--- trunk/OOPSE/libmdtools/SimSetup.cpp 2003/06/19 19:11:53 557 +++ trunk/OOPSE/libmdtools/SimSetup.cpp 2003/08/13 19:21:53 693 @@ -1,8 +1,11 @@ +#include #include #include #include +#include #include "SimSetup.hpp" +#include "ReadWrite.hpp" #include "parse_me.h" #include "Integrator.hpp" #include "simError.h" @@ -14,18 +17,28 @@ // some defines for ensemble and Forcefield cases -#define NVE_ENS 0 -#define NVT_ENS 1 -#define NPT_ENS 2 +#define NVE_ENS 0 +#define NVT_ENS 1 +#define NPTi_ENS 2 +#define NPTf_ENS 3 +#define NPTim_ENS 4 +#define NPTfm_ENS 5 #define FF_DUFF 0 #define FF_LJ 1 +#define FF_EAM 2 +using namespace std; SimSetup::SimSetup(){ + + isInfoArray = 0; + nInfo = 1; + stamps = new MakeStamps(); globals = new Globals(); + #ifdef IS_MPI strcpy( checkPointMsg, "SimSetup creation successful" ); MPIcheckPoint(); @@ -37,6 +50,13 @@ void SimSetup::parseFile( char* fileName ){ delete globals; } +void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { + info = the_info; + nInfo = theNinfo; + isInfoArray = 1; +} + + void SimSetup::parseFile( char* fileName ){ #ifdef IS_MPI @@ -72,1183 +92,1583 @@ void SimSetup::createSim( void ){ #endif // is_mpi -void SimSetup::createSim( void ){ +void SimSetup::createSim(void){ - MakeStamps *the_stamps; - Globals* the_globals; int i, j, k, globalAtomIndex; - int ensembleCase; - int ffCase; - - ensembleCase = -1; - ffCase = -1; + // gather all of the information from the Bass file - // get the stamps and globals; - the_stamps = stamps; - the_globals = globals; + gatherInfo(); - // set the easy ones first - simnfo->target_temp = the_globals->getTargetTemp(); - simnfo->dt = the_globals->getDt(); - simnfo->run_time = the_globals->getRunTime(); + // creation of complex system objects - // get the ones we know are there, yet still may need some work. - n_components = the_globals->getNComponents(); - strcpy( force_field, the_globals->getForceField() ); + sysObjectsCreation(); - if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; - else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; - else{ - sprintf( painCave.errMsg, - "SimSetup Error. Unrecognized force field -> %s\n", - force_field ); - painCave.isFatal = 1; - simError(); - } + // check on the post processing info - // get the ensemble: - strcpy( ensemble, the_globals->getEnsemble() ); + finalInfoCheck(); - if( !strcasecmp( ensemble, "NVE" )) ffCase = NVE_ENS; - else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS; - else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS; - else{ - sprintf( painCave.errMsg, - "SimSetup Warning. Unrecognized Ensemble -> %s, " - "reverting to NVE for this simulation.\n", - ensemble ); - painCave.isFatal = 0; - simError(); - strcpy( ensemble, "NVE" ); - ensembleCase = NVE_ENS; - } - strcpy( simnfo->ensemble, ensemble ); + // initialize the system coordinates + if( !isInfoArray ) initSystemCoords(); -// 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(); -// } + // make the output filenames -// 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(); -// } + makeOutNames(); + + // make the integrator + + makeIntegrator(); + +#ifdef IS_MPI + mpiSim->mpiRefresh(); +#endif -// 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(); -// } + // initialize the Fortran -// } else if ( !strcasecmp( ensemble, "NVT") ) { -// the_extendedsystem = new ExtendedSystem( simnfo ); -// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); + initFortran(); -// 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(); -// } - strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); - simnfo->usePBC = the_globals->getPBC(); - - int usesDipoles = 0; - switch( ffCase ){ - case FF_DUFF: - the_ff = new DUFF(); - usesDipoles = 1; - break; +} - case FF_LJ: - the_ff = LJFF(); - break; - default: - sprintf( painCave.errMsg, - "SimSetup Error. Unrecognized force field in case statement.\n"); - painCave.isFatal = 1; - simError(); - } +void SimSetup::makeMolecules( void ){ -#ifdef IS_MPI - strcpy( checkPointMsg, "ForceField creation successful" ); - MPIcheckPoint(); -#endif // is_mpi + int k,l; + int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; + molInit molInfo; + DirectionalAtom* dAtom; + LinkedAssign* extras; + LinkedAssign* current_extra; + AtomStamp* currentAtom; + BondStamp* currentBond; + BendStamp* currentBend; + TorsionStamp* currentTorsion; - // get the components and calculate the tot_nMol and indvidual n_mol - the_components = the_globals->getComponents(); - components_nmol = new int[n_components]; - comp_stamps = new MoleculeStamp*[n_components]; + bond_pair* theBonds; + bend_set* theBends; + torsion_set* theTorsions; - if( !the_globals->haveNMol() ){ - // we don't have the total number of molecules, so we assume it is - // given in each component + + //init the forceField paramters - tot_nmol = 0; - for( i=0; ireadParams(); - if( !the_components[i]->haveNMol() ){ - // we have a problem - sprintf( painCave.errMsg, - "SimSetup Error. No global NMol or component NMol" - " given. Cannot calculate the number of atoms.\n" ); - painCave.isFatal = 1; - simError(); - } + + // init the atoms - tot_nmol += the_components[i]->getNMol(); - components_nmol[i] = the_components[i]->getNMol(); - } - } - else{ - sprintf( painCave.errMsg, - "SimSetup error.\n" - "\tSorry, the ability to specify total" - " nMols and then give molfractions in the components\n" - "\tis not currently supported." - " Please give nMol in the components.\n" ); - painCave.isFatal = 1; - simError(); + double ux, uy, uz, u, uSqr; + + for(k=0; kgetNMol(); - - // //we have the total number of molecules, now we check for molfractions - // for( i=0; ihaveMolFraction() ){ - - // if( !the_components[i]->haveNMol() ){ - // //we have a problem - // std::cerr << "SimSetup error. Neither molFraction nor " - // << " nMol was given in component - - } + the_ff->setSimInfo( &(info[k]) ); -#ifdef IS_MPI - strcpy( checkPointMsg, "Have the number of components" ); - MPIcheckPoint(); -#endif // is_mpi - - // make an array of molecule stamps that match the components used. - // also extract the used stamps out into a separate linked list - - simnfo->nComponents = n_components; - simnfo->componentsNmol = components_nmol; - simnfo->compStamps = comp_stamps; - simnfo->headStamp = new LinkedMolStamp(); - - char* id; - LinkedMolStamp* headStamp = simnfo->headStamp; - LinkedMolStamp* currentStamp = NULL; - for( i=0; igetType(); - comp_stamps[i] = NULL; + atomOffset = 0; + excludeOffset = 0; + for(i=0; imatch( id ); - if( comp_stamps[i] == NULL ){ + molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); + molInfo.nBonds = comp_stamps[stampID]->getNBonds(); + molInfo.nBends = comp_stamps[stampID]->getNBends(); + molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); + molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; - // extract the component from the list; + molInfo.myAtoms = &(info[k].atoms[atomOffset]); + molInfo.myExcludes = &(info[k].excludes[excludeOffset]); + molInfo.myBonds = new Bond*[molInfo.nBonds]; + molInfo.myBends = new Bend*[molInfo.nBends]; + molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; + + theBonds = new