Main class for SCFT or PS-FTS simulation of one system. More...

#include <System.h>

Inheritance diagram for Pscf::Rpc::System< D >:

Public Member Functions
Construction and Destruction
	System ()
	Constructor.

	~System ()
	Destructor.

Lifetime (Main Actions)
void	setOptions (int argc, char **argv)
	Process command line options.

virtual void	readParam (std::istream &in)
	Read input parameters (with opening and closing lines).

void	readParam ()
	Read input parameters from default param file.

virtual void	readParameters (std::istream &in)
	Read body of parameter block (without opening and closing lines).

void	readCommands (std::istream &in)
	Read and process commands from an input stream.

void	readCommands ()
	Read and process commands from the default command file.

W Field (Chemical Potential Field) Modifiers
void	readWBasis (const std::string &filename)
	Read chemical potential fields in symmetry adapted basis format.

void	readWRGrid (const std::string &filename)
	Read chemical potential fields in real space grid (r-grid) format.

void	setWBasis (DArray< DArray< double > > const &fields)
	Set chemical potential fields, in symmetry-adapted basis format.

void	setWRGrid (DArray< RField< D > > const &fields)
	Set new w fields, in real-space (r-grid) format.

void	estimateWfromC (const std::string &filename)
	Construct trial w-fields from c-fields in symmetry-adapted form.

Unit Cell Modifiers
void	setUnitCell (UnitCell< D > const &unitCell)
	Set parameters of the associated unit cell.

void	setUnitCell (typename UnitCell< D >::LatticeSystem lattice, FSArray< double, 6 > const &parameters)
	Set state of the associated unit cell.

void	setUnitCell (FSArray< double, 6 > const &parameters)
	Set parameters of the associated unit cell.

Primary Field Theory Computations
void	compute (bool needStress=false)
	Solve the modified diffusion equation once, without iteration.

int	iterate (bool isContinuation=false)
	Iteratively solve a SCFT problem.

void	sweep ()
	Sweep in parameter space, solving an SCF problem at each point.

void	simulate (int nStep)
	Perform a field theoretic simulation (PS-FTS).

Thermodynamic Properties
void	computeFreeEnergy ()
	Compute free energy density and pressure for current fields.

double	fHelmholtz () const
	Get precomputed Helmoltz free energy per monomer / kT.

double	pressure () const
	Get precomputed pressure x monomer volume / kT.

Thermodynamic Data Output
void	writeParamNoSweep (std::ostream &out) const
	Write parameter file to an ostream, omitting any sweep block.

void	writeThermo (std::ostream &out)
	Write thermodynamic properties to a file.

void	writeStress (std::ostream &out)
	Write stress properties to a file.

Field Output
void	writeWBasis (const std::string &filename) const
	Write chemical potential fields in symmetrized basis format.

void	writeWRGrid (const std::string &filename) const
	Write chemical potential fields in real space grid (r-grid) format.

void	writeCBasis (const std::string &filename) const
	Write concentration fields in symmetrized basis format.

void	writeCRGrid (const std::string &filename) const
	Write concentration fields in real space grid (r-grid) format.

void	writeBlockCRGrid (const std::string &filename) const
	Write c-fields for all blocks and solvents in r-grid format.

Propagator Output
void	writeQSlice (std::string const &filename, int polymerId, int blockId, int directionId, int segmentId) const
	Write slice of a propagator at fixed s in r-grid format.

void	writeQTail (std::string const &filename, int polymerId, int blockId, int directionId) const
	Write the final slice of a propagator in r-grid format.

void	writeQ (std::string const &filename, int polymerId, int blockId, int directionId) const
	Write one propagator for one block, in r-grid format.

void	writeQAll (std::string const &basename)
	Write all propagators of all blocks, each to a separate file.

Crystallographic Information
void	writeWaves (std::string const &filename) const
	Output information about waves.

void	writeStars (std::string const &filename) const
	Output information about stars and symmetrized basis functions.

void	writeGroup (std::string const &filename) const
	Output all elements of the space group.

Field File Manipulation and Analysis
void	basisToRGrid (const std::string &inFileName, const std::string &outFileName)
	Convert a field from symmetrized basis format to r-grid format.

void	rGridToBasis (const std::string &inFileName, const std::string &outFileName)
	Convert a field from real-space grid to symmetrized basis format.

void	kGridToRGrid (const std::string &inFileName, const std::string &outFileName)
	Convert fields from Fourier (k-grid) to real-space (r-grid) format.

void	rGridToKGrid (const std::string &inFileName, const std::string &outFileName)
	Convert fields from real-space (r-grid) to Fourier (k-grid) format.

void	kGridToBasis (const std::string &inFileName, const std::string &outFileName)
	Convert fields from Fourier (k-grid) to symmetrized basis format.

void	basisToKGrid (const std::string &inFileName, const std::string &outFileName)
	Convert fields from symmetrized basis to Fourier (k-grid) format.

void	compare (const DArray< DArray< double > > field1, const DArray< DArray< double > > field2)
	Compare arrays of fields in basis format, output a report.

void	compare (const DArray< RField< D > > field1, const DArray< RField< D > > field2)
	Compare two fields in r-grid format, output a report.

bool	checkRGridFieldSymmetry (const std::string &inFileName, double epsilon=1.0E-8)
	Check if r-grid fields have the declared space group symmetry.

void	scaleFieldsBasis (const std::string &inFileName, const std::string &outFileName, double factor)
	Multiply all components of an array of basis fields by a scalar.

void	scaleFieldsRGrid (const std::string &inFileName, const std::string &outFileName, double factor) const
	Multiply all elements of an array of r-grid fields by a scalar.

void	expandRGridDimension (const std::string &inFileName, const std::string &outFileName, int d, DArray< int > newGridDimensions)
	Expand the number of spatial dimensions of an r-grid field.

void	replicateUnitCell (const std::string &inFileName, const std::string &outFileName, IntVec< D > const &replicas)
	Replicate the crystal unit cell to create a larger cell.

Timers
void	writeTimers (std::ostream &out)
	Write timer information to an output stream.

void	clearTimers ()
	Clear timers.

Field Accessors
WFieldContainer< D > const &	w () const
	Get container of chemical potential fields (w fields).

CFieldContainer< D > const &	c () const
	Get container of monomer concentration fields (c fields).

WFieldContainer< D > &	h ()
	Get container of external potential fields (reference).

WFieldContainer< D > const &	h () const
	Get container of external potential fields (const reference).

Mask< D > &	mask ()
	Get the mask (field to which total density is constrained).

Mask< D > const &	mask () const
	Get the mask by const reference.

Member Object Accessors
Mixture< D > &	mixture ()
	Get the Mixture by non-const reference.

Mixture< D > const &	mixture () const
	Get the Mixture by const reference.

Interaction &	interaction ()
	Get Interaction (excess free energy model) by reference.

