Update Doxygen documentation with json block examples

src/model/BloodVessel.h

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

src/model/BloodVesselJunction.h

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

src/model/ChamberElastanceInductor.h

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

src/model/ChamberSphere.h

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

src/model/ClosedLoopCoronaryLeftBC.h

@@ -12,6 +12,22 @@
 /**
  * @brief Left side of closed loop coronary boundary condition
  * ClosedLoopCoronaryBC.
+ *
+ * ### Usage in json configuration file
+ *
+ *     "boundary_conditions": [
+ *          {
+ *              "bc_name": "LCA",
+ *              "bc_type": "ClosedLoopCoronaryLeft",
+ *              "bc_values": {
+ *                  "Ra": 9.307638231,
+ *                  "Ram": 15.124912126,
+ *                  "Rv": 33.270958757,
+ *                  "Cim": 0.003737025,
+ *                  "Ca": 0.000552427
+ *              }
+ *          }
+ *     ]
  */
 class ClosedLoopCoronaryLeftBC : public ClosedLoopCoronaryBC {
  public:

src/model/ClosedLoopCoronaryRightBC.h

@@ -12,6 +12,22 @@
 /**
  * @brief Right side of closed loop coronary boundary condition
  * ClosedLoopCoronaryBC.
+ *
+ * ### Usage in json configuration file
+ *
+ *     "boundary_conditions": [
+ *         {
+ *             "bc_name": "RCA",
+ *             "bc_type": "ClosedLoopCoronaryRight",
+ *             "bc_values": {
+ *                 "Ra": 5.757416349,
+ *                 "Ram": 9.355801566,
+ *                 "Rv": 20.580381989,
+ *                 "Cim": 0.003463134,
+ *                 "Ca": 0.001055957
+ *             }
+ *         }
+ *     ]
  */
 class ClosedLoopCoronaryRightBC : public ClosedLoopCoronaryBC {
  public:

src/model/ClosedLoopHeartPulmonary.h

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

src/model/ClosedLoopRCRBC.h

@@ -82,6 +82,22 @@
  * * `1` Capacitance
  * * `2` Distal resistance
  *
+ * ### Usage in json configuration file
+ *
+ *     "boundary_conditions": [
+ *         {
+ *             "bc_name": "RCR_aorta",
+ *             "bc_type": "ClosedLoopRCR",
+ *             "bc_values": {
+ *                 "_comment_": "R_total = 1.570879*0.948914 = 1.490629075, Rp =
+ * 0.09*R_total, Rd = 0.91*R_total, C = 0.228215*1.044637", "Rp": 0.134156617,
+ *                 "Rd": 1.356472458,
+ *                 "C": 0.238401833,
+ *                 "closed_loop_outlet": true
+ *             }
+ *         }
+ *     ]
+ *
  * ### Internal variables
  *
  * Names of internal variables in this block's output:

src/model/FlowReferenceBC.h

@@ -50,6 +50,25 @@
  *
  * * `0` Flow
  *
+ * ### Usage in json configuration file
+ *
+ *     "boundary_conditions": [
+ *         {
+ *             "bc_name": "INFLOW",
+ *             "bc_type": "FLOW",
+ *             "bc_values": {
+ *                 "Q": [
+ *                     5.0,
+ *                     5.0
+ *                 ],
+ *                 "t": [
+ *                     0.0,
+ *                     1.0
+ *                 ]
+ *             }
+ *         }
+ *     ]
+ *
  * ### Internal variables
  *
  * This block has no internal variables.

src/model/Junction.h

@@ -63,6 +63,22 @@
  * \underbrace{1}_{P_i} & \dots & \underbrace{1}_{P_j} & \dots\end{array}\right]
  * \quad \mathrm{with} \quad i \neq j \f]
  *
+ * ### Usage in json configuration file
+ *
+ *     "junctions": [
+ *         {
+ *             "inlet_vessels": [
+ *                 0
+ *             ],
+ *             "junction_name": "J0",
+ *             "junction_type": "NORMAL_JUNCTION",
+ *             "outlet_vessels": [
+ *                 1,
+ *                 2
+ *             ]
+ *         }
+ *     ]
+ *
  * ### Internal variables
  *
  * This block has no internal variables.

src/model/OpenLoopCoronaryBC.h

@@ -80,6 +80,31 @@
  * * `5` Pim: Intramyocardial pressure
  * * `6` Pv: Venous pressure
  *
+ * ### Usage in json configuration file
+ *
+ *     "boundary_conditions": [
+ *         {
+ *             "bc_name": "OUT",
+ *             "bc_type": "CORONARY",
+ *             "bc_values": {
+ *                 "Ca": 0.0001,
+ *                 "Cc": 0.0001,
+ *                 "Pim": [
+ *                     1000.0,
+ *                     1000.0
+ *                 ],
+ *                 "P_v": 0.0,
+ *                 "Ra1": 100.0,
+ *                 "Ra2": 100.0,
+ *                 "Rv1": 100.0,
+ *                 "t": [
+ *                     0.0,
+ *                     1.0
+ *                 ]
+ *             }
+ *         }
+ *     ]
+ *
  * ### Internal variables
  *
  * Names of internal variables in this block's output:

src/model/PressureReferenceBC.h

@@ -51,6 +51,25 @@
  *
  * * `0` Pressure
  *
+ * ### Usage in json configuration file
+ *
+ *     "boundary_conditions": [
+ *         {
+ *             "bc_name": "OUT",
+ *             "bc_type": "PRESSURE",
+ *             "bc_values": {
+ *                 "P": [
+ *                     1000.0,
+ *                     1000.0
+ *                 ],
+ *                 "t": [
+ *                     0.0,
+ *                     1.0
+ *                 ]
+ *             }
+ *         }
+ *     ]
+ *
  * ### Internal variables
  *
  * This block has no internal variables.

src/model/ResistanceBC.h

@@ -50,6 +50,19 @@
  * * `0` Resistance
  * * `1` Distal pressure
  *
+ * ### Usage in json configuration file
+ *
+ *     "boundary_conditions": [
+ *         {
+ *             "bc_name": "OUT",
+ *             "bc_type": "RESISTANCE",
+ *             "bc_values": {
+ *                 "R": 100.0,
+ *                 "Pd": 1000.0
+ *             }
+ *         }
+ *     ]
+ *
  * ### Internal variables
  *
  * This block has no internal variables.