SSAGES  0.1
A MetaDynamics Package
Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
SSAGES::Meta Class Reference

"Vanilla" multi-dimensional Metadynamics. More...

#include <Meta.h>

Inheritance diagram for SSAGES::Meta:
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Public Member Functions

 Meta (const MPI_Comm &world, const MPI_Comm &comm, double height, const std::vector< double > &widths, const std::vector< double > &lowerb, const std::vector< double > &upperb, const std::vector< double > &lowerk, const std::vector< double > &upperk, Grid< Vector > *grid, unsigned int hillfreq, unsigned int frequency)
 Constructor. More...
 
void PreSimulation (Snapshot *snapshot, const class CVManager &cvmanager) override
 Pre-simulation hook. More...
 
void PostIntegration (Snapshot *snapshot, const class CVManager &cvmanager) override
 Post-integration hook. More...
 
void PostSimulation (Snapshot *snapshot, const class CVManager &cvmanager) override
 Post-simulation hook. More...
 
void LoadHills (const std::string &filename)
 Load hills from file. More...
 
 ~Meta ()
 Destructor.
 
- Public Member Functions inherited from SSAGES::Method
 Method (uint frequency, const MPI_Comm &world, const MPI_Comm &comm)
 Constructor. More...
 
void SetCVMask (const std::vector< uint > &mask)
 Sets the collective variable mask.
 
virtual ~Method ()
 Destructor.
 
- Public Member Functions inherited from SSAGES::EventListener
 EventListener (uint frequency)
 Constructor. More...
 
uint GetFrequency () const
 Get frequency of event listener. More...
 
virtual ~EventListener ()
 Destructor.
 

Static Public Member Functions

static MetaBuild (const Json::Value &json, const MPI_Comm &world, const MPI_Comm &comm, const std::string &path)
 
- Static Public Member Functions inherited from SSAGES::Method
static MethodBuildMethod (const Json::Value &json, const MPI_Comm &world, const MPI_Comm &comm, const std::string &path)
 Build a derived method from JSON node. More...
 

Private Member Functions

void AddHill (const CVList &cvs, int iteration)
 Adds a new hill. More...
 
void CalcBiasForce (const CVList &cvs)
 Computes the bias force. More...
 
void PrintHill (const Hill &hill, int interation)
 Prints the new hill to file. More...
 

Private Attributes

std::vector< Hillhills_
 Hills.
 
double height_
 Hill height.
 
std::vector< double > widths_
 Hill widths.
 
std::vector< double > derivatives_
 Derivatives and temporary storage vectors.
 
std::vector< double > tder_
 
std::vector< double > dx_
 
unsigned int hillfreq_
 Frequency of new hills.
 
Grid< Vector > * grid_
 CV Grid.
 
std::vector< double > upperb_
 Bounds.
 
std::vector< double > lowerb_
 
std::vector< double > upperk_
 Bound restraints.
 
std::vector< double > lowerk_
 
std::ofstream hillsout_
 Output stream for hill data.
 

Additional Inherited Members

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

Detailed Description

"Vanilla" multi-dimensional Metadynamics.

Implementation of a "vanilla" multi-dimensional Metadynamics method with no bells and whistles.

Definition at line 68 of file Meta.h.

Constructor & Destructor Documentation

SSAGES::Meta::Meta ( const MPI_Comm &  world,
const MPI_Comm &  comm,
double  height,
const std::vector< double > &  widths,
const std::vector< double > &  lowerb,
const std::vector< double > &  upperb,
const std::vector< double > &  lowerk,
const std::vector< double > &  upperk,
Grid< Vector > *  grid,
unsigned int  hillfreq,
unsigned int  frequency 
)
inline

Constructor.

Parameters
worldMPI global communicator.
commMPI local communicator.
heightHeight of the hills to be deposited.
widthsWidth of the hills to be deposited.
hillfreqFrequency of depositing hills.
frequencyFrequency of invoking this method.

Constructs an instance of Metadynamics method.

Note
The size of "widths" should be commensurate with the number of CV's expected.

Definition at line 132 of file Meta.h.

