Changeset 6829d2 for src/Fragmentation/Summation/Containers

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.

Location:

src/Fragmentation/Summation/Containers

Files:

• MPQCData.cpp (modified) (1 diff)
• MPQCData.hpp (modified) (3 diffs)

src/Fragmentation/Summation/Containers/MPQCData.cpp

@@ -139 +139 @@
         +toString(instance.sampled_grid.getWindowGridPoints())+" and was "+toString(window_gridpoints));
     instance.positions = other.positions;
+    instance.atomicnumbers = other.atomicnumbers;
     instance.charges = other.charges;
     instance.times = other.times;

src/Fragmentation/Summation/Containers/MPQCData.hpp

@@ -110 +110 @@
   SamplingGrid sampled_grid;
 
-  // nuclei positions and charges
+  // nuclei positions, atomic numbers and charges
   std::vector< std::vector<double> > positions;
+  std::vector< unsigned int > atomicnumbers;
   std::vector<double> charges;
 
@@ -161 +162 @@
     ar & positions;
     ar & charges;
+    if (version > 3)
+      ar & atomicnumbers;
     ar & times.total_walltime;
     ar & times.total_cputime;
@@ -174 +177 @@
 };
 
-BOOST_CLASS_VERSION(MPQCData, 3)
+BOOST_CLASS_VERSION(MPQCData, 4)
 
 std::ostream & operator<<(std::ostream &ost, const MPQCData &data);