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######################################################## |
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# |
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# Copyright (c) 2003-2008 by University of Queensland |
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# Earth Systems Science Computational Center (ESSCC) |
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# http://www.uq.edu.au/esscc |
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# |
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# Primary Business: Queensland, Australia |
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# Licensed under the Open Software License version 3.0 |
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# http://www.opensource.org/licenses/osl-3.0.php |
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# |
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######################################################## |
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|
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__copyright__="""Copyright (c) 2003-2008 by University of Queensland |
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Earth Systems Science Computational Center (ESSCC) |
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http://www.uq.edu.au/esscc |
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Primary Business: Queensland, Australia""" |
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__license__="""Licensed under the Open Software License version 3.0 |
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http://www.opensource.org/licenses/osl-3.0.php""" |
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__url__="http://www.uq.edu.au/esscc/escript-finley" |
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|
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from esys.escript import * |
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from esys.escript.linearPDEs import LinearPDE, TransportPDE |
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from esys.escript.pdetools import Projector |
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from esys import finley |
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import math |
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|
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|
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|
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from esys.escript import * |
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from esys.finley import finley |
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from esys.escript.linearPDEs import LinearPDE |
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from esys.escript.pdetools import Projector |
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import sys |
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|
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|
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class LevelSet: |
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""" |
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The level set method tracking an interface defined by the zero contour of the level set function phi. |
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it is assumed the phi(x)<0 defines the volume of interest. |
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|
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""" |
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def __init__(self,domain,phi,reinit_max=10,reinit_each=2,smooth=2.): |
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""" |
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set up the level set method |
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|
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@param domain: the domain where the level set is used |
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@param phi: the initial level set function |
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@param reinit_max: maximum number of reinitalization steps |
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@param reinit_each: phi is reinitialized every reinit_each step |
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@param smooth: smoothing width |
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""" |
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self.__domain = domain |
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self.__phi = phi |
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self.__reinit_max = reinit_max |
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self.__reinit_each = reinit_each |
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self.__PDE = LinearPDE(domain) |
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self.__PDE.setReducedOrderOn() |
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self.__PDE.setValue(D=1.0) |
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self.__PDE.setSolverMethod(solver=LinearPDE.PCG) |
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self.__reinitPDE = LinearPDE(domain, numEquations=1) |
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self.__reinitPDE.setReducedOrderOn() |
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self.__reinitPDE.setValue(D=1.0) |
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self.__reinitPDE.setSolverMethod(solver=LinearPDE.LUMPING) |
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self.__h = inf(domain.getSize()) |
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self.__smooth = smooth |
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self.__n_step=0 |
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|
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def __advect(self, velocity, dt): |
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""" |
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advects the level set function in the presense of a velocity field. |
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|
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This implementation uses the 2-step Taylor-Galerkin method |
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@param velocity: velocity field |
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@param dt: dime increment |
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@return: the advected level set function |
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""" |
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Y = self.__phi-dt/2.*inner(velocity,grad(self.__phi)) |
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self.__PDE.setValue(Y=Y) |
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phi_half = self.__PDE.getSolution() |
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Y = self.__phi-dt*inner(velocity,grad(phi_half)) |
