Dear Christop, Sorry for not clear explanantions. - Do you have ALUGrid installed? I have installed ALUGrid and I can run test_boxco2. So I think about the installation everything should be OK.
- Is ALUGrid found? (check config.log in the dumux folder, search for "Summary" check what it states for ALUGrid) Here is the Summary part of config.log: ------------------------------------------------------------------------------ - SUMMARY - ------------------------------------------------------------------------------ dune-common.............: version 2.2.0 (/home/mojdeh/dumux/dune-common-2.2.0) dune-geometry...........: version 2.2.0 (/home/mojdeh/dumux/dune-geometry-2.2.0) dune-grid...............: version 2.2.0 (/home/mojdeh/dumux/dune-grid-2.2.0) dune-istl...............: version 2.2.0 (/home/mojdeh/dumux/dune-istl-2.2.0) dune-localfunctions.....: version 2.2.0 (/home/mojdeh/dumux/dune-localfunctions-2.2.0) ALBERTA.................: no ALUGrid.................: version 1.52 (parallel) (/usr/local) AlgLib for DUNE.........: no AmiraMesh...............: no BLAS....................: yes Build DuMuX handbook....: no (Configure parameter --enable-documentation not specified) GMP.....................: no Grape...................: no METIS...................: yes MPI.....................: no OpenGL..................: yes (add GL_LIBS to LDADD manually, etc.) ParMETIS................: no SuperLU-DIST............: no SuperLU.................: yes (version 4.2 or older, post 2005) UG......................: no Valgrind client requests: no psurface................: no quadruple precision math: no ------------------------------------------------------------------------------ - Do you use an opts file? If yes, please attach it. The optim.opts file is attached. - Does test_boxco2 work with ALUGrid for you? Yes - What are your modifications in test_boxmpnc? Can you send a diff/patch of your changes? The diff/patch files are attached. Thank you very much for your time, Mojdeh ----- Original Message ----- > Send Dumux mailing list submissions to > [email protected] > To subscribe or unsubscribe via the World Wide Web, visit > https://listserv.uni-stuttgart.de/mailman/listinfo/dumux > or, via email, send a message with subject or body 'help' to > [email protected] > You can reach the person managing the list at > [email protected] > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Dumux digest..." > Today's Topics: > 1. Re: Dumux Digest, Vol 40, Issue 8 (mojdeh rasoulzadeh) > 2. Re: Dumux Digest, Vol 40, Issue 8 (Christoph Gr?ninger ) > 3. Re: Buildsystem and compiler problems (Christoph Gr?ninger ) > ---------------------------------------------------------------------- > Message: 1 > Date: Fri, 30 May 2014 12:07:31 +0200 (CEST) > From: mojdeh rasoulzadeh <[email protected]> > Subject: Re: [DuMuX] Dumux Digest, Vol 40, Issue 8 > To: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="utf-8" > Dear Christoph, > Thank you for your reply. > I guess in test_boxmpnc.cc file when checking 'HAVE_ALUGRID' it is > stopped. Apparently there is no ALUGRID. > Besided when make test_boxmpnc the resulting comments include no > ALUGrid which is different from the case when I make test_boxco2. > Rgds, > Mojdeh > ----- Original Message ----- > > Send Dumux mailing list submissions to > > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > > https://listserv.uni-stuttgart.de/mailman/listinfo/dumux > > or, via email, send a message with subject or body 'help' to > > [email protected] > > You can reach the person managing the list at > > [email protected] > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Dumux digest..." > > Today's Topics: > > 1. Buildsystem and compiler problems (Markus Blatt) > > 2. Using ALUGrid in MpNc (mojdeh rasoulzadeh) > > 3. Re: Using ALUGrid in MpNc (Christoph Gr?ninger ) > > 4. Re: Buildsystem and compiler problems (Christoph Gr?ninger ) > > 5. Re: Buildsystem and compiler problems (Markus