source: src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp@ 2a0a9e3

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 2a0a9e3 was e4afb4, checked in by Frederik Heber <heber@…>, 15 years ago

Huge refactoring: Introduction of Traits to Actions.

This change is really big but the introduction of the Trait concept (at least
in its current light form) is so fundamental that lots of pieces had to be
changed in order to get everything working.

The main point why it was necessary to add these traits in the first place was
to comfortably allow for adding extension of Actions information-wise, i.e.
with stuff that is only important for the QtUI, such as icons, or tooltips, ...
This extra information should not be stored with Action itself, as it has
nothing to do with the workings of the Action. And neither should it get
stored with some blown-out-of-proportions MapOfActions class ...

The gist of the change is as follows:

  • OptionTrait contains the token, description, shortform and type of an option, such as ("position", "position in space, none, typeid(Vector)).
  • ActionTrait is the derived form for actions where additionally MenuPosition and MenuName are stored (and probably more to come for the GUI), also we have a set of OptionTrait instances, one for each option of the Action.
  • Action then contains this ActionTrait, specialized for each Action.
  • the preprocessor macros have been enhanced to gather all this information from the .def files.
  • MapOfActions is gone. Completely. Most of its use was to store this extra information and the ValueStorage part now is just in class ValueStorage.
  • ValueStorage is no more an interface to MapOfActions but as the name says a (type-safe) ValueStorage.

Listing the (remaining) changes in alphabetical order of the class:

  • Action
    • member value ::name dropped, ::getName() uses ActionTraits::getName()
    • new define NODEFAULT which is used in paramdefaults in .def files
    • all derived actions classes such as Process, Calculations, MakroAction,... have been adapated to use the ActionTrait concept as well.
  • ActionHistory
    • extraced RedoAction and UndoAction, shifted implementation into their own object files and they use .def files as well (i.e. streamlined with method used for other actions)
  • MenuDescription
    • contain information on Menus such as name, ...
    • new unit test checks for consistency
  • molecule
    • const member functions: Copy(), Output() and OutputBonds()
  • OptionRegistry
    • new registry class for options only
    • we want the same type throughout the code for each token, e.g. "position"
    • the registry containts checks for consistency
  • OptionTrait
    • default values are specified in paramdefaults, none are given by NODEFAULT
    • introduced default for translate-atoms, point-correlation, pair-correlation
  • Registry pattern
    • new unit test, but only sceleton code so far
  • ...Query, also ...Pipe
    • atoms, molecule and elements are now all const
    • also ValueStorage's signatures all have const therein
  • ValueStorage
    • set/queryCurrentValue from MapOfActions
    • at times VectorValue has been in .def files where Vector was in the signature. This is cleared. Such stuff is only present for e.g. BoxVector being queried as a Vector. But this is a feature and intended.
  • World
    • most of the (un)selection functions now work on const atoms and molecules
    • in one case we need a const_cast to remove this, but this is intentional, as the vector of selected atoms stores non-const pointers and this is ok.

There is only one test which had to be changed slightly because a specific
option token as "position" must now have the same type everywhere, e.g. always
Vector.

  • TESTFIX: Simple_configuration/2: --position -> --domain-position (and associated to BoxVector)
  • Property mode set to 100644
File size: 3.4 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8/*
9 * SurfaceCorrelationAction.cpp
10 *
11 * Created on: May 9, 2010
12 * Author: heber
13 */
14
15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19
20#include "Helpers/MemDebug.hpp"
21
22#include "analysis_correlation.hpp"
23#include "boundary.hpp"
24#include "linkedcell.hpp"
25#include "Helpers/Verbose.hpp"
26#include "Helpers/Log.hpp"
27#include "element.hpp"
28#include "molecule.hpp"
29#include "periodentafel.hpp"
30#include "tesselation.hpp"
31#include "LinearAlgebra/Vector.hpp"
32#include "World.hpp"
33
34#include <iostream>
35#include <string>
36
37using namespace std;
38
39#include "Actions/AnalysisAction/SurfaceCorrelationAction.hpp"
40
41// and construct the stuff
42#include "SurfaceCorrelationAction.def"
43#include "Action_impl_pre.hpp"
44
45/** =========== define the function ====================== */
46Action::state_ptr AnalysisSurfaceCorrelationAction::performCall() {
47 int ranges[3] = {1, 1, 1};
48 ofstream output;
49 ofstream binoutput;
50 string type;
51 BinPairMap *binmap = NULL;
52
53 // obtain information
54 getParametersfromValueStorage();
55
56 // execute action
57 output.open(params.outputname.string().c_str());
58 binoutput.open(params.binoutputname.string().c_str());
59 ASSERT(params.Boundary != NULL, "No molecule specified for SurfaceCorrelation.");
60 const double radius = 4.;
61 double LCWidth = 20.;
62 if (params.BinEnd > 0) {
63 if (params.BinEnd > 2.*radius)
64 LCWidth = params.BinEnd;
65 else
66 LCWidth = 2.*radius;
67 }
68
69 // get the boundary
70 class Tesselation *TesselStruct = NULL;
71 const LinkedCell *LCList = NULL;
72 // find biggest molecule
73 std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
74 std::cout << "There are " << molecules.size() << " selected molecules." << std::endl;
75 LCList = new LinkedCell(*params.Boundary, LCWidth);
76 FindNonConvexBorder(params.Boundary, TesselStruct, LCList, radius, NULL);
77 CorrelationToSurfaceMap *surfacemap = NULL;
78 if (params.periodic)
79 surfacemap = PeriodicCorrelationToSurface( molecules, params.elements, TesselStruct, LCList, ranges);
80 else
81 surfacemap = CorrelationToSurface( molecules, params.elements, TesselStruct, LCList);
82 delete LCList;
83 OutputCorrelationToSurface(&output, surfacemap);
84 // check whether radius was appropriate
85 {
86 double start; double end;
87 GetMinMax( surfacemap, start, end);
88 if (LCWidth < end)
89 DoeLog(1) && (eLog()<< Verbose(1) << "Linked Cell width is smaller than the found range of values! Bins can only be correct up to: " << radius << "." << endl);
90 }
91 binmap = BinData( surfacemap, params.BinWidth, params.BinStart, params.BinEnd );
92 OutputCorrelation ( &binoutput, binmap );
93 delete TesselStruct; // surfacemap contains refs to triangles! delete here, not earlier!
94 delete(binmap);
95 delete(surfacemap);
96 output.close();
97 binoutput.close();
98 return Action::success;
99}
100
101Action::state_ptr AnalysisSurfaceCorrelationAction::performUndo(Action::state_ptr _state) {
102 return Action::success;
103}
104
105Action::state_ptr AnalysisSurfaceCorrelationAction::performRedo(Action::state_ptr _state){
106 return Action::success;
107}
108
109bool AnalysisSurfaceCorrelationAction::canUndo() {
110 return true;
111}
112
113bool AnalysisSurfaceCorrelationAction::shouldUndo() {
114 return true;
115}
116/** =========== end of function ====================== */
Note: See TracBrowser for help on using the repository browser.