def adder():
form = Forms(request.form)
if request.method == 'POST':
con = sql.connect("studentdb.db")
cur = con.cursor()
idnumNew = form.idnumNew.data
fnameNew = form.fnameNew.data
mnameNew = form.mnameNew.data
lnameNew = form.lnameNew.data
sexNew = form.sexNew.data
courseidNew = form.courseidNew.data
cur.execute("SELECT * FROM students WHERE idnum = ?", (idnumNew,))
if cur.fetchone() is not None:
flash('Id number already taken', 'error')
return render_template("add.html", form=form)
elif not form.validate():
flash("Please don't leave any blank", 'error')
return render_template("add.html", form=form)
elif form.validate():
student = models.Student(idnum = idnumNew, fname = fnameNew, mname = mnameNew, lname = lnameNew, sex = sexNew,courseid = courseidNew)
student.add()
flash('Student successfully added', 'success')
return render_template("studentDatabase.html")
else:
return render_template("add.html", form=form)
con.close()
def __init__(self, username, password, email, firstname, lastname, age,
country, highestqualification, workexperiences, skillsets,
awards, bio):
Forms.__init__(self, username, password)
self.__email = email
self.__firstname = firstname
self.__lastname = lastname
self.__age = age
self.__country = country
self.__highestqualification = highestqualification
self.__workexperiences = workexperiences
self.__skillsets = skillsets
self.__awards = awards
self.__bio = bio
def signup():
form = Forms()
error = ""
if (request.method == 'POST' and form.validate_on_submit()):
username = request.form['username']
hash_password = make_pw_hash(request.form['password1'])
user = User.query.filter_by(username=username).first()
if (not user): #create new user
session['username'] = username
user = User(username, hash_password)
db.session.add(user)
db.session.commit()
return redirect('/post')
else: #duplicated user
error = "Duplicated user!"
return render_template('signup.html', form=form, error=error)
def login():
form = Forms()
error = ""
if (request.method == 'POST'):
username = request.form['username']
user = User.query.filter_by(username=username).first()
password = request.form['password1']
if (user):
if (check_pw_hash(password, user.password)):
session['username'] = username
return redirect('/post')
else:
flash("Invalid password!")
error = "Invalid Password!"
#return render_template('login.html',form=form,error=error)
else:
flash("Username does not exist!")
error = "Username does not exist!"
#return redirect('/login')
return render_template('login.html', form=form, error=error)
def fenics(sim_params, file_inputs, output_params, passive_params, hs_params,
cell_ion_params, monodomain_params, windkessel_params, pso):
i, j = indices(2)
#global i
#global j
# We don't do pressure control simulations, probably will get rid of this.
ispressurectrl = False
#------------------## Load in all information and set up simulation --------
## Assign input/output parameters
output_path = output_params["output_path"][0]
casename = file_inputs["casename"][0]
# Assign parameters for Windkessel
# will be moving circulatory to its own module and pass in dictionary
# similar to cell_ion module
Cao = windkessel_params["Cao"][0]
Cven = windkessel_params["Cven"][0]
Vart0 = windkessel_params["Vart0"][0]
Vven0 = windkessel_params["Vven0"][0]
Rao = windkessel_params["Rao"][0]
Rven = windkessel_params["Rven"][0]
Rper = windkessel_params["Rper"][0]
V_ven = windkessel_params["V_ven"][0]
V_art = windkessel_params["V_art"][0]
# -------- Assign parameters for active force calculation ----------------
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]
hsl_min_threshold = hs_params["myofilament_parameters"]["passive_l_slack"][
0]
hsl_max_threshold = hs_params["myofilament_parameters"][
"hsl_max_threshold"][0]
xfiber_fraction = hs_params["myofilament_parameters"]["xfiber_fraction"][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 # +2 for binding sites on/off
# Need to work out a general way to set this based on the scheme
n_vector_indices = [[0, 0], [1, 1], [2, 2 + no_of_x_bins - 1]]
#------------ Start setting up simulation ---------------------------------
sim_duration = sim_params["sim_duration"][0]
save_output = sim_params["save_output"][0]
step_size = sim_params["sim_timestep"][0]
loading_number = sim_params["loading_number"][0]
if sim_params["sim_geometry"][0] == "ventricle" or sim_params[
"sim_geometry"][0] == "ventricle_lclee_2" or sim_params[
"sim_geometry"][0] == "ventricle_physloop":
# For ventricle for now, specify number of cardiac cycles
cycles = sim_params["sim_type"][1]
meshfilename = sim_params["sim_type"][2]
# Cardiac cycle length and number of cycles will be general
# For now, just including this info in the input file
BCL = sim_duration # ms
hsl0 = hs_params["initial_hs_length"][
0] # this is now set when creating mesh
no_of_time_steps = int(cycles * BCL / step_size)
no_of_cell_time_steps = int(BCL / step_size)
deg = 4
parameters["form_compiler"]["quadrature_degree"] = deg
parameters["form_compiler"]["representation"] = "quadrature"
# Clear out any old results files
os.system("rm " + output_path + "*.pvd")
os.system("rm " + output_path + "*.vtu")
#--------------- Load in mesh, initialize things from it -------------------
mesh = Mesh()
f = HDF5File(mpi_comm_world(), meshfilename, 'r')
f.read(mesh, casename, False)
if casename == "ellipsoidal":
#loading_number = 25;
ugrid = vtk_py.convertXMLMeshToUGrid(mesh)
ugrid = vtk_py.rotateUGrid(ugrid, sx=0.11, sy=0.11, sz=0.11)
mesh = vtk_py.convertUGridToXMLMesh(ugrid)
#don't need to do the vtk_py mesh stuff
else: #assuming we are using a patient specific mesh
ugrid = vtk_py.convertXMLMeshToUGrid(mesh)
ugrid = vtk_py.rotateUGrid(ugrid, sx=0.1, sy=0.1, sz=0.1)
mesh = vtk_py.convertUGridToXMLMesh(ugrid)
no_of_int_points = 14 * np.shape(mesh.cells())[0]
print "num_int_points" + str(no_of_int_points)
facetboundaries = MeshFunction("size_t", mesh, 2)
edgeboundaries = MeshFunction("size_t", mesh, 1)
# set surface id numbers:
topid = 4
LVendoid = 2
epiid = 1
# Define referential facet normal
N = FacetNormal(mesh)
# Define spatial coordinate system used in rigid motion constraint
X = SpatialCoordinate(mesh)
# --------- Initialize finite elements -----------------------------------
# Vector element at gauss points (for fibers)
VQuadelem = VectorElement("Quadrature",
mesh.ufl_cell(),
degree=deg,
quad_scheme="default")
VQuadelem._quad_scheme = 'default'
# General quadrature element whose points we will evaluate myosim at
Quadelem = FiniteElement("Quadrature",
tetrahedron,
degree=deg,
quad_scheme="default")
Quadelem._quad_scheme = 'default'
# Vector element for displacement
Velem = VectorElement("CG", mesh.ufl_cell(), 2, quad_scheme="default")
Velem._quad_scheme = 'default'
# Quadrature element for pressure
Qelem = FiniteElement("CG", mesh.ufl_cell(), 1, quad_scheme="default")
Qelem._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'
# 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])
# ------- Define function spaces on mesh using above elements --------------
# Quadrature space for information needed at gauss points, such as
# hsl, cb_force, passive forces, etc.
Quad = FunctionSpace(mesh, Quadelem)
# Function space for myosim populations
Quad_vectorized_Fspace = FunctionSpace(
mesh, MixedElement(n_array_length * [Quadelem]))
# Function space for local coordinate system (fiber, sheet, sheet-normal)
fiberFS = FunctionSpace(mesh, VQuadelem)
# Mixed function space for displacement, pressure, rigid body constraint
if (ispressurectrl):
W = FunctionSpace(mesh, MixedElement([Velem, Qelem, VRelem]))
else:
W = FunctionSpace(mesh, MixedElement([Velem, Qelem, Relem, VRelem]))
