#include <gromacs/applied_forces/awh/biasparams.h>
Constant parameters for the bias.
Switch to turn off update skips, useful for testing.
| Enumerator |
|---|
| no |
Allow update skips (when supported by the method)
|
| yes |
Disable update skips.
|
Constructor.
The local Boltzmann target distibution is defined by 1) Adding the sampled weights instead of the target weights to the reference weight histogram. 2) Scaling the weights of these samples by the beta scaling factor. 3) Setting the target distribution equal the reference weight histogram. This requires the following special update settings: localWeightScaling = targetParam idealWeighthistUpdate = false Note: these variables could in principle be set to something else also for other target distribution types. However, localWeightScaling < 1 is in general expected to give lower efficiency and, except for local Boltzmann, idealWeightHistUpdate = false gives (in my experience) unstable, non-converging results.
- Parameters
-
| [in] | awhParams | AWH parameters. |
| [in] | awhBiasParams | Bias parameters. |
| [in] | dimParams | Bias dimension parameters. |
| [in] | beta | 1/(k_B T) in units of 1/(kJ/mol), should be > 0. |
| [in] | mdTimeStep | The MD time step. |
| [in] | numSharingSimulations | The number of simulations to share the bias across. |
| [in] | gridAxis | The grid axes. |
| [in] | disableUpdateSkips | If to disable update skips, useful for testing. |
| [in] | biasIndex | Index of the bias. |
| bool gmx::BiasParams::isCheckCoveringStep |
( |
int64_t |
step | ) |
const |
|
inline |
Returns if to do checks for covering in the initial stage.
To avoid overhead due to expensive checks, we do not check at every free energy update. However, if checks are performed too rarely the detection of coverings will be delayed, ultimately affecting free energy convergence.
- Parameters
-
- Returns
- true at steps where checks should be performed.
- Note
- Only returns true at free energy update steps.
| bool gmx::BiasParams::isCheckHistogramForAnomaliesStep |
( |
int64_t |
step | ) |
const |
|
inline |
Returns if to perform checks for anomalies in the histogram.
To avoid overhead due to expensive checks, we do not check at every free energy update. These checks are only used for warning the user and can be made as infrequently as neccessary without affecting the algorithm itself.
- Parameters
-
- Returns
- true at steps where checks should be performed.
- Note
- Only returns true at free energy update steps.
- Todo:
- Currently this function just calls isCheckCoveringStep but the checks could be done less frequently.
| bool gmx::BiasParams::isSampleCoordStep |
( |
int64_t |
step | ) |
const |
|
inline |
Returns whether we should sample the coordinate.
- Parameters
-
| [in] | step | The MD step number. |
| bool gmx::BiasParams::isUpdateFreeEnergyStep |
( |
int64_t |
step | ) |
const |
|
inline |
Returns whether we should update the free energy.
- Parameters
-
| [in] | step | The MD step number. |
| bool gmx::BiasParams::isUpdateTargetStep |
( |
int64_t |
step | ) |
const |
|
inline |
Returns whether we should update the target distribution.
- Parameters
-
| [in] | step | The MD step number. |
| bool gmx::BiasParams::skipUpdates |
( |
| ) |
const |
|
inline |
Check if the parameters permit skipping updates.
Generally, we can skip updates of points that are non-local at the time of the update if we for later times, when the points with skipped updates have become local, know exactly how to apply the previous updates. The free energy updates only depend on local sampling, but the histogram rescaling factors generally depend on the histogram size (all samples). If the histogram size is kept constant or the scaling factors are trivial, this is not a problem. However, if the histogram growth is scaled down by some factor the size at the time of the update needs to be known. It would be fairly simple to, for a deterministically growing histogram, backtrack and calculate this value, but currently we just disallow this case. This is not a restriction because it only affects the local Boltzmann target type for which every update is currently anyway global because the target is always updated globally.
- Returns
- true when we can skip updates.
| const int gmx::BiasParams::biasIndex_ |
Index of the bias, used as a second random seed and for priting.
| const bool gmx::BiasParams::convolveForce |
True if we convolve the force, false means use MC between umbrellas.
Type of target distribution.
| const double gmx::BiasParams::freeEnergyCutoffInKT |
Free energy cut-off in kT for cut-off target distribution.
| const bool gmx::BiasParams::idealWeighthistUpdate |
Update reference weighthistogram using the target distribution? Otherwise use the realized distribution.
| const double gmx::BiasParams::initialErrorInKT |
Estimated initial free energy error in kT.
| const double gmx::BiasParams::initialHistogramSize |
Initial reference weight histogram size.
| const double gmx::BiasParams::localWeightScaling |
Scaling factor applied to a sample before adding it to the reference weight histogram (= 1, usually).
| const int gmx::BiasParams::numSamplesUpdateFreeEnergy_ |
Number of samples per free energy update.
| const double gmx::BiasParams::targetMetricScalingLimit |
The upper limit for the scaling factor based on the friction metric.
The lower limit is the inverse.
| const double gmx::BiasParams::temperatureScaleFactor |
Temperature scaling factor for temperature scaled targed distributions.
| const double gmx::BiasParams::updateWeight |
The probability weight accumulated for each update.
The documentation for this class was generated from the following files:
1.8.5