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MEmodel3.py
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from dolfin import *
import numpy as np
import os as os
from ..utils.nsolver import NSolver as NSolver
from ..utils.oops_objects_MRC2 import biventricle_mesh as biv_mechanics_mesh
from ..utils.oops_objects_MRC2 import lv_mesh as lv_mechanics_mesh
from ..utils.oops_objects_MRC2 import PV_Elas
from ..utils.oops_objects_MRC2 import update_mesh
from ..utils.oops_objects_MRC2 import printout
from ..utils.edgetypebc import *
from forms_MRC2 import Forms
from activeforms_MRC2 import activeForms
from ..utils.mesh_partitionMeshforEP_J import defCPP_Matprop, defCPP_Matprop_DIsch
from ..utils.mesh_scale_create_fiberFiles import create_EDFibers
class MEmodel(object):
def __init__(self, params, SimDet):
self.parameters = self.default_parameters()
self.parameters.update(params)
self.SimDet = SimDet
self.isLV = SimDet["isLV"]
self.deg_me = SimDet["GiccioneParams"]["deg"]
if(self.isLV):
self.Mesh = lv_mechanics_mesh(self.parameters, SimDet)
else:
self.Mesh = biv_mechanics_mesh(self.parameters, SimDet)
f0_me_Gauss = self.Mesh.f0
s0_me_Gauss = self.Mesh.s0
n0_me_Gauss = self.Mesh.n0
self.mesh_me = self.Mesh.mesh
self.facetboundaries_me = self.Mesh.facetboundaries
self.edgeboundaries_me = self.Mesh.edgeboundaries
self.ds_me = self.Mesh.ds
self.dx_me = self.Mesh.dx
LVendoid = self.SimDet["LVendoid"]
dsendo = self.ds_me(LVendoid, domain = self.mesh_me, subdomain_data = self.facetboundaries_me)
self.LVendo_area_me = Expression(("val"), val=0.0, degree=2)
self.LVendo_area_me.val = assemble(Constant(1.0) * dsendo, form_compiler_parameters={"representation":"uflacs"})
self.f0_me = f0_me_Gauss
self.s0_me = s0_me_Gauss
self.n0_me = n0_me_Gauss
self.LVCavityvol = Expression(("vol"), vol=0.0, degree=2)
self.RVCavityvol = Expression(("vol"), vol=0.0, degree=2)
self.isincomp = SimDet["GiccioneParams"]["incompressible"]
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
Velem = VectorElement("CG", self.mesh_me.ufl_cell(), 2, quad_scheme="default")
Qelem = FiniteElement("CG", self.mesh_me.ufl_cell(), 1, quad_scheme="default")
Qelem._quad_scheme = 'default'
Relem = FiniteElement("Real", self.mesh_me.ufl_cell(), 0, quad_scheme="default")
Relem._quad_scheme = 'default'
Quadelem = FiniteElement("Quadrature", self.mesh_me.ufl_cell(), degree=self.deg_me, quad_scheme="default")
Quadelem._quad_scheme = 'default'
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
Telem2 = TensorElement("Quadrature", self.mesh_me.ufl_cell(), degree=self.deg_me, shape=2*(3,), quad_scheme='default')
Telem2._quad_scheme = 'default'
for e in Telem2.sub_elements():
e._quad_scheme = 'default'
Telem4 = TensorElement("Quadrature", self.mesh_me.ufl_cell(), degree=self.deg_me, shape=4*(3,), quad_scheme='default')
Telem4._quad_scheme = 'default'
for e in Telem4.sub_elements():
e._quad_scheme = 'default'
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
# Mixed Element for rigid body motion
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
VRelem = MixedElement([Relem, Relem, Relem]) #, Relem]) #, Relem])
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
if(self.isincomp):
if(self.isLV):
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
self.W = FunctionSpace(self.mesh_me, MixedElement([Velem, Qelem, Relem]))
else:
self.W = FunctionSpace(self.mesh_me, MixedElement([Velem, Qelem, Relem, VRelem]))
else:
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
self.W = FunctionSpace(self.mesh_me, MixedElement([Velem, Qelem, Relem, Relem]))
else:
self.W = FunctionSpace(self.mesh_me, MixedElement([Velem, Qelem, Relem, Relem, VRelem]))
else:
if(self.isLV):
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
self.W = FunctionSpace(self.mesh_me, MixedElement([Velem, Relem]))
else:
self.W = FunctionSpace(self.mesh_me, MixedElement([Velem, Relem, VRelem]))
else:
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
self.W = FunctionSpace(self.mesh_me, MixedElement([Velem, Relem, Relem]))
else:
self.W = FunctionSpace(self.mesh_me, MixedElement([Velem, Relem, Relem, VRelem]))
self.Quad = FunctionSpace(self.mesh_me, Quadelem)
self.TF = FunctionSpace(self.mesh_me, Telem2)
self.Q = FunctionSpace(self.mesh_me,'CG',1)
self.QDG = FunctionSpace(self.mesh_me, 'DG', 0)
self.V_CG1 = VectorFunctionSpace(self.mesh_me,'CG',1)
self.we_n = Function(self.W.sub(0).collapse())
self.w_me = Function(self.W)
self.w_me_n = Function(self.W)
self.dw_me = TrialFunction(self.W)
self.wtest_me = TestFunction(self.W)
self.Ftotal, self.Jac, self.bcs = self.Problem()
def default_parameters(self):
return {
"probeloc": [3.5, 0.0, -2.0]
};
def unloading(self, params):
default_params = {"EDP":12, "maxit":20, "restol":1e-3, "drestol":1e-4, "EDPtol": 1e-1, "volinc":1, "LVangle":[60,-60], "Sheetangle":[0.1,-0.1]}
default_params.update(params)
EDP = default_params["EDP"]
LVangle = default_params["LVangle"]
Sheetangle = default_params["Sheetangle"]
maxit = default_params["maxit"]
restol = default_params["restol"]
drestol = default_params["drestol"]
EDPtol = default_params["EDPtol"]
LVendoid = self.SimDet["LVendoid"]
volinc = default_params["volinc"]
outputfolder = self.parameters[ "outputfolder"]
folderName = self.parameters["foldername"]
outfolder = outputfolder + folderName + 'deformation_unloadED/'
targetmesh = Mesh(self.Mesh.mesh)
xtarget = project(SpatialCoordinate(self.mesh_me), self.V_CG1).vector()
comm_me = self.mesh_me.mpi_comm()
if(MPI.rank(comm_me) == 0):
if not os.path.isdir(outfolder):
os.makedirs(outfolder)
if(MPI.rank(comm_me) == 0):
fdataPV = open(outfolder + "BiV_unloadPV.txt", "w", 0)
hdf = HDF5File(comm_me, outfolder + 'Data_unload.h5', "w")
it = 0
res = 1e9
dres = 0
alpha = 1.0
while(1):
it_load = 0
self.LVCavityvol.vol = self.GetLVV()
LVP = self.GetLVP()*0.0075
LVV = self.GetLVV()
printout("Iteration number = " + str(it), comm_me )
printout("Pressure = " + str(LVP) + " Vol = " + str(LVV), comm_me)
if(MPI.rank(comm_me) == 0):
print >> fdataPV, it, LVP, LVV
hdf.write(self.mesh_me, "unloading"+str(it)+"/mesh")
hdf.write(self.GetDisplacement(), "unloading"+str(it)+"/u_loading", it_load)
while(1):
self.LVCavityvol.vol += volinc
self.Solver().solvenonlinear()
LVP = self.GetLVP()*0.0075
LVV = self.GetLVV()
if(LVP > EDP):
print "Decrease load step"
self.LVCavityvol.vol -= volinc
volinc = volinc/2.0
continue;
printout("Loading iteration number = " + str(it_load), comm_me)
printout("Pressure = " + str(LVP) + " Vol = " + str(LVV), comm_me)
if(MPI.rank(comm_me) == 0):
print >> fdataPV, it, LVP, LVV
hdf.write(self.GetDisplacement(), "unloading"+str(it)+"/u_loading", it_load)
if(abs(LVP - EDP) < EDPtol):
#Get Residual
x = project(SpatialCoordinate(self.mesh_me) + self.GetDisplacement(), self.V_CG1).vector()
res_new = norm(x - xtarget, 'L2')
dres = abs(res_new - res)
res = res_new
printout("Residual = " + str(res) + " dResidual = " + str(dres), comm_me)
# Reset volume increment
volinc = default_params["volinc"]
break;
it_load += 1
if(it > maxit or res < restol or dres < drestol):
self.Reset()
break;
else:
dispCG1 = project(-alpha*self.GetDisplacement(), self.V_CG1)
