Changeset 7b4261

Timestamp:

May 6, 2008, 9:48:00 AM (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:

db066d

Parents:

63382d

Message:

MatrixContainer::MatrixContainer() debug message fixes only, ForceMatrix::ParseIndices() re-done parsing of Forces-Factors file

ParseIndices() was hacked down to just ...[j]=j entries in the belief that we do not need ForcesFactors anymore. However, we do due to the saturated hydrogen and hence the index parsing thrown out before is needed again. This caused joiner to return faulty forces of course.

File:

• src/parser.cpp (modified) (4 diffs)

src/parser.cpp

@@ -287 +287 @@
             if (m != -1) { // if it's not an added hydrogen
               for (int l=0;l<RowCounter[ KeySet.OrderSet[Order][CurrentFragment] ];l++) { // look for the corresponding index in the current fragment
-                //cout << "Comparing " << m << " with " << Matrix.Indices[ KeySet.OrderSet[Order][CurrentFragment] ][l] << "." << endl;
+                //cout << "Comparing " << m << " with " << MatrixValues.Indices[ KeySet.OrderSet[Order][CurrentFragment] ][l] << "." << endl;
                 if (m == MatrixValues.Indices[ KeySet.OrderSet[Order][CurrentFragment] ][l]) {
                   m = l;
@@ -306 +306 @@
               }
             }
-          //if ((ColumnCounter>1) && (RowCounter >= 1))
-            //cout << "Fragments[ KeySet.OrderSet[" << i << "][" << CurrentFragment << "]=" << KeySet.OrderSet[Order][CurrentFragment] << " ][" << RowCounter[0]-1 << "][" << 1 << "] = " <<  Fragments[ KeySet.OrderSet[Order][CurrentFragment] ][RowCounter[0]-1][1] << endl;
+          //if ((ColumnCounter>1) && (RowCounter[0]-1 >= 1))
+            //cout << "Fragments[ KeySet.OrderSet[" << Order << "][" << CurrentFragment << "]=" << KeySet.OrderSet[Order][CurrentFragment] << " ][" << RowCounter[0]-1 << "][" << 1 << "] = " <<  Matrix[ KeySet.OrderSet[Order][CurrentFragment] ][RowCounter[0]-1][1] << endl;
           }
         } else {
-          //cout << "Fragment " << KeySet.OrderSet[SubOrder][j] << " is not contained in fragment " << KeySet. KeySet.OrderSet[Order][CurrentFragment] << "." << endl;
+          //cout << "Fragment " << KeySet.OrderSet[SubOrder][j] << " is not contained in fragment " << KeySet.OrderSet[Order][CurrentFragment] << "." << endl;
         }
       }
     }
-    //cout << "Final Fragments[ KeySet.OrderSet[" << Order << "][" << CurrentFragment << "]=" << KeySet.OrderSet[Order][CurrentFragment] << " ][" << KeySet.AtomCounter[0]-1 << "][" << 1 << "] = " <<  Fragments[ KeySet.OrderSet[Order][CurrentFragment] ][KeySet.AtomCounter[0]-1][1] << endl;
+    //cout << "Final Fragments[ KeySet.OrderSet[" << Order << "][" << CurrentFragment << "]=" << KeySet.OrderSet[Order][CurrentFragment] << " ][" << KeySet.AtomCounter[0]-1 << "][" << 1 << "] = " <<  Matrix[ KeySet.OrderSet[Order][CurrentFragment] ][KeySet.AtomCounter[0]-1][1] << endl;
   }
   
@@ -422 +422 @@
 bool ForceMatrix::ParseIndices(char *name) 
 {
+  ifstream input;
+  char *FragmentNumber = NULL;
+  char filename[1023];
+  stringstream line;
+  
   cout << "Parsing force indices." << endl;
   Indices = (int **) Malloc(sizeof(int *)*(MatrixCounter+1), "ForceMatrix::ParseIndices: **Indices");
-  for (int i=0;i<MatrixCounter;i++) {
+  line << name << FRAGMENTPREFIX << FORCESFILE;
+  input.open(line.str().c_str(), ios::in);
+  //cout << "Opening " << line.str() << " ... "  << input << endl;
+  if (input == NULL) {
+    cout << endl << "Unable to open " << line.str() << ", is the directory correct?" << endl;
+    return false;
+  }
+  for (int i=0;(i<MatrixCounter) && (!input.eof());i++) {
+    // get the number of atoms for this fragment
+    input.getline(filename, 1023);
+    line.str(filename);
+    // parse the values
     Indices[i] = (int *) Malloc(sizeof(int)*RowCounter[i], "ForceMatrix::ParseIndices: *Indices[]");
-    for(int j=0;j<RowCounter[i];j++)
-      Indices[i][j] = j;
+    FragmentNumber = FixedDigitNumber(MatrixCounter, i);
+    cout << FRAGMENTPREFIX << FragmentNumber << "[" << RowCounter[i] << "]:";
+    Free((void **)&FragmentNumber, "ForceMatrix::ParseIndices: *FragmentNumber");
+    for(int j=0;(j<RowCounter[i]) && (!line.eof());j++) {
+      line >> Indices[i][j];
+      cout << " " << Indices[i][j];
+    }
+    cout << endl;
   }
   Indices[MatrixCounter] = (int *) Malloc(sizeof(int)*RowCounter[MatrixCounter], "ForceMatrix::ParseIndices: *Indices[]");
@@ -433 +455 @@
     Indices[MatrixCounter][j] = j;
   }
+  input.close();
   return true;
 };