.. toctree:: :maxdepth: 2 spirit.chain <spirit.chain> spirit.configuration <spirit.configuration> spirit.constants <spirit.constants> spirit.geometry <spirit.geometry> spirit.hamiltonian <spirit.hamiltonian> spirit.htst <spirit.htst> spirit.io <spirit.io> spirit.log <spirit.log> spirit.parameters <parameters> spirit.quantities <spirit.quantities> spirit.simulation <spirit.simulation> spirit.state <spirit.state> spirit.system <spirit.system> spirit.transition <spirit.transition>