Detailed Description
Save / load configuration from / to an archive.
The virtual functions readConfig and writeConfig, which take file objects parameters, read from or write to files that stores archives of type Serializable::IArchive or Serializable::OArchive. The loadConfig and saveConfig methods take archive object arguments.
Definition at line 31 of file SerializeConfigIo.h.
#include <SerializeConfigIo.h>
Public Member Functions | |
| SerializeConfigIo () | |
| Default constructor. More... | |
| SerializeConfigIo (Simulation &simulation) | |
| Constructor. More... | |
| virtual void | readConfig (std::ifstream &file, MaskPolicy maskPolicy) |
| Read configuration file. More... | |
| virtual void | writeConfig (std::ofstream &file) |
| Write configuration file. More... | |
| void | loadConfig (Serializable::IArchive &ar, MaskPolicy maskPolicy) |
| Load configuration from an archive. More... | |
| void | saveConfig (Serializable::OArchive &ar) |
| Save configuration. More... | |
 Public Member Functions inherited from DdMd::ConfigIo | |
| 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... | |
| 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 | 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... | |
| Public Member Functions inherited from Util::ParamComponent | |
| virtual | ~ParamComponent () |
| Destructor. More... | |
| void | setIndent (const ParamComponent &parent, bool next=true) |
| Set indent level. More... | |
| std::string | indent () const |
| Return indent string for this object (string of spaces). More... | |
| template<class Archive > | |
| void | serialize (Archive &ar, const unsigned int version) |
| Serialize this ParamComponent as a string. More... | |
| Public Member Functions inherited from Util::Serializable | |
| virtual | ~Serializable () |
| Destructor. More... | |
| Public Member Functions inherited from Util::MpiFileIo | |
| MpiFileIo () | |
| Constructor. More... | |
| MpiFileIo (const MpiFileIo &other) | |
| Copy constructor. More... | |
| bool | isIoProcessor () const |
| Can this processor do file I/O ? More... | |
| void | setIoCommunicator (MPI::Intracomm &communicator) |
| Set the communicator. More... | |
| void | clearCommunicator () |
| Clear (nullify) the communicator. More... | |
| bool | hasIoCommunicator () const |
| Does this object have an associated MPI communicator? More... | |
| MPI::Intracomm & | ioCommunicator () const |
| Get the MPI communicator by reference. More... | |
Additional Inherited Members | |
| Public Types inherited from Util::Serializable | |
| typedef BinaryFileOArchive | OArchive |
| Type of output archive used by save method. More... | |
| typedef BinaryFileIArchive | IArchive |
| Type of input archive used by load method. More... | |
| Static Public Member Functions inherited from Util::ParamComponent | |
| static void | initStatic () |
| Initialize static echo member to false. More... | |
| static void | setEcho (bool echo=true) |
| Enable or disable echoing for all subclasses of ParamComponent. More... | |
| static bool | echo () |
| Get echo parameter. More... | |
| Protected Member Functions inherited from DdMd::ConfigIo | |
| 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... | |
| 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... | |
Constructor & Destructor Documentation
| DdMd::SerializeConfigIo::SerializeConfigIo | ( | ) |
Default constructor.
Definition at line 44 of file SerializeConfigIo.cpp.
References Util::ParamComposite::setClassName().
| DdMd::SerializeConfigIo::SerializeConfigIo | ( | Simulation & | simulation | ) |
Constructor.
- Parameters
-
simulation parent Simulation object.
Definition at line 51 of file SerializeConfigIo.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().
Member Function Documentation
|
virtual |
Read configuration file.
Call on all processors, but reads from file only on master.
This function opens and reads a file on the master, and distributes atom data among the processors. This calls loadConfig() internally, and thus has all the preconditions of loadConfig().
- Parameters
-
file input file stream (must be open on master) maskPolicy MaskPolicy to be used in setting atom masks
Implements DdMd::ConfigIo.
Definition at line 295 of file SerializeConfigIo.cpp.
References DdMd::ConfigIo::domain(), loadConfig(), and UTIL_THROW.
|
virtual |
Write configuration file.
Call on all processors, but file must be open only on master.
This function opens and writes a file on the master, collecting atom data from all processors. It calls saveConfig() internally.
- Parameters
-
file output file stream (must be open on master)
Implements DdMd::ConfigIo.
Definition at line 310 of file SerializeConfigIo.cpp.
References DdMd::ConfigIo::domain(), saveConfig(), and UTIL_THROW.
| void DdMd::SerializeConfigIo::loadConfig | ( | Serializable::IArchive & | ar, |
| MaskPolicy | maskPolicy | ||
| ) |
Load configuration from an archive.
Call on all processors, but save from archive only on master.
- Precondition
- There are no atoms, ghosts, or groups.
- AtomStorage is set for scaled / generalized coordinates
- Postcondition
- atomic coordinates are scaled / generalized
- there are no ghosts
- Parameters
-
ar input archive maskPolicy MaskPolicy to be used in setting atom masks
Definition at line 84 of file SerializeConfigIo.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::groups(), DdMd::Atom::hasAtomContext(), 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().
Referenced by readConfig().
| void DdMd::SerializeConfigIo::saveConfig | ( | Serializable::OArchive & | ar | ) |
Save configuration.
Call on all processors, but uses archive only on master.
This function allows the AtomStorage to be set for either generalized or Cartesian coordinates, but always saves Cartesian atom coordinates to the archive. In either case, it does not modify any Atom position values, or change the coordinates system setting of the AtomStorage.
Usage: Atomic coordinates are Cartesian on input and output when this function is used by an Integrator to write a restart file, but are scaled / generalized on input and ouput when it is called by writeConfig() to implement the WRITE_CONFIG command within the Simulation::readCommand() function.
- Parameters
-
ar output archive
Definition at line 227 of file SerializeConfigIo.cpp.
References DdMd::ConfigIo::angleCollector(), DdMd::ConfigIo::angleStorage(), DdMd::ConfigIo::atomCollector(), DdMd::AtomContext::atomId, 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::groups(), DdMd::Atom::hasAtomContext(), DdMd::Atom::id(), DdMd::AtomStorage::isCartesian(), DdMd::AtomContext::moleculeId, DdMd::AtomStorage::nAtomTotal(), DdMd::AtomCollector::nextPtr(), DdMd::Atom::position(), DdMd::AtomCollector::send(), DdMd::AtomCollector::setup(), DdMd::AtomContext::speciesId, Simp::OrthorhombicBoundary::transformGenToCart(), DdMd::Atom::typeId(), and DdMd::Atom::velocity().
Referenced by writeConfig().
The documentation for this class was generated from the following files:
