src/brains/SimInfo.cpp

/*
 * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
 * 
 * Contact: oopse@oopse.org
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */

/**
 * @file SimInfo.cpp
 * @author    tlin
 * @date  11/02/2004
 * @version 1.0
 */

#include <algorithm>

#include "brains/SimInfo.hpp"
#include "utils/MemoryUtils.hpp"

namespace oopse {

SimInfo::SimInfo(const std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, 
                                ForceField* ff, Globals* globals) : 
                                forceField_(ff), globals_(globals), nAtoms_(0), nBonds_(0), 
                                nBends_(0), nTorsions_(0), nRigidBodies_(0), nIntegrableObjects_(0), 
                                nCutoffGroups_(0), nConstraints_(0), nZConstraint_(0), sman_(NULL) {

    std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
    int nCutoffAtoms; // number of atoms belong to cutoff groups
    int ngroups;          //total cutoff groups defined in meta-data file
    MoleculeStamp* molStamp;
    int nMolWithSameStamp;
    CutoffGroupStamp* cgStamp;
    int nAtomsIngroups;
    int nCutoffGroupsInStamp;    

    nGlobalAtoms_ =  0;
    ngroups = 0;
    
    for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
        molStamp = i->first;
        nMolWithSameStamp = i->second;
        
        addMoleculeStamp(molStamp, nMolWithSameStamp);
        
        nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;   
        
        nAtomsIngroups = 0;
        nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
        
        for (int j=0; j < nCutoffGroupsInStamp; j++) {
            cgStamp = molStamp->getCutoffGroup(j);
            nAtomsIngroups += cgStamp->getNMembers();
        }

        ngroups += *nMolWithSameStamp;
        nCutoffAtoms += nAtomsIngroups * nMolWithSameStamp;                
    }

    //every free atom (atom does not belong to cutoff groups) is a cutoff group
    //therefore the total number of cutoff groups in the system is equal to 
    //the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
    //file plus the number of cutoff groups defined in meta-data file
    nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + ngroups;

    //initialize globalGroupMembership_, every element of this array will be 0
    globalGroupMembership_.insert(globalGroupMembership_.end(), nGlobalAtoms_, 0);

    nGlobalMols_ = molStampIds_.size();

#ifdef IS_MPI    
    molToProcMap_.resize(nGlobalMols_);
#endif
    
}

SimInfo::~SimInfo() {
    //MemoryUtils::deleteVectorOfPointer(molecules_);

    MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
    
    delete sman_;
    delete globals_;
    delete forceField_;

}


bool SimInfo::addMolecule(Molecule* mol) {
    MoleculeIterator i;

    i = molecules_.find(mol->getGlobalIndex());
    if (i != molecules_.end() ) {

        molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
        
        nAtoms_ += mol->getNAtoms();
        nBonds_ += mol->getNBonds();
        nBends_ += mol->getNBends();
        nTorsions_ += mol->getNTorsions();
        nRigidBodies_ += mol->getNRigidBodies();
        nIntegrableObjects_ += mol->getNIntegrableObjects();
        nCutoffGroups_ += mol->getNCutoffGroups();
        nConstraints_ += mol->getNConstraints();

        return true;
    } else {
        return false;
    }
}

bool SimInfo::removeMolecule(Molecule* mol) {
    MoleculeIterator i;
    i = molecules_.find(mol->getGlobalIndex());

    if (i != molecules_.end() ) {

        assert(mol == i->second);
        
        nAtoms_ -= mol->getNAtoms();
        nBonds_ -= mol->getNBonds();
        nBends_ -= mol->getNBends();
        nTorsions_ -= mol->getNTorsions();
        nRigidBodies_ -= mol->getNRigidBodies();
        nIntegrableObjects_ -= mol->getNIntegrableObjects();
        nCutoffGroups_ -= mol->getNCutoffGroups();
        nConstraints_ -= mol->getNConstraints();

        molecules_.erase(mol->getGlobalIndex());

        delete mol;
        
        return true;
    } else {
        return false;
    }


}    

        
Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
    i = molecules_.begin();
    return i == molecules_.end() ? NULL : *i;
}    

Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
    ++i;
    return i == molecules_.end() ? NULL : *i;    
}


void SimInfo::calcNdf() {
    int ndf_local;
    MoleculeIterator i;
    std::vector<StuntDouble*>::iterator j;
    Molecule* mol;
    StuntDouble* integrableObject;

    ndf_local = 0;
    