Blatt) > > ---------------------------------------------------------------------- > > Message: 1 > > Date: Thu, 29 May 2014 18:29:25 +0200 > > From: Markus Blatt <[email protected]> > > Subject: [DuMuX] Buildsystem and compiler problems > > To: [email protected] > > Message-ID: <[email protected]> > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > I am having problems with the compiler support and build system of > > dumux. > > I am using g++-4.6, but am having problems compiling dumux: > > [ 33%] Building CXX object > > test/decoupled/2p2c/CMakeFiles/test_multiphysics2p2c. > > dir/test_multiphysics2p2c.cc.o > > In file included from > > /home/mblatt/src/dune/release/dumux/dumux/decoupled/2p2c/f > > vpressure2p2c.hh:29:0, > > from > > /home/mblatt/src/dune/release/dumux/dumux/decoupled/2p2c/fvpressure2p2cmultiphysics.hh:23, > > from > > /home/mblatt/src/dune/release/dumux/test/decoupled/2p2c/test_multiphysics2p2cproblem.hh:35, > > from > > /home/mblatt/src/dune/release/dumux/test/decoupled/2p2c/test_multiphysics2p2c.cc:33: > > /home/mblatt/src/dune/release/dumux/dumux/decoupled/2p2c/fvpressurecompositional.hh:398:20: > > sorry, unimplemented: non-static data member initializers > > make[4]: *** > > [test/decoupled/2p2c/CMakeFiles/test_multiphysics2p2c.dir/test_multiphysics2p2c.cc.o] > > Fehler 1 > > make[3]: *** > > [test/decoupled/2p2c/CMakeFiles/test_multiphysics2p2c.dir/all] > > Fehler > > 2 > > make[2]: *** > > [test/decoupled/2p2c/CMakeFiles/_test_decoupled_2p2c.dir/rule] > > Fehler > > 2 > > make[1]: *** [_test_decoupled_2p2c] Fehler 2 > > Do I need to use a newer g++? > > Additionally I am unable to build dumux using the autotools as > > there > > are several Makefile.am that contain entries like: > > fv_HEADER=*.hh > > which breaks make on my system: > > make[6]: Entering directory > > `/home/mblatt/src/dune/release/dumux/build-auto/dumux/decoupled/1p/diffusion/fv' > > make[6]: *** Keine Regel vorhanden, um das Target ?*.hh?, > > ben?tigt von ?all-am?, zu erstellen. Schluss. > > My automake version is 1.11.6 and the autoconf version is 2.69. > > Cheers, > > Markus > > -- > > Dr. Markus Blatt - HPC-Simulation-Software & Services > > http://www.dr-blatt.de > > Hans-Bunte-Str. 8-10, 69123 Heidelberg, Germany, USt-Id: > > DE279960836 > > Tel.: +49 (0) 160 97590858 > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: not available > > Type: application/pgp-signature > > Size: 836 bytes > > Desc: Digital signature > > Url : > > http://listserv.uni-stuttgart.de/pipermail/dumux/attachments/20140529/de279eba/attachment-0001.sig > > ------------------------------ > > Message: 2 > > Date: Thu, 29 May 2014 19:12:04 +0200 (CEST) > > From: mojdeh rasoulzadeh <[email protected]> > > Subject: [DuMuX] Using ALUGrid in MpNc > > To: [email protected] > > Message-ID: > > <[email protected]> > > Content-Type: text/plain; charset="utf-8" > > Dear DuMuxes, > > I have installed ALUGrid and succesfully built DuMux and run > > test_boxco2 example using ALUGrids. > > Now, I am trying to use ALUGrid in MpNc test files. > > I made the required modifications in problem and spatial parameter > > files, like including headers etc. > > I rebuild DuMux and DUNE. > > But the run is skipped becuase of the reason 'no ALUGird'. > > Is there sth else I should do? > > Thank you in advance, > > Mojdeh > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: > > http://listserv.uni-stuttgart.de/pipermail/dumux/attachments/20140529/b6f97ce8/attachment-0001.htm > > ------------------------------ > > Message: 3 > > Date: Thu, 29 May 2014 19:20:31 +0200 > > From: "Christoph Gr?ninger " > > <[email protected]> > > Subject: Re: [DuMuX] Using ALUGrid in MpNc > > To: DuMuX User Forum <[email protected]> > > Message-ID: <[email protected]> > > Content-Type: text/plain;charset=utf-8; format="flowed" > > Hi Mojdeh, > > sounds right what you did. > > > But the run is skipped becuase of the reason 'no ALUGird'. > > > Is there sth else I should do? > > I couldn't