Dear Zhenghuai Guo,
Sorry for the late response. You're doing everything correct except your
elements are not isoparametric, as temporary_mesh_deformator requires (this
is it's current limitation, of course).
Geometric transformation of your elements is linear (you generated linear
triangles with three vertices in GMSH), while the element type is FEM_PK(2,
2), meaning
that they have 6 degrees of freedom per element. You either need to create
quadratic mesh in GMSH (it has a button "Order" or something), or,
alternatively, you'd need to use FEM_PK(2, 1) linear interpolation
in your code.
Regarding the software I use for meshing. I used to use GMSH a lot as well.
It does a good job once you learn it's ways. It's quite ok for reasonably
small meshes. Now we use Getfem in our company and have our internal
in-house mesher.
Best regards,
Andriy
On Mon, 17 Dec 2018 at 02:28, Zhenghuai Guo <[email protected]>
wrote:
> Hi Andriy,
>
>
>
> Could you please again help me for the following?
>
>
>
> 1. I generate an mesh from gmsh (‘Mesh_3.msh’ as attached). Then I run
> the code ‘myexperiment.cc’ as attached. It is basically for isotropic
> linear eleasticity.
>
> Everything is fine *if I delete the line 101* ‘auto deformator =
> getfem::temporary_mesh_deformator<getfem::model_real_plain_vector>(mf_u, U,
> true, false);’
>
>
>
> I can get a displacement field as in the figure below
>
>
>
>
>
>
>
>
>
> *If I activate this line 101, then I get *
>
>
>
> *Level 3 Warning in getfem_import.cc, line 233: All regions must have
> different number!*
>
> *Mesh loaded*
>
> *Mesh exported: 'mesh.vtk'*
>
> *defined boundary: 'bound for whole boundary' 'Dirichlet_boundary for
> Dirichlet boundary' 'Neumann_boundary for Neumann boundary'*
>
> *set fem mf_u: 'FEM_PK(2, 2)'*
>
> *set mim mim: 'IM_TRIANGLE(2)'*
>
> *model bullt: 'model'*
>
> *add variable: 'u'*
>
> *add scalar_data lambda, mu: 'lambda' 'mu'*
>
> *add fixed_size_data Dirichlet_value, Fdata: 'Dirichlet_value' 'Fdata'*
>
> *add_isotropic_linearized_elasticity_brick*
>
> *add_Dirichlet_condition_with_multipliers*
>
> *add_source_term_brick*
>
> *Trace 2 in getfem_models.cc, line 4325: Mass term assembly for Dirichlet
> condition*
>
> *Trace 2 in getfem_models.cc, line 4362: Source term assembly for
> Dirichlet condition*
>
> *Trace 2 in getfem_models.cc, line 3446: Generic linear assembly brick:
> generic matrix assembly*
>
> *Trace 2 in getfem_models.cc, line 4325: Mass term assembly for Dirichlet
> condition*
>
> *Trace 2 in getfem_models.cc, line 4362: Source term assembly for
> Dirichlet condition*
>
> *Trace 2 in getfem_models.cc, line 3293: Generic source term assembly*
>
> *Trace 2 in getfem_models.cc, line 3300: Source term: generic source term
> assembly*
>
> *Trace 2 in getfem_models.cc, line 3307: Source term: generic matrix
> assembly*
>
> *condition number: 14972.4*
>
> *model solved*
>
> *terminate called after throwing an instance of 'gmm::gmm_error'*
>
> * what(): Error in ../src/getfem/getfem_deformable_mesh.h, line 112 void
> getfem::temporary_mesh_deformator<VECTOR>::deforming_mesh_(VECTOR&) [with
> VECTOR = std::vector<double>]:*
>
> *dimension of dof is greater than 3*
>
>
>
> and the displacement field is as in the below figure
>
>
>
>
>
> I try to find out what the error means and solve, and I still can’t. The
> line 101 ‘auto deformator =
> getfem::temporary_mesh_deformator<getfem::model_real_plain_vector>(mf_u, U,
> true, false);’ is after line where I export the displacement field U, but
> the line 101 affect the export of U, which I don’t understand.
>
>
>
> Could you please advise about this?
>
>
>
>
>
> 1. Could you please let me know what software or approach you normally
> use for mesh generation for import to Getfem?
>
>
>
>
>
> Thank you very much
>
> Regards
>
> Zhenghuai Guo
>
>
>
> *From:* Zhenghuai Guo
> *Sent:* Tuesday, December 11, 2018 12:15 AM
> *To:* [email protected]
> *Cc:* [email protected]
> *Subject:* RE: [Getfem-users] mesh_deformation
>
>
>
> Oh Thank you Andriy, I think I got confused by myself. The reason is that
> I already used getfem::vtk_export exp("mesh.vtk", false); above.
