def __init__(self, problem, solver_params_solid, solver_params_flow0d):
self.pb = problem
# initialize solver instances
self.solversmall = SolidmechanicsFlow0DSolver(self.pb.pbsmall,
solver_params_solid,
solver_params_flow0d)
self.solverlarge = SolidmechanicsSolver(self.pb.pblarge,
solver_params_solid)
# read restart information
if self.pb.restart_cycle > 0:
self.pb.pbsmall.pbs.simname = self.pb.simname_small + str(
self.pb.restart_cycle)
self.pb.pblarge.simname = self.pb.simname_large + str(
self.pb.restart_cycle)
self.pb.pbsmall.pbs.io.readcheckpoint(self.pb.pbsmall.pbs,
self.pb.restart_cycle)
self.pb.pblarge.io.readcheckpoint(self.pb.pblarge,
self.pb.restart_cycle)
self.pb.pbsmall.pbf.readrestart(self.pb.pbsmall.pbs.simname,
self.pb.restart_cycle)
# no need to do after restart
self.pb.pbsmall.pbs.prestress_initial = False
# induce the perturbation
self.pb.pbsmall.induce_perturbation()
# next small scale run is a resumption of a previous one
self.pb.pbsmall.restart_multiscale = True
def __init__(self, problem, solver_params_solid, solver_params_flow0d):
self.pb = problem
self.solver_params_solid = solver_params_solid
self.solver_params_flow0d = solver_params_flow0d
# initialize nonlinear solver class
self.solnln = solver_nonlin.solver_nonlinear_constraint_monolithic(
self.pb, self.pb.pbs.V_u, self.pb.pbs.V_p,
self.solver_params_solid, self.solver_params_flow0d)
if self.pb.pbs.prestress_initial:
# add coupling work to prestress weak form
self.pb.pbs.weakform_prestress_u -= self.pb.work_coupling_prestr
# initialize solid mechanics solver
self.solverprestr = SolidmechanicsSolver(self.pb.pbs,
self.solver_params_solid)
class SolidmechanicsConstraintSolver():
def __init__(self, problem, solver_params_solid, solver_params_constr):
self.pb = problem
self.solver_params_solid = solver_params_solid
self.solver_params_constr = solver_params_constr
self.solve_type = self.solver_params_solid['solve_type']
# initialize nonlinear solver class
self.solnln = solver_nonlin.solver_nonlinear_constraint_monolithic(
self.pb, self.pb.pbs.V_u, self.pb.pbs.V_p,
self.solver_params_solid, self.solver_params_constr)
if self.pb.pbs.prestress_initial:
# add coupling work to prestress weak form
self.pb.pbs.weakform_prestress_u -= self.pb.work_coupling_prestr
# initialize solid mechanics solver
self.solverprestr = SolidmechanicsSolver(self.pb.pbs,
self.solver_params_solid)
def solve_problem(self):
start = time.time()
# print header
utilities.print_problem(self.pb.problem_physics, self.pb.pbs.comm,
self.pb.pbs.ndof)
# read restart information
if self.pb.pbs.restart_step > 0:
self.pb.pbs.io.readcheckpoint(self.pb.pbs,
self.pb.pbs.restart_step)
self.pb.pbs.simname += '_r' + str(self.pb.pbs.restart_step)
self.pb.set_pressure_fem(self.pb.lm_old, self.pb.coupfuncs_old)