    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; 
               integrableObject = mol->nextIntegrableObject(j)) {

            ndf_local += 3;

            if (integrableObject->isDirectional()) {
                if (integrableObject->isLinear()) {
                    ndf_local += 2;
                } else {
                    ndf_local += 3;
                }
            }
            
        }//end for (integrableObject)
    }// end for (mol)
    
    // n_constraints is local, so subtract them on each processor
    ndf_local -= nConstraints_;

#ifdef IS_MPI
    MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
#else
    ndf_ = ndf_local;
#endif

    // nZconstraints_ is global, as are the 3 COM translations for the 
    // entire system:
    ndf_ = ndf_ - 3 - nZconstraints_;

}

void SimInfo::calcNdfRaw() {
    int ndfRaw_local;

    MoleculeIterator i;
    std::vector<StuntDouble*>::iterator j;
    Molecule* mol;
    StuntDouble* integrableObject;

    // Raw degrees of freedom that we have to set
    ndfRaw_local = 0;
    
    for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
        for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
               integrableObject = mol->nextIntegrableObject(j)) {

            ndfRaw_local += 3;

            if (integrableObject->isDirectional()) {
                if (integrableObject->isLinear()) {
                    ndfRaw_local += 2;
                } else {
                    ndfRaw_local += 3;
                }
            }
            
        }
    }
    
#ifdef IS_MPI
    MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
#else
    ndfRaw_ = ndfRaw_local;
#endif
}

void SimInfo::calcNdfTrans() {
    int ndfTrans_local;

    ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;


#ifdef IS_MPI
    MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
#else
    ndfTrans_ = ndfTrans_local;
#endif

    ndfTrans_ = ndfTrans_ - 3 - nZconstraints_;
 
}

void SimInfo::addExcludePairs(Molecule* mol) {
    std::vector<Bond*>::iterator bondIter;
    std::vector<Bend*>::iterator bendIter;
    std::vector<Torsion*>::iterator torsionIter;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    int a;
    int b;
    int c;
    int d;
    
    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
        a = bond->getAtomA()->getGlobalIndex();
        b = bond->getAtomB()->getGlobalIndex();        
        exclude_.addPair(a, b);
    }

    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
        a = bend->getAtomA()->getGlobalIndex();
        b = bend->getAtomB()->getGlobalIndex();        
        c = bend->getAtomC()->getGlobalIndex();

        exclude_.addPair(a, b);
        exclude_.addPair(a, c);
        exclude_.addPair(b, c);        
    }

    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
        a = torsion->getAtomA()->getGlobalIndex();
        b = torsion->getAtomB()->getGlobalIndex();        
        c = torsion->getAtomC()->getGlobalIndex();        
        d = torsion->getAtomD()->getGlobalIndex();        

        exclude_.addPair(a, b);
        exclude_.addPair(a, c);
        exclude_.addPair(a, d);
        exclude_.addPair(b, c);
        exclude_.addPair(b, d);
        exclude_.addPair(c, d);        
    }

    
}

void SimInfo::removeExcludePairs(Molecule* mol) {
    std::vector<Bond*>::iterator bondIter;
    std::vector<Bend*>::iterator bendIter;
    std::vector<Torsion*>::iterator torsionIter;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    int a;
    int b;
    int c;
    int d;
    
    for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
        a = bond->getAtomA()->getGlobalIndex();
        b = bond->getAtomB()->getGlobalIndex();        
        exclude_.removePair(a, b);
    }

    for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
        a = bend->getAtomA()->getGlobalIndex();
        b = bend->getAtomB()->getGlobalIndex();        
        c = bend->getAtomC()->getGlobalIndex();

        exclude_.removePair(a, b);
        exclude_.removePair(a, c);
        exclude_.removePair(b, c);        
    }

    for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
        a = torsion->getAtomA()->getGlobalIndex();
        b = torsion->getAtomB()->getGlobalIndex();        
        c = torsion->getAtomC()->getGlobalIndex();        
        d = torsion->getAtomD()->getGlobalIndex();        

        exclude_.removePair(a, b);
        exclude_.removePair(a, c);
        exclude_.removePair(a, d);
        exclude_.removePair(b, c);
        exclude_.removePair(b, d);
        exclude_.removePair(c, d);        
    }

}


void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
    int curStampId;

    //index from 0
    curStampId = molStampIds_.size();

    moleculeStamps_.push_back(molStamp);
    molStampIds_.insert(molStampIds_.end(), nmol, curStampId)
}

void SimInfo::update() {

#ifdef IS_MPI
    setupFortranParallel();
#endif

    setupFortranSim();

    calcNdf();
    calcNdfRaw();
    calcNdfTrans();
}

std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
    typename SimInfo::MoleculeIterator mi;
    Molecule* mol;
    typename Molecule::AtomIterator ai;
    Atom* atom;
    std::set<AtomType*> atomTypes;

