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chuckv |
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#include <iostream> |
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#include <cstdlib> |
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#include <cstring> |
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#include <cmath> |
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#include <vector> |
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#include "simError.h" |
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#include "SimInfo.hpp" |
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#include "ReadWrite.hpp" |
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#include "latticeBuilder.hpp" |
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#include "MoLocator.hpp" |
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#include "sysBuild.hpp" |
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#include "nanoBuilder.hpp" |
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nanoBuilder::nanoBuilder(int thisIsRandom, int thisHasVacancies, |
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int thisLatticeType, double thisParticleRadius, |
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double thisCoreRadius, double thisVacancyFraction, |
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double thisVacancyRadius, |
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double thisLatticeSpacing, |
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double solute_X, |
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int &hasError){ |
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int Errors; |
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int foundCore,foundShell; |
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int i; |
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//Zero variables |
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particleRadius = 0.0; |
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coreRadius = 0.0; |
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vacancyFraction = 0.0; |
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vacancyRadius = 0.0; |
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shellRadius = 0.0; |
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latticeSpacing = 0.0; |
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buildNmol = 0; |
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nCoreMolecules = 0; |
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nShellMolecules = 0; |
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atomCount = 0; |
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coreAtomCount = 0; |
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shellAtomCount = 0; |
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moleculeCount = 0; |
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foundCore = 0; |
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foundShell = 0; |
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totalMolecules = 0; |
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coreHasOrientation = 0; |
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shellHasOrientation = 0; |
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nInterface = 0; |
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nMol = 0; |
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hasError = 0; |
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Errors = 0; |
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isRandom = thisIsRandom; |
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hasVacancies = thisHasVacancies; |
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latticeType = thisLatticeType; |
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particleRadius = thisParticleRadius; |
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coreRadius = thisCoreRadius; |
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vacancyFraction = thisVacancyFraction; |
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latticeSpacing = thisLatticeSpacing; |
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soluteX = solute_X; //Mole fraction for random particle. |
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for (i=0;bsInfo.nComponents;i++){ |
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if( !strcmp( bsInfo.compStamps[i]->getID(),bsInfo.coreName )){ |
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foundCore = 1; |
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coreStamp = bsInfo.compStamps[i]; |
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nCoreMolecules = bsInfo.componentsNmol[i]; |
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} |
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if( !strcmp( bsInfo.compStamps[i]->getID(),bsInfo.shellName)){ |
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foundShell = 1; |
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shellStamp = bsInfo.compStamps[i]; |
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nShellMolecules = bsInfo.componentsNmol[i]; |
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} |
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} |
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if( !foundCore ){ |
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hasError = 1; |
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return; |
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} |
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if( !foundShell ){ |
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hasError = 1; |
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return; |
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} |
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Errors = sanityCheck(); |
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if (Errors){ |
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hasError = 1; |
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return; |
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} |
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nCoreModelAtoms = coreStamp->getNAtoms(); |
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nShellModelAtoms = shellStamp->getNAtoms(); |
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// We assume that if the core or shell model has more then one atom |
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// the model has an orientational component... |
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if (nCoreModelAtoms > 1) coreHasOrientation = 1; |
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if (nShellModelAtoms > 1) shellHasOrientation = 1; |
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maxModelNatoms = std::max(nCoreModelAtoms,nShellModelAtoms); |
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/* If we specify a number of atoms in bass, we will try to build a nanopartice |
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with that number. |
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*/ |
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if ((nShellMolecules != 0) && (nCoreMolecules != 0)){ |
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totalMolecules = nShellMolecules + nCoreMolecules; |
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nCells = ceil(pow((double)totalMolecules/4.0, 1/3)); |
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buildNmol = 1; |
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} |
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else { |
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nCells = 2.0 * particleRadius/latticeSpacing; |
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shellRadius = particleRadius - coreRadius; |
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} |
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// Initialize random seed |
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srand48( RAND_SEED ); |
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} |
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nanoBuilder::~nanoBuilder(){ |
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} |
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// Checks to make sure we aren't doing something the builder can't do. |
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int nanoBuilder::sanityCheck(void){ |
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// Right now we only do bimetallic nanoparticles |
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if (bsInfo.nComponents > 2) return 1; |
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//Check for vacancies and random |
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if (hasVacancies && isRandom) return 1; |
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// make sure we aren't trying to build a core larger then the total particle size |
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if ((coreRadius >= particleRadius) && (particleRadius != 0)) return 1; |
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// we initialize the lattice spacing to be 0.0, if the lattice spacing is still 0.0 |
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// we have a problem |
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if (latticeSpacing == 0.0) return 1; |
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// Check to see if we are specifing the number of atoms in the particle correctly. |
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if ((nShellMolecules == 0) && (nCoreMolecules != 0)){ |
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cerr << "nShellParticles is zero and nCoreParticles != 0" << "\n"; |
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return 1; |
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} |
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// Make sure there are more then two components if we are building a randomly mixed particle. |
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if ((bsInfo.nComponents < 2) && (isRandom)){ |
