Changeset f731ae for src/analyzer.cpp

Timestamp:

Oct 18, 2008, 3:05:54 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, 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:

b12a35, eeec8f

Parents:

85d278

Message:

ColumnCounter -> *ColumnCounter

columns of the MatrixContainer class may now be variable over each matrix. This was changed globally to allow for varying column numbers of the new class HessianMatrix.

File:

• src/analyzer.cpp (modified) (12 diffs)

src/analyzer.cpp

@@ -93 +93 @@
 
   // ---------- Parse the TE Factors into an array -----------------
-  if (!Energy.ParseIndices()) return 1;
-  if (Hcorrected) Hcorrection.ParseIndices();
+  if (!Energy.InitialiseIndices()) return 1;
+  if (Hcorrected) Hcorrection.InitialiseIndices();
   
   // ---------- Parse the Force indices into an array ---------------
@@ -132 +132 @@
   output << endl << "Total Energy" << endl << "==============" << endl << Energy.Header << endl;
   for(int j=0;j<Energy.RowCounter[Energy.MatrixCounter];j++) {
-    for(int k=0;k<Energy.ColumnCounter;k++)
+    for(int k=0;k<Energy.ColumnCounter[Energy.MatrixCounter];k++)
       output << scientific << Energy.Matrix[ Energy.MatrixCounter ][j][k] << "\t";
     output << endl;
@@ -140 +140 @@
   output << endl << "Total Forces" << endl << "===============" << endl << Force.Header << endl;
   for(int j=0;j<Force.RowCounter[Force.MatrixCounter];j++) {
-    for(int k=0;k<Force.ColumnCounter;k++)
+    for(int k=0;k<Force.ColumnCounter[Force.MatrixCounter];k++)
       output << scientific << Force.Matrix[ Force.MatrixCounter ][j][k] << "\t";
     output << endl;
@@ -149 +149 @@
     output << endl << "Total Shieldings" << endl << "===============" << endl << Shielding.Header << endl;
     for(int j=0;j<Shielding.RowCounter[Shielding.MatrixCounter];j++) {
-      for(int k=0;k<Shielding.ColumnCounter;k++)
+      for(int k=0;k<Shielding.ColumnCounter[Shielding.MatrixCounter];k++)
         output << scientific << Shielding.Matrix[ Shielding.MatrixCounter ][j][k] << "\t";
       output << endl;
@@ -157 +157 @@
     output << endl << "Total Shieldings PAS" << endl << "===============" << endl << ShieldingPAS.Header << endl;
     for(int j=0;j<ShieldingPAS.RowCounter[ShieldingPAS.MatrixCounter];j++) {
-      for(int k=0;k<ShieldingPAS.ColumnCounter;k++)
+      for(int k=0;k<ShieldingPAS.ColumnCounter[ShieldingPAS.MatrixCounter];k++)
         output << scientific << ShieldingPAS.Matrix[ ShieldingPAS.MatrixCounter ][j][k] << "\t";
       output << endl;
@@ -166 +166 @@
   output << endl << "Total Times" << endl << "===============" << endl << Time.Header << endl;
   for(int j=0;j<Time.RowCounter[Time.MatrixCounter];j++) {
-    for(int k=0;k<Time.ColumnCounter;k++) {
+    for(int k=0;k<Time.ColumnCounter[Time.MatrixCounter];k++) {
       output << scientific << Time.Matrix[ Time.MatrixCounter ][j][k] << "\t";
     }
@@ -173 +173 @@
   output << endl;
   output.close();
-  for(int k=0;k<Time.ColumnCounter;k++)
+  for(int k=0;k<Time.ColumnCounter[Time.MatrixCounter];k++)
     Time.Matrix[ Time.MatrixCounter ][ Time.RowCounter[Time.MatrixCounter] ][k] = Time.Matrix[ Time.MatrixCounter ][Time.RowCounter[Time.MatrixCounter]-1][k];
 
@@ -187 +187 @@
   if (!OpenOutputFile(output2, argv[3], "DeltaSimTime-Order.dat" )) return false;
   for(int j=Time.RowCounter[Time.MatrixCounter];j--;)
-    for(int k=Time.ColumnCounter;k--;) {
+    for(int k=Time.ColumnCounter[Time.MatrixCounter];k--;) {
       Time.Matrix[ Time.MatrixCounter ][j][k] = 0.;
     }
@@ -196 +196 @@
     for(int i=KeySet.FragmentsPerOrder[BondOrder];i--;)
       for(int j=Time.RowCounter[Time.MatrixCounter];j--;)
-        for(int k=Time.ColumnCounter;k--;) {
+        for(int k=Time.ColumnCounter[Time.MatrixCounter];k--;) {
           Time.Matrix[ Time.MatrixCounter ][j][k] += Time.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
         }
@@ -202 +202 @@
     output << BondOrder+1 << "\t" << counter;
     output2 << BondOrder+1 << "\t" << counter;
-    for(int k=0;k<Time.ColumnCounter;k++) {
+    for(int k=0;k<Time.ColumnCounter[Time.MatrixCounter];k++) {
       output << "\t" << scientific << Time.Matrix[ Time.MatrixCounter ][ Time.RowCounter[Time.MatrixCounter]-1 ][k];
       if (fabs(Time.Matrix[ Time.MatrixCounter ][ Time.RowCounter[Time.MatrixCounter] ][k]) > MYEPSILON)
@@ -224 +224 @@
     for(int j=0;j<ShieldingPAS.RowCounter[ShieldingPAS.MatrixCounter];j++) {
       output << j << "\t";
-      for(int k=0;k<ShieldingPAS.ColumnCounter;k++)
+      for(int k=0;k<ShieldingPAS.ColumnCounter[ShieldingPAS.MatrixCounter];k++)
         output << scientific <<  ShieldingPAS.Matrix[ ShieldingPAS.MatrixCounter ][j][k] << "\t"; //*(((k>1) && (k<6))? 1.e6 : 1.) << "\t";
       output << endl;
@@ -256 +256 @@
   for(int j=0;j<Force.RowCounter[Force.MatrixCounter];j++) {
     output << j << "\t";
-    for(int k=0;k<Force.ColumnCounter;k++)
+    for(int k=0;k<Force.ColumnCounter[Force.MatrixCounter];k++)
       output << scientific <<  Force.Matrix[ Force.MatrixCounter ][j][k] << "\t";
     output << endl;