Changeset f5724f for src


Ignore:
Timestamp:
Aug 12, 2013, 11:30:33 AM (11 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:
93909a
Parents:
24e19e
git-author:
Frederik Heber <heber@…> (07/26/13 09:08:31)
git-committer:
Frederik Heber <heber@…> (08/12/13 11:30:33)
Message:

Moved all FragmentationActions related to potentials into own menu and folder.

  • changed class names Fragmentation... -> Potential...
  • changed tokens in GlobalListOfActions.
  • added menu entry "potential" and CommandLineParser program_options variable.
  • moved regression tests into own folder as well and renamed folder in files.
Location:
src
Files:
5 edited
12 moved

Legend:

Unmodified
Added
Removed

  • src/Actions/GlobalListOfActions.hpp

    r24e19e rf5724f  
    123123  (SelectionNotShapeByName) \
    124124  (FragmentationAnalyseFragmentationResults) \
    125   (FragmentationFitParticleCharges) \
    126125  (FragmentationFragmentation) \
    127   (FragmentationParseHomologies) \
    128   (FragmentationSaveHomologies) \
    129126  (FragmentationStoreSaturatedFragment) \
     127  (PotentialFitParticleCharges) \
     128  (PotentialParseHomologies) \
     129  (PotentialSaveHomologies) \
    130130  (FillRegularGrid) \
    131131  (FillSurface) \
    … …  
    159159    BOOST_PP_SEQ_PUSH_BACK( \
    160160        GLOBALLISTOFACTIONS_JOBMARKET, \
    161         FragmentationFitPotential \
     161        PotentialFitPotential \
    162162    )
    163163#else

  • src/Actions/Makefile.am

    r24e19e rf5724f  
    6060  ${MOLECULEACTIONSOURCE} \
    6161  ${PARSERACTIONSOURCE} \
     62  ${POTENTIALACTIONSOURCE} \
    6263  ${RANDONNUMBERSSOURCE} \
    6364  ${SELECTIONATOMACTIONSOURCE} \
    … …  
    7980  ${MOLECULEACTIONHEADER} \
    8081  ${PARSERACTIONHEADER} \
     82  ${POTENTIALACTIONHEADER} \
    8183  ${RANDONNUMBERSHEADER} \
    8284  ${SELECTIONATOMACTIONHEADER} \
    … …  
    98100  ${MOLECULEACTIONDEFS} \
    99101  ${PARSERACTIONDEFS} \
     102  ${POTENTIALACTIONDEFS} \
    100103  ${RANDONNUMBERSDEFS} \
    101104  ${SELECTIONATOMACTIONDEFS} \
    … …  
    214217FRAGMENTATIONACTIONSOURCE = \
    215218  Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp \
    216   Actions/FragmentationAction/FitParticleChargesAction.cpp \
    217219  Actions/FragmentationAction/FragmentationAction.cpp \
    218   Actions/FragmentationAction/ParseHomologiesAction.cpp \
    219   Actions/FragmentationAction/SaveHomologiesAction.cpp \
    220220  Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp
    221221FRAGMENTATIONACTIONHEADER = \
    222222  Actions/FragmentationAction/AnalyseFragmentationResultsAction.hpp \
    223   Actions/FragmentationAction/FitParticleChargesAction.hpp \
    224223  Actions/FragmentationAction/FragmentationAction.hpp \
    225   Actions/FragmentationAction/ParseHomologiesAction.hpp \
    226   Actions/FragmentationAction/SaveHomologiesAction.hpp \
    227224  Actions/FragmentationAction/StoreSaturatedFragmentAction.hpp
    228225FRAGMENTATIONACTIONDEFS = \
    229226  Actions/FragmentationAction/AnalyseFragmentationResultsAction.def \
    230   Actions/FragmentationAction/FitParticleChargesAction.def  \
    231227  Actions/FragmentationAction/FragmentationAction.def \
    232   Actions/FragmentationAction/ParseHomologiesAction.def \
    233   Actions/FragmentationAction/SaveHomologiesAction.def \
    234228  Actions/FragmentationAction/StoreSaturatedFragmentAction.def
    235229
    … …  
    248242  Actions/FragmentationAction/ParseFragmentJobsAction.def
    249243endif
    250 
    251 if CONDLEVMAR
    252 FRAGMENTATIONACTIONSOURCE += \
    253   Actions/FragmentationAction/FitPotentialAction.cpp
    254 FRAGMENTATIONACTIONHEADER += \
    255   Actions/FragmentationAction/FitPotentialAction.hpp
    256 FRAGMENTATIONACTIONDEFS += \
    257   Actions/FragmentationAction/FitPotentialAction.def
    258 endif
    259 
    260244
    261245GRAPHACTIONSOURCE = \
    … …  
    351335  Actions/ParserAction/SetOutputFormatsAction.def \
    352336  Actions/ParserAction/SetTremoloAtomdataAction.def
     337
     338POTENTIALACTIONSOURCE = \
     339  Actions/PotentialAction/FitParticleChargesAction.cpp \
     340  Actions/PotentialAction/ParseHomologiesAction.cpp \
     341  Actions/PotentialAction/SaveHomologiesAction.cpp
     342POTENTIALACTIONHEADER = \
     343  Actions/PotentialAction/FitParticleChargesAction.hpp \
     344  Actions/PotentialAction/ParseHomologiesAction.hpp \
     345  Actions/PotentialAction/SaveHomologiesAction.hpp
     346POTENTIALACTIONDEFS = \
     347  Actions/PotentialAction/FitParticleChargesAction.def  \
     348  Actions/PotentialAction/ParseHomologiesAction.def \
     349  Actions/PotentialAction/SaveHomologiesAction.def
     350
     351if CONDLEVMAR
     352POTENTIALACTIONSOURCE += \
     353  Actions/PotentialAction/FitPotentialAction.cpp
     354POTENTIALACTIONHEADER += \
     355  Actions/PotentialAction/FitPotentialAction.hpp
     356POTENTIALACTIONDEFS += \
     357  Actions/PotentialAction/FitPotentialAction.def
     358endif
    353359
    354360RANDONNUMBERSSOURCE =\

