def fenics(sim_params,file_inputs,output_params,passive_params,hs_params,cell_ion_params,monodomain_params,windkessel_params,pso):
# marking these as indices because this is a function called from fenics_driver
i,j = indices(2)
#------------------## Load in all information and set up simulation --------
output_path = output_params["output_path"][0]
displacementfile = File(output_path + "u_disp.pvd")
save_output = sim_params["save_output"][0]
filament_compliance_factor = hs_params["myofilament_parameters"]["filament_compliance_factor"][0]
no_of_states = hs_params["myofilament_parameters"]["num_states"][0]
no_of_attached_states = hs_params["myofilament_parameters"]["num_attached_states"][0]
no_of_detached_states = no_of_states-no_of_attached_states
no_of_transitions = hs_params["myofilament_parameters"]["num_transitions"][0]
state_attached = hs_params["myofilament_parameters"]["state_attached"][0]
cb_extensions = hs_params["myofilament_parameters"]["cb_extensions"][0]
k_cb_multiplier = hs_params["myofilament_parameters"]["k_cb_multiplier"][0]
k_cb_pos = hs_params["myofilament_parameters"]["k_cb_pos"][0]
k_cb_neg = hs_params["myofilament_parameters"]["k_cb_neg"][0]
cb_number_density = hs_params["cb_number_density"][0]
alpha_value = hs_params["myofilament_parameters"]["alpha"][0]
x_bin_min = hs_params["myofilament_parameters"]["bin_min"][0]
x_bin_max = hs_params["myofilament_parameters"]["bin_max"][0]
x_bin_increment = hs_params["myofilament_parameters"]["bin_width"][0]
work_loop = sim_params["work_loop"][0]
## --------- Set up information for active force calculation ------------------
# Create x interval for cross-bridges
xx = np.arange(x_bin_min, x_bin_max + x_bin_increment, x_bin_increment)
# Define number of intervals cross-bridges are defined over
no_of_x_bins = np.shape(xx)[0]
# Define the length of the populations vector
n_array_length = no_of_attached_states * no_of_x_bins + no_of_detached_states + 2
print "n array length = " + str(n_array_length)
n_vector_indices = [[0,0], [1,1], [2,2+no_of_x_bins-1]]
hsl0 = hs_params["initial_hs_length"][0]
step_size = sim_params["sim_timestep"][0]
sim_duration = sim_params["sim_duration"][0]
time_steps = int(sim_duration/step_size +1)
Ca_flag = 4
constant_pCa = 6.5
fdataCa = open(output_path + "calcium_.txt", "w", 0)
pk1file = File(output_path + "pk1_act_on_f0.pvd")
hsl_file = File(output_path + "hsl_mesh.pvd")
# holder for reaction force at right end
fx_rxn = np.zeros((time_steps))
shorten_flag = 0 # switches to one if shortening begins
# Define the cylinder
x = 10.0
y = 0.0
z = 0.0
cyl_top = Point(x,y,z)
cyl_bottom = Point(0,0,0)
top_radius = 1.0
bottom_radius = 1.0
segments = 4
geometry = mshr.Cylinder(cyl_top,cyl_bottom,top_radius,bottom_radius,segments)
# Create the mesh
mesh = mshr.generate_mesh(geometry,20)
# Save the mesh
File('cylinder_3.pvd') << mesh
no_of_int_points = 4 * np.shape(mesh.cells())[0]
# General quadrature element whose points we will evaluate myosim at
Quadelem = FiniteElement("Quadrature", tetrahedron, degree=2, quad_scheme="default")
Quadelem._quad_scheme = 'default'
# Vector element at gauss points (for fibers)
VQuadelem = VectorElement("Quadrature", mesh.ufl_cell(), degree=2, quad_scheme="default")
VQuadelem._quad_scheme = 'default'
# Real element for rigid body motion boundary condition
Relem = FiniteElement("Real", mesh.ufl_cell(), 0, quad_scheme="default")
Relem._quad_scheme = 'default'
