# Tutorials

The following tutorials are also located in the code repository with the same path as the html (e.g., in /path/to/feasst/plugin/[name]/tutorial/).

Basic tutorials:

Build and test models:

- Lennard Jones potential test
- Reference configuration of SPC/E water in non-cuboid domain
- Average energy of a bulk SPC/E fluid in the canonical ensemble
- Lennard Jones Alpha potential test
- User defined tabular potentials
- Example TwoBodyAlpha potential: Feynman-Hibbs
- Make your own custom two body model
- Make your own custom analysis
- Make your own custom Action

Flat-histogram simulations:

- Ideal gas equation of state using grand canonical ensemble transition-matrix Monte Carlo
- Grand canonical ensemble transition-matrix Monte Carlo
- Analysis of a one-phase (supercritical) simulation
- Analysis of a two-phase (phase separated) simulation
- Grand Canonical Flat Histogram Simulation of Lennard-Jones
- Grand Canonical Flat Histogram Simulation of SPC/E
- Grand Canonical Flat Histogram Simulation of RPM
- Grand Canonical Flat Histogram Simulation of Hard Spheres.
- Grand Canonical Flat Histogram Simulation of Patchy Trimers
- Grand Canonical Flat Histogram Simulation of Kern-Frenkel Patches
- Grand Canonical Flat Histogram Simulation at low temperature
- Grand Canonical Flat Histogram Simulation of TraPPE alkanes
- Efficiency of 1 or 2 bin Grand Canonical Flat Histogram Simulations

Others:

- Slab, cylindrical, spherical and mixed confinement
- Simulation of a single freely-jointed chain
- Simulation of a single chain
- Simulation of a single 20-bead linear chain
- Scattering calculations for hard sphere coarse-grained mAb models
- Temperature extrapolation of the radius of gyration
- Monte Carlo with rigid cluster moves
- Compare scattering calculations for hard spheres
- Post process scattering calculations from file.
- Beta expanded ensemble
- Expanded Ensemble Grand Canonical Flat Histogram Simulation of RPM
- Second virial coefficient calculation of a Trimer using Mayer-Sampling
- Second virial coefficient calculation of TraPPE ethane using Mayer-Sampling
- Second virial coefficient calculation of a Kern-Frenkel patch using Mayer-Sampling
- Virial coefficients of all-atom mAb domains.
- Virial coefficients of 7-bead coarse-grained mAb model.
- Block average analysis for correlated data
- Prefetch example
- Test of an anisotropic, textured square well potential.
- Compare standard vs FFTW scattering calculations for hard spheres
- Semi-Grand Canonical Flat Histogram Simulation of a binary LJ mixture
- Semi-Grand Canonical Flat Histogram Simulation of CO2 and N2
- Compare XYZ (ascii) with netCDF

## Text file interface

The above tutorials feature the text-based interface of FEASST. The text interface comprises the names of all Classes and their constructor arguments. Thus, most users will want to search the documentation for these classes. Documentation for a particular class can be found by searching the list of all capabilities (typically, using ctrl-f). All available arguments for that class can then be found in the list of “args” of that class, or its base classes.

For developers, the bash command “grep” is also an option to search for more information on classes and their arguments. For example, if you would like more information on RandomMT19937 but are not sure where to find it, you could search headers files

```
grep -r --include=*.h RandomMT19937
```

And find that the class is part of the Math plugin.

## Python and C++ interface

FEASST may also be called directly in Python and C++ as a library. Note that the Python and C++ interfaces may change with minor version. Thus, the Python and C++ interfaces are not recommended for beginning users.