updating testcases part 1

testcases/injectionWGrains/inject.py → testcases/deprecated/injectionWGrains/inject.py

@@ -63,7 +63,7 @@ fluid.set_open_boundary("Bottom",velocity=[0,outerBndV])
 ii = 0
 t = 0
 
-fluid.export_vtk(outputdir,0,0)
+fluid.write_vtk(outputdir,0,0)
 
 tic = time.clock()
 while t < tEnd : 
@@ -73,6 +73,6 @@ while t < tEnd :
     #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.clock() - tic))

testcases/injectionWGrains/inject1fGrains.py → testcases/deprecated/injectionWGrains/inject1fGrains.py

@@ -25,6 +25,7 @@
 # Injection of fluid in granular matrix immersed in the same fluid
 from migflow import fluid
 from migflow import scontact
+from migflow import time_integration
 
 import numpy as np
 import os
@@ -56,10 +57,10 @@ ii = 0
 
 
 # physical parameters
-g =  -9.81                 # gravity
+g =  np.array([0,-9.81])                 # gravity
 rho = 1000
 nu = 1e-6                            # kinematic viscosity
-r = 5e-4
+r = 1e-3
 N = 20000
 lx = .222
 ly = .16
@@ -88,28 +89,16 @@ fluid.set_open_boundary("Bottom",velocity=[0,outerBndV])
 ii = 0
 t = 0
 
-fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
-fluid.export_vtk(outputdir,0,0)
-fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
-tic = time.clock()
+fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity(),p.contact_forces())
+fluid.write_vtk(outputdir,0,0)
+tic = time.time()
 while t < tEnd : 
-    #Fluid solver
-    fluid.implicit_euler(dt)
-    forces = fluid.compute_node_force(dt)
-    #Computation of the new velocities
-    vn = p.velocity() + forces * dt / p.mass()
-    vmax = np.max(np.hypot(vn[:, 0], vn[:, 1]))
-    #number of sub time step
-    nsub = max(2, int(np.ceil((vmax * dt * 4)/min(p.r()))))
-    print("NSUB", nsub,"VMAX",vmax, "VMAX * dt", vmax * dt, "r", min(p.r()))
-    #Contact solver
-    for i in range(nsub) :
-        p.iterate(dt/nsub, forces)  
+    time_integration.iterate(fluid,p,dt,min_nsub=5,external_particles_forces=g*p.mass()) 
     t += dt
     #Output files writting
     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.clock() - tic))
+    print("%i : %.2g/%.2g (cpu %.6g)" % (ii, t, tEnd, time.time() - tic))

testcases/injectionWGrains/inject2f.py → testcases/deprecated/injectionWGrains/inject2f.py

@@ -24,6 +24,7 @@
 # TESTCASE DESCRIPTION
 # Injection of a light fluid in a heavier fluid
 from migflow import fluid
+from migflow import time_integration
 
 import numpy as np
 import os
@@ -74,8 +75,6 @@ fluid.set_wall_boundary("Lateral")
 fluid.set_open_boundary("Top",pressure=0,concentration=0)
 fluid.set_open_boundary("Bottom",velocity=[0,outerBndV],concentration=1)
 
-#fluid.set_concentration_cg(np.where(fluid.coordinates()[:,1]>0.32,1,0))
-
 ii = 0
 t = 0
 
@@ -83,11 +82,11 @@ fluid.export_vtk(outputdir,0,0)
 tic = time.time()
 while t < tEnd : 
     #Fluid solver
-    fluid.implicit_euler(dt)
+    time_integration.iterate(fluid,None,dt)
     t += dt
     #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))

testcases/injectionWGrains/inject2fGrains.py → testcases/deprecated/injectionWGrains/inject2fGrains.py

@@ -27,6 +27,7 @@
 from migflow import fluid
 from migflow import scontact
 from pylmgc90 import pre
+from migflow import time_integration
 import numpy as np
 import os
 import time
@@ -54,13 +55,13 @@ if not os.path.isdir(outputdir) :
 
