Viscosity - Advanced Options Dialog Box
Set an option for pre-averaging the stress tensors.
To open this dialog box, click the Advanced Options button in the Viscosity Panel.
Selecting the tau range for fitting of the linear region prior to running the simulations is non-trivial and varies by system. Some information is given below, but it is important to note that the range can be adjusted in the Viscosity Viewer Panel, where the curve can be inspected, and refitting can be done to obtain better values.
- Features
- Additional Resources
Viscosity - Advanced Options Dialog Box Features
- Pre-average every N stress tensors option and text box
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Average the stress tensors in groups of N. Each group is consecutive, and the average of the group is written out for use in the fitting. The time interval corresponding to the number of stress tensors in each group is reported (N times the energy group recording interval). The averaging is expected to reduce the noise in the autocorrelation function, and reduce disk space.
- Additional Properties section
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Specify additional properties to be calculated. The values are returned as entry properties.
- Calculate viscosity via Einstein-Helfand method option
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Calculate the viscosity from the Einstein relations for the time integral of the pressure tensor [49]. The viscosity is derived from a linear fit of the mean square displacement (MSD) of this integral over a specified range. This is useful as a check on the viscosity determined by the Green–Kubo method: if the results are different, it may mean that one or other of the fitting regions is poorly chosen. This method requires longer simulation times to reach the point where the pressure tensor loses correlation.
- Include Tau values from min ns to max ns for fitting option
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Specify the range of tau values for the linear fit to obtain the viscosity. The viscosity is determined from the long time behavior of the pressure tensor MSD, where the pressure tensor becomes decorrelated from itself, and the MSD curve is linear. The onset of the linear region shifts to longer tau as viscosity increases. The upper end of the range should be set at a point before the MSD curve becomes too noisy.
- Calculate diffusion coefficient via mean squared displacement option
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Calculate the self-diffusion coefficient of the system, using the mean squared displacement (MSD) of the molecular center-of-mass positions. The diffusion calculation is derived for dynamics in a Brownian regime (uncorrelated random walks).
- Include Tau values from min ns to max ns for fitting option
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Specify the range of tau values for determining the diffusion coefficient. The defaults are chosen to avoid the ballistic region at very short tau values where the MSD curve tends to be parabolic, and the region at long tau values where there is less sampling and deviation from linearity due to the noise in the averaged data.
In very slow diffusing cases, the MSD curve may actually be sub-linear. If the MSD does not become linear at longer tau, you may need to run longer simulations.
- Reset button
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Reset the panel to its default settings.