# V isn't used? Could define function spaces V: Velem, Q:Qelem,VR: VRelem, then W = V*W*VR
# but below W is explicitly defined using the elements?
# could define these once and use them for all projections
#V = VectorFunctionSpace(mesh, 'CG', 2)
#TF = TensorFunctionSpace(mesh, 'DG', 1)
#Q = FunctionSpace(mesh,'CG',1)
# ------ Initalize functions on above spaces -------------------------------
# fiber, sheet, and sheet-normal functions
f0 = Function(fiberFS)
print f0.vector().array()
print np.shape(f0.vector())
#print "free indices of f0 " + str(f0.free_indices())
s0 = Function(fiberFS)
n0 = Function(fiberFS)
# function for original hsl distribution
hsl0_transmural = Function(Quad)
# These are now functions because they don't have to be uniform
c_param = Function(Quad)
c2_param = Function(Quad)
c3_param = Function(Quad)
# Setting the value of the passive functions
c_param.vector()[:] = passive_params["c"][0]
c2_param.vector()[:] = passive_params["c2"][0]
c3_param.vector()[:] = passive_params["c3"][0]
# Go ahead and read in rest of info from mesh file and close
# mesh lclee created doesn't have hsl0 variation
f.read(hsl0_transmural, casename + "/" + "hsl0")
f.read(f0, casename + "/" + "eF")
f.read(s0, casename + "/" + "eS")
f.read(n0, casename + "/" + "eN")
# read in more mesh info, using MeshFunction for these
f.read(facetboundaries, casename + "/" + "facetboundaries")
f.read(edgeboundaries, casename + "/" + "edgeboundaries")
# finished with the mesh file, close it
f.close()
#print f0[0]
#print np.shape(f0.vector().array())
# define rest of needed functions
# mixed function for solver
w = Function(W)
# define trial function
dw = TrialFunction(W)
# define test function
wtest = TestFunction(W)
# separate out individual functions for displacement, pressure, bdry
if (ispressurectrl):
du, dp, dc11 = TrialFunctions(W)
(u, p, c11) = split(w)
(v, q, v11) = TestFunctions(W)
else:
du, dp, dpendo, dc11 = TrialFunctions(W)
(u, p, pendo, c11) = split(w)
#(u,p, pendo,c11,lm11) = w.split(True)
(v, q, qendo, v11) = TestFunctions(W)
# function for myosim populations
y_vec = Function(Quad_vectorized_Fspace)
# not explicitly defined as a function, but product
#hsl = sqrt(dot(f0, Cmat*f0))*hsl0_transmural
# Store old hsl and use for calculation of delta_hsl
hsl_old = Function(Quad)
# ------- Set up files for saving information -----------------------------
# save initial mesh information
File(output_path + "facetboundaries.pvd") << facetboundaries
File(output_path + "edgeboundaries.pvd") << edgeboundaries
File(output_path + "fiber.pvd") << project(
f0, VectorFunctionSpace(mesh, "CG", 1))
File(output_path + "sheet.pvd") << project(
s0, VectorFunctionSpace(mesh, "CG", 1))
File(output_path + "sheet-normal.pvd") << project(
n0, VectorFunctionSpace(mesh, "CG", 1))
# Define paraview files to visualize on mesh
displacementfile = File(output_path + "u_disp.pvd")
pk1file = File(output_path + "pk1_act_on_f0.pvd")
hsl_file = File(output_path + "hsl_mesh.pvd")
alpha_file = File(output_path + "alpha_mesh.pvd")
# Instead, initialize file for each of these arrays, and append each time step?
"""calcium_df = pd.DataFrame(np.zeros((no_of_time_steps+1,no_of_int_points)),dtype='f8')
active_stress_df = pd.DataFrame(np.zeros((no_of_time_steps+1,no_of_int_points)),dtype='f8')
myofiber_passive_stress_df = pd.DataFrame(np.zeros((no_of_time_steps+1,no_of_int_points)),dtype='f8')
gucc_fiber_pstress_df = pd.DataFrame(np.zeros((no_of_time_steps+1,no_of_int_points)),dtype='f8')
gucc_trans_pstress_df = pd.DataFrame(np.zeros((no_of_time_steps+1,no_of_int_points)),dtype='f8')
gucc_shear_pstress_df = pd.DataFrame(np.zeros((no_of_time_steps+1,no_of_int_points)),dtype='f8')
alpha_df = pd.DataFrame(np.zeros((no_of_time_steps+1,no_of_int_points)),dtype='f8')
filament_overlap_df = pd.DataFrame(np.zeros((no_of_time_steps+1,no_of_int_points)),dtype='f8')
delta_hsl_df = pd.DataFrame(np.zeros((no_of_time_steps+1,no_of_int_points)),dtype='f8')"""
calcium = np.zeros(no_of_time_steps)
calcium_ds = pd.DataFrame(np.zeros(no_of_int_points), index=None)
calcium_ds = calcium_ds.transpose()
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(no_of_time_steps + 1), index=None)
tarray_ds = tarray_ds.transpose()
tarray = np.zeros(no_of_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()
#overlaparray = np.zeros((no_of_time_steps+1,no_of_int_points)) # need from previous step
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()
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, no_of_time_steps))
j4_fluxes = np.zeros((no_of_int_points, no_of_time_steps))
y_interp = np.zeros((no_of_int_points + 1) * n_array_length)
#test_cbf_storage = pd.Series(np.zeros(no_of_int_points))
# Saving pressure/volume data
# define communicator
comm = mesh.mpi_comm()
if (MPI.rank(comm) == 0):
fdataPV = open(output_path + "PV_.txt", "w", 0)
"""hsl_data_file = open(output_path + "hsl_file.txt", "w", 0)
cbforce_file = open(output_path + "cbforce.txt", "w", 0)
calcium_data_file = open(output_path + "calcium.txt", "w", 0)
myosim_fiber_passive_file = open(output_path + "fiber_passive.txt", "w", 0)
guccione_fiber_pstress_file = open(output_path + "gucc_fiber.txt", "w", 0)
guccione_trans_pstress_file = open(output_path + "gucc_trans.txt", "w", 0)
guccione_shear_pstress_file = open(output_path + "gucc_shear.txt", "w", 0)
alpha_txt_file = open(output_path + "alpha.txt", "w", 0)
overlap_file = open(output_path + "overlap.txt", "w", 0)"""
#--------- some miscellaneous definitions ----------------------------------
isincomp = True #False
# initialize LV cavity volume
LVCavityvol = Expression(("vol"), vol=0.0, degree=2)
y_vec_array_new = np.zeros(no_of_int_points * n_array_length)
#Press = Expression(("P"), P=0.0, degree=0)
#Kspring = Constant(100)
if (ispressurectrl):
pendo = []
# ------- Dirichlet bdry for fixing base in z ------------------------------
bctop = DirichletBC(
W.sub(0).sub(2), Expression(("0.0"), degree=2), facetboundaries, topid)
bcs = [bctop]
# ------- Set parameters for forms file, where stresses and things are calculated
params = {
"mesh": mesh,
"facetboundaries": facetboundaries,
"facet_normal": N,
"mixedfunctionspace": W,
"mixedfunction": w,
"displacement_variable": u,
"pressure_variable": p,
"lv_volconst_variable": pendo,
"lv_constrained_vol": LVCavityvol,
"LVendoid": LVendoid,
"LVendo_comp": 2,
"fiber": f0,
"sheet": s0,
"sheet-normal": n0,
"incompressible": isincomp,
"Kappa": Constant(1e5)
}
# Update params from loaded in parameters from json file
params.update(passive_params)
params["c"] = c_param
params["c2"] = c2_param
params["c3"] = c3_param
# initialize the forms module
uflforms = Forms(params)
# --------- Calculate quantities from form file used in weak form ----------
LVCavityvol.vol = uflforms.LVcavityvol()
print("cavity-vol = ", LVCavityvol.vol)
# Get deformation gradient
Fmat = uflforms.Fmat()
# Get right cauchy stretch tensor
Cmat = (Fmat.T * Fmat)
# Get Green strain tensor
Emat = uflforms.Emat()
# jacobian of deformation gradient
J = uflforms.J()
# facet normal in current config
n = J * inv(Fmat.T) * N
# integration measure
dx = dolfin.dx(mesh, metadata={"integration_order": 2})
# get passive material strain energy function
Wp = uflforms.PassiveMatSEF()
