Changeset 2a0eb0 for src

Timestamp:

Dec 3, 2012, 9:49:06 AM (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:

3501d2

Parents:

34e74fd

git-author:

Frederik Heber <heber@…> (09/19/12 09:47:16)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:49:06)

Message:

FragmentationAction now works on selected atoms, split into molecules.

• i.e. we still call Fragmentation on a specific molecule but fragmentMolecule() receives a vector of ids to use in its AtomMask. This is however not yet implemented.
• TESTFIX: added --select-molecules-atoms to all fragmentation calls.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAction.cpp (modified) (3 diffs)
• Fragmentation/AdaptivityMap.cpp (modified) (1 diff)
• Fragmentation/AtomMask.hpp (modified) (2 diffs)
• Fragmentation/Fragmentation.cpp (modified) (5 diffs)
• Fragmentation/Fragmentation.hpp (modified) (2 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -44 +44 @@
 
 #include <iostream>
+#include <map>
 #include <string>
+#include <vector>
 
 #include "Actions/FragmentationAction/FragmentationAction.hpp"
@@ -56 +58 @@
 Action::state_ptr FragmentationFragmentationAction::performCall() {
   clock_t start,end;
-  molecule *mol = NULL;
-  int ExitFlag = 0;
+  int ExitFlag = -1;
+  World &world = World::getInstance();
 
+  // inform about used parameters
   LOG(0, "STATUS: Fragmenting molecular system with current connection matrix maximum bond distance "
       << params.distance.get() << " up to "
@@ -65 +68 @@
       << params.types.get() << "." << std::endl);
 
+  // check for selected atoms
+  if (world.beginAtomSelection() == world.endAtomSelection()) {
+    ELOG(1, "There are not atoms selected for fragmentation.");
+    return Action::failure;
+  }
+
+  // go through all atoms, note down their molecules and group them
+  typedef std::multimap<molecule *, atom *> clusters_t;
+  clusters_t clusters;
+  for (World::AtomSelectionConstIterator iter = world.beginAtomSelection();
+      iter != world.endAtomSelection(); ++iter) {
+    clusters.insert( std::make_pair(iter->second->getMolecule(), iter->second) );
+  }
+  LOG(1, "INFO: There are " << clusters.size()  << " molecules to consider.");
+
   DepthFirstSearchAnalysis DFS;
-  for (World::MoleculeSelectionConstIterator iter = World::getInstance().beginMoleculeSelection(); iter != World::getInstance().endMoleculeSelection(); ++iter) {
-    mol = iter->second;
-    ASSERT(mol != NULL, "No molecule has been picked for fragmentation.");
-    LOG(2, "INFO: Fragmenting molecule with bond distance " << params.distance.get() << " angstroem, order of " << params.order.get() << ".");
-    start = clock();
-    if (mol->hasBondStructure()) {
-      Fragmentation Fragmenter(mol, params.DoSaturation.get() ? DoSaturate : DontSaturate);
-      Fragmenter.setOutputTypes(params.types.get());
-      ExitFlag = Fragmenter.FragmentMolecule(params.order.get(), params.prefix.get(), DFS);
+  start = clock();
+  // go through all keys (i.e. all molecules)
+  clusters_t::const_iterator advanceiter;
+  for (clusters_t::const_iterator iter = clusters.begin();
+      iter != clusters.end();
+      iter = advanceiter) {
+    // get iterator to past last atom in this molecule
+    molecule * mol = iter->first;
+    advanceiter = clusters.upper_bound(mol);
+
+    // copy molecule's atoms' ids as parameters to Fragmentation's AtomMask
+    std::vector<atomId_t> mols_atomids;
+    std::transform(iter, advanceiter, std::back_inserter(mols_atomids),
+        boost::bind( &atom::getNr,
+            boost::bind( &clusters_t::value_type::second, _1 ))
+    );
+    LOG(2, "INFO: Fragmenting in molecule " << mol->getName() << " in " << clusters.count(mol) 
+        << " atoms, out of " << mol->getAtomCount() << ".");
+    Fragmentation Fragmenter(mol, params.DoSaturation.get() ? DoSaturate : DontSaturate);
+    Fragmenter.setOutputTypes(params.types.get());
+
+    // perform fragmentation
+    LOG(0, std::endl << " ========== Fragmentation of molecule " << mol->getName() << " ========================= ");
+    {
+      const int tempFlag = Fragmenter.FragmentMolecule(mols_atomids, params.order.get(), params.prefix.get(), DFS);
+      if ((ExitFlag == 2) && (tempFlag != 2))
+        ExitFlag = tempFlag; // if there is one molecule that needs further fragmentation, it overrides others
+      if (ExitFlag == -1)
+        ExitFlag = tempFlag; // if we are the first, we set the standard
     }
-    World::getInstance().setExitFlag(ExitFlag);
-    end = clock();
-    LOG(0, "STATUS: Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s.");
   }
+  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/Fragmentation/AdaptivityMap.cpp