>
> Then I do getfem::vtk_export exp("results/displacement_" +
> std::to_string(n) + ".vtk", false); It gave error of exp was previously
> declared.
>
>
>
> Now it works. Thank you .
>
>
>
> Regards
>
> Zhenghuai Guo
>
>
>
> *From:* Andriy Andreykiv <[email protected]>
> *Sent:* Tuesday, December 11, 2018 12:02 AM
> *To:* Zhenghuai Guo <[email protected]>
> *Subject:* Re: [Getfem-users] mesh_deformation
>
>
>
> " But in C++, I can’t repeatedly use getfem::vtk_export exp(filename,
> false) in each time step with a new filename value. "
>
> Why? Yes you can. For instance, if you have a step number
>
> int step;
>
> and you increment it then you simply post-process inside the loop:
>
> for (step = 0; step < NStep; ++step)
>
> {
>
> //calculation
>
> getfem::vtk_export exp("result_" + std::to_string(step) + ".vtk", false);
>
> }
>
> Best regards,
>
> Andriy
>
>
>
>
>
> On Mon, 10 Dec 2018 at 13:57, Zhenghuai Guo <[email protected]>
> wrote:
>
> Thank you Roman,
>
>
>
> I will need to digest what you suggested and will let you know how it goes.
>
>
>
> In the meantime, can you please advise: *how to export a time series mf
> in .VTK format in C++*.
>
>
>
> In Python, it is quite easy using
> ‘model.export_to_vtk('results/displacement_%d.vtk' % n, U) ‘in each time
> step. The file names can be set to be displacement _1.vtk , displacement
> _2.vtk, displacement _3.vtk and so on.
>
>
>
> But in C++, I can’t repeatedly use getfem::vtk_export exp(filename, false)
> in each time step with a new filename value.
>
>
>
> Please advise.
>
>
>
> Thank you very much
>
> Regards
>
> Zhenghuai Guo
>
>
>
> *From:* Roman Putanowicz <[email protected]>
> *Sent:* Sunday, December 9, 2018 8:17 PM
> *To:* Zhenghuai Guo <[email protected]>
> *Cc:* [email protected]
> *Subject:* Re: [Getfem-users] mesh_deformation
>
>
>
> Dear Zhenghuai Guo,
>
> Probably this is not exactly what you requested, but I think can be
> helpful. Instead of dealing
> with mesh connectivity you could use features of mesh_fem. To get the
> positions of points
> on face you can do:
>
> mesh_fem -> dofs_on_face -> poins related to dofs.
>
> In mesh_fem there is a method:
> ind_dof_face_ct
> getfem::mesh_fem::ind_basic_dof_of_face_of_elements(size_type_cv, short f);
>
> It gives an array of dof numbers lying on a convex face.
> Then you can use the method:
> base_node::mesh_fem::point_of_basic_dof
> <http://download-mirror.savannah.gnu.org/releases/getfem/doc/getfem_reference/classgetfem_1_1mesh__fem.html#a5df7a24fdfc24ec21d43fb44b1c44536>
> (size_type d);
>
> The only thing to be careful is to properly select mesh_fem type, for
> instance Lagrangian one with
> linear shape functions.
>
> This way of getting points on face may seem strange but it is a direct use
> of GetFEM API
> and you will not have do dig deeper into GetFEM internals.
>
> Regards,
>
> Roman
>
>
> December 9, 2018 9:43 AM, "Zhenghuai Guo" <[email protected]>
> wrote:
>
> Hi Andriy,
>
> Your advice help me a lot. I now try to make some simple c++ script in
> getfem. The compile and
> build works fine.
>
> I have one more question: how to get the points in a particular face, if
> we know the convex and
> fact index?
>
> I can see that we can do ‘mesh.convex(i).points()’ or ‘mesh.points()[i]’.
> But we can’t do
> ‘mesh.faces(i).points()’.
>
> The reason I ask for this is that I would like to have the capacity to
> define region based spatial
> coordinates.
>
> Could you please advise?
>
> Thank you very much
>
> Zhenghuai Guo
>
> From: Andriy Andreykiv <[email protected]>
> Sent: Monday, December 3, 2018 5:12 AM
> To: Zhenghuai Guo <[email protected]>
> Cc: [email protected]
> Subject: Re: [Getfem-users] mesh_deformation
>
> Dear Zhenghuai Guo,
>
> The installation and building of getfem and the tests are explained in the
> manual.