#Active force calculation------------------------------------------------------
# can we move this to the forms file?
# define 'active_params' as dict and send to forms?
#hsl = sqrt(dot(f0, Cmat*f0))*hsl0_transmural # must project if want to set directly
hsl = sqrt(dot(f0, Cmat * f0)) * hsl0
#f0 = 1/k(U(f0) - f0)
delta_hsl = hsl - hsl_old
cb_force = Constant(0.0)
y_vec_split = split(y_vec)
print "shape of y_vec_split is " + str(np.shape(y_vec_split))
for jj in range(no_of_states):
f_holder = Constant(0.0)
if state_attached[jj] == 1:
cb_ext = cb_extensions[jj]
for k in range(no_of_x_bins):
temp_holder = Constant(0.0)
dxx = xx[k] + delta_hsl * filament_compliance_factor
n_pop = y_vec_split[n_vector_indices[jj][0] + k]
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 + temp_holder
#f_holder = f_holder + conditional(gt(temp_holder,0.0),temp_holder,0.0)
f_holder = f_holder * cb_number_density * 1e-9
f_holder = f_holder * alpha_value
cb_force = cb_force + f_holder
cb_force = cb_force * conditional(gt(cb_force, 0.0), 1.0, 0.0)
# use cb_force to form active stress tensor
print np.shape(f0)
Pactive = cb_force * as_tensor(
f0[i] * f0[j], (i, j)) + xfiber_fraction * cb_force * as_tensor(
s0[i] * s0[j], (i, j)) + xfiber_fraction * cb_force * as_tensor(
n0[i] * n0[j], (i, j))
# -------- pre-allocation and initialization -------------------------------
tstep = 0
#t = 0
LVcav_array = np.zeros(no_of_time_steps + 1)
LVcav_array[0] = uflforms.LVcavityvol()
Pcav_array = np.zeros(no_of_time_steps + 1)
Pcav_array[0] = uflforms.LVcavitypressure() * 0.0075
# Contraction phase
#tarray = []
# Get array of cross-bridge populations
y_vec_array = y_vec.vector().get_local()[:]
hsl_array = project(sqrt(dot(f0, Cmat * f0)) * hsl0,
Quad).vector().get_local()[:]
#delta_hsl_array = np.zeros(no_of_int_points)
for init_counter in range(0, n_array_length * no_of_int_points,
n_array_length):
# Initializing myosin heads in the off state
y_vec_array[init_counter] = 1
# Initialize all binding sites to off state
y_vec_array[init_counter - 2] = 1
Pg, Pff, alpha = uflforms.stress()
# Pg is guccione stress tensor as first Piola-Kirchhoff
# 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()[:]
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()[:]
# ------ Define terms for variational problem ------------------------------
# passive material contribution
F1 = derivative(Wp, w, wtest) * dx
# active stress contribution (Pactive is PK1, transform to PK2)
F2 = inner(Fmat * Pactive, grad(v)) * dx
# volumetric stress
if (ispressurectrl):
pressure = Expression(("p"), p=0.0, degree=2)
F3 = inner(pressure * n, v) * ds(LVendoid)
else:
Wvol = uflforms.LVV0constrainedE()
F3 = derivative(Wvol, w, wtest)
# 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
# ----- Set up solver, using default but can use LCLee nsolver -------------
solverparams = {
"Jacobian": Jac,
"F": Ftotal,
"w": w,
"boundary_conditions": bcs,
"Type": 0,
"mesh": mesh,
"mode": 0
}
solver = NSolver(solverparams)
# -----------------------------
# Loading phase
#print "memory growth before loading:"
#obg.show_growth()
print("cavity-vol = ", LVCavityvol.vol)
for lmbda_value in range(0, loading_number):
print "Loading phase step = ", lmbda_value
LVCavityvol.vol += 0.004 #LCL change to smaller value
p_cav = uflforms.LVcavitypressure()
V_cav = uflforms.LVcavityvol()
hsl_array_old = hsl_array
#solver.solvenonlinear()
solve(Ftotal == 0,
w,
bcs,
J=Jac,
form_compiler_parameters={"representation": "uflacs"})
hsl_array = project(hsl, Quad).vector().get_local()[:] # for Myosim
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
delta_hsl_array = hsl_array - hsl_array_old
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()[:]
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()[:]
if (MPI.rank(comm) == 0):
print >> fdataPV, 0.0, p_cav * 0.0075, 0.0, 0.0, V_cav, 0.0, 0.0, 0.0
displacementfile << w.sub(0)
pk1temp = project(inner(f0, Pactive * f0),
FunctionSpace(mesh, 'DG', 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
alpha_temp = project(alphas, FunctionSpace(mesh, 'DG', 0))
alpha_temp.rename("alpha_temp", "alpha_temp")
alpha_file << alpha_temp
print("cavity-vol = ", LVCavityvol.vol)
print("p_cav = ", uflforms.LVcavitypressure())
# Closed-loop phase
# 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
# For now, uniform properties
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)
# Initialize cell ion module
cell_ion = cell_ion_driver.cell_ion_driver(cell_ion_params)
# Initialize calcium
calcium[0] = cell_ion.calculate_concentrations(0, 0)
#dumped_populations = np.zeros((no_of_time_steps+1, no_of_int_points, n_array_length))
dumped_populations = np.zeros((no_of_int_points, n_array_length))
counter = 0
cell_counter = 0
cycle = 0
AV_old = 0
MV_old = 1
systole = 0
#print "memory growth before closed loop"
#obg.show_growth()
while (cycle < cycles):
p_cav = uflforms.LVcavitypressure()
V_cav = uflforms.LVcavityvol()
tstep = tstep + step_size
cycle = math.floor(tstep / BCL)
cell_time = tstep - cycle * BCL
if (MPI.rank(comm) == 0):
print "Cycle number = ", cycle, " cell time = ", cell_time, " tstep = ", tstep, " step_size = ", step_size
#print >>fdataPV, tstep, p_cav*0.0075 , V_cav, Myosim.Get_Ca()
Part = 1.0 / Cao * (V_art - Vart0)
Pven = 1.0 / Cven * (V_ven - Vven0)
PLV = p_cav
if (MPI.rank(comm) == 0):
print "P_ven = ", Pven
print "P_LV = ", PLV
print "P_art = ", Part
if (PLV <= Part):
Qao = 0.0
AV_new = 0
else:
Qao = 1.0 / Rao * (PLV - Part)
AV_new = 1
if (PLV >= Pven):
Qmv = 0.0
MV_new = 0
else:
Qmv = 1.0 / Rven * (Pven - PLV)
MV_new = 1
Qper = 1.0 / Rper * (Part - Pven)
if (MV_old == 1 and MV_new == 0):
systole = 1
if (AV_old == 1 and AV_new == 0):
systole = 0
MV_old = MV_new
AV_old = AV_new
if (MPI.rank(comm) == 0):
print "Q_mv = ", Qmv
print "Q_ao = ", Qao
print "Q_per = ", Qper
if (systole == 1):
print "********systole**********"
else:
print "***diastole***"
"""V_cav_prev = V_cav
V_art_prev = V_art
V_ven_prev = V_ven
p_cav_prev = p_cav"""
V_cav = V_cav + step_size * (Qmv - Qao)
V_art = V_art + step_size * (Qao - Qper)
V_ven = V_ven + step_size * (Qper - Qmv)
LVCavityvol.vol = V_cav
if (MPI.rank(comm) == 0):
print "V_ven = ", V_ven
print "V_LV = ", V_cav
print "V_art = ", V_art
#LVcav_array.append(V_cav)
LVcav_array[counter] = V_cav
Pcav_array[counter] = p_cav * 0.0075
#Pcav_array.append(p_cav*0.0075)
if (counter > 0 and (int(counter / no_of_cell_time_steps)
== (counter / no_of_cell_time_steps))):
cell_counter = 0
cell_counter += 1
print "cell_counter = ", cell_counter
"""for i in range(no_of_int_points):
for j in range(n_array_length):
dumped_populations[counter, i, j] = y_vec_array[i * n_array_length + j]"""
# Initialize MyoSim solution holder
#y_vec_array_new = np.zeros(no_of_int_points*n_array_length)
# Update calcium
calcium[counter] = cell_ion.calculate_concentrations(
cycle, tstep) #LCL Commented off
# Now print out volumes, pressures, calcium
if (MPI.rank(comm) == 0):
print >> fdataPV, tstep, p_cav * 0.0075, Part * .0075, Pven * .0075, V_cav, V_ven, V_art, calcium[
counter]
# Quick hack
if counter == 0:
overlap_counter = 1
else:
overlap_counter = counter
# Going to try to loop through integration points in python, not in fenics script
#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[counter], n_array_length, cell_time, overlaparray[overlap_counter,:])
#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[counter], n_array_length, cell_time)
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[counter], n_array_length,
tstep, hs_params_list[mm])
for i in range(no_of_int_points):
for j in range(n_array_length):
dumped_populations[i, j] = y_interp[i * n_array_length + j]
y_vec_array = y_vec_array_new # for Myosim
#Kurtis moved to here
y_vec.vector()[:] = y_vec_array # for PDE
hsl_array_old = hsl_array
#print hsl_array_old
# Kurtis assigning hsl_old function for newton iteration
hsl_old.vector()[:] = hsl_array_old[:]
###########################################################################
#solver.solvenonlinear()
#++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
solve(Ftotal == 0,
w,
bcs,
J=Jac,
form_compiler_parameters={"representation": "uflacs"})
"""try:
solve(Ftotal == 0, w, bcs, J = Jac, form_compiler_parameters={"representation":"uflacs"})
except:
print "Newton Iteration non-convergence, saving myosim info"
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 + "gucc_fiber", gucc_fiber)
np.save(output_path + "gucc_trans", gucc_trans)
np.save(output_path + "gucc_shear", gucc_shear)
np.save(output_path + "deltahsl", deltahslarray)
