Changes in / [e38750:dace6c]

Files:

• src/Actions/AtomAction/AddAction.cpp (modified) (3 diffs)
• src/Actions/AtomAction/AddAction.def (modified) (1 diff)
• src/Actions/AtomAction/SaturateAction.cpp (modified) (1 diff)
• src/Actions/WorldAction/SetBoundaryConditionsAction.def (modified) (1 diff)
• src/Atom/atom.cpp (modified) (1 diff)
• src/Element/element.cpp (modified) (1 diff)
• src/Element/elements_db.cpp (modified) (2 diffs)
• src/Element/unittests/ElementUnitTest.cpp (modified) (1 diff)
• src/Fragmentation/Exporters/SaturatedBond.cpp (modified) (1 diff)
• src/Graph/BondGraph.hpp (modified) (2 diffs)
• src/Parameters/Specifics/Value_element.cpp (modified) (2 diffs)
• src/Parameters/Specifics/Value_elements.cpp (modified) (1 diff)
• src/Parser/MpqcParser.cpp (modified) (2 diffs)
• src/Parser/MpqcParser_Parameters.cpp (modified) (3 diffs)
• src/Parser/MpqcParser_Parameters.hpp (modified) (4 diffs)
• src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) (4 diffs)
• src/UIElements/CommandLineUI/CommandLineParser.cpp (modified) (2 diffs)
• src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) (2 diffs)
• src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) (2 diffs)
• src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) (4 diffs)
• src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp (modified) (4 diffs)
• src/World.cpp (modified) (1 diff)
• src/molecule.cpp (modified) (11 diffs)
• src/molecule.hpp (modified) (4 diffs)
• tests/regression/Atoms/Add/post/test.in (modified) (1 diff)
• tests/regression/Atoms/Add/post/test.pdb (modified) (1 diff)
• tests/regression/Atoms/Remove/post/test.in (modified) (1 diff)
• tests/regression/Atoms/Saturate/post/saturated_carbon.xyz (modified) (1 diff)
• tests/regression/Atoms/Saturate/post/saturated_nitrogen.xyz (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/doublewater.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/empty.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/test.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/testCLHF.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/testCLKS.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/testMBPT2.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/post/testMBPT2_R12.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testCLHF.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testCLHF_n.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testCLHF_n_ascend_ids.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testCLHF_n_mixed_ids.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testCLKS.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testMBPT2.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/testMBPT2_R12.in (modified) (1 diff)
• tests/regression/Parser/Mpqc/pre/water.in (modified) (1 diff)
• tests/regression/Parser/SetParameters/Mpqc/post/testCLHF.in (modified) (1 diff)
• tests/regression/Parser/SetParameters/Mpqc/pre/testCLHF.in (modified) (1 diff)

src/Actions/AtomAction/AddAction.cpp

@@ -55 +55 @@
 #include "Action_impl_pre.hpp"
 /** =========== define the function ====================== */
-
-atom * getNewAtom(const AtomAddAction::AtomAddParameters &_params)
-{
-  atom * first = World::getInstance().createAtom();
-  first->setType(_params.elemental.get());
-  first->setPosition(_params.position.get());
-
-  return first;
-}
-
-std::vector<atomId_t> createAtoms(
-    const AtomAddAction::AtomAddParameters &_params,
-    std::vector<molecule *> &_molecules)
-{
-  std::vector<atomId_t> ids;
-  if (!_molecules.empty()) {
-    if (_molecules.size() == 1) {
-        atom *first = getNewAtom(_params);
-        molecule *mol = *_molecules.begin();
-        LOG(1, "Adding new atom with element " << first->getType()->getName()
-            << " at " << (first->getPosition()) << " to selected molecule "
-            << mol->getName()+".");
-        mol->AddAtom(first);
-      ids.push_back(first->getId());
-    }
-  } else {
-    atom *first = getNewAtom(_params);
-    molecule *mol = World::getInstance().createMolecule();
-    mol->setName("none");
-    mol->AddAtom(first);
-    LOG(1, "Adding new atom with element " << first->getType()->getName()
-        << " at " << (first->getPosition()) << " to new molecule.");
-    ids.push_back(first->getId());
-  }
-
-  return ids;
-}
-
 ActionState::ptr AtomAddAction::performCall() {
   // execute action
-  std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
-  std::vector<atomId_t> ids = createAtoms(params, molecules);
-
-  if (molecules.size() > 1)
-     return Action::failure;
-  else
-    return ActionState::ptr(new AtomAddState(ids, params));
+  atom * first = World::getInstance().createAtom();
+  first->setType(params.elemental.get());
+  first->setPosition(params.position.get());
+  LOG(1, "Adding new atom with element " << first->getType()->getName() << " at " << (first->getPosition()) << ".");
+  // TODO: remove when all of World's atoms are stored.
+  std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
+  if (!molecules.empty()) {
+    std::vector<molecule *>::iterator iter = molecules.begin();
+    (*iter)->AddAtom(first);
+  }
+  return ActionState::ptr(new AtomAddState(first->getId(), params));
 }
 
@@ -107 +73 @@
   AtomAddState *state = assert_cast<AtomAddState*>(_state.get());
 
-  for (std::vector<atomId_t>::const_iterator iter = state->ids.begin();
-      iter != state->ids.end(); ++iter) {
-    LOG(1, "Removing atom with id " << *iter << ".");
-    World::getInstance().destroyAtom(*iter);
-  }
+  LOG(1, "Removing atom with id " << state->id << ".");
+  World::getInstance().destroyAtom(state->id);
 
   return ActionState::ptr(_state);
@@ -119 +82 @@
   AtomAddState *state = assert_cast<AtomAddState*>(_state.get());
 
-  std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
-  std::vector<atomId_t> newids = createAtoms(params, molecules);
+  atom * first = World::getInstance().createAtom();
+  first->setType(state->params.elemental.get());
+  first->setPosition(state->params.position.get());
+  LOG(1, "Re-adding new atom with element " << state->params.elemental.get()->getName() << " at " << state->params.position.get() << ".");
+  // TODO: remove when all of World's atoms are stored.
+  std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
+  if (!molecules.empty()) {
+    std::vector<molecule *>::iterator iter = molecules.begin();
+    (*iter)->AddAtom(first);
+  }
+  if (first->getId() != state->id)
+    if (!first->changeId(state->id)) {
+      STATUS("Could not change atom id "+toString(first->getId())+"->"+toString(state->id)+".");
+      return Action::failure;
+    }
 
-  if (newids.size() != state->ids.size()) {
-    STATUS("Could not recreate all atoms after undo.");
-    for (std::vector<atomId_t>::const_iterator iter = newids.begin(); iter != newids.end();++iter)
-      World::getInstance().destroyAtom(*iter);
-    return Action::failure;
-  }
-
-  std::vector<atomId_t>::const_iterator newiter = newids.begin();
-  std::vector<atomId_t>::const_iterator olditer = state->ids.begin();
-  bool status=true;
-  for (; newiter != newids.end(); ++newiter, ++olditer) {
-    atom * first = World::getInstance().getAtom(AtomById(*newiter));
-    ASSERT( first != NULL,
-        "AtomAddAction::performRedo() - re-created atom not present?");
-    if (first->getId() != *olditer)
-      if (!first->changeId(*olditer)) {
-        STATUS("Could not change atom id "+toString(first->getId())+"->"+toString(*olditer)+".");
-        // remove all created atoms
-        for (std::vector<atomId_t>::const_iterator iter = state->ids.begin(); iter != olditer;++iter)
-          World::getInstance().destroyAtom(*iter);
-        olditer = state->ids.end();
-        for (std::vector<atomId_t>::const_iterator iter = newiter; iter != newids.end();++iter)
-          World::getInstance().destroyAtom(*iter);
-        status = false;
-        break;
-      }
-  }
-  ASSERT( olditer == state->ids.end(),
-      "AtomAddAction::performRedo() - after all unequal amount of ids in new and old?");
-
-  if (!status) {
-    return Action::failure;
-  } else
-    return ActionState::ptr(_state);
+  return ActionState::ptr(_state);
 }
 

src/Actions/AtomAction/AddAction.def

@@ -27 +27 @@
 (BoxVectorValidator())
 
-#define statetypes (std::vector<atomId_t>)
-#define statereferences (ids)
+#define statetypes (const atomId_t)
+#define statereferences (id)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS

src/Actions/AtomAction/SaturateAction.cpp

@@ -79 +79 @@
     // add the hydrogens
     const Vector AtomsPosition = _atom->getPosition();
-    double typical_distance = _atom->getType()->getHBondDistance(0);
+    double typical_distance = _atom->getType()->getHBondDistance(1);
     if (typical_distance == -1.)
       typical_distance = 1.;

src/Actions/WorldAction/SetBoundaryConditionsAction.def

@@ -18 +18 @@
 #define paramtypes (std::vector< std::string >)
 #define paramtokens ("set-boundary-conditions")
-#define paramdescriptions ("new boundary conditions as list of three strings, e.g. 'Wrap Bounce Ignore'")
+#define paramdescriptions ("new boundary conditions as list of three strings, e.g. 'wrap wrap ignore'")
 #undef paramdefaults
 #define paramreferences (newconditions)

src/Atom/atom.cpp

@@ -264 +264 @@
   // first we move ourselves in the world
   // the world lets us know if that succeeded
-  atomId_t oldid = id;
   if(world->changeAtomId(id,newId,this)){
     OBSERVE;
     id = newId;
-    if (mol != NULL)
-      mol->changeAtomId(oldid, newId);
     NOTIFY(IndexChanged);
     return true;

src/Element/element.cpp

@@ -64 +64 @@
     color[i] = (unsigned char)0;
   for (size_t i =0; i<3;++i)
-    HBondDistance[i] = -1.;
-  for (size_t i =0; i<3;++i)
-    HBondAngle[i] = -1.;
+    HBondDistance[i] = 0.;
+  for (size_t i =0; i<3;++i)
+    HBondAngle[i] = 0.;
 };
 

src/Element/elements_db.cpp

@@ -258 +258 @@
 const char *HbonddistanceDB =\
 "#atomic number bond distances for single, double and triple bond (-1 no bond)\n\
-1       0.741283  -1. -1.\n\
-2       0  -1. -1.\n\
-3       1.65217  -1. -1.\n\
-4       1.3455  -1. -1.\n\
-5       1.1962  1.19 1.18\n\
-6       1.09234  1.076 1.06\n\
-7       1.00154  1.02 1.01\n\
-8       0.941566  0.957 -1.\n\
-9       0.958865  -1. -1.\n\
-10      0  -1. -1.\n\
-11      1.9426  -1. -1.\n\
-12      1.73705  -1. -1.\n\
-13      1.60991  -1. -1.\n\
-14      1.49796  1.48 1.48\n\
-15      1.39145  -1. -1.\n\
-16      1.32987  -1. -1.\n\
-17      1.31403  -1. -1.\n\
-18      0  -1. -1.\n\
-19      2.38168  -1. -1.\n\
-20      2.39602  -1. -1.\n\
-21      1.69169  -1. -1.\n\
-22      1.69817  -1. -1.\n\
-23      1.75022  -1. -1.\n\
-24      1.79185  -1. -1.\n\
-25      1.49581  -1. -1.\n\
-26      1.76215  -1. -1.\n\
-27      1.4284  -1. -1.\n\
-28      1.56442  -1. -1.\n\
-29      2.00512  -1. -1.\n\
-30      1.55672  -1. -1.\n\
-31      1.58872  -1. -1.\n\
-32      1.5484  -1. -1.\n\
-33      1.47208  -1. -1.\n\
-34      1.43322  -1. -1.\n\
-35      1.45079  -1. -1.\n\
-36      0  -1. -1.\n\
+1       0.74    -1      -1\n\
+2       0.77429209      -1      -1\n\
+5       1.23    1.19    1.18\n\
+6       1.09    1.076   1.06\n\
+7       1.04    1.02    1.01\n\
+8       0.96    0.957   -1\n\
+14      1.48    1.48    1.48\n\
+15      1.42    -1      -1\n\
+16      1.35    -1      -1\n\
+17      1.29    -1      -1\n\
+20      1.09    1.09    -1\n\
+34      1.47    -1      -1\n\
+35      1.44    -1      -1\n\
 ";
 
@@ -303 +280 @@
 7       0       110     106.67\n\
 8       0       104.5   -1\n\
-11  0 -1 -1\n\
 14      0       120     109.47\n\
 15      0       -1      -1\n\

src/Element/unittests/ElementUnitTest.cpp

@@ -110 +110 @@
   CPPUNIT_ASSERT_EQUAL( 0, testelement->getNoValenceOrbitals() );
   for (size_t i = 0; i < 3; ++i)
-    CPPUNIT_ASSERT_EQUAL( -1., testelement->getHBondDistance(i) );
+    CPPUNIT_ASSERT_EQUAL( 0., testelement->getHBondDistance(i) );
   for (size_t i = 0; i < 3; ++i)
-    CPPUNIT_ASSERT_EQUAL( -1., testelement->getHBondAngle(i) );
+    CPPUNIT_ASSERT_EQUAL( 0., testelement->getHBondAngle(i) );
 }
 

src/Fragmentation/Exporters/SaturatedBond.cpp

@@ -64 +64 @@
       saturated_atom.getElement().getHBondDistance(saturated_bond.getDegree()-1);
   ASSERT( HydrogenDistance > 0.,
-      "SaturatedBond::SaturatedBond() - negative bond distance for "
-      +saturated_atom.getElement().getName());
+      "SaturatedBond::SaturatedBond() - negative bond distance");
   const double HydrogenAngle =
       saturated_atom.getElement().getHBondAngle(saturated_bond.getDegree()-1);
   ASSERT( HydrogenAngle >= 0.,
-      "SaturatedBond::SaturatedBond() - negative bond angle for "
-      +saturated_atom.getElement().getName());
+      "SaturatedBond::SaturatedBond() - negative bond angle");
   LOG(5, "DEBUG: Hydrogen distance is " << HydrogenDistance
       << ", angle is " << HydrogenAngle);

src/Graph/BondGraph.hpp

@@ -221 +221 @@
               neighboriter != ListOfNeighbors.end();
               ++neighboriter) {
-            const atom * const OtherWalker = dynamic_cast<const atom *>(*neighboriter);
-            ASSERT(OtherWalker != NULL,
-                "BondGraph::CreateAdjacency() - TesselPoint "
-                +(*neighboriter)->getName()+" that was not an atom retrieved from LinkedList");
-            if (OtherWalker->getId() > Walker->getId()) {  // just to not add bonds from both sides
+            if ((*neighboriter) > Walker) {  // just to not add bonds from both sides
+              const atom * const OtherWalker = dynamic_cast<const atom *>(*neighboriter);
+              ASSERT(OtherWalker != NULL,
+                  "BondGraph::CreateAdjacency() - TesselPoint "
+                  +(*neighboriter)->getName()+" that was not an atom retrieved from LinkedList");
               LOG(4, "INFO: Current other atom is " << *OtherWalker << ".");
 
@@ -245 +245 @@
               }
             } else {
-              LOG(4, "REJECT: Not Adding: Wrong order.");
+              LOG(5, "REJECT: Not Adding: Wrong order.");
             }
           }

src/Parameters/Specifics/Value_element.cpp

@@ -35 +35 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include <boost/lexical_cast.hpp>
-
 #include "Value_element.hpp"
 
@@ -47 +45 @@
 static const element * FindElementByString(const std::string &_value)
 {
-  const element * elem = NULL;
-  try {
-    const int tempvalue = boost::lexical_cast<atomicNumber_t>(_value);
-    elem = World::getInstance().getPeriode()->FindElement(tempvalue);
-  } catch( boost::bad_lexical_cast &e) {
-    elem = World::getInstance().getPeriode()->FindElement(_value);
-  }
-  return elem;
+  static ConvertTo<atomicNumber_t> converter;
+  const element * _element =
+      World::getInstance().getPeriode()->FindElement(converter(_value));
+  return _element;
 }
 

src/Parameters/Specifics/Value_elements.cpp

@@ -57 +57 @@
   for(tokenizer::iterator beg=tok.begin();
       beg != tok.end();++beg) {
-    const element * elem = NULL;
-    try {
-      const int tempvalue = boost::lexical_cast<atomicNumber_t>(*beg);
-      elem = World::getInstance().getPeriode()->FindElement(tempvalue);
-    } catch( boost::bad_lexical_cast &e) {
-      elem = World::getInstance().getPeriode()->FindElement(*beg);
-    }
-    ASSERT( elem != NULL,
+    const int tempvalue = boost::lexical_cast<atomicNumber_t>(*beg);
+    const element * _element =
+        World::getInstance().getPeriode()->FindElement(tempvalue);
+    ASSERT( _element != NULL,
         "FindElementsByString() - cannnot find element "
-        +toString(*beg)+" in periodentafel.");
-    elements.push_back(elem);
+        +toString(tempvalue)+" in periodentafel.");
+    elements.push_back(_element);
   }
   return elements;

src/Parser/MpqcParser.cpp

@@ -309 +309 @@
     *file << "% Created by MoleCuilder" << endl;
     *file << "mpqc: (" << endl;
-    *file << "\tcheckpoint = no" << endl;
     *file << "\tsavestate = " << getParams().getParameter(MpqcParser_Parameters::savestateParam) << endl;
     *file << "\tdo_gradient = " << getParams().getParameter(MpqcParser_Parameters::do_gradientParam) << endl;
@@ -375 +374 @@
       ELOG(0, "Unknown level of theory requested for MPQC output file.");
     }
-    const std::string jobtype = getParams().getParameter(MpqcParser_Parameters::jobtypeParam);
-    if (jobtype == getParams().getJobtypeName(MpqcParser_Parameters::Optimization)) {
-      *file << "\t% optimizer object for the molecular geometry" << endl;
-      *file << "\topt<QNewtonOpt>: (" << endl;
-      *file << "\t\tfunction = $..:mole" << endl;
-      *file << "\t\tupdate<BFGSUpdate>: ()" << endl;
-      *file << "\t\tconvergence<MolEnergyConvergence>: (" << endl;
-      *file << "\t\t\tcartesian = yes" << endl;
-      *file << "\t\t\tenergy = $..:..:mole" << endl;
-      *file << "\t\t)" << endl;
-      *file << "\t)" << endl;
-    }
     *file << ")" << endl;
     *file << "molecule<Molecule>: (" << endl;

src/Parser/MpqcParser_Parameters.cpp

@@ -69 +69 @@
     ParamNames[integrationParam] = "integration";
     ParamNames[theoryParam] = "theory";
-    ParamNames[jobtypeParam] = "jobtype";
   }
 
@@ -87 +86 @@
   }
   //InvertMap<TheoryNamesType,TheoryLookupType>(TheoryNames,TheoryLookup);
-
-  // create Jobs parameter
-  {
-    ValidJobtypes.clear();
-    ValidJobtypes.resize(unknownJob);
-    ValidJobtypes[Default]="Default";
-    ValidJobtypes[Optimization]="Optimization";
-    appendParameter(
-        new Parameter<std::string>(
-            ParamNames[jobtypeParam],
-            ValidJobtypes,
-            ValidJobtypes[Default]));
-  }
 
   // create integration parameter
@@ -191 +177 @@
 }
 
-/** Getter for name of a specific Parameter.
- *
- * @param param index among enum Jobtype
- * @return name of the desired Jobtype
- */
-const std::string &MpqcParser_Parameters::getJobtypeName(const enum Jobtype jobtype) const
-{
-  return ValidJobtypes[jobtype];
-}
-
 /** Getter for the name of specific of IntegrationMethod.
  *

src/Parser/MpqcParser_Parameters.hpp

@@ -58 +58 @@
     integrationParam,//!< integrationParam, integration method to use in MBPT2 R12
     theoryParam,     //!< theoryParam, level of theory to use
-    jobtypeParam,    //!< jobtypeParam, job type to use
     unknownParam};   //!< unknownParam, designates an unknown parameter
 
@@ -70 +69 @@
     MBPT2_R12,  //!< Moeller Plesset Perturbation Theory second order with R12 integral
     unknownTheory //!< designates an unknown theory
-  };
-
-  /** Enumeration of all known jobtypes.
-   *
-   */
-  enum Jobtype {
-    Default,       //!< standard energy and force calculation
-    Optimization,       //!< additional optimization of geometry
-    unknownJob //!< designates an unknown job
   };
 
@@ -103 +93 @@
   const std::string &getParameterName(const enum Parameters param) const;
   const std::string &getTheoryName(const enum Theory theory) const;
-  const std::string &getJobtypeName(const enum Jobtype jobtype) const;
   const std::string &getIntegrationMethodName(const enum IntegrationMethod integration) const;
 
@@ -110 +99 @@
   //!> vector with all available theories in same order as enum Theory.
   std::vector<std::string> ValidTheories;
-
-  //!> vector with all available jobtypes in same order as enum Jobs.
-  std::vector<std::string> ValidJobtypes;
 
   //!> vector with all available integration methods in same order as enum IntegrationMethod.

