espressopp.interaction.Tabulated

espressopp.interaction.Tabulated(itype, filename, cutoff)

Defines a tabulated potential.

Parameters:
  • itype (int) – interpolation type (1,2, or 3 for linear, Akima, or cubic splines)
  • filename (string) – table filename
  • cutoff (real or "infinity") – (default: infinity) interaction cutoff
espressopp.interaction.VerletListAdressTabulated(vl, fixedtupleList)

Defines a verletlist-based AdResS interaction using tabulated potentials for both AT and CG interactions.

Parameters:
  • vl (shared_ptr<VerletListAdress>) – Verletlist AdResS object
  • fixedtupleList (shared_ptr<FixedTupleListAdress>) – FixedTupleList object
espressopp.interaction.VerletListAdressTabulated.setPotentialAT(type1, type2, potential)

Sets the AT potential in VerletListAdressTabulated interaction for interacting particles of type1 and type2.

Parameters:
  • type1 (int) – particle type 1
  • type2 (int) – particle type 2
  • potential (shared_ptr<Tabulated>) – tabulated interaction potential object
espressopp.interaction.VerletListAdressTabulated.setPotentialCG(type1, type2, potential)

Sets the CG potential in VerletListAdressTabulated interaction for interacting particles of type1 and type2.

Parameters:
  • type1 (int) – particle type 1
  • type2 (int) – particle type 2
  • potential (shared_ptr<Tabulated>) – tabulated interaction potential object
espressopp.interaction.VerletListAdressCGTabulated(vl, fixedtupleList)

Defines only the CG part of a verletlist-based AdResS interaction using a tabulated potential for the CG interaction. It’s defined as a “NonbondedSlow” interaction (which multiple time stepping integrators can make use of).

Parameters:
  • vl (shared_ptr<VerletListAdress>) – Verletlist AdResS object
  • fixedtupleList (shared_ptr<FixedTupleListAdress>) – FixedTupleList object
espressopp.interaction.VerletListAdressCGTabulated.setPotential(type1, type2, potential)

Sets the CG potential in VerletListAdressCGTabulated interaction for interacting particles of type1 and type2.

Parameters:
  • type1 (int) – particle type 1
  • type2 (int) – particle type 2
  • potential (shared_ptr<Tabulated>) – tabulated interaction potential object
espressopp.interaction.VerletListAdressCGTabulated.getPotential(type1, type2)

Gets the CG potential in VerletListAdressCGTabulated interaction for interacting particles of type1 and type2.

Parameters:
  • type1 (int) – particle type 1
  • type2 (int) – particle type 2
Return type:

shared_ptr<Tabulated>
espressopp.interaction.VerletListAdressCGTabulated.getVerletList()

Gets the verletlist used in VerletListAdressCGTabulated interaction.

Return type:shared_ptr<VerletListAdress>
espressopp.interaction.VerletListHadressTabulated(vl, fixedtupleList)

Defines a verletlist-based H-AdResS interaction using tabulated potentials for both AT and CG interactions.

Parameters:
  • vl (shared_ptr<VerletListAdress>) – Verletlist AdResS object
  • fixedtupleList (shared_ptr<FixedTupleListAdress>) – FixedTupleList object
espressopp.interaction.VerletListHadressTabulated.setPotentialAT(type1, type2, potential)

Sets the AT potential in VerletListHadressTabulated interaction for interacting particles of type1 and type2.

Parameters:
  • type1 (int) – particle type 1
  • type2 (int) – particle type 2
  • potential (shared_ptr<Tabulated>) – tabulated interaction potential object
espressopp.interaction.VerletListHadressTabulated.setPotentialCG(type1, type2, potential)

Sets the CG potential in VerletListHadressTabulated interaction for interacting particles of type1 and type2.

Parameters:
  • type1 (int) – particle type 1
  • type2 (int) – particle type 2
  • potential (shared_ptr<Tabulated>) – tabulated interaction potential object
espressopp.interaction.VerletListHadressCGTabulated(vl, fixedtupleList)

Defines only the CG part of a verletlist-based H-AdResS interaction using a tabulated potential for the CG interaction. It’s defined as a “NonbondedSlow” interaction (which multiple time stepping integrators can make use of).

Parameters:
  • vl (shared_ptr<VerletListAdress>) – Verletlist AdResS object
  • fixedtupleList (shared_ptr<FixedTupleListAdress>) – FixedTupleList object
espressopp.interaction.VerletListHadressCGTabulated.setPotential(type1, type2, potential)

Sets the CG potential in VerletListHadressCGTabulated interaction for interacting particles of type1 and type2.

