|
| From: | Wen Jiang |
| Subject: | Re: [Getfem-users] Problems on MacOS 10.9.2 |
| Date: | Tue, 15 Apr 2014 09:56:59 -0400 |
Send Getfem-users mailing list submissions to
address@hidden
To subscribe or unsubscribe via the World Wide Web, visit
https://mail.gna.org/listinfo/getfem-users
or, via email, send a message with subject or body 'help' to
address@hidden
You can reach the person managing the list at
address@hidden
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Getfem-users digest..."
Today's Topics:
1. Re: High level generic assembly procedures (Yves Renard)
2. Problems on MacOS 10.9.2 (Stephan Gekle)
3. history variables at gauss point (Wen Jiang)
4. Re: history variables at gauss point (Yves Renard)
----------------------------------------------------------------------
Message: 1
Date: Mon, 14 Apr 2014 12:34:49 +0200
From: Yves Renard <address@hidden>
To: Marco Pischedda <address@hidden>
Cc: address@hidden
Subject: Re: [Getfem-users] High level generic assembly procedures
Message-ID: <address@hidden>
Content-Type: text/plain; charset=UTF-8
It should work. Did you recompile the library after the update ? May be
it did not reconize "sinc".
The _expression_ "sqr(rho(1))+sqr(rho(2))+sqr(rho(3))" can be replaced by
"Norm_sqr(rho)" if rho is a vector with three components.
Yves.
Le 14/04/2014 11:49, Marco Pischedda a ?crit :
> Ok,
>
> thank you. I have some problem with the function
> sinc(sqr(rho(1))+sqr(rho(2))+sqr(rho(3))), I receive this error:
>
> "Unknown variable, function, operator or data"
> terminate called after throwing an instance of 'gmm::gmm_error'
> what(): Error in
> ../../getfem-svn/getfem/src/getfem_generic_assembly.cc, line 4269 :
> Error in assembly string
>
>
> rho is a finite element variable, i.e
> workspace.add_fem_variable("rho", mf_rho, Irho, rho);
>
> Thanks
>
> Marco
>
> 2014-04-14 11:34 GMT+02:00 Yves Renard <address@hidden>:
>> Dear Marco,
>>
>> May be it is too much specific to add a new function to the langage (you
>> may if you think it is better). However, you also may use
>> (1 -cos(t))/t^2 = (sinc(t))^2 / (1+cos(t))
>>
>>
>> Yves.
>>
>>
>>
>>
>>
>> Le 14/04/2014 11:23, Marco Pischedda a ?crit :
>>> Dear Yves,
>>>
>>> thank you for your answer.
>>> Is there also something for the function (1-cos(phi))/(phi*phi) when
>>> phi tends to zero?
>>>
>>> Thanks in advance
>>>
>>> Marco
>>>
>>>
>>>
>>> 2014-04-13 10:44 GMT+02:00 Yves Renard <address@hidden>:
>>>> Dear Marco,
>>>>
>>>> The message "WARNING: detected wrong equivalent nodes" is a debugging message which can be ignored, it serves to control the efficiency of the hash codes for the semantic trees produced by the generic assembly.
>>>>
>>>> For the moment, their is no conditional expressions in the language. However, you can use pos_part and neg_part.
>>>> Concerning the cardinal sine function (sin(t)/t) I added it to the language. It is called "sinc" now in the generic assembly.
>>>>
>>>> Yves.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ----- Original Message -----
>>>> From: "Marco Pischedda" <address@hidden>
>>>> To: "Yves Renard" <address@hidden>
>>>> Cc: address@hidden
>>>> Sent: Friday, April 11, 2014 9:28:22 AM
>>>> Subject: Re: [Getfem-users] High level generic assembly procedures
>>>>
>>>> Dear Yves,
>>>>
>>>> thank you for your answer. I understand how to impose the boundary condition.
>>>> I have another question: in my formulation I'm assembling a term
>>>> A(rho)*f.Test_f, where A(rho) is a symmetric matrix defined as
>>>> follows:
>>>>
>>>> " [-sqr(rho(2))-sqr(rho(3)), rho(1)*rho(2), rho(1)*rho(3);"
>>>> " rho(1)*rho(2), -sqr(rho(1))-sqr(rho(3)), rho(2)*rho(3);"
>>>> " rho(1)*rho(3), rho(2)*rho(3) , -sqr(rho(1))-sqr(rho(2))]";
>>>>
>>>> where rho and f are two FemVariables. When I'm assembling this term I
>>>> receive this warning message: "WARNING: detected wrong equivalent
>>>> nodes".
>>>> What does it mean?
