NEEMP:Reports: Difference between revisions

Revision as of 16:49, 23 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 and can be obtained running NEEMP in calculation or quality validation mode with the option --chg-stats-out (see here for details).

**Figure 8:** 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

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


Figure 2: Detailed view of the LR parametrization settings for two distinct NEEMP executions differing in the best-performance selection metrics (R² in left side image and RMSD in the right side image).	Figure 10: Abridged output for the k search progress. For each k value a set of parameters is generated and evaluated. In this particular instance, the parameters set with the lowest RMSD value is chosen.

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   |-
   | [[File:set3_DE_RMSD_B3LYP_6311G_NPA_cross_ideal_all-summary.png| 620px]]
-  | [[File:set3_DE_RMSD_B3LYP_6311G_NPA_cross_ideal_all-O1.png| 620px]]
+  | [[File:set3_DE_RMSD_B3LYP_6311G_NPA_cross_ideal_all-O1.png| 420px]]
   |-
   |'''''Figure 2:''''' Detailed view of the '''LR''' parametrization settings for two distinct '''NEEMP''' executions differing in the best-performance selection metrics (''R<sup>2</sup>'' in left side image and ''RMSD'' in the right side image).
   | '''''Figure 10:''''' Abridged output for the k search progress. For each k value a set of parameters is generated and evaluated. In this particular instance, the parameters set with the lowest ''RMSD'' value is chosen.
   |}