# in case we want to prestress with MULF (Gee et al. 2010) prior to solving the 3D-0D problem
if self.pb.pbs.prestress_initial and self.pb.pbs.restart_step == 0:
# solve solid prestress problem
self.solverprestr.solve_initial_prestress()
del self.solverprestr
else:
# set flag definitely to False if we're restarting
self.pb.pbs.prestress_initial = False
self.pb.constr, self.pb.constr_old = [], []
for i in range(self.pb.num_coupling_surf):
lm_sq, lm_old_sq = allgather_vec(self.pb.lm,
self.pb.comm), allgather_vec(
self.pb.lm_old, self.pb.comm)
con = assemble_scalar(self.pb.cq[i])
con = self.pb.pbs.comm.allgather(con)
self.pb.constr.append(sum(con))
self.pb.constr_old.append(sum(con))
# consider consistent initial acceleration
if self.pb.pbs.timint != 'static' and self.pb.pbs.restart_step == 0:
# weak form at initial state for consistent initial acceleration solve
weakform_a = self.pb.pbs.deltaW_kin_old + self.pb.pbs.deltaW_int_old - self.pb.pbs.deltaW_ext_old - self.pb.work_coupling_old
jac_a = derivative(weakform_a, self.pb.pbs.a_old,
self.pb.pbs.du) # actually linear in a_old
# solve for consistent initial acceleration a_old
self.solnln.solve_consistent_ini_acc(weakform_a, jac_a,
self.pb.pbs.a_old)
# write mesh output
self.pb.pbs.io.write_output(self.pb.pbs, writemesh=True)
# solid constraint main time loop
for N in range(self.pb.pbs.restart_step + 1,
self.pb.pbs.numstep_stop + 1):
wts = time.time()
# current time
t = N * self.pb.pbs.dt
# set time-dependent functions
self.pb.pbs.ti.set_time_funcs(self.pb.pbs.ti.funcs_to_update,
self.pb.pbs.ti.funcs_to_update_vec,
t)
# take care of active stress
if self.pb.pbs.have_active_stress and self.pb.pbs.active_stress_trig == 'ode':
self.pb.pbs.evaluate_active_stress_ode(t)
# solve
self.solnln.newton(self.pb.pbs.u,
self.pb.pbs.p,
self.pb.lm,
t,
locvar=self.pb.pbs.theta,
locresform=self.pb.pbs.r_growth,
locincrform=self.pb.pbs.del_theta)
# update time step
self.pb.pbs.ti.update_timestep(
self.pb.pbs.u, self.pb.pbs.u_old, self.pb.pbs.v_old,
self.pb.pbs.a_old, self.pb.pbs.p, self.pb.pbs.p_old,
self.pb.pbs.internalvars, self.pb.pbs.internalvars_old,
self.pb.pbs.ti.funcs_to_update,
self.pb.pbs.ti.funcs_to_update_old,
self.pb.pbs.ti.funcs_to_update_vec,
self.pb.pbs.ti.funcs_to_update_vec_old)
# update old pressures on solid
self.pb.lm.assemble(), self.pb.lm_old.axpby(1.0, 0.0, self.pb.lm)
self.pb.set_pressure_fem(self.pb.lm_old, self.pb.coupfuncs_old)
# update old 3D constraint variable
for i in range(self.pb.num_coupling_surf):
self.pb.constr_old[i] = self.pb.constr[i]
# solve time for time step
wte = time.time()
wt = wte - wts
# print time step info to screen
self.pb.pbs.ti.print_timestep(N, t, wt=wt)
# write output and restart info
self.pb.pbs.io.write_output(self.pb.pbs, N=N, t=t)
if self.pb.comm.rank == 0: # only proc 0 should print this
print('Time for computation: %.4f s (= %.2f min)' %
(time.time() - start, (time.time() - start) / 60.))
