SSAGES::Umbrella Class Reference

Umbrella sampling method. More...

#include <Umbrella.h>

Inheritance diagram for SSAGES::Umbrella:

Public Member Functions
	Umbrella (const MPI_Comm &world, const MPI_Comm &comm, const std::vector< double > &kspring, const std::vector< double > &centers, std::string name, unsigned int frequency)
	Constructor. More...
	Umbrella (const MPI_Comm &world, const MPI_Comm &comm, const std::vector< double > &kspring, const std::vector< double > &centers0, const std::vector< double > &centers1, size_t timesteps, std::string name, unsigned int frequency)
	Constructor. More...
void	PreSimulation (Snapshot *snapshot, const class CVManager &cvmanager) override
	Method call prior to simulation initiation. More...
void	PostIntegration (Snapshot *snapshot, const class CVManager &cvmanager) override
	Method call post integration. More...
void	PostSimulation (Snapshot *snapshot, const class CVManager &cvmanager) override
	Method call post simulation. More...
void	SetOutputFrequency (int outfreq)
	Set output frequency. More...
void	SetAppend (bool append)
	Set append mode. More...
Public Member Functions inherited from SSAGES::Method
	Method (unsigned int frequency, const MPI_Comm &world, const MPI_Comm &comm)
	Constructor. More...
void	SetCVMask (const std::vector< unsigned int > &mask)
	Sets the collective variable mask. More...
virtual	~Method ()
	Destructor.
Public Member Functions inherited from SSAGES::EventListener
	EventListener (unsigned int frequency)
	Constructor. More...
unsigned int	GetFrequency () const
	Get frequency of event listener. More...
virtual	~EventListener ()
	Destructor.

Static Public Member Functions
static Umbrella *	Build (const Json::Value &json, const MPI_Comm &world, const MPI_Comm &comm, const std::string &path)
	Build a derived method from JSON node. More...
Static Public Member Functions inherited from SSAGES::Method
static Method *	BuildMethod (const Json::Value &json, const MPI_Comm &world, const MPI_Comm &comm, const std::string &path)
	Build a derived method from JSON node. More...
Static Public Member Functions inherited from SSAGES::EventListener
static unsigned int	GetWalkerID (const MPI_Comm &world, const MPI_Comm &comm)
	Get walker ID number of specified communicator. More...
static unsigned int	GetNumWalkers (const MPI_Comm &world, const MPI_Comm &comm)
	Get total number of walkers in the simulation. More...
static bool	IsMasterRank (const MPI_Comm &comm)
	Check if current processor is master. More...

Private Member Functions
double	GetCurrentCenter (size_t iteration, size_t i)
	Get the current center of the umbrella at a given iteration. More...
void	PrintUmbrella (const CVList &cvs, size_t iteration)
	Print umbrella values. More...

Private Attributes
std::vector< double >	kspring_
	Vector of spring constants.
size_t	time_
	Amount of time over which to scale centers.
std::string	filename_
	Output filename.
int	outfreq_
	Frequency of outputting data.
std::ofstream	umbrella_
	Output stream for umbrella data.
bool	append_
	Append to output files?
std::vector< double >	centers0_
std::vector< double >	centers1_

Additional Inherited Members
Protected Attributes inherited from SSAGES::Method
mxx::comm	world_
	Global MPI communicator.
mxx::comm	comm_
	Local MPI communicator.
std::vector< unsigned int >	cvmask_
	Mask which identifies which CVs to act on.

Detailed Description

Umbrella sampling method.

Umbrella sampling method to constrain an arbitrary number of CVs at specified equilibrium distances.

Definition at line 35 of file Umbrella.h.

Constructor & Destructor Documentation

Umbrella() [1/2]

SSAGES::Umbrella::Umbrella ( const MPI_Comm &  world, const MPI_Comm &  comm, const std::vector< double > &  kspring, const std::vector< double > &  centers, std::string  name, unsigned int  frequency  )

inline

Constructor.

Parameters

world	MPI global communicator.
comm	MPI local communicator.
kspring	List of spring constants.
centers	List of spring equilibrium positions.
name	Filename.
frequency	Frequency with which this method is applied.

