OOPSE/utils/nanoBuilder.cpp

#include <iostream>

#include <cstdlib>
#include <cstring>
#include <cmath>
#include <vector>

#include "simError.h"
#include "SimInfo.hpp"
#include "ReadWrite.hpp"

#include "latticeBuilder.hpp"
#include "MoLocator.hpp"
#include "sysBuild.hpp"
#include "nanoBuilder.hpp"

nanoBuilder::nanoBuilder(int thisIsRandom, int thisHasVacancies,
                         int thisLatticeType, double thisParticleRadius, 
                         double thisCoreRadius, double thisVacancyFraction,
                         double thisVacancyRadius,
                         double thisLatticeSpacing, 
                         double solute_X,
                         int &hasError){
  int Errors;
  int foundCore,foundShell;
  int i;
  
  //Zero variables
  particleRadius = 0.0;
  coreRadius = 0.0;
  vacancyFraction = 0.0;
  vacancyRadius = 0.0;
  shellRadius = 0.0;
  latticeSpacing = 0.0;

  buildNmol = 0;

  nCoreMolecules = 0;
  nShellMolecules = 0;

  atomCount = 0;
  coreAtomCount = 0;
  shellAtomCount = 0;

  
  moleculeCount = 0; 
  foundCore  = 0;
  foundShell = 0;
  totalMolecules = 0;
  coreHasOrientation = 0;
  shellHasOrientation = 0;
  nInterface = 0;
  nMol = 0;

  hasError = 0;
  Errors = 0;


  isRandom        = thisIsRandom;
  hasVacancies    = thisHasVacancies;
  latticeType     = thisLatticeType;
  particleRadius  = thisParticleRadius;
  coreRadius      = thisCoreRadius;
  vacancyFraction = thisVacancyFraction;
  latticeSpacing  = thisLatticeSpacing;
  soluteX = solute_X; //Mole fraction for random particle.


  for (i=0;bsInfo.nComponents;i++){
    if( !strcmp( bsInfo.compStamps[i]->getID(),bsInfo.coreName )){
      foundCore = 1;
      coreStamp = bsInfo.compStamps[i];
      nCoreMolecules = bsInfo.componentsNmol[i];
    }
    if( !strcmp( bsInfo.compStamps[i]->getID(),bsInfo.shellName)){
      foundShell = 1;
      shellStamp = bsInfo.compStamps[i];
      nShellMolecules = bsInfo.componentsNmol[i];

    }    

  }


  if( !foundCore ){
    hasError = 1;
    return;
  }
  if( !foundShell ){
    hasError = 1;
    return;
  }


  Errors = sanityCheck();

  if (Errors){
    hasError = 1;
    return;
  }


  nCoreModelAtoms  = coreStamp->getNAtoms();
  nShellModelAtoms = shellStamp->getNAtoms();
  

  // We assume that if the core or shell model has more then one atom
  // the model has an orientational component...
  if (nCoreModelAtoms > 1)    coreHasOrientation = 1;
  if (nShellModelAtoms > 1)   shellHasOrientation = 1;
  
  maxModelNatoms = std::max(nCoreModelAtoms,nShellModelAtoms);
  
  /* If we specify a number of atoms in bass, we will try to build a nanopartice
     with that number.
  */
 

  if ((nShellMolecules != 0) && (nCoreMolecules != 0)){
    totalMolecules = nShellMolecules + nCoreMolecules;
    nCells = ceil(pow((double)totalMolecules/4.0, 1/3));
    buildNmol = 1;
  }
  else {
    nCells = 2.0 * particleRadius/latticeSpacing;
    shellRadius = particleRadius - coreRadius;
  }


  // Initialize random seed
  srand48( RAND_SEED );

  
}


nanoBuilder::~nanoBuilder(){
}


// Checks to make sure we aren't doing something the builder can't do.
int nanoBuilder::sanityCheck(void){

  // Right now we only do bimetallic nanoparticles  
  if (bsInfo.nComponents > 2) return 1;

  //Check for vacancies and random
  if (hasVacancies && isRandom) return 1;

  // make sure we aren't trying to build a core larger then the total particle size
  if ((coreRadius >= particleRadius) && (particleRadius != 0)) return 1;

  // we initialize the lattice spacing to be 0.0, if the lattice spacing is still 0.0
  // we have a problem
  if (latticeSpacing == 0.0) return 1;

  // Check to see if we are specifing the number of atoms in the particle correctly.
  if ((nShellMolecules == 0) && (nCoreMolecules != 0)){
    cerr << "nShellParticles is zero and nCoreParticles != 0" << "\n";
    return 1;
  } 
  // Make sure there are more then two components if we are building a randomly mixed particle.
  if ((bsInfo.nComponents < 2) && (isRandom)){
    cerr << "Two Components are needed to build a random particle." << "\n";
  }
  // Make sure both the core and shell models specify a target nmol.
  if ((nShellMolecules != 0) && (nCoreMolecules == 0)){
    cerr << "nCoreParticles is zero and nShellParticles != 0" << "\n";
    return 1;
  } 
  
  return 0;