sys.stdout.flush()
class SolidmechanicsFlow0DMultiscaleGrowthRemodelingSolver():
def __init__(self, problem, solver_params_solid, solver_params_flow0d):
self.pb = problem
# initialize solver instances
self.solversmall = SolidmechanicsFlow0DSolver(self.pb.pbsmall,
solver_params_solid,
solver_params_flow0d)
self.solverlarge = SolidmechanicsSolver(self.pb.pblarge,
solver_params_solid)
# read restart information
if self.pb.restart_cycle > 0:
self.pb.pbsmall.pbs.simname = self.pb.simname_small + str(
self.pb.restart_cycle)
self.pb.pblarge.simname = self.pb.simname_large + str(
self.pb.restart_cycle)
self.pb.pbsmall.pbs.io.readcheckpoint(self.pb.pbsmall.pbs,
self.pb.restart_cycle)
self.pb.pblarge.io.readcheckpoint(self.pb.pblarge,
self.pb.restart_cycle)
self.pb.pbsmall.pbf.readrestart(self.pb.pbsmall.pbs.simname,
self.pb.restart_cycle)
# no need to do after restart
self.pb.pbsmall.pbs.prestress_initial = False
# induce the perturbation
self.pb.pbsmall.induce_perturbation()
# next small scale run is a resumption of a previous one
self.pb.pbsmall.restart_multiscale = True
def solve_problem(self):
start = time.time()
# print header
utilities.print_problem(self.pb.problem_physics, self.pb.comm)
# multiscale growth and remodeling solid 0D flow main time loop
for N in range(self.pb.restart_cycle + 1, self.pb.N_cycles + 1):
wts = time.time()
# time offset from previous small scale times
self.pb.pbsmall.t_prev = (self.pb.pbsmall.pbf.ti.cycle[0] - 1
) * self.pb.pbsmall.pbf.cardvasc0D.T_cycl
# change output names
self.pb.pbsmall.pbs.simname = self.pb.simname_small + str(N)
self.pb.pblarge.simname = self.pb.simname_large + str(N)
self.set_state_small()
if not self.pb.restart_from_small:
if self.pb.comm.rank == 0:
print(
"Solving small scale 3D-0D coupled solid-flow0d problem:"
)
sys.stdout.flush()
# solve small scale 3D-0D coupled solid-flow0d problem with fixed growth
self.solversmall.solve_problem()
# next small scale run is a resumption of a previous one
self.pb.pbsmall.restart_multiscale = True
if self.pb.write_checkpoints:
# write checkpoint for potential restarts
self.pb.pbsmall.pbs.io.writecheckpoint(
self.pb.pbsmall.pbs, N)
self.pb.pbsmall.pbf.writerestart(
self.pb.pbsmall.pbs.simname, N, ms=True)
else:
# read small scale checkpoint if we restart from this scale
self.pb.pbsmall.pbs.io.readcheckpoint(
self.pb.pbsmall.pbs, self.pb.restart_cycle + 1)
self.pb.pbsmall.pbf.readrestart(self.pb.pbsmall.pbs.simname,
self.pb.restart_cycle + 1,
ms=True)
# induce the perturbation
if not self.pb.pbsmall.pbf.have_induced_pert:
self.pb.pbsmall.induce_perturbation()
# no need to do after restart
self.pb.pbsmall.pbs.prestress_initial = False
# set flag to False again
self.pb.restart_from_small = False
# next small scale run is a resumption of a previous one
self.pb.pbsmall.restart_multiscale = True
# set large scale state
self.set_state_large(N)
# compute volume prior to G&R
vol_prior = self.compute_volume_large()
if self.pb.comm.rank == 0:
print(
"Solving large scale solid growth and remodeling problem:")
sys.stdout.flush()
# solve large scale static G&R solid problem with fixed loads
self.solverlarge.solve_problem()
# compute volume after G&R
vol_after = self.compute_volume_large()
if self.pb.write_checkpoints:
# write checkpoint for potential restarts
self.pb.pblarge.io.writecheckpoint(self.pb.pblarge, N)
# relative volume increase over large scale run
volchange = (vol_after - vol_prior) / vol_prior
if self.pb.comm.rank == 0:
print('Volume change due to growth: %.4e' % (volchange))
sys.stdout.flush()
# check if below tolerance
if abs(volchange) <= self.pb.tol_outer:
break
if self.pb.comm.rank == 0: # only proc 0 should print this
print('Time for full multiscale computation: %.4f s (= %.2f min)' %
(time.time() - start, (time.time() - start) / 60.))