@@ -211 +211 @@
       AtomMask.setTrue(No);
       status = true;
-    //} else
+    //} else {
+      //AtomMask.setFalse(No);
       //LOG(2, "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", however MinimumRingSize of " << MinimumRingSize[Walker->getNr()] << " does not allow further adaptive increase.");
+    //}
   }
   return status;

src/Fragmentation/AtomMask.hpp

@@ -18 +18 @@
 #include "types.hpp"
 
+#include <vector>
+
 /** AtomMask is a filter for a atomic ids. The bit is either true or false.
  *
@@ -23 +25 @@
 struct AtomMask_t : public Mask_t<atomId_t>
 {
+  typedef std::vector<atomId_t> atoms_t;
+  AtomMask_t(const atoms_t &atoms) {
+    for (atoms_t::const_iterator iter = atoms.begin();
+        iter != atoms.end(); ++iter)
+      setTrue(*iter);
+  }
 
 };

src/Fragmentation/Fragmentation.cpp

@@ -91 +91 @@
  * of vertex indices: Global always means the index in "this" molecule, whereas local refers to the molecule or
  * subgraph in the MoleculeListClass.
+ * \param atomids atoms to fragment, used in AtomMask
  * \param Order up to how many neighbouring bonds a fragment contains in BondOrderScheme::BottumUp scheme
  * \param prefix prefix string for every fragment file name (may include path)
@@ -96 +97 @@
  * \return 1 - continue, 2 - stop (no fragmentation occured)
  */
-int Fragmentation::FragmentMolecule(int Order, std::string prefix, DepthFirstSearchAnalysis &DFS)
+int Fragmentation::FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, std::string prefix, DepthFirstSearchAnalysis &DFS)
 {
   MoleculeListClass *BondFragments = NULL;
@@ -108 +109 @@
   Graph TotalGraph;     // graph with all keysets however local numbers
   int TotalNumberOfKeySets = 0;
-  AtomMask_t AtomMask;
+  AtomMask_t AtomMask(atomids);
 
   LOG(0, endl);
@@ -157 +158 @@
 
   // ===== 4. check globally whether there's something to do actually (first adaptivity check)
-  FragmentationToDo = FragmentationToDo && ParseOrderAtSiteFromFile(prefix);
+  FragmentationToDo = FragmentationToDo && ParseOrderAtSiteFromFile(atomids, prefix);
 
   // =================================== Begin of FRAGMENTATION ===============================
@@ -566 +567 @@
 /** Parses pairs(Atom::Nr, Atom::AdaptiveOrder) from file and stores in molecule's Atom's.
  * Atoms not present in the file get "0".
+ * \param atomids atoms to fragment, used in AtomMask
  * \param &path path to file ORDERATSITEFILEe
  * \return true - file found and scanned, false - file not found
  * \sa ParseKeySetFile() and CheckAdjacencyFileAgainstMolecule() as this is meant to be used in conjunction with the two
  */
-bool Fragmentation::ParseOrderAtSiteFromFile(std::string &path)
+bool Fragmentation::ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, std::string &path)
 {
   typedef unsigned char order_t;
   typedef std::map<atomId_t, order_t> OrderArray_t;
   OrderArray_t OrderArray;
-  AtomMask_t MaxArray;
+  AtomMask_t MaxArray(atomids);
   bool status;
   int AtomNr, value;

src/Fragmentation/Fragmentation.hpp

@@ -36 +36 @@
   ~Fragmentation();
 
-  int FragmentMolecule(int Order, std::string prefix, DepthFirstSearchAnalysis &DFS);
+  int FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, std::string prefix, DepthFirstSearchAnalysis &DFS);
 
   void setOutputTypes(const std::vector<std::string> &types);
@@ -50 +50 @@
   bool CheckOrderAtSite(AtomMask_t &AtomMask, Graph *GlobalKeySetList, int Order, std::string path, bool LoopDoneAlready);
   bool StoreOrderAtSiteFile(std::string &path);
-  bool ParseOrderAtSiteFromFile(std::string &path);
+  bool ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, std::string &path);
 
   // storing fragments