4.2 Base Classes

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Base classes for mcSim and mdSim

The mcSim and mdSim programs use several base classes that can be extended by users to implement new algorithms, molecular species, and file formats, which are all defined in the McMd or Simp namespace. Among these are:

• Simp::Species, a molecular species
• McMd::McMove, a MC Markov move
• McMd::MdIntegrator, an MD integration algorithm
• McMd::Analyzer, a data analysis or output operation
• McMd::ConfigIo, a configuration file reader and writer
• McMd::TrajectoryReader, an MD trajectory file reader
• McMd::Perturbation, which defines a free energy perturbation

In order to implement, for instance, a new data analysis operation in mcSim and/or MdSim, the user must thus write a subclass of the McMd::Analyzer base class. The McMd namespace also contains a set of potential energy base classes:

• McMd::McPairPotential, a nonbonded pair interaction for MC simulations
• McMd::MdPairPotential, a nonbonded pair interaction for MD simulations
• McMd::BondPotential, a covalent two-body bond potential
• McMd::AnglePotential, a covalent three-body angle potential
• McMd::AnglePotential, a covalent four-body dihedral potential
• McMd::ExternalPotential, an external one-body potential

The BondPotential, AnglePotential, DihedralPotential, and ExternalPotential classes are used in both MC and MD simulations. Two different classes, McPairPotential and MdPairPotential, are provided for nonbonded interations in MC and MD simulations, because of differences in the algorithms and types of calculations required in MC and MD simulations

Base classes for ddSim

The base classes used by the ddSim parallel MD program are defined in the DdMd namespace. Several have names identical to names of analogous classes in the McMd namespace. These base classes include:

• DdMd::ConfigIo, a configuration file format
• DdMd::Analyzer, a data analysis or output operation
• DdMd::Integrator, an MD integration algorithm
• DdMd::Modifier, a algorithm that can modify the system during integration

The DdMd namespace also contains the following potential energy classes

• DdMd::PairPotential, a nonbonded pair interaction for MD simulations
• DdMd::BondPotential, a covalent two-body bond potential
• DdMd::AnglePotential, a covalent three-body angle potential
• DdMd::AnglePotential, a covalent four-body dihedral potential
• DdMd::ExternalPotential, a external one-body potential

Implementation of subclasses of these DdMd base classes generally require interprocessor communication.

Potential energy classes

Subclasses of the potential energy classes in either the McMd or DdMd namespaces are implemented differently than the other base classes discussed above. Each subclass of a "potential" classes is implemented as an instantiation of a class template that takes a simpler "interaction" class as an argument. Consequences of this peculiarity are discussed in more detail here.

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