Changeset a1e929 for src

Timestamp:

Jun 21, 2010, 1:07:58 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:

d3dff06

Parents:

2f40c0e

Message:

Case 'p' is now handled by CommandLineUI.

• ~XyzParser() did destroy falsely its own comment.
• TremoloParser and XyzParser used include with Parser path.
• ParserLoadXyzAction:
  • corrected NAME.
  • uses XyzParser and adds all new atoms to the first present molecule.
• CommandLineWindow::display() - now states when action is launched or found absent.
• builder.cpp: cleanup() - purges ChangeTracker
• ParseCommandLineOptions() - sets configPresent to present without check (as parsing is done afterwards, but arguments of other cases will be thrown away in case of empty world)

Location:

src

Files:

• Actions/MapOfActions.cpp (modified) (1 diff)
• Actions/ParserAction/LoadXyzAction.cpp (modified) (4 diffs)
• Parser/TremoloParser.hpp (modified) (1 diff)
• Parser/XyzParser.cpp (modified) (1 diff)
• Parser/XyzParser.hpp (modified) (1 diff)
• UIElements/CommandLineUI/CommandLineWindow.cpp (modified) (1 diff)
• builder.cpp (modified) (3 diffs)

src/Actions/MapOfActions.cpp

@@ -266 +266 @@
   generic.insert("nonconvex-envelope");
         generic.insert("pair-correlation");
-//      generic.insert("parse-xyz");
+        generic.insert("parse-xyz");
 //  generic.insert("principal-axis-system");
   generic.insert("remove-atom");

src/Actions/ParserAction/LoadXyzAction.cpp

@@ -8 +8 @@
 #include "Helpers/MemDebug.hpp"
 
+using namespace std;
+
 #include "Actions/ParserAction/LoadXyzAction.hpp"
 #include "Parser/XyzParser.hpp"
 
 #include <iostream>
+#include <set>
 #include <string>
+#include <vector>
 
-using namespace std;
 
 #include "UIElements/UIFactory.hpp"
@@ -21 +24 @@
 
 #include "atom.hpp"
+#include "log.hpp"
 #include "molecule.hpp"
+#include "verbose.hpp"
+#include "World.hpp"
 
 /****** ParserLoadXyzAction *****/
@@ -37 +43 @@
 //};
 
-const char ParserLoadXyzAction::NAME[] = "LoadXyz";
+const char ParserLoadXyzAction::NAME[] = "parse-xyz";
 
 ParserLoadXyzAction::ParserLoadXyzAction() :
@@ -48 +54 @@
 Action::state_ptr ParserLoadXyzAction::performCall() {
   string filename;
-  XyzParser parser;
   Dialog *dialog = UIFactory::getInstance().makeDialog();
 
-  dialog->queryString("filename",&filename, "Filename of the xyz file");
+  dialog->queryString(NAME,&filename, NAME);
 
   if(dialog->display()) {
+    DoLog(1) && (Log() << Verbose(1) << "Parsing xyz file for new atoms." << endl);
     // parse xyz file
     ifstream input;
     input.open(filename.c_str());
-    if (!input.fail())
+    if (!input.fail()) {
+      // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
+      set <atom*> UniqueList;
+      {
+        vector<atom *> ListBefore = World::getInstance().getAllAtoms();
+        for (vector<atom *>::iterator runner = ListBefore.begin();runner != ListBefore.end(); ++runner)
+          UniqueList.insert(*runner);
+      }
+      XyzParser parser; // briefly instantiate a parser which is removed at end of focus
       parser.load(&input);
+      {
+        vector<atom *> ListAfter = World::getInstance().getAllAtoms();
+        pair< set<atom *>::iterator, bool > Inserter;
+        if (UniqueList.size() != ListAfter.size()) { // only create if new atoms have been parsed
+          MoleculeListClass *molecules = World::getInstance().getMolecules();
+          molecule *mol= NULL;
+          if (molecules->ListOfMolecules.empty()) {
+            mol = World::getInstance().createMolecule();
+            molecules->insert(mol);
+          } else {
+            mol = *(molecules->ListOfMolecules.begin());
+          }
+          for (vector<atom *>::iterator runner = ListAfter.begin(); runner != ListAfter.end(); ++runner) {
+            Inserter = UniqueList.insert(*runner);
+            if (Inserter.second) { // if not present, then new (just parsed) atom, add ...
+              cout << "Adding new atom " << **runner << " to new mol." << endl;
+              mol->AddAtom(*runner);
+            }
+          }
+          mol->doCountAtoms();
+        } else {
+          cout << "No atoms parsed?" << endl;
+        }
+      }
+    } else {
+      DoeLog(1) && (eLog() << Verbose(1) << "Could not open file " << filename << "." << endl);
+    }
     input.close();
   }

src/Parser/TremoloParser.hpp

@@ -10 +10 @@
 
 #include <string>
-#include "FormatParser.hpp"
+#include "Parser/FormatParser.hpp"
 
 /**

src/Parser/XyzParser.cpp

@@ -27 +27 @@
  */
 XyzParser::~XyzParser() {
-  delete(&comment);
 }
 

src/Parser/XyzParser.hpp

@@ -10 +10 @@
 
 #include <string>
-#include "FormatParser.hpp"
+#include "Parser/FormatParser.hpp"
 
 /**

src/UIElements/CommandLineUI/CommandLineWindow.cpp

@@ -83 +83 @@
   // go through all possible actions
   for (std::list<std::string>::iterator CommandRunner = CommandLineParser::getInstance().SequenceOfActions.begin(); CommandRunner != CommandLineParser::getInstance().SequenceOfActions.end(); ++CommandRunner) {
-    cout << "Checking presence of " << *CommandRunner << endl;
-    if (ActionRegistry::getInstance().isActionByNamePresent(*CommandRunner))
+    cout << "Checking presence of " << *CommandRunner << ": ";
+    if (ActionRegistry::getInstance().isActionByNamePresent(*CommandRunner)) {
+      cout << "calling " << *CommandRunner << endl;
       ActionRegistry::getInstance().getActionByName(*CommandRunner)->call();
+    } else {
+      cout << "absent." << endl;
+    }
   }
 }

src/builder.cpp

@@ -79 +79 @@
 #include "UIElements/Dialog.hpp"
 #include "Menu/ActionMenuItem.hpp"
+#include "Parser/ChangeTracker.hpp"
 #include "Actions/ActionRegistry.hpp"
 #include "Actions/ActionHistory.hpp"
@@ -1691 +1692 @@
               } else {
                 SaveFlag = true;
-                DoLog(1) && (Log() << Verbose(1) << "Parsing xyz file for new atoms." << endl);
-                if (!mol->AddXYZFile(argv[argptr]))
-                  DoLog(2) && (Log() << Verbose(2) << "File not found." << endl);
-                else {
-                  DoLog(2) && (Log() << Verbose(2) << "File found and parsed." << endl);
-                  configPresent = present;
-                }
+                configPresent = present;
+                ArgcList.insert(argptr-1);
+                ArgcList.insert(argptr);
+                argptr+=1;
               }
               break;
@@ -2181 +2179 @@
 
 void cleanUp(){
+  ChangeTracker::purgeInstance();
   World::purgeInstance();
   logger::purgeInstance();