sys.stdout.flush()
def set_state_small(self):
# set delta small to large
u_delta = PETSc.Vec().createMPI(
(self.pb.pblarge.u.vector.getLocalSize(),
self.pb.pblarge.u.vector.getSize()),
bsize=self.pb.pblarge.u.vector.getBlockSize(),
comm=self.pb.comm)
u_delta.waxpy(-1.0, self.pb.pbsmall.pbs.u_set.vector,
self.pb.pblarge.u.vector)
if self.pb.pbsmall.pbs.incompressible_2field:
p_delta = PETSc.Vec().createMPI(
(self.pb.pblarge.p.vector.getLocalSize(),
self.pb.pblarge.p.vector.getSize()),
bsize=self.pb.pblarge.p.vector.getBlockSize(),
comm=self.pb.comm)
p_delta.waxpy(-1.0, self.pb.pbsmall.pbs.p_set.vector,
self.pb.pblarge.p.vector)
# update small scale variables - add delta from growth to last small scale displacement
self.pb.pbsmall.pbs.u.vector.axpy(1.0, u_delta)
self.pb.pbsmall.pbs.u.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
self.pb.pbsmall.pbs.u_old.vector.axpy(1.0, u_delta)
self.pb.pbsmall.pbs.u_old.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
if self.pb.pbsmall.pbs.incompressible_2field:
self.pb.pbsmall.pbs.p.vector.axpy(1.0, p_delta)
self.pb.pbsmall.pbs.p.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
self.pb.pbsmall.pbs.p_old.vector.axpy(1.0, p_delta)
self.pb.pbsmall.pbs.p_old.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
#self.pb.pbsmall.pbs.v_old.vector.set(0.0)
#self.pb.pbsmall.pbs.v_old.vector.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
#self.pb.pbsmall.pbs.a_old.vector.set(0.0)
#self.pb.pbsmall.pbs.a_old.vector.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
# 0D variables s and s_old are already correctly set from the previous small scale run (end values)
# set constant prescribed growth stretch for subsequent small scale
self.pb.pbsmall.pbs.theta.vector.axpby(1.0, 0.0,
self.pb.pblarge.theta.vector)
self.pb.pbsmall.pbs.theta.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
self.pb.pbsmall.pbs.theta_old.vector.axpby(
1.0, 0.0, self.pb.pblarge.theta.vector)
self.pb.pbsmall.pbs.theta_old.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
def set_state_large(self, N):
# update large scale variables
# only needed once - set prestressing history deformation gradient and spring offset from small scale
if self.pb.prestress_initial and N == 1:
self.pb.pblarge.F_hist.vector.axpby(
1.0, 0.0, self.pb.pbsmall.pbs.F_hist.vector)
self.pb.pblarge.F_hist.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
self.pb.pblarge.u_pre.vector.axpby(
1.0, 0.0, self.pb.pbsmall.pbs.u_pre.vector)
self.pb.pblarge.u_pre.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
self.pb.pblarge.u_set.vector.axpby(1.0, 0.0,
self.pb.pbsmall.pbs.u_set.vector)
self.pb.pblarge.u_set.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
self.pb.pblarge.u.vector.axpby(1.0, 0.0,
self.pb.pbsmall.pbs.u_set.vector)
self.pb.pblarge.u.vector.ghostUpdate(addv=PETSc.InsertMode.INSERT,
mode=PETSc.ScatterMode.FORWARD)
if self.pb.pblarge.incompressible_2field:
self.pb.pblarge.p.vector.axpby(1.0, 0.0,
self.pb.pbsmall.pbs.p_set.vector)
