modif testcases

testcases/Test-3d/funnel/funnel.py

@@ -24,7 +24,7 @@ def genInitialPosition(filename, rhop) :
     
     p.position()[:, 1] += .15/2 
     print(len(p.position()[:, 1]))
-    p.write(filename)
+    p.write_vtk(filename, 0, 0)
 
 
 outputdir = "outputFunnelG"
@@ -49,69 +49,48 @@ tEnd = 100
 #numerical parameters
 lcmin = 0.001 # approx r*100 but should match the mesh size
 dt = 1e-3
-alpha = 2.5e-5
+alpha = 2.5e-4
 epsilon = alpha*lcmin**2 /nu#2e-2*c*h*2#2e-2*c*h # ?? not sure ??1e-5
 print('epsilon',epsilon)
 
 shutil.copy("mesh.msh", outputdir +"/mesh.msh")
 #scontact2Interface.MeshLoader(p, "funnel.msh", ("Funnel", "Top", "Bottom", "Lateral"))
-p.write(outputdir+"/part-00000")
 
-genInitialPosition(outputdir + "/part-00000", rhop)
 
-p = scontact3.ParticleProblem(outputdir+"/part-00000")
+genInitialPosition(outputdir, rhop)
+
+p = scontact3.ParticleProblem()
+p.read_vtk(outputdir,0)
 
 #print("r = %g, m = %g\n" %  (p.r()[0], p.mass()[0]))
 print("RHOP = %g" % rhop)
 outf = 100
 
 strong_boundaries = [("Top",0,.0),("Top",1,0.),("Top",2,0.),("Box",1,0.),("Box",0,0.),("Box",2,0.),("Top",3,0.)]#("Top",3,0.),("Top",1,0.),("Top",0,0.),("Top",2,0.),("Box",1,0.),("Box",0,0.),("Box",2,0.)]
-fluid = fluid.fluid_problem("mesh.msh",g,nu*rho,rho,epsilon,strong_boundaries)
+fluid = fluid.fluid_problem("mesh.msh",g,nu*rho,rho,epsilon,strong_boundaries, 1)
 
 print("Initialisation fluid done!\n")
 fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
 print("Initialisation particles done!\n")
-fluid.export(outputdir,0,0)
 
-ii = 0
 tic = time.clock()
-#forces = g*p.mass()
-while t < tEnd and ii < 50: 
-    ticf = time.clock()
+fluid.export_vtk(outputdir,0,0)
+forces = g*p.mass()
+fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
+while t < tEnd : 
+    fluid.implicit_euler(dt)
     forces = fluid.compute_node_force(dt)
-    tocf = time.clock()
-    print("Time to compute the force : %.6e\n" % (tocf-ticf))
-    #print(forces)
-
-    ticp = time.clock()
     vn = p.velocity() + forces * dt / p.mass()
-    vmax = np.max((vn[:, 0]**2+ vn[:, 1]**2+vn[:,2]**2)**0.5)
-    nsub = max(1, int(np.ceil((vmax * dt * 4)/min(10*p.r()))))
+    vmax = np.max(np.hypot(vn[:, 0], vn[:, 1]))
+    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()))
     for i in range(nsub) :
-        p.iterate(dt/nsub, forces) 
-    tocp = time.clock() 
-    print("Time to move the grains : %.6e\n" % (tocp-ticp))
-
-    ticfp = time.clock()
+        p.iterate(dt/nsub, forces)  
     fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
-    tocfp = time.clock()
-    print("Time to create the particle fluid : %.6e\n" % (tocfp-ticfp))
-
-    tice = time.clock()
-    fluid.implicit_euler(dt)
-    toce = time.clock()
-    print("Time to solve the fluid : %.6e\n" % (toce-tice))
-
     t += dt
     if ii %outf == 0 :
         ioutput = int(ii/outf) + 1
         p.write_vtk(outputdir, ioutput, t)
-        p.write(outputdir+"/part-%05d" % ioutput)
-        p.write_boundary_vtk(outputdir, ioutput, t)
-        fluid.export(outputdir, t, ioutput)
-
+        fluid.export_vtk(outputdir, t, ioutput)
     ii += 1
     print("%i : %.2g/%.2g (cpu %.6g)" % (ii, t, tEnd, time.clock() - tic))
-    if ii==400:
-        break

