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

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:	128
Committed:	Thu Oct 3 21:52:46 2002 UTC (21 years, 9 months ago) by chuckv
File size:	17074 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	chuckv	128	void SimSetup::testMe(void){
46			bassDiag* dumpMe = new bassDiag(globals,stamps);
47			dumpMe->dumpStamps();
48			delete dumpMe;
49			}
50
51	mmeineke	10	void SimSetup::createSim( void ){
52
53			MakeStamps *the_stamps;
54			Globals* the_globals;
55			int i;
56
57			// get the stamps and globals;
58			the_stamps = stamps;
59			the_globals = globals;
60
61			// set the easy ones first
62			simnfo->target_temp = the_globals->getTargetTemp();
63			simnfo->dt = the_globals->getDt();
64			simnfo->run_time = the_globals->getRunTime();
65
66			// get the ones we know are there, yet still may need some work.
67			n_components = the_globals->getNComponents();
68			strcpy( force_field, the_globals->getForceField() );
69			strcpy( ensemble, the_globals->getEnsemble() );
70	chuckv	124
71	mmeineke	10	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
72			else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
73			else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
74			else{
75	chuckv	124	std::cerr<< "SimSetup Error. Unrecognized force field -> "
76	mmeineke	10	<< force_field << "\n";
77			exit(8);
78			}
79
80			// get the components and calculate the tot_nMol and indvidual n_mol
81			the_components = the_globals->getComponents();
82			components_nmol = new int[n_components];
83			comp_stamps = new MoleculeStamp*[n_components];
84	chuckv	124
85	mmeineke	10	if( !the_globals->haveNMol() ){
86	chuckv	124	// we don't have the total number of molecules, so we assume it is
87	mmeineke	10	// given in each component
88
89			tot_nmol = 0;
90			for( i=0; i<n_components; i++ ){
91	chuckv	124
92	mmeineke	10	if( !the_components[i]->haveNMol() ){
93			// we have a problem
94			std::cerr << "SimSetup Error. No global NMol or component NMol"
95			<< " given. Cannot calculate the number of atoms.\n";
96			exit( 8 );
97			}
98
99			tot_nmol += the_components[i]->getNMol();
100			components_nmol[i] = the_components[i]->getNMol();
101			}
102			}
103			else{
104			std::cerr << "NOT A SUPPORTED FEATURE\n";
105	chuckv	124
106	mmeineke	10	// tot_nmol = the_globals->getNMol();
107	chuckv	124
108	mmeineke	10	// //we have the total number of molecules, now we check for molfractions
109			// for( i=0; i<n_components; i++ ){
110	chuckv	124
111	mmeineke	10	// if( !the_components[i]->haveMolFraction() ){
112	chuckv	124
113	mmeineke	10	// if( !the_components[i]->haveNMol() ){
114			// //we have a problem
115			// std::cerr << "SimSetup error. Neither molFraction nor "
116			// << " nMol was given in component
117
118			}
119
120			// make an array of molecule stamps that match the components used.