self.pb.pblarge.p.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
# constant large scale active tension
self.pb.pblarge.tau_a.vector.axpby(
1.0, 0.0, self.pb.pbsmall.pbs.tau_a_set.vector)
self.pb.pblarge.tau_a.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
if self.pb.pblarge.have_frank_starling:
self.pb.pblarge.amp_old.vector.axpby(
1.0, 0.0, self.pb.pbsmall.pbs.amp_old_set.vector)
self.pb.pblarge.amp_old.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
# pressures from growth set point
self.pb.pbsmall.pbf.cardvasc0D.set_pressure_fem(
self.pb.pbsmall.pbf.s_set, self.pb.pbsmall.pbf.cardvasc0D.v_ids,
self.pb.pbsmall.pr0D, self.pb.neumann_funcs)
# growth thresholds from set point
self.pb.pblarge.growth_thres.vector.axpby(
1.0, 0.0, self.pb.pbsmall.pbs.growth_thres.vector)
self.pb.pblarge.growth_thres.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
def compute_volume_large(self):
J_all = as_ufl(0)
for n in range(self.pb.pblarge.num_domains):
J_all += self.pb.pblarge.ki.J(
self.pb.pblarge.u) * self.pb.pblarge.dx_[n]
vol = assemble_scalar(J_all)
vol = self.pb.comm.allgather(vol)
volume_large = sum(vol)
if self.pb.comm.rank == 0:
print('Volume of myocardium: %.4e' % (volume_large))
sys.stdout.flush()
return volume_large
class SolidmechanicsFlow0DSolver():
def __init__(self, problem, solver_params_solid, solver_params_flow0d):
self.pb = problem
self.solver_params_solid = solver_params_solid
self.solver_params_flow0d = solver_params_flow0d
self.solve_type = self.solver_params_solid['solve_type']
# initialize nonlinear solver class
self.solnln = solver_nonlin.solver_nonlinear_constraint_monolithic(
self.pb, self.pb.pbs.V_u, self.pb.pbs.V_p,
self.solver_params_solid, self.solver_params_flow0d)
if self.pb.pbs.prestress_initial:
# add coupling work to prestress weak form
self.pb.pbs.weakform_prestress_u -= self.pb.work_coupling_prestr
# initialize solid mechanics solver
self.solverprestr = SolidmechanicsSolver(self.pb.pbs,
self.solver_params_solid)
def solve_problem(self):
start = time.time()
# print header
utilities.print_problem(self.pb.problem_physics, self.pb.pbs.comm,
self.pb.pbs.ndof)
# read restart information
if self.pb.pbs.restart_step > 0:
self.pb.pbs.io.readcheckpoint(self.pb.pbs,
self.pb.pbs.restart_step)
self.pb.pbf.readrestart(self.pb.pbs.simname,
self.pb.pbs.restart_step)
self.pb.pbs.simname += '_r' + str(self.pb.pbs.restart_step)
# set pressure functions for old state - s_old already initialized by 0D flow problem
if self.pb.coupling_type == 'monolithic_direct':
self.pb.pbf.cardvasc0D.set_pressure_fem(
self.pb.pbf.s_old, self.pb.pbf.cardvasc0D.v_ids, self.pb.pr0D,
self.pb.coupfuncs_old)
if self.pb.coupling_type == 'monolithic_lagrange':
self.pb.pbf.cardvasc0D.set_pressure_fem(
self.pb.lm_old, list(range(self.pb.num_coupling_surf)),
self.pb.pr0D, self.pb.coupfuncs_old)
# in case we want to prestress with MULF (Gee et al. 2010) prior to solving the 3D-0D problem
if self.pb.pbs.prestress_initial and self.pb.pbs.restart_step == 0:
# solve solid prestress problem
self.solverprestr.solve_initial_prestress()
