Changeset 1a3c26


Ignore:
Timestamp:
Jul 26, 2010, 5:03:48 PM (15 years ago)
Author:
Frederik Heber <heber@…>
Branches:
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, 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
Children:
215b89
Parents:
4ff081
Message:

All MoleculeActions contain now a ActionCall.hpp function.

Location:
src/Actions/MoleculeAction
Files:
22 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/MoleculeAction/BondFileAction.cpp

    r4ff081 r1a3c26  
    99
    1010#include "Actions/MoleculeAction/BondFileAction.hpp"
     11#include "Actions/ActionCalls.hpp"
     12#include "log.hpp"
     13#include "molecule.hpp"
     14#include "verbose.hpp"
     15#include "World.hpp"
    1116
    1217#include <iostream>
    … …  
    2025#include "UIElements/ValueStorage.hpp"
    2126
    22 #include "log.hpp"
    23 #include "molecule.hpp"
    24 #include "verbose.hpp"
    25 #include "World.hpp"
    2627
    2728/****** MoleculeBondFileAction *****/
    … …  
    4849{}
    4950
     51void MoleculeBondFile(std::string &bondfile) {
     52  ValueStorage::getInstance().setCurrentValue(MoleculeBondFileAction::NAME, bondfile);
     53  ActionRegistry::getInstance().getActionByName(MoleculeBondFileAction::NAME)->call(Action::NonInteractive);
     54};
     55
    5056Dialog* MoleculeBondFileAction::createDialog() {
    5157  Dialog *dialog = UIFactory::getInstance().makeDialog();
    … …  
    5561  return dialog;
    5662}
    57 
    5863
    5964Action::state_ptr MoleculeBondFileAction::performCall() {

  • src/Actions/MoleculeAction/BondFileAction.hpp

    r4ff081 r1a3c26  
    1515
    1616class MoleculeBondFileAction : public Action {
     17  friend void MoleculeBondFile(std::string &bondfile);
     18
    1719public:
    1820  MoleculeBondFileAction();

  • src/Actions/MoleculeAction/ChangeNameAction.cpp

    r4ff081 r1a3c26  
    99
    1010#include "Actions/MoleculeAction/ChangeNameAction.hpp"
     11#include "Actions/ActionCalls.hpp"
     12#include "atom.hpp"
     13#include "molecule.hpp"
    1114
    1215#include <iostream>
    … …  
    1821#include "UIElements/Dialog.hpp"
    1922#include "UIElements/ValueStorage.hpp"
    20 
    21 #include "atom.hpp"
    22 #include "molecule.hpp"
    2323
    2424/****** MoleculeChangeNameAction *****/
    … …  
    4444MoleculeChangeNameAction::~MoleculeChangeNameAction()
    4545{}
     46
     47void MoleculeChangeName(std::string &name) {
     48  ValueStorage::getInstance().setCurrentValue(MoleculeChangeNameAction::NAME, name);
     49  ActionRegistry::getInstance().getActionByName(MoleculeChangeNameAction::NAME)->call(Action::NonInteractive);
     50};
    4651
    4752Dialog* MoleculeChangeNameAction::createDialog() {

  • src/Actions/MoleculeAction/ChangeNameAction.hpp

    r4ff081 r1a3c26  
    1515
    1616class MoleculeChangeNameAction : public Action {
     17  friend void MoleculeChangeName(std::string &name);
     18
    1719public:
    1820  MoleculeChangeNameAction();

