src/types/MoleculeStamp.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */

#include <functional> 
#include <iostream>
#include <sstream>
#include "types/MoleculeStamp.hpp"
#include "utils/Tuple.hpp"
#include "utils/MemoryUtils.hpp"
namespace oopse {

template<class ContainerType>
std::string containerToString(ContainerType& cont) {
    std::ostringstream oss;
    oss << "(";
    typename ContainerType::iterator i = cont.begin();
    if (i != cont.end()) {
        oss << *i;
        ++i;
    }
    for (; i != cont.end();++i) {
        oss << ", ";
        oss << *i;
    }
    oss << ")";
    return oss.str();
}

MoleculeStamp::MoleculeStamp() {
    DefineParameter(Name, "name");
    
    deprecatedKeywords_.insert("nAtoms");
    deprecatedKeywords_.insert("nBonds");
    deprecatedKeywords_.insert("nBends");
    deprecatedKeywords_.insert("nTorsions");
    deprecatedKeywords_.insert("nRigidBodies");
    deprecatedKeywords_.insert("nCutoffGroups");
    
}

MoleculeStamp::~MoleculeStamp() {
    MemoryUtils::deletePointers(atomStamps_);
    MemoryUtils::deletePointers(bondStamps_);
    MemoryUtils::deletePointers(bendStamps_);
    MemoryUtils::deletePointers(torsionStamps_);
    MemoryUtils::deletePointers(rigidBodyStamps_);
    MemoryUtils::deletePointers(cutoffGroupStamps_);
    MemoryUtils::deletePointers(fragmentStamps_);    
}

bool MoleculeStamp::addAtomStamp( AtomStamp* atom) {
    bool ret = addIndexSensitiveStamp(atomStamps_, atom);
    if (!ret) {
         std::cout<< "Error in Molecule " << getName()  << ": multiple atoms have the same indices"<< atom->getIndex() <<"\n";
    }
    return ret;
    
}

bool MoleculeStamp::addBondStamp( BondStamp* bond) {
    bondStamps_.push_back(bond);
    return true;
}

bool MoleculeStamp::addBendStamp( BendStamp* bend) {
    bendStamps_.push_back(bend);
    return true;
}

bool MoleculeStamp::addTorsionStamp( TorsionStamp* torsion) {
    torsionStamps_.push_back(torsion);
    return true;
}

bool MoleculeStamp::addRigidBodyStamp( RigidBodyStamp* rigidbody) {
    bool ret = addIndexSensitiveStamp(rigidBodyStamps_, rigidbody);
    if (!ret) {
        std::cout<< "Error in Molecule " << getName()  << ": multiple rigidbodies have the same indices: " << rigidbody->getIndex() <<"\n";
    }
    return ret;
}

bool MoleculeStamp::addCutoffGroupStamp( CutoffGroupStamp* cutoffgroup) {
    cutoffGroupStamps_.push_back(cutoffgroup);
    return true;
}

bool MoleculeStamp::addFragmentStamp( FragmentStamp* fragment) {
    return addIndexSensitiveStamp(fragmentStamps_, fragment);
}
    
void MoleculeStamp::validate() {
    DataHolder::validate();

    atom2Rigidbody.resize(getNAtoms()); 
    // negative number means atom is a free atom, does not belong to rigidbody
    //every element in atom2Rigidbody has unique negative number at the very beginning
    for(int i = 0; i < atom2Rigidbody.size(); ++i) {
        atom2Rigidbody[i] = -1 - i;
    }
    for (int i = 0; i < getNRigidBodies(); ++i) {
        RigidBodyStamp* rbStamp = getRigidBodyStamp(i);
        std::vector<int> members = rbStamp->getMembers();
        for(std::vector<int>::iterator j = members.begin(); j != members.end(); ++j) {
            atom2Rigidbody[*j] = i;                 
        }
    }

    checkAtoms();
    checkBonds();
    fillBondInfo();
    checkBends();
    checkTorsions();
    checkRigidBodies();
    checkCutoffGroups();
    checkFragments();

    int nrigidAtoms = 0;
    for (int i = 0; i < getNRigidBodies(); ++i) {
        RigidBodyStamp* rbStamp = getRigidBodyStamp(i);
        nrigidAtoms += rbStamp->getNMembers();
    }
    nintegrable_ = getNAtoms()+ getNRigidBodies() - nrigidAtoms;

 }

void MoleculeStamp::checkAtoms() {
    std::vector<AtomStamp*>::iterator ai = std::find(atomStamps_.begin(), atomStamps_.end(), static_cast<AtomStamp*>(NULL));
    if (ai != atomStamps_.end()) {
        std::cout << "Error in Molecule " << getName() << ": atom[" << ai - atomStamps_.begin()<< "] is missing\n";
    }

}

void MoleculeStamp::checkBonds() {
    //make sure index is not out of range
    int natoms = getNAtoms();
    for(int i = 0; i < getNBonds(); ++i) {
        BondStamp* bondStamp = getBondStamp(i);
        if (bondStamp->getA() >=  natoms && bondStamp->getB() >= natoms) {
            std::cout << "Error in Molecule " << getName() <<  ": bond(" << bondStamp->getA() << ", " << bondStamp->getB() << ") is invalid\n";
        }
    }
    
