Changeset 091838 for src/Parser

Timestamp:

Oct 26, 2011, 12:31:00 PM (13 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:

babcc1

Parents:

3a9091

git-author:

Frederik Heber <heber@…> (10/20/11 23:48:40)

git-committer:

Frederik Heber <heber@…> (10/26/11 12:31:00)

Message:

FormatParserStorage now explicitly needs to know which formats to store automatically.

• new functions FormatParserStorage::setOutputFormat() for giving this info.
• FormatParserStorage::SaveAll() only calls setOstream if the format is desired.
• FIX: FormatParser_common::FormatParser_common() forget to initialize saveStream.
• FormatParser_common::update() only stores when saveStream is not NULL, i.e. set.
• SetOutputFormatsAction now uses add and setOutputFormat().
• InputAction also adds the format of the input file.

Note that this is needed to allow various output formats for BondFragments in
Fragmentation without these formats eventually also being used for the writing
of the main input file.

Location:

src/Parser

Files:

• FormatParserStorage.cpp (modified) (4 diffs)
• FormatParserStorage.hpp (modified) (2 diffs)
• FormatParser_common.cpp (modified) (2 diffs)

src/Parser/FormatParserStorage.cpp

@@ -49 +49 @@
   ParserStream.resize(ParserTypes_end, NULL);
   ParserPresent.resize(ParserTypes_end, false);
+  ParserDesiredOutputFormat.resize(ParserTypes_end, false);
 
 #include "ParserTypes.def"
@@ -122 +123 @@
   for (ParserTypes iter = ParserTypes_begin; iter < ParserTypes_end; ++iter)
     if (ParserPresent[iter]) {
-      if (ParserStream[iter]->is_open())
-        ParserStream[iter]->close();
-      delete ParserStream[iter];
+      if (ParserStream[iter] != NULL) {
+        if (ParserStream[iter]->is_open())
+          ParserStream[iter]->close();
+        delete ParserStream[iter];
+      }
       delete ParserList[iter];
     }
@@ -137 +140 @@
 };
 
-
+/** Sets \a type as a format to be stored on call of SaveAll.
+ *
+ * @param type type to add to desired output formats
+ */
+void FormatParserStorage::setOutputFormat(ParserTypes type)
+{
+  LOG(0, "STATUS: Adding " << ParserNames[type] << " type to output.");
+  ParserDesiredOutputFormat[type] = true;
+}
+
+/** Sets \a type as a format to be stored on call of SaveAll.
+ *
+ * @param type type to add to desired output formats
+ */
+void FormatParserStorage::setOutputFormat(std::string type)
+{
+  std::map<std::string, ParserTypes>::const_iterator iter = ParserLookupNames.find(type);
+  ASSERT(iter != ParserLookupNames.end(),
+      "FormatParserStorage::setOutputFormat() - output format "+type+" is unknown.");
+  setOutputFormat(iter->second);
+}
+
+/** Saves the world in the desired output formats.
+ *
+ */
 void FormatParserStorage::SaveAll()
 {
   std::string filename;
   for (ParserTypes iter = ParserTypes_begin; iter < ParserTypes_end; ++iter)
-    if (ParserPresent[iter]) {
+    if (ParserPresent[iter] && ParserDesiredOutputFormat[iter]) {
       filename = prefix;
       filename += ".";
@@ -174 +201 @@
   if (ptype != ParserTypes_end) {
     if (ParserAddFunction.find(ptype) != ParserAddFunction.end()) {
-      LOG(0, "STATUS: Adding " << ParserNames[ptype] << " type to output.");
       (getInstance().*(ParserAddFunction[ptype]))(); // we still need an object to work on ...
       return true;

src/Parser/FormatParserStorage.hpp

@@ -41 +41 @@
   bool saveSelectedMolecules(std::ostream &output, std::string suffix);
   bool saveWorld(std::ostream &output, std::string suffix);
+
+  void setOutputFormat(ParserTypes type);
+  void setOutputFormat(std::string type);
   
   FormatParserInterface &get(ParserTypes _type);
@@ -63 +66 @@
   // which parser is already present
   std::vector<bool> ParserPresent;
+
+  // which parser is already present
+  std::vector<bool> ParserDesiredOutputFormat;
 
   // default suffix of each parser type

src/Parser/FormatParser_common.cpp

@@ -33 +33 @@
  */
 FormatParser_common::FormatParser_common(FormatParser_Parameters *_parameters) :
-  Observer("FormatParser_common")
+  Observer("FormatParser_common"),
+  saveStream(NULL)
 {
   parameters = _parameters;
@@ -58 +59 @@
  */
 void FormatParser_common::update(Observable *publisher) {
-  if (!saveStream) {
-    cerr << "Please invoke setOstream() so the parser knows where to save the World's data." << endl;
-    return;
+  if (saveStream != NULL) { // only store when a saveStream is given
+    std::vector<atom *> atoms = World::getInstance().getAllAtoms();
+    save(saveStream, atoms);
   }
-
-  std::vector<atom *> atoms = World::getInstance().getAllAtoms();
-  save(saveStream, atoms);
 }