# Quadrature space for information needed at gauss points, such as
# hsl, cb_force, passive forces, etc.
Quad = FunctionSpace(mesh, Quadelem)
# Initialize the half-sarcomere class. Its methods will be used to solve for cell populations
hs = half_sarcomere.half_sarcomere(hs_params,1)
# Need to create a list of dictionaries for parameters for each gauss point
hs_params_list = [{}]*no_of_int_points
passive_params_list = [{}]*no_of_int_points
# Initialize ion class (get calcium transient from here)
cell_ion = cell_ion_driver.cell_ion_driver(cell_ion_params)
calcium = np.zeros(time_steps)
calcium[0] = cell_ion.calculate_concentrations(0,0)
for jj in np.arange(np.shape(hs_params_list)[0]):
hs_params_list[jj] = copy.deepcopy(hs_params)
passive_params_list[jj] = copy.deepcopy(passive_params)
# Create a simple expression to test if x_coord is > 9.0
# making last 10% of cylinder spring elements
tester = Expression("x[0]",degree=1)
digitation = Expression("pow(x[1],2) + pow(x[2],2) + 0.5",degree=1)
point_radius = Expression("sqrt(pow(x[1],2)+pow(x[2],2))",degree=1)
# Project the expression onto the mesh
temp_tester_values = project(tester,FunctionSpace(mesh,"DG",1),form_compiler_parameters={"representation":"uflacs"})
dig_values = project(digitation,FunctionSpace(mesh,"DG",1),form_compiler_parameters={"representation":"uflacs"})
point_rad_values = project(point_radius,FunctionSpace(mesh,"DG",1),form_compiler_parameters={"representation":"uflacs"})
# Interpolate onto the FunctionSpace for quadrature points
temp_tester = interpolate(temp_tester_values,Quad)
dig = interpolate(dig_values,Quad)
point_rad = interpolate(point_rad_values,Quad)
# Create array of the expression values
temp_tester_array = temp_tester.vector().get_local()
dig_array = dig.vector().get_local()
point_rad_array = point_rad.vector().get_local()
parameters["form_compiler"]["quadrature_degree"]=2
parameters["form_compiler"]["representation"] = "quadrature"
# defining parts of the model where the boundary condition should be applied later
# where x[0] = 0
class Left(SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return on_boundary and abs(x[0]) < tol
# where x[0] = 10
class Right(SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return on_boundary and abs(x[0]-10.0) < tol
class Fix_y(SubDomain):
def inside(self, x, on_boundary):
tol = 1E-1
return near(x[0],0.0,tol) and near(x[1],0.0,tol)
class Fix_y_right(SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return near(x[0],10.0,tol) and near(x[1],0.0,tol)
class Fix_z_right(SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return near(x[0],10.0,tol) and near(x[2],0.0,tol)
class Fix_z(SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return (near(x[0],0.0,tol) and near(x[2],0.0,tol))
# now test_marker_fcn has value of 1 on right boundary always
# Define spatial coordinate system used in rigid motion constraint
X = SpatialCoordinate (mesh)
facetboundaries = MeshFunction('size_t', mesh, mesh.topology().dim()-1)
edgeboundaries = MeshFunction('size_t', mesh, mesh.topology().dim()-2)
facetboundaries.set_all(0)
left = Left()
right = Right()
fix_y = Fix_y()
fix_y_right = Fix_y_right()
fix_z = Fix_z()
fix_z_right = Fix_z_right()
#horizontal = Horizontal()
#lower = Lower()
#front = Front()
#
left.mark(facetboundaries, 1)
right.mark(facetboundaries, 2)
fix_y.mark(facetboundaries, 3)
#horizontal.mark(facetboundaries,4)