newmesh, newboundaries = update_mesh(targetmesh, dispCG1, self.facetboundaries_me)
#Update mesh
self.Reset()
self.mesh_me.coordinates()[:, 0] = newmesh.coordinates()[:, 0]
self.mesh_me.coordinates()[:, 1] = newmesh.coordinates()[:, 1]
self.mesh_me.coordinates()[:, 2] = newmesh.coordinates()[:, 2]
self.facetboundaries_me.set_values(newboundaries.array())
# Update LV endo surface area for imposing BC
dsendo = self.ds_me(LVendoid, domain = self.mesh_me, subdomain_data = self.facetboundaries_me)
self.LVendo_area_me.val = assemble(Constant(1.0) * dsendo, form_compiler_parameters={"representation":"uflacs"})
self.mesh_me.bounding_box_tree().build(self.mesh_me)
#Update fiber
default_params.update({"meshName":"unloadfiber_"+str(it)})
f0_me_Gauss, s0_me_Gauss, n0_me_Gauss, deformedMesh, deformedBoundary = self.GetDeformedBasis(default_params)
self.f0_me = f0_me_Gauss
self.s0_me = s0_me_Gauss
self.n0_me = n0_me_Gauss
self.f0_me = self.f0_me/sqrt(inner(self.f0_me, self.f0_me))
self.s0_me = self.s0_me/sqrt(inner(self.s0_me, self.s0_me))
self.n0_me = self.n0_me/sqrt(inner(self.n0_me, self.n0_me))
# Restate problem
self.Ftotal, self.Jac, self.bcs = self.Problem()
it += 1
# Write mesh
f = HDF5File(comm_me, outfolder + "UnloadMesh.hdf5", 'w')
f.write(self.mesh_me, "UnloadMesh")
f.close()
f = dolfin.HDF5File(comm_me, outfolder + "UnloadMesh.hdf5", 'a')
f.write(self.facetboundaries_me, "UnloadMesh"+"/"+"facetboundaries")
f.write(self.edgeboundaries_me, "UnloadMesh"+"/"+"edgeboundaries")
f.write(f0_me_Gauss, "UnloadMesh"+"/"+"eF")
f.write(s0_me_Gauss, "UnloadMesh"+"/"+"eS")
f.write(n0_me_Gauss, "UnloadMesh"+"/"+"eN")
#np.savez(outfolder+"Udata.npz", f0_me_Gauss=f0_me_Gauss.vector().array()[:], \
# s0_me_Gauss=s0_me_Gauss.vector().array()[:], \
# n0_me_Gauss=n0_me_Gauss.vector().array()[:], \
# )
#File(outfolder+"facetboundaries.pvd") << self.facetboundaries_me
#File(outfolder+"mesh.pvd") << self.mesh_me
f.close()
#os.system("cp " + outfolder + "UnloadMesh.hdf5" + " " + outfolder + "UnloadMesh_refine.hdf5")
return it_load, volinc, LVV, self.Solver()
def set_BCs(self):
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
# Using bubble element
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
#baseconstraint = project(Expression(("0.0"), degree=2), W.sub(0).sub(2).collapse())
#bctop = DirichletBC(W.sub(0).sub(2), baseconstraint, facetboundaries, topid)
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
facetboundaries = self.facetboundaries_me
edgeboundaries = self.edgeboundaries_me
topid = self.SimDet["topid"]
W = self.W
bctop = DirichletBC(W.sub(0).sub(2), Expression(("0.0"), degree = 2), facetboundaries, topid)
#bctop = DirichletBC(W.sub(0), Expression(("0.0", "0.0", "0.0"), degree = 2), facetboundaries, topid)
endoring = pick_endoring_bc(method="cpp")(edgeboundaries, 1)
bcedge = DirichletBC(W.sub(0), Expression(("0.0", "0.0", "0.0"), degree = 0), endoring, method="pointwise")
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
bcs = [bctop]
else:
#bcs = [bctop]
bcs = [bctop]
#bcs = [] # changing top constraint
#bcs = [bctop, bcedge]
return bcs
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
def Problem(self):
GuccioneParams = self.SimDet["GiccioneParams"]
topid = self.SimDet["topid"]
LVendoid = self.SimDet["LVendoid"]
RVendoid = self.SimDet["RVendoid"]
epiid = self.SimDet["epiid"]
isincomp = GuccioneParams["incompressible"]
deg_me = GuccioneParams["deg"]
mesh_me = self.mesh_me
facetboundaries_me = self.facetboundaries_me
f0_me = self.f0_me
s0_me = self.s0_me
n0_me = self.n0_me
