Changeset f714979 for src/molecules.cpp

Timestamp:

Dec 8, 2008, 2:16:34 PM (16 years ago)

Author:

Christian Neuen <neuen@…>

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:

caf5d6

Parents:

a8bcea6

Message:

Another update w.r.t. the Tesselation.
Some signs switched, but atom indices might be misused.

File:

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

src/molecules.cpp

@@ -1677 +1677 @@
 
 /** Creates an adjacency list of the molecule.
+ * We obtain an outside file with the indices of atoms which are bondmembers.
+ */
+void molecule::CreateAdjacencyList2(ofstream *out, ifstream *input)
+{
+
+        // 1 We will parse bonds out of the dbond file created by tremolo.
+                        int atom1, atom2, temp;
+                        atom *Walker, *OtherWalker;
+
+                if (!input)
+                {
+                        cout << Verbose(1) << "Opening silica failed \n";
+                };
+
+                        *input >> ws >> atom1;
+                        *input >> ws >> atom2;
+                cout << Verbose(1) << "Scanning file\n";
+                while (!input->eof()) // Check whether we read everything already
+                {
+                                *input >> ws >> atom1;
+                                *input >> ws >> atom2;
+                        if(atom2<atom1) //Sort indices of atoms in order
+                        {
+                                temp=atom1;
+                                atom1=atom2;
+                                atom2=temp;
+                        };
+
+                        Walker=start;
+                        while(Walker-> nr != atom1) // Find atom corresponding to first index
+                        {
+                                Walker = Walker->next;
+                        };
+                        OtherWalker = Walker->next;
+                        while(OtherWalker->nr != atom2) // Find atom corresponding to second index
+                        {
+                                OtherWalker= OtherWalker->next;
+                        };
+                        AddBond(Walker, OtherWalker); //Add the bond between the two atoms with respective indices.
+                        BondCount++; //Increase bond count of molecule
+                }
+
+                CreateListOfBondsPerAtom(out);
+
+};
+
+
+/** Creates an adjacency list of the molecule.
  * Generally, we use the CSD approach to bond recognition, that is the the distance
  * between two atoms A and B must be within [Rcov(A)+Rcov(B)-t,Rcov(A)+Rcov(B)+t] with
@@ -1694 +1742 @@
  * \param IsAngstroem whether coordinate system is gauged to Angstroem or Bohr radii
  */
-void molecule::CreateAdjacencyList2(ofstream *out, ifstream *input)// ofstream* out, double bonddistance, bool IsAngstroem)
-{
-
-        // 1 We will parse bonds out of the dbond file created by tremolo.
-                        int atom1, atom2, temp;
-                        atom *Walker, *OtherWalker;
-
-                if (!input)
-                {
-                        cout << Verbose(1) << "Opening silica failed \n";
-                };
-
-                        *input >> ws >> atom1;
-                        *input >> ws >> atom2;
-                cout << Verbose(1) << "Scanning file\n";
-                while (!input->eof()) // Check whether we read 2 items
-                {
-                                *input >> ws >> atom1;
-                                *input >> ws >> atom2;
-                        if(atom2<atom1) //Sort indizes of atoms in order
-                        {
-                                temp=atom1;
-                                atom1=atom2;
-                                atom2=temp;
-                        };
-
-                        Walker=start;
-                        while(Walker-> nr != atom1) // Find atom corresponding to first index
-                        {
-                                Walker = Walker->next;
-                        };
-                        OtherWalker = Walker->next;
-                        while(OtherWalker->nr != atom2) // Find atom corresponding to second index
-                        {
-                                OtherWalker= OtherWalker->next;
-                        };
-                        AddBond(Walker, OtherWalker); //Add the bond between the two atoms with respective indices.
-                        BondCount++; //Increase bond count of molecule
-                }
-
-                CreateListOfBondsPerAtom(out);
-
-};
 void molecule::CreateAdjacencyList(ofstream *out, double bonddistance, bool IsAngstroem)
 {