follow what you did and what the exact error > > message is. Is it a compile-time or runtime error? > > Bye > > Christoph > > -- > > Das Kommt darauf an, in welchen Zeitr?umen du rechnest. F?r > > Geologen: > > ja, in naher Zukunft :-) [Stefan Seyfried in suse-laptop] > > ------------------------------ > > Message: 4 > > Date: Thu, 29 May 2014 19:52:16 +0200 > > From: "Christoph Gr?ninger " > > <[email protected]> > > Subject: Re: [DuMuX] Buildsystem and compiler problems > > To: Markus Blatt <[email protected]>, DuMuX User Forum > > <[email protected]> > > Message-ID: <[email protected]> > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Markus! > > > Do I need to use a newer g++? > > Yes and no. No, because we require GCC 4.5 or newer so it > > should work. Yes, because this bug slipped in due to lack > > of continuous testing with older compilers. With GCC 4.8 > > and a recent Clang it works. > > Thanks for the heads-up. Please find attached a patch > > which is untested as I don't have a GCC on this machine. > > > Additionally I am unable to build dumux using the autotools > > > as there are several Makefile.am that contain entries like: > > > > > > fv_HEADER=*.hh > > > > > > which breaks make on my system: > > [..] > > > My automake version is 1.11.6 and the autoconf version is 2.69. > > Phew, it should not be your version of autoconf or automake, > > as > > we use this pattern for a long time. I just checked and your > > are > > right, the automake guys have wired arguments to not support > > wildcards in automake files. > > I guess it works with GNU make (gmake) and you have maybe > > some other make flavor? > > Bye > > Christoph > > [1] > > https://www.gnu.org/software/automake/manual/html_node/Wildcards.html#Wildcards > > -- > > Das Kommt darauf an, in welchen Zeitr?umen du rechnest. F?r > > Geologen: > > ja, in naher Zukunft :-) [Stefan Seyfried in suse-laptop] > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: dumux-gcc46.patch > > Type: application/octet-stream > > Size: 1823 bytes > > Desc: not available > > Url : > > http://listserv.uni-stuttgart.de/pipermail/dumux/attachments/20140529/1ebc21ff/dumux-gcc46-0001.dll > > ------------------------------ > > Message: 5 > > Date: Fri, 30 May 2014 11:06:57 +0200 > > From: Markus Blatt <[email protected]> > > Subject: Re: [DuMuX] Buildsystem and compiler problems > > To: DuMuX User Forum <[email protected]> > > Message-ID: <[email protected]> > > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > thanks for the patch. > > On Thu, May 29, 2014 at 07:52:16PM +0200, Christoph Gr?ninger > > wrote: > > > >which breaks make on my system: > > > [..] > > > >My automake version is 1.11.6 and the autoconf version is 2.69. > > > > > > Phew, it should not be your version of autoconf or automake, as > > > we use this pattern for a long time. I just checked and your are > > > right, the automake guys have wired arguments to not support > > > wildcards in automake files. > > > I guess it works with GNU make (gmake) and you have maybe > > > some other make flavor? > > I do have gnumake: > > make --version > > GNU Make 3.81 > > Copyright (C) 2006 Free Software Foundation, Inc. > > This is free software; see the source for copying conditions. > > There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A > > PARTICULAR PURPOSE. > > Cheers, > > Markus > > -- > > Dr. Markus Blatt - HPC-Simulation-Software & Services > > http://www.dr-blatt.de > > Hans-Bunte-Str. 8-10, 69123 Heidelberg, Germany, USt-Id: > > DE279960836 > > Tel.: +49 (0) 160 97590858 > > -------------- next part -------------- > > A non-text attachment was scrubbed... > > Name: not available > > Type: application/pgp-signature > > Size: 836 bytes > > Desc: Digital signature > > Url : > > http://listserv.uni-stuttgart.de/pipermail/dumux/attachments/20140530/760d2cf7/attachment-0001.sig > > ------------------------------ > > _______________________________________________ > > Dumux mailing list > > [email protected] > > https://listserv.uni-stuttgart.de/mailman/listinfo/dumux > > End of Dumux Digest, Vol 40, Issue 8 > > ************************************ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://listserv.uni-stuttgart.de/pipermail/dumux/attachments/20140530/393d520d/attachment-0001.htm > ------------------------------ > Message: 2 > Date: Fri, 30 May 2014 12:40:50 +0200 > From: "Christoph Gr?ninger " > <[email protected]> > Subject: Re: [DuMuX] Dumux Digest, Vol 40, Issue 8 > To: DuMuX User Forum <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain;charset=utf-8; format="flowed" > Hi Mojdeh, > I do neither understand your problem nor your questions. > Please > tell us more about what you try and what you expect. Otherwise > I won't be able to help you. > - Do you have ALUGrid installed? > - Is ALUGrid found? (check config.log in the dumux folder, > search for "Summary" check what it states for ALUGrid) > - Do you use an opts file? If yes, please attach it. > - Does test_boxco2 work with ALUGrid for you? > - What are your modifications in test_boxmpnc? Can you send > a diff/patch of your changes? > Bye > Christoph > -- > Das Kommt darauf an, in welchen Zeitr?umen du rechnest. F?r > Geologen: > ja, in naher Zukunft :-) [Stefan Seyfried in suse-laptop] > ------------------------------ > Message: 3 > Date: Fri, 30 May 2014 12:44:52 +0200 > From: "Christoph Gr?ninger " > <[email protected]> > Subject: Re: [DuMuX] Buildsystem and compiler problems > To: Markus Blatt <[email protected]>, DuMuX User Forum > <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain;charset=iso-8859-1; format="flowed" > Hi Markus! > > thanks for the patch. > Thanks for your feedback. Was this the only problem with > GCC 4.6? If yes, then I'll apply my patch. > >> I guess it works with GNU make (gmake) and you have maybe > >> some other make flavor? > > > > I do have gnumake: > No good ideas left. Can you send my your Makefile by private > mail? Maybe a direct comparison with my local file will > provide > an insight. > Bye > Christoph > -- > Das Kommt darauf an, in welchen Zeitr?umen du rechnest. F?r > Geologen: > ja, in naher Zukunft :-) [Stefan Seyfried in suse-laptop] > ------------------------------ > _______________________________________________ > Dumux mailing list > [email protected] > https://listserv.uni-stuttgart.de/mailman/listinfo/dumux > End of Dumux Digest, Vol 40, Issue 9 > ************************************
--- obstacleproblem.hh 2014-05-20 16:41:48.000000000 +0200
+++ obstacleproblem1.hh 2014-05-30 11:05:35.000000000 +0200
@@ -25,10 +25,18 @@
#ifndef DUMUX_OBSTACLEPROBLEM_HH
#define DUMUX_OBSTACLEPROBLEM_HH
-#include <dune/common/parametertreeparser.hh>
-#include <dune/grid/io/file/dgfparser/dgfug.hh>
+
+#if HAVE_ALUGRID
+#include <dune/grid/alugrid/2d/alugrid.hh>
+#else
+#warning ALUGrid is necessary for this test.
+#endif
+
#include <dune/grid/io/file/dgfparser/dgfs.hh>
-#include <dune/grid/io/file/dgfparser/dgfyasp.hh>
+//#include <dune/common/parametertreeparser.hh>
+//#include <dune/grid/io/file/dgfparser/dgfug.hh>
+//#include <dune/grid/io/file/dgfparser/dgfyasp.hh>
+#include <dumux/boxmodels/common/intersectiontovertexbc.hh>
#include <dumux/boxmodels/mpncu/mpncmodel.hh>
#include <dumux/boxmodels/common/porousmediaboxproblem.hh>
@@ -54,7 +62,12 @@
NEW_TYPE_TAG(ObstacleProblem, INHERITS_FROM(BoxMPNC, ObstacleSpatialParams));
// Set the grid type
-SET_TYPE_PROP(ObstacleProblem, Grid, Dune::YaspGrid<1>);
+#if HAVE_ALUGRID
+SET_TYPE_PROP(ObstacleProblem, Grid, Dune::ALUGrid<2, 2, Dune::cube,
Dune::nonconforming>);
+#else
+SET_TYPE_PROP(ObstacleProblem, Grid, Dune::YaspGrid<2>);
+#endif
+
// Set the problem property
SET_TYPE_PROP(ObstacleProblem,
Problem,
@@ -176,13 +189,15 @@
typedef typename GridView::template Codim<dim>::Entity Vertex;
typedef typename GridView::Intersection Intersection;
typedef typename GET_PROP_TYPE(TypeTag, FVElementGeometry)
FVElementGeometry;