src/Parser/unittests/ParserMpqcUnitTest.cpp

@@ -63 +63 @@
 static string waterMpqc_CLHF ="% Created by MoleCuilder\n\
 mpqc: (\n\
-\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\
@@ -87 +86 @@
 static string waterMpqc_CLKS ="% Created by MoleCuilder\n\
 mpqc: (\n\
-\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\
@@ -112 +110 @@
 static string waterMpqc_MBPT2 ="% Created by MoleCuilder\n\
 mpqc: (\n\
-\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\
@@ -141 +138 @@
 static string waterMpqc_MBPT2_R12 ="% Created by MoleCuilder\n\
 mpqc: (\n\
-\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\

src/UIElements/CommandLineUI/CommandLineParser.cpp

@@ -390 +390 @@
 //            currentOption->hasDefaultValue() ?
 //                  po::value < const element * >()->default_value(boost::lexical_cast<const element *>(currentOption->getDefaultValue().c_str())) :
-                  po::value < std::string >(),
+                  po::value < int >(),
                   currentOption->getDescription().c_str())
         ;
@@ -399 +399 @@
 //            currentOption->hasDefaultValue() ?
 //                  po::value < std::vector<const element *> >()->default_value(boost::lexical_cast< std::vector<const element *> >(currentOption->getDefaultValue().c_str())) :
-                  po::value < std::vector<std::string> >()->multitoken(),
+                  po::value < std::vector<int> >()->multitoken(),
                   currentOption->getDescription().c_str())
         ;

src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp

@@ -36 +36 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include <string>
-
 #include "CommandLineUI/Query/CommandLineQuery.hpp"
 #include "CommandLineUI/CommandLineParser.hpp"
@@ -56 +54 @@
   // TODO: vector of ints and removing first is not correctly implemented yet. How to remove from a vector?
   periodentafel *periode = World::getInstance().getPeriode();
+  int Z = -1;
   if (CommandLineParser::getInstance().vm.count(getTitle())) {
-    std::string argument("none");
     try {
-      argument = CommandLineParser::getInstance().vm[getTitle()].as< std::string >();
-      try {
-        int Z = -1;
-        Z = boost::lexical_cast<int>(argument);
-        temp = periode->FindElement(Z);
-      } catch(boost::bad_lexical_cast &e) {
-        temp = periode->FindElement(argument);
-      }
+      Z = CommandLineParser::getInstance().vm[getTitle()].as< int >();
     } catch(boost::bad_any_cast &e) {
+      Z = -1;
       return false;
     }
+    temp = periode->FindElement(Z);
     ASSERT(temp != NULL, "Invalid element specified in ElementCommandLineQuery");
     return true;

src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp

@@ -36 +36 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include <string>
-
 #include "CommandLineUI/Query/CommandLineQuery.hpp"
 #include "CommandLineUI/CommandLineParser.hpp"
@@ -53 +51 @@
 {}
 
-template <typename T>
-std::vector<const element *> getElementsFromInput(const std::vector<std::string> &_input)
-{
-  periodentafel *periode = World::getInstance().getPeriode();
-  std::vector<const element *> result;
-  const element *temp_element;
-  for (typename std::vector<std::string>::const_iterator ZRunner = _input.begin(); ZRunner != _input.end(); ++ZRunner) {
-    const T argument = boost::lexical_cast<T>(*ZRunner);
-    temp_element = periode->FindElement(argument);
-    ASSERT(temp_element != NULL, "Invalid element specified in ElementCommandLineQuery");
-    result.push_back(temp_element);
-  }
-  return result;
-}
-
 bool CommandLineDialog::ElementsCommandLineQuery::handle() {
   // TODO: vector of ints and removing first is not correctly implemented yet. How to remove from a vector?
+  periodentafel *periode = World::getInstance().getPeriode();
+  std::vector<int> AllElements;
   if (CommandLineParser::getInstance().vm.count(getTitle())) {
     try {
-      std::vector<std::string> AllArguments;
-      AllArguments = CommandLineParser::getInstance().vm[getTitle()].as< vector<std::string> >();
-      try {
-        temp = getElementsFromInput<int>(AllArguments);
-      } catch(boost::bad_lexical_cast &e) {
-        try {
-        temp = getElementsFromInput<std::string>(AllArguments);
-        } catch(boost::bad_lexical_cast &e) {
-          return false;
-        }
-      }
+      AllElements = CommandLineParser::getInstance().vm[getTitle()].as< vector<int> >();
     } catch(boost::bad_any_cast &e) {
+      AllElements.clear();
       return false;
     }
-    if (temp.empty())
-      return false;
-    else
-      return true;
+    const element *temp_element;
+    for (vector<int>::iterator ZRunner = AllElements.begin(); ZRunner != AllElements.end(); ++ZRunner) {
+      temp_element = periode->FindElement(*ZRunner);
+      ASSERT(temp_element != NULL, "Invalid element specified in ElementCommandLineQuery");
+      temp.push_back(temp_element);
+    }
+    return true;
   }
   return false;

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp

@@ -85 +85 @@
 const Observable::channels_t GLMoleculeObject_molecule::AtomsChannels(getAtomsChannels());
 const Observable::channels_t GLMoleculeObject_molecule::HullChannels(getAllAtomicChangesChannels());
-const Observable::channels_t GLMoleculeObject_molecule::BoundingBoxChannels(1, molecule::BoundingBoxChanged);
+const Observable::channels_t GLMoleculeObject_molecule::BoundingBoxChannels(getAllAtomicChangesChannels());
 const Observable::channels_t GLMoleculeObject_molecule::IndexChannels(1, molecule::IndexChanged);
 const Observable::channels_t GLMoleculeObject_molecule::NameChannels(1, molecule::MoleculeNameChanged);
@@ -403 +403 @@
 }
 