fix_z.mark(facetboundaries,5)
marker_space = FunctionSpace(mesh,'CG',1)
bc_right_test = DirichletBC(marker_space,Constant(1),facetboundaries,2)
test_marker_fcn = Function(marker_space)
bc_right_test.apply(test_marker_fcn.vector())
File(output_path + "facetboundaries.pvd") << facetboundaries
#lower.mark(facetboundaries, 4)
#front.mark(facetboundaries, 5)
#
ds = dolfin.ds(subdomain_data = facetboundaries)
#
###############################################################################
isincomp = True#False
N = FacetNormal (mesh)
#Cparam = Constant(1.0e2)
TF = TensorFunctionSpace(mesh, 'DG', 1)
Velem = VectorElement("Lagrange", tetrahedron, 2, quad_scheme="default")
Velem._quad_scheme = 'default'
Qelem = FiniteElement("Lagrange", tetrahedron, 1, quad_scheme="default")
Qelem._quad_scheme = 'default'
# Mixed element for rigid body motion. One each for x, y displacement. One each for
# x, y, z rotation
VRelem = MixedElement([Relem, Relem, Relem, Relem, Relem])
W = FunctionSpace(mesh, MixedElement([Velem,Qelem,VRelem]))
x_dofs = W.sub(0).sub(0).dofmap().dofs()
Quad_vectorized_Fspace = FunctionSpace(mesh, MixedElement(n_array_length*[Quadelem]))
# Kurtis trying to initialize vectors
fiberFS = FunctionSpace(mesh, VQuadelem)
f0 = Function(fiberFS)
s0 = Function(fiberFS)
n0 = Function(fiberFS)
f0_diff = Function(fiberFS)
c_param = Function(Quad)
c2_param = Function(Quad)
c3_param = Function(Quad)
File(output_path + "fiber1.pvd") << project(f0, VectorFunctionSpace(mesh, "DG", 0))
m_x = 1.0
m_y = 0.0
m_z = 0.0
width = sim_params["width"][0]
#x_comps = r.normal(m_x,width,no_of_int_points)
#y_comps = r.normal(m_y,width,no_of_int_points)
#z_comps = r.normal(m_z,width,no_of_int_points)
for jj in np.arange(no_of_int_points):
#if (temp_tester_array[jj] < dig_array[jj]) or (temp_tester_array[jj] > -dig_array[jj] + 10.0):
if (temp_tester_array[jj] > 9.0) or (temp_tester_array[jj] < 1.0):
# inside left end
f0.vector()[jj*3] = 1.0
f0.vector()[jj*3+1] = 0.0
f0.vector()[jj*3+2] = 0.0
hs_params_list[jj]["myofilament_parameters"]["k_3"][0] = 0.0
#passive_params_list[jj]["c"][0] = 2000
c_param.vector()[jj] = 400
c2_param.vector()[jj] = 250
c3_param.vector()[jj] = 10
else:
# In middle region, assign fiber vector
# find radius of point
temp_radius = point_rad_array[jj]
if np.abs(temp_radius - top_radius) < 0.01:
temp_width = 0.0
else:
temp_width = width*(1.0-(temp_radius*temp_radius/(top_radius*top_radius)))
f0.vector()[jj*3] = r.normal(m_x,temp_width,1)[0]
f0.vector()[jj*3+1] = r.normal(m_y,temp_width,1)[0]
f0.vector()[jj*3+2] = r.normal(m_z,temp_width,1)[0]
c_param.vector()[jj] = 1000
c2_param.vector()[jj] = 250
c3_param.vector()[jj] = 15
"""f0.vector()[kk*3] = x_comps[kk]
# assign y component
f0.vector()[kk*3+1] = y_comps[kk]
# z component would look like
f0.vector()[kk*3+2] = z_comps[kk]"""
f0 = f0/sqrt(inner(f0,f0))
#f0_norm = project(sqrt(inner(f0,f0)),FunctionSpace(mesh,"CG",1))
#print "norm is " + str(f0_norm.vector().array())
#stop
f0_diff = f0 - Constant((1.,0.,0.))
long_axis = Function(fiberFS)
for nn in np.arange(no_of_int_points):
long_axis.vector()[nn*3] = 0.0
long_axis.vector()[nn*3+1] = 0.0
long_axis.vector()[nn*3+2] = 1.0
#s0 = f0 + f0_diff # sum object
#n0 = cross(f0,s0) # cross object
#s0 = project(Constant((0,1,0))+f0_diff,VectorFunctionSpace(mesh, "DG", 0))
s0 = cross(long_axis,f0)
s0 = s0/sqrt(inner(s0,s0))
File(output_path + "sheet.pvd") << project(s0,VectorFunctionSpace(mesh, "DG", 0))
