Changeset 0d1ad0 for src/Parser

Timestamp:

Jun 25, 2010, 9:42:28 AM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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, 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

Children:

04488a, 0c5eeb, 93987b

Parents:

6d574a (diff), a356f2 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'stable' into StructureRefactoring

Conflicts:

molecuilder/src/World.cpp

Location:

src/Parser

Files:

• ChangeTracker.cpp (modified) (3 diffs)
• ChangeTracker.hpp (modified) (2 diffs)
• FormatParser.cpp (modified) (2 diffs)
• FormatParserStorage.cpp (added)
• FormatParserStorage.hpp (added)
• MpqcParser.cpp (added)
• MpqcParser.hpp (added)
• PcpParser.cpp (added)
• PcpParser.hpp (added)
• TremoloParser.cpp (modified) (2 diffs)
• TremoloParser.hpp (modified) (1 diff)
• XyzParser.cpp (modified) (2 diffs)
• XyzParser.hpp (modified) (1 diff)

src/Parser/ChangeTracker.cpp

@@ -7 +7 @@
 
 #include "Helpers/MemDebug.hpp"
+#include "Parser/ChangeTracker.hpp"
+#include "Patterns/Singleton_impl.hpp"
 
-#include "ChangeTracker.hpp"
-
-ChangeTracker* ChangeTracker::instance = NULL;
 
 /**
@@ -27 +26 @@
 ChangeTracker::~ChangeTracker() {
   World::getInstance().signOff(this);
-}
-
-/**
- * Returns the change tracker instance.
- *
- * \return this
- */
-ChangeTracker* ChangeTracker::get() {
-  if (instance == NULL) {
-    instance = new ChangeTracker();
-  }
-
-  return instance;
-}
-
-/**
- * Destroys the change tracker instance. Be careful, the change tracker is a
- * singleton and destruction might lead to a loss of consistency.
- */
-void ChangeTracker::destroy() {
-  delete instance;
-  instance = NULL;
 }
 
@@ -76 +53 @@
   }
 }
+
+CONSTRUCT_SINGLETON(ChangeTracker)

src/Parser/ChangeTracker.hpp

@@ -18 +18 @@
  * changes to it.
  */
-class ChangeTracker : public Observable {
+class ChangeTracker : public Singleton<ChangeTracker>, public Observable {
+  friend class Singleton<ChangeTracker>;
 public:
   void saveStatus();
@@ -31 +32 @@
   bool isConsistent;
   static ChangeTracker* instance;
+
+  // private constructor and destructor due to singleton
   ChangeTracker();
   ~ChangeTracker();

src/Parser/FormatParser.cpp

@@ -19 +19 @@
   Observer("FormatParser")
 {
-  ChangeTracker::get()->signOn(this);
+  ChangeTracker::getInstance().signOn(this);
   saveStream = NULL;
 }
@@ -27 +27 @@
  */
 FormatParser::~FormatParser() {
-  ChangeTracker::get()->signOff(this);
+  ChangeTracker::getInstance().signOff(this);
 }
 

src/Parser/TremoloParser.cpp

@@ -49 +49 @@
   knownKeys["GrpTypeNo"] = TremoloKey::GrpTypeNo;
   knownKeys["torsion"] = TremoloKey::torsion;
+
+  // default behavior: use all possible keys on output
+  for (std::map<std::string, TremoloKey::atomDataKey>::iterator iter = knownKeys.begin(); iter != knownKeys.end(); ++iter)
+    usedFields.push_back(iter->first);
 }
 
@@ -193 +197 @@
 
   lineStream << line.substr(offset);
+  usedFields.clear();
   while (lineStream.good()) {
     lineStream >> keyword;

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);
 }
 
@@ -58 +57 @@
  */
 void XyzParser::save(ostream* file) {
+  if (comment == "") {
+    time_t now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
+    comment = "\tCreated by molecuilder on ";
+    // ctime ends in \n\0, we have to cut away the newline
+    std::string time(ctime(&now));
+    size_t pos = time.find('\n');
+    if (pos != 0)
+      comment += time.substr(0,pos);
+    else
+      comment += time;
+  }
   *file << World::getInstance().numAtoms() << endl << comment << endl;
 
   vector<atom*> atoms = World::getInstance().getAllAtoms();
   for(vector<atom*>::iterator it = atoms.begin(); it != atoms.end(); it++) {
-    *file << fixed << (*it)->getType()->symbol << "\t" << (*it)->x[0] << "\t" << (*it)->x[1] << "\t" << (*it)->x[2] << endl;
+    *file << noshowpoint << (*it)->getType()->symbol << "\t" << (*it)->x[0] << "\t" << (*it)->x[1] << "\t" << (*it)->x[2] << endl;
   }
 }

src/Parser/XyzParser.hpp

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