source: src/World.cpp@ c48641

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
 */

/*
 * World.cpp
 *
 *  Created on: Feb 3, 2010
 *      Author: crueger
 */

// include config.h
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include "CodePatterns/MemDebug.hpp"

#include "World.hpp"

#include <functional>

#include "Actions/ActionTrait.hpp"
#include "Actions/ManipulateAtomsProcess.hpp"
#include "Atom/atom.hpp"
#include "Atom/AtomObserver.hpp"
#include "Box.hpp"
#include "CodePatterns/Assert.hpp"
#include "config.hpp"
#include "Descriptors/AtomDescriptor.hpp"
#include "Descriptors/AtomDescriptor_impl.hpp"
#include "Descriptors/AtomSelectionDescriptor.hpp"
#include "Descriptors/MoleculeDescriptor.hpp"
#include "Descriptors/MoleculeDescriptor_impl.hpp"
#include "Descriptors/MoleculeSelectionDescriptor.hpp"
#include "Descriptors/SelectiveIterator_impl.hpp"
#include "Element/periodentafel.hpp"
#include "Graph/BondGraph.hpp"
#include "Graph/DepthFirstSearchAnalysis.hpp"
#include "Helpers/defs.hpp"
#include "LinearAlgebra/RealSpaceMatrix.hpp"
#include "LinkedCell/LinkedCell_Controller.hpp"
#include "LinkedCell/PointCloudAdaptor.hpp"
#include "molecule.hpp"
#include "MoleculeListClass.hpp"
#include "Thermostats/ThermoStatContainer.hpp"
#include "WorldTime.hpp"

#include "IdPool_impl.hpp"

#include "CodePatterns/IteratorAdaptors.hpp"
#include "CodePatterns/Singleton_impl.hpp"
#include "CodePatterns/Observer/Channels.hpp"
#include "CodePatterns/Observer/ObservedContainer_impl.hpp"

using namespace MoleCuilder;

/******************************* Notifications ************************/


atom* World::_lastchangedatom = NULL;
molecule* World::_lastchangedmol = NULL;

/******************************* getter and setter ************************/
periodentafel *&World::getPeriode()
{
  return periode;
}

BondGraph *&World::getBondGraph()
{
  return BG;
}

void World::setBondGraph(BondGraph *_BG){
  delete (BG);
  BG = _BG;
}

config *&World::getConfig(){
  return configuration;
}

// Atoms

atom* World::getAtom(AtomDescriptor descriptor){
  return descriptor.find();
}

World::AtomComposite World::getAllAtoms(AtomDescriptor descriptor){
  return descriptor.findAll();
}

World::AtomComposite World::getAllAtoms(){
  return getAllAtoms(AllAtoms());
}

int World::numAtoms(){
  return atoms.size();
}

// Molecules

molecule *World::getMolecule(MoleculeDescriptor descriptor){
  return descriptor.find();
}

std::vector<molecule*> World::getAllMolecules(MoleculeDescriptor descriptor){
  return descriptor.findAll();
}

std::vector<molecule*> World::getAllMolecules(){
  return getAllMolecules(AllMolecules());
}

int World::numMolecules(){
  return molecules_deprecated->ListOfMolecules.size();
}

// system

Box& World::getDomain() {
  return *cell_size;
}

void World::setDomain(const RealSpaceMatrix &mat){
  OBSERVE;
  *cell_size = mat;
}

void World::setDomain(double * matrix)
{
  OBSERVE;
  RealSpaceMatrix M = ReturnFullMatrixforSymmetric(matrix);
  cell_size->setM(M);
}

