/svZeroDSolver-Archived

A Python lumped-parameter solver for blood flow and pressure in hemodynamic networks

Primary LanguagePythonOtherNOASSERTION

This repository has been archived and is no longer maintained. It has been replaced by a new 0D solver with the same name.

About svZeroDSolver

svZeroDSolver is a Python code that simulates the hemodynamics in zero-dimensional (0D) lumped parameter models of vascular networks. These 0D models are governed by differential algebraic equations (DAEs).

The solver uses a highly modular framework to model the vascular anatomy, using individual 0D elements to represent different parts of the vascular anatomy (and boundary conditions). The individual 0D elements and their associated governing equations defined in blocks.py. In solver.py, the blocks are assembled and simulated using the generalized-alpha time-stepping method defined in time_integration.py.

The svZeroDSolver Python files are in the svzerodsolver Python package directory.

svZeroDSolver currently supports the following vascular 0D modeling options and boundary conditions:

Vascular 0D elements:

  • Resistor
  • Resistor-capacitor
  • Resistor-inductor
  • Resistor-capacitor-inductor

Boundary conditions:

  • Pressure
  • Resistor
  • RCR
  • Coronary
  • Flow

Installation

svZeroDSolver and all its dependencies can be installed easily via pip.

pip install git+https://github.com/SimVascular/svZeroDSolver.git

For Contributers

The following guide provides all necessary steps to install your local svZeroDSolver repository via pip in editable mode to allow for local code changes to reflect in the package.

If you are contributing to svZeroDSolver, it is highly recommended to use a virtual environment like Miniconda. After installing Miniconda you can create a new environment and enter it using:

conda create -n zerodsolver python=3.9
conda activate zerodsolver

After that, enter the repository folder and install the svZeroDSolver with development related dependencies using:

pip install -e .[dev]

If you are using the zsh shell, enter: pip install -e ".[dev]"

Usage

Command line

To run svZeroDSolver form the command line, run:

zerod SOLVER_INPUT_FILE

For more information about command line options, enter:

zerod --help

As a python module

import svzerodsolver
svzerodsolver.solver.set_up_and_run_0d_simulation('input.json')

This variant enables running svZeroDSolver within a user-defined Python code (e.g. parameter optimization, uncertainty quantification)