mdtools/interface_implementation/SimSetup.cpp

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

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

#ifdef IS_MPI
#include "mpiBASS.h"
#include "bassDiag.hpp"
#endif

SimSetup::SimSetup(){
  stamps = new MakeStamps();
  globals = new Globals();
}

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

void SimSetup::parseFile( char* fileName ){

  inFileName = fileName;
  set_interface_stamps( stamps, globals );
#ifdef IS_MPI
  mpiEventInit();
#endif
  yacc_BASS( fileName );
#ifdef IS_MPI
  throwMPIEvent(NULL);
#endif

}

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

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

}


void SimSetup::testMe(void){
  bassDiag* dumpMe = new bassDiag(globals,stamps);
  dumpMe->dumpStamps();
  delete dumpMe;
}
#endif
void SimSetup::createSim( void ){

  MakeStamps *the_stamps;
  Globals* the_globals;
  int i;

  // 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() );
  strcpy( ensemble, the_globals->getEnsemble() );

  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
  else{
    std::cerr<< "SimSetup Error. Unrecognized force field -> "
             << force_field << "\n";
    exit(8);
  }

  // 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; i<n_components; i++ ){

      if( !the_components[i]->haveNMol() ){
        // we have a problem
        std::cerr << "SimSetup Error. No global NMol or component NMol"
                  << " given. Cannot calculate the number of atoms.\n";
        exit( 8 );
      }

      tot_nmol += the_components[i]->getNMol();
      components_nmol[i] = the_components[i]->getNMol();
    }
  }
  else{
    std::cerr << "NOT A SUPPORTED FEATURE\n";

//     tot_nmol = the_globals->getNMol();

//     //we have the total number of molecules, now we check for molfractions
//     for( i=0; i<n_components; i++ ){

//       if( !the_components[i]->haveMolFraction() ){

//      if( !the_components[i]->haveNMol() ){
//        //we have a problem
//        std::cerr << "SimSetup error. Neither molFraction nor "
//                  << " nMol was given in component

  }

  // make an array of molecule stamps that match the components used.

  for( i=0; i<n_components; i++ ){

    comp_stamps[i] =
      the_stamps->getMolecule( the_components[i]->getType() );
  }


  // caclulate the number of atoms, bonds, bends and torsions

  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;

  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;

  // create the atom and short range interaction arrays

  the_atoms = new Atom*[tot_atoms];
  Atom::createArrays(tot_atoms);
  the_molecules = new Molecule[tot_nmol];


  if( tot_SRI ){
    the_sris = new SRI*[tot_SRI];
    the_excludes = new ex_pair[tot_SRI];
  }

  // set the arrays into the SimInfo object

  simnfo->atoms = the_atoms;
  simnfo->sr_interactions = the_sris;
  simnfo->n_exclude = tot_SRI;
  simnfo->excludes = the_excludes;


  // initialize the arrays

  the_ff->setSimInfo( simnfo );

  makeAtoms();

  if( tot_bonds ){
    makeBonds();
  }

  if( tot_bends ){
    makeBends();
  }

  if( tot_torsions ){
    makeTorsions();
  }

  //  makeMolecules();

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

  if( simnfo->n_dipoles ){

    if( !the_globals->haveRRF() ){
      std::cerr << "SimSetup Error, system has dipoles, but no rRF was set.\n";
      exit(8);
    }
    if( !the_globals->haveDielectric() ){
      std::cerr << "SimSetup Error, system has dipoles, but no"
                << " dielectric was set.\n";
      exit(8);
    }

    simnfo->rRF        = the_globals->getRRF();
    simnfo->dielectric = the_globals->getDielectric();
  }

  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() ){
      std::cerr << "SimSetup error, no periodic BoxX size given.\n";
      exit(8);
    }
    simnfo->box_x = the_globals->getBoxX();

    if( !the_globals->haveBoxY() ){
      std::cerr << "SimSetup error, no periodic BoxY size given.\n";
      exit(8);
    }
    simnfo->box_y = the_globals->getBoxY();

    if( !the_globals->haveBoxZ() ){
      std::cerr << "SimSetup error, no periodic BoxZ size given.\n";
      exit(8);
    }
    simnfo->box_z = the_globals->getBoxZ();
  }


//   if( the_globals->haveInitialConfig() ){
//        InitializeFromFile* fileInit;
//     fileInit = new InitializeFromFile( the_globals->getInitialConfig() );

