Green’s Functions

We will here describe the inheritance hierarchy for generating Green’s functions, in order to use and extend it properly. The runtime creation of Green’s functions objects relies on the Factory Method pattern [GHJV94][Ale01], implemented through the generic Factory class.

The top-level header, _i.e._ to be included in client code, is Green.hpp. The common interface to all Green’s function classes is specified by the IGreensFunction class, this is non-templated. All other classes are templated. The Green’s functions are registered to the factory based on a label encoding: type, derivative, and dielectric profile. The only allowed labels must be listed in src/green/Green.hpp. If they are not, they can not be selected at run time.

../_images/green.svg

IGreensFunction

class IGreensFunction

Interface for Green’s function classes.

We

define as Green’s function a function:
\[ G(\mathbf{r}, \mathbf{r}^\prime) : \mathbb{R}^6 \rightarrow \mathbb{R} \]
Green’s functions and their directional derivatives appear as kernels of the \(\mathcal{S}\) and \(\mathcal{D}\) integral operators. Forming the matrix representation of these operators requires performing integrations over surface finite elements. Since these Green’s functions present a Coulombic divergence, the diagonal elements of the operators will diverge unless appropriately formulated. This is possible, but requires explicit access to the subtype of this abstract base object. This justifies the need for the singleLayer and doubleLayer functions. The code uses the Non-Virtual Interface (NVI) idiom.
Author
Luca Frediani and Roberto Di Remigio
Date
2012-2016

Subclassed by pcm::green::GreensFunction< DerivativeTraits, dielectric_profile::Anisotropic >, pcm::green::GreensFunction< DerivativeTraits, dielectric_profile::Sharp >, pcm::green::GreensFunction< DerivativeTraits, dielectric_profile::Uniform >, pcm::green::GreensFunction< DerivativeTraits, dielectric_profile::Yukawa >, pcm::green::GreensFunction< DerivativeTraits, ProfilePolicy >, pcm::green::GreensFunction< Stencil, ProfilePolicy >

Unnamed Group

double kernelS(const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Methods to sample the Green’s function and its probe point directional derivative

Returns value of the kernel of the \(\mathcal{S}\) integral operator, i.e. the value of the Greens’s function for the pair of points p1, p2: \( G(\mathbf{p}_1, \mathbf{p}_2)\)

Note
This is the Non-Virtual Interface (NVI)
Parameters
  • p1: first point
  • p2: second point

double kernelD(const Eigen::Vector3d &direction, const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Returns value of the kernel of the \(\mathcal{D}\) integral operator for the pair of points p1, p2: \( [\boldsymbol{\varepsilon}\nabla_{\mathbf{p_2}}G(\mathbf{p}_1, \mathbf{p}_2)]\cdot \mathbf{n}_{\mathbf{p}_2}\) To obtain the kernel of the \(\mathcal{D}^\dagger\) operator call this methods with \(\mathbf{p}_1\) and \(\mathbf{p}_2\) exchanged and with \(\mathbf{n}_{\mathbf{p}_2} = \mathbf{n}_{\mathbf{p}_1}\)

Note
This is the Non-Virtual Interface (NVI)
Parameters
  • direction: the direction
  • p1: first point
  • p2: second point

Unnamed Group

double singleLayer(const Element &e, double factor) const

Methods to compute the diagonal of the matrix representation of the S and D operators by approximate collocation.

Calculates an element on the diagonal of the matrix representation of the S operator using an approximate collocation formula.

Note
This is the Non-Virtual Interface (NVI)
Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

double doubleLayer(const Element &e, double factor) const

Calculates an element of the diagonal of the matrix representation of the D operator using an approximate collocation formula.

