Changeset 56fb09

Timestamp:

Jun 30, 2010, 8:35:38 AM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

5ec8e3

Parents:

51a5c8 (diff), 8e0c63 (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.

Message:

Merge branch 'stable' into StructureRefactoring

Files:

• src/Actions/MoleculeAction/VerletIntegrationAction.cpp (modified) (1 diff)
• src/CommandLineParser.hpp (modified) (1 diff)
• src/Parser/FormatParserStorage.cpp (modified) (3 diffs)
• src/Parser/FormatParserStorage.hpp (modified) (1 diff)
• src/Parser/PcpParser.cpp (modified) (1 diff)
• src/UIElements/CommandLineUI/CommandLineUIFactory.hpp (modified) (1 diff)
• src/UIElements/Dialog.hpp (modified) (1 diff)
• src/UIElements/TextUI/TextWindow.cpp (modified) (4 diffs)
• src/UIElements/TextUI/TextWindow.hpp (modified) (1 diff)
• src/UIElements/UIFactory.hpp (modified) (1 diff)
• src/atom_trajectoryparticle.cpp (modified) (1 diff)
• src/atom_trajectoryparticle.hpp (modified) (1 diff)
• src/molecule.hpp (modified) (1 diff)
• src/molecule_dynamics.cpp (modified) (5 diffs)
• src/molecule_geometry.cpp (modified) (1 diff)
• src/parser.cpp (modified) (7 diffs)
• src/tesselationhelpers.cpp (modified) (1 diff)
• tests/regression/testsuite-molecules.at (modified) (1 diff)

src/Actions/MoleculeAction/VerletIntegrationAction.cpp

@@ -62 +62 @@
     char outputname[MAXSTRINGSIZE];
     strcpy(outputname, filename.c_str());
-    if (!mol->VerletForceIntegration(outputname, *(World::getInstance().getConfig())))
+    if (!mol->VerletForceIntegration(outputname, *(World::getInstance().getConfig()), 0))
       DoLog(2) && (Log() << Verbose(2) << "File not found." << endl);
     else