N_me = FacetNormal (mesh_me)
W_me = self.W
Q_me = self.Q
TF_me = self.TF
w_me = self.w_me
w_me_n = self.w_me_n
dw_me = self.dw_me
wtest_me = self.wtest_me
bcs_elas = self.set_BCs()
if(isincomp):
if(self.isLV):
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
du, dp, dlv_pendo = TrialFunctions(W_me)
(u_me, p_me, lv_pendo) = split(w_me)
(u_me_n, p_me_n, lv_pendo_n) = split(w_me_n)
(v_me, q_me, lv_qendo) = TestFunctions(W_me)
rv_pendo = []
LVendo_comp = 2
RVendo_comp = 1000
else:
du, dp, dlv_pendo, dc = TrialFunctions(W_me)
(u_me, p_me, lv_pendo, c_me) = split(w_me)
(u_me_n, p_me_n, lv_pendo_n, c_me_n) = split(w_me_n)
(v_me, q_me, lv_qendo, cq) = TestFunctions(W_me)
rv_pendo = []
LVendo_comp = 2
RVendo_comp = 1000
else:
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
du, dp, dlv_pendo, drv_pendo = TrialFunctions(W_me)
(u_me, p_me, lv_pendo, rv_pendo) = split(w_me)
(u_me_n, p_me_n, lv_pendo_n, rv_pendo_n) = split(w_me_n)
(v_me, q_me, lv_qendo, rv_qendo) = TestFunctions(W_me)
LVendo_comp = 2
RVendo_comp = 3
else:
du, dp, dlv_pendo, drv_pendo, dc = TrialFunctions(W_me)
(u_me, p_me, lv_pendo, rv_pendo, c_me) = split(w_me)
(u_me_n, p_me_n, lv_pendo_n, rv_pendo_n, c_me_n) = split(w_me_n)
(v_me, q_me, lv_qendo, rv_qendo, cq) = TestFunctions(W_me)
LVendo_comp = 2
RVendo_comp = 3
else:
if(self.isLV):
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
du, dlv_pendo = TrialFunctions(W_me)
(u_me, lv_pendo) = split(w_me)
(v_me, lv_qendo) = TestFunctions(W_me)
p_me = Function(Q_me)
rv_pendo = []
LVendo_comp = 1
RVendo_comp = 1000
else:
du, dlv_pendo, dc = TrialFunctions(W_me)
(u_me, lv_pendo, c_me) = split(w_me)
(v_me, lv_qendo, cq) = TestFunctions(W_me)
p_me = Function(Q_me)
rv_pendo = []
LVendo_comp = 1
RVendo_comp = 1000
else:
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
du, dlv_pendo, drv_pendo = TrialFunctions(W_me)
(u_me, lv_pendo, rv_pendo) = split(w_me)
(v_me, lv_qendo, rv_qendo) = TestFunctions(W_me)
p_me = Function(Q_me)
LVendo_comp = 1
RVendo_comp = 2
else:
du, dlv_pendo, drv_pendo, dc = TrialFunctions(W_me)
(u_me, lv_pendo, rv_pendo, c_me) = split(w_me)
(v_me, lv_qendo, rv_qendo, cq) = TestFunctions(W_me)
p_me = Function(Q_me)
LVendo_comp = 1
RVendo_comp = 2
self.t_a = Function(self.Quad)
self.t_a.vector()[:] = 0
#ls0 = 1.85
#Tact = GuccioneParams["Tmax"]
ds_me = self.ds_me
dx_me = self.dx_me
LVendo_area_me = self.LVendo_area_me
params= {"mesh": mesh_me,
"facetboundaries": facetboundaries_me,
"facet_normal": N_me,
"mixedfunctionspace": W_me,
"mixedfunction": w_me,
"displacement_variable": u_me,
"pressure_variable": p_me,
"lv_volconst_variable": lv_pendo,
"lv_constrained_vol":self.LVCavityvol,
"rv_volconst_variable": rv_pendo,
"rv_constrained_vol":self.RVCavityvol,
"LVendoid": LVendoid,
"RVendoid": RVendoid,
"epiid": epiid,
"LVendo_comp": LVendo_comp,
"RVendo_comp": RVendo_comp,
"fiber": f0_me,
"sheet": s0_me,
"sheet-normal": n0_me,
"growth_tensor": None,
"material model": GuccioneParams["Passive model"],
"material params": GuccioneParams["Passive params"],
"incompressible" : GuccioneParams["incompressible"],
"LVendo_area" : LVendo_area_me
}
uflforms = Forms(params)
self.uflforms = uflforms
activeparams = {"mesh": mesh_me,
"dx":dx_me,
"deg" : GuccioneParams["deg"],
"facetboundaries": facetboundaries_me,
"facet_normal": N_me,
"displacement_variable": u_me,
"pressure_variable": p_me,
"fiber": f0_me,
"sheet": s0_me,
"sheet-normal": n0_me,
"t_a": self.t_a,
"Threshold_Potential": 0.9,
"growth_tensor": None,
}
if("Active model" in GuccioneParams.keys()):
