--- trunk/OOPSE/libmdtools/SimSetup.cpp 2003/04/10 20:08:56 489 +++ trunk/OOPSE/libmdtools/SimSetup.cpp 2003/07/31 19:59:34 660 @@ -1,6 +1,8 @@ +#include #include #include #include +#include #include "SimSetup.hpp" #include "parse_me.h" @@ -12,10 +14,36 @@ SimSetup::SimSetup(){ #include "mpiSimulation.hpp" #endif +// some defines for ensemble and Forcefield cases + +#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 NVEZCONS_ENS 6 +#define NVTZCONS_ENS 7 +#define NPTiZCONS_ENS 8 +#define NPTfZCONS_ENS 9 +#define NPTimZCONS_ENS 10 +#define NPTfmZCONS_ENS 11 + +#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(); @@ -27,6 +55,13 @@ 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 @@ -64,720 +99,50 @@ void SimSetup::createSim( void ){ void SimSetup::createSim( void ){ - MakeStamps *the_stamps; - Globals* the_globals; - ExtendedSystem* the_extendedsystem; - int i, j; - - // get the stamps and globals; - the_stamps = stamps; - the_globals = globals; - - // set the easy ones first - simnfo->target_temp = the_globals->getTargetTemp(); - simnfo->dt = the_globals->getDt(); - simnfo->run_time = the_globals->getRunTime(); - - // 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(); - - 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", - force_field ); - painCave.isFatal = 1; - simError(); - } - -#ifdef IS_MPI - strcpy( checkPointMsg, "ForceField creation successful" ); - MPIcheckPoint(); -#endif // is_mpi - + int i, j, k, globalAtomIndex; - - // 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]; - - if( !the_globals->haveNMol() ){ - // we don't have the total number of molecules, so we assume it is - // given in each component - - 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(); - - - // tot_nmol = the_globals->getNMol(); - - // //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 - - } - -#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(); + // gather all of the information from the Bass file - char* id; - LinkedMolStamp* headStamp = simnfo->headStamp; - LinkedMolStamp* currentStamp = NULL; - for( i=0; igetType(); - comp_stamps[i] = NULL; - - // check to make sure the component isn't already in the list + // creation of complex system objects - comp_stamps[i] = headStamp->match( id ); - if( comp_stamps[i] == NULL ){ - - // extract the component from the list; - - 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(); - } - - headStamp->add( currentStamp ); - comp_stamps[i] = headStamp->match( id ); - } - } + sysObjectsCreation(); -#ifdef IS_MPI - strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); - MPIcheckPoint(); -#endif // is_mpi + // check on the post processing info + finalInfoCheck(); + // initialize the system coordinates - - // caclulate the number of atoms, bonds, bends and torsions - - 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; - - 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; - + initSystemCoords(); -#ifdef IS_MPI - // divide the molecules among processors here. - - mpiSim = new mpiSimulation( simnfo ); - - + // make the output filenames - globalIndex = mpiSim->divideLabor(); - - // set up the local variables + makeOutNames(); + + // make the integrator - 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; - for( i=0; igetNAtoms(); - local_bonds += comp_stamps[i]->getNBonds(); - local_bends += comp_stamps[i]->getNBends(); - local_torsions += comp_stamps[i]->getNTorsions(); - localMol++; - } - allMol++; - } - } - 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(); - } - - simnfo->n_bonds = local_bonds; - simnfo->n_bends = local_bends; - simnfo->n_torsions = local_torsions; - simnfo->n_SRI = local_SRI; - simnfo->n_mol = localMol; - - strcpy( checkPointMsg, "Passed nlocal consistency check." ); - MPIcheckPoint(); - - -#endif // is_mpi - - - // create the atom and short range interaction arrays - - Atom::createArrays(simnfo->n_atoms); - the_atoms = new Atom*[simnfo->n_atoms]; - the_molecules = new Molecule[simnfo->n_mol]; - int molIndex; - - // initialize the molecule's stampID's - -#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; - for(i=0; in_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; - } - - // set the arrays into the SimInfo object - - simnfo->atoms = the_atoms; - simnfo->molecules = the_molecules; - simnfo->nGlobalExcludes = 0; - simnfo->excludes = the_excludes; - - - // get some of the tricky things that may still be in the globals - - - if( the_globals->haveBox() ){ - simnfo->box_x = the_globals->getBox(); - simnfo->box_y = the_globals->getBox(); - simnfo->box_z = the_globals->getBox(); - } - 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; - } - 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(); - - if( !the_globals->haveBoxZ() ){ - sprintf( painCave.errMsg, - "SimSetup error, no periodic BoxZ size given.\n" ); - painCave.isFatal = 1; - simError(); - } - simnfo->box_z = the_globals->getBoxZ(); - } - -#ifdef IS_MPI - strcpy( checkPointMsg, "Box size set up" ); - MPIcheckPoint(); -#endif // is_mpi - - - // initialize the arrays - - the_ff->setSimInfo( simnfo ); - - makeMolecules(); - simnfo->identArray = new int[simnfo->n_atoms]; - simnfo->molMembershipArray = new int[simnfo->n_atoms]; - for(i=0; in_atoms; i++){ - simnfo->identArray[i] = the_atoms[i]->getIdent(); - } - for(i=0; i< simnfo->n_mol; i++) { - the_molecules[i].atomicRollCall(simnfo->molMembershipArray); - } - - 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(); - } - } - } - -#ifdef IS_MPI - strcpy( checkPointMsg, "electrostatic parameters check out" ); - MPIcheckPoint(); -#endif // is_mpi - - 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 - - delete fileInit; - } - else{ - -#ifdef IS_MPI - - // no init from bass + makeIntegrator(); - sprintf( painCave.errMsg, - "Cannot intialize a parallel simulation without an initial configuration file.\n" ); - painCave.isFatal; - simError(); - -#else - - initFromBass(); - - -#endif - } - #ifdef IS_MPI - strcpy( checkPointMsg, "Successfully read in the initial configuration" ); - MPIcheckPoint(); -#endif // is_mpi - - - - - - - -#ifdef IS_MPI - if( worldRank == 0 ){ -#endif // is_mpi - - if( the_globals->haveFinalConfig() ){ - strcpy( simnfo->finalName, the_globals->getFinalConfig() ); - } - 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" ); - } - } - } - - // make the sample and status out names - - strcpy( simnfo->sampleName, inFileName ); - char* endTest; - int nameLength = strlen( simnfo->sampleName ); - endTest = &(simnfo->sampleName[nameLength - 5]); - if( !strcmp( endTest, ".bass" ) ){ - strcpy( endTest, ".dump" ); - } - 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" ); - } - } - - strcpy( simnfo->statusName, inFileName ); - nameLength = strlen( simnfo->statusName ); - endTest = &(simnfo->statusName[nameLength - 5]); - if( !strcmp( endTest, ".bass" ) ){ - strcpy( endTest, ".stat" ); - } - else if( !strcmp( endTest, ".BASS" ) ){ - strcpy( endTest, ".stat" ); - } - else{ - endTest = &(simnfo->statusName[nameLength - 4]); - if( !strcmp( endTest, ".bss" ) ){ - strcpy( endTest, ".stat" ); - } - else if( !strcmp( endTest, ".mdl" ) ){ - strcpy( endTest, ".stat" ); - } - else{ - strcat( simnfo->statusName, ".stat" ); - } - } - -#ifdef IS_MPI - } -#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 - - if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); - - -// // make the longe range forces and the integrator - -// new AllLong( simnfo ); - - - if( !strcmp( force_field, "TraPPE_Ex" ) ){ - new Symplectic(simnfo, the_ff, the_extendedsystem); - } - else if( !strcmp( force_field, "LJ" ) ){ - new Verlet( *simnfo, the_ff, the_extendedsystem ); - } - else { - std::cerr << "I'm a bug.