n0 = project(cross(f0,s0),VectorFunctionSpace(mesh, "DG", 0))
n0 = n0/sqrt(inner(n0,n0))
File(output_path + "sheet_normal.pvd") << project(n0,VectorFunctionSpace(mesh, "DG", 0))
File(output_path + "fiber.pvd") << project(f0, VectorFunctionSpace(mesh, "CG", 1))
#test_tensor = as_tensor(f0*f0)
# assigning BCs
u_D = Expression(("u_D"), u_D = 0.0, degree = 2)
bcleft= DirichletBC(W.sub(0).sub(0), Constant((0.0)), facetboundaries, 1) # u1 = 0 on left face
bcright= DirichletBC(W.sub(0).sub(0), u_D, facetboundaries, 2)
bcfix_y = DirichletBC(W.sub(0).sub(1), Constant((0.0)), fix_y, method="pointwise")
bcfix_z = DirichletBC(W.sub(0).sub(2), Constant((0.0)), fix_z, method="pointwise") # at one vertex u = v = w = 0
bcfix_y_right = DirichletBC(W.sub(0).sub(1), Constant((0.0)),fix_y_right, method="pointwise")
bcfix_z_right = DirichletBC(W.sub(0).sub(2), Constant((0.0)),fix_z_right, method="pointwise")
#bchorizontal = DirichletBC(W.sub(0).sub(1), Constant((0.0)), horizontal, method="pointwise")
#bclower= DirichletBC(W.sub(0).sub(2), Constant((0.0)), facetboundaries, 4) # u3 = 0 on lower face
#bcfront= DirichletBC(W.sub(0).sub(1), Constant((0.0)), facetboundaries, 5) # u2 = 0 on front face
#bcs = [bcleft, bclower, bcfront, bcright,bcfix]
bcs = [bcleft, bcright,bcfix_y,bcfix_z,bcfix_y_right,bcfix_z_right]
du,dp,dc11 = TrialFunctions(W)
w = Function(W)
dw = TrialFunction(W)
(u,p,c11) = split(w)
(v,q,v11) = TestFunctions(W)
wtest = TestFunction(W)
params= {"mesh": mesh,
"facetboundaries": facetboundaries,
"facet_normal": N,
"mixedfunctionspace": W,
"mixedfunction": w,
"displacement_variable": u,
"pressure_variable": p,
"fiber": f0,
"sheet": s0,
"sheet-normal": n0,
#"C_param": Cparam,
"incompressible": isincomp,
"Kappa":Constant(1e5)}
params.update(passive_params)
params["c"] = c_param
params["c2"] = c2_param
params["c3"] = c3_param
uflforms = Forms(params)
Fmat = uflforms.Fmat()
Cmat = (Fmat.T*Fmat)
Emat = uflforms.Emat()
J = uflforms.J()
n = J*inv(Fmat.T)*N
dx = dolfin.dx(mesh,metadata = {"integration_order":2})
#Ematrix = project(Emat, TF)
Wp = uflforms.PassiveMatSEF()
#Active force calculation------------------------------------------------------
y_vec = Function(Quad_vectorized_Fspace)
hsl = sqrt(dot(f0, Cmat*f0))*hsl0
hsl_old = Function(Quad)
#hsl_old = hsl
delta_hsl = hsl - hsl_old
#delta_hsl = 0.0
#f_holder = Constant(0.0)
cb_force = Constant(0.0)
y_vec_split = split(y_vec)
#print "shape of yvecsplit " + str(np.shape(y_vec_split))
for jj in range(no_of_states):
f_holder = Constant(0.0)
temp_holder = Constant(0.0)
if state_attached[jj] == 1:
cb_ext = cb_extensions[jj]
for kk in range(no_of_x_bins):
dxx = xx[kk] + delta_hsl * filament_compliance_factor
n_pop = y_vec_split[n_vector_indices[jj][0] + kk]
temp_holder = n_pop * k_cb_multiplier[jj] * (dxx + cb_ext) * conditional(gt(dxx + cb_ext,0.0), k_cb_pos, k_cb_neg)
#temp_holder = temp_holder*conditional(gt(abs(dxx),x_bin_max),0.0,1.0)
#f_holder = f_holder + conditional(gt(temp_holder,0.0),temp_holder,0.0)
f_holder = f_holder + temp_holder
f_holder = f_holder * cb_number_density * 1e-9
f_holder = f_holder * alpha_value
cb_force = cb_force + f_holder
#print "rank" + str(f0.rank())
Pactive = cb_force * as_tensor(f0[i]*f0[j], (i,j))
Press = Expression(("P"), P=0.0, degree=0)
# Automatic differentiation #####################################################################################################
F1 = derivative(Wp, w, wtest)*dx