testcases/depot-2d/mesh1.geo

-L = 0.014;
-H = 0.076;
-y = 0;
-lc = 0.001;
-
-Point(1) = {-L, H, 0, lc};
-Point(2) = {-L, -H, 0, lc};
-Point(3) = {L, -H, 0, lc};
-Point(4) = {L, H, 0, lc};
-Line(1) = {1, 2};
-Line(2) = {2, 3};
-Line(3) = {3, 4};
-Line(4) = {4, 1};
-Line Loop(1) = {1:4};
-
-Plane Surface(1) = {1};
-Physical Line("Box") = {1,2,3};
-Physical Line("Top") = {4};
-Physical Surface("Domain") = {1};
-Physical Point("PtFix") = {1};

testcases/depot-2d/run.py

-import pyfefp
-import scontact2
-from pyfefp import scontact2Interface
-import numpy as np
-import time
-import os
-from pyfefp.legendre import *
-
-def genInitialPosition(filename, r, lx, ly, rhop) :
-    p = scontact2.ParticleProblem()
-    scontact2Interface.MeshLoader(p, "mesh.msh", ["Top", "Box"])
-    x = np.arange(lx-r, -lx + r*0.999, 2 * -r)
-    y = np.arange(ly-r, -ly + r*0.999, 2 * -r)
-    x, y = np.meshgrid(x, y)
-    x = x.flat
-    y = y.flat
-    for i in range(len(x)) :
-        p.addParticle((x[i], y[i]), r, r**2 * np.pi * rhop);
-    p.position()[:, 1] += 4
-    p.write(filename)
-
-dt = 0.005
-tEnd = 2
-
-outputdir = "output"
-if not os.path.isdir(outputdir) :
-    os.makedirs(outputdir)
-rhop=2500
-d = 0.005
-mu = 0.001
-rho = 1000
-ii = 0
-
-filename = outputdir + "/part-00000"
-genInitialPosition(filename, d, 2, 1, rhop)
-
-
-## scontact
-p = scontact2Interface.ScontactInterface(outputdir+"/part-%05d"%ii)
-
-## lmgc
-#from pyfefp import lmgc2Interface
-#lmgc2Interface.scontactToLmgc90(filename)
-#p = lmgc2Interface.LmgcInterface()
-
-g =  [0, -9.81]
-print("r = %g, m = %g\n" %  (p.r()[0], p.mass()[0]))
-print("dtmax = %g Re_p/u = %g" % (p.mass()[0] / (150 * mu * d), d * rho * 0.3/mu))
-print("RHOP = %g" % rhop)
-outf = 5
-fluid = pyfefp.FluidSolver("mesh.msh", dt, rhop=rhop, rho=rho, mu=mu, g = g, epsilon=1e-02, imex=False, TypeEMu=TriangleP1, TypeEMp=TriangleP1)
-fluid.add_boundary_condition("Box", 0, 0.)
-fluid.add_boundary_condition("Box", 1, 0.)
-fluid.add_boundary_condition("Top", 0, 0.)
-fluid.add_boundary_condition("Top", 1, 0.)
-fluid.add_boundary_condition("Top", 2, 0.)
-fluid.complete()
-
-t = 0
-p.write_vtk(outputdir, ii, t)
-
-fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
-fluid.write_solution(outputdir, ii, t, "vtk")
-
-tic = time.clock()
-while t < tEnd :
-    forces = fluid.solve()
-    vn = p.velocity() + forces * dt / p.mass()
-    vmax = np.max(np.hypot(vn[:, 0], vn[:, 1]))
-    nsub = max(1, int(np.ceil((vmax * dt * 2)/min(p.r()))))
-    print("NSUB", nsub,"VMAX",vmax, "VMAX * dt", vmax * dt, "r", min(p.r()))
-    for i in range(nsub) :
-        p.iterate(dt/nsub, forces)
-    fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
-    t += dt
-    if ii %outf == 0 :
-        ioutput = int(ii/outf) + 1
-        p.write_vtk(outputdir, ioutput, t)
-        p.write(outputdir, ioutput, t)
-        fluid.write_solution(outputdir, ioutput, t, "vtk")
-    ii += 1
-    print("%i : %.2g/%.2g (cpu %.2g)" % (ii, t, tEnd, time.clock() - tic))

