Changes in / [dace6c:e38750]

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
-  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));
+  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));
 }
 
@@ -73 +107 @@
   AtomAddState *state = assert_cast<AtomAddState*>(_state.get());
 
-  LOG(1, "Removing atom with id " << state->id << ".");
-  World::getInstance().destroyAtom(state->id);
+  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);
+  }
 
   return ActionState::ptr(_state);
@@ -82 +119 @@
   AtomAddState *state = assert_cast<AtomAddState*>(_state.get());
 
-  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);
+  std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
+  std::vector<atomId_t> newids = createAtoms(params, molecules);
+
+  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;
   }
-  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;
-    }
 
-  return ActionState::ptr(_state);
+  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);
 }
 

src/Actions/AtomAction/AddAction.def

@@ -27 +27 @@
 (BoxVectorValidator())
 
-#define statetypes (const atomId_t)
-#define statereferences (id)
+#define statetypes (std::vector<atomId_t>)
+#define statereferences (ids)
 
 // 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(1);
+    double typical_distance = _atom->getType()->getHBondDistance(0);
     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 wrap ignore'")
+#define paramdescriptions ("new boundary conditions as list of three strings, e.g. 'Wrap Bounce 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] = 0.;
-  for (size_t i =0; i<3;++i)
-    HBondAngle[i] = 0.;
+    HBondDistance[i] = -1.;
+  for (size_t i =0; i<3;++i)
+    HBondAngle[i] = -1.;
 };
 

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       0.74    -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\
+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\
 ";
 
@@ -280 +303 @@
 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( 0., testelement->getHBondDistance(i) );
+    CPPUNIT_ASSERT_EQUAL( -1., testelement->getHBondDistance(i) );
   for (size_t i = 0; i < 3; ++i)
-    CPPUNIT_ASSERT_EQUAL( 0., testelement->getHBondAngle(i) );
+    CPPUNIT_ASSERT_EQUAL( -1., 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");
+      "SaturatedBond::SaturatedBond() - negative bond distance for "
+      +saturated_atom.getElement().getName());
   const double HydrogenAngle =
       saturated_atom.getElement().getHBondAngle(saturated_bond.getDegree()-1);
   ASSERT( HydrogenAngle >= 0.,
-      "SaturatedBond::SaturatedBond() - negative bond angle");
+      "SaturatedBond::SaturatedBond() - negative bond angle for "
+      +saturated_atom.getElement().getName());
   LOG(5, "DEBUG: Hydrogen distance is " << HydrogenDistance
       << ", angle is " << HydrogenAngle);

src/Graph/BondGraph.hpp

@@ -221 +221 @@
               neighboriter != ListOfNeighbors.end();
               ++neighboriter) {
-            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");
+            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
               LOG(4, "INFO: Current other atom is " << *OtherWalker << ".");
 
@@ -245 +245 @@
               }
             } else {
-              LOG(5, "REJECT: Not Adding: Wrong order.");
+              LOG(4, "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"
 
@@ -45 +47 @@
 static const element * FindElementByString(const std::string &_value)
 {
-  static ConvertTo<atomicNumber_t> converter;
-  const element * _element =
-      World::getInstance().getPeriode()->FindElement(converter(_value));
-  return _element;
+  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;
 }
 

src/Parameters/Specifics/Value_elements.cpp

@@ -57 +57 @@
   for(tokenizer::iterator beg=tok.begin();
       beg != tok.end();++beg) {
-    const int tempvalue = boost::lexical_cast<atomicNumber_t>(*beg);
-    const element * _element =
-        World::getInstance().getPeriode()->FindElement(tempvalue);
-    ASSERT( _element != NULL,
+    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,
         "FindElementsByString() - cannnot find element "
-        +toString(tempvalue)+" in periodentafel.");
-    elements.push_back(_element);
+        +toString(*beg)+" in periodentafel.");
+    elements.push_back(elem);
   }
   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;
@@ -374 +375 @@
       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 +88 @@
   //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
   {
@@ -177 +191 @@
 }
 
+/** 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
 
@@ -69 +70 @@
     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
   };
 
@@ -93 +103 @@
   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;
 
@@ -99 +110 @@
   //!> 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\
@@ -86 +87 @@
 static string waterMpqc_CLKS ="% Created by MoleCuilder\n\
 mpqc: (\n\
+\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\
@@ -110 +112 @@
 static string waterMpqc_MBPT2 ="% Created by MoleCuilder\n\
 mpqc: (\n\
+\tcheckpoint = no\n\
 \tsavestate = no\n\
 \tdo_gradient = yes\n\
@@ -138 +141 @@
 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 < int >(),
+                  po::value < std::string >(),
                   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<int> >()->multitoken(),
+                  po::value < std::vector<std::string> >()->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"
@@ -54 +56 @@
   // 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 {
-      Z = CommandLineParser::getInstance().vm[getTitle()].as< int >();
+      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);
+      }
     } 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"
@@ -51 +53 @@
 {}
 