 # physical parameters
 alpha = 0*np.pi/4.
-g =  -9.81*np.cos(alpha)                 # gravity
+g =  np.array([0,-9.81])                 # gravity
 rho0 = 1.117                             # fluid density
 rho1 = 1000
 nu1 = 1.57e-5                            # kinematic viscosity
 nu0 = 1e-6
 tEnd = 10                                # final time
-r = 5e-4
+r = 1e-3
 N = 10000*3
 lx = .222
 ly = .14*2
@@ -69,8 +70,6 @@ rhop = 2500
 dt = .0005                               # time step
 
 genInitialPosition(outputdir, N, r, lx, ly, rhop)
-
-friction=0.3
 p = scontact.ParticleProblem(2)
 p.read_vtk(outputdir,0)
 # number of iterations between output files
@@ -87,42 +86,21 @@ fluid.load_msh("mesh.msh")
 fluid.set_wall_boundary("Bottom")
 fluid.set_wall_boundary("Lateral")
 fluid.set_open_boundary("Top",pressure=0, concentration=1)
-fluid.set_open_boundary("Injection",velocity=[0, outerBndV], concentration=1)
-
-fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
+fluid.set_open_boundary("Injection",velocity=[0, outerBndV(1)], concentration=1)
+fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity(),p.contact_forces())
 
-#set initial_condition
-print(fluid.solution().shape, fluid.coordinates().shape)
-fluid.solution()[fluid.coordinates()[:,1]>0.3,3] = 1
 
-fluid.export_vtk(outputdir,0,0)
+fluid.write_vtk(outputdir,0,0)
 
 ii = 0
 tic = time.time()
-
-fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
 while t < tEnd : 
-#Adaptation of the mesh. Args are minimal mesh radius, maximal mesh radius and number of elements
-    #Fluid solver
-    fluid.implicit_euler(dt, newton_max_it=20)
-    if (ii%50==0 and ii != 0):
-       fluid.adapt_mesh(8e-2,3e-3,10000)
-    forces = fluid.compute_node_force(dt)
-    #Computation of the new velocities
-    vn = p.velocity() + forces * dt / p.mass()
-    vmax = np.max(np.hypot(vn[:, 0], vn[:, 1]))
-    #number of sub time step
-    nsub = max(1, int(np.ceil((vmax * dt * 4)/min(p.r()))))
-    print("NSUB", nsub,"VMAX",vmax, "VMAX * dt", vmax * dt, "r", min(p.r()))
-    #Contact solver
-    for i in range(nsub) :
-        p.iterate(dt/nsub, forces)  
+    time_integration.iterate(fluid,p,dt,external_particles_forces=g*p.mass()) 
     t += dt
-    fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
     #Output files writting
     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))

testcases/injectionWGrains/inject2fGrainsReload.py → testcases/deprecated/injectionWGrains/inject2fGrainsReload.py

@@ -38,7 +38,7 @@ if not os.path.isdir(outputdir) :
 
 #physical parameters
 alpha = 0*np.pi/4.
-g =  -9.81*np.cos(alpha)                                      # gravity
+g =  np.array([0,-9.81])                                 # gravity
 rho0 = 1.117                                      # fluid density
 rho1 = 1000
 nu1 = 1.57e-5                                   # kinematic viscosity
@@ -75,37 +75,20 @@ fluid.import_vtk(outputrel+"/fluid_%05d.vtu"%iReload)
 