del self.solverprestr
else:
# set flag definitely to False if we're restarting
self.pb.pbs.prestress_initial = False
if self.pb.coupling_type == 'monolithic_direct':
# old 3D coupling quantities (volumes or fluxes)
self.pb.pbf.c = []
for i in range(self.pb.num_coupling_surf):
cq = assemble_scalar(self.pb.cq_old[i])
cq = self.pb.pbs.comm.allgather(cq)
self.pb.pbf.c.append(sum(cq) * self.pb.cq_factor[i])
if self.pb.coupling_type == 'monolithic_lagrange':
self.pb.pbf.c, self.pb.constr, self.pb.constr_old = [], [], []
for i in range(self.pb.num_coupling_surf):
lm_sq, lm_old_sq = allgather_vec(self.pb.lm,
self.pb.comm), allgather_vec(
self.pb.lm_old,
self.pb.comm)
self.pb.pbf.c.append(lm_sq[i])
con = assemble_scalar(self.pb.cq_old[i])
con = self.pb.pbs.comm.allgather(con)
self.pb.constr.append(sum(con) * self.pb.cq_factor[i])
self.pb.constr_old.append(sum(con) * self.pb.cq_factor[i])
if bool(self.pb.pbf.chamber_models):
self.pb.pbf.y = []
for ch in self.pb.pbf.chamber_models:
if self.pb.pbf.chamber_models[ch]['type'] == '0D_elast':
self.pb.pbf.y.append(
self.pb.pbs.ti.timecurves(
self.pb.pbf.chamber_models[ch]['activation_curve'])
(self.pb.pbs.t_init))
# initially evaluate 0D model at old state
self.pb.pbf.cardvasc0D.evaluate(self.pb.pbf.s_old, self.pb.pbs.dt,
self.pb.pbs.t_init, self.pb.pbf.df_old,
self.pb.pbf.f_old, None, self.pb.pbf.c,
self.pb.pbf.y, self.pb.pbf.aux_old)
# consider consistent initial acceleration
if self.pb.pbs.timint != 'static' and self.pb.pbs.restart_step == 0 and not self.pb.restart_multiscale:
# weak form at initial state for consistent initial acceleration solve
weakform_a = self.pb.pbs.deltaW_kin_old + self.pb.pbs.deltaW_int_old - self.pb.pbs.deltaW_ext_old - self.pb.work_coupling_old
jac_a = derivative(weakform_a, self.pb.pbs.a_old,
self.pb.pbs.du) # actually linear in a_old
# solve for consistent initial acceleration a_old
self.solnln.solve_consistent_ini_acc(weakform_a, jac_a,
self.pb.pbs.a_old)
# write mesh output
self.pb.pbs.io.write_output(self.pb.pbs, writemesh=True)
# solid 0D flow main time loop
for N in range(self.pb.pbs.restart_step + 1,
self.pb.pbs.numstep_stop + 1):
wts = time.time()
# current time
t = N * self.pb.pbs.dt + self.pb.t_prev # t_prev for multiscale analysis (time from previous cycles)
# offset time for multiple cardiac cycles
t_off = (
self.pb.pbf.ti.cycle[0] - 1
) * self.pb.pbf.cardvasc0D.T_cycl # zero if T_cycl variable is not specified
# set time-dependent functions
self.pb.pbs.ti.set_time_funcs(self.pb.pbs.ti.funcs_to_update,
self.pb.pbs.ti.funcs_to_update_vec,
t - t_off)
# take care of active stress
if self.pb.pbs.have_active_stress and self.pb.pbs.active_stress_trig == 'ode':
self.pb.pbs.evaluate_active_stress_ode(t - t_off)
# activation curves for 0D chambers (if present)
self.pb.pbf.evaluate_activation(t - t_off)
# solve
self.solnln.newton(self.pb.pbs.u,
self.pb.pbs.p,
self.pb.pbf.s,
t - t_off,
locvar=self.pb.pbs.theta,
locresform=self.pb.pbs.r_growth,
locincrform=self.pb.pbs.del_theta)
