mdtools/interface_implementation/SimSetup.cpp

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

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

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 MPI
  mpiEventInit();
#endif
  yacc_BASS( fileName );
#ifdef MPI
  throwMPIEvent(NULL);
#endif

}

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

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

}
#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];
  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;
          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;
        }
        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:	124
Committed:	Mon Sep 30 20:35:42 2002 UTC (21 years, 9 months ago) by chuckv
File size:	16950 byte(s)
Log Message:	* empty log message *
#	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	chuckv	124	#include "mpiInterface.h"
10	mmeineke	10
11			SimSetup::SimSetup(){
12			stamps = new MakeStamps();
13			globals = new Globals();
14			}
15
16			SimSetup::~SimSetup(){
17			delete stamps;
18			delete globals;
19			}
20
21			void SimSetup::parseFile( char* fileName ){
22
23			inFileName = fileName;
24			set_interface_stamps( stamps, globals );
25	chuckv	124	#ifdef MPI
26			mpiEventInit();
27			#endif
28	mmeineke	10	yacc_BASS( fileName );
29	chuckv	124	#ifdef MPI
30			throwMPIEvent(NULL);
31			#endif
32
33	mmeineke	10	}
34
35	chuckv	124	#ifdef MPI
36			void SimSetup::receiveParse(void){
37
38			set_interface_stamps( stamps, globals );
39			mpiEventInit();
40			mpiEventLoop();
41
42			}
43			#endif
44
45	mmeineke	10	void SimSetup::createSim( void ){
46
47			MakeStamps *the_stamps;
48			Globals* the_globals;
49			int i;
50
51			// get the stamps and globals;
52			the_stamps = stamps;
53			the_globals = globals;
54
55			// set the easy ones first
56			simnfo->target_temp = the_globals->getTargetTemp();
57			simnfo->dt = the_globals->getDt();
58			simnfo->run_time = the_globals->getRunTime();
59
60			// get the ones we know are there, yet still may need some work.
61			n_components = the_globals->getNComponents();
62			strcpy( force_field, the_globals->getForceField() );
63			strcpy( ensemble, the_globals->getEnsemble() );
64	chuckv	124
65	mmeineke	10	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
66			else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
67			else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
68			else{
69	chuckv	124	std::cerr<< "SimSetup Error. Unrecognized force field -> "
70	mmeineke	10	<< force_field << "\n";
71			exit(8);
72			}
73
74			// get the components and calculate the tot_nMol and indvidual n_mol
75			the_components = the_globals->getComponents();
76			components_nmol = new int[n_components];
77			comp_stamps = new MoleculeStamp*[n_components];
78	chuckv	124
79	mmeineke	10	if( !the_globals->haveNMol() ){
80	chuckv	124	// we don't have the total number of molecules, so we assume it is
81	mmeineke	10	// given in each component
82
83			tot_nmol = 0;
84			for( i=0; i<n_components; i++ ){
85	chuckv	124
86	mmeineke	10	if( !the_components[i]->haveNMol() ){
87			// we have a problem
88			std::cerr << "SimSetup Error. No global NMol or component NMol"
89			<< " given. Cannot calculate the number of atoms.\n";
90			exit( 8 );
91			}
92
93			tot_nmol += the_components[i]->getNMol();
94			components_nmol[i] = the_components[i]->getNMol();
95			}
96			}
97			else{
98			std::cerr << "NOT A SUPPORTED FEATURE\n";
99	chuckv	124
100	mmeineke	10	// tot_nmol = the_globals->getNMol();
101	chuckv	124
102	mmeineke	10	// //we have the total number of molecules, now we check for molfractions
103			// for( i=0; i<n_components; i++ ){
104	chuckv	124
105	mmeineke	10	// if( !the_components[i]->haveMolFraction() ){
106	chuckv	124
107	mmeineke	10	// if( !the_components[i]->haveNMol() ){
108			// //we have a problem
109			// std::cerr << "SimSetup error. Neither molFraction nor "
110			// << " nMol was given in component
111
112			}
113
114			// make an array of molecule stamps that match the components used.
115
116			for( i=0; i<n_components; i++ ){
117
118	chuckv	124	comp_stamps[i] =
119	mmeineke	10	the_stamps->getMolecule( the_components[i]->getType() );
120			}
121
122
123	chuckv	124
124	mmeineke	10	// caclulate the number of atoms, bonds, bends and torsions
125
126			tot_atoms = 0;
127			tot_bonds = 0;
128			tot_bends = 0;
129			tot_torsions = 0;
130			for( i=0; i<n_components; i++ ){
131	chuckv	124
132	mmeineke	10	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
133			tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
134			tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
135			tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
136			}
137	chuckv	124
138	mmeineke	10	tot_SRI = tot_bonds + tot_bends + tot_torsions;
139	chuckv	124
140	mmeineke	10	simnfo->n_atoms = tot_atoms;
141			simnfo->n_bonds = tot_bonds;
142			simnfo->n_bends = tot_bends;
143			simnfo->n_torsions = tot_torsions;
144			simnfo->n_SRI = tot_SRI;
145
146			// create the atom and short range interaction arrays
147	chuckv	124
148	mmeineke	10	the_atoms = new Atom*[tot_atoms];
149	mmeineke	113	the_molecules = new Molecule[tot_nmol];
150	chuckv	124
151
152	mmeineke	10	if( tot_SRI ){
153			the_sris = new SRI*[tot_SRI];
154			the_excludes = new ex_pair[tot_SRI];
155			}
156
157			// set the arrays into the SimInfo object
158
159			simnfo->atoms = the_atoms;
160			simnfo->sr_interactions = the_sris;
161			simnfo->n_exclude = tot_SRI;
162			simnfo->excludes = the_excludes;
163
164	chuckv	124
165	mmeineke	10	// initialize the arrays
166	chuckv	124
167	mmeineke	10	the_ff->setSimInfo( simnfo );
168	chuckv	124
169	mmeineke	10	makeAtoms();
170
171			if( tot_bonds ){
172			makeBonds();
173			}
174
175			if( tot_bends ){
176			makeBends();
177			}
178
179			if( tot_torsions ){
180			makeTorsions();
181			}
182
183			// makeMolecules();
184
185			// get some of the tricky things that may still be in the globals
186
187			if( simnfo->n_dipoles ){
188
189			if( !the_globals->haveRRF() ){
190			std::cerr << "SimSetup Error, system has dipoles, but no rRF was set.\n";
191			exit(8);
192			}
193			if( !the_globals->haveDielectric() ){
194			std::cerr << "SimSetup Error, system has dipoles, but no"
195			<< " dielectric was set.\n";
196			exit(8);
197			}
198
199			simnfo->rRF = the_globals->getRRF();
200			simnfo->dielectric = the_globals->getDielectric();
201			}
202
203			if( the_globals->haveBox() ){
204			simnfo->box_x = the_globals->getBox();
205			simnfo->box_y = the_globals->getBox();
206			simnfo->box_z = the_globals->getBox();
207			}
208			else if( the_globals->haveDensity() ){
209	chuckv	124
210	mmeineke	10	double vol;
211			vol = (double)tot_nmol / the_globals->getDensity();
212			simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
213			simnfo->box_y = simnfo->box_x;
214			simnfo->box_z = simnfo->box_x;
215			}
216			else{
217			if( !the_globals->haveBoxX() ){
218			std::cerr << "SimSetup error, no periodic BoxX size given.\n";
219			exit(8);
220			}
221			simnfo->box_x = the_globals->getBoxX();
222
223			if( !the_globals->haveBoxY() ){
224			std::cerr << "SimSetup error, no periodic BoxY size given.\n";
225			exit(8);
226			}
227			simnfo->box_y = the_globals->getBoxY();
228
229			if( !the_globals->haveBoxZ() ){
230			std::cerr << "SimSetup error, no periodic BoxZ size given.\n";
231			exit(8);
232			}
233			simnfo->box_z = the_globals->getBoxZ();
234			}
235
236	chuckv	124