testcases/depot-2d/runart.py

-import pyfefp
-import scontact2
-from pyfefp import scontact2Interface
-import numpy as np
-import time
-import os
-from pyfefp.legendre import *
-
-def genInitialPosition(filename, r, lx, ly, rhop) :
-    p = scontact2.ParticleProblem()
-    scontact2Interface.MeshLoader(p, "mesh1.msh", ["Top", "Box"])
-    x = np.arange(lx-r, -lx + r*0.999, -2.1*r)
-    y = np.arange(ly-r, -ly + r*0.999, -2.1*r)
-    x, y = np.meshgrid(x, y)
-    x = x.flat
-    y = y.flat
-    for i in range(len(x)) :
-        p.addParticle((x[i], y[i]), r, r**2 * np.pi * rhop);
-    p.position()[:, 1] += 0.07542
-    p.write(filename)
-
-
-dt = 0.005
-tEnd = 110
-
-outputdir = "outputarttestpl1"
-if not os.path.isdir(outputdir) :
-    os.makedirs(outputdir)
-rhop=2500
-d = 0.000045
-mu = 0.001
-rho = 1000
-ii = 0
-
-filename = outputdir + "/part-00000"
-genInitialPosition(filename, d/2, 0.014, 0.00055, rhop)
-
-
-## scontact
-p = scontact2Interface.ScontactInterface(outputdir+"/part-%05d"%ii)
-
-## lmgc
-#from pyfefp import lmgc2Interface
-#lmgc2Interface.scontactToLmgc90(filename)
-#p = lmgc2Interface.LmgcInterface()
-
-g =  [0, -9.81]
-print("r = %g, m = %g\n" %  (p.r()[0], p.mass()[0]))
-print("dtmax = %g Re_p/u = %g" % (p.mass()[0] / (150 * mu * d), d * rho * 0.3/mu))
-print("RHOP = %g" % rhop)
-outf = 10
-fluid = pyfefp.FluidSolver("mesh1.msh", dt, rhop=rhop, rho=rho, g = g, mu=mu, epsilon=1e-04, imex=False, TypeEMu=TriangleP1, TypeEMp=TriangleP1)
-fluid.add_boundary_condition("Box", 0, 0.)
-fluid.add_boundary_condition("Box", 1, 0.)
-fluid.add_boundary_condition("Top", 0, 0.)
-fluid.add_boundary_condition("Top", 1, 0.)
-fluid.add_boundary_condition("Top", 2, 0.)
-fluid.complete()
-
-t = 0
-p.write_vtk(outputdir, ii, t)
-p.write(outputdir, ii, t)
-p.write_boundary_vtk(outputdir, ii, t)
-
-fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
-fluid.write_solution(outputdir, ii, t, "vtk")
-
-tic = time.clock()
-while t < tEnd :
-    forces = fluid.solve()
-    vn = p.velocity() + forces * dt / p.mass()
-    vmax = np.max(np.hypot(vn[:, 0], vn[:, 1]))
-    nsub = max(1, int(np.ceil((vmax * dt * 2)/min(p.r()))))
-    print("NSUB", nsub,"v", vn[:, 1],"VMAX",vmax, "VMAX * dt", vmax * dt, "r", min(p.r()))
-    for i in range(nsub) :
-        p.iterate(dt/nsub, forces)
-    fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
-    t += dt
-    #dt=min(0.05,d/vmax)
-    print("dt",dt)
-    if ii %outf == 0 :
-        ioutput = int(ii/outf) + 1
-        p.write_vtk(outputdir, ioutput, t)
-        p.write(outputdir, ioutput, t)
-        p.write_boundary_vtk(outputdir, ioutput, t)
-        fluid.write_solution(outputdir, ioutput, t, "vtk")
-    ii += 1
-    print("%i : %.2g/%.2g (cpu %.2g)" % (ii, t, tEnd, time.clock() - tic))