    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {

        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
            atomTypes.insert(atom->getAtomType());
        }
        
    }

    return atomTypes;        
}

void SimInfo::setupSimType() {
    std::set<AtomType*>::iterator i;
    std::set<AtomType*> atomTypes;
    atomTypes = getUniqueAtomTypes();
    
    int useLennardJones = 0;
    int useElectrostatic = 0;
    int useEAM = 0;
    int useCharge = 0;
    int useDirectional = 0;
    int useDipole = 0;
    int useGayBerne = 0;
    int useSticky = 0;
    int useShape = 0; 
    int useFLARB = 0; //it is not in AtomType yet
    int useDirectionalAtom = 0;    
    int useElectrostatics = 0;
    //usePBC and useRF are from globals
    bool usePBC = globals_->getPBC();
    bool useRF = globals_->getUseRF();

    //loop over all of the atom types
    for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
        useLennardJones |= i->isLennardJones();
        useElectrostatic |= i->isElectrostatic();
        useEAM |= i->isEAM();
        useCharge |= i->isCharge();
        useDirectional |= i->isDirectional();
        useDipole |= i->isDipole();
        useGayBerne |= i->isGayBerne();
        useSticky |= i->isSticky();
        useShape |= i->isShape(); 
    }

    if (useSticky || useDipole || useGayBerne || useShape) {
        useDirectionalAtom = 1;
    }

    if (useCharge || useDipole) {
        useElectrostatics = 1;
    }

#ifdef IS_MPI    
    int temp;

    temp = usePBC;
    MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useDirectionalAtom;
    MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useLennardJones;
    MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useElectrostatics;
    MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useCharge;
    MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useDipole;
    MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useSticky;
    MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useGayBerne;
    MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useEAM;
    MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useShape;
    MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);   

    temp = useFLARB;
    MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    

    temp = useRF;
    MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);    
    
#endif

    fInfo_.SIM_uses_PBC = usePBC;    
    fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
    fInfo_.SIM_uses_LennardJones = useLennardJones;
    fInfo_.SIM_uses_Electrostatics = useElectrostatics;    
    fInfo_.SIM_uses_Charges = useCharge;
    fInfo_.SIM_uses_Dipoles = useDipole;
    fInfo_.SIM_uses_Sticky = useSticky;
    fInfo_.SIM_uses_GayBerne = useGayBerne;
    fInfo_.SIM_uses_EAM = useEAM;
    fInfo_.SIM_uses_Shapes = useShape;
    fInfo_.SIM_uses_FLARB = useFLARB;
    fInfo_.SIM_uses_RF = useRF;

    if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
        fInfo_.dielect = dielectric;
    } else {
        fInfo_.dielect = 0.0;
    }

}

void SimInfo::setupFortranSim() {
    int isError;
    int nExclude;
    std::vector<int> fortranGlobalGroupMembership;
    
    nExclude = exclude_.getSize();
    isError = 0;

    //globalGroupMembership_ is filled by SimCreator    
    for (int i = 0; i < nGlobalAtoms_; i++) {
        fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
    }

    //calculate mass ratio of cutoff group
    std::vector<double> mfact;
    typename SimInfo::MoleculeIterator mi;
    Molecule* mol;
    typename Molecule::CutoffGroupIterator ci;
    CutoffGroup* cg;
    typename Molecule::AtomIterator ai;
    Atom* atom;
    double totalMass;

    //to avoid memory reallocation, reserve enough space for mfact
    mfact.reserve(getNCutoffGroups());
    
    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {

            totalMass = cg->getMass();
            for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
                        mfact.push_back(atom->getMass()/totalMass);
            }

        }       
    }

    //fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
    std::vector<int> identArray;

    //to avoid memory reallocation, reserve enough space identArray
    identArray.reserve(getNAtoms());
    
    for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {        
        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
            identArray.push_back(atom->getIdent());
        }
    }    

    //setup fortran simulation
    //gloalExcludes and molMembershipArray should go away (They are never used)
    //why the hell fortran need to know molecule?
    //OOPSE = Object-Obfuscated Parallel Simulation Engine
    
    setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, exclude_->getExcludeList(), 
                  &nGlobalExcludes, globalExcludes, molMembershipArray, 
                  &mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); 

    if( isError ){

        sprintf( painCave.errMsg,
                 "There was an error setting the simulation information in fortran.\n" );
        painCave.isFatal = 1;
        painCave.severity = OOPSE_ERROR;
        simError();
    }

