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, 7 months ago) by gezelter
File size:	14931 byte(s)
Log Message:	made some minor changes to allow compilation with the portland group compilers
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	2204	/**
43			* @file MoleculeCreator.cpp
44			* @author tlin
45			* @date 11/04/2004
46			* @time 13:44am
47			* @version 1.0
48			*/
49	gezelter	1930
50			#include <cassert>
51	gezelter	2508	#include <typeinfo>
52	gezelter	1930	#include <set>
53
54			#include "brains/MoleculeCreator.hpp"
55			#include "primitives/GhostBend.hpp"
56	tim	1957	#include "primitives/GhostTorsion.hpp"
57	gezelter	1930	#include "types/DirectionalAtomType.hpp"
58			#include "types/FixedBondType.hpp"
59			#include "utils/simError.h"
60			#include "utils/StringUtils.hpp"
61
62			namespace oopse {
63	tim	2346
64	gezelter	2204	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
65			int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
66	gezelter	1930
67	tim	2469	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName());
68	gezelter	1930
69			//create atoms
70			Atom* atom;
71			AtomStamp* currentAtomStamp;
72			int nAtom = molStamp->getNAtoms();
73			for (int i = 0; i < nAtom; ++i) {
74	tim	2469	currentAtomStamp = molStamp->getAtomStamp(i);
75	gezelter	2204	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
76			mol->addAtom(atom);
77	gezelter	1930	}
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	tim	2469	currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
86	gezelter	2204	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
87			mol->addRigidBody(rb);
88	gezelter	1930	}
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	tim	2469	currentBondStamp = molStamp->getBondStamp(i);
97	gezelter	2204	bond = createBond(ff, mol, currentBondStamp);
98			mol->addBond(bond);
99	gezelter	1930	}
100
101			//create bends
102			Bend* bend;
103			BendStamp* currentBendStamp;
104			int nBends = molStamp->getNBends();
105			for (int i = 0; i < nBends; ++i) {
106	tim	2469	currentBendStamp = molStamp->getBendStamp(i);
107	gezelter	2204	bend = createBend(ff, mol, currentBendStamp);
108			mol->addBend(bend);
109	gezelter	1930	}
110
111			//create torsions
112			Torsion* torsion;
113			TorsionStamp* currentTorsionStamp;
114			int nTorsions = molStamp->getNTorsions();
115			for (int i = 0; i < nTorsions; ++i) {
116	tim	2469	currentTorsionStamp = molStamp->getTorsionStamp(i);
117	gezelter	2204	torsion = createTorsion(ff, mol, currentTorsionStamp);
118			mol->addTorsion(torsion);
119	gezelter	1930	}
120
121			//create cutoffGroups
122			CutoffGroup* cutoffGroup;
123			CutoffGroupStamp* currentCutoffGroupStamp;
124			int nCutoffGroups = molStamp->getNCutoffGroups();
125			for (int i = 0; i < nCutoffGroups; ++i) {
126	tim	2469	currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
127	gezelter	2204	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
128			mol->addCutoffGroup(cutoffGroup);
129	gezelter	1930	}
130
131			//every free atom is a cutoff group
132	tim	2346	std::vector<Atom*> freeAtoms;
133			std::vector<Atom*>::iterator ai;
134			std::vector<Atom*>::iterator fai;
135	gezelter	1930
136			//add all atoms into allAtoms set
137	tim	2346	for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
138			freeAtoms.push_back(atom);
139	gezelter	1930	}
140
141			Molecule::CutoffGroupIterator ci;
142			CutoffGroup* cg;
143
144			for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
145
146	gezelter	2204	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
147	tim	2346	//erase the atoms belong to cutoff groups from freeAtoms vector
148			freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom), freeAtoms.end());
149	gezelter	2204	}
150	gezelter	1930
151			}
152
153			//loop over the free atoms and then create one cutoff group for every single free atom
154	tim	2346
155	gezelter	1930	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
156	gezelter	2204	cutoffGroup = createCutoffGroup(mol, *fai);
157			mol->addCutoffGroup(cutoffGroup);
158	gezelter	1930	}
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	gezelter	2204	}
168	gezelter	1930
169
170	gezelter	2204	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
171			LocalIndexManager* localIndexMan) {
172	gezelter	1930	AtomType * atomType;
173			Atom* atom;
174
175			atomType = ff->getAtomType(stamp->getType());
176
177			if (atomType == NULL) {
178	gezelter	2204	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
179	tim	2469	stamp->getType().c_str());
180	gezelter	1930
181	gezelter	2204	painCave.isFatal = 1;
182			simError();
183	gezelter	1930	}
184
185			//below code still have some kind of hard-coding smell
186			if (atomType->isDirectional()){
187
188	gezelter	2204	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
189	gezelter	1930
190	gezelter	2204	if (dAtomType == NULL) {
191			sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
192	gezelter	1930
193	gezelter	2204	painCave.isFatal = 1;
194			simError();
195			}
196	gezelter	1930
197	gezelter	2204	DirectionalAtom* dAtom;
198			dAtom = new DirectionalAtom(dAtomType);
199			atom = dAtom;
200	gezelter	1930	}
201			else{
202	gezelter	2204	atom = new Atom(atomType);
203	gezelter	1930	}
204
205			atom->setLocalIndex(localIndexMan->getNextAtomIndex());
206
207			return atom;
208	gezelter	2204	}
209	gezelter	1930
210	gezelter	2204	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp molStamp, Molecule mol,
211			RigidBodyStamp* rbStamp,
212			LocalIndexManager* localIndexMan) {
213	gezelter	1930	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	gezelter	2204	//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	tim	2469	atom = mol->getAtomAt(rbStamp->getMemberAt(i));
224			atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));
225	gezelter	2204	rb->addAtom(atom, atomStamp);
226	gezelter	1930	}
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	gezelter	2087	std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10);
241			rb->setType(mol->getType() + "_RB_" + s.c_str());
242	tim	1976
243	gezelter	1930	return rb;
244	gezelter	2204	}
245	gezelter	1930
246	gezelter	2204	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
247	gezelter	1930	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	gezelter	2204	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
260			atomA->getType().c_str(),
261			atomB->getType().c_str());
262	gezelter	1930
263	gezelter	2204	painCave.isFatal = 1;
264			simError();
265	gezelter	1930	}
266			return new Bond(atomA, atomB, bondType);
267	gezelter	2204	}
268	gezelter	1930
269	gezelter	2204	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
270	tim	2469	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	gezelter	1930
277	tim	2469	assert( atomA && atomB && atomC);
278	gezelter	1930
279	tim	2469	BendType* bendType = ff->getBendType(atomA->getType().c_str(), atomB->getType().c_str(), atomC->getType().c_str());
280	gezelter	1930
281	tim	2469	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	gezelter	2204	}
290	gezelter	1930
291	tim	2469	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	gezelter	2204	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	gezelter	1930
303	gezelter	2204	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
304	gezelter	1930
305	gezelter	2204	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	gezelter	1930
311	gezelter	2204	painCave.isFatal = 1;
312			simError();
313			}
314	gezelter	1930
315	tim	2469	bend = new GhostBend(normalAtom, ghostAtom, bendType);
316	gezelter	1930
317	tim	2469	}
318
319			return bend;
320			}
321	gezelter	1930
322	tim	2469	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
323	gezelter	1930
324	tim	2469	Torsion* torsion = NULL;
325			std::vector<int> torsionAtoms = stamp->getMembers();
326			if (torsionAtoms.size() < 3) {
327			return torsion;
328	gezelter	1930	}
329
330	tim	2469	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
331			Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
332			Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
333	gezelter	1930
334	tim	2469	if (torsionAtoms.size() == 4) {
335			Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
336	gezelter	1930
337	gezelter	2204	assert(atomA && atomB && atomC && atomD);
338	tim	1957
339	gezelter	2204	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
340			atomC->getType(), atomD->getType());
341	gezelter	1930
342	gezelter	2204	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	tim	1957
349	gezelter	2204	painCave.isFatal = 1;
350			simError();
351			}
352	tim	1957
353	gezelter	2204	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
354	gezelter	1930	}
355	tim	1957	else {
356
357	tim	2469	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
358	gezelter	2204	if (dAtom == NULL) {
359			sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
360			painCave.isFatal = 1;
361			simError();
362			}
363	tim	1957
364	gezelter	2204	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
365			atomC->getType(), "GHOST");
366	tim	1957
367	gezelter	2204	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	tim	1957
374	gezelter	2204	painCave.isFatal = 1;
375			simError();
376			}
377	tim	1957
378	gezelter	2204	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
379	tim	1957	}
380
381			return torsion;
382	gezelter	2204	}
383	gezelter	1930
384	gezelter	2204	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
385	gezelter	1930	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	tim	2469	atom = mol->getAtomAt(stamp->getMemberAt(i));
393	gezelter	2204	assert(atom);
394			cg->addAtom(atom);
395	gezelter	1930	}
396
397			return cg;
398	gezelter	2204	}
399	gezelter	1930
400	gezelter	2204	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
401	gezelter	1930	CutoffGroup* cg;
402			cg = new CutoffGroup();
403			cg->addAtom(atom);
404			return cg;
405	gezelter	2204	}
406	gezelter	1930
407	gezelter	2204	void MoleculeCreator::createConstraintPair(Molecule* mol) {
408	gezelter	1930
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	gezelter	2204	BondType* bt = bond->getBondType();
415	gezelter	1930
416	gezelter	2204	//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	gezelter	1930
423	gezelter	2204	if (typeid(FixedBondType) == typeid(*bt)) {
424			FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
425	gezelter	1930
426	gezelter	2204	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	gezelter	1930	}
432
433			//rigidbody -- rigidbody constraint is not support yet
434	gezelter	2204	}
435	gezelter	1930
436	gezelter	2204	void MoleculeCreator::createConstraintElem(Molecule* mol) {
437	gezelter	1930
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	gezelter	2204	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
444			if (sdSet.find(sdA) == sdSet.end()){
445			sdSet.insert(sdA);
446			mol->addConstraintElem(new ConstraintElem(sdA));
447			}
448	gezelter	1930
449	gezelter	2204	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
450			if (sdSet.find(sdB) == sdSet.end()){
451			sdSet.insert(sdB);
452			mol->addConstraintElem(new ConstraintElem(sdB));
453			}
454	gezelter	1930
455			}
456
457	gezelter	2204	}
458	gezelter	1930
459			}