Note
This is the Non-Virtual Interface (NVI)
Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

Unnamed Group

virtual double kernelS_impl(const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const = 0

Methods to sample the Green’s function and its probe point directional derivative

Returns value of the kernel of the \(\mathcal{S}\) integral operator, i.e. the value of the Greens’s function for the pair of points p1, p2: \( G(\mathbf{p}_1, \mathbf{p}_2)\)

Parameters
  • p1: first point
  • p2: second point

virtual double kernelD_impl(const Eigen::Vector3d &direction, const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const = 0

Returns value of the kernel of the \(\mathcal{D}\) integral operator for the pair of points p1, p2: \( [\boldsymbol{\varepsilon}\nabla_{\mathbf{p_2}}G(\mathbf{p}_1, \mathbf{p}_2)]\cdot \mathbf{n}_{\mathbf{p}_2}\) To obtain the kernel of the \(\mathcal{D}^\dagger\) operator call this methods with \(\mathbf{p}_1\) and \(\mathbf{p}_2\) exchanged and with \(\mathbf{n}_{\mathbf{p}_2} = \mathbf{n}_{\mathbf{p}_1}\)

Parameters
  • direction: the direction
  • p1: first point
  • p2: second point

Unnamed Group

virtual double singleLayer_impl(const Element &e, double factor) const = 0

Methods to compute the diagonal of the matrix representation of the S and D operators by approximate collocation.

Calculates an element on the diagonal of the matrix representation of the S operator using an approximate collocation formula.

Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

virtual double doubleLayer_impl(const Element &e, double factor) const = 0

Calculates an element of the diagonal of the matrix representation of the D operator using an approximate collocation formula.

Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

Public Functions

virtual bool uniform() const = 0

Whether the Green’s function describes a uniform environment

virtual double permittivity() const = 0

Returns a dielectric permittivity

GreensFunction

template <typename DerivativeTraits, typename ProfilePolicy>
class GreensFunction : public pcm::IGreensFunction

Templated interface for Green’s functions.

Author
Luca Frediani and Roberto Di Remigio
Date
2012-2016
Template Parameters
  • DerivativeTraits: evaluation strategy for the function and its derivatives
  • ProfilePolicy: dielectric profile type

Unnamed Group

double derivativeSource(const Eigen::Vector3d &normal_p1, const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Methods to sample the Green’s function directional derivatives

Returns value of the directional derivative of the Greens’s function for the pair of points p1, p2: \( \nabla_{\mathbf{p_1}}G(\mathbf{p}_1, \mathbf{p}_2)\cdot \mathbf{n}_{\mathbf{p}_1}\) Notice that this method returns the directional derivative with respect to the source point.

Parameters
  • normal_p1: the normal vector to p1
  • p1: first point
  • p2: second point

virtual double derivativeProbe(const Eigen::Vector3d &normal_p2, const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Returns value of the directional derivative of the Greens’s function for the pair of points p1, p2: \( \nabla_{\mathbf{p_2}}G(\mathbf{p}_1, \mathbf{p}_2)\cdot \mathbf{n}_{\mathbf{p}_2}\) Notice that this method returns the directional derivative with respect to the probe point.

Parameters
  • normal_p2: the normal vector to p2
  • p1: first point
  • p2: second point

Unnamed Group

Eigen::Vector3d gradientSource(const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Methods to sample the Green’s function gradients

Returns full gradient of Greens’s function for the pair of points p1, p2: \( \nabla_{\mathbf{p_1}}G(\mathbf{p}_1, \mathbf{p}_2)\) Notice that this method returns the gradient with respect to the source point.

Parameters
  • p1: first point
  • p2: second point

Eigen::Vector3d gradientProbe(const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Returns full gradient of Greens’s function for the pair of points p1, p2: \( \nabla_{\mathbf{p_2}}G(\mathbf{p}_1, \mathbf{p}_2)\) Notice that this method returns the gradient with respect to the probe point.