>>>>
>>>> Then I have an _expression_ "sin(phi)/phi", how can I insert an "if
>>>> condition" (i.e if phi<1e-8) in the _expression_ when "phi" tends to
>>>> zero?
>>>>
>>>> Thanks in advance
>>>>
>>>> Marco
>>>>
>>>>
>>>>
>>>> 2014-04-08 15:29 GMT+02:00 Yves Renard <address@hidden>:
>>>>> Dear Marco,
>>>>>
>>>>> No, "Grad_u.Test_p +p.Grad_Test_u+p.Test_u + p(0)u(0)-p(L)u(L)" is not
>>>>> valid. The _expression_ of an assembly string is to be evaluated at each
>>>>> Gauss point of the concerned region. An _expression_ such as "p(0)" will
>>>>> be understand to be the component 0 of p which is not valid because the
>>>>> first component is 1.
>>>>> If you want to add some _expression_ on a boundary (an extremity of the
>>>>> intervall [0, L] here) then it is possible but not in the same assembly
>>>>> string. In your example you have to add the assembly string "p.u" at the
>>>>> boundary x=0 and "-p.u" at the boundary x=L.
>>>>>
>>>>> However, if you need to prescribe a Dirichlet boundary condition, the
>>>>> best would be to use a corresponding model brick (if you use the model
>>>>> system).
>>>>>
>>>>>
>>>>> Yves.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Le 07/04/2014 15:43, Marco Pischedda a ?crit :
>>>>>> Hi,
>>>>>>
>>>>>> how can I impose the boundary condition with high level generic
>>>>>> assembly? For example I want to assemble "Grad_u.Test_p +
>>>>>> p.Grad_Test_u+p.Test_u" and then imposing the value of p on the
>>>>>> boundaries of the 1d domain, i.e x=0 and x=L. It is possible
>>>>>> to write "Grad_u.Test_p +p.Grad_Test_u+p.Test_u + p(0)u(0)-p(L)u(L)",
>>>>>> i.e can I insert the boundaries conditions in the assembling string?
>>>>>>
>>>>>> Thanks in advance
>>>>>>
>>>>>> Marco
>>>>>>
>>>>>>
>>>>>> 2014-04-03 9:52 GMT+02:00 Marco Pischedda <address@hidden>:
>>>>>>> Dear Yves,
>>>>>>>
>>>>>>> thank you for bug correction, now it works.
>>>>>>>
>>>>>>>> Concerning your question on Grad_u for a vector field, it is usually an
>>>>>>>> order two tensor (a matrix) except in 1D.
>>>>>>> Ok that's good.
>>>>>>>
>>>>>>> I will let you know if there are other problems.
>>>>>>>
>>>>>>> Thank you
>>>>>>>
>>>>>>> Marco
>>>>>>>
>>>>>>> 2014-04-03 9:25 GMT+02:00 Yves Renard <address@hidden>:
>>>>>>>> Dear Marco,
>>>>>>>>
>>>>>>>> Concerning your question on Grad_u for a vector field, it is usually an
>>>>>>>> order two tensor (a matrix) except in 1D.
>>>>>>>> I tried to to the best to make the most operations "dimension
>>>>>>>> indepedent" so there is some permitivity in the langage (components of
>>>>>>>> size 1 are sometimes ignored).
>>>>>>>> Remember also that you can have the _expression_ of any term with the
>>>>>>>> commant Print. For instance "Print( Grad_u).Test_p" will print the
>>>>>>>> gradient of u on each Gauss point. It does a lot of print, but at least,
>>>>>>>> you can see the format of the term.
>>>>>>>>
>>>>>>>> Yves.
>>>>>>>>
>>>>>>>>
>>>>>>>> Le 02/04/2014 17:21, Marco Pischedda a ?crit :
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I have other questions:
>>>>>>>>>
>>>>>>>>> - I tried to assemble separately the following terms:
>>>>>>>>> "Grad_u.Test_p" , "p.Grad_Test_u", "p.Test_u" and the code works correctly.
>>>>>>>>> Then I want to assemble the sum of this terms, i.e: "Grad_u.Test_p +
>>>>>>>>> p.Grad_Test_u+p.Test_u"
>>>>>>>>> but I receive the following error:
>>>>>>>>>
>>>>>>>>> Addition or substraction of incompatible expressions or of different sizes
>>>>>>>>> terminate called after throwing an instance of 'gmm::gmm_error'
>>>>>>>>> what(): Error in getfem_generic_assembly.cc, line 3591 :
>>>>>>>>> Error in assembly string
>>>>>>>>> Aborted
>>>>>>>>>
>>>>>>>>> - I'm working in 1d problem with vectors as unknowns. Grad_u is
>>>>>>>>> therefore a vector or is a tensor? When I do Grad_u.Test_p the
>>>>>>>>> result is a scalar or a vector? Test_p is a vector or a scalar?