Interaction const &	interaction () const
	Get Interaction (excess free energy model) by const reference.

Domain< D > const &	domain () const
	Get Domain by const reference.

Iterator< D > &	iterator ()
	Get the Iterator by non-const reference.

Iterator< D > const &	iterator () const
	Get the Iterator by const reference.

Simulator< D > &	simulator ()
	Get the Simulator for field theoretic simulation.

FileMaster &	fileMaster ()
	Get the FileMaster.

FileMaster const &	fileMaster () const
	Get the FileMaster by const reference.

Homogeneous::Mixture &	homogeneous ()
	Get homogeneous mixture (for reference calculations).

Homogeneous::Mixture const &	homogeneous () const
	Get const homogeneous mixture (for reference calculations).

Boolean Queries
bool	hasIterator () const
	Does this system have an Iterator object?

bool	hasSweep () const
	Does this system have a Sweep object?

bool	hasSimulator () const
	Does this system have an initialized Simulator?

bool	hasExternalFields () const
	Does this system have external potential fields?

bool	hasMask () const
	Does this system have a mask (inhomogeneous density constraint)?

bool	hasCFields () const
	Have c fields been computed from the current w fields?

bool	hasFreeEnergy () const
	Has the free energy been computed from the current w fields?

Public Member Functions inherited from Util::ParamComposite
	ParamComposite ()
	Constructor.

	ParamComposite (const ParamComposite &other)
	Copy constructor.

	ParamComposite (int capacity)
	Constructor.

virtual	~ParamComposite ()
	Virtual destructor.

void	resetParam ()
	Resets ParamComposite to its empty state.

virtual void	readParamOptional (std::istream &in)
	Read optional parameter file block.

virtual void	writeParam (std::ostream &out) const
	Write all parameters to an output stream.

virtual void	load (Serializable::IArchive &ar)
	Load all parameters from an input archive.

virtual void	loadOptional (Serializable::IArchive &ar)
	Load an optional ParamComposite.

virtual void	loadParameters (Serializable::IArchive &ar)
	Load state from archive, without adding Begin and End lines.

virtual void	save (Serializable::OArchive &ar)
	Saves all parameters to an archive.

void	saveOptional (Serializable::OArchive &ar)
	Saves isActive flag, and then calls save() iff isActive is true.

void	readParamComposite (std::istream &in, ParamComposite &child, bool next=true)
	Add and read a required child ParamComposite.

void	readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true)
	Add and attempt to read an optional child ParamComposite.

template<typename Type >
ScalarParam< Type > &	read (std::istream &in, const char *label, Type &value)
	Add and read a new required ScalarParam < Type > object.

template<typename Type >
ScalarParam< Type > &	readOptional (std::istream &in, const char *label, Type &value)
	Add and read a new optional ScalarParam < Type > object.

template<typename Type >
CArrayParam< Type > &	readCArray (std::istream &in, const char label, Type value, int n)
	Add and read a required C array parameter.

template<typename Type >
CArrayParam< Type > &	readOptionalCArray (std::istream &in, const char label, Type value, int n)
	Add and read an optional C array parameter.

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.

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.

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.

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.

template<typename Type , int N>
FSArrayParam< Type, N > &	readFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size)
	Add and read a required FSArray < Type, N > array parameter.

template<typename Type , int N>
FSArrayParam< Type, N > &	readOptionalFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size)
	Add and read an optional FSArray < Type, N > array parameter.

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.

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.

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.

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.

template<typename Type >
DSymmMatrixParam< Type > &	readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n)
	Add and read a required symmetrix DMatrix.

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.

Begin &	readBegin (std::istream &in, const char *label, bool isRequired=true)
	Add and read a class label and opening bracket.

End &	readEnd (std::istream &in)
	Add and read the closing bracket.

Blank &	readBlank (std::istream &in)
	Add and read a new Blank object, representing a blank line.

void	loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load a required child ParamComposite.

void	loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true)
	Add and load an optional child ParamComposite if isActive.

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired)
	Add and load a new ScalarParam < Type > object.

template<typename Type >
ScalarParam< Type > &	loadParameter (Serializable::IArchive &ar, const char *label, Type &value)
	Add and load new required ScalarParam < Type > object.

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.

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.

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.

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.

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.

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.

template<typename Type , int N>
FSArrayParam< Type, N > &	loadFSArray (Serializable::IArchive &ar, const char *label, FSArray< Type, N > &array, int size, bool isRequired)
	Add and load an FSArray < Type, N > array parameter.

template<typename Type , int N>
FSArrayParam< Type, N > &	loadFSArray (Serializable::IArchive &ar, const char *label, FSArray< Type, N > &array, int size)
	Add and load a required FSArray < Type > array parameter.

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.

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.

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.

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.

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.

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.

void	addParamComposite (ParamComposite &child, bool next=true)
	Add a child ParamComposite object to the format array.

Begin &	addBegin (const char *label)
	Add a Begin object representing a class name and bracket.

End &	addEnd ()
	Add a closing bracket.

Blank &	addBlank ()
	Create and add a new Blank object, representing a blank line.

std::string	className () const
	Get class name string.

bool	isRequired () const
	Is this ParamComposite required in the input file?

bool	isActive () const
	Is this parameter active?

Public Member Functions inherited from Util::ParamComponent
virtual	~ParamComponent ()
	Destructor.

void	setIndent (const ParamComponent &parent, bool next=true)
	Set indent level.

std::string	indent () const
	Return indent string for this object (string of spaces).

template<class Archive >
void	serialize (Archive &ar, const unsigned int version)
	Serialize this ParamComponent as a string.

Public Member Functions inherited from Util::Serializable
virtual	~Serializable ()
	Destructor.

Public Member Functions inherited from Util::MpiFileIo
	MpiFileIo ()
	Constructor.

	MpiFileIo (const MpiFileIo &other)
	Copy constructor.

bool	isIoProcessor () const
	Can this processor do file I/O ?

void	setIoCommunicator (MPI::Intracomm &communicator)
	Set the communicator.

void	clearCommunicator ()
	Clear (nullify) the communicator.

bool	hasIoCommunicator () const
	Does this object have an associated MPI communicator?

MPI::Intracomm &	ioCommunicator () const
	Get the MPI communicator by reference.

Additional Inherited Members
Public Types inherited from Util::Serializable
typedef BinaryFileOArchive	OArchive
	Type of output archive used by save method.

typedef BinaryFileIArchive	IArchive
	Type of input archive used by load method.

Static Public Member Functions inherited from Util::ParamComponent
static void	initStatic ()
	Initialize static echo member to false.

static void	setEcho (bool echo=true)
	Enable or disable echoing for all subclasses of ParamComponent.

static bool	echo ()
	Get echo parameter.

