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[9];
  
  int nCellSites;
  int iref;
  int appNMols;
  int latticeCount = 0;
 
  int nAtoms;
  int nCoreAtomCounter = 0;
  int nShellAtomCounter = 0;
  int hasError;

  int i;

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

  DumpWriter* writer;
  SimInfo* simnfo;

  Lattice::Lattice *myLattice;
  MoLocator::MoLocator *coreLocate;
  MoLocator::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<9;i++) simnfo->Hmat[i] = 0;
  simnfo->Hmat[0] = 1;
  simnfo->Hmat[4] = 1;
  simnfo->Hmat[8] = 1;

  // 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:	589
Committed:	Thu Jul 10 19:53:50 2003 UTC (21 years ago) by chuckv
File size:	15076 byte(s)
Log Message:	Added nanoBuilder and a general Lattice builder.
#	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
18
19	nanoBuilder::nanoBuilder(int thisIsRandom, int thisHasVacancies,
20	int thisLatticeType, double thisParticleRadius,
21	double thisCoreRadius, double thisVacancyFraction,
22	double thisVacancyRadius,
23	double thisLatticeSpacing,
24	double solute_X,
25	int &hasError){
26	int Errors;
27	int foundCore,foundShell;
28	int i;
29
30	//Zero variables
31	particleRadius = 0.0;
32	coreRadius = 0.0;
33	vacancyFraction = 0.0;
34	vacancyRadius = 0.0;
35	shellRadius = 0.0;
36	latticeSpacing = 0.0;
37
38	buildNmol = 0;
39
40	nCoreMolecules = 0;
41	nShellMolecules = 0;
42
43	atomCount = 0;
44	coreAtomCount = 0;
45	shellAtomCount = 0;
46
47
48
49	moleculeCount = 0;
50	foundCore = 0;
51	foundShell = 0;
52	totalMolecules = 0;
53	coreHasOrientation = 0;
54	shellHasOrientation = 0;
55	nInterface = 0;
56	nMol = 0;
57
58	hasError = 0;
59	Errors = 0;
60
61
62	isRandom = thisIsRandom;
63	hasVacancies = thisHasVacancies;
64	latticeType = thisLatticeType;
65	particleRadius = thisParticleRadius;
66	coreRadius = thisCoreRadius;
67	vacancyFraction = thisVacancyFraction;
68	latticeSpacing = thisLatticeSpacing;
69	soluteX = solute_X; //Mole fraction for random particle.
70
71
72
73
74
75	for (i=0;bsInfo.nComponents;i++){
76	if( !strcmp( bsInfo.compStamps[i]->getID(),bsInfo.coreName )){
77	foundCore = 1;
78	coreStamp = bsInfo.compStamps[i];
79	nCoreMolecules = bsInfo.componentsNmol[i];
80	}
81	if( !strcmp( bsInfo.compStamps[i]->getID(),bsInfo.shellName)){
82	foundShell = 1;
83	shellStamp = bsInfo.compStamps[i];
84	nShellMolecules = bsInfo.componentsNmol[i];
85
86	}
87
88	}
89
90
91
92	if( !foundCore ){
93	hasError = 1;
94	return;
95	}
96	if( !foundShell ){
97	hasError = 1;
98	return;
99	}
100
101
102
103	Errors = sanityCheck();
104
105	if (Errors){
106	hasError = 1;
107	return;
108	}
109
110
111
112
113
114
115
116	nCoreModelAtoms = coreStamp->getNAtoms();
117	nShellModelAtoms = shellStamp->getNAtoms();
118
119
120	// We assume that if the core or shell model has more then one atom
121	// the model has an orientational component...
122	if (nCoreModelAtoms > 1) coreHasOrientation = 1;
123	if (nShellModelAtoms > 1) shellHasOrientation = 1;
124
125	maxModelNatoms = std::max(nCoreModelAtoms,nShellModelAtoms);
126
127	/* If we specify a number of atoms in bass, we will try to build a nanopartice
128	with that number.