Parameters:
  • type1 (int) – particle type 1
  • type2 (int) – particle type 2
  • potential (shared_ptr<Tabulated>) – tabulated interaction potential object
espressopp.interaction.VerletListHadressCGTabulated.getPotential(type1, type2)

Gets the CG potential in VerletListHadressCGTabulated interaction for interacting particles of type1 and type2.

Parameters:
  • type1 (int) – particle type 1
  • type2 (int) – particle type 2
Return type:

shared_ptr<Tabulated>
espressopp.interaction.VerletListHadressCGTabulated.getVerletList()

Gets the verletlist used in VerletListHadressCGTabulated interaction.

Return type:shared_ptr<VerletListAdress>
espressopp.interaction.VerletListTabulated(vl)

Defines a verletlist-based interaction using a tabulated potential.

Parameters:vl (shared_ptr<VerletList>) – Verletlist object
espressopp.interaction.VerletListTabulated.getPotential(type1, type2)

Gets the tabulated interaction potential in VerletListTabulated for interacting particles of type1 and type2.

Parameters:
  • type1 (int) – particle type 1
  • type2 (int) – particle type 2
Return type:

shared_ptr<Tabulated>
espressopp.interaction.VerletListTabulated.setPotential(type1, type2, potential)

Sets the tabulated interaction potential in VerletListTabulated for interacting particles of type1 and type2.

Parameters:
  • type1 (int) – particle type 1
  • type2 (int) – particle type 2
  • potential (shared_ptr<Tabulated>) – tabulated interaction potential object
espressopp.interaction.CellListTabulated(stor)

Defines a CellList-based interaction using a tabulated potential.

Parameters:stor (shared_ptr <storage::Storage>) – storage object
espressopp.interaction.CellListTabulated.setPotential(type1, type2, potential)

Sets the tabulated interaction potential in CellListTabulated for interacting particles of type1 and type2.

Parameters:
  • type1 (int) – particle type 1
  • type2 (int) – particle type 2
  • potential (shared_ptr<Tabulated>) – tabulated interaction potential object
espressopp.interaction.FixedPairListTabulated(system, vl, potential)

Defines a FixedPairList-based interaction using a tabulated potential.

Parameters:
  • system (shared_ptr<System>) – system object
  • vl (shared_ptr<FixedPairList>) – FixedPairList list object
  • potential (shared_ptr<Tabulated>) – tabulated potential object
espressopp.interaction.FixedPairListTabulated.setPotential(potential)

Sets the tabulated interaction potential in FixedPairListTabulated for interacting particles.

Parameters:potential (shared_ptr<Tabulated>) – tabulated potential object
espressopp.interaction.FixedPairListTypesTabulated(system, fpl)
Parameters:
espressopp.interaction.FixedPairListTypesTabulated.setPotential(type1, type2, potential)

Defines bond potential for interaction between particles of types type1-type2-type3.

Parameters:
espressopp.interaction.FixedPairListPIadressTabulated(system, fpl, fixedtupleList, potential, ntrotter, speedup)

Defines tabulated bonded pair potential for interactions based on the fixedtuplelist in the context of Path Integral AdResS. When the speedup flag is set, it will use only the centroids in the classical region, otherwise all Trotter beads. In the quantum region, always all Trotter beads are used.

Parameters:
espressopp.interaction.FixedPairListPIadressTabulated.setPotential(potential)

Sets the potential.

Parameters:potential (espressopp.interaction.Potential) – The potential object.
espressopp.interaction.FixedPairListPIadressTabulated.getPotential()

Gets the potential.

Returns:the potential
Return type:shared_ptr < Potential >
espressopp.interaction.FixedPairListPIadressTabulated.setFixedPairList(fpl)

Sets the FixedPairList.

Parameters:fpl (espressopp.FixedPairList) – The FixedPairList object.
espressopp.interaction.FixedPairListPIadressTabulated.getFixedPairList()

Gets the FixedPairList.

Returns:the FixedPairList
Return type:shared_ptr < FixedPairList >
espressopp.interaction.FixedPairListPIadressTabulated.setFixedTupleList(fixedtupleList)

Sets the FixedTupleList.

Parameters:fixedtupleList (espressopp.FixedTupleListAdress) – The FixedTupleListAdress object.
espressopp.interaction.FixedPairListPIadressTabulated.getFixedTupleList()

Gets the FixedTupleList.

Returns:the FixedTupleList
Return type:shared_ptr < FixedTupleListAdress >
espressopp.interaction.FixedPairListPIadressTabulated.setNTrotter(ntrotter)

Sets the Trotter number NTrotter.