#ifdef IS_MPI
    sprintf( checkPointMsg,
       "succesfully sent the simulation information to fortran.\n");
    MPIcheckPoint();
#endif // is_mpi
}


#ifdef IS_MPI
void SimInfo::setupFortranParallel() {
    
    //SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
    std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
    std::vector<int> localToGlobalCutoffGroupIndex;
    typename SimInfo::MoleculeIterator mi;
    typename Molecule::AtomIterator ai;
    typename Molecule::CutoffGroupIterator ci;
    Molecule* mol;
    Atom* atom;
    CutoffGroup* cg;
    mpiSimData parallelData;
    int isError;

    for (mol = beginMolecule(mi); mol != NULL; mol  = nextMolecule(mi)) {

        //local index(index in DataStorge) of atom is important
        for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
            localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
        }

        //local index of cutoff group is trivial, it only depends on the order of travesing
        for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
            localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
        }        
        
    }

    //fill up mpiSimData struct
    parallelData.nMolGlobal = getNGlobalMolecules();
    parallelData.nMolLocal = getNMolecules();
    parallelData.nAtomsGlobal = getNGlobalAtoms();
    parallelData.nAtomsLocal = getNAtoms();
    parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
    parallelData.nGroupsLocal = getNCutoffGroups();
    parallelData.myNode = worldRank;
    MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors));

    //pass mpiSimData struct and index arrays to fortran
    setFsimParallel(parallelData, &(parallelData->nAtomsLocal),
                    &localToGlobalAtomIndex[0],  &(parallelData->nGroupsLocal),
                    &localToGlobalCutoffGroupIndex[0], &isError);

    if (isError) {
        sprintf(painCave.errMsg,
                "mpiRefresh errror: fortran didn't like something we gave it.\n");
        painCave.isFatal = 1;
        simError();
    }

    sprintf(checkPointMsg, " mpiRefresh successful.\n");
    MPIcheckPoint();


}

#endif

void SimInfo::addProperty(GenericData* genData) {
    properties_.addProperty(genData);  
}

void SimInfo::removeProperty(const std::string& propName) {
    properties_.removeProperty(propName);  
}

void SimInfo::clearProperties() {
    properties_.clearProperties(); 
}

std::vector<std::string> SimInfo::getPropertyNames() {
    return properties_.getPropertyNames();  
}
      
std::vector<GenericData*> SimInfo::getProperties() { 
    return properties_.getProperties(); 
}

GenericData* SimInfo::getPropertyByName(const std::string& propName) {
    return properties_.getPropertyByName(propName); 
}


