espressopp/espressopp

#  Copyright (C) 2012,2013, 2019
#      Max Planck Institute for Polymer Research
#  Copyright (C) 2008,2009,2010,2011
#      Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
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#  This file is part of ESPResSo++.
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r"""
*********************************
espressopp.interaction.FENECapped
*********************************

A capped FENE potential avoiding calculation of unreasonably large bonded forces. It is usually applied at the
equilibration stage of a simulation and helps a polymer system to relax. After the system has reached
its equilibrium the capped potential should be substituted by a regular FENE, :py:class:`espressopp.interaction.FENE`.

The capped FENE potential is employed as:

.. math::

        U = -\frac{1}{2}r_{max}^2  K \cdot
                 log \left[1 - \left(\frac{D - r_0}{r_{max}}\right)^2\right],

where

.. math::

    D = min \left(r, r_{\it{cap}}\right).

.. py:class:: espressopp.interaction.FENECapped(K = 30.0, r0 = 0.0, rMax = 1.5, cutoff = inf, r_cap = 1.0, shift = 0.0)

    :param real K: attractive force strength (in :math:`\epsilon / \sigma^2` units)
    :param real r0: displacement parameter (in :math:`sigma` units)
    :param real rMax: size parameter (in :math:`sigma` units)
    :param real cutoff: cutoff radius
    :param real r_cap: radius of capping (in :math:`sigma` units)
    :param real shift: shift of the potential


After setting up the potential you have to apply it to the particles in the pair list (bondlist):

.. py:class:: espressopp.interaction.FixedPairListFENECapped(system, bondlist, potential)

    :param object system: system object :func:`espressopp.System`
    :param list bondlist: list of bonds :func:`espressopp.FixedPairList`
    :param object potential: bonded potential, in this case :func:`espressopp.interaction.FENECapped`

    **Methods**

    .. py:method:: getFixedPairList()

        :rtype: A Python list of pairs (the bondlist)

    .. py:method:: getPotential()

        :rtype: potential object

    .. py:method:: setFixedPairList(bondlist)

        :param list bondlist: fixed-pair list (bondlist)

    .. py:method:: setPotential(potential)

        :param object potential: a potential applied to all pairs in the bondlist

**Example of usage**

>>> Please, refer to the example of FENE potential

Go to FENE-example :py:class:`espressopp.interaction.FENE`

"""
from espressopp import pmi, infinity
from espressopp.esutil import *

from espressopp.interaction.Potential import *
from espressopp.interaction.Interaction import *
from _espressopp import interaction_FENECapped, interaction_FixedPairListFENECapped

class FENECappedLocal(PotentialLocal, interaction_FENECapped):

    def __init__(self, K=30.0, r0=0.0, rMax=1.5,
                 cutoff=infinity, r_cap=1.0, shift=0.0):
        """Initialize the local FENE object."""
        if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
            if shift == "auto":
                cxxinit(self, interaction_FENECapped, K, r0, rMax, cutoff, r_cap)
            else:
                cxxinit(self, interaction_FENECapped, K, r0, rMax, cutoff, r_cap, shift)

class FixedPairListFENECappedLocal(InteractionLocal, interaction_FixedPairListFENECapped):

    def __init__(self, system, bondlist, potential):
        if not (pmi._PMIComm and pmi._PMIComm.isActive()) or pmi._MPIcomm.rank in pmi._PMIComm.getMPIcpugroup():
            cxxinit(self, interaction_FixedPairListFENECapped, system, bondlist, 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 FENECapped(Potential):
        pmiproxydefs = dict(
            cls = 'espressopp.interaction.FENECappedLocal',
            pmiproperty = ['K', 'r0', 'rMax', 'r_cap']
            )

    class FixedPairListFENECapped(Interaction, metaclass=pmi.Proxy):
        pmiproxydefs = dict(
            cls =  'espressopp.interaction.FixedPairListFENECappedLocal',
            pmicall = ['setPotential','getPotential','setFixedPairList', 'getFixedPairList']
            )