Changeset d67150

Timestamp:

Apr 8, 2009, 11:27:50 AM (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:

63f06e

Parents:

3af1f0

Message:

Lots of bugfixes, some name changes and new functions

BUGFIX:

• molecule::molecule did not initialise IndexNr and ActiveFlag
• molecule::SetNameFromFilename() was missing terminal \0 at end of constructed name
• molecule::CenterInBox() translates and zeros Center
• molecule::CenterEdge() also zeros Center
• molecule::CenterOrigin(): dropped parameter *center as molecule::Center is now used, translated and center then set to zero

Changes:

• molecule::CenterGravity() now is called CenterPeriodic() and just calls DeterminePeriodicCenter with molecule::Center as parameter
• molecule::DetermineCenter() variable is now called center to stop confusion with molecule::Center
• molecule::PrincipalAxisSystem() uses CenterAtVector with DetermineCenterOfGravity()
• molecule::IsEqualToWithinThreshold() now uses molecule::DeterminePeriodicCenter() due to name change
• molecule:SetNameFromFilename() now expects constant *filename

New:

• molecule:CenterAtVector() adds given vector to molecule::Center

Location:

src

Files:

• molecules.cpp (modified) (15 diffs)
• molecules.hpp (modified) (1 diff)

src/molecules.cpp

@@ -63 +63 @@
         cell_size[1] = cell_size[3] = cell_size[4]= 0.;
         strcpy(name,"none");
+        IndexNr  = -1;
+        ActiveFlag = false;
 };
 
@@ -602 +604 @@
  * \param *filename filename
  */
-void molecule::SetNameFromFilename(char *filename)
+void molecule::SetNameFromFilename(const char *filename)
 {
   int length = 0;
   char *molname = strrchr(filename, '/')+sizeof(char);  // search for filename without dirs
-  char *endname = strrchr(filename, '.');
+  char *endname = strchr(molname, '.');
   if ((endname == NULL) || (endname < molname))
     length = strlen(molname);
@@ -612 +614 @@
     length = strlen(molname) - strlen(endname);
   strncpy(name, molname, length);
+  name[length]='\0';
 };
 
@@ -667 +670 @@
                 max->AddVector(BoxLengths);
                 max->Scale(0.5);
-                Translate(max);
+    Translate(max);
+    Center.Zero();
         }
 
@@ -707 +711 @@
                 max->AddVector(min);
                 Translate(min);
+                Center.Zero();
         }
         delete(min);
@@ -716 +721 @@
  * \param *center return vector for translation vector
  */
-void molecule::CenterOrigin(ofstream *out, Vector *center)
+void molecule::CenterOrigin(ofstream *out)
 {
         int Num = 0;
         atom *ptr = start->next;        // start at first in list
 
-        for(int i=NDIM;i--;) // zero center vector
-                center->x[i] = 0.;
+        Center.Zero();
 
         if (ptr != end) {        //list not empty?
@@ -728 +732 @@
                         ptr = ptr->next;
                         Num++;
-                        center->AddVector(&ptr->x);
-                }
-                center->Scale(-1./Num); // divide through total number (and sign for direction)
-                Translate(center);
+                        Center.AddVector(&ptr->x);
+                }
+                Center.Scale(-1./Num); // divide through total number (and sign for direction)
+          Translate(&Center);
+          Center.Zero();
         }
 };
@@ -796 +801 @@
  * \param *center return vector for translation vector
  */
-void molecule::CenterGravity(ofstream *out, Vector *center)
-{
-        if (center == NULL) {
-                DetermineCenter(*center);
-                Translate(center);
-                delete(center);
-        } else {
-                Translate(center);
-        }
+void molecule::CenterPeriodic(ofstream *out)
+{
+        DeterminePeriodicCenter(Center);
+};
+
+/** Centers the center of gravity of the atoms at (0,0,0).
+ * \param *out output stream for debugging
+ * \param *center return vector for translation vector
+ */
+void molecule::CenterAtVector(ofstream *out, Vector *newcenter)
+{
+  Center.CopyVector(newcenter);
 };
 
@@ -853 +861 @@
 
 /** Determines center of molecule (yet not considering atom masses).
- * \param Center reference to return vector
- */
-void molecule::DetermineCenter(Vector &Center)
+ * \param center reference to return vector
+ */
+void molecule::DeterminePeriodicCenter(Vector &center)
 {
         atom *Walker = start;
@@ -865 +873 @@
 
         do {
-                Center.Zero();
+                center.Zero();
                 flag = true;
                 while (Walker->next != end) {
@@ -892 +900 @@
                                 Testvector.AddVector(&Translationvector);
                                 Testvector.MatrixMultiplication(matrix);
-                                Center.AddVector(&Testvector);
+                                center.AddVector(&Testvector);
                                 cout << Verbose(1) << "vector is: ";
                                 Testvector.Output((ofstream *)&cout);
@@ -905 +913 @@
                                                 Testvector.AddVector(&Translationvector);
                                                 Testvector.MatrixMultiplication(matrix);
-                                                Center.AddVector(&Testvector);
+                                                center.AddVector(&Testvector);
                                                 cout << Verbose(1) << "Hydrogen vector is: ";
                                                 Testvector.Output((ofstream *)&cout);
@@ -916 +924 @@
         } while (!flag);
         Free((void **)&matrix, "molecule::DetermineCenter: *matrix");
-        Center.Scale(1./(double)AtomCount);
+        center.Scale(1./(double)AtomCount);
 };
 
@@ -929 +937 @@
         Vector *CenterOfGravity = DetermineCenterOfGravity(out);
 
-        CenterGravity(out, CenterOfGravity);
+        CenterAtVector(out, CenterOfGravity);
 
         // reset inertia tensor
@@ -4494 +4502 @@
         if (result) {
                 *out << Verbose(5) << "Calculating Centers of Gravity" << endl;
-                DetermineCenter(CenterOfGravity);
-                OtherMolecule->DetermineCenter(OtherCenterOfGravity);
+                DeterminePeriodicCenter(CenterOfGravity);
+                OtherMolecule->DeterminePeriodicCenter(OtherCenterOfGravity);
                 *out << Verbose(5) << "Center of Gravity: ";
                 CenterOfGravity.Output(out);

src/molecules.hpp

@@ -251 +251 @@
         bool CenterInBox(ofstream *out, Vector *BoxLengths);
         void CenterEdge(ofstream *out, Vector *max);
-        void CenterOrigin(ofstream *out, Vector *max);
-        void CenterGravity(ofstream *out, Vector *max);
+        void CenterOrigin(ofstream *out);
+        void CenterPeriodic(ofstream *out);
+        void CenterAtVector(ofstream *out, Vector *newcenter);
         void Translate(const Vector *x);
         void Mirror(const Vector *x);
         void Align(Vector *n);
         void Scale(double **factor);
-        void DetermineCenter(Vector &center);
+        void DeterminePeriodicCenter(Vector &center);
         Vector * DetermineCenterOfGravity(ofstream *out);
         Vector * DetermineCenterOfAll(ofstream *out);
-        void SetNameFromFilename(char *filename);
+        void SetNameFromFilename(const char *filename);
         void SetBoxDimension(Vector *dim);
         double * ReturnFullMatrixforSymmetric(double *cell_size);