Changes in / [677e13:0430e3]

Files:

• src/Descriptors/MoleculeFormulaDescriptor.cpp (deleted)
• src/Descriptors/MoleculeFormulaDescriptor.hpp (deleted)
• src/Descriptors/MoleculeFormulaDescriptor_impl.hpp (deleted)
• src/Descriptors/MoleculePtrDescriptor.cpp (modified) (1 diff)
• src/Exceptions/ParseError.cpp (deleted)
• src/Exceptions/ParseError.hpp (deleted)
• src/Formula.cpp (deleted)
• src/Formula.hpp (deleted)
• src/Helpers/Range.hpp (deleted)
• src/Makefile.am (modified) (5 diffs)
• src/World.cpp (modified) (12 diffs)
• src/World.hpp (modified) (3 diffs)
• src/config.cpp (modified) (3 diffs)
• src/molecule.cpp (modified) (12 diffs)
• src/molecule.hpp (modified) (5 diffs)
• src/molecule_dynamics.cpp (modified) (1 diff)
• src/moleculelist.cpp (modified) (2 diffs)
• src/periodentafel.cpp (modified) (2 diffs)
• src/periodentafel.hpp (modified) (3 diffs)
• src/unittests/FormulaUnittest.cpp (deleted)
• src/unittests/FormulaUnittest.hpp (deleted)
• src/unittests/Makefile.am (modified) (4 diffs)
• test_all.sh (modified) (2 diffs)

src/Descriptors/MoleculePtrDescriptor.cpp

@@ -10 +10 @@
 #include "MoleculePtrDescriptor.hpp"
 #include "MoleculePtrDescriptor_impl.hpp"
-
-#include "Patterns/ObservedContainer_impl.hpp"
 
 #include "molecule.hpp"

src/Makefile.am

@@ -77 +77 @@
   Actions/Process.hpp
 
-EXCEPTIONSOURCE = \
-  Exceptions/CustomException.cpp \
-  Exceptions/IllegalTypeException.cpp \
-  Exceptions/LinearDependenceException.cpp \
-  Exceptions/MathException.cpp \
-  Exceptions/MissingValueException.cpp \
-  Exceptions/NotInvertibleException.cpp \
-  Exceptions/ParseError.cpp \
-  Exceptions/SkewException.cpp \
-  Exceptions/ZeroVectorException.cpp
+EXCEPTIONSOURCE = Exceptions/CustomException.cpp \
+        Exceptions/IllegalTypeException.cpp \
+        Exceptions/LinearDependenceException.cpp \
+        Exceptions/MathException.cpp \
+        Exceptions/MissingValueException.cpp \
+        Exceptions/NotInvertibleException.cpp \
+        Exceptions/SkewException.cpp \
+        Exceptions/ZeroVectorException.cpp
                                   
-EXCEPTIONHEADER = \
-  Exceptions/CustomException.hpp \
-  Exceptions/IllegalTypeException.hpp \
-  Exceptions/LinearDependenceException.hpp \
-  Exceptions/MathException.hpp \
-  Exceptions/MissingValueException.hpp \
-  Exceptions/NotInvertibleException.hpp \
-  Exceptions/ParseError.hpp \
-  Exceptions/SkewException.hpp \
-  Exceptions/ZeroVectorException.hpp
+EXCEPTIONHEADER = Exceptions/CustomException.hpp \
+        Exceptions/IllegalTypeException.hpp \
+        Exceptions/LinearDependenceException.hpp \
+        Exceptions/MathException.hpp \
+        Exceptions/MissingValueException.hpp \
+        Exceptions/NotInvertibleException.hpp \
+        Exceptions/SkewException.hpp \
+        Exceptions/ZeroVectorException.hpp
 
 PARSERSOURCE = \
@@ -155 +151 @@
   Descriptors/AtomTypeDescriptor.cpp \
   Descriptors/MoleculeDescriptor.cpp \
-  Descriptors/MoleculeFormulaDescriptor.cpp \
   Descriptors/MoleculeIdDescriptor.cpp \
   Descriptors/MoleculeNameDescriptor.cpp \
@@ -167 +162 @@
   Descriptors/AtomTypeDescriptor.hpp \
   Descriptors/MoleculeDescriptor.hpp \
-  Descriptors/MoleculeFormulaDescriptor.hpp \
   Descriptors/MoleculeIdDescriptor.hpp \
   Descriptors/MoleculeNameDescriptor.hpp \
@@ -208 +202 @@
   ellipsoid.cpp \
   errorlogger.cpp \
-  Formula.cpp \
   graph.cpp \
   helpers.cpp \
@@ -259 +252 @@
   ellipsoid.hpp \
   errorlogger.hpp \
-  Formula.hpp \
   graph.hpp \
   helpers.hpp \

src/World.cpp

@@ -234 +234 @@
     atomIdPool_t::iterator iter=atomIdPool.begin();
     atomId_t id = iter->first;
-    range<atomId_t> newRange = makeRange(id+1,iter->last);
+    pair<atomId_t,atomId_t> newRange = make_pair(id+1,iter->second);
     // we wont use this iterator anymore, so we don't care about invalidating
     atomIdPool.erase(iter);
-    if(newRange.first<newRange.last){
+    if(newRange.first<newRange.second){
       atomIdPool.insert(newRange);
     }
@@ -247 +247 @@
 
 void World::releaseAtomId(atomId_t id){
-  atomIdPool.insert(makeRange(id,id+1));
+  atomIdPool.insert(make_pair(id,id+1));
   defragAtomIdPool();
 }
@@ -253 +253 @@
 bool World::reserveAtomId(atomId_t id){
   if(id>=currAtomId ){
-    range<atomId_t> newRange = makeRange(currAtomId,id);
-    if(newRange.first<newRange.last){
+    pair<atomId_t,atomId_t> newRange = make_pair(currAtomId,id);
+    if(newRange.first<newRange.second){
       atomIdPool.insert(newRange);
     }
@@ -263 +263 @@
   // look for a range that matches the request
   for(atomIdPool_t::iterator iter=atomIdPool.begin();iter!=atomIdPool.end();++iter){
-    if(iter->isBefore(id)){
-      // we have covered all available ranges... nothing to be found here
+    if(iter->first>id){
+      // we have coverd all available ranges... nothing to be found here
       break;
     }
     // no need to check first, since it has to be <=id, since otherwise we would have broken out
-    if(!iter->isBeyond(id)){
+    if(iter->second > id){
       // we found a matching range... get the id from this range
 
       // split up this range at the point of id
-      range<atomId_t> bottomRange = makeRange(iter->first,id);
-      range<atomId_t> topRange = makeRange(id+1,iter->last);
+      pair<atomId_t,atomId_t> bottomRange = make_pair(iter->first,id);
+      pair<atomId_t,atomId_t> topRange = make_pair(id+1,iter->second);
       // remove this range
       atomIdPool.erase(iter);
-      if(bottomRange.first<bottomRange.last){
+      if(bottomRange.first<bottomRange.second){
         atomIdPool.insert(bottomRange);
       }
-      if(topRange.first<topRange.last){
+      if(topRange.first<topRange.second){
         atomIdPool.insert(topRange);
       }
@@ -301 +301 @@
     atomIdPool_t::iterator next = iter;
     next++;
-    if(next!=atomIdPool.end() && (next->first==iter->last)){
+    if(next!=atomIdPool.end() && (next->first==iter->second)){
       // merge the two ranges
-      range<atomId_t> newRange = makeRange(iter->first,next->last);
+      pair<atomId_t,atomId_t> newRange = make_pair(iter->first,next->second);
       atomIdPool.erase(iter);
       atomIdPool.erase(next);
@@ -317 +317 @@
     atomIdPool_t::iterator iter = atomIdPool.end();
     iter--;
-    if(iter->last==currAtomId){
+    if(iter->second==currAtomId){
       currAtomId=iter->first;
       atomIdPool.erase(iter);
@@ -333 +333 @@
     moleculeIdPool_t::iterator iter=moleculeIdPool.begin();
     moleculeId_t id = iter->first;
-    range<moleculeId_t> newRange = makeRange(id+1,iter->last);
+    pair<moleculeId_t,moleculeId_t> newRange = make_pair(id+1,iter->second);
     // we wont use this iterator anymore, so we don't care about invalidating
     moleculeIdPool.erase(iter);
-    if(newRange.first<newRange.last){
+    if(newRange.first<newRange.second){
       moleculeIdPool.insert(newRange);
     }
@@ -346 +346 @@
 