237			// if( the_globals->haveInitialConfig() ){
238			// InitializeFromFile* fileInit;
239			// fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
240
241			// fileInit->read_xyz( simnfo ); // default velocities on
242
243			// delete fileInit;
244			// }
245			// else{
246
247	mmeineke	10	initFromBass();
248
249
250	chuckv	124	// }
251
252			// if( the_globals->haveFinalConfig() ){
253			// strcpy( simnfo->finalName, the_globals->getFinalConfig() );
254			// }
255			// else{
256			// strcpy( simnfo->finalName, inFileName );
257			// char* endTest;
258			// int nameLength = strlen( simnfo->finalName );
259			// endTest = &(simnfo->finalName[nameLength - 5]);
260			// if( !strcmp( endTest, ".bass" ) ){
261			// strcpy( endTest, ".eor" );
262			// }
263			// else if( !strcmp( endTest, ".BASS" ) ){
264			// strcpy( endTest, ".eor" );
265			// }
266			// else{
267			// endTest = &(simnfo->finalName[nameLength - 4]);
268			// if( !strcmp( endTest, ".bss" ) ){
269			// strcpy( endTest, ".eor" );
270			// }
271			// else if( !strcmp( endTest, ".mdl" ) ){
272			// strcpy( endTest, ".eor" );
273			// }
274			// else{
275			// strcat( simnfo->finalName, ".eor" );
276			// }
277			// }
278			// }
279
280			// // make the sample and status out names
281
282			// strcpy( simnfo->sampleName, inFileName );
283			// char* endTest;
284			// int nameLength = strlen( simnfo->sampleName );
285			// endTest = &(simnfo->sampleName[nameLength - 5]);
286			// if( !strcmp( endTest, ".bass" ) ){
287			// strcpy( endTest, ".dump" );
288			// }
289			// else if( !strcmp( endTest, ".BASS" ) ){
290			// strcpy( endTest, ".dump" );
291			// }
292			// else{
293			// endTest = &(simnfo->sampleName[nameLength - 4]);
294			// if( !strcmp( endTest, ".bss" ) ){
295			// strcpy( endTest, ".dump" );
296			// }
297			// else if( !strcmp( endTest, ".mdl" ) ){
298			// strcpy( endTest, ".dump" );
299			// }
300			// else{
301			// strcat( simnfo->sampleName, ".dump" );
302			// }
303			// }
304
305			// strcpy( simnfo->statusName, inFileName );
306			// nameLength = strlen( simnfo->statusName );
307			// endTest = &(simnfo->statusName[nameLength - 5]);
308			// if( !strcmp( endTest, ".bass" ) ){
309			// strcpy( endTest, ".stat" );
310			// }
311			// else if( !strcmp( endTest, ".BASS" ) ){
312			// strcpy( endTest, ".stat" );
313			// }
314			// else{
315			// endTest = &(simnfo->statusName[nameLength - 4]);
316			// if( !strcmp( endTest, ".bss" ) ){
317			// strcpy( endTest, ".stat" );
318			// }
319			// else if( !strcmp( endTest, ".mdl" ) ){
320			// strcpy( endTest, ".stat" );
321			// }
322			// else{
323			// strcat( simnfo->statusName, ".stat" );
324			// }
325			// }
326
327
328	mmeineke	10	// set the status, sample, and themal kick times
329
330			if( the_globals->haveSampleTime() ){
331	chuckv	124	simnfo->sampleTime = the_globals->getSampleTime();
332	mmeineke	10	simnfo->statusTime = simnfo->sampleTime;
333			simnfo->thermalTime = simnfo->sampleTime;
334			}
335			else{
336	chuckv	124	simnfo->sampleTime = the_globals->getRunTime();
337	mmeineke	10	simnfo->statusTime = simnfo->sampleTime;
338			simnfo->thermalTime = simnfo->sampleTime;
339			}
340
341			if( the_globals->haveStatusTime() ){
342			simnfo->statusTime = the_globals->getStatusTime();
343			}
344
345			if( the_globals->haveThermalTime() ){
346			simnfo->thermalTime = the_globals->getThermalTime();
347			}
348
