Virtual Cell Finite Volume PDE solver

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  • License: MIT License
  • Author: Jim Schaff
  • Requires: Python >=3.10
  • Provides-Extra: test
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vcell-fvsolver

Virtual Cell Finite Volume solver virtualcell/vcell-fvsolver is a reaction-diffusion-advection PDE solver for computational cell biology. This solver is used within the Virtual Cell modeling and simulation application virtualcell/vcell and as a component in the Virtual Cell Python API virtualcell/pyvcell (coming soon).

The Virtual Cell Project

The Virtual Cell is a modeling and simulation framework for computational biology. For details see http://vcell.org and http://github.com/virtualcell.

Docker container

the vcell-fvsolver is available as a docker container at ghcr.io/virtualcell/vcell-fvsolver.

Standalone executables

FiniteVolume executable can be build on Windows, MacOS, and Linux (see .github/workflows/cd.yml for details). The executables are available in the release section of this repository.

Python API - pyvcell_fvsolver

The Python API for the VCell Finite Volume solver is a low level wrapper which accepts VCell solver input files (.fvinput, .vcg) and generates the output files (.log, .zip, .mesh, .meshmetrics, .hdf5). The .functions file is not used by the solver, but is helpful for interpreting the results in the context of the original model.

This package is intended to be used by the Virtual Cell Python API virtualcell/pyvcell (coming soon).

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