>>>>>>>>>
>>>>>>>>> Thanks in Advance
>>>>>>>>>
>>>>>>>>> Marco
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 2014-04-01 17:51 GMT+02:00 Marco Pischedda <address@hidden>:
>>>>>>>>>> Ok thank you,
>>>>>>>>>>
>>>>>>>>>> I tried it and it works. I will let you know if there are other problems.
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> Marco
>>>>>>>>>>
>>>>>>>>>> 2014-04-01 17:16 GMT+02:00 Yves Renard <address@hidden>:
>>>>>>>>>>> Dear Marco,
>>>>>>>>>>>
>>>>>>>>>>> All seems to me correct in your implementation. This is probably just
>>>>>>>>>>> the test line 2074 of getfem_generic_assembly.cc
>>>>>>>>>>> which is not correct for one-dimensionnal problems.
>>>>>>>>>>>
>>>>>>>>>>> I think the test should be
>>>>>>>>>>>
>>>>>>>>>>> GA_DEBUG_ASSERT((qdim == 1 && t.sizes()[0] == N) ||
>>>>>>>>>>> (t.sizes()[1] == N && t.sizes()[0] == qdim) ||
>>>>>>>>>>> (N == 1 && t.sizes()[0] == qdim),
>>>>>>>>>>> "dimensions mismatch");
>>>>>>>>>>>
>>>>>>>>>>> May be you can try this. I will validate it if it works.
>>>>>>>>>>>
>>>>>>>>>>> Regards,
>>>>>>>>>>>
>>>>>>>>>>> Yves.
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Le 01/04/2014 16:56, Marco Pischedda a ?crit :
>>>>>>>>>>>> Dear Yves,
>>>>>>>>>>>>
>>>>>>>>>>>> thank you for your fast answer.
>>>>>>>>>>>>
>>>>>>>>>>>> I have another question:
>>>>>>>>>>>>
>>>>>>>>>>>> - I have a monodimensional problem but the unknowns are vectorial. I
>>>>>>>>>>>> set the vectorial
>>>>>>>>>>>> dimension of the unknows with mf_u.set_qdim(3) and with mf_p.set_qdim(3).
>>>>>>>>>>>> When I define the _expression_ " Grad_u.Test_p " i receive the following error:
>>>>>>>>>>>>
>>>>>>>>>>>> terminate called after throwing an instance of 'gmm::gmm_error'
>>>>>>>>>>>> what(): Error in
>>>>>>>>>>>> ../../getfem-svn/getfem/src/getfem_generic_assembly.cc, line 2074 :
>>>>>>>>>>>> dimensions mismatch
>>>>>>>>>>>>
>>>>>>>>>>>> Grad_u should be a 2nd order tensor, while Test_p should be a vector.
>>>>>>>>>>>> I suppose the
>>>>>>>>>>>> problem is that Grad_u is interpreted as a vector while Test_p is
>>>>>>>>>>>> interpreted as a scalar.
>>>>>>>>>>>> How can I use the high level generic assembly procedures on vectorial problems
>>>>>>>>>>>> defined on a monodimensional computational domain?
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks in advance
>>>>>>>>>>>>
>>>>>>>>>>>> Marco
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> 2014-04-01 8:42 GMT+02:00 Yves Renard <address@hidden>:
>>>>>>>>>>>>> Dear Marco,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Yes, your code is correct and it should work correctly.
>>>>>>>>>>>>> Note that you can also use the high level generic assembly with the
>>>>>>>>>>>>> model object using a generic assembly brick.
>>>>>>>>>>>>> Note also that high level assembly is only available in the svn
>>>>>>>>>>>>> repository version of Getfem
>>>>>>>>>>>>> (and a very recent version, at least r4570 because a bug have been
>>>>>>>>>>>>> corrected on coupled problems recently).
>>>>>>>>>>>>>
>>>>>>>>>>>>> Yves.
