Gromacs
2023.1

#include <gromacs/applied_forces/awh/biasstate.h>
The state of a bias.
The bias state has the current coordinate state: its value and the grid point it maps to (the grid point of the umbrella potential if needed). It contains a vector with the state for each point on the grid. It also counts the number of updates issued and tracks which points have been sampled since last update. Finally, the convergence state is a global property set ultimately by the histogram size histogramSize in the subclass HistogramSize, since the update sizes are ~ 1/histogramSize.
Public Member Functions  
BiasState (const AwhBiasParams &awhBiasParams, double histogramSizeInitial, ArrayRef< const DimParams > dimParams, const BiasGrid &grid, const BiasSharing *biasSharing)  
Constructor. More...  
void  restoreFromHistory (const AwhBiasHistory &biasHistory, const BiasGrid &grid) 
Restore the bias state from history. More...  
void  broadcast (const t_commrec *commRecord) 
Broadcast the bias state over the MPI ranks in this simulation. More...  
void  initHistoryFromState (AwhBiasHistory *biasHistory) const 
Allocate and initialize a bias history with the given bias state. More...  
void  updateHistory (AwhBiasHistory *biasHistory, const BiasGrid &grid) const 
Update the bias state history with the current state. More...  
void  initGridPointState (const AwhBiasParams &awhBiasParams, ArrayRef< const DimParams > dimParams, const BiasGrid &grid, const BiasParams ¶ms, const std::string &filename, int numBias) 
Initialize the state of grid coordinate points. More...  
int  warnForHistogramAnomalies (const BiasGrid &grid, int biasIndex, double t, FILE *fplog, int maxNumWarnings) const 
Performs statistical checks on the collected histograms and warns if issues are detected. More...  
double  calcUmbrellaForceAndPotential (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, int point, ArrayRef< const double > neighborLambdaDhdl, ArrayRef< double > force) const 
Calculates and sets the force the coordinate experiences from an umbrella centered at the given point. More...  
void  calcConvolvedForce (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, ArrayRef< const double > probWeightNeighbor, ArrayRef< const double > neighborLambdaDhdl, ArrayRef< double > forceWorkBuffer, ArrayRef< double > force) const 
Calculates and sets the convolved force acting on the coordinate. More...  
double  moveUmbrella (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, ArrayRef< const double > probWeightNeighbor, ArrayRef< const double > neighborLambdaDhdl, ArrayRef< double > biasForce, int64_t step, int64_t seed, int indexSeed, bool onlySampleUmbrellaGridpoint) 
Move the center point of the umbrella potential. More...  
void  doSkippedUpdatesForAllPoints (const BiasParams ¶ms) 
Do all previously skipped updates. Public for use by tests. More...  
void  doSkippedUpdatesInNeighborhood (const BiasParams ¶ms, const BiasGrid &grid) 
Do previously skipped updates in this neighborhood. More...  
void  setCoordValue (const BiasGrid &grid, const awh_dvec coordValue) 
Update the reaction coordinate value. More...  
void  updateFreeEnergyAndAddSamplesToHistogram (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, const BiasParams ¶ms, double t, int64_t step, FILE *fplog, std::vector< int > *updateList) 
Performs an update of the bias. More...  
double  updateProbabilityWeightsAndConvolvedBias (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, ArrayRef< const double > neighborLambdaEnergies, std::vector< double, AlignedAllocator< double >> *weight) const 
Update the probability weights and the convolved bias. More...  
void  sampleProbabilityWeights (const BiasGrid &grid, ArrayRef< const double > probWeightNeighbor) 
Take samples of the current probability weights for future updates and analysis. More...  
void  sampleCoordAndPmf (const std::vector< DimParams > &dimParams, const BiasGrid &grid, ArrayRef< const double > probWeightNeighbor, double convolvedBias) 
Sample the reaction coordinate and PMF for future updates or analysis. More...  
double  calcConvolvedBias (ArrayRef< const DimParams > dimParams, const BiasGrid &grid, const awh_dvec &coordValue) const 
Calculates the convolved bias for a given coordinate value. More...  
void  getPmf (ArrayRef< float >) const 
Fills the given array with PMF values. More...  
const CoordState &  coordState () const 
Returns the current coordinate state.  
const std::vector< PointState > &  points () const 
Returns a const reference to the point state.  
bool  inInitialStage () const 
Returns true if we are in the initial stage.  