src/CommandLineParser.hpp

@@ -17 +17 @@
 #include <list>
 
+/** This class is a wrapper for boost::program_options.
+ *
+ * <h1> CommandLine Howto </h1>
+ * <h2> Introduction </h2>
+ *
+ * The UIFactory is a base class for the User Interaction. There are three UI specializations:
+ * Text, GUI and CommandLine. Accessing functionality via the CommandLine UI is explained here.
+ *
+ * First, an Action has to be written for the specific functionality. This Action should
+ * be added in Actions/...Action in the respective subdirectory of the following types:
+ *  -# Analysis: Analysis actions like evaluating pair correlation, bonds, ...
+ *  -# Atom: adding, removing, manipulating atoms
+ *  -# Cmd: specifying data bases, verbosity, ...
+ *  -# Fragmentation: fragmenting a system, performing graph analysis, ...
+ *  -# Molecule: adding, removing, manipulating molecules
+ *  -# Parser: Parsing files (loading, saving)
+ *  -# Tesselation: obtaining (non)convex surface of a molecule, embedding, ...
+ *  -# World: Setting Box dimensions, default name of new molecules, ...
+ *
+ *  The CommandLineUIFactory is a specialization of the UIFactory for parsing command
+ *  line parameters, generating and executing actions there from.
+ *
+ *  The idea of the CommandLineFactory is explained elsewhere, here we would like to give a
+ *  receipe for creating new actions.
+ *
+ * <h3>Introducing new actions</h3>
+ *
+ * Let us now introduce what to do if a new action is to be implemented. Here, we use the
+ * CommandLineVersionAction as an example.
+ * This consists if basically three parts:
+ * 1. Create the files, write the classes and make them compilable
+ *   - Create new source and header files in one of the above subfolders in the Actions folder,
+ *     e.g. create VersionAction.cpp and VersionAction.hpp in Actions/Cmd/
+ *   - Give it a sensible class name, the convention is <type><what it does>Action,
+ *     where <type> is basically the naming (written out) of the subdirectory,
+ *     e.g. class CommandLineVersionAction.
+ *   - Add the source and header file to the respective variables in molecuilder/src/Makefile.am,
+ *     e.g. if you add a Cmd action the variables are CMDACTIONSOURCE and CMDACTIONHEADER,
+ *     such that they get compiled.
+ * 2. Add an instance to the CommandLineUIFactory, such that they are known to the UI.
+ *   - Add the header file as an include to UIElements/CommandLineWindow.cpp, e.g.
+ *     #include "Actions/Cmd/VersionAction.hpp"
+ *   - Add an instance of your class to the specific populater-function in
+ *     UIElements/CommandLineWindow.cpp, e.g. for the above Cmd action, add to populateCmdActions()
+ *     add new CommandLineVersionAction().
+ *     This will automatically register in the ActionRegistry.
+ * 3. Give them an option name, short hand an description, such that they can be referenced from
+ *    the command line.
+ *   - think of a new key name, e.g. "version", which is the long form of the command parameter,
+ *     i.e. --version).
+ *   - add this key to every map of MapofActions, i.e. to
+ *     - MapofActions::DescriptionMap: the description which appears as help and tooltip
+ *     - MapofActions::ShortFormMap: the short form of the command parameter (e.g. -v)
+ *     - MapofActions::ValueMap: the value the command parameter has (do not create if it does not need one)
+ *   - If your action requires additional parameters, these need to be added in the same manner as in
+ *     the list item above.
+ *
+ *  Don't forget to write the actual code. :)
+ *
+ * <h3>Writing an action</h3>
+ *
+ *  As you write a new action you may think in terms of the command line, i.e. you want to use this
+ *  new functionality you add by calling molecuilder as: ./molecuilder --super-action foobar.txt, where
+ *  the key of your new action would be "super-action". While this is fine, keep in mind, that your action
+ *  should be useable for the other UI specializations as well, i.e. from the menu and the GUI. Therefore,
+ *  -# Don't use cin to ask the user for input: Use Query...()!
+ *  -# Rather don't use cout/cerrs, but either give Log() or eLog() or use QueryEmpty() if you want to give
+ *     the user specific information what you ask of him.
+ *
+ */
 class CommandLineParser : public Singleton<CommandLineParser> {
   friend class Singleton<CommandLineParser>;

src/Parser/FormatParserStorage.cpp

@@ -38 +38 @@
 {
   ParserList.resize(ParserTypes_end, NULL);
+  ParserStream.resize(ParserTypes_end, NULL);
   ParserPresent.resize(ParserTypes_end, false);
   ParserSuffix.resize(ParserTypes_end, "");
@@ -54 +55 @@
 {
   for (ParserTypes iter = ParserTypes_begin; iter < ParserTypes_end; ++iter)
-    if (ParserPresent[iter])
+    if (ParserPresent[iter]) {
+      if (ParserStream[iter]->is_open())
+        ParserStream[iter]->close();
+      delete ParserStream[iter];
       delete ParserList[iter];
+    }
 }
 
@@ -75 +80 @@
       filename += ".";
       filename += ParserSuffix[iter];
-      std::ofstream *file = new std::ofstream(filename.c_str());
-      ParserList[iter]->setOstream((std::ostream *)file);
+      ParserStream[iter] = new std::ofstream(filename.c_str());
+      ParserList[iter]->setOstream((std::ostream *)ParserStream[iter]);
     }
 }

src/Parser/FormatParserStorage.hpp

@@ -57 +57 @@
   std::vector<FormatParser *> ParserList;
 
+  // list of allocated strams
+  std::vector<std::ofstream *> ParserStream;
+
   // which parser is already present
   std::vector<bool> ParserPresent;

src/Parser/PcpParser.cpp

@@ -88 +88 @@
   IsAngstroem = 1;
   RelativeCoord = 0;
+  StructOpt = 0;
   MaxTypes = 0;
 }

src/UIElements/CommandLineUI/CommandLineUIFactory.hpp

@@ -11 +11 @@
 #include "UIFactory.hpp"
 