}

    
int nanoBuilder::buildNanoParticle( void ){

  int ix;
  int iy;
  int iz;
  double *rx;
  double *ry;
  double *rz;
  double pos[3];
  double A[3][3];
  double HmatI[3][3];
  
  int nCellSites;
  int iref;
  int appNMols;
  int latticeCount = 0;
 
  int nAtoms;
  int nCoreAtomCounter = 0;
  int nShellAtomCounter = 0;
  int hasError;

  int i, j;

  int interfaceIndex = 0;
  double dist;
  double distsq;
  int latticeNpoints;
  int shesActualSizetoMe = 0;

  DumpWriter* writer;
  SimInfo* simnfo;

  Lattice *myLattice;
  MoLocator *coreLocate;
  MoLocator *shellLocate;


  Atom** atoms;

  hasError = 0;

  myLattice = new Lattice(FCC_LATTICE_TYPE,latticeSpacing);
  /*
  latticeNpoints = myLattice.getNpoints();

  // Initializd atom vector to approximate size. 
  switch (buildType){

  case BUILD_NMOL_PARTICLE:

    break;
  case BUILD_CORE_SHELL_VACANCY:
   // Make space in the vector for all atoms except the last full cells
    // We will have to add at most (latticeNpoints-1)^3 to vector 
    appNMols = latticeNPoints * pow((double)(nCells - 1),3);
    moleculeVector.pushBack();

  default:
    // Make space in the vector for all atoms except the last full cells
    // We will have to add at most (latticeNpoints-1)^3 to vector 
    appNMols = latticeNPoints * pow((double)(nCells - 1),3);

  }
  */
  

  // Create molocator and atom arrays.
  coreLocate  = new MoLocator(coreStamp);
  shellLocate = new MoLocator(shellStamp);
 
  
  for(iz=-nCells;iz < nCells;iz++){ 
    for(iy=-nCells;iy<nCells;iy++){      
      for(ix=-nCells;ix<nCells;ix++){
        nCellSites = myLattice->getLatticePoints(&rx,&ry,&rz,
                                                 ix,iy,iz);
        for (iref=1;iref<nCellSites;iref++){
          latticeCount++;
          
          pos[0] = rx[iref];
          pos[1] = ry[iref];
          pos[2] = rz[iref];
          
          distsq = rx[iref]*rx[iref] + ry[iref]*ry[iref] +rz[iref]*rz[iref];
          dist = sqrt(distsq);
          
          switch(buildType){

          case BUILD_CORE_SHELL:
            nanoBuilder::buildWithCoreShell(dist,pos);
            break;
          case BUILD_CORE_SHELL_VACANCY:
            nanoBuilder::buildWithVacancies(dist,pos);
            break;

          case BUILD_RANDOM_PARTICLE:
            nanoBuilder::buildRandomlyMixed(dist,pos);
            break;
          case BUILD_NMOL_PARTICLE:
            nanoBuilder::buildNmolParticle(dist,pos);
          }
        }
      }
    }
  }


  // Create vacancies
  if (hasVacancies) buildVacancies();

  // Find the size of the atom vector not including Null atoms
  for (i=0;i<moleculeVector.size();i++){
    if (! moleculeVector[i].isVacancy){
      shesActualSizetoMe++;
      nAtoms = moleculeVector[i].myStamp->getNAtoms();
    }
  }

// Make a random particle.
  if (isRandom){
    placeRandom(shesActualSizetoMe); 

  // Loop back thru and count natoms since they may have changed
    for (i=0;i<moleculeVector.size();i++){
      if (! moleculeVector[i].isVacancy){
        shesActualSizetoMe++;
        nAtoms = moleculeVector[i].myStamp->getNAtoms();
      }
    }
  }


  Atom::createArrays( nAtoms );
  atoms = new Atom*[nAtoms];

 
  shesActualSizetoMe = 0;
  /*  Use the information from the molecule vector to place the atoms.
   */
  for (i= 0;i<moleculeVector.size();i++){
    if (! moleculeVector[i].isVacancy) {
      orientationMunger( A );
      if( moleculeVector[i].isCore){
        nCoreAtomCounter =+ nCoreModelAtoms;
        coreLocate->placeMol(moleculeVector[i].pos,A,atoms,nShellAtomCounter);
      }
      else {
        nShellAtomCounter =+ nShellModelAtoms;
        shellLocate->placeMol(moleculeVector[i].pos,A,atoms,nCoreAtomCounter);
      }
      shesActualSizetoMe++;
    }
  }