 void World::releaseMoleculeId(moleculeId_t id){
-  moleculeIdPool.insert(makeRange(id,id+1));
+  moleculeIdPool.insert(make_pair(id,id+1));
   defragMoleculeIdPool();
 }
@@ -352 +352 @@
 bool World::reserveMoleculeId(moleculeId_t id){
   if(id>=currMoleculeId ){
-    range<moleculeId_t> newRange = makeRange(currMoleculeId,id);
-    if(newRange.first<newRange.last){
+    pair<moleculeId_t,moleculeId_t> newRange = make_pair(currMoleculeId,id);
+    if(newRange.first<newRange.second){
       moleculeIdPool.insert(newRange);
     }
@@ -362 +362 @@
   // look for a range that matches the request
   for(moleculeIdPool_t::iterator iter=moleculeIdPool.begin();iter!=moleculeIdPool.end();++iter){
-    if(iter->isBefore(id)){
+    if(iter->first>id){
       // we have coverd all available ranges... nothing to be found here
       break;
     }
     // no need to check first, since it has to be <=id, since otherwise we would have broken out
-    if(!iter->isBeyond(id)){
+    if(iter->second > id){
       // we found a matching range... get the id from this range
 
       // split up this range at the point of id
-      range<moleculeId_t> bottomRange = makeRange(iter->first,id);
-      range<moleculeId_t> topRange = makeRange(id+1,iter->last);
+      pair<moleculeId_t,moleculeId_t> bottomRange = make_pair(iter->first,id);
+      pair<moleculeId_t,moleculeId_t> topRange = make_pair(id+1,iter->second);
       // remove this range
       moleculeIdPool.erase(iter);
-      if(bottomRange.first<bottomRange.last){
+      if(bottomRange.first<bottomRange.second){
         moleculeIdPool.insert(bottomRange);
       }
-      if(topRange.first<topRange.last){
+      if(topRange.first<topRange.second){
         moleculeIdPool.insert(topRange);
       }
@@ -400 +400 @@
     moleculeIdPool_t::iterator next = iter;
     next++;
-    if(next!=moleculeIdPool.end() && (next->first==iter->last)){
+    if(next!=moleculeIdPool.end() && (next->first==iter->second)){
       // merge the two ranges
-      range<moleculeId_t> newRange = makeRange(iter->first,next->last);
+      pair<moleculeId_t,moleculeId_t> newRange = make_pair(iter->first,next->second);
       moleculeIdPool.erase(iter);
       moleculeIdPool.erase(next);
@@ -416 +416 @@
     moleculeIdPool_t::iterator iter = moleculeIdPool.end();
     iter--;
-    if(iter->last==currMoleculeId){
+    if(iter->second==currMoleculeId){
       currMoleculeId=iter->first;
       moleculeIdPool.erase(iter);

src/World.hpp

@@ -24 +24 @@
 #include "Patterns/Singleton.hpp"
 #include "Patterns/ObservedContainer.hpp"
-#include "Helpers/Range.hpp"
 
 // include config.h
@@ -361 +360 @@
   AtomSet atoms;
   AtomSet selectedAtoms;
-  typedef std::set<range<atomId_t> > atomIdPool_t;
+  typedef std::set<std::pair<atomId_t, atomId_t> > atomIdPool_t;
   /**
    * stores the pool for all available AtomIds below currAtomId
@@ -374 +373 @@
   MoleculeSet molecules;
   MoleculeSet selectedMolecules;
-  typedef std::set<range<atomId_t> > moleculeIdPool_t;
+  typedef std::set<std::pair<moleculeId_t, moleculeId_t> > moleculeIdPool_t;
   /**
    * stores the pool for all available AtomIds below currAtomId

src/config.cpp

@@ -1031 +1031 @@
 {
   bool result = true;
+  // bring MaxTypes up to date
+  mol->CountElements();
   const Matrix &domain = World::getInstance().getDomain().getM();
   ofstream * const output = new ofstream(filename, ios::out);
@@ -1136 +1138 @@
     *output << "IsAngstroem\t" << config::IsAngstroem << "\t# 0 - Bohr, 1 - Angstroem" << endl;
     *output << "RelativeCoord\t" << config::RelativeCoord << "\t# whether ion coordinates are relative (1) or absolute (0)" << endl;
-    *output << "MaxTypes\t" << mol->getElementCount() <<  "\t# maximum number of different ion types" << endl;
+    *output << "MaxTypes\t" << mol->ElementCount <<  "\t# maximum number of different ion types" << endl;
     *output << endl;
     result = result && mol->Checkout(output);
@@ -1531 +1533 @@
     mol->SetNameFromFilename(ConfigFileName);
     molecules->SimpleMultiMerge(mol, src, N);
+    mol->doCountAtoms();
+    mol->CountElements();
     //mol->CalculateOrbitals(*this);
     delete[](src);