  • src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

    r4ff081 r1a3c26  
    99
    1010#include "Actions/MoleculeAction/FillWithMoleculeAction.hpp"
     11#include "Actions/ActionCalls.hpp"
     12#include "atom.hpp"
     13#include "bondgraph.hpp"
     14#include "boundary.hpp"
     15#include "config.hpp"
     16#include "molecule.hpp"
     17#include "verbose.hpp"
     18#include "World.hpp"
     19
    1120
    1221#include <iostream>
    … …  
    1827#include "UIElements/Dialog.hpp"
    1928#include "UIElements/ValueStorage.hpp"
    20 
    21 #include "atom.hpp"
    22 #include "bondgraph.hpp"
    23 #include "boundary.hpp"
    24 #include "config.hpp"
    25 #include "molecule.hpp"
    26 #include "verbose.hpp"
    27 #include "World.hpp"
    2829
    2930/****** MoleculeFillWithMoleculeAction *****/
    … …  
    4950MoleculeFillWithMoleculeAction::~MoleculeFillWithMoleculeAction()
    5051{}
     52
     53void MoleculeFillWithMolecule(std::string &fillername, Vector &distances, Vector &lengths, double MaxDistance, bool DoRotate) {
     54  ValueStorage::getInstance().setCurrentValue(MoleculeFillWithMoleculeAction::NAME, fillername);
     55  ValueStorage::getInstance().setCurrentValue("distances", distances);
     56  ValueStorage::getInstance().setCurrentValue("lengths", lengths);
     57  ValueStorage::getInstance().setCurrentValue("DoRotate", MaxDistance);
     58  ValueStorage::getInstance().setCurrentValue("MaxDistance", DoRotate);
     59  ActionRegistry::getInstance().getActionByName(MoleculeFillWithMoleculeAction::NAME)->call(Action::NonInteractive);
     60};
    5161
    5262Dialog* MoleculeFillWithMoleculeAction::createDialog() {

  • src/Actions/MoleculeAction/FillWithMoleculeAction.hpp

    r4ff081 r1a3c26  
    1111#include "Actions/Action.hpp"
    1212#include "Actions/Process.hpp"
     13#include "vector.hpp"
    1314
    1415class MoleculeListClass;
    1516
    1617class MoleculeFillWithMoleculeAction : public Action {
     18  friend void MoleculeFillWithMolecule(std::string &fillername, Vector &distances, Vector &lengths, double MaxDistance, bool DoRotate);
     19
    1720public:
    1821  MoleculeFillWithMoleculeAction();

  • src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp

    r4ff081 r1a3c26  
    99
    1010#include "Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp"
     11#include "Actions/ActionCalls.hpp"
     12#include "atom.hpp"
     13#include "defs.hpp"
     14#include "log.hpp"
     15#include "molecule.hpp"
     16#include "verbose.hpp"
     17#include "World.hpp"
    1118
    1219#include <iostream>
    … …  
    2027#include "UIElements/ValueStorage.hpp"
    2128
    22 #include "atom.hpp"
    23 #include "defs.hpp"
    24 #include "log.hpp"
    25 #include "molecule.hpp"
    26 #include "verbose.hpp"
    27 #include "World.hpp"
    2829
    2930/****** MoleculeLinearInterpolationofTrajectoriesAction *****/
    … …  
    4950MoleculeLinearInterpolationofTrajectoriesAction::~MoleculeLinearInterpolationofTrajectoriesAction()
    5051{}
     52
     53void MoleculeLinearInterpolationofTrajectories(std::string &filename, int start, int end, bool IdMapping) {
     54  ValueStorage::getInstance().setCurrentValue(MoleculeLinearInterpolationofTrajectoriesAction::NAME, filename);
     55  ValueStorage::getInstance().setCurrentValue("start-step", start);
     56  ValueStorage::getInstance().setCurrentValue("end-step", end);
     57  ValueStorage::getInstance().setCurrentValue("id-mapping", IdMapping);
     58  ActionRegistry::getInstance().getActionByName(MoleculeLinearInterpolationofTrajectoriesAction::NAME)->call(Action::NonInteractive);
     59};
    5160
    5261Dialog* MoleculeLinearInterpolationofTrajectoriesAction::createDialog() {

  • src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp

    r4ff081 r1a3c26  
    1515
    1616class MoleculeLinearInterpolationofTrajectoriesAction : public Action {
     17  friend void MoleculeLinearInterpolationofTrajectories(std::string &filename, int start, int end, bool IdMapping);
     18
    1719public:
    1820  MoleculeLinearInterpolationofTrajectoriesAction();

