source: src/World.cpp@ 5f8660a

/*
 * Project: MoleCuilder
 * Description: creates and alters molecular systems
 * Copyright (C)  2010 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 "Helpers/MemDebug.hpp"

#include "World.hpp"

#include <functional>

#include "atom.hpp"
#include "config.hpp"
#include "molecule.hpp"
#include "periodentafel.hpp"
#include "ThermoStatContainer.hpp"
#include "Descriptors/AtomDescriptor.hpp"
#include "Descriptors/AtomDescriptor_impl.hpp"
#include "Descriptors/MoleculeDescriptor.hpp"
#include "Descriptors/MoleculeDescriptor_impl.hpp"
#include "Descriptors/SelectiveIterator_impl.hpp"
#include "Actions/ManipulateAtomsProcess.hpp"
#include "Helpers/Assert.hpp"
#include "Box.hpp"
#include "LinearAlgebra/Matrix.hpp"
#include "defs.hpp"

#include "Patterns/Singleton_impl.hpp"
#include "Patterns/ObservedContainer_impl.hpp"

using namespace std;

const unsigned int MAX_POOL_FRAGMENTATION=20;
const unsigned int MAX_FRAGMENTATION_SKIPS=100;

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

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 Matrix &mat){
  OBSERVE;
  *cell_size = mat;
}

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

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 = getNextMoleculeId();
  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);
  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){
  OBSERVE;
  molecule *mol = molecules[id];
  ASSERT(mol,"Molecule id that was meant to be destroyed did not exist");
  DeleteMolecule(mol);
  molecules.erase(id);
  releaseMoleculeId(id);
}

atom *World::createAtom(){
  OBSERVE;
  atomId_t id = getNextAtomId();
  ASSERT(!atoms.count(id),"proposed id did not specify an unused ID");
  atom *res = NewAtom(id);
  res->setWorld(this);
  // store the atom by ID
  atoms[res->getId()] = res;
  return res;
}


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

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

void World::destroyAtom(atomId_t id) {
  OBSERVE;
  atom *atom = atoms[id];
  ASSERT(atom,"Atom ID that was meant to be destroyed did not exist");
  DeleteAtom(atom);
  atoms.erase(id);
  releaseAtomId(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(reserveAtomId(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(reserveMoleculeId(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){
  return new ManipulateAtomsProcess(op, descr,name,true);
}

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);
}
/******************************* IDManagement *****************************/

// Atoms

atomId_t World::getNextAtomId(){
  // try to find an Id in the pool;
  if(!atomIdPool.empty()){
    atomIdPool_t::iterator iter=atomIdPool.begin();
    atomId_t id = iter->first;
    range<atomId_t> newRange = makeRange(id+1,iter->last);
    // we wont use this iterator anymore, so we don't care about invalidating
    atomIdPool.erase(iter);
    if(newRange.first<newRange.last){
      atomIdPool.insert(newRange);
    }
    return id;
  }
  // Nothing in the pool... we are out of luck
  return currAtomId++;
}

void World::releaseAtomId(atomId_t id){
  atomIdPool.insert(makeRange(id,id+1));
  defragAtomIdPool();
}

bool World::reserveAtomId(atomId_t id){
  if(id>=currAtomId ){
    range<atomId_t> newRange = makeRange(currAtomId,id);
    if(newRange.first<newRange.last){
      atomIdPool.insert(newRange);
    }
    currAtomId=id+1;
    defragAtomIdPool();
    return true;
  }
  // look for a range that matches the request
  for(atomIdPool_t::iterator iter=atomIdPool.begin();iter!=atomIdPool.end();++iter){
    if(iter->isBefore(id)){
      // we have covered all available ranges... nothing to be found here
      break;
    }
    // no need to check first, since it has to be <=id, since otherwise we would have broken out
    if(!iter->isBeyond(id)){
      // we found a matching range... get the id from this range

      // split up this range at the point of id
      range<atomId_t> bottomRange = makeRange(iter->first,id);
      range<atomId_t> topRange = makeRange(id+1,iter->last);
      // remove this range
      atomIdPool.erase(iter);
      if(bottomRange.first<bottomRange.last){
        atomIdPool.insert(bottomRange);
      }
      if(topRange.first<topRange.last){
        atomIdPool.insert(topRange);
      }
      defragAtomIdPool();
      return true;
    }
  }
  // this ID could not be reserved
  return false;
}

void World::defragAtomIdPool(){
  // check if the situation is bad enough to make defragging neccessary
  if((numAtomDefragSkips<MAX_FRAGMENTATION_SKIPS) &&
     (atomIdPool.size()<lastAtomPoolSize+MAX_POOL_FRAGMENTATION)){
    ++numAtomDefragSkips;
    return;
  }
  for(atomIdPool_t::iterator iter = atomIdPool.begin();iter!=atomIdPool.end();){
    // see if this range is adjacent to the next one
    atomIdPool_t::iterator next = iter;
    next++;
    if(next!=atomIdPool.end() && (next->first==iter->last)){
      // merge the two ranges
      range<atomId_t> newRange = makeRange(iter->first,next->last);
      atomIdPool.erase(iter);
      atomIdPool.erase(next);
      pair<atomIdPool_t::iterator,bool> res = atomIdPool.insert(newRange);
      ASSERT(res.second,"Id-Pool was confused");
      iter=res.first;
      continue;
    }
    ++iter;
  }
  if(!atomIdPool.empty()){
    // check if the last range is at the border
    atomIdPool_t::iterator iter = atomIdPool.end();
    iter--;
    if(iter->last==currAtomId){
      currAtomId=iter->first;
      atomIdPool.erase(iter);
    }
  }
  lastAtomPoolSize=atomIdPool.size();
  numAtomDefragSkips=0;
}