\n"; - fprintf( stderr, "Ima bug. stderr %s\n", force_field); - } -#ifdef IS_MPI mpiSim->mpiRefresh(); #endif // initialize the Fortran + initFortran(); - simnfo->refreshSim(); - - if( !strcmp( simnfo->mixingRule, "standard") ){ - the_ff->initForceField( LB_MIXING_RULE ); - } - else if( !strcmp( simnfo->mixingRule, "explicit") ){ - the_ff->initForceField( EXPLICIT_MIXING_RULE ); - } - else{ - sprintf( painCave.errMsg, - "SimSetup Error: unknown mixing rule -> \"%s\"\n", - simnfo->mixingRule ); - painCave.isFatal = 1; - simError(); - } -#ifdef IS_MPI - strcpy( checkPointMsg, - "Successfully intialized the mixingRule for Fortran." ); - MPIcheckPoint(); -#endif // is_mpi } void SimSetup::makeMolecules( void ){ int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; - molInit info; + molInit molInfo; DirectionalAtom* dAtom; LinkedAssign* extras; LinkedAssign* current_extra; @@ -802,36 +167,36 @@ void SimSetup::makeMolecules( void ){ atomOffset = 0; excludeOffset = 0; - for(i=0; in_mol; i++){ + for(i=0; in_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; + 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; - 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]; + molInfo.myAtoms = &the_atoms[atomOffset]; + molInfo.myExcludes = &the_excludes[excludeOffset]; + molInfo.myBonds = new Bond*[molInfo.nBonds]; + molInfo.myBends = new Bend*[molInfo.nBends]; + molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; - theBonds = new bond_pair[info.nBonds]; - theBends = new bend_set[info.nBends]; - theTorsions = new torsion_set[info.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); - simnfo->n_oriented++; - info.myAtoms[j] = dAtom; + info->n_oriented++; + molInfo.myAtoms[j] = dAtom; ux = currentAtom->getOrntX(); uy = currentAtom->getOrntY(); @@ -849,19 +214,19 @@ void SimSetup::makeMolecules( void ){ dAtom->setSUz( uz ); } else{ - info.myAtoms[j] = new GeneralAtom(j + atomOffset); + molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); } - info.myAtoms[j]->setType( currentAtom->getType() ); + molInfo.myAtoms[j]->setType( currentAtom->getType() ); #ifdef IS_MPI - info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); + molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); #endif // is_mpi } // make the bonds - for(j=0; jgetBond( j ); theBonds[j].a = currentBond->getA() + atomOffset; @@ -888,10 +253,10 @@ void SimSetup::makeMolecules( void ){ the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); #endif //is_mpi } - excludeOffset += info.nBonds; + excludeOffset += molInfo.nBonds; //make the bends - for(j=0; jgetBend( j ); theBends[j].a = currentBend->getA() + atomOffset; @@ -974,9 +339,9 @@ void SimSetup::makeMolecules( void ){ the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); #endif //is_mpi } - excludeOffset += info.nBends; + excludeOffset += molInfo.nBends; - for(j=0; jgetTorsion( j ); theTorsions[j].a = currentTorsion->getA() + atomOffset; @@ -1004,21 +369,21 @@ void SimSetup::makeMolecules( void ){ the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); #endif //is_mpi } - excludeOffset += info.nTorsions; + excludeOffset += molInfo.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 ); + 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 ); - the_molecules[i].initialize( info ); + the_molecules[i].initialize( molInfo ); - atomOffset += info.nAtoms; + atomOffset += molInfo.nAtoms; delete[] theBonds; delete[] theBends; delete[] theTorsions; @@ -1054,9 +419,9 @@ void SimSetup::initFromBass( void ){ have_extra =1; n_cells = (int)temp3 - 1; - cellx = simnfo->box_x / temp3; - celly = simnfo->box_y / temp3; - cellz = simnfo->box_z / temp3; + cellx = info->boxL[0] / temp3; + celly = info->boxL[1] / temp3; + cellz = info->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 ); @@ -1071,9 +436,9 @@ void SimSetup::initFromBass( void ){ } else{ n_cells = (int)temp3; - cellx = simnfo->box_x / temp3; - celly = simnfo->box_y / temp3; - cellz = simnfo->box_z / temp3; + cellx = info->boxL[0] / temp3; + celly = info->boxL[1] / temp3; + cellz = info->boxL[2] / temp3; } current_mol = 0; @@ -1153,10 +518,10 @@ void