Class containing a snapshot of the current simulation in time. More...

#include <Snapshot.h>

Public Member Functions
	Snapshot (const MPI_Comm &comm, unsigned int wid)
	Constructor. More...

size_t	GetIteration () const
	Get the current iteration. More...

size_t	GetTargetIterations () const
	Get target iterations. More...

double	GetTemperature () const
	Get current temperature. More...

double	GetEnergy () const
	Get per-particle energy. More...

const Matrix3 &	GetHMatrix () const
	Get system H-matrix. More...

const Matrix3 &	GetVirial () const
	Get box virial. More...

Matrix3 &	GetVirial ()
	Get box virial. More...

const Vector3 &	GetOrigin () const
	Get origin of the system. More...

const Bool3 &	IsPeriodic () const
	Get periodicity of three dimensions. More...

double	GetVolume () const
	Get system volume. More...

double	GetKb () const
	Get system Kb. More...

double	GetDielectric () const
	Get dielectric constant. More...

double	Getqqrd2e () const
	Get qqrd2e value. More...

const mxx::comm &	GetCommunicator () const
	Get communicator for walker. More...

unsigned	GetWalkerID () const
	Get walker ID. More...

unsigned	GetNumAtoms () const
	Get number of atoms in this snapshot. More...

void	SetIteration (size_t iteration)
	Set the iteration. More...

void	SetTargetIterations (int target)
	Set target iterations. More...

void	SetTemperature (double temperature)
	Change the temperature. More...

void	SetEnergy (double energy)
	Change the energy. More...

void	SetHMatrix (const Matrix3 &hmat)
	Change the Box H-matrix. More...

void	SetVirial (const Matrix3 &virial)
	Change the box virial. More...

void	SetOrigin (const Vector3 &origin)
	Change the box origin. More...

void	SetPeriodicity (const Bool3 &isperiodic)
	Change the periodicity of the system. More...

void	SetKb (double kb)
	Change the kb. More...

void	SetDielectric (double dielectric)
	Set the dielectric constant. More...

void	Setqqrd2e (double qqrd2e)
	Set the value for qqrd2e. More...

void	SetNumAtoms (unsigned int natoms)
	Set number of atoms in this snapshot. More...

const std::vector< Vector3 > &	GetPositions () const
	Access the particle positions. More...

std::vector< Vector3 > &	GetPositions ()
	Access the particle positions. More...

const std::vector< Vector3 > &	GetVelocities () const
	Access the particle velocities. More...

std::vector< Vector3 > &	GetVelocities ()
	Access the particle velocities. More...

const std::vector< Vector3 > &	GetForces () const
	Access the per-particle forces. More...

std::vector< Vector3 > &	GetForces ()
	Access the per-particle forces. More...

const std::vector< double > &	GetMasses () const
	Const access to the particle masses. More...

std::vector< double > &	GetMasses ()
	Const access to the particle masses. More...

Vector3	ScaleVector (const Vector3 &v) const
	Scale a vector into fractional coordinates. More...

void	ApplyMinimumImage (Vector3 *v) const
	Apply minimum image to a vector. More...

Vector3	ApplyMinimumImage (const Vector3 &v) const
	Apply minimum image to a vector. More...

double	TotalMass (const Label &indices) const
	Compute the total mass of a group of particles based on index. More...

Vector3	CenterOfMass (const Label &indices, bool mass_weight=true) const
	Compute center of mass of a group of atoms based on index. More...

const Label &	GetAtomIDs () const
	Access the atom IDs. More...

Label &	GetAtomIDs ()
	Access the atom IDs. More...

int	GetLocalIndex (int id) const
	Gets the local atom index corresponding to an atom ID. More...

void	GetLocalIndices (const Label &ids, Label *indices) const

const std::vector< double > &	GetCharges () const
	Access the atom charges. More...

std::vector< double > &	GetCharges ()
	Access the atom charges. More...

const Label &	GetAtomTypes () const
	Access the atom types. More...

Label &	GetAtomTypes ()
	Access the atom types. More...

const std::string &	GetSnapshotID () const
	Access the snapshot ID. More...

std::string &	GetSnapshotID ()
	Access the snapshot ID. More...

bool	HasChanged () const
	Query if Snapshot was modified. More...

void	Changed (bool state)
	Set the "changed" flag of the Snapshot. More...

std::vector< double >	SerializePositions ()
	Return the serialized positions across all local cores. More...

std::vector< double >	SerializeVelocities ()
	Return the serialized velocities across all local cores. More...

std::vector< int >	SerializeIDs ()
	Return the serialized IDs across all local cores. More...

	~Snapshot ()
	Destructor.

Private Attributes
mxx::comm	comm_
	Local snapshot (walker) communicator.

unsigned int	wid_
	Walker ID.

unsigned int	nlocal_
	Number of atoms located on this snapshot.

std::string	ID_
	ID string.

Matrix3	H_
	Parrinello-Rahman box H-matrix.

Matrix3	Hinv_
	Parinello-Rahman box inverse.

Matrix3	virial_
	Virial tensor.

Vector3	origin_
	Box origin.

