Simpatico
v1.10
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Native / default format for configuration files.
DdMdOrderedConfigIo is a ConfigIo that implements the default configuration file format for ddSim, like DdMdConfigIo, but that outputs atoms in sequential order, sorted by atom id.
Definition at line 32 of file DdMdOrderedConfigIo.h.
#include <DdMdOrderedConfigIo.h>
Public Member Functions | |
DdMdOrderedConfigIo (bool hasMolecules) | |
Default constructor. More... | |
DdMdOrderedConfigIo (Simulation &simulation, bool hasMolecules) | |
Constructor. More... | |
virtual void | readConfig (std::ifstream &file, MaskPolicy maskPolicy) |
Read configuration file. More... | |
virtual void | writeConfig (std::ofstream &file) |
Write configuration file. More... | |
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ConfigIo () | |
Default constructor. More... | |
ConfigIo (Simulation &simulation) | |
Constructor. More... | |
virtual | ~ConfigIo () |
Destructor. More... | |
void | associate (Domain &domain, Boundary &boundary, AtomStorage &atomStorage, BondStorage &bondStorage, AngleStorage &angleStorage, DihedralStorage &dihedralStorage, Buffer &buffer) |
Associate with related objects. More... | |
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ParamComposite () | |
Constructor. More... | |
ParamComposite (const ParamComposite &other) | |
Copy constructor. More... | |
ParamComposite (int capacity) | |
Constructor. More... | |
virtual | ~ParamComposite () |
Virtual destructor. More... | |
void | resetParam () |
Resets ParamComposite to its empty state. More... | |
virtual void | readParam (std::istream &in) |
Read the parameter file block. More... | |
virtual void | readParamOptional (std::istream &in) |
Read optional parameter file block. More... | |
virtual void | readParameters (std::istream &in) |
Read the body of parameter block, without begin and end lines. 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... | |
virtual void | loadParameters (Serializable::IArchive &ar) |
Load state from archive, without adding Begin and End lines. More... | |
virtual void | save (Serializable::OArchive &ar) |
Saves all parameters to an archive. More... | |
void | saveOptional (Serializable::OArchive &ar) |
Saves isActive flag, and then calls save() iff isActive is true. More... | |
void | readParamComposite (std::istream &in, ParamComposite &child, bool next=true) |
Add and read a required child ParamComposite. More... | |
void | readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true) |
Add and attempt to read an optional child ParamComposite. More... | |
template<typename Type > | |
ScalarParam< Type > & | read (std::istream &in, const char *label, Type &value) |
Add and read a new required ScalarParam < Type > object. More... | |
template<typename Type > | |
ScalarParam< Type > & | readOptional (std::istream &in, const char *label, Type &value) |
Add and read a new optional ScalarParam < Type > object. More... | |
template<typename Type > | |
CArrayParam< Type > & | readCArray (std::istream &in, const char *label, Type *value, int n) |
Add and read a required C array parameter. More... | |
template<typename Type > | |
CArrayParam< Type > & | readOptionalCArray (std::istream &in, const char *label, Type *value, int n) |
Add and read an optional C array parameter. More... | |
template<typename Type > | |
DArrayParam< Type > & | readDArray (std::istream &in, const char *label, DArray< Type > &array, int n) |
Add and read a required DArray < Type > parameter. More... | |
template<typename Type > | |
DArrayParam< Type > & | readOptionalDArray (std::istream &in, const char *label, DArray< Type > &array, int n) |
Add and read an optional DArray < Type > parameter. More... | |
template<typename Type , int N> | |
FArrayParam< Type, N > & | readFArray (std::istream &in, const char *label, FArray< Type, N > &array) |
Add and read a required FArray < Type, N > array parameter. More... | |
template<typename Type , int N> | |
FArrayParam< Type, N > & | readOptionalFArray (std::istream &in, const char *label, FArray< Type, N > &array) |
Add and read an optional FArray < Type, N > array parameter. More... | |
template<typename Type > | |
CArray2DParam< Type > & | readCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np) |
Add and read a required CArray2DParam < Type > 2D C-array. More... | |
template<typename Type > | |
CArray2DParam< Type > & | readOptionalCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np) |
Add and read an optional CArray2DParam < Type > 2D C-array parameter. More... | |
template<typename Type > | |
DMatrixParam< Type > & | readDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n) |
Add and read a required DMatrix < Type > matrix parameter. More... | |
template<typename Type > | |
DMatrixParam< Type > & | readOptionalDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n) |
Add and read an optional DMatrix < Type > matrix parameter. More... | |
template<typename Type > | |
DSymmMatrixParam< Type > & | readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n) |
Add and read a required symmetrix DMatrix. More... | |
template<typename Type > | |
DSymmMatrixParam< Type > & | readOptionalDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n) |
Add and read an optional DMatrix matrix parameter. More... | |
Begin & | readBegin (std::istream &in, const char *label, bool isRequired=true) |
Add and read a class label and opening bracket. More... | |
End & | readEnd (std::istream &in) |
Add and read the closing bracket. More... | |
Blank & | readBlank (std::istream &in) |
Add and read a new Blank object, representing a blank line. More... | |
void | loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true) |
Add and load a required child ParamComposite. More... | |
void | loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true) |
Add and load an optional child ParamComposite if isActive. More... | |
template<typename Type > | |
ScalarParam< Type > & | loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired) |
Add and load a new ScalarParam < Type > object. More... | |
template<typename Type > | |
ScalarParam< Type > & | loadParameter (Serializable::IArchive &ar, const char *label, Type &value) |
Add and load new required ScalarParam < Type > object. More... | |
template<typename Type > | |
CArrayParam< Type > & | loadCArray (Serializable::IArchive &ar, const char *label, Type *value, int n, bool isRequired) |
Add a C array parameter and load its elements. More... | |
template<typename Type > | |
CArrayParam< Type > & | loadCArray (Serializable::IArchive &ar, const char *label, Type *value, int n) |
Add and load a required CArrayParam< Type > array parameter. More... | |
template<typename Type > | |
DArrayParam< Type > & | loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired) |
Add an load a DArray < Type > array parameter. More... | |
template<typename Type > | |
DArrayParam< Type > & | loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n) |
Add and load a required DArray< Type > array parameter. More... | |
template<typename Type , int N> | |
FArrayParam< Type, N > & | loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired) |
Add and load an FArray < Type, N > fixed-size array parameter. More... | |
template<typename Type , int N> | |
FArrayParam< Type, N > & | loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array) |
Add and load a required FArray < Type > array parameter. More... | |
template<typename Type > | |
CArray2DParam< Type > & | loadCArray2D (Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np, bool isRequired) |
Add and load a CArray2DParam < Type > C 2D array parameter. More... | |
template<typename Type > | |
CArray2DParam< Type > & | loadCArray2D (Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np) |
Add and load a required < Type > matrix parameter. More... | |
template<typename Type > | |
DMatrixParam< Type > & | loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired) |
Add and load a DMatrixParam < Type > matrix parameter. More... | |
template<typename Type > | |
DMatrixParam< Type > & | loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n) |
Add and load a required DMatrixParam < Type > matrix parameter. More... | |
template<typename Type > | |
DSymmMatrixParam< Type > & | loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired) |
Add and load a symmetric DSymmMatrixParam < Type > matrix parameter. More... | |
template<typename Type > | |
DSymmMatrixParam< Type > & | loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n) |
Add and load a required DSymmMatrixParam < Type > matrix parameter. More... | |
void | addParamComposite (ParamComposite &child, bool next=true) |
Add a child ParamComposite object to the format array. More... | |
Begin & | addBegin (const char *label) |
Add a Begin object representing a class name and bracket. More... | |
End & | addEnd () |
Add a closing bracket. More... | |
Blank & | addBlank () |
Create and add a new Blank object, representing a blank line. More... | |
std::string | className () const |
Get class name string. More... | |
bool | isRequired () const |
Is this ParamComposite required in the input file? More... | |
bool | isActive () const |
Is this parameter active? More... | |
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virtual | ~ParamComponent () |
Destructor. More... | |
void | setIndent (const ParamComponent &parent, bool next=true) |
Set indent level. More... | |
std::string | indent () const |
Return indent string for this object (string of spaces). More... | |
template<class Archive > | |
void | serialize (Archive &ar, const unsigned int version) |
Serialize this ParamComponent as a string. More... | |
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virtual | ~Serializable () |
Destructor. More... | |
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MpiFileIo () | |
Constructor. More... | |
MpiFileIo (const MpiFileIo &other) | |
Copy constructor. More... | |
bool | isIoProcessor () const |
Can this processor do file I/O ? More... | |
void | setIoCommunicator (MPI::Intracomm &communicator) |
Set the communicator. More... | |
void | clearCommunicator () |
Clear (nullify) the communicator. More... | |
bool | hasIoCommunicator () const |
Does this object have an associated MPI communicator? More... | |
MPI::Intracomm & | ioCommunicator () const |
Get the MPI communicator by reference. More... | |
Additional Inherited Members | |
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typedef BinaryFileOArchive | OArchive |
Type of output archive used by save method. More... | |
typedef BinaryFileIArchive | IArchive |
Type of input archive used by load method. More... | |
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static void | initStatic () |
Initialize static echo member to false. More... | |
static void | setEcho (bool echo=true) |
Enable or disable echoing for all subclasses of ParamComponent. More... | |
static bool | echo () |
Get echo parameter. More... | |
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void | setAtomMasks () |
Set Mask data on all atoms. More... | |
Domain & | domain () |
Get the Domain by reference. More... | |
Boundary & | boundary () |
Get Boundary by reference. More... | |
AtomStorage & | atomStorage () |
Get AtomStorage by reference. More... | |
AtomDistributor & | atomDistributor () |
Get the AtomDistributor by reference. More... | |
AtomCollector & | atomCollector () |
Get the AtomCollector by reference. More... | |
BondStorage & | bondStorage () |
Get BondStorage by reference. More... | |
GroupDistributor< 2 > & | bondDistributor () |
Get the bondDistributor by reference. More... | |
GroupCollector< 2 > & | bondCollector () |
Get the bond collector by reference. More... | |
AngleStorage & | angleStorage () |
Get AngleStorage by reference. More... | |
GroupDistributor< 3 > & | angleDistributor () |
Get the angle distributor by reference. More... | |
GroupCollector< 3 > & | angleCollector () |
Get the angle collector by reference. More... | |
DihedralStorage & | dihedralStorage () |
Get DihedralStorage by reference. More... | |
GroupDistributor< 4 > & | dihedralDistributor () |
Get the dihedral distributor by reference. More... | |
GroupCollector< 4 > & | dihedralCollector () |
Get the dihedral collector by reference. More... | |
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void | setClassName (const char *className) |
Set class name string. More... | |
void | setIsRequired (bool isRequired) |
Set or unset the isActive flag. More... | |
void | setIsActive (bool isActive) |
Set or unset the isActive flag. More... | |
void | setParent (ParamComponent ¶m, bool next=true) |
Set this to the parent of a child component. More... | |
void | addComponent (ParamComponent ¶m, bool isLeaf=true) |
Add a new ParamComponent object to the format array. More... | |
template<typename Type > | |
ScalarParam< Type > & | add (std::istream &in, const char *label, Type &value, bool isRequired=true) |
Add a new required ScalarParam < Type > object. More... | |
template<typename Type > | |
CArrayParam< Type > & | addCArray (std::istream &in, const char *label, Type *value, int n, bool isRequired=true) |
Add (but do not read) a required C array parameter. More... | |
template<typename Type > | |
DArrayParam< Type > & | addDArray (std::istream &in, const char *label, DArray< Type > &array, int n, bool isRequired=true) |
Add (but do not read) a DArray < Type > parameter. More... | |
template<typename Type , int N> | |
FArrayParam< Type, N > & | addFArray (std::istream &in, const char *label, FArray< Type, N > &array, bool isRequired=true) |
Add (but do not read) a FArray < Type, N > array parameter. More... | |
template<typename Type > | |
CArray2DParam< Type > & | addCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np, bool isRequired=true) |
Add (but do not read) a CArray2DParam < Type > 2D C-array. More... | |
template<typename Type > | |
DMatrixParam< Type > & | addDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired=true) |
Add and read a required DMatrix < Type > matrix parameter. More... | |
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ParamComponent () | |
Constructor. More... | |
ParamComponent (const ParamComponent &other) | |
Copy constructor. More... | |
DdMd::DdMdOrderedConfigIo::DdMdOrderedConfigIo | ( | bool | hasMolecules | ) |
Default constructor.
hasMolecules | Set true to include AtomContext info. |
Definition at line 44 of file DdMdOrderedConfigIo.cpp.
References Util::ParamComposite::setClassName().
DdMd::DdMdOrderedConfigIo::DdMdOrderedConfigIo | ( | Simulation & | simulation, |
bool | hasMolecules | ||
) |
Constructor.
simulation | parent Simulation object. |
hasMolecules | Set true to include AtomContext info. |
Definition at line 52 of file DdMdOrderedConfigIo.cpp.
References DdMd::GroupDistributor< N >::add(), DdMd::ConfigIo::domain(), DdMd::GroupDistributor< N >::newPtr(), DdMd::GroupDistributor< N >::receive(), DdMd::GroupDistributor< N >::send(), Util::ParamComposite::setClassName(), and DdMd::GroupDistributor< N >::setup().
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virtual |
Read configuration file.
This routine opens and reads a file on the master, and distributes atom data among the processors.
file | input file stream |
maskPolicy | MaskPolicy to be used in setting atom masks |
Implements DdMd::ConfigIo.
Definition at line 90 of file DdMdOrderedConfigIo.cpp.
References DdMd::AtomDistributor::addAtom(), DdMd::ConfigIo::angleDistributor(), DdMd::ConfigIo::angleStorage(), DdMd::ConfigIo::atomDistributor(), DdMd::AtomContext::atomId, DdMd::ConfigIo::atomStorage(), Util::bcast(), DdMd::ConfigIo::bondDistributor(), DdMd::ConfigIo::bondStorage(), DdMd::ConfigIo::boundary(), DdMd::GroupStorage< N >::computeNTotal(), DdMd::Atom::context(), DdMd::ConfigIo::dihedralDistributor(), DdMd::ConfigIo::dihedralStorage(), DdMd::ConfigIo::domain(), DdMd::Atom::hasAtomContext(), DdMd::Group< N >::id(), DdMd::GroupStorage< N >::isValid(), DdMd::AtomContext::moleculeId, DdMd::AtomDistributor::newAtomPtr(), DdMd::GroupCollector< N >::nextPtr(), DdMd::GroupStorage< N >::nTotal(), DdMd::Atom::position(), DdMd::AtomDistributor::receive(), DdMd::GroupCollector< N >::send(), DdMd::AtomDistributor::send(), DdMd::ConfigIo::setAtomMasks(), DdMd::Atom::setId(), DdMd::Atom::setTypeId(), DdMd::GroupCollector< N >::setup(), DdMd::AtomDistributor::setup(), DdMd::AtomContext::speciesId, DdMd::AtomStorage::totalAtomCapacity(), Simp::OrthorhombicBoundary::transformCartToGen(), UTIL_THROW, DdMd::AtomDistributor::validate(), and DdMd::Atom::velocity().
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virtual |
Write configuration file.
This routine opens and writes a file on the master, collecting atom and group data from all processors. Atoms and Groups are output in order, sorted by global id.
file | output file stream |
Implements DdMd::ConfigIo.
Definition at line 284 of file DdMdOrderedConfigIo.cpp.
References DdMd::ConfigIo::angleCollector(), DdMd::ConfigIo::angleStorage(), DdMd::ConfigIo::atomCollector(), DdMd::ConfigIo::atomStorage(), DdMd::ConfigIo::bondCollector(), DdMd::ConfigIo::bondStorage(), DdMd::ConfigIo::boundary(), DdMd::GroupStorage< N >::capacity(), DdMd::AtomStorage::computeNAtomTotal(), DdMd::Atom::context(), DdMd::ConfigIo::dihedralCollector(), DdMd::ConfigIo::dihedralStorage(), DdMd::ConfigIo::domain(), DdMd::Atom::hasAtomContext(), DdMd::Atom::id(), DdMd::AtomStorage::isCartesian(), DdMd::AtomStorage::nAtomTotal(), DdMd::AtomCollector::nextPtr(), DdMd::Atom::position(), DdMd::AtomCollector::send(), DdMd::AtomCollector::setup(), Simp::OrthorhombicBoundary::transformGenToCart(), DdMd::Atom::typeId(), UTIL_THROW, and DdMd::Atom::velocity().