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> Le 31/03/2014 14:00, Marco Pischedda a ?crit :
>>>>>>>>>>>>>> Dear all,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> I want to use the high level generic assembly procedures in order to
>>>>>>>>>>>>>> use the automatic differentation for calculating the Jacobian of a
>>>>>>>>>>>>>> non-linear problem.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> For example I want to calculate the Jacobian of two vectorial
>>>>>>>>>>>>>> equations in the unknowns "u" and "p". The first vectorial equation is
>>>>>>>>>>>>>> (u+p).Test_u while the second is (u+p).Test_p.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> It is correct the following code?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> gmm::sub_interval Iu(0, ndofs_u);
>>>>>>>>>>>>>> gmm::sub_interval Ip(ndofs_u,ndofs_p);
>>>>>>>>>>>>>> workspace.add_fem_variable("u", mf_u, Iu, U);
>>>>>>>>>>>>>> workspace.add_fem_variable("p", mf_p, Ip, P);
>>>>>>>>>>>>>> workspace.add_expression("(u+p).Test_u + (u+p).Test_p",mim);
>>>>>>>>>>>>>> getfem::model_real_sparse_matrix Jac(ndofs_u+ndofs_p, ndofs_u+ndofs_p);
>>>>>>>>>>>>>> workspace.set_assembled_matrix(Jac);
>>>>>>>>>>>>>> workspace.assembly(2);
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> In the matrix Jac I have the Jacobian of the system?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks in advance
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Marco
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Getfem-users mailing list
>>>>>>>>>>>>>> address@hidden
>>>>>>>>>>>>>> https://mail.gna.org/listinfo/getfem-users
>>>>>>>>>>>>> --
>>>>>>>>>>>>>
>>>>>>>>>>>>> Yves Renard (address@hidden) tel : (33) 04.72.43.87.08
>>>>>>>>>>>>> Pole de Mathematiques, INSA-Lyon fax : (33) 04.72.43.85.29
>>>>>>>>>>>>> 20, rue Albert Einstein
>>>>>>>>>>>>> 69621 Villeurbanne Cedex, FRANCE
>>>>>>>>>>>>> http://math.univ-lyon1.fr/~renard
>>>>>>>>>>>>>
>>>>>>>>>>>>> ---------
>>>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> Yves Renard (address@hidden) tel : (33) 04.72.43.87.08
>>>>>>>>>>> Pole de Mathematiques, INSA-Lyon fax : (33) 04.72.43.85.29
>>>>>>>>>>> 20, rue Albert Einstein
>>>>>>>>>>> 69621 Villeurbanne Cedex, FRANCE
>>>>>>>>>>> http://math.univ-lyon1.fr/~renard
>>>>>>>>>>>
>>>>>>>>>>> ---------
>>>>>>>>>>>
>>>>>>>> --
>>>>>>>>
>>>>>>>> Yves Renard (address@hidden) tel : (33) 04.72.43.87.08
>>>>>>>> Pole de Mathematiques, INSA-Lyon fax : (33) 04.72.43.85.29
>>>>>>>> 20, rue Albert Einstein
>>>>>>>> 69621 Villeurbanne Cedex, FRANCE
>>>>>>>> http://math.univ-lyon1.fr/~renard
>>>>>>>>
>>>>>>>> ---------
>>>>>>>>
>>>>> --
>>>>>
>>>>> Yves Renard (address@hidden) tel : (33) 04.72.43.87.08
>>>>> Pole de Mathematiques, INSA-Lyon fax : (33) 04.72.43.85.29
>>>>> 20, rue Albert Einstein
>>>>> 69621 Villeurbanne Cedex, FRANCE
>>>>> http://math.univ-lyon1.fr/~renard
>>>>>
>>>>> ---------
>>>>>
>>
>> --
>>
>> Yves Renard (address@hidden) tel : (33) 04.72.43.87.08
>> Pole de Mathematiques, INSA-Lyon fax : (33) 04.72.43.85.29
>> 20, rue Albert Einstein
>> 69621 Villeurbanne Cedex, FRANCE
>> http://math.univ-lyon1.fr/~renard
>>
>> ---------
>>
--
Yves Renard (address@hidden) tel : (33) 04.72.43.87.08
Pole de Mathematiques, INSA-Lyon fax : (33) 04.72.43.85.29
20, rue Albert Einstein
69621 Villeurbanne Cedex, FRANCE
http://math.univ-lyon1.fr/~renard
---------
------------------------------
Message: 2
Date: Mon, 14 Apr 2014 21:30:03 +0200
From: Stephan Gekle <address@hidden>
To: address@hidden
Subject: [Getfem-users] Problems on MacOS 10.9.2
Message-ID: <address@hidden>
Content-Type: text/plain; charset=ISO-8859-15; format=flowed
Dear all,
I try to compile GetFem++ on my Mac 10.9.2. and I keep getting the
following error message:
libtool: compile: g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../src -I..
-DGMM_USES_BLAS -I/Users/stephangekle/getfem/include
-I/Users/stephangekle/getfem/include -DGMM_USES_LAPACK -arch i386
-mmacosx-version-min=10.5 -MT getfem_superlu.lo -MD -MP -MF
.deps/getfem_superlu.Tpo -c getfem_superlu.cc -fno-common -DPIC -o
getfem_superlu.o
In file included from getfem_superlu.cc:22:
In file included from ./getfem/getfem_superlu.h:47:
In file included from ./getfem/getfem_config.h:155:
In file included from ./getfem/bgeot_config.h:50:
In file included from ./gmm/gmm_kernel.h:51:
./gmm/gmm_blas_interface.h:158:12: warning: 'cdotu_' has C-linkage
specified, but returns user-defined type 'std::complex<float>' which is
incompatible with C [-Wreturn-type-c-linkage]
BLAS_C cdotu_(...); BLAS_Z zdotu_(...);
^
./gmm/gmm_blas_interface.h:158:32: warning: 'zdotu_' has C-linkage
specified, but returns user-defined type 'std::complex<double>' which is
incompatible with C [-Wreturn-type-c-linkage]
BLAS_C cdotu_(...); BLAS_Z zdotu_(...);
^
./gmm/gmm_blas_interface.h:159:12: warning: 'cdotc_' has C-linkage
specified, but returns user-defined type 'std::complex<float>' which is
incompatible with C [-Wreturn-type-c-linkage]
BLAS_C cdotc_(...); BLAS_Z zdotc_(...);
^
./gmm/gmm_blas_interface.h:159:32: warning: 'zdotc_' has C-linkage
specified, but returns user-defined type 'std::complex<double>' which is
incompatible with C [-Wreturn-type-c-linkage]
BLAS_C cdotc_(...); BLAS_Z zdotc_(...);
^
In file included from getfem_superlu.cc:42:
../superlu/slu_ddefs.h:140:16: error: conflicting types for 'countnz'
extern void countnz (const int, int *, int *, int *, GlobalLU_t *);
^
../superlu/slu_sdefs.h:140:16: note: previous declaration is here
extern void countnz (const int, int *, int *, int *, GlobalLU_t *);
[ more similar errors follow]
It seems that the Mac compiler has a more severe type-checking than
other versions and that's why it goes wrong?
Any suggestions are greatly appreciated!
Thanks a lot and best regards,
Stephan
------------------------------
Message: 3
Date: Mon, 14 Apr 2014 23:13:06 -0400
From: Wen Jiang <address@hidden>
To: "address@hidden" <address@hidden>
Subject: [Getfem-users] history variables at gauss point
Message-ID:
<address@hidden>
Content-Type: text/plain; charset="utf-8"
Dear all,
I am wondering whether it is possible to store some history variables at
each gauss point and later use them in assembly procedure. Thanks.
Regards,
Wen
-------------- next part --------------
An HTML attachment was scrubbed...
URL: </public/getfem-users/attachments/20140414/e2832bda/attachment.html>
------------------------------
Message: 4
Date: Tue, 15 Apr 2014 08:24:21 +0200
From: Yves Renard <address@hidden>
To: address@hidden
Subject: Re: [Getfem-users] history variables at gauss point
Message-ID: <address@hidden>
Content-Type: text/plain; charset="iso-8859-1"
Dear Wen,
This is not finalised, but there is a structure called im_data (see
src/getfem/getfem_im_data.h) who aims to store some data on Gauss points
on which you can interpolate and that you can use in the high-level
generic assembly.
Yves.
Le 15/04/2014 05:13, Wen Jiang a ?crit :
> Dear all,
>
> I am wondering whether it is possible to store some history variables
> at each gauss point and later use them in assembly procedure. Thanks.
>
> Regards,
> Wen
>
>
> _______________________________________________
> Getfem-users mailing list
> address@hidden
> https://mail.gna.org/listinfo/getfem-users
--
Yves Renard (address@hidden) tel : (33) 04.72.43.87.08
Pole de Mathematiques, INSA-Lyon fax : (33) 04.72.43.85.29
20, rue Albert Einstein
69621 Villeurbanne Cedex, FRANCE
http://math.univ-lyon1.fr/~renard
---------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: </public/getfem-users/attachments/20140415/53f37f4a/attachment.html>
------------------------------
Subject: Digest Footer
_______________________________________________
Getfem-users mailing list
address@hidden
https://mail.gna.org/listinfo/getfem-users
------------------------------
End of Getfem-users Digest, Vol 92, Issue 10
********************************************
| [Prev in Thread] | Current Thread | [Next in Thread] |