  //      shellLocate.placeMol(pos, A, moleculeVector,shellAtomCount);

  for (i=0;i<3;i++) 
    for (j=0; j<3; j++) 
      simnfo->Hmat[i][j] = 0.0;

  simnfo->Hmat[0][0] = 1.0;
  simnfo->Hmat[1][1] = 1.0;
  simnfo->Hmat[2][2] = 1.0;
  
  // set up the SimInfo object

  simnfo = new SimInfo();
  simnfo->n_atoms = nAtoms;
  
  sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix );
  sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix );

  simnfo->atoms = atoms;
  
  // set up the writer and write out
  
  writer = new DumpWriter( simnfo );
  writer->writeFinal(0.0);

    // clean up  

  delete[] myLattice;

  return hasError;
} 

// Begin Builder routines------------------------------->

/* Builds a standard core-shell nanoparticle.
*/
void nanoBuilder::buildWithCoreShell(double dist, double pos[3]){

  
  if ( dist <= particleRadius ){
    moleculeVector.push_back(myMol);
    
    if (dist <= coreRadius){
      coreAtomCount =+ nCoreModelAtoms;
      moleculeVector[moleculeCount].pos[0] = pos[0]; 
      moleculeVector[moleculeCount].pos[1] = pos[1]; 
      moleculeVector[moleculeCount].pos[2] = pos[2]; 
      moleculeVector[moleculeCount].myStamp = coreStamp;
      moleculeVector[moleculeCount].isCore = 1;
      moleculeVector[moleculeCount].isShell = 0;
      
    }
    // Place shell
    else{
      shellAtomCount =+ nShellModelAtoms;
      moleculeVector[moleculeCount].pos[0] = pos[0]; 
      moleculeVector[moleculeCount].pos[1] = pos[1]; 
      moleculeVector[moleculeCount].pos[2] = pos[2]; 
      moleculeVector[moleculeCount].myStamp = shellStamp;
      moleculeVector[moleculeCount].isCore = 0;
      moleculeVector[moleculeCount].isShell = 1;
      
    }
    moleculeCount++;
  }      
  
}
/*
Builds a core-shell nanoparticle and tracks the number of molecules at the
interface between the core-shell. These are recorded in vacancyInterface which is just
an integer vector. 
*/
void nanoBuilder::buildWithVacancies(double dist, double pos[3]){
  if ( dist <= particleRadius ){

    moleculeVector.push_back(myMol);
    if (dist <= coreRadius){
        
      coreAtomCount =+ nCoreModelAtoms;
      moleculeVector[moleculeCount].pos[0] = pos[0]; 
      moleculeVector[moleculeCount].pos[1] = pos[1]; 
      moleculeVector[moleculeCount].pos[2] = pos[2]; 
      moleculeVector[moleculeCount].myStamp = coreStamp;
      moleculeVector[moleculeCount].isCore = 1;
      moleculeVector[moleculeCount].isShell = 0;

      if ((dist >= coreRadius - vacancyRadius/2.0) && 
          (dist <= coreRadius + vacancyRadius/2.0)){
        
        vacancyInterface.push_back(moleculeCount);
        nInterface++;
      }
    } else {
      // Place shell
      shellAtomCount =+ nShellModelAtoms;
      moleculeVector[moleculeCount].pos[0] = pos[0]; 
      moleculeVector[moleculeCount].pos[1] = pos[1]; 
      moleculeVector[moleculeCount].pos[2] = pos[2]; 
      moleculeVector[moleculeCount].myStamp = shellStamp;
      moleculeVector[moleculeCount].isCore = 0;
      moleculeVector[moleculeCount].isShell = 1;

    }
    moleculeCount++;
  }


}

/* Builds a core-shell nanoparticle where the number of core and shell
 molecules is known.
*/
void nanoBuilder::buildNmolParticle(double dist, double pos[3]){
  static int nMolCounter = 0;
  static int nCoreMolCounter = 0;
  
  
  if (nMolCounter < totalMolecules){
    moleculeVector.push_back(myMol);
    if (nCoreMolCounter < nCoreMolecules){
      
      coreAtomCount =+ nCoreModelAtoms;
      moleculeVector[moleculeCount].pos[0] = pos[0]; 
      moleculeVector[moleculeCount].pos[1] = pos[1]; 
      moleculeVector[moleculeCount].pos[2] = pos[2]; 
      moleculeVector[moleculeCount].myStamp = coreStamp;
      moleculeVector[moleculeCount].isCore = 1;
      moleculeVector[moleculeCount].isShell = 0;
      
      
    } else {
      shellAtomCount =+ nShellModelAtoms;
      moleculeVector[moleculeCount].pos[0] = pos[0]; 
      moleculeVector[moleculeCount].pos[1] = pos[1]; 
      moleculeVector[moleculeCount].pos[2] = pos[2]; 
      moleculeVector[moleculeCount].myStamp = shellStamp;
      moleculeVector[moleculeCount].isCore = 0;
      moleculeVector[moleculeCount].isShell = 1;
      