bond_pair[molInfo.nBonds]; + theBends = new bend_set[molInfo.nBends]; + theTorsions = new torsion_set[molInfo.nTorsions]; + + // make the Atoms + + for(j=0; jgetAtom( j ); + if( currentAtom->haveOrientation() ){ + + dAtom = new DirectionalAtom( (j + atomOffset), + info[k].getConfiguration() ); + info[k].n_oriented++; + molInfo.myAtoms[j] = dAtom; + + ux = currentAtom->getOrntX(); + uy = currentAtom->getOrntY(); + uz = currentAtom->getOrntZ(); + + uSqr = (ux * ux) + (uy * uy) + (uz * uz); + + u = sqrt( uSqr ); + ux = ux / u; + uy = uy / u; + uz = uz / u; + + dAtom->setSUx( ux ); + dAtom->setSUy( uy ); + dAtom->setSUz( uz ); + } + else{ + molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), + info[k].getConfiguration() ); + } + molInfo.myAtoms[j]->setType( currentAtom->getType() ); + +#ifdef IS_MPI - currentStamp = the_stamps->extractMolStamp( id ); - if( currentStamp == NULL ){ - sprintf( painCave.errMsg, - "SimSetup error: Component \"%s\" was not found in the " - "list of declared molecules\n", - id ); - painCave.isFatal = 1; - simError(); + molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); + +#endif // is_mpi + } + + // make the bonds + for(j=0; jgetBond( j ); + theBonds[j].a = currentBond->getA() + atomOffset; + theBonds[j].b = currentBond->getB() + atomOffset; + + exI = theBonds[j].a; + exJ = theBonds[j].b; + + // exclude_I must always be the smaller of the pair + if( exI > exJ ){ + tempEx = exI; + exI = exJ; + exJ = tempEx; + } +#ifdef IS_MPI + tempEx = exI; + exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; + tempEx = exJ; + exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; + + info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); +#else // isn't MPI + + info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); +#endif //is_mpi } + excludeOffset += molInfo.nBonds; - headStamp->add( currentStamp ); - comp_stamps[i] = headStamp->match( id ); + //make the bends + for(j=0; jgetBend( j ); + theBends[j].a = currentBend->getA() + atomOffset; + theBends[j].b = currentBend->getB() + atomOffset; + theBends[j].c = currentBend->getC() + atomOffset; + + if( currentBend->haveExtras() ){ + + extras = currentBend->getExtras(); + current_extra = extras; + + while( current_extra != NULL ){ + if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ + + switch( current_extra->getType() ){ + + case 0: + theBends[j].ghost = + current_extra->getInt() + atomOffset; + theBends[j].isGhost = 1; + break; + + case 1: + theBends[j].ghost = + (int)current_extra->getDouble() + atomOffset; + theBends[j].isGhost = 1; + break; + + default: + sprintf( painCave.errMsg, + "SimSetup Error: ghostVectorSource was neither a " + "double nor an int.\n" + "-->Bend[%d] in %s\n", + j, comp_stamps[stampID]->getID() ); + painCave.isFatal = 1; + simError(); + } + } + + else{ + + sprintf( painCave.errMsg, + "SimSetup Error: unhandled bend assignment:\n" + " -->%s in Bend[%d] in %s\n", + current_extra->getlhs(), + j, comp_stamps[stampID]->getID() ); + painCave.isFatal = 1; + simError(); + } + + current_extra = current_extra->getNext(); + } + } + + if( !theBends[j].isGhost ){ + + exI = theBends[j].a; + exJ = theBends[j].c; + } + else{ + + exI = theBends[j].a; + exJ = theBends[j].b; + } + + // exclude_I must always be the smaller of the pair + if( exI > exJ ){ + tempEx = exI; + exI = exJ; + exJ = tempEx; + } +#ifdef IS_MPI + tempEx = exI; + exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; + tempEx = exJ; + exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; + + info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); +#else // isn't MPI + info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); +#endif //is_mpi + } + excludeOffset += molInfo.nBends; + + for(j=0; jgetTorsion( j ); + theTorsions[j].a = currentTorsion->getA() + atomOffset; + theTorsions[j].b = currentTorsion->getB() + atomOffset; + theTorsions[j].c = currentTorsion->getC() + atomOffset; + theTorsions[j].d = currentTorsion->getD() + atomOffset; + + exI = theTorsions[j].a; + exJ = theTorsions[j].d; + + // exclude_I must always be the smaller of the pair + if( exI > exJ ){ + tempEx = exI; + exI = exJ; + exJ = tempEx; + } +#ifdef IS_MPI + tempEx = exI; + exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; + tempEx = exJ; + exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; + + info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); +#else // isn't MPI + info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); +#endif //is_mpi + } + excludeOffset += molInfo.nTorsions; + + + // send the arrays off to the forceField for init. + + the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); + the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); + the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); + the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); + + + info[k].molecules[i].initialize( molInfo ); + + + atomOffset += molInfo.nAtoms; + delete[] theBonds; + delete[] theBends; + delete[] theTorsions; } } - + #ifdef IS_MPI - strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); + sprintf( checkPointMsg, "all molecules initialized succesfully" ); MPIcheckPoint(); #endif // is_mpi + // clean up the forcefield + the_ff->calcRcut(); + the_ff->cleanMe(); + +} +void SimSetup::initFromBass( void ){ - // caclulate the number of atoms, bonds, bends and torsions + int i, j, k; + int n_cells; + double cellx, celly, cellz; + double temp1, temp2, temp3; + int n_per_extra; + int n_extra; + int have_extra, done; - tot_atoms = 0; - tot_bonds = 0; - tot_bends = 0; - tot_torsions = 0; - for( i=0; igetNAtoms(); - tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); - tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); - tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); - } + double vel[3]; + vel[0] = 0.0; + vel[1] = 0.0; + vel[2] = 0.0; - tot_SRI = tot_bonds + tot_bends + tot_torsions; + temp1 = (double)tot_nmol / 4.0; + temp2 = pow( temp1, ( 1.0 / 3.0 ) ); + temp3 = ceil( temp2 ); - simnfo->n_atoms = tot_atoms; - simnfo->n_bonds = tot_bonds; - simnfo->n_bends = tot_bends; - simnfo->n_torsions = tot_torsions; - simnfo->n_SRI = tot_SRI; - simnfo->n_mol = tot_nmol; - - simnfo->molMembershipArray = new int[tot_atoms]; + have_extra =0; + if( temp2 < temp3 ){ // we have a non-complete lattice + have_extra =1; -#ifdef IS_MPI + n_cells = (int)temp3 - 1; + cellx = info[0].boxL[0] / temp3; + celly = info[0].boxL[1] / temp3; + cellz = info[0].boxL[2] / temp3; + n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); + temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); + n_per_extra = (int)ceil( temp1 ); - // divide the molecules among processors here. - - mpiSim = new mpiSimulation( simnfo ); - - globalIndex = mpiSim->divideLabor(); - - // set up the local variables - - int localMol, allMol; - int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; - - int* mol2proc = mpiSim->getMolToProcMap(); - int* molCompType = mpiSim->getMolComponentType(); - - allMol = 0; - localMol = 0; - local_atoms = 0; - local_bonds = 0; - local_bends = 0; - local_torsions = 0; - globalAtomIndex = 0; - - - for( i=0; igetNAtoms(); - local_bonds += comp_stamps[i]->getNBonds(); - local_bends += comp_stamps[i]->getNBends(); - local_torsions += comp_stamps[i]->getNTorsions(); - localMol++; - } - for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { - simnfo->molMembershipArray[globalAtomIndex] = allMol; - globalAtomIndex++; - } - - allMol++; + if( n_per_extra > 4){ + sprintf( painCave.errMsg, + "SimSetup error. There has been an error in constructing" + " the non-complete lattice.