// Molecules

moleculeId_t World::getNextMoleculeId(){
  // try to find an Id in the pool;
  if(!moleculeIdPool.empty()){
    moleculeIdPool_t::iterator iter=moleculeIdPool.begin();
    moleculeId_t id = iter->first;
    range<moleculeId_t> newRange = makeRange(id+1,iter->last);
    // we wont use this iterator anymore, so we don't care about invalidating
    moleculeIdPool.erase(iter);
    if(newRange.first<newRange.last){
      moleculeIdPool.insert(newRange);
    }
    return id;
  }
  // Nothing in the pool... we are out of luck
  return currMoleculeId++;
}

void World::releaseMoleculeId(moleculeId_t id){
  moleculeIdPool.insert(makeRange(id,id+1));
  defragMoleculeIdPool();
}

bool World::reserveMoleculeId(moleculeId_t id){
  if(id>=currMoleculeId ){
    range<moleculeId_t> newRange = makeRange(currMoleculeId,id);
    if(newRange.first<newRange.last){
      moleculeIdPool.insert(newRange);
    }
    currMoleculeId=id+1;
    defragMoleculeIdPool();
    return true;
  }
  // look for a range that matches the request
  for(moleculeIdPool_t::iterator iter=moleculeIdPool.begin();iter!=moleculeIdPool.end();++iter){
    if(iter->isBefore(id)){
      // we have coverd all available ranges... nothing to be found here
      break;
    }
    // no need to check first, since it has to be <=id, since otherwise we would have broken out
    if(!iter->isBeyond(id)){
      // we found a matching range... get the id from this range

      // split up this range at the point of id
      range<moleculeId_t> bottomRange = makeRange(iter->first,id);
      range<moleculeId_t> topRange = makeRange(id+1,iter->last);
      // remove this range
      moleculeIdPool.erase(iter);
      if(bottomRange.first<bottomRange.last){
        moleculeIdPool.insert(bottomRange);
      }
      if(topRange.first<topRange.last){
        moleculeIdPool.insert(topRange);
      }
      defragMoleculeIdPool();
      return true;
    }
  }
  // this ID could not be reserved
  return false;
}

void World::defragMoleculeIdPool(){
  // check if the situation is bad enough to make defragging neccessary
  if((numMoleculeDefragSkips<MAX_FRAGMENTATION_SKIPS) &&
     (moleculeIdPool.size()<lastMoleculePoolSize+MAX_POOL_FRAGMENTATION)){
    ++numMoleculeDefragSkips;
    return;
  }
  for(moleculeIdPool_t::iterator iter = moleculeIdPool.begin();iter!=moleculeIdPool.end();){
    // see if this range is adjacent to the next one
    moleculeIdPool_t::iterator next = iter;
    next++;
    if(next!=moleculeIdPool.end() && (next->first==iter->last)){
      // merge the two ranges
      range<moleculeId_t> newRange = makeRange(iter->first,next->last);
      moleculeIdPool.erase(iter);
      moleculeIdPool.erase(next);
      pair<moleculeIdPool_t::iterator,bool> res = moleculeIdPool.insert(newRange);
      ASSERT(res.second,"Id-Pool was confused");
      iter=res.first;
      continue;
    }
    ++iter;
  }
  if(!moleculeIdPool.empty()){
    // check if the last range is at the border
    moleculeIdPool_t::iterator iter = moleculeIdPool.end();
    iter--;
    if(iter->last==currMoleculeId){
      currMoleculeId=iter->first;
      moleculeIdPool.erase(iter);
    }
  }
  lastMoleculePoolSize=moleculeIdPool.size();
  numMoleculeDefragSkips=0;
}

/******************************* 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::selectAtom(atom *atom){
  ASSERT(atom,"Invalid pointer in selection of atom");
  selectedAtoms[atom->getId()]=atom;
}

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

void World::unselectAtom(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)(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(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)(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(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(atom *atom) const {
  return selectedAtoms.find(atom->getId()) != 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::selectMolecule(molecule *mol){
  ASSERT(mol,"Invalid pointer to molecule in selection");
  selectedMolecules[mol->getId()]=mol;
}

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

void World::unselectMolecule(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)(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(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(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(molecule *mol) const {
  return selectedMolecules.find(mol->getId()) != 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::MoleculeSelectionIterator World::beginMoleculeSelection(){
  return selectedMolecules.begin();
}

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

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

World::World() :
    Observable("World"),
    periode(new periodentafel),
    configuration(new config),
    Thermostats(new ThermoStatContainer),
    ExitFlag(0),
    atoms(this),
    selectedAtoms(this),
    currAtomId(0),
    lastAtomPoolSize(0),
    numAtomDefragSkips(0),
    molecules(this),
    selectedMolecules(this),
    currMoleculeId(0),
    molecules_deprecated(new MoleculeListClass(this))
{
  cell_size = new Box;
  Matrix domain;
  domain.at(0,0) = 20;
  domain.at(1,1) = 20;
  domain.at(2,2) = 20;
  cell_size->setM(domain);
  defaultName = "none";
  molecules_deprecated->signOn(this);
}

World::~World()
{
  molecules_deprecated->signOff(this);
  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();
  delete periode;
  delete configuration;
  delete Thermostats;
}

// Explicit instantiation of the singleton mechanism at this point

CONSTRUCT_SINGLETON(World)

CONSTRUCT_OBSERVEDCONTAINER(World::AtomSTLSet)

CONSTRUCT_OBSERVEDCONTAINER(World::MoleculeSTLSet)

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

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