//     fileInit->read_xyz( simnfo ); // default velocities on

//     delete fileInit;
//   }
//   else{

    initFromBass();


//   }

//   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" );
//     }
//   }


  // 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" ) ) new Verlet( *simnfo );
  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo );
  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo );
}

void SimSetup::makeAtoms( void ){

  int i, j, k, index;
  double ux, uy, uz, uSqr, u;
  AtomStamp* current_atom;
  DirectionalAtom* dAtom;
  int molIndex, molStart, molEnd, nMemb;


  molIndex = 0;
  index = 0;
  for( i=0; i<n_components; i++ ){

    for( j=0; j<components_nmol[i]; j++ ){

      molStart = index;
      nMemb = comp_stamps[i]->getNAtoms();
      for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){

        current_atom = comp_stamps[i]->getAtom( k );
        if( current_atom->haveOrientation() ){

          dAtom = new DirectionalAtom(index);
          simnfo->n_oriented++;
          the_atoms[index] = dAtom;

          ux = current_atom->getOrntX();
          uy = current_atom->getOrntY();
          uz = current_atom->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{
          the_atoms[index] = new GeneralAtom(index);
        }
        the_atoms[index]->setType( current_atom->getType() );
        the_atoms[index]->setIndex( index );

        // increment the index and repeat;
        index++;
      }

      molEnd = index -1;
      the_molecules[molIndex].setNMembers( nMemb );
      the_molecules[molIndex].setStartAtom( molStart );
      the_molecules[molIndex].setEndAtom( molEnd );
      molIndex++;

    }
  }

  the_ff->initializeAtoms();
}

void SimSetup::makeBonds( void ){

  int i, j, k, index, offset;
  bond_pair* the_bonds;
  BondStamp* current_bond;

  the_bonds = new bond_pair[tot_bonds];
  index = 0;
  offset = 0;
  for( i=0; i<n_components; i++ ){

    for( j=0; j<components_nmol[i]; j++ ){

      for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){

        current_bond = comp_stamps[i]->getBond( k );
        the_bonds[index].a = current_bond->getA() + offset;
        the_bonds[index].b = current_bond->getB() + offset;

        the_excludes[index].i = the_bonds[index].a;
        the_excludes[index].j = the_bonds[index].b;

        // increment the index and repeat;
        index++;
      }
      offset += comp_stamps[i]->getNAtoms();
    }
  }

  the_ff->initializeBonds( the_bonds );
}

void SimSetup::makeBends( void ){

  int i, j, k, index, offset;
  bend_set* the_bends;
  BendStamp* current_bend;

  the_bends = new bend_set[tot_bends];
  index = 0;
  offset = 0;
  for( i=0; i<n_components; i++ ){

    for( j=0; j<components_nmol[i]; j++ ){

      for( k=0; k<comp_stamps[i]->getNBends(); k++ ){

        current_bend = comp_stamps[i]->getBend( k );
        the_bends[index].a = current_bend->getA() + offset;
        the_bends[index].b = current_bend->getB() + offset;
        the_bends[index].c = current_bend->getC() + offset;

        the_excludes[index + tot_bonds].i = the_bends[index].a;
        the_excludes[index + tot_bonds].j = the_bends[index].c;

        // increment the index and repeat;
        index++;
      }
      offset += comp_stamps[i]->getNAtoms();
    }
  }

  the_ff->initializeBends( the_bends );
}

void SimSetup::makeTorsions( void ){

  int i, j, k, index, offset;
  torsion_set* the_torsions;
  TorsionStamp* current_torsion;

  the_torsions = new torsion_set[tot_torsions];
  index = 0;
  offset = 0;
  for( i=0; i<n_components; i++ ){

    for( j=0; j<components_nmol[i]; j++ ){

      for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){

        current_torsion = comp_stamps[i]->getTorsion( k );
        the_torsions[index].a = current_torsion->getA() + offset;
        the_torsions[index].b = current_torsion->getB() + offset;
        the_torsions[index].c = current_torsion->getC() + offset;
        the_torsions[index].d = current_torsion->getD() + offset;

        the_excludes[index + tot_bonds + tot_bends].i = the_torsions[index].a;
        the_excludes[index + tot_bonds + tot_bends].j = the_torsions[index].d;

        // increment the index and repeat;
        index++;
      }
      offset += comp_stamps[i]->getNAtoms();
    }
  }

  the_ff->initializeTorsions( the_torsions );
}

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 = simnfo->box_x / temp3;
    celly = simnfo->box_y / temp3;
    cellz = simnfo->box_z / temp3;
    n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
    temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
    n_per_extra = (int)ceil( temp1 );

    if( n_per_extra > 4){
      std::cerr << "THere has been an error in constructing the non-complete lattice.\n";
      exit(8);
    }
  }
  else{
    n_cells = (int)temp3;
    cellx = simnfo->box_x / temp3;
    celly = simnfo->box_y / temp3;
    cellz = simnfo->box_z / temp3;
  }

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

  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<simnfo->n_atoms; i++ ){
    simnfo->atoms[i]->set_vx( 0.0 );
    simnfo->atoms[i]->set_vy( 0.0 );
    simnfo->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() ){
      std::cerr << "Component " << comp_stamps[current_comp]->getID()
                << ", atom " << current_atom->getType()
                << " does not have a position specified.\n"
                << "The initialization routine is unable to give a start"
                << " position.\n";
      exit(8);
    }

    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++;
  }
}
Revision:	145
Committed:	Fri Oct 18 15:34:21 2002 UTC (21 years, 8 months ago) by mmeineke
File size:	17171 byte(s)
Log Message:	finished adding the static storage arrays to the atom class
#	User	Rev	Content
1	mmeineke	10	#include <cstdlib>
2			#include <iostream>
3			#include <cmath>
4
5			#include "SimSetup.hpp"
6			#include "parse_me.h"
7			#include "LRI.hpp"
8			#include "Integrator.hpp"
9	mmeineke	144
10	chuckv	131	#ifdef IS_MPI
11	chuckv	139	#include "mpiBASS.h"
12	chuckv	131	#include "bassDiag.hpp"
13			#endif
14	mmeineke	10
15			SimSetup::SimSetup(){
16			stamps = new MakeStamps();
17			globals = new Globals();
18			}
19
20			SimSetup::~SimSetup(){
21			delete stamps;
22			delete globals;
23			}
24
25			void SimSetup::parseFile( char* fileName ){
26
27			inFileName = fileName;
28			set_interface_stamps( stamps, globals );
29	chuckv	131	#ifdef IS_MPI
30	chuckv	124	mpiEventInit();
31			#endif
32	mmeineke	10	yacc_BASS( fileName );
33	chuckv	131	#ifdef IS_MPI
34	chuckv	124	throwMPIEvent(NULL);
35			#endif
36
37	mmeineke	10	}
38
39	chuckv	131	#ifdef IS_MPI
40	chuckv	124	void SimSetup::receiveParse(void){
41
42			set_interface_stamps( stamps, globals );
43			mpiEventInit();
44			mpiEventLoop();
45
46			}
47
48	chuckv	131
49	chuckv	128	void SimSetup::testMe(void){
50			bassDiag* dumpMe = new bassDiag(globals,stamps);
51			dumpMe->dumpStamps();
52			delete dumpMe;
53			}
54	chuckv	131	#endif
55	mmeineke	10	void SimSetup::createSim( void ){
56
57			MakeStamps *the_stamps;
58			Globals* the_globals;
59			int i;
60
61			// get the stamps and globals;
62			the_stamps = stamps;
63			the_globals = globals;
64
65			// set the easy ones first
66			simnfo->target_temp = the_globals->getTargetTemp();
67			simnfo->dt = the_globals->getDt();
68			simnfo->run_time = the_globals->getRunTime();
69
70			// get the ones we know are there, yet still may need some work.
71			n_components = the_globals->getNComponents();
72			strcpy( force_field, the_globals->getForceField() );
73			strcpy( ensemble, the_globals->getEnsemble() );
74	chuckv	124
75	mmeineke	10	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
76			else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
77			else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
78			else{
79	chuckv	124	std::cerr<< "SimSetup Error. Unrecognized force field -> "
80	mmeineke	10	<< force_field << "\n";
81			exit(8);
82			}
83
84			// get the components and calculate the tot_nMol and indvidual n_mol
85			the_components = the_globals->getComponents();
86			components_nmol = new int[n_components];
87			comp_stamps = new MoleculeStamp*[n_components];
88	chuckv	124
89	mmeineke	10	if( !the_globals->haveNMol() ){
90	chuckv	124	// we don't have the total number of molecules, so we assume it is
91	mmeineke	10	// given in each component
92
93			tot_nmol = 0;
94			for( i=0; i<n_components; i++ ){
95	chuckv	124
96	mmeineke	10	if( !the_components[i]->haveNMol() ){
97			// we have a problem
98			std::cerr << "SimSetup Error. No global NMol or component NMol"
99			<< " given. Cannot calculate the number of atoms.\n";
100			exit( 8 );
101			}
102
103			tot_nmol += the_components[i]->getNMol();
104			components_nmol[i] = the_components[i]->getNMol();
105			}
106			}
107			else{
108			std::cerr << "NOT A SUPPORTED FEATURE\n";
109	chuckv	124
110	mmeineke	10	// tot_nmol = the_globals->getNMol();
111	chuckv	124
112	mmeineke	10	// //we have the total number of molecules, now we check for molfractions
113			// for( i=0; i<n_components; i++ ){
114	chuckv	124
115	mmeineke	10	// if( !the_components[i]->haveMolFraction() ){
116	chuckv	124
117	mmeineke	10	// if( !the_components[i]->haveNMol() ){
118			// //we have a problem
119			// std::cerr << "SimSetup error. Neither molFraction nor "
120			// << " nMol was given in component
121
122			}
123
124			// make an array of molecule stamps that match the components used.
125
126			for( i=0; i<n_components; i++ ){
127
128	chuckv	124	comp_stamps[i] =
129	mmeineke	10	the_stamps->getMolecule( the_components[i]->getType() );
130			}
131
132
133	chuckv	124
134	mmeineke	10	// caclulate the number of atoms, bonds, bends and torsions
135
136			tot_atoms = 0;
137			tot_bonds = 0;
138			tot_bends = 0;
139			tot_torsions = 0;
140			for( i=0; i<n_components; i++ ){
141	chuckv	124
142	mmeineke	10	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
143			tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
144			tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
145			tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
146			}
147	chuckv	124
148	mmeineke	10	tot_SRI = tot_bonds + tot_bends + tot_torsions;
149	chuckv	124
150	mmeineke	10	simnfo->n_atoms = tot_atoms;
151			simnfo->n_bonds = tot_bonds;
152			simnfo->n_bends = tot_bends;
153			simnfo->n_torsions = tot_torsions;
154			simnfo->n_SRI = tot_SRI;
155
156			// create the atom and short range interaction arrays
157	chuckv	124
158	mmeineke	10	the_atoms = new Atom*[tot_atoms];
159	mmeineke	145	Atom::createArrays(tot_atoms);
160	mmeineke	113	the_molecules = new Molecule[tot_nmol];
161	chuckv	124
162
163	mmeineke	10	if( tot_SRI ){
164			the_sris = new SRI*[tot_SRI];
165			the_excludes = new ex_pair[tot_SRI];
166			}
167
168			// set the arrays into the SimInfo object
169
170			simnfo->atoms = the_atoms;
171			simnfo->sr_interactions = the_sris;
172			simnfo->n_exclude = tot_SRI;
173			simnfo->excludes = the_excludes;
174
175	chuckv	124
176	mmeineke	10	// initialize the arrays
177	chuckv	124
178	mmeineke	10	the_ff->setSimInfo( simnfo );
179	chuckv	124
180	mmeineke	10	makeAtoms();
181
182			if( tot_bonds ){
183			makeBonds();
184			}
185
186			if( tot_bends ){
187			makeBends();
188			}
189
190			if( tot_torsions ){
191			makeTorsions();
192			}
193
194			// makeMolecules();
195
196			// get some of the tricky things that may still be in the globals
197
198			if( simnfo->n_dipoles ){
199
200			if( !the_globals->haveRRF() ){
201			std::cerr << "SimSetup Error, system has dipoles, but no rRF was set.\n";
202			exit(8);
203			}
204			if( !the_globals->haveDielectric() ){
