Add 3D motion of non spherical objects (chaos-polymtl#979)

Description of the problem
This PR aims to add support for the coupled angular motion of any 3D object. This includes the coupling with the fluid and the DEM interaction between these objects. The following elements are added: integration of the Euler angles in the DEM and in the CFD coupling, relevant parameters for the inertia and volume of the objects, A function to evaluate the distance between the two objects using the intersection of their level-set and their bounding box, a set of three boolean parameters that aimed at limiting the number of call to the DEM calculation.
While implementing these features, two bugs were found: A bug that affected the evaluation of the force when two particles were in contact. This bug was changing the force evaluation on a particle depending on the number of processors that were used. This bug comes from overconstrained cells (cells with all their DOF imposed by boundary conditions were poorly treated in the force evaluation). This modification changed the results of a few tests where contact played a role. However, the solution's behavior does not change significantly, and new results still agree well with previous results for cases with particle contact. The modification to the function generate_cut_cell_map and force_evaluation only addresses this bug.
Another bug for the evaluation of the gradient of superquadric was found. The gradient had a sign error if evaluated inside of the particle. The evaluation of the supequadric was also optimized by avoiding overshoot.
The new inertia required a modification of the load particle from the file option. To add the possibility of defining the inertia matrix in the load particle from the file option, we modified the syntax to be semicolon-separated instead of space-separated and added the volume variable.
Description of the solution
Add support for integrating the Euler angle in the coupling formulation and in the DEM. Move all the DEM calculations for contact force in the ib_particle_dem to take the contact point into account correctly and simplify the code.
Add the new function in the shape classes called distance_to_shape. This function looks for the minimum of the level set defined by the intersection of two shapes. Using this minimum, we can evaluate the overlap of the two shapes. This function combines a Cartesian search with a gradient direction search and a numerical gradient descent.
How Has This Been Tested?
A new test was added that modeled two ellipsoids in contact with each other and a wall.
All previous tests were verified, and an investigation was performed when the results were modified (e.g., pp_contact_test).
Previous examples were tested and run successfully.
A modified example was performed to test multiple superquadric shapes (64).
Documentation
The documentation was updated to reflect the new options and add some tips on using the new feature.
Future changes
This feature version remains experimental, and more tests and validation should be performed. An example with a validation case should be added.

Co-authored-by: Pierre <[email protected]>
Co-authored-by: Bruno Blais <[email protected]>
Co-authored-by: Olivier Guévremont <[email protected]>
Co-authored-by: OGaboriault <[email protected]>
Co-authored-by: Victor Oliveira Ferreira <[email protected]>
Co-authored-by: PierreLaurentinCS <[email protected]>
Former-commit-id: 72412e7

Author: 6 people

applications_tests/lethe-fluid-sharp/CMakeLists.txt

@@ -13,7 +13,7 @@ file(COPY check_point.triangulation DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/che
 file(COPY check_point.triangulation.info DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/check_point.${_build_type}/mpirun=1/")
 file(COPY check_point.triangulation_fixed.data DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/check_point.${_build_type}/mpirun=1/")
 file(COPY ib_force.00.dat DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/check_point.${_build_type}/mpirun=1/")
-file(COPY particles DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/load_particles_from_file_test.${_build_type}/mpirun=1/")
+file(COPY particles.input DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/load_particles_from_file_test.${_build_type}/mpirun=1/")
 file(COPY rbf_test_shape.input DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/flow_around_rbf.${_build_type}/mpirun=1/")
 file(COPY helix_composite_shape DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/cavatappi_composite_test.${_build_type}/mpirun=1/")
 file(COPY spooky_composite_shape DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/spooky_composite_test.${_build_type}/mpirun=1/")
@@ -29,4 +29,5 @@ if(CMAKE_BUILD_TYPE STREQUAL "Debug")
   set_tests_properties(lethe-fluid-sharp/pp_lubrication_test.debug PROPERTIES TIMEOUT 2000)
   set_tests_properties(lethe-fluid-sharp/coupled_moving_stokes.mpirun=2.debug PROPERTIES TIMEOUT 2000)
   set_tests_properties(lethe-fluid-sharp/pw_contact_test.debug PROPERTIES TIMEOUT 2000)
+  set_tests_properties(lethe-fluid-sharp/two_non_sphere_contact.debug PROPERTIES TIMEOUT 2000)
 endif()

