OOPSE/libmdtools/SimSetup.cpp

#include <cstdlib>
#include <iostream>
#include <cmath>

#include "SimSetup.hpp"
#include "parse_me.h"
#include "Integrator.hpp"
#include "simError.h"

#ifdef IS_MPI
#include "mpiBASS.h"
#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 FF_DUFF 0
#define FF_LJ   1


SimSetup::SimSetup(){
  stamps = new MakeStamps();
  globals = new Globals();
  
#ifdef IS_MPI
  strcpy( checkPointMsg, "SimSetup creation successful" );
  MPIcheckPoint();
#endif // IS_MPI
}

SimSetup::~SimSetup(){
  delete stamps;
  delete globals;
}

void SimSetup::parseFile( char* fileName ){

#ifdef IS_MPI
  if( worldRank == 0 ){
#endif // is_mpi
    
    inFileName = fileName;
    set_interface_stamps( stamps, globals );
    
#ifdef IS_MPI
    mpiEventInit();
#endif

    yacc_BASS( fileName );

#ifdef IS_MPI
    throwMPIEvent(NULL);
  }
  else receiveParse();
#endif

}

#ifdef IS_MPI
void SimSetup::receiveParse(void){

    set_interface_stamps( stamps, globals );
    mpiEventInit();
    MPIcheckPoint();
    mpiEventLoop();

}

#endif // is_mpi

void SimSetup::createSim( void ){

  MakeStamps *the_stamps;
  Globals* the_globals;
  int i, j, k, globalAtomIndex;
  
  // gather all of the information from the Bass file
  
  gatherInfo();

  // creation of complex system objects

  sysObjectsCreation();


  // initialize the arrays

 
  makeMolecules();
  info->identArray = new int[info->n_atoms];
  for(i=0; i<info->n_atoms; i++){
    info->identArray[i] = the_atoms[i]->getIdent();
  }
  

  // check on the post processing info
  
  finalInfoCheck();


  // initialize the system coordinates

  initSystemCoords();
  

  // make the output filenames

  makeOutNames();
   
 
  // make the integrator
  
  
  NVT*  myNVT = NULL;
  NPTi* myNPTi = NULL;
  NPTf* myNPTf = NULL;
  NPTim* myNPTim = NULL;
  NPTfm* myNPTfm = NULL;

  switch( ensembleCase ){

  case NVE_ENS:
    new NVE( info, the_ff );
    break;

  case NVT_ENS:
    myNVT = new NVT( info, the_ff );
    myNVT->setTargetTemp(the_globals->getTargetTemp());

    if (the_globals->haveTauThermostat()) 
      myNVT->setTauThermostat(the_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( the_globals->getTargetTemp() );

    if (the_globals->haveTargetPressure())
      myNPTi->setTargetPressure(the_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( the_globals->haveTauThermostat() )
      myNPTi->setTauThermostat( the_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( the_globals->haveTauBarostat() )
      myNPTi->setTauBarostat( the_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( the_globals->getTargetTemp());

    if (the_globals->haveTargetPressure())
      myNPTf->setTargetPressure(the_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( the_globals->haveTauThermostat() )
      myNPTf->setTauThermostat( the_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( the_globals->haveTauBarostat() )
      myNPTf->setTauBarostat( the_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( the_globals->getTargetTemp());

    if (the_globals->haveTargetPressure())
      myNPTim->setTargetPressure(the_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( the_globals->haveTauThermostat() )
      myNPTim->setTauThermostat( the_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( the_globals->haveTauBarostat() )
      myNPTim->setTauBarostat( the_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( the_globals->getTargetTemp());

    if (the_globals->haveTargetPressure())
      myNPTfm->setTargetPressure(the_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( the_globals->haveTauThermostat() )
      myNPTfm->setTauThermostat( the_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( the_globals->haveTauBarostat() )
      myNPTfm->setTauBarostat( the_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();
  }


#ifdef IS_MPI
  mpiSim->mpiRefresh();
#endif

  // initialize the Fortran


  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::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;

  
  //init the forceField paramters

  the_ff->readParams();