Protected Member Functions inherited from Util::ParamComposite
void	setClassName (const char *className)
	Set class name string.

void	setIsRequired (bool isRequired)
	Set or unset the isActive flag.

void	setIsActive (bool isActive)
	Set or unset the isActive flag.

void	setParent (ParamComponent &param, bool next=true)
	Set this to the parent of a child component.

void	addComponent (ParamComponent &param, bool isLeaf=true)
	Add a new ParamComponent object to the format array.

template<typename Type >
ScalarParam< Type > &	add (std::istream &in, const char *label, Type &value, bool isRequired=true)
	Add a new required ScalarParam < Type > object.

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.

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.

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.

template<typename Type , int N>
FSArrayParam< Type, N > &	addFSArray (std::istream &in, const char *label, FSArray< Type, N > &array, int size, bool isRequired=true)
	Add (but do not read) a FSArray < Type, N > array parameter.

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.

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.

Protected Member Functions inherited from Util::ParamComponent
	ParamComponent ()
	Constructor.

	ParamComponent (const ParamComponent &other)
	Copy constructor.

Detailed Description

template<int D>
class Pscf::Rpc::System< D >

Main class for SCFT or PS-FTS simulation of one system.

A System has (among other member components):

a Mixture (container for polymer and solvent solvers)
an Interaction (list of binary chi parameters)
a Domain (description of unit cell and discretization)
a container of monomer chemical potential fields
a container of monomer concentration fields

A System may also optionally own Iterator, Sweep, and Simulator (BdSimulator or McSimulator) components. Iterator and Sweep objects are only used for SCFT calculations. A Simulator object is only used for PS-FTS calculations (i.e., field theoretic simulations that use a partial saddle-point approximation).

System is a class template with an integer template parameter D = 1, 2, or 3 that represents the dimension of space. Many related components are also class templates of the same type. Names such as System, Mixture, Domain, etc. mentioned above are thus names of class templates, whereas actual class names are of the form Mixture<D>, Interaction<D>, etc. with D=1, 2, or 3.

Usage of a System<D> object in the main program looks something like this:

System<D> system;
system.setOptions(argc, argv);
system.readParam();
system.readCommands();

where argc, and argv are parameters containing information about command line arguments that must be passed from the main program. This is implemented as function template Pscf::Rpc::run in the file src/rpc/pscf_pc.cpp.

Constructor & Destructor Documentation

◆ System()

template<int D>

Pscf::Rpc::System< D >::System ( )

Constructor.

Definition at line 54 of file rpc/System.tpp.

References Pscf::Rpc::System< D >::domain(), Util::BracketPolicy::set(), and Util::ParamComposite::setClassName().

◆ ~System()

template<int D>

Pscf::Rpc::System< D >::~System ( )

Destructor.

Definition at line 99 of file rpc/System.tpp.

Member Function Documentation

◆ setOptions()

template<int D>

void Pscf::Rpc::System< D >::setOptions	(	int	argc,
		char **	argv )

Process command line options.

This function takes the same arguments as any C/C++ main program function. The arguments of the main function should d be passed to this function unaltered, to allow this function to process the command line options.

Parameters

argc	number of command line arguments
argv	array of pointers to command line arguments

Definition at line 128 of file rpc/System.tpp.

References Util::Log::file(), Util::ParamComponent::setEcho(), UTIL_CHECK, and UTIL_THROW.

Referenced by Pscf::Rpc::run().

◆ readParam() [1/2]

template<int D>

void Pscf::Rpc::System< D >::readParam ( std::istream & in )

virtual

Read input parameters (with opening and closing lines).

Parameters

in	input parameter stream

Reimplemented from Util::ParamComposite.

Definition at line 305 of file rpc/System.tpp.

Referenced by Pscf::Rpc::run().

◆ readParam() [2/2]

template<int D>

void Pscf::Rpc::System< D >::readParam ( )

Read input parameters from default param file.

This function reads the parameter file set by the -p command line option.

Definition at line 316 of file rpc/System.tpp.

◆ readParameters()

template<int D>

void Pscf::Rpc::System< D >::readParameters ( std::istream & in )

virtual

Read body of parameter block (without opening and closing lines).

Parameters

in	input parameter stream

Reimplemented from Util::ParamComposite.

Definition at line 230 of file rpc/System.tpp.

References Util::ParamComponent::echo(), Util::Log::file(), and UTIL_CHECK.

◆ readCommands() [1/2]

template<int D>

void Pscf::Rpc::System< D >::readCommands ( std::istream & in )

Read and process commands from an input stream.

Parameters

in	command script input stream

Definition at line 323 of file rpc/System.tpp.

References Util::DArray< T >::allocate(), Pscf::Prdc::expandRGridDimension(), Util::Log::file(), Pscf::Prdc::hasSymmetry(), Pscf::Prdc::replicateUnitCell(), and UTIL_CHECK.

Referenced by Pscf::Rpc::run().

◆ readCommands() [2/2]

template<int D>

void Pscf::Rpc::System< D >::readCommands ( )

Read and process commands from the default command file.

This function reads the parameter file set by the -c command line option.

Definition at line 737 of file rpc/System.tpp.

References UTIL_THROW.

◆ readWBasis()

template<int D>

void Pscf::Rpc::System< D >::readWBasis ( const std::string & filename )

Read chemical potential fields in symmetry adapted basis format.

This function opens and reads the file named by the "filename" string parameter, which must contain chemical potential fields in symmetry-adapted basis format. The function sets the system w fields equal to those given in this file, by copying the coefficients of the basis expansion and computing values on a real-space grid (r-grid format).

Upon exit, both w().basis() and w().rgrid() are set, w().hasData and w().isSymmetric() return true, while hasCFields() and hasFreeEnergy() return false. Unit cell parameters are set to values read from the field file header.

SCFT calculations that use an iterator that preserves space group symmetry must set an initial field using a function that creates fields that can be represented in symmetry adapted basis form, such as this function, setWBasis, or estimateWFromC.

Parameters

filename name of input w-field file in basis format

Definition at line 751 of file rpc/System.tpp.

References Pscf::Prdc::readFieldHeader(), and UTIL_CHECK.

◆ readWRGrid()

template<int D>

void Pscf::Rpc::System< D >::readWRGrid ( const std::string & filename )

Read chemical potential fields in real space grid (r-grid) format.

This function opens and reads the file with the name given by the "filename" string, which must contain chemical potential fields in real space grid (r-grid) format. The function sets values for the system w fields in r-grid format. It does not attempt to set field values in symmetry-adapted basis format, because it cannot assume that the r-grid field exhibits the declared space group symmetry. On exit, w().rgrid() is reset and w().hasData() returns true, while w().isSymmetric(), hasCFields() and hasFreeEnergy() return false. Unit cell parameters are set to values read from the field file header.

Initial chemical potential fields for field theoretic simulations are normally initialized using a function that sets the fields in r-grid format, such as this function or setWRGrid.