121
122			for( i=0; i<n_components; i++ ){
123
124	chuckv	124	comp_stamps[i] =
125	mmeineke	10	the_stamps->getMolecule( the_components[i]->getType() );
126			}
127
128
129	chuckv	124
130	mmeineke	10	// caclulate the number of atoms, bonds, bends and torsions
131
132			tot_atoms = 0;
133			tot_bonds = 0;
134			tot_bends = 0;
135			tot_torsions = 0;
136			for( i=0; i<n_components; i++ ){
137	chuckv	124
138	mmeineke	10	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
139			tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
140			tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
141			tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
142			}
143	chuckv	124
144	mmeineke	10	tot_SRI = tot_bonds + tot_bends + tot_torsions;
145	chuckv	124
146	mmeineke	10	simnfo->n_atoms = tot_atoms;
147			simnfo->n_bonds = tot_bonds;
148			simnfo->n_bends = tot_bends;
149			simnfo->n_torsions = tot_torsions;
150			simnfo->n_SRI = tot_SRI;
151
152			// create the atom and short range interaction arrays
153	chuckv	124
154	mmeineke	10	the_atoms = new Atom*[tot_atoms];
155	mmeineke	113	the_molecules = new Molecule[tot_nmol];
156	chuckv	124
157
158	mmeineke	10	if( tot_SRI ){
159			the_sris = new SRI*[tot_SRI];
160			the_excludes = new ex_pair[tot_SRI];
161			}
162
163			// set the arrays into the SimInfo object
164
165			simnfo->atoms = the_atoms;
166			simnfo->sr_interactions = the_sris;
167			simnfo->n_exclude = tot_SRI;
168			simnfo->excludes = the_excludes;
169
170	chuckv	124
171	mmeineke	10	// initialize the arrays
172	chuckv	124
173	mmeineke	10	the_ff->setSimInfo( simnfo );
174	chuckv	124
175	mmeineke	10	makeAtoms();
176
177			if( tot_bonds ){
178			makeBonds();
179			}
180
181			if( tot_bends ){
182			makeBends();
183			}
184
185			if( tot_torsions ){
186			makeTorsions();
187			}
188
189			// makeMolecules();
190
191			// get some of the tricky things that may still be in the globals
192
193			if( simnfo->n_dipoles ){
194
195			if( !the_globals->haveRRF() ){
196			std::cerr << "SimSetup Error, system has dipoles, but no rRF was set.\n";
197			exit(8);
198			}
199			if( !the_globals->haveDielectric() ){
200			std::cerr << "SimSetup Error, system has dipoles, but no"
201			<< " dielectric was set.\n";
202			exit(8);
203			}
204
205			simnfo->rRF = the_globals->getRRF();
206			simnfo->dielectric = the_globals->getDielectric();
207			}
208
209			if( the_globals->haveBox() ){
210			simnfo->box_x = the_globals->getBox();
211			simnfo->box_y = the_globals->getBox();
212			simnfo->box_z = the_globals->getBox();
213			}
214			else if( the_globals->haveDensity() ){
215	chuckv	124
216	mmeineke	10	double vol;
217			vol = (double)tot_nmol / the_globals->getDensity();
218			simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
219			simnfo->box_y = simnfo->box_x;
220			simnfo->box_z = simnfo->box_x;
221			}
222			else{
223			if( !the_globals->haveBoxX() ){
224			std::cerr << "SimSetup error, no periodic BoxX size given.\n";
225			exit(8);
226			}
227			simnfo->box_x = the_globals->getBoxX();
228
229			if( !the_globals->haveBoxY() ){
230			std::cerr << "SimSetup error, no periodic BoxY size given.\n";
231			exit(8);
232			}
233			simnfo->box_y = the_globals->getBoxY();
234
235			if( !the_globals->haveBoxZ() ){
236			std::cerr << "SimSetup error, no periodic BoxZ size given.\n";
237			exit(8);
238			}
239			simnfo->box_z = the_globals->getBoxZ();
240			}
241
242	chuckv	124
243			// if( the_globals->haveInitialConfig() ){
244			// InitializeFromFile* fileInit;
245			// fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
246
247			// fileInit->read_xyz( simnfo ); // default velocities on
248
249			// delete fileInit;
250			// }
251			// else{
252
253	mmeineke	10	initFromBass();
254
255
256	chuckv	124	// }
257
258			// if( the_globals->haveFinalConfig() ){
259			// strcpy( simnfo->finalName, the_globals->getFinalConfig() );
260			// }
261			// else{
262			// strcpy( simnfo->finalName, inFileName );
263			// char* endTest;
264			// int nameLength = strlen( simnfo->finalName );
265			// endTest = &(simnfo->finalName[nameLength - 5]);
266			// if( !strcmp( endTest, ".bass" ) ){
267			// strcpy( endTest, ".eor" );
268			// }
269			// else if( !strcmp( endTest, ".BASS" ) ){
270			// strcpy( endTest, ".eor" );
271			// }
272			// else{
273			// endTest = &(simnfo->finalName[nameLength - 4]);
274			// if( !strcmp( endTest, ".bss" ) ){
275			// strcpy( endTest, ".eor" );
276			// }
277			// else if( !strcmp( endTest, ".mdl" ) ){
278			// strcpy( endTest, ".eor" );
279			// }
280			// else{
281			// strcat( simnfo->finalName, ".eor" );
282			// }
283			// }
284			// }
285
286			// // make the sample and status out names
287
288			// strcpy( simnfo->sampleName, inFileName );
289			// char* endTest;
290			// int nameLength = strlen( simnfo->sampleName );
291			// endTest = &(simnfo->sampleName[nameLength - 5]);
292			// if( !strcmp( endTest, ".bass" ) ){
293			// strcpy( endTest, ".dump" );
294			// }
295			// else if( !strcmp( endTest, ".BASS" ) ){
296			// strcpy( endTest, ".dump" );
297			// }
298			// else{
299			// endTest = &(simnfo->sampleName[nameLength - 4]);
300			// if( !strcmp( endTest, ".bss" ) ){
301			// strcpy( endTest, ".dump" );
302			// }
303			// else if( !strcmp( endTest, ".mdl" ) ){
304			// strcpy( endTest, ".dump" );
305			// }
306			// else{
307			// strcat( simnfo->sampleName, ".dump" );
308			// }
309			// }
310
311			// strcpy( simnfo->statusName, inFileName );
312			// nameLength = strlen( simnfo->statusName );
313			// endTest = &(simnfo->statusName[nameLength - 5]);
314			// if( !strcmp( endTest, ".bass" ) ){
315			// strcpy( endTest, ".stat" );
316			// }
317			// else if( !strcmp( endTest, ".BASS" ) ){
318			// strcpy( endTest, ".stat" );
319			// }
320			// else{
321			// endTest = &(simnfo->statusName[nameLength - 4]);
322			// if( !strcmp( endTest, ".bss" ) ){
323			// strcpy( endTest, ".stat" );
324			// }
325			// else if( !strcmp( endTest, ".mdl" ) ){
326			// strcpy( endTest, ".stat" );
327			// }
328			// else{
329			// strcat( simnfo->statusName, ".stat" );
330			// }
331			// }
332
333
334	mmeineke	10	// set the status, sample, and themal kick times
335
336			if( the_globals->haveSampleTime() ){
337	chuckv	124	simnfo->sampleTime = the_globals->getSampleTime();
338	mmeineke	10	simnfo->statusTime = simnfo->sampleTime;
339			simnfo->thermalTime = simnfo->sampleTime;
340			}
341			else{
342	chuckv	124	simnfo->sampleTime = the_globals->getRunTime();
343	mmeineke	10	simnfo->statusTime = simnfo->sampleTime;
344			simnfo->thermalTime = simnfo->sampleTime;
345			}
346
347			if( the_globals->haveStatusTime() ){
348			simnfo->statusTime = the_globals->getStatusTime();
349			}
350
351			if( the_globals->haveThermalTime() ){
352			simnfo->thermalTime = the_globals->getThermalTime();
353			}
354