Create instance of umbrella with spring constants "kspring", and centers "centers". Note the sizes of the vectors should be commensurate with the number of CVs.

Definition at line 98 of file Umbrella.h.

                                         : 
        Method(frequency, world, comm), kspring_(kspring), centers0_(centers),
        centers1_(centers), time_(0), filename_(name), outfreq_(1), append_(false)
        {
        }

Umbrella() [2/2]

SSAGES::Umbrella::Umbrella ( const MPI_Comm &  world, const MPI_Comm &  comm, const std::vector< double > &  kspring, const std::vector< double > &  centers0, const std::vector< double > &  centers1, size_t  timesteps, std::string  name, unsigned int  frequency  )

inline

Constructor.

Parameters

world	MPI global communicator.
comm	MPI local communicator.
kspring	List of spring constants.
centers0	List of starting spring equilibrium positions.
centers1	List of ending spring equilibrium positions.
timesteps	Number of timesteps over which to scale centers.
name	Filename.
frequency	Frequency with which this method is applied.

Create instance of umbrella with spring constants "kspring", and centers "centers". Note the sizes of the vectors should be commensurate with the number of CVs.

Definition at line 124 of file Umbrella.h.

                                         : 
        Method(frequency, world, comm), kspring_(kspring), centers0_(centers0),
        centers1_(centers1), time_(timesteps), filename_(name), outfreq_(1)
        {
        }

Member Function Documentation

Build()

Umbrella * SSAGES::Umbrella::Build ( const Json::Value &  json, const MPI_Comm &  world, const MPI_Comm &  comm, const std::string &  path  )

static

Build a derived method from JSON node.

Parameters

json	JSON Value containing all input information.
world	MPI global communicator.
comm	MPI local communicator.
path	Path for JSON path specification.

Returns

Pointer to the Method built. nullptr if an unknown error occurred.

This function builds a registered method from a JSON node. The difference between this function and "Build" is that this automatically determines the appropriate derived type based on the JSON node information.

Note

Object lifetime is the caller's responsibility.

Definition at line 112 of file Umbrella.cpp.

    {
        ObjectRequirement validator;
        Value schema;
        CharReaderBuilder rbuilder;
        CharReader* reader = rbuilder.newCharReader();
 
        reader->parse(JsonSchema::UmbrellaMethod.c_str(),
                      JsonSchema::UmbrellaMethod.c_str() + JsonSchema::UmbrellaMethod.size(),
                      &schema, nullptr);
        validator.Parse(schema, path);
 
        // Validate inputs.
        validator.Validate(json, path);
        if(validator.HasErrors())
            throw BuildException(validator.GetErrors());
 
        unsigned int wid = GetWalkerID(world, comm);
        unsigned int wcount = GetNumWalkers(world, comm);
        bool ismulti = wcount > 1;
 
        std::vector<std::vector<double>> ksprings;
        for(auto& s : json["ksprings"])
        {
            std::vector<double> kspring;
            if(s.isArray())
                for(auto& k : s)
                    kspring.push_back(k.asDouble());
            else
                kspring.push_back(s.asDouble());
            
            ksprings.push_back(kspring);
        }
 
        std::vector<std::vector<double>> centers0, centers1;
        if(json.isMember("centers"))
        {
            for(auto& s : json["centers"])
            {
                std::vector<double> center;
                if(s.isArray())
                    for(auto& k : s)
                        center.push_back(k.asDouble());
                else
                    center.push_back(s.asDouble());
                
                centers0.push_back(center);
            }
        }
        else if(json.isMember("centers0") && json.isMember("centers1") && json.isMember("timesteps"))
        {
            for(auto& s : json["centers0"])
            {           
                std::vector<double> center;
                if(s.isArray())
                    for(auto& k : s)
                        center.push_back(k.asDouble());
                else
                    center.push_back(s.asDouble());
                
                centers0.push_back(center);
            }
 
            for(auto& s : json["centers1"])
            {           
                std::vector<double> center;
                if(s.isArray())
                    for(auto& k : s)
                        center.push_back(k.asDouble());
                else
                    center.push_back(s.asDouble());
                
                centers1.push_back(center);
            }
        }
        else
            throw BuildException({"Either \"centers\" or \"timesteps\", \"centers0\" and \"centers1\" must be defined for umbrella."});
 
        if(ksprings[0].size() != centers0[0].size())
            throw BuildException({"Need to define a spring for every center or a center for every spring!"});
        
        // If only one set of center/ksprings are specified. Fill it up for multi.
        if(ismulti)
        {
            if(ksprings.size() == 1)
                for(size_t i = 1; i < wcount; ++i)
                    ksprings.push_back(ksprings[0]);
            else if(ksprings.size() != wcount)
                throw std::invalid_argument(path + ": Multi-walker simulations requires that the number of \"ksprings\" match the number of walkers.");
            if(centers0.size() == 1)
                for(size_t i = 1; i < wcount; ++i)
                    centers0.push_back(centers0[0]);
            else if(centers0.size() != wcount)
                throw std::invalid_argument(path + ": Multi-walker simulations requires that the number of \"centers\"/\"centers0\" match the number of walkers.");
            if(centers1.size() == 1)
                for(size_t i = 1; i < wcount; ++i)
                    centers1.push_back(centers1[0]);
            else if(centers1.size()) // centers1 is optional.
                throw std::invalid_argument(path + ": Multi-walker simulations requires that the number of \"centers1\" match the number of walkers.");
        }
 
        auto freq = json.get("frequency", 1).asInt();
 
        size_t timesteps = 0;
        if(json.isMember("timesteps"))
        {
            if(json["timesteps"].isArray())
                timesteps = json["timesteps"][wid].asUInt();
            else
                timesteps = json["timesteps"].asUInt();
        }
 
        std::string name = "umbrella.dat";
        if(json["output_file"].isArray())
            name = json["output_file"][wid].asString();
        else if(ismulti)
            throw std::invalid_argument(path + ": Multi-walker simulations require a separate output file for each.");
        else
            name = json["output_file"].asString();
 
        Umbrella* m = nullptr;
        if(timesteps == 0)
            m = new Umbrella(world, comm, ksprings[wid], centers0[wid], name, freq);
        else
            m = new Umbrella(world, comm, ksprings[wid], centers0[wid], centers1[wid], timesteps, name, freq);
 
        m->SetOutputFrequency(json.get("output_frequency",0).asInt());
        m->SetAppend(json.get("append", false).asBool());
        
        return m;
    }

References Json::Requirement::GetErrors(), Json::Requirement::HasErrors(), Json::ObjectRequirement::Parse(), SetAppend(), SetOutputFrequency(), and Json::ObjectRequirement::Validate().

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GetCurrentCenter()

double SSAGES::Umbrella::GetCurrentCenter ( size_t  iteration, size_t  i  )

inlineprivate

Get the current center of the umbrella at a given iteration.

Parameters

iteration	Current iteration of the Snapshot.
i	index (iterator) for CV.

Returns

Center of umbrella at current iteration

Definition at line 68 of file Umbrella.h.

        {
            // We are at the end.
            if(iteration >= time_) return centers1_[i];
 
            // Scale linearly.
            return (centers1_[i] - centers0_[i])/time_*iteration + centers0_[i]; 
        }

References centers0_, and time_.

PostIntegration()

void SSAGES::Umbrella::PostIntegration ( Snapshot *  snapshot, const class CVManager &  cvmanager  )

overridevirtual

Method call post integration.

Parameters

snapshot	Pointer to the simulation snapshot.
cvmanager	Collective variable manager.

This function will be called after each integration step.

Implements SSAGES::Method.

Definition at line 57 of file Umbrella.cpp.

    {
        // Get necessary info.
        auto cvs = cvmanager.GetCVs(cvmask_);
        auto& forces = snapshot->GetForces();
        auto& virial = snapshot->GetVirial();
 
        for(size_t i = 0; i < cvs.size(); ++i)
        {
            // Get current CV and gradient.
            auto& cv = cvs[i];
            auto& grad = cv->GetGradient();
            auto& boxgrad = cv->GetBoxGradient();
            // Compute dV/dCV.
            auto center = GetCurrentCenter(snapshot->GetIteration(), i);
            auto D = kspring_[i]*cv->GetDifference(center);
 
            // Update forces.
            for(size_t j = 0; j < forces.size(); ++j)
                forces[j] -= D*grad[j];
            
            // Update virial.
            virial += D*boxgrad;
        }
 
        if(snapshot->GetIteration() % outfreq_ == 0)
            PrintUmbrella(cvs, snapshot->GetIteration());
    }

References SSAGES::CVManager::GetCVs(), SSAGES::Snapshot::GetForces(), SSAGES::Snapshot::GetIteration(), and SSAGES::Snapshot::GetVirial().

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PostSimulation()

void SSAGES::Umbrella::PostSimulation ( Snapshot *  snapshot, const class CVManager &  cvmanager  )

overridevirtual

Method call post simulation.

Parameters

snapshot	Pointer to the simulation snapshot.
cvmanager	Collective variable manager.

This function will be called after the end of the simulation run.

Implements SSAGES::Method.

Definition at line 86 of file Umbrella.cpp.

    {
        if(IsMasterRank(comm_))
            umbrella_.close();
    }

PreSimulation()

void SSAGES::Umbrella::PreSimulation ( Snapshot *  snapshot, const class CVManager &  cvmanager  )

overridevirtual

Method call prior to simulation initiation.

Parameters

snapshot	Pointer to the simulation snapshot.
cvmanager	Collective variable manager.

This function will be called before the simulation is started.

Implements SSAGES::Method.

Definition at line 33 of file Umbrella.cpp.

    {
        if(IsMasterRank(comm_))
        {
            if(append_)
                umbrella_.open(filename_.c_str(), std::ofstream::out | std::ofstream::app);
            else
            {
                // Write out header.
                umbrella_.open(filename_.c_str(), std::ofstream::out);
                umbrella_ << "#";
                umbrella_ << "Iteration ";
 
                auto cvs = cvmanager.GetCVs(cvmask_);
                for(size_t i = 0; i < cvs.size(); ++i)
                    umbrella_ << "cv_" + std::to_string(i) << " ";
 
                for(size_t i = 0; i < cvs.size() - 1; ++i)
                    umbrella_ << "center_" + std::to_string(i) << " ";
                umbrella_ << "center_" + std::to_string(cvs.size() - 1) << std::endl;
            }
        }
    }

References SSAGES::CVManager::GetCVs().

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PrintUmbrella()

void SSAGES::Umbrella::PrintUmbrella ( const CVList &  cvs, size_t  iteration  )

private

Print umbrella values.

Parameters

cvs	List of CVs.
iteration	Current iteration.

Definition at line 92 of file Umbrella.cpp.

    {
        if(IsMasterRank(comm_))
        {
            umbrella_.precision(8);
            umbrella_ << iteration << " ";
 
            // Print out CV values first.
            for(auto& cv : cvs)
                umbrella_ << cv->GetValue() << " ";
            
            // Print out target (center) of each CV.
            for(size_t i = 0; i < cvs.size() - 1; ++i)
                umbrella_ << GetCurrentCenter(iteration, i) << " ";
            umbrella_ << GetCurrentCenter(iteration, cvs.size() - 1);
 
            umbrella_ << std::endl;
        }
    }

SetAppend()

void SSAGES::Umbrella::SetAppend ( bool  append )

inline

Set append mode.

Parameters

append

Whether to enable or disable append mode.

Definition at line 159 of file Umbrella.h.

        {
            append_ = append;
        }

References append_.

Referenced by Build().

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SetOutputFrequency()

void SSAGES::Umbrella::SetOutputFrequency ( int  outfreq )

inline

Set output frequency.

Parameters

outfreq

New value for output frequency.

Definition at line 150 of file Umbrella.h.

        {
            outfreq_ = outfreq;
        }

References outfreq_.

Referenced by Build().

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Member Data Documentation

centers0_

std::vector<double> SSAGES::Umbrella::centers0_

private

Vector of equilibrium distances.

Definition at line 43 of file Umbrella.h.

Referenced by GetCurrentCenter().

---

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

• /home/michael/development/SSAGES/src/Methods/Umbrella.h
• /home/michael/development/SSAGES/src/Methods/Umbrella.cpp