-molecule::BoundingBoxInfo GLMoleculeObject_molecule::initBoundingBox() const
-{
-  molecule::BoundingBoxInfo info;
+GLMoleculeObject_molecule::BoundingBoxInfo GLMoleculeObject_molecule::initBoundingBox() const
+{
+  BoundingBoxInfo info;
   info.position = zeroVec;
   info.radius = 0.;
@@ -411 +411 @@
 }
 
-molecule::BoundingBoxInfo GLMoleculeObject_molecule::updateBoundingBox() const
-{
-  molecule::BoundingBoxInfo info = BoundingBox.get();
+GLMoleculeObject_molecule::BoundingBoxInfo GLMoleculeObject_molecule::updateBoundingBox() const
+{
+  BoundingBoxInfo info = BoundingBox.get();
   const molecule * const _molecule = getMolecule(MolIndex.get());
   if (_molecule != NULL) {
@@ -472 +472 @@
 void GLMoleculeObject_molecule::resetBoundingBox()
 {
-  molecule::BoundingBoxInfo info = BoundingBox.get();
+  BoundingBoxInfo info = BoundingBox.get();
   setPosition(QVector3D(info.position[0], info.position[1], info.position[2]));
   setScale(info.radius + 0.3); // getBoundingSphere() only sees atoms as points, so make the box a bit bigger

src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.hpp

@@ -24 +24 @@
 #include "GLMoleculeObject_bond.hpp"
 
-#include "molecule.hpp"
-
 class atom;
 class bond;
 class GLMoleculeObject_atom;
 class GLWorldScene;
+class molecule;
 
 class GLMoleculeObject_molecule : public GLMoleculeObject, public Observer
@@ -110 +109 @@
   typedef std::set<atomId_t> atoms_t;
 
-  molecule::BoundingBoxInfo initBoundingBox() const;
+  /** Structure for the required information on the bounding box.
+   *
+   */
+  struct BoundingBoxInfo {
+    //!> position of center
+    Vector position;
+    //!> radius of sphere
+    double radius;
+  };
+
+  /** Structure for the required information on the tesselation hull.
+   *
+   */
+  struct TesselationHullInfo {
+  };
+
+  BoundingBoxInfo initBoundingBox() const;
 
   QGeometryData updateTesselationHull() const;
-  molecule::BoundingBoxInfo updateBoundingBox() const;
+  BoundingBoxInfo updateBoundingBox() const;
   atoms_t updateAtoms();
   moleculeId_t updateIndex() const;
@@ -138 +153 @@
   boost::function<std::string ()> MolNameUpdater;
   boost::function<QGeometryData ()> TesselationHullUpdater;
-  boost::function<molecule::BoundingBoxInfo ()> BoundingBoxUpdater;
+  boost::function<BoundingBoxInfo ()> BoundingBoxUpdater;
   boost::function<atoms_t ()> PresentAtomsUpdater;
 
@@ -148 +163 @@
   Cacheable<QGeometryData> TesselationHull;
   //!> contains newest version of the bounding box on request
-  ObservedValue<molecule::BoundingBoxInfo> BoundingBox;
+  ObservedValue<BoundingBoxInfo> BoundingBox;
   //!> contains the current live set of atoms for the molecule
   ObservedValue<atoms_t> PresentAtoms;

src/World.cpp

@@ -396 +396 @@
   if (isAtomSelected(id))
     selectedAtoms.erase(id);
+  atoms.erase(id);
   DeleteAtom(atom);
-  atoms.erase(id);
   atomIdPool.releaseId(id);
   // remove molecule if empty

src/molecule.cpp

@@ -36 +36 @@
 
 #include <algorithm>
-#include <boost/assign.hpp>
 #include <boost/bind.hpp>
 #include <boost/foreach.hpp>
@@ -51 +50 @@
 #include "CodePatterns/enumeration.hpp"
 #include "CodePatterns/Log.hpp"
-#include "CodePatterns/Observer/Observable.hpp"
 #include "CodePatterns/Observer/Notification.hpp"
 #include "config.hpp"
@@ -69 +67 @@
 #include "WorldTime.hpp"
 
-using namespace boost::assign;
-
-// static entities
-static Observable::channels_t getBoundingBoxChannels()
-{
-  Observable::channels_t channels;
-  channels += molecule::AtomInserted, molecule::AtomRemoved, molecule::AtomMoved;
-  return channels;
-}
 
 /************************************* Functions for class molecule *********************************/
@@ -94 +83 @@
   BondCount(this,boost::bind(&molecule::doCountBonds,this),"BondCount"),
   atomIdPool(1, 20, 100),
-  BoundingBoxSweepingAxis(std::vector<AtomDistanceMap_t>(NDIM)),
   _lastchangedatomid(-1),
   last_atom(0)
@@ -104 +92 @@
     OurChannel->addChannel(type);
 
