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Significant improvements! #5

Merged
merged 2 commits into from
Jul 21, 2024
Merged

Significant improvements! #5

merged 2 commits into from
Jul 21, 2024

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paulsaxe
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  • Simplified error analysis to safe approach of analyzing the diffusion constants over runs.
  • Improved fitting of the curves to focus on the central linear portion. There are reasonable defaults but the user can adjust as needed.
  • Provided a combined average and error bars when both the MSF approach and Helfand moments are used.
  • Capture temperature, pressure, and cell size from the MD step, providing 1/L as a result since the true diffusion constants are found by extrapolating to 1/L = 0.
  • Provided control over the number of steps for the expensive numerical integration in the Helfand moments, providing a reasonable default of 1000.

paulsaxe added 2 commits July 21, 2024 17:34
@paulsaxe
Significant improvements!
0247b3c 
    * Simplified error analysis to safe approach of analyzing the diffusion constants
      over runs.
    * Improved fitting of the curves to focus on the central linear portion. There are
      reasonable defaults but the user can adjust as needed.
    * Provided a combined average and error bars when both the MSF approach and Helfand
      moments are used.
    * Capture temperature, pressure, and cell size from the MD step, providing 1/L as a
      result since the true diffusion constants are found by extrapolating to 1/L = 0.
    * Provided control over the number of steps for the expensive numerical integration
      in the Helfand moments, providing a reasonable default of 1000.
@paulsaxe
Significant improvements!
17254de 
    * Simplified error analysis to safe approach of analyzing the diffusion constants
      over runs.
    * Improved fitting of the curves to focus on the central linear portion. There are
      reasonable defaults but the user can adjust as needed.
    * Provided a combined average and error bars when both the MSF approach and Helfand
      moments are used.
    * Capture temperature, pressure, and cell size from the MD step, providing 1/L as a
      result since the true diffusion constants are found by extrapolating to 1/L = 0.
    * Provided control over the number of steps for the expensive numerical integration
      in the Helfand moments, providing a reasonable default of 1000.
@paulsaxe paulsaxe added the enhancement New feature or request label Jul 21, 2024
@paulsaxe paulsaxe requested a review from seamm July 21, 2024 21:39
seamm
seamm approved these changes Jul 21, 2024
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LGTM

@seamm seamm merged commit a710b7f into main Jul 21, 2024
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@seamm seamm seamm approved these changes

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@paulsaxe @seamm