--- trunk/OOPSE/libmdtools/SimInfo.cpp 2004/04/15 16:18:26 1113 +++ trunk/OOPSE/libmdtools/SimInfo.cpp 2004/05/27 00:48:12 1198 @@ -42,11 +42,10 @@ SimInfo::SimInfo(){ thermalTime = 0.0; currentTime = 0.0; rCut = 0.0; - ecr = 0.0; - est = 0.0; + rSw = 0.0; haveRcut = 0; - haveEcr = 0; + haveRsw = 0; boxIsInit = 0; resetTime = 1e99; @@ -63,7 +62,10 @@ SimInfo::SimInfo(){ useReactionField = 0; useGB = 0; useEAM = 0; + useThermInt = 0; + haveCutoffGroups = false; + excludes = Exclude::Instance(); myConfiguration = new SimState(); @@ -71,6 +73,8 @@ SimInfo::SimInfo(){ has_minimizer = false; the_minimizer =NULL; + ngroup = 0; + wrapMeSimInfo( this ); } @@ -83,7 +87,7 @@ SimInfo::~SimInfo(){ for(i = properties.begin(); i != properties.end(); i++) delete (*i).second; - + } void SimInfo::setBox(double newBox[3]) { @@ -326,8 +330,12 @@ int SimInfo::getNDF(){ for(int i = 0; i < integrableObjects.size(); i++){ ndf_local += 3; - if (integrableObjects[i]->isDirectional()) - ndf_local += 3; + if (integrableObjects[i]->isDirectional()) { + if (integrableObjects[i]->isLinear()) + ndf_local += 2; + else + ndf_local += 3; + } } // n_constraints is local, so subtract them on each processor: @@ -356,8 +364,12 @@ int SimInfo::getNDFraw() { for(int i = 0; i < integrableObjects.size(); i++){ ndfRaw_local += 3; - if (integrableObjects[i]->isDirectional()) - ndfRaw_local += 3; + if (integrableObjects[i]->isDirectional()) { + if (integrableObjects[i]->isLinear()) + ndfRaw_local += 2; + else + ndfRaw_local += 3; + } } #ifdef IS_MPI @@ -431,62 +443,55 @@ void SimInfo::refreshSim(){ n_exclude = excludes->getSize(); excl = excludes->getFortranArray(); - + #ifdef IS_MPI n_global = mpiSim->getTotAtoms(); #else n_global = n_atoms; #endif - + isError = 0; - + + getFortranGroupArray(this, mfact, ngroup, groupList, groupStart); + //it may not be a good idea to pass the address of first element in vector + //since c++ standard does not require vector to be stored continuously in meomory + //Most of the compilers will organize the memory of vector continuously setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, - &nGlobalExcludes, globalExcludes, molMembershipArray, - &isError ); - + &nGlobalExcludes, globalExcludes, molMembershipArray, + &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError); + if( isError ){ - + sprintf( painCave.errMsg, - "There was an error setting the simulation information in fortran.\n" ); + "There was an error setting the simulation information in fortran.\n" ); painCave.isFatal = 1; simError(); } - + #ifdef IS_MPI sprintf( checkPointMsg, "succesfully sent the simulation information to fortran.\n"); MPIcheckPoint(); #endif // is_mpi - + this->ndf = this->getNDF(); this->ndfRaw = this->getNDFraw(); this->ndfTrans = this->getNDFtranslational(); } void SimInfo::setDefaultRcut( double theRcut ){ - + haveRcut = 1; rCut = theRcut; - - ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; - - notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); -} - -void SimInfo::setDefaultEcr( double theEcr ){ - - haveEcr = 1; - ecr = theEcr; + rList = rCut + 1.0; - ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; - - notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); + notifyFortranCutOffs( &rCut, &rSw, &rList ); } -void SimInfo::setDefaultEcr( double theEcr, double theEst ){ +void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ - est = theEst; - setDefaultEcr( theEcr ); + rSw = theRsw; + setDefaultRcut( theRcut ); } @@ -498,42 +503,21 @@ void SimInfo::checkCutOffs( void ){ if( rCut > maxCutoff ){ sprintf( painCave.errMsg, - "LJrcut is too large for the current periodic box.\n" - "\tCurrent Value of LJrcut = %G at time %G\n " + "cutoffRadius is too large for the current periodic box.\n" + "\tCurrent Value of cutoffRadius = %G at time %G\n " "\tThis is larger than half of at least one of the\n" "\tperiodic box vectors. Right now, the Box matrix is:\n" - "\n, %G" + "\n" "\t[ %G %G %G ]\n" "\t[ %G %G %G ]\n" "\t[ %G %G %G ]\n", - rCut, currentTime, maxCutoff, + rCut, currentTime, Hmat[0][0], Hmat[0][1], Hmat[0][2], Hmat[1][0], Hmat[1][1], Hmat[1][2], Hmat[2][0], Hmat[2][1], Hmat[2][2]); painCave.isFatal = 1; simError(); - } - - if( haveEcr ){ - if( ecr > maxCutoff ){ - sprintf( painCave.errMsg, - "electrostaticCutoffRadius is too large for the current\n" - "\tperiodic box.\n\n" - "\tCurrent Value of ECR = %G at time %G\n " - "\tThis is larger than half of at least one of the\n" - "\tperiodic box vectors. Right now, the Box matrix is:\n" - "\n" - "\t[ %G %G %G ]\n" - "\t[ %G %G %G ]\n" - "\t[ %G %G %G ]\n", - ecr, currentTime, - Hmat[0][0], Hmat[0][1], Hmat[0][2], - Hmat[1][0], Hmat[1][1], Hmat[1][2], - Hmat[2][0], Hmat[2][1], Hmat[2][2]); - painCave.isFatal = 1; - simError(); - } - } + } } else { // initialize this stuff before using it, OK? sprintf( painCave.errMsg, @@ -581,13 +565,54 @@ GenericData* SimInfo::getProperty(const string& propNa return NULL; } -vector SimInfo::getProperties(){ - vector result; - map::iterator i; +void getFortranGroupArray(SimInfo* info, vector& mfact, int& ngroup, + vector& groupList, vector& groupStart){ + Molecule* myMols; + Atom** myAtoms; + int numAtom; + int curIndex; + double mtot; + int numMol; + int numCutoffGroups; + CutoffGroup* myCutoffGroup; + vector::iterator iterCutoff; + Atom* cutoffAtom; + vector::iterator iterAtom; + int atomIndex; + double totalMass; - for(i = properties.begin(); i != properties.end(); i++) - result.push_back((*i).second); - - return result; + mfact.clear(); + groupList.clear(); + groupStart.clear(); + + //Be careful, fortran array begin at 1 + curIndex = 1; + + myMols = info->molecules; + numMol = info->n_mol; + for(int i = 0; i < numMol; i++){ + numCutoffGroups = myMols[i].getNCutoffGroups(); + for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL; + myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ + + totalMass = myCutoffGroup->getMass(); + + for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; + cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ + mfact.push_back(cutoffAtom->getMass()/totalMass); + groupList.push_back(cutoffAtom->getIndex() + 1); + } + + groupStart.push_back(curIndex); + curIndex += myCutoffGroup->getNumAtom(); + + }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff)) + + }//end for(int i = 0; i < numMol; i++) + + + //The last cutoff group need more element to indicate the end of the cutoff + groupStart.push_back(curIndex); + ngroup = groupStart.size() - 1; }