diff --git a/.gitignore b/.gitignore index d7aab593..e98bf815 100644 --- a/.gitignore +++ b/.gitignore @@ -2,6 +2,7 @@ dist/ build/ libext/ tests/tmp/ +doc/examples/tmp/ __pycache__/ .pytest_cache/ *.egg-info/ diff --git a/doc/examples/flow0d_heart_cycle.py b/doc/examples/flow0d_heart_cycle.py new file mode 100644 index 00000000..0f478cf1 --- /dev/null +++ b/doc/examples/flow0d_heart_cycle.py @@ -0,0 +1,232 @@ +#!/usr/bin/env python3 + +""" +This example demonstrates how to simulate a cardiac cycle using a lumped-parameter (0D) model for the heart chambers and the entire circulation. Multiple heart beats are run +until a periodic state criterion is met (which compares variable values at the beginning to those at the end of a cycle, and stops if the relative change is less than +a specified value, here 'eps_periodic' in the TIME_PARAMS dictionary). The problem is set up such that periodicity is reached after 5 heart cycles. + +INSTRUCTIONS: +Run the simulation, either in one of the provided Docker containers or using your own FEniCSx/Ambit installation, using the command +python3 flow0d_heart_cycle.py + +For postprocessing of the time courses of pressures, volumes, and fluxes of the 0D model, make sure to have Gnuplot (and TeX) installed. +Navigate to the output folder (tmp/) and execute the script flow0d_plot.py (which lies in ambit/src/ambit_fe/postprocess/): +flow0d_plot.py -s flow0d_heart_cycle -n 100 +A folder 'plot_flow0d_heart_cycle' is created inside tmp/. Look at the results of pressures (p), volumes (V), and fluxes (q,Q) over time. +Subscripts v, at, ar, ven refer to 'ventricular', 'atrial', 'arterial', and 'venous', respectively. Superscripts l, r, sys, pul refer to 'left', 'right', 'systemic', and +'pulmonary', respectively. +Try to understand the time courses of the respective pressures, as well as the plots of ventricular pressure over volume. +Check that the overall system volume is constant and around 4-5 liters. +""" + +import ambit_fe + +import sys +import numpy as np +from pathlib import Path + + +def main(): + + basepath = str(Path(__file__).parent.absolute()) + + """ + Parameters for input/output + """ + IO_PARAMS = {# problem type 'flow0d' indicates a pure ODE problem of pressure-flow relationships + 'problem_type' : 'flow0d', + # at which step frequency to write results (set to 0 in order to not write any output) + 'write_results_every' : 1, + # where to write the output to + 'output_path' : basepath+'/tmp', + # the 'midfix' for all simulation result file names: will be results__.txt + 'simname' : 'flow0d_heart_cycle'} + + """ + Parameters for the nonlinear solution scheme (Newton solver) + """ + SOLVER_PARAMS = {# residual and increment tolerances + 'tol_res' : 1.0e-8, + 'tol_inc' : 1.0e-8} + + """ + Parameters for the 0D model time integration scheme + """ + TIME_PARAMS = {'maxtime' : 10*1.0, + 'numstep' : 10*100, + # the 0D model time integration scheme: we use a One-Step-theta method with theta = 0.5, which corresponds to the trapezoidal rule + 'timint' : 'ost', + 'theta_ost' : 0.5, + # do initial time step using backward scheme (theta=1), to avoid fluctuations for quantities whose d/dt is zero + 'initial_backwardeuler' : True, + # the initial conditions of the 0D ODE model (defined below) + 'initial_conditions' : init(), + # the periodic state criterion tolerance + 'eps_periodic' : 0.03, + # which variables to check for periodicity (default, 'allvar') + 'periodic_checktype' : ['allvar']} + + MODEL_PARAMS = {# the type of 0D model: 'syspul' refers to the closed-loop systemic+pulmonary circulation model + 'modeltype' : 'syspul', + # the parameters of the 0D model (defined below) + 'parameters' : param(), + # models for cardiac chambers: all four are 0D time-varying elastance models, activated with different time curves (curve no. 2 for ventricles, curve no. 1 for atria, cf. below) + 'chamber_models' : {'lv' : {'type' : '0D_elast', 'activation_curve' : 2}, + 'rv' : {'type' : '0D_elast', 'activation_curve' : 2}, + 'la' : {'type' : '0D_elast', 'activation_curve' : 1}, + 'ra' : {'type' : '0D_elast', 'activation_curve' : 1}}, + # models for valves: all are piecewise-linear pressure-dependent ('pwlin_pres', default) + 'valvelaws' : {'av' : ['pwlin_pres'], # aortic valve + 'mv' : ['pwlin_pres'], # mitral valve + 'pv' : ['pwlin_pres'], # pulmonary valve + 'tv' : ['pwlin_pres']}} # tricuspid valve + + + # define your time curves here (syntax: tcX refers to curve X) + class time_curves(): + + # the activation curves for the contraction of the 0D atria + def tc1(self, t): + + act_dur = 2.*param()['t_ed'] + t0 = 0. + + if t >= t0 and t <= t0 + act_dur: + return 0.5*(1.-np.cos(2.*np.pi*(t-t0)/act_dur)) + else: + return 0.0 + + # the activation curves for the contraction of the 0D ventricles + def tc2(self, t): + + act_dur = 1.8*(param()['t_es'] - param()['t_ed']) + t0 = param()['t_ed'] + + if t >= t0 and t <= t0 + act_dur: + return 0.5*(1.-np.cos(2.*np.pi*(t-t0)/act_dur)) + else: + return 0.0 + + + # problem setup + problem = ambit_fe.ambit_main.Ambit(IO_PARAMS, TIME_PARAMS, SOLVER_PARAMS, constitutive_params=MODEL_PARAMS, time_curves=time_curves()) + + # solve time-dependent problem + problem.solve_problem() + + + +def init(): + + # values in kg-mm-s unit system + + return {'q_vin_l_0' : 0.0, # initial left ventricular in-flow + 'p_at_l_0' : 0.599950804034, # initial left atrial pressure + 'q_vout_l_0' : 0.0, # initial left ventricular out-flow + 'p_v_l_0' : 0.599950804034, # initial left ventricular pressure + 'p_ar_sys_0' : 9.68378038166, # initial systemic arterial pressure + 'q_ar_sys_0' : 0.0, # initial systemic arterial flux + 'p_ven_sys_0' : 2.13315841434, # initial systemic venous pressure + 'q_ven_sys_0' : 0.0, # initial systemic venous flux + 'q_vin_r_0' : 0.0, # initial right ventricular in-flow + 'p_at_r_0' : 0.0933256806275, # initial right atrial pressure + 'q_vout_r_0' : 0.0, # initial right ventricular out-flow + 'p_v_r_0' : 0.0933256806275, # initial right ventricular pressure + 'p_ar_pul_0' : 3.22792679389, # initial pulmonary arterial pressure + 'q_ar_pul_0' : 0.0, # initial pulmonary arterial flux + 'p_ven_pul_0' : 1.59986881076, # initial pulmonary venous pressure + 'q_ven_pul_0' : 0.0} # initial pulmonary venous flux + + +def param(): + + # parameters in kg-mm-s unit system + + R_ar_sys = 120.0e-6 # systemic arterial resistance + tau_ar_sys = 1.0311433159 # systemic arterial Windkessel time constant + tau_ar_pul = 0.3 # pulmonary arterial resistance + + # Diss Hirschvogel tab. 2.7 + C_ar_sys = tau_ar_sys/R_ar_sys # systemic arterial compliance + Z_ar_sys = R_ar_sys/20. # systemic arterial characteristic impedance + R_ven_sys = R_ar_sys/5. # systemic venous resistance + C_ven_sys = 30.*C_ar_sys # systemic venous compliance + R_ar_pul = R_ar_sys/8. # pulmonary arterial resistance + C_ar_pul = tau_ar_pul/R_ar_pul # pulmonary arterial compliance + R_ven_pul = R_ar_pul # pulmonary venous resistance + C_ven_pul = 2.5*C_ar_pul # pulmonary venous resistance + + L_ar_sys = 0.667e-6 # systemic arterial inertance + L_ven_sys = 0. # systemic venous inertance + L_ar_pul = 0. # pulmonary arterial inertance + L_ven_pul = 0. # pulmonary venous inertance + + # timings + t_ed = 0.2 # end-diastolic time + t_es = 0.53 # end-systolic time + T_cycl = 1.0 # cardiac cycle time + + # atrial elastances + E_at_max_l = 2.9e-5 # maximum left atrial elastance + E_at_min_l = 9.0e-6 # minimum left atrial elastance + E_at_max_r = 1.8e-5 # maximum right atrial elastance + E_at_min_r = 8.0e-6 # minimum right atrial elastance + # ventricular elastances + E_v_max_l = 30.0e-5 # maximum left ventricular elastance + E_v_min_l = 12.0e-6 # minimum left ventricular elastance + E_v_max_r = 20.0e-5 # maximum right ventricular elastance + E_v_min_r = 10.0e-6 # minimum right ventricular elastance + + + return {'R_ar_sys' : R_ar_sys, + 'C_ar_sys' : C_ar_sys, + 'L_ar_sys' : L_ar_sys, + 'Z_ar_sys' : Z_ar_sys, + 'R_ar_pul' : R_ar_pul, + 'C_ar_pul' : C_ar_pul, + 'L_ar_pul' : L_ar_pul, + 'R_ven_sys' : R_ven_sys, + 'C_ven_sys' : C_ven_sys, + 'L_ven_sys' : L_ven_sys, + 'R_ven_pul' : R_ven_pul, + 'C_ven_pul' : C_ven_pul, + 'L_ven_pul' : L_ven_pul, + # atrial elastances + 'E_at_max_l' : E_at_max_l, + 'E_at_min_l' : E_at_min_l, + 'E_at_max_r' : E_at_max_r, + 'E_at_min_r' : E_at_min_r, + # ventricular elastances + 'E_v_max_l' : E_v_max_l, + 'E_v_min_l' : E_v_min_l, + 'E_v_max_r' : E_v_max_r, + 'E_v_min_r' : E_v_min_r, + # valve resistances + 'R_vin_l_min' : 1.0e-6, # mitral valve open resistance + 'R_vin_l_max' : 1.0e1, # mitral valve closed resistance + 'R_vout_l_min' : 1.0e-6, # aortic valve open resistance + 'R_vout_l_max' : 1.0e1, # aortic valve closed resistance + 'R_vin_r_min' : 1.0e-6, # tricuspid valve open resistance + 'R_vin_r_max' : 1.0e1, # tricuspid valve closed resistance + 'R_vout_r_min' : 1.0e-6, # pulmonary valve open resistance + 'R_vout_r_max' : 1.0e1, # pulmonary valve closed resistance + # timings + 't_ed' : t_ed, + 't_es' : t_es, + 'T_cycl' : T_cycl, + # unstressed compartment volumes (only for post-processing, since 0D model is formulated in fluxes = dVolume/dt) + 'V_at_l_u' : 5e3, # unstressed left atrial volume + 'V_at_r_u' : 4e3, # unstressed right atrial volume + 'V_v_l_u' : 10e3, # unstressed left ventricular volume + 'V_v_r_u' : 8e3, # unstressed right ventricular volume + 'V_ar_sys_u' : 611e3, # unstressed systemic arterial volume + 'V_ar_pul_u' : 123e3, # unstressed pulmonary arterial volume + 'V_ven_sys_u' : 2596e3, # unstressed systemic venous volume + 'V_ven_pul_u' : 120e3} # unstressed pulmonary venous volume + + + + +if __name__ == "__main__": + + main() diff --git a/doc/examples/input/fib_fiber_indices_nodal.txt b/doc/examples/input/fib_fiber_indices_nodal.txt new file mode 100644 index 00000000..291777c5 --- /dev/null +++ b/doc/examples/input/fib_fiber_indices_nodal.txt @@ -0,0 +1,2609 @@ +106 -0.20220215676290684 0.9211510778743675 -0.33255823479703506 +25 -0.019972145377264883 0.025932145310121474 0.9994641750701444 +26 -0.015536915637324122 0.054332860359199944 0.9984019954595778 +616 -0.02386096728423881 0.05680663492148137 0.9981000252826159 +1448 -0.22933584123204745 0.9197511844272548 -0.3185323071072248 +105 -0.343743231769059 0.881633384362821 -0.32336228319011107 +1447 -0.09611015767844333 0.9392792795787905 -0.3294195995155318 +617 -0.023819815585153614 0.014928115481945586 0.9996048057875908 +1500 -0.14637118393368923 0.9408180096447101 -0.3056745806278579 +107 -0.07003350757317289 0.9368439871172223 -0.34266405066669103 +553 -0.03103842915993965 0.02647442041342038 0.9991675139730359 +429 -0.028324110747055542 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doc/examples/input/heart3D_boundary.xdmf index d6d8a584..90e6c81d 100644 --- a/tests/input/heart3D_boundary.xdmf +++ b/doc/examples/input/heart3D_boundary.xdmf @@ -11519,19 +11519,5 @@ - - - - 13 - 14 - - - - - 1 - 2 - - - diff --git a/tests/input/heart3D_domain.xdmf b/doc/examples/input/heart3D_domain.xdmf similarity index 100% rename from tests/input/heart3D_domain.xdmf rename to doc/examples/input/heart3D_domain.xdmf diff --git a/doc/examples/solid_flow0d_heart_cycle.py b/doc/examples/solid_flow0d_heart_cycle.py new file mode 100644 index 00000000..b989b7c4 --- /dev/null +++ b/doc/examples/solid_flow0d_heart_cycle.py @@ -0,0 +1,351 @@ +#!/usr/bin/env python3 + +""" +This example demonstrates how to set up and simulate a two-chamber (left and right ventricular) solid mechanics heart model coupled to a closed-loop +0D circulatory system. A full dynamic heart cycle of duration 1 s is simulated, where the active contraction is modeled by a prescribed active stress approach. +Passive material behavior of the heart muscle is governed by the Holzapfel-Ogden anisotropic strain energy function and a strain rate-dependent viscous +model. +We start the simulation with "prestressing" using the MULF method (Gee et al. 2010, Schein and Gee 2021), which allows to imprint loads without changing the geometry, +where the solid is loaded to the initial left and right ventricular pressures. +Thereafter, we kickstart the dynamic simulation with passive ventricular filling by the systole of the atria (0D chamber models). Ventricular systole +happens in t \in [0.2 s, 0.53 s], hence lasting a third of the whole cycle time. After systole, the heart relaxes and eventually fills to about the same pressure +as it has been initialized to. + +NOTE: For demonstrative purposes, a fairly coarse finite element discretization is chosen here, which by no means yields a spatially converged solution and which +may be prone to locking phenomena. The user may increse the parameter 'order_disp' in the FEM_PARAMS section from 1 to 2 (and maybe increase 'quad_degree' to 6) +such that quadratic finite element ansatz functions (instead of linear ones) are used. While this will increase accuracy and mitigate locking, computation time will +increase. + +INSTRUCTIONS: +Run the simulation, either in one of the provided Docker containers or using your own FEniCSx/Ambit installation, using the command +mpiexec -n 1 python3 solid_flow0d_heart_cycle.py +It is fully sufficient to use one core (mpiexec -n 1) for the presented setup, while you might want to use more (e.g., mpiexec -n 4) is you increase 'order_disp' to 2. + +Open the results file results_solid_flow0d_heart_cycle_displacement.xdmf in Paraview, and visualize the deformation over the heart cycle. + +For postprocessing of the time courses of pressures, volumes, and fluxes of the 0D model, make sure to have Gnuplot (and TeX) installed. +Navigate to the output folder (tmp/) and execute the script flow0d_plot.py (which lies in ambit/src/ambit_fe/postprocess/): +flow0d_plot.py -s solid_flow0d_heart_cycle +A folder 'plot_solid_flow0d_heart_cycle' is created inside tmp/. Look at the results of pressures (p), volumes (V), and fluxes (q,Q) over time. +Subscripts v, at, ar, ven refer to 'ventricular', 'atrial', 'arterial', and 'venous', respectively. Superscripts l, r, sys, pul refer to 'left', 'right', 'systemic', and +'pulmonary', respectively. +Try to understand the time courses of the respective pressures, as well as the plots of ventricular pressure over volume. +Check that the overall system volume is constant and around 4-5 liters. +""" + +import ambit_fe + +import sys +import numpy as np +from pathlib import Path + + +def main(): + + basepath = str(Path(__file__).parent.absolute()) + + + """ + Parameters for input/output + """ + IO_PARAMS = {# problem type 'solid_flow0d' indicates a coupling of the individual problems 'solid' and 