205			std::cerr << "SimSetup Error, system has dipoles, but no"
206			<< " dielectric was set.\n";
207			exit(8);
208			}
209
210			simnfo->rRF = the_globals->getRRF();
211			simnfo->dielectric = the_globals->getDielectric();
212			}
213
214			if( the_globals->haveBox() ){
215			simnfo->box_x = the_globals->getBox();
216			simnfo->box_y = the_globals->getBox();
217			simnfo->box_z = the_globals->getBox();
218			}
219			else if( the_globals->haveDensity() ){
220	chuckv	124
221	mmeineke	10	double vol;
222			vol = (double)tot_nmol / the_globals->getDensity();
223			simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
224			simnfo->box_y = simnfo->box_x;
225			simnfo->box_z = simnfo->box_x;
226			}
227			else{
228			if( !the_globals->haveBoxX() ){
229			std::cerr << "SimSetup error, no periodic BoxX size given.\n";
230			exit(8);
231			}
232			simnfo->box_x = the_globals->getBoxX();
233
234			if( !the_globals->haveBoxY() ){
235			std::cerr << "SimSetup error, no periodic BoxY size given.\n";
236			exit(8);
237			}
238			simnfo->box_y = the_globals->getBoxY();
239
240			if( !the_globals->haveBoxZ() ){
241			std::cerr << "SimSetup error, no periodic BoxZ size given.\n";
242			exit(8);
243			}
244			simnfo->box_z = the_globals->getBoxZ();
245			}
246
247	chuckv	124
248			// if( the_globals->haveInitialConfig() ){
249			// InitializeFromFile* fileInit;
250			// fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
251
252			// fileInit->read_xyz( simnfo ); // default velocities on
253
254			// delete fileInit;
255			// }
256			// else{
257
258	mmeineke	10	initFromBass();
259
260
261	chuckv	124	// }
262
263			// if( the_globals->haveFinalConfig() ){
264			// strcpy( simnfo->finalName, the_globals->getFinalConfig() );
265			// }
266			// else{
267			// strcpy( simnfo->finalName, inFileName );
268			// char* endTest;
269			// int nameLength = strlen( simnfo->finalName );
270			// endTest = &(simnfo->finalName[nameLength - 5]);
271			// if( !strcmp( endTest, ".bass" ) ){
272			// strcpy( endTest, ".eor" );
273			// }
274			// else if( !strcmp( endTest, ".BASS" ) ){
275			// strcpy( endTest, ".eor" );
276			// }
277			// else{
278			// endTest = &(simnfo->finalName[nameLength - 4]);
279			// if( !strcmp( endTest, ".bss" ) ){
280			// strcpy( endTest, ".eor" );
281			// }
282			// else if( !strcmp( endTest, ".mdl" ) ){
283			// strcpy( endTest, ".eor" );
284			// }
285			// else{
286			// strcat( simnfo->finalName, ".eor" );
287			// }
288			// }
289			// }
290
291			// // make the sample and status out names
292
293			// strcpy( simnfo->sampleName, inFileName );
294			// char* endTest;
295			// int nameLength = strlen( simnfo->sampleName );
296			// endTest = &(simnfo->sampleName[nameLength - 5]);
297			// if( !strcmp( endTest, ".bass" ) ){
298			// strcpy( endTest, ".dump" );
299			// }
300			// else if( !strcmp( endTest, ".BASS" ) ){
301			// strcpy( endTest, ".dump" );
302			// }
303			// else{
304			// endTest = &(simnfo->sampleName[nameLength - 4]);
305			// if( !strcmp( endTest, ".bss" ) ){
306			// strcpy( endTest, ".dump" );
307			// }
308			// else if( !strcmp( endTest, ".mdl" ) ){
309			// strcpy( endTest, ".dump" );
310			// }
311			// else{
312			// strcat( simnfo->sampleName, ".dump" );
313			// }
314			// }
315
316			// strcpy( simnfo->statusName, inFileName );
317			// nameLength = strlen( simnfo->statusName );
318			// endTest = &(simnfo->statusName[nameLength - 5]);
319			// if( !strcmp( endTest, ".bass" ) ){
320			// strcpy( endTest, ".stat" );
321			// }
322			// else if( !strcmp( endTest, ".BASS" ) ){
323			// strcpy( endTest, ".stat" );
324			// }
325			// else{
326			// endTest = &(simnfo->statusName[nameLength - 4]);
327			// if( !strcmp( endTest, ".bss" ) ){
