OOPSE/libmdtools/SimSetup.cpp

#include <algorithm>
#include <cstdlib>
#include <iostream>
#include <cmath>
#include <string>

#include "SimSetup.hpp"
#include "ReadWrite.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
#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();
#endif // IS_MPI
}

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

  int i, j, k, globalAtomIndex;
  
  // gather all of the information from the Bass file

  std::cerr << "gathering info\n";

  gatherInfo();

  // creation of complex system objects

  std::cerr << "creating system objects\n";

  sysObjectsCreation();

  // check on the post processing info
  
  std::cerr << "performing final info check.\n";

  finalInfoCheck();

  // initialize the system coordinates

  std::cerr << "about to init coords\n";

  if( !isInfoArray ) initSystemCoords();  

  // make the output filenames

  makeOutNames();
   
  // make the integrator
  
  makeIntegrator();
  
#ifdef IS_MPI
  mpiSim->mpiRefresh();
#endif

  // initialize the Fortran

  initFortran();


}


void SimSetup::makeMolecules( void ){

  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;

  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;
  
  for(k=0; k<nInfo; k++){
    
    the_ff->setSimInfo( &(info[k]) );

    atomOffset = 0;
    excludeOffset = 0;
    for(i=0; i<info[k].n_mol; i++){
    
      stampID = info[k].molecules[i].getStampID();

      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;
      
      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; j<molInfo.nAtoms; j++){
        
        currentAtom = comp_stamps[stampID]->getAtom( 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
      
        molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
      
#endif // is_mpi
      } 
    
    // make the bonds
      for(j=0; j<molInfo.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 = 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;
      
      //make the bends
      for(j=0; j<molInfo.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 = 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; j<molInfo.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 = 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
  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;

  double vel[3];
  vel[0] = 0.0;
  vel[1] = 0.0;
  vel[2] = 0.0;

  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[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 );

    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[0].boxL[0] / temp3;
    celly = info[0].boxL[1] / temp3;
    cellz = info[0].boxL[2] / 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[0].n_atoms; i++ ){
    info[0].atoms[i]->setVel( vel );
  }
}

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

  int k;
  AtomStamp* current_atom;
  DirectionalAtom* dAtom;
  double rotMat[3][3];
  double pos[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();
    }
    
    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 );

    if( info[0].atoms[current_atom_ndx]->isDirectional() ){

      dAtom = (DirectionalAtom *)info[0].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 ){
  int i,j,k;

  ensembleCase = -1;
  ffCase = -1;

  // set the easy ones first

  for( i=0; i<nInfo; i++){
    info[i].target_temp = globals->getTargetTemp();
    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;
  }  
  
  for(i=0; i<nInfo; i++){
    
    strcpy( info[i].ensemble, ensemble );

    // get the mixing rule

    strcpy( info[i].mixingRule, globals->getMixingRule() );
    info[i].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; 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
  
  for(i=0; i<nInfo; i++){

    if( globals->haveSampleTime() ){
      info[i].sampleTime = globals->getSampleTime();
      info[i].statusTime = info[i].sampleTime;
      info[i].thermalTime = info[i].sampleTime;
    }
    else{
      info[i].sampleTime = globals->getRunTime();
      info[i].statusTime = info[i].sampleTime;
      info[i].thermalTime = info[i].sampleTime;
    }
    
    if( globals->haveStatusTime() ){
      info[i].statusTime = globals->getStatusTime();
    }
    
    if( globals->haveThermalTime() ){
      info[i].thermalTime = globals->getThermalTime();
    }

    // check for the temperature set flag

    if( globals->haveTempSet() ) info[i].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[i].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[i].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[i].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;
  int i;

  for(i=0; i<nInfo; i++){
    // check electrostatic parameters
    
    index = 0;
    usesDipoles = 0;
    while( (index < info[i].n_atoms) && !usesDipoles ){
      usesDipoles = (info[i].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[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 );
      }
    }  
  }

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

}

void SimSetup::initSystemCoords( void ){
  int i;
  
  char* inName;

  std::cerr << "Setting atom Coords\n";

  (info[0].getConfiguration())->createArrays( info[0].n_atoms );
  
  for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
  
  if( globals->haveInitialConfig() ){
    
    InitializeFromFile* fileInit;
#ifdef IS_MPI // is_mpi
    if( worldRank == 0 ){
#endif //is_mpi
      inName = globals->getInitialConfig();
      fileInit = new InitializeFromFile( inName );
#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 ){
  
  int k;

  
  for(k=0; k<nInfo; k++){

#ifdef IS_MPI
    if( worldRank == 0 ){
#endif // is_mpi
      
      if( globals->haveFinalConfig() ){
        strcpy( info[k].finalName, globals->getFinalConfig() );
      }
      else{
        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{
            strcat( info[k].finalName, ".eor" );
          }
        }
      }
      