'flow0d' + 'problem_type' : 'solid_flow0d', + # the meshes for the domain and boundary topology are specified separately + 'mesh_domain' : basepath+'/input/heart3D_domain.xdmf', + 'mesh_boundary' : basepath+'/input/heart3D_boundary.xdmf', + # since we use fiber orientations in both the passive as well as active model, we need to specify those fields + 'fiber_data' : [basepath+'/input/fib_fiber_indices_nodal.txt', + basepath+'/input/fib_sheet_indices_nodal.txt'], + 'order_fib_input' : 1, + # at which step frequency to write results (set to 0 in order to not write any output) + 'write_results_every' : 1, + # where to write the output to + 'output_path' : basepath+'/tmp/', + # which results to write: here, all 3D fields need to be specified, while the 0D model results are output nevertheless + 'results_to_write' : ['displacement','fibers'], + # the 'midfix' for all simulation result file names: will be results__.xdmf/.h5 + 'simname' : 'solid_flow0d_heart_cycle'} + + """ + Parameters for the linear and nonlinear solution schemes + """ + SOLVER_PARAMS = {# this specifies which linear solution strategy to use; since this problem has less than 10'000 degrees of freedom, we comfortably can use a direct solver + 'solve_type' : 'direct', + # residual and increment tolerances: first value for the solid mechanics problem (momentum balance), second value for the 3D-0D constraint problem + 'tol_res' : [1e-8, 1e-6], + 'tol_inc' : [1e-8, 1e-6], + # subsolver tolerances for the 0D model solver: tolerances for residual and increment + 'subsolver_params' : {'tol_res' : 1e-6, + 'tol_inc' : 1e-6}} + + """ + Parameters for the solid mechanics time integration scheme, plus the global time parameters + """ + TIME_PARAMS_SOLID = {# the maximum simulation time - here, we want our heart cycle to last 1 s + 'maxtime' : 1.0, + # the number of time steps which the simulation time is divided into - so here, a time step lasts 1/500 s = 0.002 s = 2 ms + 'numstep' : 500, + # the solid mechanics time integration scheme: we use the Generalized-alpha method with a spectral radius of 0.8 + 'timint' : 'genalpha', + 'rho_inf_genalpha' : 0.8} + + """ + Parameters for the 0D model time integration scheme + """ + TIME_PARAMS_FLOW0D = {# the 0D model time integration scheme: we use a One-Step-theta method with theta = 0.5, which corresponds to the trapezoidal rule + 'timint' : 'ost', + 'theta_ost' : 0.5, + # do initial time step using backward scheme (theta=1), to avoid fluctuations for quantities whose d/dt is zero + 'initial_backwardeuler' : True, + # the initial conditions of the 0D ODE model (defined below) + 'initial_conditions' : init()} + + """ + Parameters for the 0D model + """ + MODEL_PARAMS_FLOW0D = {# the type of 0D model: 'syspul' refers to the closed-loop systemic+pulmonary circulation model + 'modeltype' : 'syspul', + # the parameters of the 0D model (defined below) + 'parameters' : param(), + # The 0D model is setup in a modular fashion which allows each of the four cardiac chambers to be either modeled as purely 0D (time-varying elastance models), + # as a 3D solid mechanics chamber, or as a 3D fluid domain. + # Since we have a biventricular heart model, our left and right ventricle (lv and rv, respectively) are of type '3D_solid', whereas the left and right atrium + # (la and ra, respectively) are treated as 0D chambers. Their elastance are controlled by time curve no. 2 (cf. below), which mimics the atrial systole. + 'chamber_models' : {'lv' : {'type' : '3D_solid'}, + 'rv' : {'type' : '3D_solid'}, + 'la' : {'type' : '0D_elast', 'activation_curve' : 2}, + 'ra' : {'type' : '0D_elast', 'activation_curve' : 2}}} + """ + Finite element parameters and parameters relating to the prestress + """ + FEM_PARAMS = {# the order of the finite element ansatz functions for the displacement + 'order_disp' : 1, + # the quadrature degree (should be > 1 but can be only 2 here for linear tetrahedral finite elements) + 'quad_degree' : 2, + # whether we want to model the heart as purely incompressible (would involve a 2-field functional with additional pressure degrees of freedom) + 'incompressible_2field' : False, + # the prestress settings: initial prestressing with the MULF method using 5 load steps and PTC (pseudo-transient continuation) for more stable load stepping + 'prestress_initial' : True, + 'prestress_numstep' : 5, + 'prestress_ptc' : True} + + """ + 3D-0D coupling parameters + """ + COUPLING_PARAMS = {# the surfaces IDs which couple to the 0D world: 1 is the left ventricle, 2 is the right (order here would be lv, rv, la, ra) + 'surface_ids' : [[1],[2]], + # the coupling type: 'monolithic_lagrange' here is a more general scheme that enforces equality of 3D and 0D fluxes/volumes via (Lagrange) multipliers, outsourcing the 0D + # solve to a sub-solver in each nonlinear iteration, whereas 'monolithic_direct' would embed the 0D system of equations directly into the monolithic system matrix + 'coupling_type' : 'monolithic_lagrange', + # for 'monolithic_lagrange', we need the pressures to be the exchanged quantities between 3D and 0D world (being the Lagrange multipliers) + 'coupling_quantity' : ['pressure','pressure'], + # the coupling variables which are enforced between 3D and 0D: can be volume or flux + 'variable_quantity' : ['flux','flux']} + + """ + Constitutive parameters for the 3D solid mechanics model of the heart + """ + MATERIALS = {# Here, we only have one region defined (hence only MAT1) - while, in principal, each element could be associated to a different material. + # the classical Holzapfel-Ogden material for passive myocardium (Holzapfel and Ogden 2009), in its deviatoric version (only for the isotropic part) + 'MAT1' : {'holzapfelogden_dev' : {'a_0' : 0.059, + 'b_0' : 8.023, + 'a_f' : 18.472, + 'b_f' : 16.026, + 'a_s' : 2.481, + 'b_s' : 11.120, + 'a_fs' : 0.216, + 'b_fs' : 11.436}, + # a volumetric material penalizing volume changes, yielding a nearly incompressible behavior + 'sussmanbathe_vol' : {'kappa' : 1e3}, + # a strain rate-dependent material + 'visco_green' : {'eta' : 0.1}, + # the active stress law that is exerted along the muscle fiber direction and controlled by time curve no. 1 (cf. below) + # this model is reponsible for the contraction of the heart + 'active_fiber' : {'sigma0' : 100.0, 'alpha_max' : 15.0, 'alpha_min' : -30.0, 'activation_curve' : 1}, + # the inertia: density + 'inertia' : {'rho0' : 1e-6}}} + + + """ + Time curves, e.g. any prescribed time-controlled/-varying loads or functions + """ + class time_curves(): + + # the activation curve for the contraction of the 3D heart ventricles + def tc1(self, t): + + K = 5. + t_contr, t_relax = 0.2, 0.53 + + alpha_max = MATERIALS['MAT1']['active_fiber']['alpha_max'] + alpha_min = MATERIALS['MAT1']['active_fiber']['alpha_min'] + + c1 = t_contr + alpha_max/(K*(alpha_max-alpha_min)) + c2 = t_relax - alpha_max/(K*(alpha_max-alpha_min)) + + # Diss Hirschvogel eq. 2.101 + return (K*(t-c1)+1.)*((K*(t-c1)+1.)>0.) - K*(t-c1)*((K*(t-c1))>0.) - K*(t-c2)*((K*(t-c2))>0.) + (K*(t-c2)-1.)*((K*(t-c2)-1.)>0.) + + # the activation curves for the contraction of the 0D atria + def tc2(self, t): + + act_dur = 2.*param()['t_ed'] + t0 = 0. + + if t >= t0 and t <= t0 + act_dur: + return 0.5*(1.-np.cos(2.*np.pi*(t-t0)/act_dur)) + else: + return 0.0 + + # The curves that contoll the prestress in each ventricular chamber: Note that we need a negative sign, since the pressure + # acts against the surface outward normal. + # We ramp up these loads linearly during the 5 prestress steps. Since the prestress phase is quasi-static, the results only + # depend on the end value, not on the type of ramp-up. Hence, any ramp-up that converges can be used. + def tc3(self, t): # LV + return -init()['p_v_l_0']*t + + def tc4(self, t): # RV + return -init()['p_v_r_0']*t + + + """ + Boundary conditions + """ + BC_DICT = { # the prestress boundary conditions, using time curves no. 3 and 4 + 'neumann_prestress' : [{'id' : [1], 'dir' : 'normal_ref', 'curve' : 3}, + {'id' : [2], 'dir' : 'normal_ref', 'curve' : 4}], + # Robin conditions (springs and dashpots) are applied to the heart's epicardium (surface ID 3) as well as to the base (surface ID 4), + # either acting in reference normal direction ('normal_ref') or in reference cartesian directions ('xyz_ref'). + # The parameters are chosen according to Hirschvogel 2018 (PhD Thesis), which yielded acceptable results regarding base and epicardial + # movement. + 'robin' : [{'type' : 'spring', 'id' : [3], 'dir' : 'normal_ref', 'stiff' : 0.075}, + {'type' : 'dashpot', 'id' : [3], 'dir' : 'normal_ref', 'visc' : 0.005}, + {'type' : 'spring', 'id' : [4], 'dir' : 'normal_ref', 'stiff' : 2.5}, + {'type' : 'dashpot', 'id' : [4], 'dir' : 'normal_ref', 'visc' : 0.0005}, + {'type' : 'spring', 'id' : [4], 'dir' : 'xyz_ref', 'stiff' : 0.25}, + {'type' : 'dashpot', 'id' : [4], 'dir' : 'xyz_ref', 'visc' : 0.0005}] } + + # Pass parameters to Ambit to set up the problem + problem = ambit_fe.ambit_main.Ambit(IO_PARAMS, [TIME_PARAMS_SOLID, TIME_PARAMS_FLOW0D], SOLVER_PARAMS, FEM_PARAMS, [MATERIALS, MODEL_PARAMS_FLOW0D], BC_DICT, time_curves=time_curves(), coupling_params=COUPLING_PARAMS) + + # Call the Ambit solver to solve the problem + problem.solve_problem() + + + +def init(): + + # values in kg-mm-s unit system + + return {'Q_v_l_0' : 0.0, # initial left ventricular flux + 'q_vin_l_0' : 0.0, # initial left ventricular in-flow + 'p_at_l_0' : 0.599950804034, # initial left atrial pressure + 'q_vout_l_0' : 0.0, # initial left ventricular out-flow + 'p_v_l_0' : 0.599950804034, # initial left ventricular pressure (will be initial value of Lagrange multiplier!) + 'p_ar_sys_0' : 9.68378038166, # initial systemic arterial pressure + 'q_ar_sys_0' : 0.0, # initial systemic arterial flux + 'p_ven_sys_0' : 2.13315841434, # initial systemic venous pressure + 'q_ven_sys_0' : 0.0, # initial systemic venous flux + 'Q_v_r_0' : 0.0, # initial right ventricular flux + 'q_vin_r_0' : 0.0, # initial right ventricular in-flow + 'p_at_r_0' : 0.0933256806275, # initial right atrial pressure + 'q_vout_r_0' : 0.0, # initial right ventricular out-flow + 'p_v_r_0' : 0.0933256806275, # initial right ventricular pressure (will be initial value of Lagrange multiplier!) + 'p_ar_pul_0' : 3.22792679389, # initial pulmonary arterial pressure + 'q_ar_pul_0' : 0.0, # initial pulmonary arterial flux + 'p_ven_pul_0' : 1.59986881076, # initial pulmonary venous pressure + 'q_ven_pul_0' : 0.0} # initial pulmonary venous flux + + +def param(): + + # parameters in kg-mm-s unit system + + R_ar_sys = 120.0e-6 # systemic arterial resistance + tau_ar_sys = 1.0311433159 # systemic arterial Windkessel time constant + tau_ar_pul = 0.3 # pulmonary arterial resistance + + # Diss Hirschvogel tab. 2.7 + C_ar_sys = tau_ar_sys/R_ar_sys # systemic arterial compliance + Z_ar_sys = R_ar_sys/20. # systemic arterial characteristic impedance + R_ven_sys = R_ar_sys/5. # systemic venous resistance + C_ven_sys = 30.*C_ar_sys # systemic venous compliance + R_ar_pul = R_ar_sys/8. # pulmonary arterial resistance + C_ar_pul = tau_ar_pul/R_ar_pul # pulmonary arterial compliance + R_ven_pul = R_ar_pul # pulmonary venous resistance + C_ven_pul = 2.5*C_ar_pul # pulmonary venous resistance + + L_ar_sys = 0.667e-6 # systemic arterial inertance + L_ven_sys = 0. # systemic venous inertance + L_ar_pul = 0. # pulmonary arterial inertance + L_ven_pul = 0. # pulmonary venous inertance + + # timings + t_ed = 0.2 # end-diastolic time + t_es = 0.53 # end-systolic time + T_cycl = 1.0 # cardiac cycle time + + # atrial elastances + E_at_max_l = 2.9e-5 # maximum left atrial elastance + E_at_min_l = 9.0e-6 # minimum left atrial elastance + E_at_max_r = 1.8e-5 # maximum right atrial elastance + E_at_min_r = 8.0e-6 # minimum right atrial elastance + # ventricular elastances - NOT used in this example, since the ventricles are 3D bodies + E_v_max_l = 30.0e-5 # maximum left ventricular elastance + E_v_min_l = 12.0e-6 # minimum left ventricular elastance + E_v_max_r = 20.0e-5 # maximum right ventricular elastance + E_v_min_r = 10.0e-6 # minimum right ventricular elastance + + + return {'R_ar_sys' : R_ar_sys, + 'C_ar_sys' : C_ar_sys, + 'L_ar_sys' : L_ar_sys, + 'Z_ar_sys' : Z_ar_sys, + 'R_ar_pul' : R_ar_pul, + 'C_ar_pul' : C_ar_pul, + 'L_ar_pul' : L_ar_pul, + 'R_ven_sys' : R_ven_sys, + 'C_ven_sys' : C_ven_sys, + 'L_ven_sys' : L_ven_sys, + 'R_ven_pul' : R_ven_pul, + 'C_ven_pul' : C_ven_pul, + 'L_ven_pul' : L_ven_pul, + # atrial elastances + 'E_at_max_l' : E_at_max_l, + 'E_at_min_l' : E_at_min_l, + 'E_at_max_r' : E_at_max_r, + 'E_at_min_r' : E_at_min_r, + # ventricular elastances + 'E_v_max_l' : E_v_max_l, + 'E_v_min_l' : E_v_min_l, + 'E_v_max_r' : E_v_max_r, + 'E_v_min_r' : E_v_min_r, + # valve resistances + 'R_vin_l_min' : 1.0e-6, # mitral valve open resistance + 'R_vin_l_max' : 1.0e1, # mitral valve closed resistance + 'R_vout_l_min' : 1.0e-6, # aortic valve open resistance + 'R_vout_l_max' : 1.0e1, # aortic valve closed resistance + 'R_vin_r_min' : 1.0e-6, # tricuspid valve open resistance + 'R_vin_r_max' : 1.0e1, # tricuspid valve closed resistance + 'R_vout_r_min' : 1.0e-6, # pulmonary valve open resistance + 'R_vout_r_max' : 1.0e1, # pulmonary valve closed resistance + # timings + 't_ed' : t_ed, + 't_es' : t_es, + 'T_cycl' : T_cycl, + # unstressed compartment volumes (only for post-processing, since 0D model is formulated in fluxes = dVolume/dt) + 'V_at_l_u' : 5e3, # unstressed left atrial volume + 'V_at_r_u' : 4e3, # unstressed right atrial volume + 'V_v_l_u' : 10e3, # unstressed left ventricular volume - NOT used here, since from 3D + 'V_v_r_u' : 8e3, # unstressed right ventricular volume - NOT used here, since from 3D + 'V_ar_sys_u' : 611e3, # unstressed systemic arterial volume + 'V_ar_pul_u' : 123e3, # unstressed pulmonary arterial volume + 'V_ven_sys_u' : 2596e3, # unstressed systemic venous volume + 'V_ven_pul_u' : 120e3} # unstressed pulmonary venous volume + + + + +if __name__ == "__main__": + + main() diff --git a/src/ambit_fe/ale/ale_kinematics_constitutive.py b/src/ambit_fe/ale/ale_kinematics_constitutive.py index ca3f0327..81073545 100644 --- a/src/ambit_fe/ale/ale_kinematics_constitutive.py +++ b/src/ambit_fe/ale/ale_kinematics_constitutive.py @@ -9,7 +9,9 @@ import ufl from .ale_material import materiallaw -# ALE kinematics and constitutive class +""" +ALE kinematics and constitutive class +""" class constitutive: diff --git a/src/ambit_fe/ale/ale_main.py b/src/ambit_fe/ale/ale_main.py index c7c015e9..c5d02e6f 100644 --- a/src/ambit_fe/ale/ale_main.py +++ b/src/ambit_fe/ale/ale_main.py @@ -23,8 +23,9 @@ from ..base import problem_base, solver_base - -# Arbitrary Lagrangian Eulerian (ALE) mechanics problem +""" +Arbitrary Lagrangian Eulerian (ALE) mechanics problem +""" class AleProblem(problem_base): @@ -57,6 +58,7 @@ def __init__(self, io_params, time_params, fem_params, constitutive_models, bc_d self.dx = ufl.Measure("dx", domain=self.io.mesh_master, metadata={'quadrature_degree': self.quad_degree}) self.ds = ufl.Measure("ds", domain=self.io.mesh_master, subdomain_data=self.io.mt_b1_master, metadata={'quadrature_degree': self.quad_degree}) + self.de = ufl.Measure("ds", domain=self.io.mesh_master, subdomain_data=self.io.mt_b2_master, metadata={'quadrature_degree': self.quad_degree}) self.localsolve = False # no idea what might have to be solved locally... self.prestress_initial = False # guess prestressing in ALE is somehow senseless... @@ -180,11 +182,11 @@ def set_variational_forms(self): # external virtual work (from Neumann or Robin boundary conditions, body forces, ...) w_neumann, w_body, w_robin = ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0) if 'neumann' in self.bc_dict.keys(): - w_neumann = self.bc.neumann_bcs(self.bc_dict['neumann'], self.V_d, self.Vd_scalar, self.ds, funcs_to_update=self.ti.funcs_to_update, funcs_to_update_vec=self.ti.funcs_to_update_vec) + w_neumann = self.bc.neumann_bcs(self.bc_dict['neumann'], self.V_d, self.Vd_scalar, [self.ds,self.de], funcs_to_update=self.ti.funcs_to_update, funcs_to_update_vec=self.ti.funcs_to_update_vec) if 'bodyforce' in self.bc_dict.keys(): w_body = self.bc.bodyforce(self.bc_dict['bodyforce'], self.V_d, self.Vd_scalar, self.dx, funcs_to_update=self.ti.funcs_to_update) if 'robin' in self.bc_dict.keys(): - w_robin = self.bc.robin_bcs(self.bc_dict['robin'], self.d, self.wel, self.ds) + w_robin = self.bc.robin_bcs(self.bc_dict['robin'], self.d, self.wel, [self.ds,self.de]) self.deltaW_ext = w_neumann + w_body + w_robin diff --git a/src/ambit_fe/ale/ale_variationalform.py b/src/ambit_fe/ale/ale_variationalform.py index fc2ba7bb..0b64d6d1 100644 --- a/src/ambit_fe/ale/ale_variationalform.py +++ b/src/ambit_fe/ale/ale_variationalform.py @@ -9,10 +9,12 @@ import ufl from ..variationalform import variationalform_base +""" +ALE variational forms class +Principle of Virtual Work +\delta \mathcal{W} = \delta \mathcal{W}_{\mathrm{int}} - \delta \mathcal{W}_{\mathrm{ext}} = 0, \quad \forall \; \delta\boldsymbol{u} +""" -# ALE variational forms class -# Principle of Virtual Work -# TeX: \delta \mathcal{W} = \delta \mathcal{W}_{\mathrm{int}} - \delta \mathcal{W}_{\mathrm{ext}} = 0, \quad \forall \; \delta\boldsymbol{u} class variationalform(variationalform_base): def __init__(self, var_d, n0=None): diff --git a/src/ambit_fe/ambit_main.py b/src/ambit_fe/ambit_main.py index 0cc5582c..46c43748 100644 --- a/src/ambit_fe/ambit_main.py +++ b/src/ambit_fe/ambit_main.py @@ -9,6 +9,9 @@ from mpi4py import MPI from . import ioroutines +""" +Ambit main class +""" class Ambit(): diff --git a/src/ambit_fe/base.py b/src/ambit_fe/base.py index bf8a83f5..d3d634db 100644 --- a/src/ambit_fe/base.py +++ b/src/ambit_fe/base.py @@ -10,6 +10,9 @@ import numpy as np from . import utilities +""" +Ambit problem and solver base classes +""" class problem_base(): diff --git a/src/ambit_fe/boundaryconditions.py b/src/ambit_fe/boundaryconditions.py index 92125922..9e60cb97 100644 --- a/src/ambit_fe/boundaryconditions.py +++ b/src/ambit_fe/boundaryconditions.py @@ -12,6 +12,9 @@ from . import expression +""" +Boundary condition classes for all problems +""" class boundary_cond(): @@ -23,6 +26,8 @@ def __init__(self, fem_params, io, vf, ti, ki=None, ff=None): self.ki = ki self.ff = ff + self.dim = self.io.mesh.topology.dim + self.quad_degree = fem_params['quad_degree'] self.dbcs = [] @@ -35,12 +40,12 @@ def dirichlet_bcs(self, bcdict, V): for d in bcdict: - try: bdim_r = d['bdim_reduction'] - except: bdim_r = 1 + try: codim = d['codimension'] + except: codim = self.dim - 1 - if bdim_r==1: mdata = self.io.mt_b1 - if bdim_r==2: mdata = self.io.mt_b2 - if bdim_r==3: mdata = self.io.mt_b3 + if codim==self.dim-1: mdata = self.io.mt_b1 + if codim==self.dim-2: mdata = self.io.mt_b2 + if codim==self.dim-3: mdata = self.io.mt_b3 func = fem.Function(V) @@ -60,33 +65,33 @@ def dirichlet_bcs(self, bcdict, V): if d['dir'] == 'all': for i in range(len(d['id'])): - self.dbcs.append( fem.dirichletbc(func, fem.locate_dofs_topological(V, self.io.mesh.topology.dim-bdim_r, mdata.indices[mdata.values == d['id'][i]])) ) + self.dbcs.append( fem.dirichletbc(func, fem.locate_dofs_topological(V, codim, mdata.indices[mdata.values == d['id'][i]])) ) elif d['dir'] == 'x': for i in range(len(d['id'])): - dofs_x = fem.locate_dofs_topological(V.sub(0), self.io.mesh.topology.dim-bdim_r, mdata.indices[mdata.values == d['id'][i]]) + dofs_x = fem.locate_dofs_topological(V.sub(0), codim, mdata.indices[mdata.values == d['id'][i]]) self.dbcs.append( fem.dirichletbc(func.sub(0), dofs_x) ) elif d['dir'] == 'y': for i in range(len(d['id'])): - dofs_y = fem.locate_dofs_topological(V.sub(1), self.io.mesh.topology.dim-bdim_r, mdata.indices[mdata.values == d['id'][i]]) + dofs_y = fem.locate_dofs_topological(V.sub(1), codim, mdata.indices[mdata.values == d['id'][i]]) self.dbcs.append( fem.dirichletbc(func.sub(1), dofs_y) ) elif d['dir'] == 'z': for i in range(len(d['id'])): - dofs_z = fem.locate_dofs_topological(V.sub(2), self.io.mesh.topology.dim-bdim_r, mdata.indices[mdata.values == d['id'][i]]) + dofs_z = fem.locate_dofs_topological(V.sub(2), codim, mdata.indices[mdata.values == d['id'][i]]) self.dbcs.append( fem.dirichletbc(func.sub(2), dofs_z) ) elif d['dir'] == '2dimX': - dofs_x = fem.locate_dofs_topological(V.sub(0), self.io.mesh.topology.dim-bdim_r, mesh.locate_entities_boundary(self.io.mesh, self.io.mesh.topology.dim-bdim_r, self.twodimX)) + dofs_x = fem.locate_dofs_topological(V.sub(0), codim, mesh.locate_entities_boundary(self.io.mesh, codim, self.twodimX)) self.dbcs.append( fem.dirichletbc(func.sub(0), dofs_x) ) elif d['dir'] == '2dimY': - dofs_y = fem.locate_dofs_topological(V.sub(1), self.io.mesh.topology.dim-bdim_r, mesh.locate_entities_boundary(self.io.mesh, self.io.mesh.topology.dim-bdim_r, self.twodimY)) + dofs_y = fem.locate_dofs_topological(V.sub(1), codim, mesh.locate_entities_boundary(self.io.mesh, codim, self.twodimY)) self.dbcs.append( fem.dirichletbc(func.sub(1), dofs_y) ) elif d['dir'] == '2dimZ': - dofs_z = fem.locate_dofs_topological(V.sub(2), self.io.mesh.topology.dim-bdim_r, mesh.locate_entities_boundary(self.io.mesh, self.io.mesh.topology.dim-bdim_r, self.twodimZ)) + dofs_z = fem.locate_dofs_topological(V.sub(2), codim, mesh.locate_entities_boundary(self.io.mesh, codim, self.twodimZ)) self.dbcs.append( fem.dirichletbc(func.sub(2), dofs_z) ) else: @@ -121,7 +126,7 @@ def dirichlet_vol(self, bcdict, V): raise RuntimeError("Need to have 'curve', 'val', or 'file' specified!") for i in range(len(d['id'])): - self.dbcs.append( fem.dirichletbc(func, fem.locate_dofs_topological(V, self.io.mesh.topology.dim, self.io.mt_d.indices[self.io.mt_d.values == d['id'][i]])) ) + self.dbcs.append( fem.dirichletbc(func, fem.locate_dofs_topological(V, self.dim, self.io.mt_d.indices[self.io.mt_d.values == d['id'][i]])) ) # function to mark x=0 @@ -144,6 +149,13 @@ def neumann_bcs(self, bcdict, V, V_real, ds_, F=None, funcs_to_update=None, func for n in bcdict: + try: codim = n['codimension'] + except: codim = self.dim - 1 + + if codim==self.dim-1: dind=0 + elif codim==self.dim-2: dind=1 + else: raise ValueError("Wrong codimension of boundary.") + if n['dir'] == 'xyz_ref': # reference xyz func = fem.Function(V) @@ -162,7 +174,7 @@ def neumann_bcs(self, bcdict, V, V_real, ds_, F=None, funcs_to_update=None, func for i in range(len(n['id'])): - w += self.vf.deltaW_ext_neumann_ref(func, ds_(n['id'][i])) + w += self.vf.deltaW_ext_neumann_ref(func, ds_[dind](n['id'][i])) elif n['dir'] == 'normal_ref': # reference normal @@ -182,7 +194,7 @@ def neumann_bcs(self, bcdict, V, V_real, ds_, F=None, funcs_to_update=None, func for i in range(len(n['id'])): - w += self.vf.deltaW_ext_neumann_normal_ref(func, ds_(n['id'][i])) + w += self.vf.deltaW_ext_neumann_normal_ref(func, ds_[dind](n['id'][i])) elif n['dir'] == 'xyz_cur': # current xyz @@ -202,7 +214,7 @@ def neumann_bcs(self, bcdict, V, V_real, ds_, F=None, funcs_to_update=None, func for i in range(len(n['id'])): - w += self.vf.deltaW_ext_neumann_cur(func, ds_(n['id'][i]), F=F) + w += self.vf.deltaW_ext_neumann_cur(func, ds_[dind](n['id'][i]), F=F) elif n['dir'] == 'normal_cur': # current normal @@ -222,7 +234,7 @@ def neumann_bcs(self, bcdict, V, V_real, ds_, F=None, funcs_to_update=None, func for i in range(len(n['id'])): - w += self.vf.deltaW_ext_neumann_normal_cur(func, ds_(n['id'][i]), F=F) + w += self.vf.deltaW_ext_neumann_normal_cur(func, ds_[dind](n['id'][i]), F=F) else: raise NameError("Unknown dir option for Neumann BC!") @@ -237,6 +249,13 @@ def neumann_prestress_bcs(self, bcdict, V, V_real, ds_, funcs_to_update=None, fu for n in bcdict: + try: codim = n['codimension'] + except: codim = self.dim - 1 + + if codim==self.dim-1: dind=0 + elif codim==self.dim-2: dind=1 + else: raise ValueError("Wrong codimension of boundary.") + if n['dir'] == 'xyz_ref': # reference xyz func = fem.Function(V) @@ -255,7 +274,7 @@ def neumann_prestress_bcs(self, bcdict, V, V_real, ds_, funcs_to_update=None, fu for i in range(len(n['id'])): - w += self.vf.deltaW_ext_neumann_ref(func, ds_(n['id'][i])) + w += self.vf.deltaW_ext_neumann_ref(func, ds_[dind](n['id'][i])) elif n['dir'] == 'normal_ref': # reference normal @@ -275,7 +294,7 @@ def neumann_prestress_bcs(self, bcdict, V, V_real, ds_, funcs_to_update=None, fu for i in range(len(n['id'])): - w += self.vf.deltaW_ext_neumann_normal_ref(func, ds_(n['id'][i])) + w += self.vf.deltaW_ext_neumann_normal_ref(func, ds_[dind](n['id'][i])) else: raise NameError("Unknown dir option for Neumann prestress BC!") @@ -290,25 +309,32 @@ def robin_bcs(self, bcdict, u, v, ds_, u_pre=None): for r in bcdict: + try: codim = r['codimension'] + except: codim = self.dim - 1 + + if codim==self.dim-1: dind=0 + elif codim==self.dim-2: dind=1 + else: raise ValueError("Wrong codimension of boundary.") + if r['type'] == 'spring': if r['dir'] == 'xyz_ref': # reference xyz for i in range(len(r['id'])): - w += self.vf.deltaW_ext_robin_spring(u, r['stiff'], ds_(r['id'][i]), u_pre) + w += self.vf.deltaW_ext_robin_spring(u, r['stiff'], ds_[dind](r['id'][i]), u_pre) elif r['dir'] == 'normal_ref': # reference normal for i in range(len(r['id'])): - w += self.vf.deltaW_ext_robin_spring_normal_ref(u, r['stiff'], ds_(r['id'][i]), u_pre) + w += self.vf.deltaW_ext_robin_spring_normal_ref(u, r['stiff'], ds_[dind](r['id'][i]), u_pre) elif r['dir'] == 'normal_cross': # cross normal for i in range(len(r['id'])): - w += self.vf.deltaW_ext_robin_spring_normal_cross(u, r['stiff'], ds_(r['id'][i]), u_pre) + w += self.vf.deltaW_ext_robin_spring_normal_cross(u, r['stiff'], ds_[dind](r['id'][i]), u_pre) else: raise NameError("Unknown dir option for Robin BC!") @@ -320,19 +346,19 @@ def robin_bcs(self, bcdict, u, v, ds_, u_pre=None): for i in range(len(r['id'])): - w += self.vf.deltaW_ext_robin_dashpot(v, r['visc'], ds_(r['id'][i])) + w += self.vf.deltaW_ext_robin_dashpot(v, r['visc'], ds_[dind](r['id'][i])) elif r['dir'] == 'normal_ref': # reference normal for i in range(len(r['id'])): - w += self.vf.deltaW_ext_robin_dashpot_normal_ref(v, r['visc'], ds_(r['id'][i])) + w += self.vf.deltaW_ext_robin_dashpot_normal_ref(v, r['visc'], ds_[dind](r['id'][i])) elif r['dir'] == 'normal_cross': # cross normal for i in range(len(r['id'])): - w += self.vf.deltaW_ext_robin_dashpot_normal_cross(v, r['visc'], ds_(r['id'][i])) + w += self.vf.deltaW_ext_robin_dashpot_normal_cross(v, r['visc'], ds_[dind](r['id'][i])) else: raise NameError("Unknown dir option for Robin BC!") @@ -352,6 +378,13 @@ def membranesurf_bcs(self, bcdict, u, v, a, ds_, ivar=None, wallfields=[]): mi=0 for m in bcdict: + try: codim = m['codimension'] + except: codim = self.dim - 1 + + if codim==self.dim-1: dind=0 + elif codim==self.dim-2: dind=1 + else: raise ValueError("Wrong codimension of boundary.") + # field for variable wall thickness if bool(wallfields): wallfield = wallfields[mi] @@ -362,8 +395,8 @@ def membranesurf_bcs(self, bcdict, u, v, a, ds_, ivar=None, wallfields=[]): idmem.append(m['id'][i]) - w += self.vf.deltaW_ext_membrane(self.ki.F(u), self.ki.Fdot(v), a, m['params'], ds_(m['id'][i]), ivar=ivar, fibfnc=self.ff, wallfield=wallfield) - bstress.append(self.vf.deltaW_ext_membrane(self.ki.F(u), self.ki.Fdot(v), a, m['params'], ds_(m['id'][i]), ivar=ivar, fibfnc=self.ff, stress=True, wallfield=wallfield)) + w += self.vf.deltaW_ext_membrane(self.ki.F(u), self.ki.Fdot(v), a, m['params'], ds_[dind](m['id'][i]), ivar=ivar, fibfnc=self.ff, wallfield=wallfield) + bstress.append(self.vf.deltaW_ext_membrane(self.ki.F(u), self.ki.Fdot(v), a, m['params'], ds_[dind](m['id'][i]), ivar=ivar, fibfnc=self.ff, stress=True, wallfield=wallfield)) mi+=1 @@ -414,13 +447,20 @@ def stabilized_neumann_bcs(self, bcdict, v, ds_, wel=None, F=None): for sn in bcdict: + try: codim = sn['codimension'] + except: codim = self.dim - 1 + + if codim==self.dim-1: dind=0 + elif codim==self.dim-2: dind=1 + else: raise ValueError("Wrong codimension of boundary.") + for i in range(len(sn['id'])): par1 = sn['par1'] try: par2 = sn['par2'] except: par2 = 0. - w += self.vf.deltaW_ext_stabilized_neumann(v, par1, par2, ds_(sn['id'][i]), w=wel, F=F) + w += self.vf.deltaW_ext_stabilized_neumann(v, par1, par2, ds_[dind](sn['id'][i]), w=wel, F=F) return w @@ -431,17 +471,24 @@ def robin_valve_bcs(self, bcdict, v, V_real, beta_, dS_, wel=None, F=None): w = ufl.as_ufl(0) if wel is None: - wel_ = ufl.constantvalue.zero(self.io.mesh.topology.dim) + wel_ = ufl.constantvalue.zero(self.dim) else: wel_ = wel for r in bcdict: + try: codim = r['codimension'] + except: codim = self.dim - 1 + + if codim==self.dim-1: dind=0 + elif codim==self.dim-2: dind=1 + else: raise ValueError("Wrong codimension of boundary.") + beta_.append( fem.Function(V_real) ) for i in range(len(r['id'])): - w += self.vf.deltaW_ext_robin_valve(v, beta_[-1], dS_(r['id'][i]), fcts='+', w=wel_, F=F) + w += self.vf.deltaW_ext_robin_valve(v, beta_[-1], dS_[dind](r['id'][i]), fcts='+', w=wel_, F=F) return w @@ -450,12 +497,19 @@ def robin_valve_bcs(self, bcdict, v, V_real, beta_, dS_, wel=None, F=None): def flux_monitor_bcs(self, bcdict, v, qdict_, wel=None, F=None): if wel is None: - wel_ = ufl.constantvalue.zero(self.io.mesh.topology.dim) + wel_ = ufl.constantvalue.zero(self.dim) else: wel_ = wel for r in bcdict: + try: codim = r['codimension'] + except: codim = self.dim - 1 + + if codim==self.dim-1: dind=0 + elif codim==self.dim-2: dind=1 + else: raise ValueError("Wrong codimension of boundary.") + q = ufl.as_ufl(0) try: internal = r['internal'] @@ -498,7 +552,7 @@ def flux_monitor_bcs(self, bcdict, v, qdict_, wel=None, F=None): def dp_monitor_bcs(self, bcdict, a_u_, a_d_, pint_u_, pint_d_, pdict, wel=None, F=None): if wel is None: - wel_ = ufl.constantvalue.zero(self.io.mesh.topology.dim) + wel_ = ufl.constantvalue.zero(self.dim) else: wel_ = wel @@ -511,6 +565,13 @@ def dp_monitor_bcs(self, bcdict, a_u_, a_d_, pint_u_, pint_d_, pdict, wel=None, for r in bcdict: + try: codim = r['codimension'] + except: codim = self.dim - 1 + + if codim==self.dim-1: dind=0 + elif codim==self.dim-2: dind=1 + else: raise ValueError("Wrong codimension of boundary.") + dom_u, dom_d = r['upstream_domain'], r['downstream_domain'] a_u, a_d, pint_u, pint_d = ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0) diff --git a/src/ambit_fe/coupling/fsi_main.py b/src/ambit_fe/coupling/fsi_main.py index c73d6826..1c24dc49 100644 --- a/src/ambit_fe/coupling/fsi_main.py +++ b/src/ambit_fe/coupling/fsi_main.py @@ -21,6 +21,9 @@ from ..base import problem_base, solver_base +""" +FSI problem class +""" class FSIProblem(problem_base): diff --git a/src/ambit_fe/flow0d/cardiovascular0D.py b/src/ambit_fe/flow0d/cardiovascular0D.py index 9ff3724d..ba8c001b 100644 --- a/src/ambit_fe/flow0d/cardiovascular0D.py +++ b/src/ambit_fe/flow0d/cardiovascular0D.py @@ -26,7 +26,7 @@ def __init__(self, init=True, ode_par=False, comm=None): # check for cardiac cycle periodicity - def cycle_check(self, var, varTc, varTc_old, aux, auxTc, auxTc_old, t, cycle, cyclerr, eps_periodic, check=['allvar'], inioutpath=None, nm='', induce_pert_after_cycl=-1): + def cycle_check(self, var, varTc, varTc_old, aux, auxTc, auxTc_old, t, cycle, cyclerr, eps_periodic, check=None, inioutpath=None, nm='', induce_pert_after_cycl=-1): if self.ode_parallel: vs, ve = var.getOwnershipRange() else: vs, ve = 0, len(var.array) @@ -38,7 +38,7 @@ def cycle_check(self, var, varTc, varTc_old, aux, auxTc, auxTc_old, t, cycle, cy varTc[vs:ve] = var[vs:ve] auxTc[:] = aux[:] - if check[0] is not None: is_periodic = self.check_periodic(varTc, varTc_old, auxTc, auxTc_old, eps_periodic, check, cyclerr) + if check is not None: is_periodic = self.check_periodic(varTc, varTc_old, auxTc, auxTc_old, eps_periodic, check, cyclerr) # definitely should not be True if we've not yet surpassed the "disease induction" cycle if cycle[0] <= induce_pert_after_cycl: diff --git a/src/ambit_fe/flow0d/cardiovascular0D_2elwindkessel.py b/src/ambit_fe/flow0d/cardiovascular0D_2elwindkessel.py index 1bcdc879..921022b7 100644 --- a/src/ambit_fe/flow0d/cardiovascular0D_2elwindkessel.py +++ b/src/ambit_fe/flow0d/cardiovascular0D_2elwindkessel.py @@ -14,8 +14,10 @@ from ..mpiroutines import allgather_vec from .. import utilities -### 2-element windkessel: C dp/dt + (p-p_ref)/R = Q, with Q:=-dV/dt (Poiseuille's flow for C=0) -# (can be reproduced with 4elwindkesselLsZ by setting Z, L = 0) +""" +2-element windkessel: C dp/dt + (p-p_ref)/R = Q, with Q:=-dV/dt (Poiseuille's flow for C=0) +(can be reproduced with 4elwindkesselLsZ by setting Z, L = 0) +""" class cardiovascular0D2elwindkessel(cardiovascular0Dbase): diff --git a/src/ambit_fe/flow0d/cardiovascular0D_4elwindkesselLpZ.py b/src/ambit_fe/flow0d/cardiovascular0D_4elwindkesselLpZ.py index 17b4c592..38c59f9d 100644 --- a/src/ambit_fe/flow0d/cardiovascular0D_4elwindkesselLpZ.py +++ b/src/ambit_fe/flow0d/cardiovascular0D_4elwindkesselLpZ.py @@ -14,15 +14,16 @@ from ..mpiroutines import allgather_vec from .. import utilities -### this implements a 4-element windkessel model with an inertance L parallel to an impedance Z, all in series -# to a compliance C parallel to a resistance R, with the original equation -# LC/Z * d2p/dt2 + (L/(RZ) + C)*dp/dt + (p-p_ref)/R - Q - (L/R + L/Z)*dQ/dt - LC*d2Q/dt2 = 0, with Q:=-dV/dt -### this is implemented as four first order ODEs: -# LC/Z * dg/dt + (L/(RZ) + C)*g + (p-p_ref)/R + q + (L/R + L/Z)*s + LC*ds/dt = 0 -# dp/dt - g = 0 -# dV/dt - q = 0 -# dq/dt - s = 0 - +""" +This implements a 4-element windkessel model with an inertance L parallel to an impedance Z, all in series +to a compliance C parallel to a resistance R, with the original equation +LC/Z * d2p/dt2 + (L/(RZ) + C)*dp/dt + (p-p_ref)/R - Q - (L/R + L/Z)*dQ/dt - LC*d2Q/dt2 = 0, with Q:=-dV/dt +This is implemented as four first order ODEs: +LC/Z * dg/dt + (L/(RZ) + C)*g + (p-p_ref)/R + q + (L/R + L/Z)*s + LC*ds/dt = 0 +dp/dt - g = 0 +dV/dt - q = 0 +dq/dt - s = 0 +""" class cardiovascular0D4elwindkesselLpZ(cardiovascular0Dbase): diff --git a/src/ambit_fe/flow0d/cardiovascular0D_4elwindkesselLsZ.py b/src/ambit_fe/flow0d/cardiovascular0D_4elwindkesselLsZ.py index 3c47526d..41d44db0 100644 --- a/src/ambit_fe/flow0d/cardiovascular0D_4elwindkesselLsZ.py +++ b/src/ambit_fe/flow0d/cardiovascular0D_4elwindkesselLsZ.py @@ -14,15 +14,15 @@ from ..mpiroutines import allgather_vec from .. import utilities -# here we make use of sympy for symbolic differention... - -### this implements a 4-element windkessel model with an inertance L in series to an impedance Z, all in series -# to a compliance C parallel to a resistance R, with the original equation -# C dp/dt + (p-p_ref)/R - (1+Z/R)*Q - (CZ + L/R)*dQ/dt - LC*d2Q/dt2 = 0, with Q:=-dV/dt -### this is implemented as three first order ODEs: -# C dp/dt + (p-p_ref)/R + (1+Z/R)*q + (CZ + L/R)*s + LC*ds/dt = 0 -# dV/dt - q = 0 -# dq/dt - s = 0 +""" +This implements a 4-element windkessel model with an inertance L in series to an impedance Z, all in series +to a compliance C parallel to a resistance R, with the original equation +C dp/dt + (p-p_ref)/R - (1+Z/R)*Q - (CZ + L/R)*dQ/dt - LC*d2Q/dt2 = 0, with Q:=-dV/dt +This is implemented as three first order ODEs: +C dp/dt + (p-p_ref)/R + (1+Z/R)*q + (CZ + L/R)*s + LC*ds/dt = 0 +dV/dt - q = 0 +dq/dt - s = 0 +""" class cardiovascular0D4elwindkesselLsZ(cardiovascular0Dbase): diff --git a/src/ambit_fe/flow0d/cardiovascular0D_CRLinoutlink.py b/src/ambit_fe/flow0d/cardiovascular0D_CRLinoutlink.py index 3b7cee6c..b33e39f3 100644 --- a/src/ambit_fe/flow0d/cardiovascular0D_CRLinoutlink.py +++ b/src/ambit_fe/flow0d/cardiovascular0D_CRLinoutlink.py @@ -14,7 +14,9 @@ from ..mpiroutines import allgather_vec from .. import utilities -# two RC models (2-element Windkessels) in series linking an in- to an outflow +""" +Two RC models (2-element Windkessels) in series linking an in- to an outflow +""" class cardiovascular0DCRLinoutlink(cardiovascular0Dbase): diff --git a/src/ambit_fe/flow0d/cardiovascular0D_coronary.py b/src/ambit_fe/flow0d/cardiovascular0D_coronary.py index 70df2385..3528052a 100644 --- a/src/ambit_fe/flow0d/cardiovascular0D_coronary.py +++ b/src/ambit_fe/flow0d/cardiovascular0D_coronary.py @@ -11,17 +11,19 @@ from .. import utilities -# coronary model with a 3-element Windkessel (ZCR, proximal part) in series with a 2-element Windkessel (CR, distal part) -# according to Vieira et al. (2018) "Patient-specific modeling of right coronary circulation vulnerability post-liver transplant in Alagille’s syndrome", PLoS ONE 13(11), e0205829 -# here their R_e is Z_corp_sys, C_e is C_corp_sys, R_p is R_corp_sys, C_i is C_cord_sys, and R_d is R_cord_sys -# the distal compliance is fed by the left ventricular pressure in order to have a phase-dependent tone of the coronary -# (coronaries almost entirely fill in diastole, not during systole) -#\begin{align} -#&C_{\mathrm{cor,p}}^{\mathrm{sys}} \left(\frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{sys}}}{\mathrm{d}t}-Z_{\mathrm{cor,p}}^{\mathrm{sys}}\frac{\mathrm{d}q_{\mathrm{cor,p,in}}^{\mathrm{sys}}}{\mathrm{d}t}\right) = q_{\mathrm{cor,p,in}}^{\mathrm{sys}} - q_{\mathrm{cor,p}}^{\mathrm{sys}}\\ -#&R_{\mathrm{cor,p}}^{\mathrm{sys}}\,q_{\mathrm{cor,p}}^{\mathrm{sys}}=p_{\mathrm{ar}}^{\mathrm{sys}}-p_{\mathrm{cor,d}}^{\mathrm{sys}} - Z_{\mathrm{cor,p}}^{\mathrm{sys}}\,q_{\mathrm{cor,p,in}}^{\mathrm{sys}}\\ -#&C_{\mathrm{cor,d}}^{\mathrm{sys}} \frac{\mathrm{d}(p_{\mathrm{cor,d}}^{\mathrm{sys}}-p_{\mathrm{v}}^{\ell})}{\mathrm{d}t} = q_{\mathrm{cor,p}}^{\mathrm{sys}} - q_{\mathrm{cor,d}}^{\mathrm{sys}}\\ -#&R_{\mathrm{cor,d}}^{\mathrm{sys}}\,q_{\mathrm{cor,d}}^{\mathrm{sys}}=p_{\mathrm{cor,d}}^{\mathrm{sys}}-p_{\mathrm{at}}^{r} -#\end{align} +""" +Coronary model with a 3-element Windkessel (ZCR, proximal part) in series with a 2-element Windkessel (CR, distal part) +according to Vieira et al. (2018) "Patient-specific modeling of right coronary circulation vulnerability post-liver transplant in Alagille’s syndrome", PLoS ONE 13(11), e0205829 +here their R_e is Z_corp_sys, C_e is C_corp_sys, R_p is R_corp_sys, C_i is C_cord_sys, and R_d is R_cord_sys +the distal compliance is fed by the left ventricular pressure in order to have a phase-dependent tone of the coronary +(coronaries almost entirely fill in diastole, not during systole) +\begin{align} +&C_{\mathrm{cor,p}}^{\mathrm{sys}} \left(\frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{sys}}}{\mathrm{d}t}-Z_{\mathrm{cor,p}}^{\mathrm{sys}}\frac{\mathrm{d}q_{\mathrm{cor,p,in}}^{\mathrm{sys}}}{\mathrm{d}t}\right) = q_{\mathrm{cor,p,in}}^{\mathrm{sys}} - q_{\mathrm{cor,p}}^{\mathrm{sys}}\\ +&R_{\mathrm{cor,p}}^{\mathrm{sys}}\,q_{\mathrm{cor,p}}^{\mathrm{sys}}=p_{\mathrm{ar}}^{\mathrm{sys}}-p_{\mathrm{cor,d}}^{\mathrm{sys}} - Z_{\mathrm{cor,p}}^{\mathrm{sys}}\,q_{\mathrm{cor,p,in}}^{\mathrm{sys}}\\ +&C_{\mathrm{cor,d}}^{\mathrm{sys}} \frac{\mathrm{d}(p_{\mathrm{cor,d}}^{\mathrm{sys}}-p_{\mathrm{v}}^{\ell})}{\mathrm{d}t} = q_{\mathrm{cor,p}}^{\mathrm{sys}} - q_{\mathrm{cor,d}}^{\mathrm{sys}}\\ +&R_{\mathrm{cor,d}}^{\mathrm{sys}}\,q_{\mathrm{cor,d}}^{\mathrm{sys}}=p_{\mathrm{cor,d}}^{\mathrm{sys}}-p_{\mathrm{at}}^{r} +\end{align} +""" class coronary_circ_ZCRp_CRd(): @@ -104,19 +106,20 @@ def print_to_screen(self, var_arr, aux, comm): utilities.print_status('{:<10s}{:<3s}{:<7.3f}'.format('p_cord_sys',' = ',var_arr[self.varmap['p_cord_sys']]), comm) - -# equivalent model to ZCRp_CRd, but individually for left and right coronary arteries -#\begin{align} -#&C_{\mathrm{cor,p}}^{\mathrm{sys},\ell} \left(\frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{sys},\ell}}{\mathrm{d}t}-Z_{\mathrm{cor,p}}^{\mathrm{sys},\ell}\frac{\mathrm{d}q_{\mathrm{cor,p,in}}^{\mathrm{sys},\ell}}{\mathrm{d}t}\right) = q_{\mathrm{cor,p,in}}^{\mathrm{sys},\ell} - q_{\mathrm{cor,p}}^{\mathrm{sys},\ell}\\ -#&R_{\mathrm{cor,p}}^{\mathrm{sys},\ell}\,q_{\mathrm{cor,p}}^{\mathrm{sys},\ell}=p_{\mathrm{ar}}^{\mathrm{sys}}-p_{\mathrm{cor,d}}^{\mathrm{sys},\ell} - Z_{\mathrm{cor,p}}^{\mathrm{sys},\ell}\,q_{\mathrm{cor,p,in}}^{\mathrm{sys},\ell}\\ -#&C_{\mathrm{cor,d}}^{\mathrm{sys},\ell} \frac{\mathrm{d}(p_{\mathrm{cor,d}}^{\mathrm{sys},\ell}-p_{\mathrm{v}}^{\ell})}{\mathrm{d}t} = q_{\mathrm{cor,p}}^{\mathrm{sys},\ell} - q_{\mathrm{cor,d}}^{\mathrm{sys},\ell}\\ -#&R_{\mathrm{cor,d}}^{\mathrm{sys},\ell}\,q_{\mathrm{cor,d}}^{\mathrm{sys},\ell}=p_{\mathrm{cor,d}}^{\mathrm{sys},\ell}-p_{\mathrm{at}}^{r}\\ -#&C_{\mathrm{cor,p}}^{\mathrm{sys},r} \left(\frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{sys},r}}{\mathrm{d}t}-Z_{\mathrm{cor,p}}^{\mathrm{sys},r}\frac{\mathrm{d}q_{\mathrm{cor,p,in}}^{\mathrm{sys},r}}{\mathrm{d}t}\right) = q_{\mathrm{cor,p,in}}^{\mathrm{sys},r} - q_{\mathrm{cor,p}}^{\mathrm{sys},r}\\ -#&R_{\mathrm{cor,p}}^{\mathrm{sys},r}\,q_{\mathrm{cor,p}}^{\mathrm{sys},r}=p_{\mathrm{ar}}^{\mathrm{sys}}-p_{\mathrm{cor,d}}^{\mathrm{sys},r} - Z_{\mathrm{cor,p}}^{\mathrm{sys},r}\,q_{\mathrm{cor,p,in}}^{\mathrm{sys},r}\\ -#&C_{\mathrm{cor,d}}^{\mathrm{sys},r} \frac{\mathrm{d}(p_{\mathrm{cor,d}}^{\mathrm{sys},r}-p_{\mathrm{v}}^{\ell})}{\mathrm{d}t} = q_{\mathrm{cor,p}}^{\mathrm{sys},r} - q_{\mathrm{cor,d}}^{\mathrm{sys},r}\\ -#&R_{\mathrm{cor,d}}^{\mathrm{sys},r}\,q_{\mathrm{cor,d}}^{\mathrm{sys},r}=p_{\mathrm{cor,d}}^{\mathrm{sys},r}-p_{\mathrm{at}}^{r}\\ -#&0=q_{\mathrm{cor,d}}^{\mathrm{sys},\ell}+q_{\mathrm{cor,d}}^{\mathrm{sys},r}-q_{\mathrm{cor,d,out}}^{\mathrm{sys}} -#\end{align} +""" +Equivalent model to ZCRp_CRd, but individually for left and right coronary arteries +\begin{align} +&C_{\mathrm{cor,p}}^{\mathrm{sys},\ell} \left(\frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{sys},\ell}}{\mathrm{d}t}-Z_{\mathrm{cor,p}}^{\mathrm{sys},\ell}\frac{\mathrm{d}q_{\mathrm{cor,p,in}}^{\mathrm{sys},\ell}}{\mathrm{d}t}\right) = q_{\mathrm{cor,p,in}}^{\mathrm{sys},\ell} - q_{\mathrm{cor,p}}^{\mathrm{sys},\ell}\\ +&R_{\mathrm{cor,p}}^{\mathrm{sys},\ell}\,q_{\mathrm{cor,p}}^{\mathrm{sys},\ell}=p_{\mathrm{ar}}^{\mathrm{sys}}-p_{\mathrm{cor,d}}^{\mathrm{sys},\ell} - Z_{\mathrm{cor,p}}^{\mathrm{sys},\ell}\,q_{\mathrm{cor,p,in}}^{\mathrm{sys},\ell}\\ +&C_{\mathrm{cor,d}}^{\mathrm{sys},\ell} \frac{\mathrm{d}(p_{\mathrm{cor,d}}^{\mathrm{sys},\ell}-p_{\mathrm{v}}^{\ell})}{\mathrm{d}t} = q_{\mathrm{cor,p}}^{\mathrm{sys},\ell} - q_{\mathrm{cor,d}}^{\mathrm{sys},\ell}\\ +&R_{\mathrm{cor,d}}^{\mathrm{sys},\ell}\,q_{\mathrm{cor,d}}^{\mathrm{sys},\ell}=p_{\mathrm{cor,d}}^{\mathrm{sys},\ell}-p_{\mathrm{at}}^{r}\\ +&C_{\mathrm{cor,p}}^{\mathrm{sys},r} \left(\frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{sys},r}}{\mathrm{d}t}-Z_{\mathrm{cor,p}}^{\mathrm{sys},r}\frac{\mathrm{d}q_{\mathrm{cor,p,in}}^{\mathrm{sys},r}}{\mathrm{d}t}\right) = q_{\mathrm{cor,p,in}}^{\mathrm{sys},r} - q_{\mathrm{cor,p}}^{\mathrm{sys},r}\\ +&R_{\mathrm{cor,p}}^{\mathrm{sys},r}\,q_{\mathrm{cor,p}}^{\mathrm{sys},r}=p_{\mathrm{ar}}^{\mathrm{sys}}-p_{\mathrm{cor,d}}^{\mathrm{sys},r} - Z_{\mathrm{cor,p}}^{\mathrm{sys},r}\,q_{\mathrm{cor,p,in}}^{\mathrm{sys},r}\\ +&C_{\mathrm{cor,d}}^{\mathrm{sys},r} \frac{\mathrm{d}(p_{\mathrm{cor,d}}^{\mathrm{sys},r}-p_{\mathrm{v}}^{\ell})}{\mathrm{d}t} = q_{\mathrm{cor,p}}^{\mathrm{sys},r} - q_{\mathrm{cor,d}}^{\mathrm{sys},r}\\ +&R_{\mathrm{cor,d}}^{\mathrm{sys},r}\,q_{\mathrm{cor,d}}^{\mathrm{sys},r}=p_{\mathrm{cor,d}}^{\mathrm{sys},r}-p_{\mathrm{at}}^{r}\\ +&0=q_{\mathrm{cor,d}}^{\mathrm{sys},\ell}+q_{\mathrm{cor,d}}^{\mathrm{sys},r}-q_{\mathrm{cor,d,out}}^{\mathrm{sys}} +\end{align} +""" class coronary_circ_ZCRp_CRd_lr(): diff --git a/src/ambit_fe/flow0d/cardiovascular0D_syspul.py b/src/ambit_fe/flow0d/cardiovascular0D_syspul.py index a05ad31a..02e34193 100644 --- a/src/ambit_fe/flow0d/cardiovascular0D_syspul.py +++ b/src/ambit_fe/flow0d/cardiovascular0D_syspul.py @@ -14,36 +14,38 @@ from ..mpiroutines import allgather_vec from .. import utilities -# systemic and pulmonary closed-loop circulation model, each heart chamber can be treated individually, -# either as 0D elastance model, volume or flux coming from a 3D solid, or interface fluxes from a 3D fluid model - -# 18 governing equations (uncomment and paste directly into a LaTeX environment): - -#% left heart and systemic circulation: -#\begin{align} -#&-Q_{\mathrm{at}}^{\ell} = q_{\mathrm{ven}}^{\mathrm{pul}} - q_{\mathrm{v,in}}^{\ell}\\ -#&\tilde{R}_{\mathrm{v,in}}^{\ell}\,q_{\mathrm{v,in}}^{\ell} = p_{\mathrm{at}}^{\ell}-p_{\mathrm{v}}^{\ell}\\ -#&-Q_{\mathrm{v}}^{\ell} = q_{\mathrm{v,in}}^{\ell} - q_{\mathrm{v,out}}^{\ell}\\ -#&\tilde{R}_{\mathrm{v,out}}^{\ell}\,q_{\mathrm{v,out}}^{\ell} = p_{\mathrm{v}}^{\ell}-p_{\mathrm{ar}}^{\mathrm{sys}}\\ -#&0 = q_{\mathrm{v,out}}^{\ell} - q_{\mathrm{ar,p}}^{\mathrm{sys}}\\ -#&I_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}q_{\mathrm{ar,p}}^{\mathrm{sys}}}{\mathrm{d}t} + Z_{\mathrm{ar}}^{\mathrm{sys}}\,q_{\mathrm{ar,p}}^{\mathrm{sys}}=p_{\mathrm{ar}}^{\mathrm{sys}}-p_{\mathrm{ar,d}}^{\mathrm{sys}}\\ -#&C_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ar,d}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar,p}}^{\mathrm{sys}} - q_{\mathrm{ar}}^{\mathrm{sys}}\\ -#&L_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}q_{\mathrm{ar}}^{\mathrm{sys}}}{\mathrm{d}t} + R_{\mathrm{ar}}^{\mathrm{sys}}\,q_{\mathrm{ar}}^{\mathrm{sys}}=p_{\mathrm{ar,d}}^{\mathrm{sys}}-p_{\mathrm{ven}}^{\mathrm{sys}}\\ -#&C_{\mathrm{ven}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ven}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar}}^{\mathrm{sys}}-q_{\mathrm{ven}}^{\mathrm{sys}}\\ -#&L_{\mathrm{ven}}^{\mathrm{sys}} \frac{\mathrm{d}q_{\mathrm{ven}}^{\mathrm{sys}}}{\mathrm{d}t} + R_{\mathrm{ven}}^{\mathrm{sys}}\, q_{\mathrm{ven}}^{\mathrm{sys}} = p_{\mathrm{ven}}^{\mathrm{sys}} - p_{\mathrm{at}}^{r} -#\end{align} - -#% right heart and pulmonary circulation: -#\begin{align} -#&-Q_{\mathrm{at}}^{r} = q_{\mathrm{ven}}^{\mathrm{sys}} - q_{\mathrm{v,in}}^{r}\\ -#&\tilde{R}_{\mathrm{v,in}}^{r}\,q_{\mathrm{v,in}}^{r} = p_{\mathrm{at}}^{r}-p_{\mathrm{v}}^{r}\\ -#&-Q_{\mathrm{v}}^{r} = q_{\mathrm{v,in}}^{r} - q_{\mathrm{v,out}}^{r}\\ -#&\tilde{R}_{\mathrm{v,out}}^{r}\,q_{\mathrm{v,out}}^{r} = p_{\mathrm{v}}^{r}-p_{\mathrm{ar}}^{\mathrm{pul}}\\ -#&C_{\mathrm{ar}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{v,out}}^{r} - q_{\mathrm{ar}}^{\mathrm{pul}}\\ -#&L_{\mathrm{ar}}^{\mathrm{pul}} \frac{\mathrm{d}q_{\mathrm{ar}}^{\mathrm{pul}}}{\mathrm{d}t} + R_{\mathrm{ar}}^{\mathrm{pul}}\,q_{\mathrm{ar}}^{\mathrm{pul}}=p_{\mathrm{ar}}^{\mathrm{pul}} -p_{\mathrm{ven}}^{\mathrm{pul}}\\ -#&C_{\mathrm{ven}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{ven}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{ar}}^{\mathrm{pul}} - q_{\mathrm{ven}}^{\mathrm{pul}}\\ -#&L_{\mathrm{ven}}^{\mathrm{pul}} \frac{\mathrm{d}q_{\mathrm{ven}}^{\mathrm{pul}}}{\mathrm{d}t} + R_{\mathrm{ven}}^{\mathrm{pul}}\, q_{\mathrm{ven}}^{\mathrm{pul}}=p_{\mathrm{ven}}^{\mathrm{pul}}-p_{\mathrm{at}}^{\ell} -#\end{align} +""" +Systemic and pulmonary closed-loop circulation model, each heart chamber can be treated individually, +either as 0D elastance model, volume or flux coming from a 3D solid, or interface fluxes from a 3D fluid model + +18 governing equations: + +left heart and systemic circulation: +\begin{align} +&-Q_{\mathrm{at}}^{\ell} = q_{\mathrm{ven}}^{\mathrm{pul}} - q_{\mathrm{v,in}}^{\ell}\\ +&\tilde{R}_{\mathrm{v,in}}^{\ell}\,q_{\mathrm{v,in}}^{\ell} = p_{\mathrm{at}}^{\ell}-p_{\mathrm{v}}^{\ell}\\ +&-Q_{\mathrm{v}}^{\ell} = q_{\mathrm{v,in}}^{\ell} - q_{\mathrm{v,out}}^{\ell}\\ +&\tilde{R}_{\mathrm{v,out}}^{\ell}\,q_{\mathrm{v,out}}^{\ell} = p_{\mathrm{v}}^{\ell}-p_{\mathrm{ar}}^{\mathrm{sys}}\\ +&0 = q_{\mathrm{v,out}}^{\ell} - q_{\mathrm{ar,p}}^{\mathrm{sys}}\\ +&I_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}q_{\mathrm{ar,p}}^{\mathrm{sys}}}{\mathrm{d}t} + Z_{\mathrm{ar}}^{\mathrm{sys}}\,q_{\mathrm{ar,p}}^{\mathrm{sys}}=p_{\mathrm{ar}}^{\mathrm{sys}}-p_{\mathrm{ar,d}}^{\mathrm{sys}}\\ +&C_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ar,d}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar,p}}^{\mathrm{sys}} - q_{\mathrm{ar}}^{\mathrm{sys}}\\ +&L_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}q_{\mathrm{ar}}^{\mathrm{sys}}}{\mathrm{d}t} + R_{\mathrm{ar}}^{\mathrm{sys}}\,q_{\mathrm{ar}}^{\mathrm{sys}}=p_{\mathrm{ar,d}}^{\mathrm{sys}}-p_{\mathrm{ven}}^{\mathrm{sys}}\\ +&C_{\mathrm{ven}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ven}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar}}^{\mathrm{sys}}-q_{\mathrm{ven}}^{\mathrm{sys}}\\ +&L_{\mathrm{ven}}^{\mathrm{sys}} \frac{\mathrm{d}q_{\mathrm{ven}}^{\mathrm{sys}}}{\mathrm{d}t} + R_{\mathrm{ven}}^{\mathrm{sys}}\, q_{\mathrm{ven}}^{\mathrm{sys}} = p_{\mathrm{ven}}^{\mathrm{sys}} - p_{\mathrm{at}}^{r} +\end{align} + +right heart and pulmonary circulation: +\begin{align} +&-Q_{\mathrm{at}}^{r} = q_{\mathrm{ven}}^{\mathrm{sys}} - q_{\mathrm{v,in}}^{r}\\ +&\tilde{R}_{\mathrm{v,in}}^{r}\,q_{\mathrm{v,in}}^{r} = p_{\mathrm{at}}^{r}-p_{\mathrm{v}}^{r}\\ +&-Q_{\mathrm{v}}^{r} = q_{\mathrm{v,in}}^{r} - q_{\mathrm{v,out}}^{r}\\ +&\tilde{R}_{\mathrm{v,out}}^{r}\,q_{\mathrm{v,out}}^{r} = p_{\mathrm{v}}^{r}-p_{\mathrm{ar}}^{\mathrm{pul}}\\ +&C_{\mathrm{ar}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{v,out}}^{r} - q_{\mathrm{ar}}^{\mathrm{pul}}\\ +&L_{\mathrm{ar}}^{\mathrm{pul}} \frac{\mathrm{d}q_{\mathrm{ar}}^{\mathrm{pul}}}{\mathrm{d}t} + R_{\mathrm{ar}}^{\mathrm{pul}}\,q_{\mathrm{ar}}^{\mathrm{pul}}=p_{\mathrm{ar}}^{\mathrm{pul}} -p_{\mathrm{ven}}^{\mathrm{pul}}\\ +&C_{\mathrm{ven}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{ven}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{ar}}^{\mathrm{pul}} - q_{\mathrm{ven}}^{\mathrm{pul}}\\ +&L_{\mathrm{ven}}^{\mathrm{pul}} \frac{\mathrm{d}q_{\mathrm{ven}}^{\mathrm{pul}}}{\mathrm{d}t} + R_{\mathrm{ven}}^{\mathrm{pul}}\, q_{\mathrm{ven}}^{\mathrm{pul}}=p_{\mathrm{ven}}^{\mathrm{pul}}-p_{\mathrm{at}}^{\ell} +\end{align} +""" class cardiovascular0Dsyspul(cardiovascular0Dbase): diff --git a/src/ambit_fe/flow0d/cardiovascular0D_syspulcap.py b/src/ambit_fe/flow0d/cardiovascular0D_syspulcap.py index 30b879a3..2bc723e5 100644 --- a/src/ambit_fe/flow0d/cardiovascular0D_syspulcap.py +++ b/src/ambit_fe/flow0d/cardiovascular0D_syspulcap.py @@ -14,42 +14,44 @@ from ..mpiroutines import allgather_vec from .. import utilities -# systemic and pulmonary closed-loop circulation model including capillary flow, each heart chamber can be treated individually, -# either as 0D elastance model, volume or flux coming from a 3D solid, or interface fluxes from a 3D fluid model - -# 36 governing equations (uncomment and paste directly into a LaTeX environment): - -#% left heart and systemic circulation: -#\begin{align} -#&-Q_{\mathrm{at}}^{\ell} = q_{\mathrm{ven}}^{\mathrm{pul}} - q_{\mathrm{v,in}}^{\ell}\nonumber\\ -#&\tilde{R}_{\mathrm{v,in}}^{\ell}\,q_{\mathrm{v,in}}^{\ell} = p_{\mathrm{at}}^{\ell}-p_{\mathrm{v}}^{\ell}\nonumber\\ -#&-Q_{\mathrm{v}}^{\ell} = q_{\mathrm{v,in}}^{\ell} - q_{\mathrm{v,out}}^{\ell}\nonumber\\ -#&\tilde{R}_{\mathrm{v,out}}^{\ell}\,q_{\mathrm{v,out}}^{\ell} = p_{\mathrm{v}}^{\ell}-p_{\mathrm{ar}}^{\mathrm{sys}}\nonumber\\ -#&0 = q_{\mathrm{v,out}}^{\ell} - q_{\mathrm{ar,p}}^{\mathrm{sys}}\nonumber\\ -#&I_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}q_{\mathrm{ar,p}}^{\mathrm{sys}}}{\mathrm{d}t} + Z_{\mathrm{ar}}^{\mathrm{sys}}\,q_{\mathrm{ar,p}}^{\mathrm{sys}}=p_{\mathrm{ar}}^{\mathrm{sys}}-p_{\mathrm{ar,d}}^{\mathrm{sys}}\nonumber\\ -#&C_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ar,d}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar,p}}^{\mathrm{sys}} - q_{\mathrm{ar}}^{\mathrm{sys}}\nonumber\\ -#&L_{\mathrm{ar}}^{\mathrm{sys}}\frac{\mathrm{d}q_{\mathrm{ar}}^{\mathrm{sys}}}{\mathrm{d}t} + R_{\mathrm{ar}}^{\mathrm{sys}}\,q_{\mathrm{ar}}^{\mathrm{sys}}=p_{\mathrm{ar,d}}^{\mathrm{sys}} -p_{\mathrm{ar,peri}}^{\mathrm{sys}}\nonumber\\ -#&\left(\sum_{j\in\{\mathrm{spl,espl,\atop msc,cer,cor}\}}\!\!\!\!\!\!\!\!\!C_{\mathrm{ar},j}^{\mathrm{sys}}\right) \frac{\mathrm{d}p_{\mathrm{ar,peri}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar}}^{\mathrm{sys}}-\!\!\!\!\!\sum_{j\in\{\mathrm{spl,espl,\atop msc,cer,cor}\}}\!\!\!\!\!\!\!\!\!q_{\mathrm{ar},j}^{\mathrm{sys}}\nonumber\\ -#&R_{\mathrm{ar},i}^{\mathrm{sys}}\,q_{\mathrm{ar},i}^{\mathrm{sys}} = p_{\mathrm{ar,peri}}^{\mathrm{sys}} - p_{\mathrm{ven},i}^{\mathrm{sys}}, \quad\scriptstyle{i\in\{\mathrm{spl,espl,\atop msc,cer,cor}\}}\nonumber\\ -#&C_{\mathrm{ven},i}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ven},i}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar},i}^{\mathrm{sys}} - q_{\mathrm{ven},i}^{\mathrm{sys}}, \quad\scriptstyle{i\in\{\mathrm{spl,espl,\atop msc,cer,cor}\}}\nonumber\\ -#&R_{\mathrm{ven},i}^{\mathrm{sys}}\,q_{\mathrm{ven},i}^{\mathrm{sys}} = p_{\mathrm{ven},i}^{\mathrm{sys}}-p_{\mathrm{ven}}^{\mathrm{sys}}, \quad\scriptstyle{i\in\{\mathrm{spl,espl,\atop msc,cer,cor}\}}\nonumber\\ -#&C_{\mathrm{ven}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ven}}^{\mathrm{sys}}}{\mathrm{d}t} = \!\!\!\!\sum_{j=\mathrm{spl,espl,\atop msc,cer,cor}}\!\!\!\!\!q_{\mathrm{ven},j}^{\mathrm{sys}}-q_{\mathrm{ven}}^{\mathrm{sys}}\nonumber\\ -#&L_{\mathrm{ven}}^{\mathrm{sys}}\frac{\mathrm{d}q_{\mathrm{ven}}^{\mathrm{sys}}}{\mathrm{d}t} + R_{\mathrm{ven}}^{\mathrm{sys}}\, q_{\mathrm{ven}}^{\mathrm{sys}} = p_{\mathrm{ven}}^{\mathrm{sys}} - p_{\mathrm{at}}^{r}\nonumber -#\end{align} - -#% right heart and pulmonary circulation: -#\begin{align} -#&-Q_{\mathrm{at}}^{r} = q_{\mathrm{ven}}^{\mathrm{sys}} - q_{\mathrm{v,in}}^{r}\nonumber\\ -#&\tilde{R}_{\mathrm{v,in}}^{r}\,q_{\mathrm{v,in}}^{r} = p_{\mathrm{at}}^{r}-p_{\mathrm{v}}^{r}\nonumber\\ -#&-Q_{\mathrm{v}}^{r} = q_{\mathrm{v,in}}^{r} - q_{\mathrm{v,out}}^{r}\nonumber\\ -#&\tilde{R}_{\mathrm{v,out}}^{r}\,q_{\mathrm{v,out}}^{r} = p_{\mathrm{v}}^{r}-p_{\mathrm{ar}}^{\mathrm{pul}}\nonumber\\ -#&C_{\mathrm{ar}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{v,out}}^{r} - q_{\mathrm{ar}}^{\mathrm{pul}}\nonumber\\ -#&L_{\mathrm{ar}}^{\mathrm{pul}}\frac{\mathrm{d}q_{\mathrm{ar}}^{\mathrm{pul}}}{\mathrm{d}t} + R_{\mathrm{ar}}^{\mathrm{pul}}\,q_{\mathrm{ar}}^{\mathrm{pul}}=p_{\mathrm{ar}}^{\mathrm{pul}} -p_{\mathrm{cap}}^{\mathrm{pul}}\nonumber\\ -#&C_{\mathrm{cap}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{cap}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{ar}}^{\mathrm{pul}} - q_{\mathrm{cap}}^{\mathrm{pul}}\nonumber\\ -#&R_{\mathrm{cap}}^{\mathrm{pul}}\,q_{\mathrm{cap}}^{\mathrm{pul}}=p_{\mathrm{cap}}^{\mathrm{pul}}-p_{\mathrm{ven}}^{\mathrm{pul}}\nonumber\\ -#&C_{\mathrm{ven}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{ven}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{cap}}^{\mathrm{pul}} - q_{\mathrm{ven}}^{\mathrm{pul}}\nonumber\\ -#&L_{\mathrm{ven}}^{\mathrm{pul}}\frac{\mathrm{d}q_{\mathrm{ven}}^{\mathrm{pul}}}{\mathrm{d}t} + R_{\mathrm{ven}}^{\mathrm{pul}}\, q_{\mathrm{ven}}^{\mathrm{pul}}=p_{\mathrm{ven}}^{\mathrm{pul}}-p_{\mathrm{at}}^{\ell}\nonumber -#\end{align} +""" +Systemic and pulmonary closed-loop circulation model including capillary flow, each heart chamber can be treated individually, +either as 0D elastance model, volume or flux coming from a 3D solid, or interface fluxes from a 3D fluid model + +36 governing equations: + +left heart and systemic circulation: +\begin{align} +&-Q_{\mathrm{at}}^{\ell} = q_{\mathrm{ven}}^{\mathrm{pul}} - q_{\mathrm{v,in}}^{\ell}\nonumber\\ +&\tilde{R}_{\mathrm{v,in}}^{\ell}\,q_{\mathrm{v,in}}^{\ell} = p_{\mathrm{at}}^{\ell}-p_{\mathrm{v}}^{\ell}\nonumber\\ +&-Q_{\mathrm{v}}^{\ell} = q_{\mathrm{v,in}}^{\ell} - q_{\mathrm{v,out}}^{\ell}\nonumber\\ +&\tilde{R}_{\mathrm{v,out}}^{\ell}\,q_{\mathrm{v,out}}^{\ell} = p_{\mathrm{v}}^{\ell}-p_{\mathrm{ar}}^{\mathrm{sys}}\nonumber\\ +&0 = q_{\mathrm{v,out}}^{\ell} - q_{\mathrm{ar,p}}^{\mathrm{sys}}\nonumber\\ +&I_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}q_{\mathrm{ar,p}}^{\mathrm{sys}}}{\mathrm{d}t} + Z_{\mathrm{ar}}^{\mathrm{sys}}\,q_{\mathrm{ar,p}}^{\mathrm{sys}}=p_{\mathrm{ar}}^{\mathrm{sys}}-p_{\mathrm{ar,d}}^{\mathrm{sys}}\nonumber\\ +&C_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ar,d}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar,p}}^{\mathrm{sys}} - q_{\mathrm{ar}}^{\mathrm{sys}}\nonumber\\ +&L_{\mathrm{ar}}^{\mathrm{sys}}\frac{\mathrm{d}q_{\mathrm{ar}}^{\mathrm{sys}}}{\mathrm{d}t} + R_{\mathrm{ar}}^{\mathrm{sys}}\,q_{\mathrm{ar}}^{\mathrm{sys}}=p_{\mathrm{ar,d}}^{\mathrm{sys}} -p_{\mathrm{ar,peri}}^{\mathrm{sys}}\nonumber\\ +&\left(\sum_{j\in\{\mathrm{spl,espl,\atop msc,cer,cor}\}}\!\!\!\!\!\!\!\!\!C_{\mathrm{ar},j}^{\mathrm{sys}}\right) \frac{\mathrm{d}p_{\mathrm{ar,peri}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar}}^{\mathrm{sys}}-\!\!\!\!\!\sum_{j\in\{\mathrm{spl,espl,\atop msc,cer,cor}\}}\!\!\!\!\!\!\!\!\!q_{\mathrm{ar},j}^{\mathrm{sys}}\nonumber\\ +&R_{\mathrm{ar},i}^{\mathrm{sys}}\,q_{\mathrm{ar},i}^{\mathrm{sys}} = p_{\mathrm{ar,peri}}^{\mathrm{sys}} - p_{\mathrm{ven},i}^{\mathrm{sys}}, \quad\scriptstyle{i\in\{\mathrm{spl,espl,\atop msc,cer,cor}\}}\nonumber\\ +&C_{\mathrm{ven},i}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ven},i}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar},i}^{\mathrm{sys}} - q_{\mathrm{ven},i}^{\mathrm{sys}}, \quad\scriptstyle{i\in\{\mathrm{spl,espl,\atop msc,cer,cor}\}}\nonumber\\ +&R_{\mathrm{ven},i}^{\mathrm{sys}}\,q_{\mathrm{ven},i}^{\mathrm{sys}} = p_{\mathrm{ven},i}^{\mathrm{sys}}-p_{\mathrm{ven}}^{\mathrm{sys}}, \quad\scriptstyle{i\in\{\mathrm{spl,espl,\atop msc,cer,cor}\}}\nonumber\\ +&C_{\mathrm{ven}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ven}}^{\mathrm{sys}}}{\mathrm{d}t} = \!\!\!\!\sum_{j=\mathrm{spl,espl,\atop msc,cer,cor}}\!\!\!\!