Parameters:ntrotter (int) – The Trotter number.
espressopp.interaction.FixedPairListPIadressTabulated.getNTrotter()

Gets the Trotter number NTrotter.

Parameters:ntrotter (int) – The Trotter number.
espressopp.interaction.FixedPairListPIadressTabulated.setSpeedup(speedup)

Sets the speedup flag.

Parameters:speedup (bool) – The speedup flag.
espressopp.interaction.FixedPairListPIadressTabulated.getSpeedup()

Gets the speedup flag.

Returns:the speedup flag
Return type:bool
espressopp.interaction.VerletListPIadressTabulated(vl, fixedtupleList, ntrotter, speedup)

Defines a non-bonded interaction using an adaptive resolution VerletList in the context of Path Integral AdResS. Two different tabulated potentials can be specified: one, which is used in the quantum region, the other one in the classical region. The interpolation proceeds according to the Path Integral AdResS scheme (see J. Chem. Phys 147, 244104 (2017)). When the speedup flag is set,it will use only the centroids in the classical region, otherwise all Trotter beads. In the quantum region, always all Trotter beads are used.

Parameters:
  • vl (espressopp.VerletListAdress) – The AdResS VerletList.
  • fixedtupleList (espressopp.FixedTupleListAdress) – The FixedTupleListAdress object.
  • ntrotter (int) – The Trotter number.
  • speedup (bool) – Boolean flag to decide whether to use centroids in classical region or all Trotter beads
espressopp.interaction.VerletListPIadressTabulated.setPotentialQM(potential)

Sets the potential for the quantum region (has to be a tabulated one).

Parameters:potential (espressopp.interaction.Potential) – The potential object.
espressopp.interaction.VerletListPIadressTabulated.setPotentialCL(potential)

Sets the potential for the classical region (has to be a tabulated one).

Parameters:potential (espressopp.interaction.Potential) – The potential object.
espressopp.interaction.VerletListPIadressTabulated.setVerletList(vl)

Sets the VerletList.

Parameters:vl (espressopp.VerletListAdress) – The VerletListAdress object.
espressopp.interaction.VerletListPIadressTabulated.getVerletList()

Gets the VerletList.

Returns:the Adress VerletList
Return type:shared_ptr<VerletListAdress>
espressopp.interaction.VerletListPIadressTabulated.setFixedTupleList(fixedtupleList)

Sets the FixedTupleList.

Parameters:fixedtupleList (espressopp.FixedTupleListAdress) – The FixedTupleListAdress object.
espressopp.interaction.VerletListPIadressTabulated.getFixedTupleList()

Gets the FixedTupleList.

Returns:the FixedTupleList
Return type:shared_ptr < FixedTupleListAdress >
espressopp.interaction.VerletListPIadressTabulated.setNTrotter(ntrotter)

Sets the Trotter number NTrotter.

Parameters:ntrotter (int) – The Trotter number.
espressopp.interaction.VerletListPIadressTabulated.getNTrotter()

Gets the Trotter number NTrotter.

Returns:the Trotter number
Return type:int
espressopp.interaction.VerletListPIadressTabulated.setSpeedup(speedup)

Sets the speedup flag.

Parameters:speedup (bool) – The speedup flag.
espressopp.interaction.VerletListPIadressTabulated.getSpeedup()

Gets the speedup flag.

Returns:the speedup flag
Return type:bool
espressopp.interaction.VerletListPIadressTabulatedLJ(vl, fixedtupleList, ntrotter, speedup)

Defines a non-bonded interaction using an adaptive resolution VerletList in the context of Path Integral AdResS. Two different potentials can be specified: one, which is used in the quantum region (tabulated), the other one in the classical region (Lennard-Jones type). The interpolation proceeds according to the Path Integral AdResS scheme (see J. Chem. Phys 147, 244104 (2017)). When the speedup flag is set,it will use only the centroids in the classical region, otherwise all Trotter beads. In the quantum region, always all Trotter beads are used.

Parameters:
  • vl (espressopp.VerletListAdress) – The AdResS VerletList.
  • fixedtupleList (espressopp.FixedTupleListAdress) – The FixedTupleListAdress object.
  • ntrotter (int) – The Trotter number.
  • speedup (bool) – Boolean flag to decide whether to use centroids in classical region or all Trotter beads
espressopp.interaction.VerletListPIadressTabulatedLJ.setPotentialQM(potential)

Sets the potential for the quantum region (has to be a tabulated one).