applications_tests/lethe-fluid-sharp/almost_blocked_channels.output

@@ -25,5 +25,5 @@ Steady iteration:        2/2
 +------------------------------------------+
 particle_ID  time     T_x       T_y       T_z      f_x       f_y       f_z      f_xv     f_yv      f_zv      f_xp     f_yp      f_zp    
           0 2.0000 0.000000  0.000000  0.000224 0.006343  0.000008 0.000000 0.001028 0.000000 0.000000 0.005315  0.000008 0.000000 
-          1 2.0000 0.000000 0.000000 -0.000082 0.006045  0.000205  0.000000 0.000703  0.000000  0.000000 0.005342  0.000205 0.000000 
+          1 2.0000  0.000000 0.000000 -0.000078 0.006030 -0.000184  0.000000 0.000689  0.000000  0.000000 0.005341 -0.000184  0.000000 
           2 2.0000  0.000000 0.000000 -0.000003 0.006767 -0.000333  0.000000 0.000019  0.000000  0.000000 0.006748 -0.000333  0.000000 

applications_tests/lethe-fluid-sharp/check_point.ib_particles

@@ -1,4 +1,4 @@
-ID        p_x                 p_y                p_z                 v_x                 v_y                 v_z                 f_x                f_y                 f_z                f_xv                f_yv               f_zv                f_xp               f_yp               f_zp               omega_x            omega_y             omega_z               T_x                T_y                 T_z         
- 0 4.9999999990595612 12.7494136219654450 4.9999996232383346 -0.0000003761755033 -0.2345512138217047 -0.0001507046661186 -0.0000002973607462 0.0916813938745119 -0.0001193103214246 -0.0000004352142015 0.0067522410450954 -0.0000012355260728 0.0000001378534553 0.0849291528294165 -0.0001180747953518 -0.0000000925905109 0.0000000000054050 -0.0000000180642693 -0.0000370364945512 0.0000000021641789 -0.0000072258579833 
- 0 5.0000000000000000 12.7500000000000000 5.0000000000000000  0.0000000000000000  0.0000000000000000  0.0000000000000000 -0.0000002973607462 0.0916813938745119 -0.0001193103214246 -0.0000004352142015 0.0067522410450954 -0.0000012355260728 0.0000001378534553 0.0849291528294165 -0.0001180747953518  0.0000000000000000 0.0000000000000000  0.0000000000000000 -0.0000370364945512 0.0000000021641789 -0.0000072258579833 
- 0 5.0000000000000000 12.7500000000000000 5.0000000000000000  0.0000000000000000  0.0000000000000000  0.0000000000000000 -0.0000002973607462 0.0916813938745119 -0.0001193103214246 -0.0000004352142015 0.0067522410450954 -0.0000012355260728 0.0000001378534553 0.0849291528294165 -0.0001180747953518  0.0000000000000000 0.0000000000000000  0.0000000000000000 -0.0000370364945512 0.0000000021641789 -0.0000072258579833 
+ID        p_x                 p_y                p_z                 v_x                 v_y                 v_z                 f_x                f_y                 f_z                f_xv                f_yv               f_zv                f_xp               f_yp               f_zp             omega_x             omega_y            theta_x             theta_y             omega_z             theta_z              T_x                 T_y                 T_z         
+ 0 4.9999999990491526 12.7494122380370598 4.9999999990518997 -0.0000003803388930 -0.2351047851757901 -0.0000003792401519 -0.0000003030496276 0.0912431404139310 -0.0000003034800620 -0.0000004409559984 0.0068324972097559 -0.0000004409875651 0.0000001379063708 0.0844106432041751 0.0000001375075031 0.0000000182775778 -0.0000000000000049 0.0000000000456939 -0.0000000000000000 -0.0000000182776528 -0.0000000000456941 0.0000073145528819 -0.0000000000000270 -0.0000073145531960 
+ 0 5.0000000000000000 12.7500000000000000 5.0000000000000000  0.0000000000000000  0.0000000000000000  0.0000000000000000 -0.0000003030496276 0.0912431404139310 -0.0000003034800620 -0.0000004409559984 0.0068324972097559 -0.0000004409875651 0.0000001379063708 0.0844106432041751 0.0000001375075031 0.0000000000000000  0.0000000000000000 0.0000000000000000  0.0000000000000000  0.0000000000000000  0.0000000000000000 0.0000073145528819 -0.0000000000000270 -0.0000073145531960 
+ 0 5.0000000000000000 12.7500000000000000 5.0000000000000000  0.0000000000000000  0.0000000000000000  0.0000000000000000 -0.0000003030496276 0.0912431404139310 -0.0000003034800620 -0.0000004409559984 0.0068324972097559 -0.0000004409875651 0.0000001379063708 0.0844106432041751 0.0000001375075031 0.0000000000000000  0.0000000000000000 0.0000000000000000  0.0000000000000000  0.0000000000000000  0.0000000000000000 0.0000073145528819 -0.0000000000000270 -0.0000073145531960 

