Changeset 1907a7 for src/helpers.cpp

Timestamp:

Apr 2, 2009, 4:12:54 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:

ca3ccc

Parents:

d8b94a

Message:

Basic implementation of Multiple molecules.

builder.cpp:

• MoleculeListClass *molecules instead of molecule *mol
• in menu replaced list of elements and atoms by list of molecules
• new option: SetActiveMolecule
• new submenus/functions that all work on MoleculeListClass:
  • EditMolecule()
  • ManipulateMolecules() (global operations on all atoms in a molecule)
  • MergeMolecules()
  • ManipulateAtoms() (local operations on single atoms)
• SaveConfig(): SimpleMultiAdd() of all molecules into a single new one that is stored with the present configuration.

molecules.hpp:

• new STL list MoleculeList
• new variables in MoleculeListClass: list of molecules as STL list
• new variables in molecule: ActiveFlag, name of molecule, Center of molecule (used on merging)

moleculelist.cpp:

• replaced listofmolecules array by STL list everywhere (only smaller changes necessary)
• new merging function: SimpleMerge, SimpleAdd, SimpleMultiMerge, SimpleMultiAdd, (EmbedMerge, ScatterMerge ... both not finished). Add does not while merge does delete the src molecules.
• new function: Enumerate(). Output of all molecules with number of atoms and chemical formula
• new function: NumberOfActiveMolecules(). Counts the number of molecules in the list with ActiveFlag set.
• new function: insert(). Inserts a molecule into the list with a unique index

molecules.cpp:

• new function: SetNameFromFilename. Takes basename of a filename and sets name accordingly.
• new function: UnlinkAtom. Only removes atom from list, does not delete it from memory.

atom.cpp:

• Output() also accepts specific comment instead of "# molecule nr ..."

File:

• src/helpers.cpp (modified) (1 diff)

src/helpers.cpp

@@ -170 +170 @@
         }
         // allocate string
-        returnstring = (char *) Malloc(sizeof(char)*(order+2), "MoleculeListClass::CreateFragmentNumberForOutput: *returnstring");
+        returnstring = (char *) Malloc(sizeof(char)*(order+2), "FixedDigitNumber: *returnstring");
         // terminate    and fill string array from end backward
         returnstring[order] = '\0';