diff --git a/README.md b/README.md index b278f93..8316f78 100644 --- a/README.md +++ b/README.md @@ -38,14 +38,6 @@ $ pydiffuser --version pydiffuser, version 0.0.1 ``` -### From source - -```console -$ git clone https://github.com/jung235/pydiffuser.git -$ cd pydiffuser -$ pip install . -``` - ## Quickstart Pydiffuser provides various stochastic models that implement a numerical simulation based on the [Monte Carlo method](https://en.wikipedia.org/wiki/Monte_Carlo_method). @@ -63,7 +55,6 @@ tracer: Trajectory = ensemble[0] # 0th particle ``` Relevant stochastic observables, such as [mean-squared displacement](https://en.wikipedia.org/wiki/Mean_squared_displacement) $\left \langle \mathbf{r}^{2}(t) \right \rangle$ and normalized [velocity autocorrelation function](https://en.wikipedia.org/wiki/Autocorrelation), can be calculated through the [methods](#observables) of `Trajectory` and `Ensemble`. -For example: ```python tamsd = tracer.get_mean_squared_displacement(lagtime=1, rolling=True) @@ -71,13 +62,13 @@ eamsd = ensemble.get_mean_squared_displacement(lagtime=1, rolling=False) eatamsd = ensemble.get_mean_squared_displacement(lagtime=1, rolling=True) ``` -You can visualize the results using [matplotlib](https://github.com/matplotlib/matplotlib). +You can visualize the trajectory using [matplotlib](https://github.com/matplotlib/matplotlib).

-The trajectory is obtained by `matplotlib.pyplot.plot(tracer.position_x1, tracer.position_x2)`. +It is obtained by `matplotlib.pyplot.plot(tracer.position_x1, tracer.position_x2)`. ## CLI @@ -94,8 +85,6 @@ rtp RunAndTumbleParticle RunAndTumbleParticleConfig smoluchowski SmoluchowskiEquation SmoluchowskiEquationConfig 1d, 2d ``` -Here, every model is the subclass of `pydiffuser.models.BaseDiffusion`, and every configuration is the subclass of `pydiffuser.utils.BaseDiffusionConfig`. - ## Features ### Observables @@ -144,12 +133,6 @@ ensemble = model.generate() # [3] ensemble.to_npy(npy_path=) # [4] ``` -After calculating the stochastic [observables](#observables), you can plot: - -

- -

- It is possible to save & load a picklable object through `pydiffuser.save` and `pydiffuser.load`. ```python