Bool3	isperiodic_
	Periodicity of box.

std::vector< Vector3 >	positions_
	Positions.

std::vector< Vector3 >	velocities_
	Velocities.

std::vector< Vector3 >	forces_
	Forces.

std::vector< double >	masses_
	Masses.

std::vector< double >	charges_
	Charges.

Label	atomids_
	List of Atom IDs.

Label	types_
	List of Atom types.

size_t	iteration_
	Iteration of Simulation.

size_t	targetiter_
	Iteration target of simulation.

double	temperature_
	Current temperature.

double	energy_
	Average per-particle energy.

double	kb_
	Kb from the MD driver.

double	dielectric_
	Dielectric.

double	qqrd2e_
	qqrd2e

bool	changed_
	`TRUE` is Simulation state changed

Detailed Description

Class containing a snapshot of the current simulation in time.

This contains information on the particle positions, velocities, etc... and additional information on the state of the system.

Definition at line 47 of file Snapshot.h.

Constructor & Destructor Documentation

◆ Snapshot()

SSAGES::Snapshot::Snapshot	(	const MPI_Comm &	comm,
		unsigned int	wid
	)

inline

Constructor.

Parameters

comm	MPI communicator
wid	Walker ID

Initialize a snapshot with MPI communicator and a correpsonding walker ID.

Definition at line 94 of file Snapshot.h.

                                                          :
         comm_(comm), wid_(wid), H_(), Hinv_(), virial_(Matrix3::Zero()), 
         origin_({0,0,0}), isperiodic_({true, true, true}), positions_(0), 
         velocities_(0), forces_(0), masses_(0), atomids_(0), types_(0),
         iteration_(0), temperature_(0), energy_(0), kb_(0)
         {}

Member Function Documentation

◆ ApplyMinimumImage() [1/2]

Vector3 SSAGES::Snapshot::ApplyMinimumImage ( const Vector3 & v ) const

inline

Apply minimum image to a vector.

Parameters

v	Vector of interest

Returns: Return new vector.

Definition at line 405 of file Snapshot.h.

         {
             Vector3 scaled = Hinv_*v;
  
             for(int i = 0; i < 3; ++i)
                 scaled[i] -= isperiodic_[i]*roundf(scaled[i]);
  
             return H_*scaled;   
         }

References H_, Hinv_, isperiodic_, and SSAGES::roundf().

Here is the call graph for this function:

◆ ApplyMinimumImage() [2/2]

void SSAGES::Snapshot::ApplyMinimumImage ( Vector3 * v ) const

inline

Apply minimum image to a vector.

Parameters

v	Vector of interest

Definition at line 390 of file Snapshot.h.

         {
             Vector3 scaled = Hinv_*(*v);
  
             for(int i = 0; i < 3; ++i)
                 scaled[i] -= isperiodic_[i]*roundf(scaled[i]);
  
             *v = H_*scaled;
         }

References H_, Hinv_, isperiodic_, and SSAGES::roundf().

Referenced by CenterOfMass(), SSAGES::AngleCV::Evaluate(), SSAGES::GyrationTensorCV::Evaluate(), SSAGES::PairwiseCV::Evaluate(), SSAGES::ParticlePositionCV::Evaluate(), SSAGES::ParticleSeparationCV::Evaluate(), SSAGES::RMSDCV::Evaluate(), SSAGES::RouseModeCV::Evaluate(), and SSAGES::TorsionalCV::Evaluate().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ CenterOfMass()

Vector3 SSAGES::Snapshot::CenterOfMass	(	const Label &	indices,
		bool	mass_weight = `true`
	)		const

inline

Compute center of mass of a group of atoms based on index.

Parameters

indices	IDs of particles of interest.
mass_weight	Mass-weighting for COM calculation.

Returns: Vector3 Center of mass of particles.

Note: Each processor passes in the local indices of the atoms of interest and this function will collect the data and compute the center of mass.; Default behavior is to use a mass-weighted average.

Definition at line 442 of file Snapshot.h.

         {
             // Store coordinates and masses in vectors to gather.
             std::vector<double> pos, mass, gpos, gmass;
             std::vector<int> pcounts(comm_.size(), 0), mcounts(comm_.size(), 0); 
             std::vector<int> pdispls(comm_.size()+1, 0), mdispls(comm_.size()+1, 0);
  
             // Calculate total mass
             double mtot = mass_weight ? TotalMass(indices) : indices.size();
  
             pcounts[comm_.rank()] = 3*indices.size();
             mcounts[comm_.rank()] = indices.size();
  
             // Reduce counts.
             MPI_Allreduce(MPI_IN_PLACE, pcounts.data(), pcounts.size(), MPI_INT, MPI_SUM, comm_);
             MPI_Allreduce(MPI_IN_PLACE, mcounts.data(), mcounts.size(), MPI_INT, MPI_SUM, comm_);
  
             // Compute displacements.
             std::partial_sum(pcounts.begin(), pcounts.end(), pdispls.begin() + 1);
             std::partial_sum(mcounts.begin(), mcounts.end(), mdispls.begin() + 1);
             
