Changeset 820a42

Timestamp:

Jan 5, 2010, 10:11:52 AM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

3e026a

Parents:

235bed

Message:

Extracted all methods from MergeMolecules Menu

• Added new action that only displays an errorMessage

Location:

src

Files:

• Actions/ErrorAction.cpp (added)
• Actions/ErrorAction.hpp (added)
• Makefile.am (modified) (1 diff)
• menu.cpp (modified) (5 diffs)
• menu.hpp (modified) (1 diff)

src/Makefile.am

@@ -5 +5 @@
 ANALYSISHEADER = analysis_bonds.hpp analysis_correlation.hpp
 
-ACTIONSSOURCE = Actions/Action.cpp Actions/MethodAction.cpp Actions/ActionSequence.cpp Actions/MakroAction.cpp
-ACTIONSHEADER = Actions/Action.hpp Actions/MethodAction.hpp Actions/ActionSequence.hpp Actions/MakroAction.hpp
+ACTIONSSOURCE = Actions/Action.cpp Actions/MethodAction.cpp Actions/ActionSequence.cpp Actions/MakroAction.cpp Actions/ErrorAction.cpp
+ACTIONSHEADER = Actions/Action.hpp Actions/MethodAction.hpp Actions/ActionSequence.hpp Actions/MakroAction.hpp Actions/ErrorAction.hpp
 
 VIEWSOURCE = Views/View.cpp Views/StringView.cpp Views/MethodStringView.cpp Views/StreamStringView.cpp

src/menu.cpp

@@ -740 +740 @@
 };
 
+void oldmenu::duplicateCell(MoleculeListClass *molecules, config *configuration) {
+  molecule *mol = NULL;
+  int axis,faktor,count,j;
+  atom *first = NULL;
+  element **Elements;
+  Vector x,y;
+  Vector **vectors;
+
+  for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
+    if ((*ListRunner)->ActiveFlag) {
+    mol = *ListRunner;
+    Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
+    Log() << Verbose(0) << "State the axis [(+-)123]: ";
+    cin >> axis;
+    Log() << Verbose(0) << "State the factor: ";
+    cin >> faktor;
+
+    mol->CountAtoms(); // recount atoms
+    if (mol->AtomCount != 0) {  // if there is more than none
+      count = mol->AtomCount;  // is changed becausing of adding, thus has to be stored away beforehand
+      Elements = new element *[count];
+      vectors = new Vector *[count];
+      j = 0;
+      first = mol->start;
+      while (first->next != mol->end) { // make a list of all atoms with coordinates and element
+        first = first->next;
+        Elements[j] = first->type;
+        vectors[j] = &first->x;
+        j++;
+      }
+      if (count != j)
+        eLog() << Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl;
+      x.Zero();
+      y.Zero();
+      y.x[abs(axis)-1] = mol->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] * abs(axis)/axis; // last term is for sign, first is for magnitude
+      for (int i=1;i<faktor;i++) {  // then add this list with respective translation factor times
+        x.AddVector(&y); // per factor one cell width further
+        for (int k=count;k--;) { // go through every atom of the original cell
+          first = new atom(); // create a new body
+          first->x.CopyVector(vectors[k]);  // use coordinate of original atom
+          first->x.AddVector(&x);     // translate the coordinates
+          first->type = Elements[k];  // insert original element
+          mol->AddAtom(first);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
+        }
+      }
+      if (mol->first->next != mol->last) // if connect matrix is present already, redo it
+        mol->CreateAdjacencyList(mol->BondDistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
+      // free memory
+      delete[](Elements);
+      delete[](vectors);
+      // correct cell size
+      if (axis < 0) { // if sign was negative, we have to translate everything
+        x.Zero();
+        x.AddVector(&y);
+        x.Scale(-(faktor-1));
+        mol->Translate(&x);
+      }
+      mol->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= faktor;
+    }
+  }
+}
+
 /** Submenu for manipulating molecules.
  * \param *periode periodentafel
@@ -777 +839 @@
 
     case 'd': // duplicate the periodic cell along a given axis, given times
-      for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
-        if ((*ListRunner)->ActiveFlag) {
-        mol = *ListRunner;
-        Log() << Verbose(0) << "Current molecule is: " << mol->IndexNr << "\t" << mol->name << endl;
-        Log() << Verbose(0) << "State the axis [(+-)123]: ";
-        cin >> axis;
-        Log() << Verbose(0) << "State the factor: ";
-        cin >> faktor;
-
-        mol->CountAtoms(); // recount atoms
-        if (mol->AtomCount != 0) {  // if there is more than none
-          count = mol->AtomCount;  // is changed becausing of adding, thus has to be stored away beforehand
-          Elements = new element *[count];
-          vectors = new Vector *[count];
-          j = 0;
-          first = mol->start;
-          while (first->next != mol->end) { // make a list of all atoms with coordinates and element
-            first = first->next;
-            Elements[j] = first->type;
-            vectors[j] = &first->x;
-            j++;
-          }
-          if (count != j)
-            eLog() << Verbose(1) << "AtomCount " << count << " is not equal to number of atoms in molecule " << j << "!" << endl;
-          x.Zero();
-          y.Zero();
-          y.x[abs(axis)-1] = mol->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] * abs(axis)/axis; // last term is for sign, first is for magnitude
-          for (int i=1;i<faktor;i++) {  // then add this list with respective translation factor times
-            x.AddVector(&y); // per factor one cell width further
-            for (int k=count;k--;) { // go through every atom of the original cell
-              first = new atom(); // create a new body
-              first->x.CopyVector(vectors[k]);  // use coordinate of original atom
-              first->x.AddVector(&x);     // translate the coordinates
-              first->type = Elements[k];  // insert original element
-              mol->AddAtom(first);        // and add to the molecule (which increments ElementsInMolecule, AtomCount, ...)
-            }
-          }
-          if (mol->first->next != mol->last) // if connect matrix is present already, redo it
-            mol->CreateAdjacencyList(mol->BondDistance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
-          // free memory
-          delete[](Elements);
-          delete[](vectors);
-          // correct cell size
-          if (axis < 0) { // if sign was negative, we have to translate everything
-            x.Zero();
-            x.AddVector(&y);
-            x.Scale(-(faktor-1));
-            mol->Translate(&x);
-          }
-          mol->cell_size[(abs(axis) == 2) ? 2 : ((abs(axis) == 3) ? 5 : 0)] *= faktor;
-        }
-      }
+      duplicateCell(molecules, configuration);
       break;
 
@@ -899 +910 @@
 
 
+void oldmenu::SimpleAddMolecules(MoleculeListClass *molecules) {
+  int src, dest;
+  molecule *srcmol = NULL, *destmol = NULL;
+  {
+    do {
+      Log() << Verbose(0) << "Enter index of destination molecule: ";
+      cin >> dest;
+      destmol = molecules->ReturnIndex(dest);
+    } while ((destmol == NULL) && (dest != -1));
+    do {
+      Log() << Verbose(0) << "Enter index of source molecule to add from: ";
+      cin >> src;
+      srcmol = molecules->ReturnIndex(src);
+    } while ((srcmol == NULL) && (src != -1));
+    if ((src != -1) && (dest != -1))
+      molecules->SimpleAdd(srcmol, destmol);
+  }
+}
+
+void oldmenu::embeddMolecules(MoleculeListClass *molecules) {
+  int src, dest;
+  molecule *srcmol = NULL, *destmol = NULL;
+  do {
+    Log() << Verbose(0) << "Enter index of matrix molecule (the variable one): ";
+    cin >> src;
+    srcmol = molecules->ReturnIndex(src);
+  } while ((srcmol == NULL) && (src != -1));
+  do {
+    Log() << Verbose(0) << "Enter index of molecule to merge into (the fixed one): ";
+    cin >> dest;
+    destmol = molecules->ReturnIndex(dest);
+  } while ((destmol == NULL) && (dest != -1));
+  if ((src != -1) && (dest != -1))
+    molecules->EmbedMerge(destmol, srcmol);
+}
+
+void oldmenu::multiMergeMolecules(MoleculeListClass *molecules) {
+  int nr;
+  molecule *mol = NULL;
+  do {
+    Log() << Verbose(0) << "Enter index of molecule to merge into: ";
+    cin >> nr;
+    mol = molecules->ReturnIndex(nr);
+  } while ((mol == NULL) && (nr != -1));
+  if (nr != -1) {
+    int N = molecules->ListOfMolecules.size()-1;
+    int *src = new int(N);
+    for(MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
+      if ((*ListRunner)->IndexNr != nr)
+        src[N++] = (*ListRunner)->IndexNr;
+    molecules->SimpleMultiMerge(mol, src, N);
+    delete[](src);
+  }
+}
+
+void oldmenu::simpleMergeMolecules(MoleculeListClass *molecules) {
+  int src, dest;
+  molecule *srcmol = NULL, *destmol = NULL;
+  {
+    do {
+      Log() << Verbose(0) << "Enter index of destination molecule: ";
+      cin >> dest;
+      destmol = molecules->ReturnIndex(dest);
+    } while ((destmol == NULL) && (dest != -1));
+    do {
+      Log() << Verbose(0) << "Enter index of source molecule to merge into: ";
+      cin >> src;
+      srcmol = molecules->ReturnIndex(src);
+    } while ((srcmol == NULL) && (src != -1));
+    if ((src != -1) && (dest != -1))
+      molecules->SimpleMerge(srcmol, destmol);
+  }
+}
+
 /** Submenu for merging molecules.
  * \param *periode periodentafel
@@ -924 +1009 @@
 
     case 'a':
-      {
-        int src, dest;
-        molecule *srcmol = NULL, *destmol = NULL;
-        {
-          do {
-            Log() << Verbose(0) << "Enter index of destination molecule: ";
-            cin >> dest;
-            destmol = molecules->ReturnIndex(dest);
-          } while ((destmol == NULL) && (dest != -1));
-          do {
-            Log() << Verbose(0) << "Enter index of source molecule to add from: ";
-            cin >> src;
-            srcmol = molecules->ReturnIndex(src);
-          } while ((srcmol == NULL) && (src != -1));
-          if ((src != -1) && (dest != -1))
-            molecules->SimpleAdd(srcmol, destmol);
-        }
-      }
+      SimpleAddMolecules(molecules);
       break;
 
     case 'e':
-      {
-        int src, dest;
-        molecule *srcmol = NULL, *destmol = NULL;
-        do {
-          Log() << Verbose(0) << "Enter index of matrix molecule (the variable one): ";
-          cin >> src;
-          srcmol = molecules->ReturnIndex(src);
-        } while ((srcmol == NULL) && (src != -1));
-        do {
-          Log() << Verbose(0) << "Enter index of molecule to merge into (the fixed one): ";
-          cin >> dest;
-          destmol = molecules->ReturnIndex(dest);
-        } while ((destmol == NULL) && (dest != -1));
-        if ((src != -1) && (dest != -1))
-          molecules->EmbedMerge(destmol, srcmol);
-      }
+      embeddMolecules(molecules);
       break;
 
     case 'm':
-      {
-        int nr;
-        molecule *mol = NULL;
-        do {
-          Log() << Verbose(0) << "Enter index of molecule to merge into: ";
-          cin >> nr;
-          mol = molecules->ReturnIndex(nr);
-        } while ((mol == NULL) && (nr != -1));
-        if (nr != -1) {
-          int N = molecules->ListOfMolecules.size()-1;
-          int *src = new int(N);
-          for(MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++)
-            if ((*ListRunner)->IndexNr != nr)
-              src[N++] = (*ListRunner)->IndexNr;
-          molecules->SimpleMultiMerge(mol, src, N);
-          delete[](src);
-        }
-      }
+      multiMergeMolecules(molecules);
       break;
 
@@ -989 +1025 @@
 
     case 't':
-      {
-        int src, dest;
-        molecule *srcmol = NULL, *destmol = NULL;
-        {
-          do {
-            Log() << Verbose(0) << "Enter index of destination molecule: ";
-            cin >> dest;
-            destmol = molecules->ReturnIndex(dest);
-          } while ((destmol == NULL) && (dest != -1));
-          do {
-            Log() << Verbose(0) << "Enter index of source molecule to merge into: ";
-            cin >> src;
-            srcmol = molecules->ReturnIndex(src);
-          } while ((srcmol == NULL) && (src != -1));
-          if ((src != -1) && (dest != -1))
-            molecules->SimpleMerge(srcmol, destmol);
-        }
-      }
+      simpleMergeMolecules(molecules);
       break;
   }

src/menu.hpp

@@ -25 +25 @@
   void perform(MoleculeListClass *, config *, periodentafel *, char *);
 
+  // methods taken from ManipulateMoleculse submenu
+  void duplicateCell(MoleculeListClass *molecules, config *configuration);
+
+  // methods taken from MergeMolecules submenu
+  void SimpleAddMolecules(MoleculeListClass *molecules);
+  void embeddMolecules(MoleculeListClass *molecules);
+  void multiMergeMolecules(MoleculeListClass *molecules);
+  void simpleMergeMolecules(MoleculeListClass *molecules);
+
 protected:
   void AddAtoms(periodentafel *, molecule *);