HistogramSize  histogramSize () const 
Returns the current histogram size.  
void  setUmbrellaGridpointToGridpoint () 
Sets the umbrella grid point to the current grid point.  
void  updateSharedCorrelationTensorTimeIntegral (const BiasParams &biasParams, const CorrelationGrid &forceCorrelation) 
Updates sharedCorrelationTensorTimeIntegral_ for all points. More...  
double  getSharedCorrelationTensorTimeIntegral (int gridPointIndex, int correlationTensorIndex) const 
Gets the time integral, shared across all ranks, of a tensor of a correlation grid point. More...  
const std::vector< double > &  getSharedPointCorrelationIntegral (int gridPointIndex) const 
Gets the time integral (all tensors), shared across all ranks, of a correlation grid point. More...  
double  getSharedCorrelationTensorVolumeElement (int gridPointIndex, int numCorrelation) const 
Gets the volume element, shared across all ranks, of a correlation grid point. More...  
gmx::BiasState::BiasState  (  const AwhBiasParams &  awhBiasParams, 
double  histogramSizeInitial,  
ArrayRef< const DimParams >  dimParams,  
const BiasGrid &  grid,  
const BiasSharing *  biasSharing  
) 
Constructor.
Constructs the global state and the point states on a provided geometric grid passed in grid
.
[in]  awhBiasParams  The Bias parameters from inputrec. 
[in]  histogramSizeInitial  The estimated initial histogram size. This is floatingpoint, since histograms use weighted entries and grow by a floatingpoint scaling factor. 
[in]  dimParams  The dimension parameters. 
[in]  grid  The bias grid. 
[in]  biasSharing  Multisim bias sharing object, can be nullptrx 
void gmx::BiasState::broadcast  (  const t_commrec *  commRecord  ) 
Broadcast the bias state over the MPI ranks in this simulation.
[in]  commRecord  Struct for communication. 
double gmx::BiasState::calcConvolvedBias  (  ArrayRef< const DimParams >  dimParams, 
const BiasGrid &  grid,  
const awh_dvec &  coordValue  
)  const 
Calculates the convolved bias for a given coordinate value.
The convolved bias is the effective bias acting on the coordinate. Since the bias here has arbitrary normalization, this only makes sense as a relative, to other coordinate values, measure of the bias.
[in]  dimParams  The bias dimensions parameters 
[in]  grid  The grid. 
[in]  coordValue  Coordinate value. 
void gmx::BiasState::calcConvolvedForce  (  ArrayRef< const DimParams >  dimParams, 
const BiasGrid &  grid,  
ArrayRef< const double >  probWeightNeighbor,  
ArrayRef< const double >  neighborLambdaDhdl,  
ArrayRef< double >  forceWorkBuffer,  
ArrayRef< double >  force  
)  const 
Calculates and sets the convolved force acting on the coordinate.
The convolved force is the weighted sum of forces from umbrellas located at each point in the grid.
[in]  dimParams  The bias dimensions parameters. 
[in]  grid  The grid. 
[in]  probWeightNeighbor  Probability weights of the neighbors. 
[in]  neighborLambdaDhdl  An array containing the dHdL at the neighboring lambda points. The array is of length numLambdas+1, where numLambdas is the number of free energy lambda states. Element 0 in the array is the dHdL of the current state and elements 1..numLambdas contain the dHdL of the system in the neighboring lambda states (also including the current state). When there are no free energy lambda state dimensions this can be empty. 
[in]  forceWorkBuffer  Force work buffer, values only used internally. 
[in,out]  force  Bias force vector to set. 
double gmx::BiasState::calcUmbrellaForceAndPotential  (  ArrayRef< const DimParams >  dimParams, 
const BiasGrid &  grid,  
int  point,  
ArrayRef< const double >  neighborLambdaDhdl,  
ArrayRef< double >  force  
)  const 
Calculates and sets the force the coordinate experiences from an umbrella centered at the given point.
The umbrella potential is an harmonic potential given by 0.5k(coord value  point value)^2. This value is also returned.
[in]  dimParams  The bias dimensions parameters. 
[in]  grid  The grid. 
[in]  point  Point for umbrella center. 
[in]  neighborLambdaDhdl  An array containing the dHdL at the neighboring lambda points. The array is of length numLambdas+1, where numLambdas is the number of free energy lambda states. Element 0 in the array is the dHdL of the current state and elements 1..numLambdas contain the dHdL of the system in the neighboring lambda states (also including the current state). When there are no free energy lambda state dimensions this can be empty. 