129	*/
130
131
132	if ((nShellMolecules != 0) && (nCoreMolecules != 0)){
133	totalMolecules = nShellMolecules + nCoreMolecules;
134	nCells = ceil(pow((double)totalMolecules/4.0, 1/3));
135	buildNmol = 1;
136	}
137	else {
138	nCells = 2.0 * particleRadius/latticeSpacing;
139	shellRadius = particleRadius - coreRadius;
140	}
141
142
143
144
145	// Initialize random seed
146	srand48( RAND_SEED );
147
148
149	}
150
151
152	nanoBuilder::~nanoBuilder(){
153	}
154
155
156	// Checks to make sure we aren't doing something the builder can't do.
157	int nanoBuilder::sanityCheck(void){
158
159	// Right now we only do bimetallic nanoparticles
160	if (bsInfo.nComponents > 2) return 1;
161
162	//Check for vacancies and random
163	if (hasVacancies && isRandom) return 1;
164
165	// make sure we aren't trying to build a core larger then the total particle size
166	if ((coreRadius >= particleRadius) && (particleRadius != 0)) return 1;
167
168	// we initialize the lattice spacing to be 0.0, if the lattice spacing is still 0.0
169	// we have a problem
170	if (latticeSpacing == 0.0) return 1;
171
172	// Check to see if we are specifing the number of atoms in the particle correctly.
173	if ((nShellMolecules == 0) && (nCoreMolecules != 0)){
174	cerr << "nShellParticles is zero and nCoreParticles != 0" << "\n";
175	return 1;
176	}
177	// Make sure there are more then two components if we are building a randomly mixed particle.
178	if ((bsInfo.nComponents < 2) && (isRandom)){
179	cerr << "Two Components are needed to build a random particle." << "\n";
180	}
181	// Make sure both the core and shell models specify a target nmol.
182	if ((nShellMolecules != 0) && (nCoreMolecules == 0)){
183	cerr << "nCoreParticles is zero and nShellParticles != 0" << "\n";
184	return 1;
185	}
186
187	return 0;
188
189	}
190
191
192
193	int nanoBuilder::buildNanoParticle( void ){
194
195	int ix;
196	int iy;
197	int iz;
198	double *rx;
199	double *ry;
200	double *rz;
201	double pos[3];
202	double A[3][3];
203	double HmatI[9];
204
205	int nCellSites;
206	int iref;
207	int appNMols;
208	int latticeCount = 0;
209
210	int nAtoms;
211	int nCoreAtomCounter = 0;
212	int nShellAtomCounter = 0;
213	int hasError;
214
215	int i;
216
217	int interfaceIndex = 0;
218	double dist;
219	double distsq;
220	int latticeNpoints;
221	int shesActualSizetoMe = 0;
222
223	DumpWriter* writer;
224	SimInfo* simnfo;
225
226	Lattice::Lattice *myLattice;
227	MoLocator::MoLocator *coreLocate;
228	MoLocator::MoLocator *shellLocate;
229
230
231	Atom** atoms;
232
233	hasError = 0;
234
235	myLattice = new Lattice(FCC_LATTICE_TYPE,latticeSpacing);
236	/*
237	latticeNpoints = myLattice.getNpoints();
238
239	// Initializd atom vector to approximate size.
240	switch (buildType){
241
242	case BUILD_NMOL_PARTICLE:
243
244	break;
245	case BUILD_CORE_SHELL_VACANCY:
246	// Make space in the vector for all atoms except the last full cells
247	// We will have to add at most (latticeNpoints-1)^3 to vector
248	appNMols = latticeNPoints * pow((double)(nCells - 1),3);
249	moleculeVector.pushBack();
250
251	default:
252	// Make space in the vector for all atoms except the last full cells
253	// We will have to add at most (latticeNpoints-1)^3 to vector
254	appNMols = latticeNPoints * pow((double)(nCells - 1),3);
255
256	}
257	*/
258
259
260
261
262	// Create molocator and atom arrays.
