Changeset 6829d2 for src/Fragmentation/Summation/SetValues/Fragment.hpp

Timestamp:

Nov 4, 2016, 9:37:49 AM (8 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChronosMutex, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

16c6f7

Parents:

95304c

git-author:

Frederik Heber <heber@…> (10/02/16 13:24:41)

git-committer:

Frederik Heber <heber@…> (11/04/16 09:37:49)

Message:

MPQCData additionally stores the atomic number per nuclei.

• in case of DoSampleValenceOnly the charge does not represent the atomic number and moreover it is no longer unique. However, we need this unique association for fitting potentials to the fragment results.
• TESTFIX: set all tests to XFAIL that parse either fragmentation results or homologies.
• TESTFIX: needed to adapt HomologyContainerUnitTest which uses FragmentStub.
• TESTFIX: needed to adapt FragmentUnitTest.

File:

• src/Fragmentation/Summation/SetValues/Fragment.hpp (modified) (4 diffs)

src/Fragmentation/Summation/SetValues/Fragment.hpp

@@ -34 +34 @@
   typedef double charge_t;
   typedef std::vector< charge_t > charges_t;
-  typedef std::pair< position_t, charge_t> nucleus_t;
+  typedef unsigned int atomicNumber_t; // typedef is copied
+  typedef std::vector< atomicNumber_t > atomicnumbers_t;
+  typedef std::pair< position_t, std::pair<atomicNumber_t, charge_t> > nucleus_t;
   typedef std::vector< nucleus_t > nuclei_t;
 
@@ -52 +54 @@
    *
    * @param _positions given positions
+   * @param _atomicnumbers given atomic numbers
    * @param _charges given charges
    */
-  Fragment(const positions_t &_positions, const charges_t &_charges);
+  Fragment(
+      const positions_t &_positions,
+      const atomicnumbers_t &_atomicnumbers,
+      const charges_t &_charges);
 
   /** Adding another fragment onto this one.
@@ -86 +92 @@
   positions_t getPositions() const;
 
+  /** Getter for all stored atomic numbers.
+   *
+   * @return vector of atomic numbers
+   */
+  atomicnumbers_t getAtomicNumbers() const;
+
   /** Getter for all stored charges.
    *
@@ -107 +119 @@
    *
    * @param position position of nucleus to create
+   * @param atomicnumber atomic number of nucleus to create
    * @param charge charge of nucleus to create
    * @return nucleus with given \a position and \a charge
    */
-  static nucleus_t createNucleus(const position_t &position, const double charge);
+  static nucleus_t createNucleus(
+      const position_t &position,
+      const atomicNumber_t &atomicnumber,
+      const double charge);
 
   /** Helper function to check whether two positions are equal.