Gillespie on a Lattice in the single occupancy limit
Features
Unimolecular and bimolecular reactions on 1D, 2D, 3D lattices.
Installation
Build
Use cmake
mkdir build
cd build
cmake ..
make
make install
The default location is /usr/local/lib
and /usr/local/include
.
Including
Use the convenient include <lattgillespie>
.
Linking
Example:
g++ -std=c++14 -O3 -llattgillespie -o main.o main.cpp
Be sure to put it into your DYLD_LIBRARY_PATH
:
export DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:/absolute/path/to/lib/folder
else use the -L
flag when linking. (-L
needed at link time; DYLD_LIBRARY_PATH
needed at runtime).
Usage
More documentation TBD!
Namespace
The namespace is lattg
.
Setting up directory for output
A directory structure must be created for the output.
Use the included Python script create_data_dirs.py
.
For example:
mkdir data
cd data
cp /path/to/create_data_dirs.py ./
python create_data_dirs.py
Before running, adjust the range for the number of directories to output.
Then, when running the main script, in the run
command, specify the data
directory in the final argument dir
, e.g.
sim.run(n_steps,verbose,write_counts,write_nns,write_latt,write_step,write_version_no,"/path/to/data");