LinkedCell::LinkedCell_View World::getLinkedCell(const double distance)
{
  // we have to grope past the ObservedContainer mechanism and transmorph the map
  // into a traversable list for the adaptor
  PointCloudAdaptor< AtomSet::set_t, MapValueIterator<AtomSet::set_t::iterator> > atomset(
      &(atoms.getContent()),
      std::string("WorldsAtoms"));
  return LCcontroller->getView(distance, atomset);
}

void World::setTime(const unsigned int _step)
{
  if (_step != WorldTime::getTime()) {
    // set new time
    WorldTime::getInstance().setTime(_step);
    // TODO: removed when BondGraph creates the adjacency
    // 1. remove all of World's molecules
    for (MoleculeIterator iter = getMoleculeIter();
        getMoleculeIter() != moleculeEnd();
        iter = getMoleculeIter()) {
      getMolecules()->erase(*iter);
      destroyMolecule(*iter);
    }
    // 2. (re-)create bondgraph
    AtomComposite Set = getAllAtoms();
    BG->CreateAdjacency(Set);

    // 3. scan for connected subgraphs => molecules
    DepthFirstSearchAnalysis DFS;
    DFS();
    DFS.UpdateMoleculeStructure();
  }
}

std::string World::getDefaultName() {
  return defaultName;
}

void World::setDefaultName(std::string name)
{
  OBSERVE;
  defaultName = name;
};

class ThermoStatContainer * World::getThermostats()
{
  return Thermostats;
}


int World::getExitFlag() {
  return ExitFlag;
}

void World::setExitFlag(int flag) {
  if (ExitFlag < flag)
    ExitFlag = flag;
}

/******************** Methods to change World state *********************/

molecule* World::createMolecule(){
  OBSERVE;
  molecule *mol = NULL;
  mol = NewMolecule();
  moleculeId_t id = moleculeIdPool.getNextId();
  ASSERT(!molecules.count(id),"proposed id did not specify an unused ID");
  mol->setId(id);
  // store the molecule by ID
  molecules[mol->getId()] = mol;
  mol->signOn(this);
  _lastchangedmol = mol;
  NOTIFY(MoleculeInserted);
  return mol;
}

void World::destroyMolecule(molecule* mol){
  OBSERVE;
  ASSERT(mol,"Molecule that was meant to be destroyed did not exist");
  destroyMolecule(mol->getId());
}

void World::destroyMolecule(moleculeId_t id){
  molecule *mol = molecules[id];
  ASSERT(mol,"Molecule id that was meant to be destroyed did not exist");
  // give notice about immediate removal
  {
    OBSERVE;
    _lastchangedmol = mol;
    NOTIFY(MoleculeRemoved);
  }
  DeleteMolecule(mol);
  if (isMoleculeSelected(id))
    selectedMolecules.erase(id);
  molecules.erase(id);
  moleculeIdPool.releaseId(id);
}

atom *World::createAtom(){
  OBSERVE;
  atomId_t id = atomIdPool.getNextId();
  ASSERT(!atoms.count(id),"proposed id did not specify an unused ID");
  atom *res = NewAtom(id);
  res->setWorld(this);
  // sign on to global atom change tracker
  AtomObserver::getInstance().AtomInserted(res);
  // store the atom by ID
  atoms[res->getId()] = res;
  _lastchangedatom = res;
  NOTIFY(AtomInserted);
  return res;
}


int World::registerAtom(atom *atom){
  OBSERVE;
  atomId_t id = atomIdPool.getNextId();
  atom->setId(id);
  atom->setWorld(this);
  atoms[atom->getId()] = atom;
  return atom->getId();
}

void World::destroyAtom(atom* atom){
  int id = atom->getId();
  destroyAtom(id);
}

void World::destroyAtom(atomId_t id) {
  atom *atom = atoms[id];
  ASSERT(atom,"Atom ID that was meant to be destroyed did not exist");
  // give notice about immediate removal
  {
    OBSERVE;
    _lastchangedatom = atom;
    NOTIFY(AtomRemoved);
  }
  DeleteAtom(atom);
  if (isAtomSelected(id))
    selectedAtoms.erase(id);
  atoms.erase(id);
  atomIdPool.releaseId(id);
}

bool World::changeAtomId(atomId_t oldId, atomId_t newId, atom* target){
  OBSERVE;
  // in case this call did not originate from inside the atom, we redirect it,
  // to also let it know that it has changed
  if(!target){
    target = atoms[oldId];
    ASSERT(target,"Atom with that ID not found");
    return target->changeId(newId);
  }
  else{
    if(atomIdPool.reserveId(newId)){
      atoms.erase(oldId);
      atoms.insert(pair<atomId_t,atom*>(newId,target));
      return true;
    }
    else{
      return false;
    }
  }
}