    //make sure bonds are unique
    std::set<std::pair<int, int> > allBonds;
    for(int i = 0; i < getNBonds(); ++i) {
        BondStamp* bondStamp= getBondStamp(i);        
        std::pair<int, int> bondPair(bondStamp->getA(), bondStamp->getB());
        //make sure bondTuple.first is always less than or equal to bondTuple.third
        if (bondPair.first > bondPair.second) {
            std::swap(bondPair.first, bondPair.second);
        }
        
        std::set<std::pair<int, int> >::iterator iter = allBonds.find(bondPair);
        if ( iter != allBonds.end()) {
            std::cout << "Error in Molecule " << getName() << ": " << "bond(" <<iter->first << ", "<< iter->second << ")appears multiple times\n";
        } else {
            allBonds.insert(bondPair);
        }
    }
    
    //make sure atoms belong to same rigidbody do not bond to each other
    for(int i = 0; i < getNBonds(); ++i) {
        BondStamp* bondStamp = getBondStamp(i);
        if (atom2Rigidbody[bondStamp->getA()] == atom2Rigidbody[bondStamp->getB()]) {
            std::cout << "Error in Molecule " << getName() << ": "<<"bond(" << bondStamp->getA() << ", " << bondStamp->getB() << ") belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n";
        }
    }
    
}

void MoleculeStamp::checkBends() {
    for(int i = 0; i < getNBends(); ++i) {
        BendStamp* bendStamp = getBendStamp(i);
        std::vector<int> bendAtoms =  bendStamp->getMembers();
        std::vector<int>::iterator j =std::find_if(bendAtoms.begin(), bendAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1));
        if (j != bendAtoms.end()) {
            std::cout << "Error in Molecule " << getName() << " : atoms of bend" << containerToString(bendAtoms) << "have invalid indices\n";
        }

        if (bendAtoms.size() == 2 ) {
            if (!bendStamp->haveGhostVectorSource()) {
                std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce is missing\n";
            }else{
                int ghostIndex = bendStamp->getGhostVectorSource();
                if (ghostIndex < getNAtoms()) {
                    if (std::find(bendAtoms.begin(), bendAtoms.end(), ghostIndex) == bendAtoms.end()) {
                      std::cout <<  "Error in Molecule " << getName() << ": ghostVectorSouce "<< ghostIndex<<"is invalid\n"; 
                    }
                    if (!getAtomStamp(ghostIndex)->haveOrientation()) {
                        std::cout <<  "Error in Molecule " << getName() << ": ghost atom must be a directioanl atom\n"; 
                    }
                }else {
                    std::cout << "Error in Molecule " << getName() <<  ": ghostVectorsource " << ghostIndex<< "  is invalid\n";
                }
            }
        } else if (bendAtoms.size() == 3 && bendStamp->haveGhostVectorSource()) {
            std::cout <<  "Error in Molecule " << getName() << ": normal bend should not have ghostVectorSouce\n"; 
        }
    }

    for(int i = 0; i < getNBends(); ++i) {
        BendStamp* bendStamp = getBendStamp(i);
        std::vector<int> bendAtoms =  bendStamp->getMembers();
        std::vector<int> rigidSet(getNRigidBodies(), 0);
        std::vector<int>::iterator j;
        for( j = bendAtoms.begin(); j != bendAtoms.end(); ++j) {
            int rigidbodyIndex = atom2Rigidbody[*j];
            if (rigidbodyIndex >= 0) {
                ++rigidSet[rigidbodyIndex];
                if (rigidSet[rigidbodyIndex] > 1) {
                    std::cout << "Error in Molecule " << getName() << ": bend" << containerToString(bendAtoms) << " belong to same rigidbody " << rigidbodyIndex << "\n";                    
                }
            }
        }
    } 
    
    
    std::set<IntTuple3> allBends;
    std::set<IntTuple3>::iterator iter;
    for(int i = 0; i < getNBends(); ++i) {
        BendStamp* bendStamp= getBendStamp(i);
        std::vector<int> bend = bendStamp->getMembers();
        if (bend.size() == 2) {
        // in case we have two ghost bend. For example, 
        // bend {
        // members (0, 1);
        //   ghostVectorSource = 0;
        // }
        // and
        // bend {
        //   members (0, 1);
        // ghostVectorSource = 0;
        // }
        // In order to distinguish them. we expand them to Tuple3.
        // the first one is expanded to (0, 0, 1) while the second one is expaned to (0, 1, 1)
             int ghostIndex = bendStamp->getGhostVectorSource();
             std::vector<int>::iterator j = std::find(bend.begin(), bend.end(), ghostIndex);
             if (j != bend.end()) {
                bend.insert(j, ghostIndex);
             }
        }
        
        IntTuple3 bendTuple(bend[0], bend[1], bend[2]);
        //make sure bendTuple.first is always less than or equal to bendTuple.third
        if (bendTuple.first > bendTuple.third) {
            std::swap(bendTuple.first, bendTuple.third);
        }
        
        iter = allBends.find(bendTuple);
        if ( iter != allBends.end()) {
            std::cout << "Error in Molecule " << getName() << ": " << "Bend appears multiple times\n";
        } else {
            allBends.insert(bendTuple);
        }
    }

    for (int i = 0; i < getNBonds(); ++i) {
        BondStamp* bondStamp = getBondStamp(i);
        int a = bondStamp->getA();
        int b = bondStamp->getB();

        AtomStamp* atomA = getAtomStamp(a);
        AtomStamp* atomB = getAtomStamp(b);

        //find bend c--a--b
        AtomStamp::AtomIter ai;
        for(int c= atomA->getFirstBondedAtom(ai);c != -1;c = atomA->getNextBondedAtom(ai))
        {
            if(b == c)
                continue;          
            
            IntTuple3 newBend(c, a, b);
            if (newBend.first > newBend.third) {
                std::swap(newBend.first, newBend.third);
            }

            if (allBends.find(newBend) == allBends.end() ) {                
                allBends.insert(newBend);
                BendStamp * newBendStamp = new BendStamp();
                newBendStamp->setMembers(newBend);
                addBendStamp(newBendStamp);
            }
        }        

        //find bend a--b--c
        for(int c= atomB->getFirstBondedAtom(ai);c != -1;c = atomB->getNextBondedAtom(ai))
        {
            if(a == c)
                continue;          

            IntTuple3 newBend( a, b, c);
            if (newBend.first > newBend.third) {
                std::swap(newBend.first, newBend.third);
            }            
            if (allBends.find(newBend) == allBends.end() ) {                
                allBends.insert(newBend);
                BendStamp * newBendStamp = new BendStamp();
                newBendStamp->setMembers(newBend);
                addBendStamp(newBendStamp);
            }
        }        
    }

}

void MoleculeStamp::checkTorsions() {
    for(int i = 0; i < getNTorsions(); ++i) {
        TorsionStamp* torsionStamp = getTorsionStamp(i);
        std::vector<int> torsionAtoms =  torsionStamp ->getMembers();
        std::vector<int>::iterator j =std::find_if(torsionAtoms.begin(), torsionAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1));
        if (j != torsionAtoms.end()) {
            std::cout << "Error in Molecule " << getName() << ": atoms of torsion" << containerToString(torsionAtoms) << " have invalid indices\n"; 
        }
    }
    
    for(int i = 0; i < getNTorsions(); ++i) {
        TorsionStamp* torsionStamp = getTorsionStamp(i);
        std::vector<int> torsionAtoms =  torsionStamp->getMembers();
        std::vector<int> rigidSet(getNRigidBodies(), 0);
        std::vector<int>::iterator j;
        for( j = torsionAtoms.begin(); j != torsionAtoms.end(); ++j) {
            int rigidbodyIndex = atom2Rigidbody[*j];
            if (rigidbodyIndex >= 0) {
                ++rigidSet[rigidbodyIndex];
                if (rigidSet[rigidbodyIndex] > 1) {
                    std::cout << "Error in Molecule " << getName() << ": torsion" << containerToString(torsionAtoms) << "is invalid\n";                  
                }
            }
        }
    }     

    std::set<IntTuple4> allTorsions;
    std::set<IntTuple4>::iterator iter;
     for(int i = 0; i < getNTorsions(); ++i) {
         TorsionStamp* torsionStamp= getTorsionStamp(i);
         std::vector<int> torsion = torsionStamp->getMembers();
         if (torsion.size() == 3) {
             int ghostIndex = torsionStamp->getGhostVectorSource();
             std::vector<int>::iterator j = std::find(torsion.begin(), torsion.end(), ghostIndex);
             if (j != torsion.end()) {
                torsion.insert(j, ghostIndex);
             }
         }

        IntTuple4 torsionTuple(torsion[0], torsion[1], torsion[2], torsion[3]);
        if (torsionTuple.first > torsionTuple.fourth) {
            std::swap(torsionTuple.first, torsionTuple.fourth);
            std::swap(torsionTuple.second, torsionTuple.third);                    
        }                

         iter = allTorsions.find(torsionTuple);
         if ( iter == allTorsions.end()) {
            allTorsions.insert(torsionTuple);
         } else {
            std::cout << "Error in Molecule " << getName() << ": " << "Torsion appears multiple times\n";
         }
     }

    for (int i = 0; i < getNBonds(); ++i) {
        BondStamp* bondStamp = getBondStamp(i);
        int b = bondStamp->getA();
        int c = bondStamp->getB();

        AtomStamp* atomB = getAtomStamp(b);
        AtomStamp* atomC = getAtomStamp(c);

        AtomStamp::AtomIter ai2;
        AtomStamp::AtomIter ai3;

        for(int a = atomB->getFirstBondedAtom(ai2);a != -1;a = atomB->getNextBondedAtom(ai2))
        {
            if(a == c)
                continue;

            for(int d = atomC->getFirstBondedAtom(ai3);d != -1;d = atomC->getNextBondedAtom(ai3))
            {
                if(d == b)
                    continue;
                
                IntTuple4 newTorsion(a, b, c, d);
                //make sure the first element is always less than or equal to the fourth element in IntTuple4
                if (newTorsion.first > newTorsion.fourth) {
                    std::swap(newTorsion.first, newTorsion.fourth);
                    std::swap(newTorsion.second, newTorsion.third);                    
                }                
                if (allTorsions.find(newTorsion) == allTorsions.end() ) {                
                    allTorsions.insert(newTorsion);
                    TorsionStamp * newTorsionStamp = new TorsionStamp();
                    newTorsionStamp->setMembers(newTorsion);
                    addTorsionStamp(newTorsionStamp);                    
                }            
            }
        }    
    }

}

void MoleculeStamp::checkRigidBodies() {
     std::vector<RigidBodyStamp*>::iterator ri = std::find(rigidBodyStamps_.begin(), rigidBodyStamps_.end(), static_cast<RigidBodyStamp*>(NULL));
     if (ri != rigidBodyStamps_.end()) {
         std::cout << "Error in Molecule " << getName() << ":rigidBody[" <<  ri - rigidBodyStamps_.begin()<< "] is missing\n";
     }

    for (int i = 0; i < getNRigidBodies(); ++i) {
        RigidBodyStamp* rbStamp = getRigidBodyStamp(i);
        std::vector<int> rigidAtoms =  rbStamp ->getMembers();
        std::vector<int>::iterator j =std::find_if(rigidAtoms.begin(), rigidAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1));
        if (j != rigidAtoms.end()) {
            std::cout << "Error in Molecule " << getName();
        }
        