\n" ); + painCave.isFatal = 1; + simError(); } } - local_SRI = local_bonds + local_bends + local_torsions; - - simnfo->n_atoms = mpiSim->getMyNlocal(); - - if( local_atoms != simnfo->n_atoms ){ - sprintf( painCave.errMsg, - "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" - " localAtom (%d) are not equal.\n", - simnfo->n_atoms, - local_atoms ); - painCave.isFatal = 1; - simError(); + else{ + n_cells = (int)temp3; + cellx = info[0].boxL[0] / temp3; + celly = info[0].boxL[1] / temp3; + cellz = info[0].boxL[2] / temp3; } - simnfo->n_bonds = local_bonds; - simnfo->n_bends = local_bends; - simnfo->n_torsions = local_torsions; - simnfo->n_SRI = local_SRI; - simnfo->n_mol = localMol; + current_mol = 0; + current_comp_mol = 0; + current_comp = 0; + current_atom_ndx = 0; - strcpy( checkPointMsg, "Passed nlocal consistency check." ); - MPIcheckPoint(); - - -#endif // is_mpi - + for( i=0; i < n_cells ; i++ ){ + for( j=0; j < n_cells; j++ ){ + for( k=0; k < n_cells; k++ ){ - // create the atom and short range interaction arrays + makeElement( i * cellx, + j * celly, + k * cellz ); - Atom::createArrays(simnfo->n_atoms); - the_atoms = new Atom*[simnfo->n_atoms]; - the_molecules = new Molecule[simnfo->n_mol]; - int molIndex; + makeElement( i * cellx + 0.5 * cellx, + j * celly + 0.5 * celly, + k * cellz ); - // initialize the molecule's stampID's + makeElement( i * cellx, + j * celly + 0.5 * celly, + k * cellz + 0.5 * cellz ); -#ifdef IS_MPI - - - molIndex = 0; - for(i=0; igetTotNmol(); i++){ - - if(mol2proc[i] == worldRank ){ - the_molecules[molIndex].setStampID( molCompType[i] ); - the_molecules[molIndex].setMyIndex( molIndex ); - the_molecules[molIndex].setGlobalIndex( i ); - molIndex++; - } - } - -#else // is_mpi - - molIndex = 0; - globalAtomIndex = 0; - for(i=0; igetNAtoms(); k++) { - simnfo->molMembershipArray[globalAtomIndex] = molIndex; - globalAtomIndex++; + makeElement( i * cellx + 0.5 * cellx, + j * celly, + k * cellz + 0.5 * cellz ); } - molIndex++; } } - -#endif // is_mpi + if( have_extra ){ + done = 0; + int start_ndx; + for( i=0; i < (n_cells+1) && !done; i++ ){ + for( j=0; j < (n_cells+1) && !done; j++ ){ - 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 = simnfo->n_SRI; - } - else{ - - Exclude::createArray( 1 ); - the_excludes = new Exclude*; - the_excludes[0] = new Exclude(0); - the_excludes[0]->setPair( 0,0 ); - simnfo->globalExcludes = new int; - simnfo->globalExcludes[0] = 0; - simnfo->n_exclude = 0; - } + if( i < n_cells ){ - // set the arrays into the SimInfo object + if( j < n_cells ){ + start_ndx = n_cells; + } + else start_ndx = 0; + } + else start_ndx = 0; - simnfo->atoms = the_atoms; - simnfo->molecules = the_molecules; - simnfo->nGlobalExcludes = 0; - simnfo->excludes = the_excludes; + for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ + makeElement( i * cellx, + j * celly, + k * cellz ); + done = ( current_mol >= tot_nmol ); - // get some of the tricky things that may still be in the globals + if( !done && n_per_extra > 1 ){ + makeElement( i * cellx + 0.5 * cellx, + j * celly + 0.5 * celly, + k * cellz ); + done = ( current_mol >= tot_nmol ); + } - - if( the_globals->haveBox() ){ - simnfo->box_x = the_globals->getBox(); - simnfo->box_y = the_globals->getBox(); - simnfo->box_z = the_globals->getBox(); + if( !done && n_per_extra > 2){ + makeElement( i * cellx, + j * celly + 0.5 * celly, + k * cellz + 0.5 * cellz ); + done = ( current_mol >= tot_nmol ); + } + + if( !done && n_per_extra > 3){ + makeElement( i * cellx + 0.5 * cellx, + j * celly, + k * cellz + 0.5 * cellz ); + done = ( current_mol >= tot_nmol ); + } + } + } + } } - else if( the_globals->haveDensity() ){ - double vol; - vol = (double)tot_nmol / the_globals->getDensity(); - simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); - simnfo->box_y = simnfo->box_x; - simnfo->box_z = simnfo->box_x; + for( i=0; isetVel( vel ); } - else{ - if( !the_globals->haveBoxX() ){ - sprintf( painCave.errMsg, - "SimSetup error, no periodic BoxX size given.\n" ); - painCave.isFatal = 1; - simError(); - } - simnfo->box_x = the_globals->getBoxX(); +} - if( !the_globals->haveBoxY() ){ - sprintf( painCave.errMsg, - "SimSetup error, no periodic BoxY size given.\n" ); - painCave.isFatal = 1; - simError(); - } - simnfo->box_y = the_globals->getBoxY(); +void SimSetup::makeElement( double x, double y, double z ){ - if( !the_globals->haveBoxZ() ){ + int k; + AtomStamp* current_atom; + DirectionalAtom* dAtom; + double rotMat[3][3]; + double pos[3]; + + for( k=0; kgetNAtoms(); k++ ){ + + current_atom = comp_stamps[current_comp]->getAtom( k ); + if( !current_atom->havePosition() ){ sprintf( painCave.errMsg, - "SimSetup error, no periodic BoxZ size given.\n" ); + "SimSetup:initFromBass error.\n" + "\tComponent %s, atom %s does not have a position specified.\n" + "\tThe initialization routine is unable to give a start" + " position.\n", + comp_stamps[current_comp]->getID(), + current_atom->getType() ); painCave.isFatal = 1; simError(); } - simnfo->box_z = the_globals->getBoxZ(); - } + + pos[0] = x + current_atom->getPosX(); + pos[1] = y + current_atom->getPosY(); + pos[2] = z + current_atom->getPosZ(); + + info[0].atoms[current_atom_ndx]->setPos( pos ); -#ifdef IS_MPI - strcpy( checkPointMsg, "Box size set up" ); - MPIcheckPoint(); -#endif // is_mpi + if( info[0].atoms[current_atom_ndx]->isDirectional() ){ + dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; - // initialize the arrays + rotMat[0][0] = 1.0; + rotMat[0][1] = 0.0; + rotMat[0][2] = 0.0; - the_ff->setSimInfo( simnfo ); + rotMat[1][0] = 0.0; + rotMat[1][1] = 1.0; + rotMat[1][2] = 0.0; - makeMolecules(); - simnfo->identArray = new int[simnfo->n_atoms]; - for(i=0; in_atoms; i++){ - simnfo->identArray[i] = the_atoms[i]->getIdent(); + rotMat[2][0] = 0.0; + rotMat[2][1] = 0.0; + rotMat[2][2] = 1.0; + + dAtom->setA( rotMat ); + } + + current_atom_ndx++; } - - if (the_globals->getUseRF() ) { - simnfo->useReactionField = 1; - - if( !the_globals->haveECR() ){ - sprintf( painCave.errMsg, - "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; - simError(); - double smallest; - smallest = simnfo->box_x; - if (simnfo->box_y <= smallest) smallest = simnfo->box_y; - if (simnfo->box_z <= smallest) smallest = simnfo->box_z; - simnfo->ecr = 0.5 * smallest; - } else { - simnfo->ecr = the_globals->getECR(); - } - if( !the_globals->haveEST() ){ - sprintf( painCave.errMsg, - "SimSetup Warning: using default value of 0.05 * the " - "electrostaticCutoffRadius for the electrostaticSkinThickness\n" - ); - painCave.isFatal = 0; - simError(); - simnfo->est = 0.05 * simnfo->ecr; - } else { - simnfo->est = the_globals->getEST(); - } - - if(!the_globals->haveDielectric() ){ - sprintf( painCave.errMsg, - "SimSetup Error: You are trying to use Reaction Field without" - "setting a dielectric constant!