Detailed Description
Ewald Coulomb potential class for MD simulations.
This class implements the k-space sums in the Ewald method for computing the Coulomb energy and forces.
Definition at line 47 of file MdEwaldPotential.h.
#include <MdEwaldPotential.h>
Inheritance diagram for McMd::MdEwaldPotential:
Public Member Functions | |
| MdEwaldPotential (System &system) | |
| Constructor. More... | |
| virtual | ~MdEwaldPotential () |
| Destructor (does nothing). More... | |
Initialization | |
| virtual void | readParameters (std::istream &in) |
| Read parameters and initialize. 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... | |
Parameters (get/set) | |
| void | set (std::string name, double value) |
| Set a parameter value, identified by a string. More... | |
| double | get (std::string name) const |
| Get a parameter value, identified by a string. More... | |
System energy and stress. | |
| virtual void | makeWaves () |
| Generate wavevectors for the current boundary and kCutoff. More... | |
| int | nWave () const |
| Current number of wavevectors with |k| < kCutoff. More... | |
| virtual void | addForces () |
| Add k-space Coulomb forces for all atoms. More... | |
| virtual void | computeEnergy () |
| Calculate the long range kspace part of Coulomb energy. More... | |
| virtual void | computeStress () |
| Compute kspace part of Coulomb pressure. More... | |
Miscellaneous Accessors | |
| EwaldRSpaceAccumulator & | rSpaceAccumulator () |
| EwaldInteraction & | ewaldInteraction () |
 Public Member Functions inherited from McMd::MdCoulombPotential | |
| MdCoulombPotential () | |
| Constructor. More... | |
| virtual | ~MdCoulombPotential () |
| Destructor (does nothing). More... | |
| bool | hasWaves () |
| Are wavevectors and k-space influence function up to date? More... | |
| void | unsetWaves () |
| Unset all data that depends on the Boundary. More... | |
| virtual void | unsetEnergy () |
| Unset k-space energy. More... | |
| double | kSpaceEnergy () |
| Get long-range k-space part of Coulomb energy. More... | |
| double | rSpaceEnergy () |
| Return short-range r-space part of Coulomb energy. More... | |
| double | energy () |
| Get total Coulomb energy. More... | |
| virtual void | unsetStress () |
| Unset k-space stress. More... | |
| Tensor | kSpaceStress () |
| Get long-range k-space part of Coulomb stress. More... | |
| Tensor | rSpaceStress () |
| Return short-range r-space part of Coulomb stress. More... | |
| Tensor | stress () |
| Get total Coulomb stress. More... | |
| void | computeStress (Tensor &stress) |
| Get total Coulomb stress. More... | |
| void | computeStress (Vector &pressures) |
| Get diagonal components of Coulomb stress. More... | |
| double | pressure () |
| Get total Coulomb pressure. More... | |
| void | computeStress (double &pressure) |
| Get the total Coulomb pressure. 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... | |
| 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... | |
| 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 ¶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... | |
| Protected Member Functions inherited from Util::ParamComponent | |
| ParamComponent () | |
| Constructor. More... | |
| ParamComponent (const ParamComponent &other) | |
| Copy constructor. More... | |
| Protected Attributes inherited from McMd::MdCoulombPotential | |
| EwaldRSpaceAccumulator | rSpaceAccumulator_ |
| Short-range real space energy and stress contributions. More... | |
| Setable< double > | kSpaceEnergy_ |
| K-space part of Coulomb energy. More... | |
| Setable< Tensor > | kSpaceStress_ |
| K-space part of Coulomb stress. More... | |
| bool | isInitialized_ |
| Have parameters been set? More... | |
| bool | hasWaves_ |
| Are waves and k-space potential up to date? Unset if boundary or parameters change. More... | |
Constructor & Destructor Documentation
| McMd::MdEwaldPotential::MdEwaldPotential | ( | System & | system | ) |
|
virtual |
Destructor (does nothing).
Definition at line 47 of file MdEwaldPotential.cpp.
Member Function Documentation
|
virtual |
Read parameters and initialize.
- Parameters
-
in input stream
Reimplemented from Util::ParamComposite.
Definition at line 53 of file MdEwaldPotential.cpp.
