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Adding offline mbar analysis #15

Merged
merged 10 commits into from
Jan 9, 2024
Merged

Adding offline mbar analysis #15

merged 10 commits into from
Jan 9, 2024

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wiederm
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@wiederm wiederm commented Jan 9, 2024

Description

This PR simplifies and removes much of the logic contained in the multistate sampler and adds support for offline free energy estimate based on MBAR.

Todos

Notable points that this PR has either accomplished or will accomplish.

  • refactor multistate class
  • store multistate energy matrix
  • add MBAR analysis
  • add free energy testcase (harmonic oscillator with different spring constant)

Status

  • Ready to go

@wiederm wiederm requested a review from chrisiacovella January 9, 2024 11:18
@wiederm wiederm changed the base branch from main to multistage January 9, 2024 11:18
@wiederm wiederm added the enhancement New feature or request label Jan 9, 2024
@wiederm wiederm changed the base branch from multistage to main January 9, 2024 13:29
@wiederm wiederm changed the base branch from main to multistage January 9, 2024 13:31
@wiederm wiederm merged commit eb927e4 into multistage Jan 9, 2024
@wiederm wiederm deleted the analyzer branch January 9, 2024 13:34
@wiederm wiederm mentioned this pull request Jan 9, 2024
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