src/molecule.cpp

@@ -49 +49 @@
 molecule::molecule(const periodentafel * const teil) :
   Observable("molecule"),
-  elemente(teil),  MDSteps(0),  BondCount(0), NoNonHydrogen(0), NoNonBonds(0),
+  elemente(teil),  MDSteps(0),  BondCount(0), ElementCount(0), NoNonHydrogen(0), NoNonBonds(0),
   NoCyclicBonds(0), BondDistance(0.),  ActiveFlag(false), IndexNr(-1),
+  formula(this,boost::bind(&molecule::calcFormula,this),"formula"),
   AtomCount(this,boost::bind(&molecule::doCountAtoms,this),"AtomCount"), last_atom(0),  InternalPointer(atoms.begin())
 {
 
+  // other stuff
+  for(int i=MAX_ELEMENTS;i--;)
+    ElementsInMolecule[i] = 0;
   strcpy(name,World::getInstance().getDefaultName().c_str());
 };
@@ -97 +101 @@
 }
 
-const Formula &molecule::getFormula(){
-  return formula;
-}
-
-unsigned int molecule::getElementCount(){
-  return formula.getElementCount();
-}
-
-bool molecule::hasElement(const element *element) const{
-  return formula.hasElement(element);
-}
-
-bool molecule::hasElement(atomicNumber_t Z) const{
-  return formula.hasElement(Z);
-}
-
-bool molecule::hasElement(const string &shorthand) const{
-  return formula.hasElement(shorthand);
+const std::string molecule::getFormula(){
+  return *formula;
+}
+
+std::string molecule::calcFormula(){
+  std::map<atomicNumber_t,unsigned int> counts;
+  stringstream sstr;
+  periodentafel *periode = World::getInstance().getPeriode();
+  for (molecule::const_iterator iter = begin(); iter != end(); ++iter) {
+    counts[(*iter)->type->getNumber()]++;
+  }
+  std::map<atomicNumber_t,unsigned int>::reverse_iterator iter;
+  for(iter = counts.rbegin(); iter != counts.rend(); ++iter) {
+    atomicNumber_t Z = (*iter).first;
+    sstr << periode->FindElement(Z)->symbol << (*iter).second;
+  }
+  return sstr.str();
 }
 
@@ -207 +210 @@
     pointer->sort = &pointer->nr;
     if (pointer->type != NULL) {
-      formula += pointer->type;
+      if (ElementsInMolecule[pointer->type->Z] == 0)
+        ElementCount++;
+      ElementsInMolecule[pointer->type->Z]++; // increase number of elements
       if (pointer->type->Z != 1)
         NoNonHydrogen++;
@@ -646 +651 @@
 
   // copy values
+  copy->CountElements();
   if (hasBondStructure()) {  // if adjaceny list is present
     copy->BondDistance = BondDistance;
@@ -768 +774 @@
   ASSERT(pointer, "Null pointer passed to molecule::RemoveAtom().");
   OBSERVE;
-  formula-=pointer->type;
+  if (ElementsInMolecule[pointer->type->Z] != 0)  { // this would indicate an error
+    ElementsInMolecule[pointer->type->Z]--;  // decrease number of atom of this element
+  } else
+    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->getName() << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
+  if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
+    ElementCount--;
   RemoveBonds(pointer);
   erase(pointer);
@@ -782 +793 @@
   if (pointer == NULL)
     return false;
-  formula-=pointer->type;
+  if (ElementsInMolecule[pointer->type->Z] != 0)  // this would indicate an error
+    ElementsInMolecule[pointer->type->Z]--; // decrease number of atom of this element
+  else
+    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->getName() << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
+  if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
+    ElementCount--;
   erase(pointer);
   return true;
@@ -855 +871 @@
 {
   int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
+  CountElements();
 
   for (int i=0;i<MAX_ELEMENTS;++i) {
@@ -881 +898 @@
 {
   int ElementNo[MAX_ELEMENTS], AtomNo[MAX_ELEMENTS];
+  CountElements();
 
   if (output == NULL) {
@@ -922 +940 @@
 bool molecule::Checkout(ofstream * const output)  const
 {
-  return formula.checkOut(output);
+  return elemente->Checkout(output, ElementsInMolecule);
 };
 
@@ -980 +998 @@
 };
 