  • src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp

    r4ff081 r1a3c26  
    99
    1010#include "Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp"
     11#include "Actions/ActionCalls.hpp"
     12#include "log.hpp"
     13#include "molecule.hpp"
     14#include "verbose.hpp"
     15
    1116
    1217#include <iostream>
    … …  
    1924#include "UIElements/Dialog.hpp"
    2025#include "UIElements/ValueStorage.hpp"
    21 
    22 #include "log.hpp"
    23 #include "molecule.hpp"
    24 #include "verbose.hpp"
    2526
    2627/****** MoleculeRotateToPrincipalAxisSystemAction *****/
    … …  
    4647MoleculeRotateToPrincipalAxisSystemAction::~MoleculeRotateToPrincipalAxisSystemAction()
    4748{}
     49
     50void MoleculeRotateToPrincipalAxisSystem() {
     51  ActionRegistry::getInstance().getActionByName(MoleculeRotateToPrincipalAxisSystemAction::NAME)->call(Action::NonInteractive);
     52};
    4853
    4954Dialog* MoleculeRotateToPrincipalAxisSystemAction::createDialog() {

  • src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp

    r4ff081 r1a3c26  
    1515
    1616class MoleculeRotateToPrincipalAxisSystemAction : public Action {
     17  friend void MoleculeRotateToPrincipalAxisSystem();
     18
    1719public:
    1820  MoleculeRotateToPrincipalAxisSystemAction();

  • src/Actions/MoleculeAction/SaveAdjacencyAction.cpp

    r4ff081 r1a3c26  
    99
    1010#include "Actions/MoleculeAction/SaveAdjacencyAction.hpp"
     11#include "Actions/ActionCalls.hpp"
     12#include "bondgraph.hpp"
     13#include "config.hpp"
     14#include "log.hpp"
     15#include "molecule.hpp"
     16#include "verbose.hpp"
     17#include "World.hpp"
     18
    1119
    1220#include <iostream>
    … …  
    1927#include "UIElements/Dialog.hpp"
    2028#include "UIElements/ValueStorage.hpp"
    21 
    22 #include "bondgraph.hpp"
    23 #include "config.hpp"
    24 #include "log.hpp"
    25 #include "molecule.hpp"
    26 #include "verbose.hpp"
    27 #include "World.hpp"
    2829
    2930/****** MoleculeSaveAdjacencyAction *****/
    … …  
    4950MoleculeSaveAdjacencyAction::~MoleculeSaveAdjacencyAction()
    5051{}
     52
     53void MoleculeSaveAdjacency(std::string &adjacencyfile) {
     54  ValueStorage::getInstance().setCurrentValue(MoleculeSaveAdjacencyAction::NAME, adjacencyfile);
     55  ActionRegistry::getInstance().getActionByName(MoleculeSaveAdjacencyAction::NAME)->call(Action::NonInteractive);
     56};
    5157
    5258Dialog* MoleculeSaveAdjacencyAction::createDialog() {

  • src/Actions/MoleculeAction/SaveAdjacencyAction.hpp

    r4ff081 r1a3c26  
    1515
    1616class MoleculeSaveAdjacencyAction : public Action {
     17  friend void MoleculeSaveAdjacency(std::string &adjacencyfile);
     18
    1719public:
    1820  MoleculeSaveAdjacencyAction();