applications_tests/lethe-fluid-sharp/check_point.mpirun=1.output

@@ -10,15 +10,15 @@ Running on 1 MPI rank(s)...
    Volume of triangulation:      1600
 
 *********************************************************************************
-Transient iteration: 2        Time: 0.005    Time step: 0.0025   CFL: 0.00378095
+Transient iteration: 2        Time: 0.005    Time step: 0.0025   CFL: 0.00378987
 *********************************************************************************
-   Number of active cells:       6815
-   Number of degrees of freedom: 33652
+   Number of active cells:       6808
+   Number of degrees of freedom: 33596
    Volume of triangulation:      1600
 particle 0 position 5 12.7483 5
-particle 0 velocity -8.57092e-07 -0.452353 -0.000107099
+particle 0 velocity -8.61756e-07 -0.45284 -8.60545e-07
 +------------------------------------------+
 |  Force  summary particles                |
 +------------------------------------------+
-particle_ID  time     T_x     omega_x    T_y    omega_y     T_z     omega_z     f_x       v_x      p_x      f_y       v_y       p_y      f_z       v_z      p_z      f_xv      f_yv     f_zv      f_xp     f_yp     f_zp   
-          0 0.0050 -0.000019 0.000000 0.000000 0.000000 -0.000012 0.000000 0.000000 -0.000001 5.000000 0.104942 -0.452353 12.748283 0.000035 -0.000107 4.999999 -0.000001 0.012389 -0.000001 0.000000 0.092552 0.000036 
+particle_ID  time    T_x    omega_x  theta_x     T_y     omega_y   theta_y     T_z     omega_z   theta_z     f_x       v_x      p_x      f_y       v_y       p_y       f_z       v_z      p_z      f_xv      f_yv     f_zv      f_xp     f_yp     f_zp   
+          0 0.0050 0.000012 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000012 0.000000 0.000000 0.000000 -0.000001 5.000000 0.104994 -0.452840 12.748280 0.000000 -0.000001 5.000000 -0.000001 0.012447 -0.000001 0.000000 0.092547 0.000000 

applications_tests/lethe-fluid-sharp/check_point.simulationcontrol

@@ -3,6 +3,6 @@ dt_0 0.0025
 dt_1 0.0025
 dt_2 0.0025
 dt_3 0.0025
-CFL  0.00378095
+CFL  0.00378987
 Time 0.0025
 Iter 1

applications_tests/lethe-fluid-sharp/check_point.triangulation_fixed.data.REMOVED.git-id

@@ -1 +1 @@
-88e6400dc7f1fed59b7dac376737a33cac1ddc78
+6e3e0351c989cdc8da9f2567fa20edbcf9a17f17