std::ostream& operator <<(ostream& o, SimInfo& info) {

    return o;
}

}//end namespace oopse
Revision:	1733
Committed:	Fri Nov 12 06:19:04 2004 UTC (19 years, 7 months ago) by tim
File size:	20008 byte(s)
Log Message:	OOPSE = Object-Obfuscated Parallel Simulation Engine
#	Content
1	/*
2	* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project
3	*
4	* Contact: oopse@oopse.org
5	*
6	* This program is free software; you can redistribute it and/or
7	* modify it under the terms of the GNU Lesser General Public License
8	* as published by the Free Software Foundation; either version 2.1
9	* of the License, or (at your option) any later version.
10	* All we ask is that proper credit is given for our work, which includes
11	* - but is not limited to - adding the above copyright notice to the beginning
12	* of your source code files, and to any copyright notice that you may distribute
13	* with programs based on this work.
14	*
15	* This program is distributed in the hope that it will be useful,
16	* but WITHOUT ANY WARRANTY; without even the implied warranty of
17	* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18	* GNU Lesser General Public License for more details.
19	*
20	* You should have received a copy of the GNU Lesser General Public License
21	* along with this program; if not, write to the Free Software
22	* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
23	*
24	*/
25
26	/**
27	* @file SimInfo.cpp
28	* @author tlin
29	* @date 11/02/2004
30	* @version 1.0
31	*/
32
33	#include <algorithm>
34
35	#include "brains/SimInfo.hpp"
36	#include "utils/MemoryUtils.hpp"
37
38	namespace oopse {
39
40	SimInfo::SimInfo(const std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs,
41	ForceField* ff, Globals* globals) :
42	forceField_(ff), globals_(globals), nAtoms_(0), nBonds_(0),
43	nBends_(0), nTorsions_(0), nRigidBodies_(0), nIntegrableObjects_(0),
44	nCutoffGroups_(0), nConstraints_(0), nZConstraint_(0), sman_(NULL) {
45
46	std::vector<std::pair<MoleculeStamp*, int> >::iterator i;
47	int nCutoffAtoms; // number of atoms belong to cutoff groups
48	int ngroups; //total cutoff groups defined in meta-data file
49	MoleculeStamp* molStamp;
50	int nMolWithSameStamp;
51	CutoffGroupStamp* cgStamp;
52	int nAtomsIngroups;
53	int nCutoffGroupsInStamp;
54
55	nGlobalAtoms_ = 0;
56	ngroups = 0;
57
58	for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) {
59	molStamp = i->first;
60	nMolWithSameStamp = i->second;
61
62	addMoleculeStamp(molStamp, nMolWithSameStamp);
63
64	nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp;
65
66	nAtomsIngroups = 0;
67	nCutoffGroupsInStamp = molStamp->getNCutoffGroups();
68
69	for (int j=0; j < nCutoffGroupsInStamp; j++) {
70	cgStamp = molStamp->getCutoffGroup(j);
71	nAtomsIngroups += cgStamp->getNMembers();
72	}
73
74	ngroups += *nMolWithSameStamp;
75	nCutoffAtoms += nAtomsIngroups * nMolWithSameStamp;
76	}
77
78	//every free atom (atom does not belong to cutoff groups) is a cutoff group
79	//therefore the total number of cutoff groups in the system is equal to
80	//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data
81	//file plus the number of cutoff groups defined in meta-data file
82	nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + ngroups;
83
84	//initialize globalGroupMembership_, every element of this array will be 0
85	globalGroupMembership_.insert(globalGroupMembership_.end(), nGlobalAtoms_, 0);
86
87	nGlobalMols_ = molStampIds_.size();
88
89	#ifdef IS_MPI
90	molToProcMap_.resize(nGlobalMols_);
91	#endif
92
93	}
94
95	SimInfo::~SimInfo() {
96	//MemoryUtils::deleteVectorOfPointer(molecules_);
97
98	MemoryUtils::deleteVectorOfPointer(moleculeStamps_);
99
100	delete sman_;
101	delete globals_;
102	delete forceField_;
103
104	}
105
106
107	bool SimInfo::addMolecule(Molecule* mol) {
108	MoleculeIterator i;
109
110	i = molecules_.find(mol->getGlobalIndex());
111	if (i != molecules_.end() ) {
112
113	molecules_.insert(make_pair(mol->getGlobalIndex(), mol));
114
115	nAtoms_ += mol->getNAtoms();
116	nBonds_ += mol->getNBonds();
117	nBends_ += mol->getNBends();
118	nTorsions_ += mol->getNTorsions();
119	nRigidBodies_ += mol->getNRigidBodies();
120	nIntegrableObjects_ += mol->getNIntegrableObjects();
121	nCutoffGroups_ += mol->getNCutoffGroups();
122	nConstraints_ += mol->getNConstraints();
123
124	return true;
125	} else {
126	return false;
127	}
128	}
129
130	bool SimInfo::removeMolecule(Molecule* mol) {
131	MoleculeIterator i;
132	i = molecules_.find(mol->getGlobalIndex());
133
134	if (i != molecules_.end() ) {
135
136	assert(mol == i->second);
137
138	nAtoms_ -= mol->getNAtoms();
139	nBonds_ -= mol->getNBonds();
140	nBends_ -= mol->getNBends();