             // Fill up mass and position vectors.
             for(auto& idx : indices)
             {
                 auto& p = positions_[idx];
                 pos.push_back(p[0]);
                 pos.push_back(p[1]);
                 pos.push_back(p[2]);
                 mass.push_back(masses_[idx]);
             }
  
             // Re-size receiving vectors. 
             gpos.resize(pdispls.back(), 0);
             gmass.resize(mdispls.back(), 1.0); // fictitious mass of 1
  
             // All-gather data.
             MPI_Allgatherv(pos.data(), pos.size(), MPI_DOUBLE, gpos.data(), pcounts.data(), pdispls.data(), MPI_DOUBLE, comm_);
             if(mass_weight) { // overwrite gmass with true mass values
                 MPI_Allgatherv(mass.data(), mass.size(), MPI_DOUBLE, gmass.data(), mcounts.data(), mdispls.data(), MPI_DOUBLE, comm_);
             }
  
             // Loop through atoms and compute mass weighted sum.
             // We march linearly through list and find nearest image
             // to each successive particle to properly unwrap object.
             Vector3 ppos = {gpos[0], gpos[1], gpos[2]}; // Previous unwrapped position.
             Vector3 cpos = ppos;
             Vector3 xcm = gmass[0]*cpos;
  
             for(size_t i = 1, j = 3; i < gmass.size(); ++i, j += 3)
             {
                 cpos = {gpos[j], gpos[j+1], gpos[j+2]};
                 cpos = ApplyMinimumImage(cpos - ppos) + ppos;
                 xcm += gmass[i]*cpos;
                 ppos = cpos;
             }
  
             return xcm/mtot;
         }

References ApplyMinimumImage(), comm_, masses_, positions_, and TotalMass().

Referenced by SSAGES::ANNCV::Evaluate(), SSAGES::GyrationTensorCV::Evaluate(), SSAGES::ParticleCoordinateCV::Evaluate(), SSAGES::ParticlePositionCV::Evaluate(), SSAGES::ParticleSeparationCV::Evaluate(), SSAGES::RMSDCV::Evaluate(), and SSAGES::RouseModeCV::Evaluate().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ Changed()

void SSAGES::Snapshot::Changed ( bool state )

inline

Set the "changed" flag of the Snapshot.

Parameters

state State to which the "changed" flag is set

Definition at line 596 of file Snapshot.h.

596 { changed_ = state; }

SSAGES::Snapshot::changed_

bool changed_

TRUE is Simulation state changed

Definition: Snapshot.h:83

References changed_.

Referenced by SSAGES::Hook::PostIntegrationHook(), SSAGES::Hook::PostSimulationHook(), and SSAGES::Hook::PreSimulationHook().

Here is the caller graph for this function:

◆ GetAtomIDs() [1/2]

Label& SSAGES::Snapshot::GetAtomIDs ( )

inline

Access the atom IDs.

Returns: List of atom IDs

Definition at line 508 of file Snapshot.h.

         {
             changed_ = true;
             return atomids_;
         }

References atomids_, and changed_.

◆ GetAtomIDs() [2/2]

const Label& SSAGES::Snapshot::GetAtomIDs ( ) const

inline

Access the atom IDs.

Returns: List of atom IDs

Definition at line 505 of file Snapshot.h.

505 { return atomids_; }

References atomids_.

Referenced by SSAGES::ForwardFlux::AppendTrajectoryFile(), SSAGES::PairwiseCV::Evaluate(), SSAGES::ForwardFlux::ReadFFSConfiguration(), and SSAGES::ForwardFlux::WriteFFSConfiguration().

Here is the caller graph for this function:

◆ GetAtomTypes() [1/2]

Label& SSAGES::Snapshot::GetAtomTypes ( )

inline

Access the atom types.

Returns: List of atom types

Definition at line 567 of file Snapshot.h.

         {
             changed_ = true; 
             return types_; 
         }

References changed_, and types_.

◆ GetAtomTypes() [2/2]

const Label& SSAGES::Snapshot::GetAtomTypes ( ) const

inline

Access the atom types.

Returns: List of atom types

Definition at line 564 of file Snapshot.h.

564 { return types_; }

References types_.

◆ GetCharges() [1/2]

std::vector<double>& SSAGES::Snapshot::GetCharges ( )

inline

Access the atom charges.

Returns: List of atom charges

Definition at line 554 of file Snapshot.h.

         {
             changed_ = true;
             return charges_;
         }

References changed_, and charges_.

◆ GetCharges() [2/2]

const std::vector<double>& SSAGES::Snapshot::GetCharges ( ) const

inline

Access the atom charges.

Returns: List of atom charges

Definition at line 551 of file Snapshot.h.

551 { return charges_; }

References charges_.

◆ GetCommunicator()

const mxx::comm& SSAGES::Snapshot::GetCommunicator ( ) const

inline

Get communicator for walker.

Returns: Communicator containing processors for simulation instance (walker).

Access the communicator containing the set of processors that belong to a single simulation box.

Definition at line 186 of file Snapshot.h.

         {
             return comm_;
         }

References comm_.

