Changeset 49f802c for src/atom.cpp

Timestamp:

Oct 9, 2009, 11:57:41 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, Candidate_v1.7.0, 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:

c111db

Parents:

f66195

Message:

Implementing templated iterators done for molecule.cpp

• new functions in class atom: atom::DistanceSquaredToVector(), atom::DistanceToVector() and atom::AddKineticToTemperature()
• above used with ActOnAllAtoms() in molecule.cpp: molecule::OutputTemperatureFromTrajectories(), molecule::OutputListOfBonds() (uses atom::OutputBondOfAtom() which gives slightly different output than before but rather with more info)
• new template SetIndexedArrayForEachAtomTo() which sets the contents of an index array according to a member function result.
• above used in molecule::IsEqualToWithinThreshold()

File:

• src/atom.cpp (modified) (2 diffs)

src/atom.cpp

@@ -222 +222 @@
 {
   if (out != NULL) {
-    *out << Verbose(4) << "Atom " << Name << "/" << nr << " with " << NumberOfBondsPerAtom[nr] << " bonds: ";
-    int TotalDegree = 0;
-    for (int j=0;j<NumberOfBondsPerAtom[nr];j++) {
-      *out << *ListOfBondsPerAtom[nr][j] << "\t";
-      TotalDegree += ListOfBondsPerAtom[nr][j]->BondDegree;
+#ifdef ADDHYDROGEN
+    if (type->Z != 1) {   // regard only non-hydrogen
+#endif
+      *out << Verbose(4) << "Atom " << Name << "/" << nr << " with " << NumberOfBondsPerAtom[nr] << " bonds: ";
+      int TotalDegree = 0;
+      for (int j=0;j<NumberOfBondsPerAtom[nr];j++) {
+        *out << *ListOfBondsPerAtom[nr][j] << "\t";
+        TotalDegree += ListOfBondsPerAtom[nr][j]->BondDegree;
+      }
+      *out << " -- TotalDegree: " << TotalDegree << endl;
+#ifdef ADDHYDROGEN
     }
-    *out << " -- TotalDegree: " << TotalDegree << endl;
+#endif
     return true;
   } else
@@ -258 +264 @@
 };
 
+/** Returns squared distance to a given vector.
+ * \param origin vector to calculate distance to
+ * \return distance squared
+ */
+double atom::DistanceSquaredToVector(Vector &origin)
+{
+  return origin.DistanceSquared(&x);
+};
+
+/** Adds kinetic energy of this atom to given temperature value.
+ * \param *temperature add on this value
+ * \param step given step of trajectory to add
+ */
+void atom::AddKineticToTemperature(double *temperature, int step) const
+{
+  for (int i=NDIM;i--;)
+    *temperature += type->mass * Trajectory.U.at(step).x[i]* Trajectory.U.at(step).x[i];
+};
+
+/** Returns distance to a given vector.
+ * \param origin vector to calculate distance to
+ * \return distance
+ */
+double atom::DistanceToVector(Vector &origin)
+{
+  return origin.Distance(&x);
+};
+
 bool operator < (atom &a, atom &b)
 {