Membrane Dynamics in 3D using Discrete Differential Geometry (Mem3DG)

Mem3DG is a flexible software package to model the membrane and its dynamics using unstructured meshes. This work is currently under heavy development, please star this repository to follow along!

Acknowledging your use of Mem3DG

Mem3DG is developed by Cuncheng Zhu, Christopher T. Lee, with contributions from others. Development of Mem3DG is funded in part by AFOSR MURI FA9550-18-1-0051, and a Hartwell Foundation Postdoctoral Fellowship.

Installation

git submodule update --init --recursive
mkdir build
cd build
cmake -DBUILD_PYDDG=ON -DWITH_NETCDF=ON -DCMAKE_BUILD_TYPE=Release ..
cmake --build . --config Release

Source released can also be obtained from PyPi.

Building pymem3dg

The python library can be built using pip:

pip install . -v

Options can be passed to scikit-build by exporting environment variables.

export SKBUILD_CONFIGURE_OPTIONS="-DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo"

Temporary notes for setting up netcdf (especially on windows...)

1. Download vcpkg and follow the instructions to install

2. Install 32 or 64 bit version of netcdf-c and netcdf-cxx4 libraries depending upon your configuration.

   vcpkg install netcdf-c:x64-windows netcdf-cxx4:x64-windows eigen3:x64-windows

   Remove the :x64-windows from the above string for the 32 bit libraries.

3. Configure the vcpkg CMake toolchain vcpkg integrate install
4. Copy and paste the -DCMAKE_TOOLCHAIN_File="..." string as an input into your CMake configuration.
5. Build as normal

The toolchain options can be passed through setup.py accordingly:

1. python setup.py build – -DCMAKE_TOOLCHAIN_FILE="C:/Users/Kieran/vcpkg/scripts/buildsystems/vcpkg.cmake" -G "Visual Studio 16 2019" -T host=x64 -A x64 – /m:6

Dependencies

• Meshes are represented using Geometry-Central.
• Optional trajectory output uses NetCDF-cxx4.

Visualization

• Optional trajectory visualization in Python uses Polyscope.
• Optional trajectory reading in Python uses NetCDF4-python.