NEEMP:Examples

This section shows several use case examples. All of them use only data from examples directory.

NB: NEEMP is case-sensitive. Please follow carefully this section for insight on the correct syntax. Additional information can be found here.

Example 1 - Info mode

./neemp -m info --atom-types-by ElemBond --sdf-file examples/set01.sdf

Prints information about training set, group atoms according to chemical element and bond order.

Figure 5: Output for the Info mode. For more information on this mode refer to Info mode section.

Example 2 - Cover mode

./neemp -m cover -sdf-file examples/set02.sdf --par-file examples/Element.par --atom-types-by Element

Calculate coverage of supplied EEM parameters and molecules set.

Figure 6: Complete output for the Cover mode summarizing information about the input files, molecules set composition and coverage. For more information on this mode refer to Cover mode section.

Example 3 - Charges mode

./neemp -m charges --sdf-file examples/set01.sdf --par-file examples/ElemBond.par --chg-out-file eem_charges --max-threads 8

Compute EEM charges and store them into the file eem_charges. Use up to 8 threads for computation.

For more information on this mode and its output, refer to Charges mode section.

For details on eem_charges output file, see CHG file paragraph, as the format is the same. The only different regards the third column, since in this case the EEM charges are listed in place of the ab-initio charges.