Parameters
  • p1: first point
  • p2: second point

Public Functions

virtual bool uniform() const

Whether the Green’s function describes a uniform environment

Protected Functions

virtual DerivativeTraits operator()(DerivativeTraits *source, DerivativeTraits *probe) const = 0

Evaluates the Green’s function given a pair of points

Parameters
  • source: the source point
  • probe: the probe point

virtual double kernelS_impl(const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Returns value of the kernel of the \(\mathcal{S}\) integral operator, i.e. the value of the Greens’s function for the pair of points p1, p2: \( G(\mathbf{p}_1, \mathbf{p}_2)\)

Note
Relies on the implementation of operator() in the subclasses and that is all subclasses need to implement. Thus this method is marked __final.
Parameters
  • p1: first point
  • p2: second point

Protected Attributes

double delta_

Step for numerical differentiation.

ProfilePolicy profile_

Permittivity profile.

Vacuum

template <typename DerivativeTraits = AD_directional>
class Vacuum : public pcm::green::GreensFunction<DerivativeTraits, dielectric_profile::Uniform>

Green’s function for vacuum.

Author
Luca Frediani and Roberto Di Remigio
Date
2012-2016
Template Parameters
  • DerivativeTraits: evaluation strategy for the function and its derivatives

Public Functions

virtual double permittivity() const

Returns a dielectric permittivity

Private Functions

DerivativeTraits operator()(DerivativeTraits *source, DerivativeTraits *probe) const

Evaluates the Green’s function given a pair of points

Parameters
  • source: the source point
  • probe: the probe point

double kernelD_impl(const Eigen::Vector3d &direction, const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Returns value of the kernel of the \(\mathcal{D}\) integral operator for the pair of points p1, p2: \( [\boldsymbol{\varepsilon}\nabla_{\mathbf{p_2}}G(\mathbf{p}_1, \mathbf{p}_2)]\cdot \mathbf{n}_{\mathbf{p}_2}\) To obtain the kernel of the \(\mathcal{D}^\dagger\) operator call this methods with \(\mathbf{p}_1\) and \(\mathbf{p}_2\) exchanged and with \(\mathbf{n}_{\mathbf{p}_2} = \mathbf{n}_{\mathbf{p}_1}\)

Parameters
  • direction: the direction
  • p1: first point
  • p2: second point

double singleLayer_impl(const Element &e, double factor) const

Methods to compute the diagonal of the matrix representation of the S and D operators by approximate collocation.

Calculates an element on the diagonal of the matrix representation of the S operator using an approximate collocation formula.

Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

double doubleLayer_impl(const Element &e, double factor) const

Calculates an element of the diagonal of the matrix representation of the D operator using an approximate collocation formula.

Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

UniformDielectric

template <typename DerivativeTraits = AD_directional>
class UniformDielectric : public pcm::green::GreensFunction<DerivativeTraits, dielectric_profile::Uniform>

Green’s function for uniform dielectric.

Author
Luca Frediani and Roberto Di Remigio
Date
2012-2016
Template Parameters
  • DerivativeTraits: evaluation strategy for the function and its derivatives

Public Functions

virtual double permittivity() const

Returns a dielectric permittivity

Private Functions

DerivativeTraits operator()(DerivativeTraits *source, DerivativeTraits *probe) const

Evaluates the Green’s function given a pair of points

Parameters
  • source: the source point
  • probe: the probe point

double kernelD_impl(const Eigen::Vector3d &direction, const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Returns value of the kernel of the \(\mathcal{D}\) integral operator for the pair of points p1, p2: \( [\boldsymbol{\varepsilon}\nabla_{\mathbf{p_2}}G(\mathbf{p}_1, \mathbf{p}_2)]\cdot \mathbf{n}_{\mathbf{p}_2}\) To obtain the kernel of the \(\mathcal{D}^\dagger\) operator call this methods with \(\mathbf{p}_1\) and \(\mathbf{p}_2\) exchanged and with \(\mathbf{n}_{\mathbf{p}_2} = \mathbf{n}_{\mathbf{p}_1}\)

Parameters
  • direction: the direction
  • p1: first point
  • p2: second point

double singleLayer_impl(const Element &e, double factor) const

Methods to compute the diagonal of the matrix representation of the S and D operators by approximate collocation.

