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:	647
Committed:	Wed Oct 5 19:34:01 2005 UTC (20 years, 1 month 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
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	507	/**
43			* @file MoleculeCreator.cpp
44			* @author tlin
45			* @date 11/04/2004
46			* @time 13:44am
47			* @version 1.0
48			*/
49	gezelter	246
50			#include <cassert>
51			#include <set>
52
53			#include "brains/MoleculeCreator.hpp"
54			#include "primitives/GhostBend.hpp"
55	tim	273	#include "primitives/GhostTorsion.hpp"
56	gezelter	246	#include "types/DirectionalAtomType.hpp"
57			#include "types/FixedBondType.hpp"
58			#include "utils/simError.h"
59			#include "utils/StringUtils.hpp"
60
61			namespace oopse {
62	tim	647
63	gezelter	507	Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp,
64			int stampId, int globalIndex, LocalIndexManager* localIndexMan) {
65	gezelter	246
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	gezelter	507	currentAtomStamp = molStamp->getAtom(i);
74			atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
75			mol->addAtom(atom);
76	gezelter	246	}
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	gezelter	507	currentRigidBodyStamp = molStamp->getRigidBody(i);
85			rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan);
86			mol->addRigidBody(rb);
87	gezelter	246	}
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	gezelter	507	currentBondStamp = molStamp->getBond(i);
96			bond = createBond(ff, mol, currentBondStamp);
97			mol->addBond(bond);
98	gezelter	246	}
99
100			//create bends
101			Bend* bend;
102			BendStamp* currentBendStamp;
103			int nBends = molStamp->getNBends();
104			for (int i = 0; i < nBends; ++i) {
105	gezelter	507	currentBendStamp = molStamp->getBend(i);
106			bend = createBend(ff, mol, currentBendStamp);
107			mol->addBend(bend);
108	gezelter	246	}
109
110			//create torsions
111			Torsion* torsion;
112			TorsionStamp* currentTorsionStamp;
113			int nTorsions = molStamp->getNTorsions();
114			for (int i = 0; i < nTorsions; ++i) {
115	gezelter	507	currentTorsionStamp = molStamp->getTorsion(i);
116			torsion = createTorsion(ff, mol, currentTorsionStamp);
117			mol->addTorsion(torsion);
118	gezelter	246	}
119
120			//create cutoffGroups
121			CutoffGroup* cutoffGroup;
122			CutoffGroupStamp* currentCutoffGroupStamp;
123			int nCutoffGroups = molStamp->getNCutoffGroups();
124			for (int i = 0; i < nCutoffGroups; ++i) {
125	gezelter	507	currentCutoffGroupStamp = molStamp->getCutoffGroup(i);
126			cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
127			mol->addCutoffGroup(cutoffGroup);
128	gezelter	246	}
129
130			//every free atom is a cutoff group
131	tim	647	std::vector<Atom*> freeAtoms;
132			std::vector<Atom*>::iterator ai;
133			std::vector<Atom*>::iterator fai;
134	gezelter	246
135			//add all atoms into allAtoms set
136	tim	647	for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
137			freeAtoms.push_back(atom);
138	gezelter	246	}
139
140			Molecule::CutoffGroupIterator ci;
141			CutoffGroup* cg;
142
143			for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
144
145	gezelter	507	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
146	tim	647	//erase the atoms belong to cutoff groups from freeAtoms vector
147			freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom), freeAtoms.end());
148	gezelter	507	}
149	gezelter	246
150			}
151
152			//loop over the free atoms and then create one cutoff group for every single free atom
153	tim	647
154	gezelter	246	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
155	gezelter	507	cutoffGroup = createCutoffGroup(mol, *fai);
156			mol->addCutoffGroup(cutoffGroup);
157	gezelter	246	}
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	gezelter	507	}
167	gezelter	246
168
169	gezelter	507	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
170			LocalIndexManager* localIndexMan) {
171	gezelter	246	AtomType * atomType;
172			Atom* atom;
173
174			atomType = ff->getAtomType(stamp->getType());
175
176			if (atomType == NULL) {
177	gezelter	507	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
178			stamp->getType());
179	gezelter	246
180	gezelter	507	painCave.isFatal = 1;
181			simError();
182	gezelter	246	}
183
184			//below code still have some kind of hard-coding smell
185			if (atomType->isDirectional()){
186
187	gezelter	507	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
188	gezelter	246
189	gezelter	507	if (dAtomType == NULL) {
190			sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
191	gezelter	246
192	gezelter	507	painCave.isFatal = 1;
193			simError();
194			}
195	gezelter	246
196	gezelter	507	DirectionalAtom* dAtom;
197			dAtom = new DirectionalAtom(dAtomType);
198			atom = dAtom;
199	gezelter	246	}
200			else{
201	gezelter	507	atom = new Atom(atomType);
202	gezelter	246	}
203
204			atom->setLocalIndex(localIndexMan->getNextAtomIndex());
205
206			return atom;
207	gezelter	507	}
208	gezelter	246
209	gezelter	507	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp molStamp, Molecule mol,
210			RigidBodyStamp* rbStamp,
211			LocalIndexManager* localIndexMan) {
212	gezelter	246	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	gezelter	507	//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	gezelter	246	}
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	gezelter	403	std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10);
240			rb->setType(mol->getType() + "_RB_" + s.c_str());
241	tim	292
242	gezelter	246	return rb;
243	gezelter	507	}
244	gezelter	246
245	gezelter	507	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) {
246	gezelter	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	gezelter	507	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
259			atomA->getType().c_str(),
260			atomB->getType().c_str());
261	gezelter	246
262	gezelter	507	painCave.isFatal = 1;
263			simError();
264	gezelter	246	}
265			return new Bond(atomA, atomB, bondType);
266	gezelter	507	}
267	gezelter	246
268	gezelter	507	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) {
269	gezelter	246	bool isGhostBend = false;
270			int ghostIndex;
271
272
273			//
274			if (stamp->haveExtras()){
275	gezelter	507	LinkedAssign* extras = stamp->getExtras();
276			LinkedAssign* currentExtra = extras;
277	gezelter	246
278	gezelter	507	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	gezelter	246
286	gezelter	507	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	gezelter	246
301			}
302
303			if (isGhostBend) {
304
305	gezelter	507	int indexA = stamp->getA();
306			int indexB= stamp->getB();
307	gezelter	246
308	gezelter	507	assert(indexA != indexB);
309	gezelter	246
310	gezelter	507	int normalIndex;
311			if (indexA == ghostIndex) {
312			normalIndex = indexB;
313			} else if (indexB == ghostIndex) {
314			normalIndex = indexA;
315			}
316	gezelter	246
317	gezelter	507	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	gezelter	246
325	gezelter	507	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
326	gezelter	246
327	gezelter	507	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	gezelter	246
333	gezelter	507	painCave.isFatal = 1;
334			simError();
335			}
336	gezelter	246
337	gezelter	507	return new GhostBend(normalAtom, ghostAtom, bendType);
338	gezelter	246
339			} else {
340
341	gezelter	507	Atom* atomA = mol->getAtomAt(stamp->getA());
342			Atom* atomB = mol->getAtomAt(stamp->getB());
343			Atom* atomC = mol->getAtomAt(stamp->getC());
344	gezelter	246
345	gezelter	507	assert( atomA && atomB && atomC);
346	gezelter	246
347	gezelter	507	BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType());
348	gezelter	246
349	gezelter	507	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	gezelter	246
355	gezelter	507	painCave.isFatal = 1;
356			simError();
357			}
358	gezelter	246
359	gezelter	507	return new Bend(atomA, atomB, atomC, bendType);
360	gezelter	246	}
361	gezelter	507	}
362	gezelter	246
363	gezelter	507	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) {
364	gezelter	246
365	tim	273	Atom* atomA = mol->getAtomAt(stamp->getA());
366			Atom* atomB = mol->getAtomAt(stamp->getB());
367			Atom* atomC = mol->getAtomAt(stamp->getC());
368			Torsion* torsion;
369	gezelter	246
370	tim	273	if (stamp->getD() != -1) {
371	gezelter	507	Atom* atomD = mol->getAtomAt(stamp->getD());
372	gezelter	246
373	gezelter	507	assert(atomA && atomB && atomC && atomD);
374	tim	273
375	gezelter	507	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
376			atomC->getType(), atomD->getType());
377	gezelter	246
378	gezelter	507	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	tim	273
385	gezelter	507	painCave.isFatal = 1;
386			simError();
387			}
388	tim	273
389	gezelter	507	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
390	gezelter	246	}
391	tim	273	else {
392
393	gezelter	507	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	tim	273
400	gezelter	507	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
401			atomC->getType(), "GHOST");
402	tim	273
403	gezelter	507	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	tim	273
410	gezelter	507	painCave.isFatal = 1;
411			simError();
412			}
413	tim	273
414	gezelter	507	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
415	tim	273	}
416
417			return torsion;
418	gezelter	507	}
419	gezelter	246
420	gezelter	507	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
421	gezelter	246	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	gezelter	507	atom = mol->getAtomAt(stamp->getMember(i));
429			assert(atom);
430			cg->addAtom(atom);
431	gezelter	246	}
432
433			return cg;
434	gezelter	507	}
435	gezelter	246
436	gezelter	507	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
437	gezelter	246	CutoffGroup* cg;
438			cg = new CutoffGroup();
439			cg->addAtom(atom);
440			return cg;
441	gezelter	507	}
442	gezelter	246
443	gezelter	507	void MoleculeCreator::createConstraintPair(Molecule* mol) {
444	gezelter	246
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	gezelter	507	BondType* bt = bond->getBondType();
451	gezelter	246
452	gezelter	507	//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	gezelter	246
459	gezelter	507	if (typeid(FixedBondType) == typeid(*bt)) {
460			FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
461	gezelter	246
462	gezelter	507	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	gezelter	246	}
468
469			//rigidbody -- rigidbody constraint is not support yet
470	gezelter	507	}
471	gezelter	246
472	gezelter	507	void MoleculeCreator::createConstraintElem(Molecule* mol) {
473	gezelter	246
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	gezelter	507	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
480			if (sdSet.find(sdA) == sdSet.end()){
481			sdSet.insert(sdA);
482			mol->addConstraintElem(new ConstraintElem(sdA));
483			}
484	gezelter	246
485	gezelter	507	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
486			if (sdSet.find(sdB) == sdSet.end()){
487			sdSet.insert(sdB);
488			mol->addConstraintElem(new ConstraintElem(sdB));
489			}
490	gezelter	246
491			}
492
493	gezelter	507	}
494	gezelter	246
495			}