+ typedef typename GET_PROP_TYPE(TypeTag, GridCreator) GridCreator;
typedef Dune::FieldVector<typename GridView::Grid::ctype, dimWorld>
GlobalPosition;
typedef Dune::FieldVector<Scalar, numPhases> PhaseVector;
typedef typename GET_PROP_TYPE(TypeTag, TimeManager) TimeManager;
public:
- ObstacleProblem(TimeManager &timeManager, const GridView &gridView)
- : ParentType(timeManager, gridView)
+ ObstacleProblem(TimeManager &timeManager,
+ const GridView &gridView)
+ : ParentType(timeManager, GridCreator::grid().leafView()),
intersectionToVertexBC_(*this)
{
eps_ = 1e-3/FluidSystem::dimensionlessLength;
temperature_ = 303; // °K
@@ -196,6 +211,12 @@
Scalar pmax = 5.0e7 * 1.25;
int np = 1000;
+ //Boundary Id Setup:
+ injectionTop_ = 3;
+ injectionBottom_ = 4;
+ dirichletBoundary_ = 1;
+ noFlowBoundary_ = 2;
+ injectionRate_= 0.01;
FluidSystem::init(Tmin, Tmax, nT, pmin, pmax, np);
}
@@ -261,29 +282,47 @@
* \param values The boundary types for the conservation equations
* \param vertex The vertex for which the boundary type is set
*/
+
void boundaryTypes(BoundaryTypes &values, const Vertex &vertex) const
{
- const GlobalPosition &globalPos = vertex.geometry().center();
-
-// if (onOutlet_(globalPos)){
-// for (int eqIdx = 0; eqIdx < numEq; ++ eqIdx) {
-// if (eqIdx<Indices::B0Idx){// for
bacteria equations just neuman boundary condition
-// values.setDirichlet(eqIdx);
-// }
-// else
-// values.setNeumann(eqIdx) ;
-// }
-// }
-// else
-// values.setAllNeumann();
-
-
-
+ intersectionToVertexBC_.boundaryTypes(values, vertex);
+ }
- if (onOutlet_(globalPos))
+ /*!
+ * \brief Specifies which kind of boundary condition should be
+ * used for which equation on a given boundary segment.
+ *
+ * \param values The boundary types for the conservation equations
+ * \param vertex The vertex for which the boundary type is set
+ */
+ void boundaryTypes(BoundaryTypes &values, const Intersection &is) const
+ {
+ int boundaryId = is.boundaryId();
+ if (boundaryId == dirichletBoundary_)
values.setAllDirichlet();
else
values.setAllNeumann();
+// const GlobalPosition &globalPos = vertex.geometry().center();
+//
+//// if (onOutlet_(globalPos)){
+//// for (int eqIdx = 0; eqIdx < numEq; ++ eqIdx) {
+//// if (eqIdx<Indices::B0Idx){// for
bacteria equations just neuman boundary condition
+//// values.setDirichlet(eqIdx);
+//// }
+//// else
+//// values.setNeumann(eqIdx) ;
+//// }
+//// }
+//// else
+//// values.setAllNeumann();
+//
+//
+//
+//
+// if (onOutlet_(globalPos))
+// values.setAllDirichlet();
+// else
+// values.setAllNeumann();
}
@@ -318,11 +357,18 @@
const unsigned int scvIdx,
const unsigned int boundaryFaceIdx) const
{
- const GlobalPosition &globalPos = element.geometry().corner(scvIdx);
+// const GlobalPosition &globalPos = element.geometry().corner(scvIdx);
+// values = 0;
+// //Scalar t= this->timeManager().time();
+// if (onInlet_(globalPos)) {
+// values[conti0EqIdx+nCompIdx] =-2.94e-13 *200/3e-9/.15;//
kg/(s*m^2)
+// }
+ int boundaryId = is.boundaryId();
+
values = 0;
- //Scalar t= this->timeManager().time();
- if (onInlet_(globalPos)) {
- values[conti0EqIdx+nCompIdx] =-2.94e-13 *200/3e-9/.15;//
kg/(s*m^2)
+ if (boundaryId == injectionBottom_)
+ {
+ values[conti0EqIdx+nCompIdx] = -injectionRate_; // kg/(s*m^2)
}
}
/*!
@@ -482,6 +528,15 @@
Scalar temperature_;
Scalar eps_;
+ Scalar injectionRate_;
+
+ int injectionTop_;
+ int injectionBottom_;
+ int dirichletBoundary_;
+ int noFlowBoundary_;
+
+ const IntersectionToVertexBC<TypeTag> intersectionToVertexBC_;
+
};
} //end namespace
--- test_mpncu.cc 2013-09-27 14:54:24.000000000 +0200
+++ test_mpncu1.cc 2014-05-28 16:54:13.000000000 +0200
@@ -54,7 +54,11 @@
int main(int argc, char** argv)
{
-
+#if HAVE_ALUGRID
typedef TTAG(ObstacleProblem) ProblemTypeTag;
return Dumux::start<ProblemTypeTag>(argc, argv, usage);
+#else
+ std::cout << "Test skipped, it needs ALUGrid." << std::endl;
+ return 77;
+#endif
}
optim.opts
Description: Binary data
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