Changeset 4e10f5 for src/Actions

Timestamp:

Jul 7, 2010, 4:08:32 PM (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, 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:

77a570

Parents:

5630bd (diff), 192f6e (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:

src/Actions/WorldAction/CenterOnEdgeAction.cpp
src/Actions/WorldAction/ChangeBoxAction.cpp
src/Actions/WorldAction/RepeatBoxAction.cpp
src/Actions/WorldAction/ScaleBoxAction.cpp
src/World.cpp
src/boundary.cpp

Location:

src/Actions

Files:

• AnalysisAction/MolecularVolumeAction.cpp (modified) (1 diff)
• AnalysisAction/PairCorrelationAction.cpp (modified) (6 diffs)
• FragmentationAction/DepthFirstSearchAction.cpp (modified) (2 diffs)
• Makefile.am (modified) (2 diffs)
• MapOfActions.cpp (modified) (16 diffs)
• MapOfActions.hpp (modified) (1 diff)
• TesselationAction/ConvexEnvelopeAction.cpp (modified) (1 diff)
• WorldAction/CenterOnEdgeAction.cpp (modified) (1 diff)
• WorldAction/OutputAction.cpp (modified) (2 diffs)
• WorldAction/SetOutputFormatsAction.cpp (added)
• WorldAction/SetOutputFormatsAction.hpp (added)

src/Actions/AnalysisAction/MolecularVolumeAction.cpp

@@ -47 +47 @@
     LCList = new LinkedCell(mol, 10.);
     config * const configuration = World::getInstance().getConfig();
-    //FindConvexBorder(mol, LCList, argv[argptr]);
+    Boundaries *BoundaryPoints = NULL;
+    //FindConvexBorder(mol, BoundaryPoints, TesselStruct, LCList, argv[argptr]);
     FindNonConvexBorder(mol, TesselStruct, LCList, 5., NULL);
     //RemoveAllBoundaryPoints(TesselStruct, mol, argv[argptr]);

src/Actions/AnalysisAction/PairCorrelationAction.cpp

@@ -82 +82 @@
     output.open(outputname.c_str());
     binoutput.open(binoutputname.c_str());
-    PairCorrelationMap *correlationmap = NULL;
     if (type == "E") {
       PairCorrelationMap *correlationmap = NULL;
@@ -89 +88 @@
       else
         correlationmap = PairCorrelation(World::getInstance().getMolecules(), elements);
-      //OutputCorrelationToSurface(&output, correlationmap);
+      OutputPairCorrelation(&output, correlationmap);
       binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
+      OutputCorrelation ( &binoutput, binmap );
+      delete(binmap);
+      delete(correlationmap);
     } else if (type == "P")  {
       cout << "Point to correlate to is  " << Point << endl;
@@ -98 +100 @@
       else
         correlationmap = CorrelationToPoint(molecules, elements, &Point);
-      //OutputCorrelationToSurface(&output, correlationmap);
+      OutputCorrelationToPoint(&output, correlationmap);
       binmap = BinData( correlationmap, BinWidth, BinStart, BinEnd );
+      OutputCorrelation ( &binoutput, binmap );
+      delete(binmap);
+      delete(correlationmap);
     } else if (type == "S") {
       ASSERT(Boundary != NULL, "No molecule specified for SurfaceCorrelation.");
@@ -106 +111 @@
       if (BinEnd > 0) {
         if (BinEnd > 2.*radius)
-            LCWidth = BinEnd;
+          LCWidth = BinEnd;
         else
           LCWidth = 2.*radius;
@@ -129 +134 @@
       else
         surfacemap = CorrelationToSurface( molecules, elements, TesselStruct, LCList);
+      delete LCList;
       OutputCorrelationToSurface(&output, surfacemap);
+      // re-set ActiveFlag
+      counter = 0;
+      for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
+        (*BigFinder)->ActiveFlag = Actives[counter++];
+      }
+      delete[] Actives;
       // check whether radius was appropriate
       {
@@ -138 +150 @@
       }
       binmap = BinData( surfacemap, BinWidth, BinStart, BinEnd );
-    } else
+      OutputCorrelation ( &binoutput, binmap );
+      delete TesselStruct;  // surfacemap contains refs to triangles! delete here, not earlier!
+      delete(binmap);
+      delete(surfacemap);
+    } else {
       return Action::failure;
-    OutputCorrelation ( &binoutput, binmap );
+    }
     output.close();
     binoutput.close();
-    delete(binmap);
-    delete(correlationmap);
     delete dialog;
     return Action::success;

