### Install svZeroDSolver package

Source: https://simvascular.github.io/svZeroDSolver/dir_93df0772b4c11809d264133600b0552f.html

Install the package from the repository root before running examples.

```bash
pip install -e .
```

--------------------------------

### Install and build with uv sync

Source: https://simvascular.github.io/svZeroDSolver/developer_guide.html

Creates a virtual environment in .venv, installs all dependencies including development tooling, and builds the current source. Useful for continuously running integration tests during development. The build is self-contained: uv supplies a compatible Python interpreter (pinned in .python-version) and the CMake/Ninja build tools, so no system-wide installation of those is required.

```bash
uv sync
```

--------------------------------

### Install with pip as an alternative

Source: https://simvascular.github.io/svZeroDSolver/developer_guide.html

The project still builds with pip install -e . The development dependencies live in a dependency group, so install them with pip install -e . --group dev (pip >= 25.1).

```bash
pip install -e .
```

```bash
pip install -e . --group dev
```

--------------------------------

### Install optional dependency groups with uv sync --group

Source: https://simvascular.github.io/svZeroDSolver/developer_guide.html

Installs application-specific dependencies. Use uv sync --group gui for the svZeroDGUI application and uv sync --group viz for the svZeroDVisualization application.

```bash
uv sync --group gui
```

```bash
uv sync --group viz
```

--------------------------------

### Install Doxygen

Source: https://simvascular.github.io/svZeroDSolver/developer_guide.html

Commands to install Doxygen on macOS or Linux systems.

```bash
brew install doxygen
```

```bash
sudo apt-get install doxygen
```

--------------------------------

### JSON configuration example for ResistanceBC

Source: https://simvascular.github.io/svZeroDSolver/_resistance_b_c_8h_source.html

Example JSON configuration snippet showing how to define a resistance boundary condition in the boundary_conditions array, with bc_name, bc_type, and bc_values containing R and Pd.

```json
"boundary_conditions": [
{
"bc_name": "OUT",
"bc_type": "RESISTANCE",
"bc_values": {
"R": 100.0,
"Pd": 1000.0
}
}
]
```

--------------------------------

### Install Python dependencies only with uv sync --no-install-project

Source: https://simvascular.github.io/svZeroDSolver/developer_guide.html

Installs only the Python dependencies without building the C++ extension. Use when working on visualization or GUI tooling.

```bash
uv sync --no-install-project
```

--------------------------------

### Sensitivity Configuration Schema

Source: https://simvascular.github.io/svZeroDSolver/tuner_configuration.html

Example YAML configuration for performing sensitivity analysis, defining model parameters and quantities of interest.

```yaml
model:
config_file: "model.json"
parameters:
- name: "LV.Emax"
bounds: [1e8, 5e8]
quantities_of_interest:
- name: Systemic arterial max pressure
expression: np.max(pressure:AV:AR_SYS)
sensitivity:
n_samples: 256
output:
directory: "sensitivity_results"
save_plots: true
```

--------------------------------

### Solver::setup_initial()

Source: https://simvascular.github.io/svZeroDSolver/_solver_8h_source.html

Sets up and initializes the simulation parameters and model.

```APIDOC
## Solver::setup_initial()

### Description
Sets up and initializes the simulation parameters and model.

```

--------------------------------

### Solver::setup_initial()

Source: https://simvascular.github.io/svZeroDSolver/_solver_8h_source.html

Sets up and initializes the simulation parameters and model.

```APIDOC
## Solver::setup_initial()

### Description
Sets up and initializes the simulation parameters and model.

### Method
void

### Parameters
None

### Returns
void
```

--------------------------------

### setup_initial()

Source: https://simvascular.github.io/svZeroDSolver/class_solver.html

Sets up and initializes the simulation parameters and model.

```APIDOC
## setup_initial()

### Description
Set up and initialize the simulation parameters and model.

### Method
setup_initial

### Signature
void Solver::setup_initial()

```

--------------------------------

### double get(double time)

Source: https://simvascular.github.io/svZeroDSolver/class_parameter.html

Gets the parameter value at the specified time.

```APIDOC
## double get(double time)

### Description
Gets the parameter value at the specified time.

### Method
get

### Parameters
- **time** (double) - Required - Time at which to evaluate the parameter.

### Returns
double - The parameter value at the given time.
```

--------------------------------

### JSON Configuration Example for ClosedLoopHeartAndPulmonary

Source: https://simvascular.github.io/svZeroDSolver/_closed_loop_heart_pulmonary_8h_source.html

Example JSON configuration for the closed_loop_blocks array, specifying outlet blocks, closed_loop_type, cardiac_cycle_period, and parameters for the heart and pulmonary model.

```json
"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
}
```