F2 = inner(Fmat*Pactive, grad(v))*dx
F3 = inner(Press*N, v)*ds(2, domain=mesh)
# constrain rigid body motion
"""L4 = inner(as_vector([c11[0], c11[1], 0.0]), u)*dx + \
inner(as_vector([0.0, 0.0, c11[2]]), cross(X, u))*dx + \
inner(as_vector([c11[3], 0.0, 0.0]), cross(X, u))*dx + \
inner(as_vector([0.0, c11[4], 0.0]), cross(X, u))*dx
F4 = derivative(L4, w, wtest)"""
Ftotal = F1 + F2 - F3 #+ F4
Jac1 = derivative(F1, w, dw)
Jac2 = derivative(F2, w, dw)
Jac3 = derivative(F3, w, dw)
#Jac4 = derivative(F4, w, dw)
Jac = Jac1 + Jac2 - Jac3 #+ Jac4
##################################################################################################################################
darray = []
"""hslarray = np.zeros((time_steps+1,no_of_int_points))
calarray = []
strarray = np.zeros((time_steps+1,no_of_int_points))
pstrarray = np.zeros((time_steps+1,no_of_int_points))
overlaparray = np.zeros((time_steps+1,no_of_int_points))"""
calcium_ds = pd.DataFrame(np.zeros(no_of_int_points),index=None)
calcium_ds = calcium_ds.transpose()
calcium = np.zeros(time_steps)
active_stress_ds = pd.DataFrame(np.zeros(no_of_int_points),index=None)
active_stress_ds = active_stress_ds.transpose()
dumped_populations_ds = pd.DataFrame(np.zeros((no_of_int_points,n_array_length)))
tarray_ds = pd.DataFrame(np.zeros(time_steps+1),index=None)
tarray_ds = tarray_ds.transpose()
tarray = np.zeros(time_steps)
p_f_array_ds = pd.DataFrame(np.zeros(no_of_int_points),index=None)
p_f_array_ds = p_f_array_ds.transpose()
pgf_array_ds = pd.DataFrame(np.zeros(no_of_int_points),index=None)
pgf_array_ds = pgf_array_ds.transpose()
pgt_array_ds = pd.DataFrame(np.zeros(no_of_int_points),index=None)
pgt_array_ds = pgt_array_ds.transpose()
pgs_array_ds =pd.DataFrame(np.zeros(no_of_int_points),index=None)
pgs_array_ds = pgs_array_ds.transpose()
temp_overlap_ds = pd.DataFrame(np.zeros(no_of_int_points),index=None)
temp_overlap_ds = temp_overlap_ds.transpose()
alpha_array_ds = pd.DataFrame(np.zeros(no_of_int_points),index=None)
alpha_array_ds = alpha_array_ds.transpose()
hsl_array_ds =pd.DataFrame(np.zeros(no_of_int_points),index=None)
hsl_array_ds = hsl_array_ds.transpose()
delta_hsl_array_ds = pd.DataFrame(np.zeros(no_of_int_points),index=None)
delta_hsl_array_ds = delta_hsl_array_ds.transpose()
y_vec_array = y_vec.vector().get_local()[:]
hsl_array = project(hsl, Quad).vector().get_local()[:]
#hsl_array = np.ones(no_of_int_points)*hsl0
delta_hsl_array = np.zeros(no_of_int_points)
for counter in range(0,n_array_length * no_of_int_points,n_array_length):
y_vec_array[counter] = 1
y_vec_array[counter-2] = 1
Pg, Pff, alpha = uflforms.stress()
# Magnitude of bulk passive stress in fiber direction
Pg_fiber = inner(f0,Pg*f0)
Pg_transverse = inner(n0,Pg*n0)
Pg_shear = inner(n0,Pg*f0)
temp_DG = project(Pff, FunctionSpace(mesh, "DG", 1), form_compiler_parameters={"representation":"uflacs"})
p_f = interpolate(temp_DG, Quad)
p_f_array = p_f.vector().get_local()[:]
temp_DG_1 = project(alpha, FunctionSpace(mesh, "DG", 1), form_compiler_parameters={"representation":"uflacs"})
alphas = interpolate(temp_DG_1, Quad)
alpha_array = alphas.vector().get_local()[:]
cb_f_array = project(cb_force, Quad).vector().get_local()[:]
dumped_populations = np.zeros((no_of_int_points, n_array_length))
y_interp = np.zeros((no_of_int_points)*n_array_length)
x_dofs = W.sub(0).sub(0).dofmap().dofs()
temp_overlap = np.zeros((no_of_int_points))
y_vec_array_new = np.zeros(((no_of_int_points)*n_array_length))
j3_fluxes = np.zeros((no_of_int_points,time_steps))
j4_fluxes = np.zeros((no_of_int_points,time_steps))
#print "shapes of stuff"
#print np.shape(temp_overlap)
#print np.shape(y_vec_array_new)
temp_astress = np.ones(no_of_int_points)
t = 0.0
#delta_hsls = np.zeros((time_steps,24))
for l in range(time_steps):
tarray[l]=(t)
# Right now, not general. The calcium depends on cycle number, just saying 0
cycle = 0
#calcium[l] = cell_ion.model_class.calculate_concentrations(cycle,t)
calcium[l] = cell_ion.calculate_concentrations(step_size,l)
#calcium[l] = cell_ion.model.calculate_concentrations(0,t)
# Looping through integration points within Python Myosim, not here
# Quick hack
if l == 0:
overlap_counter = 1
else:
overlap_counter = l
# Because we want to be able to change contractility parameters for each
# gauss point, we need to loop through the gauss points here
#temp_overlap, y_interp, y_vec_array_new = implement.update_simulation(hs, step_size, delta_hsl_array, hsl_array, y_vec_array, p_f_array, cb_f_array, calcium[l], n_array_length, t,overlaparray[overlap_counter,:])
#print "hs list dict " + str(hs_params_list
#print "y_vec_new " + str(y_vec_array_new)
for mm in np.arange(no_of_int_points):
#print hsl_array[mm]
temp_overlap[mm], y_interp[mm*n_array_length:(mm+1)*n_array_length], y_vec_array_new[mm*n_array_length:(mm+1)*n_array_length] = implement.update_simulation(hs, step_size, delta_hsl_array[mm], hsl_array[mm], y_vec_array[mm*n_array_length:(mm+1)*n_array_length], p_f_array[mm], cb_f_array[mm], calcium[l], n_array_length, t,hs_params_list[mm])
temp_flux_dict, temp_rate_dict = implement.return_rates_fenics(hs)
#print temp_flux_dict["J3"]
j3_fluxes[mm,l] = sum(temp_flux_dict["J3"])
j4_fluxes[mm,l] = sum(temp_flux_dict["J4"])
# print y_vec_array_new[0:53]
y_vec_array = y_vec_array_new # for Myosim
print " num gauss points " + str(no_of_int_points)
print "y_vec shape" + str(np.shape(y_vec_array))
print "y_interp shape" + str(np.shape(y_interp))
for m in range(no_of_int_points):
for k in range(n_array_length):
dumped_populations[m, k] = y_interp[m * n_array_length + k]
#print "shapes of stuff"
#print np.shape(y_vec.vector())
#print np.shape(y_vec_array)
y_vec.vector()[:] = y_vec_array # for PDE
# print y_vec_array[0:53]
hsl_array_old = hsl_array
# trying to implement a work loop
if work_loop:
if l>0:
temp_astress = cb_f_array[:]
temp_astress = temp_astress[temp_astress > 0.0]
if np.shape(temp_astress)[0] == 0:
temp_astress=0.0
"""if l > 2:
u_check = project(u,VectorFunctionSpace(mesh,"CG",2))
disp_value = u_check.vector()[test_marker_fcn.vector()==1]
print "displacement after shortening on right is = " + str(disp_value[0])
u_D.u_D=disp_value[0]"""
if np.average(temp_astress>=50000):
Press.P=50000
bcs = [bcleft,bcfix_y,bcfix_z,bcfix_y_right,bcfix_z_right]
shorten_flag = 1
else:
if shorten_flag < 0:
u_D.u_D = u_D.u_D
Press.P=0.0
if shorten_flag > 0:
u_check = project(u,VectorFunctionSpace(mesh,"CG",2))
disp_value = u_check.vector()[test_marker_fcn.vector()==1]
print "displacement after shortening on right is = " + str(disp_value[0])
u_D.u_D=disp_value[0]
shorten_flag = -1
bcs = [bcleft,bcright,bcfix_y,bcfix_z,bcfix_y_right,bcfix_z_right]
