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

[Yves Renard]

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

---------