--------------------------------

### setup_integrator()

Source: https://simvascular.github.io/svZeroDSolver/class_solver.html

Sets up the integrator.

```APIDOC
## setup_integrator()

### Description
Set up integrator.

### Method
setup_integrator

### Signature
void Solver::setup_integrator()

```

--------------------------------

### Solver::setup_integrator()

Source: https://simvascular.github.io/svZeroDSolver/_solver_8h_source.html

Sets up the integrator for the simulation.

```APIDOC
## Solver::setup_integrator()

### Description
Sets up the integrator.

### Method
void

### Parameters
None

### Returns
void
```

--------------------------------

### Solver::setup_integrator()

Source: https://simvascular.github.io/svZeroDSolver/_solver_8h_source.html

Sets up the integrator for time discretization.

```APIDOC
## Solver::setup_integrator()

### Description
Sets up the integrator for time discretization.

```

--------------------------------

### get_num_triplets()

Source: https://simvascular.github.io/svZeroDSolver/class_block.html

Get number of triplets of element.

```APIDOC
## get_num_triplets()

### Description
Get number of triplets of element. Number of triplets that the element contributes to the global system (relevant for sparse memory reservation).

### Method
Virtual member function

### Signature
`TripletsContributions Block::get_num_triplets()`

### Returns
- `TripletsContributions` - Number of triplets of element
```

--------------------------------

### Python: SV0DTuner(config_file)

Source: https://simvascular.github.io/svZeroDSolver/tuner_api.html

Primary optimization API class. Initializes the tuner with a configuration file.

```APIDOC
## [Python] SV0DTuner(config_file: str)

### Description
Initializes the primary optimization API with a configuration file.

### Constructor Parameters
- **config_file** (str) - Required - Path to the tuning YAML configuration file.
```

--------------------------------

### Python: SensitivityAnalyzer.run()

Source: https://simvascular.github.io/svZeroDSolver/tuner_api.html

Runs the sensitivity analysis and returns a dictionary keyed by QoI name.

```APIDOC
## [Python] SensitivityAnalyzer.run() -> Dict

### Description
Runs the sensitivity analysis and returns a dictionary keyed by QoI name.

### Returns
- **Dict** - Sensitivity results keyed by QoI name, each containing: first_order (Dict[str, float]), total_order (Dict[str, float]), mean, std, min, max (float).
```

--------------------------------

### get_num_triplets() const

Source: https://simvascular.github.io/svZeroDSolver/class_model.html

Get number of triplets all elements.

```APIDOC
## get_num_triplets() const

### Description
Get number of triplets all elements.

### Method
Member function

### Signature
TripletsContributions get_num_triplets() const

### Returns
- **TripletsContributions** - The number of triplets.

```

--------------------------------

### Model::get_parameter_value

Source: https://simvascular.github.io/svZeroDSolver/_model_8h_source.html

Gets the current value of a parameter.

```APIDOC
## Model::get_parameter_value

### Description
Gets the current value of a parameter.

### Method
double get_parameter_value(int param_id) const

### Parameters
- **param_id** (int) - Required - Identifier of the parameter.

### Returns
- **double** - Current value of the parameter.
```

--------------------------------

### Optimization Configuration Schema

Source: https://simvascular.github.io/svZeroDSolver/tuner_configuration.html

Example YAML configuration for setting up an optimization task, including model path, parameter bounds, target objectives, and algorithm settings.

```yaml
model:
config_file: "model.json"
parameters:
- name: "LV.Emax"
bounds: [1e7, 1e9]
scaling: log
targets:
- name: Systemic arterial max pressure
type: scalar
expression: np.max(pressure:AV:AR_SYS)
target_value: 13065
relative_bounds: 5%
weight: 1.0
objective:
norm: L1
optimization:
algorithm: "differential_evolution"
terminate_at_zero: true
maxiter: 200
output:
directory: "optimization_results"
save_history: true
save_plots: true
save_final_config: true
```

--------------------------------

### get_parameter(int param_id)

Source: https://simvascular.github.io/svZeroDSolver/class_model.html

Get a parameter by its global ID.

```APIDOC
## get_parameter(int param_id)

### Description
Get a parameter by its global ID.

### Method
Member function

### Signature
Parameter* get_parameter(int param_id)

### Parameters
- **param_id** (int) - Required - The global ID of the parameter.

### Returns
- **Parameter*** - Pointer to the parameter.