        
    }

  }
}


/* Builds a randomly mixed nanoparticle. We build the particle to be 
 entirely the core model, then randomly switch identities after the particle is built.
*/ 
void nanoBuilder::buildRandomlyMixed(double dist, double pos[3]){


  if ( dist <= particleRadius ){
    moleculeCount++;


    moleculeVector[moleculeCount].pos[0] = pos[0]; 
    moleculeVector[moleculeCount].pos[1] = pos[1]; 
    moleculeVector[moleculeCount].pos[2] = pos[2]; 
    moleculeVector[moleculeCount].myStamp = coreStamp;
    moleculeVector[moleculeCount].isCore = 1;
    moleculeVector[moleculeCount].isShell = 0;
    
  }     


}


// -----------------------END Builder routines.


//------------------------Begin Helper routines.
void nanoBuilder::placeRandom(int totalMol){
  int nSolute;
  int nSolvent;
  int i;
  int notfound;
  double solute_x;
  double solvent_x;
  
  int tester;

  nSolute = floor(soluteX * (double)totalMolecules); //CHECK ME
  nSolvent = totalMolecules - nSolute;
  
  solute_x = (double)nSolute/(double)totalMolecules;
  solvent_x = 1.0 - solute_x;
  
  
  for(i=0;nSolute-1;i++){
    notfound = 1;
    
    while(notfound){
      
      tester = floor((double)totalMolecules * drand48()); //Pick a molecule
      
      if (moleculeVector[tester].isCore){ // Make sure we select a core atom to change
          
        moleculeVector[tester].isCore  = 0;
        moleculeVector[tester].isShell = 1;
        moleculeVector[tester].myStamp = shellStamp;
        notfound = 0; //set notfound = false.
      }
        
    }
      
  }
}


void nanoBuilder::buildVacancies(void){
  int i;  
  int* VacancyList; //logical nInterface long.
  int notfound;
  int index = 0;
  int nVacancies;
  int tester;

  if (nInterface != 0){
    nVacancies = floor((double)nInterface * vacancyFraction);

    VacancyList = new int[nInterface];
    
    // make vacancy list all false
    for(i=0;i<nInterface-1;i++){
      VacancyList[i] = 0;
    }
    
    // Build a vacancy list....    
    for(i=0;nVacancies-1;i++){
      notfound = 1;
      while(notfound){
        
        tester = floor((double)nInterface * drand48());
      
        if(! VacancyList[tester]){
          VacancyList[tester] = 1;
          notfound = 0;
        }
        
      }
    }
  }
  // Loop through and kill the vacancies from atom vector.

  for (i=0;i<nInterface;i++){
    if (VacancyList[i]){
      moleculeVector[vacancyInterface[i]].isVacancy = 1;   
    } // End Vacancy List
  } // for nInterface
  

    delete[] VacancyList;
}


void nanoBuilder::orientationMunger(double rot[3][3]){

  double theta, phi, psi;
  double cosTheta;

  // select random phi, psi, and cosTheta

  phi = 2.0 * M_PI * drand48();
  psi = 2.0 * M_PI * drand48();
  cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1

  theta = acos( cosTheta );

  rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
  rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
  rot[0][2] = sin(theta) * sin(psi);

  rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
  rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
  rot[1][2] = sin(theta) * cos(psi);

  rot[2][0] = sin(phi) * sin(theta);
  rot[2][1] = -cos(phi) * sin(theta);
  rot[2][2] = cos(theta);