+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 {
-      AllElements = CommandLineParser::getInstance().vm[getTitle()].as< vector<int> >();
+      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;
+        }
+      }
     } catch(boost::bad_any_cast &e) {
-      AllElements.clear();
       return false;
     }
-    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;
+    if (temp.empty())
+      return false;
+    else
+      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(getAllAtomicChangesChannels());
+const Observable::channels_t GLMoleculeObject_molecule::BoundingBoxChannels(1, molecule::BoundingBoxChanged);
 const Observable::channels_t GLMoleculeObject_molecule::IndexChannels(1, molecule::IndexChanged);
 const Observable::channels_t GLMoleculeObject_molecule::NameChannels(1, molecule::MoleculeNameChanged);
@@ -403 +403 @@
 }
 
-GLMoleculeObject_molecule::BoundingBoxInfo GLMoleculeObject_molecule::initBoundingBox() const
-{
-  BoundingBoxInfo info;
+molecule::BoundingBoxInfo GLMoleculeObject_molecule::initBoundingBox() const
+{
+  molecule::BoundingBoxInfo info;
   info.position = zeroVec;
   info.radius = 0.;
@@ -411 +411 @@
 }
 
-GLMoleculeObject_molecule::BoundingBoxInfo GLMoleculeObject_molecule::updateBoundingBox() const
-{
-  BoundingBoxInfo info = BoundingBox.get();
+molecule::BoundingBoxInfo GLMoleculeObject_molecule::updateBoundingBox() const
+{
+  molecule::BoundingBoxInfo info = BoundingBox.get();
   const molecule * const _molecule = getMolecule(MolIndex.get());
   if (_molecule != NULL) {
@@ -472 +472 @@
 void GLMoleculeObject_molecule::resetBoundingBox()
 {
-  BoundingBoxInfo info = BoundingBox.get();
+  molecule::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
@@ -109 +110 @@
   typedef std::set<atomId_t> atoms_t;
 
-  /** 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;
+  molecule::BoundingBoxInfo initBoundingBox() const;
 
   QGeometryData updateTesselationHull() const;
-  BoundingBoxInfo updateBoundingBox() const;
+  molecule::BoundingBoxInfo updateBoundingBox() const;
   atoms_t updateAtoms();
   moleculeId_t updateIndex() const;
@@ -153 +138 @@
   boost::function<std::string ()> MolNameUpdater;
   boost::function<QGeometryData ()> TesselationHullUpdater;
-  boost::function<BoundingBoxInfo ()> BoundingBoxUpdater;
+  boost::function<molecule::BoundingBoxInfo ()> BoundingBoxUpdater;
   boost::function<atoms_t ()> PresentAtomsUpdater;
 
@@ -163 +148 @@
   Cacheable<QGeometryData> TesselationHull;
   //!> contains newest version of the bounding box on request
-  ObservedValue<BoundingBoxInfo> BoundingBox;
+  ObservedValue<molecule::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);
+  DeleteAtom(atom);
   atoms.erase(id);
-  DeleteAtom(atom);
   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>
@@ -50 +51 @@
 #include "CodePatterns/enumeration.hpp"
 #include "CodePatterns/Log.hpp"
+#include "CodePatterns/Observer/Observable.hpp"
 #include "CodePatterns/Observer/Notification.hpp"
 #include "config.hpp"
@@ -67 +69 @@
 #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 *********************************/
@@ -83 +94 @@
   BondCount(this,boost::bind(&molecule::doCountBonds,this),"BondCount"),
   atomIdPool(1, 20, 100),
+  BoundingBoxSweepingAxis(std::vector<AtomDistanceMap_t>(NDIM)),
   _lastchangedatomid(-1),
   last_atom(0)
@@ -92 +104 @@
     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(){
@@ -170 +187 @@
 }
 
+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
@@ -227 +264 @@
   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());
@@ -240 +285 @@
 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()){
-    ++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;
+  if (iter != const_cast<const molecule &>(*this).end())
+    return erase(iter);
+  else
+    return iter;
 }
 
@@ -269 +299 @@
   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());
@@ -1038 +1076 @@
 }
 
+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)
 {
@@ -1057 +1116 @@
         // 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"
@@ -115 +121 @@
     MoleculeNameChanged,
     IndexChanged,
+    BoundingBoxChanged,
     AboutToBeRemoved,
     NotificationType_MAX
@@ -238 +245 @@
   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.
    *
@@ -260 +278 @@
 
 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 0-   00         10.000  10.000  10.000  0.00  0.00           H 0
+ATOM      1 H01 0non 01         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 Jan 28 20:57:11 2015, time step 0
+        Created by molecuilder on Wed Sep 30 19:50:39 2015, time step 0
 C       10      10      10
-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
+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

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

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