of element in intallBE0d integral
+    `BoundaryBE`, `InternalBE` to know if border element (BE) is on true boundary of not.
+    update `nElementonB` in case on no manifold data (value greater > 2) in meshL, MeshS case ..
+    add code to use jump, mean of test functuon on MeshL case. ( not in mesh3 ) to compute RHS.
+  - add getcwd() function in shell plugin to get the current working dir
+  - add nuVertex to get the vextex on element in some int?
+
+* Changed
+  - PETSc 3.16.1
+
+* Deprecated
+  - SLEPc and SLEPc-complex have been part of PETSc and PETSc-complex for multiple releases and are now deprecated
+
+* Fixed
+  - examples/potential.edp correct problem in times loops and BC
+  - tutorial/mortar-DN-4.edp correct problem of region number in meshL
+  - fix problem in Curve mesh and intallBE , vertex number is wrong 
+  - portability issue on arm64-apple with `make petsc-slepc`
+  - fix assertion failure with `transfer` and `transferMat` with some finite elements
+
+
+Version 4.11: new features (4 apr 2022) 
+=========================
+
+* Added
+  - add computation scalar product of R3 example :  ( N'*Tl)
+  - add tools to do compution with R3 vector see tutorial/calculus.edp
+  - add an example tutorial/tgv-test.edp see see what tgv do on matrix build. 
+  - add R3 Th.be(k).N to  get the normal of boundary element (in all mesh type)
+  - 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 
+  - 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 
+     solidangle(O,Th3[k],nuface) // triangular face is face nuface of tet Th3[k]
+     solidangle(O,ThS[k]) // triangular face is ThS[k]
+     solidangle(O,A,B,C) // triangular face i (A,B,C) 
+     Volume(O,Th3.be(ke)) // O, triangular face is the boundary face 
+     Volume(O,Th3[k],nuface) // O, triangular face is face nuface of tet Th3[k]
+     Volume(O,ThS[k]) // O, triangular face is ThS[k]
+     Volume(O,A,B,C) // (O,A,B,C) tet ..
+  - in bem pluging add array of HMatrix    
+  -  examples/3d/Connectivite-3d.edp or /3dSurf/Connectivite-S.edp of test. 
+  - 3 function mapk, mapkk, mapkk to set a function in fourier space with k parametre 
+   R3 K; // le fourier variable allway 3d (sorry)
+   int n1=16,n2=8, n3=4; 
+   real[int] tab1(nx,tab2(nx*ny),tab3(nx*ny*nz);
+   mapk(tab1,K,sqr(K.x));
+   mapkk(tab2,ny,K,K.norm2);
+   mapkkk(tab3,ny,nz,K,K.norm2);
+   //  Remark you can change K by P (current point)     
+  - in SurfaceMesh.ipd fonction to build a Isocaedron and a Sphere from this Isocaedron
+  - new finite element on MeshS  this  finite element is the ortogonal of RT0 on surface, or 
+    Nelelec Finite Element on triangle with one DoF per mesh edge and where the DoF is the 
+    current on  Edge in orientate edge by number of vertices.  
+  -  plugin Element_P3pnc for new 2d finite element P3pnc (P3 + 2 bulles)  noncoforming  (continuite of P2 mod)   
+    and add 2 examples with this new finite element 
+      examples/plugin/cavityNewtowP3pnc.edp examples/plugin/testFE-P3pnc.edp
+  - function to set dirichlet Boundary conditon on matrix A (real ou compex) trought  an real[int] 
+      (if none zero => set BC ) 
+    setBC(A,au1[],-2); and the example 
+        examples/3d/Elasticity-simple-support-BC.edp
+  
+* Changed
+  - the beaviour of linear solver UMFPACK, CHOLMOD in case of error , now FreeFEm exit on ExecError like in MUMPS
+  - PETSc 3.17.0
+
+
+* Removed
+  -map function  in plugin dfft 
+
+* Fixed
+  - pow(int,int) now call int version not complex version..
+  - correct the normal the N implicite variable   on meshL case 
+  - correct version dump in banner FreeFem++ - version 4.10 (V ...
+  - correct  in CPU time on big mesh due to do bad HCode in HashTable.hpp
+  - bug in array of finite element on meshhS, meshL (ie.  `fespace Vh(ThS,[P1,P1]);` ) 
+
+