solve(Ftotal == 0, w, bcs, J = Jac, form_compiler_parameters={"representation":"uflacs"},solver_parameters={"newton_solver":{"relative_tolerance":1e-8},"newton_solver":{"maximum_iterations":50},"newton_solver":{"absolute_tolerance":1e-8}})
"""np.save(output_path +"dumped_populations", dumped_populations)
np.save(output_path + "tarray", tarray)
np.save(output_path + "stress_array", strarray)
np.save(output_path + "hsl", hslarray)
np.save(output_path + "overlap", overlaparray)
np.save(output_path + "pstress_array",pstrarray)
#np.save(output_path + "alpha_array",alphaarray)
np.save(output_path + "calcium",calarray)"""
displacementfile << w.sub(0)
pk1temp = project(inner(f0,Pactive*f0),FunctionSpace(mesh,'CG',1))
pk1temp.rename("pk1temp","pk1temp")
pk1file << pk1temp
hsl_temp = project(hsl,FunctionSpace(mesh,'DG',1))
hsl_temp.rename("hsl_temp","hsl")
#hsl_file << hsl_temp
hsl_old.vector()[:] = project(hsl, Quad).vector().get_local()[:] # for PDE
hsl_array = project(hsl, Quad).vector().get_local()[:] # for Myosim
delta_hsl_array = project(sqrt(dot(f0, Cmat*f0))*hsl0, Quad).vector().get_local()[:] - hsl_array_old # for Myosim
#delta_hsls[l] = delta_hsl_array
temp_DG = project(Pff, FunctionSpace(mesh, "DG", 1), form_compiler_parameters={"representation":"uflacs"})
p_f = interpolate(temp_DG, Quad)
p_f_array = p_f.vector().get_local()[:]
for ii in range(np.shape(hsl_array)[0]):
if p_f_array[ii] < 0.0:
p_f_array[ii] = 0.0
temp_DG_2 = project(Pg_fiber, FunctionSpace(mesh, "DG", 1), form_compiler_parameters={"representation":"uflacs"})
pgf = interpolate(temp_DG_2, Quad)
pgf_array = pgf.vector().get_local()[:]
temp_DG_3 = project(Pg_transverse, FunctionSpace(mesh, "DG", 1), form_compiler_parameters={"representation":"uflacs"})
pgt = interpolate(temp_DG_3, Quad)
pgt_array = pgt.vector().get_local()[:]
temp_DG_4 = project(Pg_shear, FunctionSpace(mesh, "DG", 1), form_compiler_parameters={"representation":"uflacs"})
pgs = interpolate(temp_DG_4, Quad)
pgs_array = pgs.vector().get_local()[:]
cb_f_array = project(cb_force, Quad).vector().get_local()[:]
#strarray.append(cb_f_array[0])
#strarray[l,:] = cb_f_array[:]
#pstrarray[l,:] = p_f_array[:]
#hslarray.append(hsl_array[0]+delta_hsl_array[0])
#hslarray[l,:] = hsl_array[:] + delta_hsl_array[:]
#overlaparray[l,:] = temp_overlap
# Calculate reaction force at right end
b = assemble(Ftotal,form_compiler_parameters={"representation":"uflacs"})
bcleft.apply(b)
bcfix_y.apply(b)
bcfix_z.apply(b)
bcfix_y_right.apply(b)
bcfix_z_right.apply(b)
f_int_total = b.copy()
for kk in x_dofs:
fx_rxn[l] += f_int_total[kk]
#bcleft.apply(f_int_total)
#FX = 0
#for kk in x_dofs:
# FX += f_int_total[i]
#fx_rxn[l] = Fx
np.save(output_path + "fx",fx_rxn)
if t <= 5:
u_D.u_D += .14
else:
u_D.u_D = u_D.u_D
#print(cb_f_array)
"""if t <= 100: # stretch to 1300
u_D.u_D += .003
if t < 500 and t > 100:
u_D.u_D =u_D.u_D
if t < 600 and t >= 500:
u_D.u_D += .0005
if t < 800 and t >=600:
u_D.u_D = u_D.u_D
if t < 900 and t >= 800:
u_D.u_D -= .0005
if t >= 900:
u_D.u_D = u_D.u_D"""
"""if t < 170 and t > 150:
u_D.u_D -= 0.005
else:
u_D.u_D = u_D.u_D"""
"""if t < 5:
u_D.u_D += 0.03
else:
u_D.u_D = u_D.u_D"""
t = t + step_size
#calarray.append(hs.Ca_conc*np.ones(no_of_int_points))
#calcium[] = hs.Ca_conc*
if save_output:
active_stress_ds.iloc[0,:] = cb_f_array[:]
active_stress_ds.to_csv(output_path + 'active_stress.csv',mode='a',header=False)
#active_stress_ds = active_stress_ds.transpose()
#hsl_array_ds.iloc[0,:] = hsl_array[:]
