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 &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;
 
  //Initialize class members from bsInfo struct that sysbuilder provides.
  isRandom        = bsInfo.isRandomParticle;
  hasVacancies    = bsInfo.hasVacancies;
  latticeType     = bsInfo.latticeType;
  particleRadius  = bsInfo.particleRadius;
  coreRadius      = bsInfo.coreRadius;
  vacancyFraction = bsInfo.vacancyFraction;
  latticeSpacing  = bsInfo.latticeSpacing;
  soluteX         = bsInfo.soluteX; //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:	598
Committed:	Mon Jul 14 21:35:45 2003 UTC (21 years ago) by chuckv
File size:	14988 byte(s)
Log Message:	added a nanoSysBuilder that takes different cmd line arguments.
#	Content
1	#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 &hasError){
18	int Errors;
19	int foundCore,foundShell;
20	int i;
21
22	//Zero variables
23	particleRadius = 0.0;
24	coreRadius = 0.0;
25	vacancyFraction = 0.0;
26	vacancyRadius = 0.0;
27	shellRadius = 0.0;
28	latticeSpacing = 0.0;
29
30	buildNmol = 0;
31
32	nCoreMolecules = 0;
33	nShellMolecules = 0;
34
35	atomCount = 0;
36	coreAtomCount = 0;
37	shellAtomCount = 0;
38
39
40
41	moleculeCount = 0;
42	foundCore = 0;
43	foundShell = 0;
44	totalMolecules = 0;
45	coreHasOrientation = 0;
46	shellHasOrientation = 0;
47	nInterface = 0;
48	nMol = 0;
49
50	hasError = 0;
51	Errors = 0;
52
53	//Initialize class members from bsInfo struct that sysbuilder provides.
54	isRandom = bsInfo.isRandomParticle;
55	hasVacancies = bsInfo.hasVacancies;
56	latticeType = bsInfo.latticeType;
57	particleRadius = bsInfo.particleRadius;
58	coreRadius = bsInfo.coreRadius;
59	vacancyFraction = bsInfo.vacancyFraction;
60	latticeSpacing = bsInfo.latticeSpacing;
61	soluteX = bsInfo.soluteX; //Mole fraction for random particle.
62
63
64
65
66
67	for (i=0;bsInfo.nComponents;i++){
68	if( !strcmp( bsInfo.compStamps[i]->getID(),bsInfo.coreName )){
69	foundCore = 1;
70	coreStamp = bsInfo.compStamps[i];
71	nCoreMolecules = bsInfo.componentsNmol[i];
72	}
73	if( !strcmp( bsInfo.compStamps[i]->getID(),bsInfo.shellName)){
74	foundShell = 1;
75	shellStamp = bsInfo.compStamps[i];
76	nShellMolecules = bsInfo.componentsNmol[i];
77
78	}
79
80	}
81
82
83
84	if( !foundCore ){
85	hasError = 1;
86	return;
87	}
88	if( !foundShell ){
89	hasError = 1;
90	return;
91	}
92
93
94
95	Errors = sanityCheck();
96
97	if (Errors){
98	hasError = 1;
99	return;
100	}
101
102
103
104
105
106
107
108	nCoreModelAtoms = coreStamp->getNAtoms();
109	nShellModelAtoms = shellStamp->getNAtoms();
110
111
112	// We assume that if the core or shell model has more then one atom
113	// the model has an orientational component...
114	if (nCoreModelAtoms > 1) coreHasOrientation = 1;
115	if (nShellModelAtoms > 1) shellHasOrientation = 1;
116
117	maxModelNatoms = std::max(nCoreModelAtoms,nShellModelAtoms);
118
119	/* If we specify a number of atoms in bass, we will try to build a nanopartice
120	with that number.