      // 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{
        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" );
        }
      }
      
      strcpy( info[k].statusName, inFileName );
      nameLength = strlen( info[k].statusName );
      endTest = &(info[k].statusName[nameLength - 5]);
      if( !strcmp( endTest, ".bass" ) ){
        strcpy( endTest, ".stat" );
      }
      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" );
        }
      }
      
#ifdef IS_MPI
    }
#endif // is_mpi
  }
}


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
  // 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; k<nInfo; k++){
    info[k].identArray = new int[info[k].n_atoms];
    for(i=0; i<info[k].n_atoms; i++){
      info[k].identArray[i] = info[k].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;
  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; i<nInfo; i++){
    info[i].nComponents = n_components;
    info[i].componentsNmol = components_nmol;
    info[i].compStamps = comp_stamps;
    info[i].headStamp = headStamp;
  }
  

  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 = 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;
  
  int *molMembershipArray;
  
  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;
  molMembershipArray = new int[tot_atoms];
  
  for(i=0; i<nInfo; i++){
    info[i].n_atoms = tot_atoms;
    info[i].n_bonds = tot_bonds;
    info[i].n_bends = tot_bends;
    info[i].n_torsions = tot_torsions;
    info[i].n_SRI = tot_SRI;
    info[i].n_mol = tot_nmol;
    
    info[i].molMembershipArray = molMembershipArray;
  } 
}

#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; 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[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;

  strcpy( checkPointMsg, "Passed nlocal consistency check." );
  MPIcheckPoint();
}
 
#endif // is_mpi


void SimSetup::makeSysArrays( void ){
  int i, j, k, l;

  Atom** the_atoms;
  Molecule* the_molecules;
  Exclude** the_excludes;

  
  for(l=0; l<nInfo; l++){
    
    // create the atom and short range interaction arrays
    
    the_atoms = new Atom*[info[l].n_atoms];
    the_molecules = new Molecule[info[l].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[l].molMembershipArray[globalAtomIndex] = molIndex;
          globalAtomIndex++;
        }
        molIndex++;
      }
    }
    
    
#endif // is_mpi


    if( info[l].n_SRI ){
    
      Exclude::createArray(info[l].n_SRI);
      the_excludes = new Exclude*[info[l].n_SRI];
      for( int ex=0; ex<info[l].n_SRI; ex++){
        the_excludes[ex] = new Exclude(ex);
      }
      info[l].globalExcludes = new int;
      info[l].n_exclude = info[l].n_SRI;
    }
    else{
    
      Exclude::createArray( 1 );
      the_excludes = new Exclude*;
      the_excludes[0] = new Exclude(0);
      the_excludes[0]->setPair( 0,0 );
      info[l].globalExcludes = new int;
      info[l].globalExcludes[0] = 0;
      info[l].n_exclude = 0;
    }

    // set the arrays into the SimInfo object

    info[l].atoms = the_atoms;
    info[l].molecules = the_molecules;
    info[l].nGlobalExcludes = 0;
    info[l].excludes = the_excludes;

    the_ff->setSimInfo( info );
    
  }
}

void SimSetup::makeIntegrator( void ){

  int k;

  NVT<RealIntegrator>*  myNVT = NULL;
  NPTi<RealIntegrator>* myNPTi = NULL;
  NPTf<RealIntegrator>* myNPTf = NULL;
  NPTim<RealIntegrator>* myNPTim = NULL;
  NPTfm<RealIntegrator>* myNPTfm = NULL;
        
  for(k=0; k<nInfo; k++){
    
    switch( ensembleCase ){
      
    case NVE_ENS:
        if (globals->haveZconstraints()){
         setupZConstraint(info[k]);
           new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
        }

        else
        new NVE<RealIntegrator>( &(info[k]), the_ff );
      break;
      
    case NVT_ENS:
        if (globals->haveZconstraints()){
         setupZConstraint(info[k]);
           myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
        }
        else
        myNVT = new NVT<RealIntegrator>( &(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<NPTi<RealIntegrator> >( &(info[k]), the_ff );
        }
        else
        myNPTi = new NPTi<RealIntegrator>( &(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<NPTf<RealIntegrator> >( &(info[k]), the_ff );
        }
        else
        myNPTf = new NPTf<RealIntegrator>( &(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<NPTim<RealIntegrator> >( &(info[k]), the_ff );
        }
        else
        myNPTim = new NPTim<RealIntegrator>( &(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<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
        }
        else
        myNPTfm = new NPTfm<RealIntegrator>( &(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();
    }
  }
}

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();
  }


#ifdef IS_MPI
  strcpy( checkPointMsg, 
          "Successfully intialized the mixingRule for Fortran." );
  MPIcheckPoint();
#endif // is_mpi

}

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();
    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);      
}
Revision:	689
Committed:	Tue Aug 12 19:56:49 2003 UTC (20 years, 10 months ago) by tim
File size:	40516 byte(s)
Log Message:	debugging globals