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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
  
/**
 * @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 OpenMD {
  
  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 inversions
    Inversion* inversion;
    InversionStamp* currentInversionStamp;
    int nInversions = molStamp->getNInversions();
    for (int i = 0; i < nInversions; ++i) {
      currentInversionStamp = molStamp->getInversionStamp(i);
      inversion = createInversion(ff, mol, currentInversionStamp);
      if (inversion != NULL ) {
        mol->addInversion(inversion);
      }
    }

    //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, localIndexMan);
      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, localIndexMan);
      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 = OpenMD_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;
  }    

  Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol, 
                                              InversionStamp* stamp) {
    
    Inversion* inversion = NULL;
    int center = stamp->getCenter();
    std::vector<int> satellites = stamp->getSatellites();
    if (satellites.size() != 3) {
        return inversion;
    }

    Atom* atomA = mol->getAtomAt(center);
    Atom* atomB = mol->getAtomAt(satellites[0]);
    Atom* atomC = mol->getAtomAt(satellites[1]);
    Atom* atomD = mol->getAtomAt(satellites[2]);
      
    assert(atomA && atomB && atomC && atomD);
    
    InversionType* inversionType = ff->getInversionType(atomA->getType(), 
                                                        atomB->getType(), 
                                                        atomC->getType(), 
                                                        atomD->getType());

    if (inversionType == NULL) {
      sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n"
              "\t(May not be a problem: not all inversions are parametrized)\n",
              atomA->getType().c_str(),
              atomB->getType().c_str(),
              atomC->getType().c_str(),
              atomD->getType().c_str());
      
      painCave.isFatal = 0;
      painCave.severity = OPENMD_INFO;
      simError();
      return NULL;
    } else {
      
      inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
      return inversion;
    }
  }
  

  CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, 
                                                  CutoffGroupStamp* stamp,
                                                  LocalIndexManager* localIndexMan) {
    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);
    }
    
    //set the local index of this cutoffGroup, global index will be set later
    cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
    
    return cg;
  }    
  
  CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
                                                  LocalIndexManager* localIndexMan) {
    CutoffGroup* cg;
    cg  = new CutoffGroup();
    cg->addAtom(atom);

    //set the local index of this cutoffGroup, global index will be set later
    cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());

    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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 6 months ago) by gezelter
File size:	18181 byte(s)
Log Message:	updated copyright notices
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	/**
44	* @file MoleculeCreator.cpp
45	* @author tlin
46	* @date 11/04/2004
47	* @time 13:44am
48	* @version 1.0
49	*/
50
51	#include <cassert>
52	#include <typeinfo>
53	#include <set>
54
55	#include "brains/MoleculeCreator.hpp"
56	#include "primitives/GhostBend.hpp"
57	#include "primitives/GhostTorsion.hpp"
58	#include "types/DirectionalAtomType.hpp"
59	#include "types/FixedBondType.hpp"
60	#include "utils/simError.h"
61	#include "utils/StringUtils.hpp"
62
63	namespace OpenMD {
64
65	Molecule* MoleculeCreator::createMolecule(ForceField* ff,
66	MoleculeStamp *molStamp,
67	int stampId, int globalIndex,
68	LocalIndexManager* localIndexMan) {
69	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName());
70
71	//create atoms
72	Atom* atom;
73	AtomStamp* currentAtomStamp;
74	int nAtom = molStamp->getNAtoms();
75	for (int i = 0; i < nAtom; ++i) {
76	currentAtomStamp = molStamp->getAtomStamp(i);
77	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
78	mol->addAtom(atom);
79	}
80
81	//create rigidbodies
82	RigidBody* rb;
83	RigidBodyStamp * currentRigidBodyStamp;
84	int nRigidbodies = molStamp->getNRigidBodies();
85
86	for (int i = 0; i < nRigidbodies; ++i) {
87	currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
88	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp,
89	localIndexMan);
90	mol->addRigidBody(rb);
91	}
92
93	//create bonds
94	Bond* bond;
95	BondStamp* currentBondStamp;
96	int nBonds = molStamp->getNBonds();
97
98	for (int i = 0; i < nBonds; ++i) {
99	currentBondStamp = molStamp->getBondStamp(i);
100	bond = createBond(ff, mol, currentBondStamp);
101	mol->addBond(bond);
102	}
103
104	//create bends
105	Bend* bend;
106	BendStamp* currentBendStamp;
107	int nBends = molStamp->getNBends();
108	for (int i = 0; i < nBends; ++i) {
109	currentBendStamp = molStamp->getBendStamp(i);
110	bend = createBend(ff, mol, currentBendStamp);
111	mol->addBend(bend);
112	}
113
114	//create torsions
115	Torsion* torsion;
116	TorsionStamp* currentTorsionStamp;
117	int nTorsions = molStamp->getNTorsions();
118	for (int i = 0; i < nTorsions; ++i) {
119	currentTorsionStamp = molStamp->getTorsionStamp(i);
120	torsion = createTorsion(ff, mol, currentTorsionStamp);
121	mol->addTorsion(torsion);
122	}
123
124	//create inversions
125	Inversion* inversion;
126	InversionStamp* currentInversionStamp;
127	int nInversions = molStamp->getNInversions();
128	for (int i = 0; i < nInversions; ++i) {
129	currentInversionStamp = molStamp->getInversionStamp(i);
130	inversion = createInversion(ff, mol, currentInversionStamp);
131	if (inversion != NULL ) {
132	mol->addInversion(inversion);
133	}
134	}
135
136	//create cutoffGroups
137	CutoffGroup* cutoffGroup;
138	CutoffGroupStamp* currentCutoffGroupStamp;
139	int nCutoffGroups = molStamp->getNCutoffGroups();
140	for (int i = 0; i < nCutoffGroups; ++i) {
141	currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
142	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, localIndexMan);
143	mol->addCutoffGroup(cutoffGroup);
144	}
145
146	//every free atom is a cutoff group
147	std::vector<Atom*> freeAtoms;
148	std::vector<Atom*>::iterator ai;
149	std::vector<Atom*>::iterator fai;
150
151	//add all atoms into allAtoms set
152	for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
153	freeAtoms.push_back(atom);
154	}
155
156	Molecule::CutoffGroupIterator ci;
157	CutoffGroup* cg;
158
159	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
160	cg = mol->nextCutoffGroup(ci)) {
161
162	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
163	//erase the atoms belong to cutoff groups from freeAtoms vector
164	freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom),
165	freeAtoms.end());
166	}
167	}
168
169	// loop over the free atoms and then create one cutoff group for
170	// every single free atom
171
172	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
173	cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan);
174	mol->addCutoffGroup(cutoffGroup);
175	}
176	//create constraints
177	createConstraintPair(mol);
178	createConstraintElem(mol);
179
180	//the construction of this molecule is finished
181	mol->complete();
182
183	return mol;
184	}
185
186
187	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol,
188	AtomStamp* stamp,
189	LocalIndexManager* localIndexMan) {
190	AtomType * atomType;
191	Atom* atom;
192
193	atomType = ff->getAtomType(stamp->getType());
194
195	if (atomType == NULL) {
196	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
197	stamp->getType().c_str());
198
199	painCave.isFatal = 1;
200	simError();
201	}
202
203	//below code still have some kind of hard-coding smell
204	if (atomType->isDirectional()){
205
206	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
207
208	if (dAtomType == NULL) {
209	sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
210
211	painCave.isFatal = 1;
212	simError();
213	}
214
215	DirectionalAtom* dAtom;
216	dAtom = new DirectionalAtom(dAtomType);
217	atom = dAtom;
218	}
219	else{
220	atom = new Atom(atomType);
221	}
222
223	atom->setLocalIndex(localIndexMan->getNextAtomIndex());
224
225	return atom;
226	}
227
228	RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
229	Molecule* mol,
230	RigidBodyStamp* rbStamp,
231	LocalIndexManager* localIndexMan) {
232	Atom* atom;
233	int nAtoms;
234	Vector3d refCoor;
235	AtomStamp* atomStamp;
236
237	RigidBody* rb = new RigidBody();
238	nAtoms = rbStamp->getNMembers();
239	for (int i = 0; i < nAtoms; ++i) {
240	//rbStamp->getMember(i) return the local index of current atom
241	//inside the molecule. It is not the same as local index of
242	//atom which is the index of atom at DataStorage class
243	atom = mol->getAtomAt(rbStamp->getMemberAt(i));
244	atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));
245	rb->addAtom(atom, atomStamp);
246	}
247
248	//after all of the atoms are added, we need to calculate the
249	//reference coordinates
250	rb->calcRefCoords();
251
252	//set the local index of this rigid body, global index will be set later
253	rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
254
255	//the rule for naming rigidbody MoleculeName_RB_Integer
256	//The first part is the name of the molecule
257	//The second part is alway fixed as "RB"
258	//The third part is the index of the rigidbody defined in meta-data file
259	//For example, Butane_RB_0 is a valid rigid body name of butane molecule
260	/*@todo replace itoa by lexi_cast /
261	std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
262	rb->setType(mol->getType() + "_RB_" + s.c_str());
263
264	return rb;
265	}
266
267	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol,
268	BondStamp* stamp) {
269	BondType* bondType;
270	Atom* atomA;
271	Atom* atomB;
272
273	atomA = mol->getAtomAt(stamp->getA());
274	atomB = mol->getAtomAt(stamp->getB());
275
276	assert( atomA && atomB);
277
278	bondType = ff->getBondType(atomA->getType(), atomB->getType());
279
280	if (bondType == NULL) {
281	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
282	atomA->getType().c_str(),
283	atomB->getType().c_str());
284
285	painCave.isFatal = 1;
286	simError();
287	}
288	return new Bond(atomA, atomB, bondType);
289	}
290
291	Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol,
292	BendStamp* stamp) {
293	Bend* bend = NULL;
294	std::vector<int> bendAtoms = stamp->getMembers();
295	if (bendAtoms.size() == 3) {
296	Atom* atomA = mol->getAtomAt(bendAtoms[0]);
297	Atom* atomB = mol->getAtomAt(bendAtoms[1]);
298	Atom* atomC = mol->getAtomAt(bendAtoms[2]);
299
300	assert( atomA && atomB && atomC);
301
302	BendType* bendType = ff->getBendType(atomA->getType().c_str(),
303	atomB->getType().c_str(),
304	atomC->getType().c_str());
305
306	if (bendType == NULL) {
307	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
308	atomA->getType().c_str(),
309	atomB->getType().c_str(),
310	atomC->getType().c_str());
311
312	painCave.isFatal = 1;
313	simError();
314	}
315
316	bend = new Bend(atomA, atomB, atomC, bendType);
317	} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
318	int ghostIndex = stamp->getGhostVectorSource();
319	int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
320	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
321	DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
322	if (ghostAtom == NULL) {
323	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
324	painCave.isFatal = 1;
325	simError();
326	}
327
328	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
329
330	if (bendType == NULL) {
331	sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
332	normalAtom->getType().c_str(),
333	ghostAtom->getType().c_str(),
334	"GHOST");
335
336	painCave.isFatal = 1;
337	simError();
338	}
339
340	bend = new GhostBend(normalAtom, ghostAtom, bendType);
341
342	}
343
344	return bend;
345	}
346
347	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
348	TorsionStamp* stamp) {
349
350	Torsion* torsion = NULL;
351	std::vector<int> torsionAtoms = stamp->getMembers();
352	if (torsionAtoms.size() < 3) {
353	return torsion;
354	}
355
356	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
357	Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
358	Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
359
360	if (torsionAtoms.size() == 4) {
361	Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
362
363	assert(atomA && atomB && atomC && atomD);
364
365	TorsionType* torsionType = ff->getTorsionType(atomA->getType(),
366	atomB->getType(),
367	atomC->getType(),
368	atomD->getType());
369	if (torsionType == NULL) {
370	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
371	atomA->getType().c_str(),
372	atomB->getType().c_str(),
373	atomC->getType().c_str(),
374	atomD->getType().c_str());
375
376	painCave.isFatal = 1;
377	simError();
378	}
379
380	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
381	}
382	else {
383
384	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
385	if (dAtom == NULL) {
386	sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
387	painCave.isFatal = 1;
388	simError();
389	}
390
391	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
392	atomC->getType(), "GHOST");
393
394	if (torsionType == NULL) {
395	sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
396	atomA->getType().c_str(),
397	atomB->getType().c_str(),
398	atomC->getType().c_str(),
399	"GHOST");
400
401	painCave.isFatal = 1;
402	simError();
403	}
404
405	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
406	}
407
408	return torsion;
409	}
410
411	Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol,
412	InversionStamp* stamp) {
413
414	Inversion* inversion = NULL;
415	int center = stamp->getCenter();
416	std::vector<int> satellites = stamp->getSatellites();
417	if (satellites.size() != 3) {
418	return inversion;
419	}
420
421	Atom* atomA = mol->getAtomAt(center);
422	Atom* atomB = mol->getAtomAt(satellites[0]);
423	Atom* atomC = mol->getAtomAt(satellites[1]);
424	Atom* atomD = mol->getAtomAt(satellites[2]);
425
426	assert(atomA && atomB && atomC && atomD);
427
428	InversionType* inversionType = ff->getInversionType(atomA->getType(),
429	atomB->getType(),
430	atomC->getType(),
431	atomD->getType());
432
433	if (inversionType == NULL) {
434	sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n"
435	"\t(May not be a problem: not all inversions are parametrized)\n",
436	atomA->getType().c_str(),
437	atomB->getType().c_str(),
438	atomC->getType().c_str(),
439	atomD->getType().c_str());
440
441	painCave.isFatal = 0;
442	painCave.severity = OPENMD_INFO;
443	simError();
444	return NULL;
445	} else {
446
447	inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
448	return inversion;
449	}
450	}
451
452
453	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
454	CutoffGroupStamp* stamp,
455	LocalIndexManager* localIndexMan) {
456	int nAtoms;
457	CutoffGroup* cg;
458	Atom* atom;
459	cg = new CutoffGroup();
460
461	nAtoms = stamp->getNMembers();
462	for (int i =0; i < nAtoms; ++i) {
463	atom = mol->getAtomAt(stamp->getMemberAt(i));
464	assert(atom);
465	cg->addAtom(atom);
466	}
467
468	//set the local index of this cutoffGroup, global index will be set later
469	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
470
471	return cg;
472	}
473
474	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
475	LocalIndexManager* localIndexMan) {
476	CutoffGroup* cg;
477	cg = new CutoffGroup();
478	cg->addAtom(atom);
479
480	//set the local index of this cutoffGroup, global index will be set later
481	cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
482
483	return cg;
484	}
485
486	void MoleculeCreator::createConstraintPair(Molecule* mol) {
487
488	//add bond constraints
489	Molecule::BondIterator bi;
490	Bond* bond;
491	for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
492
493	BondType* bt = bond->getBondType();
494
495	//class Parent1 {};
496	//class Child1 : public Parent {};
497	//class Child2 : public Parent {};
498	//Child1* ch1 = new Child1();
499	//Child2* ch2 = dynamic_cast<Child2*>(ch1);
500	//the dynamic_cast is succeed in above line. A compiler bug?
501
502	if (typeid(FixedBondType) == typeid(*bt)) {
503	FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
504
505	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
506	ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
507	ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
508	mol->addConstraintPair(consPair);
509	}
510	}
511
512	//rigidbody -- rigidbody constraint is not support yet
513	}
514
515	void MoleculeCreator::createConstraintElem(Molecule* mol) {
516
517	ConstraintPair* consPair;
518	Molecule::ConstraintPairIterator cpi;
519	std::set<StuntDouble*> sdSet;
520	for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
521
522	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
523	if (sdSet.find(sdA) == sdSet.end()){
524	sdSet.insert(sdA);
525	mol->addConstraintElem(new ConstraintElem(sdA));
526	}
527
528	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
529	if (sdSet.find(sdB) == sdSet.end()){
530	sdSet.insert(sdB);
531	mol->addConstraintElem(new ConstraintElem(sdB));
532	}
533
534	}
535
536	}
537
538	}