}


Revision:	592
Committed:	Fri Jul 11 14:49:17 2003 UTC (21 years ago) by gezelter
File size:	15106 byte(s)
Log Message:	Fixed Hmat and some namespace strangeness
#	User	Rev	Content
1	chuckv	589	#include <iostream>
2
3			#include <cstdlib>
4			#include <cstring>
5			#include <cmath>
6			#include <vector>
7
8			#include "simError.h"
9			#include "SimInfo.hpp"
10			#include "ReadWrite.hpp"
11
12			#include "latticeBuilder.hpp"
13			#include "MoLocator.hpp"
14			#include "sysBuild.hpp"
15			#include "nanoBuilder.hpp"
16
17			nanoBuilder::nanoBuilder(int thisIsRandom, int thisHasVacancies,
18			int thisLatticeType, double thisParticleRadius,
19			double thisCoreRadius, double thisVacancyFraction,
20			double thisVacancyRadius,
21			double thisLatticeSpacing,
22			double solute_X,
23			int &hasError){
24			int Errors;
25			int foundCore,foundShell;
26			int i;
27	gezelter	592
28	chuckv	589	//Zero variables
29			particleRadius = 0.0;
30			coreRadius = 0.0;
31			vacancyFraction = 0.0;
32			vacancyRadius = 0.0;
33			shellRadius = 0.0;
34			latticeSpacing = 0.0;
35
36			buildNmol = 0;
37
38			nCoreMolecules = 0;
39			nShellMolecules = 0;
40
41			atomCount = 0;
42			coreAtomCount = 0;
43			shellAtomCount = 0;
44
45
46
47			moleculeCount = 0;
48			foundCore = 0;
49			foundShell = 0;
50			totalMolecules = 0;
51			coreHasOrientation = 0;
52			shellHasOrientation = 0;
53			nInterface = 0;
54			nMol = 0;
55
56			hasError = 0;
57			Errors = 0;
58
59
60			isRandom = thisIsRandom;
61			hasVacancies = thisHasVacancies;
62			latticeType = thisLatticeType;
63			particleRadius = thisParticleRadius;
64			coreRadius = thisCoreRadius;
65			vacancyFraction = thisVacancyFraction;
66			latticeSpacing = thisLatticeSpacing;
67			soluteX = solute_X; //Mole fraction for random particle.
68
69
70
71
72
73			for (i=0;bsInfo.nComponents;i++){
74			if( !strcmp( bsInfo.compStamps[i]->getID(),bsInfo.coreName )){
75			foundCore = 1;
76			coreStamp = bsInfo.compStamps[i];
77			nCoreMolecules = bsInfo.componentsNmol[i];
78			}
79			if( !strcmp( bsInfo.compStamps[i]->getID(),bsInfo.shellName)){
80			foundShell = 1;
81			shellStamp = bsInfo.compStamps[i];
82			nShellMolecules = bsInfo.componentsNmol[i];
83
84			}
85
86			}
87
88
89
90			if( !foundCore ){
91			hasError = 1;
92			return;
93			}
94			if( !foundShell ){
95			hasError = 1;
96			return;
97			}
98
99
100
101			Errors = sanityCheck();
102
103			if (Errors){
104			hasError = 1;
105			return;
106			}
107
108
109
110
111
112
113
114			nCoreModelAtoms = coreStamp->getNAtoms();
115			nShellModelAtoms = shellStamp->getNAtoms();
116
117
118			// We assume that if the core or shell model has more then one atom
119			// the model has an orientational component...
120			if (nCoreModelAtoms > 1) coreHasOrientation = 1;
121			if (nShellModelAtoms > 1) shellHasOrientation = 1;
122
123			maxModelNatoms = std::max(nCoreModelAtoms,nShellModelAtoms);
124
125			/* If we specify a number of atoms in bass, we will try to build a nanopartice
126			with that number.
127			*/
128
129
130			if ((nShellMolecules != 0) && (nCoreMolecules != 0)){
131			totalMolecules = nShellMolecules + nCoreMolecules;
132			nCells = ceil(pow((double)totalMolecules/4.0, 1/3));
133			buildNmol = 1;
134			}
135			else {
136			nCells = 2.0 * particleRadius/latticeSpacing;
137			shellRadius = particleRadius - coreRadius;
138			}
139
140
141
142
143			// Initialize random seed
144			srand48( RAND_SEED );
145
146
147			}
148
149
150			nanoBuilder::~nanoBuilder(){
151			}
152
153
154			// Checks to make sure we aren't doing something the builder can't do.
155			int nanoBuilder::sanityCheck(void){
156
157			// Right now we only do bimetallic nanoparticles
158			if (bsInfo.nComponents > 2) return 1;
159
160			//Check for vacancies and random
161			if (hasVacancies && isRandom) return 1;
162
163			// make sure we aren't trying to build a core larger then the total particle size
164			if ((coreRadius >= particleRadius) && (particleRadius != 0)) return 1;
165
166			// we initialize the lattice spacing to be 0.0, if the lattice spacing is still 0.0
167			// we have a problem
168			if (latticeSpacing == 0.0) return 1;
169
170			// Check to see if we are specifing the number of atoms in the particle correctly.
