Dem volume solid objects #1169

OGaboriault · 2024-06-10T19:02:39Z

Description

Solid objects are currently only using simplex. This can be problematic since double contacts can occur at the junction of two triangles. This PR aims at introducing solid objects built from volume elements, which could solve this problem. The contact between particle and volume 3D object is not implemented yet. Only in the creation and the displacement.

Testing

A new test has been implemented. (volume_solid_object_displacement.cc)

Documentation

Old simulation parameters have been renamed. The center of rotation was being defined by 3 parameters.

Subsection center of rotation and its three parameters (x, y and z) have been replaced by one parameter named center of rotation using a list of doubles.

A new subsection solid surfaces need to be used when defining solid object in the parameter file.

Miscellaneous (will be removed when merged)

Checklist (will be removed when merged)

See this page for more information about the pull request process.
Code related list:

All in-code documentation related to this PR is up to date (Doxygen format)
Lethe documentation is up to date
New feature has unit test(s) (preferred) or application test(s)
The branch is rebased onto master
Changelog (CHANGELOG.md) is up to date
Code is indented with indent-all and .prm files (examples and tests) with prm-indent

Pull request related list:

Labels are applied
There are at least 2 reviewers (or 1 if small feature) excluding the responsible for the merge
If this PR closes an issue or is related to a project, it is linked in the "Projects" or "Development" section
If the fix is temporary, an issue is opened
The PR description is cleaned and ready for merge

acdaigneault

Some general comments before a start the review:

I'm not sure the title of the PR is representative of the content for the current work. For me this is more an introduction to 3D (volume) solid object than a moving manifold thing.
I would add the comment from Miscellaneous to the description. In this case especially, this is an important info since the work is not at a full working state.
I saw you modified the application tests parameter files. Did you check the example files? (EDIT: just saw the failed test about it, so I guess you flaged it x))
Since the volume solid objects are not fully working (as it is for 2d solid object), I would put a huge warning as soon in the "solid_object_parameters.h" to not use it yet.
About the PR description, please give the name of the old parameters and the new ones

I will look at the code content probably tomorrow :)

acdaigneault · 2024-06-10T19:41:58Z

doc/source/parameters/dem/floating_mesh.rst

@@ -10,45 +10,37 @@ Floating meshes (solid objects) are finite (limited) auxiliary objects that can
 .. note:: 
    At the moment, solid objects (floating meshes) in Lethe have to be defined using triangular (simplex) meshes. Only triangular 2D meshes of 3D surfaces in 3D DEM simulations are presently supported. Quadrilateral 2D meshes of 3D surfaces and 1D mesh of 2D surfaces are not supported at the moment.

-This subsection explains the solid objects (floating meshes) information. First of all, the ``number of solids`` is specified. Then, for each solid object, we need a ``mesh`` subsection. In these subsections, the ``type``, ``initial refinement``, and other properties of the objects are defined. Note that ``simplex`` must be ``true`` for all the objects since the solid objects are defined using simplex meshes. For more information on mesh subsection, visit `CFD mesh <https://chaos-polymtl.github.io/lethe/documentation/parameters/cfd/mesh.html>`_
+This subsection explains the solid objects (floating meshes) information. First of all, the ``number of solids`` is specified. Then, for each solid object, we need a ``mesh`` subsection. In these subsections, the ``type``, ``initial refinement``, and other properties of the objects are defined. Note that currently, only ``two dimensions`` solid object are usable. The ``simplex`` parameter must be set to ``true`` for all the objects since 2D solid objects are defined using simplex meshes. For more information on mesh subsection, visit `CFD mesh <https://chaos-polymtl.github.io/lethe/documentation/parameters/cfd/mesh.html>`_


I suggest we agree on the name of the floating mesh/solid object? what do you thing?
The page is "Floating Mesh (Solid Objects)" but here it says "...the solid objects (floating meshes)..." x)
We should choose one for good!

I would use solid object exclusively. If we both agree on this, I could do a PR to fix this.

It will needs many in-code changes tho. Floating wall also needs to change.
We can agree on Solid object and virtual wall :D ?

Yup I agree with this. Virtual wall especially is a very good nomenclature.

acdaigneault · 2024-06-10T19:47:01Z

doc/source/parameters/dem/floating_mesh.rst

@@ -59,7 +51,7 @@ This subsection explains the solid objects (floating meshes) information. First

 * In the subsection ``angular velocity``, we define the angular velocity of the floating mesh.

