Changeset fcd7b6 for src/atom.cpp

Timestamp:

Oct 7, 2009, 1:11:28 PM (16 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:

681a8a

Parents:

e9f8f9

git-author:

Frederik Heber <heber@…> (10/07/09 12:14:15)

git-committer:

Frederik Heber <heber@…> (10/07/09 13:11:28)

Message:

In molecule::OutputTrajectories() ActOnAllAtoms() with new function atom::OutputTrajectory() is used.

For this to work, I had to change the Trajectory struct that was so far included in molecule.hpp to be incorporated directly into the class atom.
NOTE: This incorporation is incomplete and a ticket (#34) has been filed to remind of this issue.
However, the trajectory is better suited to reside in atom anyway and was probably just put in molecule due to memory prejudices against STL vector<>.
Functions in molecule.cpp, config.cpp, molecule_geometry.cpp and molecule_dynamics.cpp were adapted (changed from Trajectories[atom *] to atom *->Trajectory).
And the atom pointer in the Trajectory structure was removed.

File:

• src/atom.cpp (modified) (4 diffs)

src/atom.cpp

@@ -64 +64 @@
   Free<int>(&ComponentNr, "atom::~atom: *ComponentNr");
   Free<char>(&Name, "atom::~atom: *Name");
+  Trajectory.R.clear();
+  Trajectory.U.clear();
+  Trajectory.F.clear();
 };
 
@@ -118 +121 @@
  * \param *comment commentary after '#' sign
  */
-bool atom::Output(int ElementNo, int AtomNo, ofstream *out, const char *comment) const
+bool atom::Output(ofstream *out, int ElementNo, int AtomNo, const char *comment) const
 {
   if (out != NULL) {
@@ -134 +137 @@
     return false;
 };
-bool atom::Output(int *ElementNo, int *AtomNo, ofstream *out, const char *comment)
+bool atom::Output(ofstream *out, int *ElementNo, int *AtomNo, const char *comment)
 {
   AtomNo[type->Z]++;  // increment number
@@ -164 +167 @@
 };
 
+/** Output of a single atom as one lin in xyz file.
+ * \param *out stream to output to
+ */
+bool atom::OutputTrajectory(ofstream *out, int *ElementNo, int *AtomNo, int step) const
+{
+  AtomNo[type->Z]++;
+  if (out != NULL) {
+    *out << "Ion_Type" << ElementNo[type->Z] << "_" << AtomNo[type->Z] << "\t"  << fixed << setprecision(9) << showpoint;
+    *out << Trajectory.R.at(step).x[0] << "\t" << Trajectory.R.at(step).x[1] << "\t" << Trajectory.R.at(step).x[2];
+    *out << "\t" << FixedIon;
+    if (Trajectory.U.at(step).Norm() > MYEPSILON)
+      *out << "\t" << scientific << setprecision(6) << Trajectory.U.at(step).x[0] << "\t" << Trajectory.U.at(step).x[1] << "\t" << Trajectory.U.at(step).x[2] << "\t";
+    if (Trajectory.F.at(step).Norm() > MYEPSILON)
+      *out << "\t" << scientific << setprecision(6) << Trajectory.F.at(step).x[0] << "\t" << Trajectory.F.at(step).x[1] << "\t" << Trajectory.F.at(step).x[2] << "\t";
+    *out << "\t# Number in molecule " << nr << endl;
+    return true;
+  } else
+    return false;
+};
+
 ostream & operator << (ostream &ost, const atom &a)
 {