Calculates an element on the diagonal of the matrix representation of the S operator using an approximate collocation formula.

Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

double doubleLayer_impl(const Element &e, double factor) const

Calculates an element of the diagonal of the matrix representation of the D operator using an approximate collocation formula.

Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

IonicLiquid

template <typename DerivativeTraits = AD_directional>
class IonicLiquid : public pcm::green::GreensFunction<DerivativeTraits, dielectric_profile::Yukawa>

Green’s functions for ionic liquid, described by the linearized Poisson-Boltzmann equation.

Author
Luca Frediani, Roberto Di Remigio
Date
2013-2016
Template Parameters
  • DerivativeTraits: evaluation strategy for the function and its derivatives

Public Functions

virtual double permittivity() const

Returns a dielectric permittivity

Private Functions

DerivativeTraits operator()(DerivativeTraits *source, DerivativeTraits *probe) const

Evaluates the Green’s function given a pair of points

Parameters
  • source: the source point
  • probe: the probe point

double kernelD_impl(const Eigen::Vector3d &direction, const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Returns value of the kernel of the \(\mathcal{D}\) integral operator for the pair of points p1, p2: \( [\boldsymbol{\varepsilon}\nabla_{\mathbf{p_2}}G(\mathbf{p}_1, \mathbf{p}_2)]\cdot \mathbf{n}_{\mathbf{p}_2}\) To obtain the kernel of the \(\mathcal{D}^\dagger\) operator call this methods with \(\mathbf{p}_1\) and \(\mathbf{p}_2\) exchanged and with \(\mathbf{n}_{\mathbf{p}_2} = \mathbf{n}_{\mathbf{p}_1}\)

Parameters
  • direction: the direction
  • p1: first point
  • p2: second point

double singleLayer_impl(const Element &e, double factor) const

Methods to compute the diagonal of the matrix representation of the S and D operators by approximate collocation.

Calculates an element on the diagonal of the matrix representation of the S operator using an approximate collocation formula.

Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

double doubleLayer_impl(const Element &e, double factor) const

Calculates an element of the diagonal of the matrix representation of the D operator using an approximate collocation formula.

Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

AnisotropicLiquid

template <typename DerivativeTraits = AD_directional>
class AnisotropicLiquid : public pcm::green::GreensFunction<DerivativeTraits, dielectric_profile::Anisotropic>

Green’s functions for anisotropic liquid, described by a tensorial permittivity.

Author
Roberto Di Remigio
Date
2016
Template Parameters
  • DerivativeTraits: evaluation strategy for the function and its derivatives

Public Functions

AnisotropicLiquid(const Eigen::Vector3d &eigen_eps, const Eigen::Vector3d &euler_ang)

Parameters
  • eigen_eps: eigenvalues of the permittivity tensors
  • euler_ang: Euler angles in degrees

virtual double permittivity() const

Returns a dielectric permittivity

Private Functions

DerivativeTraits operator()(DerivativeTraits *source, DerivativeTraits *probe) const

Evaluates the Green’s function given a pair of points

Parameters
  • source: the source point
  • probe: the probe point

double kernelD_impl(const Eigen::Vector3d &direction, const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Returns value of the kernel of the \(\mathcal{D}\) integral operator for the pair of points p1, p2: \( [\boldsymbol{\varepsilon}\nabla_{\mathbf{p_2}}G(\mathbf{p}_1, \mathbf{p}_2)]\cdot \mathbf{n}_{\mathbf{p}_2}\) To obtain the kernel of the \(\mathcal{D}^\dagger\) operator call this methods with \(\mathbf{p}_1\) and \(\mathbf{p}_2\) exchanged and with \(\mathbf{n}_{\mathbf{p}_2} = \mathbf{n}_{\mathbf{p}_1}\)

Parameters
  • direction: the direction
  • p1: first point
  • p2: second point

double singleLayer_impl(const Element &e, double factor) const

Methods to compute the diagonal of the matrix representation of the S and D operators by approximate collocation.