  • src/Actions/MoleculeAction/SaveBondsAction.cpp

    r4ff081 r1a3c26  
    99
    1010#include "Actions/MoleculeAction/SaveBondsAction.hpp"
     11#include "Actions/ActionCalls.hpp"
     12#include "bondgraph.hpp"
     13#include "config.hpp"
     14#include "log.hpp"
     15#include "molecule.hpp"
     16#include "verbose.hpp"
     17#include "World.hpp"
     18
    1119
    1220#include <iostream>
    … …  
    1927#include "UIElements/Dialog.hpp"
    2028#include "UIElements/ValueStorage.hpp"
    21 
    22 #include "bondgraph.hpp"
    23 #include "config.hpp"
    24 #include "log.hpp"
    25 #include "molecule.hpp"
    26 #include "verbose.hpp"
    27 #include "World.hpp"
    2829
    2930/****** MoleculeSaveBondsAction *****/
    … …  
    4950MoleculeSaveBondsAction::~MoleculeSaveBondsAction()
    5051{}
     52
     53void MoleculeSaveBonds(std::string &bondsfile) {
     54  ValueStorage::getInstance().setCurrentValue(MoleculeSaveBondsAction::NAME, bondsfile);
     55  ActionRegistry::getInstance().getActionByName(MoleculeSaveBondsAction::NAME)->call(Action::NonInteractive);
     56};
    5157
    5258Dialog* MoleculeSaveBondsAction::createDialog() {

  • src/Actions/MoleculeAction/SaveBondsAction.hpp

    r4ff081 r1a3c26  
    1515
    1616class MoleculeSaveBondsAction : public Action {
     17  friend void MoleculeSaveBonds(std::string &bondsfile);
     18
    1719public:
    1820  MoleculeSaveBondsAction();

  • src/Actions/MoleculeAction/SaveTemperatureAction.cpp

    r4ff081 r1a3c26  
    99
    1010#include "Actions/MoleculeAction/SaveTemperatureAction.hpp"
     11#include "Actions/ActionCalls.hpp"
     12#include "log.hpp"
     13#include "molecule.hpp"
     14#include "verbose.hpp"
     15#include "World.hpp"
    1116
    1217#include <iostream>
    … …  
    1924#include "UIElements/Dialog.hpp"
    2025#include "UIElements/ValueStorage.hpp"
    21 
    22 #include "log.hpp"
    23 #include "molecule.hpp"
    24 #include "verbose.hpp"
    25 #include "World.hpp"
    2626
    2727/****** MoleculeSaveTemperatureAction *****/
    … …  
    4747MoleculeSaveTemperatureAction::~MoleculeSaveTemperatureAction()
    4848{}
     49
     50void MoleculeSaveTemperature(std::string &temperaturefile) {
     51  ValueStorage::getInstance().setCurrentValue(MoleculeSaveTemperatureAction::NAME, temperaturefile);
     52  ActionRegistry::getInstance().getActionByName(MoleculeSaveTemperatureAction::NAME)->call(Action::NonInteractive);
     53};
    4954
    5055Dialog* MoleculeSaveTemperatureAction::createDialog() {

  • src/Actions/MoleculeAction/SaveTemperatureAction.hpp

    r4ff081 r1a3c26  
    1515
    1616class MoleculeSaveTemperatureAction : public Action {
     17  friend void MoleculeSaveTemperature(std::string &temperaturefile);
     18
    1719public:
    1820  MoleculeSaveTemperatureAction();

  • src/Actions/MoleculeAction/SuspendInWaterAction.cpp

    r4ff081 r1a3c26  
    99
    1010#include "Actions/MoleculeAction/SuspendInWaterAction.hpp"
     11#include "Actions/ActionCalls.hpp"
     12#include "boundary.hpp"
     13#include "config.hpp"
     14#include "log.hpp"
     15#include "verbose.hpp"
     16#include "World.hpp"
    1117
    1218#include <iostream>
    … …  
    1824#include "UIElements/Dialog.hpp"
    1925#include "UIElements/ValueStorage.hpp"
    20 
    21 #include "boundary.hpp"
    22 #include "config.hpp"
    23 #include "log.hpp"
    24 #include "verbose.hpp"
    25 #include "World.hpp"
    2626
    2727/****** MoleculeSuspendInWaterAction *****/
    … …  
    4747MoleculeSuspendInWaterAction::~MoleculeSuspendInWaterAction()
    4848{}
     49
     50void MoleculeSuspendInWater(double density) {
     51  ValueStorage::getInstance().setCurrentValue(MoleculeSuspendInWaterAction::NAME, density);
     52  ActionRegistry::getInstance().getActionByName(MoleculeSuspendInWaterAction::NAME)->call(Action::NonInteractive);
     53};
    4954
    5055Dialog* MoleculeSuspendInWaterAction::createDialog() {