-  // cannot initialize in initializer body as then channels have not been setup yet
-  BoundingBox.reset(
-      new Cacheable<BoundingBoxInfo>(
-          this, boost::bind(&molecule::updateBoundingBox, boost::cref(this)), "molecule_BoundingBox", getBoundingBoxChannels()));
-
   strcpy(name,World::getInstance().getDefaultName().c_str());
-}
+};
 
 molecule *NewMolecule(){
@@ -187 +170 @@
 }
 
-bool molecule::changeAtomId(int oldId, int newId)
-{
-  OBSERVE;
-  if ((!atomIds.contains( oldId )) || (atomIds.contains( newId )))
-    return false;
-  atomIds.erase( oldId );
-  atomIds.insert( newId );
-  // also update BoundingBoxSweepingAxis
-  for (int i=0;i<NDIM;++i) {
-    AtomDistanceMap_t::left_iterator iter = BoundingBoxSweepingAxis[i].left.find(oldId);
-    ASSERT(iter != BoundingBoxSweepingAxis[i].left.end(),
-        "molecule::changeAtomId() - could not find atom "+toString(oldId)
-        +" in BoundingBoxSweepingAxis.");
-    const double component = iter->second;
-    BoundingBoxSweepingAxis[i].left.erase(iter);
-    BoundingBoxSweepingAxis[i].left.insert( std::make_pair(newId, component) );
-  }
-  return true;
-}
-
 bool molecule::changeId(moleculeId_t newId){
   // first we move ourselves in the world
@@ -264 +227 @@
   atomIds.erase( _atom->getId() );
   {
-    BoundingBoxInfo oldinfo = updateBoundingBox();
-    for (int i=0;i<NDIM;++i)
-      BoundingBoxSweepingAxis[i].left.erase( _atom->getId() );
-    BoundingBoxInfo newinfo = updateBoundingBox();
-    if (oldinfo != newinfo)
-      NOTIFY(BoundingBoxChanged);
-  }
-  {
     NOTIFY(AtomNrChanged);
     atomIdPool.releaseId(_atom->getNr());
@@ -285 +240 @@
 molecule::const_iterator molecule::erase( atom * key )
 {
+  OBSERVE;
+  {
+    _lastchangedatomid = key->getId();
+    NOTIFY(AtomRemoved);
+  }
   const_iterator iter = const_cast<const molecule &>(*this).find(key);
-  if (iter != const_cast<const molecule &>(*this).end())
-    return erase(iter);
-  else
-    return iter;
+  if (iter != const_cast<const molecule &>(*this).end()){
+    ++iter;
+    atomIds.erase( key->getId() );
+    {
+      NOTIFY(AtomNrChanged);
+      atomIdPool.releaseId(key->getNr());
+      LocalToGlobalId.erase(key->getNr());
+      key->setNr(-1);
+    }
+    NOTIFY(FormulaChanged);
+    formula-=key->getType();
+    key->removeFromMolecule();
+  }
+  return iter;
 }
 
@@ -299 +269 @@
   std::pair<iterator,bool> res = atomIds.insert(key->getId());
   if (res.second) { // push atom if went well
-    {
-      BoundingBoxInfo oldinfo = updateBoundingBox();
-      for (int i=0;i<NDIM;++i)
-        BoundingBoxSweepingAxis[i].left.insert( std::make_pair(key->getId(), key->getPosition()[i]));
-      BoundingBoxInfo newinfo = updateBoundingBox();
-      if (oldinfo != newinfo)
-        NOTIFY(BoundingBoxChanged);
-    }
     NOTIFY(AtomNrChanged);
     key->setNr(atomIdPool.getNextId());
@@ -1076 +1038 @@
 }
 
-molecule::BoundingBoxInfo molecule::updateBoundingBox() const
-{
-  BoundingBoxInfo info;
-  Vector min = zeroVec;
-  Vector max = zeroVec;
-  for (int i=0;i<NDIM;++i) {
-    if (!BoundingBoxSweepingAxis[i].right.empty()) {
-      min[i] = BoundingBoxSweepingAxis[i].right.begin()->first;
-      max[i] = BoundingBoxSweepingAxis[i].right.rbegin()->first;
-    }
-  }
-  info.radius = (.5*(max-min)).Norm();
-  info.position = .5*(max+min);
-  return info;
-}
-
-molecule::BoundingBoxInfo molecule::getBoundingBox() const
-{
-  return **BoundingBox;
-}
-
 void molecule::update(Observable *publisher)
 {
@@ -1116 +1057 @@
         // emit others about one of our atoms moved
         _lastchangedatomid = _atom->getId();
-        // update entry in map
-        BoundingBoxInfo oldinfo = updateBoundingBox();
-        for (int i=0;i<NDIM;++i) {
-          AtomDistanceMap_t::left_iterator iter = BoundingBoxSweepingAxis[i].left.find(_atom->getId());
-          ASSERT(iter != BoundingBoxSweepingAxis[i].left.end(),
-              "molecule::recieveNotification() - could not find atom "+toString(_atom->getId())
-              +" in BoundingBoxSweepingAxis.");
-          BoundingBoxSweepingAxis[i].left.erase(iter);
-          BoundingBoxSweepingAxis[i].left.insert(
-              std::make_pair(_atom->getId(), _atom->getPosition()[i]) );
-        }
-        BoundingBoxInfo newinfo = updateBoundingBox();
         OBSERVE;
         NOTIFY(AtomMoved);
-        if (oldinfo != newinfo)
-          NOTIFY(BoundingBoxChanged);
         break;
       }

src/molecule.hpp

@@ -22 +22 @@
 
 #include <string>
-
-#include <boost/bimap/bimap.hpp>
-#include <boost/bimap/unordered_set_of.hpp>
-#include <boost/bimap/multiset_of.hpp>
-#include <boost/optional.hpp>
-#include <boost/shared_ptr.hpp>
 
 #include "AtomIdSet.hpp"
@@ -121 +115 @@
     MoleculeNameChanged,
     IndexChanged,
-    BoundingBoxChanged,
     AboutToBeRemoved,
     NotificationType_MAX
@@ -245 +238 @@
   bool changeAtomNr(int oldNr, int newNr, atom* target=0);
 
