Changeset 05e2ed for src/Parser/TremoloParser.hpp

Timestamp:

Dec 14, 2012, 1:02:50 PM (12 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:

fc41df

Parents:

67ab71

git-author:

Frederik Heber <heber@…> (10/25/12 08:29:25)

git-committer:

Frederik Heber <heber@…> (12/14/12 13:02:50)

Message:

FIX: TremoloParser did not load/save imprData or torsion correctly.

• this error was introduced when incorporating local-global-maps and conversions where this was not correctly done for the improper and torsion string:
  • conversion from local to global on load was present but went over all atoms, not just newly parsed ones. adapt.. now gets atom vector as param.
  • save did no global-local conversion. For this we generalized adaptIdDependentDataString() to get a function pointer converting ids.
• TEST: We added a new regression test on this matter where a .data file with impropers is loaded and stored.

File:

• src/Parser/TremoloParser.hpp (modified) (3 diffs)

src/Parser/TremoloParser.hpp

@@ -14 +14 @@
 #endif
 
+#include <boost/function.hpp>
 #include <string>
 
@@ -99 +100 @@
   void readNeighbors(std::stringstream* line, const int numberOfNeighbors, const int atomId);
   void processNeighborInformation(const std::vector<atomId_t> &atoms);
-  void adaptImprData();
-  void adaptTorsion();
-  std::string adaptIdDependentDataString(std::string data);
+  void adaptImprData(const std::vector<atomId_t> &atoms);
+  void adaptTorsion(const std::vector<atomId_t> &atoms);
+  std::string adaptIdDependentDataString(const std::string &data, const boost::function<int (const int)> &idgetter);
   bool isUsedField(const usedFields_t &fields, const std::string &fieldName) const;
   void writeNeighbors(std::ostream* file, const int numberOfNeighbors, const atom* currentAtom);
@@ -140 +141 @@
    */
   TremoloAtomInfoContainer defaultAdditionalData;
+
+  //!> bound function to convert id to global id, stored to avoid creation many times
+  const boost::function<int (const int)> idglobalizer;
+
+  //!> bound function to convert id to local id, stored to avoid creation many times
+  const boost::function<int (const int)> idlocalizer;
 };