  • src/Actions/PotentialAction/FitParticleChargesAction.cpp

    r24e19e rf5724f  
    5050#include <string>
    5151
    52 #include "Actions/FragmentationAction/FitParticleChargesAction.hpp"
     52#include "Actions/PotentialAction/FitParticleChargesAction.hpp"
    5353
    5454#include "Potentials/PartialNucleiChargeFitter.hpp"
    … …  
    109109}
    110110
    111 Action::state_ptr FragmentationFitParticleChargesAction::performCall() {
     111Action::state_ptr PotentialFitParticleChargesAction::performCall() {
    112112
    113113  // fragment specifies the homology fragment to use
    … …  
    155155}
    156156
    157 Action::state_ptr FragmentationFitParticleChargesAction::performUndo(Action::state_ptr _state) {
     157Action::state_ptr PotentialFitParticleChargesAction::performUndo(Action::state_ptr _state) {
    158158  return Action::success;
    159159}
    160160
    161 Action::state_ptr FragmentationFitParticleChargesAction::performRedo(Action::state_ptr _state){
     161Action::state_ptr PotentialFitParticleChargesAction::performRedo(Action::state_ptr _state){
    162162  return Action::success;
    163163}
    164164
    165 bool FragmentationFitParticleChargesAction::canUndo() {
     165bool PotentialFitParticleChargesAction::canUndo() {
    166166  return false;
    167167}
    168168
    169 bool FragmentationFitParticleChargesAction::shouldUndo() {
     169bool PotentialFitParticleChargesAction::shouldUndo() {
    170170  return false;
    171171}

  • src/Actions/PotentialAction/FitParticleChargesAction.def

    r24e19e rf5724f  
    3333
    3434// some defines for all the names, you may use ACTION, STATE and PARAMS
    35 #define CATEGORY Fragmentation
    36 #define MENUNAME "fragmentation"
    37 #define MENUPOSITION 9
     35#define CATEGORY Potential
     36#define MENUNAME "potential"
     37#define MENUPOSITION 4
    3838#define ACTIONNAME FitParticleCharges
    3939#define TOKEN "fit-particle-charges"

  • src/Actions/PotentialAction/FitPotentialAction.cpp

    r24e19e rf5724f  
    4747#include <sstream>
    4848
    49 #include "Actions/FragmentationAction/FitPotentialAction.hpp"
     49#include "Actions/PotentialAction/FitPotentialAction.hpp"
    5050
    5151#include "CodePatterns/Log.hpp"
    … …  
    113113}
    114114
    115 Action::state_ptr FragmentationFitPotentialAction::performCall() {
     115Action::state_ptr PotentialFitPotentialAction::performCall() {
    116116  // fragment specifies the homology fragment to use
    117117  SerializablePotential::ParticleTypes_t fragmentnumbers;
    … …  
    211211  FunctionModel *model = new CompoundPotential(graph);
    212212  ASSERT( model != NULL,
    213       "FragmentationFitPotentialAction::performCall() - model is NULL.");
     213      "PotentialFitPotentialAction::performCall() - model is NULL.");
    214214
    215215  /******************** TRAINING ********************/
    … …  
    339339}
    340340
    341 Action::state_ptr FragmentationFitPotentialAction::performUndo(Action::state_ptr _state) {
     341Action::state_ptr PotentialFitPotentialAction::performUndo(Action::state_ptr _state) {
    342342  return Action::success;
    343343}
    344344
    345 Action::state_ptr FragmentationFitPotentialAction::performRedo(Action::state_ptr _state){
     345Action::state_ptr PotentialFitPotentialAction::performRedo(Action::state_ptr _state){
    346346  return Action::success;
    347347}
    348348
    349 bool FragmentationFitPotentialAction::canUndo() {
     349bool PotentialFitPotentialAction::canUndo() {
    350350  return false;
    351351}
    352352
    353 bool FragmentationFitPotentialAction::shouldUndo() {
     353bool PotentialFitPotentialAction::shouldUndo() {
    354354  return false;
    355355}

  • src/Actions/PotentialAction/FitPotentialAction.def

    r24e19e rf5724f  
    4242
    4343// some defines for all the names, you may use ACTION, STATE and PARAMS
    44 #define CATEGORY Fragmentation
    45 #define MENUNAME "fragmentation"
    46 #define MENUPOSITION 6
     44#define CATEGORY Potential
     45#define MENUNAME "potential"
     46#define MENUPOSITION 3
    4747#define ACTIONNAME FitPotential
    4848#define TOKEN "fit-potential"

  • src/Actions/PotentialAction/ParseHomologiesAction.cpp

    r24e19e rf5724f  
    4747#include "World.hpp"
    4848
    49 #include "Actions/FragmentationAction/ParseHomologiesAction.hpp"
     49#include "Actions/PotentialAction/ParseHomologiesAction.hpp"
    5050
    5151using namespace MoleCuilder;
    … …  
    7676}
    7777
    78 Action::state_ptr FragmentationParseHomologiesAction::performCall()
     78Action::state_ptr PotentialParseHomologiesAction::performCall()
    7979{
    8080  // append all keysets to homology file
    … …  
    9191}
    9292
    93 Action::state_ptr FragmentationParseHomologiesAction::performUndo(Action::state_ptr _state) {
     93Action::state_ptr PotentialParseHomologiesAction::performUndo(Action::state_ptr _state) {
    9494  return Action::success;
    9595}
    9696
    97 Action::state_ptr FragmentationParseHomologiesAction::performRedo(Action::state_ptr _state){
     97Action::state_ptr PotentialParseHomologiesAction::performRedo(Action::state_ptr _state){
    9898  return Action::success;
    9999}
    100100
    101 bool FragmentationParseHomologiesAction::canUndo() {
     101bool PotentialParseHomologiesAction::canUndo() {
    102102  return false;
    103103}
    104104
    105 bool FragmentationParseHomologiesAction::shouldUndo() {
     105bool PotentialParseHomologiesAction::shouldUndo() {
    106106  return false;
    107107}

  • src/Actions/PotentialAction/ParseHomologiesAction.def

    r24e19e rf5724f  
    2424
    2525// some defines for all the names, you may use ACTION, STATE and PARAMS
    26 #define CATEGORY Fragmentation
    27 #define MENUNAME "fragmentation"
    28 #define MENUPOSITION 7
     26#define CATEGORY Potential
     27#define MENUNAME "potential"
     28#define MENUPOSITION 1
    2929#define ACTIONNAME ParseHomologies
    3030#define TOKEN "parse-homologies"