src/Actions/FragmentationAction/DepthFirstSearchAction.cpp

@@ -49 +49 @@
     MoleculeLeafClass *Subgraphs = NULL;      // list of subgraphs from DFS analysis
     int *MinimumRingSize = new int[mol->getAtomCount()];
-    atom ***ListOfLocalAtoms = NULL;
+    atom **ListOfAtoms = NULL;
     class StackClass<bond *> *BackEdgeStack = NULL;
     class StackClass<bond *> *LocalBackEdgeStack = NULL;
@@ -58 +58 @@
       while (Subgraphs->next != NULL) {
         Subgraphs = Subgraphs->next;
-        Subgraphs->FillBondStructureFromReference(mol, FragmentCounter, ListOfLocalAtoms, false);  // we want to keep the created ListOfLocalAtoms
+        ListOfAtoms = NULL;
+        Subgraphs->FillBondStructureFromReference(mol, ListOfAtoms, false);  // we want to keep the created ListOfLocalAtoms
         LocalBackEdgeStack = new StackClass<bond *> (Subgraphs->Leaf->BondCount);
-        Subgraphs->Leaf->PickLocalBackEdges(ListOfLocalAtoms[FragmentCounter], BackEdgeStack, LocalBackEdgeStack);
+        Subgraphs->Leaf->PickLocalBackEdges(ListOfAtoms, BackEdgeStack, LocalBackEdgeStack);
         Subgraphs->Leaf->CyclicStructureAnalysis(LocalBackEdgeStack, MinimumRingSize);
         delete(LocalBackEdgeStack);
         delete(Subgraphs->previous);
+        delete[](ListOfAtoms);  // and here we remove it
         FragmentCounter++;
       }
       delete(Subgraphs);
-      for (int i=0;i<FragmentCounter;i++)
-        delete[](ListOfLocalAtoms[i]);
-      delete[](ListOfLocalAtoms);
     }
     delete(BackEdgeStack);

src/Actions/Makefile.am

@@ -126 +126 @@
   WorldAction/ScaleBoxAction.cpp \
   WorldAction/SetDefaultNameAction.cpp \
-  WorldAction/SetGaussianBasisAction.cpp               
+  WorldAction/SetGaussianBasisAction.cpp \
+  WorldAction/SetOutputFormatsAction.cpp
 WORLDACTIONHEADER = \
   WorldAction/AddEmptyBoundaryAction.hpp \
@@ -139 +140 @@
   WorldAction/ScaleBoxAction.hpp \
   WorldAction/SetDefaultNameAction.hpp \
-  WorldAction/SetGaussianBasisAction.hpp
+  WorldAction/SetGaussianBasisAction.hpp \
+  WorldAction/SetOutputFormatsAction.hpp               
 

src/Actions/MapOfActions.cpp

@@ -67 +67 @@
 #include "Actions/WorldAction/SetDefaultNameAction.hpp"
 #include "Actions/WorldAction/SetGaussianBasisAction.hpp"
+#include "Actions/WorldAction/SetOutputFormatsAction.hpp"
 #include "Actions/Values.hpp"
 
