NEEMP:Reports: Difference between revisions

Revision as of 17:00, 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 6 and can be obtained running NEEMP in calculation or 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.

.

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 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 1: / Line 1: @@
-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 <code>--chg-stats-out</code> (see [[NEEMP:Examples#Example 4 - Quality validation | here]] for details).
+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 ''calculation'' or ''quality validation'' mode with the option <code>--chg-stats-out</code> (see [[NEEMP:Examples#Example 4 - Quality validation | here]] for details).
 <br style="clear:both" />
-[[File:chg_stats.png | thumb | 900px | center | '''''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.]].
+[[File:chg_stats.png | thumb | 900px | center | '''''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.]].
 To generate the graphs the scripts must be called in the simple following way:
@@ Line 24: / Line 24: @@
 * ''./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 7''''' and '''''8''''' demonstrate as the correlation graphs include both all atom and individual atomic types dependency.
 {| class="wikitable" border="1" style="margin: 1em 1em 1em 1em;" width="650px"
@@ Line 31: / Line 31: @@
   | [[File:set3_DE_RMSD_B3LYP_6311G_NPA_cross_ideal_all-O1.png| 520px]]
   |-
-  |'''''Figure :''''' All atom correlation graph between ''QM charges'' (x axis) and ''EEM charges'' (y axis).
+  |'''''Figure 7:''''' All atom correlation graph between ''QM charges'' (x axis) and ''EEM charges'' (y axis).
-  | '''''Figure :''''' Correlation graph between ''QM charges'' (x axis) and ''EEM charges'' (y axis) for ''O1'' atomic type (oxygen with just single bonds).
+  | '''''Figure 8:''''' Correlation graph between ''QM charges'' (x axis) and ''EEM charges'' (y axis) for ''O1'' atomic type (oxygen with just single bonds).
   |}