Add ElementCoordinatesMappingLocal class #655

norihiro-w · 2015-04-23T11:00:04Z

This PR is a part of #595 and adds mapping of lower dimensional elements (e.g. line in 2D, tri in 3D) between global and local coordinates. The mapping functionality will be used during calculation of shape functions and mapping of tensor material properties like permeability.

norihiro-w · 2015-04-23T11:02:35Z

Remark: one of the tests is not working right now due to an issue in computeRotationMatrixToXY.(). Tom will fix it (#659).

endJunction · 2015-04-23T12:22:47Z

GeoLib/AnalyticalGeometry.h

@@ -60,11 +60,28 @@ Orientation getOrientation (const GeoLib::Point* p0,
 * @param plane_normal the normal of the plane the polygon is located in
 * @param d parameter from the plane equation
 */
-void getNewellPlane (const std::vector<GeoLib::Point*>& pnts,
+template <class T_POINT>
+void getNewellPlane (const std::vector<T_POINT*>& pnts,


From the function name it is not clear what is modified and how.
Is it possible to return the normal vector and the distance, instead of modifying values?

Update: never mind the Newell, I didn't know the Newell's method for computing a plane from a polygon.

You are right, we should rename the method to something like getSupportingPlane. The algorithm uses Newell's method, described in the book "Real-Time Collision Detection" from Christer Ericson. This fact is also missing in the documentation.
@norihiro-w Should I update the branch or should we make a separate PR?

you can make a separate PR

norihiro-w · 2015-04-24T09:24:05Z

This PR should be merged after #659 by Tom. I will rebase my commits to it

norihiro-w · 2015-04-24T12:02:40Z

rebased to #659

endJunction · 2015-04-24T15:48:12Z

MeshLib/CoordinateSystem.h

+ */
+struct CoordinateSystemType
+{
+    enum type


Better to use enum class directly.

i initially tried to use it but changed it to this way because the code is shorter and simpler as I don't need to make cast (from enum class to int) each time whenever bit operation is used.

TomFischer · 2015-04-27T07:43:26Z

@norihiro-w Please let me know if I should help you fixing some of the issues.

TomFischer · 2015-04-27T11:17:35Z

MeshLib/ElementCoordinatesMappingLocal.cpp

+    // rotate the point coordinates
+    for(unsigned i = 0; i < ele.getNNodes(); i++)
+    {
+        Eigen::Vector3d  x_new = matR2local * Eigen::Map<Eigen::Vector3d>(const_cast<double*>(vec_pt[i]->getCoords()));


Is there an obstacle to implement something like

MeshLib::Node operator*(EigenMatrix const& mat, MeshLib::Node const& node)

or

MathLib::Point3d operator*(EigenMatrix mat, MathLib::Point3d const& )?

I would prefer the second version, which is more general.

This would be
(1) more readable for the user and
(2) save some lines of code and
(3) omit some copies.

updated. please see ee35769

Small changes.

… size(), transposeInPlace(), setIdentity()

…inatesMappingLocal

norihiro-w · 2015-05-28T14:17:56Z

got the following errors with MSVC2013(Express). is there anyone having idea what to do? strangely the error does not appear on Jenkins.

Error   28  error C2280: 'ProcessLib::GroundwaterFlow::LocalAssemblerData<NumLib::ShapeLine2,NumLib::IntegrationGaussRegular<0x01>,GlobalMatrix_,GlobalVector_>::LocalAssemblerData(void)' : attempting to reference a deleted function C:\Users\watanabe\Documents\GitHub\ogs\AssemblerLib\LocalDataInitializer.h  59  1   ogs
Error   35  error C2542: 'NumLibFemIsoTest<Type>::D' : class object has no constructor for initialization   C:\Users\watanabe\Documents\GitHub\ogs\Tests\NumLib\TestFe.cpp  104 1   testrunner
Error   36  error C2542: 'NumLibFemIsoTest<Type>::expectedM' : class object has no constructor for initialization   C:\Users\watanabe\Documents\GitHub\ogs\Tests\NumLib\TestFe.cpp  104 1   testrunner
Error   37  error C2542: 'NumLibFemIsoTest<Type>::expectedK' : class object has no constructor for initialization   C:\Users\watanabe\Documents\GitHub\ogs\Tests\NumLib\TestFe.cpp  104 1   testrunner
Error   38  error C1903: unable to recover from previous error(s); stopping compilation C:\Users\watanabe\Documents\GitHub\ogs\Tests\NumLib\TestFe.cpp  109 1   testrunner

endJunction · 2015-05-28T15:37:40Z

I compiled the code with clang in RelWithDebInfo, which run through OK. But running tests ended in a SEGV for the:

[----------] 3 tests from NumLibFemIsoTest/5, where TypeParam = (anonymous namespace)::TestCase<FeTestData::TestFeLINE2, EigenFixedShapeMatrixPolicy>
[ RUN      ] NumLibFemIsoTest/5.CheckMassMatrix

test.
Running it in gdb does not always result in a SEGV: output and the backtrace here

