espressopp.Particle¶

The Particle class. Particles are used to model atoms, coarse-grained beads, etc. and are the central part of all simulations. They are stored in the storage and their time evolution can be modeled using an integrator. Importantly, particles have various properties which the user and other modules can make use of and which can be accessed. They are listed below.

class espressopp.Particle(pid, storage)¶

The particle class.

Parameters:	pid (int) – the particle id storage (storage) – the storage object

Real3D espressopp.Particle.pos: position

Real3D espressopp.Particle.v: velocity

Real3D espressopp.Particle.f: force

Real3D espressopp.Particle.modepos: normal mode coordinate (position in normal mode space)

Real3D espressopp.Particle.modemom: normal mode momentum (momentum in normal mode space)

Real3D espressopp.Particle.fm: normal mode force (force in normal mode space)

int espressopp.Particle.type: particle type

int espressopp.Particle.res_id: molecule id (eg. chain id)

int espressopp.Particle.pib: path integral bead number (Trotter number)

real espressopp.Particle.q: charge

real espressopp.Particle.mass: mass

real espressopp.Particle.varmass: variable mass (for path integral-based adaptive resolution simulations)

real espressopp.Particle.radius: particle radius

real espressopp.Particle.vradius: radial velocity

real espressopp.Particle.fradius: radial force

real espressopp.Particle.lambda_adr: particle’s resolution parameter (used in adaptive resolution simulations)

real espressopp.Particle.lambda_adrd: particle’s gradient of the resolution function in the direction of resolution change (used in adaptive resolution simulations)

bool espressopp.Particle.isGhost: boolean flag to indicate whether particle is ghost particle or not

Int3D espressopp.Particle.imageBox: particle’s image box

real espressopp.Particle.extVar: auxiliary variable associated with the particle (used in generalized Langevin friction)

real espressopp.Particle.drift_f: particle’s drift force in the direction of resolution change (used in adaptive resolution simulations)

real espressopp.Particle.state: particle state (used in AssociationReaction)

class espressopp.Particle.ParticleLocal(pid, storage)¶

The local particle.

Throws an exception: * when the particle does not exists locally

TODO: Should throw an exception: * when a ghost particle is to be written * when data is to be read from a ghost that is not available