Simpatico  v1.10
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Simp::EwaldInteraction Class Reference

Detailed Description

Implementation of r-space and k-space Ewald Coulomb interactions.

This class defines the standard Ewald decomposition of a coulomb potential. The total pair potential is 1/(4 pi epsilon r). The short-range part is erfc(alpha r)/(4 pi epsilon r). The Gaussian smeared k-space potential for square wavenumber kSq is given by V(k) = exp(-kSq/(4*alpha^2))/(epsilon kSq).

Definition at line 32 of file EwaldInteraction.h.

#include <EwaldInteraction.h>

Inheritance diagram for Simp::EwaldInteraction:
Util::ParamComposite Util::ParamComponent Util::Serializable Util::MpiFileIo

Public Member Functions

 EwaldInteraction ()
 Default constructor. More...
 
 EwaldInteraction (const EwaldInteraction &other)
 Copy constructor. More...
 
EwaldInteractionoperator= (const EwaldInteraction &other)
 Assignment. More...
 
 ~EwaldInteraction ()
 Default destructor. More...
 
Mutators
void readParameters (std::istream &in)
 Read epsilon, alpha, and rCutoff. More...
 
virtual void loadParameters (Serializable::IArchive &ar)
 Load internal state from an archive. More...
 
virtual void save (Serializable::OArchive &ar)
 Save internal state to an archive. More...
 
void set (std::string name, double value)
 Modify a parameter, identified by a string. More...
 
Energy and Force Computations
double rSpaceEnergy (double rSq, double qProduct) const
 Returns r-space interaction energy for a single pair of atoms. More...
 
double rSpaceForceOverR (double rSq, double qProduct) const
 Return ratio of scalar pair interaction force to pair separation. More...
 
double kSpacePotential (double kSq) const
 Return regularized Fourier-space potential. More...
 
Parameter Accessors
double epsilon () const
 Get dielectric permittivity. More...
 
double alpha () const
 Get Ewald smearing parameter alpha (inverse length). More...
 
double rSpaceCutoff () const
 Get real space cutoff. More...
 
double rSpaceCutoffSq () const
 Get real space cutoff squared. More...
 
double get (std::string name) const
 Get a parameter value, identified by a string. More...
 
- Public Member Functions inherited from Util::ParamComposite
 ParamComposite ()
 Constructor. More...
 
 ParamComposite (const ParamComposite &other)
 Copy constructor. More...
 
 ParamComposite (int capacity)
 Constructor. More...
 
virtual ~ParamComposite ()
 Virtual destructor. More...
 
void resetParam ()
 Resets ParamComposite to its empty state. More...
 
virtual void readParam (std::istream &in)
 Read the parameter file block. More...
 
virtual void readParamOptional (std::istream &in)
 Read optional parameter file block. More...
 
virtual void writeParam (std::ostream &out)
 Write all parameters to an output stream. More...
 
virtual void load (Serializable::IArchive &ar)
 Load all parameters from an input archive. More...
 
virtual void loadOptional (Serializable::IArchive &ar)
 Load an optional ParamComposite. More...
 
void saveOptional (Serializable::OArchive &ar)
 Saves isActive flag, and then calls save() iff isActive is true. More...
 
void readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
 Add and read a required child ParamComposite. More...
 
void readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
 Add and attempt to read an optional child ParamComposite. More...
 
template<typename Type >
ScalarParam< Type > & read (std::istream &in, const char *label, Type &value)
 Add and read a new required ScalarParam < Type > object. More...
 
template<typename Type >
ScalarParam< Type > & readOptional (std::istream &in, const char *label, Type &value)
 Add and read a new optional ScalarParam < Type > object. More...
 
template<typename Type >
CArrayParam< Type > & readCArray (std::istream &in, const char *label, Type *value, int n)
 Add and read a required C array parameter. More...
 
template<typename Type >
CArrayParam< Type > & readOptionalCArray (std::istream &in, const char *label, Type *value, int n)
 Add and read an optional C array parameter. More...
 
template<typename Type >
DArrayParam< Type > & readDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
 Add and read a required DArray < Type > parameter. More...
 
template<typename Type >
DArrayParam< Type > & readOptionalDArray (std::istream &in, const char *label, DArray< Type > &array, int n)
 Add and read an optional DArray < Type > parameter. More...
 