    }    
}

void MoleculeStamp::checkCutoffGroups() {

    for(int i = 0; i < getNCutoffGroups(); ++i) {
        CutoffGroupStamp* cutoffGroupStamp = getCutoffGroupStamp(i);
        std::vector<int> cutoffGroupAtoms =  cutoffGroupStamp ->getMembers();
        std::vector<int>::iterator j =std::find_if(cutoffGroupAtoms.begin(), cutoffGroupAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1));
        if (j != cutoffGroupAtoms.end()) {
            std::cout << "Error in Molecule " << getName() << ": cutoffGroup" << " is out of range\n"; 
        }
    }    
}

void MoleculeStamp::checkFragments() {

    std::vector<FragmentStamp*>::iterator fi = std::find(fragmentStamps_.begin(), fragmentStamps_.end(), static_cast<FragmentStamp*>(NULL));
    if (fi != fragmentStamps_.end()) {
        std::cout << "Error in Molecule " << getName() << ":fragment[" <<  fi - fragmentStamps_.begin()<< "] is missing\n";
    }
    
}

void MoleculeStamp::fillBondInfo() {

    for (int i = 0; i < getNBonds(); ++i) {
        BondStamp* bondStamp = getBondStamp(i);
        int a = bondStamp->getA();
        int b = bondStamp->getB();
        AtomStamp* atomA = getAtomStamp(a);
        AtomStamp* atomB = getAtomStamp(b);
        atomA->addBond(i);
        atomA->addBondedAtom(b);
        atomB->addBond(i);        
        atomB->addBondedAtom(a);

    }
}


//Function Name: isBondInSameRigidBody
//Return true is both atoms of the bond belong to the same rigid body, otherwise return false
bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){
  int rbA;
  int rbB;
  int consAtomA;
  int consAtomB;

  if (!isAtomInRigidBody(bond->getA(),rbA, consAtomA))
    return false;

  if(!isAtomInRigidBody(bond->getB(),rbB, consAtomB) )
    return false;

  if(rbB == rbA)
    return true;
  else
    return false;
}

// Function Name: isAtomInRigidBody 
//return false if atom does not belong to a rigid body, otherwise return true 
bool MoleculeStamp::isAtomInRigidBody(int atomIndex){
  return atom2Rigidbody[atomIndex] >=0 ;
   
}

// Function Name: isAtomInRigidBody 
//return false if atom does not belong to a rigid body otherwise return true and set whichRigidBody 
//and consAtomIndex
//atomIndex : the index of atom in component
//whichRigidBody: the index of rigidbody in component
//consAtomIndex:  the position of joint atom apears in  rigidbody's definition
bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){

  
  whichRigidBody = -1;
  consAtomIndex = -1;

  if (atom2Rigidbody[atomIndex] >=0) {
    whichRigidBody = atom2Rigidbody[atomIndex];
    RigidBodyStamp* rbStamp = getRigidBodyStamp(whichRigidBody);
    int numAtom = rbStamp->getNMembers();
    for(int j = 0; j < numAtom; j++) {
      if (rbStamp->getMemberAt(j) == atomIndex){
        consAtomIndex = j;
        return true;
      }
    }
  }

  return false;
   
}

//return the position of joint atom apears in  rigidbody's definition
//for the time being, we will use the most inefficient algorithm, the complexity is O(N2)
//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first
std::vector<std::pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){
  RigidBodyStamp* rbStamp1;
  RigidBodyStamp* rbStamp2;
  int natomInRb1;
  int natomInRb2;
  int atomIndex1;
  int atomIndex2;
  std::vector<std::pair<int, int> > jointAtomIndexPair;
  
  rbStamp1 = this->getRigidBodyStamp(rb1);
  natomInRb1 =rbStamp1->getNMembers();

  rbStamp2 = this->getRigidBodyStamp(rb2);
  natomInRb2 =rbStamp2->getNMembers();

  for(int i = 0; i < natomInRb1; i++){
    atomIndex1 = rbStamp1->getMemberAt(i);
      
    for(int j= 0; j < natomInRb1; j++){
      atomIndex2 = rbStamp2->getMemberAt(j);

      if(atomIndex1 == atomIndex2){
        jointAtomIndexPair.push_back(std::make_pair(i, j));
        break;
      }
      