141	nTorsions_ -= mol->getNTorsions();
142	nRigidBodies_ -= mol->getNRigidBodies();
143	nIntegrableObjects_ -= mol->getNIntegrableObjects();
144	nCutoffGroups_ -= mol->getNCutoffGroups();
145	nConstraints_ -= mol->getNConstraints();
146
147	molecules_.erase(mol->getGlobalIndex());
148
149	delete mol;
150
151	return true;
152	} else {
153	return false;
154	}
155
156
157	}
158
159
160	Molecule* SimInfo::beginMolecule(MoleculeIterator& i) {
161	i = molecules_.begin();
162	return i == molecules_.end() ? NULL : *i;
163	}
164
165	Molecule* SimInfo::nextMolecule(MoleculeIterator& i) {
166	++i;
167	return i == molecules_.end() ? NULL : *i;
168	}
169
170
171	void SimInfo::calcNdf() {
172	int ndf_local;
173	MoleculeIterator i;
174	std::vector<StuntDouble*>::iterator j;
175	Molecule* mol;
176	StuntDouble* integrableObject;
177
178	ndf_local = 0;
179
180	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
181	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
182	integrableObject = mol->nextIntegrableObject(j)) {
183
184	ndf_local += 3;
185
186	if (integrableObject->isDirectional()) {
187	if (integrableObject->isLinear()) {
188	ndf_local += 2;
189	} else {
190	ndf_local += 3;
191	}
192	}
193
194	}//end for (integrableObject)
195	}// end for (mol)
196
197	// n_constraints is local, so subtract them on each processor
198	ndf_local -= nConstraints_;
199
200	#ifdef IS_MPI
201	MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
202	#else
203	ndf_ = ndf_local;
204	#endif
205
206	// nZconstraints_ is global, as are the 3 COM translations for the
207	// entire system:
208	ndf_ = ndf_ - 3 - nZconstraints_;
209
210	}
211
212	void SimInfo::calcNdfRaw() {
213	int ndfRaw_local;
214
215	MoleculeIterator i;
216	std::vector<StuntDouble*>::iterator j;
217	Molecule* mol;
218	StuntDouble* integrableObject;
219
220	// Raw degrees of freedom that we have to set
221	ndfRaw_local = 0;
222
223	for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) {
224	for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL;
225	integrableObject = mol->nextIntegrableObject(j)) {
226
227	ndfRaw_local += 3;
228
229	if (integrableObject->isDirectional()) {
230	if (integrableObject->isLinear()) {
231	ndfRaw_local += 2;
232	} else {
233	ndfRaw_local += 3;
234	}
235	}
236
237	}
238	}
239
240	#ifdef IS_MPI
241	MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
242	#else
243	ndfRaw_ = ndfRaw_local;
244	#endif
245	}
246
247	void SimInfo::calcNdfTrans() {
248	int ndfTrans_local;
249
250	ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_;
251
252
253	#ifdef IS_MPI
254	MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
255	#else
256	ndfTrans_ = ndfTrans_local;
257	#endif
258
259	ndfTrans_ = ndfTrans_ - 3 - nZconstraints_;
260
261	}
262
263	void SimInfo::addExcludePairs(Molecule* mol) {
264	std::vector<Bond*>::iterator bondIter;
265	std::vector<Bend*>::iterator bendIter;
266	std::vector<Torsion*>::iterator torsionIter;
267	Bond* bond;
268	Bend* bend;
269	Torsion* torsion;
270	int a;
271	int b;
272	int c;
273	int d;
274
275	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
276	a = bond->getAtomA()->getGlobalIndex();
277	b = bond->getAtomB()->getGlobalIndex();
278	exclude_.addPair(a, b);
279	}
280
281	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
282	a = bend->getAtomA()->getGlobalIndex();
283	b = bend->getAtomB()->getGlobalIndex();
284	c = bend->getAtomC()->getGlobalIndex();
285
286	exclude_.addPair(a, b);
287	exclude_.addPair(a, c);
288	exclude_.addPair(b, c);
289	}
290
291	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
292	a = torsion->getAtomA()->getGlobalIndex();
293	b = torsion->getAtomB()->getGlobalIndex();
294	c = torsion->getAtomC()->getGlobalIndex();
295	d = torsion->getAtomD()->getGlobalIndex();
296
297	exclude_.addPair(a, b);
298	exclude_.addPair(a, c);
299	exclude_.addPair(a, d);
300	exclude_.addPair(b, c);
301	exclude_.addPair(b, d);
302	exclude_.addPair(c, d);
303	}
304
305
306	}
307
308	void SimInfo::removeExcludePairs(Molecule* mol) {
309	std::vector<Bond*>::iterator bondIter;
310	std::vector<Bend*>::iterator bendIter;
311	std::vector<Torsion*>::iterator torsionIter;
312	Bond* bond;
313	Bend* bend;
314	Torsion* torsion;
315	int a;
316	int b;
317	int c;
318	int d;
319
320	for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
321	a = bond->getAtomA()->getGlobalIndex();
322	b = bond->getAtomB()->getGlobalIndex();
323	exclude_.removePair(a, b);
324	}
325
326	for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
327	a = bend->getAtomA()->getGlobalIndex();
328	b = bend->getAtomB()->getGlobalIndex();
329	c = bend->getAtomC()->getGlobalIndex();
330
331	exclude_.removePair(a, b);
