Syncing up ericchansen/q2mm and q2mm/q2mm#26
Merged
ericchansen merged 29 commits intoericchansen:masterfrom Jun 8, 2016
Merged
Syncing up ericchansen/q2mm and q2mm/q2mm#26ericchansen merged 29 commits intoericchansen:masterfrom
ericchansen merged 29 commits intoericchansen:masterfrom
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NImag is the same value as the number of negative frequencies. Some optimized structures have additional negative frequencies that have small magnitudes.
… be sorted within 'CDAT' and 'RDAT'. This is done in the same fashion as in compare.py. Prior to this change the ref and calc data was not in the same order and gave an incorrect comparison. It might be better to actually have this sort function already built into calculate.py, or to have loop.py call the dictionaries from compare.py.
Updated Filetypes
Ignored 0cb9ee5. - Not a useful commit. Only added demo text. Added 0924b02. - Added the old Rh FF. Added e080aa3. - Added helpful information to FF. Ignored 53c0618. - Deleted useless commit cb9ee577bdc99ea52a. Added 4667898. - Modified regex for reading Gaussian archives. The change from NImag=[10] (accepts 1 or 0 imaginary frequencies) to NImag=[0-9] (accepts 0 through 9 imaginary frequencies) was helpful. However, it should be NImag=\d+ to be the most robust. Will make this change soon. Ignored b5faa7e. - Unnecessary merge commit. Added 9d281d1. - Fixed variable misname in calculate.py. Added 5949029. - Added helpful information to Rh FF. Ignored 9aa4b29. - Added sorting to compare.py. However, this was handled more efficiently by an earlier commit in this repository, bbeb5e9. Added ab7440a. - Contains more robust handling of torsional data points. However, this method can still lead to errors and needs to be addressed. Actually, this entire process of getting geometric data from the .mmo is inefficient. It should really just be done from the .mae and some sort of connectivity scheme. Still, that's a lot of coding to ask for. Also removed some references to no longer used datatypes. Ignored 998fad2. - This is a merge commit from something that already exists in this repository. Ignored 6ccc25f. - This was a commit that already exists in this repository and was added to Q2MM/q2mm from the wrong fork.
Previously used NImag=[0-9] as the regex to detect the number of imaginary frequencies. However, NImag=\d+ is more robust.
…cchansen-master Conflicts: filetypes.py
…cchansen-master
Added FF for sulfones and combined FF.
Improved handling of reference data files and removed sorting of data
For any parameter that is 0.0 (many torsions). This now only picks out the parameters that are nonzero. If a user wants to optimize any parameter, then they simply have to use a nonzero value in the mm3.fld file, which should already be done.
Sorting was still present in RDAT and CDAT, and so those lines of code were removed. Added section with COMP command now allows you to just print out results on the front end if you do not put any output option. Added a new command for a loop input file called WGHT or weight. This allows as user to adjust the default weights of a data type without having to edit the constants.py textfile.
Clean up, and feature addition to loop.py
This reverts commit 69f9c1d. The option --nozero already existed, which does the same thing as what is in this commit, but is more flexible for the user.
Two identical FF's were in the ForceFields folder. I kept the one that uses the all lowercase naming scheme. I think it looks better.
Attempting to merge everyone's changes
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* ESP RMS for a charge scheme This is code that was borrowed from Anna Tomberg and modified to fit the Q2MM organization. Simply put I added two new commands "-mgESP" and "-mjESP" which take two files filename.mae,filename.chk and filename.mae,filename.in, respectively. I have not finished coding the "-mjESP" section, as I do not know of anyone who really wants the Jaguar end of this. For a loop, use the following syntax: RDAT -r some_ref_text_file.txt CDAT -mgESP filename.mae,filename.chk This will take filename.mae and determine the partial charges from the force field and then write them into a gaussian com file (filename.ESP.q2mm.com) which will calculate the RMS when compared to the ESP found in filename.chk. I added a few things into constants.py that should be expanded. 1) Gaussian methods with just a few common functions that we have used in the lab 2) CHELPG radii that are used. This is important for metals that do not have built in radii. A GaussCom class was added to filetypes, and the GaussLog class was modified to read in the RMS from the resulting filename.ESP.q2mm.log file. I have not yet checked to see how compatible this code is with more data types. I imagine there is probably some sorting errors that happen. * Bug: Early Return in GaussLog class After adding in the ESP_fit commit previously I included an early return argument in the read_out function of the GaussLog class. This had been remedied so it shouldn't be a problem anymore. * Will add comments later. * Minor bug fixes There were bugs where atom objects would not have consistent properties, such as an atom type corresponding to Ru but still contained old information from the merging process such as the atomic number.
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There's been a lot of changes, some good, some not so good, some not well documented. Anyway, we need to sync things up every now and then.