Changeset 35b698 for src/molecule.hpp

Timestamp:

Jun 23, 2010, 3:52:50 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:

d0fbec

Parents:

dc0d21

git-author:

Frederik Heber <heber@…> (06/23/10 15:20:35)

git-committer:

Frederik Heber <heber@…> (06/23/10 15:52:50)

Message:

BIG CHANGE: config::load and config::save in ParseCommandLineOptions() and main() replaced with FormatParser replacements.

Fragmentation:

• FragmentMolecule() - configuration is not needed anymore, but a path (including prefix)
• class molecule:
  • lots of changes from char * to std:string (due to above): LinearInterpolationBetweenConfiguration(), CheckOrderAtSite(), StoreBondsToFile(), StoreAdjacencyToFile(), CheckAdjacencyFileAgainstMolecule(), CheckAdjacencyFileAgainstMolecule_Init(), ParseOrderAtSiteFromFile(), StoreOrderAtSiteFile(), StoreForcesFile(), ScanAdaptiveFileIntoMap(), StoreForcesFile(), AddHydrogenCorrection(), OutputConfigForListOfFragments()
  • in all above functions, also stringstreams have been replaced by simple strings and file != NULL by file.good()
  • no more CalculateOrbitals(), shifted to class PcpParser
• FragmentationAction: argument of -f is now the prefix, molecule is obtained by molecule-by-id
• no more strcpy needed in: MoleculeLinearInterpolationofTrajectoriesAction, MoleculeSaveAdjacencyAction, MoleculeSaveBondsAction
• oldmenu::FragmentAtoms() - needs to ask for path with prefix now
• config: RetrieveConfigPathAndName() and configpath removed (replaced by above path with prefix)
• changes due to this removal: SaveConfig(), config::Load(), config::LoadOld()

• FIX: MoleculeFillWithMoleculeAction: filler atoms have to be removed before the system can be stored to file.
• FIX: PcpParser::load() - has to put the molecule also into World's MoleculeListClass (otherwise the name cannot be set right after loading)

• ParseCommandLineOptions()
  • new parameter BondGraphFileName and creation of bond graph is done in main()
  • no more config::load, just parser->load(), ConfigFileName is set extra and we always set configPresent to present.
  • FIX: filename is only set when no molecule was allocated before
  • FIX: case 't' and 'f' had wrong argc checks
• main()
  • FormatParserStorage is set with mpqc, pcp and xyz
  • BondGraph is constructed from new string BondGrapghFileName

• new Libparser.a
• all sources from PARSER subdir are compiled into libparser such that only ParserUnitTest is recompiled.

Testfixes:

• testsuite-fragmentation - changes to due to different -f calling syntax.
• most of the xyz files had to be replaced due to a single whitespace at the end of each entry: Domain/6, Simple_configuration/2, Simple_configuration/3, Simple_configuration/4, Simple_configuration/5, Simple_configuration/8
• in many cases were the number orbitals (and thus MaxMinStopStep) wrong: Filling/1, Simple_configuration/4, Simple_configuration/5

Signed-off-by: Frederik Heber <heber@…>

File:

• src/molecule.hpp (modified) (4 diffs)

src/molecule.hpp

@@ -261 +261 @@
   /// Count and change present atoms' coordination.
   void CountElements();
-  void CalculateOrbitals(class config &configuration);
   bool CenterInBox();
   bool BoundInBox();
@@ -288 +287 @@
   double MinimiseConstrainedPotential(atom **&permutation, int startstep, int endstep, bool IsAngstroem);
   void EvaluateConstrainedForces(int startstep, int endstep, atom **PermutationMap, ForceMatrix *Force);
-  bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, const char *prefix, config &configuration, bool MapByIdentity);
+  bool LinearInterpolationBetweenConfiguration(int startstep, int endstep, std::string &prefix, config &configuration, bool MapByIdentity);
         
   bool CheckBounds(const Vector *x) const;
@@ -320 +319 @@
 
   /// Fragment molecule by two different approaches:
-  int FragmentMolecule(int Order, config *configuration);
-  bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
-  bool StoreBondsToFile(char *path, char *filename);
-  bool StoreAdjacencyToFile(char *path, char *filename);
-  bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
-  bool ParseOrderAtSiteFromFile(char *path);
-  bool StoreOrderAtSiteFile(char *path);
-  bool StoreForcesFile(MoleculeListClass *BondFragments, char *path, int *SortIndex);
+  int FragmentMolecule(int Order, std::string &prefix);
+  bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, std::string path = "");
+  bool StoreBondsToFile(std::string &filename, std::string path = "");
+  bool StoreAdjacencyToFile(std::string &filename, std::string path = "");
+  bool CheckAdjacencyFileAgainstMolecule(std::string &path, atom **ListOfAtoms);
+  bool ParseOrderAtSiteFromFile(std::string &path);
+  bool StoreOrderAtSiteFile(std::string &path);
+  bool StoreForcesFile(MoleculeListClass *BondFragments, std::string &path, int *SortIndex);
   bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
   bool CreateFatherLookupTable(atom **&LookupTable, int count = 0);
@@ -376 +375 @@
   ~MoleculeListClass();
 
-  bool AddHydrogenCorrection(char *path);
-  bool StoreForcesFile(char *path, int *SortIndex);
+  bool AddHydrogenCorrection(std::string &path);
+  bool StoreForcesFile(std::string &path, int *SortIndex);
   void insert(molecule *mol);
   void erase(molecule *mol);
   molecule * ReturnIndex(int index);
-  bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
+  bool OutputConfigForListOfFragments(std::string &prefix, int *SortIndex);
   int NumberOfActiveMolecules();
   void Enumerate(ostream *out);