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self.__PDE.setValue(Y=Y) |
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phi = self.__PDE.getSolution() |
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print "LevelSet: Advection step done" |
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return phi |
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|
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def __reinitialise(self): |
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""" |
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reinializes the level set |
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|
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It solves the |
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|
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@return: reinitalized level set |
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""" |
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phi=self.__phi |
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s = sign(phi.interpolate(Function(self.__domain))) |
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g=grad(phi) |
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w = s*g/(length(g)+1e-10) |
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dtau = 0.5*self.__h |
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iter =0 |
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mask = whereNegative(abs(phi)-1.*self.__h) |
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self.__reinitPDE.setValue(q=mask, r=phi) |
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g=grad(phi) |
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while (iter<=self.__reinit_max): |
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Y = phi+(dtau/2.)*(s-inner(w,g)) |
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self.__reinitPDE.setValue(Y = Y) |
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phi_half = self.__reinitPDE.getSolution() |
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Y = phi+dtau*(s-inner(w,grad(phi_half))) |
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self.__reinitPDE.setValue(Y = Y) |
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phi = self.__reinitPDE.getSolution() |
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g=grad(phi) |
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error = Lsup(length(g)*whereNegative(abs(phi.interpolate(g.getFunctionSpace()))-3.0*self.__h)) |
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print "LevelSet:reinitialization: iteration :", iter, " error:", error |
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iter +=1 |
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return phi |
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|
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def getTimeStepSize(self,velocity): |
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""" |
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returns a new dt for a given velocity using the courant coundition |
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|
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@param velocity: velocity field |
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""" |
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self.__velocity=velocity |
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dt=0.5*self.__h/sup(length(velocity)) |
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return dt |
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|
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def update(self,dt): |
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""" |
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sets a new velocity and updates the level set fuction |
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|
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@param dt: time step forward |
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""" |
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self.__phi=self.__advect(self.__velocity, dt) |
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self.__n_step+=1 |
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if self.__n_step%self.__reinit_each ==0: self.__phi = self.__reinitialise() |
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return self.__phi |
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|
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def update_phi(self, velocity, dt): |
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""" |
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updates phi under the presense of a velocity field |
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If dt is small this call is equivalent to call |
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|
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dt=LevelSet.getTimeStepSize(velocity) |
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phi=LevelSet.update(dt) |
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|
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otherwise substepping is used. |
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@param velocity: velocity field |
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@param dt: time step forward |
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""" |
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dt2=self.getTimeStepSize(velocity) |
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n=math.ceil(dt/dt2) |
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dt_new=dt/n |
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for i in range(n): |
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phi=self.update(dt_new) |
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t+=dt_new |
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return phi |
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|
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|
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def getVolume(self): |
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""" |
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return the volume of the phi(x)<0 region |
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""" |
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return integrate(whereNegative(self.__phi.interpolate(Function(self.__domain)))) |
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|
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def getSurface(self,rel_width_factor=0.5): |
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""" |
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return a mask for phi(x)=1 region |
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|
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@param rel_width_factor: relative wideth of region around zero contour. |
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""" |
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return whereNegative(abs(self.__phi)-rel_width_factor*self.__h) |
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|
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def getH(self): |
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""" |
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returns mesh size |
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""" |
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return self.__h |
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|
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def getDomain(self): |
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""" |
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returns domain |
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""" |
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return self.__domain |
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|
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def getLevelSetFunction(self): |
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""" |
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returns the level set function |
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""" |
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return self.__phi |
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|
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def update_parameter_sharp(self, param_neg=-1, param_pos=1, phi=None): |
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""" |
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creates a function whith param_neg where phi<0 and param_pos where phi>0 (no smoothing) |
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|
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@param param_neg: value of parameter on the negative side (phi<0) |
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@param param_pos: value of parameter on the positve side (phi>0) |
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@param phi: level set funtion to be used. if not present the current level set is used. |
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""" |
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mask_neg = whereNegative(self.__phi) |
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mask_pos = whereNonNegative(self.__phi) |
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param = param_pos*mask_pos + param_neg*mask_neg |
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return param |
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|
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def update_parameter(self, param_neg=-1, param_pos=1, phi=None, smoothing_width=None): |
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""" |
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creates a smoothed function whith param_neg where phi<0 and param_pos where phi>0 which is smoothed over a length |
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smoothing_width accross the interface |
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|
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@param smoothing_width: width of the smoothing zone relative to mesh size. If not present the initial value of C{smooth} is used. |
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""" |
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if smoothing_width==None: smoothing_width = self.__smooth |
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if phi==None: phi=self.__phi |
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s=self.__makeInterface(phi,smoothing_width) |
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return ((param_pos-param_neg)*s+param_pos+param_neg)/2 |
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|
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def __makeInterface(self,phi,smoothing_width): |
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""" |
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creates a smooth interface from -1 to 1 over the length 2*h*smoothing_width where -1 is used where the level set is negative |
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and 1 where the level set is 1 |
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""" |
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s=smoothing_width*self.__h |
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phi_on_h=interpolate(phi,Function(self.__domain)) |
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mask_neg = whereNonNegative(-s-phi_on_h) |
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mask_pos = whereNonNegative(phi_on_h-s) |
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mask_interface = 1.-mask_neg-mask_pos |
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interface=phi_on_h/s |
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return - mask_neg + mask_pos + mask_interface * interface |
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|
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def makeCharacteristicFunction(self, contour=0, phi=None, positiveSide=True, smoothing_width=None): |
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""" |
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makes a smooth charateristic function of the region phi(x)>contour if positiveSide and phi(x)<contour otherwise. |
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|
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@param phi: level set funtion to be used. if not present the current level set is used. |
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@param smoothing_width: width of the smoothing zone relative to mesh size. If not present the initial value of C{smooth} is used. |
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""" |
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if phi==None: phi=self.__phi |
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if smoothing_width == None: smoothing_width=self.__smooth |
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s=self.__makeInterface(phi=phi-contour,smoothing_width=smoothing_width) |
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if positiveSide: |
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return (1+s)/2 |
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else: |
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return (1-s)/2 |
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|
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def setTolerance(self,tolerance=1e-3): |
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self.__PDE.setTolerance(tolerance) |
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self.__reinitPDE.setTolerance(tolerance) |
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|
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|
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class LevelSet2(object): |
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def __init__(self,phi,reinit_max=10,reinit_each=2,smooth=2.): |
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""" |
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initialize model |
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""" |
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self.__domain = phi.getDomain() |
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x=self.__domain.getX() |
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diam=0 |
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for i in range(self.__domain.getDim()): |
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xi=x[i] |
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diam+=(inf(xi)-sup(xi))**2 |
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self.__diam=sqrt(diam) |
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self.__h = sup(Function(self.__domain).getSize()) |
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self.__reinit_each=reinit_each |
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self.__reinit_max = reinit_max |
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self.__smooth = smooth |
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self.__phi = phi |
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self.__update_count=0 |
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self.velocity = None |
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|
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#================================================== |
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self.__FC=True |
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if self.__FC: |
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self.__fc=TransportPDE(self.__domain,num_equations=1,theta=0.5) |
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# self.__fc.setReducedOrderOn() |
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self.__fc.setValue(M=Scalar(1.,Function(self.__domain))) |
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self.__fc.setInitialSolution(phi+self.__diam) |
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else: |
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self.__fcpde = LinearPDE(self.__domain,numEquations=1, numSolutions=1) |
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self.__fcpde.setSolverMethod(solver=LinearPDE.LUMPING) |
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self.__fcpde.setReducedOrderOn() |
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self.__fcpde.setSymmetryOn() |
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self.__fcpde.setValue(D=1.) |
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|
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#======================================= |
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self.__reinitFC=False |
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if self.__reinitFC: |
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self.__reinitfc=TransportPDE(self.__domain,num_equations=1,theta=1.0) |
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self.__reinitfc.setValue(M=Scalar(1.,Function(self.__domain))) |
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self.__reinitfc.setTolerance(1.e-5) |
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else: |
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self.__reinitPde = LinearPDE(self.__domain,numEquations=1, numSolutions=1) |
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# self.__reinitPde.setSolverMethod(solver=LinearPDE.LUMPING) |
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self.__reinitPde.setReducedOrderOn() |
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self.__reinitPde.setSymmetryOn() |
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self.__reinitPde.setValue(D=1.) |
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self.__reinitPde.setTolerance(1.e-2) |
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# self.__reinitPde.setSolverMethod(preconditioner=LinearPDE.ILU0) |
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#======================================= |
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self.__updateInterface() |
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print "phi range:",inf(phi), sup(phi) |
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|
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def setFixedRegion(self,mask,contour=0): |
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q=whereNonPositive(abs(self.__phi-contour)-self.__h)*mask |
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# self.__fc.setValue(q=q) |
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self.__reinitPde.setValue(q=q) |
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|
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|
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def __updateInterface(self): |
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self.__smoothed_char=self.__makeInterface(self.__phi) |
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|
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|
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|
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|
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def update(self,dt): |
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""" |
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sets a new velocity and updates the level set fuction |
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|
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@param dt: time step forward |
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""" |
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if self.__FC: |
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self.__phi=self.__fc.solve(dt, verbose=False)-self.__diam |
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else: |
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self.__fcpde.setValue(Y = self.__phi-(dt/2.)*inner(self.velocity,grad(self.__phi))) |
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phi_half = self.__fcpde.getSolution() |
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self.__fcpde.setValue(Y = self.__phi-dt*inner(self.velocity,grad(phi_half))) |
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self.__phi= self.__fcpde.getSolution() |
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self.__update_count += 1 |
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if self.__update_count%self.__reinit_each == 0: |
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self.__phi=self.__reinitialise(self.__phi) |
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if self.__FC: |
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self.__fc.setInitialSolution(self.__phi+self.__diam) |
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self.__updateInterface() |