  
  // init the atoms

  double ux, uy, uz, u, uSqr;
  
  atomOffset = 0;
  excludeOffset = 0;
  for(i=0; i<info->n_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; j<info.nAtoms; j++){
      
      currentAtom = comp_stamps[stampID]->getAtom( j );
      if( currentAtom->haveOrientation() ){
        
        dAtom = new DirectionalAtom(j + atomOffset);
        info->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 );
      }
      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; j<info.nBonds; j++){
      
      currentBond = comp_stamps[stampID]->getBond( 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; j<info.nBends; j++){
      
      currentBend = comp_stamps[stampID]->getBend( 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 = 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.nBends;

    for(j=0; j<info.nTorsions; j++){
      
      currentTorsion = comp_stamps[stampID]->getTorsion( 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 = 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.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_molecules[i].initialize( info );


    atomOffset += info.nAtoms;
    delete[] theBonds;
    delete[] theBends;
    delete[] theTorsions;
  }

#ifdef IS_MPI
  sprintf( checkPointMsg, "all molecules initialized succesfully" );
  MPIcheckPoint();
#endif // is_mpi

  // clean up the forcefield
  the_ff->calcRcut();
  the_ff->cleanMe();

}

void SimSetup::initFromBass( void ){

  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;

  temp1 = (double)tot_nmol / 4.0;
  temp2 = pow( temp1, ( 1.0 / 3.0 ) );
  temp3 = ceil( temp2 );

  have_extra =0;
  if( temp2 < temp3 ){ // we have a non-complete lattice
    have_extra =1;

    n_cells = (int)temp3 - 1;
    cellx = info->boxLx / temp3;
    celly = info->boxLy / temp3;
    cellz = info->boxLz / 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 );

    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();
    }
  }
  else{
    n_cells = (int)temp3;
    cellx = info->boxLx / temp3;
    celly = info->boxLy / temp3;
    cellz = info->boxLz / temp3;
  }

  current_mol = 0;
  current_comp_mol = 0;
  current_comp = 0;
  current_atom_ndx = 0;

  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 );
      }
    }
  }

  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( i < n_cells ){

          if( j < n_cells ){
            start_ndx = n_cells;
          }
          else start_ndx = 0;
        }
        else start_ndx = 0;

        for( k=start_ndx; k < (n_cells+1) && !done; k++ ){

          makeElement( i * cellx,
                       j * celly,
                       k * cellz );
          done = ( current_mol >= tot_nmol );

          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( !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( i=0; i<info->n_atoms; i++ ){
    info->atoms[i]->set_vx( 0.0 );
    info->atoms[i]->set_vy( 0.0 );
    info->atoms[i]->set_vz( 0.0 );
  }
}

void SimSetup::makeElement( double x, double y, double z ){

  int k;
  AtomStamp* current_atom;
  DirectionalAtom* dAtom;
  double rotMat[3][3];

  for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){

    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();
    }

    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() ){

      dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];

      rotMat[0][0] = 1.0;
      rotMat[0][1] = 0.0;
      rotMat[0][2] = 0.0;

      rotMat[1][0] = 0.0;
      rotMat[1][1] = 1.0;
      rotMat[1][2] = 0.0;

      rotMat[2][0] = 0.0;
      rotMat[2][1] = 0.0;
      rotMat[2][2] = 1.0;

      dAtom->setA( rotMat );
    }

    current_atom_ndx++;
  }

  current_mol++;
  current_comp_mol++;

  if( current_comp_mol >= components_nmol[current_comp] ){

    current_comp_mol = 0;
    current_comp++;
  }
}


void SimSetup::gatherInfo( void ){

  ensembleCase = -1;
  ffCase = -1;

  // get the stamps and globals;
  the_stamps = stamps;
  the_globals = globals;

  // set the easy ones first
  info->target_temp = the_globals->getTargetTemp();
  info->dt = the_globals->getDt();
  info->run_time = the_globals->getRunTime();
  n_components = the_globals->getNComponents();


  // get the forceField

  strcpy( force_field, the_globals->getForceField() );

  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();
  }

  // get the ensemble

  strcpy( ensemble, the_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;
  }  
  strcpy( info->ensemble, ensemble );

  // get the mixing rule

  strcpy( info->mixingRule, the_globals->getMixingRule() );
  info->usePBC = the_globals->getPBC();
        
  
  // get the components and calculate the tot_nMol and indvidual n_mol
 
  the_components = the_globals->getComponents();
  components_nmol = new int[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; i<n_components; i++ ){

