src/interaction/Morse.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.Morse
****************************
This class provides methods to compute forces and energies of
the Morse potential.
.. math::
U = \varepsilon \left(e^{-2 \alpha (r - r_{min})} - 2 e^{-\alpha (r - r_{min})}\right)
.. function:: espressopp.interaction.Morse(epsilon, alpha, rMin, cutoff, shift)
:param epsilon: (default: 1.0)
:param alpha: (default: 1.0)
:param rMin: (default: 0.0)
:param cutoff: (default: infinity)
:param shift: (default: "auto")
:type epsilon: real
:type alpha: real
:type rMin: real
:type cutoff:
:type shift:
.. function:: espressopp.interaction.VerletListMorse(vl)
:param vl:
:type vl:
.. function:: espressopp.interaction.VerletListMorse.getPotential(type1, type2)
:param type1:
:param type2:
:type type1:
:type type2:
:rtype:
.. function:: espressopp.interaction.VerletListMorse.setPotential(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.VerletListAdressMorse(vl, fixedtupleList)
:param vl:
:param fixedtupleList:
:type vl:
:type fixedtupleList:
.. function:: espressopp.interaction.VerletListAdressMorse.setPotentialAT(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.VerletListAdressMorse.setPotentialCG(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.VerletListHadressMorse(vl, fixedtupleList)
:param vl:
:param fixedtupleList:
:type vl:
:type fixedtupleList:
.. function:: espressopp.interaction.VerletListHadressMorse.setPotentialAT(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.VerletListHadressMorse.setPotentialCG(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.CellListMorse(stor)
:param stor:
:type stor:
.. function:: espressopp.interaction.CellListMorse.setPotential(type1, type2, potential)
:param type1:
:param type2:
:param potential:
:type type1:
:type type2:
:type potential:
.. function:: espressopp.interaction.FixedPairListMorse(system, vl, potential)
:param system:
:param vl:
:param potential:
:type system:
:type vl:
:type potential:
.. function:: espressopp.interaction.FixedPairListMorse.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_Morse, \
interaction_VerletListMorse, \
interaction_VerletListAdressMorse, \
interaction_VerletListHadressMorse, \
interaction_CellListMorse, \
interaction_FixedPairListMorse
class MorseLocal(PotentialLocal, interaction_Morse):
def __init__(self, epsilon=1.0, alpha=1.0, rMin=0.0,
cutoff=infinity, shift="auto"):
"""Initialize the local Morse object."""
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
if shift =="auto":
cxxinit(self, interaction_Morse,
epsilon, alpha, rMin, cutoff)
else:
cxxinit(self, interaction_Morse,
epsilon, alpha, rMin, cutoff, shift)
class VerletListMorseLocal(InteractionLocal, interaction_VerletListMorse):
def __init__(self, vl):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, interaction_VerletListMorse, 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)
class VerletListAdressMorseLocal(InteractionLocal, interaction_VerletListAdressMorse):
def __init__(self, vl, fixedtupleList):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, interaction_VerletListAdressMorse, 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.setPotentialAT(self, type1, type2, potential)
class VerletListHadressMorseLocal(InteractionLocal, interaction_VerletListHadressMorse):
def __init__(self, vl, fixedtupleList):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, interaction_VerletListHadressMorse, 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.setPotentialAT(self, type1, type2, potential)
class CellListMorseLocal(InteractionLocal, interaction_CellListMorse):
def __init__(self, stor):
if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
cxxinit(self, interaction_CellListMorse, 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 FixedPairListMorseLocal(InteractionLocal, interaction_FixedPairListMorse):
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_FixedPairListMorse, 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)
if pmi.isController:
class Morse(Potential):
'The Morse potential.'
pmiproxydefs = dict(
cls = 'espressopp.interaction.MorseLocal',
pmiproperty = ['epsilon', 'alpha', 'rMin']
)
class VerletListMorse(Interaction, metaclass=pmi.Proxy):
pmiproxydefs = dict(
cls = 'espressopp.interaction.VerletListMorseLocal',
pmicall = ['setPotential','getPotential']
)
class VerletListAdressMorse(Interaction, metaclass=pmi.Proxy):
pmiproxydefs = dict(
cls = 'espressopp.interaction.VerletListAdressMorseLocal',
pmicall = ['setPotentialAT', 'setPotentialCG']
)
class VerletListHadressMorse(Interaction, metaclass=pmi.Proxy):
pmiproxydefs = dict(
cls = 'espressopp.interaction.VerletListHadressMorseLocal',
pmicall = ['setPotentialAT', 'setPotentialCG']
)
class CellListMorse(Interaction, metaclass=pmi.Proxy):
pmiproxydefs = dict(
cls = 'espressopp.interaction.CellListMorseLocal',
pmicall = ['setPotential']
)
class FixedPairListMorse(Interaction, metaclass=pmi.Proxy):
pmiproxydefs = dict(
cls = 'espressopp.interaction.FixedPairListMorseLocal',
pmicall = ['setPotential']
)