2.9.1 Potential Energy Functions (Interactions)

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The potential energy used by any Simpatico simulation may contain:

• a non-bonded pair interaction
• bond, angle and dihedral 2,3 and 4-body covalent interactions
• an external 1-body potential

Specific functional forms for each type of interaction are implemented by "interaction" classes. The same set of interaction classes are available for use in all simulation programs.

The choice of which functional form to use for specific type of potential energy (e.g., pair, bond, etc.) is specified in the parameter file by an associated "style" string parameter (e.g., pairStyle or bondStyle). The value of each such string parameter gives the name of the desired interaction class.

User documentation for each interaction class documents the format of the block of potential energy parameters required for that interaction. This block must apppear in the parameter file within the parameter file block for the associated potential energy class. For example, in a ddSim simulation with bondStyle == "HarmonicBond", the BondPotential{ ... } parameter block must include the the block of potential energy parameters appropriate for a HarmonicBond interaction.

• Pair Interactions
  • LJPair - truncated Lennard-Jones
  • WcaPair - Weeks-Chandler-Anderson (purely repulsive Lennard-Jones)
  • DpdPair - soft potential typical of dissipative particle dynamics (DPD) simulations

• Bond Interactions
  • HarmonicBond - harmonic bond
  • HarmonicL0Bond - harmonic bond with zero rest length (i.e., a Gaussian spring)
  • FeneBond - finitely extensible bond

• Angle Interactions
  • CosineAngle - proportional to the cosine of the bending angle
  • CosineSqAngle - proportional to the square of cosine of bending angle
  • HarmonicAngle - harmonic in bending angle

• Dihedral Interactions
  • CosineDihedral - proportional to cosine of dihedral angle
  • MultiHarmonicDihedral - Fourier expansion in dihedral angle

• External Interactions
  • LamellarOrderExternal - designed to induce layers
  • SlitExternal - 1D confinement to a slit
  • BoxExternal - 3D confinement to a box
  • OrthoBoxExternal - 3D confinement to a box (orthorhombic variant)

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