-  friend bool atom::changeId(atomId_t newId);
-  /**
-   * used when changing an ParticleInfo::Id.
-   * Note that this number is global (and the molecule uses it to know which atoms belong to it)
-   *
-   * @param oldId old Id
-   * @param newId new Id to set
-   * @return indicates wether the change could be done or not.
-   */
-  bool changeAtomId(int oldId, int newId);
-
   /** Updates the internal lookup fro local to global indices.
    *
@@ -278 +260 @@
 
 public:
-
-  /** Structure for the required information on the bounding box.
-   *
-   */
-  struct BoundingBoxInfo {
-    //!> position of center
-    Vector position;
-    //!> radius of sphere
-    double radius;
-
-    /** Equivalence operator for bounding box.
-     *
-     * \return true - both bounding boxes have same position and radius
-     */
-    bool operator==(const BoundingBoxInfo &_other) const
-    {  return (radius == _other.radius) && (position == _other.position); }
-
-    /** Inequivalence operator for bounding box.
-     *
-     * \return true - bounding boxes have either different positions or different radii or both
-     */
-    bool operator!=(const BoundingBoxInfo &_other) const
-    { return !(*this == _other); }
-  };
-
-private:
-
-  /** Returns the current bounding box.
-   *
-   * \return Shape with center and extension of box
-   */
-  BoundingBoxInfo updateBoundingBox() const;
-
-  // stuff for keeping bounding box up-to-date efficiently
-
-  //!> Cacheable for the bounding box, ptr such that
-  boost::shared_ptr< Cacheable<BoundingBoxInfo> > BoundingBox;
-  /** Bimap storing atomic ids and the component per axis.
-   *
-   * We need a bimap in order to have the components sorted and be able to
-   * access max and min values in linear time and also access the ids in
-   * constant time in order to update the map, when atoms move, are inserted,
-   * or removed.
-   */
-  typedef boost::bimaps::bimap<
-          boost::bimaps::unordered_set_of< atomId_t >,
-          boost::bimaps::multiset_of< double, std::greater<double> >
-      > AtomDistanceMap_t;
-  std::vector<AtomDistanceMap_t> BoundingBoxSweepingAxis;
-
-public:
-
-  /** Returns the current bounding box of this molecule.
-   *
-   * \return bounding box info with center and radius
-   */
-  BoundingBoxInfo getBoundingBox() const;
 
   /** Function to create a bounding spherical shape for the currently associated atoms.

tests/regression/Atoms/Add/post/test.in

@@ -1 +1 @@
 % Created by MoleCuilder
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Atoms/Add/post/test.pdb

@@ -1 +1 @@
 REMARK created by molecuilder on Wed Feb  2 18:06:07 2011
-ATOM      1 H01 0non 01         10.000  10.000  10.000  0.00  0.00           H 0
+ATOM      1 H01 0-   00         10.000  10.000  10.000  0.00  0.00           H 0
 END

tests/regression/Atoms/Remove/post/test.in

@@ -1 +1 @@
 % Created by MoleCuilder
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Atoms/Saturate/post/saturated_carbon.xyz

@@ -1 +1 @@
 5
-        Created by molecuilder on Wed Sep 30 19:50:39 2015, time step 0
+        Created by molecuilder on Wed Jan 28 20:57:11 2015, time step 0
 C       10      10      10
-H       11.0923 10      10
-H       9.63589 11.0299 10
-H       9.63589 9.48507 10.8919
-H       9.63589 9.48507 9.10811
+H       11.076  10      10
+H       9.64133 11.0145 10
+H       9.64133 9.49277 10.8786
+H       9.64133 9.49277 9.12145

tests/regression/Atoms/Saturate/post/saturated_nitrogen.xyz

@@ -1 +1 @@
 4
-        Created by molecuilder on Wed Sep 30 19:50:40 2015, time step 0
+        Created by molecuilder on Wed Jan 28 21:41:39 2015, time step 0
 N       10      10      10
-H       11.0015 10      10
-H       9.49923 10.866  10
-H       9.49923 9.13397 10
+H       11.02   10      10
+H       9.49    10.866  10
+H       9.49    9.13397 10

tests/regression/Parser/Mpqc/post/doublewater.in

@@ -1 +1 @@
 % Created by MoleCuilder
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/post/empty.in

@@ -1 +1 @@
 % Created by MoleCuilder
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/post/test.in

@@ -1 +1 @@
 % Created by MoleCuilder
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/post/testCLHF.in

@@ -1 +1 @@
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/post/testCLKS.in

@@ -1 +1 @@
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/post/testMBPT2.in

@@ -1 +1 @@
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/post/testMBPT2_R12.in

@@ -1 +1 @@
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testCLHF.in

@@ -1 +1 @@
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testCLHF_n.in

@@ -1 +1 @@
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testCLHF_n_ascend_ids.in

@@ -1 +1 @@
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testCLHF_n_mixed_ids.in

@@ -1 +1 @@
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testCLKS.in

@@ -1 +1 @@
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testMBPT2.in

@@ -1 +1 @@
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/testMBPT2_R12.in

@@ -1 +1 @@
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/Mpqc/pre/water.in

@@ -1 +1 @@
 % Created by MoleCuilder
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/SetParameters/Mpqc/post/testCLHF.in

@@ -1 +1 @@
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes

tests/regression/Parser/SetParameters/Mpqc/pre/testCLHF.in

@@ -1 +1 @@
 mpqc: (
-        checkpoint = no
         savestate = no
         do_gradient = yes