Welcome to wlcsim’s documentation!¶
This code is designed to efficiently simulate the wormlike chain polymer model using various coarse-grainings where applicable.
For very stiff polymers, the usual wormlike chain is simulated.
For relatively more flexible polymers, the “stretchable, shearable” chain is used.
For VERY stretchable polymers, a purely Gaussian chain is used.
## To Run
make in the top level directory will build the simulator
from source. The executable created (
wlcsim.exe) will use the parameters in
input/input and write its output to the
Descriptions of the available parameters can be found at their definitions and
where they are read in
src/wlcsim/params.f03. Example input files are
usually more useful, and can be found in the
To force a rerun without having to manually delete all the old output files, you
can also simply type
make run at any time.
There are several ways to easily visualize simulation output. There are PyMol
scripts in the
python -m wlcsim.plot_wlcsim
from the repo’s top level directory will launch a GUI designed to visualize BD
simulations, and one can of course simply use the output in the
directory, which contains rank two arrays of shape
num_beads*num_polymers-by-3, with one file per time point. By default,
specifying multiple polymers just simulates them in parallel in the same
reaction volume, no interactions are assumed.
To scan parameters, the Python script
scan_wlcsim.py should be used. It takes
care of saving the current git commit_hash, all inputs, etc. into a unique
directory, and preventing race conditions even on shared filesystems, among
This codebase is internal to the Spakowitz lab and is not guaranteed to be bug-free at any point. For battle-tested versions of our software, please see the links in the relevant papers.