Changeset e4b5de for src

Timestamp:

Jun 8, 2010, 1:49:27 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:

8540f0

Parents:

48ab70a

Message:

Case 'f' is now handled by CommandLineUI.

• FragmentationFragmentationAction::handle() has not been implemented, copied from ParseCommandLineOptions()
• FIX: FragmentationFragmentationAction had wrong NAME.
• World has new ExitFlag variable and getter and setter functions.
• TESTFIX: Fragmentation/3 does not copy all BondFragment* files from pre but runs Fragmentation twice and tests the ExitFlag. This makes the test more independent and closer to what it's suppose to test (i.e. iterative fragmentation with increasing order).
• TESTFIX: removed all Fragmentation/3/pre/BondFragment* files
• FIX: CommandLineWindow::populateFragmentationActions() was missing two of its three actions still.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAction.cpp (modified) (2 diffs)
• Actions/MapOfActions.cpp (modified) (4 diffs)
• UIElements/CommandLineUI/CommandLineWindow.cpp (modified) (2 diffs)
• World.cpp (modified) (2 diffs)
• World.hpp (modified) (2 diffs)
• builder.cpp (modified) (3 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -25 +25 @@
 #include "Actions/MapOfActions.hpp"
 
-const char FragmentationFragmentationAction::NAME[] = "subspace-dissect";
+const char FragmentationFragmentationAction::NAME[] = "fragment-mol";
 
 FragmentationFragmentationAction::FragmentationFragmentationAction() :
@@ -36 +36 @@
 Action::state_ptr FragmentationFragmentationAction::performCall() {
   Dialog *dialog = UIFactory::getInstance().makeDialog();
+  clock_t start,end;
+  molecule *mol = NULL;
+  double distance = -1.;
+  int order = 0;
+  config *configuration = World::getInstance().getConfig();
+  int ExitFlag = 0;
 
-  dialog->queryEmpty(NAME, MapOfActions::getInstance().getDescription(NAME));
+  cout << "pre-dialog"<< endl;
+  dialog->queryMolecule(NAME, &mol, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryDouble("distance", &distance, MapOfActions::getInstance().getDescription("distance"));
+  dialog->queryInt("order", &order, MapOfActions::getInstance().getDescription("order"));
 
   if(dialog->display()) {
+    cout << "POST-dialog"<< endl;
+    ASSERT(mol != NULL, "No molecule has been picked for fragmentation.");
+    DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with bond distance " << distance << " angstroem, order of " << order << "." << endl);
+    DoLog(0) && (Log() << Verbose(0) << "Creating connection matrix..." << endl);
+    start = clock();
+    mol->CreateAdjacencyList(distance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
+    DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl);
+    if (mol->hasBondStructure()) {
+      ExitFlag = mol->FragmentMolecule(order, configuration);
+    }
+    World::getInstance().setExitFlag(ExitFlag);
+    end = clock();
+    DoLog(0) && (Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl);
     delete dialog;
     return Action::success;

src/Actions/MapOfActions.cpp

@@ -120 +120 @@
   DescriptionMap["MaxDistance"] = "maximum distance in space";
   DescriptionMap["molecule-by-id"] = "index of a molecule";
+  DescriptionMap["order"] = "order of a discretization, dissection, ...";
   DescriptionMap["output-file"] = "name of the output file";
   DescriptionMap["periodic"] = "system is constraint to periodic boundary conditions (y/n)";
@@ -216 +217 @@
   TypeMap["MaxDistance"] = Double;
   TypeMap["molecule-by-id"] = Molecule;
+  TypeMap["order"] = Integer;
   TypeMap["output-file"] = String;
   TypeMap["periodic"] = Boolean;
@@ -241 +243 @@
 //      generic.insert("fastparsing");
   generic.insert("fill-molecule");
-//  generic.insert("fragment-mol");
+  generic.insert("fragment-mol");
   generic.insert("help");
 //      generic.insert("linear-interpolate");
@@ -285 +287 @@
 
