NEEMP:Examples - Revision history

Francesco: /* Example 7 - Coverage validation */

2016-07-07T15:03:50Z

Example 7 - Coverage validation

← Older revision		Revision as of 15:03, 7 July 2016
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	;./neemp -m cover -sdf-file examples/set02.sdf --par-file examples/ElemBond.par		;./neemp -m cover -sdf-file examples/set02.sdf --par-file examples/ElemBond.par

	:Calculate coverage of supplied molecules set given a specific parameter set. For more information on this mode refer to [[NEEMP:Modes#Coverage validation \| ~~Cover~~ validation]] section.		:Calculate coverage of supplied molecules set given a specific parameter set. For more information on this mode refer to [[NEEMP:Modes#Coverage validation \| Coverage validation]] section.
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Krab1k at 10:44, 5 July 2016

2016-07-05T10:44:02Z

← Older revision		Revision as of 10:44, 5 July 2016
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	=Example 5 - Parametrization mode simple discard=		=Example 5 - Parametrization mode simple discard=

	;./neemp -m params -p lr-full --sdf-file examples/set01.sdf --chg-file examples/set01.chg --discard simple -v ~~--check-charges~~ --limit-iters 600 --limit-time <nowiki>00:30:00</nowiki>		;./neemp -m params -p lr-full --sdf-file examples/set01.sdf --chg-file examples/set01.chg --discard simple -v --limit-iters 600 --limit-time <nowiki>00:30:00</nowiki>

	:Perform simple discarding with '''LR''' approach and print its progress. Issue warning about molecules with abnormal values of statistical descriptors. The duration of the discarding procedure can be at most 600 iterations or 30 minutes (time format HH:MM:SS), whichever is reached first.		:Perform simple discarding with '''LR''' approach and print its progress. Issue warning about molecules with abnormal values of statistical descriptors. The duration of the discarding procedure can be at most 600 iterations or 30 minutes (time format HH:MM:SS), whichever is reached first.

Francesco at 16:59, 29 June 2016

2016-06-29T16:59:44Z

← Older revision		Revision as of 16:59, 29 June 2016
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	[[File:info_mode.png \| thumb \| 400px \| center \| '''''Figure 10:''''' Information about structures set ''examples/set01.sdf''.]]		[[File:info_mode.png \| thumb \| 400px \| center \| '''''Figure 9:''''' Information about structures set ''examples/set01.sdf''.]]

	=Example 2 - Calculation mode=		=Example 2 - Calculation mode=
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	\| [[File:ksearch2.png\| 700px]]		\| [[File:ksearch2.png\| 700px]]
	\|-		\|-
	\| '''''Figure 11:''''' Detailed view of the parametrization settings from the execution of the above command. In particular note the usage of a different evaluating statistics (''RMSD'') and the custom range for the k search.		\| '''''Figure 10:''''' Detailed view of the parametrization settings from the execution of the above command. In particular note the usage of a different evaluating statistics (''RMSD'') and the custom range for the k search.
	\| '''''Figure 12:''''' Abridged output for the k search progress. For each k value a set of parameters is generated and evaluated. In this particular instance, the parameters set with the lowest ''RMSD'' value is chosen.		\| '''''Figure 11:''''' Abridged output for the k search progress. For each k value a set of parameters is generated and evaluated. In this particular instance, the parameters set with the lowest ''RMSD'' value is chosen.
	\|}		\|}

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	[[File:simple_discard.png \| thumb \| 800px \| center \| '''''Figure 13:''''' Abridged output for the simple discard progress. The simple discarding requires as many iterations as the number of molecules in the set, unless the iterations or time limits are reached first. In this case the training set contains only 500 structures so the iteration limit doesn't affect the discarding. The time limit still holds on the other hand. Refer to the [[NEEMP:Modes#Linear Regression (LR) \| parametrization paragraph]] for details.]]		[[File:simple_discard.png \| thumb \| 800px \| center \| '''''Figure 12:''''' Abridged output for the simple discard progress. The simple discarding requires as many iterations as the number of molecules in the set, unless the iterations or time limits are reached first. In this case the training set contains only 500 structures so the iteration limit doesn't affect the discarding. The time limit still holds on the other hand. Refer to the [[NEEMP:Modes#Linear Regression (LR) \| parametrization paragraph]] for details.]]