applications_tests/lethe-fluid-sharp/coupled_moving_stokes.mpirun=2.output

@@ -10,30 +10,30 @@ Initial refinement in box - Step  1 of 1
 *******************************************************************************
 Transient iteration: 1        Time: 0.05     Time step: 0.05     CFL: 0       
 *******************************************************************************
-div u : 1.51111759282e-12
-error at the weak BC : 0.000124532067334
-L2 error velocity : 0.00158956635639 L2 error pressure: 0.0369356315003
-particle 0 position 0.997440813995 3.1785691023e-08 3.17858210487e-08
-particle 0 velocity -0.0511837200951 6.35713820461e-07 6.35716420975e-07
+div u : 2.43466360896e-12
+error at the weak BC : 0.000124532071685
+L2 error velocity : 0.00158956636743 L2 error pressure: 0.0369356375109
+particle 0 position 0.997440813986 3.18006235858e-08 3.1777347325e-08
+particle 0 velocity -0.0511837202703 6.36012471716e-07 6.355469465e-07
 +------------------------------------------+
 |  Force  summary particles                |
 +------------------------------------------+
-particle_ID  time       T_x           omega_x          T_y          omega_y           T_z           omega_z          f_x             v_x            p_x            f_y            v_y            p_y            f_z            v_z            p_z            f_xv           f_yv           f_zv           f_xp           f_yp            f_zp       
-          0 0.0500 0.000000000003 -0.000000000001 0.000452352958 0.000022626318 -0.000452352983 -0.000022626308 0.444942072384 -0.051183720095 0.997440813995 0.000013318039 0.000000635714 0.000000031786 0.000013317934 0.000000635716 0.000000031786 0.297188540782 0.000030193254 0.000030193209 0.147753531602 -0.000016875215 -0.000016875275 
+particle_ID  time        T_x          omega_x        theta_x          T_y          omega_y        theta_y           T_z           omega_z         theta_z          f_x             v_x            p_x            f_y            v_y            p_y            f_z            v_z            p_z            f_xv           f_yv           f_zv           f_xp           f_yp            f_zp       
+          0 0.0500 -0.000000000009 0.000000000008 0.000000000001 0.000452372620 0.000022619123 0.000001130956 -0.000452372613 -0.000022619130 -0.000001130956 0.444942080268 -0.051183720270 0.997440813986 0.000013306229 0.000000636012 0.000000031801 0.000013325152 0.000000635547 0.000000031777 0.297188544175 0.000030187635 0.000030195825 0.147753536094 -0.000016881406 -0.000016870673 
 
 ********************************************************************************
 Transient iteration: 2        Time: 0.125    Time step: 0.075    CFL: 0.0165057
 ********************************************************************************
-div u : 2.52610974673e-13
-error at the weak BC : 0.000587329285947
-L2 error velocity : 0.00405753965331 L2 error pressure: 0.120586738881
-particle 0 position 0.990003390197 9.87350627607e-08 9.87268312447e-08
-particle 0 velocity -0.127954808973 1.04682497146e-06 1.04664503159e-06
+div u : -3.1632465744e-13
+error at the weak BC : 0.000587329285964
+L2 error velocity : 0.00405753969248 L2 error pressure: 0.120586739061
+particle 0 position 0.99000339018 9.78804030564e-08 9.7824826966e-08
+particle 0 velocity -0.127954809041 1.02809447901e-06 1.02768473111e-06
 +------------------------------------------+
 |  Force  summary particles                |
 +------------------------------------------+
-particle_ID  time       T_x           omega_x          T_y          omega_y           T_z           omega_z          f_x             v_x            p_x             f_y            v_y            p_y             f_z            v_z            p_z            f_xv           f_yv           f_zv           f_xp           f_yp            f_zp       
-          0 0.1250 0.000000000008 -0.000000000001 0.001065407562 0.000085270095 -0.001065407586 -0.000085270082 1.142169660134 -0.127954808973 0.990003390197 -0.000000026369 0.000001046825 0.000000098735 -0.000000018913 0.000001046645 0.000000098727 0.746122264854 0.000021299506 0.000021302689 0.396047395281 -0.000021325875 -0.000021321602 
+particle_ID  time        T_x          omega_x        theta_x          T_y          omega_y        theta_y           T_z           omega_z         theta_z          f_x             v_x            p_x            f_y            v_y            p_y            f_z            v_z            p_z            f_xv           f_yv           f_zv           f_xp           f_yp            f_zp       
+          0 0.1250 -0.000000000020 0.000000000012 0.000000000030 0.001065372636 0.000085281721 0.000007527085 -0.001065372583 -0.000085281728 -0.000007527086 1.142169660645 -0.127954809041 0.990003390180 0.000000749759 0.000001028094 0.000000097880 0.000000759448 0.000001027685 0.000000097825 0.746122265860 0.000021631083 0.000021637296 0.396047394785 -0.000020881324 -0.000020877848 
  time    error_velocity   error_pressure 
-0.0500 1.589566356387e-03         0.0369 
-0.1250 4.057539653314e-03         0.1206 
+0.0500 1.589566367434e-03         0.0369 
+0.1250 4.057539692476e-03         0.1206 