328			// strcpy( endTest, ".stat" );
329			// }
330			// else if( !strcmp( endTest, ".mdl" ) ){
331			// strcpy( endTest, ".stat" );
332			// }
333			// else{
334			// strcat( simnfo->statusName, ".stat" );
335			// }
336			// }
337
338
339	mmeineke	10	// set the status, sample, and themal kick times
340
341			if( the_globals->haveSampleTime() ){
342	chuckv	124	simnfo->sampleTime = the_globals->getSampleTime();
343	mmeineke	10	simnfo->statusTime = simnfo->sampleTime;
344			simnfo->thermalTime = simnfo->sampleTime;
345			}
346			else{
347	chuckv	124	simnfo->sampleTime = the_globals->getRunTime();
348	mmeineke	10	simnfo->statusTime = simnfo->sampleTime;
349			simnfo->thermalTime = simnfo->sampleTime;
350			}
351
352			if( the_globals->haveStatusTime() ){
353			simnfo->statusTime = the_globals->getStatusTime();
354			}
355
356			if( the_globals->haveThermalTime() ){
357			simnfo->thermalTime = the_globals->getThermalTime();
358			}
359
360			// check for the temperature set flag
361
362			if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
363	chuckv	124
364
365	mmeineke	10	// make the longe range forces and the integrator
366	chuckv	124
367	mmeineke	10	new AllLong( simnfo );
368	chuckv	124
369	mmeineke	10	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo );
370			if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo );
371			if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo );
372			}
373
374			void SimSetup::makeAtoms( void ){
375	chuckv	124
376	mmeineke	10	int i, j, k, index;
377			double ux, uy, uz, uSqr, u;
378			AtomStamp* current_atom;
379			DirectionalAtom* dAtom;
380	mmeineke	117	int molIndex, molStart, molEnd, nMemb;
381	mmeineke	10
382	chuckv	124
383	mmeineke	117	molIndex = 0;
384	mmeineke	10	index = 0;
385			for( i=0; i<n_components; i++ ){
386	chuckv	124
387	mmeineke	10	for( j=0; j<components_nmol[i]; j++ ){
388	chuckv	124
389	mmeineke	117	molStart = index;
390			nMemb = comp_stamps[i]->getNAtoms();
391	mmeineke	10	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
392	chuckv	124
393	mmeineke	10	current_atom = comp_stamps[i]->getAtom( k );
394	chuckv	124	if( current_atom->haveOrientation() ){
395	mmeineke	10
396	mmeineke	145	dAtom = new DirectionalAtom(index);
397	mmeineke	10	simnfo->n_oriented++;
398			the_atoms[index] = dAtom;
399	chuckv	124
400	mmeineke	10	ux = current_atom->getOrntX();
401			uy = current_atom->getOrntY();
402			uz = current_atom->getOrntZ();
403	chuckv	124
404	mmeineke	10	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
405	chuckv	124
406	mmeineke	10	u = sqrt( uSqr );
407			ux = ux / u;
408			uy = uy / u;
409			uz = uz / u;
410	chuckv	124
411	mmeineke	10	dAtom->setSUx( ux );
412			dAtom->setSUy( uy );
413			dAtom->setSUz( uz );
414			}
415			else{
416	mmeineke	145	the_atoms[index] = new GeneralAtom(index);
417	mmeineke	10	}
418			the_atoms[index]->setType( current_atom->getType() );
419			the_atoms[index]->setIndex( index );
420	chuckv	124
421	mmeineke	10	// increment the index and repeat;
422			index++;
423			}
424	chuckv	124
425	mmeineke	117	molEnd = index -1;
426			the_molecules[molIndex].setNMembers( nMemb );
427			the_molecules[molIndex].setStartAtom( molStart );
428			the_molecules[molIndex].setEndAtom( molEnd );
429			molIndex++;
430
431	mmeineke	10	}
432			}
433	chuckv	124
434	mmeineke	10	the_ff->initializeAtoms();
435			}
436
437			void SimSetup::makeBonds( void ){
438
439			int i, j, k, index, offset;
440			bond_pair* the_bonds;
441			BondStamp* current_bond;
442
443			the_bonds = new bond_pair[tot_bonds];
444			index = 0;
445			offset = 0;
446			for( i=0; i<n_components; i++ ){
447	chuckv	124
448	mmeineke	10	for( j=0; j<components_nmol[i]; j++ ){
449	chuckv	124
450	mmeineke	10	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