-* In the subsection ``center of rotation``, we define the center of rotation of the solid object (in the case of rotational motion).
+* The ``center of rotation`` defines the center of rotation of the solid object (in the case of rotational motion).


I'm not sure about it, but maybe the center of rotation should also be a function.
What happens when your mesh moves in x but the rotation axis is in the xy plan? (let say reproducing a rolling cylinder on a surface)

The center of rotation is being translated following the translational velocity function, so it follows the solid object.

It is like if you were adding a vertex on the solid. This new "vertex" is being translated like every other vertex.

This is a non issue. I can explain it more in detail with you this week.

Thanks I get it now, I just did not know that the point was translated

Yeah otherwise it's a pain in the ass to code
It could be good to add a note that says that the center of rotation is translated with the translational velocity

We could also change the way we handle rotation. Solid surface have a tendency to deform when put into rotation.

We could define the object in its frame of reference and add the rotation matrix to the object.

Instead of translating every vertex individually, we could translate the frame of reference and to the whole rotation from the start. I don't know what would be the computational cost of this procedure. TBD

include/core/solid_objects_parameters.h

acdaigneault · 2024-06-10T19:50:04Z

include/core/solid_objects_parameters.h

+    // Cast to std::shared_ptr<Function<dim>> after parameter declaration
+    translational_velocity = translational_velocity_parsed;
+    angular_velocity       = angular_velocity_parsed;


I don't understand why this step?

translational_velocity and angular_velocity used to be Functions::ParsedFunction<dim>. The only way to define a ParsedFunction is to parse a prm file, which is not really nice when making a test. This is why they need to be of type std::shared_ptr<Function<dim>>

The Function class doesn't have the declare_parameter and parse_parameter functions ( they are only implemented in the ParsedFunction class)

In essence, if I don't use those two temporary variables, I'm not able to use the declare_parameter and parse_parameter functions or I'm not able to define a random function for my test.

Oh ok, got it

Yeah that's a bit convoluted, but I'm not sure there's an easier solution than this other than to do a dynamic typechecking there.
I think this is ok though, Just comment it so we know why you are doing this. LIke add a comment that explains why you are declaring these shared_ptr to not use them afterwards. If Audrey asked the question, it means from the comments it was not clear.

blaisb

I suggest we start using the name solid_surfaces and solid_volumes to refer to <2,3> and <3,3> solid objects. I feel this would make our life much, much easier from now on to clearly define a nomenclature.
I would improve some of your comments to make them clearer. I left a few comments there and there regarding this

CHANGELOG.md

applications_tests/lethe-particles/floating_mesh.prm

blaisb · 2024-06-11T05:48:39Z

doc/source/parameters/dem/floating_mesh.rst

@@ -10,45 +10,37 @@ Floating meshes (solid objects) are finite (limited) auxiliary objects that can
 .. note:: 
    At the moment, solid objects (floating meshes) in Lethe have to be defined using triangular (simplex) meshes. Only triangular 2D meshes of 3D surfaces in 3D DEM simulations are presently supported. Quadrilateral 2D meshes of 3D surfaces and 1D mesh of 2D surfaces are not supported at the moment.

-This subsection explains the solid objects (floating meshes) information. First of all, the ``number of solids`` is specified. Then, for each solid object, we need a ``mesh`` subsection. In these subsections, the ``type``, ``initial refinement``, and other properties of the objects are defined. Note that ``simplex`` must be ``true`` for all the objects since the solid objects are defined using simplex meshes. For more information on mesh subsection, visit `CFD mesh <https://chaos-polymtl.github.io/lethe/documentation/parameters/cfd/mesh.html>`_
+This subsection explains the solid objects (floating meshes) information. First of all, the ``number of solids`` is specified. Then, for each solid object, we need a ``mesh`` subsection. In these subsections, the ``type``, ``initial refinement``, and other properties of the objects are defined. Note that currently, only ``two dimensions`` solid object are usable. The ``simplex`` parameter must be set to ``true`` for all the objects since 2D solid objects are defined using simplex meshes. For more information on mesh subsection, visit `CFD mesh <https://chaos-polymtl.github.io/lethe/documentation/parameters/cfd/mesh.html>`_


