uniformisation lecture/ecriture VTK

python/fluid.py

@@ -326,13 +326,12 @@ class FluidProblem :
             bnds[bname.value] = nodes
         return bnds
 
-    def export_vtk(self, output_dir, t, it,stab=False) :
+    def write_vtk(self, output_dir, it ,t, stab=False):
         """Writes output file for post-visualization.
-
         Keyword arguments:
         output_dir -- Output directory
-        t -- Computation time
         it -- Computation iteration
+        t -- Computation time
         stab -- If True exports the stabilisation parametres in the output files
         """
         v = self.solution()[:,:self._dim]
@@ -359,12 +358,17 @@ class FluidProblem :
         offsets = np.cumsum(np.repeat([self._dim+1],connectivity.shape[0])).astype(np.int32)
         VTK.write(output_dir+"/fluid",it,t,(types,connectivity,offsets),self.coordinates(),data,field_data,cell_data)
 
-    def import_vtk(self, filename) :
+    def export_vtk(self, output_dir, t, it, stab=False) :
+        print("Careful this function is deprecated... \n\tUse write_vtk instead !")
+        self.write_vtk(output_dir, it, t, stab)
+
+    def read_vtk(self, dirname, i):
         """Reads output file to reload computation.
 
         Keyword arguments:
         filename -- Name of the file to read
         """
+        filename = dirname + "/fluid_%05d.vtu"%i
         x,cells,data,cdata,fdata = VTK.read(filename)
         mesh_boundaries = {name[9:]:nodes for name,nodes in fdata.items() if name.startswith("Boundary ")}
         cbnd_names = (c_char_p*len(mesh_boundaries))(*(i.encode() for i in mesh_boundaries.keys()))
@@ -390,6 +394,34 @@ class FluidProblem :
         self.old_porosity()[:] = data["old_porosity"]
         self.sys = None
 
+
+    def import_vtk(self, filename) :
+        print("Careful this function is deprecated... \n\tUse read_vtk instead !")
+        x,cells,data,cdata,fdata = VTK.read(filename)
+        mesh_boundaries = {name[9:]:nodes for name,nodes in fdata.items() if name.startswith("Boundary ")}
+        cbnd_names = (c_char_p*len(mesh_boundaries))(*(i.encode() for i in mesh_boundaries.keys()))
+        el = cells["connectivity"].reshape([-1,self._dim+1])
+        nbnd = len(mesh_boundaries)
+        bnds = np.vstack(list(mesh_boundaries.values()))
+        bnd_tags = np.repeat(list(range(nbnd)),list([v.shape[0] for v in mesh_boundaries.values()]))
+        bnd_tags = np.require(bnd_tags,np.int32,"C")
+        self._lib.mesh_new_from_elements.restype = c_void_p
+        _mesh = c_void_p(self._lib.mesh_new_from_elements(
+                c_int(x.shape[0]),_np2c(x,np.float64),
+                c_int(el.shape[0]),_np2c(el,np.int32),
+                c_int(bnds.shape[0]),_np2c(bnds,np.int32),
+                _np2c(bnd_tags,np.int32),c_int(len(cbnd_names)),cbnd_names,
+                _np2c(data["parent_node_id"],np.int32) if "parent_node_id"  in data else None))
+        self._lib.fluid_problem_set_mesh(self._fp, _mesh)
+        sol = self.solution()
+        sol[:,:self._dim] = data["velocity"][:,:self._dim]
+        sol[:,[self._dim]] = data["pressure"]
+        if self._n_fluids == 2 :
+            self.concentration_dg()[:] = cdata["concentration"]
+        self.porosity()[:] = data["porosity"]
+        self.old_porosity()[:] = data["old_porosity"]
+        self.sys = None
+        
     def compute_node_force(self, dt) :
         """Computes the forces to apply on each grain resulting from the fluid motion.
 

python/scontact.py

@@ -454,10 +454,9 @@ class ParticleProblem :
         
         periodicX, periodicCells,_, periodicCellsData, periodicFieldsData = VTK.read(dirname+"/periodicBoundaries_%05d.vtu"%i)
         entityTransformation = periodicFieldsData["Entity_transformation"]
-        entity_ids = np.hstack(periodicCellsData["Entity_id"])
+        entity_ids = periodicCellsData["Entity_id"].ravel()
         periodicOffsets = np.hstack([[0], periodicCells["offsets"]])
         periodicEl = periodicCells["connectivity"]
-
         # add entity
         for entity_id in range(np.shape(entityTransformation)[0]):
             trans = tuple(entityTransformation[entity_id])

validation/cavity/cavity.py

@@ -85,7 +85,7 @@ class Poiseuille(unittest.TestCase) :
         #s[:,3] = -rho*g*(1-x[:,1])
 