# get midpoint dof values for post-processing (has to be called before update!)
self.pb.pbf.cardvasc0D.midpoint_avg(
self.pb.pbf.s, self.pb.pbf.s_old,
self.pb.pbf.s_mid), self.pb.pbf.cardvasc0D.midpoint_avg(
self.pb.pbf.aux, self.pb.pbf.aux_old, self.pb.pbf.aux_mid)
# update time step - solid and 0D model
self.pb.pbs.ti.update_timestep(
self.pb.pbs.u, self.pb.pbs.u_old, self.pb.pbs.v_old,
self.pb.pbs.a_old, self.pb.pbs.p, self.pb.pbs.p_old,
self.pb.pbs.internalvars, self.pb.pbs.internalvars_old,
self.pb.pbs.ti.funcs_to_update,
self.pb.pbs.ti.funcs_to_update_old,
self.pb.pbs.ti.funcs_to_update_vec,
self.pb.pbs.ti.funcs_to_update_vec_old)
self.pb.pbf.cardvasc0D.update(self.pb.pbf.s, self.pb.pbf.df,
self.pb.pbf.f, self.pb.pbf.s_old,
self.pb.pbf.df_old,
self.pb.pbf.f_old, self.pb.pbf.aux,
self.pb.pbf.aux_old)
if self.pb.have_multiscale_gandr:
self.set_homeostatic_threshold(t), self.set_growth_trigger(
t - t_off)
# update old pressures on solid
if self.pb.coupling_type == 'monolithic_direct':
self.pb.pbf.cardvasc0D.set_pressure_fem(
self.pb.pbf.s_old, self.pb.pbf.cardvasc0D.v_ids,
self.pb.pr0D, self.pb.coupfuncs_old)
if self.pb.coupling_type == 'monolithic_lagrange':
self.pb.lm.assemble(), self.pb.lm_old.axpby(
1.0, 0.0, self.pb.lm)
self.pb.pbf.cardvasc0D.set_pressure_fem(
self.pb.lm_old, list(range(self.pb.num_coupling_surf)),
self.pb.pr0D, self.pb.coupfuncs_old)
# update old 3D fluxes
for i in range(self.pb.num_coupling_surf):
self.pb.constr_old[i] = self.pb.constr[i]
# solve time for time step
wte = time.time()
wt = wte - wts
# print to screen
self.pb.pbf.cardvasc0D.print_to_screen(self.pb.pbf.s_mid,
self.pb.pbf.aux_mid)
# print time step info to screen
self.pb.pbf.ti.print_timestep(N, t, self.pb.pbs.numstep, wt=wt)
# check for periodicity in cardiac cycle and stop if reached (only for syspul* models - cycle counter gets updated here)
is_periodic = self.pb.pbf.cardvasc0D.cycle_check(
self.pb.pbf.s,
self.pb.pbf.sTc,
self.pb.pbf.sTc_old,
t - t_off,
self.pb.pbf.ti.cycle,
self.pb.pbf.ti.cycleerror,
self.pb.pbf.eps_periodic,
check=self.pb.pbf.periodic_checktype,
inioutpath=self.pb.pbf.output_path_0D,
nm=self.pb.pbs.simname,
induce_pert_after_cycl=self.pb.pbf.perturb_after_cylce)
# induce some disease/perturbation for cardiac cycle (i.e. valve stenosis or leakage)
if self.pb.pbf.perturb_type is not None and not self.pb.pbf.have_induced_pert:
self.pb.induce_perturbation()
# write output and restart info
self.pb.pbs.io.write_output(self.pb.pbs, N=N, t=t)
# raw txt file output of 0D model quantities
if self.pb.pbf.write_results_every_0D > 0 and N % self.pb.pbf.write_results_every_0D == 0:
self.pb.pbf.cardvasc0D.write_output(self.pb.pbf.output_path_0D,
t, self.pb.pbf.s_mid,
self.pb.pbf.aux_mid,
self.pb.pbs.simname)
# write 0D restart info - old and new quantities are the same at this stage (except cycle values sTc)
if self.pb.pbs.io.write_restart_every > 0 and N % self.pb.pbs.io.write_restart_every == 0:
self.pb.pbf.writerestart(self.pb.pbs.simname, N)
if is_periodic:
if self.pb.comm.rank == 0:
print(
"Periodicity reached after %i heart cycles with cycle error %.4f! Finished. :-)"
% (self.pb.pbf.ti.cycle[0] - 1,
self.pb.pbf.ti.cycleerror[0]))
sys.stdout.flush()
break
if self.pb.comm.rank == 0: # only proc 0 should print this
print('Time for computation: %.4f s (= %.2f min)' %
(time.time() - start, (time.time() - start) / 60.))
