Editing ChargeCalculator:FAQ (section)

=How do I add EEM parameters if they do not exist?=

EEM, the empirical approach used by '''ACC''' to calculate atomic charges, operates with atom types primarily based on chemical elements. When uploading the input file, '''ACC''' seeks to establish the chemical element of each atom, so that it can assign a suitable atom type, and subsequently EEM parameters. If '''ACC''' does not recognize the chemical element for an atom, it will report an <span style="color:#DAA520">''unknown chemical element name''</span> warning. If '''ACC''' recognizes the chemical element but cannot find any EEM parameters associated with it, it will report <span style="color:#DAA520">''Missing Atoms''</span>. Either way, '''ACC''' will not include this atom in the atomic charge calculation. 

To make sure that even such problematic atoms are included in the calculation, you must use a custom EEM parameter set. At this point, if you have not done so till now, please have a look at [[ChargeCalculator:FAQ#How_do_I_read_the_XML_file_with_EEM_parameters.3F | how to read the XML file with EEM parameters]] before you proceed.

First, in the table with EEM parameter sets, click on one of the [[ChargeCalculator:FAQ#How_do_I_choose_a_suitable_EEM_parameter_set.3F | suitable built-in parameter sets]] already available. Basic information about the set will be displayed in the panel to the right of the table. Then click the black ''View XML'' button at the top of this panel with information. A new tab will open in your browser where the content of the EEM parameter set will be displayed in XML format. Copy the content of this page, then return to the '''ACC Setup page'''. Click the black ''Add'' button on top of the table with parameter sets. A small window will open, where you select all the content (CTRL+A) and replace it with the content of the parameter set you previously viewed and copied (CTRL+V).

You now have a copy of the built-in EEM parameter set. The idea is that you will need to actually define a new atom type and corresponding EEM parameters for the chemical element that is unknown or for which no EEM parameters are available. Pick a chemical element that has similar chemical properties (especially electronegativity and hardness) to the new chemical element you wish to introduce. Copy the whole content between the start and closing ''Element'' tags, and then paste this content inside the ''Parameters'' tag, but outside other ''Element'' tags. Now modify the attribute ''Name'' to the chemical element you wish to include. Then, inside each ''Bond'' tags, you will find the values for parameters ''A'' and ''B''. You may keep these values, or modify them. You may repeat this procedure for as many new chemical elements as you need.

Save the new EEM parameter set with a unique name. '''ACC''' will validate the syntax and let you know if any further modifications are necessary. When you return to the '''ACC Setup page''', select your new parameter set from the table. When you start your computation, the atoms with previously unknown chemical elements or missing EEM parameters will now be included in the calculation, although the EEM parameters might not be optimal.

Note that you need not copy/paste content and make modifications as described here. You can directly use the XML form provided in the window which opens when you click the ''Add'' button, as long as you respect the XML syntax.