171			if ((nShellMolecules == 0) && (nCoreMolecules != 0)){
172			cerr << "nShellParticles is zero and nCoreParticles != 0" << "\n";
173			return 1;
174			}
175			// Make sure there are more then two components if we are building a randomly mixed particle.
176			if ((bsInfo.nComponents < 2) && (isRandom)){
177			cerr << "Two Components are needed to build a random particle." << "\n";
178			}
179			// Make sure both the core and shell models specify a target nmol.
180			if ((nShellMolecules != 0) && (nCoreMolecules == 0)){
181			cerr << "nCoreParticles is zero and nShellParticles != 0" << "\n";
182			return 1;
183			}
184
185			return 0;
186
187			}
188
189
190
191			int nanoBuilder::buildNanoParticle( void ){
192
193			int ix;
194			int iy;
195			int iz;
196			double *rx;
197			double *ry;
198			double *rz;
199			double pos[3];
200			double A[3][3];
201	gezelter	592	double HmatI[3][3];
202	chuckv	589
203			int nCellSites;
204			int iref;
205			int appNMols;
206			int latticeCount = 0;
207
208			int nAtoms;
209			int nCoreAtomCounter = 0;
210			int nShellAtomCounter = 0;
211			int hasError;
212
213	gezelter	592	int i, j;
214	chuckv	589
215			int interfaceIndex = 0;
216			double dist;
217			double distsq;
218			int latticeNpoints;
219			int shesActualSizetoMe = 0;
220
221			DumpWriter* writer;
222			SimInfo* simnfo;
223
224	gezelter	592	Lattice *myLattice;
225			MoLocator *coreLocate;
226			MoLocator *shellLocate;
227	chuckv	589
228
229			Atom** atoms;
230
231			hasError = 0;
232
233			myLattice = new Lattice(FCC_LATTICE_TYPE,latticeSpacing);
234			/*
235			latticeNpoints = myLattice.getNpoints();
236
237			// Initializd atom vector to approximate size.
238			switch (buildType){
239
240			case BUILD_NMOL_PARTICLE:
241
242			break;
243			case BUILD_CORE_SHELL_VACANCY:
244			// Make space in the vector for all atoms except the last full cells
245			// We will have to add at most (latticeNpoints-1)^3 to vector
246			appNMols = latticeNPoints * pow((double)(nCells - 1),3);
247			moleculeVector.pushBack();
248
249			default:
250			// Make space in the vector for all atoms except the last full cells
251			// We will have to add at most (latticeNpoints-1)^3 to vector
252			appNMols = latticeNPoints * pow((double)(nCells - 1),3);
253
254			}
255			*/
256
257
258
259
260			// Create molocator and atom arrays.
261			coreLocate = new MoLocator(coreStamp);
262			shellLocate = new MoLocator(shellStamp);
263
264
265
266
267
268
269			for(iz=-nCells;iz < nCells;iz++){
270			for(iy=-nCells;iy<nCells;iy++){
271			for(ix=-nCells;ix<nCells;ix++){
272			nCellSites = myLattice->getLatticePoints(&rx,&ry,&rz,
273			ix,iy,iz);
274			for (iref=1;iref<nCellSites;iref++){
275			latticeCount++;
276
277			pos[0] = rx[iref];
278			pos[1] = ry[iref];
279			pos[2] = rz[iref];
280
281			distsq = rx[iref]rx[iref] + ry[iref]ry[iref] +rz[iref]*rz[iref];
282			dist = sqrt(distsq);
283
284			switch(buildType){
285
286			case BUILD_CORE_SHELL:
287			nanoBuilder::buildWithCoreShell(dist,pos);
288			break;
289			case BUILD_CORE_SHELL_VACANCY:
290			nanoBuilder::buildWithVacancies(dist,pos);
291			break;
292
293			case BUILD_RANDOM_PARTICLE:
294			nanoBuilder::buildRandomlyMixed(dist,pos);
295			break;
296			case BUILD_NMOL_PARTICLE:
297			nanoBuilder::buildNmolParticle(dist,pos);
298			}
299			}
300			}
301			}
302			}
303
304
305
306			// Create vacancies
307			if (hasVacancies) buildVacancies();
308
309			// Find the size of the atom vector not including Null atoms
310			for (i=0;i<moleculeVector.size();i++){
311			if (! moleculeVector[i].isVacancy){
312			shesActualSizetoMe++;
313			nAtoms = moleculeVector[i].myStamp->getNAtoms();
314			}
315			}
316
317			// Make a random particle.
318			if (isRandom){
319			placeRandom(shesActualSizetoMe);
320
321			// Loop back thru and count natoms since they may have changed
322			for (i=0;i<moleculeVector.size();i++){
323			if (! moleculeVector[i].isVacancy){
324			shesActualSizetoMe++;
325			nAtoms = moleculeVector[i].myStamp->getNAtoms();
326			}
327			}
328			}
329
330
331			Atom::createArrays( nAtoms );
332			atoms = new Atom*[nAtoms];
333
334
335
336			shesActualSizetoMe = 0;
337			/* Use the information from the molecule vector to place the atoms.
338			*/
339			for (i= 0;i<moleculeVector.size();i++){
