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Update Doxygen documentation with json block examples (SimVascular#189)
1 parent aa2ec73 commit 9ee68ed

16 files changed

Lines changed: 332 additions & 1 deletion

‎src/model/BloodVessel.h‎

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@@ -112,6 +112,23 @@
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* * `2` Inductance
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* * `3` Stenosis coefficient
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*
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* ### Usage in json configuration file
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*
117+
* "vessels": [
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* {
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* "vessel_id": 0,
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* "vessel_length": 10.0,
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* "vessel_name": "branch0_seg0",
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* "zero_d_element_type": "BloodVessel",
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* "zero_d_element_values": {
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* "R_poiseuille": 100.0,
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* "C": 1.0e-5,
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* "L": 1.0e-6,
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* "stenosis_coefficient": 0.0
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* }
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* }
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* ]
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*
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* ### Internal variables
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*
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* This block has no internal variables.

‎src/model/BloodVesselJunction.h‎

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@@ -113,6 +113,40 @@
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* * `i+num_outlets` Inductance for inner blood vessel `i`
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* * `i+2*num_outlets` Stenosis coefficient for inner blood vessel `i`
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*
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* ### Usage in json configuration file
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*
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* "junctions": [
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* {
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* "inlet_vessels": [
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* 0
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* ],
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* "junction_name": "J0",
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* "junction_type": "BloodVesselJunction",
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* "junction_values": {
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* "R_poiseuille": [
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* 100,
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* 200
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* ],
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* "C": [
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* 0.0,
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* 0.0
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* ],
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* "L": [
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* 0.0,
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* 0.0
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* ],
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* "stenosis_coefficient": [
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* 0.0,
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* 0.0
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* ]
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* },
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* "outlet_vessels": [
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* 1,
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* 2
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* ]
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* }
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* ]
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*
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* ### Internal variables
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*
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* This block has no internal variables.

‎src/model/ChamberElastanceInductor.h‎

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@@ -109,6 +109,27 @@
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* * `5` t_twitch: Twitch time
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* * `6` Impedance: Impedance of the outflow
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*
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* ### Usage in json configuration file
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*
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* "chambers": [
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* {
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* "type": "ChamberElastanceInductor",
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* "name": "ventricle",
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* "values": {
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* "Emax": 1.057,
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* "Emin": 0.091,
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* "Vrd": 26.1,
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* "Vrs": 18.0,
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* "t_active": 0.2,
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* "t_twitch": 0.3,
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* "Impedance": 0.000351787
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* }
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* }
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* ],
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* "initial_condition": {
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* "Vc:ventricle": 96.07
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* }
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*
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* ### Internal variables
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*
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* Names of internal variables in this block's output:
@@ -119,7 +140,7 @@
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class ChamberElastanceInductor : public Block {
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public:
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/**
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* @brief Construct a new BloodVessel object
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* @brief Construct a new ChamberElastanceInductor object
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*
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* @param id Global ID of the block
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* @param model The model to which the block belongs

‎src/model/ChamberSphere.h‎

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@@ -93,6 +93,32 @@
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* * `tdias` - Diastole timing parameter \f$t_\text{dias}\f$
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* * `steepness` - Activation steepness parameter \f$\gamma\f$
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*
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* ### Usage in json configuration file
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*
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* "vessels": [
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* {
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* "boundary_conditions": {},
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* "vessel_id": 1,
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* "vessel_length": 1.0,
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* "vessel_name": "ventricle",
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* "zero_d_element_type": "ChamberSphere",
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* "zero_d_element_values": {
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* "rho" : 1e3,
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* "thick0" : 0.01,
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* "radius0" : 0.05,
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* "W1" : 10e3,
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* "W2" : 40,
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* "eta" : 10.0,
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* "sigma_max" : 185e3,
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* "alpha_max": 30.0,
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* "alpha_min": -30.0,
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* "tsys": 0.170,
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* "tdias": 0.484,
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* "steepness": 0.005
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* }
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* }
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* ]
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*
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* ### Internal variables
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*
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* Names of internal variables in this block's output:

‎src/model/ClosedLoopCoronaryLeftBC.h‎

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/**
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* @brief Left side of closed loop coronary boundary condition
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* ClosedLoopCoronaryBC.
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*
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* ### Usage in json configuration file
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*
18+
* "boundary_conditions": [
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* {
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* "bc_name": "LCA",
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* "bc_type": "ClosedLoopCoronaryLeft",
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* "bc_values": {
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* "Ra": 9.307638231,
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* "Ram": 15.124912126,
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* "Rv": 33.270958757,
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* "Cim": 0.003737025,
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* "Ca": 0.000552427
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* }
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* }
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* ]
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*/
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class ClosedLoopCoronaryLeftBC : public ClosedLoopCoronaryBC {
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public:

‎src/model/ClosedLoopCoronaryRightBC.h‎

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/**
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* @brief Right side of closed loop coronary boundary condition
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* ClosedLoopCoronaryBC.
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*
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* ### Usage in json configuration file
17+
*
18+
* "boundary_conditions": [
19+
* {
20+
* "bc_name": "RCA",
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* "bc_type": "ClosedLoopCoronaryRight",
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* "bc_values": {
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* "Ra": 5.757416349,
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* "Ram": 9.355801566,
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* "Rv": 20.580381989,
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* "Cim": 0.003463134,
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* "Ca": 0.001055957
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* }
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* }
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* ]
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*/
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class ClosedLoopCoronaryRightBC : public ClosedLoopCoronaryBC {
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public:

‎src/model/ClosedLoopHeartPulmonary.h‎

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@@ -59,6 +59,54 @@
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* * `25` Right atrium resting volume
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* * `26` Left atrium resting volume
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*
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* ### Usage in json configuration file
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*
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* "closed_loop_blocks": [
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* {
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* "outlet_blocks": [
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* "branch0_seg0"
68+
* ],
69+
* "closed_loop_type": "ClosedLoopHeartAndPulmonary",
70+
* "cardiac_cycle_period": 1.0169,
71+
* "parameters": {
72+
* "Tsa": 0.40742,
73+
* "tpwave": 8.976868,
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* "Erv_s": 2.125279,
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* "Elv_s": 3.125202,
76+
* "iml": 0.509365,
77+
* "imr": 0.806369,
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* "Lrv_a": 0.000186865,
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* "Rrv_a": 0.035061704,
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* "Lra_v": 0.000217032,
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* "Rra_v": 0.007887459,
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* "Lla_v": 0.000351787,
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* "Rla_v": 0.005310825,
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* "Rlv_ao": 0.034320234,
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* "Llv_a": 0.000110776,
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* "Vrv_u": 9.424629,
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* "Vlv_u": 5.606007,
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* "Rpd": 0.098865401,
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* "Cp": 1.090989,
90+
* "Cpa": 0.556854,
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* "Kxp_ra": 9.22244,
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* "Kxv_ra": 0.004837,
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* "Emax_ra": 0.208858,
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* "Vaso_ra": 4.848742,
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* "Kxp_la": 9.194992,
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* "Kxv_la": 0.008067,
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* "Emax_la": 0.303119,
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* "Vaso_la": 9.355754
99+
* }
100+
* }
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* ],
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* "initial_condition": {
103+
* "V_RA:CLH": 38.43,
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* "V_RV:CLH": 96.07,
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* "V_LA:CLH": 38.43,
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* "V_LV:CLH": 96.07,
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* "P_pul:CLH": 8.0
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* }
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*
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* ### Internal variables
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*
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* Names of internal variables in this block's output:

‎src/model/ClosedLoopRCRBC.h‎

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* * `1` Capacitance
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* * `2` Distal resistance
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*
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* ### Usage in json configuration file
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*
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* "boundary_conditions": [
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* {
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* "bc_name": "RCR_aorta",
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* "bc_type": "ClosedLoopRCR",
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* "bc_values": {
92+
* "_comment_": "R_total = 1.570879*0.948914 = 1.490629075, Rp =
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* 0.09*R_total, Rd = 0.91*R_total, C = 0.228215*1.044637", "Rp": 0.134156617,
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* "Rd": 1.356472458,
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* "C": 0.238401833,
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* "closed_loop_outlet": true
97+
* }
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* }
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* ]
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*
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* ### Internal variables
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*
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* Names of internal variables in this block's output:

‎src/model/FlowReferenceBC.h‎

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*
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* * `0` Flow
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*
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* ### Usage in json configuration file
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*
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* "boundary_conditions": [
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* {
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* "bc_name": "INFLOW",
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* "bc_type": "FLOW",
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* "bc_values": {
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* "Q": [
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* 5.0,
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* 5.0
63+
* ],
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* "t": [
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* 0.0,
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* 1.0
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* ]
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* }
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* }
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* ]
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*
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* ### Internal variables
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*
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* This block has no internal variables.

‎src/model/Junction.h‎

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* \underbrace{1}_{P_i} & \dots & \underbrace{1}_{P_j} & \dots\end{array}\right]
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* \quad \mathrm{with} \quad i \neq j \f]
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*
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* ### Usage in json configuration file
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*
68+
* "junctions": [
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* {
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* "inlet_vessels": [
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* 0
72+
* ],
73+
* "junction_name": "J0",
74+
* "junction_type": "NORMAL_JUNCTION",
75+
* "outlet_vessels": [
76+
* 1,
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* 2
78+
* ]
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* }
80+
* ]
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*
6682
* ### Internal variables
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*
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* This block has no internal variables.

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