Parameters:potential (espressopp.interaction.Potential) – The potential object.
espressopp.interaction.VerletListPIadressTabulatedLJ.setPotentialCL(potential)

Sets the potential for the classical region (has to be a Lennard-Jones type one).

Parameters:potential (espressopp.interaction.Potential) – The potential object.
espressopp.interaction.VerletListPIadressTabulatedLJ.setVerletList(vl)

Sets the VerletList.

Parameters:vl (espressopp.VerletListAdress) – The VerletListAdress object.
espressopp.interaction.VerletListPIadressTabulatedLJ.getVerletList()

Gets the VerletList.

Returns:the Adress VerletList
Return type:shared_ptr<VerletListAdress>
espressopp.interaction.VerletListPIadressTabulatedLJ.setFixedTupleList(fixedtupleList)

Sets the FixedTupleList.

Parameters:fixedtupleList (espressopp.FixedTupleListAdress) – The FixedTupleListAdress object.
espressopp.interaction.VerletListPIadressTabulatedLJ.getFixedTupleList()

Gets the FixedTupleList.

Returns:the FixedTupleList
Return type:shared_ptr < FixedTupleListAdress >
espressopp.interaction.VerletListPIadressTabulatedLJ.setNTrotter(ntrotter)

Sets the Trotter number NTrotter.

Parameters:ntrotter (int) – The Trotter number.
espressopp.interaction.VerletListPIadressTabulatedLJ.getNTrotter()

Gets the Trotter number NTrotter.

Returns:the Trotter number
Return type:int
espressopp.interaction.VerletListPIadressTabulatedLJ.setSpeedup(speedup)

Sets the speedup flag.

Parameters:speedup (bool) – The speedup flag.
espressopp.interaction.VerletListPIadressTabulatedLJ.getSpeedup()

Gets the speedup flag.

Returns:the speedup flag
Return type:bool
espressopp.interaction.VerletListPIadressNoDriftTabulated(vl, fixedtupleList, ntrotter, speedup)

Defines a non-bonded interaction using an adaptive resolution VerletList in the context of Path Integral AdResS. One tabulated potential can be specified, which is used thoughout the whole system. Hence, only the quantumness of the particles changes, but not the forcefield (see J. Chem. Phys 147, 244104 (2017)). When the speedup flag is set,it will use only the centroids in the classical region, otherwise all Trotter beads. In the quantum region, always all Trotter beads are used.

Parameters:
  • vl (espressopp.VerletListAdress) – The AdResS VerletList.
  • fixedtupleList (espressopp.FixedTupleListAdress) – The FixedTupleListAdress object.
  • ntrotter (int) – The Trotter number.
  • speedup (bool) – Boolean flag to decide whether to use centroids in classical region or all Trotter beads
espressopp.interaction.VerletListPIadressNoDriftTabulated.setPotential(potential)

Sets the potential which is used throughout the whole system (has to be a tabulated one).

Parameters:potential (espressopp.interaction.Potential) – The potential object.
espressopp.interaction.VerletListPIadressNoDriftTabulated.setVerletList(vl)

Sets the VerletList.

Parameters:vl (espressopp.VerletListAdress) – The VerletListAdress object.
espressopp.interaction.VerletListPIadressNoDriftTabulated.getVerletList()

Gets the VerletList.

Returns:the Adress VerletList
Return type:shared_ptr<VerletListAdress>
espressopp.interaction.VerletListPIadressNoDriftTabulated.setFixedTupleList(fixedtupleList)

Sets the FixedTupleList.

Parameters:fixedtupleList (espressopp.FixedTupleListAdress) – The FixedTupleListAdress object.
espressopp.interaction.VerletListPIadressNoDriftTabulated.getFixedTupleList()

Gets the FixedTupleList.

Returns:the FixedTupleList
Return type:shared_ptr < FixedTupleListAdress >
espressopp.interaction.VerletListPIadressNoDriftTabulated.setNTrotter(ntrotter)

Sets the Trotter number NTrotter.

Parameters:ntrotter (int) – The Trotter number.
espressopp.interaction.VerletListPIadressNoDriftTabulated.getNTrotter()

Gets the Trotter number NTrotter.

Returns:the Trotter number
Return type:int
espressopp.interaction.VerletListPIadressNoDriftTabulated.setSpeedup(speedup)

Sets the speedup flag.

Parameters:speedup (bool) – The speedup flag.
espressopp.interaction.VerletListPIadressNoDriftTabulated.getSpeedup()

Gets the speedup flag.

Returns:the speedup flag
Return type:bool
class espressopp.interaction.Tabulated.Tabulated

The Tabulated potential.