activeparams.update({"material model" : GuccioneParams["Active model"]})
if("Active params" in GuccioneParams.keys()):
activeparams.update({"material params" : GuccioneParams["Active params"]})
if("HomogenousActivation" in GuccioneParams.keys()):
activeparams.update({"HomogenousActivation" : GuccioneParams["HomogenousActivation"]})
else:
activeparams.update({"HomogenousActivation" : True})
if self.SimDet["Ischemia"] == True:
kParam = {}
#mId_List = SimDet["mId_List"]
kParam["kabNormal"] = self.SimDet["kabNormal"]
kParam["kNormal"] = self.SimDet["kNormal"]
kappA = defCPP_Matprop(mesh = mesh, mId = bivMesh.AHAid, k = kParam)
activeparams["Tmax"] = kappA
activeforms = activeForms(activeparams)
self.activeforms = activeforms
F_ED = Function(TF_me)
Fmat = uflforms.Fmat()
Cmat = (Fmat.T*Fmat)
Emat = uflforms.Emat()
J = uflforms.J()
n_me = J*inv(Fmat.T)*N_me
Wp_me = uflforms.PassiveMatSEF()
LV_Wvol = uflforms.LVV0constrainedE()
if(not self.isLV):
RV_Wvol = uflforms.RVV0constrainedE()
Sactive = activeforms.PK2StressTensor()
#printout("Total active force = " + str(assemble(activeforms.PK1Stress()*dx_me)), comm_me)
X_me = SpatialCoordinate(mesh_me)
#Kspring = Constant(50) #Original
Kspring = Constant(1.0)#(3.0) #New
#Kspringb = Constant(100)
Kspringtop = Constant(5.0)
F1 = derivative(Wp_me, w_me, wtest_me)*dx_me
if(self.isLV):
F2 = derivative(LV_Wvol, w_me, wtest_me)
else:
F2 = derivative(LV_Wvol + RV_Wvol, w_me, wtest_me)
if("active_region" in self.SimDet.keys() and self.SimDet["active_region"]):
print "Active region = ", self.SimDet["active_region"]
region_cnt = 0
for regionid in self.SimDet["active_region"]:
if(region_cnt == 0):
F4 = inner(Fmat*Sactive, grad(v_me))*(dx_me(int(regionid)))
print "Assigning active stress to ", regionid
else:
F4 += inner(Fmat*Sactive, grad(v_me))*(dx_me(int(regionid)))
print "Assigning active stress to ", regionid
region_cnt += 1
else:
F4 = inner(Fmat*Sactive, grad(v_me))*dx_me
Ftotal = F1 + F2 + F4
#F3 = -Kspring*inner(u_me,v_me)*ds_me(epiid)
#F3 = -Kspring*inner(dot(u_me,n_me)*n_me,v_me)*ds_me(epiid)
#Ftotal += F3
#F6 = -Kspringtop*inner(u_me,v_me)*ds_me(LVendoid)
#F6 = -Kspringtop*inner(u_me,v_me)*ds_me(topid)
#F6 = -Kspringtop*inner(dot(u_me,n_me)*n_me,v_me)*ds_me(topid)
#Ftotal += F6
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
F3 = -Kspring*inner(u_me,v_me)*ds_me(epiid)
Ftotal += F3
else:
Wrigid = inner(as_vector([c_me[0], c_me[1], 0.0]), u_me) + \
inner(as_vector([0.0, 0.0, c_me[2]]), cross(X_me, u_me)) #+ \
#inner(as_vector([c_me[3], 0.0, 0.0]), cross(X_me, u_me)) + \
#inner(as_vector([0.0, c_me[4], 0.0]), cross(X_me, u_me))
F5 = derivative(Wrigid, w_me, wtest_me)*dx_me
#F5 = derivative(Wrigid, w_me, wtest_me)*ds_me(LVendoid)
Ftotal += F5
Jac1 = derivative(F1, w_me, dw_me)
Jac2 = derivative(F2, w_me, dw_me)
Jac4 = derivative(F4, w_me, dw_me)
#Jac6 = derivative(F6, w_me, dw_me)
Jac = Jac1 + Jac2 + Jac4
#Jac3 = derivative(F3, w_me, dw_me)
#Jac += Jac3
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
Jac3 = derivative(F3, w_me, dw_me)
Jac += Jac3
else:
Jac5 = derivative(F5, w_me, dw_me)
Jac += Jac5
#Jac6 = derivative(F6, w_me, dw_me)
#Jac += Jac6
# Initialize LV cavity volume
self.LVCavityvol.vol = uflforms.LVcavityvol()
if(not self.isLV):
self.RVCavityvol.vol = uflforms.RVcavityvol()
if(not self.isLV):
self.RVP_cav = uflforms.RVcavitypressure()
self.RVV_cav = uflforms.RVcavityvol()
return Ftotal, Jac, bcs_elas
def Solver(self):
solverparams = {"Jacobian": self.Jac,
"F": self.Ftotal,
"w": self.w_me,
"boundary_conditions": self.bcs,
"Type": 0,
"mesh": self.mesh_me,
"mode": 1
}