340			if (! moleculeVector[i].isVacancy) {
341			orientationMunger( A );
342			if( moleculeVector[i].isCore){
343			nCoreAtomCounter =+ nCoreModelAtoms;
344			coreLocate->placeMol(moleculeVector[i].pos,A,atoms,nShellAtomCounter);
345			}
346			else {
347			nShellAtomCounter =+ nShellModelAtoms;
348			shellLocate->placeMol(moleculeVector[i].pos,A,atoms,nCoreAtomCounter);
349			}
350			shesActualSizetoMe++;
351			}
352			}
353
354
355			// shellLocate.placeMol(pos, A, moleculeVector,shellAtomCount);
356
357	gezelter	592	for (i=0;i<3;i++)
358			for (j=0; j<3; j++)
359			simnfo->Hmat[i][j] = 0.0;
360	chuckv	589
361	gezelter	592	simnfo->Hmat[0][0] = 1.0;
362			simnfo->Hmat[1][1] = 1.0;
363			simnfo->Hmat[2][2] = 1.0;
364
365	chuckv	589	// set up the SimInfo object
366	gezelter	592
367	chuckv	589	simnfo = new SimInfo();
368			simnfo->n_atoms = nAtoms;
369
370			sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix );
371			sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix );
372
373			simnfo->atoms = atoms;
374
375			// set up the writer and write out
376
377			writer = new DumpWriter( simnfo );
378			writer->writeFinal(0.0);
379
380			// clean up
381
382			delete[] myLattice;
383
384			return hasError;
385			}
386
387			// Begin Builder routines------------------------------->
388
389			/* Builds a standard core-shell nanoparticle.
390			*/
391			void nanoBuilder::buildWithCoreShell(double dist, double pos[3]){
392
393
394			if ( dist <= particleRadius ){
395			moleculeVector.push_back(myMol);
396
397			if (dist <= coreRadius){
398			coreAtomCount =+ nCoreModelAtoms;
399			moleculeVector[moleculeCount].pos[0] = pos[0];
400			moleculeVector[moleculeCount].pos[1] = pos[1];
401			moleculeVector[moleculeCount].pos[2] = pos[2];
402			moleculeVector[moleculeCount].myStamp = coreStamp;
403			moleculeVector[moleculeCount].isCore = 1;
404			moleculeVector[moleculeCount].isShell = 0;
405
406			}
407			// Place shell
408			else{
409			shellAtomCount =+ nShellModelAtoms;
410			moleculeVector[moleculeCount].pos[0] = pos[0];
411			moleculeVector[moleculeCount].pos[1] = pos[1];
412			moleculeVector[moleculeCount].pos[2] = pos[2];
413			moleculeVector[moleculeCount].myStamp = shellStamp;
414			moleculeVector[moleculeCount].isCore = 0;
415			moleculeVector[moleculeCount].isShell = 1;
416
417			}
418			moleculeCount++;
419			}
420
421			}
422			/*
423			Builds a core-shell nanoparticle and tracks the number of molecules at the
424			interface between the core-shell. These are recorded in vacancyInterface which is just
425			an integer vector.
426			*/
427			void nanoBuilder::buildWithVacancies(double dist, double pos[3]){
428			if ( dist <= particleRadius ){
429
430			moleculeVector.push_back(myMol);
431			if (dist <= coreRadius){
432
433			coreAtomCount =+ nCoreModelAtoms;
434			moleculeVector[moleculeCount].pos[0] = pos[0];
435			moleculeVector[moleculeCount].pos[1] = pos[1];
436			moleculeVector[moleculeCount].pos[2] = pos[2];
437			moleculeVector[moleculeCount].myStamp = coreStamp;
438			moleculeVector[moleculeCount].isCore = 1;
439			moleculeVector[moleculeCount].isShell = 0;
440
441			if ((dist >= coreRadius - vacancyRadius/2.0) &&
442			(dist <= coreRadius + vacancyRadius/2.0)){
443
444			vacancyInterface.push_back(moleculeCount);
445			nInterface++;
446			}
447			} else {
448			// Place shell
449			shellAtomCount =+ nShellModelAtoms;
450			moleculeVector[moleculeCount].pos[0] = pos[0];
451			moleculeVector[moleculeCount].pos[1] = pos[1];
452			moleculeVector[moleculeCount].pos[2] = pos[2];
453			moleculeVector[moleculeCount].myStamp = shellStamp;
454			moleculeVector[moleculeCount].isCore = 0;
455			moleculeVector[moleculeCount].isShell = 1;
456
457			}
458			moleculeCount++;
459			}
460
461
462
463			}
464
465			/* Builds a core-shell nanoparticle where the number of core and shell
466			molecules is known.
467			*/
468			void nanoBuilder::buildNmolParticle(double dist, double pos[3]){
469			static int nMolCounter = 0;
470			static int nCoreMolCounter = 0;
471
472
473			if (nMolCounter < totalMolecules){
474			moleculeVector.push_back(myMol);
475			if (nCoreMolCounter < nCoreMolecules){
476
477			coreAtomCount =+ nCoreModelAtoms;
478			moleculeVector[moleculeCount].pos[0] = pos[0];