355			// check for the temperature set flag
356
357			if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
358	chuckv	124
359
360	mmeineke	10	// make the longe range forces and the integrator
361	chuckv	124
362	mmeineke	10	new AllLong( simnfo );
363	chuckv	124
364	mmeineke	10	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo );
365			if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo );
366			if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo );
367			}
368
369			void SimSetup::makeAtoms( void ){
370	chuckv	124
371	mmeineke	10	int i, j, k, index;
372			double ux, uy, uz, uSqr, u;
373			AtomStamp* current_atom;
374			DirectionalAtom* dAtom;
375	mmeineke	117	int molIndex, molStart, molEnd, nMemb;
376	mmeineke	10
377	chuckv	124
378	mmeineke	117	molIndex = 0;
379	mmeineke	10	index = 0;
380			for( i=0; i<n_components; i++ ){
381	chuckv	124
382	mmeineke	10	for( j=0; j<components_nmol[i]; j++ ){
383	chuckv	124
384	mmeineke	117	molStart = index;
385			nMemb = comp_stamps[i]->getNAtoms();
386	mmeineke	10	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
387	chuckv	124
388	mmeineke	10	current_atom = comp_stamps[i]->getAtom( k );
389	chuckv	124	if( current_atom->haveOrientation() ){
390	mmeineke	10
391			dAtom = new DirectionalAtom;
392			simnfo->n_oriented++;
393			the_atoms[index] = dAtom;
394	chuckv	124
395	mmeineke	10	ux = current_atom->getOrntX();
396			uy = current_atom->getOrntY();
397			uz = current_atom->getOrntZ();
398	chuckv	124
399	mmeineke	10	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
400	chuckv	124
401	mmeineke	10	u = sqrt( uSqr );
402			ux = ux / u;
403			uy = uy / u;
404			uz = uz / u;
405	chuckv	124
406	mmeineke	10	dAtom->setSUx( ux );
407			dAtom->setSUy( uy );
408			dAtom->setSUz( uz );
409			}
410			else{
411			the_atoms[index] = new GeneralAtom;
412			}
413			the_atoms[index]->setType( current_atom->getType() );
414			the_atoms[index]->setIndex( index );
415	chuckv	124
416	mmeineke	10	// increment the index and repeat;
417			index++;
418			}
419	chuckv	124
420	mmeineke	117	molEnd = index -1;
421			the_molecules[molIndex].setNMembers( nMemb );
422			the_molecules[molIndex].setStartAtom( molStart );
423			the_molecules[molIndex].setEndAtom( molEnd );
424			molIndex++;
425
426	mmeineke	10	}
427			}
428	chuckv	124
429	mmeineke	10	the_ff->initializeAtoms();
430			}
431
432			void SimSetup::makeBonds( void ){
433
434			int i, j, k, index, offset;
435			bond_pair* the_bonds;
436			BondStamp* current_bond;
437
438			the_bonds = new bond_pair[tot_bonds];
439			index = 0;
440			offset = 0;
441			for( i=0; i<n_components; i++ ){
442	chuckv	124
443	mmeineke	10	for( j=0; j<components_nmol[i]; j++ ){
444	chuckv	124
445	mmeineke	10	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
446	chuckv	124
447	mmeineke	10	current_bond = comp_stamps[i]->getBond( k );
448			the_bonds[index].a = current_bond->getA() + offset;
449			the_bonds[index].b = current_bond->getB() + offset;
450
451			the_excludes[index].i = the_bonds[index].a;
452			the_excludes[index].j = the_bonds[index].b;
453
454			// increment the index and repeat;
455			index++;
456			}
457			offset += comp_stamps[i]->getNAtoms();
458			}
459			}
460	chuckv	124
461	mmeineke	10	the_ff->initializeBonds( the_bonds );
462			}
463
464			void SimSetup::makeBends( void ){
465
466			int i, j, k, index, offset;
467			bend_set* the_bends;
468			BendStamp* current_bend;
469
470			the_bends = new bend_set[tot_bends];