263	coreLocate = new MoLocator(coreStamp);
264	shellLocate = new MoLocator(shellStamp);
265
266
267
268
269
270
271	for(iz=-nCells;iz < nCells;iz++){
272	for(iy=-nCells;iy<nCells;iy++){
273	for(ix=-nCells;ix<nCells;ix++){
274	nCellSites = myLattice->getLatticePoints(&rx,&ry,&rz,
275	ix,iy,iz);
276	for (iref=1;iref<nCellSites;iref++){
277	latticeCount++;
278
279	pos[0] = rx[iref];
280	pos[1] = ry[iref];
281	pos[2] = rz[iref];
282
283	distsq = rx[iref]rx[iref] + ry[iref]ry[iref] +rz[iref]*rz[iref];
284	dist = sqrt(distsq);
285
286	switch(buildType){
287
288	case BUILD_CORE_SHELL:
289	nanoBuilder::buildWithCoreShell(dist,pos);
290	break;
291	case BUILD_CORE_SHELL_VACANCY:
292	nanoBuilder::buildWithVacancies(dist,pos);
293	break;
294
295	case BUILD_RANDOM_PARTICLE:
296	nanoBuilder::buildRandomlyMixed(dist,pos);
297	break;
298	case BUILD_NMOL_PARTICLE:
299	nanoBuilder::buildNmolParticle(dist,pos);
300	}
301	}
302	}
303	}
304	}
305
306
307
308	// Create vacancies
309	if (hasVacancies) buildVacancies();
310
311	// Find the size of the atom vector not including Null atoms
312	for (i=0;i<moleculeVector.size();i++){
313	if (! moleculeVector[i].isVacancy){
314	shesActualSizetoMe++;
315	nAtoms = moleculeVector[i].myStamp->getNAtoms();
316	}
317	}
318
319	// Make a random particle.
320	if (isRandom){
321	placeRandom(shesActualSizetoMe);
322
323	// Loop back thru and count natoms since they may have changed
324	for (i=0;i<moleculeVector.size();i++){
325	if (! moleculeVector[i].isVacancy){
326	shesActualSizetoMe++;
327	nAtoms = moleculeVector[i].myStamp->getNAtoms();
328	}
329	}
330	}
331
332
333	Atom::createArrays( nAtoms );
334	atoms = new Atom*[nAtoms];
335
336
337
338	shesActualSizetoMe = 0;
339	/* Use the information from the molecule vector to place the atoms.
340	*/
341	for (i= 0;i<moleculeVector.size();i++){
342	if (! moleculeVector[i].isVacancy) {
343	orientationMunger( A );
344	if( moleculeVector[i].isCore){
345	nCoreAtomCounter =+ nCoreModelAtoms;
346	coreLocate->placeMol(moleculeVector[i].pos,A,atoms,nShellAtomCounter);
347	}
348	else {
349	nShellAtomCounter =+ nShellModelAtoms;
350	shellLocate->placeMol(moleculeVector[i].pos,A,atoms,nCoreAtomCounter);
351	}
352	shesActualSizetoMe++;
353	}
354	}
355
356
357	// shellLocate.placeMol(pos, A, moleculeVector,shellAtomCount);
358
359	for (i=0;i<9;i++) simnfo->Hmat[i] = 0;
360	simnfo->Hmat[0] = 1;
361	simnfo->Hmat[4] = 1;
362	simnfo->Hmat[8] = 1;
363
364	// set up the SimInfo object
365	simnfo = new SimInfo();
366	simnfo->n_atoms = nAtoms;
367
368
369	sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix );
370	sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix );
371
372	simnfo->atoms = atoms;
373
374	// set up the writer and write out
375
376	writer = new DumpWriter( simnfo );
377	writer->writeFinal(0.0);
378
379	// clean up
380
381	delete[] myLattice;
382
383	return hasError;
384	}
385
386	// Begin Builder routines------------------------------->
387
388	/* Builds a standard core-shell nanoparticle.
