Changeset 1b62f3
- Timestamp:
- Jul 8, 2008, 1:12:55 PM (16 years ago)
- 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:
- 0378e2
- Parents:
- 68cb0f
- File:
-
- 1 edited
Legend:
- Unmodified
- Added
- Removed
-
src/molecules.cpp
r68cb0f r1b62f3 3746 3746 bool flag = true; 3747 3747 3748 *out << Verbose( 1) << "Begin of ScanForPeriodicCorrection." << endl;3748 *out << Verbose(2) << "Begin of ScanForPeriodicCorrection." << endl; 3749 3749 3750 3750 ColorList = (enum Shading *) Malloc(sizeof(enum Shading)*AtomCount, "molecule::ScanForPeriodicCorrection: *ColorList"); … … 3760 3760 for (int i=NDIM;i--;) { 3761 3761 tmp = fabs(Binder->leftatom->x.x[i] - Binder->rightatom->x.x[i]); 3762 *out << Verbose(3) << "Checking " << i << "th distance of " << *Binder->leftatom << " to " << *Binder->rightatom << ": " << tmp << "." << endl;3762 //*out << Verbose(3) << "Checking " << i << "th distance of " << *Binder->leftatom << " to " << *Binder->rightatom << ": " << tmp << "." << endl; 3763 3763 if (tmp > BondDistance) { 3764 3764 OtherBinder = Binder->next; // note down binding partner for later re-insertion 3765 3765 unlink(Binder); // unlink bond 3766 *out << Verbose(2) << "Correcting at bond " << *Binder << "." << endl;3766 //*out << Verbose(2) << "Correcting at bond " << *Binder << "." << endl; 3767 3767 flag = true; 3768 3768 break; … … 3778 3778 } 3779 3779 TranslationVector.MatrixMultiplication(matrix); 3780 *out << "Translation vector is ";3780 *out << Verbose(3) << "Translation vector is "; 3781 3781 TranslationVector.Output(out); 3782 3782 *out << endl; … … 3802 3802 link(Binder, OtherBinder); 3803 3803 } else { 3804 *out << Verbose( 2) << "No corrections for this fragment." << endl;3804 *out << Verbose(3) << "No corrections for this fragment." << endl; 3805 3805 } 3806 3806 //delete(CompStack); … … 3811 3811 Free((void **)&ColorList, "molecule::ScanForPeriodicCorrection: *ColorList"); 3812 3812 Free((void **)&matrix, "molecule::ScanForPeriodicCorrection: *matrix"); 3813 *out << Verbose( 1) << "End of ScanForPeriodicCorrection." << endl;3813 *out << Verbose(2) << "End of ScanForPeriodicCorrection." << endl; 3814 3814 }; 3815 3815
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