Changeset b12a35 for src/joiner.cpp

Timestamp:

Oct 30, 2008, 4:17:23 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:

05d2b2

Parents:

f731ae

git-author:

Frederik Heber <heber@…> (10/19/08 13:57:23)

git-committer:

Frederik Heber <heber@…> (10/30/08 16:17:23)

Message:

HessianMatrix implemented fully, but not yet working, probably due to wrong matrix generation in script file (convertHessian.py)

HessianMatrix::IsSymmetric was though to be needed, but is NOT. As we regard full matrices, we don't need to add onto mirrored indices as well
Joiner and Analyzer have seen some small changes and bugfixes: NoHessian was not also always looked at when needed and so on

File:

• src/joiner.cpp (modified) (9 diffs)

src/joiner.cpp

@@ -37 +37 @@
   stringstream prefix;
   char *dir = NULL;
-  bool Hcorrected = true;
+  bool NoHCorrection = false;
   bool NoHessian = false;
 
@@ -68 +68 @@
   // ------------- Parse through all Fragment subdirs --------
   if (!Energy.ParseFragmentMatrix(argv[1], dir, EnergySuffix, 0,0)) return 1;
-  Hcorrected = Hcorrection.ParseFragmentMatrix(argv[1], "", HCORRECTIONSUFFIX, 0,0);
+  if (!Hcorrection.ParseFragmentMatrix(argv[1], "", HCORRECTIONSUFFIX, 0,0)) {
+    NoHCorrection = true;
+    cout << "No HCorrection matrices found, skipping these." << endl;
+  }
   if (!Force.ParseFragmentMatrix(argv[1], dir, ForcesSuffix, 0,0)) return 1;
   if (!Hessian.ParseFragmentMatrix(argv[1], dir, HessianSuffix, 0,0)) {
     NoHessian = true;
-    cout << "No hessian matrices found, skipping those.";
+    cout << "No hessian matrices found, skipping these." << endl;
   }
   if (periode != NULL) { // also look for PAS values
@@ -81 +84 @@
   // ---------- Parse the TE Factors into an array -----------------
   if (!Energy.InitialiseIndices()) return 1;
-  if (Hcorrected) Hcorrection.InitialiseIndices();
+  if (!NoHCorrection) 
+    Hcorrection.InitialiseIndices();
   
   // ---------- Parse the Force indices into an array ---------------
@@ -87 +91 @@
 
   // ---------- Parse the Hessian (=force) indices into an array ---------------
-  if (!Hessian.InitialiseIndices((class MatrixContainer *)&Force)) return 1;
+  if (!NoHessian)
+    if (!Hessian.InitialiseIndices((class MatrixContainer *)&Force)) return 1;
 
   // ---------- Parse the shielding indices into an array ---------------
@@ -100 +105 @@
   if (!KeySet.ParseManyBodyTerms()) return 1;
   if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return 1;
-  if (Hcorrected)  HcorrectionFragments.AllocateMatrix(Hcorrection.Header, Hcorrection.MatrixCounter, Hcorrection.RowCounter, Hcorrection.ColumnCounter);
+  if (!NoHCorrection)  
+    HcorrectionFragments.AllocateMatrix(Hcorrection.Header, Hcorrection.MatrixCounter, Hcorrection.RowCounter, Hcorrection.ColumnCounter);
   if (!ForceFragments.AllocateMatrix(Force.Header, Force.MatrixCounter, Force.RowCounter, Force.ColumnCounter)) return 1;
   if (!NoHessian)
@@ -126 +132 @@
     cout << "Summing energy of order " << BondOrder+1 << " ..." << endl;
     if (!EnergyFragments.SumSubManyBodyTerms(Energy, KeySet, BondOrder)) return 1;
-    if (Hcorrected) { 
+    if (!NoHCorrection) { 
       HcorrectionFragments.SumSubManyBodyTerms(Hcorrection, KeySet, BondOrder);
       if (!Energy.SumSubEnergy(EnergyFragments, &HcorrectionFragments, KeySet, BondOrder, 1.)) return 1;
-      if (Hcorrected) Hcorrection.SumSubEnergy(HcorrectionFragments, NULL, KeySet, BondOrder, 1.);
+      Hcorrection.SumSubEnergy(HcorrectionFragments, NULL, KeySet, BondOrder, 1.);
     } else 
       if (!Energy.SumSubEnergy(EnergyFragments, NULL, KeySet, BondOrder, 1.)) return 1;
@@ -159 +165 @@
     if (!Force.WriteLastMatrix(argv[1], (prefix.str()).c_str(), ForcesSuffix)) return 1;
     // hessian
-    if (!Hessian.WriteLastMatrix(argv[1], (prefix.str()).c_str(), HessianSuffix)) return 1;
+    if (!NoHessian)
+      if (!Hessian.WriteLastMatrix(argv[1], (prefix.str()).c_str(), HessianSuffix)) return 1;
     // shieldings
     if (periode != NULL) { // also look for PAS values
@@ -170 +177 @@
   prefix << dir << EnergyFragmentSuffix;
   if (!EnergyFragments.WriteTotalFragments(argv[1], (prefix.str()).c_str())) return 1;
-  if (Hcorrected) {
+  if (!NoHCorrection) {
     prefix.str(" ");
     prefix << dir << HcorrectionFragmentSuffix;
@@ -195 +202 @@
   // write last matrices as fragments into central dir (not subdir as above), for analyzer to know index bounds
   if (!Energy.WriteLastMatrix(argv[1], dir, EnergyFragmentSuffix)) return 1;
-  if (Hcorrected) Hcorrection.WriteLastMatrix(argv[1], dir, HcorrectionFragmentSuffix);
+  if (!NoHCorrection) Hcorrection.WriteLastMatrix(argv[1], dir, HcorrectionFragmentSuffix);
   if (!Force.WriteLastMatrix(argv[1], dir, ForceFragmentSuffix)) return 1;
   if (!NoHessian)