np.save(output_path + "pstress_array",pstrarray)
#np.save(output_path + "alpha_array",alphaarray)
np.save(output_path + "calcium",calarray)"""
#++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
cb_f_array[:] = project(cb_force, Quad).vector().get_local()[:]
hsl_array = project(hsl, Quad).vector().get_local()[:] # for Myosim
delta_hsl_array = hsl_array - hsl_array_old
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_1 = project(
alpha,
FunctionSpace(mesh, "DG", 1),
form_compiler_parameters={"representation": "uflacs"})
alphas = interpolate(temp_DG_1, Quad)
alpha_array = alphas.vector().get_local()[:]
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()[:]
displacementfile << w.sub(0)
pk1temp = project(inner(f0, Pactive * f0),
FunctionSpace(mesh, 'DG', 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
alpha_temp = project(alphas, FunctionSpace(mesh, 'DG', 0))
alpha_temp.rename("alpha_temp", "alpha_temp")
alpha_file << alpha_temp
print "shape of time array" + str(np.shape(tarray))
tarray[counter] = tstep
counter += 1
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[counter]
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[counter] = tarray[counter]
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)
#overlaparray[counter,:] = temp_overlap
if (MPI.rank(comm) == 0):
fdataPV.close()
#fdataCa.close()
#fluxes, rates = implement.return_rates_fenics(hs)
# Generate dictionary for output
"""outputs = {
"rates": rates,
"dumped_populations": dumped_populations,
"tarray": tarray,
"strarray": strarray,
"pstrarray": pstrarray,
"gucc_fiber": gucc_fiber,
"gucc_trans": gucc_trans,
"gucc_shear": gucc_shear,
"alphaarray": alphaarray,
"calarray": calarray,
"hsl": hslarray,
"overlap": overlaparray
}"""
success = 1
return (success)
def fenics(sim_params,file_inputs,output_params,passive_params,hs_params,cell_ion_params,monodomain_params,windkessel_params,pso):
i,j = indices(2)
m,k = indices(2)
output_path = output_params["output_path"][0]
displacementfile = File(output_path + "u_disp.pvd")
filament_compliance_factor = hs_params["myofilament_parameters"]["filament_compliance_factor"][0]
# filament_compliance_factor = 0.5
no_of_states = hs_params["myofilament_parameters"]["num_states"][0]
#no_of_states = 3
#no_of_attached_states = 1
#no_of_detached_states = 2
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]
#no_of_transitions = 4
#state_attached = [0, 0, 1]
#cb_extensions = [ 0, 0, 4.75642]
#k_cb_multiplier = [ 1.0, 1.0, 1.0]
#k_cb_pos = 0.001
#k_cb_neg = 0.001
#cb_number_density = 7.67e16
#alpha_value = 1.0
#x_bin_min = -12
#x_bin_max = +12
#x_bin_increment = 0.5
xx = np.arange(x_bin_min, x_bin_max + x_bin_increment, x_bin_increment)
no_of_x_bins = np.shape(xx)[0]
n_array_length = no_of_attached_states * no_of_x_bins + no_of_detached_states + 2
n_vector_indices = [[0,0], [1,1], [2,2+no_of_x_bins-1]]
#hsl0 = 1000
hsl0 = hs_params["initial_hs_length"][0]
#time_steps = 401
#time_steps = 2
#step_size = 0.5
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)
fx_rxn = np.zeros((time_steps))
#prev_ca = np.load("calcium_10.npy")
#prev_ca = prev_ca[:,0]
#xml_struct = ut.parse('pm_test10.xml')
#hs_params = xml_struct.single_circulation_simulation.half_sarcomere
hs = half_sarcomere.half_sarcomere(hs_params,1)
cell_ion = cell_ion_driver.cell_ion_driver(cell_ion_params)
calcium = np.zeros(time_steps)
calcium[0] = cell_ion.calculate_concentrations(0,0)
parameters["form_compiler"]["quadrature_degree"]=2
parameters["form_compiler"]["representation"] = "quadrature"
#
#os.system("rm *.pvd")
#os.system("rm *.vtu")
# 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]-1.0) < tol
# where x[2] = 0
class Lower(SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return on_boundary and abs(x[2]) < tol
# where x[1] = 0
class Front(SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return on_boundary and abs(x[1]) < tol
# where x[0], x[1] and x[2] = 0
class Fix(SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return on_boundary and abs(x[0]) < tol and abs(x[1]) < tol and abs(x[2]) < tol
#
#
mesh = UnitCubeMesh(1,1,1)
#mesh.cells()
no_of_int_points = 4 * np.shape(mesh.cells())[0]
temp_overlap = np.zeros((no_of_int_points))
y_vec_array_new = np.zeros(((no_of_int_points)*n_array_length))
hs_params_list = [{}]*no_of_int_points
for jj in np.arange(np.shape(hs_params_list)[0]):
hs_params_list[jj] = copy.deepcopy(hs_params)
#plot(mesh)
#plt.show()
#f0 = Constant((1.0, 0.0, 0.0))
s0 = Constant((0.0, 1.0, 0.0))
n0 = Constant((0.0, 0.0, 1.0))
facetboundaries = MeshFunction('size_t', mesh, mesh.topology().dim()-1)
facetboundaries.set_all(0)
left = Left()
right = Right()
fix = Fix()
lower = Lower()
front = Front()
#
left.mark(facetboundaries, 1)
right.mark(facetboundaries, 2)
fix.mark(facetboundaries, 3)
lower.mark(facetboundaries, 4)
front.mark(facetboundaries, 5)
File(output_path + "facetboundaries.pvd") << facetboundaries
#
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'
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'
W = FunctionSpace(mesh, MixedElement([Velem,Qelem]))
x_dofs = W.sub(0).sub(0).dofmap().dofs()
Quad = FunctionSpace(mesh, Quadelem)
c_param = Function(Quad)
c2_param = Function(Quad)
c3_param = Function(Quad)
c_param.vector()[:] = passive_params["c"][0]
c2_param.vector()[:] = passive_params["c2"][0]
c3_param.vector()[:] = passive_params["c3"][0]
# Putting them back in the "passive_params" dictionary so that when
# the dictionary is updated below, it reflects these changes
passive_params["c"] = c_param
passive_params["c2"] = c2_param
passive_params["c3"] = c3_param
Quad_vectorized_Fspace = FunctionSpace(mesh, MixedElement(n_array_length*[Quadelem]))
# Assigning initial fiber angles
fiberFS = FunctionSpace(mesh, VQuadelem)
f0 = Function(fiberFS)
#s0 = Function(fiberFS)
#n0 = Function(fiberFS)
for i in np.arange(no_of_int_points):
f0.vector()[i*3] = 1./sqrt(2.)
#f0.vector()[i*3] = 1.
#f0.vector()[i*3+1] = 0.
f0.vector()[i*3+1] = 1./sqrt(2.)
f0.vector()[i*3+2] = 0.
File(output_path + "fiber_init.pvd") << project(f0, VectorFunctionSpace(mesh, "DG", 0))
#print f0.type()
#f0 = f0/sqrt(inner(f0,f0))
temp_f = Function(fiberFS)
f = Function(fiberFS)
f_diff = Function(fiberFS)
scaled_fdiff = Function(fiberFS)
# 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 = DirichletBC(W.sub(0), Constant((0.0, 0.0, 0.0)), fix, method="pointwise") # at one vertex u = v = w = 0
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]
du,dp = TrialFunctions(W)
w = Function(W)
dw = TrialFunction(W)
(u,p) = split(w)
(v,q) = 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)
uflforms = Forms(params)
Fmat = uflforms.Fmat()
Cmat = (Fmat.T*Fmat)
Emat = uflforms.Emat()
Umat = uflforms.Umat()
kappa = 1.0
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)
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
Pactive = cb_force * as_tensor(f0[m]*f0[k], (m,k))
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)
Ftotal = F1 + F2 - F3
Jac1 = derivative(F1, w, dw)
Jac2 = derivative(F2, w, dw)
Jac3 = derivative(F3, w, dw)
Jac = Jac1 + Jac2 - Jac3
##################################################################################################################################
# Contraction phase
'''header_file = open("./C++/hs.h","r")
code = header_file.read()
header_file.close()
ext_module = compile_extension_module(code=code, source_directory="C++", sources=["hs.cpp", "mf.cpp", "Ca.cpp", "base_parameters.cpp"],
additional_system_headers=["petscvec.h"],
include_dirs=[".", os.path.abspath("C++"),"/usr/include", "./C++"],
library_dirs = ['/usr/lib/x86_64-linux-gnu'],
libraries = ['libgsl.a'])
Myosim = ext_module.hs()
_FE_params = {"step_size": step_size};
Myosim.FE_params.update(_FE_params)
_Ca_params = {"Ca_flag": Ca_flag};
Myosim.Ca_params.update(_Ca_params)
_Ca_params = {"constant_pCa": constant_pCa};
Myosim.Ca_params.update(_Ca_params)'''
darray = []
tarray = []
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))
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
# Starting all in on state for Debugging
y_vec_array[counter] = 1
y_vec_array[counter-2] = 1
Pg, Pff, alpha = uflforms.stress()
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()[:]
'''P,S,T = uflforms.stress()
Pff = inner(f0,P*f0)
p_f = project(Pff, Quad)
p_f_array = p_f.vector().get_local()[:]'''
#p_f = np.load("/home/fenics/shared/python_dev/test_10/passive_forces.npy")
cb_f_array = project(cb_force, Quad).vector().get_local()[:]
dumped_populations = np.zeros((time_steps, no_of_int_points, n_array_length))
y_interp = np.zeros(no_of_int_points*n_array_length)