389	*/
390	void nanoBuilder::buildWithCoreShell(double dist, double pos[3]){
391
392
393	if ( dist <= particleRadius ){
394	moleculeVector.push_back(myMol);
395
396	if (dist <= coreRadius){
397	coreAtomCount =+ nCoreModelAtoms;
398	moleculeVector[moleculeCount].pos[0] = pos[0];
399	moleculeVector[moleculeCount].pos[1] = pos[1];
400	moleculeVector[moleculeCount].pos[2] = pos[2];
401	moleculeVector[moleculeCount].myStamp = coreStamp;
402	moleculeVector[moleculeCount].isCore = 1;
403	moleculeVector[moleculeCount].isShell = 0;
404
405	}
406	// Place shell
407	else{
408	shellAtomCount =+ nShellModelAtoms;
409	moleculeVector[moleculeCount].pos[0] = pos[0];
410	moleculeVector[moleculeCount].pos[1] = pos[1];
411	moleculeVector[moleculeCount].pos[2] = pos[2];
412	moleculeVector[moleculeCount].myStamp = shellStamp;
413	moleculeVector[moleculeCount].isCore = 0;
414	moleculeVector[moleculeCount].isShell = 1;
415
416	}
417	moleculeCount++;
418	}
419
420	}
421	/*
422	Builds a core-shell nanoparticle and tracks the number of molecules at the
423	interface between the core-shell. These are recorded in vacancyInterface which is just
424	an integer vector.
425	*/
426	void nanoBuilder::buildWithVacancies(double dist, double pos[3]){
427	if ( dist <= particleRadius ){
428
429	moleculeVector.push_back(myMol);
430	if (dist <= coreRadius){
431
432	coreAtomCount =+ nCoreModelAtoms;
433	moleculeVector[moleculeCount].pos[0] = pos[0];
434	moleculeVector[moleculeCount].pos[1] = pos[1];
435	moleculeVector[moleculeCount].pos[2] = pos[2];
436	moleculeVector[moleculeCount].myStamp = coreStamp;
437	moleculeVector[moleculeCount].isCore = 1;
438	moleculeVector[moleculeCount].isShell = 0;
439
440	if ((dist >= coreRadius - vacancyRadius/2.0) &&
441	(dist <= coreRadius + vacancyRadius/2.0)){
442
443	vacancyInterface.push_back(moleculeCount);
444	nInterface++;
445	}
446	} else {
447	// Place shell
448	shellAtomCount =+ nShellModelAtoms;
449	moleculeVector[moleculeCount].pos[0] = pos[0];
450	moleculeVector[moleculeCount].pos[1] = pos[1];
451	moleculeVector[moleculeCount].pos[2] = pos[2];
452	moleculeVector[moleculeCount].myStamp = shellStamp;
453	moleculeVector[moleculeCount].isCore = 0;
454	moleculeVector[moleculeCount].isShell = 1;
455
456	}
457	moleculeCount++;
458	}
459
460
461
462	}
463
464	/* Builds a core-shell nanoparticle where the number of core and shell
465	molecules is known.
466	*/
467	void nanoBuilder::buildNmolParticle(double dist, double pos[3]){
468	static int nMolCounter = 0;
469	static int nCoreMolCounter = 0;
470
471
472	if (nMolCounter < totalMolecules){
473	moleculeVector.push_back(myMol);
474	if (nCoreMolCounter < nCoreMolecules){
475
476	coreAtomCount =+ nCoreModelAtoms;
477	moleculeVector[moleculeCount].pos[0] = pos[0];
478	moleculeVector[moleculeCount].pos[1] = pos[1];
479	moleculeVector[moleculeCount].pos[2] = pos[2];
480	moleculeVector[moleculeCount].myStamp = coreStamp;
481	moleculeVector[moleculeCount].isCore = 1;
482	moleculeVector[moleculeCount].isShell = 0;
483
484
485	} else {
486	shellAtomCount =+ nShellModelAtoms;
487	moleculeVector[moleculeCount].pos[0] = pos[0];
488	moleculeVector[moleculeCount].pos[1] = pos[1];
489	moleculeVector[moleculeCount].pos[2] = pos[2];
490	moleculeVector[moleculeCount].myStamp = shellStamp;
491	moleculeVector[moleculeCount].isCore = 0;
492	moleculeVector[moleculeCount].isShell = 1;
493
494
495	}
496
497	}
498	}
499
500
501	/* Builds a randomly mixed nanoparticle. We build the particle to be
502	entirely the core model, then randomly switch identities after the particle is built.
