--- trunk/OOPSE/libmdtools/SimSetup.cpp 2003/03/27 19:21:42 422 +++ trunk/OOPSE/libmdtools/SimSetup.cpp 2003/06/17 21:56:15 555 @@ -66,7 +66,8 @@ void SimSetup::createSim( void ){ MakeStamps *the_stamps; Globals* the_globals; - int i, j; + ExtendedSystem* the_extendedsystem; + int i, j, k, globalAtomIndex; // get the stamps and globals; the_stamps = stamps; @@ -80,18 +81,85 @@ void SimSetup::createSim( void ){ // get the ones we know are there, yet still may need some work. n_components = the_globals->getNComponents(); strcpy( force_field, the_globals->getForceField() ); + + // get the ensemble and set up an extended system if we need it: strcpy( ensemble, the_globals->getEnsemble() ); + if( !strcasecmp( ensemble, "NPT" ) ) { + the_extendedsystem = new ExtendedSystem( simnfo ); + the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); + if (the_globals->haveTargetPressure()) + the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use the constant pressure\n" + " ensemble, you must set targetPressure.\n" + " This was found in the BASS file.\n"); + painCave.isFatal = 1; + simError(); + } + + if (the_globals->haveTauThermostat()) + the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); + else if (the_globals->haveQmass()) + the_extendedsystem->setQmass(the_globals->getQmass()); + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use one of the constant temperature\n" + " ensembles, you must set either tauThermostat or qMass.\n" + " Neither of these was found in the BASS file.\n"); + painCave.isFatal = 1; + simError(); + } + + if (the_globals->haveTauBarostat()) + the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use the constant pressure\n" + " ensemble, you must set tauBarostat.\n" + " This was found in the BASS file.\n"); + painCave.isFatal = 1; + simError(); + } + + } else if ( !strcasecmp( ensemble, "NVT") ) { + the_extendedsystem = new ExtendedSystem( simnfo ); + the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); + + if (the_globals->haveTauThermostat()) + the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); + else if (the_globals->haveQmass()) + the_extendedsystem->setQmass(the_globals->getQmass()); + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use one of the constant temperature\n" + " ensembles, you must set either tauThermostat or qMass.\n" + " Neither of these was found in the BASS file.\n"); + painCave.isFatal = 1; + simError(); + } + + } else if ( !strcasecmp( ensemble, "NVE") ) { + } else { + sprintf( painCave.errMsg, + "SimSetup Warning. Unrecognized Ensemble -> %s, " + "reverting to NVE for this simulation.\n", + ensemble ); + painCave.isFatal = 0; + simError(); + strcpy( ensemble, "NVE" ); + } strcpy( simnfo->ensemble, ensemble ); strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); simnfo->usePBC = the_globals->getPBC(); - - - if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); - else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); - else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); - else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); + int usesDipoles = 0; + if( !strcmp( force_field, "TraPPE_Ex" ) ){ + the_ff = new TraPPE_ExFF(); + usesDipoles = 1; + } + else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); else{ sprintf( painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", @@ -230,20 +298,17 @@ void SimSetup::createSim( void ){ simnfo->n_torsions = tot_torsions; simnfo->n_SRI = tot_SRI; simnfo->n_mol = tot_nmol; - + simnfo->molMembershipArray = new int[tot_atoms]; + #ifdef IS_MPI // divide the molecules among processors here. mpiSim = new mpiSimulation( simnfo ); - - globalIndex = mpiSim->divideLabor(); - - // set up the local variables int localMol, allMol; @@ -258,11 +323,14 @@ void SimSetup::createSim( void ){ local_bonds = 0; local_bends = 0; local_torsions = 0; + globalAtomIndex = 0; + + for( i=0; igetNAtoms(); local_bonds += comp_stamps[i]->getNBonds(); @@ -270,12 +338,16 @@ void SimSetup::createSim( void ){ local_torsions += comp_stamps[i]->getNTorsions(); localMol++; } - allMol++; + for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { + simnfo->molMembershipArray[globalAtomIndex] = allMol; + globalAtomIndex++; + } + + allMol++; } } local_SRI = local_bonds + local_bends + local_torsions; - simnfo->n_atoms = mpiSim->getMyNlocal(); if( local_atoms != simnfo->n_atoms ){ @@ -318,6 +390,8 @@ void SimSetup::createSim( void ){ if(mol2proc[i] == worldRank ){ the_molecules[molIndex].setStampID( molCompType[i] ); + the_molecules[molIndex].setMyIndex( molIndex ); + the_molecules[molIndex].setGlobalIndex( i ); molIndex++; } } @@ -325,9 +399,16 @@ void SimSetup::createSim( void ){ #else // is_mpi molIndex = 0; + globalAtomIndex = 0; for(i=0; igetNAtoms(); k++) { + simnfo->molMembershipArray[globalAtomIndex] = molIndex; + globalAtomIndex++; + } molIndex++; } } @@ -337,10 +418,12 @@ void SimSetup::createSim( void ){ if( simnfo->n_SRI ){ + Exclude::createArray(simnfo->n_SRI); the_excludes = new Exclude*[simnfo->n_SRI]; + for( int ex=0; exn_SRI; ex++) the_excludes[ex] = new Exclude(ex); simnfo->globalExcludes = new int; - simnfo->n_exclude = tot_SRI; + simnfo->n_exclude = simnfo->n_SRI; } else{ @@ -356,6 +439,7 @@ void SimSetup::createSim( void ){ // set the arrays into the SimInfo object simnfo->atoms = the_atoms; + simnfo->molecules = the_molecules; simnfo->nGlobalExcludes = 0; simnfo->excludes = the_excludes; @@ -459,11 +543,11 @@ void SimSetup::createSim( void ){ } simnfo->dielectric = the_globals->getDielectric(); } else { - if (simnfo->n_dipoles) { + if (usesDipoles) { if( !the_globals->haveECR() ){ sprintf( painCave.errMsg, - "SimSetup Warning: using default value of 1/2 the smallest" + "SimSetup Warning: using default value of 1/2 the smallest " "box length for the electrostaticCutoffRadius.\n" "I hope you have a very fast processor!\n"); painCave.isFatal = 0; @@ -479,7 +563,7 @@ void SimSetup::createSim( void ){ if( !the_globals->haveEST() ){ sprintf( painCave.errMsg, - "SimSetup Warning: using default value of 5% of the" + "SimSetup Warning: using default value of 5%% of the " "electrostaticCutoffRadius for the " "electrostaticSkinThickness\n" ); @@ -650,19 +734,23 @@ void SimSetup::createSim( void ){ if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); -// // make the longe range forces and the integrator + // make the integrator -// new AllLong( simnfo ); - if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); - if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); - if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); - if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); - + if( !strcmp( ensemble, "TraPPE_Ex" ) ){ + new Symplectic(simnfo, the_ff, the_extendedsystem); + } + else if( !strcmp( force_field, "LJ" ) ){ + new Verlet( *simnfo, the_ff, the_extendedsystem ); + } +#ifdef IS_MPI + mpiSim->mpiRefresh(); +#endif // initialize the Fortran - + + simnfo->refreshSim(); if( !strcmp( simnfo->mixingRule, "standard") ){ @@ -699,14 +787,21 @@ void SimSetup::makeMolecules( void ){ BondStamp* currentBond; BendStamp* currentBend; TorsionStamp* currentTorsion; + + bond_pair* theBonds; + bend_set* theBends; + torsion_set* theTorsions; + //init the forceField paramters the_ff->readParams(); - // init the molecules + // init the atoms + double ux, uy, uz, u, uSqr; + atomOffset = 0; excludeOffset = 0; for(i=0; in_mol; i++){ @@ -723,7 +818,7 @@ void SimSetup::makeMolecules( void ){ info.myExcludes = &the_excludes[excludeOffset]; info.myBonds = new Bond*[info.nBonds]; info.myBends = new Bend*[info.nBends]; - info.myTorsions = new Torsions*[info.nTorsions]; + info.myTorsions = new Torsion*[info.nTorsions]; theBonds = new bond_pair[info.nBonds]; theBends = new bend_set[info.nBends]; @@ -733,7 +828,7 @@ void SimSetup::makeMolecules( void ){ for(j=0; jgetAtom( j ); + currentAtom = comp_stamps[stampID]->getAtom( j ); if( currentAtom->haveOrientation() ){ dAtom = new DirectionalAtom(j + atomOffset); @@ -774,8 +869,8 @@ void SimSetup::makeMolecules( void ){ theBonds[j].a = currentBond->getA() + atomOffset; theBonds[j].b = currentBond->getB() + atomOffset; - exI = theBonds[i].a; - exJ = theBonds[i].b; + exI = theBonds[j].a; + exJ = theBonds[j].b; // exclude_I must always be the smaller of the pair if( exI > exJ ){ @@ -791,6 +886,7 @@ void SimSetup::makeMolecules( void ){ the_excludes[j+excludeOffset]->setPair( exI, exJ ); #else // isn't MPI + the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); #endif //is_mpi } @@ -806,7 +902,7 @@ void SimSetup::makeMolecules( void ){ if( currentBend->haveExtras() ){ - extras = current_bend->getExtras(); + extras = currentBend->getExtras(); current_extra = extras; while( current_extra != NULL ){ @@ -828,7 +924,7 @@ void SimSetup::makeMolecules( void ){ default: sprintf( painCave.errMsg, - "SimSetup Error: ghostVectorSource was neiter a " + "SimSetup Error: ghostVectorSource was neither a " "double nor an int.\n" "-->Bend[%d] in %s\n", j, comp_stamps[stampID]->getID() ); @@ -922,12 +1018,23 @@ void SimSetup::makeMolecules( void ){ the_molecules[i].initialize( info ); + + atomOffset += info.nAtoms; + delete[] theBonds; + delete[] theBends; + delete[] theTorsions; } +#ifdef IS_MPI + sprintf( checkPointMsg, "all molecules initialized succesfully" ); + MPIcheckPoint(); +#endif // is_mpi + // clean up the forcefield the_ff->calcRcut(); the_ff->cleanMe(); + } void SimSetup::initFromBass( void ){