Changeset 681a8a

Timestamp:

Oct 7, 2009, 1:16:13 PM (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:

23b830

Parents:

fcd7b6

Message:

in molecule::OutputTrajectoriesXYZ() ActOnAllAtoms used by new function atom::OutputTrajectoryXYZ().

Location:

src

Files:

• atom.cpp (modified) (1 diff)
• atom.hpp (modified) (1 diff)
• molecule.cpp (modified) (2 diffs)

src/atom.cpp

@@ -187 +187 @@
 };
 
+/** Output of a single atom as one lin in xyz file.
+ * \param *out stream to output to
+ */
+bool atom::OutputTrajectoryXYZ(ofstream *out, int step) const
+{
+  if (out != NULL) {
+    *out << type->symbol << "\t";
+    *out << Trajectory.R.at(step).x[0] << "\t";
+    *out << Trajectory.R.at(step).x[1] << "\t";
+    *out << Trajectory.R.at(step).x[2] << endl;
+    return true;
+  } else
+    return false;
+};
+
 ostream & operator << (ostream &ost, const atom &a)
 {

src/atom.hpp

@@ -64 +64 @@
   bool OutputXYZLine(ofstream *out) const;
   bool OutputTrajectory(ofstream *out, int *ElementNo, int *AtomNo, int step) const;
+  bool OutputTrajectoryXYZ(ofstream *out, int step) const;
+
   void EqualsFather ( atom *ptr, atom **res );
   void CorrectFather();

src/molecule.cpp

@@ -757 +757 @@
           ElementNo[i] = current++;
       }
-      ActOnAllAtoms( &atom::OutputTrajectory, out, ElementNo, AtomNo, step ); // (bool (atom::*)(int *, int *, ofstream *, const char *))
+      ActOnAllAtoms( &atom::OutputTrajectory, out, ElementNo, AtomNo, step );
     }
     return true;
@@ -799 +799 @@
 bool molecule::OutputTrajectoriesXYZ(ofstream *out)
 {
-  atom *walker = NULL;
   int No = 0;
   time_t now;
 
-  now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
-  walker = start;
-  while (walker->next != end) { // go through every atom and count
-    walker = walker->next;
-    No++;
-  }
   if (out != NULL) {
+    now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
     for (int step=0;step<MDSteps;step++) {
-      *out << No << "\n\tCreated by molecuilder, step " << step << ", on " << ctime(&now);
-      walker = start;
-      while (walker->next != end) { // go through every atom of this element
-        walker = walker->next;
-        *out << walker->type->symbol << "\t" << walker->Trajectory.R.at(step).x[0] << "\t" << walker->Trajectory.R.at(step).x[1] << "\t" << walker->Trajectory.R.at(step).x[2] << endl;
-      }
+      *out << AtomCount << "\n\tCreated by molecuilder, step " << step << ", on " << ctime(&now);
+      ActOnAllAtoms( &atom::OutputTrajectoryXYZ, out, step );
     }
     return true;