Changeset f60d95

Timestamp:

Aug 9, 2013, 2:20:36 PM (12 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:

ff09f3

Parents:

58fcbe5

git-author:

Frederik Heber <heber@…> (07/25/13 17:39:27)

git-committer:

Frederik Heber <heber@…> (08/09/13 14:20:36)

Message:

PartialNucleiChargeFitter writes potential, solution, and residuum to CSV files in DEBUG.

Location:

src/Potentials

Files:

• PartialNucleiChargeFitter.cpp (modified) (2 diffs)
• PartialNucleiChargeFitter.hpp (modified) (1 diff)

src/Potentials/PartialNucleiChargeFitter.cpp

@@ -187 +187 @@
       "PartialNucleiChargeFitter::PartialNucleiChargeFitter() - not enough or more than calculated sample points.");
 
+#ifndef NDEBUG
+  // write vector as paraview csv file file
+  {
+    size_t N[3];
+    size_t index = 0;
+    std::ofstream paraview_output("solution.csv");
+    paraview_output << "x coord,y coord,z coord,scalar" << std::endl;
+    for(N[0]=0; N[0] < total[0]; ++N[0]) {
+      for(N[1]=0; N[1] < total[1]; ++N[1]) {
+        for(N[2]=0; N[2] < total[2]; ++N[2]) {
+          paraview_output
+              << (double)N[0]/(double)total[0] << ","
+              << (double)N[1]/(double)total[1] << ","
+              << (double)N[2]/(double)total[2] << ","
+              << SampledPotential.at(index++) << std::endl;
+        }
+      }
+    }
+    paraview_output.close();
+  }
+#endif
 
   LOG(1, "INFO: I masked " << masked_points << " points in right-hand-side.");
@@ -275 +296 @@
           SampledPotential);
 
-  LOG(4, "DEBUG: Solution vector is " << (*PotentialFromCharges) * (*PartialCharges) << ".");
+//  LOG(4, "DEBUG: Solution vector is " << (*PotentialFromCharges) * (*PartialCharges) << ".");
 
   // calculate residual vector
   VectorContent residuum = (*PotentialFromCharges) * (*PartialCharges) - SampledPotential;
+
+#ifndef NDEBUG
+  // write solution to file
+  writeMatrix();
+
+  // write vector as paraview csv file file
+  {
+    size_t N[3];
+    size_t index = 0;
+    std::ofstream paraview_output("residuum.csv");
+    paraview_output << "x coord,y coord,z coord,scalar" << std::endl;
+    for(N[0]=0; N[0] < total[0]; ++N[0]) {
+      for(N[1]=0; N[1] < total[1]; ++N[1]) {
+        for(N[2]=0; N[2] < total[2]; ++N[2]) {
+          paraview_output
+              << (double)N[0]/(double)total[0] << ","
+              << (double)N[1]/(double)total[1] << ","
+              << (double)N[2]/(double)total[2] << ","
+              << residuum.at(index++) << std::endl;
+        }
+      }
+    }
+    paraview_output.close();
+  }
+#endif
+
+  // calculate L1 and L2 errors
+  double residuum_l1 = 0.;
+  for (size_t i=0; i< residuum.getDimension(); ++i)
+    if (residuum_l1 < residuum[i])
+      residuum_l1 = residuum[i];
+  LOG(1, "INFO: L2-Norm of residuum is " << residuum.Norm() << ".");
+  LOG(1, "INFO: L1-Norm of residuum is " << residuum_l1 << ".");
+
   return residuum.Norm();
+}
+
+void PartialNucleiChargeFitter::writeMatrix()
+{
+  constructMatrix();
+
+  // write matrix as paraview csv file file
+    size_t N[3];
+    size_t index=0;
+    std::string filename = std::string("potential.csv");
+    std::ofstream paraview_output(filename.c_str());
+    paraview_output << "x coord,y coord,z coord,scalar" << std::endl;
+    for(N[0]=0; N[0] < total[0]; ++N[0]) {
+      for(N[1]=0; N[1] < total[1]; ++N[1]) {
+        for(N[2]=0; N[2] < total[2]; ++N[2]) {
+          double sum = 0.;
+          for (size_t nuclei_index = 0; nuclei_index < positions.size(); ++nuclei_index) {
+            sum+= PotentialFromCharges->at(index, nuclei_index)*PartialCharges->at(nuclei_index);
+          }
+          paraview_output
+              << (double)N[0]/(double)total[0] << ","
+              << (double)N[1]/(double)total[1] << ","
+              << (double)N[2]/(double)total[2] << ","
+              << sum << std::endl;
+          index++;
+        }
+      }
+    }
+    paraview_output.close();
 }
 

src/Potentials/PartialNucleiChargeFitter.hpp

@@ -105 +105 @@
    charges_t getSolutionAsCharges_t() const;
 
+   void writeMatrix();
+
 private:
    /** Helper function to construct the problem Matrix A.