#hsl_array_ds.to_csv(output_path + 'half_sarcomere_lengths.csv',mode='a',header=False)
calcium_ds.iloc[0,:] = calcium[l]
calcium_ds.to_csv(output_path + 'calcium.csv',mode='a',header=False)
#for i in range(no_of_int_points):
# dumped_populations_ds.iloc[i,:] = dumped_populations[i,:]
#dumped_populations_ds.to_csv(output_path + 'populations.csv',mode='a',header=False)
tarray_ds[l] = tarray[l]
tarray_ds.to_csv(output_path + 'time.csv',mode='a',header=False)
#p_f_array_ds.iloc[0,:] = p_f_array[:]
#p_f_array_ds.to_csv(output_path + 'myofiber_passive.csv',mode='a',header=False)
#pgf_array_ds.iloc[0,:] = pgf_array[:]
#pgf_array_ds.to_csv(output_path + 'gucc_fiber_pstress.csv',mode='a',header=False)
#pgt_array_ds.iloc[0,:] = pgt_array[:]
#pgt_array_ds.to_csv(output_path + 'gucc_trans_pstress.csv',mode='a',header=False)
#pgs_array_ds.iloc[0,:] = pgs_array[:]
#pgs_array_ds.to_csv(output_path + 'gucc_shear_pstress.csv',mode='a',header=False)
#temp_overlap_ds.iloc[0,:] = temp_overlap[:]
#temp_overlap_ds.to_csv(output_path + 'overlap.csv',mode='a',header=False)
#alpha_array_ds.iloc[0,:] = alpha_array[:]
#alpha_array_ds.to_csv(output_path + 'alpha.csv',mode='a',header=False)
#delta_hsl_array_ds.iloc[0,:] = delta_hsl_array[:]
#delta_hsl_array_ds.to_csv(output_path + 'delta_hsl.csv',mode='a',header=False)
# Update Fiber orientation
#f0 = f0+step_size*(Cmat*f0-f0)/sqrt(inner(Cmat*f0-f0,Cmat*f0-f0))
#target_vec = Cmat*f0
#print target_vec.type()
#target_diff = target_vec - f0
#target_diff = target_diff/sqrt(inner(target_diff,target_diff))
#f0 = f0 + step_size*target_diff
#File(output_path + "fiber_" +str(t)+ ".pvd") << project(f0, VectorFunctionSpace(mesh, "CG", 1))
"""for m in range(no_of_int_points):
for k in range(n_array_length):
dumped_populations[l, m, k] = y_vec_array[m * n_array_length + k]"""
rate_constants = np.zeros((no_of_x_bins,no_of_transitions + 1))
#for l in range(no_of_x_bins):
# for m in range(no_of_transitions + 1):
# rate_constants[l,m] = Myosim.dump_rate_constants(l, m, 0)
fluxes, rates = implement.return_rates_fenics(hs)
#np.save("/home/fenics/shared/python_dev/test_10_pm/rates",rates)
#np.save("/home/fenics/shared/python_dev/test_10_pm/dumped_populations",dumped_populations)
#np.save("/home/fenics/shared/python_dev/test_10_pm/tarray",tarray)
#np.save("/home/fenics/shared/python_dev/test_10_pm/stress_array",strarray)
#np.save("/home/fenics/shared/python_dev/test_10_pm/pstress_array",p_f)
#np.save("/home/fenics/shared/python_dev/test_10_pm/calcium",calarray)
#np.save("/home/fenics/shared/test_10/displacements",darray)
#np.save("/home/fenics/shared/python_dev/test_10_pm/HSL",hslarray)
#np.save("/home/fenics/shared/test_10/DHSL",delta_hsls)
"""outputs = {
"rates": rates,
"dumped_populations": dumped_populations,
"tarray": tarray,
"strarray": strarray,
"pstrarray": pstrarray,
"alphaarray": darray,
"calarray": calarray,
"hsl": hslarray,
#"overlap": overlaparray
}"""
outputs = {}
"""np.save(output_path +"dumped_populations", dumped_populations)
np.save(output_path + "tarray", tarray)
np.save(output_path + "stress_array", strarray)
np.save(output_path + "hsl", hslarray)
np.save(output_path + "overlap", overlaparray)
np.save(output_path + "pstress_array",pstrarray)
np.save(output_path + "j3",j3_fluxes)
np.save(output_path + "j4",j4_fluxes)
#np.save(output_path + "alpha_array",alphaarray)
np.save(output_path + "calcium",calarray)"""
fdataCa.close()
return(outputs)