NEEMP:Reports: Difference between revisions
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Along with '''NEEMP''' we provide an handy python script to generate charge correlation graphs and quality assay reports, namely '''''nut-report.py'''''. To run the above-mentioned script, ''python'' and ''R'' packages must be installed in the system. | Along with '''NEEMP''' we provide an handy python script to generate charge correlation graphs and quality assay reports, namely '''''nut-report.py'''''. To run the above-mentioned script, ''python'' and ''R'' packages must be installed in the system. | ||
'''''Figure 5''''' displays the required input file in which for each atom the difference between the ''reference QM charge'' and the ''EEM charge'' is calculated. Such a file can be obtained running '''NEEMP''' in ''quality validation'' mode with the option <code>--chg-stats-out</code> (see [[NEEMP:Examples#Example 8 - Quality validation | example]] or [[NEEMP:Modes#Quality validation | quality validation]] for details). | '''''Figure 5''''' displays the required input file in which for each atom the difference between the ''reference QM charge'' and the ''EEM charge'' is calculated. Such a file can be obtained running '''NEEMP''' in ''quality validation'' mode with the option <code>--chg-stats-out</code> (see [[NEEMP:Examples#Example 8 - Quality validation | example]] or [[NEEMP:Modes#Quality validation | quality validation]] for details). | ||
'''''<u>SCRIPT BASIC USAGE:</u>''''' ''./nut-report.py chg-stats-out-file'' | |||
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[[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.]]. | [[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.]]. | ||
'''''Figure 6''''' and '''''7''''' 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. | ||
Revision as of 09:44, 29 June 2016
Along with NEEMP we provide an handy python script to generate charge correlation graphs and quality assay reports, namely nut-report.py. To run the above-mentioned script, python and R packages must be installed in the system.
Figure 5 displays the required input file in which for each atom the difference between the reference QM charge and the EEM charge is calculated. Such a file can be obtained running NEEMP in quality validation mode with the option --chg-stats-out (see example or quality validation for details).
SCRIPT BASIC USAGE: ./nut-report.py chg-stats-out-file
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Figure 6 and 7 demonstrate as the correlation graphs include both all atom and individual atomic types dependency.
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| 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). |