121	*/
122
123
124	if ((nShellMolecules != 0) && (nCoreMolecules != 0)){
125	totalMolecules = nShellMolecules + nCoreMolecules;
126	nCells = ceil(pow((double)totalMolecules/4.0, 1/3));
127	buildNmol = 1;
128	}
129	else {
130	nCells = 2.0 * particleRadius/latticeSpacing;
131	shellRadius = particleRadius - coreRadius;
132	}
133
134
135
136
137	// Initialize random seed
138	srand48( RAND_SEED );
139
140
141	}
142
143
144	nanoBuilder::~nanoBuilder(){
145	}
146
147
148	// Checks to make sure we aren't doing something the builder can't do.
149	int nanoBuilder::sanityCheck(void){
150
151	// Right now we only do bimetallic nanoparticles
152	if (bsInfo.nComponents > 2) return 1;
153
154	//Check for vacancies and random
155	if (hasVacancies && isRandom) return 1;
156
157	// make sure we aren't trying to build a core larger then the total particle size
158	if ((coreRadius >= particleRadius) && (particleRadius != 0)) return 1;
159
160	// we initialize the lattice spacing to be 0.0, if the lattice spacing is still 0.0
161	// we have a problem
162	if (latticeSpacing == 0.0) return 1;
163
164	// Check to see if we are specifing the number of atoms in the particle correctly.
165	if ((nShellMolecules == 0) && (nCoreMolecules != 0)){
166	cerr << "nShellParticles is zero and nCoreParticles != 0" << "\n";
167	return 1;
168	}
169	// Make sure there are more then two components if we are building a randomly mixed particle.
170	if ((bsInfo.nComponents < 2) && (isRandom)){
171	cerr << "Two Components are needed to build a random particle." << "\n";
172	}
173	// Make sure both the core and shell models specify a target nmol.
174	if ((nShellMolecules != 0) && (nCoreMolecules == 0)){
175	cerr << "nCoreParticles is zero and nShellParticles != 0" << "\n";
176	return 1;
177	}
178
179	return 0;
180
181	}
182
183
184
185	int nanoBuilder::buildNanoParticle( void ){
186
187	int ix;
188	int iy;
189	int iz;
190	double *rx;
191	double *ry;
192	double *rz;
193	double pos[3];
194	double A[3][3];
195	double HmatI[3][3];
196
197	int nCellSites;
198	int iref;
199	int appNMols;
200	int latticeCount = 0;
201
202	int nAtoms;
203	int nCoreAtomCounter = 0;
204	int nShellAtomCounter = 0;
205	int hasError;
206
207	int i, j;
208
209	int interfaceIndex = 0;
210	double dist;
211	double distsq;
212	int latticeNpoints;
213	int shesActualSizetoMe = 0;
214
215	DumpWriter* writer;
216	SimInfo* simnfo;
217
218	Lattice *myLattice;
219	MoLocator *coreLocate;
220	MoLocator *shellLocate;
221
222
223	Atom** atoms;
224
225	hasError = 0;
226
227	myLattice = new Lattice(FCC_LATTICE_TYPE,latticeSpacing);
228	/*
229	latticeNpoints = myLattice.getNpoints();
230
231	// Initializd atom vector to approximate size.
232	switch (buildType){
233
234	case BUILD_NMOL_PARTICLE:
235
236	break;
237	case BUILD_CORE_SHELL_VACANCY:
238	// Make space in the vector for all atoms except the last full cells
239	// We will have to add at most (latticeNpoints-1)^3 to vector
240	appNMols = latticeNPoints * pow((double)(nCells - 1),3);
241	moleculeVector.pushBack();
242
243	default:
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
248	}
249	*/
250
251
252
253
254	// Create molocator and atom arrays.