>
> After getfem is installed, you can build all the examples with the command:
>
> make tests
>
> If you want to build a specific example, say laplacian_with_bricks, just
> type
>
> make laplacian_with_bricks
>
> The make script will call the compiler to build the object file and
> subsequently link it against
> the library.
>
> Your attempt to build elastostatic example is close, but not sufficient:
> you're compiling your
> code, but not
>
> linking against getfem. When you type "make laplacian_with_bricks", you
> will see the output of the
> exact
>
> commands necessary to compile and link against the library. You can use
> these exact commands to
> build
>
> your source file into an getfem based program.
>
> Best regards,
>
> Andriy
>
> On Sat, 1 Dec 2018 at 21:16, Zhenghuai Guo <[email protected]>
> wrote:
>
> Dear Andriy,
>
> I try your suggestions - using im_data for the coefficients - in python
> which are working fine.
> Thank you very much.
>
> But I still have problem in deforming the mesh in Python – simply don’t
> know how to call the
> ‘temporary_mesh_deformator’ in Python. I guess I should do it in C++.
>
> I don’t really use C++ too much. Could you please let me know where the
> demos are for the C++?
>
> I can see that in the folder ‘getfem-5.3/tests’, there are some ‘.cc’ test
> files – are they the
> demos? I try to compile it : ‘g++ elastostatic.cc -o elastostatic’, but it
> did not go through (give
> the message as attached). I am not sure if I did it right or simply
> because I did not install the
> getfem right in the first place.
>
> Could you please advise?
>
> Thank you very much
>
> Kind regards
>
> Zhenghuai Guo
>
> From: Andriy Andreykiv <[email protected]>
> Sent: Wednesday, November 21, 2018 9:53 PM
> To: Zhenghuai Guo <[email protected]>; [email protected]
> Subject: Re: [Getfem-users] mesh_deformation
>
> Dear Zhenghuai Guo,
>
> For 1 you don't need to do anything. All the variables in the next step
> remain from the last step.
> In some cases, if your variable has two versions (old and current, for
> instance) you need to call
> model::next_iter() to copy all the old versions of variable to the current.
>
> But if the variable doesn't have the two versions you don't need that.
> Normally we want to have two
> versions of variables when our formulations use their increments.
>
> For 2 you don't really need to add the linear elastic term with your own
> code, as the actual
> function add_isotropic_linearized_elasticity_brick uses high-level
> assembly internally. Here is
> it's source code
>
> from getfem_models.cc
>
> size_type add_isotropic_linearized_elasticity_brick(model &md, const
> mesh_im &mim, const
> std::string &varname, const std::string &dataexpr1, const std::string
> &dataexpr2, size_type region,
> const std::string &dataname3) { std::string test_varname = "Test_" +
> sup_previous_and_dot_to_varname(varname); std::string expr1 =
> "((("+dataexpr1+")*(Div_"+varname+"-Div_"+dataname3
> +"))*Id(meshdim)+(2*("+dataexpr2+"))*(Sym(Grad_"+varname
> +")-Sym(Grad_"+dataname3+"))):Grad_"
> +test_varname; std::string expr2 =
> "(Div_"+varname+"*(("+dataexpr1+")*Id(meshdim))"
> +"+(2*("+dataexpr2+"))*Sym(Grad_"+varname+")):Grad_"+test_varname;
> ga_workspace workspace(md,
> true); workspace.add_expression(expr2, mim, region); model::varnamelist
> vl, vl_test1, vl_test2, dl;
> bool is_lin = workspace.used_variables(vl, vl_test1, vl_test2, dl, 2); if
> (is_lin) { pbrick pbr =
> std::make_shared<iso_lin_elasticity_new_brick> (expr2, dataname3);
> model::termlist tl;
> tl.push_back(model::term_description(varname,
> sup_previous_and_dot_to_varname(varname), true)); if
> (dataname3.size()) dl.push_back(dataname3); return md.add_brick(pbr, vl,
> dl, tl, model::mimlist(1,
> &mim), region); } else { return add_nonlinear_generic_assembly_brick (md,
> mim, dataname3.size() ?
> expr1 : expr2, region, false, false, "Linearized isotropic elasticity
> (with nonlinear
> dependance)"); }}
> It's c++, but python logic would be similar.
>
> Regarding the source code you've attached, I see that you still add the
> elastic constants as a
> fixed size data. As I mentioned in the last email, you need to have
> different constants for every
> integration point
>
> of your model. Hence they have to be im_data.