if("abs_tol" in self.SimDet.keys()):
solverparams.update({"abs_tol":self.SimDet["abs_tol"]})
if("rel_tol" in self.SimDet.keys()):
solverparams.update({"rel_tol":self.SimDet["rel_tol"]})
solver_eals = NSolver(solverparams)
return solver_eals
def GetDisplacement(self):
if(self.isLV):
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
u, p, lv_pendo = self.w_me.split(deepcopy=True)
rv_pendo = []
else:
u, p, lv_pendo, self.c = self.w_me.split(deepcopy=True)
rv_pendo = []
else:
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
u, p, lv_pendo, rv_pendo = self.w_me.split(deepcopy=True)
else:
u, p, lv_pendo, rv_pendo, self.c = self.w_me.split(deepcopy=True)
u.rename("u_", "u_")
return u
def UpdateVar(self):
self.w_me_n.assign(self.w_me)
def Reset(self):
self.w_me.assign(self.w_me_n)
def GetP(self):
if(self.isLV):
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
u, p, lv_pendo = self.w_me.split(deepcopy=True)
rv_pendo = []
else:
u, p, lv_pendo, self.c = self.w_me.split(deepcopy=True)
rv_pendo = []
else:
if("springbc" in self.SimDet.keys() and self.SimDet["springbc"]):
u, p, lv_pendo, rv_pendo = self.w_me.split(deepcopy=True)
else:
u, p, lv_pendo, rv_pendo, self.c = self.w_me.split(deepcopy=True)
p.rename("p_", "p_")
return p
def GetFmat(self):
return self.uflforms.Fmat()
def GetFiberstrain(self, F_ref):
return self.uflforms.fiberstrain_1(F_ref=F_ref)
#################################################################################
def GetFiberstrainUL(self):
F_Identity = Identity(self.GetDisplacement().ufl_domain().geometric_dimension())
return self.uflforms.fiberstrain_1(F_ref=F_Identity)
def GetFiberstrainUL_2(self):
F_Identity = Identity(self.GetDisplacement().ufl_domain().geometric_dimension())
return self.uflforms.fiberstrain_2(F_ref=F_Identity)
def GetFiberstrainUL_3(self):
F_Identity = Identity(self.GetDisplacement().ufl_domain().geometric_dimension())
return self.uflforms.fiberstrain_3(F_ref=F_Identity)
def GetFiberstrainUL_4(self):
F_Identity = Identity(self.GetDisplacement().ufl_domain().geometric_dimension())
return self.uflforms.fiberstrain_4(F_ref=F_Identity)
#######################################################################################
def GetSheetstrainUL(self):
F_Identity = Identity(self.GetDisplacement().ufl_domain().geometric_dimension())
return self.uflforms.sheetstrain(F_ref=F_Identity)
def GetSheetnormalstrainUL(self):
F_Identity = Identity(self.GetDisplacement().ufl_domain().geometric_dimension())
return self.uflforms.normalstrain(F_ref=F_Identity)
def GetFiberstrainalmansiUL(self):
F_Identity = Identity(self.GetDisplacement().ufl_domain().geometric_dimension())
return self.uflforms.fiberstrainalmansi(F_ref=F_Identity)
def GetIMP(self):
return self.uflforms.IMP()
def GetIMP2(self):
return self.uflforms.IMP2()
def GetfstressTcauchy(self, AHA_segments):
return self.uflforms.FiberCauchyStress() + self.activeforms.CalculateFiberCauchyStress(VolSeg = AHA_segments) #self.activeforms.fiberstress()
####################################################################################################################
def GetfstressTPK2(self, AHA_segments):
return self.uflforms.fiberstress_1() + self.activeforms.CalculateFiberPK2Stress_1(VolSeg = AHA_segments) #self.activeforms.fiberstress()
def GetfstressTPK2_2(self, AHA_segments):
return self.uflforms.fiberstress_2() + self.activeforms.CalculateFiberPK2Stress_2(VolSeg = AHA_segments) #self.activeforms.fiberstress()
def GetfstressTPK2_3(self, AHA_segments):