\n" - ); - painCave.isFatal = 1; - simError(); - } - simnfo->dielectric = the_globals->getDielectric(); - } else { - if (usesDipoles) { - - if( !the_globals->haveECR() ){ - sprintf( painCave.errMsg, - "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; - simError(); - double smallest; - smallest = simnfo->box_x; - if (simnfo->box_y <= smallest) smallest = simnfo->box_y; - if (simnfo->box_z <= smallest) smallest = simnfo->box_z; - simnfo->ecr = 0.5 * smallest; - } else { - simnfo->ecr = the_globals->getECR(); - } - - if( !the_globals->haveEST() ){ - sprintf( painCave.errMsg, - "SimSetup Warning: using default value of 5%% of the " - "electrostaticCutoffRadius for the " - "electrostaticSkinThickness\n" - ); - painCave.isFatal = 0; - simError(); - simnfo->est = 0.05 * simnfo->ecr; - } else { - simnfo->est = the_globals->getEST(); - } - } - } + current_mol++; + current_comp_mol++; -#ifdef IS_MPI - strcpy( checkPointMsg, "electrostatic parameters check out" ); - MPIcheckPoint(); -#endif // is_mpi + if( current_comp_mol >= components_nmol[current_comp] ){ - if( the_globals->haveInitialConfig() ){ - - InitializeFromFile* fileInit; -#ifdef IS_MPI // is_mpi - if( worldRank == 0 ){ -#endif //is_mpi - fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); -#ifdef IS_MPI - }else fileInit = new InitializeFromFile( NULL ); -#endif - fileInit->read_xyz( simnfo ); // default velocities on + current_comp_mol = 0; + current_comp++; + } +} - delete fileInit; - } - else{ -#ifdef IS_MPI +void SimSetup::gatherInfo( void ){ + int i,j,k; - // no init from bass + ensembleCase = -1; + ffCase = -1; + + // set the easy ones first + + for( i=0; igetTargetTemp(); + info[i].dt = globals->getDt(); + info[i].run_time = globals->getRunTime(); + } + n_components = globals->getNComponents(); + + + // get the forceField + + strcpy( force_field, globals->getForceField() ); + + if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; + else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; + else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; + else{ + sprintf( painCave.errMsg, + "SimSetup Error. Unrecognized force field -> %s\n", + force_field ); + painCave.isFatal = 1; + simError(); + } + + // get the ensemble + + strcpy( ensemble, globals->getEnsemble() ); + + if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; + else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; + else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) + ensembleCase = NPTi_ENS; + else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; + else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; + else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; + else{ + sprintf( painCave.errMsg, + "SimSetup Warning. Unrecognized Ensemble -> %s, " + "reverting to NVE for this simulation.\n", + ensemble ); + painCave.isFatal = 0; + simError(); + strcpy( ensemble, "NVE" ); + ensembleCase = NVE_ENS; + } - sprintf( painCave.errMsg, - "Cannot intialize a parallel simulation without an initial configuration file.\n" ); - painCave.isFatal; - simError(); + for(i=0; igetMixingRule() ); + info[i].usePBC = globals->getPBC(); + } -#else + // get the components and calculate the tot_nMol and indvidual n_mol + + the_components = globals->getComponents(); + components_nmol = new int[n_components]; - initFromBass(); + if( !globals->haveNMol() ){ + // we don't have the total number of molecules, so we assume it is + // given in each component -#endif - } + tot_nmol = 0; + for( i=0; ihaveNMol() ){ + // we have a problem + sprintf( painCave.errMsg, + "SimSetup Error. No global NMol or component NMol" + " given. Cannot calculate the number of atoms.\n" ); + painCave.isFatal = 1; + simError(); + } + tot_nmol += the_components[i]->getNMol(); + components_nmol[i] = the_components[i]->getNMol(); + } + } + else{ + sprintf( painCave.errMsg, + "SimSetup error.\n" + "\tSorry, the ability to specify total" + " nMols and then give molfractions in the components\n" + "\tis not currently supported." + " Please give nMol in the components.\n" ); + painCave.isFatal = 1; + simError(); + } - - + // set the status, sample, and thermal kick times + for(i=0; ihaveFinalConfig() ){ - strcpy( simnfo->finalName, the_globals->getFinalConfig() ); + if( globals->haveSampleTime() ){ + info[i].sampleTime = globals->getSampleTime(); + info[i].statusTime = info[i].sampleTime; + info[i].thermalTime = info[i].sampleTime; } else{ - strcpy( simnfo->finalName, inFileName ); - char* endTest; - int nameLength = strlen( simnfo->finalName ); - endTest = &(simnfo->finalName[nameLength - 5]); - if( !strcmp( endTest, ".bass" ) ){ - strcpy( endTest, ".eor" ); - } - else if( !strcmp( endTest, ".BASS" ) ){ - strcpy( endTest, ".eor" ); - } - else{ - endTest = &(simnfo->finalName[nameLength - 4]); - if( !strcmp( endTest, ".bss" ) ){ - strcpy( endTest, ".eor" ); - } - else if( !strcmp( endTest, ".mdl" ) ){ - strcpy( endTest, ".eor" ); - } - else{ - strcat( simnfo->finalName, ".eor" ); - } - } + info[i].sampleTime = globals->getRunTime(); + info[i].statusTime = info[i].sampleTime; + info[i].thermalTime = info[i].sampleTime; } - // make the sample and status out names + if( globals->haveStatusTime() ){ + info[i].statusTime = globals->getStatusTime(); + } - strcpy( simnfo->sampleName, inFileName ); - char* endTest; - int nameLength = strlen( simnfo->sampleName ); - endTest = &(simnfo->sampleName[nameLength - 5]); - if( !strcmp( endTest, ".bass" ) ){ - strcpy( endTest, ".dump" ); + if( globals->haveThermalTime() ){ + info[i].thermalTime = globals->getThermalTime(); } - else if( !strcmp( endTest, ".BASS" ) ){ - strcpy( endTest, ".dump" ); - } - else{ - endTest = &(simnfo->sampleName[nameLength - 4]); - if( !strcmp( endTest, ".bss" ) ){ - strcpy( endTest, ".dump" ); - } - else if( !strcmp( endTest, ".mdl" ) ){ - strcpy( endTest, ".dump" ); - } - else{ - strcat( simnfo->sampleName, ".dump" ); - } - } + + // check for the temperature set flag + + if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); - strcpy( simnfo->statusName, inFileName ); - nameLength = strlen( simnfo->statusName ); - endTest = &(simnfo->statusName[nameLength - 5]); - if( !strcmp( endTest, ".bass" ) ){ - strcpy( endTest, ".stat" ); + // get some of the tricky things that may still be in the globals + + double boxVector[3]; + if( globals->haveBox() ){ + boxVector[0] = globals->getBox(); + boxVector[1] = globals->getBox(); + boxVector[2] = globals->getBox(); + + info[i].setBox( boxVector ); } - else if( !strcmp( endTest, ".BASS" ) ){ - strcpy( endTest, ".stat" ); - } + else if( globals->haveDensity() ){ + + double vol; + vol = (double)tot_nmol / globals->getDensity(); + boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); + boxVector[1] = boxVector[0]; + boxVector[2] = boxVector[0]; + + info[i].setBox( boxVector ); + } else{ - endTest = &(simnfo->statusName[nameLength - 4]); - if( !strcmp( endTest, ".bss" ) ){ - strcpy( endTest, ".stat" ); + if( !globals->haveBoxX() ){ + sprintf( painCave.errMsg, + "SimSetup error, no periodic BoxX size given.