testcases/depot-2d/scontact.opt

-alpha 0
-beta 0
-scale 2.120488091862423
-shift 0 1.400000000000001
-visible 3 3 3 3 3 3 3 3 3 3

testcases/drop-3d/metzger/adapt/mesh.geo

-L = 0.05;
-H = 0.6;
-P = 0.02;
-y = 0;
-lc = 0.01;
-
-Point(1) = {-L, H, -P, lc};
-Point(2) = {-L, 0, -P, lc};
-Point(3) = {L, 0, -P, lc};
-Point(4) = {L, H, -P, lc};
-Point(5) = {-L, H, P, lc};
-Point(6) = {-L, 0, P, lc};
-Point(7) = {L, 0, P, lc};
-Point(8) = {L, H, P, lc};
-
-Line(1) = {1, 2};
-Line(2) = {2, 3};
-Line(3) = {3, 4};
-Line(4) = {4, 1};
-Line(5) = {5, 6};
-Line(6) = {6, 7};
-Line(7) = {7, 8};
-Line(8) = {8, 5};
-Line(9) = {5, 1};
-Line(10) = {4, 8};
-Line(11) = {2, 6};
-Line(12) = {3, 7};
-
-Line Loop(1) = {1:4};
-Line Loop(2) = {5:8};
-Line Loop(3) = {9,-4,10,8};
-Line Loop(4) = {2,12,-6,-11};
-Line Loop(5) = {12,7,-10,-3};
-Line Loop(6) = {1,11,-5,9};
-
-Plane Surface(1) = {1};
-Plane Surface(2) = {2};
-Plane Surface(3) = {3};
-Plane Surface(4) = {4};
-Plane Surface(5) = {5};
-Plane Surface(6) = {6};
-Surface Loop(1) = {1,-3,-2,4,1,-5,-2,6};
-Volume(1) = {1};
-Physical Surface("Z") = {1,2};
-Physical Surface("X") = {5,6};
-Physical Surface("Top") = {3};
-Physical Surface("Bottom") = {4};
-Physical Volume("Domain") = {1};
-Physical Point("PtFix") = {1};
-Mesh.Algorithm = 5;
-
-Merge "lc.pos";
-Field[1] = PostView;
-Field[1].IView = 0;
-Background Field = 1;
-
-Mesh.CharacteristicLengthExtendFromBoundary = 0;
-Mesh.CharacteristicLengthFromPoints = 0;

