Changeset fac58f for src/Parser/TremoloParser.cpp

Timestamp:

Jul 24, 2015, 4:44:35 PM (10 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:

f3b597

Parents:

99db9b

git-author:

Frederik Heber <heber@…> (06/02/15 08:52:11)

git-committer:

Frederik Heber <heber@…> (07/24/15 16:44:35)

Message:

Converted FormatParser::save() to using vector of const atom ptrs.

• required to change all save() functions in all parsers.

File:

• src/Parser/TremoloParser.cpp (modified) (8 diffs)

src/Parser/TremoloParser.cpp

@@ -178 +178 @@
  * \param atoms atoms to store
  */
-void FormatParser< tremolo >::save(std::ostream* file, const std::vector<atom *> &AtomList) {
+void FormatParser< tremolo >::save(
+    std::ostream* file,
+    const std::vector<const atom *> &AtomList) {
   LOG(2, "DEBUG: Saving changes to tremolo.");
 
@@ -203 +205 @@
 
   // store particles
-  for (std::vector<atom*>::const_iterator  atomIt = AtomList.begin();
+  for (std::vector<const atom*>::const_iterator  atomIt = AtomList.begin();
       atomIt != AtomList.end(); ++atomIt)
     saveLine(file, *atomIt);
@@ -297 +299 @@
  * \param atoms atoms to store
  */
-void FormatParser< tremolo >::distributeContinuousIds(const std::vector<atom *> &AtomList)
+void FormatParser< tremolo >::distributeContinuousIds(
+    const std::vector<const atom *> &AtomList)
 {
   resetIdAssociations();
   atomId_t lastid = 0;
-  for (std::vector<atom*>::const_iterator atomIt = AtomList.begin();
+  for (std::vector<const atom*>::const_iterator atomIt = AtomList.begin();
       atomIt != AtomList.end(); ++atomIt)
     associateLocaltoGlobalId(++lastid, (*atomIt)->getId());
@@ -368 +371 @@
  * \param reference to the atom of which information should be written
  */
-void FormatParser< tremolo >::saveLine(std::ostream* file, const atom* currentAtom)
+void FormatParser< tremolo >::saveLine(
+    std::ostream* file,
+    const atom * const currentAtom)
 {
   TremoloKey::atomDataKey currentField;
@@ -495 +500 @@
  * \param reference to the atom of which to take the neighbor information
  */
-void FormatParser< tremolo >::writeNeighbors(std::ostream* file, const int numberOfNeighbors, const atom* currentAtom) {
+void FormatParser< tremolo >::writeNeighbors(
+    std::ostream* file,
+    const int numberOfNeighbors,
+    const atom * const currentAtom) {
   const BondList& ListOfBonds = currentAtom->getListOfBonds();
   // sort bonded indices
@@ -752 +760 @@
  * \param atomid world id of the atom the information belongs to
  */
-void FormatParser< tremolo >::readNeighbors(std::stringstream* line, const int numberOfNeighbors, const int atomId) {
+void FormatParser< tremolo >::readNeighbors(
+    std::stringstream* line,
+    const int numberOfNeighbors,
+    const int atomId) {
   int neighborId = 0;
   for (int i = 0; i < numberOfNeighbors; i++) {
@@ -772 +783 @@
  * \return true if the field name is used
  */
-bool FormatParser< tremolo >::isUsedField(const usedFields_t &fields, const std::string &fieldName) const
+bool FormatParser< tremolo >::isUsedField(
+    const usedFields_t &fields,
+    const std::string &fieldName) const
 {
   bool fieldNameExists = false;
@@ -792 +805 @@
  * @param atoms vector with all newly added (global) atomic ids
  */
-void FormatParser< tremolo >::processNeighborInformation(const std::vector<atomId_t> &atoms) {
+void FormatParser< tremolo >::processNeighborInformation(
+    const std::vector<atomId_t> &atoms) {
   if (!isUsedField(usedFields_load, "neighbors")) {
     return;