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/AtomType.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);
    
    // Does this molecule stamp define a total constrained charge value?
    // If so, let the created molecule know about it.

    if (molStamp->haveConstrainTotalCharge() ) {
      mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() );
    }

    //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()){

      DirectionalAtom* dAtom;
      dAtom = new DirectionalAtom(atomType);
      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:	1775
Committed:	Wed Aug 8 18:45:52 2012 UTC (12 years, 8 months ago) by gezelter
File size:	18169 byte(s)
Log Message:	Tracking down a strange bug report. Fixing some output. Fixing some samples.
#	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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	507	/**
44			* @file MoleculeCreator.cpp
45			* @author tlin
46			* @date 11/04/2004
47			* @time 13:44am
48			* @version 1.0
49			*/
50	gezelter	246
51			#include <cassert>
52	gezelter	809	#include <typeinfo>
53	gezelter	246	#include <set>
54
55			#include "brains/MoleculeCreator.hpp"
56			#include "primitives/GhostBend.hpp"
57	tim	273	#include "primitives/GhostTorsion.hpp"
58	gezelter	1710	#include "types/AtomType.hpp"
59	gezelter	246	#include "types/FixedBondType.hpp"
60			#include "utils/simError.h"
61			#include "utils/StringUtils.hpp"
62
63	gezelter	1390	namespace OpenMD {
64	tim	647
65	gezelter	1277	Molecule* MoleculeCreator::createMolecule(ForceField* ff,
66			MoleculeStamp *molStamp,
67			int stampId, int globalIndex,
68			LocalIndexManager* localIndexMan) {
69	tim	770	Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName());
70	gezelter	1715
71	gezelter	246	//create atoms
72			Atom* atom;
73			AtomStamp* currentAtomStamp;
74			int nAtom = molStamp->getNAtoms();
75			for (int i = 0; i < nAtom; ++i) {
76	tim	770	currentAtomStamp = molStamp->getAtomStamp(i);
77	gezelter	507	atom = createAtom(ff, mol, currentAtomStamp, localIndexMan);
78			mol->addAtom(atom);
79	gezelter	246	}
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	tim	770	currentRigidBodyStamp = molStamp->getRigidBodyStamp(i);
88	gezelter	1277	rb = createRigidBody(molStamp, mol, currentRigidBodyStamp,
89			localIndexMan);
90	gezelter	507	mol->addRigidBody(rb);
91	gezelter	246	}
92	gezelter	1277
93	gezelter	246	//create bonds
94			Bond* bond;
95			BondStamp* currentBondStamp;
96			int nBonds = molStamp->getNBonds();
97
98			for (int i = 0; i < nBonds; ++i) {
99	tim	770	currentBondStamp = molStamp->getBondStamp(i);
100	gezelter	507	bond = createBond(ff, mol, currentBondStamp);
101			mol->addBond(bond);
102	gezelter	246	}
103
104			//create bends
105			Bend* bend;
106			BendStamp* currentBendStamp;
107			int nBends = molStamp->getNBends();
108			for (int i = 0; i < nBends; ++i) {
109	tim	770	currentBendStamp = molStamp->getBendStamp(i);
110	gezelter	507	bend = createBend(ff, mol, currentBendStamp);
111			mol->addBend(bend);
112	gezelter	246	}
113
114			//create torsions
115			Torsion* torsion;
116			TorsionStamp* currentTorsionStamp;
117			int nTorsions = molStamp->getNTorsions();
118			for (int i = 0; i < nTorsions; ++i) {
119	tim	770	currentTorsionStamp = molStamp->getTorsionStamp(i);
120	gezelter	507	torsion = createTorsion(ff, mol, currentTorsionStamp);
121			mol->addTorsion(torsion);
122	gezelter	246	}
123
124	gezelter	1277	//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	gezelter	246	//create cutoffGroups
137			CutoffGroup* cutoffGroup;
138			CutoffGroupStamp* currentCutoffGroupStamp;
139			int nCutoffGroups = molStamp->getNCutoffGroups();
140			for (int i = 0; i < nCutoffGroups; ++i) {
141	tim	770	currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i);
142	gezelter	1540	cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, localIndexMan);
143	gezelter	507	mol->addCutoffGroup(cutoffGroup);
144	gezelter	246	}
145
146			//every free atom is a cutoff group
147	tim	647	std::vector<Atom*> freeAtoms;
148			std::vector<Atom*>::iterator ai;
149			std::vector<Atom*>::iterator fai;
150	gezelter	246
151			//add all atoms into allAtoms set
152	tim	647	for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) {
153			freeAtoms.push_back(atom);
154	gezelter	246	}
155
156			Molecule::CutoffGroupIterator ci;
157			CutoffGroup* cg;
158
159	gezelter	1277	for (cg = mol->beginCutoffGroup(ci); cg != NULL;
160			cg = mol->nextCutoffGroup(ci)) {
161
162	gezelter	507	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
163	gezelter	1277	//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	gezelter	246	}
168
169	gezelter	1277	// loop over the free atoms and then create one cutoff group for
170			// every single free atom
171	tim	647
172	gezelter	246	for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) {
173	gezelter	1540	cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan);
174	gezelter	507	mol->addCutoffGroup(cutoffGroup);
175	gezelter	246	}
176			//create constraints
177			createConstraintPair(mol);
178			createConstraintElem(mol);
179
180	gezelter	1715	// Does this molecule stamp define a total constrained charge value?