 
-        fluid.export_vtk(outputdir,0,0)
+        fluid.write_vtk(outputdir,0,0)
 
         ii = 0
         tic = time.time()
@@ -96,7 +96,7 @@ class Poiseuille(unittest.TestCase) :
             #Output files writting
             if ii %outf == 0 :
                 ioutput = int(ii/outf) + 1
-                fluid.export_vtk(outputdir, t, ioutput)
+                fluid.write_vtk(outputdir, ioutput, t)
             ii += 1
             print("%i : %.2g/%.2g (cpu %.6g)" % (ii, t, tEnd, time.time() - tic))
             

validation/darcy/darcy.py

@@ -71,7 +71,7 @@ class Darcy(unittest.TestCase) :
                     x[i] = x[i]+x_r
                 if y[i]+y_r<L-r and y[i]+y_r>r-L:
                     y[i] = y[i]+y_r
-                p.add_particle((x[i], y[i]), r, r**2 * np.pi * rhop);
+                p.add_particle((x[i], y[i]), r, r**2 * np.pi * rhop)
             p.write_vtk(filename,0,0)
 
         n_test = 10
@@ -115,7 +115,7 @@ class Darcy(unittest.TestCase) :
             fluid.set_wall_boundary("Top",velocity=[0,0])
             fp = np.zeros_like(fluid.porosity())
             fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity(), p.contact_forces())
-            fluid.export_vtk(outputdir,0,0)
+            fluid.write_vtk(outputdir,0,0)
 
             t = 0
             ii = 0
@@ -129,7 +129,7 @@ class Darcy(unittest.TestCase) :
                 if ii %outf == 0 :
                     ioutput = int(ii/outf) + 1
                     p.write_vtk(outputdir, ioutput, t)
-                    fluid.export_vtk(outputdir, t, ioutput)
+                    fluid.write_vtk(outputdir, ioutput, t)
                 ii += 1
                 print("%i : %.2g/%.2g (cpu %.6g)" % (ii, t, tEnd, time.time() - tic))
             

validation/dieSwell/dieSwell.py

@@ -105,7 +105,7 @@ class DieSwell(unittest.TestCase):
         #
         fs = time_integration.FreeSurface(fluid,"TopRight","BottomRight",isCentered=False)
 
-        fluid.export_vtk(outputdir,0,0)
+        fluid.write_vtk(outputdir,0,0)
         tic = time.time()
         #
         # COMPUTATION LOOP
@@ -120,7 +120,7 @@ class DieSwell(unittest.TestCase):
             # Output files writting
             if ii %outf == 0 :
                 ioutput = int(ii/outf) + 1
-                fluid.export_vtk(outputdir, t, ioutput)
+                fluid.write_vtk(outputdir, ioutput, t)
             ii += 1
             print("%i : %.2g/%.2g (cpu %.6g)" % (ii, t, tEnd, time.time() - tic))
         swelling_experiment = 1.02                  # Value from "Goren, S. L., & Wronski, S. (1966). 

validation/oneGrain/oneGrain.py

@@ -87,7 +87,7 @@ class Poiseuille(unittest.TestCase) :
 
             fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity(), p.contact_forces())
 
-            fluid.export_vtk(outputdir,0,0)
+            fluid.write_vtk(outputdir,0,0)
 
             G = p.mass()*g
             ii = 0
@@ -98,7 +98,7 @@ class Poiseuille(unittest.TestCase) :
                 #Output files writting
                 if ii %outf == 0 :
                     ioutput = int(ii/outf) + 1
-                    fluid.export_vtk(outputdir, t, ioutput)
+                    fluid.write_vtk(outputdir, ioutput, t)
                     p.write_vtk(outputdir, ioutput, t)
                 ii += 1
                 print("%i : %.2g/%.2g (cpu %.6g)" % (ii, t, tEnd, time.time() - tic))

validation/periodic2d/periodic2d.py

@@ -69,8 +69,8 @@ class Periodic2d(unittest.TestCase):
         p.add_particle((r,0.5),r,r**2*np.pi*rhop)
         p.add_particle((L - 2*r,0.5),r,r**2*np.pi*rhop)
         p.velocity()[1,0] = 0.5
-
         p.write_vtk(outputdir,0,0)
+        p.read_vtk(outputdir,0)
 
         #Object fluid creation + Boundary condition of the fluid (field 0 is horizontal velocity; field 1 is vertical velocity; field 2 is pressure)
         fluid = mbfluid.FluidProblem(2,g,mu,rho,petsc_solver_type="-pc_type lu")
@@ -87,7 +87,7 @@ class Periodic2d(unittest.TestCase):
 
         #set initial_condition
         fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity(),p.contact_forces())
-        fluid.export_vtk(outputdir,0,0)
+        fluid.write_vtk(outputdir,0,0)
 
         #Initial time and iteration
         t = 0
@@ -99,10 +99,13 @@ class Periodic2d(unittest.TestCase):
         #
         # COMPUTATION LOOP
         #
+        haveCrossed = 0
         while t < tEnd :
             # Time integration
             time_integration.iterate(fluid,p,dt,external_particles_forces=G)
 