142  :
143  Method(frequency, world, comm), hills_(), height_(height), widths_(widths),
144  derivatives_(0), tder_(0), dx_(0), hillfreq_(hillfreq), grid_(grid),
145  upperb_(upperb), lowerb_(lowerb), upperk_(upperk), lowerk_(lowerk)
146  {
147  }
unsigned int hillfreq_
Frequency of new hills.
Definition: Meta.h:84
std::vector< double > upperb_
Bounds.
Definition: Meta.h:90
Method(uint frequency, const MPI_Comm &world, const MPI_Comm &comm)
Constructor.
Definition: Method.h:61
std::vector< Hill > hills_
Hills.
Definition: Meta.h:72
std::vector< double > upperk_
Bound restraints.
Definition: Meta.h:93
std::vector< double > derivatives_
Derivatives and temporary storage vectors.
Definition: Meta.h:81
Grid< Vector > * grid_
CV Grid.
Definition: Meta.h:87
std::vector< double > widths_
Hill widths.
Definition: Meta.h:78
double height_
Hill height.
Definition: Meta.h:75

Member Function Documentation

void SSAGES::Meta::AddHill ( const CVList cvs,
int  iteration 
)
private

Adds a new hill.

Parameters
cvsList of CVs.
iterationCurrent iteration.

Definition at line 168 of file Meta.cpp.

References SSAGES::gaussian(), and SSAGES::gaussianDerv().

169  {
170  int n = cvs.size();
171 
172  // Assume we have the same number of procs per walker.
173  int nwalkers = world_.size()/comm_.size();
174 
175  // We need to exchange CV values across the walkers
176  // and to each proc on a walker.
177  std::vector<double> cvals(n*nwalkers, 0);
178 
179  if(comm_.rank() == 0)
180  {
181  for(auto i = 0, j = world_.rank()/comm_.size()*n; i < n; ++i,++j)
182  cvals[j] = cvs[i]->GetValue();
183  }
184 
185  // Reduce across all processors and add hills.
186  MPI_Allreduce(MPI_IN_PLACE, cvals.data(), n*nwalkers, MPI_DOUBLE, MPI_SUM, world_);
187 
188  for(int i = 0; i < n*nwalkers; i += n)
189  {
190  std::vector<double> cval(cvals.begin() + i, cvals.begin() + i + n);
191  hills_.emplace_back(cval, widths_, height_);
192 
193  // Write hill to file.
194  if(world_.rank() == 0)
195  PrintHill(hills_.back(), iteration);
196  }
197 
198  // If grid is defined, add bias onto grid.
199  if(grid_ != nullptr)
200  {
201  std::vector<double> dx(n, 0.0), df(n, 1.0);
202  auto& hill = hills_.back();
203  for(auto it = grid_->begin(); it != grid_->end(); ++it)
204  {
205  auto& val = *it;
206  auto coord = it.coordinates();
207 
208  // Compute difference between grid point and current val.
209  for(size_t i = 0; i < n; ++i)
210  {
211  dx[i] = -cvs[i]->GetDifference(coord[i]);
212  df[i] = 1.;
213  }
214 
215  // Compute derivative.
216  for(size_t i = 0; i < n; ++i)
217  {
218  for(size_t j = 0; j < n; ++j)
219  {
220  if(j != i)
221  df[i] *= gaussian(dx[j], hill.width[j]);
222  else
223  df[i] *= gaussianDerv(dx[j], hill.width[j]);
224  }
225  }
226 
227  // Add to grid.
228  for(size_t i = 0; i < n; ++i)
229  val[i] += height_*df[i];
230  }
231  }
232  }
double gaussian(double dx, double sigma)
Evlauate Gaussian. Helper function.
Definition: Meta.cpp:42
mxx::comm comm_
Local MPI communicator.
Definition: Method.h:47
double gaussianDerv(double dx, double sigma)
Evaluate Gaussian derivative. Helper function.
Definition: Meta.cpp:54
mxx::comm world_
Global MPI communicator.
Definition: Method.h:46
void PrintHill(const Hill &hill, int interation)
Prints the new hill to file.
Definition: Meta.cpp:236
iterator begin()
Return iterator at first grid point.
Definition: Grid.h:524
std::vector< Hill > hills_
Hills.
Definition: Meta.h:72
Grid< Vector > * grid_
CV Grid.
Definition: Meta.h:87
std::vector< double > widths_
Hill widths.
Definition: Meta.h:78
double height_
Hill height.
Definition: Meta.h:75
iterator end()
Return iterator after last valid grid point.
Definition: Grid.h:537

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

Definition at line 332 of file Meta.cpp.

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

336  {
337  ObjectRequirement validator;
338  Value schema;
339  Reader reader;
340 
341  reader.parse(JsonSchema::MetadynamicsMethod, schema);
342  validator.Parse(schema, path);
343 
344  // Validate inputs.
345  validator.Validate(json, path);
346  if(validator.HasErrors())
347  throw BuildException(validator.GetErrors());
348 
349  std::vector<double> widths;
350  for(auto& s : json["widths"])
351  widths.push_back(s.asDouble());
352 
353  std::vector<double> lowerb, upperb, lowerk, upperk;
354  Grid<Vector>* grid = nullptr;
355  if(json.isMember("grid"))
356  grid = Grid<Vector>::BuildGrid(json.get("grid", Json::Value()));
357  else if(!json.isMember("lower_bounds") || !json.isMember("upper_bounds"))
358  throw BuildException({
359  "#/Method/Metadynamics: Both upper_bounds and lower_bounds "
360  "must be defined if grid is not being used."});
361 
362  // Assume all vectors are the same size.
363  for(int i = 0; i < json["lower_bound_restraints"].size(); ++i)
364  {
365  lowerk.push_back(json["lower_bound_restraints"][i].asDouble());
366  upperk.push_back(json["upper_bound_restraints"][i].asDouble());
367  lowerb.push_back(json["lower_bounds"][i].asDouble());
368  upperb.push_back(json["upper_bounds"][i].asDouble());
369  }
370 
371  auto height = json.get("height", 1.0).asDouble();
372  auto hillfreq = json.get("hill_frequency", 1).asInt();
373  auto freq = json.get("frequency", 1).asInt();
374 
375  auto* m = new Meta(
376  world, comm, height, widths,
377  lowerb, upperb, lowerk, upperk,
378  grid, hillfreq, freq
379  );
380 
381  if(json.isMember("load_hills"))
382  m->LoadHills(json["load_hills"].asString());
383 
384  return m;
385  }
bool HasErrors()
Check if errors have occured.
Definition: Requirement.h:86
virtual void Parse(Value json, const std::string &path) override
Parse JSON value to generate Requirement(s).
Meta(const MPI_Comm &world, const MPI_Comm &comm, double height, const std::vector< double > &widths, const std::vector< double > &lowerb, const std::vector< double > &upperb, const std::vector< double > &lowerk, const std::vector< double > &upperk, Grid< Vector > *grid, unsigned int hillfreq, unsigned int frequency)
Constructor.
Definition: Meta.h:132
std::vector< std::string > GetErrors()
Get list of error messages.
Definition: Requirement.h:92
Requirements on an object.
static Grid< Vector > * BuildGrid(const Json::Value &json)
Set up the grid.
Definition: Grid.h:127
virtual void Validate(const Value &json, const std::string &path) override
Validate JSON value.

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void SSAGES::Meta::CalcBiasForce ( const CVList cvs)
private

Computes the bias force.

Parameters
cvsList of CVs.

Definition at line 253 of file Meta.cpp.

References SSAGES::gaussian(), and SSAGES::gaussianDerv().

254  {
255  // Reset bias and derivatives.
256  double bias = 0.;
257  auto n = cvs.size();
258 
259  // Reset vectors.
260  std::fill(derivatives_.begin(), derivatives_.end(), 0);
261 
262  // Look up and apply grid bias.
263  if(grid_ != nullptr)
264  {
265  bool inbounds = true;
266  std::vector<double> val(n, 0.);
267  for(size_t i = 0; i < n; ++i)
268  {
269  val[i] = cvs[i]->GetValue();
270  if(val[i] < grid_->GetLower(i) || val[i] > grid_->GetUpper(i))
271  inbounds = false;
272  }
273 
274  if(inbounds)
275  {
276  auto frc = (*grid_)[val];
277  for(size_t i = 0; i < n; ++i)
278  derivatives_[i] = frc[i];
279  }
280  else
281  {
282  if(comm_.rank() == 0)
283  {
284  std::cerr << "Metadynamics: out of bounds ( ";
285  for(auto& v : val)
286  std::cerr << v << " ";
287  std::cerr << ")" << std::endl;
288  }
289  }
290  }
291  else
292  {
293  // Loop through hills and calculate the bias force.
294  for(auto& hill : hills_)
295  {
296  auto tbias = 1.;
297  std::fill(tder_.begin(), tder_.end(), 1.0);
298  std::fill(dx_.begin(), dx_.end(), 1.0);
299 
300  for(size_t i = 0; i < n; ++i)
301  {
302  dx_[i] = cvs[i]->GetDifference(hill.center[i]);
303  tbias *= gaussian(dx_[i], hill.width[i]);
304  }
305 
306  for(size_t i = 0; i < n; ++i)
307  for(size_t j = 0; j < n; ++j)
308  {
309  if(j != i)
310  tder_[i] *= gaussian(dx_[j], hill.width[j]);
311  else
312  tder_[i] *= gaussianDerv(dx_[j], hill.width[j]);
313  }
314 
315  bias += height_ * tbias;
316  for(size_t i = 0; i < n; ++i)
317  derivatives_[i] += height_*tder_[i];
318  }
319  }
320 
321  // Restraints.
322  for(size_t i = 0; i < n; ++i)
323  {
324  auto cval = cvs[i]->GetValue();
325  if(cval < lowerb_[i])
326  derivatives_[i] += lowerk_[i]*(cval - lowerb_[i]);
327  else if(cval > upperb_[i])
328  derivatives_[i] += upperk_[i]*(cval - upperb_[i]);
329  }
330  }
double gaussian(double dx, double sigma)
Evlauate Gaussian. Helper function.
Definition: Meta.cpp:42
mxx::comm comm_
Local MPI communicator.
Definition: Method.h:47
double gaussianDerv(double dx, double sigma)
Evaluate Gaussian derivative. Helper function.
Definition: Meta.cpp:54
std::vector< double > upperb_
Bounds.
Definition: Meta.h:90
std::vector< Hill > hills_
Hills.
Definition: Meta.h:72
std::vector< double > upperk_
Bound restraints.
Definition: Meta.h:93
const std::vector< double > GetLower() const
Return the lower edges of the Grid.
Definition: GridBase.h:227
const std::vector< double > GetUpper() const
Return the upper edges of the Grid.
Definition: GridBase.h:258
std::vector< double > derivatives_
Derivatives and temporary storage vectors.
Definition: Meta.h:81
Grid< Vector > * grid_
CV Grid.
Definition: Meta.h:87
double height_
Hill height.
Definition: Meta.h:75

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void SSAGES::Meta::LoadHills ( const std::string &  filename)

Load hills from file.

Parameters
filenameFile name containing hills.
Note
File format must match the output written by this method and the dimensionality of the hills must match the initialized Meta class.

Definition at line 136 of file Meta.cpp.

137  {
138  std::ifstream file(filename);
139  std::string line;
140 
141  auto dim = widths_.size();
142  double iteration = 0, height = 0;
143  std::vector<double> width(dim, 0.), center(dim, 0);
144 
145  // First line is a comment.
146  std::getline(file, line);
147  while(std::getline(file, line))
148  {
149  std::istringstream iss(line);
150  iss >> iteration; // Not really using this.
151 
152  // Load centers.
153  for(size_t i = 0; i < dim; ++i)
154  iss >> center[i];
155 
156  // Load widths.
157  for(size_t i = 0; i < dim; ++i)
158  iss >> width[i];
159 
160  // Load height.
161  iss >> height;
162 
163  hills_.emplace_back(center, width, height);
164  }
165  }
std::vector< Hill > hills_
Hills.
Definition: Meta.h:72
std::vector< double > widths_
Hill widths.
Definition: Meta.h:78
void SSAGES::Meta::PostIntegration ( Snapshot snapshot,
const class CVManager cvmanager 
)
overridevirtual

Post-integration hook.

Parameters
snapshotCurrent simulation snapshot.
cvmanagerCollective variable manager.

Implements SSAGES::Method.

Definition at line 100 of file Meta.cpp.

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

101  {
102  auto cvs = cvmanager.GetCVs(cvmask_);
103  // Add hills when needed.
104  if(snapshot->GetIteration() % hillfreq_ == 0)
105  AddHill(cvs, snapshot->GetIteration());
106 
107  // Always calculate the current bias.
108  CalcBiasForce(cvs);
109 
110  // Take each CV and add its biased forces to the atoms
111  // using the chain rule.
112  auto& forces = snapshot->GetForces();
113  auto& virial = snapshot->GetVirial();
114 
115  for(size_t i = 0; i < cvs.size(); ++i)
116  {
117  auto& grad = cvs[i]->GetGradient();
118  auto& boxgrad = cvs[i]->GetBoxGradient();
119 
120  // Update the forces in snapshot by adding in the force bias from each
121  // CV to each atom based on the gradient of the CV.
122  for (size_t j = 0; j < forces.size(); ++j)
123  for(size_t k = 0; k < 3; ++k)
124  forces[j][k] -= derivatives_[i]*grad[j][k];
125 
126  virial += derivatives_[i]*boxgrad;
127  }
128  }
unsigned int hillfreq_
Frequency of new hills.
Definition: Meta.h:84
void CalcBiasForce(const CVList &cvs)
Computes the bias force.
Definition: Meta.cpp:253
std::vector< uint > cvmask_
Mask which identifies which CVs to act on.
Definition: Method.h:50
std::vector< double > derivatives_
Derivatives and temporary storage vectors.
Definition: Meta.h:81
void AddHill(const CVList &cvs, int iteration)
Adds a new hill.
Definition: Meta.cpp:168

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void SSAGES::Meta::PostSimulation ( Snapshot snapshot,
const class CVManager cvmanager 
)
overridevirtual

Post-simulation hook.

Parameters
snapshotCurrent simulation snapshot.
cvmanagerCollective variable manager.

Implements SSAGES::Method.

Definition at line 131 of file Meta.cpp.

132  {
133  }
void SSAGES::Meta::PreSimulation ( Snapshot snapshot,
const class CVManager cvmanager 
)
overridevirtual

Pre-simulation hook.

Parameters
snapshotCurrent simulation snapshot.
cvmanagerCollective variable manager.

Implements SSAGES::Method.

Definition at line 62 of file Meta.cpp.

References SSAGES::CVManager::GetCVs(), and SSAGES::Snapshot::GetTargetIterations().

63  {
64  auto cvs = cvmanager.GetCVs(cvmask_);
65  // Write ouput file header.
66  if(world_.rank() == 0)
67  {
68  hillsout_.open("hills.out");
69  hillsout_ << "#Iteration ";
70 
71  for(size_t i = 0; i < cvs.size(); ++i)
72  hillsout_ << "center." << i << " ";
73 
74  for(size_t i = 0; i < cvs.size(); ++i)
75  hillsout_ << "sigma." << i << " ";
76 
77  hillsout_ << "height" << std::endl;
78 
79  hillsout_.close();
80  }
81 
82  // Initialize grid to zero.
83  if(grid_ != nullptr)
84  {
85  Vector vec = Vector::Zero(cvs.size());
86  std::fill(grid_->begin(), grid_->end(), vec);
87  }
88 
89  auto n = snapshot->GetTargetIterations();
90  n = n ? n : 1e5; // Pre-allocate at least something.
91 
92  hills_.reserve(n+1);
93  widths_.reserve(n+1);
94  derivatives_.resize(cvs.size());
95  tder_.resize(cvs.size());
96  dx_.resize(cvs.size());
97  }
Eigen::VectorXd Vector
Arbitrary length vector.
Definition: types.h:30
mxx::comm world_
Global MPI communicator.
Definition: Method.h:46
iterator begin()
Return iterator at first grid point.
Definition: Grid.h:524
std::vector< Hill > hills_
Hills.
Definition: Meta.h:72
std::vector< uint > cvmask_
Mask which identifies which CVs to act on.
Definition: Method.h:50
std::vector< double > derivatives_
Derivatives and temporary storage vectors.
Definition: Meta.h:81
Grid< Vector > * grid_
CV Grid.
Definition: Meta.h:87
std::vector< double > widths_
Hill widths.
Definition: Meta.h:78
std::ofstream hillsout_
Output stream for hill data.
Definition: Meta.h:116
iterator end()
Return iterator after last valid grid point.
Definition: Grid.h:537

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void SSAGES::Meta::PrintHill ( const Hill hill,
int  interation 
)
private

Prints the new hill to file.

Parameters
hillHill to be printed.
iterationCurrent iteration.

Definition at line 236 of file Meta.cpp.

References SSAGES::Hill::center, and SSAGES::Hill::width.

237  {
238  hillsout_.open("hills.out", std::fstream::app);
239 
240  hillsout_ << iteration << " ";
241  hillsout_.precision(8);
242 
243  for(auto& cv : hill.center)
244  hillsout_ << cv << " ";
245 
246  for(auto& w : hill.width)
247  hillsout_ << w << " ";
248 
249  hillsout_ << height_ << std::endl;
250  hillsout_.close();
251  }
std::ofstream hillsout_
Output stream for hill data.
Definition: Meta.h:116
double height_
Hill height.
Definition: Meta.h:75

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