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A list of short term action items #1

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13 tasks done
wehs7661 opened this issue Jul 20, 2022 · 1 comment
Closed
13 tasks done

A list of short term action items #1

wehs7661 opened this issue Jul 20, 2022 · 1 comment
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enhancement New feature or request

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wehs7661 commented Jul 20, 2022 •
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  • Modify the weight-combining methods - Should combine the weights from all replicas that sample the state of interest
  • Improve the section of "Theory and Implementation" in the documentation for the package
    • Finish the section of weight-combining methods
    • Finish the section of replica swapping methods
  • Develop a function for printing out a summary of the simulation ensemble after the ensemble is done.
    • When the weights of each replica got equilibrated
    • How many exchanges were rejected/accepted.
  • Develop methods for data analysis
    • Simple analysis for plotting the state index time-series/histograms
    • Calculation of the state transition matrix
    • Calculation of the replica transition matrix
    • Calculation of the overlap matrix
    • Free energy calculations
@wehs7661 wehs7661 added the enhancement New feature or request label Jul 28, 2022
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wehs7661 commented Feb 3, 2023

Closing the issue now as all the action items have been completed.

@wehs7661 wehs7661 closed this as completed Feb 3, 2023
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