503	*/
504	void nanoBuilder::buildRandomlyMixed(double dist, double pos[3]){
505
506
507	if ( dist <= particleRadius ){
508	moleculeCount++;
509
510
511	moleculeVector[moleculeCount].pos[0] = pos[0];
512	moleculeVector[moleculeCount].pos[1] = pos[1];
513	moleculeVector[moleculeCount].pos[2] = pos[2];
514	moleculeVector[moleculeCount].myStamp = coreStamp;
515	moleculeVector[moleculeCount].isCore = 1;
516	moleculeVector[moleculeCount].isShell = 0;
517
518	}
519
520
521
522	}
523
524
525	// -----------------------END Builder routines.
526
527
528
529	//------------------------Begin Helper routines.
530	void nanoBuilder::placeRandom(int totalMol){
531	int nSolute;
532	int nSolvent;
533	int i;
534	int notfound;
535	double solute_x;
536	double solvent_x;
537
538	int tester;
539
540	nSolute = floor(soluteX * (double)totalMolecules); //CHECK ME
541	nSolvent = totalMolecules - nSolute;
542
543	solute_x = (double)nSolute/(double)totalMolecules;
544	solvent_x = 1.0 - solute_x;
545
546
547
548
549	for(i=0;nSolute-1;i++){
550	notfound = 1;
551
552	while(notfound){
553
554	tester = floor((double)totalMolecules * drand48()); //Pick a molecule
555
556	if (moleculeVector[tester].isCore){ // Make sure we select a core atom to change
557
558	moleculeVector[tester].isCore = 0;
559	moleculeVector[tester].isShell = 1;
560	moleculeVector[tester].myStamp = shellStamp;
561	notfound = 0; //set notfound = false.
562	}
563
564	}
565
566	}
567	}
568
569
570	void nanoBuilder::buildVacancies(void){
571	int i;
572	int* VacancyList; //logical nInterface long.
573	int notfound;
574	int index = 0;
575	int nVacancies;
576	int tester;
577
578	if (nInterface != 0){
579	nVacancies = floor((double)nInterface * vacancyFraction);
580
581	VacancyList = new int[nInterface];
582
583	// make vacancy list all false
584	for(i=0;i<nInterface-1;i++){
585	VacancyList[i] = 0;
586	}
587
588	// Build a vacancy list....
589	for(i=0;nVacancies-1;i++){
590	notfound = 1;
591	while(notfound){
592
593	tester = floor((double)nInterface * drand48());
594
595	if(! VacancyList[tester]){
596	VacancyList[tester] = 1;
597	notfound = 0;
598	}
599
600	}
601	}
602	}
603	// Loop through and kill the vacancies from atom vector.
604
605	for (i=0;i<nInterface;i++){
606	if (VacancyList[i]){
607	moleculeVector[vacancyInterface[i]].isVacancy = 1;
608	} // End Vacancy List
609	} // for nInterface
610
611
612	delete[] VacancyList;
613	}
614
615
616
617
618	void nanoBuilder::orientationMunger(double rot[3][3]){
619
620	double theta, phi, psi;
621	double cosTheta;
622
623	// select random phi, psi, and cosTheta
624
625	phi = 2.0 * M_PI * drand48();
626	psi = 2.0 * M_PI * drand48();
627	cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1
628
629	theta = acos( cosTheta );
630
631	rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
632	rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
633	rot[0][2] = sin(theta) * sin(psi);
634
635	rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
636	rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
637	rot[1][2] = sin(theta) * cos(psi);
638
639	rot[2][0] = sin(phi) * sin(theta);
640	rot[2][1] = -cos(phi) * sin(theta);
641	rot[2][2] = cos(theta);
642
643	}
644
645
646
647
648
649
650