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Request for logging of intermediate data #8

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ericchansen opened this issue Aug 26, 2015 · 3 comments
Open

Request for logging of intermediate data #8

ericchansen opened this issue Aug 26, 2015 · 3 comments
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@ericchansen
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Older versions of the code generated tables of data in files par.one, par.ref, and par.tot. A description of the files can be found in Per-Ola Norrby and Tommy Liljefors, J. Comput. Chem. 1998, 19, 1146-1166. It would be nice to still have access to these files or perhaps something similar.
@ericchansen
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There have been a lot of updates in regards to this. For the desired level of verbosity, try adjusting the logging levels in the constants module. For more information on logging levels, please refer to the documentation.

I'm going to add an option to write the Jacobian matrix to a file. Once this has been completed, I'll consider this issue closed.

@ericchansen
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I think once the Jacobian read and write functionality is added, this issue can be closed.

ericchansen added a commit that referenced this issue Jun 13, 2016
@ericchansen
Merge pull request #8 from ericchansen/master
0209a71 
I know I'm outspoken against merging one's own code into master without someone else reviewing it 1st, but I sort of need to do this to start working on what's going on with the bugs in simplex. Sorry!

There's no major changes in here though.

While debugging recent changes, I set whether or not to use many of the gradient methods to False. That was strictly for my testing, and I never meant to commit that into master. Within here, I changed them all back to True in commit 5fae1a1.
Added in more retries for MacroModel jobs. See commits 7fea00a and ebb75f1.
Tony made a nice regex change in commit 0902093.
@ericchansen
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Commit cb36b4c has helped move this issue forward significantly. This enabled one to restart the gradient optimization from the parameter central differentiation file.

I think all that is needed now is the option to print or write the Jacobian.

This probably will necessitate that gradient be runnable from the command line with argument handling.

ericchansen added a commit that referenced this issue Jun 29, 2016
@ericchansen
Moved calculation of derivatives outside NR
e3fca18 
Derivatives are now calculcated every time.

Unfortunately, there is still no way to calculate derivatives if we
restart the job from a par_diff_???.txt file.

References issue #22 and #8.
ericchansen added a commit that referenced this issue Jun 29, 2016
@ericchansen
Moved calculation of derivatives outside NR
6034a16 
Derivatives are now calculcated every time.

Unfortunately, there is still no way to calculate derivatives if we
restart the job from a par_diff_???.txt file.

References issue #22 and #8.
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@ericchansen