Add the 'evalplateau' command. Other misc. fixes.#821

Merged

drroe merged 70 commits intoAmber-MD:masterfrom

drroe:EvalEquilibration

Jun 14, 2020

Commits on Nov 25, 2019

DRR - Initial incarnation of evalequilibration
Daniel R. Roe
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DRR - Enable evalequil
Daniel R. Roe
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DRR - Start to determine direction of relaxation
Daniel R. Roe
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DRR - Use forward declares.
Daniel R. Roe
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DRR - Fix up includes for forward declares in Array1D.h
Daniel R. Roe
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DRR - use Array1D
Daniel R. Roe
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DRR - Add non linear curve fitting and final curve output
Daniel R. Roe
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DRR - Add nonlinear fit stats printout
Daniel R. Roe
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DRR - Ensure A1 parameter guess starts out < 0 (improves convergence)
Daniel R. Roe
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DRR - Try adding an offset to X. I think the incoming X values will need to be shifted as well.
Daniel R. Roe
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Commits on Nov 26, 2019

DRR - Use an offset so that when fitting, the first X value is always 1. With the addition of the A2 parameter, we're saying we dont know exactly where on the exponential curve the data starts.
Daniel R. Roe
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DRR - Allow stats to be redirected to a file.
Daniel R. Roe
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DRR - Add some documentation
Daniel R. Roe
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DRR - More docs
Daniel R. Roe
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DRR - Start adding results
Daniel R. Roe
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DRR - Make blocks respect noexitonerror
Daniel R. Roe
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DRR - Add calculation of difference of last half of data from long-time estimate
Daniel R. Roe
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DRR - New forms of exponentials that are more consistent with each other and with first order decay. Bounded by A0 OP A2 (where OP is + for decay and - for inverse) and A2 at times 0 and infinity
Daniel R. Roe
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DRR - Remove obsolete code
Daniel R. Roe
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DRR - Make it easier to add more results data sets
Daniel R. Roe
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DRR - Add final fit parameters to results
Daniel R. Roe
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DRR - Add determination of equilibrated via cutoffs
Daniel R. Roe
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DRR - Add slope calculation
Daniel R. Roe
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DRR - Fix equation forms in output
Daniel R. Roe
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DRR - Add 1st half avg calc. Make sure printing to statsout
Daniel R. Roe
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DRR - Add equil. time
Daniel R. Roe
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DRR - Get F value from regression
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DRR - Save regression F value
Daniel R. Roe
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DRR - Use offset so X values start at 0. This gives proper weight to the t=0 case where the first value should be close to A0+A2 or A2-A0
Daniel R. Roe
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DRR - Try out new equation
Daniel R. Roe
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Commits on Dec 3, 2019

Commits on Dec 5, 2019

DRR - Create default cut
drroe
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DRR - Improve strip warning message
Daniel R. Roe
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DRR - Add topresnum keyword for pdb output to use topology residue numbering instead of original
Daniel R. Roe
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DRR - Update pdb trajout documentation
Daniel R. Roe
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Commits on Dec 17, 2019

Merge branch 'master' into EvalEquilibration
Daniel R. Roe
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Commits on Jan 8, 2020

Merge branch 'master' into EvalEquilibration
drroe
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Commits on Jan 17, 2020

Merge branch 'master' into EvalEquilibration
Daniel R. Roe
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Commits on Jan 28, 2020

Merge branch 'master' into EvalEquilibration
drroe
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Commits on Jan 31, 2020

Merge branch 'master' into EvalEquilibration
Daniel R. Roe
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DRR - Fix missing include from forward declare
Daniel R. Roe
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Commits on Feb 19, 2020

Merge branch 'master' into EvalEquilibration
Daniel R. Roe
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Commits on Feb 20, 2020

Merge branch 'master' into EvalEquilibration
Daniel R. Roe
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Commits on May 14, 2020

Merge branch 'master' into EvalEquilibration
drroe
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Commits on May 29, 2020

Commits on Jun 10, 2020

Merge branch 'master' into EvalEquilibration
drroe
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Commits on Jun 13, 2020

Commits on Jun 14, 2020

Revamp how hidden commands are defined. Instead of making a separate category, add a flag that marks the command as hidden. This allows the command to retain its underlying category and so things l…
drroe
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