Changeset bfd839 for src/Legacy

Timestamp:

May 27, 2010, 9:17:11 AM (15 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:

b32dbb

Parents:

f2f4ae

Message:

Changed and added counting of hydrogen bonds to menu.

• CountHydrogenBonds() now receives two interface elements. This was needed to overcome double-couting in CSH-experiments.
• Unit test CountHBonds has been changed accordingly, but not test for the new feature has been added.
• case 'H' in builder.cpp is now used for counting hydrogen bonds not for giving help screen
• option has been added to MeasureAtoms() menu

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

File:

• src/Legacy/oldmenu.cpp (modified) (3 diffs)

src/Legacy/oldmenu.cpp

@@ -8 +8 @@
 
 #include "Legacy/oldmenu.hpp"
+#include "analysis_bonds.hpp"
 #include "analysis_correlation.hpp"
 #include "World.hpp"
@@ -501 +502 @@
   Log() << Verbose(0) << " f - calculate temperature from current velocity" << endl;
   Log() << Verbose(0) << " g - output all temperatures per step from velocities" << endl;
+  Log() << Verbose(0) << " h - count the number of hydrogen bonds" << endl;
   Log() << Verbose(0) << "all else - go back" << endl;
   Log() << Verbose(0) << "===============================================" << endl;
@@ -591 +593 @@
         output->close();
         delete(output);
+      }
+      break;
+    case 'h':
+      {
+        int Z1;
+        cout << "Please enter first interface element: ";
+        cin >> Z1;
+        const element * InterfaceElement = World::getInstance().getPeriode()->FindElement(Z1);
+        int Z2;
+        cout << "Please enter second interface element: ";
+        cin >> Z2;
+        const element * InterfaceElement2 = World::getInstance().getPeriode()->FindElement(Z2);
+        cout << endl << "There are " << CountHydrogenBridgeBonds(World::getInstance().getMolecules(), InterfaceElement, InterfaceElement2) << " hydrogen bridges with connections to " << (InterfaceElement != 0 ? InterfaceElement->name : "None") << " and " << (InterfaceElement2 != 0 ? InterfaceElement2->name : "None") << "." << endl;
       }
       break;