Changeset d067d45 for src/datacreator.cpp

Timestamp:

Jul 23, 2009, 1:45:24 PM (15 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:

51c910

Parents:

ce5ac3 (diff), 437922 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

git-author:

Frederik Heber <heber@…> (07/23/09 12:34:47)

git-committer:

Frederik Heber <heber@…> (07/23/09 13:45:24)

Message:

Merge branch 'MultipleMolecules'

Conflicts:

molecuilder/src/analyzer.cpp
molecuilder/src/atom.cpp
molecuilder/src/boundary.cpp
molecuilder/src/boundary.hpp
molecuilder/src/builder.cpp
molecuilder/src/config.cpp
molecuilder/src/datacreator.hpp
molecuilder/src/helpers.cpp
molecuilder/src/joiner.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/molecules.cpp
molecuilder/src/molecules.hpp
molecuilder/src/parser.cpp
molecuilder/src/parser.hpp
molecuilder/src/vector.cpp
molecuilder/src/verbose.cpp

merges:

• analyzer.cpp: all from HEAD, Hessian stuff
• atom.cpp: ostream & operator << (ostream &ost, const atom &a), 2nd param is const
• boundary.cpp: DoSingleStepOutput, VRMLSUffix, HULLEPSILON, Get_center_of_sphere(), Find_next_suitable_point_via_Angle_of_Sphere() and all of tesselation stuff from MultipleMolecules; DoRaster3DOutput, ~BoundaryLineSet(), ~Tesselation() from HEAD; write_raster3d_file with some changes from MultipleMolecules
• boundary.hpp: all from MultipleMolecules
• builder.cpp: all in ParseCommandLineOptions() from MultipleMolecules
• config.cpp: all from HEAD, is stuff from ThermoStat and ConstrainedMD
• datacreator.hpp: all from HEAD, Hessian stuff
• helpers.cpp: all from HEAD, ReAlloc() differed just by indentation
• moleculelist.cpp: all from MultipleMolecules, has to do with introduced molecule centers
• molecules.cpp: all from HEAD, was ConstrainedMD stuff
• molecules.hpp: ConstrainedMD and VerletForceIntegration from HEAD, moleculelist stuff from MultipleMolecules
• parser.cpp: all from HEAD, ColumnCounter is *ColumnCounter there
• parser.hpp: all from HEAD
• vector.cpp: completely from MultipleMolecules (more lines)
• verbose.cpp: all from HEAD

compilation fixes:

• CheckPresenceOfTriangle() from MultipleMolecules
• MoleculeListClass::ListOfMolecules has changed to STL list, hence use insert(), ReturnIndex() and MoleculeListClass::OutputConfigForListOfFragments
• MoleculeListClass::OutputConfigForListOfFragments() had fragmentprefix instead of FRAGMENTPREFIX
• parser.hpp: EnergyMatrix::ParseIndices() declaration was missing

File:

• src/datacreator.cpp (modified) (27 diffs)

src/datacreator.cpp

@@ -1 +1 @@
 /** \file datacreator.cpp
  *
- * Declarations of assisting functions in creating data and plot files. 
- *    
+ * Declarations of assisting functions in creating data and plot files.
+ *
  */
 
@@ -27 +27 @@
   }
   return true;
-}; 
+};
 
 /** Opens a file for appending with \a *filename in \a *dir.
@@ -45 +45 @@
   }
   return true;
-}; 
+};
 
 /** Plots an energy vs. order.
@@ -54 +54 @@
  * \return true if file was written successfully
  */
-bool CreateDataEnergyOrder(class EnergyMatrix &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; 
+bool CreateDataEnergyOrder(class EnergyMatrix &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;
@@ -87 +87 @@
  * \return true if file was written successfully
  */
-bool CreateDataDeltaEnergyOrder(class EnergyMatrix &Energy, class EnergyMatrix &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; 
+bool CreateDataDeltaEnergyOrder(class EnergyMatrix &Energy, class EnergyMatrix &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;
@@ -130 +130 @@
 
   filename << prefix << ".dat";
-  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false; 
+  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false;
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
@@ -162 +162 @@
 
   filename << prefix << ".dat";
-  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false; 
+  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false;
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
@@ -188 +188 @@
  * \return true if file was written successfully
  */
-bool CreateDataDeltaForcesOrderPerAtom(class ForceMatrix &Force, class ForceMatrix &Fragments, class KeySetsContainer &KeySet, char *dir, char *prefix, char *msg, char *datum) 
+bool CreateDataDeltaForcesOrderPerAtom(class ForceMatrix &Force, class ForceMatrix &Fragments, class KeySetsContainer &KeySet, char *dir, char *prefix, char *msg, char *datum)
 {
   stringstream filename;
@@ -195 +195 @@
 
   filename << prefix << ".dat";
-  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false; 
+  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false;
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
@@ -205 +205 @@
     // errors per atom
     output << endl << "#Order\t" << BondOrder+1 << endl;
-    for(int j=0;j<Fragments.RowCounter[ Fragments.MatrixCounter ];j++) { 
+    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++) {
@@ -213 +213 @@
             norm += Force.Matrix[Force.MatrixCounter][ j ][l+m]*Force.Matrix[Force.MatrixCounter][ j ][l+m];
           norm = sqrt(norm);
-        }                                                                                                           
+        }                                                                                                    
 //        if (norm < MYEPSILON)
           output << scientific << Fragments.Matrix[Fragments.MatrixCounter][ j ][l] << "\t";
@@ -235 +235 @@
  * \return true if file was written successfully
  */
-bool CreateDataForcesOrderPerAtom(class ForceMatrix &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; 
+bool CreateDataForcesOrderPerAtom(class ForceMatrix &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;
@@ -250 +250 @@
     // errors per atom
     output << endl << "#Order\t" << BondOrder+1 << endl;
-    for(int j=0;j<Fragments.RowCounter[ Fragments.MatrixCounter ];j++) { 
+    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++)
@@ -390 +390 @@
 