\n" ); + painCave.isFatal = 1; + simError(); } - else if( !strcmp( endTest, ".mdl" ) ){ - strcpy( endTest, ".stat" ); + boxVector[0] = globals->getBoxX(); + + if( !globals->haveBoxY() ){ + sprintf( painCave.errMsg, + "SimSetup error, no periodic BoxY size given.\n" ); + painCave.isFatal = 1; + simError(); } - else{ - strcat( simnfo->statusName, ".stat" ); + boxVector[1] = globals->getBoxY(); + + if( !globals->haveBoxZ() ){ + sprintf( painCave.errMsg, + "SimSetup error, no periodic BoxZ size given.\n" ); + painCave.isFatal = 1; + simError(); } + boxVector[2] = globals->getBoxZ(); + + info[i].setBox( boxVector ); } + + } #ifdef IS_MPI - } + strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); + MPIcheckPoint(); #endif // is_mpi - - // set the status, sample, and themal kick times - - if( the_globals->haveSampleTime() ){ - simnfo->sampleTime = the_globals->getSampleTime(); - simnfo->statusTime = simnfo->sampleTime; - simnfo->thermalTime = simnfo->sampleTime; - } - else{ - simnfo->sampleTime = the_globals->getRunTime(); - simnfo->statusTime = simnfo->sampleTime; - simnfo->thermalTime = simnfo->sampleTime; - } - if( the_globals->haveStatusTime() ){ - simnfo->statusTime = the_globals->getStatusTime(); - } +} - if( the_globals->haveThermalTime() ){ - simnfo->thermalTime = the_globals->getThermalTime(); - } - // check for the temperature set flag +void SimSetup::finalInfoCheck( void ){ + int index; + int usesDipoles; + int i; - if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); - - - // make the integrator - - - if( !strcmp( ensemble, "TraPPE_Ex" ) ){ - new Symplectic(simnfo, the_ff, the_extendedsystem); + for(i=0; ihasDipole(); + index++; + } + +#ifdef IS_MPI + int myUse = usesDipoles; + MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); +#endif //is_mpi + + double theEcr, theEst; + + if (globals->getUseRF() ) { + info[i].useReactionField = 1; + + if( !globals->haveECR() ){ + sprintf( painCave.errMsg, + "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; + simError(); + double smallest; + smallest = info[i].boxL[0]; + if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; + if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; + theEcr = 0.5 * smallest; + } else { + theEcr = globals->getECR(); + } + + if( !globals->haveEST() ){ + sprintf( painCave.errMsg, + "SimSetup Warning: using default value of 0.05 * the " + "electrostaticCutoffRadius for the electrostaticSkinThickness\n" + ); + painCave.isFatal = 0; + simError(); + theEst = 0.05 * theEcr; + } else { + theEst= globals->getEST(); + } + + info[i].setEcr( theEcr, theEst ); + + if(!globals->haveDielectric() ){ + sprintf( painCave.errMsg, + "SimSetup Error: You are trying to use Reaction Field without" + "setting a dielectric constant!\n" + ); + painCave.isFatal = 1; + simError(); + } + info[i].dielectric = globals->getDielectric(); + } + else { + if (usesDipoles) { + + if( !globals->haveECR() ){ + sprintf( painCave.errMsg, + "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; + simError(); + double smallest; + smallest = info[i].boxL[0]; + if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; + if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; + theEcr = 0.5 * smallest; + } else { + theEcr = globals->getECR(); + } + + if( !globals->haveEST() ){ + sprintf( painCave.errMsg, + "SimSetup Warning: using default value of 0.05 * the " + "electrostaticCutoffRadius for the " + "electrostaticSkinThickness\n" + ); + painCave.isFatal = 0; + simError(); + theEst = 0.05 * theEcr; + } else { + theEst= globals->getEST(); + } + + info[i].setEcr( theEcr, theEst ); + } + } } - else if( !strcmp( force_field, "LJ" ) ){ - new Verlet( *simnfo, the_ff, the_extendedsystem ); - } #ifdef IS_MPI - mpiSim->mpiRefresh(); -#endif + strcpy( checkPointMsg, "post processing checks out" ); + MPIcheckPoint(); +#endif // is_mpi - // initialize the Fortran +} +void SimSetup::initSystemCoords( void ){ + int i; + + char* inName; - simnfo->refreshSim(); + + (info[0].getConfiguration())->createArrays( info[0].n_atoms ); - if( !strcmp( simnfo->mixingRule, "standard") ){ - the_ff->initForceField( LB_MIXING_RULE ); + for(i=0; isetCoords(); + + if( globals->haveInitialConfig() ){ + + InitializeFromFile* fileInit; +#ifdef IS_MPI // is_mpi + if( worldRank == 0 ){ +#endif //is_mpi + inName = globals->getInitialConfig(); + double* tempDouble = new double[1000000]; + fileInit = new InitializeFromFile( inName ); +#ifdef IS_MPI + }else fileInit = new InitializeFromFile( NULL ); +#endif + fileInit->readInit( info ); // default velocities on + + delete fileInit; } - else if( !strcmp( simnfo->mixingRule, "explicit") ){ - the_ff->initForceField( EXPLICIT_MIXING_RULE ); - } else{ + +#ifdef IS_MPI + + // no init from bass + sprintf( painCave.errMsg, - "SimSetup Error: unknown mixing rule -> \"%s\"\n", - simnfo->mixingRule ); - painCave.isFatal = 1; + "Cannot intialize a parallel simulation without an initial configuration file.\n" ); + painCave.isFatal; simError(); + +#else + + initFromBass(); + + +#endif } - - + #ifdef IS_MPI - strcpy( checkPointMsg, - "Successfully intialized the mixingRule for Fortran." ); + strcpy( checkPointMsg, "Successfully read in the initial configuration" ); MPIcheckPoint(); #endif // is_mpi + } -void SimSetup::makeMolecules( void ){ - - int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; - molInit info; - DirectionalAtom* dAtom; - LinkedAssign* extras; - LinkedAssign* current_extra; - AtomStamp* currentAtom; - BondStamp* currentBond; - BendStamp* currentBend; - TorsionStamp* currentTorsion; - - bond_pair* theBonds; - bend_set* theBends; - torsion_set* theTorsions; - +void SimSetup::makeOutNames( void ){ - //init the forceField paramters + int k; - the_ff->readParams(); - - // init the atoms + for(k=0; kn_mol; i++){ - - stampID = the_molecules[i].getStampID(); - - info.nAtoms = comp_stamps[stampID]->getNAtoms(); - info.nBonds = comp_stamps[stampID]->getNBonds(); - info.nBends = comp_stamps[stampID]->getNBends(); - info.nTorsions = comp_stamps[stampID]->getNTorsions(); - info.nExcludes = info.nBonds + info.nBends + info.nTorsions; - - info.myAtoms = &the_atoms[atomOffset]; - info.myExcludes = &the_excludes[excludeOffset]; - info.myBonds = new Bond*[info.nBonds]; - info.myBends = new Bend*[info.nBends]; - info.myTorsions = new Torsion*[info.nTorsions]; - - theBonds = new bond_pair[info.nBonds]; - theBends = new bend_set[info.nBends]; - theTorsions = new torsion_set[info.nTorsions]; - - // make the Atoms - - for(j=0; jgetAtom( j ); - if( currentAtom->haveOrientation() ){ - - dAtom = new DirectionalAtom(j + atomOffset); - simnfo->n_oriented++; - info.myAtoms[j] = dAtom; - - ux = currentAtom->getOrntX(); - uy = currentAtom->getOrntY(); - uz = currentAtom->getOrntZ(); - - uSqr = (ux * ux) + (uy * uy) + (uz * uz); - - u = sqrt( uSqr ); - ux = ux / u; - uy = uy / u; - uz = uz / u; - - dAtom->setSUx( ux ); - dAtom->setSUy( uy ); - dAtom->setSUz( uz ); + if( globals->haveFinalConfig() ){ + strcpy( info[k].finalName, globals->getFinalConfig() ); } else{ - info.myAtoms[j] = new GeneralAtom(j + atomOffset); - } - info.myAtoms[j]->setType( currentAtom->getType() ); - -#ifdef