SSAGES  0.8.5
Software Suite for Advanced General Ensemble Simulations
Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
SSAGES::GyrationTensorCV Class Reference

Collective variable on components of the gyration tensor. More...

#include <GyrationTensorCV.h>

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Public Member Functions

 GyrationTensorCV (const Label &atomids, GyrationTensor component)
 Constructor. More...
 
 GyrationTensorCV (const Label &atomids, GyrationTensor component, bool dimx, bool dimy, bool dimz)
 Constructor. More...
 
void Initialize (const Snapshot &snapshot) override
 Initialize necessary variables. More...
 
void Evaluate (const Snapshot &snapshot) override
 Evaluate the CV. More...
 
- Public Member Functions inherited from SSAGES::CollectiveVariable
 CollectiveVariable ()
 Constructor.
 
virtual ~CollectiveVariable ()
 Destructor.
 
virtual void Initialize (const class Snapshot &)
 Initialize CV. More...
 
virtual void Evaluate (const class Snapshot &)=0
 Evaluate CV. More...
 
double GetValue () const
 Get current value of the CV. More...
 
virtual double GetMinimumImage (double) const
 Returns the minimum image of a CV based on the input location. More...
 
virtual double GetPeriodicValue (double location) const
 Apply periodic boundaries to a given value. More...
 
const std::vector< Vector3 > & GetGradient () const
 Get current gradient of the CV. More...
 
const Matrix3GetBoxGradient () const
 Get gradient contribution to box. More...
 
const std::array< double, 2 > & GetBoundaries ()
 Get CV boundaries. More...
 
virtual double GetDifference (double location) const
 

Static Public Member Functions

static GyrationTensorCVBuild (const Json::Value &json, const std::string &path)
 Set up collective variable. More...
 
- Static Public Member Functions inherited from SSAGES::CollectiveVariable
static CollectiveVariableBuildCV (const Json::Value &json, const std::string &path)
 Set up collective variable. More...
 

Private Attributes

Label atomids_
 IDs of the atoms used for calculation.
 
GyrationTensor component_
 Component of gyration tensor to compute.
 
Bool3 dim_
 Each dimension determines if it is applied by the CV.
 

Additional Inherited Members

- Protected Attributes inherited from SSAGES::CollectiveVariable
std::vector< Vector3grad_
 Gradient vector dCv/dxi.
 
Matrix3 boxgrad_
 Gradient w.r.t box vectors dCv/dHij.
 
double val_
 Current value of CV.
 
std::array< double, 2 > bounds_
 Bounds on CV.
 

Detailed Description

Collective variable on components of the gyration tensor.

Collective variable on components of gyration tensor. Depending on the user selection, this will specify a principal moment, radius of gyration, or another shape descriptor.

Definition at line 56 of file GyrationTensorCV.h.

Constructor & Destructor Documentation

SSAGES::GyrationTensorCV::GyrationTensorCV ( const Label atomids,
GyrationTensor  component 
)
inline

Constructor.

Parameters
atomidsIDs of the atoms defining gyration tensor.
componentSpecification of component to compute.

Construct a GyrationTensorCV.

Definition at line 74 of file GyrationTensorCV.h.

Referenced by Build().

74  :
75  atomids_(atomids), component_(component), dim_{true, true, true}
76  {
77  }
GyrationTensor component_
Component of gyration tensor to compute.
Label atomids_
IDs of the atoms used for calculation.
Bool3 dim_
Each dimension determines if it is applied by the CV.

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SSAGES::GyrationTensorCV::GyrationTensorCV ( const Label atomids,
GyrationTensor  component,
bool  dimx,
bool  dimy,
bool  dimz 
)
inline

Constructor.

Parameters
atomidsIDs of the atoms defining gyration tensor.
componentSpecification of component to compute.
dimxIf True, include x dimension.
dimyIf True, include y dimension.
dimzIf True, include z dimension.

Construct a GyrationTensorCV.

Definition at line 90 of file GyrationTensorCV.h.

90  :
91  atomids_(atomids), component_(component), dim_{dimx, dimy, dimz}
92  {
93  }
GyrationTensor component_
Component of gyration tensor to compute.
Label atomids_
IDs of the atoms used for calculation.
Bool3 dim_
Each dimension determines if it is applied by the CV.

Member Function Documentation

static GyrationTensorCV* SSAGES::GyrationTensorCV::Build ( const Json::Value &  json,
const std::string &  path 
)
inlinestatic

Set up collective variable.

Parameters
jsonJSON input value.
pathPath for JSON path specification.
Returns
Pointer to the CV built by this function. nullptr in case of unknown error.