SimSetup::initFromBass( void ){ } - 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 ); + for( i=0; in_atoms; i++ ){ + info->atoms[i]->set_vx( 0.0 ); + info->atoms[i]->set_vy( 0.0 ); + info->atoms[i]->set_vz( 0.0 ); } } @@ -1217,3 +582,1193 @@ void SimSetup::makeElement( double x, double y, double current_comp++; } } + + +void SimSetup::gatherInfo( void ){ + int i,j,k; + + ensembleCase = -1; + ffCase = -1; + + // get the stamps and globals; + stamps = stamps; + globals = globals; + + // set the easy ones first + info->target_temp = globals->getTargetTemp(); + info->dt = globals->getDt(); + info->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 if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; + else if( !strcasecmp( ensemble, "NVTZCONS")) ensembleCase = NVTZCONS_ENS; + else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT")) + ensembleCase = NPTiZCONS_ENS; + else if( !strcasecmp( ensemble, "NPTfCONS")) ensembleCase = NPTfZCONS_ENS; + else if( !strcasecmp( ensemble, "NPTimZCONS")) ensembleCase = NPTimZCONS_ENS; + else if( !strcasecmp( ensemble, "NPTfmCONS")) ensembleCase = NPTfmZCONS_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( info->ensemble, ensemble ); + + // get the mixing rule + + strcpy( info->mixingRule, globals->getMixingRule() ); + info->usePBC = globals->getPBC(); + + + // get the components and calculate the tot_nMol and indvidual n_mol + + the_components = globals->getComponents(); + components_nmol = new int[n_components]; + + + if( !globals->haveNMol() ){ + // we don't have the total number of molecules, so we assume it is + // given in each component + + 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 + + if( globals->haveSampleTime() ){ + info->sampleTime = globals->getSampleTime(); + info->statusTime = info->sampleTime; + info->thermalTime = info->sampleTime; + } + else{ + info->sampleTime = globals->getRunTime(); + info->statusTime = info->sampleTime; + info->thermalTime = info->sampleTime; + } + + if( globals->haveStatusTime() ){ + info->statusTime = globals->getStatusTime(); + } + + if( globals->haveThermalTime() ){ + info->thermalTime = globals->getThermalTime(); + } + + // check for the temperature set flag + + if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); + + // 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->setBox( boxVector ); + } + 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->setBox( boxVector ); + } + else{ + if( !globals->haveBoxX() ){ + sprintf( painCave.errMsg, + "SimSetup error, no periodic BoxX size given.\n" ); + painCave.isFatal = 1; + simError(); + } + boxVector[0] = globals->getBoxX(); + + if( !globals->haveBoxY() ){ + sprintf( painCave.errMsg, + "SimSetup error, no periodic BoxY size given.\n" ); + painCave.isFatal = 1; + simError(); + } + 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->setBox( boxVector ); + } + + + +#ifdef IS_MPI + strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); + MPIcheckPoint(); +#endif // is_mpi + +} + + +void SimSetup::finalInfoCheck( void ){ + int index; + int usesDipoles; + + + // check electrostatic parameters + + index = 0; + usesDipoles = 0; + while( (index < info->n_atoms) && !usesDipoles ){ + usesDipoles = ((info->atoms)[index])->hasDipole(); + 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->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->boxL[0]; + if (info->boxL[1] <= smallest) smallest = info->boxL[1]; + if (info->boxL[2] <= smallest) smallest = info->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->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->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->boxL[0]; + if (info->boxL[1] <= smallest) smallest = info->boxL[1]; + if (info->boxL[2] <= smallest) smallest = info->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->setEcr( theEcr, theEst ); + } + } + +#ifdef IS_MPI + strcpy( checkPointMsg, "post processing checks