349			// check for the temperature set flag
350
351			if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
352	chuckv	124
353
354	mmeineke	10	// make the longe range forces and the integrator
355	chuckv	124
356	mmeineke	10	new AllLong( simnfo );
357	chuckv	124
358	mmeineke	10	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo );
359			if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo );
360			if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo );
361			}
362
363			void SimSetup::makeAtoms( void ){
364	chuckv	124
365	mmeineke	10	int i, j, k, index;
366			double ux, uy, uz, uSqr, u;
367			AtomStamp* current_atom;
368			DirectionalAtom* dAtom;
369	mmeineke	117	int molIndex, molStart, molEnd, nMemb;
370	mmeineke	10
371	chuckv	124
372	mmeineke	117	molIndex = 0;
373	mmeineke	10	index = 0;
374			for( i=0; i<n_components; i++ ){
375	chuckv	124
376	mmeineke	10	for( j=0; j<components_nmol[i]; j++ ){
377	chuckv	124
378	mmeineke	117	molStart = index;
379			nMemb = comp_stamps[i]->getNAtoms();
380	mmeineke	10	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
381	chuckv	124
382	mmeineke	10	current_atom = comp_stamps[i]->getAtom( k );
383	chuckv	124	if( current_atom->haveOrientation() ){
384	mmeineke	10
385			dAtom = new DirectionalAtom;
386			simnfo->n_oriented++;
387			the_atoms[index] = dAtom;
388	chuckv	124
389	mmeineke	10	ux = current_atom->getOrntX();
390			uy = current_atom->getOrntY();
391			uz = current_atom->getOrntZ();
392	chuckv	124
393	mmeineke	10	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
394	chuckv	124
395	mmeineke	10	u = sqrt( uSqr );
396			ux = ux / u;
397			uy = uy / u;
398			uz = uz / u;
399	chuckv	124
400	mmeineke	10	dAtom->setSUx( ux );
401			dAtom->setSUy( uy );
402			dAtom->setSUz( uz );
403			}
404			else{
405			the_atoms[index] = new GeneralAtom;
406			}
407			the_atoms[index]->setType( current_atom->getType() );
408			the_atoms[index]->setIndex( index );
409	chuckv	124
410	mmeineke	10	// increment the index and repeat;
411			index++;
412			}
413	chuckv	124
414	mmeineke	117	molEnd = index -1;
415			the_molecules[molIndex].setNMembers( nMemb );
416			the_molecules[molIndex].setStartAtom( molStart );
417			the_molecules[molIndex].setEndAtom( molEnd );
418			molIndex++;
419
420	mmeineke	10	}
421			}
422	chuckv	124
423	mmeineke	10	the_ff->initializeAtoms();
424			}
425
426			void SimSetup::makeBonds( void ){
427
428			int i, j, k, index, offset;
429			bond_pair* the_bonds;
430			BondStamp* current_bond;
431
432			the_bonds = new bond_pair[tot_bonds];
433			index = 0;
434			offset = 0;
435			for( i=0; i<n_components; i++ ){
436	chuckv	124
437	mmeineke	10	for( j=0; j<components_nmol[i]; j++ ){
438	chuckv	124
439	mmeineke	10	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
440	chuckv	124
441	mmeineke	10	current_bond = comp_stamps[i]->getBond( k );
442			the_bonds[index].a = current_bond->getA() + offset;
443			the_bonds[index].b = current_bond->getB() + offset;
444
445			the_excludes[index].i = the_bonds[index].a;
446			the_excludes[index].j = the_bonds[index].b;
447
448			// increment the index and repeat;
449			index++;
450			}
451			offset += comp_stamps[i]->getNAtoms();
452			}
453			}
454	chuckv	124
455	mmeineke	10	the_ff->initializeBonds( the_bonds );
456			}
457
458			void SimSetup::makeBends( void ){
459
460			int i, j, k, index, offset;
461			bend_set* the_bends;
462			BendStamp* current_bend;
463
464			the_bends = new bend_set[tot_bends];
465			index = 0;
466			offset = 0;
467			for( i=0; i<n_components; i++ ){
468	chuckv	124
469	mmeineke	10	for( j=0; j<components_nmol[i]; j++ ){
470	chuckv	124
471	mmeineke	10	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
472	chuckv	124
473	mmeineke	10	current_bend = comp_stamps[i]->getBend( k );
474			the_bends[index].a = current_bend->getA() + offset;
475			the_bends[index].b = current_bend->getB() + offset;
476			the_bends[index].c = current_bend->getC() + offset;
477
478			the_excludes[index + tot_bonds].i = the_bends[index].a;
479			the_excludes[index + tot_bonds].j = the_bends[index].c;
480
481			// increment the index and repeat;
482			index++;
483			}
484			offset += comp_stamps[i]->getNAtoms();
485			}
486			}
487	chuckv	124
488	mmeineke	10	the_ff->initializeBends( the_bends );
489			}
490
491			void SimSetup::makeTorsions( void ){
492
493			int i, j, k, index, offset;
494			torsion_set* the_torsions;
495			TorsionStamp* current_torsion;
496
497			the_torsions = new torsion_set[tot_torsions];
498			index = 0;
499			offset = 0;
500			for( i=0; i<n_components; i++ ){
501	chuckv	124
502	mmeineke	10	for( j=0; j<components_nmol[i]; j++ ){
503	chuckv	124
504	mmeineke	10	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
505	chuckv	124
506	mmeineke	10	current_torsion = comp_stamps[i]->getTorsion( k );
507			the_torsions[index].a = current_torsion->getA() + offset;
508			the_torsions[index].b = current_torsion->getB() + offset;
509			the_torsions[index].c = current_torsion->getC() + offset;
510			the_torsions[index].d = current_torsion->getD() + offset;
511
512			the_excludes[index + tot_bonds + tot_bends].i = the_torsions[index].a;
513			the_excludes[index + tot_bonds + tot_bends].j = the_torsions[index].d;
514
515			// increment the index and repeat;
516			index++;
517			}
518			offset += comp_stamps[i]->getNAtoms();
519			}
520			}
521	chuckv	124
522	mmeineke	10	the_ff->initializeTorsions( the_torsions );
523			}
524
525			void SimSetup::initFromBass( void ){
526
527			int i, j, k;
528			int n_cells;
529			double cellx, celly, cellz;
530			double temp1, temp2, temp3;
531			int n_per_extra;
532			int n_extra;
533			int have_extra, done;
534
535			temp1 = (double)tot_nmol / 4.0;
536			temp2 = pow( temp1, ( 1.0 / 3.0 ) );
537			temp3 = ceil( temp2 );
538
539			have_extra =0;
540			if( temp2 < temp3 ){ // we have a non-complete lattice
541			have_extra =1;
542
543			n_cells = (int)temp3 - 1;
544			cellx = simnfo->box_x / temp3;
545			celly = simnfo->box_y / temp3;
546			cellz = simnfo->box_z / temp3;
547			n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
548			temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
549			n_per_extra = (int)ceil( temp1 );
550
551			if( n_per_extra > 4){
552			std::cerr << "THere has been an error in constructing the non-complete lattice.\n";
553			exit(8);
554			}
555			}
556			else{
557			n_cells = (int)temp3;
558			cellx = simnfo->box_x / temp3;
559			celly = simnfo->box_y / temp3;
560			cellz = simnfo->box_z / temp3;
561			}
562	chuckv	124
563	mmeineke	10	current_mol = 0;
564			current_comp_mol = 0;
565			current_comp = 0;
566			current_atom_ndx = 0;
567	chuckv	124
568	mmeineke	10	for( i=0; i < n_cells ; i++ ){
569			for( j=0; j < n_cells; j++ ){
570			for( k=0; k < n_cells; k++ ){
571	chuckv	124
572	mmeineke	10	makeElement( i * cellx,
573			j * celly,
574			k * cellz );
575	chuckv	124
