View source for Mod:Hunt Research Group/Jan generate esp

=using Jan's code to generate and evaluate an esp from given partial charges on a particular mesh=
==introduction==
*we want to create esp cube files from given partial charges and compare these
*to compare cube files they must have the same internal structure (ie same number of points)
*see the wiki and gaussian website for cubegen "http://gaussian.com/cubegen/" and cubman "http://gaussian.com/cubman/"  for more info on generating gaussian cubes with the same structure
*here we will be using one cube file as a template for the one to be produced thus allowing for comparison
*the best comparison point is the "real" esp created earlier ie the gaussian cube generated esp file

==create our own ESP from given partial charges and mesh==
*the script we need is '''rep_esp.py'''
*creates a gaussian cube file of the esp
*for instructions run with -h argument "rep_esp.py -h"
*required arguments are
::input charge type=name the charges to be extracted options are 'mulliken', 'nbo', 'aim', 'mk', 'chelp', 'chelpg', 'hly', or 'list' if the charges are to be provided from a text file
::input charge file = file to extract charges from this can be a gaussian.log file or a text file if you have used resp
::template cube file = name of file with a template esp, this is necessary to compare the cube files
*then add -o file to direct the output to a named cube file (remove the .cub extension)
*for example creating a cube file from the gaussian mk charges, and the resp_mk charges
<pre>
rep_esp.py mk ch3oh_mk.log ch3oh_esp.cub -o ch3oh_mk_esp
rep_esp.py list resp_charges_mk.txt ch3oh_esp.cub -o ch3oh_resp_mk_esp
</pre>

==compare our ESP files==
*we want to compare the partial charge derived esp cube files to the "proper" esp obtained from the electronic density
*for this we use '''field_diff.py'''
*required arguments are
::input cube file=real esp cube file file.cub
::input charge file = file to extract charges from this can be a gaussian.log file or a text file if you have used resp
::template cube file = name of file with a template esp, this is necessary to compare the cube files
*options include
::"-o filename"  (remove the .cub extension) to direct the output to a named cube file
::"--absolute" to get the absolute error (ie all positive)
::"--relative" to get the relative value ie the error divided by the value of the field at this point '''some problems here!'''
::"--exclude density.cub iso-value distance" to exclude points lying closer than the electron density iso-surface given,
:::: for this you need to specify an electron density cube denisty.cube, an iso-value and a distance?

{| style="background-color:#ffffff; border-style:none; border-width:0px"
|colspan="2" style="background-color:#cccccc;"|
:field_diff.py ch3oh_esp.cub ch3oh_resp_mk_esp.cub -o ch3oh_real_vs_resp_mk_diff_esp 
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*open the cub file in gaussview and play around with the iso-surface values
*starting with 0.004 is a good option
*here I have compared the real esp and the esp generated from the 
:: equivalenced mk charges, remember this is a difference!
|[[File:Esp_diff_real_vs_resp_mk_1.png |300px|thumb|right|esp 0.004 difference iso-surface for ch3oh]]
|-
|colspan="2" style="background-color:#cccccc;"|
:field_diff.py --exclude ch3oh_den.cub 0.008 0.001 ch3oh_esp.cub ch3oh_resp_mk_esp.cub -o ch3oh_real_vs_resp_mk_exclude_diff_esp
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*not sure what use this is but
*excluded within the 0.008 density sphere (this contour is shown in slightly deeper colour)
*rest is a contour plot of the esp difference
*and the 3D is the difference iso-surface at 0.004
|[[File:Esp_diff_real_vs_resp_mk_exlude_1.png |300px|thumb|right|esp difference with exclusion zone for ch3oh]]
|}