@@ -72 +73 @@
 {
   VectorValue VV;
-  if (values.size() != 3) {
-    cerr <<  "Specified vector does not have three components but " << values.size() << endl;
+  std::vector<std::string> components;
+
+  // split comma-separated values
+  if (values.size() != 1) {
+    cerr <<  "Not one vector but " << components.size() << " given " << endl;
+    throw boost::program_options::validation_error("Unequal to one vector given");
+  }
+  std::string argument(values.at(0));
+  std::string::iterator Aiter = argument.begin();
+  std::string::iterator Biter = argument.begin();
+  for (; Aiter != argument.end(); ++Aiter) {
+    if (*Aiter == ',') {
+      components.push_back(string(Biter,Aiter));
+      do {
+        Aiter++;
+      } while (*Aiter == ' ' || *Aiter == '\t');
+      Biter = Aiter;
+    }
+  }
+  components.push_back(string(Biter,argument.end()));
+
+  if (components.size() != 3) {
+    cerr <<  "Specified vector does not have three components but " << components.size() << endl;
     throw boost::program_options::validation_error("Specified vector does not have three components");
   }
-  VV.x = boost::lexical_cast<double>(values.at(0));
-  VV.y = boost::lexical_cast<double>(values.at(1));
-  VV.z = boost::lexical_cast<double>(values.at(2));
+  VV.x = boost::lexical_cast<double>(components.at(0));
+  VV.y = boost::lexical_cast<double>(components.at(1));
+  VV.z = boost::lexical_cast<double>(components.at(2));
   v = boost::any(VectorValue(VV));
 }
@@ -85 +107 @@
 {
   BoxValue BV;
-  if (values.size() != 6) {
-    cerr <<  "Specified vector does not have three components but " << values.size() << endl;
+  std::vector<std::string> components;
+
+  // split comma-separated values
+  if (values.size() != 1) {
+    cerr <<  "Not one vector but " << components.size() << " given " << endl;
+    throw boost::program_options::validation_error("Unequal to one vector given");
+  }
+  std::string argument(values.at(0));
+  std::string::iterator Aiter = argument.begin();
+  std::string::iterator Biter = argument.begin();
+  for (; Aiter != argument.end(); ++Aiter) {
+    if (*Aiter == ',') {
+      components.push_back(string(Biter,Aiter));
+      do {
+        Aiter++;
+      } while (*Aiter == ' ' || *Aiter == '\t');
+      Biter = Aiter;
+    }
+  }
+  components.push_back(string(Biter,argument.end()));
+
+  if (components.size() != 6) {
+    cerr <<  "Specified vector does not have three components but " << components.size() << endl;
     throw boost::program_options::validation_error("Specified symmetric box matrix does not have six components");
   }
-  BV.xx = boost::lexical_cast<double>(values.at(0));
-  BV.xy = boost::lexical_cast<double>(values.at(1));
-  BV.xz = boost::lexical_cast<double>(values.at(2));
-  BV.yy = boost::lexical_cast<double>(values.at(3));
-  BV.yz = boost::lexical_cast<double>(values.at(4));
-  BV.zz = boost::lexical_cast<double>(values.at(5));
+  BV.xx = boost::lexical_cast<double>(components.at(0));
+  BV.xy = boost::lexical_cast<double>(components.at(1));
+  BV.xz = boost::lexical_cast<double>(components.at(2));
+  BV.yy = boost::lexical_cast<double>(components.at(3));
+  BV.yz = boost::lexical_cast<double>(components.at(4));
+  BV.zz = boost::lexical_cast<double>(components.at(5));
   v = boost::any(BoxValue(BV));
 }
@@ -130 +173 @@
   DescriptionMap["input"] = "specify input files";
   DescriptionMap["linear-interpolate"] = "linear interpolation in discrete steps between start and end position of a molecule";
+  DescriptionMap["molecular-volume"] = "calculate the volume of a given molecule";
   DescriptionMap["nonconvex-envelope"] = "create the non-convex envelope for a molecule";
-  DescriptionMap["molecular-volume"] = "calculate the volume of a given molecule";
-  DescriptionMap["output"] = "specify output formats";
+  DescriptionMap["output"] = "write output files";
+  DescriptionMap["set-output"] = "specify output formats";
   DescriptionMap["pair-correlation"] = "pair correlation analysis between two elements, element and point or element and surface";
   DescriptionMap["parse-xyz"] = "parse xyz file into World";
@@ -140 +184 @@
   DescriptionMap["repeat-box"] = "create periodic copies of the simulation box per axis";
   DescriptionMap["rotate-to-pas"] = "calculate the principal axis system of the specified molecule and rotate specified axis to align with main axis";
-  DescriptionMap["set-basis"] = "set the name of the gaussian basis set for MPQC";
   DescriptionMap["save-adjacency"] = "name of the adjacency file to write to";
   DescriptionMap["save-bonds"] = "name of the bonds file to write to";
@@ -146 +189 @@
   DescriptionMap["SaveXyz"] = "save world as xyz file";
   DescriptionMap["scale-box"] = "scale box and atomic positions inside";
+  DescriptionMap["set-basis"] = "set the name of the gaussian basis set for MPQC";
+  DescriptionMap["set-output"] = "specify output formats";
   DescriptionMap["subgraph-dissect"] = "dissect the molecular system into molecules representing disconnected subgraphs";
   DescriptionMap["suspend-in-water"] = "suspend the given molecule in water such that in the domain the mean density is as specified";
@@ -189 +234 @@
   ShortFormMap["center-in-box"] = "b";
   ShortFormMap["change-element"] = "E";
-  ShortFormMap["convex-envelope"] = "o";
+//  ShortFormMap["convex-envelope"] = "x";
   ShortFormMap["default-molname"] = "X";
   ShortFormMap["depth-first-search"] = "D";
@@ -200 +245 @@
   ShortFormMap["linear-interpolate"] = "L";
   ShortFormMap["nonconvex-envelope"] = "N";
+//  ShortFormMap["output"] = "o";
   ShortFormMap["pair-correlation"] = "C";
   ShortFormMap["parse-xyz"] = "p";
@@ -211 +257 @@
   ShortFormMap["scale-box"] = "s";
   ShortFormMap["set-basis"] = "M";
+  ShortFormMap["set-output"] = "o";
   ShortFormMap["subgraph-dissect"] = "I";
   ShortFormMap["suspend-in-water"] = "u";
@@ -238 +285 @@
   TypeMap["molecular-volume"] = Molecule;
   TypeMap["nonconvex-envelope"] = Molecule;
-  TypeMap["output"] = String;
+  TypeMap["output"] = None;
   TypeMap["parse-xyz"] = String;
   TypeMap["pair-correlation"] = String;
@@ -251 +298 @@
   TypeMap["scale-box"] = Vector;
   TypeMap["set-basis"] = String;
+  TypeMap["set-output"] = ListOfString;
   TypeMap["subgraph-dissect"] = None;
   TypeMap["suspend-in-water"] = Double;
@@ -349 +397 @@
   MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "default-molname") );
   MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "set-basis") );
+  MenuContainsActionMap.insert( pair<std::string, std::string> ("world", "set-output") );
 
