Simpatico
v1.10
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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>
Public Member Functions | |
EwaldInteraction () | |
Default constructor. More... | |
EwaldInteraction (const EwaldInteraction &other) | |
Copy constructor. More... | |
EwaldInteraction & | operator= (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... | |
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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... | |
Begin & | readBegin (std::istream &in, const char *label, bool isRequired=true) |
Add and read a class label and opening bracket. More... | |
End & | readEnd (std::istream &in) |
Add and read the closing bracket. More... | |
Blank & | readBlank (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... | |
Begin & | addBegin (const char *label) |
Add a Begin object representing a class name and bracket. More... | |
End & | addEnd () |
Add a closing bracket. More... | |
Blank & | addBlank () |
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... | |
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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... | |
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virtual | ~Serializable () |
Destructor. More... | |
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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 | |
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typedef BinaryFileOArchive | OArchive |
Type of output archive used by save method. More... | |
typedef BinaryFileIArchive | IArchive |
Type of input archive used by load method. More... | |
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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... | |
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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 ¶m, bool next=true) |
Set this to the parent of a child component. More... | |
void | addComponent (ParamComponent ¶m, 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... | |
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ParamComponent () | |
Constructor. More... | |
ParamComponent (const ParamComponent &other) | |
Copy constructor. More... | |
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.
other | EwaldInteraction to be copied. |
Definition at line 36 of file EwaldInteraction.cpp.
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inline |
Default destructor.
Definition at line 58 of file EwaldInteraction.h.
References alpha(), epsilon(), kSpacePotential(), loadParameters(), readParameters(), rSpaceCutoff(), rSpaceCutoffSq(), rSpaceEnergy(), rSpaceForceOverR(), and save().
EwaldInteraction & Simp::EwaldInteraction::operator= | ( | const EwaldInteraction & | other | ) |
Assignment.
other | EwaldInteraction from which data is copied. |
Definition at line 50 of file EwaldInteraction.cpp.
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virtual |
Read epsilon, alpha, and rCutoff.
in | input parameter stream |
Reimplemented from Util::ParamComposite.
Definition at line 66 of file EwaldInteraction.cpp.
Referenced by McMd::MdEwaldPotential::readParameters(), McMd::MdSpmePotential::readParameters(), and ~EwaldInteraction().
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virtual |
Load internal state from an archive.
ar | input/loading archive |
Reimplemented from Util::ParamComposite.
Definition at line 78 of file EwaldInteraction.cpp.
Referenced by McMd::MdEwaldPotential::loadParameters(), McMd::MdSpmePotential::loadParameters(), and ~EwaldInteraction().
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virtual |
Save internal state to an archive.
ar | output/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.
name | parameter name |
value | new value of parameter |
Definition at line 101 of file EwaldInteraction.cpp.
References UTIL_THROW.
Referenced by McMd::MdEwaldPotential::set(), and McMd::MdSpmePotential::set().
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inline |
Returns r-space interaction energy for a single pair of atoms.
rSpaceEnergy = qProduct*erfc(r*alpha)/(4*pi*epsilon*r)
rSq | square of distance between atoms |
qProduct | product of charges |
Definition at line 235 of file EwaldInteraction.h.
Referenced by McMd::MdEwaldPairPotentialImpl< Interaction >::computeEnergy(), and ~EwaldInteraction().
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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
rSq | square of distance between atoms |
qProduct | product of charges |
Definition at line 246 of file EwaldInteraction.h.
Referenced by McMd::MdEwaldPairPotentialImpl< Interaction >::addForces(), McMd::MdEwaldPairPotentialImpl< Interaction >::computeStress(), and ~EwaldInteraction().
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inline |
Return regularized Fourier-space potential.
kSq | square of wavenumber |
Definition at line 258 of file EwaldInteraction.h.
Referenced by McMd::MdEwaldPotential::makeWaves(), McMd::MdSpmePotential::makeWaves(), and ~EwaldInteraction().
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inline |
Get dielectric permittivity.
Definition at line 208 of file EwaldInteraction.h.
Referenced by McMd::MdEwaldPotential::computeEnergy(), McMd::MdSpmePotential::computeEnergy(), and ~EwaldInteraction().
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inline |
Get Ewald smearing parameter alpha (inverse length).
Definition at line 214 of file EwaldInteraction.h.
Referenced by McMd::MdEwaldPotential::computeEnergy(), McMd::MdSpmePotential::computeEnergy(), McMd::MdSpmePotential::computeStress(), McMd::MdEwaldPotential::computeStress(), and ~EwaldInteraction().
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inline |
Get real space cutoff.
Definition at line 221 of file EwaldInteraction.h.
Referenced by McMd::MdEwaldPairPotentialImpl< Interaction >::loadParameters(), McMd::MdEwaldPairPotentialImpl< Interaction >::readParameters(), and ~EwaldInteraction().
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inline |
Get real space cutoff squared.
Definition at line 228 of file EwaldInteraction.h.
Referenced by McMd::MdEwaldPairPotentialImpl< Interaction >::addForces(), McMd::MdEwaldPairPotentialImpl< Interaction >::computeEnergy(), McMd::MdEwaldPairPotentialImpl< Interaction >::computeStress(), and ~EwaldInteraction().
double Simp::EwaldInteraction::get | ( | std::string | name | ) | const |
Get a parameter value, identified by a string.
name | parameter 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().