uq
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uq [2018/11/27 16:12] – [Optional parameters] slongbottom | uq [2018/12/03 11:08] – [Hessian Bracketing Algorithm] slongbottom | ||
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- | This generates an ensemble of potentials whose spread can be used to quantify the uncertainties in the fitted parameters. Taking an uncorrelated subsample of the MCMC output forms a potential ensemble representing the uncertainties in each parameter by the ensemble spread and covariance. Propagating the uncertainty represented by the ensemble members through molecular dynamics, the resultant uncertainties in quantities of interest can be obtained. For an example of this see ((Longbottom, | + | This generates an ensemble of potentials whose spread can be used to quantify the uncertainties in the fitted parameters. Taking an uncorrelated subsample of the MCMC output forms a potential ensemble representing the uncertainties in each parameter by the ensemble spread and covariance. Propagating the uncertainty represented by the ensemble members through molecular dynamics, the resultant uncertainties in quantities of interest can be obtained. For an example of this see ((Longbottom, |
===== The Ensemble Method ===== | ===== The Ensemble Method ===== | ||
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where $\lambda_j$ are the hessian eigenvalues, | where $\lambda_j$ are the hessian eigenvalues, | ||
- | The MCMC algorithm samples potentials from the distribution at a temperature, | + | The MCMC algorithm samples potentials from the distribution at a temperature, |
+ | ===== Hessian Bracketing Algorithm ===== | ||
+ | |||
+ | **Only use this if you know what you are doing! ** | ||
+ | |||
+ | If '' | ||
+ | |||
+ | If the landscape at this scale is not harmonic, the eigenvalues of the hessian will be negative. In this case a reduced sampling temperature may be required and the user should think about improving the reference data being fit to, as well as the suitability and possible limitations of the potential model being used. | ||
===== Parameters ===== | ===== Parameters ===== | ||
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^ parameter name | parameter type | default value | | ^ parameter name | parameter type | default value | | ||
- | | short explanation ||| | + | | short explanation. ||| |
==== Required parameters | ==== Required parameters | ||
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^ **acc_rescaling*** | float | (none) | | ^ **acc_rescaling*** | float | (none) | | ||
- | | R value to tune MCMC acceptance rate ||| | + | | R value to tune MCMC acceptance rate. ||| |
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^ **acc_moves*** | integer | (none) | | ^ **acc_moves*** | integer | (none) | | ||
- | | Number of accepted MCMC moves required ||| | + | | Number of accepted MCMC moves required. ||| |
==== Optional parameters | ==== Optional parameters | ||
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- | ^ **hess_pert** | float | (none) | + | ^ **hess_pert** | float | 0.00001 |
- | | Percentage parameter perturbation in Hessian finite difference calculation. ||| | + | | Percentage parameter perturbation in Hessian finite difference calculation. |
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| Alternative MCMC step perturbation maximum value in max('' | | Alternative MCMC step perturbation maximum value in max('' | ||
+ | |<100% 33% 33% 33%>| | ||
+ | ^ **write_ensemble** | integer | 0 | | ||
+ | | Writes a potential file every '' | ||