   filename << prefix << ".dat";
-  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false; 
+  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false;
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum << endl;
@@ -411 +411 @@
  * \param &KeySet KeySetsContainer with associations of each fragment to a bond order
  * \param BondOrder current bond order
- */ 
+ */
 void CreateMaxFragmentOrder(class MatrixContainer &Fragments, class KeySetsContainer &KeySet, int BondOrder)
 {
@@ -420 +420 @@
           Fragments.Matrix[ Fragments.MatrixCounter ][j][k] = Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
       }
-    }      
+    }
   }
 };
@@ -428 +428 @@
  * \param &KeySet KeySetsContainer with associations of each fragment to a bond order
  * \param BondOrder current bond order
- */ 
+ */
 void CreateMinFragmentOrder(class MatrixContainer &Fragments, class KeySetsContainer &KeySet, int BondOrder)
 {
@@ -443 +443 @@
           Fragments.Matrix[ Fragments.MatrixCounter ][j][k] = Fragments.Matrix[ KeySet.OrderSet[BondOrder][i] ][j][k];
       }
-    }      
+    }
   }
 };
@@ -455 +455 @@
 
   filename << prefix << ".dat";
-  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false; 
+  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false;
   cout << msg << endl;
   output << "# " << msg << ", created on " << datum;
@@ -496 +496 @@
     do {
       for (int m=NDIM;m--;) {
-        stored += Force.Matrix[MatrixNumber][ k ][l+m] 
+        stored += Force.Matrix[MatrixNumber][ k ][l+m]
               * Force.Matrix[MatrixNumber][ k ][l+m];
-        Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l+m]  = Force.Matrix[MatrixNumber][ k ][l+m]; 
+        Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l+m]  = Force.Matrix[MatrixNumber][ k ][l+m];
       }
       k++;
@@ -505 +505 @@
       double tmp = 0;
       for (int m=NDIM;m--;)
-        tmp += Force.Matrix[MatrixNumber][ k ][l+m] 
+        tmp += Force.Matrix[MatrixNumber][ k ][l+m]
               * Force.Matrix[MatrixNumber][ k ][l+m];
       if ((fabs(tmp) > MYEPSILON) && (tmp < stored)) {  // current force is greater than stored
         for (int m=NDIM;m--;)
-          Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l+m]  = Force.Matrix[MatrixNumber][ k ][l+m]; 
+          Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l+m]  = Force.Matrix[MatrixNumber][ k ][l+m];
         stored = tmp;
       }
@@ -531 +531 @@
       double norm = 0.;
       for (int m=NDIM;m--;)
-        norm += Force.Matrix[MatrixNumber][ k ][l+m] 
+        norm += Force.Matrix[MatrixNumber][ k ][l+m]
               * Force.Matrix[MatrixNumber][ k ][l+m];
       tmp += sqrt(norm);
@@ -553 +553 @@
       double tmp = 0;
       for (int m=NDIM;m--;)
-        tmp += Force.Matrix[MatrixNumber][ k ][l+m] 
+        tmp += Force.Matrix[MatrixNumber][ k ][l+m]
               * Force.Matrix[MatrixNumber][ k ][l+m];
       if (tmp > stored) {  // current force is greater than stored
         for (int m=NDIM;m--;)
-          Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l+m]  = Force.Matrix[MatrixNumber][ k ][l+m]; 
+          Force.Matrix[MatrixNumber][ Force.RowCounter[MatrixNumber] ][l+m]  = Force.Matrix[MatrixNumber][ k ][l+m];
         stored = tmp;
       }
@@ -592 +592 @@
  * \param *key position of key
  * \param *logscale axis for logscale
- * \param *extraline extra set lines if desired 
+ * \param *extraline extra set lines if desired
  * \param mxtics small tics at ...
  * \param xtics large tics at ...
- * \param *xlabel label for x axis  
+ * \param *xlabel label for x axis
  * \param *ylabel label for y axis
- */ 
+ */
 void CreatePlotHeader(ofstream &output, const char *prefix, const int keycolumns, const char *key, const char *logscale, const char *extraline, const int mxtics, const int xtics, const char *xlabel, const char *ylabel)
 {
@@ -626 +626 @@
  * \param mxtics small tics at ...
  * \param xtics large tics at ...
- * \param xlabel label for x axis  
+ * \param xlabel label for x axis
  * \param xlabel label for x axis
  * \param *xrange xrange
@@ -634 +634 @@
  * \param (*CreatePlotLines) function reference that writes a single plot line
  * \return true if file was written successfully
- */   
+ */
 bool CreatePlotOrder(class MatrixContainer &Matrix, const class KeySetsContainer &KeySet, const char *dir, const char *prefix, const int keycolumns, const char *key, const char *logscale, const char *extraline, const int mxtics, const int xtics, const char *xlabel, const char *ylabel, const char *xrange, const char *yrange, const char *xargument, const char *uses, void (*CreatePlotLines)(ofstream &, class MatrixContainer &, const char *, const char *, const char *))
 {
@@ -641 +641 @@
 
   filename << prefix << ".pyx";
-  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false; 
+  if (!OpenOutputFile(output, dir, filename.str().c_str())) return false;
   CreatePlotHeader(output, prefix, keycolumns, key, logscale, extraline, mxtics, xtics, xlabel, ylabel);
   output << "plot " << xrange << " " << yrange << " \\" << endl;
   CreatePlotLines(output, Matrix, prefix, xargument, uses);
-  output.close();  
+  output.close();
   return true;
 };