Granular Collapse

paraview_utils/show_problem.py

@@ -74,6 +74,7 @@ def showFluidVelocity(fluid, renderView):
     fluidVelocity.Function = 'velocity/porosity'
     RenameSource('Fluid Velocity', fluidVelocity)
     fluidVelocityDisplay = Show(fluidVelocity, renderView)
+    ColorBy(fluidVelocityDisplay, ('POINTS', 'FluidVelocity', 'Magnitude'))
     fluidVelocityDisplay.SetScalarBarVisibility(renderView, True)
     Hide(fluidVelocity)
     return fluidVelocity

python/scontact.py

@@ -433,10 +433,13 @@ class ParticleProblem :
         x,cells,d,cdata,fdata = VTK.read(dirname+"/boundaries_%05d.vtu"%i)
         tagnames =  VTK.string_array_decode(fdata["TagNames"])
         tagmap = {}
+        print(fdata)
+        print(tagnames)
         for j,n in enumerate(tagnames) :
             tagmap[j] = self._lib.particleProblemGetTagId(self._p,n)
         offsets = np.hstack([[0],cells["offsets"]])
         el = cells["connectivity"]
+        print(tagmap)
         tags = np.vectorize(tagmap.get)(cdata["Tag"])
         materials = cdata["Material"]
         for idx in np.where(cells["types"] == 1)[0] :

testcases/avalanch/monodisperseAvalanch/depot.py

+from migflow import time_integration
+from migflow import scontact
+
+import numpy as np
+import os
+import subprocess
+import time
+import shutil
+import random
+
+SEED = np.random.seed(0) 
+def genInitialPosition(filename, r, H, lx, rhop) :
+    """Set all the particles centre positions and create the particles objects to add in the computing structure
+
+    Keyword arguments:
+    filename -- name of the output file
+    r -- max radius of the particles
+    ly - particles area height
+    lx -- particles area width
+    rhop -- particles density
+    """
+    # Particles structure builder
+    p = scontact.ParticleProblem(2)
+    # Load mesh.msh file specifying physical boundaries names
+    p.load_msh_boundaries("meshDepot.msh", ["Top", "Lateral", "Bottom"])
+
+    #Definition of the points where the particles are located
+    x = np.arange(r-1e-8, lx-r+1e-8, 2*r)
+    y = np.arange(r-1e-8, H-r-1e-8, 2*r)
+    x, y = np.meshgrid(x, y)
+    x = x.flat
+    y = y.flat
+    # Add a grain at each centre position
+    for i in range(len(x)) :
+        R = r*(1-np.random.random()/2)
+        Xi = x[i] + np.random.random()/10000
+        p.add_particle((Xi, y[i]), R, R**2 * np.pi * rhop)
+    p.write_vtk(filename,0,0)
+
+dir_path = os.path.dirname(os.path.realpath(__file__))
+os.chdir(dir_path)
+outputdir = "outputDepot"
+if not os.path.isdir(outputdir) :
+    os.makedirs(outputdir)
+subprocess.call(["gmsh", "-2", "meshDepot.geo","-clscale","1"])
+
+# Physical parameters
+g = np.array([0,-9.81])
+rhop = 9000                                     # particle density
+r = .2e-2                                      # particle radius
+# Geometrical parameters
+L = 0.1
+H = 0.1
+
+# Numerical parameters
+tEnd = 0.5
+dt = 0.0025                                       # time step
+outf = 5                                        # number of iterations between output files
+
+genInitialPosition(outputdir,r,H,L,rhop)
+p = scontact.ParticleProblem(2)
+p.read_vtk(outputdir,0)
+
+G = np.zeros((p.n_particles(),p.dim()))
+G[:,1] = g[1]*p.mass()[:,0]
+t = 0
+ii = 0
+tic = time.time()
+#
+# COMPUTATION LOOP
+#
+while t < tEnd :
+    # Time integration
+    time_integration.iterate(None,p,dt,external_particles_forces=G)
+    #Output files writting
+    t += dt
+    if ii %outf == 0 :
+        ioutput = int(ii/outf) + 1
+        p.write_vtk(outputdir, ioutput, t)
+    ii += 1
+    print("%i : %.2g/%.2g (cpu %.6g)" % (ii, t, tEnd, time.time() - tic))
\ No newline at end of file