471			index = 0;
472			offset = 0;
473			for( i=0; i<n_components; i++ ){
474	chuckv	124
475	mmeineke	10	for( j=0; j<components_nmol[i]; j++ ){
476	chuckv	124
477	mmeineke	10	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
478	chuckv	124
479	mmeineke	10	current_bend = comp_stamps[i]->getBend( k );
480			the_bends[index].a = current_bend->getA() + offset;
481			the_bends[index].b = current_bend->getB() + offset;
482			the_bends[index].c = current_bend->getC() + offset;
483
484			the_excludes[index + tot_bonds].i = the_bends[index].a;
485			the_excludes[index + tot_bonds].j = the_bends[index].c;
486
487			// increment the index and repeat;
488			index++;
489			}
490			offset += comp_stamps[i]->getNAtoms();
491			}
492			}
493	chuckv	124
494	mmeineke	10	the_ff->initializeBends( the_bends );
495			}
496
497			void SimSetup::makeTorsions( void ){
498
499			int i, j, k, index, offset;
500			torsion_set* the_torsions;
501			TorsionStamp* current_torsion;
502
503			the_torsions = new torsion_set[tot_torsions];
504			index = 0;
505			offset = 0;
506			for( i=0; i<n_components; i++ ){
507	chuckv	124
508	mmeineke	10	for( j=0; j<components_nmol[i]; j++ ){
509	chuckv	124
510	mmeineke	10	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
511	chuckv	124
512	mmeineke	10	current_torsion = comp_stamps[i]->getTorsion( k );
513			the_torsions[index].a = current_torsion->getA() + offset;
514			the_torsions[index].b = current_torsion->getB() + offset;
515			the_torsions[index].c = current_torsion->getC() + offset;
516			the_torsions[index].d = current_torsion->getD() + offset;
517
518			the_excludes[index + tot_bonds + tot_bends].i = the_torsions[index].a;
519			the_excludes[index + tot_bonds + tot_bends].j = the_torsions[index].d;
520
521			// increment the index and repeat;
522			index++;
523			}
524			offset += comp_stamps[i]->getNAtoms();
525			}
526			}
527	chuckv	124
528	mmeineke	10	the_ff->initializeTorsions( the_torsions );
529			}
530
531			void SimSetup::initFromBass( void ){
532
533			int i, j, k;
534			int n_cells;
535			double cellx, celly, cellz;
536			double temp1, temp2, temp3;
537			int n_per_extra;
538			int n_extra;
539			int have_extra, done;
540
541			temp1 = (double)tot_nmol / 4.0;
542			temp2 = pow( temp1, ( 1.0 / 3.0 ) );
543			temp3 = ceil( temp2 );
544
545			have_extra =0;
546			if( temp2 < temp3 ){ // we have a non-complete lattice
547			have_extra =1;
548
549			n_cells = (int)temp3 - 1;
550			cellx = simnfo->box_x / temp3;
551			celly = simnfo->box_y / temp3;
552			cellz = simnfo->box_z / temp3;
553			n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
554			temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
555			n_per_extra = (int)ceil( temp1 );
556
557			if( n_per_extra > 4){
558			std::cerr << "THere has been an error in constructing the non-complete lattice.\n";
559			exit(8);
560			}
561			}
562			else{
563			n_cells = (int)temp3;
564			cellx = simnfo->box_x / temp3;
565			celly = simnfo->box_y / temp3;
566			cellz = simnfo->box_z / temp3;
567			}
568	chuckv	124
569	mmeineke	10	current_mol = 0;
570			current_comp_mol = 0;
571			current_comp = 0;
572			current_atom_ndx = 0;
573	chuckv	124
574	mmeineke	10	for( i=0; i < n_cells ; i++ ){
575			for( j=0; j < n_cells; j++ ){
576			for( k=0; k < n_cells; k++ ){
577	chuckv	124
578	mmeineke	10	makeElement( i * cellx,
579			j * celly,
580			k * cellz );
581	chuckv	124
