Gromacs
2024.4
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#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 sub-class 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 CorrelationGrid &forceCorrelation, 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, const CorrelationGrid &forceCorrelation, 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, bool shareAcrossAllRanks) |
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... | |
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 floating-point, since histograms use weighted entries and grow by a floating-point 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. |
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 CorrelationGrid & | forceCorrelation, | ||
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] | forceCorrelation | The force correlation statistics for every grid point. |
[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, | ||
const CorrelationGrid & | forceCorrelation, | ||
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] | forceCorrelation | The force correlation statistics for every grid point. |
[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(point|value), 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, | ||
bool | shareAcrossAllRanks | ||
) |
Updates sharedCorrelationTensorTimeIntegral_ for all points.
[in] | biasParams | The bias parameters. |
[in] | forceCorrelation | The force correlation grid. |
[in] | shareAcrossAllRanks | Share the data across all ranks? Otherwise only the main ranks. |
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. |