    }

  }

  return jointAtomIndexPair;
}

}
Revision:	2543
Committed:	Wed Jan 11 18:41:01 2006 UTC (18 years, 5 months ago) by gezelter
File size:	21928 byte(s)
Log Message:	Fixed a spelling error
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	#include <functional>
43	#include <iostream>
44	#include <sstream>
45	#include "types/MoleculeStamp.hpp"
46	#include "utils/Tuple.hpp"
47	#include "utils/MemoryUtils.hpp"
48	namespace oopse {
49
50	template<class ContainerType>
51	std::string containerToString(ContainerType& cont) {
52	std::ostringstream oss;
53	oss << "(";
54	typename ContainerType::iterator i = cont.begin();
55	if (i != cont.end()) {
56	oss << *i;
57	++i;
58	}
59	for (; i != cont.end();++i) {
60	oss << ", ";
61	oss << *i;
62	}
63	oss << ")";
64	return oss.str();
65	}
66
67	MoleculeStamp::MoleculeStamp() {
68	DefineParameter(Name, "name");
69
70	deprecatedKeywords_.insert("nAtoms");
71	deprecatedKeywords_.insert("nBonds");
72	deprecatedKeywords_.insert("nBends");
73	deprecatedKeywords_.insert("nTorsions");
74	deprecatedKeywords_.insert("nRigidBodies");
75	deprecatedKeywords_.insert("nCutoffGroups");
76
77	}
78
79	MoleculeStamp::~MoleculeStamp() {
80	MemoryUtils::deletePointers(atomStamps_);
81	MemoryUtils::deletePointers(bondStamps_);
82	MemoryUtils::deletePointers(bendStamps_);
83	MemoryUtils::deletePointers(torsionStamps_);
84	MemoryUtils::deletePointers(rigidBodyStamps_);
85	MemoryUtils::deletePointers(cutoffGroupStamps_);
86	MemoryUtils::deletePointers(fragmentStamps_);
87	}
88
89	bool MoleculeStamp::addAtomStamp( AtomStamp* atom) {
90	bool ret = addIndexSensitiveStamp(atomStamps_, atom);
91	if (!ret) {
92	std::cout<< "Error in Molecule " << getName() << ": multiple atoms have the same indices"<< atom->getIndex() <<"\n";
93	}
94	return ret;
95
96	}
97
98	bool MoleculeStamp::addBondStamp( BondStamp* bond) {
99	bondStamps_.push_back(bond);
100	return true;
101	}
102
103	bool MoleculeStamp::addBendStamp( BendStamp* bend) {
104	bendStamps_.push_back(bend);
105	return true;
106	}
107
108	bool MoleculeStamp::addTorsionStamp( TorsionStamp* torsion) {
109	torsionStamps_.push_back(torsion);
110	return true;
111	}
112
113	bool MoleculeStamp::addRigidBodyStamp( RigidBodyStamp* rigidbody) {
114	bool ret = addIndexSensitiveStamp(rigidBodyStamps_, rigidbody);
115	if (!ret) {
116	std::cout<< "Error in Molecule " << getName() << ": multiple rigidbodies have the same indices: " << rigidbody->getIndex() <<"\n";
117	}
118	return ret;
119	}
120
121	bool MoleculeStamp::addCutoffGroupStamp( CutoffGroupStamp* cutoffgroup) {
122	cutoffGroupStamps_.push_back(cutoffgroup);
123	return true;
124	}
125
126	bool MoleculeStamp::addFragmentStamp( FragmentStamp* fragment) {
127	return addIndexSensitiveStamp(fragmentStamps_, fragment);
128	}
129
130	void MoleculeStamp::validate() {
131	DataHolder::validate();
132
133	atom2Rigidbody.resize(getNAtoms());
134	// negative number means atom is a free atom, does not belong to rigidbody
135	//every element in atom2Rigidbody has unique negative number at the very beginning
136	for(int i = 0; i < atom2Rigidbody.size(); ++i) {
137	atom2Rigidbody[i] = -1 - i;
138	}
139	for (int i = 0; i < getNRigidBodies(); ++i) {
140	RigidBodyStamp* rbStamp = getRigidBodyStamp(i);
141	std::vector<int> members = rbStamp->getMembers();
142	for(std::vector<int>::iterator j = members.begin(); j != members.end(); ++j) {
143	atom2Rigidbody[*j] = i;
144	}
145	}
146
147	checkAtoms();
148	checkBonds();
149	fillBondInfo();
150	checkBends();
151	checkTorsions();
152	checkRigidBodies();
153	checkCutoffGroups();
154	checkFragments();
155
156	int nrigidAtoms = 0;
157	for (int i = 0; i < getNRigidBodies(); ++i) {
158	RigidBodyStamp* rbStamp = getRigidBodyStamp(i);
159	nrigidAtoms += rbStamp->getNMembers();
160	}
161	nintegrable_ = getNAtoms()+ getNRigidBodies() - nrigidAtoms;
162
163	}
164
165	void MoleculeStamp::checkAtoms() {
166	std::vector<AtomStamp>::iterator ai = std::find(atomStamps_.begin(), atomStamps_.end(), static_cast<AtomStamp>(NULL));
167	if (ai != atomStamps_.end()) {
168	std::cout << "Error in Molecule " << getName() << ": atom[" << ai - atomStamps_.begin()<< "] is missing\n";
169	}
170
171	}
172
173	void MoleculeStamp::checkBonds() {
174	//make sure index is not out of range
175	int natoms = getNAtoms();
176	for(int i = 0; i < getNBonds(); ++i) {
177	BondStamp* bondStamp = getBondStamp(i);
178	if (bondStamp->getA() >= natoms && bondStamp->getB() >= natoms) {
179	std::cout << "Error in Molecule " << getName() << ": bond(" << bondStamp->getA() << ", " << bondStamp->getB() << ") is invalid\n";
180	}
181	}
182
183	//make sure bonds are unique
184	std::set<std::pair<int, int> > allBonds;
185	for(int i = 0; i < getNBonds(); ++i) {
186	BondStamp* bondStamp= getBondStamp(i);
187	std::pair<int, int> bondPair(bondStamp->getA(), bondStamp->getB());
188	//make sure bondTuple.first is always less than or equal to bondTuple.third
189	if (bondPair.first > bondPair.second) {
190	std::swap(bondPair.first, bondPair.second);
191	}
192
193	std::set<std::pair<int, int> >::iterator iter = allBonds.find(bondPair);
194	if ( iter != allBonds.end()) {
195	std::cout << "Error in Molecule " << getName() << ": " << "bond(" <<iter->first << ", "<< iter->second << ")appears multiple times\n";
196	} else {
197	allBonds.insert(bondPair);
198	}
199	}
200
201	//make sure atoms belong to same rigidbody do not bond to each other
202	for(int i = 0; i < getNBonds(); ++i) {
203	BondStamp* bondStamp = getBondStamp(i);
204	if (atom2Rigidbody[bondStamp->getA()] == atom2Rigidbody[bondStamp->getB()]) {
205	std::cout << "Error in Molecule " << getName() << ": "<<"bond(" << bondStamp->getA() << ", " << bondStamp->getB() << ") belong to same rigidbody " << atom2Rigidbody[bondStamp->getA()] << "\n";
206	}
207	}
208
209	}
210
211	void MoleculeStamp::checkBends() {
212	for(int i = 0; i < getNBends(); ++i) {
213	BendStamp* bendStamp = getBendStamp(i);
214	std::vector<int> bendAtoms = bendStamp->getMembers();
215	std::vector<int>::iterator j =std::find_if(bendAtoms.begin(), bendAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1));
216	if (j != bendAtoms.end()) {
217	std::cout << "Error in Molecule " << getName() << " : atoms of bend" << containerToString(bendAtoms) << "have invalid indices\n";
218	}
219
220	if (bendAtoms.size() == 2 ) {
221	if (!bendStamp->haveGhostVectorSource()) {
222	std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce is missing\n";
223	}else{
224	int ghostIndex = bendStamp->getGhostVectorSource();
225	if (ghostIndex < getNAtoms()) {
226	if (std::find(bendAtoms.begin(), bendAtoms.end(), ghostIndex) == bendAtoms.end()) {
227	std::cout << "Error in Molecule " << getName() << ": ghostVectorSouce "<< ghostIndex<<"is invalid\n";
228	}
229	if (!getAtomStamp(ghostIndex)->haveOrientation()) {
230	std::cout << "Error in Molecule " << getName() << ": ghost atom must be a directioanl atom\n";
231	}
232	}else {
233	std::cout << "Error in Molecule " << getName() << ": ghostVectorsource " << ghostIndex<< " is invalid\n";
234	}
235	}
236	} else if (bendAtoms.size() == 3 && bendStamp->haveGhostVectorSource()) {
237	std::cout << "Error in Molecule " << getName() << ": normal bend should not have ghostVectorSouce\n";
238	}
239	}
240
241	for(int i = 0; i < getNBends(); ++i) {
242	BendStamp* bendStamp = getBendStamp(i);
243	std::vector<int> bendAtoms = bendStamp->getMembers();
244	std::vector<int> rigidSet(getNRigidBodies(), 0);
245	std::vector<int>::iterator j;
246	for( j = bendAtoms.begin(); j != bendAtoms.end(); ++j) {
247	int rigidbodyIndex = atom2Rigidbody[*j];
248	if (rigidbodyIndex >= 0) {
249	++rigidSet[rigidbodyIndex];
250	if (rigidSet[rigidbodyIndex] > 1) {
251	std::cout << "Error in Molecule " << getName() << ": bend" << containerToString(bendAtoms) << " belong to same rigidbody " << rigidbodyIndex << "\n";
252	}
253	}
254	}
255	}
256
257
258	std::set<IntTuple3> allBends;
259	std::set<IntTuple3>::iterator iter;
260	for(int i = 0; i < getNBends(); ++i) {
261	BendStamp* bendStamp= getBendStamp(i);
262	std::vector<int> bend = bendStamp->getMembers();
263	if (bend.size() == 2) {
264	// in case we have two ghost bend. For example,
265	// bend {
266	// members (0, 1);
267	// ghostVectorSource = 0;
268	// }
269	// and
270	// bend {
271	// members (0, 1);
272	// ghostVectorSource = 0;
273	// }
274	// In order to distinguish them. we expand them to Tuple3.
275	// the first one is expanded to (0, 0, 1) while the second one is expaned to (0, 1, 1)
276	int ghostIndex = bendStamp->getGhostVectorSource();
277	std::vector<int>::iterator j = std::find(bend.begin(), bend.end(), ghostIndex);
278	if (j != bend.end()) {
279	bend.insert(j, ghostIndex);
280	}
281	}
282
283	IntTuple3 bendTuple(bend[0], bend[1], bend[2]);
284	//make sure bendTuple.first is always less than or equal to bendTuple.third
285	if (bendTuple.first > bendTuple.third) {
286	std::swap(bendTuple.first, bendTuple.third);
287	}
288
289	iter = allBends.find(bendTuple);
290	if ( iter != allBends.end()) {
291	std::cout << "Error in Molecule " << getName() << ": " << "Bend appears multiple times\n";
292	} else {
293	allBends.insert(bendTuple);
294	}
295	}
296
297	for (int i = 0; i < getNBonds(); ++i) {
298	BondStamp* bondStamp = getBondStamp(i);
299	int a = bondStamp->getA();
300	int b = bondStamp->getB();
301
302	AtomStamp* atomA = getAtomStamp(a);
303	AtomStamp* atomB = getAtomStamp(b);
304
305	//find bend c--a--b
306	AtomStamp::AtomIter ai;
307	for(int c= atomA->getFirstBondedAtom(ai);c != -1;c = atomA->getNextBondedAtom(ai))
308	{
309	if(b == c)
310	continue;
311
312	IntTuple3 newBend(c, a, b);
313	if (newBend.first > newBend.third) {
314	std::swap(newBend.first, newBend.third);
315	}
316
317	if (allBends.find(newBend) == allBends.end() ) {
318	allBends.insert(newBend);
319	BendStamp * newBendStamp = new BendStamp();
320	newBendStamp->setMembers(newBend);
321	addBendStamp(newBendStamp);
322	}
323	}
324
325	//find bend a--b--c
326	for(int c= atomB->getFirstBondedAtom(ai);c != -1;c = atomB->getNextBondedAtom(ai))
327	{
328	if(a == c)
329	continue;
330
331	IntTuple3 newBend( a, b, c);
332	if (newBend.first > newBend.third) {
333	std::swap(newBend.first, newBend.third);
334	}
335	if (allBends.find(newBend) == allBends.end() ) {
336	allBends.insert(newBend);
337	BendStamp * newBendStamp = new BendStamp();
338	newBendStamp->setMembers(newBend);
339	addBendStamp(newBendStamp);
340	}
341	}
342	}
343
344	}
345
346	void MoleculeStamp::checkTorsions() {
347	for(int i = 0; i < getNTorsions(); ++i) {
348	TorsionStamp* torsionStamp = getTorsionStamp(i);
349	std::vector<int> torsionAtoms = torsionStamp ->getMembers();
350	std::vector<int>::iterator j =std::find_if(torsionAtoms.begin(), torsionAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1));
351	if (j != torsionAtoms.end()) {
352	std::cout << "Error in Molecule " << getName() << ": atoms of torsion" << containerToString(torsionAtoms) << " have invalid indices\n";
353	}
354	}
355
356	for(int i = 0; i < getNTorsions(); ++i) {
357	TorsionStamp* torsionStamp = getTorsionStamp(i);
358	std::vector<int> torsionAtoms = torsionStamp->getMembers();
359	std::vector<int> rigidSet(getNRigidBodies(), 0);
360	std::vector<int>::iterator j;
361	for( j = torsionAtoms.begin(); j != torsionAtoms.end(); ++j) {
362	int rigidbodyIndex = atom2Rigidbody[*j];
363	if (rigidbodyIndex >= 0) {
364	++rigidSet[rigidbodyIndex];
365	if (rigidSet[rigidbodyIndex] > 1) {
366	std::cout << "Error in Molecule " << getName() << ": torsion" << containerToString(torsionAtoms) << "is invalid\n";
367	}
368	}
369	}
370	}
371
372	std::set<IntTuple4> allTorsions;
373	std::set<IntTuple4>::iterator iter;
374	for(int i = 0; i < getNTorsions(); ++i) {
375	TorsionStamp* torsionStamp= getTorsionStamp(i);
376	std::vector<int> torsion = torsionStamp->getMembers();
377	if (torsion.size() == 3) {
378	int ghostIndex = torsionStamp->getGhostVectorSource();
379	std::vector<int>::iterator j = std::find(torsion.begin(), torsion.end(), ghostIndex);
380	if (j != torsion.end()) {
381	torsion.insert(j, ghostIndex);
382	}
383	}
384
385	IntTuple4 torsionTuple(torsion[0], torsion[1], torsion[2], torsion[3]);
386	if (torsionTuple.first > torsionTuple.fourth) {
387	std::swap(torsionTuple.first, torsionTuple.fourth);
388	std::swap(torsionTuple.second, torsionTuple.third);
389	}
390
391	iter = allTorsions.find(torsionTuple);
392	if ( iter == allTorsions.end()) {
393	allTorsions.insert(torsionTuple);
394	} else {
395	std::cout << "Error in Molecule " << getName() << ": " << "Torsion appears multiple times\n";
396	}
397	}
398
399	for (int i = 0; i < getNBonds(); ++i) {
400	BondStamp* bondStamp = getBondStamp(i);
401	int b = bondStamp->getA();
402	int c = bondStamp->getB();
403
404	AtomStamp* atomB = getAtomStamp(b);
405	AtomStamp* atomC = getAtomStamp(c);
406
407	AtomStamp::AtomIter ai2;
408	AtomStamp::AtomIter ai3;
409
410	for(int a = atomB->getFirstBondedAtom(ai2);a != -1;a = atomB->getNextBondedAtom(ai2))
411	{
412	if(a == c)
413	continue;
414
415	for(int d = atomC->getFirstBondedAtom(ai3);d != -1;d = atomC->getNextBondedAtom(ai3))
416	{
417	if(d == b)
418	continue;
419
420	IntTuple4 newTorsion(a, b, c, d);
421	//make sure the first element is always less than or equal to the fourth element in IntTuple4
422	if (newTorsion.first > newTorsion.fourth) {
423	std::swap(newTorsion.first, newTorsion.fourth);
424	std::swap(newTorsion.second, newTorsion.third);
425	}
426	if (allTorsions.find(newTorsion) == allTorsions.end() ) {
427	allTorsions.insert(newTorsion);
428	TorsionStamp * newTorsionStamp = new TorsionStamp();
429	newTorsionStamp->setMembers(newTorsion);
430	addTorsionStamp(newTorsionStamp);
431	}
432	}
433	}
434	}
435
436	}
437
438	void MoleculeStamp::checkRigidBodies() {
439	std::vector<RigidBodyStamp>::iterator ri = std::find(rigidBodyStamps_.begin(), rigidBodyStamps_.end(), static_cast<RigidBodyStamp>(NULL));
440	if (ri != rigidBodyStamps_.end()) {
441	std::cout << "Error in Molecule " << getName() << ":rigidBody[" << ri - rigidBodyStamps_.begin()<< "] is missing\n";
442	}
443
444	for (int i = 0; i < getNRigidBodies(); ++i) {
445	RigidBodyStamp* rbStamp = getRigidBodyStamp(i);
446	std::vector<int> rigidAtoms = rbStamp ->getMembers();
447	std::vector<int>::iterator j =std::find_if(rigidAtoms.begin(), rigidAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1));
448	if (j != rigidAtoms.end()) {
449	std::cout << "Error in Molecule " << getName();
450	}
451
452	}
453	}
454
455	void MoleculeStamp::checkCutoffGroups() {
456
457	for(int i = 0; i < getNCutoffGroups(); ++i) {
458	CutoffGroupStamp* cutoffGroupStamp = getCutoffGroupStamp(i);
459	std::vector<int> cutoffGroupAtoms = cutoffGroupStamp ->getMembers();
460	std::vector<int>::iterator j =std::find_if(cutoffGroupAtoms.begin(), cutoffGroupAtoms.end(), std::bind2nd(std::greater<int>(), getNAtoms()-1));
461	if (j != cutoffGroupAtoms.end()) {
462	std::cout << "Error in Molecule " << getName() << ": cutoffGroup" << " is out of range\n";
463	}
464	}
465	}
466
467	void MoleculeStamp::checkFragments() {
468
469	std::vector<FragmentStamp>::iterator fi = std::find(fragmentStamps_.begin(), fragmentStamps_.end(), static_cast<FragmentStamp>(NULL));
470	if (fi != fragmentStamps_.end()) {
471	std::cout << "Error in Molecule " << getName() << ":fragment[" << fi - fragmentStamps_.begin()<< "] is missing\n";
472	}
473
474	}
475
476	void MoleculeStamp::fillBondInfo() {
477
478	for (int i = 0; i < getNBonds(); ++i) {
479	BondStamp* bondStamp = getBondStamp(i);
480	int a = bondStamp->getA();
481	int b = bondStamp->getB();
482	AtomStamp* atomA = getAtomStamp(a);
483	AtomStamp* atomB = getAtomStamp(b);
484	atomA->addBond(i);
485	atomA->addBondedAtom(b);
486	atomB->addBond(i);
487	atomB->addBondedAtom(a);
488
489	}
490	}
491
492
493
494	//Function Name: isBondInSameRigidBody
495	//Return true is both atoms of the bond belong to the same rigid body, otherwise return false
496	bool MoleculeStamp::isBondInSameRigidBody(BondStamp* bond){
497	int rbA;
498	int rbB;
499	int consAtomA;
500	int consAtomB;
501
502	if (!isAtomInRigidBody(bond->getA(),rbA, consAtomA))
503	return false;
504
505	if(!isAtomInRigidBody(bond->getB(),rbB, consAtomB) )
506	return false;
507
508	if(rbB == rbA)
509	return true;
510	else
511	return false;
512	}
513
514	// Function Name: isAtomInRigidBody
515	//return false if atom does not belong to a rigid body, otherwise return true
516	bool MoleculeStamp::isAtomInRigidBody(int atomIndex){
517	return atom2Rigidbody[atomIndex] >=0 ;
518
519	}
520
521	// Function Name: isAtomInRigidBody
522	//return false if atom does not belong to a rigid body otherwise return true and set whichRigidBody
523	//and consAtomIndex
524	//atomIndex : the index of atom in component
525	//whichRigidBody: the index of rigidbody in component
526	//consAtomIndex: the position of joint atom apears in rigidbody's definition
527	bool MoleculeStamp::isAtomInRigidBody(int atomIndex, int& whichRigidBody, int& consAtomIndex){
528
529
530
531	whichRigidBody = -1;
532	consAtomIndex = -1;
533
534	if (atom2Rigidbody[atomIndex] >=0) {
535	whichRigidBody = atom2Rigidbody[atomIndex];
536	RigidBodyStamp* rbStamp = getRigidBodyStamp(whichRigidBody);
537	int numAtom = rbStamp->getNMembers();
538	for(int j = 0; j < numAtom; j++) {
539	if (rbStamp->getMemberAt(j) == atomIndex){
540	consAtomIndex = j;
541	return true;
542	}
543	}
544	}
545
546	return false;
547
548	}
549
550	//return the position of joint atom apears in rigidbody's definition
551	//for the time being, we will use the most inefficient algorithm, the complexity is O(N2)
552	//actually we could improve the complexity to O(NlgN) by sorting the atom index in rigid body first
553	std::vector<std::pair<int, int> > MoleculeStamp::getJointAtoms(int rb1, int rb2){
554	RigidBodyStamp* rbStamp1;
555	RigidBodyStamp* rbStamp2;
556	int natomInRb1;
557	int natomInRb2;
558	int atomIndex1;
559	int atomIndex2;
560	std::vector<std::pair<int, int> > jointAtomIndexPair;
561
562	rbStamp1 = this->getRigidBodyStamp(rb1);
563	natomInRb1 =rbStamp1->getNMembers();
564
565	rbStamp2 = this->getRigidBodyStamp(rb2);
566	natomInRb2 =rbStamp2->getNMembers();
567
568	for(int i = 0; i < natomInRb1; i++){
569	atomIndex1 = rbStamp1->getMemberAt(i);
570
571	for(int j= 0; j < natomInRb1; j++){
572	atomIndex2 = rbStamp2->getMemberAt(j);
573
574	if(atomIndex1 == atomIndex2){
575	jointAtomIndexPair.push_back(std::make_pair(i, j));
576	break;
577	}
578
579	}
580
581	}
582
583	return jointAtomIndexPair;
584	}
585
586	}