Detailed Description
A reversible, symplectic NPH integrator (Anderson barostat).
Integration algorithm based on Martyna,Tobias and Klein (J. Chem. Phys. 101, 4177-4189, 1994).
- See also
- param file format
Definition at line 29 of file ddMd/integrators/NphIntegrator.h.
#include <NphIntegrator.h>
Inheritance diagram for DdMd::NphIntegrator:
Public Member Functions | |
| NphIntegrator (Simulation &simulation) | |
| Constructor. More... | |
| ~NphIntegrator () | |
| Destructor. More... | |
| void | readParameters (std::istream &in) |
| Read required parameters. More... | |
| void | loadParameters (Serializable::IArchive &ar) |
| Load parameters from an input restart archive. More... | |
| void | save (Serializable::OArchive &ar) |
| Save state to an input restart archive. More... | |
 Public Member Functions inherited from DdMd::TwoStepIntegrator | |
| TwoStepIntegrator (Simulation &simulation) | |
| Constructor. More... | |
| ~TwoStepIntegrator () | |
| Destructor. More... | |
| void | run (int nStep) |
| Run a simulation. More... | |
| Public Member Functions inherited from DdMd::Integrator | |
| Integrator (Simulation &simulation) | |
| Constructor. More... | |
| ~Integrator () | |
| Destructor. More... | |
| virtual void | clear () |
| Set integrator to initial state and clears all statistics. More... | |
| virtual void | outputStatistics (std::ostream &out) |
| Output timing statistics from a run. More... | |
| double | time () const |
| Get average time per processor of previous run. More... | |
| int | iStep () const |
| Get current time step index. More... | |
| Public Member Functions inherited from Util::ParamComposite | |
| ParamComposite () | |
| Constructor. More... | |
| ParamComposite (const ParamComposite &other) | |
| Copy constructor. More... | |
| ParamComposite (int capacity) | |
| Constructor. More... | |
| virtual | ~ParamComposite () |
| Virtual destructor. More... | |
| void | resetParam () |
| Resets ParamComposite to its empty state. More... | |
| virtual void | readParam (std::istream &in) |
| Read the parameter file block. More... | |
| virtual void | readParamOptional (std::istream &in) |
| Read optional parameter file block. More... | |
| virtual void | writeParam (std::ostream &out) |
| Write all parameters to an output stream. More... | |
| virtual void | load (Serializable::IArchive &ar) |
| Load all parameters from an input archive. More... | |
| virtual void | loadOptional (Serializable::IArchive &ar) |
| Load an optional ParamComposite. More... | |
| void | saveOptional (Serializable::OArchive &ar) |
| Saves isActive flag, and then calls save() iff isActive is true. More... | |
| void | readParamComposite (std::istream &in, ParamComposite &child, bool next=true) |
| Add and read a required child ParamComposite. More... | |
| void | readParamCompositeOptional (std::istream &in, ParamComposite &child, bool next=true) |
| Add and attempt to read an optional child ParamComposite. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | read (std::istream &in, const char *label, Type &value) |
| Add and read a new required ScalarParam < Type > object. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | readOptional (std::istream &in, const char *label, Type &value) |
| Add and read a new optional ScalarParam < Type > object. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | readCArray (std::istream &in, const char *label, Type *value, int n) |
| Add and read a required C array parameter. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | readOptionalCArray (std::istream &in, const char *label, Type *value, int n) |
| Add and read an optional C array parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | readDArray (std::istream &in, const char *label, DArray< Type > &array, int n) |
| Add and read a required DArray < Type > parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | readOptionalDArray (std::istream &in, const char *label, DArray< Type > &array, int n) |
| Add and read an optional DArray < Type > parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | readFArray (std::istream &in, const char *label, FArray< Type, N > &array) |
| Add and read a required FArray < Type, N > array parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | readOptionalFArray (std::istream &in, const char *label, FArray< Type, N > &array) |
| Add and read an optional FArray < Type, N > array parameter. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | readCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np) |
| Add and read a required CArray2DParam < Type > 2D C-array. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | readOptionalCArray2D (std::istream &in, const char *label, Type *value, int m, int n, int np) |
| Add and read an optional CArray2DParam < Type > 2D C-array parameter. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | readDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n) |