181			// If so, let the created molecule know about it.
182
183	gezelter	1718	if (molStamp->haveConstrainTotalCharge() ) {
184			mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() );
185	gezelter	1715	}
186
187	gezelter	246	//the construction of this molecule is finished
188			mol->complete();
189	gezelter	1277
190	gezelter	246	return mol;
191	gezelter	507	}
192	gezelter	246
193
194	gezelter	1277	Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol,
195			AtomStamp* stamp,
196			LocalIndexManager* localIndexMan) {
197	gezelter	246	AtomType * atomType;
198			Atom* atom;
199
200			atomType = ff->getAtomType(stamp->getType());
201	gezelter	1277
202	gezelter	246	if (atomType == NULL) {
203	gezelter	507	sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]",
204	tim	770	stamp->getType().c_str());
205	gezelter	246
206	gezelter	507	painCave.isFatal = 1;
207			simError();
208	gezelter	246	}
209	gezelter	1775
210	gezelter	246	//below code still have some kind of hard-coding smell
211			if (atomType->isDirectional()){
212	gezelter	1775
213	gezelter	507	DirectionalAtom* dAtom;
214	gezelter	1710	dAtom = new DirectionalAtom(atomType);
215	gezelter	507	atom = dAtom;
216	gezelter	246	}
217			else{
218	gezelter	507	atom = new Atom(atomType);
219	gezelter	246	}
220
221			atom->setLocalIndex(localIndexMan->getNextAtomIndex());
222
223			return atom;
224	gezelter	507	}
225	gezelter	1277
226			RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp,
227			Molecule* mol,
228	gezelter	507	RigidBodyStamp* rbStamp,
229			LocalIndexManager* localIndexMan) {
230	gezelter	246	Atom* atom;
231			int nAtoms;
232			Vector3d refCoor;
233			AtomStamp* atomStamp;
234
235			RigidBody* rb = new RigidBody();
236			nAtoms = rbStamp->getNMembers();
237			for (int i = 0; i < nAtoms; ++i) {
238	gezelter	1277	//rbStamp->getMember(i) return the local index of current atom
239			//inside the molecule. It is not the same as local index of
240			//atom which is the index of atom at DataStorage class
241	tim	770	atom = mol->getAtomAt(rbStamp->getMemberAt(i));
242			atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i));
243	gezelter	507	rb->addAtom(atom, atomStamp);
244	gezelter	246	}
245
246	gezelter	1277	//after all of the atoms are added, we need to calculate the
247			//reference coordinates
248	gezelter	246	rb->calcRefCoords();
249
250			//set the local index of this rigid body, global index will be set later
251			rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex());
252
253			//the rule for naming rigidbody MoleculeName_RB_Integer
254			//The first part is the name of the molecule
255			//The second part is alway fixed as "RB"
256			//The third part is the index of the rigidbody defined in meta-data file
257			//For example, Butane_RB_0 is a valid rigid body name of butane molecule
258			/*@todo replace itoa by lexi_cast /
259	gezelter	1390	std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10);
260	gezelter	403	rb->setType(mol->getType() + "_RB_" + s.c_str());
261	tim	292
262	gezelter	246	return rb;
263	gezelter	507	}
264	gezelter	246
265	gezelter	1277	Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol,
266			BondStamp* stamp) {
267	gezelter	246	BondType* bondType;
268			Atom* atomA;
269			Atom* atomB;
270	gezelter	1277
271	gezelter	246	atomA = mol->getAtomAt(stamp->getA());
272			atomB = mol->getAtomAt(stamp->getB());
273	gezelter	1277
274	gezelter	246	assert( atomA && atomB);
275
276			bondType = ff->getBondType(atomA->getType(), atomB->getType());
277
278			if (bondType == NULL) {
279	gezelter	507	sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]",
280			atomA->getType().c_str(),
281			atomB->getType().c_str());
282	gezelter	1277
283	gezelter	507	painCave.isFatal = 1;
284			simError();
285	gezelter	246	}
286			return new Bond(atomA, atomB, bondType);
287	gezelter	507	}
288	gezelter	1277
289			Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol,
290			BendStamp* stamp) {
291	tim	770	Bend* bend = NULL;
292			std::vector<int> bendAtoms = stamp->getMembers();
293			if (bendAtoms.size() == 3) {
294			Atom* atomA = mol->getAtomAt(bendAtoms[0]);