 rel = 1
 
-fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity(),rel)
+fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity(),p.contact_forces())
 ii = (iReload-1)*outf+1
 t=ii*dt
-tic = time.clock()
+tic = time.time()
 outf1 = 25
 ii1 = 0
 while t < tEnd : 
-#Adaptation of the mesh. Args are minimal mesh radius, maximal mesh radius and number of elements
-    #Fluid solver
-    fluid.implicit_euler(dt)
-    if (ii%65==0 and ii != 0):
-       fluid.adapt_mesh(8e-2,3e-3,10000)
-
-    rel = 0
-    forces = fluid.compute_node_force(dt)
-    #Computation of the new velocities
-    vn = p.velocity() + forces * dt / p.mass()
-    vmax = np.max(np.hypot(vn[:, 0], vn[:, 1]))
-    #number of sub time step
-    nsub = max(1, int(np.ceil((vmax * dt * 4)/min(p.r()))))
-    print("NSUB", nsub,"VMAX",vmax, "VMAX * dt", vmax * dt, "r", min(p.r()))
-    #Contact solver
-    for i in range(nsub) :
-        p.iterate(dt/nsub, forces)  
-    fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
+    time_integration.iterate(fluid,p,dt,external_particles_forces=g*p.mass())
     #Output files writting
     if ii %outf1 == 0 :
         ioutput = int(ii1/outf1) + 1
         print("IOUTPUT",ioutput,"TIME",t,"II", ii)
         p.write_vtk(outputdir, ioutput, t)
-        fluid.export_vtk(outputdir, t, ioutput)
+        fluid.write_vtk(outputdir, ioutput, t)
     t += dt
     ii += 1
     ii1 += 1

testcases/dieSwell/dieSwell.py

@@ -79,7 +79,7 @@ fluid.set_open_boundary("Right", pressure = 0)
 #
 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
@@ -94,7 +94,7 @@ while t < tEnd :
     # 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))
 print(f"\tSwelling = {swelling}")

testcases/drag-2d/depot/depot.py

@@ -37,11 +37,11 @@ def genInitialPosition(filename, r, H, ly, lx, rin, rhop) :
     rhop -- particles density        
     """
     # Particles structure builder
-    p = scontact.ParticleProblem(2)
+    p = scontact.ParticleProblem(2,True)
     # Load mesh.msh file specifying physical boundaries names
     p.load_msh_boundaries("mesh.msh", ["Inner","Left","Right","Bottom"],material="Steel")
-    x = np.arange(-lx+r, lx-r, 2*r)
-    y = np.arange(-ly+r, H-r, 2*r)
+    x = np.arange(-lx+r, lx-r, 2.1*r)
+    y = np.arange(-ly+r, H-r, 2.1*r)
 
     #Definition of the points where the particles are located
     x, y = np.meshgrid(x, y)
@@ -49,7 +49,7 @@ def genInitialPosition(filename, r, H, ly, lx, rin, rhop) :
     y = y.flat
     # Add a grain at each centre position
     for i in range(len(x)) :
-        r1 = np.random.uniform(0.4*r,r)
+        r1 = np.random.uniform(0.8*r,r)
         if x[i]**2 + y[i]**2 > (rin+r1)**2:
           p.add_particle((x[i], y[i]), r1, r**2 * np.pi * rhop,"Sand")
     p.write_vtk(filename,0,0)
@@ -70,16 +70,17 @@ tEnd = 10                                     # final time
 # Geometrical parameters
 ly = 0.7                                      # particles area height
 lx = 0.15                                     # particles area widht
-H = 2                                         # domain height
+H = 1.3                                         # domain height
 #
 # PARTICLE PROBLEM
 #
 # Initialise particles
 genInitialPosition(outputdir, r, H, ly, lx, rin, rhop)
-p = scontact.ParticleProblem(2,True,True)
-p.set_friction_coefficient(0.3,"Sand","Sand")
-p.set_friction_coefficient(0.3,"Sand","Steel")
+p = scontact.ParticleProblem(2,True)
 p.read_vtk(outputdir,0)
+p.set_friction_coefficient(0.2,"Sand","Sand")
+p.set_friction_coefficient(0.2,"Sand","Steel")
+
 # Initial time and iteration
 t         =  0
 ii        =  0
@@ -87,7 +88,7 @@ ii        =  0
 # COMPUTATION LOOP
 #
 while t < tEnd :
-    time_integration.iterate(None, p, dt, min_nsub=1,contact_tol = 5e-7,external_particles_forces=g*p.mass())
+    time_integration.iterate(None, p, dt, min_nsub=1,external_particles_forces=g*p.mass())
     t += dt
     # Output files writting
     if ii %outf == 0 :