Parameters

filename name of input w-field file in r-grid format

Definition at line 781 of file rpc/System.tpp.

References Pscf::Prdc::readFieldHeader(), and UTIL_CHECK.

◆ setWBasis()

template<int D>

void Pscf::Rpc::System< D >::setWBasis ( DArray< DArray< double > > const & fields )

Set chemical potential fields, in symmetry-adapted basis format.

This function sets values for w fields in both symmetry adapted and r-grid format by copying coefficient values provided in the "fields" container that is passed as an argument, and computing values on a real-space grid. Upon return, values of both w().basis() and w().rgrid() are set, while w().hasData() and w().isSymmetric() return true, and hasCFields() and hasFreeEnergy() hasFreeEnergy() return false. Unit cell parameters are left unchanged.

Parameters

fields array of new w (chemical potential) fields

Definition at line 867 of file rpc/System.tpp.

References UTIL_CHECK.

◆ setWRGrid()

template<int D>

void Pscf::Rpc::System< D >::setWRGrid ( DArray< RField< D > > const & fields )

Set new w fields, in real-space (r-grid) format.

This function set values for w fields in r-grid format, but does not set components the symmetry-adapted basis format. Upon return, w.rgrid() is reset and w().hasData() returns true, while w().isSymmetric(), hasCFields() and hasFreeEnergy() all return false. Unit cell parameters are left unchanged.

Parameters

fields array of new w (chemical potential) fields

Definition at line 882 of file rpc/System.tpp.

References UTIL_CHECK.

◆ estimateWfromC()

template<int D>

void Pscf::Rpc::System< D >::estimateWfromC ( const std::string & filename )

Construct trial w-fields from c-fields in symmetry-adapted form.

This function reads concentration fields in symmetrized basis format and constructs an initial guess for corresponding chemical potential fields by setting the Lagrange multiplier field xi to zero. The result is stored in the System w fields container.

Upon return, w().hasData() and w().isSymmetric() return true, while hasCFields() and hasFreeEnergy() return false. Unit cell parameters are set to those read from the c field file header.

Parameters

filename name of input c-field file (basis format)

Definition at line 812 of file rpc/System.tpp.

References Util::DArray< T >::allocate(), Pscf::Prdc::readFieldHeader(), and UTIL_CHECK.

◆ setUnitCell() [1/3]

template<int D>

void Pscf::Rpc::System< D >::setUnitCell ( UnitCell< D > const & unitCell )

Set parameters of the associated unit cell.

The lattice (i.e., lattice system type) set in the UnitCell<D> unitCell input parameter must agree with any lattice enum value that was set previously in the parameter file, or an Exception is thrown.

If a space group has been set but a basis has not yet been constructed, then this and the other setUnitCell member functions wll all construct a symmetry-adapted basis and then allocate memory for fields stored in a symmetry adapted basis format.

Parameters

unitCell new UnitCell<D> (i.e., new parameters)

Definition at line 896 of file rpc/System.tpp.

◆ setUnitCell() [2/3]

template<int D>

void Pscf::Rpc::System< D >::setUnitCell	(	typename UnitCell< D >::LatticeSystem< D >	lattice,
		FSArray< double, 6 > const &	parameters )

Set state of the associated unit cell.

The "lattice" (lattice system) enumeration parameter must agree with any lattice value that was set previously in the parameter file.

See description of setUnitCell(UnitCell<D> const &) for other side effects.

Parameters

lattice	lattice system
parameters	array of new unit cell parameters.

Definition at line 911 of file rpc/System.tpp.

◆ setUnitCell() [3/3]

template<int D>

void Pscf::Rpc::System< D >::setUnitCell ( FSArray< double, 6 > const & parameters )

Set parameters of the associated unit cell.

The lattice type must have been set before this function is called. The logical size of the FSArray<double, 6> "parameters" array must match the expected number of parameters for the current lattice type.

See description of setUnitCell(UnitCell<D> const &) for other side effects.

Parameters

parameters array of new unit cell parameters.

Definition at line 926 of file rpc/System.tpp.

◆ compute()

template<int D>

void Pscf::Rpc::System< D >::compute ( bool needStress = false )

Solve the modified diffusion equation once, without iteration.

This function calls the Mixture::compute() function to solve the statistical mechanics problem for a non-interacting system subjected to the currrent chemical potential fields. This requires solution of the modified diffusion equation for all polymers, computation of Boltzmann weights for all solvents, computation of molecular partition functions for all species, computation of concentration fields for blocks and solvents, and computation of overall concentrations for all monomer types. This function does not compute the canonical (Helmholtz) free energy or grand-canonical free energy (i.e., pressure). Upon return, the flag hasCFields is set true.

If argument needStress == true, then this function also calls Mixture<D>::computeStress() to compute the stress.

Precondition: The w().hasData() flag must be true on entry, to confirm that chemical potential fields have been set.

Parameters

needStress true if stress is needed, false otherwise

Definition at line 942 of file rpc/System.tpp.

References UTIL_CHECK.

◆ iterate()

template<int D>

int Pscf::Rpc::System< D >::iterate ( bool isContinuation = false )

Iteratively solve a SCFT problem.

This function calls the iterator to solve the SCFT problem for the current mixture and system parameters, using the current chemical potential fields and current unit cell parameter values as initial guesses. On exit, hasCFields is set true whether or not convergence is obtained to within the desired tolerance.
The Helmholtz free energy and pressure are computed only if convergence is obtained.

Precondition: Function hasIterator() must return true.; Function w().hasData() flag must return true.; Function w().isSymmetric() flag must return true if the chosen iterator uses a symmetry adapted basis, and so requires this.

Returns: returns 0 for successful convergence, 1 for failure.

Parameters

isContinuation true if continuation within a sweep.

Definition at line 971 of file rpc/System.tpp.

References Util::Log::file(), and UTIL_CHECK.

◆ sweep()

template<int D>

void Pscf::Rpc::System< D >::sweep ( )

Sweep in parameter space, solving an SCF problem at each point.

This function uses a Sweep object that was initialized in the parameter file to solve the SCF problem at a sequence of points along a contour in parameter space. The nature of this sequence of points is determined by implementation of a subclass of Sweep and the parameters passed to the sweep object in the parameter file. The Iterator that is initialized in the parameter file is called at each state point.

Precondition: Function hasSweep() must return true.; All preconditions of the iterate() function must be satisfied

Definition at line 1007 of file rpc/System.tpp.

References Util::Log::file(), and UTIL_CHECK.

Referenced by pscfpp.output.Sweep::__getitem__(), pscfpp.output.Sweep::__init__(), pscfpp.output.Sweep::__len__(), pscfpp.output.Sweep::summary(), and pscfpp.output.Sweep::summaryString().

◆ simulate()

template<int D>

void Pscf::Rpc::System< D >::simulate ( int nStep )

Perform a field theoretic simulation (PS-FTS).

Perform a field theoretic simulation using the partial saddle-point approximation (PS-FTS). The type of calculation (BD or MC) is determined by the type of Simulator (BdSimulator or McSimulator) that created in the parameter file. The number of BD steps or attempted MC moves to be performed is given by the parameter "nStep" .

Precondition: Function hasSimulator() must return true.; Function w().hasData() must return true.

Parameters

nStep number of simulation steps

Definition at line 1022 of file rpc/System.tpp.

References UTIL_CHECK.

◆ computeFreeEnergy()

template<int D>

void Pscf::Rpc::System< D >::computeFreeEnergy ( )

Compute free energy density and pressure for current fields.

This function should be called after a successful call of System::iterate() or Iterator::solve(). Resulting values of Helhmoltz free energy per monomer and non-dimensional pressure (-1 times grand canonical free energy per monomer) are stored in private member variables and can be accessed by the fHelmholtz() and pressure() functions.

Definition at line 1083 of file rpc/System.tpp.

References Pscf::PolymerTmpl< Block >::length(), Pscf::PolymerTmpl< Block >::mu(), Pscf::Species::mu(), Pscf::PolymerTmpl< Block >::phi(), Pscf::Species::phi(), Pscf::SolventSpecies::size(), and UTIL_CHECK.

◆ fHelmholtz()

template<int D>

double Pscf::Rpc::System< D >::fHelmholtz ( ) const

inline

Get precomputed Helmoltz free energy per monomer / kT.

The value retrieved by this function is computed by the computeFreeEnergy() function.

Definition at line 1314 of file rpc/System.h.

References UTIL_CHECK.

Referenced by pscfpp.output.Thermo::__init__(), and pscfpp.output.Thermo::read().

◆ pressure()

template<int D>

double Pscf::Rpc::System< D >::pressure ( ) const

inline

Get precomputed pressure x monomer volume / kT.

The value retrieved by this function is computed by the computeFreeEnergy() function. The value is -1 times the grand canonical free energy per monomer divided by kT.

Definition at line 1322 of file rpc/System.h.

References UTIL_CHECK.

Referenced by pscfpp.output.Thermo::__init__(), and pscfpp.output.Thermo::read().

◆ writeParamNoSweep()

template<int D>

void Pscf::Rpc::System< D >::writeParamNoSweep ( std::ostream & out ) const

Write parameter file to an ostream, omitting any sweep block.

This function writes the Mixture, Interaction, and Domain blocks of a parameter file, as well as any Iterator block, but omits any Sweep or Simulator blocks. The intent is to produce an output during an SCFT sweep that only refers to parameters relevant to a single state point, in form that could be used a a parameter file for a a single SCFT calculation.

Parameters

out	output stream

Definition at line 1307 of file rpc/System.tpp.

◆ writeThermo()

template<int D>

void Pscf::Rpc::System< D >::writeThermo ( std::ostream & out )

Write thermodynamic properties to a file.

This function outputs Helmholtz free energy per monomer, pressure (in units of kT per monomer volume), the volume fraction and chemical potential of each species, and all unit cell parameters.

Calling writeParamNoSweep and writeThermo in succession with the same output stream will produce a single file containing both input parameters and resulting thermodynamic properties.

Parameters

out	output stream

Definition at line 1323 of file rpc/System.tpp.

◆ writeStress()

template<int D>

void Pscf::Rpc::System< D >::writeStress ( std::ostream & out )

Write stress properties to a file.

This function outputs derivatives of SCFT free energy w/ respect to each unit cell parameters.

The log output created by an Iterator upon convergence should call writeStress after writeThermo if and only if the iterator is not flexible.

Parameters

out	output stream

Definition at line 1387 of file rpc/System.tpp.

◆ writeWBasis()

template<int D>

void Pscf::Rpc::System< D >::writeWBasis ( const std::string & filename ) const

Write chemical potential fields in symmetrized basis format.

Parameters

filename name of output file

Definition at line 1403 of file rpc/System.tpp.

References UTIL_CHECK.

◆ writeWRGrid()

template<int D>

void Pscf::Rpc::System< D >::writeWRGrid ( const std::string & filename ) const

Write chemical potential fields in real space grid (r-grid) format.

Parameters

filename name of output file

Definition at line 1417 of file rpc/System.tpp.

References UTIL_CHECK.

◆ writeCBasis()

template<int D>

void Pscf::Rpc::System< D >::writeCBasis ( const std::string & filename ) const

Write concentration fields in symmetrized basis format.

Parameters

filename name of output file

Definition at line 1430 of file rpc/System.tpp.

References UTIL_CHECK.

◆ writeCRGrid()

template<int D>

void Pscf::Rpc::System< D >::writeCRGrid ( const std::string & filename ) const

Write concentration fields in real space grid (r-grid) format.

Parameters

filename name of output file

Definition at line 1444 of file rpc/System.tpp.

References UTIL_CHECK.

◆ writeBlockCRGrid()

template<int D>

void Pscf::Rpc::System< D >::writeBlockCRGrid ( const std::string & filename ) const

Write c-fields for all blocks and solvents in r-grid format.

Writes concentrations for all blocks of all polymers and all solvent species in r-grid format. Columns associated with blocks appear ordered by polymer id and block id, with blocks of the same polymer listed sequentially, followed by columns associated with solvent species ordered by solvent id.

Parameters

filename name of output file

Definition at line 1458 of file rpc/System.tpp.

References UTIL_CHECK.

◆ writeQSlice()

template<int D>

void Pscf::Rpc::System< D >::writeQSlice	(	std::string const &	filename,
		int	polymerId,
		int	blockId,
		int	directionId,
		int	segmentId ) const

Write slice of a propagator at fixed s in r-grid format.

Parameters

filename	name of output file
polymerId	integer id of the polymer
blockId	integer id of the block within the polymer
directionId	integer id of the direction (0 or 1)
segmentId	integer integration step index

Definition at line 1480 of file rpc/System.tpp.

References Pscf::PolymerTmpl< Block >::nBlock(), Pscf::PolymerTmpl< Block >::propagator(), Pscf::Rpc::Propagator< D >::q(), and UTIL_CHECK.

◆ writeQTail()

template<int D>

void Pscf::Rpc::System< D >::writeQTail	(	std::string const &	filename,
		int	polymerId,
		int	blockId,
		int	directionId ) const

Write the final slice of a propagator in r-grid format.

Parameters

filename	name of output file
polymerId	integer id of the polymer
blockId	integer id of the block within the polymer
directionId	integer id of the direction (0 or 1)

Definition at line 1504 of file rpc/System.tpp.

References Pscf::PolymerTmpl< Block >::nBlock(), Pscf::PolymerTmpl< Block >::propagator(), Pscf::Rpc::Propagator< D >::tail(), and UTIL_CHECK.

◆ writeQ()

template<int D>

void Pscf::Rpc::System< D >::writeQ	(	std::string const &	filename,
		int	polymerId,
		int	blockId,
		int	directionId ) const

Write one propagator for one block, in r-grid format.

Parameters

filename	name of output file
polymerId	integer id of the polymer
blockId	integer id of the block within the polymer
directionId	integer id of the direction (0 or 1)

Definition at line 1526 of file rpc/System.tpp.

References Pscf::PolymerTmpl< Block >::nBlock(), Pscf::Rpc::Propagator< D >::ns(), Pscf::PolymerTmpl< Block >::propagator(), Pscf::Rpc::Propagator< D >::q(), and UTIL_CHECK.

◆ writeQAll()

template<int D>

void Pscf::Rpc::System< D >::writeQAll ( std::string const & basename )

Write all propagators of all blocks, each to a separate file.

Write all propagators for both directions for all blocks of all polymers, with each propagator in a separate file. The function writeQ is called internally for each propagator, and is passed an automatically generated file name. The file name for each propagator is given by a string of the form (basename)_(ip)_(ib)_(id), where (basename) denotes the value of the std::string function parameter basename, and where (ip), (ib), and (id) denote the string representations of a polymer indiex ip, a block index ib, and direction index id, with id = 0 or 1. For example, if basename == "out/q", then the file name of the propagator for direction 1 of block 2 of polymer 0 would be "out/q_0_2_1".

Parameters

basename common prefix for output file names

Definition at line 1568 of file rpc/System.tpp.

References Util::toString().

◆ writeWaves()

template<int D>

void Pscf::Rpc::System< D >::writeWaves ( std::string const & filename ) const

Output information about waves.

This function opens a file with the specified filename, calls Basis<D>::outputWaves, and closes the file before returning.

Parameters

filename name of output file

Definition at line 1612 of file rpc/System.tpp.

References UTIL_CHECK.

◆ writeStars()

template<int D>

void Pscf::Rpc::System< D >::writeStars ( std::string const & filename ) const

Output information about stars and symmetrized basis functions.

This function opens a file with the specified filename, calls Basis<D>::outputStars, and closes the file before returning.

Parameters

filename name of output file

Definition at line 1595 of file rpc/System.tpp.

References UTIL_CHECK.

◆ writeGroup()

template<int D>

void Pscf::Rpc::System< D >::writeGroup ( std::string const & filename ) const

Output all elements of the space group.

Parameters

filename name of output file

Definition at line 1630 of file rpc/System.tpp.

References UTIL_CHECK.

◆ basisToRGrid()

template<int D>

void Pscf::Rpc::System< D >::basisToRGrid	(	const std::string &	inFileName,
		const std::string &	outFileName )

Convert a field from symmetrized basis format to r-grid format.

This function reads a field file in basis format, converts the fields to r-grid format, and writes the fields in r-grid format to a different file.

This and other field conversion functions do not change the w or c fields stored by this System - all required calculations are performed using mutable temporary memory.

Parameters

inFileName	name of input file (basis format)
outFileName	name of output file (r-grid format)

Definition at line 1642 of file rpc/System.tpp.

References Pscf::Prdc::FieldIoReal< D, RFRT, RFKT, FFTT >::convertBasisToRGrid(), Pscf::Prdc::readFieldHeader(), Pscf::Prdc::FieldIoReal< D, RFRT, RFKT, FFTT >::readFieldsBasis(), UTIL_CHECK, and Pscf::Rpc::FieldIo< D >::writeFieldsRGrid().

◆ rGridToBasis()

template<int D>

void Pscf::Rpc::System< D >::rGridToBasis	(	const std::string &	inFileName,
		const std::string &	outFileName )

Convert a field from real-space grid to symmetrized basis format.

This function checks if the input fields have the declared space group symmetry, and prints a warning if it detects deviations that exceed some small threshhold, but proceeds to attempt the conversion even if such an error is detected. Converting a field that does not have the declared space group symmetry to basis format is a destructive operation that modifies the field in unpredictable ways.

Parameters

inFileName	name of input file (r-grid format)
outFileName	name of output file (basis format)

Definition at line 1667 of file rpc/System.tpp.

References Pscf::Prdc::FieldIoReal< D, RFRT, RFKT, FFTT >::convertRGridToBasis(), Pscf::Prdc::readFieldHeader(), Pscf::Rpc::FieldIo< D >::readFieldsRGrid(), UTIL_CHECK, and Pscf::Prdc::FieldIoReal< D, RFRT, RFKT, FFTT >::writeFieldsBasis().

◆ kGridToRGrid()

template<int D>

void Pscf::Rpc::System< D >::kGridToRGrid	(	const std::string &	inFileName,
		const std::string &	outFileName )

Convert fields from Fourier (k-grid) to real-space (r-grid) format.

Parameters

inFileName	name of input file (k-grid format)
outFileName	name of output file (r-grid format)

Definition at line 1692 of file rpc/System.tpp.

References Pscf::Prdc::readFieldHeader(), Pscf::Rpc::FieldIo< D >::readFieldsKGrid(), and Pscf::Rpc::FieldIo< D >::writeFieldsRGrid().

◆ rGridToKGrid()

template<int D>

void Pscf::Rpc::System< D >::rGridToKGrid	(	const std::string &	inFileName,
		const std::string &	outFileName )

Convert fields from real-space (r-grid) to Fourier (k-grid) format.

Parameters

inFileName	name of input file (r-grid format)
outFileName	name of output file (k-grid format)

Definition at line 1718 of file rpc/System.tpp.

References Pscf::Prdc::readFieldHeader(), Pscf::Rpc::FieldIo< D >::readFieldsRGrid(), and Pscf::Rpc::FieldIo< D >::writeFieldsKGrid().

◆ kGridToBasis()

template<int D>

void Pscf::Rpc::System< D >::kGridToBasis	(	const std::string &	inFileName,
		const std::string &	outFileName )

Convert fields from Fourier (k-grid) to symmetrized basis format.

This function checks if the input fields have the declared space group symmetry, and prints a warning if it detects deviations that exceed some small threshhold, but proceeds to attempt the conversion even if such an error is detected. Converting a field that does not have the declared space group symmetry to basis format is a destructive operation that modifies the field in unpredictable ways.

Parameters

inFileName	name of input file (k-grid format)
outFileName	name of output file (basis format)

Definition at line 1745 of file rpc/System.tpp.

References Pscf::Prdc::readFieldHeader(), and UTIL_CHECK.

◆ basisToKGrid()

template<int D>

void Pscf::Rpc::System< D >::basisToKGrid	(	const std::string &	inFileName,
		const std::string &	outFileName )

Convert fields from symmetrized basis to Fourier (k-grid) format.

Parameters

inFileName	name of input file (basis format)
outFileName	name of output file (k-grid format)

Definition at line 1771 of file rpc/System.tpp.

References Pscf::Prdc::readFieldHeader(), and UTIL_CHECK.

◆ compare() [1/2]

template<int D>

void Pscf::Rpc::System< D >::compare	(	const DArray< DArray< double > >	field1,
		const DArray< DArray< double > >	field2 )

Compare arrays of fields in basis format, output a report.

Outputs maximum and root-mean-squared differences to the standard Log file.

Parameters

field1	first array of fields (basis format)
field2	second array of fields (basis format)

Definition at line 1872 of file rpc/System.tpp.

References Pscf::FieldComparison< FT >::compare(), Util::Log::file(), Pscf::FieldComparison< FT >::maxDiff(), Pscf::FieldComparison< FT >::rmsDiff(), and UTIL_CHECK.

◆ compare() [2/2]

template<int D>

void Pscf::Rpc::System< D >::compare	(	const DArray< RField< D > >	field1,
		const DArray< RField< D > >	field2 )

Compare two fields in r-grid format, output a report.

Outputs maximum and root-mean-squared differences to the standard Log file.

Parameters

field1	first array of fields (r-grid format)
field2	second array of fields (r-grid format)

Definition at line 1892 of file rpc/System.tpp.

References Pscf::FieldComparison< FT >::compare(), Util::Log::file(), Pscf::FieldComparison< FT >::maxDiff(), and Pscf::FieldComparison< FT >::rmsDiff().

◆ checkRGridFieldSymmetry()

template<int D>

bool Pscf::Rpc::System< D >::checkRGridFieldSymmetry	(	const std::string &	inFileName,
		double	epsilon = 1.0E-8 )

Check if r-grid fields have the declared space group symmetry.

Parameters

inFileName	name of input file
epsilon	error threshold used when testing for symmetry

Returns: true if fields all have symmetry, false otherwise

Definition at line 1798 of file rpc/System.tpp.

References Pscf::Prdc::readFieldHeader(), and UTIL_CHECK.

◆ scaleFieldsBasis()

template<int D>

void Pscf::Rpc::System< D >::scaleFieldsBasis	(	const std::string &	inFileName,
		const std::string &	outFileName,
		double	factor )

Multiply all components of an array of basis fields by a scalar.

Parameters

inFileName	name of input field file
outFileName	name of file for rescaled output fields
factor	factor by which to multiply all field elements

Definition at line 1832 of file rpc/System.tpp.

References Pscf::Prdc::readFieldHeader(), Pscf::Prdc::FieldIoReal< D, RFRT, RFKT, FFTT >::readFieldsBasis(), Pscf::Prdc::FieldIoReal< D, RFRT, RFKT, FFTT >::scaleFieldsBasis(), and Pscf::Prdc::FieldIoReal< D, RFRT, RFKT, FFTT >::writeFieldsBasis().

◆ scaleFieldsRGrid()

template<int D>

void Pscf::Rpc::System< D >::scaleFieldsRGrid	(	const std::string &	inFileName,
		const std::string &	outFileName,
		double	factor ) const

Multiply all elements of an array of r-grid fields by a scalar.

Parameters

inFileName	name of input field file
outFileName	name of file for rescaled output fields
factor	factor by which to multiply all field elements

Definition at line 1855 of file rpc/System.tpp.

References Pscf::Rpc::FieldIo< D >::readFieldsRGrid(), Pscf::Prdc::FieldIoReal< D, RFRT, RFKT, FFTT >::scaleFieldsRGrid(), and Pscf::Rpc::FieldIo< D >::writeFieldsRGrid().

◆ expandRGridDimension()

template<int D>

void Pscf::Rpc::System< D >::expandRGridDimension	(	const std::string &	inFileName,
		const std::string &	outFileName,
		int	d,
		DArray< int >	newGridDimensions )

Expand the number of spatial dimensions of an r-grid field.

This function reads a D-dimensional field and outputs a field in a format appropriate for d-dimensional space, for d > D, by assuming that all field values are independent of coordinates associated with the added dimensions. It can thus create a file representing a field with lamellar (D=1) or hexagonal (D=2) symmetry on a 3D (d=3) grid.

Element i of array newGridDimensions contains the number of grid points in added dimension D + i. This array must have a capacity d - D.

Parameters

inFileName	filename name of input field file
outFileName	filename name of output field file
d	intended dimensions (d > D)
newGridDimensions	number of grid points in added dimensions

Definition at line 1037 of file rpc/System.tpp.

References UTIL_CHECK.

◆ replicateUnitCell()

template<int D>

void Pscf::Rpc::System< D >::replicateUnitCell	(	const std::string &	inFileName,
		const std::string &	outFileName,
		IntVec< D > const &	replicas )

Replicate the crystal unit cell to create a larger cell.

This function reads a D-dimensional field and replicates the unit cell a specified number of times in each D direction

Element i of array replicas contains the number of replication times in direction i.

Parameters

inFileName	filename name of input field file
outFileName	filename name of output field file
replicas	the number of replicas in each D direction

Definition at line 1061 of file rpc/System.tpp.

◆ writeTimers()

template<int D>

void Pscf::Rpc::System< D >::writeTimers ( std::ostream & out )

Write timer information to an output stream.

Parameters

out	output stream

Definition at line 1277 of file rpc/System.tpp.

References Util::Log::file().

◆ clearTimers()

template<int D>

void Pscf::Rpc::System< D >::clearTimers ( )

Clear timers.

Definition at line 1293 of file rpc/System.tpp.

◆ w()

template<int D>

WFieldContainer< D > const & Pscf::Rpc::System< D >::w ( ) const

inline

Get container of chemical potential fields (w fields).

Definition at line 1253 of file rpc/System.h.

◆ c()

template<int D>

CFieldContainer< D > const & Pscf::Rpc::System< D >::c ( ) const

inline

Get container of monomer concentration fields (c fields).

Definition at line 1259 of file rpc/System.h.

◆ h() [1/2]

template<int D>

WFieldContainer< D > & Pscf::Rpc::System< D >::h ( )

inline

Get container of external potential fields (reference).

Definition at line 1264 of file rpc/System.h.

Referenced by Pscf::Rpc::ExtGenFilm< D >::isGenerated().

◆ h() [2/2]

template<int D>

WFieldContainer< D > const & Pscf::Rpc::System< D >::h ( ) const

inline

Get container of external potential fields (const reference).

Definition at line 1269 of file rpc/System.h.

◆ mask() [1/2]

template<int D>

Mask< D > & Pscf::Rpc::System< D >::mask ( )

inline

Get the mask (field to which total density is constrained).

Definition at line 1274 of file rpc/System.h.

Referenced by Pscf::Rpc::MaskGenFilm< D >::isGenerated().