Here is the caller graph for this function:

◆ GetDielectric()

double SSAGES::Snapshot::GetDielectric ( ) const

inline

Get dielectric constant.

Returns: dielectric constant.

Definition at line 171 of file Snapshot.h.

171 { return dielectric_; }

SSAGES::Snapshot::dielectric_

double dielectric_

Dielectric.

Definition: Snapshot.h:81

References dielectric_.

◆ GetEnergy()

double SSAGES::Snapshot::GetEnergy ( ) const

inline

Get per-particle energy.

Returns: Current average per-particle energy

Definition at line 123 of file Snapshot.h.

123 { return energy_; }

References energy_.

◆ GetForces() [1/2]

std::vector<Vector3>& SSAGES::Snapshot::GetForces ( )

inline

Access the per-particle forces.

Returns: List of per-particle forces

Definition at line 354 of file Snapshot.h.

         {
             changed_ = true; 
             return forces_; 
         }

References changed_, and forces_.

◆ GetForces() [2/2]

const std::vector<Vector3>& SSAGES::Snapshot::GetForces ( ) const

inline

Access the per-particle forces.

Returns: List of per-particle forces

Definition at line 351 of file Snapshot.h.

351 { return forces_; }

References forces_.

Referenced by SSAGES::ABF::PostIntegration(), SSAGES::ANN::PostIntegration(), SSAGES::BFS::PostIntegration(), SSAGES::CFF::PostIntegration(), SSAGES::ElasticBand::PostIntegration(), SSAGES::FiniteTempString::PostIntegration(), SSAGES::Meta::PostIntegration(), SSAGES::Swarm::PostIntegration(), SSAGES::Umbrella::PostIntegration(), and SSAGES::ForwardFlux::ReadFFSConfiguration().

Here is the caller graph for this function:

◆ GetHMatrix()

const Matrix3& SSAGES::Snapshot::GetHMatrix ( ) const

inline

Get system H-matrix.

Returns: Parrinello-Rahman H-matrix of simulation box

Definition at line 129 of file Snapshot.h.

129 { return H_; }

References H_.

◆ GetIteration()

size_t SSAGES::Snapshot::GetIteration ( ) const

inline

Get the current iteration.

Returns: Current Iteration

Definition at line 105 of file Snapshot.h.

105 {return iteration_; }

References iteration_.

Referenced by SSAGES::Logger::PostIntegration(), SSAGES::ANN::PostIntegration(), SSAGES::BFS::PostIntegration(), SSAGES::CFF::PostIntegration(), SSAGES::Meta::PostIntegration(), SSAGES::Umbrella::PostIntegration(), and SSAGES::Hook::PostIntegrationHook().

Here is the caller graph for this function:

◆ GetKb()

double SSAGES::Snapshot::GetKb ( ) const

inline

Get system Kb.

Returns: Kb of the current simulation box

Definition at line 165 of file Snapshot.h.

165 { return kb_; }

References kb_.

Referenced by SSAGES::BFS::PostIntegration(), SSAGES::ANN::PreSimulation(), and SSAGES::CFF::PreSimulation().

Here is the caller graph for this function:

◆ GetLocalIndex()

int SSAGES::Snapshot::GetLocalIndex ( int id ) const

inline

Gets the local atom index corresponding to an atom ID.

Parameters

id Atom ID.

Returns: Local atom index or -1 if not found.

Definition at line 519 of file Snapshot.h.

         {
  
             auto s = std::find(atomids_.begin(), atomids_.end(), id);
             if(s == atomids_.end())
                 return -1;
             else
                 return s - atomids_.begin();
         }

References atomids_.

Referenced by SSAGES::AlphaRMSDCV::Evaluate(), SSAGES::AngleCV::Evaluate(), SSAGES::AntiBetaRMSDCV::Evaluate(), SSAGES::PairwiseCV::Evaluate(), SSAGES::ParallelBetaRMSDCV::Evaluate(), SSAGES::TorsionalCV::Evaluate(), GetLocalIndices(), SSAGES::GyrationTensorCV::Initialize(), SSAGES::PairwiseCV::Initialize(), SSAGES::ParticleCoordinateCV::Initialize(), SSAGES::ParticlePositionCV::Initialize(), SSAGES::ParticleSeparationCV::Initialize(), SSAGES::RMSDCV::Initialize(), SSAGES::RouseModeCV::Initialize(), SSAGES::FiniteTempString::PostIntegration(), and SSAGES::Swarm::PostIntegration().

Here is the caller graph for this function:

◆ GetLocalIndices()

void SSAGES::Snapshot::GetLocalIndices	(	const Label &	ids,
		Label *	indices
	)		const

inline

Gets the local atom indices corresponding to atom IDs in the vector.

Parameters

ids	Vector of atom ID's.
indices	Pointer to container for local atom indices.

Note: If atom does not exist on processor, it will be ignored.

Definition at line 537 of file Snapshot.h.

         {
             for(auto& id : ids)
             {
                 auto idx = GetLocalIndex(id);
                 if(idx != -1)
                     indices->push_back(idx);
             }
         }

References GetLocalIndex().