255	coreLocate = new MoLocator(coreStamp);
256	shellLocate = new MoLocator(shellStamp);
257
258
259
260
261
262
263	for(iz=-nCells;iz < nCells;iz++){
264	for(iy=-nCells;iy<nCells;iy++){
265	for(ix=-nCells;ix<nCells;ix++){
266	nCellSites = myLattice->getLatticePoints(&rx,&ry,&rz,
267	ix,iy,iz);
268	for (iref=1;iref<nCellSites;iref++){
269	latticeCount++;
270
271	pos[0] = rx[iref];
272	pos[1] = ry[iref];
273	pos[2] = rz[iref];
274
275	distsq = rx[iref]rx[iref] + ry[iref]ry[iref] +rz[iref]*rz[iref];
276	dist = sqrt(distsq);
277
278	switch(buildType){
279
280	case BUILD_CORE_SHELL:
281	nanoBuilder::buildWithCoreShell(dist,pos);
282	break;
283	case BUILD_CORE_SHELL_VACANCY:
284	nanoBuilder::buildWithVacancies(dist,pos);
285	break;
286
287	case BUILD_RANDOM_PARTICLE:
288	nanoBuilder::buildRandomlyMixed(dist,pos);
289	break;
290	case BUILD_NMOL_PARTICLE:
291	nanoBuilder::buildNmolParticle(dist,pos);
292	}
293	}
294	}
295	}
296	}
297
298
299
300	// Create vacancies
301	if (hasVacancies) buildVacancies();
302
303	// Find the size of the atom vector not including Null atoms
304	for (i=0;i<moleculeVector.size();i++){
305	if (! moleculeVector[i].isVacancy){
306	shesActualSizetoMe++;
307	nAtoms = moleculeVector[i].myStamp->getNAtoms();
308	}
309	}
310
311	// Make a random particle.
312	if (isRandom){
313	placeRandom(shesActualSizetoMe);
314
315	// Loop back thru and count natoms since they may have changed
316	for (i=0;i<moleculeVector.size();i++){
317	if (! moleculeVector[i].isVacancy){
318	shesActualSizetoMe++;
319	nAtoms = moleculeVector[i].myStamp->getNAtoms();
320	}
321	}
322	}
323
324
325	Atom::createArrays( nAtoms );
326	atoms = new Atom*[nAtoms];
327
328
329
330	shesActualSizetoMe = 0;
331	/* Use the information from the molecule vector to place the atoms.
332	*/
333	for (i= 0;i<moleculeVector.size();i++){
334	if (! moleculeVector[i].isVacancy) {
335	orientationMunger( A );
336	if( moleculeVector[i].isCore){
337	nCoreAtomCounter += nCoreModelAtoms;
338	coreLocate->placeMol(moleculeVector[i].pos,A,atoms,nShellAtomCounter);
339	}
340	else {
341	nShellAtomCounter += nShellModelAtoms;
342	shellLocate->placeMol(moleculeVector[i].pos,A,atoms,nCoreAtomCounter);
343	}
344	shesActualSizetoMe++;
345	}
346	}
347
348
349	// shellLocate.placeMol(pos, A, moleculeVector,shellAtomCount);
350
351	for (i=0;i<3;i++)
352	for (j=0; j<3; j++)
353	simnfo->Hmat[i][j] = 0.0;
354
355	simnfo->Hmat[0][0] = 1.0;
356	simnfo->Hmat[1][1] = 1.0;
357	simnfo->Hmat[2][2] = 1.0;
358
359	// set up the SimInfo object
360
361	simnfo = new SimInfo();
362	simnfo->n_atoms = nAtoms;
363
364	sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix );
365	sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix );
366
367	simnfo->atoms = atoms;
368
369	// set up the writer and write out
370
371	writer = new DumpWriter( simnfo );
372	writer->writeFinal(0.0);
373
374	// clean up
375
376	delete[] myLattice;
377
378	return hasError;
379	}
380
381	// Begin Builder routines------------------------------->
382
383	/* Builds a standard core-shell nanoparticle.