out" ); + MPIcheckPoint(); +#endif // is_mpi + +} + +void SimSetup::initSystemCoords( void ){ + + if( globals->haveInitialConfig() ){ + + InitializeFromFile* fileInit; +#ifdef IS_MPI // is_mpi + if( worldRank == 0 ){ +#endif //is_mpi + fileInit = new InitializeFromFile( globals->getInitialConfig() ); +#ifdef IS_MPI + }else fileInit = new InitializeFromFile( NULL ); +#endif + fileInit->readInit( info ); // default velocities on + + delete fileInit; + } + else{ + +#ifdef IS_MPI + + // no init from bass + + sprintf( painCave.errMsg, + "Cannot intialize a parallel simulation without an initial configuration file.\n" ); + painCave.isFatal; + simError(); + +#else + + initFromBass(); + + +#endif + } + +#ifdef IS_MPI + strcpy( checkPointMsg, "Successfully read in the initial configuration" ); + MPIcheckPoint(); +#endif // is_mpi + +} + + +void SimSetup::makeOutNames( void ){ + +#ifdef IS_MPI + if( worldRank == 0 ){ +#endif // is_mpi + + if( globals->haveFinalConfig() ){ + strcpy( info->finalName, globals->getFinalConfig() ); + } + else{ + strcpy( info->finalName, inFileName ); + char* endTest; + int nameLength = strlen( info->finalName ); + endTest = &(info->finalName[nameLength - 5]); + if( !strcmp( endTest, ".bass" ) ){ + strcpy( endTest, ".eor" ); + } + else if( !strcmp( endTest, ".BASS" ) ){ + strcpy( endTest, ".eor" ); + } + else{ + endTest = &(info->finalName[nameLength - 4]); + if( !strcmp( endTest, ".bss" ) ){ + strcpy( endTest, ".eor" ); + } + else if( !strcmp( endTest, ".mdl" ) ){ + strcpy( endTest, ".eor" ); + } + else{ + strcat( info->finalName, ".eor" ); + } + } + } + + // make the sample and status out names + + strcpy( info->sampleName, inFileName ); + char* endTest; + int nameLength = strlen( info->sampleName ); + endTest = &(info->sampleName[nameLength - 5]); + if( !strcmp( endTest, ".bass" ) ){ + strcpy( endTest, ".dump" ); + } + else if( !strcmp( endTest, ".BASS" ) ){ + strcpy( endTest, ".dump" ); + } + else{ + endTest = &(info->sampleName[nameLength - 4]); + if( !strcmp( endTest, ".bss" ) ){ + strcpy( endTest, ".dump" ); + } + else if( !strcmp( endTest, ".mdl" ) ){ + strcpy( endTest, ".dump" ); + } + else{ + strcat( info->sampleName, ".dump" ); + } + } + + strcpy( info->statusName, inFileName ); + nameLength = strlen( info->statusName ); + endTest = &(info->statusName[nameLength - 5]); + if( !strcmp( endTest, ".bass" ) ){ + strcpy( endTest, ".stat" ); + } + else if( !strcmp( endTest, ".BASS" ) ){ + strcpy( endTest, ".stat" ); + } + else{ + endTest = &(info->statusName[nameLength - 4]); + if( !strcmp( endTest, ".bss" ) ){ + strcpy( endTest, ".stat" ); + } + else if( !strcmp( endTest, ".mdl" ) ){ + strcpy( endTest, ".stat" ); + } + else{ + strcat( info->statusName, ".stat" ); + } + } + +#ifdef IS_MPI + } +#endif // is_mpi + +} + + +void SimSetup::sysObjectsCreation( void ){ + + int i; + + // create the forceField + + createFF(); + + // extract componentList + + compList(); + + // calc the number of atoms, bond, bends, and torsions + + calcSysValues(); + +#ifdef 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(); + info->identArray = new int[info->n_atoms]; + for(i=0; in_atoms; i++){ + info->identArray[i] = the_atoms[i]->getIdent(); + } + + + +} + + +void SimSetup::createFF( void ){ + + switch( ffCase ){ + + case FF_DUFF: + the_ff = new DUFF(); + break; + + case FF_LJ: + the_ff = new LJFF(); + break; + + 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 + strcpy( checkPointMsg, "ForceField creation successful" ); + MPIcheckPoint(); +#endif // is_mpi + +} + + +void SimSetup::compList( void ){ + + int i; + + 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 + + info->nComponents = n_components; + info->componentsNmol = components_nmol; + info->compStamps = comp_stamps; + info->headStamp = new LinkedMolStamp(); + + char* id; + LinkedMolStamp* headStamp = info->headStamp; + LinkedMolStamp* currentStamp = NULL; + for( i=0; igetType(); + comp_stamps[i] = NULL; + + // check