Gromacs
2019-beta3
|
Functions | |
int64_t | calcTargetUpdateInterval (const AwhParams &awhParams, const AwhBiasParams &awhBiasParams) |
Determines the interval for updating the target distribution. More... | |
int64_t | calcCheckCoveringInterval (const AwhParams &awhParams, const std::vector< DimParams > &dimParams, const std::vector< GridAxis > &gridAxis) |
Determines the step interval for checking for covering. More... | |
double | gaussianGeometryFactor (gmx::ArrayRef< const double > xArray) |
Returns an approximation of the geometry factor used for initializing the AWH update size. More... | |
double | getInitialHistogramSizeEstimate (const std::vector< DimParams > &dimParams, const AwhBiasParams &awhBiasParams, const std::vector< GridAxis > &gridAxis, double beta, double samplingTimestep) |
Estimate a reasonable initial reference weight histogram size. More... | |
int | getNumSharedUpdate (const AwhBiasParams &awhBiasParams, int numSharingSimulations) |
Returns the number of simulations sharing bias updates. More... | |
int64_t gmx::anonymous_namespace{biasparams.cpp}::calcCheckCoveringInterval | ( | const AwhParams & | awhParams, |
const std::vector< DimParams > & | dimParams, | ||
const std::vector< GridAxis > & | gridAxis | ||
) |
Determines the step interval for checking for covering.
[in] | awhParams | AWH parameters. |
[in] | dimParams | Parameters for the dimensions of the coordinate. |
[in] | gridAxis | The Grid axes. |
int64_t gmx::anonymous_namespace{biasparams.cpp}::calcTargetUpdateInterval | ( | const AwhParams & | awhParams, |
const AwhBiasParams & | awhBiasParams | ||
) |
Determines the interval for updating the target distribution.
The interval value is based on the target distrbution type (this could be made a user-option but there is most likely no big need for tweaking this for most users).
[in] | awhParams | AWH parameters. |
[in] | awhBiasParams | Bias parameters. |
double gmx::anonymous_namespace{biasparams.cpp}::gaussianGeometryFactor | ( | gmx::ArrayRef< const double > | xArray | ) |
Returns an approximation of the geometry factor used for initializing the AWH update size.
The geometry factor is defined as the following sum of Gaussians: sum_{k!=0} exp(-0.5*(k*pi*x)^2)/(pi*k)^2, where k is a xArray.size()-dimensional integer vector with k_i in {0,1,..}.
[in] | xArray | Array to evaluate. |
double gmx::anonymous_namespace{biasparams.cpp}::getInitialHistogramSizeEstimate | ( | const std::vector< DimParams > & | dimParams, |
const AwhBiasParams & | awhBiasParams, | ||
const std::vector< GridAxis > & | gridAxis, | ||
double | beta, | ||
double | samplingTimestep | ||
) |
Estimate a reasonable initial reference weight histogram size.
[in] | dimParams | Parameters for the dimensions of the coordinate. |
[in] | awhBiasParams | Bias parameters. |
[in] | gridAxis | The Grid axes. |
[in] | beta | 1/(k_B T). |
[in] | samplingTimestep | Sampling frequency of probability weights. |
int gmx::anonymous_namespace{biasparams.cpp}::getNumSharedUpdate | ( | const AwhBiasParams & | awhBiasParams, |
int | numSharingSimulations | ||
) |
Returns the number of simulations sharing bias updates.
[in] | awhBiasParams | Bias parameters. |
[in] | numSharingSimulations | The number of simulations to share the bias across. |