>
> Best regards,
>
> Andriy
>
> On Sun, 18 Nov 2018 at 20:47, Zhenghuai Guo <[email protected]>
> wrote:
>
>
>
> Dear Andriy,
>
> Thank you for the advice. You understand correctly about what I am trying
> to achieve. The problems
> I am having now are to how to (1) use an updated deformed mesh and (2)
> consider the
> displacement/stress value of previous timestep as the initial condition at
> each new time step.
>
> Could you please advise about the following?
>
> * If I use Isotropic_linearized_elastic_brick, how can I pass the
> displacement and stress values
> from one time step to another? At each timestep, I would like the initial
> condition to take into
> account the state (e.g. displacement and stress) of last timestep. I am
> not sure maybe it does it
> automatically or not.
> * I am trying to use high level assembly string language to carry out
> linear elasticity. I am
> guessing, by doing this I can be more free. And maybe I can consider the
> displacement/stress value
> of previous timestep as the initial condition at each new time step.
> Could you please have a look at the attached small code? I try to add the
> assembly string of
> isotropic linear elasticity by
> md.add_linear_term(mim,'(clambda*Trace(Grad_u)*Id(qdim(u)) +
> cmu*(Grad_u+Grad_u’)):Grad_Test_u ')
>
> but, when I run the code, it appear with some problem – although it does
> not give error, but it
> does not proceed and the python shell is restarted. Could you please
> advise about this issue?
>
> Thank you very much
>
> Regards
>
> Zhenghuai Guo
>
> From: Andriy Andreykiv <[email protected]>
> Sent: Friday, November 16, 2018 11:03 PM
> To: Zhenghuai Guo <[email protected]>
> Cc: [email protected]
> Subject: Re: [Getfem-users] mesh_deformation
>
> Dear Zhenghuai Guo,
>
> If I understand correctly, you're trying to model creep with contact. If
> so, then you can probably
> assume that your elastic properties are weakly coupled with stress. In
> that case you can probably
> just update your elastic properties every time step.
>
> So, you need to write a loop where you change the properties every step.
> Here are some ideas
>
> 1) Your elastic properties lambda and mu cannot be fixed sized constants,
> as they will depend on
> stress values throughout the domain. The logical way to handle this is
>
> by setting them as a so-called im_data, which is a field defined on Gauss
> points (on mesh_im
> class). Please look up documentation or source how to add im_data.
>
> 2) Isotropic linearized elastic brick does not compute and store stress
> field. You will need to
> define stress field as im_data too and compute it from your solution
>
> using probably high-level assembly syntax
>
> ga_interpolation_im_data(md, "lambda*Trace(Grad_u)*Id(qdim(u)) +
> mu*(Grad_u+Grad_u'))" , im_data
> &imd_stress, base_vector &stress_result_vector);
>
> 3) The whole calculation should look like this:
>
> initialize the elastic properties as im_data
>
> create im_data for the stress
>
> add contact bricks
>
> while(t < T)
>
> {
>
> md.solve();
>
> compute the stresses from the displacement field using high-level assembly
> syntax interpolations
> compute the new values for the elastic properties with high-level assembly
> syntax interpolations
> post-process;
> t = t + delta T;
> }
>
> Best regards,
> Andriy
>
> On Fri, 16 Nov 2018 at 04:42, Zhenghuai Guo <[email protected]>
> wrote:
>
> Dear Andriy,
>
> I am planning to do a time dependent deformation with consideration of the
> contact and friction. I
> would like to apply the elasticity theory with Young’s modulus being a
> function of time and local
> stress value.
>
> Could you please advise about the following?
>
> * If I use add_isotropic_linearized_elasticity_brick (mim, varname,
> dataname_lambda, dataname_mu,
> region=None), how can I make the Young’s modulus time and stress
> dependent? In the test examples
> e.g. in demo_tripod.py, Young’s modulus is only added by the method
> add_initialized_data as a
> constant scalar value.
> * If I carry out elasticity formulation by a approach like the one in
> demo_tripod_alt.py using low
> level approach to building the linear system by hand, can I in the
> meantime apply together the
> bricks framework e.g.
> add_master_contact_boundary_to_large_sliding_contact_brick(indbrick, mim,
> region, dispname, wname=None)?