Suggested change

This subsection explains the solid objects (floating meshes) information. First of all, the ``number of solids`` is specified. Then, for each solid object, we need a ``mesh`` subsection. In these subsections, the ``type``, ``initial refinement``, and other properties of the objects are defined. Note that currently, only ``two dimensions`` solid object are usable. The ``simplex`` parameter must be set to ``true`` for all the objects since 2D solid objects are defined using simplex meshes. For more information on mesh subsection, visit `CFD mesh <https://chaos-polymtl.github.io/lethe/documentation/parameters/cfd/mesh.html>`_

This subsection explains the solid objects (floating meshes) information. First of all, the ``number of solids`` is specified. Then, for each solid object, we need a ``mesh`` subsection. In these subsections, the ``type``, ``initial refinement``, and other properties of the objects are defined. Note that currently, only two dimensional solid objects, meaning surfaces, are usable. The ``simplex`` parameter must be set to ``true`` for all the objects since 2D solid objects are defined using simplex meshes. For more information on mesh subsection, visit `CFD mesh <https://chaos-polymtl.github.io/lethe/documentation/parameters/cfd/mesh.html>`_

I would try to add a mention that this is a dim=2 spacedim=3 triangulation. This would make it clear for anyone familiar with deal.II

blaisb · 2024-06-11T05:49:38Z

doc/source/parameters/dem/floating_mesh.rst

@@ -59,7 +51,7 @@ This subsection explains the solid objects (floating meshes) information. First

 * In the subsection ``angular velocity``, we define the angular velocity of the floating mesh.

-* In the subsection ``center of rotation``, we define the center of rotation of the solid object (in the case of rotational motion).
+* The ``center of rotation`` defines the center of rotation of the solid object (in the case of rotational motion).


Yeah otherwise it's a pain in the ass to code
It could be good to add a note that says that the center of rotation is translated with the translational velocity

blaisb · 2024-06-11T05:54:52Z

source/dem/dem.cc

@@ -1556,7 +1600,7 @@ DEMSolver<dim>::solve()
                           triangulation,
                           particle_handler,
                           insertion_object,
-                           solids,
+                           solids_2d,


maybe solid_surfaces and solide_volumes would be the better name here.

I like it (surface/volume)!

blaisb · 2024-06-11T05:55:28Z

include/dem/dem.h

+  std::vector<std::shared_ptr<SerialSolid<dim - 1, dim>>> solids_2d;
+  std::vector<std::shared_ptr<SerialSolid<dim, dim>>>     solids_3d;


maybe solid_surfaces and solid_volumes?

Forget about my comment earlier. This answer my question. :)

blaisb · 2024-06-11T05:56:28Z

source/core/serial_solid.cc

+  translational_velocity =
+    std::make_shared<Functions::ParsedFunction<spacedim>>(spacedim);
+  angular_velocity =
+    std::make_shared<Functions::ParsedFunction<spacedim>>(spacedim);
+  translational_velocity = param->translational_velocity;
+  angular_velocity       = param->angular_velocity;


If those are shared point (translational velocity and angular velocity) you don't need to allocate them. You just set them to be equal to the other ones because they should point to the same functions
Otherwise you can call the copy constructor, but there is no need to allocate to then erase the pointer.

source/core/serial_solid.cc

blaisb · 2024-06-11T05:57:50Z

source/core/serial_solid.cc

+    simulation_control->get_output_name() + ".solid_object." +
+    Utilities::int_to_string(dim, 1) + "." + Utilities::int_to_string(id, 2);


I would really start calling them solid surfaces and solid volumes from now on.

applications_tests/lethe-particles/moving_float.prm

oguevremont · 2024-06-11T14:59:44Z

doc/source/parameters/dem/floating_mesh.rst

+       end
+
+       set center of rotation    = 0., 0., 0.
+       set output solid object = true


The indentation should be fixed here

include/core/solid_objects_parameters.h

include/dem/data_containers.h

oguevremont · 2024-06-11T15:32:03Z

tests/dem/volume_solid_object_displacement.cc

+
+  // Functions
+  std::vector<double> translational_vector = {1., 0., 0.};
+  std::vector<double> angular_vector = {-0.39269908169, 0., 0.}; //  0.125 * pi


