Changeset fa649a for src/boundary.cpp

Timestamp:

Nov 2, 2009, 12:50:57 PM (15 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:

7218f8

Parents:

34e0013

Message:

Small changes.

• VolumeOfConvexEnvelope() - setprecision corrected
• BUGFIX: PrepareClustersinWater() - IsAngstroem was set to NULL instead of true
• config::Load(), ..LoadOld() - get MoleculeListClass instead of molecule
• config::TestSyntax() - removed unncessary molecule parameter
• ParseCommandLineOptions() - no mol is created anymore, this is done when parsing in config::Load(), mol is set to first active instead
• config.cpp: Lots of ^{M (dos EOL) removed}
• have const molecule * const ref now: MoleculeLeafClass::FillBondStructureFromReference(), molecule::PickLocalBackEdges(), DepthFirstSearchAnalysis_CheckForaNewComponent(), DepthFirstSearchAnalysis_ProbeAlongUnusedBond()
• are const member functions now - necessary due to periodentafel being a const pointer: molecule::ResetAllBondsToUnused(), molecule::FindNextUnused(), molecule::SetNextComponentNumber(), molecule::CyclicStructureAnalysis(), CyclicStructureAnalysis_AssignRingSizetoNonCycleMembers(), molecule::OutputGraphInfoPerBond(), molecule::OutputGraphInfoPerAtom(), molecule::CyclicBondAnalysis(), molecule::CyclicStructureAnalysis(), molecule::GetColor(), molecule::CorrectBondDegree(), molecule::OutputBondsList()
• in molecule NoNonHydrogen, NoNonBonds and NoCyclicBonds are mutable
• molecule constructor rewritten with respect to ticket #4 (shorten constructors)

File:

• src/boundary.cpp (modified) (3 diffs)

src/boundary.cpp

@@ -649 +649 @@
       const double h = x.Norm(); // distance of CoG to triangle
       const double PyramidVolume = (1. / 3.) * G * h; // this formula holds for _all_ pyramids (independent of n-edge base or (not) centered peak)
-      *out << Verbose(2) << "Area of triangle is " << G << " "
+      *out << Verbose(2) << "Area of triangle is " << setprecision(10) << G << " "
           << (IsAngstroem ? "angstrom" : "atomiclength") << "^2, height is "
           << h << " and the volume is " << PyramidVolume << " "
@@ -655 +655 @@
       volume += PyramidVolume;
     }
-  *out << Verbose(0) << "RESULT: The summed volume is " << setprecision(10)
+  *out << Verbose(0) << "RESULT: The summed volume is " << setprecision(8)
       << volume << " " << (IsAngstroem ? "angstrom" : "atomiclength") << "^3."
       << endl;
@@ -705 +705 @@
 void PrepareClustersinWater(ofstream *out, config *configuration, molecule *mol, double ClusterVolume, double celldensity)
 {
-  bool IsAngstroem = NULL;
+  bool IsAngstroem = true;
   double *GreatestDiameter = NULL;
   Boundaries *BoundaryPoints = NULL;