```

--------------------------------

### Build Documentation Locally

Source: https://simvascular.github.io/svZeroDSolver/developer_guide.html

Command to trigger the Doxygen build process for local documentation generation.

```bash
doxygen docs/Doxyfile
```

--------------------------------

### Run optimization

Source: https://simvascular.github.io/svZeroDSolver/dir_93df0772b4c11809d264133600b0552f.html

Execute the optimization process using the specified tuning configuration file.

```bash
svzerodtuner optimize tuning_nelder_mead.yaml
```

--------------------------------

### Solver::get_times() const

Source: https://simvascular.github.io/svZeroDSolver/_solver_8h_source.html

Gets the time steps of the result.

```APIDOC
## Solver::get_times() const

### Description
Gets the time steps of the result.

### Method
std::vector<double>

### Parameters
None

### Returns
std::vector<double> - The time steps.
```

--------------------------------

### get_num_blocks(bool internal=false) const

Source: https://simvascular.github.io/svZeroDSolver/class_model.html

Get the number of blocks in the model.

```APIDOC
## get_num_blocks(bool internal=false) const

### Description
Get the number of blocks in the model.

### Method
Member function

### Signature
int get_num_blocks(bool internal=false) const

### Parameters
- **internal** (bool) - Optional - Whether to include internal blocks. Default is false.

### Returns
- **int** - The number of blocks.

```

--------------------------------

### Python: SensitivityAnalyzer(config_file)

Source: https://simvascular.github.io/svZeroDSolver/tuner_api.html

Primary sensitivity analysis API class. Initializes the analyzer with a configuration file.

```APIDOC
## [Python] SensitivityAnalyzer(config_file: str)

### Description
Initializes the primary sensitivity analysis API with a configuration file.

### Constructor Parameters
- **config_file** (str) - Required - Path to the tuning YAML configuration file.
```

--------------------------------

### get_parameter_value(int param_id) const

Source: https://simvascular.github.io/svZeroDSolver/class_model.html

Get the current value of a parameter.

```APIDOC
## get_parameter_value(int param_id) const

### Description
Get the current value of a parameter.

### Method
Member function

### Signature
double get_parameter_value(int param_id) const

### Parameters
- **param_id** (int) - Required - The ID of the parameter.

### Returns
- **double** - The current value of the parameter.

```

--------------------------------

### setup_dofs function call

Source: https://simvascular.github.io/svZeroDSolver/add_block.html

The setup_dofs function typically only calls Block::setup_dofs_ with the number of equations and internal variable names.

```cpp
Block::setup_dofs_(DOFHandler &dofhandler, int num_equations, const std::list<std::string> &internal_var_names)
```

--------------------------------

### get_node_name(int node_id) const

Source: https://simvascular.github.io/svZeroDSolver/class_model.html

Get the name of a node by its ID.

```APIDOC
## get_node_name(int node_id) const

### Description
Get the name of a node by its ID.

### Method
Member function

### Signature
std::string get_node_name(int node_id) const

### Parameters
- **node_id** (int) - Required - The ID of the node.

### Returns
- **std::string** - The name of the node.

```

--------------------------------

### Model::setup_initial_state_dependent_parameters

Source: https://simvascular.github.io/svZeroDSolver/_model_8h_source.html

Sets up model parameters that depend on the initial state.

```APIDOC
## Model::setup_initial_state_dependent_parameters

### Description
Sets up model parameters that depend on the initial state.

### Method
void setup_initial_state_dependent_parameters(State initial_state)

### Parameters
- **initial_state** (State) - Required - The initial state vector.
```

--------------------------------

### get_block_name(int block_id) const

Source: https://simvascular.github.io/svZeroDSolver/class_model.html

Get the name of a block by its ID.

```APIDOC
## get_block_name(int block_id) const

### Description
Get the name of a block by its ID.

### Method
Member function

### Signature
std::string get_block_name(int block_id) const

### Parameters
- **block_id** (int) - Required - The ID of the block.

### Returns
- **std::string** - The name of the block.

```

--------------------------------

### get_block(int block_id) const

Source: https://simvascular.github.io/svZeroDSolver/class_model.html

Get a block by its global ID.

```APIDOC
## get_block(int block_id) const

### Description
Get a block by its global ID.

### Method
Member function

### Signature
Block* get_block(int block_id) const

### Parameters
- **block_id** (int) - Required - The global ID of the block.

### Returns
- **Block*** - Pointer to the block with the given ID.

```

--------------------------------

### Run tuning with svzerodtuner optimize

Source: https://simvascular.github.io/svZeroDSolver/dir_af714cb40d7a7d9dc52f0362415ea8fd.html

Run one of the tuning configurations with the CLI. Two configs are provided: tuning_nelder_mead.yaml and tuning_differential_evolution.yaml. Nelder-Mead has produced more stable convergence for this model.

```bash
svzerodtuner optimize tuning_nelder_mead.yaml
```

```bash
svzerodtuner optimize tuning_differential_evolution.yaml
```

--------------------------------

### Model::get_largest_windkessel_time_constant

Source: https://simvascular.github.io/svZeroDSolver/_model_8h_source.html

Gets the largest Windkessel time constant in the model.

```APIDOC
## Model::get_largest_windkessel_time_constant

### Description
Gets the largest Windkessel time constant in the model.

### Method
double get_largest_windkessel_time_constant()

### Returns
- **double** - Largest Windkessel time constant of the model.
```