template<typename Type , int N>
FArrayParam< Type, N > & readFArray (std::istream &in, const char *label, FArray< Type, N > &array)
 Add and read a required FArray < Type, N > array parameter. More...
 
template<typename Type , int N>
FArrayParam< Type, N > & readOptionalFArray (std::istream &in, const char *label, FArray< Type, N > &array)
 Add and read an optional FArray < Type, N > array parameter. More...
 
template<typename Type >
CArray2DParam< Type > & readCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np)
 Add and read a required CArray2DParam < Type > 2D C-array. More...
 
template<typename Type >
CArray2DParam< Type > & readOptionalCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np)
 Add and read an optional CArray2DParam < Type > 2D C-array parameter. More...
 
template<typename Type >
DMatrixParam< Type > & readDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
 Add and read a required DMatrix < Type > matrix parameter. More...
 
template<typename Type >
DMatrixParam< Type > & readOptionalDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n)
 Add and read an optional DMatrix < Type > matrix parameter. More...
 
template<typename Type >
DSymmMatrixParam< Type > & readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
 Add and read a required symmetrix DMatrix. More...
 
template<typename Type >
DSymmMatrixParam< Type > & readOptionalDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
 Add and read an optional DMatrix matrix parameter. More...
 
BeginreadBegin (std::istream &in, const char *label, bool isRequired=true)
 Add and read a class label and opening bracket. More...
 
EndreadEnd (std::istream &in)
 Add and read the closing bracket. More...
 
BlankreadBlank (std::istream &in)
 Add and read a new Blank object, representing a blank line. More...
 
void loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
 Add and load a required child ParamComposite. More...
 
void loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
 Add and load an optional child ParamComposite if isActive. More...
 
template<typename Type >
ScalarParam< Type > & loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)
 Add and load a new ScalarParam < Type > object. More...
 
template<typename Type >
ScalarParam< Type > & loadParameter (Serializable::IArchive &ar, const char *label, Type &value)
 Add and load new required ScalarParam < Type > object. More...
 
template<typename Type >
CArrayParam< Type > & loadCArray (Serializable::IArchive &ar, const char *label, Type *value, int n, bool isRequired)
 Add a C array parameter and load its elements. More...
 
template<typename Type >
CArrayParam< Type > & loadCArray (Serializable::IArchive &ar, const char *label, Type *value, int n)
 Add and load a required CArrayParam< Type > array parameter. More...
 
template<typename Type >
DArrayParam< Type > & loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired)
 Add an load a DArray < Type > array parameter. More...
 
template<typename Type >
DArrayParam< Type > & loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n)
 Add and load a required DArray< Type > array parameter. More...
 
template<typename Type , int N>
FArrayParam< Type, N > & loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired)
 Add and load an FArray < Type, N > fixed-size array parameter. More...
 
template<typename Type , int N>
FArrayParam< Type, N > & loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array)
 Add and load a required FArray < Type > array parameter. More...
 
template<typename Type >
CArray2DParam< Type > & loadCArray2D (Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np, bool isRequired)
 Add and load a CArray2DParam < Type > C 2D array parameter. More...
 
template<typename Type >
CArray2DParam< Type > & loadCArray2D (Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np)
 Add and load a required < Type > matrix parameter. More...
 
template<typename Type >
DMatrixParam< Type > & loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired)
 Add and load a DMatrixParam < Type > matrix parameter. More...
 
template<typename Type >
DMatrixParam< Type > & loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n)
 Add and load a required DMatrixParam < Type > matrix parameter. More...
 
template<typename Type >
DSymmMatrixParam< Type > & loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired)
 Add and load a symmetric DSymmMatrixParam < Type > matrix parameter. More...
 
template<typename Type >
DSymmMatrixParam< Type > & loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n)
 Add and load a required DSymmMatrixParam < Type > matrix parameter. More...
 
void addParamComposite (ParamComposite &child, bool next=true)
 Add a child ParamComposite object to the format array. More...
 
BeginaddBegin (const char *label)
 Add a Begin object representing a class name and bracket. More...
 
EndaddEnd ()
 Add a closing bracket. More...
 
BlankaddBlank ()
 Create and add a new Blank object, representing a blank line. More...
 
std::string className () const
 Get class name string. More...
 
bool isRequired () const
 Is this ParamComposite required in the input file? More...
 
bool isActive () const
 Is this parameter active? More...
 