> Thank you very much
>
> Best regards
>
> Zhenghuai Guo
>
> From: Andriy Andreykiv <[email protected]>
> Sent: Thursday, November 8, 2018 8:56 PM
> To: Zhenghuai Guo <[email protected]>
> Cc: [email protected]
> Subject: Re: [Getfem-users] mesh_deformation
>
> Dear Zhenghuai Guo,
>
> You can build getfem and getfem based programs using either GCC c++
> compiler for Linux based
> systems
> (read Page 5 of the user doc:
> http://download-mirror.savannah.gnu.org/releases/getfem/doc/gmm_userdoc.pdf
> )
> or with Microsoft Visual Studio (you can use free Community edition). You
> can find MSVC solution in
> msvc directory of the distribution.
> Unfortunately, the solution for MSVC is not kept up-to-date and you would
> need to re-add all getfem
> sources to it to make it work.
>
> You can deform your mesh with a simple call:
> auto deformator = temporary_mesh_deformator(mf, U, true, false);
> //the first true means "deform on creation", the second false means "do
> not restore the mesh back
> when temporary_mesh_deformator reaches the end of life"
> mf - is the mesh_fem for your displacement field and U is the displacement
> vector with
> gmm::vect_size(U) = mf.nb_dof();
>
> Best regards,
> Andriy
>
> On Thu, 8 Nov 2018 at 01:15, Zhenghuai Guo <[email protected]>
> wrote:
>
> Dear Andriy,
>
> Thank you for your explanation.
>
> Regarding creep, at the moment I only use liner_elasticity_brick with
> young’s modulus being changed
> on each time-step. This is just to start with. I am new in Getfem in fact.
>
> Could you please advise about the follows?
>
> * Are you using c++ to run getfem? If so, can you give some hints how I
> can to it? I can’t see any
> instruction about setting up for c++.
> * If you don’t use c++, how do you normally use the
> getfem::temporary_mesh_deformator (from
> getfem_deformable_mesh.h) or other C functions?
> I was trying to see if it is possible to use this function in Python
> interface by using SWIG or
> Python.Boost. But it is far beyond my knowledge.
>
> Thank you very much
>
> Regards
>
> Zhenghuai Guo
>
> From: Andriy Andreykiv <[email protected]>
> Sent: Wednesday, November 7, 2018 8:32 PM
> To: Zhenghuai Guo <[email protected]>
> Cc: [email protected]
> Subject: Re: [Getfem-users] mesh_deformation
>
> Dear Zhenghuai Guo,
>
> I don't use Python interface much, but your assumption is correct, using
> getfem::temporary_mesh_deformator (from getfem_deformable_mesh.h) you can
> apply displacement field
> to the mesh.
> By default temporary_mesh_deformator will deform the mesh and un-deform it
> in the destructor,
> unless you build it with the argument to_be_restored=false.
> I only assume that you can do it with Python too.
>
> I'm not really experienced with creep, but intuitively I would assume that
> you can also use large
> deformation formulation to account for the change in geometry.
> Or it's not how you intend it?
>
> In your follow up email you are asking about the usage of mesh slices.
> From what I know it's used
> primarily for post-processing, not calculation. If you intend to use it
> solely for
> post-processing than you can easily achieve it nowadays with Paraview,
> were you import a vtk file,
> warp the result with a displacement field and take a desired slice.
>
> Best regards,
> Andriy
> On Sat, 3 Nov 2018 at 12:33, Zhenghuai Guo <[email protected]>
> wrote:
>
> Dear Sir or Madam,
>
> Could you please advise how I and deform a mesh according to a
> displacement field?
>
> I am trying to simulate a time dependent deformation of a cylinder like
> object using
> python-interface. After applying stress the object creeps with time.
>
> I think I can just go with many small time steps. In each time step, I
> would like to update and
> deform the mesh according to the displacement calculated as a function of
> time. And the deformed
> mesh will be an input for next time step.
>
> I can see there is some related information such as (1)
> ‘getfem_deformable_mesh.h’ in page 18 in
>
> https://download-mirror.savannah.gnu.org/releases/getfem/doc/getfem_project.pdf
> (2)
> ‘getfem::slicer_apply_deformation’ in
> http://getfem.org/userdoc/export.html#getfem::slicer_apply_deformation .
> But I can find details
> examples.
>
> Thank you very much
>
> Zhenghuai Guo
>
> Tyree Xray CT network facility, School of Minerals and Energy Engineering
> Resources, UNSW Sydney
>
>
> - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> Roman Putanowicz, PhD <[email protected]>
> Institute for Computational Civil Engng (L-5)
> Dept. of Civil Engng, Cracow Univ. of Technology
> www.l5.pk.edu.pl, tel. +48 12 628 2569, fax 2034
>
>