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|
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def setTolerance(self,tolerance=1e-3): |
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if self.__FC: |
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self.__fc.setTolerance(tolerance) |
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|
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def __reinitialise(self,phi): |
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print "reintialization started:" |
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s=self.__makeInterface(phi,1.) |
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print "phi range:",inf(phi), sup(phi) |
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g=grad(phi) |
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w=s*g/(length(g)+EPSILON) |
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#======================================================= |
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# # positive part: |
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# phi_p=wherePositive(phi)*phi |
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# self.__reinitfc.setInitialSolution(phi_p) |
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# self.__reinitfc.setValue(C=-wherePositive(s)*w,Y=wherePositive(s)*s,q=whereNonPositive(phi)) |
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# dtau=self.__h |
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# print "step size: dt (pos)= ",dtau |
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# print "phi_p range:",inf(phi_p), sup(phi_p) |
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# iter=0 |
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# while (iter<=self.__reinit_max): |
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# phi_p=self.__reinitfc.solve(dtau) |
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# print "phi_p range:",inf(phi_p), sup(phi_p) |
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# iter+=1 |
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# # negative part: |
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# phi_n=-whereNegative(phi)*phi |
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# self.__reinitfc.setInitialSolution(phi_n) |
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# self.__reinitfc.setValue(C=-whereNegative(s)*w,Y=-whereNegative(s)*s,q=whereNonNegative(phi)) |
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# # dtau=self.__reinitfc.getSafeTimeStepSize() |
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# dtau=self.__h |
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# print "step size: dt (neg)= ",dtau |
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# print "phi_n range:",inf(phi_n), sup(phi_n) |
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# iter=0 |
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# while (iter<=self.__reinit_max): |
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# phi_n=self.__reinitfc.solve(dtau) |
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# print "phi_n range:",inf(phi_n), sup(phi_n) |
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# iter+=1 |
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# phi=phi_p-phi_n |
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# print "phi range:",inf(phi), sup(phi) |
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# print "reintialization completed." |
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# return phi |
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|
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#======================================================= |
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if self.__reinitFC: |
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self.__reinitfc.setValue(C=-w,Y=s) |
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self.__reinitfc.setInitialSolution(phi+self.__diam) |
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dtau=self.__reinitfc.getSafeTimeStepSize() |
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# dtau = 0.5*inf(Function(self.__domain).getSize()) |
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else: |
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dtau = 0.5*inf(Function(self.__domain).getSize()) |
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print "step size: dt = ",dtau,inf(abs(phi.interpolate(Function(self.__domain)))/abs(s-inner(w,grad(phi)))) |
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iter =0 |
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# self.__reinitPde.setValue(q=whereNegative(abs(phi)-2*self.__h), r=phi) |
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# self.__reinitPde.setValue(r=phi) |
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while (iter<=self.__reinit_max): |
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phi_old=phi |
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if self.__reinitFC: |
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phi = self.__reinitfc.solve(dtau)-self.__diam |
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else: |
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self.__reinitPde.setValue(Y = phi+(dtau/2.)*(s-inner(w,grad(phi)))) |
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phi_half = self.__reinitPde.getSolution() |
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self.__reinitPde.setValue(Y = phi+dtau*(s-inner(w,grad(phi_half)))) |
| 395 |
# g=grad(phi) |
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# S=inner(w,grad(phi)) |
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# self.__reinitPde.setValue(Y = phi+dtau*(s-S),X=dtau**2/2*w*(s-S)) |
| 398 |
phi = self.__reinitPde.getSolution() |
| 399 |
change = Lsup(phi-phi_old)/self.__diam |
| 400 |
print "phi range:",inf(phi), sup(phi) |
| 401 |
print "iteration :", iter, " change:", change |
| 402 |
iter +=1 |
| 403 |
print "reintialization completed." |
| 404 |
return phi |
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|
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def createParameter(self,value_negative=-1.,value_positive=1): |
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out = (value_negative+value_positive)/2. + self.__smoothed_char * ((value_positive-value_negative)/2.) |
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return out |
| 409 |
|
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|
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#================ things from here onwards are not used nor tested: ========================================== |
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|
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|
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def getCharacteristicFunction(self): |
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return self.__smoothed_char |