Referenced by SSAGES::ANNCV::Evaluate(), SSAGES::GyrationTensorCV::Evaluate(), SSAGES::PairwiseCV::Evaluate(), SSAGES::ParticleCoordinateCV::Evaluate(), SSAGES::ParticlePositionCV::Evaluate(), SSAGES::ParticleSeparationCV::Evaluate(), SSAGES::RMSDCV::Evaluate(), SSAGES::RouseModeCV::Evaluate(), SSAGES::AlphaRMSDCV::Initialize(), SSAGES::AngleCV::Initialize(), SSAGES::ANNCV::Initialize(), SSAGES::AntiBetaRMSDCV::Initialize(), SSAGES::ParallelBetaRMSDCV::Initialize(), SSAGES::RMSDCV::Initialize(), SSAGES::TorsionalCV::Initialize(), and SSAGES::RouseModeCV::setMasses().

Here is the call graph for this function:

Here is the caller graph for this function:

◆ GetMasses() [1/2]

std::vector<double>& SSAGES::Snapshot::GetMasses ( )

inline

Const access to the particle masses.

Returns: List of Masses

Note that the Masses can be either stored as per-atom or per-type depending on the Lammps Atom type used.

Definition at line 370 of file Snapshot.h.

         {
             changed_ = true; 
             return masses_; 
         }

References changed_, and masses_.

◆ GetMasses() [2/2]

const std::vector<double>& SSAGES::Snapshot::GetMasses ( ) const

inline

Const access to the particle masses.

Returns: List of Masses

Note that the Masses can be either stored as per-atom or per-type depending on the Lammps Atom type used.

Definition at line 367 of file Snapshot.h.

367 { return masses_; }

References masses_.

Referenced by SSAGES::GyrationTensorCV::Evaluate(), SSAGES::ParticleCoordinateCV::Evaluate(), SSAGES::ParticlePositionCV::Evaluate(), SSAGES::ParticleSeparationCV::Evaluate(), SSAGES::RMSDCV::Evaluate(), SSAGES::RouseModeCV::Evaluate(), SSAGES::RMSDCV::Initialize(), SSAGES::ABF::PostIntegration(), and SSAGES::CFF::PostIntegration().

Here is the caller graph for this function:

◆ GetNumAtoms()

unsigned SSAGES::Snapshot::GetNumAtoms ( ) const

inline

Get number of atoms in this snapshot.

Returns: Number of atoms in this snapshot

Definition at line 202 of file Snapshot.h.

202 { return nlocal_; }

SSAGES::Snapshot::nlocal_

unsigned int nlocal_

Number of atoms located on this snapshot.

Definition: Snapshot.h:54

References nlocal_.

Here is the caller graph for this function:

◆ GetOrigin()

const Vector3& SSAGES::Snapshot::GetOrigin ( ) const

inline

Get origin of the system.

Returns: Vector containing coordinates of box origin.

Definition at line 147 of file Snapshot.h.

147 { return origin_; }

References origin_.

◆ GetPositions() [1/2]

std::vector<Vector3>& SSAGES::Snapshot::GetPositions ( )

inline

Access the particle positions.

Returns: List of particle positions

Definition at line 328 of file Snapshot.h.

         { 
             changed_ = true;
             return positions_; 
         }

References changed_, and positions_.

◆ GetPositions() [2/2]

const std::vector<Vector3>& SSAGES::Snapshot::GetPositions ( ) const

inline

Access the particle positions.

Returns: List of particle positions

Definition at line 325 of file Snapshot.h.

325 { return positions_; }

References positions_.

Here is the caller graph for this function:

◆ Getqqrd2e()

double SSAGES::Snapshot::Getqqrd2e ( ) const

inline

Get qqrd2e value.

Returns: Value of qqrd2e.

Definition at line 177 of file Snapshot.h.

177 { return qqrd2e_; }

SSAGES::Snapshot::qqrd2e_

double qqrd2e_

qqrd2e

Definition: Snapshot.h:82

References qqrd2e_.

◆ GetSnapshotID() [1/2]

std::string& SSAGES::Snapshot::GetSnapshotID ( )

inline

Access the snapshot ID.

Returns: Snapshot ID

Definition at line 580 of file Snapshot.h.

         {
             changed_ = true; 
             return ID_; 
         }

References changed_, and ID_.

◆ GetSnapshotID() [2/2]

const std::string& SSAGES::Snapshot::GetSnapshotID ( ) const

inline

Access the snapshot ID.

Returns: Snapshot ID

Definition at line 577 of file Snapshot.h.

577 { return ID_; }

References ID_.

◆ GetTargetIterations()

size_t SSAGES::Snapshot::GetTargetIterations ( ) const

inline

Get target iterations.

Returns: Target Iterations

Definition at line 111 of file Snapshot.h.

111 {return targetiter_; }

SSAGES::Snapshot::targetiter_

size_t targetiter_

Iteration target of simulation.

Definition: Snapshot.h:76

References targetiter_.

Referenced by SSAGES::Meta::PreSimulation().

Here is the caller graph for this function:

◆ GetTemperature()

double SSAGES::Snapshot::GetTemperature ( ) const

inline

Get current temperature.

Returns: System temperature

Definition at line 117 of file Snapshot.h.

117 {return temperature_; }

References temperature_.

◆ GetVelocities() [1/2]

std::vector<Vector3>& SSAGES::Snapshot::GetVelocities ( )

inline

Access the particle velocities.

Returns: List of particle velocities

Definition at line 341 of file Snapshot.h.

         {
             changed_ = true;
             return velocities_; 
         }

References changed_, and velocities_.

◆ GetVelocities() [2/2]

const std::vector<Vector3>& SSAGES::Snapshot::GetVelocities ( ) const

inline

Access the particle velocities.

Returns: List of particle velocities

Definition at line 338 of file Snapshot.h.

338 { return velocities_; }

References velocities_.

Referenced by SSAGES::ForwardFlux::AppendTrajectoryFile(), SSAGES::ABF::PostIntegration(), SSAGES::CFF::PostIntegration(), SSAGES::Swarm::PostIntegration(), SSAGES::ForwardFlux::ReadFFSConfiguration(), and SSAGES::ForwardFlux::WriteFFSConfiguration().

Here is the caller graph for this function:

◆ GetVirial() [1/2]

Matrix3& SSAGES::Snapshot::GetVirial ( )

inline

Get box virial.

Returns: Virial tensor of the simulation box.

Definition at line 141 of file Snapshot.h.

141 { return virial_; }

References virial_.

◆ GetVirial() [2/2]

const Matrix3& SSAGES::Snapshot::GetVirial ( ) const

inline

Get box virial.

Returns: Virial tensor of the simulation box.

Definition at line 135 of file Snapshot.h.

135 { return virial_; }

References virial_.

Referenced by SSAGES::ANN::PostIntegration(), SSAGES::BFS::PostIntegration(), SSAGES::CFF::PostIntegration(), SSAGES::Meta::PostIntegration(), and SSAGES::Umbrella::PostIntegration().

Here is the caller graph for this function:

◆ GetVolume()

double SSAGES::Snapshot::GetVolume ( ) const

inline

Get system volume.

Returns: Volume of the current simulation box

Definition at line 159 of file Snapshot.h.

159 { return H_.determinant(); }

References H_.

Referenced by SSAGES::BoxVolumeCV::Evaluate().

Here is the caller graph for this function:

◆ GetWalkerID()

unsigned SSAGES::Snapshot::GetWalkerID ( ) const

inline

Get walker ID.

Returns: ID of the Walker

Definition at line 195 of file Snapshot.h.

195 { return wid_; }

References wid_.

Referenced by SSAGES::BFS::PreSimulation(), and SSAGES::StringMethod::PreSimulation().

Here is the caller graph for this function:

◆ HasChanged()

bool SSAGES::Snapshot::HasChanged ( ) const

inline

Query if Snapshot was modified.

Returns: True if Snapshot was modified, else return False

Definition at line 590 of file Snapshot.h.

590 { return changed_; }

References changed_.

Referenced by SSAGES::Hook::PostIntegrationHook(), SSAGES::Hook::PostSimulationHook(), and SSAGES::Hook::PreSimulationHook().

Here is the caller graph for this function:

◆ IsPeriodic()

const Bool3& SSAGES::Snapshot::IsPeriodic ( ) const

inline

Get periodicity of three dimensions.

Returns: Three dimensional boolean containing periodicity of each dimension.

Definition at line 153 of file Snapshot.h.

153 {return isperiodic_; }

References isperiodic_.

◆ ScaleVector()

Vector3 SSAGES::Snapshot::ScaleVector ( const Vector3 & v ) const

inline

Scale a vector into fractional coordinates.

Parameters

v	Vector of interest

Returns: Scaled vector in fractional coordinates

Definition at line 381 of file Snapshot.h.

         {
             return Hinv_*(v-origin_);
         }

References Hinv_, and origin_.

◆ SerializeIDs()

std::vector<int> SSAGES::Snapshot::SerializeIDs ( )

inline

Return the serialized IDs across all local cores.

Returns: IDs across all local cores.

Definition at line 673 of file Snapshot.h.

         {
             std::vector<int> mcounts(comm_.size(), 0); 
             std::vector<int> mdispls(comm_.size()+1, 0);
  
             mcounts[comm_.rank()] = nlocal_;
  
             // Reduce counts.
             MPI_Allreduce(MPI_IN_PLACE, mcounts.data(), mcounts.size(), MPI_INT, MPI_SUM, comm_);
  
             // Compute displacements.
             std::partial_sum(mcounts.begin(), mcounts.end(), mdispls.begin() + 1);
  
             // Re-size receiving vectors.
             std::vector<int> IDs;
             IDs.resize(mdispls.back(), 0);
  
             // All-gather data.
             MPI_Allgatherv(atomids_.data(), atomids_.size(), MPI_INT, IDs.data(), mcounts.data(), mdispls.data(), MPI_INT, comm_);
             return IDs;
         }

References atomids_, comm_, and nlocal_.

Referenced by SSAGES::FiniteTempString::PostIntegration(), and SSAGES::Swarm::PostIntegration().

Here is the caller graph for this function:

◆ SerializePositions()

std::vector<double> SSAGES::Snapshot::SerializePositions ( )

inline

Return the serialized positions across all local cores.

Returns: Positions across all local cores.

Definition at line 602 of file Snapshot.h.

         {
  
             std::vector<int> pcounts(comm_.size(), 0); 
             std::vector<int> pdispls(comm_.size()+1, 0);
  
             pcounts[comm_.rank()] = 3*nlocal_;
  
             // Reduce counts.
             MPI_Allreduce(MPI_IN_PLACE, pcounts.data(), pcounts.size(), MPI_INT, MPI_SUM, comm_);
  
             // Compute displacements.
             std::partial_sum(pcounts.begin(), pcounts.end(), pdispls.begin() + 1);
  
             // Re-size receiving vectors.
             std::vector<double> positions;
             positions.resize(pdispls.back(), 0);
  
             std::vector<double> ptemp;
             
             for(auto& p : positions_)
             {
                 ptemp.push_back(p[0]);
                 ptemp.push_back(p[1]);
                 ptemp.push_back(p[2]);
             }
  
             // All-gather data.
             MPI_Allgatherv(ptemp.data(), ptemp.size(), MPI_DOUBLE, positions.data(), pcounts.data(), pdispls.data(), MPI_DOUBLE, comm_);
             return positions;
         }

References comm_, nlocal_, and positions_.

Referenced by SSAGES::FiniteTempString::PostIntegration(), and SSAGES::Swarm::PostIntegration().

Here is the caller graph for this function:

◆ SerializeVelocities()

std::vector<double> SSAGES::Snapshot::SerializeVelocities ( )

inline

Return the serialized velocities across all local cores.

Returns: Velocities across all local cores.

Definition at line 638 of file Snapshot.h.

         {
             std::vector<int> vcounts(comm_.size(), 0); 
             std::vector<int> vdispls(comm_.size()+1, 0);
  
             vcounts[comm_.rank()] = 3*nlocal_;
  
             // Reduce counts.
             MPI_Allreduce(MPI_IN_PLACE, vcounts.data(), vcounts.size(), MPI_INT, MPI_SUM, comm_);
  
             // Compute displacements.
             std::partial_sum(vcounts.begin(), vcounts.end(), vdispls.begin() + 1);
  
             // Re-size receiving vectors.
             std::vector<double> velocities;
             velocities.resize(vdispls.back(), 0);
  
             std::vector<double> vtemp;
             
             for(auto& v : velocities_)
             {
                 vtemp.push_back(v[0]);
                 vtemp.push_back(v[1]);
                 vtemp.push_back(v[2]);
             }
  
             // All-gather data.
             MPI_Allgatherv(vtemp.data(), vtemp.size(), MPI_DOUBLE, velocities.data(), vcounts.data(), vdispls.data(), MPI_DOUBLE, comm_);
             return velocities;
         }

References comm_, nlocal_, and velocities_.

Referenced by SSAGES::Swarm::PostIntegration().

Here is the caller graph for this function:

◆ SetDielectric()

void SSAGES::Snapshot::SetDielectric ( double dielectric )

inline

Set the dielectric constant.

Parameters

dielectric Value for the dielectric constant.

Definition at line 299 of file Snapshot.h.

         { 
             dielectric_ = dielectric;
             changed_ = true;
         }

References changed_, and dielectric_.

◆ SetEnergy()

void SSAGES::Snapshot::SetEnergy ( double energy )

inline

Change the energy.

Parameters

energy New value for the energy

Definition at line 238 of file Snapshot.h.

         {
             energy_ = energy;
             changed_ = true;
         }

References changed_, and energy_.

◆ SetHMatrix()

void SSAGES::Snapshot::SetHMatrix ( const Matrix3 & hmat )

inline

Change the Box H-matrix.

Parameters

hmat	New H-matrix for the system

Definition at line 248 of file Snapshot.h.

         {
             H_ = hmat;
             Hinv_ = hmat.inverse();
             changed_ = true;
         }

References changed_, H_, and Hinv_.

◆ SetIteration()

void SSAGES::Snapshot::SetIteration ( size_t iteration )

inline

Set the iteration.

Parameters

iteration New value for the iteration

Definition at line 208 of file Snapshot.h.

         {
             iteration_ = iteration; 
             changed_ = true; 
         }

References changed_, and iteration_.

◆ SetKb()

void SSAGES::Snapshot::SetKb ( double kb )

inline

Change the kb.

Parameters

kb	New value for the kb

Definition at line 289 of file Snapshot.h.

         {
             kb_ = kb;
             changed_ = true;
         }

References changed_, and kb_.

◆ SetNumAtoms()

void SSAGES::Snapshot::SetNumAtoms ( unsigned int natoms )

inline

Set number of atoms in this snapshot.

Parameters

natoms Number of atoms in this snapshot

Definition at line 319 of file Snapshot.h.

319 { nlocal_ = natoms; }

References nlocal_.

◆ SetOrigin()

void SSAGES::Snapshot::SetOrigin ( const Vector3 & origin )

inline

Change the box origin.

Parameters

origin New origin for the system

Definition at line 269 of file Snapshot.h.

         {
             origin_ = origin; 
             changed_ = true;
         }

References changed_, and origin_.

◆ SetPeriodicity()

void SSAGES::Snapshot::SetPeriodicity ( const Bool3 & isperiodic )

inline

Change the periodicity of the system.

Parameters

isperiodic Periodicity of three dimensions

Definition at line 279 of file Snapshot.h.

         {
             isperiodic_ = isperiodic;
             changed_ = true;
         }

References changed_, and isperiodic_.

◆ Setqqrd2e()

void SSAGES::Snapshot::Setqqrd2e ( double qqrd2e )

inline

Set the value for qqrd2e.

Parameters

qqrd2e Value for qqrd2e.

Definition at line 309 of file Snapshot.h.

         { 
             qqrd2e_ = qqrd2e;
             changed_ = true;
         }

References changed_, and qqrd2e_.

◆ SetTargetIterations()

void SSAGES::Snapshot::SetTargetIterations ( int target )

inline

Set target iterations.

Parameters

target New value for target iterations

Definition at line 218 of file Snapshot.h.

         {
             targetiter_ = target; 
             changed_ = true; 
         }

References changed_, and targetiter_.

◆ SetTemperature()

void SSAGES::Snapshot::SetTemperature ( double temperature )

inline

Change the temperature.

Parameters

temperature New value for the temperature

Definition at line 228 of file Snapshot.h.

         { 
             temperature_ = temperature;
             changed_ = true;
         }

References changed_, and temperature_.

◆ SetVirial()

void SSAGES::Snapshot::SetVirial ( const Matrix3 & virial )

inline

Change the box virial.

Parameters

virial New virial tensor for the system.

Definition at line 259 of file Snapshot.h.

         {
             virial_ = virial; 
             changed_ = true;
         }

References changed_, and virial_.

◆ TotalMass()

double SSAGES::Snapshot::TotalMass ( const Label & indices ) const

inline

Compute the total mass of a group of particles based on index.

Parameters

indices IDs of particles of interest.

Returns: double Total mass of particles.

Note: This function reduces the mass across the communicator associated with the snapshot.

Definition at line 423 of file Snapshot.h.

         {
             auto mtot = 0.;
             for(auto& i : indices)
                 mtot += masses_[i];
             MPI_Allreduce(MPI_IN_PLACE, &mtot, 1, MPI_DOUBLE, MPI_SUM, comm_);
             return mtot;
         }

References comm_, and masses_.

Referenced by CenterOfMass(), SSAGES::GyrationTensorCV::Evaluate(), SSAGES::ParticleCoordinateCV::Evaluate(), SSAGES::ParticlePositionCV::Evaluate(), SSAGES::ParticleSeparationCV::Evaluate(), SSAGES::RMSDCV::Evaluate(), and SSAGES::RouseModeCV::setMasses().

Here is the caller graph for this function:

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

/home/michael/development/SSAGES/src/Snapshot.h

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Snapshot()

Member Function Documentation

◆ ApplyMinimumImage() [1/2]

◆ ApplyMinimumImage() [2/2]

◆ CenterOfMass()

◆ Changed()

◆ GetAtomIDs() [1/2]

◆ GetAtomIDs() [2/2]

◆ GetAtomTypes() [1/2]

◆ GetAtomTypes() [2/2]

◆ GetCharges() [1/2]

◆ GetCharges() [2/2]

◆ GetCommunicator()

◆ GetDielectric()

◆ GetEnergy()

◆ GetForces() [1/2]

◆ GetForces() [2/2]

◆ GetHMatrix()

◆ GetIteration()

◆ GetKb()

◆ GetLocalIndex()

◆ GetLocalIndices()

◆ GetMasses() [1/2]

◆ GetMasses() [2/2]

◆ GetNumAtoms()

◆ GetOrigin()

◆ GetPositions() [1/2]

◆ GetPositions() [2/2]

◆ Getqqrd2e()

◆ GetSnapshotID() [1/2]

◆ GetSnapshotID() [2/2]

◆ GetTargetIterations()

◆ GetTemperature()

◆ GetVelocities() [1/2]

◆ GetVelocities() [2/2]

◆ GetVirial() [1/2]

◆ GetVirial() [2/2]

◆ GetVolume()

◆ GetWalkerID()

◆ HasChanged()

◆ IsPeriodic()

◆ ScaleVector()

◆ SerializeIDs()

◆ SerializePositions()

◆ SerializeVelocities()

◆ SetDielectric()

◆ SetEnergy()

◆ SetHMatrix()

◆ SetIteration()

◆ SetKb()

◆ SetNumAtoms()

◆ SetOrigin()

◆ SetPeriodicity()

◆ Setqqrd2e()

◆ SetTargetIterations()

◆ SetTemperature()

◆ SetVirial()

◆ TotalMass()