bool World::changeMoleculeId(moleculeId_t oldId, moleculeId_t newId, molecule* target){
  OBSERVE;
  // in case this call did not originate from inside the atom, we redirect it,
  // to also let it know that it has changed
  if(!target){
    target = molecules[oldId];
    ASSERT(target,"Molecule with that ID not found");
    return target->changeId(newId);
  }
  else{
    if(moleculeIdPool.reserveId(newId)){
      molecules.erase(oldId);
      molecules.insert(pair<moleculeId_t,molecule*>(newId,target));
      return true;
    }
    else{
      return false;
    }
  }
}

ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name,AtomDescriptor descr){
  ActionTrait manipulateTrait(name);
  return new ManipulateAtomsProcess(op, descr,manipulateTrait,false);
}

ManipulateAtomsProcess* World::manipulateAtoms(boost::function<void(atom*)> op,std::string name){
  return manipulateAtoms(op,name,AllAtoms());
}

/********************* Internal Change methods for double Callback and Observer mechanism ********/

void World::doManipulate(ManipulateAtomsProcess *proc){
  proc->signOn(this);
  {
    OBSERVE;
    proc->doManipulate(this);
  }
  proc->signOff(this);
}
/******************************* Iterators ********************************/

// external parts with observers

CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet,AtomDescriptor);

World::AtomIterator
World::getAtomIter(AtomDescriptor descr){
    return AtomIterator(descr,atoms);
}

World::AtomIterator
World::getAtomIter(){
    return AtomIterator(AllAtoms(),atoms);
}

World::AtomIterator
World::atomEnd(){
  return AtomIterator(AllAtoms(),atoms,atoms.end());
}

CONSTRUCT_SELECTIVE_ITERATOR(molecule*,World::MoleculeSet,MoleculeDescriptor);

World::MoleculeIterator
World::getMoleculeIter(MoleculeDescriptor descr){
    return MoleculeIterator(descr,molecules);
}

World::MoleculeIterator
World::getMoleculeIter(){
    return MoleculeIterator(AllMolecules(),molecules);
}

World::MoleculeIterator
World::moleculeEnd(){
  return MoleculeIterator(AllMolecules(),molecules,molecules.end());
}

// Internal parts, without observers

// Build the AtomIterator from template
CONSTRUCT_SELECTIVE_ITERATOR(atom*,World::AtomSet::set_t,AtomDescriptor);


World::internal_AtomIterator
World::getAtomIter_internal(AtomDescriptor descr){
  return internal_AtomIterator(descr,atoms.getContent());
}

World::internal_AtomIterator
World::atomEnd_internal(){
  return internal_AtomIterator(AllAtoms(),atoms.getContent(),atoms.end_internal());
}

// build the MoleculeIterator from template
CONSTRUCT_SELECTIVE_ITERATOR(molecule*,World::MoleculeSet::set_t,MoleculeDescriptor);

World::internal_MoleculeIterator World::getMoleculeIter_internal(MoleculeDescriptor descr){
  return internal_MoleculeIterator(descr,molecules.getContent());
}

World::internal_MoleculeIterator World::moleculeEnd_internal(){
  return internal_MoleculeIterator(AllMolecules(),molecules.getContent(),molecules.end_internal());
}

