References
Input file
Command Line Interface
Python API
Start KIMMDY from a python script or the command line
| cmd | Functions for starting KIMMDY either from python or the command line. |
Topology
Topology modules
| topology.topology | |
| topology.ff | |
| topology.utils | |
| topology.atomic | Atomic datatypes for the topology such as Atom, Bond, Angle, Dihedral, etc. |
| parsing.TopologyDict | A raw representation of a topology file returned by read_top. |
Modules
Modules
| analysis | Analysis tools for KIMMDY runs. |
| cmd | Functions for starting KIMMDY either from python or the command line. |
| config | Read and validate kimmdy.yml configuration files |
| constants | Constants used throughout KIMMDY |
| coordinates | coordinate, topology and plumed modification functions |
| kmc | Kinetic Monte Carlo (KMC) classes and functions. |
| parsing | All read_<…> and write_<…> functions. |
| plugins | Plugin base classes and basic instances thereof. |
| recipe | Contains the Reaction Recipe, RecipeStep and RecipeCollection. |
| runmanager | The Runmanager is the main entry point of the program. |
| schema | Handle the schema for the config file. |
| tasks | The tasks module holds the TaskFiles class which organizes input and |
| tools | Standalone tools that are complementary to KIMMDY. |
| utils | Utilities for building plugins, shell convenience functions and GROMACS related functions |
Reaction Plugins
Reaction plugins bundled with KIMMDY and the protocol to add a new reaction plugin to KIMMDY
| homolysis.reaction.Homolysis | Homolytic bond breaking leading to 2 radicals. |
| hat_naive.reaction.NaiveHAT | Naive HAT reaction, selects hydrogens at random |
| dummyreaction.reaction.DummyReaction | Dummy reaction, returns empty RecipeCollection |