src/interaction/LennardJonesGeneric.py
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ESPResSo++ is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
r"""
******************************************
espressopp.interaction.LennardJonesGeneric
******************************************
This class provides methods to compute forces and energies of
a generic Lennard Jones potential with arbitrary integers a and b.
.. math::
V(r) = 4 \varepsilon \left[ \left( \frac{\sigma}{r} \right)^{a} -
\left( \frac{\sigma}{r} \right)^{b} \right]
.. function:: espressopp.interaction.LennardJonesGeneric(epsilon, sigma, a, b, cutoff, shift)
:param epsilon: (default: 1.0)
:param sigma: (default: 1.0)
:param a: (default: 12)
:param b: (default: 6)
:param cutoff: (default: infinity)
:param shift: (default: "auto")
:type epsilon: real
:type sigma: real
:type a: int
:type b: int
:type cutoff:
:type shift:
.. function:: espressopp.interaction.VerletListLennardJonesGeneric(vl)
:param vl:
:type vl:
.. function:: espressopp.interaction.VerletListLennardJonesGeneric.getPotential(type1, type2)
:param type1:
:param type2:
:type type1:
:type type2:
:rtype:
.. function:: espressopp.interaction.VerletListLennardJonesGeneric.getVerletList()
:rtype: A Python list of lists.
.. function:: espressopp.interaction.VerletListLennardJonesGeneric.setPotential(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.VerletListAdressLennardJonesGeneric(vl, fixedtupleList)
:param vl:
:param fixedtupleList:
:type vl:
:type fixedtupleList:
.. function:: espressopp.interaction.VerletListAdressLennardJonesGeneric.setPotentialAT(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.VerletListAdressLennardJonesGeneric.setPotentialCG(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.VerletListAdressLennardJonesGeneric2(vl, fixedtupleList)
:param vl:
:param fixedtupleList:
:type vl:
:type fixedtupleList:
.. function:: espressopp.interaction.VerletListAdressLennardJonesGeneric2.setPotentialAT(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.VerletListAdressLennardJonesGeneric2.setPotentialCG(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.VerletListHadressLennardJonesGeneric(vl, fixedtupleList)
:param vl:
:param fixedtupleList:
:type vl:
:type fixedtupleList:
.. function:: espressopp.interaction.VerletListHadressLennardJonesGeneric.setPotentialAT(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.VerletListHadressLennardJonesGeneric.setPotentialCG(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.VerletListHadressLennardJonesGeneric2(vl, fixedtupleList, KTI)
:param vl:
:param fixedtupleList:
:param KTI: (default: False)
:type vl:
:type fixedtupleList:
:type KTI:
.. function:: espressopp.interaction.VerletListHadressLennardJonesGeneric2.setPotentialAT(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.VerletListHadressLennardJonesGeneric2.setPotentialCG(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.CellListLennardJonesGeneric(stor)
:param stor:
:type stor:
.. function:: espressopp.interaction.CellListLennardJonesGeneric.setPotential(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.FixedPairListLennardJonesGeneric(system, vl, potential)
:param system:
:param vl:
:param potential:
:type system:
:type vl:
:type potential:
.. function:: espressopp.interaction.FixedPairListLennardJonesGeneric.getFixedPairList()
:rtype: A Python list of lists.
.. function:: espressopp.interaction.FixedPairListLennardJonesGeneric.getPotential()
:rtype:
.. function:: espressopp.interaction.FixedPairListLennardJonesGeneric.setFixedPairList(fixedpairlist)
:param fixedpairlist:
:type fixedpairlist:
.. function:: espressopp.interaction.FixedPairListLennardJonesGeneric.setPotential(potential)
:param potential:
:type potential:
"""
from espressopp import pmi, infinity
from espressopp.esutil import *
from espressopp.interaction.Potential import *
from espressopp.interaction.Interaction import *
from _espressopp import interaction_LennardJonesGeneric, \
interaction_VerletListLennardJonesGeneric, \
interaction_VerletListAdressLennardJonesGeneric, \
interaction_VerletListAdressLennardJonesGeneric2, \
interaction_VerletListHadressLennardJonesGeneric, \
interaction_VerletListHadressLennardJonesGeneric2, \
interaction_CellListLennardJonesGeneric, \
interaction_FixedPairListLennardJonesGeneric
class LennardJonesGenericLocal(PotentialLocal, interaction_LennardJonesGeneric):
def __init__(self, epsilon=1.0, sigma=1.0, a=12, b=6,
cutoff=infinity, shift="auto"):
"""Initialize the local generic Lennard Jones object."""
