NEEMP:Examples: Difference between revisions
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For details on ''eem_charges'' output file, see [[NEEMP:files#CHG file | 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'''. | For details on ''eem_charges'' output file, see [[NEEMP:files#CHG file | 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'''. | ||
=Example 4= | =Example 4 - Cross mode= | ||
;./neemp -m cross --sdf-file examples/set02.sdf --chg-file examples/charges.chg --par-file examples/Element.par --atom-types-by Element 2> warns > log | ;./neemp -m cross --sdf-file examples/set02.sdf --chg-file examples/charges.chg --par-file examples/Element.par --atom-types-by Element 2> warns > log | ||
:Perform cross-validation of EEM parameters for atoms grouped by element only. Save standard output into the file ''log'' and warnings into the file ''warns''. | :Perform cross-validation of EEM parameters for atoms grouped by element only. Save standard output into the file ''log'' and warnings into the file ''warns''. | ||
For more information on this mode click [[NEEMP:Modes#Cross-validation (-m cross) | here]]. | |||
=Example 5= | =Example 5= | ||
Revision as of 13:41, 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.
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.
Example 4 - Cross mode
- ./neemp -m cross --sdf-file examples/set02.sdf --chg-file examples/charges.chg --par-file examples/Element.par --atom-types-by Element 2> warns > log
- Perform cross-validation of EEM parameters for atoms grouped by element only. Save standard output into the file log and warnings into the file warns.
For more information on this mode click here.