295			Atom* atomB = mol->getAtomAt(bendAtoms[1]);
296			Atom* atomC = mol->getAtomAt(bendAtoms[2]);
297	gezelter	1277
298	tim	770	assert( atomA && atomB && atomC);
299	gezelter	1277
300			BendType* bendType = ff->getBendType(atomA->getType().c_str(),
301			atomB->getType().c_str(),
302			atomC->getType().c_str());
303
304	tim	770	if (bendType == NULL) {
305			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
306			atomA->getType().c_str(),
307			atomB->getType().c_str(),
308			atomC->getType().c_str());
309	gezelter	1277
310	tim	770	painCave.isFatal = 1;
311			simError();
312	gezelter	507	}
313	gezelter	1277
314	tim	770	bend = new Bend(atomA, atomB, atomC, bendType);
315			} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) {
316			int ghostIndex = stamp->getGhostVectorSource();
317			int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1];
318	gezelter	507	Atom* normalAtom = mol->getAtomAt(normalIndex) ;
319			DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex));
320			if (ghostAtom == NULL) {
321			sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
322			painCave.isFatal = 1;
323			simError();
324			}
325	gezelter	246
326	gezelter	507	BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST");
327	gezelter	246
328	gezelter	507	if (bendType == NULL) {
329			sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]",
330			normalAtom->getType().c_str(),
331			ghostAtom->getType().c_str(),
332			"GHOST");
333	gezelter	246
334	gezelter	507	painCave.isFatal = 1;
335			simError();
336			}
337	gezelter	1277
338	tim	770	bend = new GhostBend(normalAtom, ghostAtom, bendType);
339	gezelter	1277
340	tim	770	}
341
342			return bend;
343			}
344	gezelter	246
345	gezelter	1277	Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol,
346			TorsionStamp* stamp) {
347	gezelter	246
348	tim	770	Torsion* torsion = NULL;
349			std::vector<int> torsionAtoms = stamp->getMembers();
350			if (torsionAtoms.size() < 3) {
351			return torsion;
352	gezelter	246	}
353
354	tim	770	Atom* atomA = mol->getAtomAt(torsionAtoms[0]);
355			Atom* atomB = mol->getAtomAt(torsionAtoms[1]);
356			Atom* atomC = mol->getAtomAt(torsionAtoms[2]);
357	gezelter	246
358	tim	770	if (torsionAtoms.size() == 4) {
359			Atom* atomD = mol->getAtomAt(torsionAtoms[3]);
360	gezelter	246
361	gezelter	507	assert(atomA && atomB && atomC && atomD);
362	tim	273
363	gezelter	1277	TorsionType* torsionType = ff->getTorsionType(atomA->getType(),
364			atomB->getType(),
365			atomC->getType(),
366			atomD->getType());
367	gezelter	507	if (torsionType == NULL) {
368			sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
369			atomA->getType().c_str(),
370			atomB->getType().c_str(),
371			atomC->getType().c_str(),
372			atomD->getType().c_str());
373	gezelter	1277
374	gezelter	507	painCave.isFatal = 1;
375			simError();
376			}
377	gezelter	1277
378	gezelter	507	torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType);
379	gezelter	246	}
380	tim	273	else {
381	gezelter	1277
382	tim	770	DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource()));
383	gezelter	507	if (dAtom == NULL) {
384			sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom");
385			painCave.isFatal = 1;
386			simError();
387			}
388	gezelter	1277
389	gezelter	507	TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(),
390			atomC->getType(), "GHOST");
391	gezelter	1277
392	gezelter	507	if (torsionType == NULL) {
393			sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]",
394			atomA->getType().c_str(),
395			atomB->getType().c_str(),
396			atomC->getType().c_str(),
397			"GHOST");
398	gezelter	1277
399	gezelter	507	painCave.isFatal = 1;
400			simError();
401			}
402	gezelter	1277
403	gezelter	507	torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType);
404	tim	273	}
405	gezelter	1277
406	tim	273	return torsion;
407	gezelter	507	}
408	gezelter	246
409	gezelter	1277	Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol,
410			InversionStamp* stamp) {
411
412			Inversion* inversion = NULL;
413			int center = stamp->getCenter();
414			std::vector<int> satellites = stamp->getSatellites();