      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();
      }

      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( the_globals->haveSampleTime() ){
    info->sampleTime = the_globals->getSampleTime();
    info->statusTime = info->sampleTime;
    info->thermalTime = info->sampleTime;
  }
  else{
    info->sampleTime = the_globals->getRunTime();
    info->statusTime = info->sampleTime;
    info->thermalTime = info->sampleTime;
  }

  if( the_globals->haveStatusTime() ){
    info->statusTime = the_globals->getStatusTime();
  }

  if( the_globals->haveThermalTime() ){
    info->thermalTime = the_globals->getThermalTime();
  }

  // check for the temperature set flag

  if( the_globals->haveTempSet() ) info->setTemp = the_globals->getTempSet();

  // get some of the tricky things that may still be in the globals

  double boxVector[3];
  if( the_globals->haveBox() ){
    boxVector[0] = the_globals->getBox();
    boxVector[1] = the_globals->getBox();
    boxVector[2] = the_globals->getBox();
    
    info->setBox( boxVector );
  }
  else if( the_globals->haveDensity() ){

    double vol;
    vol = (double)tot_nmol / the_globals->getDensity();
     boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
     boxVector[1] = boxVector[0];
     boxVector[2] = boxVector[0];

    info->setBox( boxVector );
  }
  else{
    if( !the_globals->haveBoxX() ){
      sprintf( painCave.errMsg,
               "SimSetup error, no periodic BoxX size given.\n" );
      painCave.isFatal = 1;
      simError();
    }
    boxVector[0] = the_globals->getBoxX();

    if( !the_globals->haveBoxY() ){
      sprintf( painCave.errMsg,
               "SimSetup error, no periodic BoxY size given.\n" );
      painCave.isFatal = 1;
      simError();
    }
    boxVector[1] = the_globals->getBoxY();

    if( !the_globals->haveBoxZ() ){
      sprintf( painCave.errMsg,
               "SimSetup error, no periodic BoxZ size given.\n" );
      painCave.isFatal = 1;
      simError();
    }
    boxVector[2] = the_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


  if (the_globals->getUseRF() ) {
    info->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 = info->boxLx;
      if (info->boxLy <= smallest) smallest = info->boxLy;
      if (info->boxLz <= smallest) smallest = info->boxLz;
      info->ecr = 0.5 * smallest;
    } else {
      info->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();
      info->est = 0.05 * info->ecr;
    } else {
      info->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();
    }
    info->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 = info->boxLx;
        if (info->boxLy <= smallest) smallest = info->boxLy;
        if (info->boxLz <= smallest) smallest = info->boxLz;
        info->ecr = 0.5 * smallest;
      } else {
        info->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();
        info->est = 0.05 * info->ecr;
      } else {
        info->est        = the_globals->getEST();
      }
    }
  }  

#ifdef IS_MPI
  strcpy( checkPointMsg, "post processing checks out" );
  MPIcheckPoint();
#endif // is_mpi

}

void SimSetup::initSystemCoords( void ){

 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( 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( the_globals->haveFinalConfig() ){
      strcpy( info->finalName, the_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 ){

  // 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();

  
}


void SimSetup::createFF( void ){

  switch( ffCase ){

  case FF_DUFF:
    the_ff = new DUFF();
    break;

  case FF_LJ:
    the_ff = new LJFF();
    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 ){

  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; i<n_components; i++ ){

    id = the_components[i]->getType();
    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 = 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 );
    }
  }

#ifdef IS_MPI
  strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
  MPIcheckPoint();
#endif // is_mpi


}

void SimSetup::calcSysValues( void ){

  tot_atoms = 0;
  tot_bonds = 0;
  tot_bends = 0;
  tot_torsions = 0;
  for( i=0; i<n_components; i++ ){
    
    tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
    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 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; i<n_components; i++ ){

    for( j=0; j<components_nmol[i]; j++ ){
      
      if( mol2proc[allMol] == worldRank ){
        
        local_atoms +=    comp_stamps[i]->getNAtoms();
        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 ){

  // 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; i<mpiSim->getTotNmol(); 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; i<n_components; i++){
    for(j=0; j<components_nmol[i]; j++ ){
      the_molecules[molIndex].setStampID( i );
      the_molecules[molIndex].setMyIndex( molIndex );
      the_molecules[molIndex].setGlobalIndex( molIndex );
      for (k = 0; k < comp_stamps[i]->getNAtoms(); 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; ex<info->n_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 );

}
Revision:	614
Committed:	Tue Jul 15 17:57:04 2003 UTC (20 years, 11 months ago) by mmeineke
File size:	35613 byte(s)
Log Message:	fixed some bugs, Changed entry_plug to info where appropriate