source: src/Actions/FragmentationAction/FitPotentialAction.def@ 503c02

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 Candidate_v1.7.0 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since 503c02 was 48d20d, checked in by Frederik Heber <heber@…>, 13 years ago

Added new action FitPotentialAction to fit empirical potentials.

  • moved functionality from levmartester into new Action.
  • removed levmartester.
  • needs both enable-levmar and path to libs/include with-levmar. This allows checking as distinct enable switch.
  • added regression test Fragmentation/FitPotential for morse and harmonic_angle fit to water molecule. Using awk to check on L2 error.
  • added take-best-of option such that fits is done as many times and best (in terms of l2 error) is used. This should make regression test FitPotential more stable (right now we take best of 5).
  • DOCU: extended construct documentation due to new PotentialTypes construct.
  • DOCU: made construct lists items appear alphabetically.
  • DOCU: extended installation documentation with VTK and levmar.
  • DOCU: also URLs for scafacos, VTK, and levmar.
  • Property mode set to 100644
File size: 2.1 KB
RevLine 
[48d20d]1/*
2 * FitPotentialAction.def
3 *
4 * Created on: Apr 08, 2013
5 * Author: heber
6 */
7
8// all includes and forward declarations necessary for non-integral types below
9#include <boost/filesystem/path.hpp>
10#include <string>
11#include <vector>
12
13#include "Parameters/Validators/RangeValidator.hpp"
14#include "Parameters/Validators/STLVectorValidator.hpp"
15#include "Parameters/Validators/Specific/ElementValidator.hpp"
16#include "Parameters/Validators/Specific/FilePresentValidator.hpp"
17#include "Parameters/Validators/Specific/PotentialTypeValidator.hpp"
18
19// i.e. there is an integer with variable name Z that can be found in
20// ValueStorage by the token "Z" -> first column: int, Z, "Z"
21// "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
22#define paramtypes (boost::filesystem::path)(std::string)(std::vector<const element *>)(std::vector<const element *>)(unsigned int)
23#define paramtokens ("homology-file")("fit-potential")("potential-charges")("fragment-charges")("take-best-of")
24#define paramdescriptions ("homology file to parse")("potential type to fit")("charges specifying the potential")("charges specifying the fragment")("take the best among this many approximations")
25#define paramdefaults (NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(NOPARAM_DEFAULT)(PARAM_DEFAULT(3))
26#define paramreferences (homology_file)(potentialtype)(charges)(fragment)(best_of_howmany)
27#define paramvalids \
28(FilePresentValidator()) \
29(PotentialTypeValidator()) \
30(STLVectorValidator< std::vector<const element *> >(1,99, ElementValidator())) \
31(STLVectorValidator< std::vector<const element *> >(1,99, ElementValidator())) \
32(RangeValidator< unsigned int>(1,99))
33
34#undef statetypes
35#undef statereferences
36
37// some defines for all the names, you may use ACTION, STATE and PARAMS
38#define CATEGORY Fragmentation
39#define MENUNAME "fragmentation"
40#define MENUPOSITION 6
41#define ACTIONNAME FitPotential
42#define TOKEN "fit-potential"
43
44
45// finally the information stored in the ActionTrait specialization
46#define DESCRIPTION "fit an empirical potential to the given part of a specified fragment"
47#undef SHORTFORM
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