t = 0.0
#delta_hsls = np.zeros((time_steps,24))
for l in range(time_steps):
tarray.append(t)
for m in range(no_of_int_points):
for k in range(n_array_length):
dumped_populations[l, m, k] = y_interp[m * n_array_length + k]
#hslarray.append(hsl_array[0])
#strarray.append(cb_f_array[0])
#pstrarray.append(p_f_array[0])
# _Ca_params = {"time_point": l};
# Myosim.Ca_params.update(_Ca_params)
#print p_f[l]
#for k in range(no_of_int_points):
# pop_holder = implement.update_simulation(hs, step_size, delta_hsl_array[k], hsl_array[k], y_vec_array[k*n_array_length:(k+1)*n_array_length],p_f_array[k], cb_f_array[k], prev_ca[l])
# y_vec_array_new = Myosim.apply_time_step(y_vec_array, delta_hsl_array, hsl_array, p_f_array, cb_f_array)
#y_vec_array_new[k*n_array_length:(k+1)*n_array_length] = pop_holder
# Right now, not general. The calcium depends on cycle number, just saying 0
cycle = 0
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
# Debugging, checking if y_input matches y_output between steps
#print y_vec_array[0:53]
# Quick hack
if l == 0:
overlap_counter = 1
else:
overlap_counter = l
#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,hs_params_list)
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])
# print y_vec_array_new[0:53]
y_vec_array = y_vec_array_new # for Myosim
y_vec.vector()[:] = y_vec_array # for PDE
# print y_vec_array[0:53]
hsl_array_old = hsl_array
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)
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()[:]
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)
f_int_total = b.copy()
for kk in x_dofs:
fx_rxn[l] += f_int_total[kk]
np.save(output_path + "fx",fx_rxn)
#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 < 20:
u_D.u_D += 0.001
else:
u_D.u_D = u_D.u_D"""
if t <= 5.0:
u_D.u_D = u_D.u_D
if t > 5.0 and t <= 10.0:
u_D.u_D += 0.03
if t > 10.0:
u_D.u_D = u_D.u_D
t = t + step_size
calarray.append(hs.Ca_conc*np.ones(no_of_int_points))
"""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]"""
#f0 += uflforms.kroon_law(fiberFS)[0] * step_size
#temp_f = project(Umat*f0,VectorFunctionSpace(mesh,"DG",1),form_compiler_parameters={"representation":"uflacs"})
#temp_f_2 = interpolate(temp_f, fiberFS)
temp_f = Umat*f0
f_mag = sqrt(inner(temp_f,temp_f))
f = temp_f/f_mag
f_diff = f-f0
scaled_fdiff = f_diff * (step_size/kappa)
scaled_f_assign = project(scaled_fdiff,VectorFunctionSpace(mesh,"DG",1),form_compiler_parameters={"representation":"uflacs"})
scaled_f_2 = interpolate(scaled_f_assign, fiberFS)
#print temp_f.type()
f0.vector()[:] += scaled_f_2.vector()[:]
File(output_path + "fiber_" + str(l) + ".pvd") << project(f0, VectorFunctionSpace(mesh, "DG", 0))
# f0.vector()[abc] += scaled_fdiff.vector()[abc]
#f0 += scaled_fdiff"""
#f0 += scaled_fdiff
#f0 = f0 + new_f_diff*step_size
#f = Umat*f0/sqrt(inner(Umat*f0,Umat*f0))
#df0 = (1.0/kappa) * (f - f0)
#f0 += df0*step_size
# File(output_path + "fiber_" + str(t) +".pvd") << project(f0, VectorFunctionSpace(mesh,"CG",1))
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
}
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)
fdataCa.close()
return(outputs)
def fenics(sim_params, file_inputs, output_params, passive_params, hs_params,
cell_ion_params, monodomain_params, windkessel_params):
global i
global j
output_path = output_params["output_path"][0]
displacementfile = File(output_path + "u_disp.pvd")
filament_compliance_factor = hs_params["myofilament_parameters"][
"filament_compliance_factor"][0]
# filament_compliance_factor = 0.5
no_of_states = hs_params["myofilament_parameters"]["num_states"][0]
#no_of_states = 3
#no_of_attached_states = 1
#no_of_detached_states = 2
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]
#no_of_transitions = 4
#state_attached = [0, 0, 1]
#cb_extensions = [ 0, 0, 4.75642]
#k_cb_multiplier = [ 1.0, 1.0, 1.0]
#k_cb_pos = 0.001
#k_cb_neg = 0.001
#cb_number_density = 7.67e16
#alpha_value = 1.0
#x_bin_min = -12
#x_bin_max = +12
#x_bin_increment = 0.5
xx = np.arange(x_bin_min, x_bin_max + x_bin_increment, x_bin_increment)
no_of_x_bins = np.shape(xx)[0]
n_array_length = no_of_attached_states * no_of_x_bins + no_of_detached_states + 2
n_vector_indices = [[0, 0], [1, 1], [2, 2 + no_of_x_bins - 1]]
#hsl0 = 1000
hsl0 = hs_params["initial_hs_length"][0]
#time_steps = 401
#time_steps = 2
#step_size = 0.5
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)
#prev_ca = np.load("calcium_10.npy")
#prev_ca = prev_ca[:,0]
#xml_struct = ut.parse('pm_test10.xml')
#hs_params = xml_struct.single_circulation_simulation.half_sarcomere
hs = half_sarcomere.half_sarcomere(hs_params, 1)
cell_ion = cell_ion_driver.cell_ion_driver(cell_ion_params)
calcium = np.zeros(time_steps)
calcium[0] = cell_ion.model_class.calculate_concentrations(0, 0)
parameters["form_compiler"]["quadrature_degree"] = 2
parameters["form_compiler"]["representation"] = "quadrature"
#
#os.system("rm *.pvd")
#os.system("rm *.vtu")
# 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.) < tol
# where x[2] = 0
class FixY(SubDomain):
def inside(self, x, on_boundary):
tol = 1e-1
return near(x[0], 0., tol) and near(x[1], 0., tol)
class FixZ(SubDomain):
def inside(self, x, on_boundary):
tol = 1e-1
return near(x[0], 0., tol) and near(x[2], 0., tol)
class FixY_right(SubDomain):
def inside(self, x, on_boundary):
tol = 1e-1
return near(x[0], 10., tol) and near(x[1], 0., tol)
class FixZ_right(SubDomain):
def inside(self, x, on_boundary):
tol = 1e-1
return near(x[0], 10., tol) and near(x[2], 0., tol)
#
#
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 = 20
geometry = mshr.Cylinder(cyl_top, cyl_bottom, top_radius, bottom_radius,
segments)
mesh = mshr.generate_mesh(geometry, 30)
no_of_int_points = 4 * np.shape(mesh.cells())[0]
#plot(mesh)
#plt.show()
VQuadelem = VectorElement("Quadrature",
mesh.ufl_cell(),
degree=2,
quad_scheme="default")
fiberFS = FunctionSpace(mesh, VQuadelem)
f0 = Function(fiberFS)
s0 = Function(fiberFS)
n0 = Function(fiberFS)
counter = 0
"""for m in np.arange(np.shape(f0.vector().array())[0]/3):
m = int(m)
#f0.vector()[m*3] = np.random.normal(1.,.3)
f0.vector()[m*3] = np.random.normal(1.,0.0)
#s0.vector()[m*3] = f0.vector().array()[m*3] - 1. #sheet vector in plane with fiber vector
s0.vector()[m*3] = 0.0
#f0.vector()[m*3+1] = np.random.normal(0.,.3)
f0.vector()[m*3+1] = np.random.normal(0.,0.0)
f0.vector()[m*3+2] = 0.0
#s0.vector()[m*3+1] = f0.vector().array()[m*3+1]
s0.vector()[m*3+1] = 1.0
s0.vector()[m*3+2] = 0.0
n0.vector()[m*3] = 0.0
n0.vector()[m*3+1] = 0.0
n0.vector()[m*3+2] = 1.0
# z component would look like
# f0.vector()[m*3+2] = something
# s0.vector()[m*3+2] = f0.vector().array()[int(m)*3+2]
#n0_holder = np.cross(f0.vector().array()[m*3:m*3+3],s0.vector().array()[m*3:m*3+3])
#n0_holder /= sqrt(np.inner(n0_holder,n0_holder))
#for n in range(3):
# n0.vector()[m*3+n] = n0_holder[n]
#s0_holder = np.cross(f0.vector().array()[m*3:m*3+3],n0.vector().array()[m*3:m*3+3])
#s0_holder /= sqrt(np.inner(s0_holder,s0_holder))
#for n in range(3):
# s0.vector()[m*3+n] = s0_holder[n]
#f0_holder = f0.vector().array()[m*3:m*3+3]
#f0_holder /= sqrt(np.inner(f0_holder,f0_holder))
#for n in range(3):
# f0.vector()[m*3+n] = f0_holder[n]"""
f0 = Constant([1.0, 0.0, 0.0])
s0 = Constant([0.0, 1.0, 0.0])
n0 = Constant([0.0, 0.0, 1.0])
File(output_path + "sheet_normal.pvd") << project(
n0, VectorFunctionSpace(mesh, "DG", 0))
File(output_path + "fiber.pvd") << project(
f0, VectorFunctionSpace(mesh, "CG", 1))
File(output_path + "sheet.pvd") << project(
s0, VectorFunctionSpace(mesh, "DG", 0))
facetboundaries = MeshFunction(
'size_t', mesh,
mesh.topology().dim() -
1) # fcn that can be evaluated at the mesh entities of 'mesh'
facetboundaries.set_all(0) #sets all values in facetboundaries to 0
left = Left()
right = Right()
fixy = FixY()
fixyright = FixY_right()
fixzright = FixZ_right()
fixz = FixZ()
#
left.mark(facetboundaries, 1)
right.mark(facetboundaries, 2)
fixy.mark(facetboundaries, 3)
fixz.mark(facetboundaries, 4)
#
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'
Quadelem = FiniteElement("Quadrature",
tetrahedron,
degree=2,
quad_scheme="default")
Quadelem._quad_scheme = 'default'
W = FunctionSpace(mesh, MixedElement([Velem, Qelem]))
Quad = FunctionSpace(mesh, Quadelem)
Quad_vectorized_Fspace = FunctionSpace(
mesh, MixedElement(n_array_length * [Quadelem]))
# assigning BCs
u_D = Expression(("u_D"), u_D=0.0, degree=2)
# BCs specified for subdomain by index
bcleft = DirichletBC(W.sub(0), Constant((0, 0, 0)), facetboundaries,
1) # u1 = 0 on left face
bcright = DirichletBC(W.sub(0), Constant((0, 0, 0)), facetboundaries, 2)
bcfixy = DirichletBC(W.sub(0).sub(1),
Constant((0.)),
fixy,
method="pointwise")
bcfixz = DirichletBC(W.sub(0).sub(2),
Constant((0.)),
fixz,
method="pointwise")
bcfixyright = DirichletBC(W.sub(0).sub(1),
Constant((0.)),
fixyright,
method="pointwise")
bcfixzright = DirichletBC(W.sub(0).sub(2),
Constant((0.)),
fixzright,
method="pointwise")
bcs = [bcleft, bcright]
du, dp = TrialFunctions(W)
w = Function(W)
dw = TrialFunction(W)
(u, p) = split(w)
(v, q) = 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)
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)
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
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)
Ftotal = F1 + F2 - F3
Jac1 = derivative(F1, w, dw)
Jac2 = derivative(F2, w, dw)
Jac3 = derivative(F3, w, dw)
Jac = Jac1 + Jac2 - Jac3
##################################################################################################################################
# Contraction phase
'''header_file = open("./C++/hs.h","r")
code = header_file.read()
header_file.close()
ext_module = compile_extension_module(code=code, source_directory="C++", sources=["hs.cpp", "mf.cpp", "Ca.cpp", "base_parameters.cpp"],
additional_system_headers=["petscvec.h"],
include_dirs=[".", os.path.abspath("C++"),"/usr/include", "./C++"],
library_dirs = ['/usr/lib/x86_64-linux-gnu'],
libraries = ['libgsl.a'])
Myosim = ext_module.hs()
_FE_params = {"step_size": step_size};
Myosim.FE_params.update(_FE_params)
_Ca_params = {"Ca_flag": Ca_flag};
Myosim.Ca_params.update(_Ca_params)
_Ca_params = {"constant_pCa": constant_pCa};
Myosim.Ca_params.update(_Ca_params)'''
darray = []
tarray = []
hslarray = []
calarray = []
strarray = []
pstrarray = []
overlaparray = np.zeros((time_steps + 1, no_of_int_points))
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
# Starting all in on state for Debugging
y_vec_array[counter] = 1
y_vec_array[counter - 2] = 1
Pg, Pff, alpha = uflforms.stress()
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()[:]
'''P,S,T = uflforms.stress()
Pff = inner(f0,P*f0)
p_f = project(Pff, Quad)
p_f_array = p_f.vector().get_local()[:]'''
#p_f = np.load("/home/fenics/shared/python_dev/test_10/passive_forces.npy")
cb_f_array = project(cb_force, Quad).vector().get_local()[:]
dumped_populations = np.zeros(
(time_steps, no_of_int_points, n_array_length))
y_interp = np.zeros(no_of_int_points * n_array_length)
# Need to create a list of dictionaries for parameters for each gauss point
hs_params_list = [{}] * no_of_int_points
temp_overlap = np.zeros((no_of_int_points))
y_vec_array_new = np.zeros(((no_of_int_points) * n_array_length))
for jj in np.arange(np.shape(hs_params_list)[0]):
hs_params_list[jj] = copy.deepcopy(hs_params)
t = 0.0
#delta_hsls = np.zeros((time_steps,24))
for l in range(time_steps):
tarray.append(t)
for m in range(no_of_int_points):
for k in range(n_array_length):
dumped_populations[l, m, k] = y_interp[m * n_array_length + k]
#hslarray.append(hsl_array[0])
#strarray.append(cb_f_array[0])
#pstrarray.append(p_f_array[0])
# _Ca_params = {"time_point": l};
# Myosim.Ca_params.update(_Ca_params)
#print p_f[l]
#for k in range(no_of_int_points):
# pop_holder = implement.update_simulation(hs, step_size, delta_hsl_array[k], hsl_array[k], y_vec_array[k*n_array_length:(k+1)*n_array_length],p_f_array[k], cb_f_array[k], prev_ca[l])
# y_vec_array_new = Myosim.apply_time_step(y_vec_array, delta_hsl_array, hsl_array, p_f_array, cb_f_array)
#y_vec_array_new[k*n_array_length:(k+1)*n_array_length] = pop_holder
# 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.model.calculate_concentrations(0,t)
# Looping through integration points within Python Myosim, not here
# Debugging, checking if y_input matches y_output between steps
#print y_vec_array[0:53]
# Quick hack
if l == 0:
overlap_counter = 1
else:
overlap_counter = l
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,
overlaparray[overlap_counter, mm], hs_params_list[mm])
#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 y_vec_array_new[0:53]
y_vec_array = y_vec_array_new # for Myosim
y_vec.vector()[:] = y_vec_array # for PDE
# print y_vec_array[0:53]
hsl_array_old = hsl_array
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)
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()[:]
cb_f_array = project(cb_force, Quad).vector().get_local()[:]
strarray.append(cb_f_array[0])
pstrarray.append(p_f_array[0])
hslarray.append(hsl_array[0] + delta_hsl_array[0])
overlaparray[l, :] = temp_overlap
#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"""
u_D.u_D = u_D.u_D
t = t + step_size
calarray.append(hs.Ca_conc * np.ones(no_of_int_points))
"""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
}
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)
fdataCa.close()
return (outputs)
def create_weak_form(mesh, fcn_spaces, functions):
# Need to set up the strain energy functions and cavity volume info
# from the forms file:
# Load in all of our relevant functions and function spaces
facetboundaries = functions["facetboundaries"]
subdomains = MeshFunction('int', mesh, 3)
X = SpatialCoordinate(mesh)
N = FacetNormal(mesh)
W = fcn_spaces["solution_space"]
w = functions["w"]
u = functions["u"]
v = functions["v"]
p = functions["p"]
f0 = functions["f0"]
s0 = functions["s0"]
n0 = functions["n0"]
c11 = functions["c11"]
wtest = functions["wtest"]
dw = functions["dw"]
# Don't really need this yet
hsl0 = 950
Fg = functions["Fg"]
M1ij = functions["M1ij"]
M2ij = functions["M2ij"]
M3ij = functions["M3ij"]
TF = fcn_spaces["growth_tensor_space"]
dolfin_functions = functions["dolfin_functions"]
pendo = functions["pendo"]
LVendoid = functions["LVendoid"]
print "LVendoid"
print LVendoid
isincomp = True
# Define some parameters
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,
"incompressible": isincomp,
"hsl0": hsl0,
"Kappa": Constant(1e5),
"growth_tensor": Fg,
"M1": M1ij,
"M2": M2ij,
"M3": M3ij,
"TF": TF
}
# update with the passive parameter functions
params.update(dolfin_functions["passive_params"])
# Need to tack on some other stuff, including an expression to keep track of
# and manipulate the cavity volume
LVCavityvol = Expression(("vol"), vol=0.0, degree=2)
Press = Expression(("P"), P=0.0, degree=0)
functions["LVCavityvol"] = LVCavityvol
functions["Press"] = Press
ventricle_params = {
"lv_volconst_variable": pendo,
"lv_constrained_vol": LVCavityvol,
"LVendoid": LVendoid,
"LVendo_comp": 2,
}
params.update(ventricle_params)
uflforms = Forms(params)
print "uflforms mesh"
print uflforms.parameters["mesh"]
# Now that the forms file is initialized, initialize specific forms
#-------------------------------
# This is needed for the forms file, but not for what we are doing yet
# I don't want to change the base functionality of anything, so I'm defining
# this here
# (there exists the capability to have hsl return to its reference length in
# an attempt to incorporate some visoelasticity)
d = u.ufl_domain().geometric_dimension()
I = Identity(d)
Fmat = I + grad(u)
J = det(Fmat)
Cmat = Fmat.T * Fmat
alpha_f = sqrt(dot(f0, Cmat * f0))
hsl = alpha_f * hsl0
functions["hsl"] = hsl
n = J * inv(Fmat.T) * N
#----------------------------------
# Passive stress contribution
Wp = uflforms.PassiveMatSEF(hsl)
# passive material contribution
F1 = derivative(Wp, w, wtest) * dx
# active stress contribution (Pactive is PK2, transform to PK1)
# temporary active stress
Pactive, cbforce = uflforms.TempActiveStress(0.0)
functions["Pactive"] = Pactive
functions["cbforce"] = cbforce
F2 = inner(Fmat * Pactive, grad(v)) * dx
# LV volume increase
Wvol = uflforms.LVV0constrainedE()
F3 = derivative(Wvol, w, wtest)
# For pressure on endo instead of volume bdry condition
F3_p = Press * inner(n, v) * ds(LVendoid)
# 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
Ftotal_growth = F1 + F3_p + F4
Jac1 = derivative(F1, w, dw)
Jac2 = derivative(F2, w, dw)
Jac3 = derivative(F3, w, dw)
Jac3_p = derivative(F3_p, w, dw)
Jac4 = derivative(F4, w, dw)
Jac = Jac1 + Jac2 + Jac3 + Jac4
Jac_growth = Jac1 + Jac3_p + Jac4
return Ftotal, Jac, Ftotal_growth, Jac_growth, uflforms, functions, Pactive
def fenics(sim_params, file_inputs, output_params, passive_params, hs_params,
cell_ion_params, monodomain_params, windkessel_params):
i, j = indices(2)
output_path = output_params["output_path"][0]
displacementfile = File(output_path + "u_disp.pvd")
filament_compliance_factor = hs_params["myofilament_parameters"][
"filament_compliance_factor"][0]
# filament_compliance_factor = 0.5
no_of_states = hs_params["myofilament_parameters"]["num_states"][0]
#no_of_states = 3
