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 <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->getID());
    
    //create atoms
    Atom* atom;
    AtomStamp* currentAtomStamp;
    int nAtom = molStamp->getNAtoms();
    for (int i = 0; i < nAtom; ++i) {
      currentAtomStamp = molStamp->getAtom(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->getRigidBody(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->getBond(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->getBend(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->getTorsion(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->getCutoffGroup(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());

      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->getMember(i));
      atomStamp= molStamp->getAtom(rbStamp->getMember(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) {
    bool isGhostBend = false;
    int ghostIndex;

    
    //
    if (stamp->haveExtras()){
      LinkedAssign* extras = stamp->getExtras();
      LinkedAssign* currentExtra = extras;

      while (currentExtra != NULL){
        if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
          switch (currentExtra->getType()){
          case 0:
            ghostIndex = currentExtra->getInt();
            isGhostBend = true;
            break;

          default:
            sprintf(painCave.errMsg,
                    "SimSetup Error: ghostVectorSource must be an int.\n");
            painCave.isFatal = 1;
            simError();
          }
        } else{
          sprintf(painCave.errMsg,
                  "SimSetup Error: unhandled bend assignment:\n");
          painCave.isFatal = 1;
          simError();
        }
        currentExtra = currentExtra->getNext();
      }
        
    }

    if (isGhostBend) {

      int indexA = stamp->getA();
      int indexB= stamp->getB();

      assert(indexA != indexB);

      int normalIndex;
      if (indexA == ghostIndex) {
        normalIndex = indexB;
      } else if (indexB == ghostIndex) {
        normalIndex = indexA;
      }
        
      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();
      }
        
      return new GhostBend(normalAtom, ghostAtom, bendType);       

    } else {
            
      Atom* atomA = mol->getAtomAt(stamp->getA());
      Atom* atomB = mol->getAtomAt(stamp->getB());
      Atom* atomC = mol->getAtomAt(stamp->getC());

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

      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();
      }

      return new Bend(atomA, atomB, atomC, bendType);       
    }
  }    

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

    Atom* atomA = mol->getAtomAt(stamp->getA());
    Atom* atomB = mol->getAtomAt(stamp->getB());
    Atom* atomC = mol->getAtomAt(stamp->getC());
    Torsion* torsion;

    if (stamp->getD() != -1) {
      Atom* atomD = mol->getAtomAt(stamp->getD());

      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*>(atomC);
      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->getMember(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:	2346
Committed:	Wed Oct 5 19:34:01 2005 UTC (18 years, 9 months ago) by tim
File size:	15341 byte(s)
Log Message:	fix a bug in creating cutoffGroup. When cutoffGroup is turned off, there is a mismatch between group and center of mass array
#	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 <set>
52
53	#include "brains/MoleculeCreator.hpp"
54	#include "primitives/GhostBend.hpp"
55	#include "primitives/GhostTorsion.hpp"
56	#include "types/DirectionalAtomType.hpp"
57	#include "types/FixedBondType.hpp"
58	#include "utils/simError.h"
59	#include "utils/StringUtils.hpp"
60
61	namespace oopse {
62
63	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
64	int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
65
66	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID());
67
68	//create atoms
69	Atom* atom;
70	AtomStamp* currentAtomStamp;
71	int nAtom = molStamp->getNAtoms();
72	for (int i = 0; i < nAtom; ++i) {
73	currentAtomStamp = molStamp->getAtom(i);
74	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
75	mol->addAtom(atom);
76	}
77
78	//create rigidbodies
79	RigidBody* rb;
80	RigidBodyStamp * currentRigidBodyStamp;
81	int nRigidbodies = molStamp->getNRigidBodies();
82
83	for (int i = 0; i < nRigidbodies; ++i) {
84	currentRigidBodyStamp = molStamp->getRigidBody(i);
85	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
86	mol->addRigidBody(rb);
87	}
88
89	//create bonds
90	Bond* bond;
91	BondStamp* currentBondStamp;
92	int nBonds = molStamp->getNBonds();
93
94	for (int i = 0; i < nBonds; ++i) {
95	currentBondStamp = molStamp->getBond(i);
96	bond = createBond(ff, mol, currentBondStamp);
97	mol->addBond(bond);
98	}
99
100	//create bends
101	Bend* bend;
102	BendStamp* currentBendStamp;
103	int nBends = molStamp->getNBends();
104	for (int i = 0; i < nBends; ++i) {
105	currentBendStamp = molStamp->getBend(i);
106	bend = createBend(ff, mol, currentBendStamp);
107	mol->addBend(bend);
108	}
109
110	//create torsions
111	Torsion* torsion;
112	TorsionStamp* currentTorsionStamp;
113	int nTorsions = molStamp->getNTorsions();
114	for (int i = 0; i < nTorsions; ++i) {
115	currentTorsionStamp = molStamp->getTorsion(i);
116	torsion = createTorsion(ff, mol, currentTorsionStamp);
117	mol->addTorsion(torsion);
118	}
119
120	//create cutoffGroups
121	CutoffGroup* cutoffGroup;
122	CutoffGroupStamp* currentCutoffGroupStamp;
123	int nCutoffGroups = molStamp->getNCutoffGroups();
124	for (int i = 0; i < nCutoffGroups; ++i) {
125	currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
126	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
127	mol->addCutoffGroup(cutoffGroup);
128	}
129
130	//every free atom is a cutoff group
131	std::vector<Atom*> freeAtoms;
132	std::vector<Atom*>::iterator ai;
133	std::vector<Atom*>::iterator fai;
134
135	//add all atoms into allAtoms set
136	for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
137	freeAtoms.push_back(atom);
138	}
139
140	Molecule::CutoffGroupIterator ci;
141	CutoffGroup* cg;
142
143	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
144
145	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
146	//erase the atoms belong to cutoff groups from freeAtoms vector
147	freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom), freeAtoms.end());
148	}
149
150	}
151
152	//loop over the free atoms and then create one cutoff group for every single free atom
153
154	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
155	cutoffGroup = createCutoffGroup(mol, *fai);
156	mol->addCutoffGroup(cutoffGroup);
157	}
158	//create constraints
159	createConstraintPair(mol);
160	createConstraintElem(mol);
161
162	//the construction of this molecule is finished
163	mol->complete();
164
165	return mol;
166	}
167
168
169	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
170	LocalIndexManager* localIndexMan) {
171	AtomType * atomType;
172	Atom* atom;
173
174	atomType = ff->getAtomType(stamp->getType());
175
176	if (atomType == NULL) {
177	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
178	stamp->getType());
179
180	painCave.isFatal = 1;
181	simError();
182	}
183
184	//below code still have some kind of hard-coding smell
185	if (atomType->isDirectional()){
186
187	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
188
189	if (dAtomType == NULL) {
190	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
191
192	painCave.isFatal = 1;
193	simError();
194	}
195
196	DirectionalAtom* dAtom;
197	dAtom = new DirectionalAtom(dAtomType);
198	atom = dAtom;
199	}
200	else{
201	atom = new Atom(atomType);
202	}
203
204	atom->setLocalIndex(localIndexMan->getNextAtomIndex());
205
206	return atom;
207	}
208
209	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp molStamp, Molecule mol,
210	RigidBodyStamp* rbStamp,
211	LocalIndexManager* localIndexMan) {
212	Atom* atom;
213	int nAtoms;
214	Vector3d refCoor;
215	AtomStamp* atomStamp;
216
217	RigidBody* rb = new RigidBody();
218	nAtoms = rbStamp->getNMembers();
219	for (int i = 0; i < nAtoms; ++i) {
220	//rbStamp->getMember(i) return the local index of current atom inside the molecule.
221	//It is not the same as local index of atom which is the index of atom at DataStorage class
222	atom = mol->getAtomAt(rbStamp->getMember(i));
223	atomStamp= molStamp->getAtom(rbStamp->getMember(i));
224	rb->addAtom(atom, atomStamp);
225	}
226
227	//after all of the atoms are added, we need to calculate the reference coordinates
228	rb->calcRefCoords();
229
230	//set the local index of this rigid body, global index will be set later
231	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
232
233	//the rule for naming rigidbody MoleculeName_RB_Integer
234	//The first part is the name of the molecule
235	//The second part is alway fixed as "RB"
236	//The third part is the index of the rigidbody defined in meta-data file
237	//For example, Butane_RB_0 is a valid rigid body name of butane molecule
238	/*@todo replace itoa by lexi_cast /
239	std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10);
240	rb->setType(mol->getType() + "_RB_" + s.c_str());
241
242	return rb;
243	}
244
245	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
246	BondType* bondType;
247	Atom* atomA;
248	Atom* atomB;
249
250	atomA = mol->getAtomAt(stamp->getA());
251	atomB = mol->getAtomAt(stamp->getB());
252
253	assert( atomA && atomB);
254
255	bondType = ff->getBondType(atomA->getType(), atomB->getType());
256
257	if (bondType == NULL) {
258	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
259	atomA->getType().c_str(),
260	atomB->getType().c_str());
261
262	painCave.isFatal = 1;
263	simError();
264	}
265	return new Bond(atomA, atomB, bondType);
266	}
267
268	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
269	bool isGhostBend = false;
270	int ghostIndex;
271
272
273	//
274	if (stamp->haveExtras()){
275	LinkedAssign* extras = stamp->getExtras();
276	LinkedAssign* currentExtra = extras;
277
278	while (currentExtra != NULL){
279	if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){
280	switch (currentExtra->getType()){
281	case 0:
282	ghostIndex = currentExtra->getInt();
283	isGhostBend = true;
284	break;
285
286	default:
287	sprintf(painCave.errMsg,
288	"SimSetup Error: ghostVectorSource must be an int.\n");
289	painCave.isFatal = 1;
290	simError();
291	}
292	} else{
293	sprintf(painCave.errMsg,
294	"SimSetup Error: unhandled bend assignment:\n");
295	painCave.isFatal = 1;
296	simError();
297	}
298	currentExtra = currentExtra->getNext();
299	}
300
301	}
302
303	if (isGhostBend) {
304
305	int indexA = stamp->getA();
306	int indexB= stamp->getB();
307
308	assert(indexA != indexB);
309
310	int normalIndex;
311	if (indexA == ghostIndex) {
312	normalIndex = indexB;
313	} else if (indexB == ghostIndex) {
314	normalIndex = indexA;
315	}
316
317	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
318	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
319	if (ghostAtom == NULL) {
320	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
321	painCave.isFatal = 1;
322	simError();
323	}
324
325	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
326
327	if (bendType == NULL) {
328	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
329	normalAtom->getType().c_str(),
330	ghostAtom->getType().c_str(),
331	"GHOST");
332
333	painCave.isFatal = 1;
334	simError();
335	}
336
337	return new GhostBend(normalAtom, ghostAtom, bendType);
338
339	} else {
340
341	Atom* atomA = mol->getAtomAt(stamp->getA());
342	Atom* atomB = mol->getAtomAt(stamp->getB());
343	Atom* atomC = mol->getAtomAt(stamp->getC());
344
345	assert( atomA && atomB && atomC);
346
347	BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
348
349	if (bendType == NULL) {
350	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
351	atomA->getType().c_str(),
352	atomB->getType().c_str(),
353	atomC->getType().c_str());
354
355	painCave.isFatal = 1;
356	simError();
357	}
358
359	return new Bend(atomA, atomB, atomC, bendType);
360	}
361	}
362
363	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
364
365	Atom* atomA = mol->getAtomAt(stamp->getA());
366	Atom* atomB = mol->getAtomAt(stamp->getB());
367	Atom* atomC = mol->getAtomAt(stamp->getC());
368	Torsion* torsion;
369
370	if (stamp->getD() != -1) {
371	Atom* atomD = mol->getAtomAt(stamp->getD());
372
373	assert(atomA && atomB && atomC && atomD);
374
375	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
376	atomC->getType(), atomD->getType());
377
378	if (torsionType == NULL) {
379	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
380	atomA->getType().c_str(),
381	atomB->getType().c_str(),
382	atomC->getType().c_str(),
383	atomD->getType().c_str());
384
385	painCave.isFatal = 1;
386	simError();
387	}
388
389	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
390	}
391	else {
392
393	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC);
394	if (dAtom == NULL) {
395	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
396	painCave.isFatal = 1;
397	simError();
398	}
399
400	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
401	atomC->getType(), "GHOST");
402
403	if (torsionType == NULL) {
404	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
405	atomA->getType().c_str(),
406	atomB->getType().c_str(),
407	atomC->getType().c_str(),
408	"GHOST");
409
410	painCave.isFatal = 1;
411	simError();
412	}
413
414	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
415	}
416
417	return torsion;
418	}
419
420	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
421	int nAtoms;
422	CutoffGroup* cg;
423	Atom* atom;
424	cg = new CutoffGroup();
425
426	nAtoms = stamp->getNMembers();
427	for (int i =0; i < nAtoms; ++i) {
428	atom = mol->getAtomAt(stamp->getMember(i));
429	assert(atom);
430	cg->addAtom(atom);
431	}
432
433	return cg;
434	}
435
436	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
437	CutoffGroup* cg;
438	cg = new CutoffGroup();
439	cg->addAtom(atom);
440	return cg;
441	}
442
443	void MoleculeCreator::createConstraintPair(Molecule* mol) {
444
445	//add bond constraints
446	Molecule::BondIterator bi;
447	Bond* bond;
448	for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
449
450	BondType* bt = bond->getBondType();
451
452	//class Parent1 {};
453	//class Child1 : public Parent {};
454	//class Child2 : public Parent {};
455	//Child1* ch1 = new Child1();
456	//Child2* ch2 = dynamic_cast<Child2*>(ch1);
457	//the dynamic_cast is succeed in above line. A compiler bug?
458
459	if (typeid(FixedBondType) == typeid(*bt)) {
460	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
461
462	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
463	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
464	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
465	mol->addConstraintPair(consPair);
466	}
467	}
468
469	//rigidbody -- rigidbody constraint is not support yet
470	}
471
472	void MoleculeCreator::createConstraintElem(Molecule* mol) {
473
474	ConstraintPair* consPair;
475	Molecule::ConstraintPairIterator cpi;
476	std::set<StuntDouble*> sdSet;
477	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
478
479	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
480	if (sdSet.find(sdA) == sdSet.end()){
481	sdSet.insert(sdA);
482	mol->addConstraintElem(new ConstraintElem(sdA));
483	}
484
485	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
486	if (sdSet.find(sdB) == sdSet.end()){
487	sdSet.insert(sdB);
488	mol->addConstraintElem(new ConstraintElem(sdB));
489	}
490
491	}
492
493	}
494
495	}