return self.uflforms.fiberstress_3() + self.activeforms.CalculateFiberPK2Stress_3(VolSeg = AHA_segments) #self.activeforms.fiberstress()
def GetfstressTPK2_4(self, AHA_segments):
return self.uflforms.fiberstress_4() + self.activeforms.CalculateFiberPK2Stress_4(VolSeg = AHA_segments) #self.activeforms.fiberstress()
###############################################################################################################################
def GetsstressTPK2(self, AHA_segments):
return self.uflforms.sheetstress() + self.activeforms.sheetstress()
def GetnstressTPK2(self, AHA_segments):
return self.uflforms.normalstress() + self.activeforms.sheetnormalstress()
def Getfstressactive(self, AHA_segments):
return self.activeforms.CalculateFiberPK2Stress_1(VolSeg = AHA_segments)
def GetFiberNaturalStrain(self, F_ED, basis_dir, AHA_segments):
F_n = self.GetFmat()
return self.activeforms.CalculateFiberNaturalStrain(F_ = F_n, F_ref = F_ED, e_fiber = basis_dir, VolSeg = AHA_segments)
def GetFiberBiotStrain(self, F_ED, basis_dir, AHA_segments):
F_n = self.GetFmat()
return self.activeforms.CalculateFiberBiotStrain(F_ = F_n, F_ref = F_ED, e_fiber = basis_dir, VolSeg = AHA_segments)
def GetFiberGreenStrain(self, F_ED, basis_dir, AHA_segments):
F_n = self.GetFmat()
return self.activeforms.CalculateFiberGreenStrain(F_ = F_n, F_ref = F_ED, e_fiber = basis_dir, VolSeg = AHA_segments)
def GetLVP(self):
return self.uflforms.LVcavitypressure()
def GetLVV(self):
return self.uflforms.LVcavityvol()
def GetRVP(self):
return self.uflforms.RVcavitypressure()
def GetRVV(self):
return self.uflforms.RVcavityvol()
def GetSActive(self):
Sactive = self.activeforms.PK2StressTensor()
Sactive_ = project(self.f0_me[i]*Sactive[i,j]*self.f0_me[j], self.QDG)
Sactive_.rename("Sact", "Sact")
return Sactive_
def GetDeformedBasis(self, params):
default_params = {"LVangle":[0,0], "SPangle":[0,0], "RVangle": [0,0], "Sheetangle": [0.1,-0.1], "meshName":'EDfile'}
default_params.update(params)
LVangle = default_params["LVangle"]
SPangle = default_params["SPangle"]
RVangle = default_params["RVangle"]
Sheetangle = default_params["Sheetangle"]
meshName = default_params["meshName"]
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
mesh_me = self.mesh_me
facetboundaries_me = self.facetboundaries_me
deg_me = self.deg_me
LVendoid = self.SimDet["LVendoid"]
RVendoid = self.SimDet["RVendoid"]
epiid = self.SimDet["epiid"]
isLV = self.isLV
meshDispFunc = VectorFunctionSpace(mesh_me, "CG", 1)
VQuadelem_me = VectorElement("Quadrature",
mesh_me.ufl_cell(),
degree=deg_me,
quad_scheme="default")
VQuadelem_me._quad_scheme = 'default'
fiberFS = FunctionSpace(mesh_me, VQuadelem_me)
meshDisplacement = project(self.GetDisplacement(), meshDispFunc)
deformedMesh, deformedBoundary = update_mesh(mesh = mesh_me, \
displacement = meshDisplacement, \
boundaries = facetboundaries_me)
outputfolder = self.parameters[ "outputfolder"]
folderName = self.parameters["foldername"]
EDmeshData = {"epiid": epiid,
"rvid": RVendoid,
"lvid": LVendoid,
"LVangle": LVangle,#[0, 0],
"Sheetangle": Sheetangle,
"Septangle": [0, 0],
"RVangle": [0, 0],
"isepiflip": False,
"isendoflip": False,
"iscaling": False,
"mesh": deformedMesh,
"facets": deformedBoundary,
"mFileName": outputfolder + folderName + '/deformation_unloadED/' ,
"isLV": isLV,
"meshName": meshName
}
eCC_ED, eLL_ED, eRR_ED = create_EDFibers(EDmeshData)
# Copy directional field from functionspace with mesh_me to deformedmesh
eCC = Function(fiberFS)
eRR = Function(fiberFS)
eLL = Function(fiberFS)
eCC.vector()[:] = eCC_ED.vector().array()[:]
eRR.vector()[:] = eRR_ED.vector().array()[:]
eLL.vector()[:] = eLL_ED.vector().array()[:]
return eCC, eRR, eLL, deformedMesh, deformedBoundary
def GetDeformedBasis2(self, params):
default_params = {"LVangle":[0,0], "SPangle":[0,0], "RVangle": [0,0], "meshName":'EDfile'}
default_params.update(params)
LVangle = default_params["LVangle"]
SPangle = default_params["SPangle"]
RVangle = default_params["RVangle"]
meshName = default_params["meshName"]
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
mesh_me = self.mesh_me
facetboundaries_me = self.facetboundaries_me
deg_me = self.deg_me
LVendoid = self.SimDet["LVendoid"]
RVendoid = self.SimDet["RVendoid"]
epiid = self.SimDet["epiid"]
isLV = self.isLV
meshDispFunc = VectorFunctionSpace(mesh_me, "CG", 1)
VQuadelem_me = VectorElement("Quadrature",
mesh_me.ufl_cell(),
degree=deg_me,
quad_scheme="default")
VQuadelem_me._quad_scheme = 'default'
fiberFS = FunctionSpace(mesh_me, VQuadelem_me)
meshDisplacement = project(self.GetDisplacement(), meshDispFunc)
deformedMesh, deformedBoundary = update_mesh(mesh = mesh_me, \
displacement = meshDisplacement, \
boundaries = facetboundaries_me)
outputfolder = self.parameters[ "outputfolder"]
folderName = self.parameters["foldername"]
EDmeshData = {"epiid": epiid,
"rvid": RVendoid,
"lvid": LVendoid,
"LVangle": [0, 0],
"Septangle": [0, 0],
"RVangle": [0, 0],
"isepiflip": False,
"isendoflip": False,
"iscaling": False,
"mesh": deformedMesh,
"facets": deformedBoundary,
"mFileName": outputfolder + folderName + '/deformation_unloadED/' ,
"isLV": isLV,
"meshName": meshName
}
eCC_ED, eLL_ED, eRR_ED = create_EDFibers(EDmeshData)
# Copy directional field from functionspace with mesh_me to deformedmesh
eCC = Function(fiberFS)
eRR = Function(fiberFS)
eLL = Function(fiberFS)
eCC.vector()[:] = eCC_ED.vector().array()[:]
eRR.vector()[:] = eRR_ED.vector().array()[:]
eLL.vector()[:] = eLL_ED.vector().array()[:]
return eCC, eRR, eLL, deformedMesh, deformedBoundary
def GetFiberDirection(self, e0, fiberfilename):
# - - - - - - - - - - - -- - - - - - - - - - - - - - - -- - - - - - -
mesh_me = self.mesh_me
facetboundaries_me = self.facetboundaries_me
deg_me = self.deg_me
LVendoid = self.SimDet["LVendoid"]
RVendoid = self.SimDet["RVendoid"]
epiid = self.SimDet["epiid"]
isLV = self.isLV
fiberFunc = VectorFunctionSpace(mesh_me, "CG", 1)
VQuadelem_me = VectorElement("Quadrature",
mesh_me.ufl_cell(),
degree=deg_me,
quad_scheme="default")
VQuadelem_me._quad_scheme = 'default'
fiberFS = FunctionSpace(mesh_me, VQuadelem_me)
f0 = project(e0, fiberFunc )
ef = Function(fiberFunc )
ef.vector().set_local(f0.vector().array().flatten())
ef.vector().apply("insert")
FiberDirFile = File(fiberfilename+"_direction.pvd")
FiberDirFile << ef
def GetFiberStretch(self, F_ED, AHA_segments):
F_n = self.GetFmat()
return self.activeforms.lmbda_ff_ED(F_ref = F_ED, VolSeg = AHA_segments)
def GetSheetStretch(self, F_ED, AHA_segments):
F_n = self.GetFmat()
return self.activeforms.lmbda_ss_ED(F_ref = F_ED, VolSeg = AHA_segments)
def GetNormalStretch(self, F_ED, AHA_segments):
F_n = self.GetFmat()
return self.activeforms.lmbda_nn_ED(F_ref = F_ED, VolSeg = AHA_segments)
def GetFiberStress(self, AHA_segments):
return self.activeforms.CalculateFiberCauchyStress(VolSeg = AHA_segments) # + self.uflforms.FiberCauchyStress()
def GetFiberStressPk2(self, AHA_segments):
return self.activeforms.CalculateFiberPK2Stress_2(VolSeg = AHA_segments)
def GetSheetStress(self, AHA_segments):
return self.activeforms.CalculateSheetCauchyStress( VolSeg = AHA_segments) #+self.uflforms.SheetCauchyStress()
def GetNormalStress(self, AHA_segments):