+/** Brings molecule::ElementCount and molecule::ElementsInMolecule up-to-date.
+ */
+void molecule::CountElements()
+{
+  for(int i=MAX_ELEMENTS;i--;)
+    ElementsInMolecule[i] = 0;
+  ElementCount = 0;
+
+  SetIndexedArrayForEachAtomTo ( ElementsInMolecule, &element::Z, &Increment, 1);
+
+  for(int i=MAX_ELEMENTS;i--;)
+    ElementCount += (ElementsInMolecule[i] != 0 ? 1 : 0);
+};
+
 /** Determines whether two molecules actually contain the same atoms and coordination.
  * \param *out output stream for debugging
@@ -998 +1030 @@
   /// first count both their atoms and elements and update lists thereby ...
   //Log() << Verbose(0) << "Counting atoms, updating list" << endl;
+  CountElements();
+  OtherMolecule->CountElements();
 
   /// ... and compare:
@@ -1007 +1041 @@
     } else Log() << Verbose(4) << "AtomCounts match: " << getAtomCount() << " == " << OtherMolecule->getAtomCount() << endl;
   }
-  /// -# Formula
+  /// -# ElementCount
   if (result) {
-    if (formula != OtherMolecule->formula) {
-      DoLog(4) && (Log() << Verbose(4) << "Formulas don't match: " << formula << " == " << OtherMolecule->formula << endl);
+    if (ElementCount != OtherMolecule->ElementCount) {
+      DoLog(4) && (Log() << Verbose(4) << "ElementCount don't match: " << ElementCount << " == " << OtherMolecule->ElementCount << endl);
       result = false;
-    } else Log() << Verbose(4) << "Formulas match: " << formula << " == " << OtherMolecule->formula << endl;
+    } else Log() << Verbose(4) << "ElementCount match: " << ElementCount << " == " << OtherMolecule->ElementCount << endl;
+  }
+  /// -# ElementsInMolecule
+  if (result) {
+    for (flag=MAX_ELEMENTS;flag--;) {
+      //Log() << Verbose(5) << "Element " <<  flag << ": " << ElementsInMolecule[flag] << " <-> " << OtherMolecule->ElementsInMolecule[flag] << "." << endl;
+      if (ElementsInMolecule[flag] != OtherMolecule->ElementsInMolecule[flag])
+        break;
+    }
+    if (flag < MAX_ELEMENTS) {
+      DoLog(4) && (Log() << Verbose(4) << "ElementsInMolecule don't match." << endl);
+      result = false;
+    } else Log() << Verbose(4) << "ElementsInMolecule match." << endl;
   }
   /// then determine and compare center of gravity for each molecule ...

src/molecule.hpp

@@ -28 +28 @@
 #include "Patterns/ObservedIterator.hpp"
 #include "Patterns/Cacheable.hpp"
-#include "Formula.hpp"
 
 #include "Descriptors/MoleculeDescriptor_impl.hpp"
@@ -98 +97 @@
     //int AtomCount;          //!< number of atoms, brought up-to-date by CountAtoms()
     int BondCount;          //!< number of atoms, brought up-to-date by CountBonds()
+    int ElementCount;       //!< how many unique elements are therein
+    int ElementsInMolecule[MAX_ELEMENTS]; //!< list whether element (sorted by atomic number) is alread present or not
     mutable int NoNonHydrogen;  //!< number of non-hydrogen atoms in molecule
     mutable int NoNonBonds;     //!< number of non-hydrogen bonds in molecule
@@ -108 +109 @@
 
   private:
-    Formula formula;
+    Cacheable<string> formula;
     Cacheable<int>    AtomCount;
     moleculeId_t id;
@@ -134 +135 @@
   void setId(moleculeId_t);
   void setName(const std::string);
-  const Formula &getFormula();
-  unsigned int getElementCount();
-  bool hasElement(const element*) const;
-  bool hasElement(atomicNumber_t) const;
-  bool hasElement(const std::string&) const;
-
+  const std::string getFormula();
+  std::string calcFormula();
 
   iterator begin();
@@ -257 +254 @@
 
   /// Count and change present atoms' coordination.
+  void CountElements();
   bool CenterInBox();
   bool BoundInBox();

src/molecule_dynamics.cpp

@@ -560 +560 @@
   ForceMatrix Force;
 
+  CountElements();  // make sure ElementsInMolecule is up to date
+
   const int AtomCount = getAtomCount();
   // check file

src/moleculelist.cpp

@@ -597 +597 @@
       periodentafel::const_iterator elemIter;
       for(elemIter=periode->begin();elemIter!=periode->end();++elemIter){
-        if ((*ListRunner)->hasElement((*elemIter).first)) { // if this element got atoms
+        if ((*ListRunner)->ElementsInMolecule[(*elemIter).first]) { // if this element got atoms
           for(molecule::iterator atomIter = (*ListRunner)->begin(); atomIter !=(*ListRunner)->end();++atomIter){
             if ((*atomIter)->type->getNumber() == (*elemIter).first) {
@@ -689 +689 @@
 