+            if np.max(p.position()[:,0]) > L:
+                haveCrossed = 1
             p.position()[:,0] = np.fmod(p.position()[:,0],L)
             ind = np.where(p.position()[:,0] <= 0)
             p.position()[ind,0] += L
@@ -111,10 +114,11 @@ class Periodic2d(unittest.TestCase):
             t += dt
             if ii %outf == 0 :
                 ioutput = int(ii/outf) + 1
-                fluid.export_vtk(outputdir, t, ioutput)
+                fluid.write_vtk(outputdir, ioutput, t)
                 p.write_vtk(outputdir, ioutput, t)
             ii += 1
             print("%i : %.2g/%.2g (cpu %.6g)" % (ii, t, tEnd, time.time() - tic))
 
             error = np.min(np.linalg.norm(p.position()[1,:] - p.position()[0,:]))
             self.assertGreater(error, r, "error is too large in periodic 2d")
+        self.assertEqual(haveCrossed, 1, "No periodic boundary in periodic 2d")

validation/periodic3d/periodic3d.py

@@ -88,7 +88,7 @@ class Periodic2d(unittest.TestCase):
         fluid.set_strong_boundary("X",3,0)
         #Set location of the particles in the mesh and compute the porosity in each computation cell
         fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity(), p.contact_forces())
-        fluid.export_vtk(outputdir,0,0)
+        fluid.write_vtk(outputdir,0,0)
 
 
         # Initial time and iteration
@@ -101,9 +101,12 @@ class Periodic2d(unittest.TestCase):
         #
         # COMPUTATION LOOP
         #
+        haveCrossed = 0
         while t < tEnd :
-            time_integration.iterate(None, p, dt,min_nsub=5, contact_tol = 1e-8,external_particles_forces=G)
+            time_integration.iterate(fluid, p, dt,min_nsub=5, contact_tol = 1e-8,external_particles_forces=G)
 
+            if np.max(p.position()[:,0]) > L:
+                haveCrossed = 1
             p.position()[:,0] = np.fmod(p.position()[:,0],L)
             ind = np.where(p.position()[:,0] <= 0)
             p.position()[ind,0] += L
@@ -113,9 +116,10 @@ class Periodic2d(unittest.TestCase):
             if ii %outf == 0 :
                 ioutput = int(ii/outf) + 1
                 p.write_vtk(outputdir, ioutput, t)
-                fluid.export_vtk(outputdir, t, ioutput)
+                fluid.write_vtk(outputdir, ioutput, t)
             ii += 1
             print("%i : %.2g/%.2g (cpu %.6g)" % (ii, t, tEnd, time.time() - tic))
 
             error = np.min(np.linalg.norm(p.position()[1,:] - p.position()[0,:]))
             self.assertGreater(error, r, "error is too large in periodic 3d")
+        self.assertEqual(haveCrossed, 1, "No periodic boundary in periodic 3d")
\ No newline at end of file

validation/poiseuille/poiseuille-2fluids.py

@@ -107,7 +107,7 @@ class Poiseuille(unittest.TestCase) :
         mu = nu0*rho
         vI = 1/(120*mu)  
 
-        fluid.export_vtk(outputdir,0,0)
+        fluid.write_vtk(outputdir,0,0)
 
         ii = 0
         tic = time.time()
@@ -118,7 +118,7 @@ class Poiseuille(unittest.TestCase) :
             #Output files writting
             if ii %outf == 0 :
                 ioutput = int(ii/outf) + 1
-                fluid.export_vtk(outputdir, t, ioutput)
+                fluid.write_vtk(outputdir, ioutput, t)
             ii += 1
             print("%i : %.2g/%.2g (cpu %.6g)" % (ii, t, tEnd, time.time() - tic))
             

validation/poiseuille/poiseuille.py

@@ -79,7 +79,7 @@ class Poiseuille(unittest.TestCase) :
 
         #set initial_condition
     
-        fluid.export_vtk(outputdir,0,0)
+        fluid.write_vtk(outputdir,0,0)
 
         ii = 0
         tic = time.time()
@@ -90,7 +90,7 @@ class Poiseuille(unittest.TestCase) :
             #Output files writting
             if ii %outf == 0 :
                 ioutput = int(ii/outf) + 1
-                fluid.export_vtk(outputdir, t, ioutput)
+                fluid.write_vtk(outputdir, ioutput, t)
             ii += 1
             print("%i : %.2g/%.2g (cpu %.6g)" % (ii, t, tEnd, time.time() - tic))
             

validation/weight/weight.py

@@ -122,7 +122,7 @@ class Weight(unittest.TestCase) :
             t += dt
             if ii %outf == 0 :
                 ioutput = int(ii/outf) + 1
-                #p.write_vtk(outputdir, ioutput, t)
+                p.write_vtk(outputdir, ioutput, t)
             print("%i : %.2g/%.2g" % (ii, t, tEnd))
         error = np.sqrt(sum(sum(forces) - bnd_forces)**2)
         error /= np.sqrt(sum(sum(forces)**2))