References Util::ParamComposite::addParamComposite(), and Simp::EwaldInteraction::readParameters().
|
virtual |
Load internal state from an archive.
- Parameters
-
ar input/loading archive
Reimplemented from Util::ParamComposite.
Definition at line 66 of file MdEwaldPotential.cpp.
References Util::ParamComposite::addParamComposite(), and Simp::EwaldInteraction::loadParameters().
|
virtual |
Save internal state to an archive.
- Parameters
-
ar output/saving archive
Reimplemented from Util::ParamComposite.
Definition at line 78 of file MdEwaldPotential.cpp.
References Simp::EwaldInteraction::save().
|
virtual |
Set a parameter value, identified by a string.
- Parameters
-
name parameter name value new value of parameter
Reimplemented from McMd::MdCoulombPotential.
Definition at line 87 of file MdEwaldPotential.cpp.
References Simp::EwaldInteraction::set(), and McMd::MdCoulombPotential::unsetWaves().
|
virtual |
Get a parameter value, identified by a string.
- Parameters
-
name parameter name
Reimplemented from McMd::MdCoulombPotential.
Definition at line 100 of file MdEwaldPotential.cpp.
References Simp::EwaldInteraction::get().
|
virtual |
Generate wavevectors for the current boundary and kCutoff.
Implements McMd::MdCoulombPotential.
Definition at line 125 of file MdEwaldPotential.cpp.
References Util::Vector::abs(), Util::GArray< Data >::append(), McMd::System::begin(), Simp::OrthorhombicBoundary::bravaisBasisVector(), Util::GArray< Data >::clear(), Util::Dimension, Util::Vector::dot(), McMd::MdCoulombPotential::hasWaves(), McMd::MdCoulombPotential::hasWaves_, Simp::EwaldInteraction::kSpacePotential(), Util::Vector::multiply(), Util::ArrayIterator< Data >::notEnd(), Util::PArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), Util::Constants::Pi, Simp::OrthorhombicBoundary::reciprocalBasisVector(), Util::GArray< Data >::reserve(), Util::GArray< Data >::resize(), Util::GArray< Data >::size(), Util::Vector::square(), Simp::OrthorhombicBoundary::transformCartToGen(), and UTIL_CHECK.
|
inlinevirtual |
Current number of wavevectors with |k| < kCutoff.
Implements McMd::MdCoulombPotential.
Definition at line 114 of file MdEwaldPotential.cpp.
|
virtual |
Add k-space Coulomb forces for all atoms.
Implements McMd::MdCoulombPotential.
Definition at line 288 of file MdEwaldPotential.cpp.
References McMd::System::begin(), Util::Dimension, Util::Constants::Im, Util::Vector::multiply(), Util::ArrayIterator< Data >::notEnd(), Util::PArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), Util::Constants::Pi, Simp::OrthorhombicBoundary::reciprocalBasisVector(), Util::GArray< Data >::size(), Simp::OrthorhombicBoundary::transformCartToGen(), Simp::OrthorhombicBoundary::volume(), and Util::Vector::zero().
|
virtual |
Calculate the long range kspace part of Coulomb energy.
Implements McMd::MdCoulombPotential.
Definition at line 378 of file MdEwaldPotential.cpp.
References Simp::EwaldInteraction::alpha(), McMd::System::begin(), McMd::MdCoulombPotential::energy(), Simp::EwaldInteraction::epsilon(), McMd::MdCoulombPotential::kSpaceEnergy_, Util::ArrayIterator< Data >::notEnd(), Util::PArrayIterator< Data >::notEnd(), McMd::Simulation::nSpecies(), Util::Constants::Pi, Util::Setable< T >::set(), and Simp::OrthorhombicBoundary::volume().
|
virtual |
Compute kspace part of Coulomb pressure.
Implements McMd::MdCoulombPotential.
Definition at line 428 of file MdEwaldPotential.cpp.
References Util::Tensor::add(), Simp::EwaldInteraction::alpha(), Util::Tensor::dyad(), Util::Tensor::Identity, McMd::MdCoulombPotential::kSpaceStress_, Util::Vector::multiply(), Simp::OrthorhombicBoundary::reciprocalBasisVector(), Simp::OrthorhombicBoundary::volume(), and Util::Tensor::zero().
The documentation for this class was generated from the following files:
