Detailed Description
StructureFactorGrid evaluates structure factors in Fourier space.
This class evaluates the structures factors for all wavevectors within a grid, within a region in which each of the h, k, l integer wavevector components (i.e., Miller indices) has an absolute magnitude less than or equal to a parameter hMax.
The class also requires a user to specify a variable lattice of enum type LatticeSystem whose value (e.g., Cubic, Orthorhombic, Triclinic) determines the symmetry group that is used to group group equivalent wavevectors into "stars". Use Triclinic to impose no symmetry.
Example: Here is parameter file for a system with nAtomType = 2, with two monomer types 0 and 1, for calculating the total, 00, and 01 correlation functions on a grid with Miller indices up and including 5:
At the end of a simulation, all of the structure factors are output in a file with a suffix *.dat. Each line in this file contains the 3 Miller indices of a wavevector, the absolute magnitude of the wavevector, and a list of nAtomTypeIdPair structure factor values for the wavevector, one for each atomTypeId pair.
- See also
- param file format
Definition at line 61 of file ddMd/analyzers/scattering/StructureFactorGrid.h.
#include <StructureFactorGrid.h>
Public Member Functions | |
| StructureFactorGrid (Simulation &simulation) | |
| Constructor. More... | |
| virtual void | readParameters (std::istream &in) |
| Read parameters from file. 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... | |
| virtual void | clear () |
| Clear all accumulators and counters. More... | |
| virtual void | sample (long iStep) |
| Add particles to StructureFactor accumulators. More... | |
| virtual void | output () |
| Output structure factors, averaged over stars. More... | |
 Public Member Functions inherited from DdMd::StructureFactor | |
| StructureFactor (Simulation &simulation) | |
| Constructor. More... | |
| ~StructureFactor () | |
| Destructor. More... | |
| Public Member Functions inherited from DdMd::Analyzer | |
| Analyzer (Simulation &simulation) | |
| Constructor. More... | |
| virtual | ~Analyzer () |
| Destructor. More... | |
| virtual void | setup () |
| Setup before simulation. 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 DdMd::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 DdMd::StructureFactor | |
| static const int | Samples = 100000 |
| Number of analyzer samples in simulation. More... | |
| Static Public Attributes inherited from DdMd::Analyzer | |
| static long | baseInterval = 1 |
| The interval for an Analyzer must be a multiple of baseInterval. More... | |
| Protected Member Functions inherited from DdMd::StructureFactor | |
| void | makeWaveVectors () |
| Update wavevectors. More... | |
| Protected Member Functions inherited from DdMd::Analyzer | |
| void | readInterval (std::istream &in) |
| Read parameter interval from file. More... | |
| void | loadInterval (Serializable::IArchive &ar) |
| Load parameter interval from input archive. More... | |
| void | saveInterval (Serializable::OArchive &ar) |
| Save interval parameter to an archive. More... | |
| void | readOutputFileName (std::istream &in) |
| Read outputFileName from file. More... | |
| void | loadOutputFileName (Serializable::IArchive &ar) |
| Load output file name to an archive. More... | |
| void | saveOutputFileName (Serializable::OArchive &ar) |
| Save output file name to an archive. More... | |
| Simulation & | simulation () |
| Get the parent Simulation 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 DdMd::StructureFactor | |
| std::ofstream | outputFile_ |
| Output file stream. More... | |
| DMatrix< double > | structureFactors_ |
| Structure factor accumulators. More... | |
| DMatrix< std::complex< double > > | fourierModes_ |
| Fourier modes of concentration. More... | |
| DMatrix< std::complex< double > > | totalFourierModes_ |
| Total fourier modes of concentration. More... | |
| DArray< IntVector > | waveIntVectors_ |
| Array of Miller index IntVectors for wavevectors. More... | |
| DArray< Vector > | waveVectors_ |
| Array of floating point wave vectors. More... | |
| DMatrix< double > | modes_ |
| Array of mode vectors. More... | |
| int | nWave_ |
| Number of wavevectors. More... | |
| int | nMode_ |
| Number of mode vectors. More... | |
| int | nSample_ |
| Number of samples thus far. More... | |
| int | nAtomType_ |
| Number of atom types, copied from Simulation::nAtomType(). More... | |
| bool | isInitialized_ |
| Has readParam been called? More... | |
| bool | isFirstStep_ |
| Is this the first step? More... | |
Constructor & Destructor Documentation
| DdMd::StructureFactorGrid::StructureFactorGrid | ( | Simulation & | simulation | ) |
Constructor.
- Parameters
-
simulation reference to parent DdMd::Simulation object
Definition at line 27 of file ddMd/analyzers/scattering/StructureFactorGrid.cpp.
References Util::ParamComposite::setClassName().
Member Function Documentation
|
virtual |
Read parameters from file.