[in,out]  force  Force vector to set. Returns the umbrella potential. 
void gmx::BiasState::doSkippedUpdatesForAllPoints  (  const BiasParams &  params  ) 
Do all previously skipped updates. Public for use by tests.
[in]  params  The bias parameters. 
void gmx::BiasState::doSkippedUpdatesInNeighborhood  (  const BiasParams &  params, 
const BiasGrid &  grid  
) 
Do previously skipped updates in this neighborhood.
[in]  params  The bias parameters. 
[in]  grid  The grid. 
void gmx::BiasState::getPmf  (  gmx::ArrayRef< float >  pmf  )  const 
Fills the given array with PMF values.
Points outside of the biasing target region will get PMF = GMX_FLOAT_MAX.
[out]  pmf  Array(ref) to be filled with the PMF values, should have the same size as the bias grid. 
double gmx::BiasState::getSharedCorrelationTensorTimeIntegral  (  int  gridPointIndex, 
int  correlationTensorIndex  
)  const 
Gets the time integral, shared across all ranks, of a tensor of a correlation grid point.
[in]  gridPointIndex  The index of the grid point from which to retrieve the tensor volume. 
[in]  correlationTensorIndex  The index of the tensor. 
double gmx::BiasState::getSharedCorrelationTensorVolumeElement  (  int  gridPointIndex, 
int  numCorrelation  
)  const 
Gets the volume element, shared across all ranks, of a correlation grid point.
[in]  gridPointIndex  The index of the grid point from which to retrieve the tensor volume. 
[in]  numCorrelation  Number of force correlation tensors. 
const std::vector< double > & gmx::BiasState::getSharedPointCorrelationIntegral  (  int  gridPointIndex  )  const 
Gets the time integral (all tensors), shared across all ranks, of a correlation grid point.
[in]  gridPointIndex  The index of the grid point from which to retrieve the tensor volume. 
void gmx::BiasState::initGridPointState  (  const AwhBiasParams &  awhBiasParams, 
ArrayRef< const DimParams >  dimParams,  
const BiasGrid &  grid,  
const BiasParams &  params,  
const std::string &  filename,  
int  numBias  
) 
Initialize the state of grid coordinate points.
[in]  awhBiasParams  Bias parameters from inputrec. 
[in]  dimParams  The dimension parameters. 
[in]  grid  The grid. 
[in]  params  The bias parameters. 
[in]  filename  Name of file to read PMF and target from. 
[in]  numBias  The number of biases. 
void gmx::BiasState::initHistoryFromState  (  AwhBiasHistory *  biasHistory  )  const 
Allocate and initialize a bias history with the given bias state.
This function will be called at the start of a new simulation. Note that this only sets the correct size and does produce a valid history object, but with all data set to zero. Actual history data is set by updateHistory.
[in,out]  biasHistory  AWH history to initialize. 
double gmx::BiasState::moveUmbrella  (  ArrayRef< const DimParams >  dimParams, 
const BiasGrid &  grid,  
ArrayRef< const double >  probWeightNeighbor,  
ArrayRef< const double >  neighborLambdaDhdl,  
ArrayRef< double >  biasForce,  
int64_t  step,  
int64_t  seed,  
int  indexSeed,  
bool  onlySampleUmbrellaGridpoint  
) 
Move the center point of the umbrella potential.
A new umbrella center is sampled from the biased distibution. Also, the bias force is updated and the new potential is return.
This function should only be called when the bias force is not being convolved. It is assumed that the probability distribution has been updated.
[in]  dimParams  Bias dimension parameters. 
[in]  grid  The grid. 
[in]  probWeightNeighbor  Probability weights of the neighbors. 
[in]  neighborLambdaDhdl  An array containing the dHdL at the neighboring lambda points. The array is of length numLambdas+1, where numLambdas is the number of free energy lambda states. Element 0 in the array is the dHdL of the current state and elements 1..numLambdas contain the dHdL of the system in the neighboring lambda states (also including the current state). When there are no free energy lambda state dimensions this can be empty. 
[in,out]  biasForce  The AWH bias force. 
[in]  step  Step number, needed for the random number generator. 
[in]  seed  Random seed. 
[in]  indexSeed  Second random seed, should be the bias Index. 
[in]  onlySampleUmbrellaGridpoint  Only sample the umbrella gridpoint without calculating force and potential. 
void gmx::BiasState::restoreFromHistory  (  const AwhBiasHistory &  biasHistory, 
const BiasGrid &  grid  
) 
Restore the bias state from history.
[in]  biasHistory  Bias history struct. 