Builds a CV from a JSON node. Returns a pointer to the built cv. If an unknown error is encountered, this function will return a nullptr, but generally it will throw a BuildException on failure.

Warning
Object lifetime is the caller's responsibility.

Definition at line 246 of file GyrationTensorCV.h.

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

Referenced by SSAGES::CollectiveVariable::BuildCV().

247  {
248  Json::ObjectRequirement validator;
249  Json::Value schema;
250  Json::CharReaderBuilder rbuilder;
251  Json::CharReader* reader = rbuilder.newCharReader();
252 
253  reader->parse(JsonSchema::GyrationTensorCV.c_str(),
254  JsonSchema::GyrationTensorCV.c_str() + JsonSchema::GyrationTensorCV.size(),
255  &schema, nullptr);
256  validator.Parse(schema, path);
257 
258  // Validate inputs.
259  validator.Validate(json, path);
260  if(validator.HasErrors())
261  throw BuildException(validator.GetErrors());
262 
263  std::vector<int> atomids;
264  for(auto& s : json["atom_ids"])
265  atomids.push_back(s.asInt());
266 
267  GyrationTensor component = Rg;
268  auto comp = json["component"].asString();
269 
270  if(comp == "Rg")
271  component = Rg;
272  else if(comp == "principal1")
273  component = principal1;
274  else if(comp == "principal2")
275  component = principal2;
276  else if(comp == "principal3")
277  component = principal3;
278  else if(comp == "asphericity")
279  component = asphericity;
280  else if(comp == "acylindricity")
281  component = acylindricity;
282  else if(comp == "shapeaniso")
283  component = shapeaniso;
284 
285  GyrationTensorCV* c;
286  if(json.isMember("dimension"))
287  {
288  auto dimx = json["dimension"][0].asBool();
289  auto dimy = json["dimension"][1].asBool();
290  auto dimz = json["dimension"][2].asBool();
291  c = new GyrationTensorCV(atomids, component, dimx, dimy, dimz);
292  }
293  else
294  c = new GyrationTensorCV(atomids, component);
295 
296  return c;
297  }
bool HasErrors()
Check if errors have occured.
Definition: Requirement.h:86
GyrationTensorCV(const Label &atomids, GyrationTensor component)
Constructor.
GyrationTensor
Define components of gyration tensor.
virtual void Parse(Value json, const std::string &path) override
Parse JSON value to generate Requirement(s).
std::vector< std::string > GetErrors()
Get list of error messages.
Definition: Requirement.h:92
Requirements on an object.
virtual void Validate(const Value &json, const std::string &path) override
Validate JSON value.

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void SSAGES::GyrationTensorCV::Evaluate ( const Snapshot snapshot)
inlineoverride

Evaluate the CV.

Parameters
snapshotCurrent simulation snapshot.

Definition at line 128 of file GyrationTensorCV.h.

References SSAGES::Snapshot::ApplyMinimumImage(), SSAGES::Snapshot::CenterOfMass(), SSAGES::Snapshot::GetCommunicator(), SSAGES::Snapshot::GetLocalIndices(), SSAGES::Snapshot::GetMasses(), SSAGES::Snapshot::GetNumAtoms(), SSAGES::Snapshot::GetPositions(), SSAGES::CollectiveVariable::grad_, SSAGES::Snapshot::TotalMass(), and SSAGES::CollectiveVariable::val_.

