Changeset 85bac0 for src/moleculelist.cpp

Timestamp:

Sep 11, 2008, 1:28:25 PM (16 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:

c30cda

Parents:

a1fe77

git-author:

Frederik Heber <heber@…> (09/09/08 15:29:58)

git-committer:

Frederik Heber <heber@…> (09/11/08 13:28:25)

Message:

Implemented molecule::LinearInterpolationBetweenConfiguration().

command line option "-L" with start and end step performs a linear interpolation between two atomic configurations. So far the mapping from initial atom labels to final labels is not yet finished, it is injective, but not yet minimal.

File:

• src/moleculelist.cpp (modified) (5 diffs)

src/moleculelist.cpp

@@ -378 +378 @@
  * \param *configuration standard configuration to attach atoms in fragment molecule to.
  * \param *SortIndex Index to map from the BFS labeling to the sequence how of Ion_Type in the config
+ * \param DoPeriodic true - call ScanForPeriodicCorrection, false - don't
+ * \param DoCentering true - call molecule::CenterEdge(), false - don't
  * \return true - success (each file was written), false - something went wrong.
  */
-bool MoleculeListClass::OutputConfigForListOfFragments(ofstream *out, config *configuration, int *SortIndex)
+bool MoleculeListClass::OutputConfigForListOfFragments(ofstream *out, const char *fragmentprefix, config *configuration, int *SortIndex, bool DoPeriodic, bool DoCentering)
 {
   ofstream outputFragment;
@@ -404 +406 @@
 
     // correct periodic
-    ListOfMolecules[i]->ScanForPeriodicCorrection(out);
+    if (DoPeriodic)
+      ListOfMolecules[i]->ScanForPeriodicCorrection(out);
 
     // output xyz file
     FragmentNumber = FixedDigitNumber(NumberOfMolecules, FragmentCounter++);
-    sprintf(FragmentName, "%s/%s%s.conf.xyz", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
+    sprintf(FragmentName, "%s/%s%s.conf.xyz", configuration->configpath, fragmentprefix, FragmentNumber);
     outputFragment.open(FragmentName, ios::out);
-    *out << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter-1 << " as XYZ ...";
+    *out << Verbose(2) << "Saving " << fragmentprefix << " No. " << FragmentNumber << "/" << FragmentCounter-1 << " as XYZ ...";
     if ((intermediateResult = ListOfMolecules[i]->OutputXYZ(&outputFragment)))
       *out << " done." << endl;
@@ -429 +432 @@
     
     // center on edge
-    ListOfMolecules[i]->CenterEdge(out, &BoxDimension);
-    ListOfMolecules[i]->SetBoxDimension(&BoxDimension);  // update Box of atoms by boundary
-    int j = -1;
-    for (int k=0;k<NDIM;k++) {
-      j += k+1;
-      BoxDimension.x[k] = 2.5* (configuration->GetIsAngstroem() ? 1. : 1./AtomicLengthToAngstroem);
-      ListOfMolecules[i]->cell_size[j] += BoxDimension.x[k]*2.;
-    }
-    ListOfMolecules[i]->Translate(&BoxDimension);
+    if (DoCentering) {
+      ListOfMolecules[i]->CenterEdge(out, &BoxDimension);
+      ListOfMolecules[i]->SetBoxDimension(&BoxDimension);  // update Box of atoms by boundary
+      int j = -1;
+      for (int k=0;k<NDIM;k++) {
+        j += k+1;
+        BoxDimension.x[k] = 2.5* (configuration->GetIsAngstroem() ? 1. : 1./AtomicLengthToAngstroem);
+        ListOfMolecules[i]->cell_size[j] += BoxDimension.x[k]*2.;
+      }
+      ListOfMolecules[i]->Translate(&BoxDimension);
+    }
 
     // also calculate necessary orbitals
@@ -445 +450 @@
     // change path in config
     //strcpy(PathBackup, configuration->configpath);
-    sprintf(FragmentName, "%s/%s%s/", PathBackup, FRAGMENTPREFIX, FragmentNumber);
+    sprintf(FragmentName, "%s/%s%s/", PathBackup, fragmentprefix, FragmentNumber);
     configuration->SetDefaultPath(FragmentName);
     
     // and save as config
-    sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
+    sprintf(FragmentName, "%s/%s%s.conf", configuration->configpath, fragmentprefix, FragmentNumber);
     outputFragment.open(FragmentName, ios::out);
-    *out << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter-1 << " as config ...";
+    *out << Verbose(2) << "Saving " << fragmentprefix << " No. " << FragmentNumber << "/" << FragmentCounter-1 << " as config ...";
     if ((intermediateResult = configuration->Save(&outputFragment, ListOfMolecules[i]->elemente, ListOfMolecules[i])))
       *out << " done." << endl;
@@ -465 +470 @@
 
     // and save as mpqc input file
-    sprintf(FragmentName, "%s/%s%s.in", configuration->configpath, FRAGMENTPREFIX, FragmentNumber);
+    sprintf(FragmentName, "%s/%s%s.in", configuration->configpath, fragmentprefix, FragmentNumber);
     outputFragment.open(FragmentName, ios::out);
-    *out << Verbose(2) << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter-1 << " as mpqc input ...";
+    *out << Verbose(2) << "Saving " << fragmentprefix << " No. " << FragmentNumber << "/" << FragmentCounter-1 << " as mpqc input ...";
     if ((intermediateResult = configuration->SaveMPQC(&outputFragment, ListOfMolecules[i])))
       *out << " done." << endl;