- Public Member Functions inherited from Util::ParamComponent
virtual ~ParamComponent ()
 Destructor. More...
 
void setIndent (const ParamComponent &parent, bool next=true)
 Set indent level. More...
 
std::string indent () const
 Return indent string for this object (string of spaces). More...
 
template<class Archive >
void serialize (Archive &ar, const unsigned int version)
 Serialize this ParamComponent as a string. More...
 
- Public Member Functions inherited from Util::Serializable
virtual ~Serializable ()
 Destructor. More...
 
- Public Member Functions inherited from Util::MpiFileIo
 MpiFileIo ()
 Constructor. More...
 
 MpiFileIo (const MpiFileIo &other)
 Copy constructor. More...
 
bool isIoProcessor () const
 Can this processor do file I/O ? More...
 
void setIoCommunicator (MPI::Intracomm &communicator)
 Set the communicator. More...
 
void clearCommunicator ()
 Clear (nullify) the communicator. More...
 
bool hasIoCommunicator () const
 Does this object have an associated MPI communicator? More...
 
MPI::Intracomm & ioCommunicator () const
 Get the MPI communicator by reference. More...
 

Additional Inherited Members

- Public Types inherited from Util::Serializable
typedef BinaryFileOArchive OArchive
 Type of output archive used by save method. More...
 
typedef BinaryFileIArchive IArchive
 Type of input archive used by load method. More...
 
- Static Public Member Functions inherited from Util::ParamComponent
static void initStatic ()
 Initialize static echo member to false. More...
 
static void setEcho (bool echo=true)
 Enable or disable echoing for all subclasses of ParamComponent. More...
 
static bool echo ()
 Get echo parameter. More...
 
- Protected Member Functions inherited from Util::ParamComposite
void setClassName (const char *className)
 Set class name string. More...
 
void setIsRequired (bool isRequired)
 Set or unset the isActive flag. More...
 
void setIsActive (bool isActive)
 Set or unset the isActive flag. More...
 
void setParent (ParamComponent &param, bool next=true)
 Set this to the parent of a child component. More...
 
void addComponent (ParamComponent &param, bool isLeaf=true)
 Add a new ParamComponent object to the format array. More...
 
template<typename Type >
ScalarParam< Type > & add (std::istream &in, const char *label, Type &value, bool isRequired=true)
 Add a new required ScalarParam < Type > object. More...
 
template<typename Type >
CArrayParam< Type > & addCArray (std::istream &in, const char *label, Type *value, int n, bool isRequired=true)
 Add (but do not read) a required C array parameter. More...
 
template<typename Type >
DArrayParam< Type > & addDArray (std::istream &in, const char *label, DArray< Type > &array, int n, bool isRequired=true)
 Add (but do not read) a DArray < Type > parameter. More...
 
template<typename Type , int N>
FArrayParam< Type, N > & addFArray (std::istream &in, const char *label, FArray< Type, N > &array, bool isRequired=true)
 Add (but do not read) a FArray < Type, N > array parameter. More...
 
template<typename Type >
CArray2DParam< Type > & addCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np, bool isRequired=true)
 Add (but do not read) a CArray2DParam < Type > 2D C-array. More...
 
template<typename Type >
DMatrixParam< Type > & addDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired=true)
 Add and read a required DMatrix < Type > matrix parameter. More...
 
- Protected Member Functions inherited from Util::ParamComponent
 ParamComponent ()
 Constructor. More...
 
 ParamComponent (const ParamComponent &other)
 Copy constructor. More...
 

Constructor & Destructor Documentation

Simp::EwaldInteraction::EwaldInteraction ( )

Default constructor.

Definition at line 26 of file EwaldInteraction.cpp.

References Util::ParamComposite::setClassName().

Simp::EwaldInteraction::EwaldInteraction ( const EwaldInteraction other)

Copy constructor.

Parameters
otherEwaldInteraction to be copied.

Definition at line 36 of file EwaldInteraction.cpp.

Simp::EwaldInteraction::~EwaldInteraction ( )
inline

Member Function Documentation

EwaldInteraction & Simp::EwaldInteraction::operator= ( const EwaldInteraction other)

Assignment.

Parameters
otherEwaldInteraction from which data is copied.

Definition at line 50 of file EwaldInteraction.cpp.

void Simp::EwaldInteraction::readParameters ( std::istream &  in)
virtual

Read epsilon, alpha, and rCutoff.