/************************** Selection of Atoms and molecules ******************/

// Atoms

void World::clearAtomSelection(){
  selectedAtoms.clear();
}

void World::invertAtomSelection(){
  // get all atoms not selected
  AtomComposite invertedSelection(getAllAtoms());
  bool (World::*predicate)(const atom*) const = &World::isSelected; // needed for type resolution of overloaded function
  AtomComposite::iterator iter =
      std::remove_if(invertedSelection.begin(), invertedSelection.end(),
          std::bind1st(std::mem_fun(predicate), this));
  invertedSelection.erase(iter, invertedSelection.end());
  // apply new selection
  selectedAtoms.clear();
  void (World::*selector)(const atom*) = &World::selectAtom; // needed for type resolution of overloaded function
  std::for_each(invertedSelection.begin(),invertedSelection.end(),
      std::bind1st(std::mem_fun(selector),this)); // func is select... see above
}

void World::selectAtom(const atom *_atom){
  // atom * is unchanged in this function, but we do store entity as changeable
  ASSERT(_atom,"Invalid pointer in selection of atom");
  selectedAtoms[_atom->getId()]=const_cast<atom *>(_atom);
}

void World::selectAtom(const atomId_t id){
  ASSERT(atoms.count(id),"Atom Id selected that was not in the world");
  selectedAtoms[id]=atoms[id];
}

void World::selectAllAtoms(AtomDescriptor descr){
  internal_AtomIterator begin = getAtomIter_internal(descr);
  internal_AtomIterator end = atomEnd_internal();
  void (World::*func)(const atom*) = &World::selectAtom; // needed for type resolution of overloaded function
  for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
}

void World::selectAtomsOfMolecule(const molecule *_mol){
  ASSERT(_mol,"Invalid pointer to molecule in selection of Atoms of Molecule");
  // need to make it const to get the fast iterators
  const molecule *mol = _mol;
  void (World::*func)(const atom*) = &World::selectAtom; // needed for type resolution of overloaded function
  for_each(mol->begin(),mol->end(),bind1st(mem_fun(func),this)); // func is select... see above
}

void World::selectAtomsOfMolecule(const moleculeId_t id){
  ASSERT(molecules.count(id),"No molecule with the given id upon Selection of atoms from molecule");
  selectAtomsOfMolecule(molecules[id]);
}

void World::unselectAtom(const atom *_atom){
  ASSERT(_atom,"Invalid pointer in unselection of atom");
  unselectAtom(_atom->getId());
}

void World::unselectAtom(const atomId_t id){
  ASSERT(atoms.count(id),"Atom Id unselected that was not in the world");
  selectedAtoms.erase(id);
}

void World::unselectAllAtoms(AtomDescriptor descr){
  internal_AtomIterator begin = getAtomIter_internal(descr);
  internal_AtomIterator end = atomEnd_internal();
  void (World::*func)(const atom*) = &World::unselectAtom; // needed for type resolution of overloaded function
  for_each(begin,end,bind1st(mem_fun(func),this)); // func is unselect... see above
}

void World::unselectAtomsOfMolecule(const molecule *_mol){
  ASSERT(_mol,"Invalid pointer to molecule in selection of Atoms of Molecule");
  // need to make it const to get the fast iterators
  const molecule *mol = _mol;
  void (World::*func)(const atom*) = &World::unselectAtom; // needed for type resolution of overloaded function
  for_each(mol->begin(),mol->end(),bind1st(mem_fun(func),this)); // func is unsselect... see above
}

void World::unselectAtomsOfMolecule(const moleculeId_t id){
  ASSERT(molecules.count(id),"No molecule with the given id upon Selection of atoms from molecule");
  unselectAtomsOfMolecule(molecules[id]);
}

size_t World::countSelectedAtoms() const {
  size_t count = 0;
  for (AtomSet::const_iterator iter = selectedAtoms.begin(); iter != selectedAtoms.end(); ++iter)
    count++;
  return count;
}

bool World::isSelected(const atom *_atom) const {
  return isAtomSelected(_atom->getId());
}

bool World::isAtomSelected(const atomId_t no) const {
  return selectedAtoms.find(no) != selectedAtoms.end();
}

const std::vector<atom *> World::getSelectedAtoms() const {
  std::vector<atom *> returnAtoms;
  returnAtoms.resize(countSelectedAtoms());
  int count = 0;
  for (AtomSet::const_iterator iter = selectedAtoms.begin(); iter != selectedAtoms.end(); ++iter)
    returnAtoms[count++] = iter->second;
  return returnAtoms;
}