to make sure the component isn't already in the list + + 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 ); + } + } + +#ifdef IS_MPI + strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); + MPIcheckPoint(); +#endif // is_mpi + + +} + +void SimSetup::calcSysValues( void ){ + int i, j, k; + + + 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; + + info->n_atoms = tot_atoms; + info->n_bonds = tot_bonds; + info->n_bends = tot_bends; + info->n_torsions = tot_torsions; + info->n_SRI = tot_SRI; + info->n_mol = tot_nmol; + + info->molMembershipArray = new int[tot_atoms]; +} + + +#ifdef IS_MPI + +void SimSetup::mpiMolDivide( void ){ + + int i, j, k; + int localMol, allMol; + int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; + + mpiSim = new mpiSimulation( info ); + + globalIndex = mpiSim->divideLabor(); + + // 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( 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++) { + info->molMembershipArray[globalAtomIndex] = allMol; + globalAtomIndex++; + } + + allMol++; + } + } + local_SRI = local_bonds + local_bends + local_torsions; + + info->n_atoms = mpiSim->getMyNlocal(); + + if( local_atoms != info->n_atoms ){ + sprintf( painCave.errMsg, + "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" + " localAtom (%d) are not equal.\n", + info->n_atoms, + local_atoms ); + painCave.isFatal = 1; + simError(); + } + + info->n_bonds = local_bonds; + info->n_bends = local_bends; + info->n_torsions = local_torsions; + info->n_SRI = local_SRI; + info->n_mol = localMol; + + strcpy( checkPointMsg, "Passed nlocal consistency check." ); + MPIcheckPoint(); +} + +#endif // is_mpi + + +void SimSetup::makeSysArrays( void ){ + int i, j, k; + + + // create the atom and short range interaction arrays + + Atom::createArrays(info->n_atoms); + the_atoms = new Atom*[info->n_atoms]; + the_molecules = new Molecule[info->n_mol]; + int molIndex; + + // initialize the molecule's stampID's + +#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++) { + info->molMembershipArray[globalAtomIndex] = molIndex; + globalAtomIndex++; + } + molIndex++; + } + } + + +#endif // is_mpi + + + if( info->n_SRI ){ + + Exclude::createArray(info->n_SRI); + the_excludes = new Exclude*[info->n_SRI]; + for( int ex=0; exn_SRI; ex++) the_excludes[ex] = new Exclude(ex); + info->globalExcludes = new int; + info->n_exclude = info->n_SRI; + } + else{ + + Exclude::createArray( 1 ); + the_excludes = new Exclude*; + the_excludes[0] = new Exclude(0); + the_excludes[0]->setPair( 0,0 ); + info->globalExcludes = new int; + info->globalExcludes[0] = 0; + info->n_exclude = 0; + } + + // set the arrays into the SimInfo object + + info->atoms = the_atoms; + info->molecules = the_molecules; + info->nGlobalExcludes = 0; + info->excludes = the_excludes; + + the_ff->setSimInfo( info ); + +} + +void SimSetup::makeIntegrator( void ){ + + NVT* myNVT = NULL; + NPTi* myNPTi = NULL; + NPTf* myNPTf = NULL; + NPTim* myNPTim = NULL; + NPTfm* myNPTfm = NULL; + ZConstraint >* myNVEZCons = NULL; + ZConstraint >* myNVTZCons = NULL; + ZConstraint >* myNPTiZCons = NULL; + ZConstraint >* myNPTfZCons = NULL; + ZConstraint >* myNPTimZCons = NULL; + ZConstraint >* myNPTfmZCons = NULL; + + cerr << "setting integrator" <( info, the_ff ); + break; + + case NVT_ENS: + myNVT = new NVT( info, 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: + myNPTi = new NPTi( info, 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: + myNPTf = new NPTf( info, 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: + myNPTim = new NPTim( info, 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: + myNPTfm = new NPTfm( info, 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; + + case NVEZCONS_ENS: + + + //setup index of z-constraint molecules, z-constraint sampel time + //and z-constraint force output name. These parameter should be known + //before constructing the z-constraint