NEEMP:Reports: Difference between revisions

Revision as of 11:57, 27 June 2016

All the graphs in NEEMP's article showing the correlation between reference charges and EEM charges, have been generated employing two python scripts, nut-report.py and nut.plot.py. The required input file must contain the charge statistics as shown in figure 6 and can be obtained running NEEMP in quality validation mode with the option --chg-stats-out (see here for details).

**Figure 6:** Close-up from charge statistics file. Along with statistics for each molecule, *ab-initio* charges (3rd column), *EEM* charges (4th column) and their difference (5th column) are also printed out.

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To generate the graphs the scripts must be called in the simple following way:

First:

./nut-report.py charge-stat-file

Figure 7 and 8 demonstrate as the correlation graphs include both all atom and individual atomic types dependency.


Figure 7: All atom correlation graph between QM charges (x axis) and EEM charges (y axis).	Figure 8: Correlation graph between QM charges (x axis) and EEM charges (y axis) for O1 atomic type (oxygen with just single bonds).

@@ Line 10: / Line 10: @@
 * ''./nut-report.py charge-stat-file''
-'''Then''':
-* ''./nut-plot.py set01-data.csv colorful 5''
-* ''./nut-plot.py set01-data.csv blackwhite 5''
-* ''./nut-plot.py set01-data.csv colorfulbig 5''
-* ''./nut-plot.py set01-data.csv colorful-zoomed  5''
-* ''./nut-plot.py set01-data.csv blackwhite-zoomed 5''
-* ''./nut-plot.py set01-data.csv colorfulbig-zoomed 5''
 '''''Figure 7''''' and '''''8''''' demonstrate as the correlation graphs include both all atom and individual atomic types dependency.