src/brains/MoleculeCreator.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.
 */
  
/**
 * @file MoleculeCreator.cpp
 * @author tlin
 * @date 11/04/2004
 * @time 13:44am
 * @version 1.0
 */

#include <cassert>
#include <typeinfo>
#include <set>

#include "brains/MoleculeCreator.hpp"
#include "primitives/GhostBend.hpp"
#include "primitives/GhostTorsion.hpp"
#include "types/DirectionalAtomType.hpp"
#include "types/FixedBondType.hpp"
#include "utils/simError.h"
#include "utils/StringUtils.hpp"

namespace oopse {
  
  Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
                                            int stampId, int globalIndex, LocalIndexManager* localIndexMan) {

    Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName());
    
    //create atoms
    Atom* atom;
    AtomStamp* currentAtomStamp;
    int nAtom = molStamp->getNAtoms();
    for (int i = 0; i < nAtom; ++i) {
      currentAtomStamp = molStamp->getAtomStamp(i);
      atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
      mol->addAtom(atom);
    }

    //create rigidbodies
    RigidBody* rb;
    RigidBodyStamp * currentRigidBodyStamp;
    int nRigidbodies = molStamp->getNRigidBodies();

    for (int i = 0; i < nRigidbodies; ++i) {
      currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
      rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
      mol->addRigidBody(rb);
    }

    //create bonds
    Bond* bond;
    BondStamp* currentBondStamp;
    int nBonds = molStamp->getNBonds();

    for (int i = 0; i < nBonds; ++i) {
      currentBondStamp = molStamp->getBondStamp(i);
      bond = createBond(ff, mol, currentBondStamp);
      mol->addBond(bond);
    }

    //create bends
    Bend* bend;
    BendStamp* currentBendStamp;
    int nBends = molStamp->getNBends();
    for (int i = 0; i < nBends; ++i) {
      currentBendStamp = molStamp->getBendStamp(i);
      bend = createBend(ff, mol, currentBendStamp);
      mol->addBend(bend);
    }

    //create torsions
    Torsion* torsion;
    TorsionStamp* currentTorsionStamp;
    int nTorsions = molStamp->getNTorsions();
    for (int i = 0; i < nTorsions; ++i) {
      currentTorsionStamp = molStamp->getTorsionStamp(i);
      torsion = createTorsion(ff, mol, currentTorsionStamp);
      mol->addTorsion(torsion);
    }

    //create cutoffGroups
    CutoffGroup* cutoffGroup;
    CutoffGroupStamp* currentCutoffGroupStamp;
    int nCutoffGroups = molStamp->getNCutoffGroups();
    for (int i = 0; i < nCutoffGroups; ++i) {
      currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
      cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
      mol->addCutoffGroup(cutoffGroup);
    }

    //every free atom is a cutoff group    
    std::vector<Atom*> freeAtoms;
    std::vector<Atom*>::iterator ai;
    std::vector<Atom*>::iterator fai;

    //add all atoms into allAtoms set
    for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
      freeAtoms.push_back(atom);
    }

    Molecule::CutoffGroupIterator ci;
    CutoffGroup* cg;
    
    for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {

      for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
           //erase the atoms belong to cutoff groups from freeAtoms vector
           freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom), freeAtoms.end());
      }

    }       
    
    //loop over the free atoms and then create one cutoff group for every single free atom
    
    for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
      cutoffGroup = createCutoffGroup(mol, *fai);
      mol->addCutoffGroup(cutoffGroup);
    }
    //create constraints
    createConstraintPair(mol);
    createConstraintElem(mol);
    
    //the construction of this molecule is finished
    mol->complete();

    return mol;
  }    


  Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp, 
                                    LocalIndexManager* localIndexMan) {
    AtomType * atomType;
    Atom* atom;

    atomType =  ff->getAtomType(stamp->getType());

    if (atomType == NULL) {
      sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
              stamp->getType().c_str());

      painCave.isFatal = 1;
      simError();
    }
    
    //below code still have some kind of hard-coding smell
    if (atomType->isDirectional()){
     
      DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
        
      if (dAtomType == NULL) {
        sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");

        painCave.isFatal = 1;
        simError();
      }

      DirectionalAtom* dAtom;
      dAtom = new DirectionalAtom(dAtomType);
      atom = dAtom;    
    }
    else{
      atom = new Atom(atomType);
    }

    atom->setLocalIndex(localIndexMan->getNextAtomIndex());

    return atom;
  }

  RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol,
                                              RigidBodyStamp* rbStamp, 
                                              LocalIndexManager* localIndexMan) {
    Atom* atom;
    int nAtoms;
    Vector3d refCoor;
    AtomStamp* atomStamp;
    
    RigidBody* rb = new RigidBody();
    nAtoms = rbStamp->getNMembers();    
    for (int i = 0; i < nAtoms; ++i) {
      //rbStamp->getMember(i) return the local index of current atom inside the molecule.
      //It is not the same as local index of atom which is the index of atom at DataStorage class
      atom = mol->getAtomAt(rbStamp->getMemberAt(i));
      atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));    
      rb->addAtom(atom, atomStamp);
    }

    //after all of the atoms are added, we need to calculate the reference coordinates
    rb->calcRefCoords();

    //set the local index of this rigid body, global index will be set later
    rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());

    //the rule for naming rigidbody MoleculeName_RB_Integer
    //The first part is the name of the molecule
    //The second part is alway fixed as "RB"
    //The third part is the index of the rigidbody defined in meta-data file
    //For example, Butane_RB_0 is a valid rigid body name of butane molecule
    /**@todo replace itoa by lexi_cast */
    std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10);
    rb->setType(mol->getType() + "_RB_" + s.c_str());

    return rb;
  }    

  Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
    BondType* bondType;
    Atom* atomA;
    Atom* atomB;

    atomA = mol->getAtomAt(stamp->getA());
    atomB = mol->getAtomAt(stamp->getB());

    assert( atomA && atomB);
    
    bondType = ff->getBondType(atomA->getType(), atomB->getType());

    if (bondType == NULL) {
      sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
              atomA->getType().c_str(),
              atomB->getType().c_str());

      painCave.isFatal = 1;
      simError();
    }
    return new Bond(atomA, atomB, bondType);    
  }    

  Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
    Bend* bend = NULL; 
    std::vector<int> bendAtoms = stamp->getMembers(); 
    if (bendAtoms.size() == 3) {
      Atom* atomA = mol->getAtomAt(bendAtoms[0]);
      Atom* atomB = mol->getAtomAt(bendAtoms[1]);
      Atom* atomC = mol->getAtomAt(bendAtoms[2]);

      assert( atomA && atomB && atomC);

      BendType* bendType = ff->getBendType(atomA->getType().c_str(), atomB->getType().c_str(), atomC->getType().c_str());

      if (bendType == NULL) {
        sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
                atomA->getType().c_str(),
                atomB->getType().c_str(),
                atomC->getType().c_str());

        painCave.isFatal = 1;
        simError();
      }

      bend = new Bend(atomA, atomB, atomC, bendType);
    } else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
      int ghostIndex = stamp->getGhostVectorSource();
      int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1]; 
      Atom* normalAtom = mol->getAtomAt(normalIndex) ;        
      DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
      if (ghostAtom == NULL) {
        sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
        painCave.isFatal = 1;
        simError();
      }
                
      BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");

      if (bendType == NULL) {
        sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
                normalAtom->getType().c_str(),
                ghostAtom->getType().c_str(),
                "GHOST");

        painCave.isFatal = 1;
        simError();
      }
        
      bend = new GhostBend(normalAtom, ghostAtom, bendType);       

    } 
    
    return bend;
  }    

  Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {

    Torsion* torsion = NULL;
    std::vector<int> torsionAtoms = stamp->getMembers();
    if (torsionAtoms.size() < 3) {
        return torsion;
    }

    Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
    Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
    Atom* atomC = mol->getAtomAt(torsionAtoms[2]);

    if (torsionAtoms.size() == 4) {
      Atom* atomD = mol->getAtomAt(torsionAtoms[3]);

      assert(atomA && atomB && atomC && atomD);
        
      TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), 
                                                    atomC->getType(), atomD->getType());

      if (torsionType == NULL) {
        sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
                atomA->getType().c_str(),
                atomB->getType().c_str(),
                atomC->getType().c_str(),
                atomD->getType().c_str());

        painCave.isFatal = 1;
        simError();
      }
        
      torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);       
    }
    else {

      DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
      if (dAtom == NULL) {
        sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
        painCave.isFatal = 1;
        simError();
      }        

      TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), 
                                                    atomC->getType(), "GHOST");

      if (torsionType == NULL) {
        sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
                atomA->getType().c_str(),
                atomB->getType().c_str(),
                atomC->getType().c_str(),
                "GHOST");

        painCave.isFatal = 1;
        simError();
      }
        
      torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);               
    }

    return torsion;
  }    

  CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
    int nAtoms;
    CutoffGroup* cg;
    Atom* atom;
    cg = new CutoffGroup();
    
    nAtoms = stamp->getNMembers();
    for (int i =0; i < nAtoms; ++i) {
      atom = mol->getAtomAt(stamp->getMemberAt(i));
      assert(atom);
      cg->addAtom(atom);
    }

    return cg;
  }    

  CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
    CutoffGroup* cg;
    cg  = new CutoffGroup();
    cg->addAtom(atom);
    return cg;
  }

  void MoleculeCreator::createConstraintPair(Molecule* mol) {

    //add bond constraints
    Molecule::BondIterator bi;
    Bond* bond;
    for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
        
      BondType* bt = bond->getBondType();

      //class Parent1 {};
      //class Child1 : public Parent {};
      //class Child2 : public Parent {};
      //Child1* ch1 = new Child1();
      //Child2* ch2 = dynamic_cast<Child2*>(ch1); 
      //the dynamic_cast is succeed in above line. A compiler bug?        

      if (typeid(FixedBondType) == typeid(*bt)) {
        FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);

        ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
        ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());            
        ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
        mol->addConstraintPair(consPair);
      }
    }

    //rigidbody -- rigidbody constraint is not support yet
  }

  void MoleculeCreator::createConstraintElem(Molecule* mol) {

    ConstraintPair* consPair;
    Molecule::ConstraintPairIterator cpi;
    std::set<StuntDouble*> sdSet;
    for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {

      StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();            
      if (sdSet.find(sdA) == sdSet.end()){
        sdSet.insert(sdA);
        mol->addConstraintElem(new ConstraintElem(sdA));
      }

      StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();            
      if (sdSet.find(sdB) == sdSet.end()){
        sdSet.insert(sdB);
        mol->addConstraintElem(new ConstraintElem(sdB));
      }
        
    }

  }
    
}
Revision:	2508
Committed:	Mon Dec 12 19:32:50 2005 UTC (18 years, 6 months ago) by gezelter
File size:	14931 byte(s)
Log Message:	made some minor changes to allow compilation with the portland group compilers
#	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	/**
43	* @file MoleculeCreator.cpp
44	* @author tlin
45	* @date 11/04/2004
46	* @time 13:44am
47	* @version 1.0
48	*/
49
50	#include <cassert>
51	#include <typeinfo>
52	#include <set>
53
54	#include "brains/MoleculeCreator.hpp"
55	#include "primitives/GhostBend.hpp"
56	#include "primitives/GhostTorsion.hpp"
57	#include "types/DirectionalAtomType.hpp"
58	#include "types/FixedBondType.hpp"
59	#include "utils/simError.h"
60	#include "utils/StringUtils.hpp"
61
62	namespace oopse {
63
64	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
65	int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
66
67	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName());
68
69	//create atoms
70	Atom* atom;
71	AtomStamp* currentAtomStamp;
72	int nAtom = molStamp->getNAtoms();
73	for (int i = 0; i < nAtom; ++i) {
74	currentAtomStamp = molStamp->getAtomStamp(i);
75	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
76	mol->addAtom(atom);
77	}
78
79	//create rigidbodies
80	RigidBody* rb;
81	RigidBodyStamp * currentRigidBodyStamp;
82	int nRigidbodies = molStamp->getNRigidBodies();
83
84	for (int i = 0; i < nRigidbodies; ++i) {
85	currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
86	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
87	mol->addRigidBody(rb);
88	}
89
90	//create bonds
91	Bond* bond;
92	BondStamp* currentBondStamp;
93	int nBonds = molStamp->getNBonds();
94
95	for (int i = 0; i < nBonds; ++i) {
96	currentBondStamp = molStamp->getBondStamp(i);
97	bond = createBond(ff, mol, currentBondStamp);
98	mol->addBond(bond);
99	}
100
101	//create bends
102	Bend* bend;
103	BendStamp* currentBendStamp;
104	int nBends = molStamp->getNBends();
105	for (int i = 0; i < nBends; ++i) {
106	currentBendStamp = molStamp->getBendStamp(i);
107	bend = createBend(ff, mol, currentBendStamp);
108	mol->addBend(bend);
109	}
110
111	//create torsions
112	Torsion* torsion;
113	TorsionStamp* currentTorsionStamp;
114	int nTorsions = molStamp->getNTorsions();
115	for (int i = 0; i < nTorsions; ++i) {
116	currentTorsionStamp = molStamp->getTorsionStamp(i);
117	torsion = createTorsion(ff, mol, currentTorsionStamp);
118	mol->addTorsion(torsion);
119	}
120
121	//create cutoffGroups
122	CutoffGroup* cutoffGroup;
123	CutoffGroupStamp* currentCutoffGroupStamp;
124	int nCutoffGroups = molStamp->getNCutoffGroups();
125	for (int i = 0; i < nCutoffGroups; ++i) {
126	currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
127	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
128	mol->addCutoffGroup(cutoffGroup);
129	}
130
131	//every free atom is a cutoff group
132	std::vector<Atom*> freeAtoms;
133	std::vector<Atom*>::iterator ai;
134	std::vector<Atom*>::iterator fai;
135
136	//add all atoms into allAtoms set
137	for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
138	freeAtoms.push_back(atom);
139	}
140
141	Molecule::CutoffGroupIterator ci;
142	CutoffGroup* cg;
143
144	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
145
146	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
147	//erase the atoms belong to cutoff groups from freeAtoms vector
148	freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom), freeAtoms.end());
149	}
150
151	}
152
153	//loop over the free atoms and then create one cutoff group for every single free atom
154
155	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
156	cutoffGroup = createCutoffGroup(mol, *fai);
157	mol->addCutoffGroup(cutoffGroup);
158	}
159	//create constraints
160	createConstraintPair(mol);
161	createConstraintElem(mol);
162
163	//the construction of this molecule is finished
164	mol->complete();
165
166	return mol;
167	}
168
169
170	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
171	LocalIndexManager* localIndexMan) {
172	AtomType * atomType;
173	Atom* atom;
174
175	atomType = ff->getAtomType(stamp->getType());
176
177	if (atomType == NULL) {
178	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
179	stamp->getType().c_str());
180
181	painCave.isFatal = 1;
182	simError();
183	}
184
185	//below code still have some kind of hard-coding smell
186	if (atomType->isDirectional()){
187
188	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
189
190	if (dAtomType == NULL) {
191	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
192
193	painCave.isFatal = 1;
194	simError();
195	}
196
197	DirectionalAtom* dAtom;
198	dAtom = new DirectionalAtom(dAtomType);
199	atom = dAtom;
200	}
201	else{
202	atom = new Atom(atomType);
203	}
204
205	atom->setLocalIndex(localIndexMan->getNextAtomIndex());
206
207	return atom;
208	}
209
210	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp molStamp, Molecule mol,
211	RigidBodyStamp* rbStamp,
212	LocalIndexManager* localIndexMan) {
213	Atom* atom;
214	int nAtoms;
215	Vector3d refCoor;
216	AtomStamp* atomStamp;
217
218	RigidBody* rb = new RigidBody();
219	nAtoms = rbStamp->getNMembers();
220	for (int i = 0; i < nAtoms; ++i) {
221	//rbStamp->getMember(i) return the local index of current atom inside the molecule.
222	//It is not the same as local index of atom which is the index of atom at DataStorage class
223	atom = mol->getAtomAt(rbStamp->getMemberAt(i));
224	atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));
225	rb->addAtom(atom, atomStamp);
226	}
227
228	//after all of the atoms are added, we need to calculate the reference coordinates
229	rb->calcRefCoords();
230
231	//set the local index of this rigid body, global index will be set later
232	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
233
234	//the rule for naming rigidbody MoleculeName_RB_Integer
235	//The first part is the name of the molecule
236	//The second part is alway fixed as "RB"
237	//The third part is the index of the rigidbody defined in meta-data file
238	//For example, Butane_RB_0 is a valid rigid body name of butane molecule
239	/*@todo replace itoa by lexi_cast /
240	std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10);
241	rb->setType(mol->getType() + "_RB_" + s.c_str());
242
243	return rb;
244	}
245
246	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
247	BondType* bondType;
248	Atom* atomA;
249	Atom* atomB;
250
251	atomA = mol->getAtomAt(stamp->getA());
252	atomB = mol->getAtomAt(stamp->getB());
253
254	assert( atomA && atomB);
255
256	bondType = ff->getBondType(atomA->getType(), atomB->getType());
257
258	if (bondType == NULL) {
259	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
260	atomA->getType().c_str(),
261	atomB->getType().c_str());
262
263	painCave.isFatal = 1;
264	simError();
265	}
266	return new Bond(atomA, atomB, bondType);
267	}
268
269	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
270	Bend* bend = NULL;
271	std::vector<int> bendAtoms = stamp->getMembers();
272	if (bendAtoms.size() == 3) {
273	Atom* atomA = mol->getAtomAt(bendAtoms[0]);
274	Atom* atomB = mol->getAtomAt(bendAtoms[1]);
275	Atom* atomC = mol->getAtomAt(bendAtoms[2]);
276
277	assert( atomA && atomB && atomC);
278
279	BendType* bendType = ff->getBendType(atomA->getType().c_str(), atomB->getType().c_str(), atomC->getType().c_str());
280
281	if (bendType == NULL) {
282	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
283	atomA->getType().c_str(),
284	atomB->getType().c_str(),
285	atomC->getType().c_str());
286
287	painCave.isFatal = 1;
288	simError();
289	}
290
291	bend = new Bend(atomA, atomB, atomC, bendType);
292	} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
293	int ghostIndex = stamp->getGhostVectorSource();
294	int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
295	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
296	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
297	if (ghostAtom == NULL) {
298	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
299	painCave.isFatal = 1;
300	simError();
301	}
302
303	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
304
305	if (bendType == NULL) {
306	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
307	normalAtom->getType().c_str(),
308	ghostAtom->getType().c_str(),
309	"GHOST");
310
311	painCave.isFatal = 1;
312	simError();
313	}
314
315	bend = new GhostBend(normalAtom, ghostAtom, bendType);
316
317	}
318
319	return bend;
320	}
321
322	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
323
324	Torsion* torsion = NULL;
325	std::vector<int> torsionAtoms = stamp->getMembers();
326	if (torsionAtoms.size() < 3) {
327	return torsion;
328	}
329
330	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
331	Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
332	Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
333
334	if (torsionAtoms.size() == 4) {
335	Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
336
337	assert(atomA && atomB && atomC && atomD);
338
339	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
340	atomC->getType(), atomD->getType());
341
342	if (torsionType == NULL) {
343	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
344	atomA->getType().c_str(),
345	atomB->getType().c_str(),
346	atomC->getType().c_str(),
347	atomD->getType().c_str());
348
349	painCave.isFatal = 1;
350	simError();
351	}
352
353	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
354	}
355	else {
356
357	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
358	if (dAtom == NULL) {
359	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
360	painCave.isFatal = 1;
361	simError();
362	}
363
364	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
365	atomC->getType(), "GHOST");
366
367	if (torsionType == NULL) {
368	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
369	atomA->getType().c_str(),
370	atomB->getType().c_str(),
371	atomC->getType().c_str(),
372	"GHOST");
373
374	painCave.isFatal = 1;
375	simError();
376	}
377
378	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
379	}
380
381	return torsion;
382	}
383
384	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
385	int nAtoms;
386	CutoffGroup* cg;
387	Atom* atom;
388	cg = new CutoffGroup();
389
390	nAtoms = stamp->getNMembers();
391	for (int i =0; i < nAtoms; ++i) {
392	atom = mol->getAtomAt(stamp->getMemberAt(i));
393	assert(atom);
394	cg->addAtom(atom);
395	}
396
397	return cg;
398	}
399
400	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
401	CutoffGroup* cg;
402	cg = new CutoffGroup();
403	cg->addAtom(atom);
404	return cg;
405	}
406
407	void MoleculeCreator::createConstraintPair(Molecule* mol) {
408
409	//add bond constraints
410	Molecule::BondIterator bi;
411	Bond* bond;
412	for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
413
414	BondType* bt = bond->getBondType();
415
416	//class Parent1 {};
417	//class Child1 : public Parent {};
418	//class Child2 : public Parent {};
419	//Child1* ch1 = new Child1();
420	//Child2* ch2 = dynamic_cast<Child2*>(ch1);
421	//the dynamic_cast is succeed in above line. A compiler bug?
422
423	if (typeid(FixedBondType) == typeid(*bt)) {
424	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
425
426	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
427	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
428	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
429	mol->addConstraintPair(consPair);
430	}
431	}
432
433	//rigidbody -- rigidbody constraint is not support yet
434	}
435
436	void MoleculeCreator::createConstraintElem(Molecule* mol) {
437
438	ConstraintPair* consPair;
439	Molecule::ConstraintPairIterator cpi;
440	std::set<StuntDouble*> sdSet;
441	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
442
443	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
444	if (sdSet.find(sdA) == sdSet.end()){
445	sdSet.insert(sdA);
446	mol->addConstraintElem(new ConstraintElem(sdA));
447	}
448
449	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
450	if (sdSet.find(sdB) == sdSet.end()){
451	sdSet.insert(sdB);
452	mol->addConstraintElem(new ConstraintElem(sdB));
453	}
454
455	}
456
457	}
458
459	}