integrator + setupZConstraint(); + + myNVEZCons = new ZConstraint >( info, the_ff ); + + break; + + + case NVTZCONS_ENS: + + setupZConstraint(); + + myNVTZCons = new ZConstraint >( info, the_ff ); + myNVTZCons->setTargetTemp(globals->getTargetTemp()); + + if (globals->haveTauThermostat()) + myNVTZCons->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 NPTiZCONS_ENS: + + setupZConstraint(); + + myNPTiZCons = new ZConstraint >( info, the_ff ); + myNPTiZCons->setTargetTemp( globals->getTargetTemp() ); + + if (globals->haveTargetPressure()) + myNPTiZCons->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() ) + myNPTiZCons->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() ) + myNPTiZCons->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 NPTfZCONS_ENS: + + setupZConstraint(); + + myNPTfZCons = new ZConstraint >( info, the_ff ); + myNPTfZCons->setTargetTemp( globals->getTargetTemp()); + + if (globals->haveTargetPressure()) + myNPTfZCons->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() ) + myNPTfZCons->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() ) + myNPTfZCons->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 NPTimZCONS_ENS: + + setupZConstraint(); + + myNPTimZCons = new ZConstraint >( info, the_ff ); + myNPTimZCons->setTargetTemp( globals->getTargetTemp()); + + if (globals->haveTargetPressure()) + myNPTimZCons->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() ) + myNPTimZCons->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() ) + myNPTimZCons->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 NPTfmZCONS_ENS: + + setupZConstraint(); + + myNPTfmZCons = new ZConstraint >( info, the_ff ); + myNPTfmZCons->setTargetTemp( globals->getTargetTemp()); + + if (globals->haveTargetPressure()) + myNPTfmZCons->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() ) + myNPTfmZCons->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() ) + myNPTfmZCons->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(); + } + +} + +void SimSetup::initFortran( void ){ + + info->refreshSim(); + + if( !strcmp( info->mixingRule, "standard") ){ + the_ff->initForceField( LB_MIXING_RULE ); + } + else if( !strcmp( info->mixingRule, "explicit") ){ + the_ff->initForceField( EXPLICIT_MIXING_RULE ); + } + else{ + sprintf( painCave.errMsg, + "SimSetup Error: unknown mixing rule -> \"%s\"\n", + info->mixingRule ); + painCave.isFatal = 1; + simError(); + } + + +#ifdef IS_MPI + strcpy( checkPointMsg, + "Successfully intialized the mixingRule for Fortran." ); + MPIcheckPoint(); +#endif // is_mpi + +} + +void SimSetup::setupZConstraint() +{ + if(globals->haveZConsTime()){ + + //add sample time of z-constraint into SimInfo's property list + DoubleData* zconsTimeProp = new DoubleData(); + zconsTimeProp->setID("zconstime"); + zconsTimeProp->setData(globals->getZConsTime()); + info->addProperty(zconsTimeProp); + } + else{ + sprintf( painCave.errMsg, + "ZConstraint error: If you use an ZConstraint\n" + " , you must set sample time.\n"); + painCave.isFatal = 1; + simError(); + } + + if(globals->haveIndexOfAllZConsMols()){ + + //add index of z-constraint molecules into SimInfo's property list + vector tempIndex = globals->getIndexOfAllZConsMols(); + + //sort the index + sort(tempIndex.begin(), tempIndex.end()); + + IndexData* zconsIndex = new IndexData(); + zconsIndex->setID("zconsindex"); + zconsIndex->setIndexData(tempIndex); + info->addProperty(zconsIndex); + } + else{ + sprintf( painCave.errMsg, + "SimSetup error: If you use an ZConstraint\n" + " , you must set index of z-constraint molecules.\n"); + painCave.isFatal = 1; + simError(); + + } + + //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(info->finalName); + + zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; + + StringData* zconsFilename = new StringData(); + zconsFilename->setID("zconsfilename"); + zconsFilename->setData(zconsOutput); + + info->addProperty(zconsFilename); + +}