Editing NEEMP:Modes (section)

===Linear Regression (LR)===

'''''<u>BASIC USAGE:</u>''''' ''./neemp -m params -p lr-full --sdf-file examples/set01.sdf --chg-file examples/set01.chg --par-out-file new_parameters.par''

'''LR''' (<code>--params-method</code> <code>lr-full</code> or <code>-p</code> <code>lr-full</code>) is the default parametrization approach in '''NEEMP''', since its application in the parametrization process is well documented and described in literature. The main extension in respect to previous version is the ability for the user to define by which metrics the best performing parameter set will be selected ('''''see figure'''''): 

:<code>-s</code> <code>R2</code> or <code>--sort-by</code> <code>R2</code> to select the parameter set with the highest squared Pearson coefficient (R<sup>2</sup>)

:<code>-s</code> <code>RMSD</code> or <code>--sort-by</code> <code>RMSD</code> to select the parameter set with the lowest atomic type root mean square difference (avg(RMSDa))

{| class="wikitable" border="1" style="margin-left: auto; margin-right: auto;" width="650px"
 |-
 | [[File:LR_full_R2.png| 600px]]
 | [[File:LR_full_RMSD.png| 600px]]
 |- 
 |colspan=2 |'''''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).
 |}

Additionally, the quality of the parameter set may benefit from the usage of a discarding procedure (<code>-d</code> <code>simple</code> or <code>--discard</code> <code>simple</code>). In fact it has been proved that using a subset of the original training set often leads to EEM charges that better agree with the reference QM charges. For useful examples on the '''LR''' parametrization approach and the discarding procedure see respectively examples [[NEEMP:Examples#Example 3 - Parametrization mode | 3]]/[[NEEMP:Examples#Example 4 - Parametrization mode k search |4]] and [[NEEMP:Examples#Example 5 - Parametrization mode simple discard|5]]. In particular the latter introduces the <code>--limit-iters</code> and <code>--limit-time</code> options, which modulate the behaviour of the discarding procedure, setting respectively an upper bound in the number of iterations and/or in the execution time.