\!q_{\mathrm{ven},j}^{\mathrm{sys}}-q_{\mathrm{ven}}^{\mathrm{sys}}\nonumber\\ +&L_{\mathrm{ven}}^{\mathrm{sys}}\frac{\mathrm{d}q_{\mathrm{ven}}^{\mathrm{sys}}}{\mathrm{d}t} + R_{\mathrm{ven}}^{\mathrm{sys}}\, q_{\mathrm{ven}}^{\mathrm{sys}} = p_{\mathrm{ven}}^{\mathrm{sys}} - p_{\mathrm{at}}^{r}\nonumber +\end{align} + +right heart and pulmonary circulation: +\begin{align} +&-Q_{\mathrm{at}}^{r} = q_{\mathrm{ven}}^{\mathrm{sys}} - q_{\mathrm{v,in}}^{r}\nonumber\\ +&\tilde{R}_{\mathrm{v,in}}^{r}\,q_{\mathrm{v,in}}^{r} = p_{\mathrm{at}}^{r}-p_{\mathrm{v}}^{r}\nonumber\\ +&-Q_{\mathrm{v}}^{r} = q_{\mathrm{v,in}}^{r} - q_{\mathrm{v,out}}^{r}\nonumber\\ +&\tilde{R}_{\mathrm{v,out}}^{r}\,q_{\mathrm{v,out}}^{r} = p_{\mathrm{v}}^{r}-p_{\mathrm{ar}}^{\mathrm{pul}}\nonumber\\ +&C_{\mathrm{ar}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{v,out}}^{r} - q_{\mathrm{ar}}^{\mathrm{pul}}\nonumber\\ +&L_{\mathrm{ar}}^{\mathrm{pul}}\frac{\mathrm{d}q_{\mathrm{ar}}^{\mathrm{pul}}}{\mathrm{d}t} + R_{\mathrm{ar}}^{\mathrm{pul}}\,q_{\mathrm{ar}}^{\mathrm{pul}}=p_{\mathrm{ar}}^{\mathrm{pul}} -p_{\mathrm{cap}}^{\mathrm{pul}}\nonumber\\ +&C_{\mathrm{cap}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{cap}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{ar}}^{\mathrm{pul}} - q_{\mathrm{cap}}^{\mathrm{pul}}\nonumber\\ +&R_{\mathrm{cap}}^{\mathrm{pul}}\,q_{\mathrm{cap}}^{\mathrm{pul}}=p_{\mathrm{cap}}^{\mathrm{pul}}-p_{\mathrm{ven}}^{\mathrm{pul}}\nonumber\\ +&C_{\mathrm{ven}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{ven}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{cap}}^{\mathrm{pul}} - q_{\mathrm{ven}}^{\mathrm{pul}}\nonumber\\ +&L_{\mathrm{ven}}^{\mathrm{pul}}\frac{\mathrm{d}q_{\mathrm{ven}}^{\mathrm{pul}}}{\mathrm{d}t} + R_{\mathrm{ven}}^{\mathrm{pul}}\, q_{\mathrm{ven}}^{\mathrm{pul}}=p_{\mathrm{ven}}^{\mathrm{pul}}-p_{\mathrm{at}}^{\ell}\nonumber +\end{align} +""" class cardiovascular0Dsyspulcap(cardiovascular0Dbase): @@ -663,45 +665,47 @@ def print_to_screen(self, var, aux): -# similar to syspulcap model, however with the coronaries branching off after the aortic valve and directly feeding back into the right atrium - -# 37 governing equations (uncomment and paste directly into a LaTeX environment): - -#% left heart and systemic circulation: -#\begin{align} -#&-Q_{\mathrm{at}}^{\ell} = q_{\mathrm{ven}}^{\mathrm{pul}} - q_{\mathrm{v,in}}^{\ell}\nonumber\\ -#&\tilde{R}_{\mathrm{v,in}}^{\ell}\,q_{\mathrm{v,in}}^{\ell} = p_{\mathrm{at}}^{\ell}-p_{\mathrm{v}}^{\ell}\nonumber\\ -#&-Q_{\mathrm{v}}^{\ell} = q_{\mathrm{v,in}}^{\ell} - q_{\mathrm{v,out}}^{\ell}\nonumber\\ -#&\tilde{R}_{\mathrm{v,out}}^{\ell}\,q_{\mathrm{v,out}}^{\ell} = p_{\mathrm{v}}^{\ell}-p_{\mathrm{ar}}^{\mathrm{sys}}\nonumber\\ -#&0 = q_{\mathrm{v,out}}^{\ell} - q_{\mathrm{ar,p}}^{\mathrm{sys}} - q_{\mathrm{ar,cor,in}}^{\mathrm{sys}}\nonumber\\ -#&I_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}q_{\mathrm{ar,p}}^{\mathrm{sys}}}{\mathrm{d}t} + Z_{\mathrm{ar}}^{\mathrm{sys}}\,q_{\mathrm{ar,p}}^{\mathrm{sys}}=p_{\mathrm{ar}}^{\mathrm{sys}}-p_{\mathrm{ar,d}}^{\mathrm{sys}}\nonumber\\ -#&C_{\mathrm{ar,cor}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar,cor,in}}^{\mathrm{sys}} - q_{\mathrm{ar,cor}}^{\mathrm{sys}}\nonumber\\ -#&R_{\mathrm{ar,cor}}^{\mathrm{sys}}\,q_{\mathrm{ar,cor}}^{\mathrm{sys}} = p_{\mathrm{ar}}^{\mathrm{sys}} - p_{\mathrm{ven,cor}}^{\mathrm{sys}}\nonumber\\ -#&C_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ar,d}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar,p}}^{\mathrm{sys}} - q_{\mathrm{ar}}^{\mathrm{sys}}\nonumber\\ -#&L_{\mathrm{ar}}^{\mathrm{sys}}\frac{\mathrm{d}q_{\mathrm{ar}}^{\mathrm{sys}}}{\mathrm{d}t} + R_{\mathrm{ar}}^{\mathrm{sys}}\,q_{\mathrm{ar}}^{\mathrm{sys}}=p_{\mathrm{ar,d}}^{\mathrm{sys}} -p_{\mathrm{ar,peri}}^{\mathrm{sys}}\nonumber\\ -#&\left(\sum_{j\in\{\mathrm{spl,espl,\atop msc,cer}\}}\!\!\!\!\!\!\!\!\!C_{\mathrm{ar},j}^{\mathrm{sys}}\right) \frac{\mathrm{d}p_{\mathrm{ar,peri}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar}}^{\mathrm{sys}}-\!\!\!\!\!\sum_{j\in\{\mathrm{spl,espl,\atop msc,cer}\}}\!\!\!\!\!\!\!\!\!q_{\mathrm{ar},j}^{\mathrm{sys}}\nonumber\\ -#&R_{\mathrm{ar},i}^{\mathrm{sys}}\,q_{\mathrm{ar},i}^{\mathrm{sys}} = p_{\mathrm{ar,peri}}^{\mathrm{sys}} - p_{\mathrm{ven},i}^{\mathrm{sys}}, \quad\scriptstyle{i\in\{\mathrm{spl,espl,\atop msc,cer}\}}\nonumber\\ -#&C_{\mathrm{ven},i}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ven},i}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar},i}^{\mathrm{sys}} - q_{\mathrm{ven},i}^{\mathrm{sys}}, \quad\scriptstyle{i\in\{\mathrm{spl,espl,\atop msc,cer}\}}\nonumber\\ -#&R_{\mathrm{ven},i}^{\mathrm{sys}}\,q_{\mathrm{ven},i}^{\mathrm{sys}} = p_{\mathrm{ven},i}^{\mathrm{sys}}-p_{\mathrm{ven}}^{\mathrm{sys}}, \quad\scriptstyle{i\in\{\mathrm{spl,espl,\atop msc,cer}\}}\nonumber\\ -#&C_{\mathrm{ven}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ven}}^{\mathrm{sys}}}{\mathrm{d}t} = \!\!\!\!\sum_{j=\mathrm{spl,espl,\atop msc,cer}}\!\!\!\!\!q_{\mathrm{ven},j}^{\mathrm{sys}}-q_{\mathrm{ven}}^{\mathrm{sys}}\nonumber\\ -#&L_{\mathrm{ven}}^{\mathrm{sys}}\frac{\mathrm{d}q_{\mathrm{ven}}^{\mathrm{sys}}}{\mathrm{d}t} + R_{\mathrm{ven}}^{\mathrm{sys}}\, q_{\mathrm{ven}}^{\mathrm{sys}} = p_{\mathrm{ven}}^{\mathrm{sys}} - p_{\mathrm{at}}^{r}\nonumber\\ -#&C_{\mathrm{ven,cor}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ven,cor}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar,cor}}^{\mathrm{sys}}-q_{\mathrm{ven,cor}}^{\mathrm{sys}}\nonumber\\ -#&R_{\mathrm{ven,cor}}^{\mathrm{sys}}\,q_{\mathrm{ven,cor}}^{\mathrm{sys}} = p_{\mathrm{ven,cor}}^{\mathrm{sys}} - p_{\mathrm{at}}^{r}\nonumber -#\end{align} - -#% right heart and pulmonary circulation: -#\begin{align} -#&-Q_{\mathrm{at}}^{r} = q_{\mathrm{ven}}^{\mathrm{sys}} + q_{\mathrm{ven,cor}}^{\mathrm{sys}} - q_{\mathrm{v,in}}^{r}\nonumber\\ -#&\tilde{R}_{\mathrm{v,in}}^{r}\,q_{\mathrm{v,in}}^{r} = p_{\mathrm{at}}^{r}-p_{\mathrm{v}}^{r}\nonumber\\ -#&-Q_{\mathrm{v}}^{r} = q_{\mathrm{v,in}}^{r} - q_{\mathrm{v,out}}^{r}\nonumber\\ -#&\tilde{R}_{\mathrm{v,out}}^{r}\,q_{\mathrm{v,out}}^{r} = p_{\mathrm{v}}^{r}-p_{\mathrm{ar}}^{\mathrm{pul}}\nonumber\\ -#&C_{\mathrm{ar}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{v,out}}^{r} - q_{\mathrm{ar}}^{\mathrm{pul}}\nonumber\\ -#&L_{\mathrm{ar}}^{\mathrm{pul}}\frac{\mathrm{d}q_{\mathrm{ar}}^{\mathrm{pul}}}{\mathrm{d}t} + R_{\mathrm{ar}}^{\mathrm{pul}}\,q_{\mathrm{ar}}^{\mathrm{pul}}=p_{\mathrm{ar}}^{\mathrm{pul}} -p_{\mathrm{cap}}^{\mathrm{pul}}\nonumber\\ -#&C_{\mathrm{cap}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{cap}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{ar}}^{\mathrm{pul}} - q_{\mathrm{cap}}^{\mathrm{pul}}\nonumber\\ -#&R_{\mathrm{cap}}^{\mathrm{pul}}\,q_{\mathrm{cap}}^{\mathrm{pul}}=p_{\mathrm{cap}}^{\mathrm{pul}}-p_{\mathrm{ven}}^{\mathrm{pul}}\nonumber\\ -#&C_{\mathrm{ven}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{ven}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{cap}}^{\mathrm{pul}} - q_{\mathrm{ven}}^{\mathrm{pul}}\nonumber\\ -#&L_{\mathrm{ven}}^{\mathrm{pul}}\frac{\mathrm{d}q_{\mathrm{ven}}^{\mathrm{pul}}}{\mathrm{d}t} + R_{\mathrm{ven}}^{\mathrm{pul}}\, q_{\mathrm{ven}}^{\mathrm{pul}}=p_{\mathrm{ven}}^{\mathrm{pul}}-p_{\mathrm{at}}^{\ell}\nonumber -#\end{align} +""" +Similar to syspulcap model, however with the coronaries branching off after the aortic valve and directly feeding back into the right atrium + +37 governing equations: + +left heart and systemic circulation: +\begin{align} +&-Q_{\mathrm{at}}^{\ell} = q_{\mathrm{ven}}^{\mathrm{pul}} - q_{\mathrm{v,in}}^{\ell}\nonumber\\ +&\tilde{R}_{\mathrm{v,in}}^{\ell}\,q_{\mathrm{v,in}}^{\ell} = p_{\mathrm{at}}^{\ell}-p_{\mathrm{v}}^{\ell}\nonumber\\ +&-Q_{\mathrm{v}}^{\ell} = q_{\mathrm{v,in}}^{\ell} - q_{\mathrm{v,out}}^{\ell}\nonumber\\ +&\tilde{R}_{\mathrm{v,out}}^{\ell}\,q_{\mathrm{v,out}}^{\ell} = p_{\mathrm{v}}^{\ell}-p_{\mathrm{ar}}^{\mathrm{sys}}\nonumber\\ +&0 = q_{\mathrm{v,out}}^{\ell} - q_{\mathrm{ar,p}}^{\mathrm{sys}} - q_{\mathrm{ar,cor,in}}^{\mathrm{sys}}\nonumber\\ +&I_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}q_{\mathrm{ar,p}}^{\mathrm{sys}}}{\mathrm{d}t} + Z_{\mathrm{ar}}^{\mathrm{sys}}\,q_{\mathrm{ar,p}}^{\mathrm{sys}}=p_{\mathrm{ar}}^{\mathrm{sys}}-p_{\mathrm{ar,d}}^{\mathrm{sys}}\nonumber\\ +&C_{\mathrm{ar,cor}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar,cor,in}}^{\mathrm{sys}} - q_{\mathrm{ar,cor}}^{\mathrm{sys}}\nonumber\\ +&R_{\mathrm{ar,cor}}^{\mathrm{sys}}\,q_{\mathrm{ar,cor}}^{\mathrm{sys}} = p_{\mathrm{ar}}^{\mathrm{sys}} - p_{\mathrm{ven,cor}}^{\mathrm{sys}}\nonumber\\ +&C_{\mathrm{ar}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ar,d}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar,p}}^{\mathrm{sys}} - q_{\mathrm{ar}}^{\mathrm{sys}}\nonumber\\ +&L_{\mathrm{ar}}^{\mathrm{sys}}\frac{\mathrm{d}q_{\mathrm{ar}}^{\mathrm{sys}}}{\mathrm{d}t} + R_{\mathrm{ar}}^{\mathrm{sys}}\,q_{\mathrm{ar}}^{\mathrm{sys}}=p_{\mathrm{ar,d}}^{\mathrm{sys}} -p_{\mathrm{ar,peri}}^{\mathrm{sys}}\nonumber\\ +&\left(\sum_{j\in\{\mathrm{spl,espl,\atop msc,cer}\}}\!\!\!\!\!\!\!\!\!C_{\mathrm{ar},j}^{\mathrm{sys}}\right) \frac{\mathrm{d}p_{\mathrm{ar,peri}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar}}^{\mathrm{sys}}-\!\!\!\!\!\sum_{j\in\{\mathrm{spl,espl,\atop msc,cer}\}}\!\!\!\!\!\!\!\!\!q_{\mathrm{ar},j}^{\mathrm{sys}}\nonumber\\ +&R_{\mathrm{ar},i}^{\mathrm{sys}}\,q_{\mathrm{ar},i}^{\mathrm{sys}} = p_{\mathrm{ar,peri}}^{\mathrm{sys}} - p_{\mathrm{ven},i}^{\mathrm{sys}}, \quad\scriptstyle{i\in\{\mathrm{spl,espl,\atop msc,cer}\}}\nonumber\\ +&C_{\mathrm{ven},i}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ven},i}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar},i}^{\mathrm{sys}} - q_{\mathrm{ven},i}^{\mathrm{sys}}, \quad\scriptstyle{i\in\{\mathrm{spl,espl,\atop msc,cer}\}}\nonumber\\ +&R_{\mathrm{ven},i}^{\mathrm{sys}}\,q_{\mathrm{ven},i}^{\mathrm{sys}} = p_{\mathrm{ven},i}^{\mathrm{sys}}-p_{\mathrm{ven}}^{\mathrm{sys}}, \quad\scriptstyle{i\in\{\mathrm{spl,espl,\atop msc,cer}\}}\nonumber\\ +&C_{\mathrm{ven}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ven}}^{\mathrm{sys}}}{\mathrm{d}t} = \!\!\!\!\sum_{j=\mathrm{spl,espl,\atop msc,cer}}\!\!\!\!\!q_{\mathrm{ven},j}^{\mathrm{sys}}-q_{\mathrm{ven}}^{\mathrm{sys}}\nonumber\\ +&L_{\mathrm{ven}}^{\mathrm{sys}}\frac{\mathrm{d}q_{\mathrm{ven}}^{\mathrm{sys}}}{\mathrm{d}t} + R_{\mathrm{ven}}^{\mathrm{sys}}\, q_{\mathrm{ven}}^{\mathrm{sys}} = p_{\mathrm{ven}}^{\mathrm{sys}} - p_{\mathrm{at}}^{r}\nonumber\\ +&C_{\mathrm{ven,cor}}^{\mathrm{sys}} \frac{\mathrm{d}p_{\mathrm{ven,cor}}^{\mathrm{sys}}}{\mathrm{d}t} = q_{\mathrm{ar,cor}}^{\mathrm{sys}}-q_{\mathrm{ven,cor}}^{\mathrm{sys}}\nonumber\\ +&R_{\mathrm{ven,cor}}^{\mathrm{sys}}\,q_{\mathrm{ven,cor}}^{\mathrm{sys}} = p_{\mathrm{ven,cor}}^{\mathrm{sys}} - p_{\mathrm{at}}^{r}\nonumber +\end{align} + +right heart and pulmonary circulation: +\begin{align} +&-Q_{\mathrm{at}}^{r} = q_{\mathrm{ven}}^{\mathrm{sys}} + q_{\mathrm{ven,cor}}^{\mathrm{sys}} - q_{\mathrm{v,in}}^{r}\nonumber\\ +&\tilde{R}_{\mathrm{v,in}}^{r}\,q_{\mathrm{v,in}}^{r} = p_{\mathrm{at}}^{r}-p_{\mathrm{v}}^{r}\nonumber\\ +&-Q_{\mathrm{v}}^{r} = q_{\mathrm{v,in}}^{r} - q_{\mathrm{v,out}}^{r}\nonumber\\ +&\tilde{R}_{\mathrm{v,out}}^{r}\,q_{\mathrm{v,out}}^{r} = p_{\mathrm{v}}^{r}-p_{\mathrm{ar}}^{\mathrm{pul}}\nonumber\\ +&C_{\mathrm{ar}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{ar}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{v,out}}^{r} - q_{\mathrm{ar}}^{\mathrm{pul}}\nonumber\\ +&L_{\mathrm{ar}}^{\mathrm{pul}}\frac{\mathrm{d}q_{\mathrm{ar}}^{\mathrm{pul}}}{\mathrm{d}t} + R_{\mathrm{ar}}^{\mathrm{pul}}\,q_{\mathrm{ar}}^{\mathrm{pul}}=p_{\mathrm{ar}}^{\mathrm{pul}} -p_{\mathrm{cap}}^{\mathrm{pul}}\nonumber\\ +&C_{\mathrm{cap}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{cap}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{ar}}^{\mathrm{pul}} - q_{\mathrm{cap}}^{\mathrm{pul}}\nonumber\\ +&R_{\mathrm{cap}}^{\mathrm{pul}}\,q_{\mathrm{cap}}^{\mathrm{pul}}=p_{\mathrm{cap}}^{\mathrm{pul}}-p_{\mathrm{ven}}^{\mathrm{pul}}\nonumber\\ +&C_{\mathrm{ven}}^{\mathrm{pul}} \frac{\mathrm{d}p_{\mathrm{ven}}^{\mathrm{pul}}}{\mathrm{d}t} = q_{\mathrm{cap}}^{\mathrm{pul}} - q_{\mathrm{ven}}^{\mathrm{pul}}\nonumber\\ +&L_{\mathrm{ven}}^{\mathrm{pul}}\frac{\mathrm{d}q_{\mathrm{ven}}^{\mathrm{pul}}}{\mathrm{d}t} + R_{\mathrm{ven}}^{\mathrm{pul}}\, q_{\mathrm{ven}}^{\mathrm{pul}}=p_{\mathrm{ven}}^{\mathrm{pul}}-p_{\mathrm{at}}^{\ell}\nonumber +\end{align} +""" class cardiovascular0Dsyspulcapcor(cardiovascular0Dsyspulcap): diff --git a/src/ambit_fe/flow0d/cardiovascular0D_syspulcaprespir.py b/src/ambit_fe/flow0d/cardiovascular0D_syspulcaprespir.py index e4e38979..a9ad8210 100644 --- a/src/ambit_fe/flow0d/cardiovascular0D_syspulcaprespir.py +++ b/src/ambit_fe/flow0d/cardiovascular0D_syspulcaprespir.py @@ -14,8 +14,10 @@ from ..mpiroutines import allgather_vec from .. import utilities -# respiratory and gas transport part of syspulcap model (Diss Hirschvogel, p. 58ff.) -# builds upon syspulcap model +""" +Respiratory and gas transport part of syspulcap model (Diss Hirschvogel, p. 58ff.) +Builds upon syspulcap model +""" class cardiovascular0Dsyspulcaprespir(cardiovascular0Dsyspulcap): diff --git a/src/ambit_fe/fluid/fluid_kinematics_constitutive.py b/src/ambit_fe/fluid/fluid_kinematics_constitutive.py index 40b0345c..b808af5c 100644 --- a/src/ambit_fe/fluid/fluid_kinematics_constitutive.py +++ b/src/ambit_fe/fluid/fluid_kinematics_constitutive.py @@ -11,8 +11,9 @@ from .fluid_material import materiallaw - -# fluid kinematics and constitutive class +""" +Fluid kinematics and constitutive class +""" class constitutive: diff --git a/src/ambit_fe/fluid/fluid_main.py b/src/ambit_fe/fluid/fluid_main.py index 341c2ac9..970c0752 100644 --- a/src/ambit_fe/fluid/fluid_main.py +++ b/src/ambit_fe/fluid/fluid_main.py @@ -25,12 +25,14 @@ from ..base import problem_base, solver_base -# fluid mechanics, governed by incompressible Navier-Stokes equations: +""" +Fluid mechanics, governed by incompressible Navier-Stokes equations: -#\begin{align} -#\rho \left(\frac{\partial\boldsymbol{v}}{\partial t} + \left(\boldsymbol{\nabla}\boldsymbol{v}\right) \boldsymbol{v}\right) = \boldsymbol{\nabla} \cdot \boldsymbol{\sigma} + \hat{\boldsymbol{b}} \quad \text{in} \; \Omega \times [0, T] \\ -#\boldsymbol{\nabla} \cdot \boldsymbol{v} = 0 \quad \text{in} \; \Omega \times [0, T] -#\end{align} +\begin{align} +\rho \left(\frac{\partial\boldsymbol{v}}{\partial t} + \left(\boldsymbol{\nabla}\boldsymbol{v}\right) \boldsymbol{v}\right) = \boldsymbol{\nabla} \cdot \boldsymbol{\sigma} + \hat{\boldsymbol{b}} \quad \text{in} \; \Omega \times [0, T] \\ +\boldsymbol{\nabla} \cdot \boldsymbol{v} = 0 \quad \text{in} \; \Omega \times [0, T] +\end{align} +""" class FluidmechanicsProblem(problem_base): @@ -66,6 +68,7 @@ def __init__(self, io_params, time_params, fem_params, constitutive_models, bc_d self.ds = ufl.Measure("ds", domain=self.io.mesh_master, subdomain_data=self.io.mt_b1_master, metadata={'quadrature_degree': self.quad_degree}) self.dS = ufl.Measure("dS", domain=self.io.mesh_master, subdomain_data=self.io.mt_b1_master, metadata={'quadrature_degree': self.quad_degree}) + self.de = ufl.Measure("ds", domain=self.io.mesh_master, subdomain_data=self.io.mt_b2_master, metadata={'quadrature_degree': self.quad_degree}) # collect domain data self.rho = [] @@ -421,23 +424,23 @@ def set_variational_forms(self): # external virtual power (from Neumann or Robin boundary conditions, body forces, ...) w_neumann, w_neumann_old, w_body, w_body_old, w_robin, w_robin_old, w_stabneumann, w_stabneumann_old, w_robin_valve, w_robin_valve_old, w_membrane, w_membrane_old = ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0) if 'neumann' in self.bc_dict.keys(): - w_neumann = self.bc.neumann_bcs(self.bc_dict['neumann'], self.V_v, self.Vd_scalar, self.ds, F=self.alevar['Fale'], funcs_to_update=self.ti.funcs_to_update, funcs_to_update_vec=self.ti.funcs_to_update_vec) - w_neumann_old = self.bc.neumann_bcs(self.bc_dict['neumann'], self.V_v, self.Vd_scalar, self.ds, F=self.alevar['Fale_old'], funcs_to_update=self.ti.funcs_to_update_old, funcs_to_update_vec=self.ti.funcs_to_update_vec_old) + w_neumann = self.bc.neumann_bcs(self.bc_dict['neumann'], self.V_v, self.Vd_scalar, [self.ds,self.de], F=self.alevar['Fale'], funcs_to_update=self.ti.funcs_to_update, funcs_to_update_vec=self.ti.funcs_to_update_vec) + w_neumann_old = self.bc.neumann_bcs(self.bc_dict['neumann'], self.V_v, self.Vd_scalar, [self.ds,self.de], F=self.alevar['Fale_old'], funcs_to_update=self.ti.funcs_to_update_old, funcs_to_update_vec=self.ti.funcs_to_update_vec_old) if 'bodyforce' in self.bc_dict.keys(): w_body = self.bc.bodyforce(self.bc_dict['bodyforce'], self.V_v, self.Vd_scalar, self.dx, F=self.alevar['Fale'], funcs_to_update=self.ti.funcs_to_update) w_body_old = self.bc.bodyforce(self.bc_dict['bodyforce'], self.V_v, self.Vd_scalar, self.dx, F=self.alevar['Fale_old'], funcs_to_update=self.ti.funcs_to_update_old) if 'robin' in self.bc_dict.keys(): - w_robin = self.bc.robin_bcs(self.bc_dict['robin'], self.v, self.ds, F=self.alevar['Fale']) - w_robin_old = self.bc.robin_bcs(self.bc_dict['robin'], self.v_old, self.ds, F=self.alevar['Fale_old']) + w_robin = self.bc.robin_bcs(self.bc_dict['robin'], self.v, [self.ds,self.de], F=self.alevar['Fale']) + w_robin_old = self.bc.robin_bcs(self.bc_dict['robin'], self.v_old, [self.ds,self.de], F=self.alevar['Fale_old']) if 'stabilized_neumann' in self.bc_dict.keys(): - w_stabneumann = self.bc.stabilized_neumann_bcs(self.bc_dict['stabilized_neumann'], self.v, self.ds, wel=self.alevar['w'], F=self.alevar['Fale']) - w_stabneumann_old = self.bc.stabilized_neumann_bcs(self.bc_dict['stabilized_neumann'], self.v_old, self.ds, wel=self.alevar['w_old'], F=self.alevar['Fale_old']) + w_stabneumann = self.bc.stabilized_neumann_bcs(self.bc_dict['stabilized_neumann'], self.v, [self.ds,self.de], wel=self.alevar['w'], F=self.alevar['Fale']) + w_stabneumann_old = self.bc.stabilized_neumann_bcs(self.bc_dict['stabilized_neumann'], self.v_old, [self.ds,self.de], wel=self.alevar['w_old'], F=self.alevar['Fale_old']) if 'robin_valve' in self.bc_dict.keys(): assert(self.num_dupl>1) # only makes sense if we have duplicate pressure domains self.have_robin_valve = True self.beta_valve, self.beta_valve_old = [], [] - w_robin_valve = self.bc.robin_valve_bcs(self.bc_dict['robin_valve'], self.v, self.Vd_scalar, self.beta_valve, self.dS, wel=self.alevar['w'], F=self.alevar['Fale']) - w_robin_valve_old = self.bc.robin_valve_bcs(self.bc_dict['robin_valve'], self.v_old, self.Vd_scalar, self.beta_valve_old, self.dS, wel=self.alevar['w_old'], F=self.alevar['Fale_old']) + w_robin_valve = self.bc.robin_valve_bcs(self.bc_dict['robin_valve'], self.v, self.Vd_scalar, self.beta_valve, [self.dS], wel=self.alevar['w'], F=self.alevar['Fale']) + w_robin_valve_old = self.bc.robin_valve_bcs(self.bc_dict['robin_valve'], self.v_old, self.Vd_scalar, self.beta_valve_old, [self.dS], wel=self.alevar['w_old'], F=self.alevar['Fale_old']) if 'flux_monitor' in self.bc_dict.keys(): self.have_flux_monitor = True self.q_, self.q_old_ = [], [] @@ -477,8 +480,8 @@ def set_variational_forms(self): self.io.readfunction(h0_func, self.bc_dict['membrane'][nm]['params']['h0']['field']) self.wallfields.append(h0_func) - w_membrane, self.idmem, self.bstress = self.bc.membranesurf_bcs(self.bc_dict['membrane'], self.ufluid, self.v, self.acc, self.ds, ivar=self.internalvars, wallfields=self.wallfields) - w_membrane_old, _, _ = self.bc.membranesurf_bcs(self.bc_dict['membrane'], self.uf_old, self.v_old, self.a_old, self.ds, ivar=self.internalvars_old, wallfields=self.wallfields) + w_membrane, self.idmem, self.bstress = self.bc.membranesurf_bcs(self.bc_dict['membrane'], self.ufluid, self.v, self.acc, [self.ds,self.de], ivar=self.internalvars, wallfields=self.wallfields) + w_membrane_old, _, _ = self.bc.membranesurf_bcs(self.bc_dict['membrane'], self.uf_old, self.v_old, self.a_old, [self.ds,self.de], ivar=self.internalvars_old, wallfields=self.wallfields) w_neumann_prestr, self.deltaW_prestr_kin = ufl.as_ufl(0), ufl.as_ufl(0) if self.prestress_initial or self.prestress_initial_only: @@ -488,10 +491,10 @@ def set_variational_forms(self): # it seems that we need some slight inertia for this to work smoothly, so let's use transient Stokes here (instead of steady Navier-Stokes or steady Stokes...) self.deltaW_prestr_kin += self.vf.deltaW_kin_stokes_transient(self.acc, self.v, self.rho[n], self.dx(N), w=self.alevar['w'], F=self.alevar['Fale']) if 'neumann_prestress' in self.bc_dict.keys(): - w_neumann_prestr = self.bc.neumann_prestress_bcs(self.bc_dict['neumann_prestress'], self.V_v, self.Vd_scalar, self.ds, funcs_to_update=self.funcs_to_update_pre, funcs_to_update_vec=self.funcs_to_update_vec_pre) + w_neumann_prestr = self.bc.neumann_prestress_bcs(self.bc_dict['neumann_prestress'], self.V_v, self.Vd_scalar, [self.ds,self.de], funcs_to_update=self.funcs_to_update_pre, funcs_to_update_vec=self.funcs_to_update_vec_pre) if 'membrane' in self.bc_dict.keys(): self.ufluid_prestr = self.v * self.dt # only incremental displacement needed, since MULF update actually yields a zero displacement after the step - w_membrane_prestr, _, _ = self.bc.membranesurf_bcs(self.bc_dict['membrane'], self.ufluid_prestr, self.v, self.acc, self.ds, ivar=self.internalvars, wallfields=self.wallfields) + w_membrane_prestr, _, _ = self.bc.membranesurf_bcs(self.bc_dict['membrane'], self.ufluid_prestr, self.v, self.acc, [self.ds,self.de], ivar=self.internalvars, wallfields=self.wallfields) self.deltaW_prestr_ext = w_neumann_prestr + w_robin + w_stabneumann + w_membrane_prestr else: assert('neumann_prestress' not in self.bc_dict.keys()) diff --git a/src/ambit_fe/fluid/fluid_variationalform.py b/src/ambit_fe/fluid/fluid_variationalform.py index f89d2ea4..ae2fee08 100644 --- a/src/ambit_fe/fluid/fluid_variationalform.py +++ b/src/ambit_fe/fluid/fluid_variationalform.py @@ -9,10 +9,12 @@ import ufl from ..variationalform import variationalform_base +""" +Fluid mechanics variational forms class +Principle of Virtual Power +\delta \mathcal{P} = \delta \mathcal{P}_{\mathrm{kin}} + \delta \mathcal{P}_{\mathrm{int}} - \delta \mathcal{P}_{\mathrm{ext}} = 0, \quad \forall \; \delta\boldsymbol{v} +""" -# fluid mechanics variational forms class -# Principle of Virtual Power -# TeX: \delta \mathcal{P} = \delta \mathcal{P}_{\mathrm{kin}} + \delta \mathcal{P}_{\mathrm{int}} - \delta \mathcal{P}_{\mathrm{ext}} = 0, \quad \forall \; \delta\boldsymbol{v} class variationalform(variationalform_base): ### Kinetic virtual power \delta \mathcal{P}_{\mathrm{kin}} diff --git a/src/ambit_fe/ioparams.py b/src/ambit_fe/ioparams.py index 7484ceb5..846423e7 100644 --- a/src/ambit_fe/ioparams.py +++ b/src/ambit_fe/ioparams.py @@ -18,6 +18,8 @@ def check_params_io(params): 'indicate_results_by', 'mesh_domain', 'mesh_boundary', + 'mesh_edge', + 'mesh_point', 'meshfile_type', 'ode_parallel', 'order_fib_input', diff --git a/src/ambit_fe/ioroutines.py b/src/ambit_fe/ioroutines.py index bb920d16..6dfbf015 100644 --- a/src/ambit_fe/ioroutines.py +++ b/src/ambit_fe/ioroutines.py @@ -36,7 +36,12 @@ def __init__(self, io_params, entity_maps, comm): except: self.output_path_pre = self.output_path self.mesh_domain = io_params['mesh_domain'] - self.mesh_boundary = io_params['mesh_boundary'] + try: self.mesh_boundary = io_params['mesh_boundary'] + except: self.mesh_boundary = None + try: self.mesh_edge = io_params['mesh_edge'] + except: self.mesh_edge = None + try: self.mesh_point = io_params['mesh_point'] + except: self.mesh_point = None try: self.fiber_data = io_params['fiber_data'] except: self.fiber_data = [] @@ -111,49 +116,73 @@ def readin_mesh(self): # for a 2D problem - b1: edge BCs, b2: point BCs # 1D problems not supported (currently...) + self.mt_b1_master, self.mt_b2_master, self.mt_b3_master = None, None, None + if self.mesh.topology.dim == 3: - try: + if self.mesh_boundary is not None: + self.mesh.topology.create_connectivity(2, self.mesh.topology.dim) with io.XDMFFile(self.comm, self.mesh_boundary, 'r', encoding=encoding) as infile: self.mt_b1 = infile.read_meshtags(self.mesh, name=self.gridname_boundary) self.mt_b1_master = self.mt_b1 - except: - pass - try: + if self.mesh_edge is not None: + self.mesh.topology.create_connectivity(1, self.mesh.topology.dim) - with io.XDMFFile(self.comm, self.mesh_boundary, 'r', encoding=encoding) as infile: - self.mt_b2 = infile.read_meshtags(self.mesh, name=self.gridname_boundary+'_b2') + with io.XDMFFile(self.comm, self.mesh_edge, 'r', encoding=encoding) as infile: + self.mt_b2 = infile.read_meshtags(self.mesh, name=self.gridname_boundary) self.mt_b2_master = self.mt_b2 - except: - pass - try: + """ + NOTE: We cannot perform line/edge integrals in 3D in an intuitive manner by + defining and using a 1-dimensional ufl ds measure. This is not yet implemented + in dolfinx. + But, we can use the mixed dimensional branch to create a submesh and collect the + integration edges, performing the integration over the 1D boundary using entitiy maps. + """ + if self.USE_MIXED_DOLFINX_BRANCH: + self.mesh_e = mesh.create_submesh(self.mesh, self.mesh.topology.dim-2, self.mt_b2_master.indices[self.mt_b2_master.values == 1])[0:2] + + edge_imap = self.mesh.topology.index_map(self.mesh.topology.dim-2) + num_edges = edge_imap.size_local + edge_imap.num_ghosts + + inv_emap = np.full(num_edges, -1) + inv_emap[self.mesh_e[1]] = np.arange(len(self.mesh_e[1])) + self.entity_maps[self.mesh_e[0]] = inv_emap + + edge_indices = self.mt_b2_master.indices[self.mt_b2_master.values == 1] + + edge_integration_entities = [] + meshutils.get_integration_entities(self.mesh, edge_indices, 1, edge_integration_entities) + + self.de = ufl.Measure("ds", domain=self.mesh, subdomain_data=[(1, edge_integration_entities)]) + + else: + raise RuntimeError("Weak integrations over edges in 3D currently only supported in mixed dolfinx branch.") + + if self.mesh_point is not None: + self.mesh.topology.create_connectivity(0, self.mesh.topology.dim) - with io.XDMFFile(self.comm, self.mesh_boundary, 'r', encoding=encoding) as infile: - self.mt_b3 = infile.read_meshtags(self.mesh, name=self.gridname_boundary+'_b3') + with io.XDMFFile(self.comm, self.mesh_point, 'r', encoding=encoding) as infile: + self.mt_b3 = infile.read_meshtags(self.mesh, name=self.gridname_boundary) self.mt_b3_master = self.mt_b3 - except: - pass elif self.mesh.topology.dim == 2: - try: + if self.mesh_boundary is not None: + self.mesh.topology.create_connectivity(1, self.mesh.topology.dim) with io.XDMFFile(self.comm, self.mesh_boundary, 'r', encoding=encoding) as infile: self.mt_b1 = infile.read_meshtags(self.mesh, name=self.gridname_boundary) self.mt_b1_master = self.mt_b1 - except: - pass - try: + if self.mesh_point is not None: + self.mesh.topology.create_connectivity(0, self.mesh.topology.dim) - with io.XDMFFile(self.comm, self.mesh_boundary, 'r', encoding=encoding) as infile: - self.mt_b2 = infile.read_meshtags(self.mesh, name=self.gridname_boundary+'_b2') + with io.XDMFFile(self.comm, self.mesh_point, 'r', encoding=encoding) as infile: + self.mt_b2 = infile.read_meshtags(self.mesh, name=self.gridname_boundary) self.mt_b2_master = self.mt_b2 - except: - pass else: raise AttributeError("Your mesh seems to be 1D! Not supported!") diff --git a/src/ambit_fe/meshutils.py b/src/ambit_fe/meshutils.py index f2db16b9..86781a49 100644 --- a/src/ambit_fe/meshutils.py +++ b/src/ambit_fe/meshutils.py @@ -84,3 +84,23 @@ def meshtags_parent_to_child(mshtags, childmsh, childmsh_emap, parentmsh, diment sub_values[child] = all_values[parent] return mesh.meshtags(childmsh, dim_c, np.arange(num_sub_ent, dtype=np.int32), sub_values) + + +def get_integration_entities(msh, entity_indices, codim, integration_entities): + + dim = msh.topology.dim + + entity_imap = msh.topology.index_map(codim) + + msh.topology.create_connectivity(dim, codim) + msh.topology.create_connectivity(codim, dim) + c_to_e = msh.topology.connectivity(dim, codim) + e_to_c = msh.topology.connectivity(codim, dim) + # loop through all relevant entities + for entity in entity_indices: + # check if this entity is owned + if entity < entity_imap.size_local: + # get a cell connected to the entity + cell = e_to_c.links(entity)[0] + local_entity = c_to_e.links(cell).tolist().index(entity) + integration_entities.extend([cell, local_entity]) diff --git a/src/ambit_fe/oderoutines.py b/src/ambit_fe/oderoutines.py index faaf0a66..3e7d95c2 100644 --- a/src/ambit_fe/oderoutines.py +++ b/src/ambit_fe/oderoutines.py @@ -13,6 +13,9 @@ from . import utilities from .mpiroutines import allgather_vec, allgather_vec_entry +""" +ODE base class +""" class ode: diff --git a/src/ambit_fe/signet/signet_hypertrophy.py b/src/ambit_fe/signet/signet_hypertrophy.py index e4207af8..57347420 100644 --- a/src/ambit_fe/signet/signet_hypertrophy.py +++ b/src/ambit_fe/signet/signet_hypertrophy.py @@ -11,8 +11,10 @@ from ..oderoutines import ode -# signalling network model, from Ryall et al. (2012) "Network Reconstruction and Systems Analysis of Cardiac Myocyte Hypertrophy Signaling", The Journal of Biological Chemistry 287(50) -# adopted form supplementary MATLAB code provided by authors +""" +Signalling network model, from Ryall et al. (2012) "Network Reconstruction and Systems Analysis of Cardiac Myocyte Hypertrophy Signaling", The Journal of Biological Chemistry 287(50) +adopted form supplementary MATLAB code provided by authors +""" class signethypertrophy(ode): diff --git