+/** This class is a specialization of the UIFactory.
+ *
+ * <h2> Introduction </h2>
+ *
+ * The UIFactory is a base class for the User Interaction. There are three UI specializations:
+ * Text, GUI and CommandLine.
+ *
+ * The idea of the command line part is as follows:
+ *
+ * All actions that can be called from the command line are instantiated via populater-functions.
+ * In the constructor of an action it is automatically registered with the ActionRegistry and can
+ * henceforth be looked up there.
+ *
+ * There is a CommandLineParser which parses the command line parameters and puts all found values
+ * into a map. Then, MainWindow::Display of the CommandLineUIFactory is called, which goes through
+ * every action (by the ActionRegistry) and looks through the parsed commands whether the action is
+ * desired.
+ *
+ * In the action itself, Query's ask for user input. In the CommandLine case, we don't want direct
+ * user interaction, but the user has to have those values already delivered along with the desired
+ * action. Hence, the Query implementations just look up the desired values in the CommandLineParser
+ * vaults. When they are not found, an exception is thrown. When all are found, the action is performed.
+ *
+ */
 class CommandLineUIFactory : public UIFactory
 {

src/UIElements/Dialog.hpp

@@ -18 +18 @@
 class Vector;
 
+
+/** Dialog is one of the two main classes of the UIFactory base class.
+ *
+ * The Dialog is meant for asking the user for information needed to perform actions he
+ * desires, such as asking for a position in space or a length.
+ *
+ * For this purpose there is the base class Query and numerous specializations for each
+ * of the types to be asked. There are primitives integer, doubles and string, but also
+ * advanced types such as element, molecule or Vector. There is also an empty query for
+ * displaying text.
+ */
 class Dialog
 {

src/UIElements/TextUI/TextWindow.cpp

@@ -7 +7 @@
 
 #include "Helpers/MemDebug.hpp"
-
-#include "TextUI/TextWindow.hpp"
 
 #include <boost/bind.hpp>
@@ -19 +17 @@
 #include "Menu/SubMenuItem.hpp"
 #include "TextUI/TextStatusIndicator.hpp"
+#include "TextUI/TextWindow.hpp"
 #include "Actions/MapOfActions.hpp"
 #include "Actions/MethodAction.hpp"
@@ -40 +39 @@
 #include <iostream>
 #include <map>
-
-using namespace std;
 
 // TODO: see what code can be moved to a base class for Graphic and Text Windows
@@ -110 +107 @@
 }
 
-char TextWindow::getSuitableShortForm(set <char> &ShortcutList, const std::string name) const
+char TextWindow::getSuitableShortForm(std::set <char> &ShortcutList, const std::string name) const
 {
   for (std::string::const_iterator CharRunner = name.begin(); CharRunner != name.end(); ++CharRunner) {

src/UIElements/TextUI/TextWindow.hpp

@@ -27 +27 @@
 
   virtual void display();
+
 private:
   // populaters

src/UIElements/UIFactory.hpp

@@ -25 +25 @@
  * only create UIelements of that certain type, so that all UIElements match. This way different
  * UIs can be handled in a concise abstract way.
+ *
+ * The main functionality is the MainWindow and the Dialog.
+ *
+ * MainWindow basically is the framework if the UI. The MainWindow has a run function which is
+ * called MainWindow::Display(), which will listen for user input and react to it via actions for
+ * as long as the user desires or tells the MainWindow to quit.
+ *
+ * Within the MainWindow Dialog classes may be instantiated which ask the user for input to
+ * certain actions he wants to perform.
+ *
  */
 class UIFactory : public Singleton<UIFactory,false>