	=Example 6 - Parametrization mode DE-MIN=		=Example 6 - Parametrization mode DE-MIN=
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	[[File:cover_mode2.png \| thumb \| 400px \| center \| '''''Figure 14:''''' Output from ''Cover mode''. In this case the parameter set ''ElemBond.par'' lacks the parameters for all the marked atomic types in ''set02.sdf'', leading to the discard of 1690 molecules. Note the resemblance with [[NEEMP:Modes#Calculation mode \| ''Calculation mode'']] output for a similar low coverage circumstance.]]		[[File:cover_mode2.png \| thumb \| 400px \| center \| '''''Figure 13:''''' Output from ''Cover mode''. In this case the parameter set ''ElemBond.par'' lacks the parameters for all the marked atomic types in ''set02.sdf'', leading to the discard of 1690 molecules. Note the resemblance with [[NEEMP:Modes#Calculation mode \| ''Calculation mode'']] output for a similar low coverage circumstance.]]

	=Example 8 - Quality validation=		=Example 8 - Quality validation=
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	[[File:chg_stats.png \| thumb \| 900px \| center \| '''''Figure 15:''''' Close-up from ''stats'' file. Along with statistics for each molecule, ''ab-initio'' charges (3rd column), ''EEM'' charges (4th column) and their difference (5th column) are also printed out.]]		[[File:chg_stats.png \| thumb \| 900px \| center \| '''''Figure 14:''''' Close-up from ''stats'' file. Along with statistics for each molecule, ''ab-initio'' charges (3rd column), ''EEM'' charges (4th column) and their difference (5th column) are also printed out.]]

Francesco: /* Example 8 - Quality validation */

2016-06-29T14:01:29Z

Example 8 - Quality validation

← Older revision		Revision as of 14:01, 29 June 2016
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	=Example 8 - Quality validation=		=Example 8 - Quality validation=

	;./neemp -m quality --sdf-file examples/set01.sdf --chg-file examples/set01.chg --par-file examples/~~Element~~.par --chg-stats-out stats ~~--atom-types-by Element~~ 2> warns > log		;./neemp -m quality --sdf-file examples/set01.sdf --chg-file examples/set01.chg --par-file examples/ElemBond.par --chg-stats-out-file stats 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''. Moreover ~~outputs~~ charge statistics for each molecule into the file ''stats''.		:Perform quality validation of EEM parameters for atoms grouped by atomic type. Save standard output into the file ''log'' and warnings into the file ''warns''. Moreover output charge statistics for each molecule into the file ''stats''.

	For more information on this mode click [[NEEMP:Modes#Quality validation \| here]].		For more information on this mode click [[NEEMP:Modes#Quality validation \| here]].
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	[[File:chg_stats.png \| thumb \| 900px \| center \| '''''Figure 12:''''' Close-up from ''stats'' file. Along with statistics for each molecule, ''ab-initio'' charges (3rd column), ''EEM'' charges (4th column) and their difference (5th column) are also printed out.]]		[[File:chg_stats.png \| thumb \| 900px \| center \| '''''Figure 15:''''' Close-up from ''stats'' file. Along with statistics for each molecule, ''ab-initio'' charges (3rd column), ''EEM'' charges (4th column) and their difference (5th column) are also printed out.]]

Francesco: /* Example 8 - Quality validation */

2016-06-29T13:58:56Z

Example 8 - Quality validation

← Older revision		Revision as of 13:58, 29 June 2016
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	=Example 8 - Quality validation=		=Example 8 - Quality validation=

	;./neemp -m ~~cross~~ --sdf-file examples/~~set02~~.sdf --chg-file examples/~~charges~~.chg --par-file examples/Element.par --chg-stats-out stats --atom-types-by Element 2> warns > log		;./neemp -m quality --sdf-file examples/set01.sdf --chg-file examples/set01.chg --par-file examples/Element.par --chg-stats-out stats --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''. Moreover outputs charge statistics for each molecule into the file ''stats''.		: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''. Moreover outputs charge statistics for each molecule into the file ''stats''.

Francesco: /* Example 7 - Coverage validation */

2016-06-29T13:40:43Z

Example 7 - Coverage validation

← Older revision		Revision as of 13:40, 29 June 2016
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	;./neemp -m cover -sdf-file examples/set02.sdf --par-file examples/ElemBond.par		;./neemp -m cover -sdf-file examples/set02.sdf --par-file examples/ElemBond.par

	:Calculate coverage of supplied molecules set given a specific parameter set.		:Calculate coverage of supplied molecules set given a specific parameter set. For more information on this mode refer to [[NEEMP:Modes#Coverage validation \| Cover validation]] section.
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	[[File:cover_mode2.png \| thumb \| 400px \| center \| '''''Figure 14:''''' Output from ''Cover mode''. In this case the parameter set ''ElemBond.par'' lacks the parameters for all the marked atomic types in ''set02.sdf'', leading to the discard of 1690 molecules. Note the resemblance with [[NEEMP:Modes#Calculation mode \| ''Calculation mode'']] output for similar low coverage circumstance~~. For more information on this mode refer to [[NEEMP:Modes#Coverage validation \| Cover validation]] section~~.]]		[[File:cover_mode2.png \| thumb \| 400px \| center \| '''''Figure 14:''''' Output from ''Cover mode''. In this case the parameter set ''ElemBond.par'' lacks the parameters for all the marked atomic types in ''set02.sdf'', leading to the discard of 1690 molecules. Note the resemblance with [[NEEMP:Modes#Calculation mode \| ''Calculation mode'']] output for a similar low coverage circumstance.]]