  • src/Actions/PotentialAction/SaveHomologiesAction.cpp

    r24e19e rf5724f  
    4747#include "World.hpp"
    4848
    49 #include "Actions/FragmentationAction/SaveHomologiesAction.hpp"
     49#include "Actions/PotentialAction/SaveHomologiesAction.hpp"
    5050
    5151using namespace MoleCuilder;
    … …  
    7979}
    8080
    81 Action::state_ptr FragmentationSaveHomologiesAction::performCall()
     81Action::state_ptr PotentialSaveHomologiesAction::performCall()
    8282{
    8383  if (!params.homology_file.get().empty()) {
    … …  
    9393}
    9494
    95 Action::state_ptr FragmentationSaveHomologiesAction::performUndo(Action::state_ptr _state) {
     95Action::state_ptr PotentialSaveHomologiesAction::performUndo(Action::state_ptr _state) {
    9696  return Action::success;
    9797}
    9898
    99 Action::state_ptr FragmentationSaveHomologiesAction::performRedo(Action::state_ptr _state){
     99Action::state_ptr PotentialSaveHomologiesAction::performRedo(Action::state_ptr _state){
    100100  return Action::success;
    101101}
    102102
    103 bool FragmentationSaveHomologiesAction::canUndo() {
     103bool PotentialSaveHomologiesAction::canUndo() {
    104104  return false;
    105105}
    106106
    107 bool FragmentationSaveHomologiesAction::shouldUndo() {
     107bool PotentialSaveHomologiesAction::shouldUndo() {
    108108  return false;
    109109}

  • src/Actions/PotentialAction/SaveHomologiesAction.def

    r24e19e rf5724f  
    2626
    2727// some defines for all the names, you may use ACTION, STATE and PARAMS
    28 #define CATEGORY Fragmentation
    29 #define MENUNAME "fragmentation"
    30 #define MENUPOSITION 8
     28#define CATEGORY Potential
     29#define MENUNAME "potential"
     30#define MENUPOSITION 2
    3131#define ACTIONNAME SaveHomologies
    3232#define TOKEN "save-homologies"

  • src/UIElements/CommandLineUI/CommandLineParser.cpp

    r24e19e rf5724f  
    7474  options("Secondary options"),
    7575  parser("Parser options"),
     76  potential("Potential options"),
    7677  selection("Selection options"),
    7778  tesselation("Tesselation options"),
    … …  
    9192  CmdParserLookup["molecule"] = &molecule;
    9293  CmdParserLookup["parser"] = &parser;
     94  CmdParserLookup["potential"] = &potential;
    9395  CmdParserLookup["selection"] = &selection;
    9496  CmdParserLookup["tesselation"] = &tesselation;

  • src/UIElements/CommandLineUI/CommandLineParser.hpp

    r24e19e rf5724f  
    6666  po::options_description options;
    6767  po::options_description parser;
     68  po::options_description potential;
    6869  po::options_description selection;
    6970  po::options_description tesselation;

  • src/UIElements/Menu/MenuDescription.cpp

    r24e19e rf5724f  
    6969  MenuPositionMap->insert(std::make_pair("graph",TopPosition("tools",4)));
    7070  MenuPositionMap->insert(std::make_pair("molecule",TopPosition("edit",3)));
     71  MenuPositionMap->insert(std::make_pair("potential",TopPosition("tools",7)));
    7172  MenuPositionMap->insert(std::make_pair("parser",TopPosition("edit",4)));
    7273  MenuPositionMap->insert(std::make_pair("selection",TopPosition("edit",5)));
    … …  
    8788  MenuDescriptionsMap->insert(std::make_pair("molecule","Parse files into system"));
    8889  MenuDescriptionsMap->insert(std::make_pair("parser","Edit molecules (load, parse, save)"));
     90  MenuDescriptionsMap->insert(std::make_pair("potential","Fit potentials and parse, save homologies"));
    8991  MenuDescriptionsMap->insert(std::make_pair("selection","Select atoms/molecules"));
    9092  MenuDescriptionsMap->insert(std::make_pair("tesselation","Tesselate molecules"));
    … …  
    104106  MenuNameMap->insert(std::make_pair("molecule","Molecules"));
    105107  MenuNameMap->insert(std::make_pair("parser","Input/Output"));
     108  MenuNameMap->insert(std::make_pair("potential","PotentialFitting"));
    106109  MenuNameMap->insert(std::make_pair("selection","Selection"));
    107110  MenuNameMap->insert(std::make_pair("tesselation","Tesselation"));
Note: See TracChangeset for help on using the changeset viewer.