Changeset bfd839

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@…>

Location:

src

Files:

• Legacy/oldmenu.cpp (modified) (3 diffs)
• analysis_bonds.cpp (modified) (5 diffs)
• analysis_bonds.hpp (modified) (1 diff)
• builder.cpp (modified) (4 diffs)
• unittests/CountBondsUnitTest.cpp (modified) (8 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;

src/analysis_bonds.cpp

@@ -123 +123 @@
  * \param *molecules molecules to count bonds
  * \param *InterfaceElement or NULL
- */
-int CountHydrogenBridgeBonds(MoleculeListClass *molecules, element * InterfaceElement = NULL)
+ * \param *Interface2Element or NULL
+ */
+int CountHydrogenBridgeBonds(MoleculeListClass *molecules, const element * InterfaceElement = NULL, const element * Interface2Element = NULL)
 {
   atom *Walker = NULL;
@@ -132 +133 @@
   double Otherangle = 0.;
   bool InterfaceFlag = false;
+  bool Interface2Flag = false;
   bool OtherHydrogenFlag = true;
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin();MolWalker != molecules->ListOfMolecules.end(); MolWalker++) {
@@ -151 +153 @@
               OtherHydrogens = 0;
               InterfaceFlag = (InterfaceElement == NULL);
+              Interface2Flag = (Interface2Element == NULL);
               for (BondList::const_iterator BondRunner = Runner->ListOfBonds.begin(); BondRunner != Runner->ListOfBonds.end(); BondRunner++) {
                 atom * const OtherAtom = (*BondRunner)->GetOtherAtom(Runner);
@@ -161 +164 @@
                 }
                 InterfaceFlag = InterfaceFlag || (OtherAtom->type == InterfaceElement);
+                Interface2Flag = Interface2Flag || (OtherAtom->type == Interface2Element);
               }
               DoLog(1) && (Log() << Verbose(1) << "Otherangle is " << Otherangle << " for " << OtherHydrogens << " hydrogens." << endl);
@@ -174 +178 @@
                   break;
               }
-              if (InterfaceFlag && OtherHydrogenFlag) {
+              if (InterfaceFlag && Interface2Flag && OtherHydrogenFlag) {
                 // on this element (Walker) we check for bond to hydrogen, i.e. part of water molecule
                 for (BondList::const_iterator BondRunner = Walker->ListOfBonds.begin(); BondRunner != Walker->ListOfBonds.end(); BondRunner++) {

src/analysis_bonds.hpp

@@ -33 +33 @@
 void MinMeanMaxBondDistanceBetweenElements(const molecule *mol, element *type1, element *type2, double &Min, double &Mean, double &Max);
 
-int CountHydrogenBridgeBonds(MoleculeListClass * const molecules, element * InterfaceElement);
+int CountHydrogenBridgeBonds(MoleculeListClass * const molecules, const element * InterfaceElement, const element * Interface2Element);
 int CountBondsOfTwo(MoleculeListClass * const molecules, const element * const first, const element * const second);
 int CountBondsOfThree(MoleculeListClass * const molecules, const element * const first, const element * const second, const element * const third);

src/builder.cpp

@@ -70 +70 @@
 #include "molecule.hpp"
 #include "periodentafel.hpp"
+#include "tesselationhelpers.hpp"
 #include "UIElements/UIFactory.hpp"
 #include "UIElements/MainWindow.hpp"
@@ -1519 +1520 @@
         switch(argv[argptr-1][1]) {
           case 'h':
-          case 'H':
           case '?':
             DoLog(0) && (Log() << Verbose(0) << "MoleCuilder suite" << endl << "==================" << endl << endl);
@@ -1538 +1538 @@
             DoLog(0) && (Log() << Verbose(0) << "\t-FF <MaxDistance> <xyz of filler> <dist_x> <dist_y> <dist_z> <epsilon> <randatom> <randmol> <DoRotate>\tFilling Box with water molecules." << endl);
             DoLog(0) && (Log() << Verbose(0) << "\t-g <file>\tParses a bond length table from the given file." << endl);
-            DoLog(0) && (Log() << Verbose(0) << "\t-h/-H/-?\tGive this help screen." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-h/-?\tGive this help screen." << endl);
+            DoLog(0) && (Log() << Verbose(0) << "\t-H\tCount Hydrogen bridge bonds." << endl);
             DoLog(0) && (Log() << Verbose(0) << "\t-I\t Dissect current system of molecules into a set of disconnected (subgraphs of) molecules." << endl);
             DoLog(0) && (Log() << Verbose(0) << "\t-j\t<path> Store all bonds to file." << endl);
@@ -1817 +1818 @@
                 if (mol != NULL)
                   mol->ActiveFlag = true;
+              }
+              break;
+            case 'H':
+              if ((argptr+1 >= argc) || (argv[argptr][0] == '-') || (argv[argptr+1][0] == '-')) {
+                ExitFlag = 255;
+                DoeLog(0) && (eLog()<< Verbose(0) << "Not enough or invalid arguments given for calculating hydrogen bridge bonds: -H <Z1> <Z2>" << endl);
+                performCriticalExit();
+              } else {
+                if (ExitFlag == 0) ExitFlag = 1;
+                const element *elemental = periode->FindElement((const int) atoi(argv[argptr]));
+                const element *elemental2 = periode->FindElement((const int) atoi(argv[argptr+1]));
+                cout << endl << "There are " << CountHydrogenBridgeBonds(molecules, elemental, elemental2) << " hydrogen bridges with connections to " << (elemental != 0 ? elemental->name : "None") << " and " << (elemental2 != 0 ? elemental2->name : "None") << "." << endl;
+                argptr+=1;
               }
               break;

src/unittests/CountBondsUnitTest.cpp

@@ -167 +167 @@
   Translator  = Vector(3,0,0);
   TestMolecule2->Translate(&Translator);
-  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL) );
-  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, oxygen) );
+  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
+  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, oxygen, NULL) );
   //OutputTestMolecule(TestMolecule2, "testmolecule2-1.xyz");
   Translator = Vector(-3,0,0);
@@ -176 +176 @@
   Translator = Vector(0,3,0);
   TestMolecule2->Translate(&Translator);
-  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL) );
+  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
   //OutputTestMolecule(TestMolecule2, "testmolecule2-2.xyz");
   Translator = Vector(0,-3,0);
@@ -185 +185 @@
   TestMolecule2->Scale((const double ** const)&mirror);
   TestMolecule2->Translate(&Translator);
-  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL) );
+  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
   //OutputTestMolecule(TestMolecule2, "testmolecule2-3.xyz");
   Translator = Vector(0,3,0);
@@ -194 +194 @@
   Translator = Vector(2,1,0);
   TestMolecule2->Translate(&Translator);
-  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL) );
+  CPPUNIT_ASSERT_EQUAL( 1 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
   //OutputTestMolecule(TestMolecule2, "testmolecule2-4.xyz");
   Translator = Vector(-2,-1,0);
@@ -202 +202 @@
   Translator = Vector(0,0,3);
   TestMolecule2->Translate(&Translator);
-  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL) );
+  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
   //OutputTestMolecule(TestMolecule2, "testmolecule2-5.xyz");
   Translator = Vector(0,0,-3);
@@ -211 +211 @@
   TestMolecule2->Scale((const double ** const)&mirror);
   TestMolecule2->Translate(&Translator);
-  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL) );
+  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
   //OutputTestMolecule(TestMolecule2, "testmolecule2-6.xyz");
   Translator = Vector(3,0,0);
@@ -221 +221 @@
   TestMolecule2->Scale((const double ** const)&mirror);
   TestMolecule2->Translate(&Translator);
-  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL) );
+  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
   //OutputTestMolecule(TestMolecule2, "testmolecule2-7.xyz");
   Translator = Vector(-3,0,0);
@@ -232 +232 @@
   TestMolecule2->Translate(&Translator);
   //OutputTestMolecule(TestMolecule2, "testmolecule2-8.xyz");
-  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL) );
+  CPPUNIT_ASSERT_EQUAL( 0 , CountHydrogenBridgeBonds(molecules, NULL, NULL) );
   Translator = Vector(0,-3,0);
   TestMolecule2->Translate(&Translator);