Valgrind's memcheck does not show any invalid reads/writes until a SEGV. (see the above gist for details)

Update: After some through testing I'm not sure if my error report is related to the MSVC compilation error.
When removing the --march=native from the clang's compiler flags, everything is green again.
Clang is version 3.6.1. With gcc 5.1.0 and -march=native there is no error.

norihiro-w · 2015-05-31T13:12:07Z

update: the test failing on Jenkins cannot be reproduced on my windows (win7, MSVC2013 with update 4, 64bit). could be there is something unitialized or machine dependent bug.

norihiro-w · 2015-06-01T11:38:19Z

rebased to HEAD

ogsbot · 2015-06-01T11:45:49Z

Jenkins: OGS-6/Win-PRs failed: https://svn.ufz.de:8443/job/OGS-6/job/Win-PRs/140/

ogsbot · 2015-06-01T12:11:37Z

Jenkins: OGS-6/Win-PRs failed: https://svn.ufz.de:8443/job/OGS-6/job/Win-PRs/141/

norihiro-w · 2015-06-01T12:13:21Z

@bilke Eigen version used in OGS6/Win-PRs seems to be bit old (3.1.4). Can you please replace it with the latest (3.2.4)?

…gen objects

ogsbot · 2015-06-01T12:56:15Z

Jenkins: OGS-6/Win-PRs failed: https://svn.ufz.de:8443/job/OGS-6/job/Win-PRs/142/

bilke · 2015-06-01T13:03:25Z

I updated eigen to 3.2.4.

Jenkins test this please!

bilke · 2015-06-01T13:31:33Z

test this please

ogsbot · 2015-06-01T13:41:37Z

Jenkins: OGS-6/Win-PRs failed: https://svn.ufz.de:8443/job/OGS-6/job/Win-PRs/143/

norihiro-w · 2015-06-01T13:50:22Z

@bilke thanks!

norihiro-w · 2015-06-01T14:05:05Z

the problem was solved!

Add ElementCoordinatesMappingLocal class

ogsbot · 2020-06-19T12:15:15Z

OpenGeoSys development has been moved to GitLab.

See this pull request on GitLab.

norihiro-w force-pushed the add-element-mapping-local branch from ddbe526 to 8e4de41 Compare April 23, 2015 11:01

norihiro-w force-pushed the add-element-mapping-local branch from 8e4de41 to 7502a77 Compare April 23, 2015 11:12

norihiro-w added the please review label Apr 23, 2015

endJunction reviewed Apr 23, 2015
View reviewed changes

norihiro-w force-pushed the add-element-mapping-local branch from 7502a77 to a39c54e Compare April 24, 2015 09:21

norihiro-w force-pushed the add-element-mapping-local branch from a39c54e to 0187921 Compare April 24, 2015 12:02

endJunction reviewed Apr 24, 2015
View reviewed changes

TomFischer reviewed Apr 27, 2015
View reviewed changes

norihiro-w added the stop review 🛑 label Apr 27, 2015

TomFischer and others added 8 commits May 28, 2015 15:28

[T/MeL] Fix warnings for unused variables.

3fe0ece

deactivate a debug function in tests

02611d4

use for each

8c11f20

rename vec_pt with vec_nodes

26d3ffb

[MeL] Consistent tabs/ws and cleanup semicolons.

4822a2f

Merge pull request #37 from endJunction/add-element-mapping-local

745b0a1

Small changes.

extend DenseMatrix to support several Eigen matrix functions: data(),…

0343c32

… size(), transposeInPlace(), setIdentity()

support DenseMatrix as a default rotation matrix type in ElementCoord…

cb6b507

…inatesMappingLocal

norihiro-w force-pushed the add-element-mapping-local branch from 96dc62f to cb6b507 Compare June 1, 2015 11:37

output found Eigen version during CMake

9d47397

need EIGEN_MAKE_ALIGNED_OPERATOR_NEW for a class having fixed size Ei…

d8b6e5d

…gen objects

fix a bug that new point was not initialized with zero

460d114

endJunction added a commit that referenced this pull request Jun 1, 2015

Merge pull request #655 from norihiro-w/add-element-mapping-local

4448b55

Add ElementCoordinatesMappingLocal class

endJunction merged commit 4448b55 into ufz:master Jun 1, 2015

norihiro-w deleted the add-element-mapping-local branch June 2, 2015 07:19

endJunction removed the please review label Jul 6, 2016

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Add ElementCoordinatesMappingLocal class #655

Add ElementCoordinatesMappingLocal class #655

norihiro-w commented Apr 23, 2015

norihiro-w commented Apr 23, 2015

endJunction Apr 23, 2015

TomFischer Apr 23, 2015

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ogsbot commented Jun 19, 2020

Add ElementCoordinatesMappingLocal class #655

Add ElementCoordinatesMappingLocal class #655

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