#no_of_attached_states = 1
#no_of_detached_states = 2
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]
#no_of_transitions = 4
#state_attached = [0, 0, 1]
#cb_extensions = [ 0, 0, 4.75642]
#k_cb_multiplier = [ 1.0, 1.0, 1.0]
#k_cb_pos = 0.001
#k_cb_neg = 0.001
#cb_number_density = 7.67e16
#alpha_value = 1.0
#x_bin_min = -12
#x_bin_max = +12
#x_bin_increment = 0.5
xx = np.arange(x_bin_min, x_bin_max + x_bin_increment, x_bin_increment)
no_of_x_bins = np.shape(xx)[0]
n_array_length = no_of_attached_states * no_of_x_bins + no_of_detached_states + 2
n_vector_indices = [[0, 0], [1, 1], [2, 2 + no_of_x_bins - 1]]
#hsl0 = 1000
hsl0 = hs_params["initial_hs_length"][0]
#time_steps = 401
#time_steps = 2
#step_size = 0.5
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)
#prev_ca = np.load("calcium_10.npy")
#prev_ca = prev_ca[:,0]
#xml_struct = ut.parse('pm_test10.xml')
#hs_params = xml_struct.single_circulation_simulation.half_sarcomere
hs = half_sarcomere.half_sarcomere(hs_params, 1)
cell_ion = cell_ion_driver.cell_ion_driver(cell_ion_params)
calcium = np.zeros(time_steps)
calcium[0] = cell_ion.model_class.calculate_concentrations(0, 0)
parameters["form_compiler"]["quadrature_degree"] = 2
parameters["form_compiler"]["representation"] = "quadrature"
#
#os.system("rm *.pvd")
#os.system("rm *.vtu")
# 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] - 1.0) < tol
# where x[2] = 0
class Lower(SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return on_boundary and abs(x[2]) < tol
# where x[1] = 0
class Front(SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return on_boundary and abs(x[1]) < tol
# where x[0], x[1] and x[2] = 0
class Fix(SubDomain):
def inside(self, x, on_boundary):
tol = 1E-14
return on_boundary and abs(x[0]) < tol and abs(x[1]) < tol and abs(
x[2]) < tol
#
#
mesh = UnitCubeMesh(1, 1, 1)
#mesh.cells()
# Vector element at gauss points (for fibers)
VQuadelem = VectorElement("Quadrature",
mesh.ufl_cell(),
degree=2,
quad_scheme="default")
VQuadelem._quad_scheme = 'default'
no_of_int_points = 4 * np.shape(mesh.cells())[0]
#print no_of_int_points
#plot(mesh)
#plt.show()
# Function space for local coordinate system (fiber, sheet, sheet-normal)
#f0.vector().array()[:] = [1.0,0.0,0.0]
#f0 = Constant((1.0, 0.0, 0.0))
s0 = Constant((0.0, 1.0, 0.0))
n0 = Constant((0.0, 0.0, 1.0))
facetboundaries = MeshFunction('size_t', mesh, mesh.topology().dim() - 1)
facetboundaries.set_all(0)
left = Left()
right = Right()
fix = Fix()
lower = Lower()
front = Front()
#
left.mark(facetboundaries, 1)
right.mark(facetboundaries, 2)
fix.mark(facetboundaries, 3)
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'
Quadelem = FiniteElement("Quadrature",
tetrahedron,
degree=2,
quad_scheme="default")
Quadelem._quad_scheme = 'default'
W = FunctionSpace(mesh, MixedElement([Velem, Qelem]))
Quad = FunctionSpace(mesh, Quadelem)
Quad_vectorized_Fspace = FunctionSpace(
mesh, MixedElement(n_array_length * [Quadelem]))
# Kurtis trying to initialize vectors
fiberFS = FunctionSpace(mesh, VQuadelem)
f0 = Function(fiberFS)
File(output_path + "fiber1.pvd") << project(
f0, VectorFunctionSpace(mesh, "CG", 1))
ugrid = vtk_py.convertXMLMeshToUGrid(mesh)
File(output_path + "fiber2.pvd") << project(
f0, VectorFunctionSpace(mesh, "CG", 1))
gdim = mesh.geometry().dim()
xdofmap = fiberFS.sub(0).dofmap().dofs()
ydofmap = fiberFS.sub(1).dofmap().dofs()
zdofmap = fiberFS.sub(2).dofmap().dofs()
xq = fiberFS.tabulate_dof_coordinates().reshape((-1, gdim))
xq0 = xq[xdofmap]
print "xq0 shape " + str(np.shape(xq0))
points = vtk.vtkPoints()
vertices = vtk.vtkCellArray()
#ugrid = vtk.vtkUnstructuredGrid()
nb_cells = ugrid.GetNumberOfCells()
print "num cells = " + str(nb_cells)
fvecs = vtk_py.createFloatArray("fvecs", 3, 24)
for i in np.arange(24):
fvecs.InsertTuple(i, [1.0, 0.0, 0.0])
cnt = 0
for pt in xq0:
points.InsertNextPoint([pt[0], pt[1], pt[2]])
vertex = vtk.vtkVertex()
vertex.GetPointIds().SetId(0, cnt)
vertices.InsertNextCell(vertex)
cnt += 1
ugrid.SetPoints(points)
ugrid.SetCells(0, vertices)
vtk_py.CreateVertexFromPoint(ugrid)
#fvecs[:] = f0.vector()[:]
#ugrid.GetCellData().AddArray(f0.vector())
ugrid.GetCellData().AddArray(fvecs)
vtk_py.writeXMLUGrid(ugrid, output_path + "fiber_ugrid.vtu")
cnt = 0
for pt in xq0:
print cnt
fvec = fvecs.GetTuple(cnt)
f0.vector()[xdofmap[cnt]] = fvec[0]
f0.vector()[ydofmap[cnt]] = fvec[1]
f0.vector()[zdofmap[cnt]] = fvec[2]
cnt += 1
mesh = vtk_py.convertUGridToXMLMesh(ugrid)
"""cnt =0
for pt in xq0:
print "assigning vector"
f0.vector()[xdofmap[cnt]] = 1.0*cnt; f0.vector()[ydofmap[cnt]] = 0.0; f0.vector()[zdofmap[cnt]] = 0.0;
cnt +=1"""
print f0[0]
print "shape of f0 " + str(np.shape(f0.vector().array()))
#print "free indices of f0 " + str(f0.free_indices())
#f0.vector()[:] = 1.0
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 = DirichletBC(W.sub(0),
Constant((0.0, 0.0, 0.0)),
fix,
method="pointwise") # at one vertex u = v = w = 0
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]
du, dp = TrialFunctions(W)
w = Function(W)
dw = TrialFunction(W)
(u, p) = split(w)
(v, q) = 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)
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(s0[i] * s0[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)
Ftotal = F1 + F2 - F3
Jac1 = derivative(F1, w, dw)
Jac2 = derivative(F2, w, dw)
Jac3 = derivative(F3, w, dw)
Jac = Jac1 + Jac2 - Jac3
##################################################################################################################################
# Contraction phase
'''header_file = open("./C++/hs.h","r")
code = header_file.read()
header_file.close()
ext_module = compile_extension_module(code=code, source_directory="C++", sources=["hs.cpp", "mf.cpp", "Ca.cpp", "base_parameters.cpp"],
additional_system_headers=["petscvec.h"],
include_dirs=[".", os.path.abspath("C++"),"/usr/include", "./C++"],
library_dirs = ['/usr/lib/x86_64-linux-gnu'],
libraries = ['libgsl.a'])
Myosim = ext_module.hs()
_FE_params = {"step_size": step_size};
Myosim.FE_params.update(_FE_params)
_Ca_params = {"Ca_flag": Ca_flag};
Myosim.Ca_params.update(_Ca_params)
_Ca_params = {"constant_pCa": constant_pCa};
Myosim.Ca_params.update(_Ca_params)'''
darray = []
tarray = []
hslarray = []
calarray = []
strarray = []
pstrarray = []
overlaparray = np.zeros((time_steps + 1, no_of_int_points))
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
# Starting all in on state for Debugging
y_vec_array[counter] = 1
y_vec_array[counter - 2] = 1
Pg, Pff, alpha = uflforms.stress()
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()[:]
'''P,S,T = uflforms.stress()
Pff = inner(f0,P*f0)
p_f = project(Pff, Quad)
p_f_array = p_f.vector().get_local()[:]'''
#p_f = np.load("/home/fenics/shared/python_dev/test_10/passive_forces.npy")
cb_f_array = project(cb_force, Quad).vector().get_local()[:]
dumped_populations = np.zeros(
(time_steps, no_of_int_points, n_array_length))
y_interp = np.zeros(no_of_int_points * n_array_length)
t = 0.0
#delta_hsls = np.zeros((time_steps,24))
for l in range(time_steps):
tarray.append(t)
for m in range(no_of_int_points):
for k in range(n_array_length):
dumped_populations[l, m, k] = y_interp[m * n_array_length + k]
#hslarray.append(hsl_array[0])
#strarray.append(cb_f_array[0])
#pstrarray.append(p_f_array[0])
# _Ca_params = {"time_point": l};
# Myosim.Ca_params.update(_Ca_params)
#print p_f[l]
#for k in range(no_of_int_points):
# pop_holder = implement.update_simulation(hs, step_size, delta_hsl_array[k], hsl_array[k], y_vec_array[k*n_array_length:(k+1)*n_array_length],p_f_array[k], cb_f_array[k], prev_ca[l])
# y_vec_array_new = Myosim.apply_time_step(y_vec_array, delta_hsl_array, hsl_array, p_f_array, cb_f_array)
#y_vec_array_new[k*n_array_length:(k+1)*n_array_length] = pop_holder
# 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.model.calculate_concentrations(0,t)
# Looping through integration points within Python Myosim, not here
# Debugging, checking if y_input matches y_output between steps
#print y_vec_array[0:53]
# Quick hack
if l == 0:
overlap_counter = 1
else:
overlap_counter = l
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 y_vec_array_new[0:53]
y_vec_array = y_vec_array_new # for Myosim
y_vec.vector()[:] = y_vec_array # for PDE
# print y_vec_array[0:53]
hsl_array_old = hsl_array
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)
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()[:]
cb_f_array = project(cb_force, Quad).vector().get_local()[:]
strarray.append(cb_f_array[0])
pstrarray.append(p_f_array[0])
hslarray.append(hsl_array[0] + delta_hsl_array[0])
