Changeset 1f1b23

Timestamp:

Feb 2, 2010, 9:43:52 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:

164a33, 8ab0407, a25aae

Parents:

790807

Message:

Possibility to store all bonds to file added.

So far we only could store the adjacency (i.e. atom along with all bond partners per line) to file.
For plotting molecules with pgfplots (and maybe for other purposes too) we need to have single tupels of two per line.
Hence, the following additions were implemented:

• new functions: BondedParticle::OutputBonds(), molecule::StoreBondsToFile()
• new ParseCommandLineOption: J stores adjacency, j stores bonds.

Location:

src

Files:

• atom_bondedparticle.cpp (modified) (2 diffs)
• atom_bondedparticle.hpp (modified) (1 diff)
• builder.cpp (modified) (3 diffs)
• molecule.hpp (modified) (1 diff)
• molecule_graph.cpp (modified) (1 diff)

src/atom_bondedparticle.cpp

@@ -56 +56 @@
  * \param *AdjacencyFile output stream
  */
-void BondedParticle::OutputAdjacency(ofstream *AdjacencyFile) const
+void BondedParticle::OutputAdjacency(ofstream * const AdjacencyFile) const
 {
   *AdjacencyFile << nr << "\t";
@@ -62 +62 @@
     *AdjacencyFile << (*Runner)->GetOtherAtom(this)->nr << "\t";
   *AdjacencyFile << endl;
+};
+
+/** Output of atom::nr along each bond partner per line.
+ * Only bonds are printed where atom::nr is smaller than the one of the bond partner.
+ * \param *AdjacencyFile output stream
+ */
+void BondedParticle::OutputBonds(ofstream * const BondFile) const
+{
+  for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); (++Runner))
+    if (nr < (*Runner)->GetOtherAtom(this)->nr)
+      *BondFile << nr << "\t" << (*Runner)->GetOtherAtom(this)->nr << "\n";
 };
 

src/atom_bondedparticle.hpp

@@ -44 +44 @@
   int CorrectBondDegree();
   void OutputBondOfAtom() const;
-  void OutputAdjacency(ofstream *AdjacencyFile) const;
+  void OutputAdjacency(ofstream * const AdjacencyFile) const;
+  void OutputBonds(ofstream * const BondFile) const;
   void OutputOrder(ofstream *file) const;
 

src/builder.cpp

@@ -1422 +1422 @@
             Log() << Verbose(0) << "\t-h/-H/-?\tGive this help screen." << endl;
             Log() << Verbose(0) << "\t-I\t Dissect current system of molecules into a set of disconnected (subgraphs of) molecules." << endl;
+            Log() << Verbose(0) << "\t-j\t<path> Store all bonds to file." << endl;
+            Log() << Verbose(0) << "\t-J\t<path> Store adjacency per atom to file." << endl;
             Log() << Verbose(0) << "\t-L <step0> <step1> <prefix>\tStore a linear interpolation between two configurations <step0> and <step1> into single config files with prefix <prefix> and as Trajectories into the current config file." << endl;
             Log() << Verbose(0) << "\t-m <0/1>\tCalculate (0)/ Align in(1) PAS with greatest EV along z axis." << endl;
@@ -1709 +1711 @@
                 CorrelationToSurfaceMap *surfacemap = PeriodicCorrelationToSurface( molecules, elemental, TesselStruct, LCList, ranges );
                 OutputCorrelationToSurface(&output, surfacemap);
-                BinPairMap *binmap = BinData( surfacemap, 0.5, 0., 0. );
+                BinPairMap *binmap = BinData( surfacemap, 0.5, 0., 20. );
                 OutputCorrelation ( &binoutput, binmap );
                 output.close();
@@ -1793 +1795 @@
               }
               break;
+
+            case 'J':
+              if (ExitFlag == 0) ExitFlag = 1;
+              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
+                ExitFlag =255;
+                eLog() << Verbose(0) << "Missing path of adjacency file: -j <path>" << endl;
+                performCriticalExit();
+              } else {
+                Log() << Verbose(0) << "Storing adjacency to path " << argv[argptr] << "." << endl;
+                configuration.BG->ConstructBondGraph(mol);
+                mol->StoreAdjacencyToFile(argv[argptr]);
+                argptr+=1;
+              }
+              break;
+
+            case 'j':
+              if (ExitFlag == 0) ExitFlag = 1;
+              if ((argptr >= argc) || (argv[argptr][0] == '-')) {
+                ExitFlag =255;
+                eLog() << Verbose(0) << "Missing path of bonds file: -j <path>" << endl;
+                performCriticalExit();
+              } else {
+                Log() << Verbose(0) << "Storing bonds to path " << argv[argptr] << "." << endl;
+                configuration.BG->ConstructBondGraph(mol);
+                mol->StoreBondsToFile(argv[argptr]);
+                argptr+=1;
+              }
+              break;
+
             case 'N':
               if (ExitFlag == 0) ExitFlag = 1;

src/molecule.hpp

@@ -269 +269 @@
   int FragmentMolecule(int Order, config *configuration);
   bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
+  bool StoreBondsToFile(char *path);
   bool StoreAdjacencyToFile(char *path);
   bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);

src/molecule_graph.cpp

@@ -992 +992 @@
   Log() << Verbose(1) << "Saving adjacency list ... ";
   if (AdjacencyFile != NULL) {
+    AdjacencyFile << "m\tn" << endl;
     ActOnAllAtoms(&atom::OutputAdjacency, &AdjacencyFile);
     AdjacencyFile.close();
+    Log() << Verbose(1) << "done." << endl;
+  } else {
+    Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl;
+    status = false;
+  }
+
+  return status;
+}
+;
+
+/** Storing the bond structure of a molecule to file.
+ * Simply stores Atom::nr and then the Atom::nr of all bond partners, one per line.
+ * \param *out output stream for debugging
+ * \param *path path to file
+ * \return true - file written successfully, false - writing failed
+ */
+bool molecule::StoreBondsToFile(char *path)
+{
+  ofstream BondFile;
+  stringstream line;
+  bool status = true;
+
+  line << path << "/" << FRAGMENTPREFIX << ADJACENCYFILE;
+  BondFile.open(line.str().c_str(), ios::out);
+  Log() << Verbose(1) << "Saving adjacency list ... ";
+  if (BondFile != NULL) {
+    BondFile << "m\tn" << endl;
+    ActOnAllAtoms(&atom::OutputBonds, &BondFile);
+    BondFile.close();
     Log() << Verbose(1) << "done." << endl;
   } else {