Changeset 20895b for molecuilder/src/atom_bondedparticle.cpp

Timestamp:

Nov 4, 2009, 5:34:05 PM (16 years ago)

Author:

Frederik Heber <heber@…>

Children:

5f1d021

Parents:

c1b76e

Message:

Extension to the periodic boundary case for analysis_correlation.cpp

• Distance() -> PeriodicDistance(): PairCorrelation(), CorrelationToPoint(), CorrelationToSurface()
• CorrelationToSurface() - goes through periodic cells given by a ranges variable and puts into map as well.
• const: ReturnFullMatrixforSymmetric() and InverseMatrix() now have const * const parameter
• InverseMatrix() shifted from class Vector into helpers.cpp
• adapted due to InverseMatrix(): molecule::CenterInBox(), molecule::BoundInBox(), molecule::TranslatePeriodically()
• new function: RDET3(), RDET2() (former #define's)
• FIX: molecule::CorrectBondDegree() would loop eternally, if bonds cannot be fully corrected.
• FIX for NULL return: Tesselation::FindClosestTrianglesToPoint(), Tesselation::GetCircleOfConnectedPoints()
• FIX: Vector::DistanceToPlane() - did not give correct sign before according to PlaneNormal orientation

other stuff:

• less output: BondedParticle::CorrectBondDegree(), molecule::CyclicStructureAnalysis()

File:

• molecuilder/src/atom_bondedparticle.cpp (modified) (3 diffs)

molecuilder/src/atom_bondedparticle.cpp

@@ -126 +126 @@
   bond *CandidateBond = NULL;
 
-  *out << Verbose(3) << "Walker " << *this << ": " << (int)this->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
+  //*out << Verbose(3) << "Walker " << *this << ": " << (int)this->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
   NoBonds = CountBonds();
   if ((int)(type->NoValenceOrbitals) > NoBonds) { // we have a mismatch, check all bonding partners for mismatch
@@ -132 +132 @@
       OtherWalker = (*Runner)->GetOtherAtom(this);
       OtherNoBonds = OtherWalker->CountBonds();
-      *out << Verbose(3) << "OtherWalker " << *OtherWalker << ": " << (int)OtherWalker->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
+      //*out << Verbose(3) << "OtherWalker " << *OtherWalker << ": " << (int)OtherWalker->type->NoValenceOrbitals << " > " << NoBonds << "?" << endl;
       if ((int)(OtherWalker->type->NoValenceOrbitals) > NoBonds) { // check if possible candidate
         if ((CandidateBond == NULL) || (ListOfBonds.size() > OtherWalker->ListOfBonds.size())) { // pick the one with fewer number of bonds first
           CandidateBond = (*Runner);
-          *out << Verbose(3) << "New candidate is " << *CandidateBond << "." << endl;
+          //*out << Verbose(3) << "New candidate is " << *CandidateBond << "." << endl;
         }
       }
@@ -144 +144 @@
       *out << Verbose(2) << "Increased bond degree for bond " << *CandidateBond << "." << endl;
     } else {
-      *out << Verbose(2) << "Could not find correct degree for atom " << *this << "." << endl;
+      //*out << Verbose(2) << "Could not find correct degree for atom " << *this << "." << endl;
       FalseBondDegree++;
     }