     // hidden arguments
-//  generic.insert("distance");
-    generic.insert("DoRotate");
-    generic.insert("distances");
-    generic.insert("lengths");
-    generic.insert("MaxDistance");
-    generic.insert("molecule-by-id");
+  generic.insert("distance");
+  generic.insert("DoRotate");
+  generic.insert("distances");
+  generic.insert("lengths");
+  generic.insert("MaxDistance");
+  generic.insert("molecule-by-id");
+  generic.insert("order");
 }
 

src/UIElements/CommandLineUI/CommandLineWindow.cpp

@@ -26 +26 @@
 #include "Actions/FragmentationAction/DepthFirstSearchAction.hpp"
 #include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
+#include "Actions/FragmentationAction/FragmentationAction.hpp"
 #include "Actions/MoleculeAction/BondFileAction.hpp"
 #include "Actions/MoleculeAction/ChangeNameAction.hpp"
@@ -119 +120 @@
 {
   new FragmentationDepthFirstSearchAction();
+  new FragmentationFragmentationAction();
+  new FragmentationSubgraphDissectionAction();
 }
 

src/World.cpp

@@ -96 +96 @@
 };
 
+int World::getExitFlag() {
+  return ExitFlag;
+}
+
+void World::setExitFlag(int flag) {
+  if (ExitFlag < flag)
+    ExitFlag = flag;
+}
 
 /******************** Methods to change World state *********************/
@@ -279 +287 @@
     periode(new periodentafel),
     configuration(new config),
+    ExitFlag(0),
     atoms(),
     currAtomId(0),

src/World.hpp

@@ -142 +142 @@
   void setDefaultName(char * name);
 
+  /*
+   * get the ExitFlag
+   */
+  int getExitFlag();
+
+  /*
+   * set the ExitFlag
+   */
+  void setExitFlag(int flag);
+
   /***** Methods to work with the World *****/
 
@@ -244 +254 @@
   static double *cell_size;
   static char *defaultName;
+  int ExitFlag;
 public:
   AtomSet atoms;

src/builder.cpp

@@ -2237 +2237 @@
             case 'f':
               if (ExitFlag == 0) ExitFlag = 1;
-              if ((argptr+1 >= argc) || (argv[argptr][0] == '-') || (!IsValidNumber(argv[argptr])) || (!IsValidNumber(argv[argptr+1]))) {
+              if ((argptr+1 >= argc) || (argv[argptr][0] == '-')) {
                 ExitFlag = 255;
                 DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments for fragmentation: -f <max. bond distance> <bond order>" << endl);
                 performCriticalExit();
               } else {
-                DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with bond distance " << argv[argptr] << " angstroem, order of " << argv[argptr+1] << "." << endl);
-                DoLog(0) && (Log() << Verbose(0) << "Creating connection matrix..." << endl);
-                start = clock();
-                mol->CreateAdjacencyList(atof(argv[argptr]), configuration.GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
-                DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl);
-                if (mol->hasBondStructure()) {
-                  ExitFlag = mol->FragmentMolecule(atoi(argv[argptr+1]), &configuration);
-                }
-                end = clock();
-                DoLog(0) && (Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl);
-                argptr+=2;
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                ArgcList.insert(argptr+1);
+                ArgcList.insert(argptr+2);
+                ArgcList.insert(argptr+3);
+                ArgcList.insert(argptr+4);
+                argptr+=5;
               }
               break;
@@ -2409 +2405 @@
       // handle arguments by ParseCommandLineOptions()
       ExitFlag = ParseCommandLineOptions(argc,argv,World::getInstance().getMolecules(),World::getInstance().getPeriode(),*World::getInstance().getConfig(), &ConfigFileName, ArgcList);
+      World::getInstance().setExitFlag(ExitFlag);
       // copy all remaining arguments to a new argv
       Arguments = new char *[ArgcList.size()];
@@ -2449 +2446 @@
   delete[](ConfigFileName);
 
+  ExitFlag = World::getInstance().getExitFlag();
   return (ExitFlag == 1 ? 0 : ExitFlag);
 }