Calculates an element on the diagonal of the matrix representation of the S operator using an approximate collocation formula.

Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

double doubleLayer_impl(const Element &e, double factor) const

Calculates an element of the diagonal of the matrix representation of the D operator using an approximate collocation formula.

Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

SphericalDiffuse

template <typename ProfilePolicy = dielectric_profile::OneLayerLog>
class SphericalDiffuse : public pcm::green::GreensFunction<Stencil, ProfilePolicy>

Green’s function for a diffuse interface with spherical symmetry.

The origin of the dielectric sphere can be changed by means of the constructor. The solution of the differential equation defining the Green’s function is

always performed assuming that the dielectric sphere is centered in the origin of the coordinate system. Whenever the public methods are invoked to “sample” the Green’s function at a pair of points, a translation of the sampling points is performed first.
Author
Hui Cao, Ville Weijo, Luca Frediani and Roberto Di Remigio
Date
2010-2015
Template Parameters
  • ProfilePolicy: functional form of the diffuse layer

Unnamed Group

int maxLGreen_

Parameters and functions for the calculation of the Green’s function, including Coulomb singularity

Maximum angular momentum in the final summation over Legendre polynomials to obtain G

std::vector<RadialFunction<detail::StateType, detail::LnTransformedRadial, Zeta>> zeta_

First independent radial solution, used to build Green’s function.

Note
The vector has dimension maxLGreen_ and has r^l behavior

std::vector<RadialFunction<detail::StateType, detail::LnTransformedRadial, Omega>> omega_

Second independent radial solution, used to build Green’s function.

Note
The vector has dimension maxLGreen_ and has r^(-l-1) behavior

double imagePotentialComponent_impl(int L, const Eigen::Vector3d &sp, const Eigen::Vector3d &pp, double Cr12) const

Returns L-th component of the radial part of the Green’s function.

Note
This function shifts the given source and probe points by the location of the dielectric sphere.
Parameters
  • L: angular momentum
  • sp: source point
  • pp: probe point
  • Cr12: Coulomb singularity separation coefficient

Unnamed Group

int maxLC_

Parameters and functions for the calculation of the Coulomb singularity separation coefficient

Maximum angular momentum to obtain C(r, r’), needed to separate the Coulomb singularity

RadialFunction<detail::StateType, detail::LnTransformedRadial, Zeta> zetaC_

First independent radial solution, used to build coefficient.

Note
This is needed to separate the Coulomb singularity and has r^l behavior

RadialFunction<detail::StateType, detail::LnTransformedRadial, Omega> omegaC_

Second independent radial solution, used to build coefficient.

Note
This is needed to separate the Coulomb singularity and has r^(-l-1) behavior

double coefficient_impl(const Eigen::Vector3d &sp, const Eigen::Vector3d &pp) const

Returns coefficient for the separation of the Coulomb singularity.

Note
This function shifts the given source and probe points by the location of the dielectric sphere.
Parameters
  • sp: first point
  • pp: second point

Public Functions

SphericalDiffuse(double e1, double e2, double w, double c, const Eigen::Vector3d &o, int l)

Constructor for a one-layer interface

Parameters
  • e1: left-side dielectric constant
  • e2: right-side dielectric constant
  • w: width of the interface layer
  • c: center of the diffuse layer
  • o: center of the sphere
  • l: maximum value of angular momentum

virtual double permittivity() const

Returns a dielectric permittivity

double coefficientCoulomb(const Eigen::Vector3d &source, const Eigen::Vector3d &probe) const

Returns Coulomb singularity separation coefficient.

