Detailed Description
Analyzer to output the total pair energy and the sum of squares of the monomeric and molecular pair energy.
See here for the parameter file format and any other user documentation.
Definition at line 38 of file MdPairEnergyCoefficients.h.
#include <MdPairEnergyCoefficients.h>
Inheritance diagram for McMd::MdPairEnergyCoefficients:
Public Member Functions | |
| MdPairEnergyCoefficients (MdSystem &system) | |
| Constructor. More... | |
| ~MdPairEnergyCoefficients () | |
| Destructor. More... | |
| virtual void | readParameters (std::istream &in) |
| Read parameters and initialize. More... | |
| virtual void | loadParameters (Serializable::IArchive &ar) |
| Load state from an archive. More... | |
| virtual void | save (Serializable::OArchive &ar) |
| Save state to archive. More... | |
| template<class Archive > | |
| void | serialize (Archive &ar, const unsigned int version) |
| Serialize to/from an archive. More... | |
| virtual void | sample (long iStep) |
| Evaluate energy and print. More... | |
| virtual void | output () |
| Output final summary and file format. More... | |
 Public Member Functions inherited from McMd::SystemAnalyzer< MdSystem > | |
| SystemAnalyzer (MdSystem &system) | |
| Constructor. More... | |
| virtual | ~SystemAnalyzer () |
| Destructor. More... | |
| Public Member Functions inherited from McMd::Analyzer | |
| Analyzer () | |
| Default constructor. More... | |
| virtual | ~Analyzer () |
| Destructor. More... | |
| template<class Archive > | |
| void | serialize (Archive &ar, const unsigned int version) |
| Serialize to/from an archive. More... | |
| virtual void | setup () |
| Complete any required initialization. More... | |
| int | interval () const |
| Get interval value. More... | |
| bool | isAtInterval (long counter) const |
| Return true iff counter is a multiple of the interval. 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 McMd::Analyzer | |
| static void | initStatic () |
| Define and initialize baseInterval. 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... | |
| Static Public Attributes inherited from McMd::Analyzer | |
| static long | baseInterval = 0 |
| The interval for an Analyzer must be a multiple of baseInterval. More... | |
| Protected Member Functions inherited from McMd::SystemAnalyzer< MdSystem > | |
| MdSystem & | system () |
| Return reference to parent system. More... | |
| Protected Member Functions inherited from McMd::Analyzer | |
| void | setFileMaster (FileMaster &fileMaster) |
| Set the FileMaster to use to open files. More... | |
| void | readInterval (std::istream &in) |
| Read interval from file, with error checking. More... | |
| void | readOutputFileName (std::istream &in) |
| Read outputFileName from file. More... | |
| void | loadInterval (Serializable::IArchive &ar) |
| Load interval from archive, with error checking. More... | |
| void | loadOutputFileName (Serializable::IArchive &ar) |
| Load output file name from archive. More... | |
| FileMaster & | fileMaster () |
| Get the FileMaster by reference. More... | |
| const std::string & | outputFileName () const |
| Return outputFileName string. More... | |
| std::string | outputFileName (const std::string &suffix) const |
| Return outputFileName string with added suffix. 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::Analyzer | |
| std::string | outputFileName_ |
| Base name of output file(s). More... | |
| long | interval_ |
| Number of simulation steps between subsequent actions. More... | |
Constructor & Destructor Documentation
| McMd::MdPairEnergyCoefficients::MdPairEnergyCoefficients | ( | MdSystem & | system | ) |
Constructor.
Definition at line 29 of file MdPairEnergyCoefficients.cpp.
References Util::ParamComposite::setClassName().
| McMd::MdPairEnergyCoefficients::~MdPairEnergyCoefficients | ( | ) |
Destructor.
Definition at line 42 of file MdPairEnergyCoefficients.cpp.
References Simp::Species::capacity(), McMd::System::simulation(), McMd::Simulation::species(), and McMd::SystemAnalyzer< MdSystem >::system().
Member Function Documentation
|
virtual |
Read parameters and initialize.
Reads output file, pair selector and maximum number of neighbors per molecule
- Parameters
-
in input parameter stream
Reimplemented from McMd::Analyzer.
Definition at line 66 of file MdPairEnergyCoefficients.cpp.
References Simp::Species::capacity(), McMd::Analyzer::fileMaster(), Util::FileMaster::openOutputFile(), McMd::Analyzer::outputFileName(), McMd::Analyzer::readInterval(), McMd::Analyzer::readOutputFileName(), McMd::System::simulation(), McMd::Simulation::species(), and McMd::SystemAnalyzer< MdSystem >::system().
|
virtual |
Load state from an archive.
- Parameters
-
ar loading (input) archive.
Reimplemented from McMd::Analyzer.
Definition at line 99 of file MdPairEnergyCoefficients.cpp.
References Simp::Species::capacity(), McMd::Analyzer::fileMaster(), McMd::Analyzer::loadInterval(), McMd::Analyzer::loadOutputFileName(), Util::FileMaster::openOutputFile(), McMd::Analyzer::outputFileName(), McMd::System::simulation(), McMd::Simulation::species(), McMd::SystemAnalyzer< MdSystem >::system(), and UTIL_THROW.
|
virtual |
Save state to archive.
- Parameters
-
ar saving (output) archive.
Reimplemented from McMd::Analyzer.
Definition at line 151 of file MdPairEnergyCoefficients.cpp.
template<class Archive >
| void McMd::MdPairEnergyCoefficients::serialize | ( | Archive & | ar, |
| const unsigned int | version | ||
| ) |
Serialize to/from an archive.
- Parameters
-
ar saving or loading archive version archive version id
Definition at line 149 of file MdPairEnergyCoefficients.h.
|
virtual |
Evaluate energy and print.
Implements McMd::Analyzer.
Definition at line 157 of file MdPairEnergyCoefficients.cpp.
References Util::DSArray< Data >::begin(), McMd::PairList::begin(), Simp::Species::capacity(), Simp::OrthorhombicBoundary::distanceSq(), McMd::PairPotential::energy(), McMd::PairIterator::getPair(), McMd::Molecule::id(), Simp::Species::id(), McMd::Analyzer::isAtInterval(), McMd::PairSelector::match(), McMd::Atom::molecule(), Util::ConstArrayIterator< Data >::notEnd(), McMd::PairIterator::notEnd(), McMd::Atom::position(), Util::Average::sample(), McMd::System::simulation(), McMd::Molecule::species(), McMd::Simulation::species(), McMd::SystemAnalyzer< MdSystem >::system(), and McMd::Atom::typeId().
|
virtual |
Output final summary and file format.
Reimplemented from McMd::Analyzer.
Definition at line 318 of file MdPairEnergyCoefficients.cpp.
References McMd::Analyzer::fileMaster(), Util::FileMaster::openOutputFile(), Util::Average::output(), McMd::Analyzer::outputFileName(), and Util::ParamComposite::writeParam().
The documentation for this class was generated from the following files:
