Changeset eeec8f for src/datacreator.cpp

Timestamp:

Oct 19, 2008, 1:57:23 PM (16 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:

84fc91

Parents:

f731ae

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/datacreator.cpp (modified) (15 diffs)

src/datacreator.cpp

@@ -63 +63 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "#Order\tFrag.No.\t" << Fragments.Header << endl;
+  output << "#Order\tFrag.No.\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
     for(int i=KeySet.FragmentsPerOrder[BondOrder];i--;) {
@@ -96 +96 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "#Order\tFrag.No.\t" << Fragments.Header << endl;
+  output << "#Order\tFrag.No.\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
   Fragments.SetLastMatrix(Energy.Matrix[Energy.MatrixCounter],0);
   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
@@ -133 +133 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "# Order\tFrag.No.\t" << Fragments.Header << endl;
+  output << "# Order\tFrag.No.\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
   Fragments.SetLastMatrix(0.,0);
   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
@@ -165 +165 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "# Order\tFrag.No.\t" << Fragments.Header << endl;
+  output << "# Order\tFrag.No.\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
   Fragments.SetLastMatrix(Force.Matrix[Force.MatrixCounter],0);
   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
@@ -198 +198 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "# AtomNo\t" << Fragments.Header << endl;
+  output << "# AtomNo\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
   Fragments.SetLastMatrix(Force.Matrix[Force.MatrixCounter], 0);
   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
@@ -244 +244 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "# AtomNo\t" << Fragments.Header << endl;
+  output << "# AtomNo\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
     //cout << "Current order is " << BondOrder << "." << endl;
@@ -262 +262 @@
 };
 
+
+/** Plot hessian error vs. vs atom vs. order.
+ * \param &Hessian HessianMatrix containing reference values (in MatrixCounter matrix)
+ * \param &Fragments HessianMatrix class containing matrix values
+ * \param KeySet KeySetContainer class holding bond KeySetContainer::Order
+ * \param *prefix prefix in filename (without ending)
+ * \param *msg message to be place in first line as a comment
+ * \param *datum current date and time
+ * \return true if file was written successfully
+ */
+bool CreateDataDeltaHessianOrderPerAtom(class HessianMatrix &Hessian, class HessianMatrix &Fragments, class KeySetsContainer &KeySet, char *dir, char *prefix, char *msg, char *datum) 
+{
+  stringstream filename;
+  ofstream output;
+  double norm = 0.;
+
+  filename << prefix << ".dat";
+  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false; 
+  cout << msg << endl;
+  output << "# " << msg << ", created on " << datum;
+  output << "# AtomNo\t" << Fragments.Header[Fragments.MatrixCounter] << endl;
+  Fragments.SetLastMatrix(Hessian.Matrix[Hessian.MatrixCounter], 0);
+  for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
+    //cout << "Current order is " << BondOrder << "." << endl;
+    Fragments.SumSubHessians(Fragments, KeySet, BondOrder, -1.);
+    // errors per atom
+    output << endl << "#Order\t" << BondOrder+1 << endl;
+    for(int j=0;j<Fragments.RowCounter[ Fragments.MatrixCounter ];j++) { 
+      output << Fragments.Indices[Fragments.MatrixCounter][j] << "\t";
+      for (int l=0;l<Fragments.ColumnCounter[ Fragments.MatrixCounter ];l++) {
+        output << scientific << Fragments.Matrix[Fragments.MatrixCounter][ j ][l] << "\t";
+      }
+      output << endl;
+    }
+    output << endl;
+  }
+  output.close();
+  return true;
+};
+
+/** Plot hessian error vs. vs atom vs. order.
+ * \param &Fragments HessianMatrix class containing matrix values
+ * \param KeySet KeySetContainer class holding bond KeySetContainer::Order
+ * \param *prefix prefix in filename (without ending)
+ * \param *msg message to be place in first line as a comment
+ * \param *datum current date and time
+ * \return true if file was written successfully
+ */
+bool CreateDataHessianOrderPerAtom(class HessianMatrix &Fragments, class KeySetsContainer &KeySet, char *dir, char *prefix, char *msg, char *datum) 
+{
+  stringstream filename;
+  ofstream output;
+
+  filename << prefix << ".dat";
+  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false; 
+  cout << msg << endl;
+  output << "# " << msg << ", created on " << datum;
+  output << "# AtomNo\t" << Fragments.Header[ Fragments.MatrixCounter ] << endl;
+  Fragments.SetLastMatrix(0., 0);
+  for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
+    //cout << "Current order is " << BondOrder << "." << endl;
+    Fragments.SumSubHessians(Fragments, KeySet, BondOrder, 1.);
+    // errors per atom
+    output << endl << "#Order\t" << BondOrder+1 << endl;
+    for(int j=0;j<Fragments.RowCounter[ Fragments.MatrixCounter ];j++) { 
+      output << Fragments.Indices[Fragments.MatrixCounter][j] << "\t";
+      for (int l=0;l<Fragments.ColumnCounter[ Fragments.MatrixCounter ];l++)
+        output << scientific << Fragments.Matrix[Fragments.MatrixCounter][ j ][l] << "\t";
+      output << endl;
+    }
+    output << endl;
+  }
+  output.close();
+  return true;
+};
+
 /** Plot matrix vs. fragment.
  */
@@ -273 +349 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum << endl;
-  output << "#Order\tFrag.No.\t" << Fragment.Header << endl;
+  output << "#Order\tFrag.No.\t" << Fragment.Header[ Fragment.MatrixCounter ] << endl;
   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
     for(int i=0;i<KeySet.FragmentsPerOrder[BondOrder];i++) {
@@ -338 +414 @@
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
-  output << "#Order\tFrag.No.\t" << Fragment.Header << endl;
+  output << "#Order\tFrag.No.\t" << Fragment.Header[ Fragment.MatrixCounter ] << endl;
   // max
   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
@@ -538 +614 @@
 void AbsEnergyPlotLine(ofstream &output, class MatrixContainer &Energy, const char *prefix, const char *xargument, const char *uses)
 {
-  stringstream line(Energy.Header);
+  stringstream line(Energy.Header[ Energy.MatrixCounter ]);
   string token;
 
@@ -562 +638 @@
 void EnergyPlotLine(ofstream &output, class MatrixContainer &Energy, const char *prefix, const char *xargument, const char *uses)
 {
-  stringstream line(Energy.Header);
+  stringstream line(Energy.Header[Energy.MatrixCounter]);
   string token;
 
@@ -586 +662 @@
 void ForceMagnitudePlotLine(ofstream &output, class MatrixContainer &Force, const char *prefix, const char *xargument, const char *uses)
 {
-  stringstream line(Force.Header);
+  stringstream line(Force.Header[Force.MatrixCounter]);
   string token;
 
@@ -617 +693 @@
 void AbsFirstForceValuePlotLine(ofstream &output, class MatrixContainer &Force, const char *prefix, const char *xargument, const char *uses)
 {
-  stringstream line(Force.Header);
+  stringstream line(Force.Header[Force.MatrixCounter]);
   string token;
 
@@ -648 +724 @@
 void BoxesForcePlotLine(ofstream &output, class MatrixContainer &Force, const char *prefix, const char *xargument, const char *uses)
 {
-  stringstream line(Force.Header);
+  stringstream line(Force.Header[Force.MatrixCounter]);
   char *fillcolor[5] = {"black", "red", "blue", "green", "cyan"};
   string token;
@@ -680 +756 @@
 void BoxesFirstForceValuePlotLine(ofstream &output, class MatrixContainer &Force, const char *prefix, const char *xargument, const char *uses)
 {
-  stringstream line(Force.Header);
+  stringstream line(Force.Header[Force.MatrixCounter]);
   char *fillcolor[5] = {"black", "red", "blue", "green", "cyan"};
   string token;