451	chuckv	124
452	mmeineke	10	current_bond = comp_stamps[i]->getBond( k );
453			the_bonds[index].a = current_bond->getA() + offset;
454			the_bonds[index].b = current_bond->getB() + offset;
455
456			the_excludes[index].i = the_bonds[index].a;
457			the_excludes[index].j = the_bonds[index].b;
458
459			// increment the index and repeat;
460			index++;
461			}
462			offset += comp_stamps[i]->getNAtoms();
463			}
464			}
465	chuckv	124
466	mmeineke	10	the_ff->initializeBonds( the_bonds );
467			}
468
469			void SimSetup::makeBends( void ){
470
471			int i, j, k, index, offset;
472			bend_set* the_bends;
473			BendStamp* current_bend;
474
475			the_bends = new bend_set[tot_bends];
476			index = 0;
477			offset = 0;
478			for( i=0; i<n_components; i++ ){
479	chuckv	124
480	mmeineke	10	for( j=0; j<components_nmol[i]; j++ ){
481	chuckv	124
482	mmeineke	10	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
483	chuckv	124
484	mmeineke	10	current_bend = comp_stamps[i]->getBend( k );
485			the_bends[index].a = current_bend->getA() + offset;
486			the_bends[index].b = current_bend->getB() + offset;
487			the_bends[index].c = current_bend->getC() + offset;
488
489			the_excludes[index + tot_bonds].i = the_bends[index].a;
490			the_excludes[index + tot_bonds].j = the_bends[index].c;
491
492			// increment the index and repeat;
493			index++;
494			}
495			offset += comp_stamps[i]->getNAtoms();
496			}
497			}
498	chuckv	124
499	mmeineke	10	the_ff->initializeBends( the_bends );
500			}
501
502			void SimSetup::makeTorsions( void ){
503
504			int i, j, k, index, offset;
505			torsion_set* the_torsions;
506			TorsionStamp* current_torsion;
507
508			the_torsions = new torsion_set[tot_torsions];
509			index = 0;
510			offset = 0;
511			for( i=0; i<n_components; i++ ){
512	chuckv	124
513	mmeineke	10	for( j=0; j<components_nmol[i]; j++ ){
514	chuckv	124
515	mmeineke	10	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
516	chuckv	124
517	mmeineke	10	current_torsion = comp_stamps[i]->getTorsion( k );
518			the_torsions[index].a = current_torsion->getA() + offset;
519			the_torsions[index].b = current_torsion->getB() + offset;
520			the_torsions[index].c = current_torsion->getC() + offset;
521			the_torsions[index].d = current_torsion->getD() + offset;
522
523			the_excludes[index + tot_bonds + tot_bends].i = the_torsions[index].a;
524			the_excludes[index + tot_bonds + tot_bends].j = the_torsions[index].d;
525
526			// increment the index and repeat;
527			index++;
528			}
529			offset += comp_stamps[i]->getNAtoms();
530			}
531			}
532	chuckv	124
533	mmeineke	10	the_ff->initializeTorsions( the_torsions );
534			}
535
536			void SimSetup::initFromBass( void ){
537
538			int i, j, k;
539			int n_cells;
540			double cellx, celly, cellz;
541			double temp1, temp2, temp3;
542			int n_per_extra;
543			int n_extra;
544			int have_extra, done;
545
546			temp1 = (double)tot_nmol / 4.0;
547			temp2 = pow( temp1, ( 1.0 / 3.0 ) );
548			temp3 = ceil( temp2 );
549
550			have_extra =0;
551			if( temp2 < temp3 ){ // we have a non-complete lattice
552			have_extra =1;
553
554			n_cells = (int)temp3 - 1;
555			cellx = simnfo->box_x / temp3;
556			celly = simnfo->box_y / temp3;
557			cellz = simnfo->box_z / temp3;
558			n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
559			temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
560			n_per_extra = (int)ceil( temp1 );
561
562			if( n_per_extra > 4){
563			std::cerr << "THere has been an error in constructing the non-complete lattice.\n";
564			exit(8);
565			}
566			}
567			else{
568			n_cells = (int)temp3;
569			cellx = simnfo->box_x / temp3;
570			celly = simnfo->box_y / temp3;
571			cellz = simnfo->box_z / temp3;
572			}
573	chuckv	124
574	mmeineke	10	current_mol = 0;