applications_tests/lethe-fluid-sharp/flow_around_ellipsoid_rectangle.output

@@ -14,8 +14,8 @@ Steady iteration:        1/2
 |  Force  summary particles                |
 +------------------------------------------+
 particle_ID  time     T_x       T_y       T_z       f_x       f_y       f_z      f_xv      f_yv      f_zv     f_xp      f_yp      f_zp    
-          0 1.0000 -0.506350 -2.821483  2.355642 18.846185 -4.486911 -2.481077  6.564591 -0.286348 0.142814 12.281594 -4.200563 -2.623891 
-          1 1.0000  2.234653 -8.563906 14.526490 37.624523 -2.431316  0.858565 16.087240 -0.775825 1.705423 21.537283 -1.655491 -0.846858 
+          0 1.0000 -0.319224 -2.790041  2.919969 18.452830 -3.919410 -2.393904  6.543322 -0.280789 0.137993 11.909508 -3.638621 -2.531897 
+          1 1.0000  2.674703 -8.038619 14.141736 38.603082 -2.852982  1.053311 16.318084 -0.718644 1.718840 22.284997 -2.134338 -0.665529 
 
 *****************************
 Steady iteration:        2/2
@@ -28,4 +28,4 @@ Steady iteration:        2/2
 +------------------------------------------+
 particle_ID  time     T_x       T_y       T_z       f_x       f_y       f_z      f_xv      f_yv      f_zv     f_xp      f_yp      f_zp    
           0 2.0000 -0.896705 -3.070480  4.070378 24.561449 -5.315848 -2.531452 10.575164 -0.140790 0.784065 13.986285 -5.175058 -3.315518 
-          1 2.0000  3.387772 -8.472651 14.771933 45.887976 -3.065652  0.564865 19.744992 -0.546630 0.981405 26.142984 -2.519022 -0.416539 
+          1 2.0000  3.561520 -8.413456 14.508845 46.100476 -3.205490  0.625000 19.752743 -0.541710 0.986115 26.347733 -2.663781 -0.361114 

applications_tests/lethe-fluid-sharp/flow_around_torus.output

@@ -14,4 +14,4 @@ Steady iteration:        1/1
 |  Force  summary particles                |
 +------------------------------------------+
 particle_ID  time     T_x        T_y        T_z        f_x      f_y       f_z       f_xv      f_yv      f_zv      f_xp      f_yp      f_zp    
-          0 1.0000 -46.057942 -57.151966 -43.196935 62.585201 2.391831 -45.330981 33.185057 -1.141109 -0.086008 29.400144 3.532939 -45.244974
+          0 1.0000 -45.046800 -56.583090 -38.752022 61.084700 2.230158 -44.936232 32.246668 -1.253914 -0.157118 28.838032 3.484073 -44.779115 

applications_tests/lethe-fluid-sharp/ib_force.00.dat

@@ -1,2 +1,2 @@
-particle_ID  time     T_x     omega_x    T_y    omega_y     T_z     omega_z     f_x       v_x      p_x      f_y       v_y       p_y       f_z       v_z      p_z      f_xv      f_yv     f_zv      f_xp     f_yp     f_zp    
-     0.0000 0.0025 -0.000037 -0.000000 0.000000 0.000000 -0.000007 -0.000000 -0.000000 -0.000000 5.000000 0.091681 -0.234551 12.749414 -0.000119 -0.000151 5.000000 -0.000000 0.006752 -0.000001 0.000000 0.084929 -0.000118 
+particle_ID  time    T_x    omega_x  theta_x     T_y     omega_y   theta_y     T_z     omega_z   theta_z     f_x       v_x      p_x      f_y       v_y       p_y       f_z       v_z      p_z      f_xv      f_yv     f_zv      f_xp     f_yp     f_zp   
+          0 0.0025 0.000007 0.000000 0.000000 -0.000000 -0.000000 -0.000000 -0.000007 -0.000000 -0.000000 -0.000000 -0.000000 5.000000 0.091243 -0.235105 12.749412 -0.000000 -0.000000 5.000000 -0.000000 0.006832 -0.000000 0.000000 0.084411 0.000000