     // also calculate necessary orbitals
+    (*ListRunner)->CountElements(); // this is a bugfix, atoms should shoulds actually be added correctly to this fragment
     //(*ListRunner)->CalculateOrbitals(*World::getInstance().getConfig);
 

src/periodentafel.cpp

@@ -125 +125 @@
  * \return pointer to element
  */
-element * const periodentafel::FindElement(const string &shorthand) const
+element * const periodentafel::FindElement(const char * const shorthand) const
 {
   element *res = 0;
@@ -205 +205 @@
     for(const_iterator iter=elements.begin(); iter !=elements.end();++iter){
       result = result && (*iter).second->Output(output);
+    }
+    return result;
+  } else
+    return false;
+};
+
+/** Prints period table to given stream.
+ * \param *output output stream
+ * \param *checkliste elements table for this molecule
+ */
+bool periodentafel::Checkout(ostream * const output, const int * const checkliste) const
+{
+  bool result = true;
+  int No = 1;
+
+  if (output != NULL) {
+    *output << "# Ion type data (PP = PseudoPotential, Z = atomic number)" << endl;
+    *output << "#Ion_TypeNr.\tAmount\tZ\tRGauss\tL_Max(PP)L_Loc(PP)IonMass\t# chemical name, symbol" << endl;
+    for(const_iterator iter=elements.begin(); iter!=elements.end();++iter){
+      if (((*iter).first < MAX_ELEMENTS) && (checkliste[(*iter).first])) {
+        (*iter).second->No = No;
+        result = result && (*iter).second->Checkout(output, No++, checkliste[(*iter).first]);
+      }
     }
     return result;

src/periodentafel.hpp

@@ -11 +11 @@
 #include <iosfwd>
 #include <map>
-#include <string>
 
 #include "unittests/periodentafelTest.hpp"
@@ -48 +47 @@
   void CleanupPeriodtable();
   element * const FindElement(atomicNumber_t) const;
-  element * const FindElement(const std::string &shorthand) const;
+  element * const FindElement(const char * const shorthand) const;
   element * const AskElement() const;
   element * const EnterElement();
@@ -57 +56 @@
   reverse_iterator rend();
   bool Output(std::ostream * const output) const;
+  bool Checkout(std::ostream * const output, const int * const checkliste) const;
   bool LoadPeriodentafel(const char * const path);
   bool StorePeriodentafel(const char * const path) const;

src/unittests/Makefile.am

@@ -21 +21 @@
   CacheableTest \
   CountBondsUnitTest \
-  FormulaUnittest \
   GSLMatrixSymmetricUnitTest \
   GSLMatrixUnitTest \
@@ -67 +66 @@
   CacheableTest.cpp \
   CountBondsUnitTest.cpp \
-  FormulaUnittest.cpp \
   gslmatrixsymmetricunittest.cpp \
   gslmatrixunittest.cpp \
@@ -104 +102 @@
   CacheableTest.hpp \
   CountBondsUnitTest.hpp \
-  FormulaUnittest.hpp \
   gslmatrixsymmetricunittest.hpp \
   gslmatrixunittest.hpp \
@@ -161 +158 @@
 CountBondsUnitTest_LDADD = ${ALLLIBS}
 
-FormulaUnittest_SOURCES = UnitTestMain.cpp FormulaUnittest.cpp FormulaUnittest.hpp
-FormulaUnittest_LDADD = ${ALLLIBS}
-
 GSLMatrixSymmetricUnitTest_SOURCES = UnitTestMain.cpp gslmatrixsymmetricunittest.cpp gslmatrixsymmetricunittest.hpp
 GSLMatrixSymmetricUnitTest_LDADD = ${GSLLIBS}

test_all.sh

@@ -129 +129 @@
   echo "Valgrinding";
   retval=0;
-  for test in src/unittests/*
+  for test in molecuilder/src/unittests/*
   do
     if [ -x "$test" ]
@@ -150 +150 @@
 
   echo "Testing with \"$2\"";
-  echo "" >> $logfile;
-  echo "" >> $logfile;
-  echo "" >> $logfile;
-  echo "Testing with \"$2\"" >> $logfile;
 
   echo -n "  Configuring: " >> $outfile;