IS_MPI - - info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); - -#endif // is_mpi - } - - // make the bonds - for(j=0; jgetBond( j ); - theBonds[j].a = currentBond->getA() + atomOffset; - theBonds[j].b = currentBond->getB() + atomOffset; - - exI = theBonds[j].a; - exJ = theBonds[j].b; - - // exclude_I must always be the smaller of the pair - if( exI > exJ ){ - tempEx = exI; - exI = exJ; - exJ = tempEx; - } -#ifdef IS_MPI - tempEx = exI; - exI = the_atoms[tempEx]->getGlobalIndex() + 1; - tempEx = exJ; - exJ = the_atoms[tempEx]->getGlobalIndex() + 1; - - the_excludes[j+excludeOffset]->setPair( exI, exJ ); -#else // isn't MPI - - the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); -#endif //is_mpi - } - excludeOffset += info.nBonds; - - //make the bends - for(j=0; jgetBend( j ); - theBends[j].a = currentBend->getA() + atomOffset; - theBends[j].b = currentBend->getB() + atomOffset; - theBends[j].c = currentBend->getC() + atomOffset; - - if( currentBend->haveExtras() ){ - - extras = currentBend->getExtras(); - current_extra = extras; - - while( current_extra != NULL ){ - if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ - - switch( current_extra->getType() ){ - - case 0: - theBends[j].ghost = - current_extra->getInt() + atomOffset; - theBends[j].isGhost = 1; - break; - - case 1: - theBends[j].ghost = - (int)current_extra->getDouble() + atomOffset; - theBends[j].isGhost = 1; - break; - - default: - sprintf( painCave.errMsg, - "SimSetup Error: ghostVectorSource was neither a " - "double nor an int.\n" - "-->Bend[%d] in %s\n", - j, comp_stamps[stampID]->getID() ); - painCave.isFatal = 1; - simError(); - } + strcpy( info[k].finalName, inFileName ); + char* endTest; + int nameLength = strlen( info[k].finalName ); + endTest = &(info[k].finalName[nameLength - 5]); + if( !strcmp( endTest, ".bass" ) ){ + strcpy( endTest, ".eor" ); + } + else if( !strcmp( endTest, ".BASS" ) ){ + strcpy( endTest, ".eor" ); + } + else{ + endTest = &(info[k].finalName[nameLength - 4]); + if( !strcmp( endTest, ".bss" ) ){ + strcpy( endTest, ".eor" ); } - + else if( !strcmp( endTest, ".mdl" ) ){ + strcpy( endTest, ".eor" ); + } else{ - - sprintf( painCave.errMsg, - "SimSetup Error: unhandled bend assignment:\n" - " -->%s in Bend[%d] in %s\n", - current_extra->getlhs(), - j, comp_stamps[stampID]->getID() ); - painCave.isFatal = 1; - simError(); + strcat( info[k].finalName, ".eor" ); } - - current_extra = current_extra->getNext(); } } - - if( !theBends[j].isGhost ){ - - exI = theBends[j].a; - exJ = theBends[j].c; + + // make the sample and status out names + + strcpy( info[k].sampleName, inFileName ); + char* endTest; + int nameLength = strlen( info[k].sampleName ); + endTest = &(info[k].sampleName[nameLength - 5]); + if( !strcmp( endTest, ".bass" ) ){ + strcpy( endTest, ".dump" ); } + else if( !strcmp( endTest, ".BASS" ) ){ + strcpy( endTest, ".dump" ); + } else{ - - exI = theBends[j].a; - exJ = theBends[j].b; + endTest = &(info[k].sampleName[nameLength - 4]); + if( !strcmp( endTest, ".bss" ) ){ + strcpy( endTest, ".dump" ); + } + else if( !strcmp( endTest, ".mdl" ) ){ + strcpy( endTest, ".dump" ); + } + else{ + strcat( info[k].sampleName, ".dump" ); + } } - // exclude_I must always be the smaller of the pair - if( exI > exJ ){ - tempEx = exI; - exI = exJ; - exJ = tempEx; + strcpy( info[k].statusName, inFileName ); + nameLength = strlen( info[k].statusName ); + endTest = &(info[k].statusName[nameLength - 5]); + if( !strcmp( endTest, ".bass" ) ){ + strcpy( endTest, ".stat" ); } -#ifdef IS_MPI - tempEx = exI; - exI = the_atoms[tempEx]->getGlobalIndex() + 1; - tempEx = exJ; - exJ = the_atoms[tempEx]->getGlobalIndex() + 1; + else if( !strcmp( endTest, ".BASS" ) ){ + strcpy( endTest, ".stat" ); + } + else{ + endTest = &(info[k].statusName[nameLength - 4]); + if( !strcmp( endTest, ".bss" ) ){ + strcpy( endTest, ".stat" ); + } + else if( !strcmp( endTest, ".mdl" ) ){ + strcpy( endTest, ".stat" ); + } + else{ + strcat( info[k].statusName, ".stat" ); + } + } - the_excludes[j+excludeOffset]->setPair( exI, exJ ); -#else // isn't MPI - the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); -#endif //is_mpi +#ifdef IS_MPI } - excludeOffset += info.nBends; +#endif // is_mpi + } +} - for(j=0; jgetTorsion( j ); - theTorsions[j].a = currentTorsion->getA() + atomOffset; - theTorsions[j].b = currentTorsion->getB() + atomOffset; - theTorsions[j].c = currentTorsion->getC() + atomOffset; - theTorsions[j].d = currentTorsion->getD() + atomOffset; - - exI = theTorsions[j].a; - exJ = theTorsions[j].d; - // exclude_I must always be the smaller of the pair - if( exI > exJ ){ - tempEx = exI; - exI = exJ; - exJ = tempEx; - } +void SimSetup::sysObjectsCreation( void ){ + + int i,k; + + // create the forceField + + createFF(); + + // extract componentList + + compList(); + + // calc the number of atoms, bond, bends, and torsions + + calcSysValues(); + #ifdef IS_MPI - tempEx = exI; - exI = the_atoms[tempEx]->getGlobalIndex() + 1; - tempEx = exJ; - exJ = the_atoms[tempEx]->getGlobalIndex() + 1; - - the_excludes[j+excludeOffset]->setPair( exI, exJ ); -#else // isn't MPI - the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); -#endif //is_mpi + // divide the molecules among the processors + + mpiMolDivide(); +#endif //is_mpi + + // create the atom and SRI arrays. Also initialize Molecule Stamp ID's + + makeSysArrays(); + + // make and initialize the molecules (all but atomic coordinates) + + makeMolecules(); + + for(k=0; kgetIdent(); } - excludeOffset += info.nTorsions; + } +} - - // send the arrays off to the forceField for init. - the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); - the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); - the_ff->initializeBends( info.nBends, info.myBends, theBends ); - the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); +void SimSetup::createFF( void ){ + switch( ffCase ){ - the_molecules[i].initialize( info ); + case FF_DUFF: + the_ff = new DUFF(); + break; + case FF_LJ: + the_ff = new LJFF(); + break; - atomOffset += info.nAtoms; - delete[] theBonds; - delete[] theBends; - delete[] theTorsions; + case FF_EAM: + the_ff = new EAM_FF(); + break; + + default: + sprintf( painCave.errMsg, + "SimSetup Error. Unrecognized force field in case statement.\n"); + painCave.isFatal = 1; + simError(); } #ifdef IS_MPI - sprintf( checkPointMsg, "all molecules initialized succesfully" ); + strcpy( checkPointMsg, "ForceField creation successful" ); MPIcheckPoint(); #endif // is_mpi - // clean up the forcefield - the_ff->calcRcut(); - the_ff->cleanMe(); - } -void SimSetup::initFromBass( void ){ - int i, j, k; - int n_cells; - double cellx, celly, cellz; - double temp1, temp2, temp3; - int n_per_extra; - int n_extra; - int have_extra, done; +void SimSetup::compList( void ){ - temp1 = (double)tot_nmol / 4.0; - temp2 = pow( temp1, ( 1.0 / 3.0 ) ); - temp3 = ceil( temp2 ); + int i; + char* id; + LinkedMolStamp* headStamp = new LinkedMolStamp(); + LinkedMolStamp* currentStamp = NULL; + comp_stamps = new MoleculeStamp*[n_components]; + + // make an array of molecule stamps that match the components used. + // also extract the used stamps out into a separate linked list + + for(i=0; ibox_x / temp3; - celly = simnfo->box_y / temp3; - cellz = simnfo->box_z / temp3; - n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); - temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); - n_per_extra = (int)ceil( temp1 ); + id = the_components[i]->getType(); + comp_stamps[i] = NULL; + + // check to make sure the component isn't already in the list - if( n_per_extra > 4){ - sprintf( painCave.errMsg, - "SimSetup error. There has been an error in constructing" - " the non-complete lattice.