384	*/
385	void nanoBuilder::buildWithCoreShell(double dist, double pos[3]){
386
387
388	if ( dist <= particleRadius ){
389	moleculeVector.push_back(myMol);
390
391	if (dist <= coreRadius){
392	coreAtomCount += nCoreModelAtoms;
393	moleculeVector[moleculeCount].pos[0] = pos[0];
394	moleculeVector[moleculeCount].pos[1] = pos[1];
395	moleculeVector[moleculeCount].pos[2] = pos[2];
396	moleculeVector[moleculeCount].myStamp = coreStamp;
397	moleculeVector[moleculeCount].isCore = 1;
398	moleculeVector[moleculeCount].isShell = 0;
399
400	}
401	// Place shell
402	else{
403	shellAtomCount += nShellModelAtoms;
404	moleculeVector[moleculeCount].pos[0] = pos[0];
405	moleculeVector[moleculeCount].pos[1] = pos[1];
406	moleculeVector[moleculeCount].pos[2] = pos[2];
407	moleculeVector[moleculeCount].myStamp = shellStamp;
408	moleculeVector[moleculeCount].isCore = 0;
409	moleculeVector[moleculeCount].isShell = 1;
410
411	}
412	moleculeCount++;
413	}
414
415	}
416	/*
417	Builds a core-shell nanoparticle and tracks the number of molecules at the
418	interface between the core-shell. These are recorded in vacancyInterface which is just
419	an integer vector.
420	*/
421	void nanoBuilder::buildWithVacancies(double dist, double pos[3]){
422	if ( dist <= particleRadius ){
423
424	moleculeVector.push_back(myMol);
425	if (dist <= coreRadius){
426
427	coreAtomCount += nCoreModelAtoms;
428	moleculeVector[moleculeCount].pos[0] = pos[0];
429	moleculeVector[moleculeCount].pos[1] = pos[1];
430	moleculeVector[moleculeCount].pos[2] = pos[2];
431	moleculeVector[moleculeCount].myStamp = coreStamp;
432	moleculeVector[moleculeCount].isCore = 1;
433	moleculeVector[moleculeCount].isShell = 0;
434
435	if ((dist >= coreRadius - vacancyRadius/2.0) &&
436	(dist <= coreRadius + vacancyRadius/2.0)){
437
438	vacancyInterface.push_back(moleculeCount);
439	nInterface++;
440	}
441	} else {
442	// Place shell
443	shellAtomCount += nShellModelAtoms;
444	moleculeVector[moleculeCount].pos[0] = pos[0];
445	moleculeVector[moleculeCount].pos[1] = pos[1];
446	moleculeVector[moleculeCount].pos[2] = pos[2];
447	moleculeVector[moleculeCount].myStamp = shellStamp;
448	moleculeVector[moleculeCount].isCore = 0;
449	moleculeVector[moleculeCount].isShell = 1;
450
451	}
452	moleculeCount++;
453	}
454
455
456
457	}
458
459	/* Builds a core-shell nanoparticle where the number of core and shell
460	molecules is known.
461	*/
462	void nanoBuilder::buildNmolParticle(double dist, double pos[3]){
463	static int nMolCounter = 0;
464	static int nCoreMolCounter = 0;
465
466
467	if (nMolCounter < totalMolecules){
468	moleculeVector.push_back(myMol);
469	if (nCoreMolCounter < nCoreMolecules){
470
471	coreAtomCount += nCoreModelAtoms;
472	moleculeVector[moleculeCount].pos[0] = pos[0];
473	moleculeVector[moleculeCount].pos[1] = pos[1];
474	moleculeVector[moleculeCount].pos[2] = pos[2];
475	moleculeVector[moleculeCount].myStamp = coreStamp;
476	moleculeVector[moleculeCount].isCore = 1;
477	moleculeVector[moleculeCount].isShell = 0;
478
479
480	} else {
481	shellAtomCount += nShellModelAtoms;
482	moleculeVector[moleculeCount].pos[0] = pos[0];
483	moleculeVector[moleculeCount].pos[1] = pos[1];
484	moleculeVector[moleculeCount].pos[2] = pos[2];
485	moleculeVector[moleculeCount].myStamp = shellStamp;
486	moleculeVector[moleculeCount].isCore = 0;
487	moleculeVector[moleculeCount].isShell = 1;
488
489
490	}
491
492	}
493	}
494
495
496	/* Builds a randomly mixed nanoparticle. We build the particle to be
497	entirely the core model, then randomly switch identities after the particle is built.