479			moleculeVector[moleculeCount].pos[1] = pos[1];
480			moleculeVector[moleculeCount].pos[2] = pos[2];
481			moleculeVector[moleculeCount].myStamp = coreStamp;
482			moleculeVector[moleculeCount].isCore = 1;
483			moleculeVector[moleculeCount].isShell = 0;
484
485
486			} else {
487			shellAtomCount =+ nShellModelAtoms;
488			moleculeVector[moleculeCount].pos[0] = pos[0];
489			moleculeVector[moleculeCount].pos[1] = pos[1];
490			moleculeVector[moleculeCount].pos[2] = pos[2];
491			moleculeVector[moleculeCount].myStamp = shellStamp;
492			moleculeVector[moleculeCount].isCore = 0;
493			moleculeVector[moleculeCount].isShell = 1;
494
495
496			}
497
498			}
499			}
500
501
502			/* Builds a randomly mixed nanoparticle. We build the particle to be
503			entirely the core model, then randomly switch identities after the particle is built.
504			*/
505			void nanoBuilder::buildRandomlyMixed(double dist, double pos[3]){
506
507
508			if ( dist <= particleRadius ){
509			moleculeCount++;
510
511
512			moleculeVector[moleculeCount].pos[0] = pos[0];
513			moleculeVector[moleculeCount].pos[1] = pos[1];
514			moleculeVector[moleculeCount].pos[2] = pos[2];
515			moleculeVector[moleculeCount].myStamp = coreStamp;
516			moleculeVector[moleculeCount].isCore = 1;
517			moleculeVector[moleculeCount].isShell = 0;
518
519			}
520
521
522
523			}
524
525
526			// -----------------------END Builder routines.
527
528
529
530			//------------------------Begin Helper routines.
531			void nanoBuilder::placeRandom(int totalMol){
532			int nSolute;
533			int nSolvent;
534			int i;
535			int notfound;
536			double solute_x;
537			double solvent_x;
538
539			int tester;
540
541			nSolute = floor(soluteX * (double)totalMolecules); //CHECK ME
542			nSolvent = totalMolecules - nSolute;
543
544			solute_x = (double)nSolute/(double)totalMolecules;
545			solvent_x = 1.0 - solute_x;
546
547
548
549
550			for(i=0;nSolute-1;i++){
551			notfound = 1;
552
553			while(notfound){
554
555			tester = floor((double)totalMolecules * drand48()); //Pick a molecule
556
557			if (moleculeVector[tester].isCore){ // Make sure we select a core atom to change
558
559			moleculeVector[tester].isCore = 0;
560			moleculeVector[tester].isShell = 1;
561			moleculeVector[tester].myStamp = shellStamp;
562			notfound = 0; //set notfound = false.
563			}
564
565			}
566
567			}
568			}
569
570
571			void nanoBuilder::buildVacancies(void){
572			int i;
573			int* VacancyList; //logical nInterface long.
574			int notfound;
575			int index = 0;
576			int nVacancies;
577			int tester;
578
579			if (nInterface != 0){
580			nVacancies = floor((double)nInterface * vacancyFraction);
581
582			VacancyList = new int[nInterface];
583
584			// make vacancy list all false
585			for(i=0;i<nInterface-1;i++){
586			VacancyList[i] = 0;
587			}
588
589			// Build a vacancy list....
590			for(i=0;nVacancies-1;i++){
591			notfound = 1;
592			while(notfound){
593
594			tester = floor((double)nInterface * drand48());
595
596			if(! VacancyList[tester]){
597			VacancyList[tester] = 1;
598			notfound = 0;
599			}
600
601			}
602			}
603			}
604			// Loop through and kill the vacancies from atom vector.
605
606			for (i=0;i<nInterface;i++){
607			if (VacancyList[i]){
608			moleculeVector[vacancyInterface[i]].isVacancy = 1;
609			} // End Vacancy List
610			} // for nInterface
611
612
613			delete[] VacancyList;
614			}
615
616
617
618
619			void nanoBuilder::orientationMunger(double rot[3][3]){
620
621			double theta, phi, psi;
622			double cosTheta;
623
624			// select random phi, psi, and cosTheta
625
626			phi = 2.0 * M_PI * drand48();
627			psi = 2.0 * M_PI * drand48();
628			cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1
629
630			theta = acos( cosTheta );
631
632			rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
633			rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
634			rot[0][2] = sin(theta) * sin(psi);
635
636			rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
637			rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
638			rot[1][2] = sin(theta) * cos(psi);
639
640			rot[2][0] = sin(phi) * sin(theta);
641			rot[2][1] = -cos(phi) * sin(theta);
642			rot[2][2] = cos(theta);
643
644			}
645
646
647
648
649
650
651