Changeset d067d45 for src/atom.cpp

Timestamp:

Jul 23, 2009, 1:45:24 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, Candidate_v1.7.0, 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:

51c910

Parents:

ce5ac3 (diff), 437922 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Frederik Heber <heber@…> (07/23/09 12:34:47)

git-committer:

Frederik Heber <heber@…> (07/23/09 13:45:24)

Message:

Merge branch 'MultipleMolecules'

Conflicts:

molecuilder/src/analyzer.cpp
molecuilder/src/atom.cpp
molecuilder/src/boundary.cpp
molecuilder/src/boundary.hpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/datacreator.hpp
molecuilder/src/helpers.cpp
molecuilder/src/joiner.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/molecules.cpp
molecuilder/src/molecules.hpp
molecuilder/src/parser.cpp
molecuilder/src/parser.hpp
molecuilder/src/vector.cpp
molecuilder/src/verbose.cpp

merges:

• analyzer.cpp: all from HEAD, Hessian stuff
• atom.cpp: ostream & operator << (ostream &ost, const atom &a), 2nd param is const
• boundary.cpp: DoSingleStepOutput, VRMLSUffix, HULLEPSILON, Get_center_of_sphere(), Find_next_suitable_point_via_Angle_of_Sphere() and all of tesselation stuff from MultipleMolecules; DoRaster3DOutput, ~BoundaryLineSet(), ~Tesselation() from HEAD; write_raster3d_file with some changes from MultipleMolecules
• boundary.hpp: all from MultipleMolecules
• builder.cpp: all in ParseCommandLineOptions() from MultipleMolecules
• config.cpp: all from HEAD, is stuff from ThermoStat and ConstrainedMD
• datacreator.hpp: all from HEAD, Hessian stuff
• helpers.cpp: all from HEAD, ReAlloc() differed just by indentation
• moleculelist.cpp: all from MultipleMolecules, has to do with introduced molecule centers
• molecules.cpp: all from HEAD, was ConstrainedMD stuff
• molecules.hpp: ConstrainedMD and VerletForceIntegration from HEAD, moleculelist stuff from MultipleMolecules
• parser.cpp: all from HEAD, ColumnCounter is *ColumnCounter there
• parser.hpp: all from HEAD
• vector.cpp: completely from MultipleMolecules (more lines)
• verbose.cpp: all from HEAD

compilation fixes:

• CheckPresenceOfTriangle() from MultipleMolecules
• MoleculeListClass::ListOfMolecules has changed to STL list, hence use insert(), ReturnIndex() and MoleculeListClass::OutputConfigForListOfFragments
• MoleculeListClass::OutputConfigForListOfFragments() had fragmentprefix instead of FRAGMENTPREFIX
• parser.hpp: EnergyMatrix::ParseIndices() declaration was missing

File:

• src/atom.cpp (modified) (6 diffs)

src/atom.cpp

@@ -1 +1 @@
 /** \file atom.cpp
- * 
+ *
  * Function implementations for the class atom.
- * 
+ *
  */
 
 #include "molecules.hpp"
- 
+
 /************************************* Functions for class atom *************************************/
 
 /** Constructor of class atom.
  */
-atom::atom() 
+atom::atom()
 {
   Name = NULL;
@@ -33 +33 @@
 /** Destructor of class atom.
  */
-atom::~atom() 
+atom::~atom()
 {
   Free((void **)&Name, "atom::~atom: *Name");
@@ -58 +58 @@
  * \param AtomNo cardinal number among these atoms of the same element
  * \param *out stream to output to
+ * \param *comment commentary after '#' sign
  */
-bool atom::Output(int ElementNo, int AtomNo, ofstream *out) const
+bool atom::Output(int ElementNo, int AtomNo, ofstream *out, const char *comment) const
 {
   if (out != NULL) {
@@ -67 +68 @@
     if (v.Norm() > MYEPSILON)
       *out << "\t" << scientific << setprecision(6) << v.x[0] << "\t" << v.x[1] << "\t" << v.x[2] << "\t";
-    *out << " # Number in molecule " << nr << endl;
+    if (comment != NULL)
+      *out << " # " << comment << endl;
+    else
+      *out << " # molecule nr " << nr << endl;
     return true;
   } else
@@ -94 +98 @@
  * \param ptr atom to compare index against
  * \return true - this one's is smaller, false - not
- */ 
+ */
 bool atom::Compare(atom &ptr)
 {
@@ -103 +107 @@
 };
 
-bool operator < (atom &a, atom &b) 
+bool operator < (atom &a, atom &b)
 {
   return a.Compare(b);