testcases/drop-3d/metzger/drop.py

-#!/usr/bin/env python
-from marblesbag import fluid3 as fluid
-from marblesbag import scontact3
-
-import numpy as np
-import os
-import time
-import shutil
-import random
-
-def genInitialPosition(r, rout, rhop, compacity) :
-    p = scontact3.ParticleProblem()
-    p.load_msh_boundaries("mesh.msh", ["Top", "Bottom","X","Z"])
-    
-    N = compacity*rout**3/(r**3)
-    e = 2*rout/(6*N/np.pi)**(1./3.)
-    
-    for x in np.arange(rout, -rout, -e):
-        for y in np.arange(rout, -rout, -e):
-            for z in np.arange(rout, -rout, -e):
-                R2 = x**2 + y**2 + z**2
-                if R2<(rout-r)**2:
-                    p.add_particle((x+random.uniform(-e/2+r,e/2-r), y+random.uniform(-e/2+r,e/2-r), z+random.uniform(-e/2+r,e/2-r)), r, 4./3.* r**3 * np.pi * rhop);
-    
-    p.position()[:, 1] += 0.52
-    print(len(p.position()[:, 1] ))
-    p.write_vtk(outputdir,0,0)
-
-
-outputdir = "MetzgerB"
-if not os.path.isdir(outputdir) :
-    os.makedirs(outputdir)
-
-t = 0
-ii = 0
-
-r=154e-6
-R = 3.3e-3
-compacity = .20
-drho = 35.4
-p = scontact3.ParticleProblem()
-#R = np.random.uniform(45e-06, 90e-06, len(x))
-
-#physical parameters
-g =  -9.81
-rhop = 2450
-nu = 1.17/1030.
-rho = 1030#rhop-drho/compacity
-V = 0.5 # todo : estimate V base on limit velocity
-tEnd = 1000
-
-#numerical parameters
-lcmin = 0.0004 # approx r*100 but should match the mesh size
-dt = 5e-5*1000
-alpha = 1e-3
-epsilon = alpha*lcmin**2/nu
-print('epsilon',epsilon)
-
-shutil.copy("mesh.msh", outputdir +"/mesh.msh")
-#scontact2Interface.MeshLoader(p, "funnel.msh", ("Funnel", "Top", "Bottom", "Lateral"))
-p.write_vtk(outputdir,0,0)
-mu = nu*rho
-
-genInitialPosition(r, R, rhop, compacity)
-
-p = scontact3.ParticleProblem()
-p.read_vtk(outputdir,0)
-
-print("r = %g, m = %g\n" %  (p.r()[0], p.mass()[0]))
-print("RHOP = %g" % rhop)
-outf = 10
-outf1 = 100000
-
-#strong_boundaries = [("Top",0,.0),("Top",1,0.),("Top",2,0.),("Box",1,0.),("Box",0,0.),("Box",2,0.),("Top",3,0.)]
-#strong_boundaries = [("Top",0,.0),("Top",1,0.),("Top",2,0.),("Bottom",0,.0),("Bottom",1,0.),("Bottom",2,0.),("X",0,.0),("X",1,0.),("X",2,0.),("Z",0,.0),("Z",1,0.),("Z",2,0.),("Top",3,0.)]
-strong_boundaries = [("Top",1,0.),("Bottom",1,0.),("X",0,.0),("Z",2,0.),("Top",3,0.)]
-fluid = fluid.fluid_problem("mesh.msh",g,nu*rho,rho,epsilon,strong_boundaries, 1)
-
-fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
-
-
-ii = 0
-jj = 0
-tEnd1 = 100
-#p.velocity()[:,1] = 2./9. *(compacity)* R**2*g*(rhop-rho)/mu
-print(p.velocity()[1,1])
-print(1-compacity)
-
-
-for jj in range(4):
-    dt1 = dt
-    t = 0
-    if jj!=0:
-        fluid.adapt_mesh(1e-3,1e-4,300000, epsilon, 1)
-    fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
-    
-    while t < tEnd1 : 
-        niter = fluid.implicit_euler(dt1)
-        forces = fluid.compute_node_force(dt1)
-        vn = p.velocity() + forces * dt1 / p.mass()
-        fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
-        if niter < 5 and dt1 < 20:
-            dt1 *= 3
-        elif niter > 5 and dt1 > dt:
-            dt1 /= 3
-        print(dt1)
-        t += dt1
-#        if ii %outf == 0 :
-#                ioutput = int(ii/outf) + 1
-#                p.write_vtk(outputdir, ioutput, t)
-#                fluid.export_vtk(outputdir, t, ioutput)
-        ii += 1
-
-ii = 0
-t = 0
-tic = time.clock()
-fluid.export_vtk(outputdir,0,0)
-forces = g*p.mass()
-fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
-while t < tEnd : 
-    if (ii%5==0 and ii != 0):
-       fluid.adapt_mesh(1e-3,1e-4,300000, epsilon, 1)
-       fluid.set_particles(p.mass(), p.volume(), p.position(), p.velocity())
-    fluid.implicit_euler(dt)
-    forces = fluid.compute_node_force(dt)
-    vn = p.velocity() + forces*dt/p.mass()
-    vmax = np.max(np.hypot(vn[:, 0], vn[:, 1]))
-    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()))
-    for i in range(nsub) :
-        p.iterate(dt/nsub, forces)  
-    fluid.set_particles(p.mass(),p.volume(),p.position(),p.velocity())
-    t += dt
-    if ii %outf == 0 :
-        ioutput = int(ii/outf) + 1
-        p.write_vtk(outputdir, ioutput, t)
-        fluid.export_vtk(outputdir, t, ioutput)
-    ii += 1
-    print("%i : %.2g/%.2g (cpu %.6g)" % (ii, t, tEnd, time.clock() - tic))