[in]  grid  The bias grid. 
void gmx::BiasState::sampleCoordAndPmf  (  const std::vector< DimParams > &  dimParams, 
const BiasGrid &  grid,  
gmx::ArrayRef< const double >  probWeightNeighbor,  
double  convolvedBias  
) 
Sample the reaction coordinate and PMF for future updates or analysis.
These samples do not affect the (future) sampling and are thus pure observables. Statisics of these are stored in the energy file.
[in]  dimParams  The bias dimensions parameters 
[in]  grid  The grid. 
[in]  probWeightNeighbor  Probability weights of the neighbors. 
[in]  convolvedBias  The convolved bias. 
void gmx::BiasState::sampleProbabilityWeights  (  const BiasGrid &  grid, 
gmx::ArrayRef< const double >  probWeightNeighbor  
) 
Take samples of the current probability weights for future updates and analysis.
Points in the current neighborhood will now have data meaning they need to be included in the local update list of the next update. Therefore, the local update range is also update here.
[in]  grid  The grid. 
[in]  probWeightNeighbor  Probability weights of the neighbors. 
Update the reaction coordinate value.
[in]  grid  The bias grid. 
[in]  coordValue  The current reaction coordinate value (there are no limits on allowed values). 
void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram  (  ArrayRef< const DimParams >  dimParams, 
const BiasGrid &  grid,  
const BiasParams &  params,  
double  t,  
int64_t  step,  
FILE *  fplog,  
std::vector< int > *  updateList  
) 
Performs an update of the bias.
The objective of the update is to use collected samples (probability weights) to improve the free energy estimate. For sake of efficiency, the update is local whenever possible, meaning that only points that have actually been sampled are accessed and updated here. For certain AWH settings or at certain steps however, global need to be performed. Besides the actual free energy update, this function takes care of ensuring future convergence of the free energy. Convergence is obtained by increasing the size of the reference weight histogram in a controlled (sometimes dynamic) manner. Also, there are AWH variables that are direct functions of the free energy or sampling history that need to be updated here, namely the target distribution and the bias function.
[in]  dimParams  The dimension parameters. 
[in]  grid  The grid. 
[in]  params  The bias parameters. 
[in]  t  Time. 
[in]  step  Time step. 
[in,out]  fplog  Log file. 
[in,out]  updateList  Work space to store a temporary list. 
void gmx::BiasState::updateHistory  (  AwhBiasHistory *  biasHistory, 
const BiasGrid &  grid  
)  const 
double gmx::BiasState::updateProbabilityWeightsAndConvolvedBias  (  ArrayRef< const DimParams >  dimParams, 
const BiasGrid &  grid,  
ArrayRef< const double >  neighborLambdaEnergies,  
std::vector< double, AlignedAllocator< double >> *  weight  
)  const 
Update the probability weights and the convolved bias.
Given a coordinate value, each grid point is assigned a probability weight, w(pointvalue), that depends on the current bias function. The sum of these weights is needed for normalizing the probability sum to 1 but also equals the effective, or convolved, biasing weight for this coordinate value. The convolved bias is needed e.g. for extracting the PMF, so we save it here since this saves us from doing extra exponential function evaluations later on.
[in]  dimParams  The bias dimensions parameters 
[in]  grid  The grid. 
[in]  neighborLambdaEnergies  An array containing the energy of the system in neighboring lambdas. The array is of length numLambdas+1, where numLambdas is the number of free energy lambda states. Element 0 in the array is the energy of the current state and elements 1..numLambdas contain the energy of the system in the neighboring lambda states (also including the current state). When there are no free energy lambda state dimensions this can be empty. 
[out]  weight  Probability weights of the neighbors, SIMD aligned. 
void gmx::BiasState::updateSharedCorrelationTensorTimeIntegral  (  const BiasParams &  biasParams, 
const CorrelationGrid &  forceCorrelation  
) 
Updates sharedCorrelationTensorTimeIntegral_ for all points.
[in]  biasParams  The bias parameters. 
[in]  forceCorrelation  The force correlation grid. 
int gmx::BiasState::warnForHistogramAnomalies  (  const BiasGrid &  grid, 
int  biasIndex,  
double  t,  
FILE *  fplog,  
int  maxNumWarnings  
)  const 
Performs statistical checks on the collected histograms and warns if issues are detected.
[in]  grid  The grid. 
[in]  biasIndex  The index of the bias we are checking for. 
[in]  t  Time. 
[in,out]  fplog  Output file for warnings. 
[in]  maxNumWarnings  Don't issue more than this number of warnings. 