// Molecules

void World::clearMoleculeSelection(){
  selectedMolecules.clear();
}

void World::invertMoleculeSelection(){
  // get all molecules not selected
  typedef std::vector<molecule *> MoleculeVector_t;
  MoleculeVector_t invertedSelection(getAllMolecules());
  bool (World::*predicate)(const molecule*) const = &World::isSelected; // needed for type resolution of overloaded function
  MoleculeVector_t::iterator iter =
      std::remove_if(invertedSelection.begin(), invertedSelection.end(),
          std::bind1st(std::mem_fun(predicate), this));
  invertedSelection.erase(iter, invertedSelection.end());
  // apply new selection
  selectedMolecules.clear();
  void (World::*selector)(const molecule*) = &World::selectMolecule; // needed for type resolution of overloaded function
  std::for_each(invertedSelection.begin(),invertedSelection.end(),
      std::bind1st(std::mem_fun(selector),this)); // func is select... see above
}

void World::selectMolecule(const molecule *_mol){
  // molecule * is unchanged in this function, but we do store entity as changeable
  ASSERT(_mol,"Invalid pointer to molecule in selection");
  selectedMolecules[_mol->getId()]=const_cast<molecule *>(_mol);
}

void World::selectMolecule(const moleculeId_t id){
  ASSERT(molecules.count(id),"Molecule Id selected that was not in the world");
  selectedMolecules[id]=molecules[id];
}

void World::selectAllMolecules(MoleculeDescriptor descr){
  internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
  internal_MoleculeIterator end = moleculeEnd_internal();
  void (World::*func)(const molecule*) = &World::selectMolecule; // needed for type resolution of overloaded function
  for_each(begin,end,bind1st(mem_fun(func),this)); // func is select... see above
}

void World::selectMoleculeOfAtom(const atom *_atom){
  ASSERT(_atom,"Invalid atom pointer in selection of MoleculeOfAtom");
  molecule *mol=_atom->getMolecule();
  // the atom might not be part of a molecule
  if(mol){
    selectMolecule(mol);
  }
}

void World::selectMoleculeOfAtom(const atomId_t id){
  ASSERT(atoms.count(id),"No such atom with given ID in selection of Molecules of Atom");\
  selectMoleculeOfAtom(atoms[id]);
}

void World::unselectMolecule(const molecule *_mol){
  ASSERT(_mol,"invalid pointer in unselection of molecule");
  unselectMolecule(_mol->getId());
}

void World::unselectMolecule(const moleculeId_t id){
  ASSERT(molecules.count(id),"No such molecule with ID in unselection");
  selectedMolecules.erase(id);
}

void World::unselectAllMolecules(MoleculeDescriptor descr){
  internal_MoleculeIterator begin = getMoleculeIter_internal(descr);
  internal_MoleculeIterator end = moleculeEnd_internal();
  void (World::*func)(const molecule*) = &World::unselectMolecule; // needed for type resolution of overloaded function
  for_each(begin,end,bind1st(mem_fun(func),this)); // func is unselect... see above
}

void World::unselectMoleculeOfAtom(const atom *_atom){
  ASSERT(_atom,"Invalid atom pointer in selection of MoleculeOfAtom");
  molecule *mol=_atom->getMolecule();
  // the atom might not be part of a molecule
  if(mol){
    unselectMolecule(mol);
  }
}

void World::unselectMoleculeOfAtom(const atomId_t id){
  ASSERT(atoms.count(id),"No such atom with given ID in selection of Molecules of Atom");\
  unselectMoleculeOfAtom(atoms[id]);
}

size_t World::countSelectedMolecules() const {
  size_t count = 0;
  for (MoleculeSet::const_iterator iter = selectedMolecules.begin(); iter != selectedMolecules.end(); ++iter)
    count++;
  return count;
}

bool World::isSelected(const molecule *_mol) const {
  return isMoleculeSelected(_mol->getId());
}

bool World::isMoleculeSelected(const moleculeId_t no) const {
  return selectedMolecules.find(no) != selectedMolecules.end();
}

const std::vector<molecule *> World::getSelectedMolecules() const {
  std::vector<molecule *> returnMolecules;
  returnMolecules.resize(countSelectedMolecules());
  int count = 0;
  for (MoleculeSet::const_iterator iter = selectedMolecules.begin(); iter != selectedMolecules.end(); ++iter)
    returnMolecules[count++] = iter->second;
  return returnMolecules;
}

/******************* Iterators over Selection *****************************/
World::AtomSelectionIterator World::beginAtomSelection(){
  return selectedAtoms.begin();
}

World::AtomSelectionIterator World::endAtomSelection(){
  return selectedAtoms.end();
}

World::AtomSelectionConstIterator World::beginAtomSelection() const{
  return selectedAtoms.begin();
}

World::AtomSelectionConstIterator World::endAtomSelection() const{
  return selectedAtoms.end();
}


World::MoleculeSelectionIterator World::beginMoleculeSelection(){
  return selectedMolecules.begin();
}

World::MoleculeSelectionIterator World::endMoleculeSelection(){
  return selectedMolecules.end();
}

World::MoleculeSelectionConstIterator World::beginMoleculeSelection() const{
  return selectedMolecules.begin();
}

World::MoleculeSelectionConstIterator World::endMoleculeSelection() const{
  return selectedMolecules.end();
}

/******************************* Singleton Stuff **************************/

World::World() :
    Observable("World"),
    BG(new BondGraph(true)),  // assume Angstroem for the moment
    periode(new periodentafel(true)),
    configuration(new config),
    Thermostats(new ThermoStatContainer),
    ExitFlag(0),
    atoms(this),
    selectedAtoms(this),
    atomIdPool(0, 20, 100),
    molecules(this),
    selectedMolecules(this),
    moleculeIdPool(0, 20,100),
    molecules_deprecated(new MoleculeListClass(this))
{
  cell_size = new Box;
  RealSpaceMatrix domain;
  domain.at(0,0) = 20;
  domain.at(1,1) = 20;
  domain.at(2,2) = 20;
  cell_size->setM(domain);
  LCcontroller = new LinkedCell::LinkedCell_Controller(*cell_size);
  defaultName = "none";
  Channels *OurChannel = new Channels;
  NotificationChannels.insert( std::make_pair( this, OurChannel) );
  for (size_t type = 0; type < (size_t)NotificationType_MAX; ++type)
    OurChannel->addChannel(type);
  molecules_deprecated->signOn(this);
}

World::~World()
{
  molecules_deprecated->signOff(this);
  delete LCcontroller;
  delete cell_size;
  delete molecules_deprecated;
  MoleculeSet::iterator molIter;
  for(molIter=molecules.begin();molIter!=molecules.end();++molIter){
    DeleteMolecule((*molIter).second);
  }
  molecules.clear();
  AtomSet::iterator atIter;
  for(atIter=atoms.begin();atIter!=atoms.end();++atIter){
    DeleteAtom((*atIter).second);
  }
  atoms.clear();

  // empty notifications
  std::map<Observable *, Channels*>::iterator iter = NotificationChannels.find(this);
  ASSERT(iter != NotificationChannels.end(),
      "World::~World() - cannot find our Channels in NotificationChannels.");
  delete iter->second;
  NotificationChannels.erase(iter);

  delete BG;
  delete periode;
  delete configuration;
  delete Thermostats;
}

// Explicit instantiation of the singleton mechanism at this point

// moleculeId_t und atomId_t sind gleicher Basistyp, deswegen nur einen von beiden konstruieren
CONSTRUCT_IDPOOL(atomId_t, uniqueId)
CONSTRUCT_IDPOOL(moleculeId_t, continuousId)

CONSTRUCT_SINGLETON(World)

CONSTRUCT_OBSERVEDCONTAINER(World::AtomSTLSet)

CONSTRUCT_OBSERVEDCONTAINER(World::MoleculeSTLSet)

/******************************* deprecated Legacy Stuff ***********************/

MoleculeListClass *&World::getMolecules() {
  return molecules_deprecated;
}