498	*/
499	void nanoBuilder::buildRandomlyMixed(double dist, double pos[3]){
500
501
502	if ( dist <= particleRadius ){
503	moleculeCount++;
504
505
506	moleculeVector[moleculeCount].pos[0] = pos[0];
507	moleculeVector[moleculeCount].pos[1] = pos[1];
508	moleculeVector[moleculeCount].pos[2] = pos[2];
509	moleculeVector[moleculeCount].myStamp = coreStamp;
510	moleculeVector[moleculeCount].isCore = 1;
511	moleculeVector[moleculeCount].isShell = 0;
512
513	}
514
515
516
517	}
518
519
520	// -----------------------END Builder routines.
521
522
523
524	//------------------------Begin Helper routines.
525	void nanoBuilder::placeRandom(int totalMol){
526	int nSolute;
527	int nSolvent;
528	int i;
529	int notfound;
530	double solute_x;
531	double solvent_x;
532
533	int tester;
534
535	nSolute = floor(soluteX * (double)totalMolecules); //CHECK ME
536	nSolvent = totalMolecules - nSolute;
537
538	solute_x = (double)nSolute/(double)totalMolecules;
539	solvent_x = 1.0 - solute_x;
540
541
542
543
544	for(i=0;nSolute-1;i++){
545	notfound = 1;
546
547	while(notfound){
548
549	tester = floor((double)totalMolecules * drand48()); //Pick a molecule
550
551	if (moleculeVector[tester].isCore){ // Make sure we select a core atom to change
552
553	moleculeVector[tester].isCore = 0;
554	moleculeVector[tester].isShell = 1;
555	moleculeVector[tester].myStamp = shellStamp;
556	notfound = 0; //set notfound = false.
557	}
558
559	}
560
561	}
562	}
563
564
565	void nanoBuilder::buildVacancies(void){
566	int i;
567	int* VacancyList; //logical nInterface long.
568	int notfound;
569	int index = 0;
570	int nVacancies;
571	int tester;
572
573	if (nInterface != 0){
574	nVacancies = floor((double)nInterface * vacancyFraction);
575
576	VacancyList = new int[nInterface];
577
578	// make vacancy list all false
579	for(i=0;i<nInterface-1;i++){
580	VacancyList[i] = 0;
581	}
582
583	// Build a vacancy list....
584	for(i=0;nVacancies-1;i++){
585	notfound = 1;
586	while(notfound){
587
588	tester = floor((double)nInterface * drand48());
589
590	if(! VacancyList[tester]){
591	VacancyList[tester] = 1;
592	notfound = 0;
593	}
594
595	}
596	}
597	}
598	// Loop through and kill the vacancies from atom vector.
599
600	for (i=0;i<nInterface;i++){
601	if (VacancyList[i]){
602	moleculeVector[vacancyInterface[i]].isVacancy = 1;
603	} // End Vacancy List
604	} // for nInterface
605
606
607	delete[] VacancyList;
608	}
609
610
611
612
613	void nanoBuilder::orientationMunger(double rot[3][3]){
614
615	double theta, phi, psi;
616	double cosTheta;
617
618	// select random phi, psi, and cosTheta
619
620	phi = 2.0 * M_PI * drand48();
621	psi = 2.0 * M_PI * drand48();
622	cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1
623
624	theta = acos( cosTheta );
625
626	rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
627	rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
628	rot[0][2] = sin(theta) * sin(psi);
629
630	rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
631	rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
632	rot[1][2] = sin(theta) * cos(psi);
633
634	rot[2][0] = sin(phi) * sin(theta);
635	rot[2][1] = -cos(phi) * sin(theta);
636	rot[2][2] = cos(theta);
637
638	}
639
640
641
642
643
644
645