Changeset b21a64 for src/bondgraph.cpp

Timestamp:

Oct 30, 2009, 3:49:38 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:

34e0013

Parents:

b70721

git-author:

Frederik Heber <heber@…> (10/30/09 15:33:51)

git-committer:

Frederik Heber <heber@…> (10/30/09 15:49:38)

Message:

BondGraph is parsed if command line switch '-g' is given.

• builder.cpp: case 'g' which gives a bond length table file which is parsed after the configuration and before other command line options.
• BondGraph::BondLengthMatrixMinMaxDistance() falls back to CovalentMinMaxDistance() if no table parsed.
• Bond Length Table was changed to have first row _and_ column each enlist all the elements and does not have a "#" in front anymore.
• The unit test has been changed accordingly.

Signed-off-by: Frederik Heber <heber@…>

File:

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

src/bondgraph.cpp

@@ -49 +49 @@
 
   // parse in matrix
-  BondLengthMatrix->ParseMatrix(filename.c_str(), 0, 0, 0);
+  BondLengthMatrix->ParseMatrix(filename.c_str(), 0, 1, 0);
 
   // find greatest distance
@@ -113 +113 @@
 void BondGraph::BondLengthMatrixMinMaxDistance(BondedParticle * const Walker, BondedParticle * const OtherWalker, double &MinDistance, double &MaxDistance, bool IsAngstroem)
 {
-  MinDistance = GetBondLength(Walker->type->Z-1, OtherWalker->type->Z-1);
-  MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
-  MaxDistance = MinDistance + BONDTHRESHOLD;
-  MinDistance -= BONDTHRESHOLD;
+  if (BondLengthMatrix->Matrix == NULL) {// safety measure if no matrix has been parsed yet
+    cerr << Verbose(1) << "WARNING:  BondLengthMatrixMinMaxDistance() called without having parsed the bond length matrix yet!" << endl;
+    CovalentMinMaxDistance(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
+  } else {
+    MinDistance = GetBondLength(Walker->type->Z-1, OtherWalker->type->Z-1);
+    MinDistance *= (IsAngstroem) ? 1. : 1. / AtomicLengthToAngstroem;
+    MaxDistance = MinDistance + BONDTHRESHOLD;
+    MinDistance -= BONDTHRESHOLD;
+  }
 };