espressopp.VerletListAdress

The VerletListAdress is the Verlet List to be used for AdResS or H-AdResS simulations. When creating the VerletListAdress one has to provide the system and specify both cutoff for the CG interaction and adrcutoff for the atomistic interaction. Often, it is important to set the atomistic adrcutoff much bigger than the actual interaction’s cutoff would be, since also the atomistic part of the VerletListAdress (adrPairs) is built based on the coarse-grained particle positions. For a much larger coarse-grained cutoff it is for example possible to also set the atomistic cutoff on the same value as the coarse-grained one.

Furthermore, the sizes of the explicit and hybrid region have to be provided (dEx and dHy in the example below) and the center of the atomistic region has to be set (adrCenter). Additionally, it can be chosen between a spherical and a slab-like geometry (sphereAdr).

The AdResS region can also be defined based on one or more particles. For a single particle, in this case a spherical region moves along with the particle. For many such region defining particles, the high-resolution/hybrid region corresponds to the overlap of the different spherical regions based on the individual particles (for details see Kreis et al., JCTC doi: 10.1021/acs.jctc.6b00440). Note that more region defining particles mean a higher computational overhead as these particles need to be communicated among all processors (also see explanations in AdResS.py). Also note that region defining particles should be normal/CG particles, not atomistic/AdResS ones.

Bascially the VerListAdress provides 4 lists:

  • adrZone: A list which holds all particles in the atomistic and hybrid region
  • cgZone: A list which holds all particles in the coarse-grained region
  • adrPairs: A list which holds all pairs which have at least one particle in the adrZone, i.e. in the atomistic or hybrid region
  • vlPairs: A list which holds all pairs which have both particles in the cgZone, i.e. in the coarse-grained region

Example - creating the VerletListAdress for a slab-type adress region fixed in space (only the x value of adrCenter is used):

>>> vl      = espressopp.VerletListAdress(system, cutoff=rc, adrcut=rc, dEx=ex_size, dHy=hy_size, adrCenter=[Lx/2, Ly/2, Lz/2])

or

>>> vl      = espressopp.VerletListAdress(system, cutoff=rc, adrcut=rc, dEx=ex_size, dHy=hy_size, adrCenter=[Lx/2, Ly/2, Lz/2], sphereAdr=False)

Example - creating the VerletListAdress for a spherical adress region centered on adrCenter and fixed in space:

>>> vl      = espressopp.VerletListAdress(system, cutoff=rc, adrcut=rc, dEx=ex_size, dHy=hy_size, adrCenter=[Lx/2, Ly/2, Lz/2], sphereAdr=True)

Example - creating the VerletListAdress for a spherical adress region centered on one particle and moving with the particle

>>> vl      = espressopp.VerletListAdress(system, cutoff=rc, adrcut=rc, dEx=ex_size, dHy=hy_size, pids=[adrCenterPID], sphereAdr=True)

Example - creating the VerletListAdress for a adress region based on the overlapping spherical regions by several particles

>>> vl      = espressopp.VerletListAdress(system, cutoff=rc, adrcut=rc, dEx=ex_size, dHy=hy_size, pids=[adrCenterPID1,adrCenterPID2,adrCenterPID3, ... ], sphereAdr=True)
espressopp.VerletListAdress(system, cutoff, adrcut, dEx, dHy, adrCenter, pids, exclusionlist, sphereAdr)
Parameters:
  • system –
  • cutoff –
  • adrcut –
  • dEx –
  • dHy –
  • adrCenter – (default: [])
  • pids – (default: [])
  • exclusionlist – (default: [])
  • sphereAdr – (default: False)
espressopp.VerletListAdress.addAdrParticles(pids, rebuild)
Parameters:
  • pids –
  • rebuild – (default: True)
Return type:
espressopp.VerletListAdress.exclude(exclusionlist)
Parameters:exclusionlist –
Return type:
espressopp.VerletListAdress.rebuild()
Return type:
espressopp.VerletListAdress.totalSize()
Return type: