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]  Vardeman & Gezelter, in progress (2009).                        
 */
  
/**
 * @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);
      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 = 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) {
    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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	17567 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
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	gezelter	809	#include <typeinfo>
52	gezelter	246	#include <set>
53
54			#include "brains/MoleculeCreator.hpp"
55			#include "primitives/GhostBend.hpp"
56	tim	273	#include "primitives/GhostTorsion.hpp"
57	gezelter	246	#include "types/DirectionalAtomType.hpp"
58			#include "types/FixedBondType.hpp"
59			#include "utils/simError.h"
60			#include "utils/StringUtils.hpp"
61
62	gezelter	1390	namespace OpenMD {
63	tim	647
64	gezelter	1277	Molecule* MoleculeCreator::createMolecule(ForceField* ff,
65			MoleculeStamp *molStamp,
66			int stampId, int globalIndex,
67			LocalIndexManager* localIndexMan) {
68	tim	770	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName());
69	gezelter	246
70			//create atoms
71			Atom* atom;
72			AtomStamp* currentAtomStamp;
73			int nAtom = molStamp->getNAtoms();
74			for (int i = 0; i < nAtom; ++i) {
75	tim	770	currentAtomStamp = molStamp->getAtomStamp(i);
76	gezelter	507	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
77			mol->addAtom(atom);
78	gezelter	246	}
79
80			//create rigidbodies
81			RigidBody* rb;
82			RigidBodyStamp * currentRigidBodyStamp;
83			int nRigidbodies = molStamp->getNRigidBodies();
84
85			for (int i = 0; i < nRigidbodies; ++i) {
86	tim	770	currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
87	gezelter	1277	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp,
88			localIndexMan);
89	gezelter	507	mol->addRigidBody(rb);
90	gezelter	246	}
91	gezelter	1277
92	gezelter	246	//create bonds
93			Bond* bond;
94			BondStamp* currentBondStamp;
95			int nBonds = molStamp->getNBonds();
96
97			for (int i = 0; i < nBonds; ++i) {
98	tim	770	currentBondStamp = molStamp->getBondStamp(i);
99	gezelter	507	bond = createBond(ff, mol, currentBondStamp);
100			mol->addBond(bond);
101	gezelter	246	}
102
103			//create bends
104			Bend* bend;
105			BendStamp* currentBendStamp;
106			int nBends = molStamp->getNBends();
107			for (int i = 0; i < nBends; ++i) {
108	tim	770	currentBendStamp = molStamp->getBendStamp(i);
109	gezelter	507	bend = createBend(ff, mol, currentBendStamp);
110			mol->addBend(bend);
111	gezelter	246	}
112
113			//create torsions
114			Torsion* torsion;
115			TorsionStamp* currentTorsionStamp;
116			int nTorsions = molStamp->getNTorsions();
117			for (int i = 0; i < nTorsions; ++i) {
118	tim	770	currentTorsionStamp = molStamp->getTorsionStamp(i);
119	gezelter	507	torsion = createTorsion(ff, mol, currentTorsionStamp);
120			mol->addTorsion(torsion);
121	gezelter	246	}
122
123	gezelter	1277	//create inversions
124			Inversion* inversion;
125			InversionStamp* currentInversionStamp;
126			int nInversions = molStamp->getNInversions();
127			for (int i = 0; i < nInversions; ++i) {
128			currentInversionStamp = molStamp->getInversionStamp(i);
129			inversion = createInversion(ff, mol, currentInversionStamp);
130			if (inversion != NULL ) {
131			mol->addInversion(inversion);
132			}
133			}
134
135	gezelter	246	//create cutoffGroups
136			CutoffGroup* cutoffGroup;
137			CutoffGroupStamp* currentCutoffGroupStamp;
138			int nCutoffGroups = molStamp->getNCutoffGroups();
139			for (int i = 0; i < nCutoffGroups; ++i) {
140	tim	770	currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
141	gezelter	507	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp);
142			mol->addCutoffGroup(cutoffGroup);
143	gezelter	246	}
144
145			//every free atom is a cutoff group
146	tim	647	std::vector<Atom*> freeAtoms;
147			std::vector<Atom*>::iterator ai;
148			std::vector<Atom*>::iterator fai;
149	gezelter	246
150			//add all atoms into allAtoms set
151	tim	647	for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
152			freeAtoms.push_back(atom);
153	gezelter	246	}
154
155			Molecule::CutoffGroupIterator ci;
156			CutoffGroup* cg;
157
158	gezelter	1277	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
159			cg = mol->nextCutoffGroup(ci)) {
160
161	gezelter	507	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
162	gezelter	1277	//erase the atoms belong to cutoff groups from freeAtoms vector
163			freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom),
164			freeAtoms.end());
165			}
166	gezelter	246	}
167
168	gezelter	1277	// loop over the free atoms and then create one cutoff group for
169			// every single free atom
170	tim	647
171	gezelter	246	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
172	gezelter	507	cutoffGroup = createCutoffGroup(mol, *fai);
173			mol->addCutoffGroup(cutoffGroup);
174	gezelter	246	}
175			//create constraints
176			createConstraintPair(mol);
177			createConstraintElem(mol);
178
179			//the construction of this molecule is finished
180			mol->complete();
181	gezelter	1277
182	gezelter	246	return mol;
183	gezelter	507	}
184	gezelter	246
185
186	gezelter	1277	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol,
187			AtomStamp* stamp,
188			LocalIndexManager* localIndexMan) {
189	gezelter	246	AtomType * atomType;
190			Atom* atom;
191
192			atomType = ff->getAtomType(stamp->getType());
193	gezelter	1277
194	gezelter	246	if (atomType == NULL) {
195	gezelter	507	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
196	tim	770	stamp->getType().c_str());
197	gezelter	246
198	gezelter	507	painCave.isFatal = 1;
199			simError();
200	gezelter	246	}
201
202			//below code still have some kind of hard-coding smell
203			if (atomType->isDirectional()){
204
205	gezelter	507	DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
206	gezelter	246
207	gezelter	507	if (dAtomType == NULL) {
208			sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType");
209	gezelter	246
210	gezelter	507	painCave.isFatal = 1;
211			simError();
212			}
213	gezelter	246
214	gezelter	507	DirectionalAtom* dAtom;
215			dAtom = new DirectionalAtom(dAtomType);
216			atom = dAtom;
217	gezelter	246	}
218			else{
219	gezelter	507	atom = new Atom(atomType);
220	gezelter	246	}
221
222			atom->setLocalIndex(localIndexMan->getNextAtomIndex());
223
224			return atom;
225	gezelter	507	}
226	gezelter	1277
227			RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
228			Molecule* mol,
229	gezelter	507	RigidBodyStamp* rbStamp,
230			LocalIndexManager* localIndexMan) {
231	gezelter	246	Atom* atom;
232			int nAtoms;
233			Vector3d refCoor;
234			AtomStamp* atomStamp;
235
236			RigidBody* rb = new RigidBody();
237			nAtoms = rbStamp->getNMembers();
238			for (int i = 0; i < nAtoms; ++i) {
239	gezelter	1277	//rbStamp->getMember(i) return the local index of current atom
240			//inside the molecule. It is not the same as local index of
241			//atom which is the index of atom at DataStorage class
242	tim	770	atom = mol->getAtomAt(rbStamp->getMemberAt(i));
243			atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));
244	gezelter	507	rb->addAtom(atom, atomStamp);
245	gezelter	246	}
246
247	gezelter	1277	//after all of the atoms are added, we need to calculate the
248			//reference coordinates
249	gezelter	246	rb->calcRefCoords();
250
251			//set the local index of this rigid body, global index will be set later
252			rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
253
254			//the rule for naming rigidbody MoleculeName_RB_Integer
255			//The first part is the name of the molecule
256			//The second part is alway fixed as "RB"
257			//The third part is the index of the rigidbody defined in meta-data file
258			//For example, Butane_RB_0 is a valid rigid body name of butane molecule
259			/*@todo replace itoa by lexi_cast /
260	gezelter	1390	std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
261	gezelter	403	rb->setType(mol->getType() + "_RB_" + s.c_str());
262	tim	292
263	gezelter	246	return rb;
264	gezelter	507	}
265	gezelter	246
266	gezelter	1277	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol,
267			BondStamp* stamp) {
268	gezelter	246	BondType* bondType;
269			Atom* atomA;
270			Atom* atomB;
271	gezelter	1277
272	gezelter	246	atomA = mol->getAtomAt(stamp->getA());
273			atomB = mol->getAtomAt(stamp->getB());
274	gezelter	1277
275	gezelter	246	assert( atomA && atomB);
276
277			bondType = ff->getBondType(atomA->getType(), atomB->getType());
278
279			if (bondType == NULL) {
280	gezelter	507	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
281			atomA->getType().c_str(),
282			atomB->getType().c_str());
283	gezelter	1277
284	gezelter	507	painCave.isFatal = 1;
285			simError();
286	gezelter	246	}
287			return new Bond(atomA, atomB, bondType);
288	gezelter	507	}
289	gezelter	1277
290			Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol,
291			BendStamp* stamp) {
292	tim	770	Bend* bend = NULL;
293			std::vector<int> bendAtoms = stamp->getMembers();
294			if (bendAtoms.size() == 3) {
295			Atom* atomA = mol->getAtomAt(bendAtoms[0]);
296			Atom* atomB = mol->getAtomAt(bendAtoms[1]);
297			Atom* atomC = mol->getAtomAt(bendAtoms[2]);
298	gezelter	1277
299	tim	770	assert( atomA && atomB && atomC);
300	gezelter	1277
301			BendType* bendType = ff->getBendType(atomA->getType().c_str(),
302			atomB->getType().c_str(),
303			atomC->getType().c_str());
304
305	tim	770	if (bendType == NULL) {
306			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
307			atomA->getType().c_str(),
308			atomB->getType().c_str(),
309			atomC->getType().c_str());
310	gezelter	1277
311	tim	770	painCave.isFatal = 1;
312			simError();
313	gezelter	507	}
314	gezelter	1277
315	tim	770	bend = new Bend(atomA, atomB, atomC, bendType);
316			} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
317			int ghostIndex = stamp->getGhostVectorSource();
318			int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
319	gezelter	507	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
320			DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
321			if (ghostAtom == NULL) {
322			sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
323			painCave.isFatal = 1;
324			simError();
325			}
326	gezelter	246
327	gezelter	507	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
328	gezelter	246
329	gezelter	507	if (bendType == NULL) {
330			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
331			normalAtom->getType().c_str(),
332			ghostAtom->getType().c_str(),
333			"GHOST");
334	gezelter	246
335	gezelter	507	painCave.isFatal = 1;
336			simError();
337			}
338	gezelter	1277
339	tim	770	bend = new GhostBend(normalAtom, ghostAtom, bendType);
340	gezelter	1277
341	tim	770	}
342
343			return bend;
344			}
345	gezelter	246
346	gezelter	1277	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
347			TorsionStamp* stamp) {
348	gezelter	246
349	tim	770	Torsion* torsion = NULL;
350			std::vector<int> torsionAtoms = stamp->getMembers();
351			if (torsionAtoms.size() < 3) {
352			return torsion;
353	gezelter	246	}
354
355	tim	770	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
356			Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
357			Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
358	gezelter	246
359	tim	770	if (torsionAtoms.size() == 4) {
360			Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
361	gezelter	246
362	gezelter	507	assert(atomA && atomB && atomC && atomD);
363	tim	273
364	gezelter	1277	TorsionType* torsionType = ff->getTorsionType(atomA->getType(),
365			atomB->getType(),
366			atomC->getType(),
367			atomD->getType());
368	gezelter	507	if (torsionType == NULL) {
369			sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
370			atomA->getType().c_str(),
371			atomB->getType().c_str(),
372			atomC->getType().c_str(),
373			atomD->getType().c_str());
374	gezelter	1277
375	gezelter	507	painCave.isFatal = 1;
376			simError();
377			}
378	gezelter	1277
379	gezelter	507	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
380	gezelter	246	}
381	tim	273	else {
382	gezelter	1277
383	tim	770	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
384	gezelter	507	if (dAtom == NULL) {
385			sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
386			painCave.isFatal = 1;
387			simError();
388			}
389	gezelter	1277
390	gezelter	507	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
391			atomC->getType(), "GHOST");
392	gezelter	1277
393	gezelter	507	if (torsionType == NULL) {
394			sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
395			atomA->getType().c_str(),
396			atomB->getType().c_str(),
397			atomC->getType().c_str(),
398			"GHOST");
399	gezelter	1277
400	gezelter	507	painCave.isFatal = 1;
401			simError();
402			}
403	gezelter	1277
404	gezelter	507	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
405	tim	273	}
406	gezelter	1277
407	tim	273	return torsion;
408	gezelter	507	}
409	gezelter	246
410	gezelter	1277	Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol,
411			InversionStamp* stamp) {
412
413			Inversion* inversion = NULL;
414			int center = stamp->getCenter();
415			std::vector<int> satellites = stamp->getSatellites();
416			if (satellites.size() != 3) {
417			return inversion;
418			}
419
420			Atom* atomA = mol->getAtomAt(center);
421			Atom* atomB = mol->getAtomAt(satellites[0]);
422			Atom* atomC = mol->getAtomAt(satellites[1]);
423			Atom* atomD = mol->getAtomAt(satellites[2]);
424
425			assert(atomA && atomB && atomC && atomD);
426
427			InversionType* inversionType = ff->getInversionType(atomA->getType(),
428			atomB->getType(),
429			atomC->getType(),
430			atomD->getType());
431
432			if (inversionType == NULL) {
433			sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n"
434			"\t(May not be a problem: not all inversions are parametrized)\n",
435			atomA->getType().c_str(),
436			atomB->getType().c_str(),
437			atomC->getType().c_str(),
438			atomD->getType().c_str());
439
440			painCave.isFatal = 0;
441	gezelter	1390	painCave.severity = OPENMD_INFO;
442	gezelter	1277	simError();
443			return NULL;
444			} else {
445
446			inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
447			return inversion;
448			}
449			}
450
451
452	gezelter	507	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) {
453	gezelter	246	int nAtoms;
454			CutoffGroup* cg;
455			Atom* atom;
456			cg = new CutoffGroup();
457
458			nAtoms = stamp->getNMembers();
459			for (int i =0; i < nAtoms; ++i) {
460	tim	770	atom = mol->getAtomAt(stamp->getMemberAt(i));
461	gezelter	507	assert(atom);
462			cg->addAtom(atom);
463	gezelter	246	}
464
465			return cg;
466	gezelter	507	}
467	gezelter	246
468	gezelter	507	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) {
469	gezelter	246	CutoffGroup* cg;
470			cg = new CutoffGroup();
471			cg->addAtom(atom);
472			return cg;
473	gezelter	507	}
474	gezelter	246
475	gezelter	507	void MoleculeCreator::createConstraintPair(Molecule* mol) {
476	gezelter	246
477			//add bond constraints
478			Molecule::BondIterator bi;
479			Bond* bond;
480			for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
481
482	gezelter	507	BondType* bt = bond->getBondType();
483	gezelter	246
484	gezelter	507	//class Parent1 {};
485			//class Child1 : public Parent {};
486			//class Child2 : public Parent {};
487			//Child1* ch1 = new Child1();
488			//Child2* ch2 = dynamic_cast<Child2*>(ch1);
489			//the dynamic_cast is succeed in above line. A compiler bug?
490	gezelter	246
491	gezelter	507	if (typeid(FixedBondType) == typeid(*bt)) {
492			FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
493	gezelter	246
494	gezelter	507	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
495			ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
496			ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
497			mol->addConstraintPair(consPair);
498			}
499	gezelter	246	}
500
501			//rigidbody -- rigidbody constraint is not support yet
502	gezelter	507	}
503	gezelter	246
504	gezelter	507	void MoleculeCreator::createConstraintElem(Molecule* mol) {
505	gezelter	246
506			ConstraintPair* consPair;
507			Molecule::ConstraintPairIterator cpi;
508			std::set<StuntDouble*> sdSet;
509			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
510
511	gezelter	507	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
512			if (sdSet.find(sdA) == sdSet.end()){
513			sdSet.insert(sdA);
514			mol->addConstraintElem(new ConstraintElem(sdA));
515			}
516	gezelter	246
517	gezelter	507	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
518			if (sdSet.find(sdB) == sdSet.end()){
519			sdSet.insert(sdB);
520			mol->addConstraintElem(new ConstraintElem(sdB));
521			}
522	gezelter	246
523			}
524
525	gezelter	507	}
526	gezelter	246
527			}