| Add and read a required DMatrix < Type > matrix parameter. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | readOptionalDMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int m, int n) |
| Add and read an optional DMatrix < Type > matrix parameter. More... | |
| template<typename Type > | |
| DSymmMatrixParam< Type > & | readDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n) |
| Add and read a required symmetrix DMatrix. More... | |
| template<typename Type > | |
| DSymmMatrixParam< Type > & | readOptionalDSymmMatrix (std::istream &in, const char *label, DMatrix< Type > &matrix, int n) |
| Add and read an optional DMatrix matrix parameter. More... | |
| Begin & | readBegin (std::istream &in, const char *label, bool isRequired=true) |
| Add and read a class label and opening bracket. More... | |
| End & | readEnd (std::istream &in) |
| Add and read the closing bracket. More... | |
| Blank & | readBlank (std::istream &in) |
| Add and read a new Blank object, representing a blank line. More... | |
| void | loadParamComposite (Serializable::IArchive &ar, ParamComposite &child, bool next=true) |
| Add and load a required child ParamComposite. More... | |
| void | loadParamCompositeOptional (Serializable::IArchive &ar, ParamComposite &child, bool next=true) |
| Add and load an optional child ParamComposite if isActive. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | loadParameter (Serializable::IArchive &ar, const char *label, Type &value, bool isRequired) |
| Add and load a new ScalarParam < Type > object. More... | |
| template<typename Type > | |
| ScalarParam< Type > & | loadParameter (Serializable::IArchive &ar, const char *label, Type &value) |
| Add and load new required ScalarParam < Type > object. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | loadCArray (Serializable::IArchive &ar, const char *label, Type *value, int n, bool isRequired) |
| Add a C array parameter and load its elements. More... | |
| template<typename Type > | |
| CArrayParam< Type > & | loadCArray (Serializable::IArchive &ar, const char *label, Type *value, int n) |
| Add and load a required CArrayParam< Type > array parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n, bool isRequired) |
| Add an load a DArray < Type > array parameter. More... | |
| template<typename Type > | |
| DArrayParam< Type > & | loadDArray (Serializable::IArchive &ar, const char *label, DArray< Type > &array, int n) |
| Add and load a required DArray< Type > array parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array, bool isRequired) |
| Add and load an FArray < Type, N > fixed-size array parameter. More... | |
| template<typename Type , int N> | |
| FArrayParam< Type, N > & | loadFArray (Serializable::IArchive &ar, const char *label, FArray< Type, N > &array) |
| Add and load a required FArray < Type > array parameter. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | loadCArray2D (Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np, bool isRequired) |
| Add and load a CArray2DParam < Type > C 2D array parameter. More... | |
| template<typename Type > | |
| CArray2DParam< Type > & | loadCArray2D (Serializable::IArchive &ar, const char *label, Type *value, int m, int n, int np) |
| Add and load a required < Type > matrix parameter. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n, bool isRequired) |
| Add and load a DMatrixParam < Type > matrix parameter. More... | |
| template<typename Type > | |
| DMatrixParam< Type > & | loadDMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int m, int n) |
| Add and load a required DMatrixParam < Type > matrix parameter. More... | |
| template<typename Type > | |
| DSymmMatrixParam< Type > & | loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n, bool isRequired) |
| Add and load a symmetric DSymmMatrixParam < Type > matrix parameter. More... | |
| template<typename Type > | |
| DSymmMatrixParam< Type > & | loadDSymmMatrix (Serializable::IArchive &ar, const char *label, DMatrix< Type > &matrix, int n) |
| Add and load a required DSymmMatrixParam < Type > matrix parameter. More... | |
| void | addParamComposite (ParamComposite &child, bool next=true) |
| Add a child ParamComposite object to the format array. More... | |
| Begin & | addBegin (const char *label) |
| Add a Begin object representing a class name and bracket. More... | |
| End & | addEnd () |
| Add a closing bracket. More... | |
| Blank & | addBlank () |
| Create and add a new Blank object, representing a blank line. More... | |
| std::string | className () const |
| Get class name string. More... | |
| bool | isRequired () const |
| Is this ParamComposite required in the input file? More... | |
| bool | isActive () const |
| Is this parameter active? More... | |
| Public Member Functions inherited from Util::ParamComponent | |
| virtual | ~ParamComponent () |
| Destructor. More... | |
| void | setIndent (const ParamComponent &parent, bool next=true) |
| Set indent level. More... | |
| std::string | indent () const |
| Return indent string for this object (string of spaces). More... | |