332	exclude_.removePair(a, c);
333	exclude_.removePair(b, c);
334	}
335
336	for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) {
337	a = torsion->getAtomA()->getGlobalIndex();
338	b = torsion->getAtomB()->getGlobalIndex();
339	c = torsion->getAtomC()->getGlobalIndex();
340	d = torsion->getAtomD()->getGlobalIndex();
341
342	exclude_.removePair(a, b);
343	exclude_.removePair(a, c);
344	exclude_.removePair(a, d);
345	exclude_.removePair(b, c);
346	exclude_.removePair(b, d);
347	exclude_.removePair(c, d);
348	}
349
350	}
351
352
353	void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) {
354	int curStampId;
355
356	//index from 0
357	curStampId = molStampIds_.size();
358
359	moleculeStamps_.push_back(molStamp);
360	molStampIds_.insert(molStampIds_.end(), nmol, curStampId)
361	}
362
363	void SimInfo::update() {
364
365	#ifdef IS_MPI
366	setupFortranParallel();
367	#endif
368
369	setupFortranSim();
370
371	calcNdf();
372	calcNdfRaw();
373	calcNdfTrans();
374	}
375
376	std::set<AtomType*> SimInfo::getUniqueAtomTypes() {
377	typename SimInfo::MoleculeIterator mi;
378	Molecule* mol;
379	typename Molecule::AtomIterator ai;
380	Atom* atom;
381	std::set<AtomType*> atomTypes;
382
383	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
384
385	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
386	atomTypes.insert(atom->getAtomType());
387	}
388
389	}
390
391	return atomTypes;
392	}
393
394	void SimInfo::setupSimType() {
395	std::set<AtomType*>::iterator i;
396	std::set<AtomType*> atomTypes;
397	atomTypes = getUniqueAtomTypes();
398
399	int useLennardJones = 0;
400	int useElectrostatic = 0;
401	int useEAM = 0;
402	int useCharge = 0;
403	int useDirectional = 0;
404	int useDipole = 0;
405	int useGayBerne = 0;
406	int useSticky = 0;
407	int useShape = 0;
408	int useFLARB = 0; //it is not in AtomType yet
409	int useDirectionalAtom = 0;
410	int useElectrostatics = 0;
411	//usePBC and useRF are from globals
412	bool usePBC = globals_->getPBC();
413	bool useRF = globals_->getUseRF();
414
415	//loop over all of the atom types
416	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
417	useLennardJones \|= i->isLennardJones();
418	useElectrostatic \|= i->isElectrostatic();
419	useEAM \|= i->isEAM();
420	useCharge \|= i->isCharge();
421	useDirectional \|= i->isDirectional();
422	useDipole \|= i->isDipole();
423	useGayBerne \|= i->isGayBerne();
424	useSticky \|= i->isSticky();
425	useShape \|= i->isShape();
426	}
427
428	if (useSticky \|\| useDipole \|\| useGayBerne \|\| useShape) {
429	useDirectionalAtom = 1;
430	}
431
432	if (useCharge \|\| useDipole) {
433	useElectrostatics = 1;
434	}
435
436	#ifdef IS_MPI
437	int temp;
438
439	temp = usePBC;
440	MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
441
442	temp = useDirectionalAtom;
443	MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
444
445	temp = useLennardJones;
446	MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
447
448	temp = useElectrostatics;
449	MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
450
451	temp = useCharge;
452	MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
453
454	temp = useDipole;
455	MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
456
457	temp = useSticky;
458	MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
459
460	temp = useGayBerne;
461	MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
462
463	temp = useEAM;
464	MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
465
466	temp = useShape;
467	MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
468
469	temp = useFLARB;
470	MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
471
472	temp = useRF;
473	MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
474
475	#endif
476
477	fInfo_.SIM_uses_PBC = usePBC;
478	fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom;
479	fInfo_.SIM_uses_LennardJones = useLennardJones;
480	fInfo_.SIM_uses_Electrostatics = useElectrostatics;
481	fInfo_.SIM_uses_Charges = useCharge;
482	fInfo_.SIM_uses_Dipoles = useDipole;
483	fInfo_.SIM_uses_Sticky = useSticky;
484	fInfo_.SIM_uses_GayBerne = useGayBerne;
485	fInfo_.SIM_uses_EAM = useEAM;
486	fInfo_.SIM_uses_Shapes = useShape;
487	fInfo_.SIM_uses_FLARB = useFLARB;
488	fInfo_.SIM_uses_RF = useRF;
489
490	if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) {
491	fInfo_.dielect = dielectric;
492	} else {
493	fInfo_.dielect = 0.0;
494	}
495
496	}
497
498	void SimInfo::setupFortranSim() {
499	int isError;
500	int nExclude;
501	std::vector<int> fortranGlobalGroupMembership;
502
503	nExclude = exclude_.getSize();
504	isError = 0;
505
506	//globalGroupMembership_ is filled by SimCreator
507	for (int i = 0; i < nGlobalAtoms_; i++) {
