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Bug #486

Formatting in g_analyze help info messes up the manual

Added by Justin Lemkul over 9 years ago. Updated over 9 years ago.

Status:
Closed
Priority:
Normal
Category:
documentation
Target version:
Affected version - extra info:
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Description

I think there are some formatting issues with the description in g_analyze. I'm still figuring out how the manual all goes together, but I think there are some problems with the newly-added text that causes the automatic parsing to get screwed up. If you look at Appendix D of the current 4.5 beta manual, the formatting goes haywire during the description of g_analyze -balfind. I think there are typos in the source code that give rise to the issues. I think the corrected section should read:

"Option [TT]-bal[tt] finds and subtracts the ultrafast \"ballistic\"",
"component from a hydrogen bond autocorrelation function by the fitting",
"of a sum of exponentials, as described in e.g.",
"O. Markovitch, J. Chem. Phys. 129:084505, 2008. The fastest term",
"is the one with the most negative coefficient in the exponential,",
"or with [TT]-d[tt], the one with most negative time derivative at time 0.",
"Option [TT]-nbalexp[tt] sets the number of exponentials to fit.[PAR]",
"Option [TT]-gem[tt] fits bimolecular rate constants ka and kb",
"(and optionally kD) to the hydrogen bond autocorrelation function",
"according to the reversible geminate recombination model. Removal of",
"the ballistic component first is strongly advised. The model is presented in",
"O. Markovitch, J. Chem. Phys. 129:084505, 2008.[PAR]",

I tried generating the g_analyze.tex file and it seems to have worked, removing a bunch of extraneous (and unmatched) {\tt formatting indicators.

History

#1 Updated by David van der Spoel over 9 years ago

Fixed, thanks for reporting.

#2 Updated by David van der Spoel over 9 years ago

FIxed!

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