| template<class Archive > | |
| void | serialize (Archive &ar, const unsigned int version) |
| Serialize this ParamComponent as a string. More... | |
| Public Member Functions inherited from Util::Serializable | |
| virtual | ~Serializable () |
| Destructor. More... | |
| Public Member Functions inherited from Util::MpiFileIo | |
| MpiFileIo () | |
| Constructor. More... | |
| MpiFileIo (const MpiFileIo &other) | |
| Copy constructor. More... | |
| bool | isIoProcessor () const |
| Can this processor do file I/O ? More... | |
| void | setIoCommunicator (MPI::Intracomm &communicator) |
| Set the communicator. More... | |
| void | clearCommunicator () |
| Clear (nullify) the communicator. More... | |
| bool | hasIoCommunicator () const |
| Does this object have an associated MPI communicator? More... | |
| MPI::Intracomm & | ioCommunicator () const |
| Get the MPI communicator by reference. More... | |
| Public Member Functions inherited from DdMd::SimulationAccess | |
| SimulationAccess (Simulation &simulation) | |
| Constructor. More... | |
| ~SimulationAccess () | |
| Destructor. More... | |
| Simulation & | simulation () |
| Get the parent simulation. More... | |
| Boundary & | boundary () |
| Get the Boundary. More... | |
| AtomStorage & | atomStorage () |
| Get the AtomStorage. More... | |
| GroupStorage< 2 > & | bondStorage () |
| Get the BondStorage. More... | |
| GroupStorage< 3 > & | angleStorage () |
| Get the AngleStorage. More... | |
| GroupStorage< 4 > & | dihedralStorage () |
| Get the angleStorage. More... | |
| PairPotential & | pairPotential () |
| Get the PairPotential. More... | |
| BondPotential & | bondPotential () |
| Get the PairPotential. More... | |
| AnglePotential & | anglePotential () |
| Get the AnglePotential. More... | |
| DihedralPotential & | dihedralPotential () |
| Get the DihedralPotential. More... | |
| ExternalPotential & | externalPotential () |
| Get the ExternalPotential. More... | |
| EnergyEnsemble & | energyEnsemble () |
| Get the EnergyEnsemble. More... | |
| BoundaryEnsemble & | boundaryEnsemble () |
| Get the BoundaryEnsemble. More... | |
| Random & | random () |
| Get the Random number generator. More... | |
| Domain & | domain () |
| Get the Domain. More... | |
| Exchanger & | exchanger () |
| Get the Exchanger. More... | |
| FileMaster & | fileMaster () |
| Get the FileMaster. More... | |
| int | nAtomType () |
| Get maximum number of atom types. More... | |
| int | nBondType () |
| Get maximum number of bond types. More... | |
| int | nAngleType () |
| Get maximum number of angle types. More... | |
| int | nDihedralType () |
| Get maximum number of dihedral types. More... | |
| bool | hasExternal () |
| Does this simulation have an external potential? More... | |
| AtomType & | atomType (int i) |
| Get an AtomType descriptor for atomtype i. More... | |
| MaskPolicy | maskedPairPolicy () const |
| Return the value of the mask policy (MaskNone or MaskBonded). More... | |
| bool | reverseUpdateFlag () const |
| Are forces evaluated by reverse communication (true) or not (false)? More... | |
Protected Member Functions | |
| void | initDynamicalState () |
| Initialize Vector nu to zero. More... | |
| void | setup () |
| Setup state just before integration. More... | |
| virtual void | integrateStep1 () |
| Execute first step of two-step integrator. More... | |
| virtual void | integrateStep2 () |
| Execute secodn step of two-step integrator. More... | |
| Protected Member Functions inherited from DdMd::Integrator | |
| void | setIsSetup () |
| Mark the integrator as having been setup at least once. More... | |
| bool | isSetup () const |
| Has the setup() method been called at least once previously? More... | |
| void | setupAtoms () |
| Setup state of atoms just before integration. More... | |
| void | computeForces () |
| Compute forces for all local atoms, with timing. More... | |
| void | computeForcesAndVirial () |
| Compute forces for all local atoms and virial, with timing. More... | |
| bool | isExchangeNeeded (double skin) |
| Determine whether an atom exchange and reneighboring is needed. More... | |
| const std::string & | saveFileName () const |
| Get restart file base name. More... | |
| int | saveInterval () const |
| Get interval for writing a restart file. 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... | |
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 Types inherited from DdMd::Integrator | |
| Protected Attributes inherited from DdMd::Integrator | |
| int | iStep_ |
| Current step number. More... | |
Constructor & Destructor Documentation
| DdMd::NphIntegrator::NphIntegrator | ( | Simulation & | simulation | ) |
Constructor.
Definition at line 32 of file ddMd/integrators/NphIntegrator.cpp.
References Util::ParamComposite::setClassName().
| DdMd::NphIntegrator::~NphIntegrator | ( | ) |
Destructor.
Definition at line 39 of file ddMd/integrators/NphIntegrator.cpp.
Member Function Documentation
|
virtual |
Read required parameters.