testcases/drag-2d/depot/mesh.geo

@@ -40,4 +40,4 @@ Line Loop(20) = {20, 21, 22, 23};
 Plane Surface(1) = {20, 10};
 Physical Surface("Domain") = {1};
 Physical Point("PtFix") = {13};
-Mesh.MshFileVersion = 2;
+Mesh.MshFileVersion = 4;

testcases/drag-2d/drag.py

@@ -43,7 +43,7 @@ dt = 1e-3                                      #time step
 t = 0                                          #initial time
 tEnd = 10                                      #final time
 ii = 0                                         #iteration number
-outf = 1000                                    #iterations between data frames  
+outf = 10                                      #iterations between data frames  
 # Define output directory
 outputdir = "output/" + vitesse[index] 
 if not os.path.isdir(outputdir) :
@@ -68,15 +68,15 @@ p2.write_vtk(outputdir, 0, 0)
 #
 # FLUID PROBLEM
 #
-#fluid = fluid.FluidProblem(2,g,[nu*rho],[rho],drag_in_stab=0)
-#fluid.load_msh("mesh.msh")
-#fluid.set_wall_boundary("Inner")
-#fluid.set_wall_boundary("Left", velocity = [0,0])
-#fluid.set_wall_boundary("Right", velocity = [0,0])
-#fluid.set_open_boundary("Bottom", velocity = [0,vit])
-#fluid.set_open_boundary("Top",pressure = 0)
-#fluid.set_particles(p2.mass(), p2.volume(), p2.position(), p2.velocity(), p2.contact_forces(),init=True)
-#fluid.export_vtk(outputdir, 0.,0)
+fluid = fluid.FluidProblem(2,g,[nu*rho],[rho],drag_in_stab=0)
+fluid.load_msh("mesh.msh")
+fluid.set_wall_boundary("Inner")
+fluid.set_wall_boundary("Left", velocity = [0,0])
+fluid.set_wall_boundary("Right", velocity = [0,0])
+fluid.set_open_boundary("Bottom", velocity = [0,vit])
+fluid.set_open_boundary("Top",pressure = 0)
+fluid.set_particles(p2.mass(), p2.volume(), p2.position(), p2.velocity(), p2.contact_forces())
+fluid.write_vtk(outputdir, 0,0)
 # 
 # COMPUTATION LOOP
 #
@@ -90,16 +90,16 @@ while t < tEnd :
        p2.add_particles(p.position(),p.r(),p.mass(),v=p.velocity(),tag="Sand",forced=p.forced_flag(),contact_forces=p.contact_forces())
      p2.remove_particles_flag( (p2.position()[:,1] + p2.r()[:,0] >-0.55))
      F = np.zeros(2)
-     #time_integration.particle_changed(fluid,p2)
-     time_integration.iterate(None,p2,dt,1,contact_tol=5e-7,external_particles_forces=g*p2.mass(),after_sub_iter=lambda n_divide : accumulate(F,n_divide))
+     fluid.set_particles(p2.mass(), p2.volume(), p2.position(), p2.velocity(), p2.contact_forces())
+     time_integration.iterate(fluid,p2,dt,1,contact_tol=5e-7,external_particles_forces=g*p2.mass(),after_sub_iter=lambda n_divide : accumulate(F,n_divide))
      with open(filename,"a") as file1:
-        #F += fluid.boundary_force()[0,:]
+        F += fluid.boundary_force()[0,:]
         file1.write( str(F[0])+";"+str(F[1])+";"+str(t)+"\n")
      t += dt   
      # Output files writing
      if ii %outf == 0 :
          ioutput = int(ii/outf) + 1
          p2.write_vtk(outputdir, ioutput, t)
-         #fluid.export_vtk(outputdir+"/Flow", t, ioutput)       
+         fluid.write_vtk(outputdir, ioutput, t)       
      ii += 1
      print("%i : %.2g/%.2g" % (ii, t, tEnd))

testcases/drag-2d/mesh.geo

@@ -40,4 +40,4 @@ Line Loop(20) = {20, 21, 22, 23};
 Plane Surface(1) = {20, 10};
 Physical Surface("Domain") = {1};
 Physical Point("PtFix") = {13};
-Mesh.MshFileVersion = 2;
+Mesh.MshFileVersion = 4;