Suggested change

std::vector<double> angular_vector = {-0.39269908169, 0., 0.}; // 0.125 * pi

std::vector<double> angular_vector = {-0.39269908169, 0., 0.}; // - 0.125 * pi

acdaigneault

First batch for the documentation.
Also please don't forget to gives the name of the old vs new parameters in the PR doc and the name of the new test :)
Also, Just verify for other "floating mesh" mention in the doc of solid objects

doc/source/parameters/dem/dem.rst

doc/source/parameters/dem/solid_objects.rst

acdaigneault

Nice :) It's sure it is not finished yet, so there are a few places that will need the distinction between surface and volume (like has_solid_objects), but this is fine to me.
Maybe I would open an issue about the fact that there are solid volume, but it needs proper implementation for contacts.

include/core/solid_objects_parameters.h

include/dem/data_containers.h

acdaigneault · 2024-06-11T20:18:52Z

include/dem/particle_wall_broad_search.h

@@ -141,19 +141,19 @@ class ParticleWallBroadSearch

  void
  particle_floating_mesh_contact_search(


The name of the function is still particle_floating_mesh_contact_search()

source/dem/dem.cc

acdaigneault · 2024-06-12T23:13:18Z

Just saw that there is a test called floating_mesh.prm if you want to change it

oguevremont · 2024-06-14T13:15:27Z

CHANGELOG.md

+
+### Changed
+
+- MINOR A new subsection ``solid surfaces`` need to be used when defining solid objects in the parameter file. For more information, see the solid object documentation. [#1169](https://github.com/chaos-polymtl/lethe/pull/1169)


Suggested change

- MINOR A new subsection ``solid surfaces`` need to be used when defining solid objects in the parameter file. For more information, see the solid object documentation. [#1169](https://github.com/chaos-polymtl/lethe/pull/1169)

- MINOR A new subsection ``solid surfaces`` needs to be used when defining solid objects in the parameter file. For more information, see the solid object documentation. [#1169](https://github.com/chaos-polymtl/lethe/pull/1169)

doc/source/examples/dem/granular-dam-break/granular-dam-break.rst

examples/dem/3d-dam-break/granular-dam-break-H-40cm.prm

examples/dem/3d-dam-break/granular-dam-break.prm

tests/dem/volume_solid_object_displacement.cc

doc/source/parameters/dem/dem.rst

doc/source/parameters/dem/solid_objects.rst

acdaigneault

The content of the Miscellaneous section is actually matters of the Documentation in the PR description.
Also, is there a reason you don't resolve the comments in the PR once the topic is discussed or modification has been applied? When I review I think that it's not done when it's still there, and this is why I do not rereview or approve. So I just want to know if there is a specific reason and next time I should just change the way I understand it :)
Otherwise, all good for me!

OGaboriault · 2024-06-17T16:56:27Z

The content of the Miscellaneous section is actually matters of the Documentation in the PR description. Also, is there a reason you don't resolve the comments in the PR once the topic is discussed or modification has been applied? When I review I think that it's not done when it's still there, and this is why I do not rereview or approve. So I just want to know if there is a specific reason and next time I should just change the way I understand it :) Otherwise, all good for me!

I don't get what you mean about the Miscellaneous section . I did add the changed parameter, do I need to do something else?

About the resolve thing, the comments remaining were not modification requests, but more like questions. I like to keep those open because sometime I'm not the one answering those question (like the one Bruno gave about the SerialSolid thing), or someone else would like to comment over my anwser.

blaisb · 2024-06-17T19:54:51Z

This is not reviewed and ready to merge until @oguevremont has approved the PR.... then I'll review/merge

blaisb

1-2 last things, seems good to go.
I presume the virtual wall (instead of floating wall) will be made in a follow-up PR?

CHANGELOG.md

blaisb · 2024-06-17T20:07:53Z

doc/source/parameters/dem/dem.rst

+Insertion information including the dimensions of the insertion box, insertion frequency, etc. are defined in the ``insertion info`` section. 
+The``mesh`` section defines the simulation triangulation and refinements. 
+In the ``DEM boundary conditions`` section, boundaries can be defined as outlets or they can get periodicity, rotation or translation.  
+In the ``floating walls`` section, hyperplanes can be added to the simulation domain. 


These were finally not renamed to virtual walls in this PR?

No, not in this PR.

blaisb · 2024-06-17T20:08:25Z

doc/source/parameters/dem/solid_objects.rst

+Solid Objects
+=============================
+
+Solid objects are finite auxiliary objects that can be stationary or in motion. Rotating impellers, sliding surfaces, and finite stoppers are examples of solid objects. The main differences between them and floating walls are:


Suggested change

Solid objects are finite auxiliary objects that can be stationary or in motion. Rotating impellers, sliding surfaces, and finite stoppers are examples of solid objects. The main differences between them and floating walls are:

Solid objects are finite auxiliary objects that can be stationary or in motion. Rotating impellers, sliding surfaces, and finite stoppers are examples of solid objects. The main differences between them and floating walls are:

Again the change to virtual wall was not made here?