src/atom_trajectoryparticle.cpp

@@ -106 +106 @@
  * \param *Force matrix with forces
  */
-void TrajectoryParticle::VelocityVerletUpdate(int NextStep, config *configuration, ForceMatrix *Force)
+void TrajectoryParticle::VelocityVerletUpdate(int NextStep, config *configuration, ForceMatrix *Force, const size_t offset)
 {
   //a = configuration.Deltat*0.5/walker->type->mass;        // (F+F_old)/2m = a and thus: v = (F+F_old)/2m * t = (F + F_old) * a
   for (int d=0; d<NDIM; d++) {
-    Trajectory.F.at(NextStep)[d] = -Force->Matrix[0][nr][d+5]*(configuration->GetIsAngstroem() ? AtomicLengthToAngstroem : 1.);
+    Trajectory.F.at(NextStep)[d] = -Force->Matrix[0][nr][d+offset]*(configuration->GetIsAngstroem() ? AtomicLengthToAngstroem : 1.);
     Trajectory.R.at(NextStep)[d] = Trajectory.R.at(NextStep-1)[d];
     Trajectory.R.at(NextStep)[d] += configuration->Deltat*(Trajectory.U.at(NextStep-1)[d]);     // s(t) = s(0) + v * deltat + 1/2 a * deltat^2

src/atom_trajectoryparticle.hpp

@@ -50 +50 @@
   void ResizeTrajectory(int MaxSteps);
   void CopyStepOnStep(int dest, int src);
-  void VelocityVerletUpdate(int MDSteps, config *configuration, ForceMatrix *Force);
+  void VelocityVerletUpdate(int MDSteps, config *configuration, ForceMatrix *Force, const size_t offset);
   void SumUpKineticEnergy( int Step, double *TotalMass, Vector *TotalVelocity ) const;
 

src/molecule.hpp

@@ -279 +279 @@
   void SetBoxDimension(Vector *dim);
   void ScanForPeriodicCorrection();
-  bool VerletForceIntegration(char *file, config &configuration);
+  bool VerletForceIntegration(char *file, config &configuration, const size_t offset);
   void Thermostats(config &configuration, double ActualTemp, int Thermostat);
   void PrincipalAxisSystem(bool DoRotate);

src/molecule_dynamics.cpp

@@ -540 +540 @@
  * have to transform them).
  * This adds a new MD step to the config file.
- * \param *out output stream for debugging
  * \param *file filename
  * \param config structure with config::Deltat, config::IsAngstroem, config::DoConstrained
- * \param delta_t time step width in atomic units
- * \param IsAngstroem whether coordinates are in angstroem (true) or bohrradius (false)
- * \param DoConstrained whether we perform a constrained (>0, target step in molecule::trajectories) or unconstrained (0) molecular dynamics, \sa molecule::MinimiseConstrainedPotential()
+ * \param offset offset in matrix file to the first force component
  * \return true - file found and parsed, false - file not found or imparsable
  * \todo This is not yet checked if it is correctly working with DoConstrained set to true.
  */
-bool molecule::VerletForceIntegration(char *file, config &configuration)
+bool molecule::VerletForceIntegration(char *file, config &configuration, const size_t offset)
 {
   Info FunctionInfo(__func__);
@@ -561 +558 @@
   CountElements();  // make sure ElementsInMolecule is up to date
 
+  const int AtomCount = getAtomCount();
   // check file
   if (input == NULL) {
@@ -571 +569 @@
       return false;
     }
-    if (Force.RowCounter[0] != getAtomCount()) {
+    if (Force.RowCounter[0] != AtomCount) {
       DoeLog(0) && (eLog()<< Verbose(0) << "Mismatch between number of atoms in file " << Force.RowCounter[0] << " and in molecule " << getAtomCount() << "." << endl);
       performCriticalExit();
@@ -578 +576 @@
     // correct Forces
     Velocity.Zero();
-    for(int i=0;i<getAtomCount();i++)
+    for(int i=0;i<AtomCount;i++)
       for(int d=0;d<NDIM;d++) {
-        Velocity[d] += Force.Matrix[0][i][d+5];
+        Velocity[d] += Force.Matrix[0][i][d+offset];
       }
-    for(int i=0;i<getAtomCount();i++)
+    for(int i=0;i<AtomCount;i++)
       for(int d=0;d<NDIM;d++) {
-        Force.Matrix[0][i][d+5] -= Velocity[d]/static_cast<double>(getAtomCount());
+        Force.Matrix[0][i][d+offset] -= Velocity[d]/static_cast<double>(AtomCount);
       }
     // solve a constrained potential if we are meant to
@@ -599 +597 @@
     //ActOnAllAtoms( &atom::ResizeTrajectory, MDSteps+10 );
 