\n" ); - painCave.isFatal = 1; - simError(); + comp_stamps[i] = headStamp->match( id ); + if( comp_stamps[i] == NULL ){ + + // extract the component from the list; + + currentStamp = stamps->extractMolStamp( id ); + if( currentStamp == NULL ){ + sprintf( painCave.errMsg, + "SimSetup error: Component \"%s\" was not found in the " + "list of declared molecules\n", + id ); + painCave.isFatal = 1; + simError(); + } + + headStamp->add( currentStamp ); + comp_stamps[i] = headStamp->match( id ); } } - else{ - n_cells = (int)temp3; - cellx = simnfo->box_x / temp3; - celly = simnfo->box_y / temp3; - cellz = simnfo->box_z / temp3; - } - current_mol = 0; - current_comp_mol = 0; - current_comp = 0; - current_atom_ndx = 0; +#ifdef IS_MPI + strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); + MPIcheckPoint(); +#endif // is_mpi - for( i=0; i < n_cells ; i++ ){ - for( j=0; j < n_cells; j++ ){ - for( k=0; k < n_cells; k++ ){ - makeElement( i * cellx, - j * celly, - k * cellz ); +} - makeElement( i * cellx + 0.5 * cellx, - j * celly + 0.5 * celly, - k * cellz ); - - makeElement( i * cellx, - j * celly + 0.5 * celly, - k * cellz + 0.5 * cellz ); - - makeElement( i * cellx + 0.5 * cellx, - j * celly, - k * cellz + 0.5 * cellz ); - } - } +void SimSetup::calcSysValues( void ){ + int i, j, k; + + int *molMembershipArray; + + tot_atoms = 0; + tot_bonds = 0; + tot_bends = 0; + tot_torsions = 0; + for( i=0; igetNAtoms(); + tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); + tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); + tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); } + + tot_SRI = tot_bonds + tot_bends + tot_torsions; + molMembershipArray = new int[tot_atoms]; + + for(i=0; idivideLabor(); - if( j < n_cells ){ - start_ndx = n_cells; - } - else start_ndx = 0; - } - else start_ndx = 0; + // set up the local variables + + mol2proc = mpiSim->getMolToProcMap(); + molCompType = mpiSim->getMolComponentType(); + + allMol = 0; + localMol = 0; + local_atoms = 0; + local_bonds = 0; + local_bends = 0; + local_torsions = 0; + globalAtomIndex = 0; - for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ - makeElement( i * cellx, - j * celly, - k * cellz ); - done = ( current_mol >= tot_nmol ); + for( i=0; i 1 ){ - makeElement( i * cellx + 0.5 * cellx, - j * celly + 0.5 * celly, - k * cellz ); - done = ( current_mol >= tot_nmol ); - } - - if( !done && n_per_extra > 2){ - makeElement( i * cellx, - j * celly + 0.5 * celly, - k * cellz + 0.5 * cellz ); - done = ( current_mol >= tot_nmol ); - } - - if( !done && n_per_extra > 3){ - makeElement( i * cellx + 0.5 * cellx, - j * celly, - k * cellz + 0.5 * cellz ); - done = ( current_mol >= tot_nmol ); - } - } + for( j=0; jgetNAtoms(); + local_bonds += comp_stamps[i]->getNBonds(); + local_bends += comp_stamps[i]->getNBends(); + local_torsions += comp_stamps[i]->getNTorsions(); + localMol++; + } + for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { + info[0].molMembershipArray[globalAtomIndex] = allMol; + globalAtomIndex++; } + + allMol++; } } + local_SRI = local_bonds + local_bends + local_torsions; + + info[0].n_atoms = mpiSim->getMyNlocal(); + + if( local_atoms != info[0].n_atoms ){ + sprintf( painCave.errMsg, + "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" + " localAtom (%d) are not equal.\n", + info[0].n_atoms, + local_atoms ); + painCave.isFatal = 1; + simError(); + } + info[0].n_bonds = local_bonds; + info[0].n_bends = local_bends; + info[0].n_torsions = local_torsions; + info[0].n_SRI = local_SRI; + info[0].n_mol = localMol; - for( i=0; in_atoms; i++ ){ - simnfo->atoms[i]->set_vx( 0.0 ); - simnfo->atoms[i]->set_vy( 0.0 ); - simnfo->atoms[i]->set_vz( 0.0 ); - } + strcpy( checkPointMsg, "Passed nlocal consistency check." ); + MPIcheckPoint(); } + +#endif // is_mpi -void SimSetup::makeElement( double x, double y, double z ){ - int k; - AtomStamp* current_atom; - DirectionalAtom* dAtom; - double rotMat[3][3]; +void SimSetup::makeSysArrays( void ){ + int i, j, k, l; - for( k=0; kgetNAtoms(); k++ ){ + Atom** the_atoms; + Molecule* the_molecules; + Exclude** the_excludes; - current_atom = comp_stamps[current_comp]->getAtom( k ); - if( !current_atom->havePosition() ){ - sprintf( painCave.errMsg, - "SimSetup:initFromBass error.\n" - "\tComponent %s, atom %s does not have a position specified.\n" - "\tThe initialization routine is unable to give a start" - " position.\n", - comp_stamps[current_comp]->getID(), - current_atom->getType() ); - painCave.isFatal = 1; - simError(); + + for(l=0; lgetTotNmol(); i++){ + + if(mol2proc[i] == worldRank ){ + the_molecules[molIndex].setStampID( molCompType[i] ); + the_molecules[molIndex].setMyIndex( molIndex ); + the_molecules[molIndex].setGlobalIndex( i ); + molIndex++; + } } + +#else // is_mpi + + molIndex = 0; + globalAtomIndex = 0; + for(i=0; igetNAtoms(); k++) { + info[l].molMembershipArray[globalAtomIndex] = molIndex; + globalAtomIndex++; + } + molIndex++; + } + } + + +#endif // is_mpi - the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); - the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); - the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); - if( the_atoms[current_atom_ndx]->isDirectional() ){ + if( info[l].n_SRI ){ + + Exclude::createArray(info[l].n_SRI); + the_excludes = new Exclude*[info[l].n_SRI]; + for( int ex=0; exsetPair( 0,0 ); + info[l].globalExcludes = new int; + info[l].globalExcludes[0] = 0; + info[l].n_exclude = 0; + } - dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; + // set the arrays into the SimInfo object - rotMat[0][0] = 1.0; - rotMat[0][1] = 0.0; - rotMat[0][2] = 0.0; + info[l].atoms = the_atoms; + info[l].molecules = the_molecules; + info[l].nGlobalExcludes = 0; + info[l].excludes = the_excludes; - rotMat[1][0] = 0.0; - rotMat[1][1] = 1.0; - rotMat[1][2] = 0.0; + the_ff->setSimInfo( info ); + + } +} - rotMat[2][0] = 0.0; - rotMat[2][1] = 0.0; - rotMat[2][2] = 1.0; +void SimSetup::makeIntegrator( void ){ - dAtom->setA( rotMat ); + int k; + + NVT* myNVT = NULL; + NPTi* myNPTi = NULL; + NPTf* myNPTf = NULL; + NPTim* myNPTim = NULL; + NPTfm* myNPTfm = NULL; + + for(k=0; khaveZconstraints()){ + setupZConstraint(info[k]); + new ZConstraint >( &(info[k]), the_ff ); + } + + else + new NVE( &(info[k]), the_ff ); + break; + + case NVT_ENS: + if (globals->haveZconstraints()){ + setupZConstraint(info[k]); + myNVT = new ZConstraint >( &(info[k]), the_ff ); + } + else + myNVT = new NVT( &(info[k]), the_ff ); + + myNVT->setTargetTemp(globals->getTargetTemp()); + + if (globals->haveTauThermostat()) + myNVT->setTauThermostat(globals->getTauThermostat()); + + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use the NVT\n" + " ensemble, you must set tauThermostat.