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
if shift =="auto":
print("here without shift")
cxxinit(self, interaction_LennardJonesGeneric,
epsilon, sigma, a, b, cutoff)
else:
print("here with shift")
cxxinit(self, interaction_LennardJonesGeneric,
epsilon, sigma, a, b, cutoff, shift)
class VerletListLennardJonesGenericLocal(InteractionLocal, interaction_VerletListLennardJonesGeneric):
def __init__(self, vl):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, interaction_VerletListLennardJonesGeneric, vl)
def setPotential(self, type1, type2, potential):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
self.cxxclass.setPotential(self, type1, type2, potential)
def getPotential(self, type1, type2):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
return self.cxxclass.getPotential(self, type1, type2)
def getVerletListLocal(self):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
return self.cxxclass.getVerletList(self)
class VerletListAdressLennardJonesGenericLocal(InteractionLocal, interaction_VerletListAdressLennardJonesGeneric):
def __init__(self, vl, fixedtupleList):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, interaction_VerletListAdressLennardJonesGeneric, vl, fixedtupleList)
def setPotentialAT(self, type1, type2, potential):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
self.cxxclass.setPotentialAT(self, type1, type2, potential)
def setPotentialCG(self, type1, type2, potential):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
self.cxxclass.setPotentialCG(self, type1, type2, potential)
class VerletListAdressLennardJonesGeneric2Local(InteractionLocal, interaction_VerletListAdressLennardJonesGeneric2):
def __init__(self, vl, fixedtupleList):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, interaction_VerletListAdressLennardJonesGeneric2, vl, fixedtupleList)
def setPotentialAT(self, type1, type2, potential):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
self.cxxclass.setPotentialAT(self, type1, type2, potential)
def setPotentialCG(self, type1, type2, potential):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
self.cxxclass.setPotentialCG(self, type1, type2, potential)
class VerletListHadressLennardJonesGenericLocal(InteractionLocal, interaction_VerletListHadressLennardJonesGeneric):
def __init__(self, vl, fixedtupleList):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, interaction_VerletListHadressLennardJonesGeneric, vl, fixedtupleList)
def setPotentialAT(self, type1, type2, potential):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
self.cxxclass.setPotentialAT(self, type1, type2, potential)
def setPotentialCG(self, type1, type2, potential):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
self.cxxclass.setPotentialCG(self, type1, type2, potential)
class VerletListHadressLennardJonesGeneric2Local(InteractionLocal, interaction_VerletListHadressLennardJonesGeneric2):
def __init__(self, vl, fixedtupleList, KTI = False):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, interaction_VerletListHadressLennardJonesGeneric2, vl, fixedtupleList, KTI)
def setPotentialAT(self, type1, type2, potential):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
self.cxxclass.setPotentialAT(self, type1, type2, potential)
def setPotentialCG(self, type1, type2, potential):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
self.cxxclass.setPotentialCG(self, type1, type2, potential)
class CellListLennardJonesGenericLocal(InteractionLocal, interaction_CellListLennardJonesGeneric):
def __init__(self, stor):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, interaction_CellListLennardJonesGeneric, stor)
def setPotential(self, type1, type2, potential):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
self.cxxclass.setPotential(self, type1, type2, potential)
class FixedPairListLennardJonesGenericLocal(InteractionLocal, interaction_FixedPairListLennardJonesGeneric):
def __init__(self, system, vl, potential):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, interaction_FixedPairListLennardJonesGeneric, system, vl, potential)
def setPotential(self, potential):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
self.cxxclass.setPotential(self, potential)
def getPotential(self):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
return self.cxxclass.getPotential(self)
def setFixedPairList(self, fixedpairlist):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
self.cxxclass.setFixedPairList(self, fixedpairlist)
def getFixedPairList(self):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
return self.cxxclass.getFixedPairList(self)
if pmi.isController:
class LennardJonesGeneric(Potential):
'The generic Lennard-Jones potential.'
pmiproxydefs = dict(
cls = 'espressopp.interaction.LennardJonesGenericLocal',
pmiproperty = ['epsilon', 'sigma', 'a', 'b']
)
class VerletListLennardJonesGeneric(Interaction, metaclass=pmi.Proxy):
pmiproxydefs = dict(
cls = 'espressopp.interaction.VerletListLennardJonesGenericLocal',
pmicall = ['setPotential', 'getPotential', 'getVerletList']
)
class VerletListAdressLennardJonesGeneric(Interaction, metaclass=pmi.Proxy):
pmiproxydefs = dict(
cls = 'espressopp.interaction.VerletListAdressLennardJonesGenericLocal',
pmicall = ['setPotentialAT', 'setPotentialCG']
)
class VerletListAdressLennardJonesGeneric2(Interaction, metaclass=pmi.Proxy):
pmiproxydefs = dict(
cls = 'espressopp.interaction.VerletListAdressLennardJonesGeneric2Local',
pmicall = ['setPotentialAT', 'setPotentialCG']
)
class VerletListHadressLennardJonesGeneric(Interaction, metaclass=pmi.Proxy):
pmiproxydefs = dict(
cls = 'espressopp.interaction.VerletListHadressLennardJonesGenericLocal',
pmicall = ['setPotentialAT', 'setPotentialCG']
)
class VerletListHadressLennardJonesGeneric2(Interaction, metaclass=pmi.Proxy):
pmiproxydefs = dict(
cls = 'espressopp.interaction.VerletListHadressLennardJonesGeneric2Local',
pmicall = ['setPotentialAT', 'setPotentialCG']
)
class CellListLennardJonesGeneric(Interaction, metaclass=pmi.Proxy):
pmiproxydefs = dict(
cls = 'espressopp.interaction.CellListLennardJonesGenericLocal',
pmicall = ['setPotential']
)
class FixedPairListLennardJonesGeneric(Interaction, metaclass=pmi.Proxy):
pmiproxydefs = dict(
cls = 'espressopp.interaction.FixedPairListLennardJonesGenericLocal',
pmicall = ['getPotential', 'setPotential', 'setFixedPairList','getFixedPairList' ]
)