Simpatico
v1.10
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A Nose-Hoover constant temperature, constant volume integrator.
Definition at line 26 of file NvtIntegrator.h.
#include <NvtIntegrator.h>
Public Member Functions | |
NvtIntegrator (Simulation &simulation) | |
Constructor. More... | |
~NvtIntegrator () | |
Destructor. More... | |
void | readParameters (std::istream &in) |
Read required parameters. More... | |
virtual void | loadParameters (Serializable::IArchive &ar) |
Load internal state from an archive. More... | |
virtual void | save (Serializable::OArchive &ar) |
Save internal state to an archive. More... | |
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TwoStepIntegrator (Simulation &simulation) | |
Constructor. More... | |
~TwoStepIntegrator () | |
Destructor. More... | |
void | run (int nStep) |
Run a simulation. More... | |
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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... | |
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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 | 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... | |
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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... | |
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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 | 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... | |
virtual void | initDynamicalState () |
Initialize internal dynamical state variables to default value. More... | |
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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... | |
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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... | |
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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int | iStep_ |
Current step number. More... | |
DdMd::NvtIntegrator::NvtIntegrator | ( | Simulation & | simulation | ) |
Constructor.
Definition at line 31 of file NvtIntegrator.cpp.
References DdMd::Simulation::energyEnsemble(), Simp::EnergyEnsemble::isIsothermal(), Util::ParamComposite::setClassName(), and UTIL_THROW.
DdMd::NvtIntegrator::~NvtIntegrator | ( | ) |
Destructor.
Definition at line 55 of file NvtIntegrator.cpp.
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virtual |
Read required parameters.
Reimplemented from DdMd::Integrator.
Definition at line 61 of file NvtIntegrator.cpp.
References Util::DArray< Data >::allocate(), Util::DArray< Data >::isAllocated(), DdMd::SimulationAccess::nAtomType(), DdMd::Simulation::nAtomType(), DdMd::Integrator::readParameters(), and DdMd::SimulationAccess::simulation().
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virtual |
Load internal state from an archive.
ar | input/loading archive |
Reimplemented from DdMd::Integrator.
Definition at line 77 of file NvtIntegrator.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().
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virtual |
Save internal state to an archive.
ar | output/saving archive |
Reimplemented from DdMd::Integrator.
Definition at line 96 of file NvtIntegrator.cpp.
References DdMd::Integrator::save().
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protectedvirtual |
Setup state just before integration.
Implements DdMd::Integrator.
Definition at line 115 of file NvtIntegrator.cpp.
References DdMd::SimulationAccess::atomStorage(), DdMd::Simulation::atomType(), Util::bcast(), Util::Array< Data >::capacity(), DdMd::Integrator::clear(), DdMd::Simulation::computeKineticEnergy(), DdMd::AtomStorage::computeNAtomTotal(), DdMd::SimulationAccess::domain(), DdMd::Simulation::energyEnsemble(), DdMd::Integrator::isSetup(), DdMd::Simulation::kineticEnergy(), DdMd::AtomType::mass(), DdMd::AtomStorage::nAtomTotal(), DdMd::SimulationAccess::nAtomType(), DdMd::Integrator::setIsSetup(), DdMd::Integrator::setupAtoms(), DdMd::SimulationAccess::simulation(), and Simp::EnergyEnsemble::temperature().
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protectedvirtual |
Execute first step of two-step integrator.
Implements DdMd::TwoStepIntegrator.
Definition at line 153 of file NvtIntegrator.cpp.
References DdMd::SimulationAccess::atomStorage(), DdMd::AtomStorage::begin(), DdMd::Simulation::energyEnsemble(), Util::Vector::multiply(), Util::PArrayIterator< Data >::notEnd(), DdMd::SimulationAccess::simulation(), and Simp::EnergyEnsemble::temperature().
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protectedvirtual |
Execute secodn step of two-step integrator.
Implements DdMd::TwoStepIntegrator.
Definition at line 178 of file NvtIntegrator.cpp.
References DdMd::SimulationAccess::atomStorage(), Util::bcast(), DdMd::AtomStorage::begin(), DdMd::Simulation::computeKineticEnergy(), DdMd::SimulationAccess::domain(), DdMd::Simulation::energyEnsemble(), DdMd::Simulation::kineticEnergy(), Util::Vector::multiply(), Util::PArrayIterator< Data >::notEnd(), Util::Signal< T >::notify(), DdMd::SimulationAccess::simulation(), Simp::EnergyEnsemble::temperature(), and DdMd::Simulation::velocitySignal().
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protectedvirtual |
Initialize internal dynamical state variables to default value.
Reimplemented from DdMd::Integrator.
Definition at line 108 of file NvtIntegrator.cpp.