508	fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1);
509	}
510
511	//calculate mass ratio of cutoff group
512	std::vector<double> mfact;
513	typename SimInfo::MoleculeIterator mi;
514	Molecule* mol;
515	typename Molecule::CutoffGroupIterator ci;
516	CutoffGroup* cg;
517	typename Molecule::AtomIterator ai;
518	Atom* atom;
519	double totalMass;
520
521	//to avoid memory reallocation, reserve enough space for mfact
522	mfact.reserve(getNCutoffGroups());
523
524	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
525	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
526
527	totalMass = cg->getMass();
528	for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) {
529	mfact.push_back(atom->getMass()/totalMass);
530	}
531
532	}
533	}
534
535	//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!)
536	std::vector<int> identArray;
537
538	//to avoid memory reallocation, reserve enough space identArray
539	identArray.reserve(getNAtoms());
540
541	for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
542	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
543	identArray.push_back(atom->getIdent());
544	}
545	}
546
547	//setup fortran simulation
548	//gloalExcludes and molMembershipArray should go away (They are never used)
549	//why the hell fortran need to know molecule?
550	//OOPSE = Object-Obfuscated Parallel Simulation Engine
551
552	setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, exclude_->getExcludeList(),
553	&nGlobalExcludes, globalExcludes, molMembershipArray,
554	&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError);
555
556	if( isError ){
557
558	sprintf( painCave.errMsg,
559	"There was an error setting the simulation information in fortran.\n" );
560	painCave.isFatal = 1;
561	painCave.severity = OOPSE_ERROR;
562	simError();
563	}
564
565	#ifdef IS_MPI
566	sprintf( checkPointMsg,
567	"succesfully sent the simulation information to fortran.\n");
568	MPIcheckPoint();
569	#endif // is_mpi
570	}
571
572
573	#ifdef IS_MPI
574	void SimInfo::setupFortranParallel() {
575
576	//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex
577	std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0);
578	std::vector<int> localToGlobalCutoffGroupIndex;
579	typename SimInfo::MoleculeIterator mi;
580	typename Molecule::AtomIterator ai;
581	typename Molecule::CutoffGroupIterator ci;
582	Molecule* mol;
583	Atom* atom;
584	CutoffGroup* cg;
585	mpiSimData parallelData;
586	int isError;
587
588	for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) {
589
590	//local index(index in DataStorge) of atom is important
591	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
592	localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1;
593	}
594
595	//local index of cutoff group is trivial, it only depends on the order of travesing
596	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
597	localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1);
598	}
599
600	}
601
602	//fill up mpiSimData struct
603	parallelData.nMolGlobal = getNGlobalMolecules();
604	parallelData.nMolLocal = getNMolecules();
605	parallelData.nAtomsGlobal = getNGlobalAtoms();
606	parallelData.nAtomsLocal = getNAtoms();
607	parallelData.nGroupsGlobal = getNGlobalCutoffGroups();
608	parallelData.nGroupsLocal = getNCutoffGroups();
609	parallelData.myNode = worldRank;
610	MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors));
611
612	//pass mpiSimData struct and index arrays to fortran
613	setFsimParallel(parallelData, &(parallelData->nAtomsLocal),
614	&localToGlobalAtomIndex[0], &(parallelData->nGroupsLocal),
615	&localToGlobalCutoffGroupIndex[0], &isError);
616
617	if (isError) {
618	sprintf(painCave.errMsg,
619	"mpiRefresh errror: fortran didn't like something we gave it.\n");
620	painCave.isFatal = 1;
621	simError();
622	}
623
624	sprintf(checkPointMsg, " mpiRefresh successful.\n");
625	MPIcheckPoint();
626
627
628	}
629
630	#endif
631
632	void SimInfo::addProperty(GenericData* genData) {
633	properties_.addProperty(genData);
634	}
635
636	void SimInfo::removeProperty(const std::string& propName) {
637	properties_.removeProperty(propName);
638	}
639
640	void SimInfo::clearProperties() {
641	properties_.clearProperties();
642	}
643
644	std::vector<std::string> SimInfo::getPropertyNames() {
645	return properties_.getPropertyNames();
646	}
647
648	std::vector<GenericData*> SimInfo::getProperties() {
649	return properties_.getProperties();
650	}
651
652	GenericData* SimInfo::getPropertyByName(const std::string& propName) {
653	return properties_.getPropertyByName(propName);
654	}
655
656
657	std::ostream& operator <<(ostream& o, SimInfo& info) {
658
659	return o;
660	}
661
662	}//end namespace oopse