sampledoc

STREAMM code description

StructureContainer Class

Object-oriented design is used throughout STREAMM to enable ease of use and the ability to update and extend its functionality. The StructureContainer class is a data structure for describing a collection of discrete particles. These particles have unique integer IDs and spatial positions and can have user specified attributes such as mass, charge and type. These particles can have 2-body (bond), 3-body (angle) and 4-body (dihedral) interactions, which are implemented by the python classes Particle, Bond, Angle and Dihedral. Impropers are special dihedral 4-body interactions.

Each of these classes has an associated container. For example, multiple Particle objects are held in an instance of a ParticleContainer class. These containers are essentially modified dictionaries that map a unique integer ID to an object. All IDs referred to by the subcontainers are consistent. The embedded docstrings for the modules containing the classes above and their related containers are:

Finally, a StructureContainer object is a container for the Particle, Bond, Angle Dihedral and Improper containers. This class is in the module structureContainer

_images/strucC.png

The StructureContainer must contain a ParticleContainer at a minimum (eg for setting Gaussian runs when no connectivity information is requested). StructureContainer objects can be created without Bonds, Angles, Dihedrals and/or Impropers, with the default empty containers being set automatically.

MPI Wrapper Class

Molecular Building-Block Assembler

Simulation Classes

These classes make use of the StructureContainer to organize data needed to run specific simulations. The Simulation class is an interface to the derived classes simulationLAMMPS1 and simulationGaussian1. The derived classes have specific methods for input/output that are specific to particular applications and projects. The intent is for users to be able to design additional derived classes for other projects and/or additional simulation packages. There is one example in the tools-tests (see test_dumpLammps) illustrating the LAMMPS simulation derived class.

External Utilities

A number of utility classes are included in STREAMM that use the core functionality described above. These utility classes are used in a number of Examples included in the documentation. The embedded docstrings for these are listed below.