Changeset 3aa8a5 for src/Actions

Timestamp:

Dec 3, 2012, 9:50:01 AM (12 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:

4694df

Parents:

5197e5

git-author:

Frederik Heber <heber@…> (09/21/12 16:22:50)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:50:01)

Message:

REFACTOR: AdjacencyList now just contains a single internal map.

• map may either be created from world for a given vector of atomids or parsed from file.
• Moved molecule::StoreAdjacencyFromFile() over to StoreToFile().
• removed atom_bondedparticle::OutputAdjacency().
• changed comparison functions into operator<,>,==,!=().
• adapted FragmentationAction and SaveAdjacencyAction due to new calls, the former also needs to check the adjacency file for existence.
• SaveAdjacencyAction does not split given filename into path and name anymore.
• TESTFIX: Fragmentation-MaxOrder is working again, removed XFAIL_IF.
• TESTFIX: Rewrite of AdjacencyListUnitTest due to heavily changed interface of AdjacencyList. Also wrongadjacencyfile3 was buggy.
• TESTFIX: regression test SaveAdjacency replaced tab by space and removed tab after last entry in test.adj.

Location:

src/Actions

Files:

• FragmentationAction/FragmentationAction.cpp (modified) (5 diffs)
• MoleculeAction/SaveAdjacencyAction.cpp (modified) (2 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -47 +47 @@
 #include "World.hpp"
 
+#include <boost/filesystem.hpp>
 #include <iostream>
 #include <map>
@@ -80 +81 @@
   // go through all atoms, note down their molecules and group them
   typedef std::multimap<molecule *, atom *> clusters_t;
+  typedef std::vector<atomId_t> atomids_t;
+  atomids_t atomids;
   clusters_t clusters;
   for (World::AtomSelectionConstIterator iter = world.beginAtomSelection();
       iter != world.endAtomSelection(); ++iter) {
     clusters.insert( std::make_pair(iter->second->getMolecule(), iter->second) );
+    atomids.push_back(iter->second->getId());
   }
   LOG(1, "INFO: There are " << clusters.size()  << " molecules to consider.");
@@ -91 +95 @@
 
   // parse in Adjacency file
-  std::ifstream File;
-  std::string filename;
-  filename = params.prefix.get() + ADJACENCYFILE;
-  File.open(filename.c_str(), ios::out);
-  AdjacencyList FileChecker(File);
+  boost::shared_ptr<AdjacencyList> FileChecker;
+  boost::filesystem::path filename(params.prefix.get() + std::string(ADJACENCYFILE));
+  if (boost::filesystem::exists(filename) && boost::filesystem::is_regular_file(filename)) {
+    std::ifstream File;
+    File.open(filename.string().c_str(), ios::out);
+    FileChecker.reset(new AdjacencyList(File));
+    File.close();
+  } else {
+    LOG(1, "INFO: Could not open default adjacency file " << filename.string() << ".");
+    FileChecker.reset(new AdjacencyList);
+  }
 
   DepthFirstSearchAnalysis DFS;
@@ -119 +129 @@
         << " atoms, out of " << mol->getAtomCount() << ".");
     const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
-    Fragmentation Fragmenter(mol, FileChecker, saturation);
+    Fragmentation Fragmenter(mol, *FileChecker, saturation);
 
     // perform fragmentation
@@ -134 +144 @@
   }
   LOG(0, "STATUS: There are " << keysetcounter << " fragments.");
+
   // store molecule's fragment to file
-  ExportGraph_ToFiles exporter(TotalGraph, saturation);
-  exporter.setPrefix(params.prefix.get());
-  exporter.setOutputTypes(params.types.get());
-  exporter();
+  {
+    ExportGraph_ToFiles exporter(TotalGraph, saturation);
+    exporter.setPrefix(params.prefix.get());
+    exporter.setOutputTypes(params.types.get());
+    exporter();
+  }
+
+  // store Adjacency to file
+  {
+    std::string filename = params.prefix.get() + ADJACENCYFILE;
+    std::ofstream AdjacencyFile;
+    AdjacencyFile.open(filename.c_str(), ios::out);
+    AdjacencyList adjacency(atomids);
+    adjacency.StoreToFile(AdjacencyFile);
+    AdjacencyFile.close();
+  }
+
   World::getInstance().setExitFlag(ExitFlag);
   end = clock();
   LOG(0, "STATUS: Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s.");
-
 
   return Action::success;

src/Actions/MoleculeAction/SaveAdjacencyAction.cpp

@@ -40 +40 @@
 
 #include "CodePatterns/Log.hpp"
-#include "Graph/BondGraph.hpp"
+#include "Graph/AdjacencyList.hpp"
 #include "molecule.hpp"
 #include "World.hpp"
@@ -55 +55 @@
   molecule *mol = NULL;
 
+  // gather all desired ids
+  typedef std::vector<atomId_t> atomids_t;
+  atomids_t atomids;
   for (World::MoleculeSelectionIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
     mol = iter->second;
-    LOG(0, "Storing adjacency to path " << params.adjacencyfile.get() << ".");
-    // TODO: sollte stream nicht filename benutzen, besser fuer unit test
-    mol->StoreAdjacencyToFile(params.adjacencyfile.get().leaf().string(), params.adjacencyfile.get().branch_path().string());
+    const molecule::atomIdSet &mol_atomids = mol->getAtomIds();
+    atomids.insert(atomids.end(), mol_atomids.begin(), mol_atomids.end());
   }
+
+  // store to file
+  AdjacencyList adjacency(atomids);
+  std::ofstream AdjacencyFile;
+  const std::string filename = params.adjacencyfile.get().string();
+  LOG(0, "STATUS: Storing adjacency of selected molecules to " << filename << ".");
+  AdjacencyFile.open(filename.c_str(), ios::out);
+  adjacency.StoreToFile(AdjacencyFile);
+  AdjacencyFile.close();
+
   return Action::success;
 }