Parameters
ininput parameter stream

Reimplemented from Util::ParamComposite.

Definition at line 66 of file EwaldInteraction.cpp.

Referenced by McMd::MdEwaldPotential::readParameters(), McMd::MdSpmePotential::readParameters(), and ~EwaldInteraction().

void Simp::EwaldInteraction::loadParameters ( Serializable::IArchive ar)
virtual

Load internal state from an archive.

Parameters
arinput/loading archive

Reimplemented from Util::ParamComposite.

Definition at line 78 of file EwaldInteraction.cpp.

Referenced by McMd::MdEwaldPotential::loadParameters(), McMd::MdSpmePotential::loadParameters(), and ~EwaldInteraction().

void Simp::EwaldInteraction::save ( Serializable::OArchive ar)
virtual

Save internal state to an archive.

Parameters
aroutput/saving archive

Reimplemented from Util::ParamComposite.

Definition at line 91 of file EwaldInteraction.cpp.

Referenced by McMd::MdEwaldPotential::save(), McMd::MdSpmePotential::save(), and ~EwaldInteraction().

void Simp::EwaldInteraction::set ( std::string  name,
double  value 
)

Modify a parameter, identified by a string.

Parameters
nameparameter name
valuenew value of parameter

Definition at line 101 of file EwaldInteraction.cpp.

References UTIL_THROW.

Referenced by McMd::MdEwaldPotential::set(), and McMd::MdSpmePotential::set().

double Simp::EwaldInteraction::rSpaceEnergy ( double  rSq,
double  qProduct 
) const
inline

Returns r-space interaction energy for a single pair of atoms.

rSpaceEnergy = qProduct*erfc(r*alpha)/(4*pi*epsilon*r)

Parameters
rSqsquare of distance between atoms
qProductproduct of charges
Returns
short range part of pair energy

Definition at line 235 of file EwaldInteraction.h.

Referenced by McMd::MdEwaldPairPotentialImpl< Interaction >::computeEnergy(), and ~EwaldInteraction().

double Simp::EwaldInteraction::rSpaceForceOverR ( double  rSq,
double  qProduct 
) const
inline

Return ratio of scalar pair interaction force to pair separation.

Multiply this quantity by the components of the separation vector to obtain the force vector. A positive value for the return value represents a repulsive force between a pair of atoms.

Precondition: The distance squared rSq must be less than cutoffSq. If rSq > cutoffSq, the return value is undefined (i.e., invalid). Usage: Test for rSq < cutoffSq before calling this function

if (rSq < interaction.rSpaceCutoffSq()) {
forceOverR = rSpaceForceOverR(rsq, i, j);
.....
}
Parameters
rSqsquare of distance between atoms
qProductproduct of charges
Returns
force magnitude divided by distance

Definition at line 246 of file EwaldInteraction.h.

Referenced by McMd::MdEwaldPairPotentialImpl< Interaction >::addForces(), McMd::MdEwaldPairPotentialImpl< Interaction >::computeStress(), and ~EwaldInteraction().

double Simp::EwaldInteraction::kSpacePotential ( double  kSq) const
inline

Return regularized Fourier-space potential.

Parameters
kSqsquare of wavenumber
Returns
exp(-kSq/(4*alpha*alpha))/(epsilon*ksq)

Definition at line 258 of file EwaldInteraction.h.

Referenced by McMd::MdEwaldPotential::makeWaves(), McMd::MdSpmePotential::makeWaves(), and ~EwaldInteraction().

double Simp::EwaldInteraction::epsilon ( ) const
inline

Get dielectric permittivity.

Returns
epsilon

Definition at line 208 of file EwaldInteraction.h.

Referenced by McMd::MdEwaldPotential::computeEnergy(), McMd::MdSpmePotential::computeEnergy(), and ~EwaldInteraction().

double Simp::EwaldInteraction::alpha ( ) const
inline
double Simp::EwaldInteraction::rSpaceCutoff ( ) const
inline
double Simp::EwaldInteraction::rSpaceCutoffSq ( ) const
inline
double Simp::EwaldInteraction::get ( std::string  name) const

Get a parameter value, identified by a string.

Parameters
nameparameter name

Definition at line 120 of file EwaldInteraction.cpp.

References Util::Constants::Pi, and UTIL_THROW.

Referenced by McMd::MdEwaldPotential::get(), and McMd::MdSpmePotential::get().


The documentation for this class was generated from the following files: