SSAGES::Snapshot Class Reference

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

#include <Snapshot.h>

Public Member Functions
	Snapshot (const MPI_Comm &comm, uint wid)
	Constructor. More...
int	GetIteration () const
	Get the current iteration. More...
int	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 (int 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< Integer3 > &	GetImageFlags () const
	Access the particles image flags. More...
std::vector< Integer3 > &	GetImageFlags ()
	Access the particles image flags. 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...
Vector3	UnwrapVector (const Vector3 &v, const Integer3 &image) const
	Unwrap a vector's real coordinates according to its image replica count. 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) const
Vector3	CenterOfMass (const Label &indices, double mtot) const
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::vector< std::vector < double > > &	GetSigmas () const
	Access the atom sigmas. More...
std::vector< std::vector < double > > &	GetSigmas ()
	Access the atom sigmas. 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.
std::vector< double >	SerializeVelocities ()
	Return the serialized velocities across all local cores.
std::vector< int >	SerializeIDs ()
	Return the serialized positions across all local cores.
	~Snapshot ()
	Destructor.

Private Attributes
mxx::comm	comm_
	Local snapshot (walker) communicator.
uint	wid_
	Walker ID.
uint	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_
Vector3	origin_
	< Virial tensor. More...
Bool3	isperiodic_
	Periodicity of box.
std::vector< Vector3 >	positions_
	Positions.
std::vector< Integer3 >	images_
	Unwrapped 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.
std::vector< std::vector < double > >	sigma_
	Sigma.
int	iteration_
	Iteration of Simulation.
int	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 43 of file Snapshot.h.

Constructor & Destructor Documentation

SSAGES::Snapshot::Snapshot ( const MPI_Comm &  comm, uint  wid  )

inline

Constructor.

Parameters

comm	MPI communicator
wid	Walker ID

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

Definition at line 92 of file Snapshot.h.

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

Member Function Documentation

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

inline

Apply minimum image to a vector.

Parameters

v	Vector of interest

Definition at line 418 of file Snapshot.h.

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

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

        {
            Vector3 scaled = Hinv_*(*v);

            for(int i = 0; i < 3; ++i)
                scaled[i] -= isperiodic_[i]*roundf(scaled[i]);

            *v = H_*scaled;
        }

Here is the call graph for this function:

Here is the caller graph for this function:

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 433 of file Snapshot.h.

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

        {
            Vector3 scaled = Hinv_*v;

            for(int i = 0; i < 3; ++i)
                scaled[i] -= isperiodic_[i]*roundf(scaled[i]);

            return H_*scaled;   
        }

Here is the call graph for this function:

Vector3 SSAGES::Snapshot::CenterOfMass ( const Label &  indices ) const

inline

Compute center of mass of a group of atoms based on idex with provided Total mass.

Parameters

indices

IDs of particles of interest.

Returns

Vector3 Center of mass of particles.

Definition at line 466 of file Snapshot.h.

References TotalMass().

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

        {
            // Get total mass.
            auto mtot = TotalMass(indices);

            return CenterOfMass(indices, mtot);         
        }

Here is the call graph for this function:

Here is the caller graph for this function:

Vector3 SSAGES::Snapshot::CenterOfMass ( const Label &  indices, double  mtot  ) const

inline

Compute center of mass of a group of atoms based on idex with provided Total mass.

Parameters

indices	IDs of particles of interest.
mtot	Total mass of particle group.

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.

Definition at line 483 of file Snapshot.h.

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

        {
            // Store coorinates 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);

            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(), 0);

            // All-gather data.
            MPI_Allgatherv(pos.data(), pos.size(), MPI_DOUBLE, gpos.data(), pcounts.data(), pdispls.data(), MPI_DOUBLE, comm_);
            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;
        }

Here is the call graph for this function:

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 645 of file Snapshot.h.

References changed_.

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

{ changed_ = state; }

Here is the caller graph for this function:

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

inline

Access the atom IDs.

Returns

List of atom IDs

Definition at line 541 of file Snapshot.h.

References atomids_.

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

{ return atomids_; }

Here is the caller graph for this function:

Label& SSAGES::Snapshot::GetAtomIDs ( )

inline

Access the atom IDs.

Returns

List of atom IDs

Definition at line 544 of file Snapshot.h.

References atomids_, and changed_.

        {
            changed_ = true;
            return atomids_;
        }

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

inline

Access the atom types.

Returns

List of atom types

Definition at line 600 of file Snapshot.h.

References types_.

Referenced by SSAGES::COPSSImage::force_pol(), and SSAGES::COPSSImage::PostIntegration().

{ return types_; }

Here is the caller graph for this function:

Label& SSAGES::Snapshot::GetAtomTypes ( )

inline

Access the atom types.

Returns

List of atom types

Definition at line 603 of file Snapshot.h.

References changed_, and types_.

        {
            changed_ = true; 
            return types_; 
        }

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

inline

Access the atom charges.

Returns

List of atom charges

Definition at line 587 of file Snapshot.h.

References charges_.

Referenced by SSAGES::COPSSImage::force_pol(), and SSAGES::COPSSImage::PostIntegration().

{ return charges_; }

Here is the caller graph for this function:

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

inline

Access the atom charges.

Returns

List of atom charges

Definition at line 590 of file Snapshot.h.

References changed_, and charges_.

        {
            changed_ = true;
            return charges_;
        }

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 184 of file Snapshot.h.

References comm_.

Referenced by SSAGES::BoxVolumeCV::Evaluate(), SSAGES::AngleCV::Evaluate(), SSAGES::TorsionalCV::Evaluate(), SSAGES::GyrationTensorCV::Evaluate(), SSAGES::PairwiseCV::Evaluate(), SSAGES::AngleCV::Initialize(), SSAGES::PairwiseCV::Initialize(), SSAGES::ParticleCoordinateCV::Initialize(), SSAGES::TorsionalCV::Initialize(), SSAGES::GyrationTensorCV::Initialize(), SSAGES::ParticlePositionCV::Initialize(), SSAGES::RouseModeCV::Initialize(), SSAGES::ParticleSeparationCV::Initialize(), and SSAGES::COPSS::PostIntegration().

        {
            return comm_;
        }

Here is the caller graph for this function:

double SSAGES::Snapshot::GetDielectric ( ) const

inline

Get dielectric constant.

Returns

dielectric constant.

Definition at line 169 of file Snapshot.h.

References dielectric_.

Referenced by SSAGES::COPSSImage::force_pol().

{ return dielectric_; }

Here is the caller graph for this function:

double SSAGES::Snapshot::GetEnergy ( ) const

inline

Get per-particle energy.

Returns

Current average per-particle energy

Definition at line 121 of file Snapshot.h.

References energy_.

{ return energy_; }

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

inline

Access the per-particle forces.

Returns

List of per-particle forces

Definition at line 362 of file Snapshot.h.

References forces_.

Referenced by SSAGES::COPSSImage::force_pol(), SSAGES::COPSS::PostIntegration(), SSAGES::ElasticBand::PostIntegration(), SSAGES::FiniteTempString::PostIntegration(), SSAGES::Swarm::PostIntegration(), SSAGES::Umbrella::PostIntegration(), SSAGES::Meta::PostIntegration(), SSAGES::COPSSImage::PostIntegration(), SSAGES::ABF::PostIntegration(), SSAGES::Basis::PostIntegration(), and SSAGES::ForwardFlux::ReadFFSConfiguration().

{ return forces_; }

Here is the caller graph for this function:

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

inline

Access the per-particle forces.

Returns

List of per-particle forces

Definition at line 365 of file Snapshot.h.

References changed_, and forces_.

        {
            changed_ = true; 
            return forces_; 
        }

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

inline

Get system H-matrix.

Returns

Parrinello-Rahman H-matrix of simulation box

Definition at line 127 of file Snapshot.h.

References H_.

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

{ return H_; }

Here is the caller graph for this function:

const std::vector<Integer3>& SSAGES::Snapshot::GetImageFlags ( ) const

inline

Access the particles image flags.

Returns

List of particle image flags

Definition at line 336 of file Snapshot.h.

References images_.

{ return images_; }

std::vector<Integer3>& SSAGES::Snapshot::GetImageFlags ( )

inline

Access the particles image flags.

Returns

List of particle image flags

Definition at line 339 of file Snapshot.h.

References changed_, and images_.

        { 
            changed_ = true;
            return images_; 
        }

int SSAGES::Snapshot::GetIteration ( ) const

inline

Get the current iteration.

Returns

Current Iteration

Definition at line 103 of file Snapshot.h.

References iteration_.

Referenced by SSAGES::Logger::PostIntegration(), SSAGES::Umbrella::PostIntegration(), SSAGES::Meta::PostIntegration(), SSAGES::Basis::PostIntegration(), and SSAGES::Hook::PostIntegrationHook().

{return iteration_; }

Here is the caller graph for this function:

double SSAGES::Snapshot::GetKb ( ) const

inline

Get system Kb.

Returns

Kb of the current simulation box

Definition at line 163 of file Snapshot.h.

References kb_.

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

{ return kb_; }

Here is the caller graph for this function:

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 555 of file Snapshot.h.

References atomids_.

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

        {

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

Here is the caller graph for this function:

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 573 of file Snapshot.h.

References GetLocalIndex().

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

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

Here is the call graph for this function:

Here is the caller graph for this function:

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 378 of file Snapshot.h.

References masses_.

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

{ return masses_; }

Here is the caller graph for this function:

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 381 of file Snapshot.h.

References changed_, and masses_.

        {
            changed_ = true; 
            return masses_; 
        }

unsigned SSAGES::Snapshot::GetNumAtoms ( ) const

inline

Get number of atoms in this snapshot.

Returns

Number of atoms in this snapshot

Definition at line 200 of file Snapshot.h.

References nlocal_.

Referenced by SSAGES::ABF::CalcBiasForce(), SSAGES::BoxVolumeCV::Evaluate(), SSAGES::AngleCV::Evaluate(), SSAGES::TorsionalCV::Evaluate(), SSAGES::ParticleCoordinateCV::Evaluate(), SSAGES::GyrationTensorCV::Evaluate(), SSAGES::ParticlePositionCV::Evaluate(), SSAGES::PairwiseCV::Evaluate(), SSAGES::RouseModeCV::Evaluate(), SSAGES::ParticleSeparationCV::Evaluate(), SSAGES::AlphaRMSDCV::Evaluate(), SSAGES::AntiBetaRMSDCV::Evaluate(), SSAGES::ParallelBetaRMSDCV::Evaluate(), SSAGES::COPSSImage::PostIntegration(), and SSAGES::ABF::PostIntegration().

{ return nlocal_; }

Here is the caller graph for this function:

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

inline

Get origin of the system.

Returns

Vector containing coordinates of box origin.

Definition at line 145 of file Snapshot.h.

References origin_.

{ return origin_; }

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

inline

Access the particle positions.

Returns

List of particle positions

Definition at line 323 of file Snapshot.h.

References positions_.

Referenced by SSAGES::ForwardFlux::AppendTrajectoryFile(), SSAGES::AngleCV::Evaluate(), SSAGES::TorsionalCV::Evaluate(), SSAGES::GyrationTensorCV::Evaluate(), SSAGES::PairwiseCV::Evaluate(), SSAGES::AlphaRMSDCV::Evaluate(), SSAGES::AntiBetaRMSDCV::Evaluate(), SSAGES::ParallelBetaRMSDCV::Evaluate(), SSAGES::COPSSImage::force_pol(), SSAGES::MockCV::Initialize(), SSAGES::FiniteTempString::PostIntegration(), SSAGES::Swarm::PostIntegration(), SSAGES::COPSSImage::PostIntegration(), SSAGES::ABF::PreSimulation(), SSAGES::ForwardFlux::ReadFFSConfiguration(), and SSAGES::ForwardFlux::WriteFFSConfiguration().

{ return positions_; }

Here is the caller graph for this function:

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

inline

Access the particle positions.

Returns

List of particle positions

Definition at line 326 of file Snapshot.h.

References changed_, and positions_.

        { 
            changed_ = true;
            return positions_; 
        }

double SSAGES::Snapshot::Getqqrd2e ( ) const

inline

Get qqrd2e value.

Returns

Value of qqrd2e.

Definition at line 175 of file Snapshot.h.

References qqrd2e_.

Referenced by SSAGES::COPSSImage::force_pol().

{ return qqrd2e_; }

Here is the caller graph for this function:

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

inline

Access the atom sigmas.

Returns

List of atom sigmas

Definition at line 613 of file Snapshot.h.

References sigma_.

{ return sigma_; }

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

inline

Access the atom sigmas.

Returns

List of atom sigmas

Definition at line 616 of file Snapshot.h.

References changed_, and sigma_.

        {
            changed_ = true; 
            return sigma_;
        }

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

inline

Access the snapshot ID.

Returns

Snapshot ID

Definition at line 626 of file Snapshot.h.

References ID_.

{ return ID_; }

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

inline

Access the snapshot ID.

Returns

Snapshot ID

Definition at line 629 of file Snapshot.h.

References changed_, and ID_.

        {
            changed_ = true; 
            return ID_; 
        }

int SSAGES::Snapshot::GetTargetIterations ( ) const

inline

Get target iterations.

Returns

Target Iterations

Definition at line 109 of file Snapshot.h.

References targetiter_.

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

{return targetiter_; }

Here is the caller graph for this function:

double SSAGES::Snapshot::GetTemperature ( ) const

inline

Get current temperature.

Returns

System temperature

Definition at line 115 of file Snapshot.h.

References temperature_.

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

{return temperature_; }

Here is the caller graph for this function:

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

inline

Access the particle velocities.

Returns

List of particle velocities

Definition at line 349 of file Snapshot.h.

References velocities_.

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

{ return velocities_; }

Here is the caller graph for this function:

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

inline

Access the particle velocities.

Returns

List of particle velocities

Definition at line 352 of file Snapshot.h.

References changed_, and velocities_.

        {
            changed_ = true;
            return velocities_; 
        }

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

inline

Get box virial.

Virial tensor of the simulation box.

Definition at line 133 of file Snapshot.h.

Referenced by SSAGES::Umbrella::PostIntegration(), SSAGES::Meta::PostIntegration(), and SSAGES::Basis::PostIntegration().

{ return virial_; }

Here is the caller graph for this function:

Matrix3& SSAGES::Snapshot::GetVirial ( )

inline

Get box virial.

Virial tensor of the simulation box.

Definition at line 139 of file Snapshot.h.

{ return virial_; }

double SSAGES::Snapshot::GetVolume ( ) const

inline

Get system volume.

Returns

Volume of the current simulation box

Definition at line 157 of file Snapshot.h.

References H_.

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

{ return H_.determinant(); }

Here is the caller graph for this function:

unsigned SSAGES::Snapshot::GetWalkerID ( ) const

inline

Get walker ID.

Returns

ID of the Walker

Definition at line 193 of file Snapshot.h.

References wid_.

Referenced by SSAGES::COPSS::PostIntegration(), SSAGES::StringMethod::PreSimulation(), and SSAGES::Basis::PreSimulation().

{ return wid_; }

Here is the caller graph for this function:

bool SSAGES::Snapshot::HasChanged ( ) const

inline

Query if Snapshot was modified.

Returns

True if Snapshot was modified, else return False

Definition at line 639 of file Snapshot.h.

References changed_.

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

{ return changed_; }

Here is the caller graph for this function:

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

inline

Get periodicity of three dimensions.

Returns

Three dimensional boolean containing periodicity of each dimension.

Definition at line 151 of file Snapshot.h.

References isperiodic_.

{return isperiodic_; }

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 392 of file Snapshot.h.

References Hinv_, and origin_.

        {
            return Hinv_*(v-origin_);
        }

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

inline

Set the dielectric constant.

Parameters

dielectric

Value for the dielectric constant.

Definition at line 297 of file Snapshot.h.

References changed_, and dielectric_.

        { 
            dielectric_ = dielectric;
            changed_ = true;
        }

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

inline

Change the energy.

Parameters

energy

New value for the energy

Definition at line 236 of file Snapshot.h.

References changed_, and energy_.

        {
            energy_ = energy;
            changed_ = true;
        }

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

inline

Change the Box H-matrix.

Parameters

hmat	New H-matrix for the system

Definition at line 246 of file Snapshot.h.

References changed_, H_, and Hinv_.

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

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

inline

Set the iteration.

Parameters

iteration

New value for the iteration

Definition at line 206 of file Snapshot.h.

References changed_, and iteration_.

        {
            iteration_ = iteration; 
            changed_ = true; 
        }

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

inline

Change the kb.

Parameters

kb	New value for the kb

Definition at line 287 of file Snapshot.h.

References changed_, and kb_.

        {
            kb_ = kb;
            changed_ = true;
        }

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 317 of file Snapshot.h.

References nlocal_.

{ nlocal_ = natoms; }

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

inline

Change the box origin.

Parameters

origin

New origin for the system

Definition at line 267 of file Snapshot.h.

References changed_, and origin_.

        {
            origin_ = origin; 
            changed_ = true;
        }

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

inline

Change the periodicity of the system.

Parameters

isperiodic

Periodicity of three dimensions

Definition at line 277 of file Snapshot.h.

References changed_, and isperiodic_.

        {
            isperiodic_ = isperiodic;
            changed_ = true;
        }

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

inline

Set the value for qqrd2e.

Parameters

qqrd2e

Value for qqrd2e.

Definition at line 307 of file Snapshot.h.

References changed_, and qqrd2e_.

        { 
            qqrd2e_ = qqrd2e;
            changed_ = true;
        }

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

inline

Set target iterations.

Parameters

target

New value for target iterations

Definition at line 216 of file Snapshot.h.

References changed_, and targetiter_.

        {
            targetiter_ = target; 
            changed_ = true; 
        }

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

inline

Change the temperature.

Parameters

temperature

New value for the temperature

Definition at line 226 of file Snapshot.h.

References changed_, and temperature_.

        { 
            temperature_ = temperature;
            changed_ = true;
        }

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

inline

Change the box virial.

Parameters

virial

New virial tensor for the system.

Definition at line 257 of file Snapshot.h.

References changed_.

        {
            virial_ = virial; 
            changed_ = true;
        }

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 451 of file Snapshot.h.

References comm_, and masses_.

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

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

Here is the caller graph for this function:

Vector3 SSAGES::Snapshot::UnwrapVector ( const Vector3 &  v, const Integer3 &  image  ) const

inline

Unwrap a vector's real coordinates according to its image replica count.

Parameters

v	Vector of interest
image	Integer vector representing mirror images in the three dimensions.

Returns

Vector3 Unwrapped vector in real coordinates. This function takes a set of (wrapped) coordinates and returns the unwrapped coordinates.

Note

This function does not require the initial coordinates to be within the simulation box.

Definition at line 409 of file Snapshot.h.

References H_.

        {
            return H_*image.cast<double>()+v;
        }

Member Data Documentation

Vector3 SSAGES::Snapshot::origin_

private

< Virial tensor.

Box origin.

Definition at line 59 of file Snapshot.h.

Referenced by GetOrigin(), ScaleVector(), and SetOrigin().

---

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

• /home/cody/SSAGES/src/Snapshot.h