129  {
130  using namespace Eigen;
131 
132  // Get local atom indices and compute COM.
133  std::vector<int> idx;
134  snapshot.GetLocalIndices(atomids_, &idx);
135 
136  // Get data from snapshot.
137  auto n = snapshot.GetNumAtoms();
138  const auto& masses = snapshot.GetMasses();
139  const auto& pos = snapshot.GetPositions();
140 
141  // Initialize gradient.
142  std::fill(grad_.begin(), grad_.end(), Vector3{0,0,0});
143  grad_.resize(n, Vector3{0,0,0});
144 
145  // Compute total and center of mass.
146  auto masstot = snapshot.TotalMass(idx);
147  Vector3 com = snapshot.CenterOfMass(idx, masstot);
148 
149  // Gyration tensor and temporary vector to store positions in inertial frame.
150  Matrix3 S = Matrix3::Zero();
151  std::vector<Vector3> ris;
152  ris.reserve(idx.size());
153  for(auto& i : idx)
154  {
155  ris.emplace_back(snapshot.ApplyMinimumImage(pos[i] - com).cwiseProduct(dim_.cast<double>()));
156  S.noalias() += masses[i]*ris.back()*ris.back().transpose();
157  }
158 
159  // Reduce gyration tensor across processors and normalize.
160  MPI_Allreduce(MPI_IN_PLACE, S.data(), S.size(), MPI_DOUBLE, MPI_SUM, snapshot.GetCommunicator());
161  S /= masstot;
162 
163  // Perform EVD. The columns are the eigenvectors.
164  // SelfAdjoint solver sorts in ascending order.
165  SelfAdjointEigenSolver<Matrix3> solver;
166  solver.computeDirect(S);
167  const auto& eigvals = solver.eigenvalues();
168  const auto& eigvecs = solver.eigenvectors();
169 
170  // Assign variables for clarity. l1 is largest.
171  auto l1 = eigvals[2],
172  l2 = eigvals[1],
173  l3 = eigvals[0];
174  const auto& n1 = eigvecs.col(2),
175  n2 = eigvecs.col(1),
176  n3 = eigvecs.col(0);
177 
178  val_ = 0;
179  auto sum = l1 + l2 + l3;
180  auto sqsum = l1*l1 + l2*l2 + l3*l3;
181  switch(component_)
182  {
183  case Rg:
184  val_ = sum;
185  break;
186  case principal1:
187  val_ = l1;
188  break;
189  case principal2:
190  val_ = l2;
191  break;
192  case principal3:
193  val_ = l3;
194  break;
195  case asphericity:
196  val_ = l1 - 0.5*(l2 + l3);
197  break;
198  case acylindricity:
199  val_ = l2 - l3;
200  break;
201  case shapeaniso:
202  val_ = 1.5*sqsum/(sum*sum) - 0.5;
203  break;
204  }
205 
206  // Compute gradient.
207  size_t j = 0;
208  for(auto& i : idx)
209  {
210  // Compute derivative of each eigenvalue and use combos in components.
211  auto dl1 = 2.*masses[i]/masstot*(1.-masses[i]/masstot)*ris[j].dot(n1)*n1;
212  auto dl2 = 2.*masses[i]/masstot*(1.-masses[i]/masstot)*ris[j].dot(n2)*n2;
213  auto dl3 = 2.*masses[i]/masstot*(1.-masses[i]/masstot)*ris[j].dot(n3)*n3;
214 
215  switch(component_)
216  {
217  case Rg:
218  grad_[i] = dl1 + dl2 + dl3;
219  break;
220  case principal1:
221  grad_[i] = dl1;
222  break;
223  case principal2:
224  grad_[i] = dl2;
225  break;
226  case principal3:
227  grad_[i] = dl3;
228  break;
229  case asphericity:
230  grad_[i] = dl1 - 0.5*(dl2 + dl3);
231  break;
232  case acylindricity:
233  grad_[i] = dl2 - dl3;
234  break;
235  case shapeaniso:
236  grad_[i] = 3.*(l1*dl1+l2*dl2+l3*dl3)/(sum*sum) -
237  3.*sqsum*(dl1+dl2+dl3)/(sum*sum*sum);
238  break;
239  }
240 
241  ++j;
242  }
243  }
Eigen::Matrix3d Matrix3
3x3 matrix.
Definition: types.h:42
GyrationTensor component_
Component of gyration tensor to compute.
std::vector< Vector3 > grad_
Gradient vector dCv/dxi.
Label atomids_
IDs of the atoms used for calculation.
Eigen::Vector3d Vector3
Three-dimensional vector.
Definition: types.h:33
double val_
Current value of CV.
Bool3 dim_
Each dimension determines if it is applied by the CV.

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void SSAGES::GyrationTensorCV::Initialize ( const Snapshot snapshot)
inlineoverride

Initialize necessary variables.

Parameters
snapshotCurrent simulation snapshot.

Definition at line 99 of file GyrationTensorCV.h.

References SSAGES::Snapshot::GetCommunicator(), and SSAGES::Snapshot::GetLocalIndex().

100  {
101  using std::to_string;
102 
103  auto n = atomids_.size();
104 
105  // Make sure atom ID's are on at least one processor.
106  std::vector<int> found(n, 0);
107  for(size_t i = 0; i < n; ++i)
108  {
109  if(snapshot.GetLocalIndex(atomids_[i]) != -1)
110  found[i] = 1;
111  }
112 
113  MPI_Allreduce(MPI_IN_PLACE, found.data(), n, MPI_INT, MPI_SUM, snapshot.GetCommunicator());
114  unsigned ntot = std::accumulate(found.begin(), found.end(), 0, std::plus<int>());
115  if(ntot != n)
116  throw BuildException({
117  "GyrationTensorCV: Expected to find " +
118  to_string(n) +
119  " atoms, but only found " +
120  to_string(ntot) + "."
121  });
122  }
Label atomids_
IDs of the atoms used for calculation.

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