◆ mask() [2/2]

template<int D>

Mask< D > const & Pscf::Rpc::System< D >::mask ( ) const

inline

Get the mask by const reference.

Definition at line 1279 of file rpc/System.h.

◆ mixture() [1/2]

template<int D>

Mixture< D > & Pscf::Rpc::System< D >::mixture ( )

inline

Get the Mixture by non-const reference.

Definition at line 1180 of file rpc/System.h.

◆ mixture() [2/2]

template<int D>

Mixture< D > const & Pscf::Rpc::System< D >::mixture ( ) const

inline

Get the Mixture by const reference.

Definition at line 1185 of file rpc/System.h.

◆ interaction() [1/2]

template<int D>

Interaction & Pscf::Rpc::System< D >::interaction ( )

inline

Get Interaction (excess free energy model) by reference.

Definition at line 1220 of file rpc/System.h.

References UTIL_ASSERT.

◆ interaction() [2/2]

template<int D>

Interaction const & Pscf::Rpc::System< D >::interaction ( ) const

inline

Get Interaction (excess free energy model) by const reference.

Definition at line 1228 of file rpc/System.h.

References UTIL_ASSERT.

◆ domain()

template<int D>

Domain< D > const & Pscf::Rpc::System< D >::domain ( ) const

inline

Get Domain by const reference.

Definition at line 1190 of file rpc/System.h.

Referenced by Pscf::Rpc::System< D >::System().

◆ iterator() [1/2]

template<int D>

Iterator< D > & Pscf::Rpc::System< D >::iterator ( )

inline

Get the Iterator by non-const reference.

Definition at line 1236 of file rpc/System.h.

References UTIL_ASSERT.

◆ iterator() [2/2]

template<int D>

Iterator< D > const & Pscf::Rpc::System< D >::iterator ( ) const

inline

Get the Iterator by const reference.

Definition at line 1244 of file rpc/System.h.

References UTIL_ASSERT.

◆ simulator()

template<int D>

Simulator< D > & Pscf::Rpc::System< D >::simulator ( )

inline

Get the Simulator for field theoretic simulation.

Definition at line 1195 of file rpc/System.h.

◆ fileMaster() [1/2]

template<int D>

FileMaster & Pscf::Rpc::System< D >::fileMaster ( )

inline

Get the FileMaster.

Access by non-const reference is used in some unit tests.

Definition at line 1200 of file rpc/System.h.

◆ fileMaster() [2/2]

template<int D>

FileMaster const & Pscf::Rpc::System< D >::fileMaster ( ) const

inline

Get the FileMaster by const reference.

Definition at line 1205 of file rpc/System.h.

◆ homogeneous() [1/2]

template<int D>

Homogeneous::Mixture & Pscf::Rpc::System< D >::homogeneous ( )

inline

Get homogeneous mixture (for reference calculations).

Definition at line 1210 of file rpc/System.h.

◆ homogeneous() [2/2]

template<int D>

Homogeneous::Mixture const & Pscf::Rpc::System< D >::homogeneous ( ) const

inline

Get const homogeneous mixture (for reference calculations).

Definition at line 1215 of file rpc/System.h.

◆ hasIterator()

template<int D>

bool Pscf::Rpc::System< D >::hasIterator ( ) const

inline

Does this system have an Iterator object?

Definition at line 1284 of file rpc/System.h.

◆ hasSweep()

template<int D>

bool Pscf::Rpc::System< D >::hasSweep ( ) const

inline

Does this system have a Sweep object?

Definition at line 1289 of file rpc/System.h.

◆ hasSimulator()

template<int D>

bool Pscf::Rpc::System< D >::hasSimulator ( ) const

inline

Does this system have an initialized Simulator?

Definition at line 1304 of file rpc/System.h.

◆ hasExternalFields()

template<int D>

bool Pscf::Rpc::System< D >::hasExternalFields ( ) const

inline

Does this system have external potential fields?

Definition at line 1294 of file rpc/System.h.

References Pscf::Prdc::MaskTmpl< D, FieldIo, RField >::hasData().

◆ hasMask()

template<int D>

bool Pscf::Rpc::System< D >::hasMask ( ) const

inline

Does this system have a mask (inhomogeneous density constraint)?

Definition at line 1299 of file rpc/System.h.

◆ hasCFields()

template<int D>

bool Pscf::Rpc::System< D >::hasCFields ( ) const

inline

Have c fields been computed from the current w fields?

Definition at line 1309 of file rpc/System.h.

◆ hasFreeEnergy()

template<int D>

bool Pscf::Rpc::System< D >::hasFreeEnergy ( ) const

inline

Has the free energy been computed from the current w fields?

Definition at line 1330 of file rpc/System.h.

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ System()

◆ ~System()

Member Function Documentation

◆ setOptions()

◆ readParam() [1/2]

◆ readParam() [2/2]

◆ readParameters()

◆ readCommands() [1/2]

◆ readCommands() [2/2]

◆ readWBasis()

◆ readWRGrid()

◆ setWBasis()

◆ setWRGrid()

◆ estimateWfromC()

◆ setUnitCell() [1/3]

◆ setUnitCell() [2/3]

◆ setUnitCell() [3/3]

◆ compute()

◆ iterate()

◆ sweep()

◆ simulate()

◆ computeFreeEnergy()

◆ fHelmholtz()

◆ pressure()

◆ writeParamNoSweep()

◆ writeThermo()

◆ writeStress()

◆ writeWBasis()

◆ writeWRGrid()

◆ writeCBasis()

◆ writeCRGrid()

◆ writeBlockCRGrid()

◆ writeQSlice()

◆ writeQTail()

◆ writeQ()

◆ writeQAll()

◆ writeWaves()

◆ writeStars()

◆ writeGroup()

◆ basisToRGrid()

◆ rGridToBasis()

◆ kGridToRGrid()

◆ rGridToKGrid()

◆ kGridToBasis()

◆ basisToKGrid()

◆ compare() [1/2]

◆ compare() [2/2]

◆ checkRGridFieldSymmetry()

◆ scaleFieldsBasis()

◆ scaleFieldsRGrid()

◆ expandRGridDimension()

◆ replicateUnitCell()

◆ writeTimers()

◆ clearTimers()

◆ w()

◆ c()

◆ h() [1/2]

◆ h() [2/2]

◆ mask() [1/2]

◆ mask() [2/2]

◆ mixture() [1/2]

◆ mixture() [2/2]

◆ interaction() [1/2]

◆ interaction() [2/2]

◆ domain()

◆ iterator() [1/2]

◆ iterator() [2/2]

◆ simulator()

◆ fileMaster() [1/2]

◆ fileMaster() [2/2]

◆ homogeneous() [1/2]

◆ homogeneous() [2/2]

◆ hasIterator()

◆ hasSweep()

◆ hasSimulator()

◆ hasExternalFields()