-    ActOnAllAtoms( &atom::VelocityVerletUpdate, MDSteps+1, &configuration, &Force);
+    ActOnAllAtoms( &atom::VelocityVerletUpdate, MDSteps+1, &configuration, &Force, (const size_t) 0);
   }
   // correct velocities (rather momenta) so that center of mass remains motionless

src/molecule_geometry.cpp

@@ -45 +45 @@
   delete[](Minv);
   delete(Center);
+  delete(CenterBox);
   return status;
 };

src/parser.cpp

@@ -76 +76 @@
 MatrixContainer::~MatrixContainer() {
   if (Matrix != NULL) {
+    // free Matrix[MatrixCounter]
+    if ((ColumnCounter != NULL) && (RowCounter != NULL) && (Matrix[MatrixCounter] != NULL))
+      for(int j=RowCounter[MatrixCounter]+1;j--;)
+        delete[](Matrix[MatrixCounter][j]);
+    //if (MatrixCounter != 0)
+    delete[](Matrix[MatrixCounter]);
+    // free all matrices but ultimate one
     for(int i=MatrixCounter;i--;) {
       if ((ColumnCounter != NULL) && (RowCounter != NULL)) {
@@ -83 +90 @@
       }
     }
-    if ((ColumnCounter != NULL) && (RowCounter != NULL) && (Matrix[MatrixCounter] != NULL))
-      for(int j=RowCounter[MatrixCounter]+1;j--;)
-        delete[](Matrix[MatrixCounter][j]);
-    if (MatrixCounter != 0)
-      delete[](Matrix[MatrixCounter]);
     delete[](Matrix);
   }
+  // free indices
   if (Indices != NULL)
     for(int i=MatrixCounter+1;i--;) {
@@ -96 +99 @@
   delete[](Indices);
   
+  // free header and counters
   if (Header != NULL)
     for(int i=MatrixCounter+1;i--;)
@@ -168 +172 @@
 
   // parse header
+  if (Header[MatrixNr] != NULL)
+    delete[] Header[MatrixNr];
   Header[MatrixNr] = new char[1024];
   for (int m=skiplines+1;m--;)
@@ -207 +213 @@
   // allocate matrix if it's not zero dimension in one direction
   if ((ColumnCounter[MatrixNr] > 0) && (RowCounter[MatrixNr] > -1)) {
+    if (Matrix[MatrixNr] != NULL)
+      delete[] Matrix[MatrixNr];
     Matrix[MatrixNr] = new double*[RowCounter[MatrixNr] + 1];
-  
+    for(int j=0;j<RowCounter[MatrixNr]+1;j++)
+      Matrix[MatrixNr][j] = 0;
+
     // parse in each entry for this matrix
     input.clear();
@@ -219 +229 @@
     strncpy(Header[MatrixNr], line.str().c_str(), 1023);  
     for(int j=0;j<RowCounter[MatrixNr];j++) {
+      if (Matrix[MatrixNr][j] != NULL)
+        delete[] Matrix[MatrixNr][j];
       Matrix[MatrixNr][j] = new double[ColumnCounter[MatrixNr]];
+      for(int k=0;k<ColumnCounter[MatrixNr];k++)
+        Matrix[MatrixNr][j][k] = 0;
+
       input.getline(filename, 1023);
       stringstream lines(filename);
@@ -229 +244 @@
         //Log() << Verbose(1) << " " << setprecision(2) << Matrix[MatrixNr][j][k] << endl;
       }
+      if (Matrix[MatrixNr][ RowCounter[MatrixNr] ] != NULL)
+        delete[] Matrix[MatrixNr][ RowCounter[MatrixNr] ];
       Matrix[MatrixNr][ RowCounter[MatrixNr] ] = new double[ColumnCounter[MatrixNr]];
       for(int j=ColumnCounter[MatrixNr];j--;)