	=Example 8 - Quality validation=		=Example 8 - Quality validation=

Francesco: /* Example 7 - Coverage validation */

2016-06-29T13:39:06Z

Example 7 - Coverage validation

← Older revision		Revision as of 13:39, 29 June 2016
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	[[File:cover_mode2.png \| thumb \| 400px \| center \| '''''Figure 14:'''''Output from ''Cover mode'' ~~summarizing information about the input files, molecules set composition and coverage~~. In this case the parameter set ''ElemBond.par'' lacks the parameters for all the marked atomic types in ''set02.sdf'', leading to the discard of 1690 molecules. Note the resemblance with [[NEEMP:Modes#Calculation mode \| ''Calculation mode'']] output for similar low coverage circumstance. For more information on this mode refer to [[NEEMP:Modes#Coverage validation \| Cover validation]] section.]]		[[File:cover_mode2.png \| thumb \| 400px \| center \| '''''Figure 14:''''' Output from ''Cover mode''. In this case the parameter set ''ElemBond.par'' lacks the parameters for all the marked atomic types in ''set02.sdf'', leading to the discard of 1690 molecules. Note the resemblance with [[NEEMP:Modes#Calculation mode \| ''Calculation mode'']] output for similar low coverage circumstance. For more information on this mode refer to [[NEEMP:Modes#Coverage validation \| Cover validation]] section.]]

	=Example 8 - Quality validation=		=Example 8 - Quality validation=

Francesco: /* Example 7 - Coverage validation */

2016-06-29T13:37:20Z

Example 7 - Coverage validation

← Older revision		Revision as of 13:37, 29 June 2016
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	[[File:cover_mode2.png \| thumb \| 400px \| center \| '''''Figure 14:''''' ~~Close up~~ from ~~the output for~~ ''Cover mode'' summarizing information about the input files, molecules set composition and coverage. In this case the parameter set ''ElemBond.par'' lacks the parameters for all the marked atomic types in ''set02.sdf'', leading to the discard of 1690 molecules. Note the ~~similarities~~ with ''Calculation mode'' output ~~in the case of~~ low coverage circumstance. For more information on this mode refer to [[NEEMP:Modes#Coverage validation \| Cover validation]] section.]]		[[File:cover_mode2.png \| thumb \| 400px \| center \| '''''Figure 14:'''''Output from ''Cover mode'' summarizing information about the input files, molecules set composition and coverage. In this case the parameter set ''ElemBond.par'' lacks the parameters for all the marked atomic types in ''set02.sdf'', leading to the discard of 1690 molecules. Note the resemblance with [[NEEMP:Modes#Calculation mode \| ''Calculation mode'']] output for similar low coverage circumstance. For more information on this mode refer to [[NEEMP:Modes#Coverage validation \| Cover validation]] section.]]

	=Example 8 - Quality validation=		=Example 8 - Quality validation=

Francesco: /* Example 7 - Coverage validation */

2016-06-29T13:32:26Z

Example 7 - Coverage validation

← Older revision		Revision as of 13:32, 29 June 2016
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	[[File:cover_mode2.png \| thumb \| 400px \| center \| '''''Figure 14:''''' ~~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#Coverage validation \| Cover validation]] section.]]		[[File:cover_mode2.png \| thumb \| 400px \| center \| '''''Figure 14:''''' Close up from the output for ''Cover mode'' summarizing information about the input files, molecules set composition and coverage. In this case the parameter set ''ElemBond.par'' lacks the parameters for all the marked atomic types in ''set02.sdf'', leading to the discard of 1690 molecules. Note the similarities with ''Calculation mode'' output in the case of low coverage circumstance. For more information on this mode refer to [[NEEMP:Modes#Coverage validation \| Cover validation]] section.]]

	=Example 8 - Quality validation=		=Example 8 - Quality validation=

Francesco: /* Example 7 - Coverage validation */

2016-06-29T13:18:44Z

Example 7 - Coverage validation

← Older revision		Revision as of 13:18, 29 June 2016
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	=Example 7 - Coverage validation=		=Example 7 - Coverage validation=

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

	:Calculate coverage of supplied ~~EEM parameters and~~ molecules set.		:Calculate coverage of supplied molecules set given a specific parameter set.
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