415			if (satellites.size() != 3) {
416			return inversion;
417			}
418
419			Atom* atomA = mol->getAtomAt(center);
420			Atom* atomB = mol->getAtomAt(satellites[0]);
421			Atom* atomC = mol->getAtomAt(satellites[1]);
422			Atom* atomD = mol->getAtomAt(satellites[2]);
423
424			assert(atomA && atomB && atomC && atomD);
425
426			InversionType* inversionType = ff->getInversionType(atomA->getType(),
427			atomB->getType(),
428			atomC->getType(),
429			atomD->getType());
430
431			if (inversionType == NULL) {
432			sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n"
433			"\t(May not be a problem: not all inversions are parametrized)\n",
434			atomA->getType().c_str(),
435			atomB->getType().c_str(),
436			atomC->getType().c_str(),
437			atomD->getType().c_str());
438
439			painCave.isFatal = 0;
440	gezelter	1390	painCave.severity = OPENMD_INFO;
441	gezelter	1277	simError();
442			return NULL;
443			} else {
444
445			inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType);
446			return inversion;
447			}
448			}
449
450
451	gezelter	1540	CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol,
452			CutoffGroupStamp* stamp,
453			LocalIndexManager* localIndexMan) {
454	gezelter	246	int nAtoms;
455			CutoffGroup* cg;
456			Atom* atom;
457			cg = new CutoffGroup();
458
459			nAtoms = stamp->getNMembers();
460			for (int i =0; i < nAtoms; ++i) {
461	tim	770	atom = mol->getAtomAt(stamp->getMemberAt(i));
462	gezelter	507	assert(atom);
463			cg->addAtom(atom);
464	gezelter	246	}
465	gezelter	1540
466			//set the local index of this cutoffGroup, global index will be set later
467			cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
468
469	gezelter	246	return cg;
470	gezelter	507	}
471	gezelter	1540
472			CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom,
473			LocalIndexManager* localIndexMan) {
474	gezelter	246	CutoffGroup* cg;
475			cg = new CutoffGroup();
476			cg->addAtom(atom);
477	gezelter	1540
478			//set the local index of this cutoffGroup, global index will be set later
479			cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex());
480
481	gezelter	246	return cg;
482	gezelter	507	}
483	gezelter	246
484	gezelter	507	void MoleculeCreator::createConstraintPair(Molecule* mol) {
485	gezelter	246
486			//add bond constraints
487			Molecule::BondIterator bi;
488			Bond* bond;
489			for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) {
490
491	gezelter	507	BondType* bt = bond->getBondType();
492	gezelter	246
493	gezelter	507	//class Parent1 {};
494			//class Child1 : public Parent {};
495			//class Child2 : public Parent {};
496			//Child1* ch1 = new Child1();
497			//Child2* ch2 = dynamic_cast<Child2*>(ch1);
498			//the dynamic_cast is succeed in above line. A compiler bug?
499	gezelter	246
500	gezelter	507	if (typeid(FixedBondType) == typeid(*bt)) {
501			FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt);
502	gezelter	246
503	gezelter	507	ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA());
504			ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB());
505			ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength());
506			mol->addConstraintPair(consPair);
507			}
508	gezelter	246	}
509
510			//rigidbody -- rigidbody constraint is not support yet
511	gezelter	507	}
512	gezelter	246
513	gezelter	507	void MoleculeCreator::createConstraintElem(Molecule* mol) {
514	gezelter	246
515			ConstraintPair* consPair;
516			Molecule::ConstraintPairIterator cpi;
517			std::set<StuntDouble*> sdSet;
518			for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) {
519
520	gezelter	507	StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble();
521			if (sdSet.find(sdA) == sdSet.end()){
522			sdSet.insert(sdA);
523			mol->addConstraintElem(new ConstraintElem(sdA));
524			}
525	gezelter	246
526	gezelter	507	StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble();
527			if (sdSet.find(sdB) == sdSet.end()){
528			sdSet.insert(sdB);
529			mol->addConstraintElem(new ConstraintElem(sdB));
530			}
531	gezelter	246
532			}
533
534	gezelter	507	}
535	gezelter	246
536			}