testcases/drop-3d/metzger/mesh.geo

-L = 0.05;
-H = 0.6;
-P = 0.02;
-y = 0;
-lc = 0.01;
-
-Point(1) = {-L, H, -P, lc};
-Point(2) = {-L, -H, -P, lc};
-Point(3) = {L, -H, -P, lc};
-Point(4) = {L, H, -P, lc};
-Point(5) = {-L, H, P, lc};
-Point(6) = {-L, -H, P, lc};
-Point(7) = {L, -H, P, lc};
-Point(8) = {L, H, P, lc};
-Point(9) = {0,H,0,lc};
-Point(10) = {0,-H,0,lc};
-
-Line(1) = {1, 2};
-Line(2) = {2, 3};
-Line(3) = {3, 4};
-Line(4) = {4, 1};
-Line(5) = {5, 6};
-Line(6) = {6, 7};
-Line(7) = {7, 8};
-Line(8) = {8, 5};
-Line(9) = {5, 1};
-Line(10) = {4, 8};
-Line(11) = {2, 6};
-Line(12) = {3, 7};
-
-Line Loop(1) = {1:4};
-Line Loop(2) = {5:8};
-Line Loop(3) = {9,-4,10,8};
-Line Loop(4) = {2,12,-6,-11};
-Line Loop(5) = {12,7,-10,-3};
-Line Loop(6) = {1,11,-5,9};
-
-Plane Surface(1) = {1};
-Plane Surface(2) = {2};
-Plane Surface(3) = {3};
-Plane Surface(4) = {4};
-Plane Surface(5) = {5};
-Plane Surface(6) = {6};
-Surface Loop(1) = {1,-3,-2,4,1,-5,-2,6};
-Volume(1) = {1};
-Physical Surface("Z") = {1,2};
-Physical Surface("X") = {5,6};
-Physical Surface("Top") = {3};
-Physical Surface("Bottom") = {4};
-Physical Volume("Domain") = {1};
-Physical Point("PtFix") = {1};
-
-
-Point(15) = {0,.52,0};
-Field[1] = Attractor;
-Field[1].NodesList = {15};
-
-Field[2] = Threshold;
-Field[2].DistMax = 0.06;
-Field[2].DistMin = 0.01;
-Field[2].LcMax = 0.008;
-Field[2].LcMin = 0.0004;
-Field[2].IField = 1;
-
-Background Field = 2;
-
-Mesh.CharacteristicLengthFromPoints = 0;
-Mesh.CharacteristicLengthExtendFromBoundary = 0;

testcases/drop-3d/testSmallerDtWithInitialCondition/adapt/mesh.geo

-L = 0.02;
-H = 0.6;
-P = 0.02;
-y = 0;
-lc = 0.01;
-
-Point(1) = {-L, H, -P, lc};
-Point(2) = {-L, -H, -P, lc};
-Point(3) = {L, -H, -P, lc};
-Point(4) = {L, H, -P, lc};
-Point(5) = {-L, H, P, lc};
-Point(6) = {-L, -H, P, lc};
-Point(7) = {L, -H, P, lc};
-Point(8) = {L, H, P, lc};
-
-Line(1) = {1, 2};
-Line(2) = {2, 3};
-Line(3) = {3, 4};
-Line(4) = {4, 1};
-Line(5) = {5, 6};
-Line(6) = {6, 7};
-Line(7) = {7, 8};
-Line(8) = {8, 5};
-Line(9) = {5, 1};
-Line(10) = {4, 8};
-Line(11) = {2, 6};
-Line(12) = {3, 7};
-
-Line Loop(1) = {1:4};
-Line Loop(2) = {5:8};
-Line Loop(3) = {9,-4,10,8};
-Line Loop(4) = {2,12,-6,-11};