Input format:
- int interval sampling interval
- string outputFileName output file base name
- int nMode number of modes
- DMatrix<double> modes mode vectors
- int hMax maximum Miller index
- LatticeSystem lattice lattice system (string)
- Parameters
-
in input parameter stream
Reimplemented from DdMd::StructureFactor.
Definition at line 38 of file ddMd/analyzers/scattering/StructureFactorGrid.cpp.
References Util::SymmetryGroup< Symmetry >::add(), Util::DMatrix< Data >::allocate(), Util::DArray< Data >::allocate(), DdMd::StructureFactor::fourierModes_, Util::SymmetryGroup< Symmetry >::makeCompleteGroup(), Util::PointGroup::makeStar(), DdMd::StructureFactor::modes_, DdMd::Simulation::nAtomType(), DdMd::StructureFactor::nAtomType_, DdMd::StructureFactor::nMode_, DdMd::StructureFactor::nSample_, DdMd::StructureFactor::nWave_, Util::PointSymmetry::R(), DdMd::Analyzer::readInterval(), DdMd::Analyzer::readOutputFileName(), DdMd::Analyzer::simulation(), Util::FSArray< Data, Capacity >::size(), DdMd::StructureFactor::structureFactors_, DdMd::StructureFactor::totalFourierModes_, UTIL_THROW, DdMd::StructureFactor::waveIntVectors_, and DdMd::StructureFactor::waveVectors_.
|
virtual |
Load internal state from an archive.
- Parameters
-
ar input/loading archive
Reimplemented from DdMd::StructureFactor.
Definition at line 242 of file ddMd/analyzers/scattering/StructureFactorGrid.cpp.
References Util::DMatrix< Data >::allocate(), Util::DArray< Data >::allocate(), DdMd::StructureFactor::fourierModes_, DdMd::Analyzer::loadInterval(), DdMd::Analyzer::loadOutputFileName(), DdMd::StructureFactor::modes_, DdMd::Simulation::nAtomType(), DdMd::StructureFactor::nAtomType_, DdMd::StructureFactor::nMode_, DdMd::StructureFactor::nSample_, DdMd::StructureFactor::nWave_, DdMd::Analyzer::simulation(), DdMd::StructureFactor::structureFactors_, DdMd::StructureFactor::totalFourierModes_, DdMd::StructureFactor::waveIntVectors_, and DdMd::StructureFactor::waveVectors_.
|
virtual |
Save internal state to an archive.
- Parameters
-
ar output/saving archive
Reimplemented from DdMd::StructureFactor.
Definition at line 283 of file ddMd/analyzers/scattering/StructureFactorGrid.cpp.
References DdMd::StructureFactor::modes_, DdMd::StructureFactor::nMode_, DdMd::StructureFactor::nSample_, DdMd::StructureFactor::nWave_, DdMd::Analyzer::saveInterval(), DdMd::Analyzer::saveOutputFileName(), DdMd::StructureFactor::structureFactors_, and DdMd::StructureFactor::waveIntVectors_.
|
virtual |
Clear all accumulators and counters.
Reimplemented from DdMd::StructureFactor.
Definition at line 302 of file ddMd/analyzers/scattering/StructureFactorGrid.cpp.
|
virtual |
Add particles to StructureFactor accumulators.
- Parameters
-
iStep step counter
Reimplemented from DdMd::StructureFactor.
Definition at line 305 of file ddMd/analyzers/scattering/StructureFactorGrid.cpp.
References DdMd::Simulation::boundary(), Util::Dimension, DdMd::Simulation::fileMaster(), DdMd::Analyzer::isAtInterval(), DdMd::StructureFactor::isFirstStep_, DdMd::StructureFactor::nMode_, Util::FileMaster::openOutputFile(), DdMd::Analyzer::outputFileName(), DdMd::StructureFactor::sample(), DdMd::Analyzer::simulation(), DdMd::StructureFactor::totalFourierModes_, UTIL_THROW, Simp::OrthorhombicBoundary::volume(), DdMd::StructureFactor::waveIntVectors_, and DdMd::StructureFactor::waveVectors_.
|
virtual |
Output structure factors, averaged over stars.
Reimplemented from DdMd::StructureFactor.
Definition at line 357 of file ddMd/analyzers/scattering/StructureFactorGrid.cpp.
References Util::Dimension, DdMd::Simulation::fileMaster(), DdMd::StructureFactor::nMode_, DdMd::StructureFactor::nSample_, Util::FileMaster::openOutputFile(), DdMd::StructureFactor::outputFile_, DdMd::Analyzer::outputFileName(), DdMd::Analyzer::simulation(), DdMd::StructureFactor::structureFactors_, DdMd::StructureFactor::waveIntVectors_, DdMd::StructureFactor::waveVectors_, and Util::ParamComposite::writeParam().
The documentation for this class was generated from the following files:
