Re: [Getfem-users] High level generic assembly procedures

[Marco Pischedda]

Ok now it works, I didn't recompile the code.

>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.
Yes correct, thank you for the suggestion.

Thank you

Marco.


2014-04-14 12:34 GMT+02:00 Yves Renard <address@hidden>:
>
> 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 écrit :
>> 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 écrit :
>>>> 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 écrit :
>>>>>>> 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 écrit :
>>>>>>>>>> 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 écrit :
>>>>>>>>>>>>> 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 écrit :
>>>>>>>>>>>>>>> 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
>
> ---------
>