NEEMP:Examples: Difference between revisions
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[[File:cover_mode2.png | thumb | 400px | center | '''''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 [[NEEMP:Modes#Cover (-m cover) | Cover mode]] section.]] | [[File:cover_mode2.png | thumb | 400px | center | '''''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 [[NEEMP:Modes#Cover (-m cover) | Cover mode]] section.]] | ||
=Example 3= | =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 | ;./neemp -m charges --sdf-file examples/set01.sdf --par-file examples/ElemBond.par --chg-out-file eem_charges --max-threads 8 | ||
Revision as of 11:38, 30 May 2016
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.
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.
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.