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|
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|
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|
| 419 |
|
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def RK2(self,L): |
| 421 |
k0=L(phi) |
| 422 |
phi_1=phi+dt*k0 |
| 423 |
k1=L(phi_1) |
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phi=phi+dt/2*(k0+k1) |
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def RK3(self,L): |
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k0=L(phi) |
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phi_1=phi+dt*L(phi) |
| 428 |
k1=L(phi_1) |
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phi_2=phi+dt/4*(k0+k1) |
| 430 |
k2=L(phi_2) |
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phi=phi+dt/6*(k0+4*k2+K1) |
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def TG(self,L): |
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k0=L(phi) |
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phi_1=phi+dt/2*k0 |
| 435 |
k1=L(phi_1) |
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phi=phi+dt*k1 |
| 437 |
|
| 438 |
|
| 439 |
def __reinitialise_old(self): |
| 440 |
#============================================= |
| 441 |
f=0.1 |
| 442 |
f2=0.3 |
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h=self.__h |
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fs=h.getFunctionSpace() |
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vol=self.getVolumeOfNegativeDomain() |
| 446 |
self.__reinitPde.setValue(D=1.0) |
| 447 |
#============ |
| 448 |
grad_phi=grad(self.__phi,fs) |
| 449 |
len_grad_phi=length(grad_phi) |
| 450 |
w=grad_phi/len_grad_phi |
| 451 |
|
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# s=wherePositive(self. __makeInterface(2.))-whereNegative(self. __makeInterface(2.)) |
| 453 |
s=self. __makeInterface(2.) |
| 454 |
# s2=whereNegative(len_grad_phi-f2)*(1-(1-len_grad_phi/f2)**2)+(1-whereNegative(len_grad_phi-f2)) |
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s2=1. |
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s=s*s2 |
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dtau=f*inf(h/abs(s)) |
| 458 |
|
| 459 |
#======================== |
| 460 |
diff=1. |
| 461 |
d=1. |
| 462 |
c =0 |
| 463 |
#============================================== |
| 464 |
TVD=integrate(length(grad_phi)) |
| 465 |
print "initial range ",inf(self.__phi),sup(self.__phi),"error:",Lsup(1.-len_grad_phi),"volume =",vol,TVD |
| 466 |
# saveVTK("test.%s.xml"%c,l=length(grad(self.__phi,fs))-1,s=s,phi=self.__phi) |
| 467 |
|
| 468 |
dtau=f*inf(h/abs(s)) |
| 469 |
while c < self.__reinit_max: # and abs(diff) >= 0.01: |
| 470 |
# |
| 471 |
grad_phi=grad(self.__phi,fs) |
| 472 |
len_grad_phi=length(grad_phi) |
| 473 |
# |
| 474 |
# s=self.__makeInterface(1.) |
| 475 |
# s2=whereNegative(len_grad_phi-f2)*(1-(1-len_grad_phi/f2)**2)+(1-whereNegative(len_grad_phi-f2)) |
| 476 |
# s=s*s2 |
| 477 |
# phi_on_h=interpolate(self.__phi,fs) |
| 478 |
# self.__reinitPde.setValue(Y =self.__phi+dtau/2*s*(1.-len_grad_phi)) |
| 479 |
# phi_half=self.__reinitPde.getSolution() |
| 480 |
# self.__reinitPde.setValue(Y =self.__phi+dtau*s*(1.-length(grad(phi_half,fs)))) |
| 481 |
# self.__reinitPde.setValue(Y =self.__phi, Y_reduced=dtau*s*(1.-inner(w,grad(phi_half,ReducedFunction(self.__domain))))) |
| 482 |
# self.__reinitPde.setValue(Y =self.__phi+dtau*(s-inner(w,grad_phi)),X=dtau/2*h*(s-inner(w,grad_phi))*w) |
| 483 |
# self.__reinitPde.setValue(Y =self.__phi+dtau*s*(1.-len_grad_phi),X=-dtau/2*h*s**2*grad_phi) |
| 484 |
self.__reinitPde.setValue(Y=self.__phi+dtau*s*(1.-len_grad_phi),X=f*dtau/2*h*abs(s)*(1.-len_grad_phi)*grad_phi/len_grad_phi) |
| 485 |
|
| 486 |
# self.__reinitPde.setValue(Y=self.__phi+dtau*s*(1.-len_grad_phi),X=f*dtau/2*h*abs(s)*(1.-len_grad_phi)*grad_phi/len_grad_phi) |
| 487 |
self.__phi, previous = self.__reinitPde.getSolution(), self.__phi |
| 488 |
# self.__updateInterface() |
| 489 |
|
| 490 |
vol,vol_old=self.getVolumeOfNegativeDomain(),vol |
| 491 |
diff=(vol-vol_old) |
| 492 |
r=Lsup(length(grad(self.__phi))-1.) |
| 493 |
TVD=integrate(length(grad(self.__phi,fs))) |
| 494 |
print "iteration :", c, "range ",inf(self.__phi),sup(self.__phi),"error :",r,"volume change:",diff,TVD |
| 495 |
# saveVTK("test.%s.xml"%(c+1),l=length(grad(self.__phi,fs)),s=s,phi=self.__phi,v=grad(self.__phi,fs)) |
| 496 |
c += 1 |
| 497 |
return |
| 498 |
#============================================== |
| 499 |
f2=0.7 |
| 500 |
h=self.__h |
| 501 |
fs=h.getFunctionSpace() |
| 502 |
vol=self.getVolumeOfNegativeDomain() |
| 503 |
s=abs(self. __makeInterface(2.)) |
| 504 |
grad_phi=grad(self.__phi,fs) |
| 505 |
len_grad_phi=length(grad_phi) |
| 506 |
|
| 507 |
#---- |
| 508 |
# aphi_on_h=abs(interpolate(self.__phi,self.__h.getFunctionSpace())) |
| 509 |
# q=2*self.__h |
| 510 |
# mask_neg = whereNegative(aphi_on_h-q) |
| 511 |
# mask_pos = wherePositive(aphi_on_h-q-self.__h) |
| 512 |
# mask_interface = 1.-mask_neg-mask_pos |
| 513 |
# s2=mask_neg + mask_interface * (q+self.__h-aphi_on_h)/self.__h |
| 514 |
#---- |
| 515 |
m=whereNonPositive(len_grad_phi-f2) |
| 516 |
s2=m*len_grad_phi/f2+(1.-m) |
| 517 |
#---- |
| 518 |
# s2=1. |
| 519 |
#---- |
| 520 |
self.__reinitPde.setValue(D=(1-s)/h**2,Y=(1-s)/h**2*self.__phi) |
| 521 |
self.__reinitPde.setValue(A=(s2*len_grad_phi+(1.-s2))*kronecker(3),X=grad_phi) |
| 522 |
# self.__reinitPde.setValue(A=(len_grad_phi-1)/len_grad_phi*kronecker(3)) |
| 523 |
# self.__reinitPde.setValue(A=kronecker(3), X=grad_phi/len_grad_phi) |
| 524 |
self.__phi = self.__reinitPde.getSolution() |
| 525 |
r=Lsup(length(grad(self.__phi))-1.) |
| 526 |
vol,vol_old=self.getVolumeOfNegativeDomain(),vol |
| 527 |
diff=(vol-vol_old)/vol |
| 528 |
print "iteration :", inf(self.__phi),sup(self.__phi),r,diff |
| 529 |
# saveVTK("test.%s.xml"%0,l=length(grad(self.__phi,fs)),s=s,phi=self.__phi,v=grad(self.__phi,fs),s2=s2) |
| 530 |
return |
| 531 |
#============================================= |
| 532 |
|
| 533 |
#============ |
| 534 |
|
| 535 |
|
| 536 |
def getVolumeOfNegativeDomain(self): |
| 537 |
""" |
| 538 |
return the current volume of domain with phi<0. |
| 539 |
""" |
| 540 |
return integrate((1.-self.__makeInterface(1.))/2.) |
| 541 |
|
| 542 |
|
| 543 |
def getBoundingBoxOfNegativeDomain(self): |
| 544 |
""" |
| 545 |
get the height of the region with phi<0 |
| 546 |
""" |
| 547 |
fs=self.__h.getFunctionSpace() |
| 548 |
mask_phi1=wherePositive(interpolate(self.__phi,fs)) |
| 549 |
mask_phi2=wherePositive(self.__phi) |
| 550 |
x1=fs.getX() |
| 551 |
x2=self.__domain.getX() |
| 552 |
out=[] |
| 553 |
for i in range(fs.getDim()): |
| 554 |
x1_i=x1[i] |
| 555 |
x2_i=x2[i] |
| 556 |
d=2*(sup(x2_i)-inf(x2_i)) |
| 557 |
offset1=d*mask_phi1 |
| 558 |
offset2=d*mask_phi2 |
| 559 |
out.append((min(inf(x1_i+offset1),inf(x2_i+offset2)),max(sup(x1_i-offset1),sup(x2_i-offset2)))) |
| 560 |
return tuple(out) |
| 561 |
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