Refactoring ibm/sbm/unfitted methods (#905)

* Yy/debug pseudopenalty 2p (#904)

* Cekees/cleanup ib (#906)

* cleaned up some tests and removed some old code

* moved notebooks to lfs

* fix bug in particle_velocity and particle_signed_distance_normal sizing

* added pressure integral to cut cell approach

* use eN_k_3d instead of eN_k_nSpace for 2d particles (#915)

* fix added mass global residual assembly; enable Pres.LevelModel

* updated added mass comparison values

* update some test files and turn off cut cell integration

* disable MeshAdapt

* turn off optimization for travis compile

* reduce size of some tests

* update optimization level to 1

.gitattributes

@@ -19,3 +19,8 @@ proteus/tests/HotStart_3P/comparison_files/T01P1_hotstart.h5 filter=lfs diff=lfs
 proteus/tests/HotStart_3P/comparison_files/T01P2_hotstart.h5 filter=lfs diff=lfs merge=lfs -text
 proteus/tests/cylinder2D/sbm_3Dmesh/comparison_files/T001_P1_sbm_3Dmesh.h5 filter=lfs diff=lfs merge=lfs -text
 proteus/tests/cylinder2D/ibm_rans2p/comparison_files/T1_ibm_rans2p.h5 filter=lfs diff=lfs merge=lfs -text
+proteus/tests/cylinder2D/conforming_rans2p/plot_lift_drag_from_pv_files.ipynb filter=lfs diff=lfs merge=lfs -text
+proteus/tests/cylinder2D/conforming_rans3p/plot_lift_drag_from_pv_files.ipynb filter=lfs diff=lfs merge=lfs -text
+proteus/tests/cylinder2D/ibm_method/plot_lift_drag_force_from_particle.ipynb filter=lfs diff=lfs merge=lfs -text
+proteus/tests/cylinder2D/ibm_rans2p/plot_lift_drag_force_from_particle.ipynb filter=lfs diff=lfs merge=lfs -text
+proteus/tests/cylinder2D/sbm_method/plot_lift_drag_force_from_particle.ipynb filter=lfs diff=lfs merge=lfs -text

.travis.yml

@@ -42,7 +42,7 @@ install:
 - export PATHSAVE=$PATH
 - export PATH=$PWD/linux2/bin:$PATH
 - export LD_LIBRARY_PATH=$PWD/linux2/lib:$LD_LIBRARY_PATH
-- PROTEUS_OPT="-O2 -UNDEBUG -w" FC=gfortran CC=mpicc CXX=mpicxx make develop N=2
+- PROTEUS_OPT="-w -O1 -UNDEBUG" FC=gfortran CC=mpicc CXX=mpicxx make develop N=2
 - export SSL_CERT_DIR=/etc/ssl/certs
 - pip install matplotlib
 

proteus/mprans/AddedMass.h

@@ -511,16 +511,16 @@ namespace proteus
                   Aij[36*eBMT+added_mass_i+6*4] += (rz*px-rx*pz)*dS;
                   Aij[36*eBMT+added_mass_i+6*5] += (rx*py-ry*px)*dS;
                 }
-              //
-              //update the element and global residual storage
-              //
-              for (int i=0;i<nDOF_test_element;i++)
-                {
-                  int eN_i = eN*nDOF_test_element+i;
-                  globalResidual[offset_u+stride_u*u_l2g[eN_i]] += elementResidual_u[i];
-                }//i
-            }//ebNE
-        }
+            }//kb
+          //
+          //update the element and global residual storage
+          //
+          for (int i=0;i<nDOF_test_element;i++)
+            {
+              int eN_i = eN*nDOF_test_element+i;
+              globalResidual[offset_u+stride_u*u_l2g[eN_i]] += elementResidual_u[i];
+            }//i
+        }//ebNE
     }
 
 

proteus/mprans/Pres.py

@@ -171,6 +171,7 @@ def postStep(self, t, firstStep=False):
                 r = 1
             else:
                 r = old_div(self.fluidModel.timeIntegration.dt, self.fluidModel.timeIntegration.dt_history[0])
+            self.model.p_sharp_dof[:] = self.model.u[0].dof + r * self.pressureIncrementModel.u[0].dof
             self.model.q_p_sharp[:] = self.model.q[('u', 0)] + r * self.pressureIncrementModel.q[('u', 0)]
             self.model.ebqe_p_sharp[:] = self.model.ebqe[('u', 0)] + r * self.pressureIncrementModel.ebqe[('u', 0)]
             self.model.q_grad_p_sharp[:] = self.model.q[('grad(u)', 0)] + r * self.pressureIncrementModel.q[('grad(u)', 0)]
@@ -354,6 +355,7 @@ def __init__(self,
             dc.nFreeDOF_global for dc in list(self.dirichletConditions.values())]
         self.nVDOF_element = sum(self.nDOF_trial_element)
         self.nFreeVDOF_global = sum(self.nFreeDOF_global)
+        self.p_sharp_dof=self.u[0].dof.copy()
         #
         NonlinearEquation.__init__(self, self.nFreeVDOF_global)
         #

proteus/mprans/PresInit.py

@@ -394,24 +394,6 @@ def __init__(self,
             self.mesh.nElements_global *
             self.mesh.nElementBoundaries_element *
             self.nElementBoundaryQuadraturePoints_elementBoundary)
-        if type(self.u[0].femSpace) == C0_AffineLinearOnSimplexWithNodalBasis:
-            # print self.nQuadraturePoints_element
-            if self.nSpace_global == 3:
-                assert(self.nQuadraturePoints_element == 5)
-            elif self.nSpace_global == 2:
-                assert(self.nQuadraturePoints_element == 6)
-            elif self.nSpace_global == 1:
-                assert(self.nQuadraturePoints_element == 3)
-
-            # print self.nElementBoundaryQuadraturePoints_elementBoundary
-            if self.nSpace_global == 3:
-                assert(self.nElementBoundaryQuadraturePoints_elementBoundary == 4)
-            elif self.nSpace_global == 2:
-                assert(self.nElementBoundaryQuadraturePoints_elementBoundary == 4)
-            elif self.nSpace_global == 1:
-                assert(self.nElementBoundaryQuadraturePoints_elementBoundary == 1)
-
-        # pdb.set_trace()
         #
         # simplified allocations for test==trial and also check if space is mixed or not
         #