   // put actions into command line category
@@ -386 +435 @@
   generic.insert("scale-box");
   generic.insert("set-basis");
+  generic.insert("set-output");
         generic.insert("subgraph-dissect");
   generic.insert("suspend-in-water");
@@ -484 +534 @@
   new WorldSetDefaultNameAction();
   new WorldSetGaussianBasisAction();
+  new WorldSetOutputFormatsAction();
 }
 
@@ -561 +612 @@
               ;
             break;
+          case ListOfString:
+            ListRunner->second->add_options()
+              (getKeyAndShortForm(*OptionRunner).c_str(),
+                  po::value< vector<std::string> >()->multitoken(),
+                  getDescription(*OptionRunner).c_str())
+              ;
+            break;
           case Axis:
             ListRunner->second->add_options()
@@ -573 +631 @@
             ListRunner->second->add_options()
               (getKeyAndShortForm(*OptionRunner).c_str(),
-                  po::value<VectorValue>()->multitoken(),
+                  po::value<VectorValue>(),
                   getDescription(*OptionRunner).c_str())
               ;

src/Actions/MapOfActions.hpp

@@ -123 +123 @@
   friend class MapOfActionsTest;
 public:
-  enum OptionTypes { None, Boolean, Integer, ListOfInts, Double, ListOfDoubles, String, Axis, Vector, Box, Molecule, ListOfMolecules, Atom, ListOfAtoms, Element, ListOfElements };
+  enum OptionTypes { None, Boolean, Integer, ListOfInts, Double, ListOfDoubles, String, ListOfString, Axis, Vector, Box, Molecule, ListOfMolecules, Atom, ListOfAtoms, Element, ListOfElements };
 
   // getter for the action descriptions and short forms

src/Actions/TesselationAction/ConvexEnvelopeAction.cpp

@@ -70 +70 @@
     DoLog(1) && (Log() << Verbose(1) << "Storing tecplot non-convex data in " << filenameNonConvex << "." << endl);
     LCList = new LinkedCell(mol, 100.);
-    //FindConvexBorder(mol, LCList, argv[argptr]);
+    Boundaries *BoundaryPoints = NULL;
+    //FindConvexBorder(mol, BoundaryPoints, TesselStruct, LCList, argv[argptr]);
     // TODO: Beide Funktionen sollten streams anstelle des Filenamen benutzen, besser fuer unit tests
     FindNonConvexBorder(mol, TesselStruct, LCList, 50., filenameNonConvex.c_str());

src/Actions/WorldAction/CenterOnEdgeAction.cpp

@@ -63 +63 @@
       domain.at(i,i) = tmp;
     }
-    cout << "new domain is: " << domain << endl;
     World::getInstance().setDomain(domain);
     // translate all atoms, such that Min is aty (0,0,0)

src/Actions/WorldAction/OutputAction.cpp

@@ -9 +9 @@
 
 #include "Actions/WorldAction/OutputAction.hpp"
+#include "Parser/ChangeTracker.hpp"
 #include "log.hpp"
 #include "verbose.hpp"
@@ -33 +34 @@
 Action::state_ptr WorldOutputAction::performCall() {
   Dialog *dialog = UIFactory::getInstance().makeDialog();
-  string defaultname;
 
-  defaultname = World::getInstance().getDefaultName();
-  dialog->queryString(NAME, &defaultname, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryEmpty(NAME, MapOfActions::getInstance().getDescription(NAME));
 
   if(dialog->display()) {
-    World::getInstance().setDefaultName(defaultname);
-    DoLog(0) && (Log() << Verbose(0) << "Default name of new molecules set to " << World::getInstance().getDefaultName() << "." << endl);
+    DoLog(0) && (Log() << Verbose(0) << "Saving world to files." << endl);
+    ChangeTracker::getInstance().saveStatus();
     delete dialog;
     return Action::success;