Changeset 390248 for src/parser.hpp

Timestamp:

Jul 24, 2008, 2:00:19 PM (17 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, Candidate_v1.7.0, 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:

958457

Parents:

c685eb

Message:

BIG change: Hcorrection included and bugfix of analyzer (wrt forces)

• Hcorrection is supplied via molecuilder which gives correction values if hydrogen atoms are to close and thus already feel each other's influence. This correction energy matrix is also parsed ans subtracted from the approximated energy matrix generated from the fragments. This impacts both on joiner, analyzer and molecuilder
• Forces were not working which had multiple causes:
  • first, we stepped back down to absolute errors which rather gives a feel about convergence (1e-6 is simply small and neglegible)
  • there may have been bugs where (either in Force or in ForceFragments) adding up took place, this is cleaned up
  • more routines have been abstracted from analyzer into datacreator functions
    • the order of ions had changed, re-run with current molecuilder, calculation and subsequent joining/analyzing brought correct results finally
• plots were bad still due to wrong axes (two more functions finding max/min values), use of wrong columns in plot file

File:

• src/parser.hpp (modified) (5 diffs)

src/parser.hpp

@@ -19 +19 @@
 
 #define EnergySuffix ".energy.all"
+#define HcorrectionSuffix ".Hcorrection.all"
 #define ForcesSuffix ".forces.all"
 #define ShieldingSuffix ".sigma_all.csv"
@@ -26 +27 @@
 #define TimeSuffix ".speed"
 #define EnergyFragmentSuffix ".energyfragment.all"
+#define HcorrectionFragmentSuffix ".Hcorrectionfragment.all"
 #define ForceFragmentSuffix ".forcefragment.all"
 #define OrderSuffix ".Order"
@@ -52 +54 @@
   bool AllocateMatrix(char *GivenHeader, int MCounter, int *RCounter, int CCounter);
   bool ResetMatrix();
+  double FindMinValue();
+  double FindMaxValue();
   bool SetLastMatrix(double value, int skipcolumns);
   bool SetLastMatrix(double **values, int skipcolumns);
@@ -66 +70 @@
   public:
     bool ParseIndices();
-    bool SumSubEnergy(class EnergyMatrix &Fragments, class KeySetsContainer &KeySet, int Order);
+    bool SumSubEnergy(class EnergyMatrix &Fragments, class EnergyMatrix *CorrectionFragments, class KeySetsContainer &KeySet, int Order, double sign);
 };
 
@@ -74 +78 @@
   public: 
     bool ParseIndices(char *name);
-    bool SumSubForces(class ForceMatrix &Fragments, class KeySetsContainer &KeySet, int Order);
+    bool SumSubForces(class ForceMatrix &Fragments, class KeySetsContainer &KeySet, int Order, double sign);
 };