Reimplemented from DdMd::Integrator.
Definition at line 45 of file ddMd/integrators/NphIntegrator.cpp.
References Util::DArray< Data >::allocate(), Util::DArray< Data >::isAllocated(), DdMd::SimulationAccess::nAtomType(), DdMd::Simulation::nAtomType(), DdMd::Integrator::readParameters(), and DdMd::SimulationAccess::simulation().
|
virtual |
Load parameters from an input restart archive.
Reimplemented from DdMd::Integrator.
Definition at line 62 of file ddMd/integrators/NphIntegrator.cpp.
References Util::DArray< Data >::allocate(), Util::DArray< Data >::isAllocated(), Util::MpiLoader< IArchive >::load(), DdMd::Integrator::loadParameters(), DdMd::SimulationAccess::nAtomType(), DdMd::Simulation::nAtomType(), and DdMd::SimulationAccess::simulation().
|
virtual |
Save state to an input restart archive.
Reimplemented from DdMd::Integrator.
Definition at line 82 of file ddMd/integrators/NphIntegrator.cpp.
References DdMd::Integrator::save().
|
protectedvirtual |
Initialize Vector nu to zero.
Reimplemented from DdMd::Integrator.
Definition at line 94 of file ddMd/integrators/NphIntegrator.cpp.
|
protectedvirtual |
Setup state just before integration.
Implements DdMd::Integrator.
Definition at line 97 of file ddMd/integrators/NphIntegrator.cpp.
References DdMd::SimulationAccess::atomStorage(), DdMd::Simulation::atomType(), Util::bcast(), DdMd::Simulation::boundaryEnsemble(), Util::Array< Data >::capacity(), DdMd::Integrator::clear(), DdMd::Simulation::computeKineticEnergy(), DdMd::AtomStorage::computeNAtomTotal(), DdMd::SimulationAccess::domain(), DdMd::Integrator::isSetup(), DdMd::AtomType::mass(), DdMd::AtomStorage::nAtomTotal(), DdMd::SimulationAccess::nAtomType(), Simp::BoundaryEnsemble::pressure(), DdMd::Integrator::setIsSetup(), DdMd::Integrator::setupAtoms(), and DdMd::SimulationAccess::simulation().
|
protectedvirtual |
Execute first step of two-step integrator.
Implements DdMd::TwoStepIntegrator.
Definition at line 133 of file ddMd/integrators/NphIntegrator.cpp.
References DdMd::SimulationAccess::atomStorage(), Util::bcast(), DdMd::AtomStorage::begin(), DdMd::Simulation::boundary(), DdMd::Simulation::boundaryEnsemble(), DdMd::Simulation::computeKineticEnergy(), DdMd::Simulation::computeKineticStress(), DdMd::Simulation::computeVirialStress(), DdMd::SimulationAccess::domain(), DdMd::Simulation::domain(), DdMd::Domain::isMaster(), DdMd::Simulation::kineticEnergy(), DdMd::Simulation::kineticStress(), Simp::OrthorhombicBoundary::lengths(), Util::Vector::multiply(), Util::PArrayIterator< Data >::notEnd(), Simp::BoundaryEnsemble::pressure(), Simp::OrthorhombicBoundary::setOrthorhombic(), DdMd::SimulationAccess::simulation(), Util::Tensor::trace(), DdMd::Simulation::virialStress(), and Simp::OrthorhombicBoundary::volume().
|
protectedvirtual |
Execute secodn step of two-step integrator.
Implements DdMd::TwoStepIntegrator.
Definition at line 265 of file ddMd/integrators/NphIntegrator.cpp.
References DdMd::SimulationAccess::atomStorage(), Util::bcast(), DdMd::AtomStorage::begin(), DdMd::Simulation::boundary(), DdMd::Simulation::computeKineticEnergy(), DdMd::Simulation::computeKineticStress(), DdMd::Simulation::computePotentialEnergies(), DdMd::Simulation::computeVirialStress(), DdMd::SimulationAccess::domain(), DdMd::Simulation::domain(), DdMd::Domain::isMaster(), DdMd::Simulation::kineticEnergy(), DdMd::Simulation::kineticStress(), Util::Vector::multiply(), Util::PArrayIterator< Data >::notEnd(), Util::Signal< T >::notify(), DdMd::Simulation::potentialEnergy(), DdMd::SimulationAccess::simulation(), Util::Tensor::trace(), DdMd::Simulation::velocitySignal(), DdMd::Simulation::virialStress(), and Simp::OrthorhombicBoundary::volume().
The documentation for this class was generated from the following files:
