Welcome to trimem’s documentation¶
Trimem is a python package for the Monte Carlo simulation of lipid membranes according to the Helfrich theory [Helfrich1973].
Installation¶
Trimem can be installed via
git clone --recurse-submodules https://github.com/bio-phys/trimem.git
pip install trimem/
We suggest the installation using the --user flag to pip. Alternatively,
we recommend to consider the usage of virtual environments to isolate the
installation of trimem, see, e.g., here.
Dependencies¶
Trimem builds upon the generic mesh data structure
OpenMesh, which
is included as a submodule that is pulled in upon git clone via the
--recurse-submodules flag, see Installation.
For the efficient utilization of shared-memory parallelism, trimem makes
use of the OpenMP application programming model
(>= v4.5) and modern C++. It thus requires relatively up-to-date
compilers (supporting at least C++17).
If not already available, the following python dependencies will be automatically installed:
numpy
scipy
h5py
meshio
Documentation and tests further require:
autograd
trimesh
sphinx
sphinx-copybutton
sphinxcontrib-programoutput
Usage¶
Trimem provides a convenient user interface via a Command line interface that is
available after Installation as mc_app under the respective binary
installation directory available to pip. For a quick-start and more
detailed documentation, please have a look at the User manual.
Alternatively, trimem can also be used as a
python library. High level functionality is exposed in
the module trimem.mc.util. For details on low level functionality,
please refer to the API reference.
Citation¶
If you use trimem for your scientific work, please consider the citation of [Siggel2022].