  • src/Actions/MoleculeAction/SuspendInWaterAction.hpp

    r4ff081 r1a3c26  
    1515
    1616class MoleculeSuspendInWaterAction : public Action {
     17  friend void MoleculeSuspendInWater(double density);
     18
    1719public:
    1820  MoleculeSuspendInWaterAction();

  • src/Actions/MoleculeAction/TranslateAction.cpp

    r4ff081 r1a3c26  
    99
    1010#include "Actions/MoleculeAction/TranslateAction.hpp"
     11#include "Actions/ActionCalls.hpp"
     12#include "log.hpp"
     13#include "molecule.hpp"
     14#include "vector.hpp"
     15#include "verbose.hpp"
     16#include "World.hpp"
    1117
    1218#include <iostream>
    … …  
    1925#include "UIElements/Dialog.hpp"
    2026#include "UIElements/ValueStorage.hpp"
    21 
    22 #include "log.hpp"
    23 #include "molecule.hpp"
    24 #include "vector.hpp"
    25 #include "verbose.hpp"
    26 #include "World.hpp"
    2727
    2828/****** MoleculeTranslateAction *****/
    … …  
    4848MoleculeTranslateAction::~MoleculeTranslateAction()
    4949{}
     50
     51void MoleculeTranslate(Vector &x, bool periodic) {
     52  ValueStorage::getInstance().setCurrentValue(MoleculeTranslateAction::NAME, x);
     53  ValueStorage::getInstance().setCurrentValue("periodic", periodic);
     54  ActionRegistry::getInstance().getActionByName(MoleculeTranslateAction::NAME)->call(Action::NonInteractive);
     55};
    5056
    5157Dialog* MoleculeTranslateAction::createDialog() {

  • src/Actions/MoleculeAction/TranslateAction.hpp

    r4ff081 r1a3c26  
    1111#include "Actions/Action.hpp"
    1212#include "Actions/Process.hpp"
     13#include "vector.hpp"
    1314
    1415class MoleculeListClass;
    1516
    1617class MoleculeTranslateAction : public Action {
     18  friend void MoleculeTranslate(Vector &x, bool periodic);
     19
    1720public:
    1821  MoleculeTranslateAction();

  • src/Actions/MoleculeAction/VerletIntegrationAction.cpp

    r4ff081 r1a3c26  
    99
    1010#include "Actions/MoleculeAction/VerletIntegrationAction.hpp"
     11#include "Actions/ActionCalls.hpp"
     12#include "log.hpp"
     13#include "molecule.hpp"
     14#include "verbose.hpp"
     15#include "World.hpp"
    1116
    1217#include <iostream>
    … …  
    1924#include "UIElements/Dialog.hpp"
    2025#include "UIElements/ValueStorage.hpp"
    21 
    22 #include "log.hpp"
    23 #include "molecule.hpp"
    24 #include "verbose.hpp"
    25 #include "World.hpp"
    2626
    2727/****** MoleculeVerletIntegrationAction *****/
    … …  
    4747MoleculeVerletIntegrationAction::~MoleculeVerletIntegrationAction()
    4848{}
     49
     50void MoleculeVerletIntegration(std::string &forcesfile) {
     51  ValueStorage::getInstance().setCurrentValue(MoleculeVerletIntegrationAction::NAME, forcesfile);
     52  ActionRegistry::getInstance().getActionByName(MoleculeVerletIntegrationAction::NAME)->call(Action::NonInteractive);
     53};
    4954
    5055Dialog* MoleculeVerletIntegrationAction::createDialog() {

  • src/Actions/MoleculeAction/VerletIntegrationAction.hpp

    r4ff081 r1a3c26  
    1515
    1616class MoleculeVerletIntegrationAction : public Action {
     17  friend void MoleculeVerletIntegration(std::string &forcesfile);
     18
    1719public:
    1820  MoleculeVerletIntegrationAction();
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