575			current_comp_mol = 0;
576			current_comp = 0;
577			current_atom_ndx = 0;
578	chuckv	124
579	mmeineke	10	for( i=0; i < n_cells ; i++ ){
580			for( j=0; j < n_cells; j++ ){
581			for( k=0; k < n_cells; k++ ){
582	chuckv	124
583	mmeineke	10	makeElement( i * cellx,
584			j * celly,
585			k * cellz );
586	chuckv	124
587	mmeineke	10	makeElement( i * cellx + 0.5 * cellx,
588			j * celly + 0.5 * celly,
589			k * cellz );
590	chuckv	124
591	mmeineke	10	makeElement( i * cellx,
592			j * celly + 0.5 * celly,
593			k * cellz + 0.5 * cellz );
594	chuckv	124
595	mmeineke	10	makeElement( i * cellx + 0.5 * cellx,
596			j * celly,
597			k * cellz + 0.5 * cellz );
598			}
599			}
600			}
601
602			if( have_extra ){
603			done = 0;
604	chuckv	124
605	mmeineke	10	int start_ndx;
606			for( i=0; i < (n_cells+1) && !done; i++ ){
607			for( j=0; j < (n_cells+1) && !done; j++ ){
608	chuckv	124
609	mmeineke	10	if( i < n_cells ){
610	chuckv	124
611	mmeineke	10	if( j < n_cells ){
612			start_ndx = n_cells;
613			}
614			else start_ndx = 0;
615			}
616			else start_ndx = 0;
617	chuckv	124
618	mmeineke	10	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
619	chuckv	124
620	mmeineke	10	makeElement( i * cellx,
621			j * celly,
622			k * cellz );
623			done = ( current_mol >= tot_nmol );
624	chuckv	124
625	mmeineke	10	if( !done && n_per_extra > 1 ){
626			makeElement( i * cellx + 0.5 * cellx,
627			j * celly + 0.5 * celly,
628			k * cellz );
629			done = ( current_mol >= tot_nmol );
630			}
631	chuckv	124
632	mmeineke	10	if( !done && n_per_extra > 2){
633			makeElement( i * cellx,
634			j * celly + 0.5 * celly,
635			k * cellz + 0.5 * cellz );
636			done = ( current_mol >= tot_nmol );
637			}
638	chuckv	124
639	mmeineke	10	if( !done && n_per_extra > 3){
640			makeElement( i * cellx + 0.5 * cellx,
641			j * celly,
642			k * cellz + 0.5 * cellz );
643			done = ( current_mol >= tot_nmol );
644			}
645			}
646			}
647			}
648			}
649	chuckv	124
650
651	mmeineke	10	for( i=0; i<simnfo->n_atoms; i++ ){
652			simnfo->atoms[i]->set_vx( 0.0 );
653			simnfo->atoms[i]->set_vy( 0.0 );
654			simnfo->atoms[i]->set_vz( 0.0 );
655			}
656			}
657
658			void SimSetup::makeElement( double x, double y, double z ){
659
660			int k;
661			AtomStamp* current_atom;
662			DirectionalAtom* dAtom;
663			double rotMat[3][3];
664
665			for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
666	chuckv	124
667	mmeineke	10	current_atom = comp_stamps[current_comp]->getAtom( k );
668			if( !current_atom->havePosition() ){
669			std::cerr << "Component " << comp_stamps[current_comp]->getID()
670			<< ", atom " << current_atom->getType()
671			<< " does not have a position specified.\n"
672			<< "The initialization routine is unable to give a start"
673			<< " position.\n";
674			exit(8);
675			}
676	chuckv	124
677	mmeineke	10	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
678			the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
679			the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
680	chuckv	124
681	mmeineke	10	if( the_atoms[current_atom_ndx]->isDirectional() ){
682	chuckv	124
683	mmeineke	10	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
684	chuckv	124
685	mmeineke	10	rotMat[0][0] = 1.0;
686			rotMat[0][1] = 0.0;
687			rotMat[0][2] = 0.0;
688
689			rotMat[1][0] = 0.0;
690			rotMat[1][1] = 1.0;
691			rotMat[1][2] = 0.0;
692
693			rotMat[2][0] = 0.0;
694			rotMat[2][1] = 0.0;
695			rotMat[2][2] = 1.0;
696
697			dAtom->setA( rotMat );
698			}
699
700			current_atom_ndx++;
701			}
702	chuckv	124
703	mmeineke	10	current_mol++;
704			current_comp_mol++;
705
706			if( current_comp_mol >= components_nmol[current_comp] ){
707	chuckv	124
708	mmeineke	10	current_comp_mol = 0;
709			current_comp++;
710			}
711			}