src/tesselationhelpers.cpp

@@ -179 +179 @@
         Info FunctionInfo(__func__);
   Vector helper;
-  double alpha, beta, gamma;
   Vector SideA = b - c;
   Vector SideB = c - a;
   Vector SideC = a - b;
-  alpha = M_PI - SideB.Angle(SideC);
-  beta = M_PI - SideC.Angle(SideA);
-  gamma = M_PI - SideA.Angle(SideB);
-  Log() << Verbose(1) << "INFO: alpha = " << alpha/M_PI*180. << ", beta = " << beta/M_PI*180. << ", gamma = " << gamma/M_PI*180. << "." << endl;
-  if (fabs(M_PI - alpha - beta - gamma) > HULLEPSILON) {
-    DoeLog(2) && (eLog()<< Verbose(2) << "GetCenterofCircumcircle: Sum of angles " << (alpha+beta+gamma)/M_PI*180. << " > 180 degrees by " << fabs(M_PI - alpha - beta - gamma)/M_PI*180. << "!" << endl);
-  }
-
-  Center->Zero();
-  helper = sin(2.*alpha) * a;
-  (*Center) += helper;
-  helper = sin(2.*beta) * b;
-  (*Center) += helper;
-  helper = sin(2.*gamma) * c;
-  (*Center) += helper;
-  Center->Scale(1./(sin(2.*alpha) + sin(2.*beta) + sin(2.*gamma)));
-  Log() << Verbose(1) << "INFO: Center (1st algo) is at " << *Center << "." << endl;
-
-//  LinearSystemOfEquations LSofEq(NDIM,NDIM);
-//  double *matrix = new double[NDIM*NDIM];
-//  matrix[0] = 0.;
-//  matrix[1] = a.DistanceSquared(b);
-//  matrix[2] = a.DistanceSquared(c);
-//  matrix[3] = a.DistanceSquared(b);
-//  matrix[4] = 0.;
-//  matrix[5] = b.DistanceSquared(c);
-//  matrix[6] = a.DistanceSquared(c);
-//  matrix[7] = b.DistanceSquared(c);
-//  matrix[8] = 0.;
-//  cout << "Matrix is: ";
-//  for (int i=0;i<NDIM*NDIM;i++)
-//    cout << matrix[i] << "\t";
-//  cout << endl;
-//  LSofEq.SetA(matrix);
-//  delete[](matrix);
-//  LSofEq.Setb(new Vector(1.,1.,1.));
-//  LSofEq.SetSymmetric(true);
-//  helper.Zero();
-//  if (!LSofEq.GetSolutionAsVector(helper)) {
-//    DoLog(0) && (eLog()<< Verbose(0) << "Could not solve the linear system in GetCenterofCircumCircle()!" << endl);
-//  }
-//  cout << "Solution is " << helper << endl;
-  // is equivalent to the three lines below
+
   helper[0] = SideA.NormSquared()*(SideB.NormSquared()+SideC.NormSquared() - SideA.NormSquared());
   helper[1] = SideB.NormSquared()*(SideC.NormSquared()+SideA.NormSquared() - SideB.NormSquared());

tests/regression/testsuite-molecules.at

@@ -37 +37 @@
 AT_KEYWORDS([Molecules])
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/5/pre/test.* .], 0)
-AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -P test.forces --molecule-by-id 0], 134, [stdout], [stderr])
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -P test.forces --molecule-by-id 0], 0, [stdout], [stderr])
 #AT_CHECK([file=test.conf; diff $file ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/5/post/$file], 0, [ignore], [ignore])
 AT_CLEANUP