\n"); + painCave.isFatal = 1; + simError(); + } + break; + + case NPTi_ENS: + if (globals->haveZconstraints()){ + setupZConstraint(info[k]); + myNPTi = new ZConstraint >( &(info[k]), the_ff ); + } + else + myNPTi = new NPTi( &(info[k]), the_ff ); + + myNPTi->setTargetTemp( globals->getTargetTemp() ); + + if (globals->haveTargetPressure()) + myNPTi->setTargetPressure(globals->getTargetPressure()); + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use a constant pressure\n" + " ensemble, you must set targetPressure in the BASS file.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauThermostat() ) + myNPTi->setTauThermostat( globals->getTauThermostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauThermostat.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauBarostat() ) + myNPTi->setTauBarostat( globals->getTauBarostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauBarostat.\n"); + painCave.isFatal = 1; + simError(); + } + break; + + case NPTf_ENS: + if (globals->haveZconstraints()){ + setupZConstraint(info[k]); + myNPTf = new ZConstraint >( &(info[k]), the_ff ); + } + else + myNPTf = new NPTf( &(info[k]), the_ff ); + + myNPTf->setTargetTemp( globals->getTargetTemp()); + + if (globals->haveTargetPressure()) + myNPTf->setTargetPressure(globals->getTargetPressure()); + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use a constant pressure\n" + " ensemble, you must set targetPressure in the BASS file.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauThermostat() ) + myNPTf->setTauThermostat( globals->getTauThermostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauThermostat.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauBarostat() ) + myNPTf->setTauBarostat( globals->getTauBarostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauBarostat.\n"); + painCave.isFatal = 1; + simError(); + } + break; + + case NPTim_ENS: + if (globals->haveZconstraints()){ + setupZConstraint(info[k]); + myNPTim = new ZConstraint >( &(info[k]), the_ff ); + } + else + myNPTim = new NPTim( &(info[k]), the_ff ); + + myNPTim->setTargetTemp( globals->getTargetTemp()); + + if (globals->haveTargetPressure()) + myNPTim->setTargetPressure(globals->getTargetPressure()); + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use a constant pressure\n" + " ensemble, you must set targetPressure in the BASS file.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauThermostat() ) + myNPTim->setTauThermostat( globals->getTauThermostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauThermostat.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauBarostat() ) + myNPTim->setTauBarostat( globals->getTauBarostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauBarostat.\n"); + painCave.isFatal = 1; + simError(); + } + break; + + case NPTfm_ENS: + if (globals->haveZconstraints()){ + setupZConstraint(info[k]); + myNPTfm = new ZConstraint >( &(info[k]), the_ff ); + } + else + myNPTfm = new NPTfm( &(info[k]), the_ff ); + + myNPTfm->setTargetTemp( globals->getTargetTemp()); + + if (globals->haveTargetPressure()) + myNPTfm->setTargetPressure(globals->getTargetPressure()); + else { + sprintf( painCave.errMsg, + "SimSetup error: If you use a constant pressure\n" + " ensemble, you must set targetPressure in the BASS file.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauThermostat() ) + myNPTfm->setTauThermostat( globals->getTauThermostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauThermostat.\n"); + painCave.isFatal = 1; + simError(); + } + + if( globals->haveTauBarostat() ) + myNPTfm->setTauBarostat( globals->getTauBarostat() ); + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an NPT\n" + " ensemble, you must set tauBarostat.\n"); + painCave.isFatal = 1; + simError(); + } + break; + + default: + sprintf( painCave.errMsg, + "SimSetup Error. Unrecognized ensemble in case statement.\n"); + painCave.isFatal = 1; + simError(); } + } +} - current_atom_ndx++; +void SimSetup::initFortran( void ){ + + info[0].refreshSim(); + + if( !strcmp( info[0].mixingRule, "standard") ){ + the_ff->initForceField( LB_MIXING_RULE ); } + else if( !strcmp( info[0].mixingRule, "explicit") ){ + the_ff->initForceField( EXPLICIT_MIXING_RULE ); + } + else{ + sprintf( painCave.errMsg, + "SimSetup Error: unknown mixing rule -> \"%s\"\n", + info[0].mixingRule ); + painCave.isFatal = 1; + simError(); + } - current_mol++; - current_comp_mol++; - if( current_comp_mol >= components_nmol[current_comp] ){ +#ifdef IS_MPI + strcpy( checkPointMsg, + "Successfully intialized the mixingRule for Fortran." ); + MPIcheckPoint(); +#endif // is_mpi - current_comp_mol = 0; - current_comp++; - } } + +void SimSetup::setupZConstraint(SimInfo& theInfo) +{ + int nZConstraints; + ZconStamp** zconStamp; + + if(globals->haveZconstraintTime()){ + + //add sample time of z-constraint into SimInfo's property list + DoubleData* zconsTimeProp = new DoubleData(); + zconsTimeProp->setID(ZCONSTIME_ID); + zconsTimeProp->setData(globals->getZconsTime()); + theInfo.addProperty(zconsTimeProp); + } + else{ + sprintf( painCave.errMsg, + "ZConstraint error: If you use an ZConstraint\n" + " , you must set sample time.\n"); + painCave.isFatal = 1; + simError(); + } + + // + nZConstraints = globals->getNzConstraints(); + theInfo.nZconstraints = nZConstraints; + + zconStamp = globals->getZconStamp(); + ZConsParaItem tempParaItem; + + ZConsParaData* zconsParaData = new ZConsParaData(); + zconsParaData->setID(ZCONSPARADATA_ID); + + for(int i = 0; i < nZConstraints; i++){ + tempParaItem.havingZPos = zconStamp[i]->haveZpos(); + tempParaItem.zPos = zconStamp[i]->getZpos(); + tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); + tempParaItem.kRatio = zconStamp[i]->getKratio(); + + zconsParaData->addItem(tempParaItem); + } + + //sort the parameters by index of molecules + zconsParaData->sortByIndex(); + + //push data into siminfo, therefore, we can retrieve later + theInfo.addProperty(zconsParaData); + + //push zconsTol into siminfo, if user does not specify + //value for zconsTol, a default value will be used + DoubleData* zconsTol = new DoubleData(); + zconsTol->setID(ZCONSTOL_ID); + if(globals->haveZconsTol()){ + zconsTol->setData(globals->getZconsTol()); + } + else{ + double defaultZConsTol = 1E-6; + sprintf( painCave.errMsg, + "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" + " , default value %f is used.\n", defaultZConsTol); + painCave.isFatal = 0; + simError(); + + zconsTol->setData(defaultZConsTol); + } + theInfo.addProperty(zconsTol); + + //Determine the name of ouput file and add it into SimInfo's property list + //Be careful, do not use inFileName, since it is a pointer which + //point to a string at master node, and slave nodes do not contain that string + + string zconsOutput(theInfo.finalName); + + zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; + + StringData* zconsFilename = new StringData(); + zconsFilename->setID(ZCONSFILENAME_ID); + zconsFilename->setData(zconsOutput); + + theInfo.addProperty(zconsFilename); +}