Changeset 2459b1 for src/moleculelist.cpp

Timestamp:

May 5, 2008, 4:19:05 PM (17 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:

3c4b08

Parents:

bd6579

Message:

ForcesFile and TEFactors are _needed_, reincorporated. UniqueFragments structure is now in BOSSANOVA

ForcesFile is again written, as we need it for the hydrogen not coming saturation (forces!)
TEFactors are back, as despite my notion they are needed in the evaluation
UniqueFragments structure is shifted from PowerSetGenerator to FragmentBOSSANOVA. Actually only for the labels - however, the if was changed to test the real indices (which are also always the same, which is better for adaptive runs) - but might be more useful there still.
analyzer and joiner again parse indices.

File:

• src/moleculelist.cpp (modified) (2 diffs)

src/moleculelist.cpp

@@ -133 +133 @@
 };
 
+
+/** Store force indices, i.e. the connection between the nuclear index in the total molecule config and the respective atom in fragment config.
+ * \param *out output stream for debugging
+ * \param *path path to file
+ * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
+ * \return true - file written successfully, false - writing failed
+ */
+bool MoleculeListClass::StoreForcesFile(ofstream *out, char *path, int *SortIndex)
+{
+  bool status = true;
+  ofstream ForcesFile;
+  stringstream line;
+  atom *Walker = NULL;
+  element *runner = NULL;
+
+  // open file for the force factors
+  *out << Verbose(1) << "Saving  force factors ... ";
+  line << path << "/" << FRAGMENTPREFIX << FORCESFILE;
+  ForcesFile.open(line.str().c_str(), ios::out);
+  if (ForcesFile != NULL) {
+    //cout << Verbose(1) << "Final AtomicForcesList: ";
+    //output << prefix << "Forces" << endl;
+    for(int j=0;j<NumberOfMolecules;j++) {
+      //if (TEList[j] != 0) {
+      runner = ListOfMolecules[j]->elemente->start;
+      while (runner->next != ListOfMolecules[j]->elemente->end) { // go through every element
+        runner = runner->next;
+        if (ListOfMolecules[j]->ElementsInMolecule[runner->Z]) { // if this element got atoms
+          Walker = ListOfMolecules[j]->start;
+          while (Walker->next != ListOfMolecules[j]->end) { // go through every atom of this element
+            Walker = Walker->next;
+            if (Walker->type->Z == runner->Z) {
+              if ((Walker->GetTrueFather() != NULL) && (Walker->GetTrueFather() != Walker)) {// if there is a rea
+                //cout << "Walker is " << *Walker << " with true father " << *( Walker->GetTrueFather()) << ", it
+                ForcesFile <<  SortIndex[Walker->GetTrueFather()->nr] << "\t";
+                } else  // otherwise a -1 to indicate an added saturation hydrogen
+                  ForcesFile << "-1\t";
+              }
+            }
+          }
+      }
+      ForcesFile << endl;
+    }
+    ForcesFile.close();
+    *out << Verbose(1) << "done." << endl;
+  } else {
+    status = false;
+    *out << Verbose(1) << "failed to open file " << line.str() << "." << endl;
+  }
+  ForcesFile.close();
+  
+  return status;
+};
+
 /** Writes a config file for each molecule in the given \a **FragmentList.
  * \param *out output stream for debugging
@@ -216 +270 @@
     Free((void **)&FragmentNumber, "MoleculeListClass::OutputConfigForListOfFragments: *FragmentNumber");
   }
-
-  // open KeySet file
-  sprintf(FragmentName, "%s/%s%s", configuration->configpath,  FRAGMENTPREFIX , KEYSETFILE);
-  output.open(FragmentName, ios::out);
-  *out << Verbose(2) << "Saving " << FRAGMENTPREFIX << " key sets of each subgraph ...";
-  for(int j=0;j<NumberOfMolecules;j++) {
-    Walker = ListOfMolecules[j]->start;
-    while(Walker->next != ListOfMolecules[j]->end) {
-      Walker = Walker->next;        
-#ifdef ADDHYDROGEN
-      if ((Walker->GetTrueFather() != NULL) && (Walker->type->Z != 1)) // if there is a real father, prints its index
-#else
-      if ((Walker->GetTrueFather() != NULL)) // if there is a real father, prints its index
-#endif 
-        output <<  Walker->GetTrueFather()->nr << "\t";
-#ifdef ADDHYDROGEN
-      else  // otherwise a -1 to indicate an added saturation hydrogen
-        output << "-1\t";
-#endif 
-    }
-    output << endl;
-  }
-  output.close();
-  *out << " done." << endl;
+  cout << " done." << endl;
   
   // printing final number