a/src/ambit_fe/signet/signet_main.py b/src/ambit_fe/signet/signet_main.py index 64f86639..1d3d3585 100644 --- a/src/ambit_fe/signet/signet_main.py +++ b/src/ambit_fe/signet/signet_main.py @@ -15,7 +15,9 @@ from ..base import problem_base, solver_base -# framework of signalling network models +""" +Framework of signalling network models +""" class SignallingNetworkProblem(problem_base): diff --git a/src/ambit_fe/solid/solid_kinematics_constitutive.py b/src/ambit_fe/solid/solid_kinematics_constitutive.py index 8c43a7ad..9d81a090 100644 --- a/src/ambit_fe/solid/solid_kinematics_constitutive.py +++ b/src/ambit_fe/solid/solid_kinematics_constitutive.py @@ -11,8 +11,9 @@ from .solid_material import materiallaw, growth, growthfunction - -# nonlinear finite strain kinematics and constitutive class +""" +Nonlinear finite strain kinematics and constitutive class +""" class constitutive: diff --git a/src/ambit_fe/solid/solid_main.py b/src/ambit_fe/solid/solid_main.py index 1a3c1ce6..100fca9f 100644 --- a/src/ambit_fe/solid/solid_main.py +++ b/src/ambit_fe/solid/solid_main.py @@ -28,12 +28,14 @@ from ..base import problem_base, solver_base -# solid mechanics governing equation +""" +Solid mechanics governing equation -#\rho_{0} \ddot{\boldsymbol{u}} = \boldsymbol{\nabla}_{0} \cdot (\boldsymbol{F}\boldsymbol{S}) + \hat{\boldsymbol{b}}_{0} \quad \text{in} \; \Omega_{0} \times [0, T] +\rho_{0} \ddot{\boldsymbol{u}} = \boldsymbol{\nabla}_{0} \cdot (\boldsymbol{F}\boldsymbol{S}) + \hat{\boldsymbol{b}}_{0} \quad \text{in} \; \Omega_{0} \times [0, T] -# can be solved together with constraint J = 1 (2-field variational principle with u and p as degrees of freedom) -#J-1 = 0 \quad \text{in} \; \Omega_{0} \times [0, T] +can be solved together with constraint J = 1 (2-field variational principle with u and p as degrees of freedom) +J-1 = 0 \quad \text{in} \; \Omega_{0} \times [0, T] +""" class SolidmechanicsProblem(problem_base): @@ -77,6 +79,8 @@ def __init__(self, io_params, time_params, fem_params, constitutive_models, bc_d self.dx = ufl.Measure("dx", domain=self.io.mesh_master, metadata={'quadrature_degree': self.quad_degree}) self.ds = ufl.Measure("ds", domain=self.io.mesh_master, subdomain_data=self.io.mt_b1_master, metadata={'quadrature_degree': self.quad_degree}) + self.de = ufl.Measure("ds", domain=self.io.mesh_master, subdomain_data=self.io.mt_b2_master, metadata={'quadrature_degree': self.quad_degree}) + # self.de = self.io.de # collect domain data self.rho0 = [] @@ -434,17 +438,17 @@ def set_variational_forms(self): # external virtual work (from Neumann or Robin boundary conditions, body forces, ...) w_neumann, w_neumann_old, w_body, w_body_old, w_robin, w_robin_old, w_membrane, w_membrane_old = ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0), ufl.as_ufl(0) if 'neumann' in self.bc_dict.keys(): - w_neumann = self.bc.neumann_bcs(self.bc_dict['neumann'], self.V_u, self.Vd_scalar, self.ds, F=self.ki.F(self.u,ext=True), funcs_to_update=self.ti.funcs_to_update, funcs_to_update_vec=self.ti.funcs_to_update_vec) - w_neumann_old = self.bc.neumann_bcs(self.bc_dict['neumann'], self.V_u, self.Vd_scalar, self.ds, F=self.ki.F(self.u_old,ext=True), funcs_to_update=self.ti.funcs_to_update_old, funcs_to_update_vec=self.ti.funcs_to_update_vec_old) + w_neumann = self.bc.neumann_bcs(self.bc_dict['neumann'], self.V_u, self.Vd_scalar, [self.ds,self.de], F=self.ki.F(self.u,ext=True), funcs_to_update=self.ti.funcs_to_update, funcs_to_update_vec=self.ti.funcs_to_update_vec) + w_neumann_old = self.bc.neumann_bcs(self.bc_dict['neumann'], self.V_u, self.Vd_scalar, [self.ds,self.de], F=self.ki.F(self.u_old,ext=True), funcs_to_update=self.ti.funcs_to_update_old, funcs_to_update_vec=self.ti.funcs_to_update_vec_old) if 'bodyforce' in self.bc_dict.keys(): w_body = self.bc.bodyforce(self.bc_dict['bodyforce'], self.V_u, self.Vd_scalar, self.dx, funcs_to_update=self.ti.funcs_to_update) w_body_old = self.bc.bodyforce(self.bc_dict['bodyforce'], self.V_u, self.Vd_scalar, self.dx, funcs_to_update=self.ti.funcs_to_update_old) if 'robin' in self.bc_dict.keys(): - w_robin = self.bc.robin_bcs(self.bc_dict['robin'], self.u, self.vel, self.ds, u_pre=self.u_pre) - w_robin_old = self.bc.robin_bcs(self.bc_dict['robin'], self.u_old, self.v_old, self.ds, u_pre=self.u_pre) + w_robin = self.bc.robin_bcs(self.bc_dict['robin'], self.u, self.vel, [self.ds,self.de], u_pre=self.u_pre) + w_robin_old = self.bc.robin_bcs(self.bc_dict['robin'], self.u_old, self.v_old, [self.ds,self.de], u_pre=self.u_pre) if 'membrane' in self.bc_dict.keys(): - w_membrane, self.idmem, self.bstress = self.bc.membranesurf_bcs(self.bc_dict['membrane'], self.u, self.vel, self.acc, self.ds) - w_membrane_old, _, _ = self.bc.membranesurf_bcs(self.bc_dict['membrane'], self.u_old, self.v_old, self.a_old, self.ds) + w_membrane, self.idmem, self.bstress = self.bc.membranesurf_bcs(self.bc_dict['membrane'], self.u, self.vel, self.acc, [self.ds,self.de]) + w_membrane_old, _, _ = self.bc.membranesurf_bcs(self.bc_dict['membrane'], self.u_old, self.v_old, self.a_old, [self.ds,self.de]) # for (quasi-static) prestressing, we need to eliminate dashpots in our external virtual work # plus no rate-dependent or inelastic constitutive models @@ -462,9 +466,9 @@ def set_variational_forms(self): if r['type'] == 'dashpot': r['visc'] = 0. bc_prestr = boundaryconditions.boundary_cond(self.fem_params, self.io, self.vf, self.ti, ki=self.ki) if 'neumann_prestress' in bc_dict_prestr.keys(): - w_neumann_prestr = bc_prestr.neumann_prestress_bcs(bc_dict_prestr['neumann_prestress'], self.V_u, self.Vd_scalar, self.ds, funcs_to_update=self.funcs_to_update_pre, funcs_to_update_vec=self.funcs_to_update_vec_pre) + w_neumann_prestr = bc_prestr.neumann_prestress_bcs(bc_dict_prestr['neumann_prestress'], self.V_u, self.Vd_scalar, [self.ds,self.de], funcs_to_update=self.funcs_to_update_pre, funcs_to_update_vec=self.funcs_to_update_vec_pre) if 'robin' in bc_dict_prestr.keys(): - w_robin_prestr = bc_prestr.robin_bcs(bc_dict_prestr['robin'], self.u, self.vel, self.ds, u_pre=self.u_pre) + w_robin_prestr = bc_prestr.robin_bcs(bc_dict_prestr['robin'], self.u, self.vel, [self.ds,self.de], u_pre=self.u_pre) self.deltaW_prestr_ext = w_neumann_prestr + w_robin_prestr else: assert('neumann_prestress' not in self.bc_dict.keys()) diff --git a/src/ambit_fe/solid/solid_variationalform.py b/src/ambit_fe/solid/solid_variationalform.py index 0a7c9a95..f6722cb2 100644 --- a/src/ambit_fe/solid/solid_variationalform.py +++ b/src/ambit_fe/solid/solid_variationalform.py @@ -9,10 +9,12 @@ import ufl from ..variationalform import variationalform_base +""" +Solid mechanics variational form class +Principle of Virtual Work +\delta \mathcal{W} = \delta \mathcal{W}_{\mathrm{kin}} + \delta \mathcal{W}_{\mathrm{int}} - \delta \mathcal{W}_{\mathrm{ext}} = 0, \quad \forall \; \delta\boldsymbol{u} +""" -# solid mechanics variational base class -# Principle of Virtual Work -# TeX: \delta \mathcal{W} = \delta \mathcal{W}_{\mathrm{kin}} + \delta \mathcal{W}_{\mathrm{int}} - \delta \mathcal{W}_{\mathrm{ext}} = 0, \quad \forall \; \delta\boldsymbol{u} class variationalform(variationalform_base): ### Kinetic virtual work diff --git a/src/ambit_fe/solver/preconditioner.py b/src/ambit_fe/solver/preconditioner.py index bf9e15b5..2b518c5e 100644 --- a/src/ambit_fe/solver/preconditioner.py +++ b/src/ambit_fe/solver/preconditioner.py @@ -12,8 +12,12 @@ from .. import utilities -### PETSc PC types: -# https://www.mcs.anl.gov/petsc/petsc4py-current/docs/apiref/petsc4py.PETSc.PC.Type-class.html +""" +Ambit preconditioner classes + +PETSc PC types: +https://www.mcs.anl.gov/petsc/petsc4py-current/docs/apiref/petsc4py.PETSc.PC.Type-class.html +""" class block_precond(): diff --git a/src/ambit_fe/solver/solver_nonlin.py b/src/ambit_fe/solver/solver_nonlin.py index 4e5f1172..a8445fd4 100644 --- a/src/ambit_fe/solver/solver_nonlin.py +++ b/src/ambit_fe/solver/solver_nonlin.py @@ -18,13 +18,17 @@ from .. import ioparams from .. import utilities -### useful infos for PETSc mats, vecs, solvers... -# https://www.mcs.anl.gov/petsc/petsc4py-current/docs/apiref/petsc4py.PETSc.Mat-class.html -# https://www.mcs.anl.gov/petsc/petsc4py-current/docs/apiref/petsc4py.PETSc.Vec-class.html -# https://www.mcs.anl.gov/petsc/documentation/faq.html -# https://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html -# https://www.mcs.anl.gov/petsc/petsc4py-current/docs/apiref/petsc4py.PETSc.KSP-class.html -# https://www.mcs.anl.gov/petsc/petsc4py-current/docs/apiref/petsc4py.PETSc.PC-class.html +""" +Ambit nonlinear solver classes + +useful infos for PETSc mats, vecs, solvers... +https://www.mcs.anl.gov/petsc/petsc4py-current/docs/apiref/petsc4py.PETSc.Mat-class.html +https://www.mcs.anl.gov/petsc/petsc4py-current/docs/apiref/petsc4py.PETSc.Vec-class.html +https://www.mcs.anl.gov/petsc/documentation/faq.html +https://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html +https://www.mcs.anl.gov/petsc/petsc4py-current/docs/apiref/petsc4py.PETSc.KSP-class.html +https://www.mcs.anl.gov/petsc/petsc4py-current/docs/apiref/petsc4py.PETSc.PC-class.html +""" # standard nonlinear solver for FEM problems class solver_nonlinear: @@ -559,7 +563,7 @@ def newton(self, t, localdata={}): tes = time.time() - # initial redidual actions due to predictor + # initial residual actions due to predictor self.residual_problem_actions(t, npr, localdata) te = time.time() - tes diff --git a/src/ambit_fe/timeintegration.py b/src/ambit_fe/timeintegration.py index 18312e86..a5e73332 100644 --- a/src/ambit_fe/timeintegration.py +++ b/src/ambit_fe/timeintegration.py @@ -12,6 +12,9 @@ from . import expression, utilities +""" +Time-integration classes for all problems +""" class timeintegration(): diff --git a/src/ambit_fe/variationalform.py b/src/ambit_fe/variationalform.py index f3382870..788154a8 100644 --- a/src/ambit_fe/variationalform.py +++ b/src/ambit_fe/variationalform.py @@ -9,7 +9,10 @@ import ufl from .mathutils import spectral_decomposition_3x3 -# variational form base class +""" +Variational form base class +""" + class variationalform_base: def __init__(self, var_u, var_p=None, du=None, dp=None, n0=None, x_ref=None, formulation=None): diff --git a/tests/input/block_edge.xdmf b/tests/input/block_edge.xdmf new file mode 100644 index 00000000..7133cae6 --- /dev/null +++ b/tests/input/block_edge.xdmf @@ -0,0 +1,36 @@ + + + + + + 0.0 0.0 1.0 + 0.0 0.0 0.0 + 0.0 1.0 1.0 + 0.0 1.0 0.0 + 1.0 0.0 1.0 + 1.0 0.0 0.0 + 1.0 1.0 1.0 + 1.0 1.0 0.0 + 0.0 0.5 0.5 + 1.0 0.5 0.5 + 0.5 0.0 0.5 + 0.5 1.0 0.5 + 0.5 0.5 0.0 + 0.5 0.5 1.0 + + + + + 4 13 + 13 2 + + + + + 1 + 1 + + + + + diff --git a/tests/input/fib_fiber_nodal_3D.txt b/tests/input/fib_fiber_nodal_3D.txt deleted file mode 100644 index 0f1b476a..00000000 --- a/tests/input/fib_fiber_nodal_3D.txt +++ /dev/null @@ -1,2609 +0,0 @@ -106 0.666031496187006 0.5343721026428089 -0.5204310732498607 -25 0.0858544914132846 0.06514595697174153 0.994175543148393 -26 0.6248475970049794 0.5874282457579282 -0.5142893510494517 -616 0.06968655188365758 0.0684862130249893 0.9952152647101344 -1448 0.6451582730183496 0.5547347872009633 -0.5253952023240055 -105 0.7248352132257272 0.4446888588958132 -0.526180323123123 -1447 0.7291994790878774 0.4302908707910324 -0.5320882316043678 -617 0.07131846120268759 0.0671769870195893 0.9951888913702015 -1500 0.5264234071382783 0.6900822540140985 -0.496653681262656 -107 0.06544103127304124 0.07281704846123693 0.9951960354017265 -553 0.06593912972138727 0.0760247092684205 0.9949232506843121 -429 0.08702077978906864 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b/tests/test_solid_pinch_edge.py new file mode 100755 index 00000000..7200d0a0 --- /dev/null +++ b/tests/test_solid_pinch_edge.py @@ -0,0 +1,102 @@ +#!/usr/bin/env python3 + +""" +- quasi-static solid mechanics +- compressible NeoHookean material +- force applied over an edge integral +""" + +import ambit_fe + +import sys +import numpy as np +from pathlib import Path +import pytest + + +@pytest.mark.solid +@pytest.mark.skip(reason="Not yet ready for testing.") +def test_main(): + + basepath = str(Path(__file__).parent.absolute()) + + # reads in restart step from the command line + try: restart_step = int(sys.argv[1]) + except: restart_step = 0 + + IO_PARAMS = {'problem_type' : 'solid', + 'USE_MIXED_DOLFINX_BRANCH' : True, + 'mesh_domain' : basepath+'/input/block_domain.xdmf', + 'mesh_boundary' : basepath+'/input/block_boundary.xdmf', + 'mesh_edge' : basepath+'/input/block_edge.xdmf', + 'write_results_every' : 1, + 'write_restart_every' : -1, + 'indicate_results_by' : 'step', + 'restart_step' : restart_step, + 'output_path' : basepath+'/tmp/', + 'results_to_write' : ['displacement'], + 'simname' : 'solid_pinch_edgeEEEII'} + + SOLVER_PARAMS = {'solve_type' : 'direct', + 'tol_res' : 1.0e-8, + 'tol_inc' : 1.0e-8, + 'maxiter' : 25, + 'divergence_continue' : None} + + TIME_PARAMS = {'maxtime' : 1.0, + 'numstep' : 10, + 'numstep_stop' : 10, + 'timint' : 'static'} + + FEM_PARAMS = {'order_disp' : 1, + 'quad_degree' : 2, + 'incompressible_2field' : False} + + #MATERIALS = {'MAT1' : {'neohooke_compressible' : {'mu' : 10., 'nu' : 0.1}}} + MATERIALS = {'MAT1' : {'neohooke_dev' : {'mu' : 10.}, + 'sussmanbathe_vol' : {'kappa' : 500.}}} + + + # define your load curves here (syntax: tcX refers to curve X, to be used in BC_DICT key 'curve' : [X,0,0], or 'curve' : X) + class time_curves(): + + def tc1(self, t): + return -8.*t + + BC_DICT = { 'neumann' : [{'id' : [6], 'dir' : 'xyz_ref', 'curve' : [0,0,1]}], + 'dirichlet' : [{'id' : [3], 'dir' : 'all', 'val' : 0.0}, + {'id' : [1], 'dir' : 'all', 'val' : 0.0, 'codimension' : 1}]}#, + #'robin' : [{'id' : [1], 'dir' : 'xyz_ref', 'type' : 'spring', 'stiff' : 1e3, 'codimension' : 1}]} + + + # problem setup + problem = ambit_fe.ambit_main.Ambit(IO_PARAMS, TIME_PARAMS, SOLVER_PARAMS, FEM_PARAMS, MATERIALS, BC_DICT, time_curves=time_curves()) + + # solve time-dependent problem + problem.solve_problem() + + + # --- results check + tol = 1.0e-6 + + check_node = [] + check_node.append(np.array([0.5, 0.5, 1.0])) + + u_corr = np.zeros(3*len(check_node)) + + ## correct results + u_corr[0] = 6.00095441680302044e-01 # x + u_corr[1] = -1.0862313365225019e-07 # y + u_corr[2] = -0.000897803340365617 # z + + check1 = ambit_fe.resultcheck.results_check_node(problem.mp.u, check_node, u_corr, problem.mp.V_u, problem.mp.comm, tol=tol, nm='u') + success = ambit_fe.resultcheck.success_check([check1], problem.mp.comm) + + if not success: + raise RuntimeError("Test failed!") + + + +if __name__ == "__main__": + + test_main()