testcases/avalanch/monodisperseAvalanch/granularCollapse.py

+# MigFlow - Copyright (C) <2010-2020>
+# <Universite catholique de Louvain (UCL), Belgium
+#  Universite de Montpellier, France>
+# 	
+# List of the contributors to the development of MigFlow: see AUTHORS file.
+# Description and complete License: see LICENSE file.
+# 	
+# This program (MigFlow) is free software: 
+# you can redistribute it and/or modify it under the terms of the GNU Lesser General 
+# Public License as published by the Free Software Foundation, either version
+# 3 of the License, or (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Lesser General Public License for more details.
+# 
+# You should have received a copy of the GNU Lesser General Public License
+# along with this program (see COPYING and COPYING.LESSER files).  If not, 
+# see <http://www.gnu.org/licenses/>.
+
+#!/usr/bin/env python
+
+# TESTCASE DESCRIPTION:
+# Collapsing of a grain column in fluid. 
+
+from migflow import fluid
+from migflow import scontact
+from migflow import time_integration
+
+import numpy as np
+import os
+import subprocess
+import time
+import shutil
+import random
+
+outputdir = "outputCollapse"
+outputdirDepot = "outputDepot"
+if not os.path.isdir(outputdir) :
+    os.makedirs(outputdir)
+subprocess.call(["gmsh", "-2", "mesh.geo","-clscale","1"])
+
+# Physical parameters
+g = np.array([0,-9.81])                     # gravity
+rhop = 9000                                 # grains density
+rho = 1000                                  # fluid density
+nu = 1e-6                                   # kinematic fluid viscosity
+
+# Geometrical parameters
+H = 0.15                                    # domain height
+L = 0.3                                   
+
+# Numerical parameters
+outf = 10                                 # number of iterations between output files
+dt = 1e-3                                 # time step
+tEnd = 10                                 # final time
+
+# 
+# PARTICLES PROBLEM
+#
+# Particles container for the current problem
+p = scontact.ParticleProblem(2)
+p.load_msh_boundaries("mesh.msh", ["Top", "Lateral", "Bottom"])
+pdepot = scontact.ParticleProblem(2)
+pdepot.read_vtk(outputdirDepot,40)
+p.add_particles(pdepot.position(),pdepot.r(),
+                pdepot.mass(),pdepot.velocity())
+p.write_vtk(outputdir, 0, 0)
+
+#
+# FLUID PROBLEM
+#
+fluid = fluid.FluidProblem(2,g,[nu*rho], [rho])
+fluid.load_msh("mesh.msh")
+fluid.set_wall_boundary("Bottom", velocity=[0,0])
+fluid.set_wall_boundary("Lateral", velocity=[0,0])
+fluid.set_wall_boundary("Top", velocity=[0,0], pressure=0)
+fluid.set_strong_boundary("Bottom",1,0)
+fluid.set_strong_boundary("Lateral",0,0)
+fluid.set_strong_boundary("Top",1,0)
+
+fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity(), p.contact_forces())
+fluid.solution()[:,2] =  (H-fluid.coordinates()[:,1])*(-g[1])*rho
+fluid.read_vtk(outputdir,0)
+
+# Initial time and iteration.
+t = 0
+ii = 0
+
+tic = time.time()
+G = np.zeros((p.n_particles(),p.dim()))
+G[:,1] = g[1]*p.mass()[:,0]
+
+#
+# COMPUTATION LOOP
+#
+while t < tEnd :
+    time_integration.iterate(fluid, p, dt, min_nsub=5, external_particles_forces=G)
+    t += dt
+    # Output files writing.
+    if ii%outf == 0 :
+        ioutput = int(ii/outf) + 1
+        p.write_vtk(outputdir, ioutput, t)
+        fluid.write_vtk(outputdir, ioutput, t)
+    ii += 1
+    print("%i : %.2g/%.2g (cpu %.6g)" % (ii, t, tEnd, time.time() - tic))

testcases/avalanch/monodisperseAvalanch/mesh.geo

+L = 0.3;
+H = 0.15;
+y = 0;
+lc = 0.01;
+
+Point(1) = {0, 0, 0, lc};
+Point(2) = {L, 0, 0, lc};
+Point(3) = {L, H, 0, lc};
+Point(4) = {0, H, 0, lc};
+Line(1) = {1, 2};
+Line(2) = {2, 3};
+Line(3) = {3, 4};
+Line(4) = {4, 1};
+Point(5) = {0,0.5,0};
+
+Line Loop(1) = {1:4};
+
+Plane Surface(1) = {1};
+Physical Line("Bottom") = {1};
+Physical Line("Lateral") = {2,4};
+Physical Line("Top") = {3};
+Physical Surface("Domain") = {1};
+Physical Point("PtFix") = {1};
+
+Mesh.CharacteristicLengthFromPoints = 1;
+Mesh.MshFileVersion = 4;

testcases/avalanch/monodisperseAvalanch/meshDepot.geo

+L = 0.1;
+H = 0.1;
+y = 0;
+lc = 0.01;
+
+Point(1) = {0, 0, 0,lc};
+Point(2) = {L, 0, 0,lc};
+Point(3) = {L, H, 0,lc};
+Point(4) = {0, H, 0,lc};
+Line(1) = {1, 2};
+Line(2) = {2, 3};
+Line(3) = {3, 4};
+Line(4) = {4, 1};
+Point(5) = {0,0.5,0};
+
+Line Loop(1) = {1:4};
+
+Plane Surface(1) = {1};
+Physical Line("Bottom") = {1};
+Physical Line("Lateral") = {2,4};
+Physical Line("Top") = {3};
+Physical Surface("Domain") = {1};
+Physical Point("PtFix") = {1};
+
+Mesh.CharacteristicLengthFromPoints = 1;
+Mesh.MshFileVersion = 4;

testcases/periodicTest/2D/grains.py

@@ -69,7 +69,6 @@ p.write_vtk(outputdir,0,0)
 
 #Initial time and iteration
 t = 0
-ii = 0
 
 ii = 0
 tic = time.time()