582	mmeineke	10	makeElement( i * cellx + 0.5 * cellx,
583			j * celly + 0.5 * celly,
584			k * cellz );
585	chuckv	124
586	mmeineke	10	makeElement( i * cellx,
587			j * celly + 0.5 * celly,
588			k * cellz + 0.5 * cellz );
589	chuckv	124
590	mmeineke	10	makeElement( i * cellx + 0.5 * cellx,
591			j * celly,
592			k * cellz + 0.5 * cellz );
593			}
594			}
595			}
596
597			if( have_extra ){
598			done = 0;
599	chuckv	124
600	mmeineke	10	int start_ndx;
601			for( i=0; i < (n_cells+1) && !done; i++ ){
602			for( j=0; j < (n_cells+1) && !done; j++ ){
603	chuckv	124
604	mmeineke	10	if( i < n_cells ){
605	chuckv	124
606	mmeineke	10	if( j < n_cells ){
607			start_ndx = n_cells;
608			}
609			else start_ndx = 0;
610			}
611			else start_ndx = 0;
612	chuckv	124
613	mmeineke	10	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
614	chuckv	124
615	mmeineke	10	makeElement( i * cellx,
616			j * celly,
617			k * cellz );
618			done = ( current_mol >= tot_nmol );
619	chuckv	124
620	mmeineke	10	if( !done && n_per_extra > 1 ){
621			makeElement( i * cellx + 0.5 * cellx,
622			j * celly + 0.5 * celly,
623			k * cellz );
624			done = ( current_mol >= tot_nmol );
625			}
626	chuckv	124
627	mmeineke	10	if( !done && n_per_extra > 2){
628			makeElement( i * cellx,
629			j * celly + 0.5 * celly,
630			k * cellz + 0.5 * cellz );
631			done = ( current_mol >= tot_nmol );
632			}
633	chuckv	124
634	mmeineke	10	if( !done && n_per_extra > 3){
635			makeElement( i * cellx + 0.5 * cellx,
636			j * celly,
637			k * cellz + 0.5 * cellz );
638			done = ( current_mol >= tot_nmol );
639			}
640			}
641			}
642			}
643			}
644	chuckv	124
645
646	mmeineke	10	for( i=0; i<simnfo->n_atoms; i++ ){
647			simnfo->atoms[i]->set_vx( 0.0 );
648			simnfo->atoms[i]->set_vy( 0.0 );
649			simnfo->atoms[i]->set_vz( 0.0 );
650			}
651			}
652
653			void SimSetup::makeElement( double x, double y, double z ){
654
655			int k;
656			AtomStamp* current_atom;
657			DirectionalAtom* dAtom;
658			double rotMat[3][3];
659
660			for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
661	chuckv	124
662	mmeineke	10	current_atom = comp_stamps[current_comp]->getAtom( k );
663			if( !current_atom->havePosition() ){
664			std::cerr << "Component " << comp_stamps[current_comp]->getID()
665			<< ", atom " << current_atom->getType()
666			<< " does not have a position specified.\n"
667			<< "The initialization routine is unable to give a start"
668			<< " position.\n";
669			exit(8);
670			}
671	chuckv	124
672	mmeineke	10	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
673			the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
674			the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
675	chuckv	124
676	mmeineke	10	if( the_atoms[current_atom_ndx]->isDirectional() ){
677	chuckv	124
678	mmeineke	10	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
679	chuckv	124
680	mmeineke	10	rotMat[0][0] = 1.0;
681			rotMat[0][1] = 0.0;
682			rotMat[0][2] = 0.0;
683
684			rotMat[1][0] = 0.0;
685			rotMat[1][1] = 1.0;
686			rotMat[1][2] = 0.0;
687
688			rotMat[2][0] = 0.0;
689			rotMat[2][1] = 0.0;
690			rotMat[2][2] = 1.0;
691
692			dAtom->setA( rotMat );
693			}
694
695			current_atom_ndx++;
696			}
697	chuckv	124
698	mmeineke	10	current_mol++;
699			current_comp_mol++;
700
701			if( current_comp_mol >= components_nmol[current_comp] ){
702	chuckv	124
703	mmeineke	10	current_comp_mol = 0;
704			current_comp++;
705			}
706			}