576	mmeineke	10	makeElement( i * cellx + 0.5 * cellx,
577			j * celly + 0.5 * celly,
578			k * cellz );
579	chuckv	124
580	mmeineke	10	makeElement( i * cellx,
581			j * celly + 0.5 * celly,
582			k * cellz + 0.5 * cellz );
583	chuckv	124
584	mmeineke	10	makeElement( i * cellx + 0.5 * cellx,
585			j * celly,
586			k * cellz + 0.5 * cellz );
587			}
588			}
589			}
590
591			if( have_extra ){
592			done = 0;
593	chuckv	124
594	mmeineke	10	int start_ndx;
595			for( i=0; i < (n_cells+1) && !done; i++ ){
596			for( j=0; j < (n_cells+1) && !done; j++ ){
597	chuckv	124
598	mmeineke	10	if( i < n_cells ){
599	chuckv	124
600	mmeineke	10	if( j < n_cells ){
601			start_ndx = n_cells;
602			}
603			else start_ndx = 0;
604			}
605			else start_ndx = 0;
606	chuckv	124
607	mmeineke	10	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
608	chuckv	124
609	mmeineke	10	makeElement( i * cellx,
610			j * celly,
611			k * cellz );
612			done = ( current_mol >= tot_nmol );
613	chuckv	124
614	mmeineke	10	if( !done && n_per_extra > 1 ){
615			makeElement( i * cellx + 0.5 * cellx,
616			j * celly + 0.5 * celly,
617			k * cellz );
618			done = ( current_mol >= tot_nmol );
619			}
620	chuckv	124
621	mmeineke	10	if( !done && n_per_extra > 2){
622			makeElement( i * cellx,
623			j * celly + 0.5 * celly,
624			k * cellz + 0.5 * cellz );
625			done = ( current_mol >= tot_nmol );
626			}
627	chuckv	124
628	mmeineke	10	if( !done && n_per_extra > 3){
629			makeElement( i * cellx + 0.5 * cellx,
630			j * celly,
631			k * cellz + 0.5 * cellz );
632			done = ( current_mol >= tot_nmol );
633			}
634			}
635			}
636			}
637			}
638	chuckv	124
639
640	mmeineke	10	for( i=0; i<simnfo->n_atoms; i++ ){
641			simnfo->atoms[i]->set_vx( 0.0 );
642			simnfo->atoms[i]->set_vy( 0.0 );
643			simnfo->atoms[i]->set_vz( 0.0 );
644			}
645			}
646
647			void SimSetup::makeElement( double x, double y, double z ){
648
649			int k;
650			AtomStamp* current_atom;
651			DirectionalAtom* dAtom;
652			double rotMat[3][3];
653
654			for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
655	chuckv	124
656	mmeineke	10	current_atom = comp_stamps[current_comp]->getAtom( k );
657			if( !current_atom->havePosition() ){
658			std::cerr << "Component " << comp_stamps[current_comp]->getID()
659			<< ", atom " << current_atom->getType()
660			<< " does not have a position specified.\n"
661			<< "The initialization routine is unable to give a start"
662			<< " position.\n";
663			exit(8);
664			}
665	chuckv	124
666	mmeineke	10	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
667			the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
668			the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
669	chuckv	124
670	mmeineke	10	if( the_atoms[current_atom_ndx]->isDirectional() ){
671	chuckv	124
672	mmeineke	10	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
673	chuckv	124
674	mmeineke	10	rotMat[0][0] = 1.0;
675			rotMat[0][1] = 0.0;
676			rotMat[0][2] = 0.0;
677
678			rotMat[1][0] = 0.0;
679			rotMat[1][1] = 1.0;
680			rotMat[1][2] = 0.0;
681
682			rotMat[2][0] = 0.0;
683			rotMat[2][1] = 0.0;
684			rotMat[2][2] = 1.0;
685
686			dAtom->setA( rotMat );
687			}
688
689			current_atom_ndx++;
690			}
691	chuckv	124
692	mmeineke	10	current_mol++;
693			current_comp_mol++;
694
695			if( current_comp_mol >= components_nmol[current_comp] ){
696	chuckv	124
697	mmeineke	10	current_comp_mol = 0;
698			current_comp++;
699			}
700			}