Changeset 0d1ad0 for src/moleculelist.cpp

Timestamp:

Jun 25, 2010, 9:42:28 AM (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, Candidate_v1.7.0, 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:

04488a, 0c5eeb, 93987b

Parents:

6d574a (diff), a356f2 (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:

molecuilder/src/World.cpp

File:

• src/moleculelist.cpp (modified) (12 diffs)

src/moleculelist.cpp

@@ -12 +12 @@
 #include "atom.hpp"
 #include "bond.hpp"
+#include "bondgraph.hpp"
 #include "boundary.hpp"
 #include "config.hpp"
@@ -379 +380 @@
  * bonded to the same atom, then we add for this pair a correction term constructed from a Morse
  * potential function fit to QM calculations with respecting to the interatomic hydrogen distance.
- * \param *out output stream for debugging
- * \param *path path to file
- */
-bool MoleculeListClass::AddHydrogenCorrection(char *path)
+ * \param &path path to file
+ */
+bool MoleculeListClass::AddHydrogenCorrection(std::string &path)
 {
   bond *Binder = NULL;
@@ -400 +400 @@
   // 0a. find dimension of matrices with constants
   line = path;
-  line.append("/");
-  line += FRAGMENTPREFIX;
   line += "1";
   line += FITCONSTANTSUFFIX;
   input.open(line.c_str());
-  if (input == NULL) {
+  if (input.fail()) {
     DoLog(1) && (Log() << Verbose(1) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
     return false;
@@ -569 +567 @@
 
 /** 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 &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(char *path,
-    int *SortIndex)
+bool MoleculeListClass::StoreForcesFile(std::string &path, int *SortIndex)
 {
   bool status = true;
-  ofstream ForcesFile;
-  stringstream line;
+  string filename(path);
+  filename += FORCESFILE;
+  ofstream ForcesFile(filename.c_str());
   periodentafel *periode=World::getInstance().getPeriode();
 
   // open file for the force factors
   DoLog(1) && (Log() << Verbose(1) << "Saving  force factors ... ");
-  line << path << "/" << FRAGMENTPREFIX << FORCESFILE;
-  ForcesFile.open(line.str().c_str(), ios::out);
-  if (ForcesFile != NULL) {
+  if (!ForcesFile.fail()) {
     //Log() << Verbose(1) << "Final AtomicForcesList: ";
     //output << prefix << "Forces" << endl;
@@ -611 +606 @@
   } else {
     status = false;
-    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << filename << "." << endl);
   }
   ForcesFile.close();
@@ -620 +615 @@
 /** Writes a config file for each molecule in the given \a **FragmentList.
  * \param *out output stream for debugging
- * \param *configuration standard configuration to attach atoms in fragment molecule to.
+ * \param &prefix path and prefix to the fragment config files
  * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
  * \return true - success (each file was written), false - something went wrong.
  */
-bool MoleculeListClass::OutputConfigForListOfFragments(config *configuration, int *SortIndex)
+bool MoleculeListClass::OutputConfigForListOfFragments(std::string &prefix, int *SortIndex)
 {
   ofstream outputFragment;
-  char FragmentName[MAXSTRINGSIZE];
+  std::string FragmentName;
   char PathBackup[MAXSTRINGSIZE];
   bool result = true;
@@ -645 +640 @@
   for (MoleculeList::iterator ListRunner = ListOfMolecules.begin(); ListRunner != ListOfMolecules.end(); ListRunner++) {
     // save default path as it is changed for each fragment
-    path = configuration->GetDefaultPath();
+    path = World::getInstance().getConfig()->GetDefaultPath();
     if (path != NULL)
       strcpy(PathBackup, path);
@@ -658 +653 @@
     // output xyz file
     FragmentNumber = FixedDigitNumber(ListOfMolecules.size(), FragmentCounter++);
-    sprintf(FragmentName, "%s/%s%s.conf.xyz", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
-    outputFragment.open(FragmentName, ios::out);
+    FragmentName = prefix + FragmentNumber + ".conf.xyz";
+    outputFragment.open(FragmentName.c_str(), ios::out);
     DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as XYZ ...");
     if ((intermediateResult = (*ListRunner)->OutputXYZ(&outputFragment)))
@@ -682 +677 @@
     for (int k = 0; k < NDIM; k++) {
       j += k + 1;
-      BoxDimension[k] = 2.5 * (configuration->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
+      BoxDimension[k] = 2.5 * (World::getInstance().getConfig()->GetIsAngstroem() ? 1. : 1. / AtomicLengthToAngstroem);
       cell_size[j] = BoxDimension[k] * 2.;
     }
@@ -689 +684 @@
     // also calculate necessary orbitals
     (*ListRunner)->CountElements(); // this is a bugfix, atoms should shoulds actually be added correctly to this fragment
-    (*ListRunner)->CalculateOrbitals(*configuration);
+    //(*ListRunner)->CalculateOrbitals(*World::getInstance().getConfig);
 
     // change path in config
-    //strcpy(PathBackup, configuration->configpath);
-    sprintf(FragmentName, "%s/%s%s/", PathBackup, FRAGMENTPREFIX, FragmentNumber);
-    configuration->SetDefaultPath(FragmentName);
+    FragmentName = PathBackup;
+    FragmentName += "/";
+    FragmentName += FRAGMENTPREFIX;
+    FragmentName += FragmentNumber;
+    FragmentName += "/";
+    World::getInstance().getConfig()->SetDefaultPath(FragmentName.c_str());
 
     // and save as config
-    sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
+    FragmentName = prefix + FragmentNumber + ".conf";
     DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as config ...");
-    if ((intermediateResult = configuration->Save(FragmentName, (*ListRunner)->elemente, (*ListRunner))))
+    if ((intermediateResult = World::getInstance().getConfig()->Save(FragmentName.c_str(), (*ListRunner)->elemente, (*ListRunner))))
       DoLog(0) && (Log() << Verbose(0) << " done." << endl);
     else
@@ -706 +704 @@
 
     // restore old config
-    configuration->SetDefaultPath(PathBackup);
+    World::getInstance().getConfig()->SetDefaultPath(PathBackup);
 
     // and save as mpqc input file
-    sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
+    FragmentName = prefix + FragmentNumber + ".conf";
     DoLog(2) && (Log() << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ...");
-    if ((intermediateResult = configuration->SaveMPQC(FragmentName, (*ListRunner))))
+    if ((intermediateResult = World::getInstance().getConfig()->SaveMPQC(FragmentName.c_str(), (*ListRunner))))
       DoLog(2) && (Log() << Verbose(2) << " done." << endl);
     else
@@ -767 +765 @@
 
   // 1. dissect the molecule into connected subgraphs
-  if (!configuration->BG->ConstructBondGraph(mol)) {
-    World::getInstance().destroyMolecule(mol);
-    DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
+  if (configuration->BG != NULL) {
+    if (!configuration->BG->ConstructBondGraph(mol)) {
+      World::getInstance().destroyMolecule(mol);
+      DoeLog(1) && (eLog()<< Verbose(1) << "There are no bonds." << endl);
+      return;
+    }
+  } else {
+    DoeLog(1) && (eLog()<< Verbose(1) << "There is no BondGraph class present to create bonds." << endl);
     return;
   }