Parameters
  • source: location of the source charge
  • probe: location of the probe charge

double Coulomb(const Eigen::Vector3d &source, const Eigen::Vector3d &probe) const

Returns singular part of the Green’s function.

Parameters
  • source: location of the source charge
  • probe: location of the probe charge

double imagePotential(const Eigen::Vector3d &source, const Eigen::Vector3d &probe) const

Returns non-singular part of the Green’s function (image potential)

Parameters
  • source: location of the source charge
  • probe: location of the probe charge

double coefficientCoulombDerivative(const Eigen::Vector3d &direction, const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Returns value of the directional derivative of the Coulomb singularity separation coefficient for the pair of points p1, p2: \( \nabla_{\mathbf{p_2}}G(\mathbf{p}_1, \mathbf{p}_2)\cdot *\mathbf{n}_{\mathbf{p}_2}\) Notice that this method returns the directional derivative with respect to the probe point, thus assuming that the direction is relative to that point.

Parameters
  • direction: the direction
  • p1: first point
  • p2: second point

double CoulombDerivative(const Eigen::Vector3d &direction, const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Returns value of the directional derivative of the singular part of the Greens’s function for the pair of points p1, p2: \( \nabla_{\mathbf{p_2}}G(\mathbf{p}_1, \mathbf{p}_2)\cdot *\mathbf{n}_{\mathbf{p}_2}\) Notice that this method returns the directional derivative with respect to the probe point, thus assuming that the direction is relative to that point.

Parameters
  • direction: the direction
  • p1: first point
  • p2: second point

double imagePotentialDerivative(const Eigen::Vector3d &direction, const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Returns value of the directional derivative of the non-singular part (image potential) of the Greens’s function for the pair of points p1, p2: \( \nabla_{\mathbf{p_2}}G(\mathbf{p}_1, \mathbf{p}_2)\cdot *\mathbf{n}_{\mathbf{p}_2}\) Notice that this method returns the directional derivative with respect to the probe point, thus assuming that the direction is relative to that point.

Parameters
  • direction: the direction
  • p1: first point
  • p2: second point

pcm::tuple<double, double> epsilon(const Eigen::Vector3d &point) const

Handle to the dielectric profile evaluation

Private Functions

Stencil operator()(Stencil *sp, Stencil *pp) const

Evaluates the Green’s function given a pair of points

Note
This takes care of the origin shift
Parameters
  • sp: the source point
  • pp: the probe point

double kernelD_impl(const Eigen::Vector3d &direction, const Eigen::Vector3d &p1, const Eigen::Vector3d &p2) const

Returns value of the kernel of the \(\mathcal{D}\) integral operator for the pair of points p1, p2: \( [\boldsymbol{\varepsilon}\nabla_{\mathbf{p_2}}G(\mathbf{p}_1, \mathbf{p}_2)]\cdot \mathbf{n}_{\mathbf{p}_2}\) To obtain the kernel of the \(\mathcal{D}^\dagger\) operator call this methods with \(\mathbf{p}_1\) and \(\mathbf{p}_2\) exchanged and with \(\mathbf{n}_{\mathbf{p}_2} = \mathbf{n}_{\mathbf{p}_1}\)

Parameters
  • direction: the direction
  • p1: first point
  • p2: second point

double singleLayer_impl(const Element &e, double factor) const

Methods to compute the diagonal of the matrix representation of the S and D operators by approximate collocation.

Calculates an element on the diagonal of the matrix representation of the S operator using an approximate collocation formula.

Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

double doubleLayer_impl(const Element &e, double factor) const

Calculates an element of the diagonal of the matrix representation of the D operator using an approximate collocation formula.

Parameters
  • e: finite element on the cavity
  • factor: the scaling factor for the diagonal elements

void initSphericalDiffuse()

This calculates all the components needed to evaluate the Green’s function

Private Members

Eigen::Vector3d origin_

Center of the dielectric sphere