OGaboriault · 2024-06-17T20:21:58Z

1-2 last things, seems good to go. I presume the virtual wall (instead of floating wall) will be made in a follow-up PR?

Yes, that what I had in mind regarding the virtual walls.

Co-authored-by: Bruno Blais <blais.bruno@gmail.com>

include/core/solid_objects_parameters.h

include/dem/particle_wall_broad_search.h

guevremont comment Co-authored-by: Olivier Guévremont <guevremont.o@gmail.com>

Description Solid objects are currently only using simplex. This can be problematic since double contacts can occur at the junction of two triangles. This PR aims at introducing solid objects built from volume elements, which could solve this problem. The contact between particle and volume 3D object is not implemented yet. Only in the creation and the displacement. Testing A new test has been implemented. (volume_solid_object_displacement.cc) Documentation Old simulation parameters have been renamed. The center of rotation was being defined by 3 parameters. Subsection center of rotation and its three parameters (x, y and z) have been replaced by one parameter named center of rotation using a list of doubles. A new subsection solid surfaces need to be used when defining solid object in the parameter file. Co-authored-by: Audrey Collard-Daigneault <71884806+acdaigneault@users.noreply.github.com> Co-authored-by: Olivier Guévremont <guevremont.o@gmail.com> Co-authored-by: Bruno Blais <blais.bruno@gmail.com>

OGaboriault added Documentation Ready for review labels Jun 10, 2024

OGaboriault requested review from oguevremont and acdaigneault June 10, 2024 19:02

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OGaboriault changed the title ~~Dem moving manifold~~ Dem volume solid objects Jun 10, 2024

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OGaboriault added 11 commits June 15, 2024 22:52

Added subsection

38e912d

Next step, map the 3d object in the bg triangulation

0ad4e50

Need to create tests

374c787

Change the parameter type

99c1e02

ParseFunction -> Function , updated application test prm

e41ce62

New parameter for the center of rotation

5e485ce

Change the type of the displacement function. Need to add a test

26880e3

Working on test, push to work on the desktop

03c56fd

Indent + test works

da5a469

Typo in the doc

f2ea67b

Doc

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OGaboriault force-pushed the dem_moving_manifold branch from d038b67 to 314b067 Compare June 16, 2024 03:28

Change function name + indent

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.msh

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Application test

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Apply suggestions from code review

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Co-authored-by: Bruno Blais <blais.bruno@gmail.com>

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guevremont comment Co-authored-by: Olivier Guévremont <guevremont.o@gmail.com>

@param

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blaisb deleted the dem_moving_manifold branch June 18, 2024 12:26

		std::vector<std::shared_ptr<SerialSolid<dim - 1, dim>>> solids_2d;
		std::vector<std::shared_ptr<SerialSolid<dim, dim>>> solids_3d;

		simulation_control->get_output_name() + ".solid_object." +
		Utilities::int_to_string(dim, 1) + "." + Utilities::int_to_string(id, 2);

	std::vector<double> angular_vector = {-0.39269908169, 0., 0.}; // 0.125 * pi
	std::vector<double> angular_vector = {-0.39269908169, 0., 0.}; // - 0.125 * pi

		@@ -141,19 +141,19 @@ class ParticleWallBroadSearch

		void
		particle_floating_mesh_contact_search(


		### Changed

		- MINOR A new subsection ``solid surfaces`` need to be used when defining solid objects in the parameter file. For more information, see the solid object documentation. [#1169](https://github.com/chaos-polymtl/lethe/pull/1169)

	Solid objects are finite auxiliary objects that can be stationary or in motion. Rotating impellers, sliding surfaces, and finite stoppers are examples of solid objects. The main differences between them and floating walls are:
	Solid objects are finite auxiliary objects that can be stationary or in motion. Rotating impellers, sliding surfaces, and finite stoppers are examples of solid objects. The main differences between them and floating walls are:

Dem volume solid objects #1169

Dem volume solid objects #1169

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OGaboriault commented Jun 10, 2024 • edited Loading

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Miscellaneous (will be removed when merged)

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