overlaparray[l, :] = temp_overlap
#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 < 20:
u_D.u_D += 0.001
else:
u_D.u_D = u_D.u_D
t = t + step_size
calarray.append(hs.Ca_conc * np.ones(no_of_int_points))
# 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
}
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)
fdataCa.close()
return (outputs)
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)
def create_weak_form(mesh, fcn_spaces, functions, arrays_and_values):
m, k = indices(2)
# Need to set up the strain energy functions and cavity volume info
# from the forms file:
# Load in all of our relevant functions and function spaces
facetboundaries = functions["facetboundaries"]
subdomains = MeshFunction('int', mesh, 3)
X = SpatialCoordinate(mesh)
N = FacetNormal(mesh)
W = fcn_spaces["solution_space"]
w = functions["w"]
u = functions["u"]
v = functions["v"]
p = functions["p"]
f0 = functions["f0"]
s0 = functions["s0"]
n0 = functions["n0"]
c11 = functions["c11"]
wtest = functions["wtest"]
dw = functions["dw"]
# Don't really need this yet
#hsl0 = 950
hsl0 = functions["hsl0"]
Fg = functions["Fg"]
M1ij = functions["M1ij"]
M2ij = functions["M2ij"]
M3ij = functions["M3ij"]
TF = fcn_spaces["growth_tensor_space"]
dolfin_functions = functions["dolfin_functions"]
pendo = functions["pendo"]
LVendoid = functions["LVendoid"]
isincomp = True
# Define some parameters
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,
"incompressible": isincomp,
"hsl0": hsl0,
"Kappa": Constant(1e5),
"growth_tensor": Fg,
"M1": M1ij,
"M2": M2ij,
"M3": M3ij,
"TF": TF
}
# update with the passive parameter functions
params.update(dolfin_functions["passive_params"])
# Need to tack on some other stuff, including an expression to keep track of
# and manipulate the cavity volume
LVCavityvol = Expression(("vol"), vol=0.0, degree=2)
Press = Expression(("P"), P=0.0, degree=0)
functions["LVCavityvol"] = LVCavityvol
functions["Press"] = Press
ventricle_params = {
"lv_volconst_variable": pendo,
"lv_constrained_vol": LVCavityvol,
"LVendoid": LVendoid,
"LVendo_comp": 2,
}
params.update(ventricle_params)
uflforms = Forms(params)
# Now that the forms file is initialized, initialize specific forms
#-------------------------------
# This is needed for the forms file, but not for what we are doing yet
# I don't want to change the base functionality of anything, so I'm defining
# this here
# (there exists the capability to have hsl return to its reference length in
# an attempt to incorporate some visoelasticity)
#d = u.ufl_domain().geometric_dimension()
#I = Identity(d)
#Fmat = I + grad(u)
#J = det(Fmat)
#Cmat = Fmat.T*Fmat
#alpha_f = sqrt(dot(f0, Cmat*f0))
#hsl = alpha_f*hsl0
#functions["hsl"] = hsl
Fmat = uflforms.Fe()
Cmat = uflforms.Cmat()
J = uflforms.J()
n = J * inv(Fmat.T) * N
alpha_f = sqrt(dot(f0, Cmat * f0))
hsl = alpha_f * functions["hsl0"]
print "hsl initial"
print project(hsl, fcn_spaces["quadrature_space"]).vector().get_local()
#----------------------------------
# Passive stress contribution
Wp = uflforms.PassiveMatSEF(hsl)
# passive material contribution
F1 = derivative(Wp, w, wtest) * dx
# active stress contribution (Pactive is PK2, transform to PK1)
# temporary active stress
#Pactive, cbforce = uflforms.TempActiveStress(0.0)
functions["hsl_old"].vector()[:] = functions["hsl0"].vector()[:]
functions["hsl_diff_from_reference"] = (
functions["hsl_old"] - functions["hsl0"]) / functions["hsl0"]
functions["pseudo_alpha"] = functions["pseudo_old"] * (
1. - (arrays_and_values["k_myo_damp"] *
(functions["hsl_diff_from_reference"])))
alpha_f = sqrt(dot(f0, Cmat *
f0)) # actual stretch based on deformation gradient
print "checking pseudo_alpha"
print functions["pseudo_alpha"].vector().get_local()
functions["hsl"] = functions["pseudo_alpha"] * alpha_f * functions["hsl0"]
functions["delta_hsl"] = functions["hsl"] - functions["hsl_old"]
cb_force = Constant(0.0)
y_vec_split = split(functions["y_vec"])
#Wp = uflforms.PassiveMatSEF(functions["hsl"])
#F1 = derivative(Wp, w, wtest)*dx
for jj in range(arrays_and_values["no_of_states"]):
f_holder = Constant(0.0)
temp_holder = 0.0
if arrays_and_values["state_attached"][jj] == 1:
cb_ext = arrays_and_values["cb_extensions"][jj]
for kk in range(arrays_and_values["no_of_x_bins"]):
dxx = arrays_and_values["xx"][
kk] + functions["delta_hsl"] * arrays_and_values[
"filament_compliance_factor"]
n_pop = y_vec_split[
arrays_and_values["n_vector_indices"][jj][0] + kk]
temp_holder = n_pop * arrays_and_values["k_cb_multiplier"][
jj] * (dxx + cb_ext) * conditional(
gt(dxx + cb_ext, 0.0), arrays_and_values["k_cb_pos"],
arrays_and_values["k_cb_neg"])
f_holder = f_holder + temp_holder
f_holder = f_holder * dolfin_functions["cb_number_density"][
-1] * 1e-9
f_holder = f_holder * arrays_and_values["alpha_value"]
cb_force = cb_force + f_holder
Pactive = cb_force * as_tensor(
functions["f0"][m] * functions["f0"][k],
(m, k)) + arrays_and_values["xfiber_fraction"] * cb_force * as_tensor(
functions["s0"][m] * functions["s0"][k],
(m,
k)) + arrays_and_values["xfiber_fraction"] * cb_force * as_tensor(
functions["n0"][m] * functions["n0"][k], (m, k))
functions["cb_force"] = cb_force
arrays_and_values["cb_f_array"] = project(
functions["cb_force"],
fcn_spaces["quadrature_space"]).vector().get_local()[:]
arrays_and_values["hsl_array"] = project(
functions["hsl"],
fcn_spaces["quadrature_space"]).vector().get_local()[:]
# calculate myofiber passive stress along f0, set negatives to zero (no compressive stress born by fibers)
total_passive_PK2, functions["Sff"] = uflforms.stress(functions["hsl"])
temp_DG = project(functions["Sff"],
FunctionSpace(mesh, "DG", 1),
form_compiler_parameters={"representation": "uflacs"})
p_f = interpolate(temp_DG, fcn_spaces["quadrature_space"])
arrays_and_values["p_f_array"] = p_f.vector().get_local()[:]
functions["Pactive"] = Pactive
#functions["cbforce"] = cbforce
F2 = inner(Fmat * Pactive, grad(v)) * dx
# LV volume increase
Wvol = uflforms.LVV0constrainedE()
F3 = derivative(Wvol, w, wtest)
# For pressure on endo instead of volume bdry condition
F3_p = Press * inner(n, v) * ds(LVendoid)
# 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
Ftotal_growth = F1 + F3_p + F4
Jac1 = derivative(F1, w, dw)
Jac2 = derivative(F2, w, dw)
Jac3 = derivative(F3, w, dw)
Jac3_p = derivative(F3_p, w, dw)
Jac4 = derivative(F4, w, dw)
Jac = Jac1 + Jac2 + Jac3 + Jac4
Jac_growth = Jac1 + Jac3_p + Jac4
return Ftotal, Jac, Ftotal_growth, Jac_growth, uflforms, functions, Pactive, arrays_and_values
import os
import sys
import argparse
from pathlib import Path
from const import Const
from forms import Forms
from games import Games
from updater import Updater
from settings import Settings
updater = Updater(Const.updateurl, Const.version)
games = Games(Const.gamesjsonpath)
settings = Settings(Const.settingsjsonpath)
forms = Forms(updater=updater, games=games, settings=settings)
parser = argparse.ArgumentParser()
parser.add_argument('--noui', action='store_true')
parser.add_argument('--name')
parser.add_argument('--path')
parser.add_argument('--host', action='store_true')
args = parser.parse_args()
if __name__ == "__main__":
if args.name is not None and args.path is not None:
if args.host is not None:
games.addgame(args.name, args.path, args.host)
else:
games.addgame(args.name, args.path)
def _get_forms(inf_desc, req_infinitive):
forms = []
verb_types = ['M', 'A', 'S']
for verb_type in verb_types:
descriptors = inf_desc[req_infinitive]
form = 'V{0}N00000'.format(verb_type)
if form not in descriptors:
continue
forms.append(Forms('Indicatiu', 'Present', 'V' + verb_type + 'IP'))
forms.append(Forms('Indicatiu', 'Imperfet', 'V' + verb_type + 'II'))
forms.append(
Forms('Indicatiu', 'Passat simple', 'V' + verb_type + 'IS'))
forms.append(Forms('Indicatiu', 'Futur', 'V' + verb_type + 'IF'))
forms.append(Forms('Indicatiu', 'Condicional', 'V' + verb_type + 'IC'))
forms.append(Forms('Subjuntiu', 'Present', 'V' + verb_type + 'SP'))
forms.append(Forms('Subjuntiu', 'Imperfet', 'V' + verb_type + 'SI'))
forms.append(Forms('Imperatiu', 'Present', 'V' + verb_type + 'M0'))
descriptors = inf_desc[req_infinitive]
for form in forms:
_set_plurals_singulars(form, descriptors)
forms.append(
Forms('Formes no personals', 'Infinitiu', 'V' + verb_type + 'N0'))
forms.append(
Forms('Formes no personals', 'Gerundi', 'V' + verb_type + 'G0'))
for form in forms[-2:]:
_set_plurals_singulars0(form, descriptors)
forms.append(
Forms('Formes no personals', 'Participi', 'V' + verb_type + 'P0'))
_set_plurals_singulars_gerundi(forms[len(forms) - 1], descriptors)
return forms