sys.stdout.flush()
# for multiscale G&R analysis
def set_homeostatic_threshold(self, t):
# time is absolute time (should only be set in first cycle)
eps = 1.0e-14
if t >= self.pb.t_gandr_setpoint - eps and t < self.pb.t_gandr_setpoint + self.pb.pbs.dt - eps:
if self.pb.comm.rank == 0:
print('Set homeostatic growth thresholds...')
sys.stdout.flush()
time.sleep(1)
growth_thresolds = []
for n in range(self.pb.pbs.num_domains):
if self.pb.pbs.mat_growth[n]:
growth_settrig = self.pb.pbs.constitutive_models[
'MAT' + str(n + 1) + '']['growth']['growth_settrig']
if growth_settrig == 'fibstretch':
growth_thresolds.append(self.pb.pbs.ma[n].fibstretch_e(
self.pb.pbs.ki.C(self.pb.pbs.u), self.pb.pbs.theta,
self.pb.pbs.fib_func[0]))
elif growth_settrig == 'volstress':
growth_thresolds.append(
tr(self.pb.pbs.ma[n].M_e(
self.pb.pbs.u,
self.pb.pbs.p,
self.pb.pbs.ki.C(self.pb.pbs.u),
ivar=self.pb.pbs.internalvars)))
else:
raise NameError(
"Unknown growth trigger to be set as homeostatic threshold!"
)
else:
growth_thresolds.append(as_ufl(0))
growth_thres_proj = project(growth_thresolds,
self.pb.pbs.Vd_scalar, self.pb.pbs.dx_)
self.pb.pbs.growth_thres.vector.ghostUpdate(
addv=PETSc.InsertMode.ADD, mode=PETSc.ScatterMode.REVERSE)
self.pb.pbs.growth_thres.interpolate(growth_thres_proj)
# for multiscale G&R analysis
def set_growth_trigger(self, t):
# time is relative time (w.r.t. heart cycle)
eps = 1.0e-14
if t >= self.pb.t_gandr_setpoint - eps and t < self.pb.t_gandr_setpoint + self.pb.pbs.dt - eps:
if self.pb.comm.rank == 0:
print('Set growth triggers...')
sys.stdout.flush()
time.sleep(1)
self.pb.pbs.u_set.vector.axpby(1.0, 0.0, self.pb.pbs.u.vector)
self.pb.pbs.u_set.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
if self.pb.pbs.incompressible_2field:
self.pb.pbs.p_set.vector.axpby(1.0, 0.0, self.pb.pbs.p.vector)
self.pb.pbs.p_set.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT,
mode=PETSc.ScatterMode.FORWARD)
self.pb.pbs.tau_a_set.vector.axpby(1.0, 0.0,
self.pb.pbs.tau_a.vector)
self.pb.pbs.tau_a_set.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
if self.pb.pbs.have_frank_starling:
self.pb.pbs.amp_old_set.vector.axpby(
1.0, 0.0, self.pb.pbs.amp_old.vector)
self.pb.pbs.amp_old_set.vector.ghostUpdate(
addv=PETSc.InsertMode.INSERT,
mode=PETSc.ScatterMode.FORWARD)
self.pb.pbf.s_set.axpby(1.0, 0.0, self.pb.pbf.s)