NEEMP:Reports: Difference between revisions

Revision as of 08:13, 29 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 5 and can be obtained running NEEMP in quality validation mode with the option --chg-stats-out (see here for details).

**Figure 5:** 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

Figure 6 and 7 demonstrate as the correlation graphs include both all atom and individual atomic types dependency.


Figure 6: All atom correlation graph between QM charges (x axis) and EEM charges (y axis).	Figure 7: 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 6''''' and  can be obtained running '''NEEMP''' in ''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 5''''' and  can be obtained running '''NEEMP''' in ''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 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.]].
+[[File:chg_stats.png | thumb | 900px | center | '''''Figure 5:''''' 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 11: / Line 11: @@
-'''''Figure 7''''' and '''''8''''' demonstrate as the correlation graphs include both all atom and individual atomic types dependency.
+'''''Figure 6''''' and '''''7''''' 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 18: / Line 18: @@
   | [[File:set3_DE_RMSD_B3LYP_6311G_NPA_cross_ideal_all-O1.png| 520px]]
   |-
-  |'''''Figure 7:''''' All atom correlation graph between ''QM charges'' (x axis) and ''EEM charges'' (y axis).
+  |'''''Figure 6:''''' 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).
+  | '''''Figure 7:''''' Correlation graph between ''QM charges'' (x axis) and ''EEM charges'' (y axis) for ''O1'' atomic type (oxygen with just single bonds).
   |}