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cerr << "Two Components are needed to build a random particle." << "\n"; |
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} |
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// Make sure both the core and shell models specify a target nmol. |
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if ((nShellMolecules != 0) && (nCoreMolecules == 0)){ |
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cerr << "nCoreParticles is zero and nShellParticles != 0" << "\n"; |
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return 1; |
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} |
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return 0; |
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} |
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int nanoBuilder::buildNanoParticle( void ){ |
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int ix; |
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int iy; |
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int iz; |
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double *rx; |
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double *ry; |
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double *rz; |
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double pos[3]; |
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double A[3][3]; |
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double HmatI[9]; |
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int nCellSites; |
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int iref; |
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int appNMols; |
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int latticeCount = 0; |
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int nAtoms; |
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int nCoreAtomCounter = 0; |
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int nShellAtomCounter = 0; |
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int hasError; |
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int i; |
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int interfaceIndex = 0; |
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double dist; |
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double distsq; |
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int latticeNpoints; |
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int shesActualSizetoMe = 0; |
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DumpWriter* writer; |
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SimInfo* simnfo; |
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Lattice::Lattice *myLattice; |
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MoLocator::MoLocator *coreLocate; |
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MoLocator::MoLocator *shellLocate; |
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Atom** atoms; |
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hasError = 0; |
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myLattice = new Lattice(FCC_LATTICE_TYPE,latticeSpacing); |
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/* |
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latticeNpoints = myLattice.getNpoints(); |
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// Initializd atom vector to approximate size. |
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switch (buildType){ |
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case BUILD_NMOL_PARTICLE: |
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break; |
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case BUILD_CORE_SHELL_VACANCY: |
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// Make space in the vector for all atoms except the last full cells |
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// We will have to add at most (latticeNpoints-1)^3 to vector |
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appNMols = latticeNPoints * pow((double)(nCells - 1),3); |
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moleculeVector.pushBack(); |
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default: |
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// Make space in the vector for all atoms except the last full cells |
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// We will have to add at most (latticeNpoints-1)^3 to vector |
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appNMols = latticeNPoints * pow((double)(nCells - 1),3); |
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} |
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*/ |
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// Create molocator and atom arrays. |
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coreLocate = new MoLocator(coreStamp); |
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shellLocate = new MoLocator(shellStamp); |
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for(iz=-nCells;iz < nCells;iz++){ |
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for(iy=-nCells;iy<nCells;iy++){ |
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for(ix=-nCells;ix<nCells;ix++){ |
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nCellSites = myLattice->getLatticePoints(&rx,&ry,&rz, |
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ix,iy,iz); |
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for (iref=1;iref<nCellSites;iref++){ |
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latticeCount++; |
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pos[0] = rx[iref]; |
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pos[1] = ry[iref]; |
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pos[2] = rz[iref]; |
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distsq = rx[iref]*rx[iref] + ry[iref]*ry[iref] +rz[iref]*rz[iref]; |
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dist = sqrt(distsq); |
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switch(buildType){ |
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case BUILD_CORE_SHELL: |
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nanoBuilder::buildWithCoreShell(dist,pos); |
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break; |
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case BUILD_CORE_SHELL_VACANCY: |
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nanoBuilder::buildWithVacancies(dist,pos); |
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break; |
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case BUILD_RANDOM_PARTICLE: |
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nanoBuilder::buildRandomlyMixed(dist,pos); |
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break; |
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case BUILD_NMOL_PARTICLE: |
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nanoBuilder::buildNmolParticle(dist,pos); |
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} |
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} |
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} |
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} |
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} |
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// Create vacancies |
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if (hasVacancies) buildVacancies(); |
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// Find the size of the atom vector not including Null atoms |
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for (i=0;i<moleculeVector.size();i++){ |
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if (! moleculeVector[i].isVacancy){ |
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shesActualSizetoMe++; |
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nAtoms = moleculeVector[i].myStamp->getNAtoms(); |
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} |
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} |
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// Make a random particle. |
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if (isRandom){ |
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placeRandom(shesActualSizetoMe); |
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// Loop back thru and count natoms since they may have changed |
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for (i=0;i<moleculeVector.size();i++){ |
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if (! moleculeVector[i].isVacancy){ |
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shesActualSizetoMe++; |
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nAtoms = moleculeVector[i].myStamp->getNAtoms(); |
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} |
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} |
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} |
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Atom::createArrays( nAtoms ); |
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atoms = new Atom*[nAtoms]; |
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shesActualSizetoMe = 0; |
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/* Use the information from the molecule vector to place the atoms. |
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*/ |
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for (i= 0;i<moleculeVector.size();i++){ |
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if (! moleculeVector[i].isVacancy) { |
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orientationMunger( A ); |
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if( moleculeVector[i].isCore){ |
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nCoreAtomCounter =+ nCoreModelAtoms; |
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coreLocate->placeMol(moleculeVector[i].pos,A,atoms,nShellAtomCounter); |
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} |
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else { |
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nShellAtomCounter =+ nShellModelAtoms; |
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shellLocate->placeMol(moleculeVector[i].pos,A,atoms,nCoreAtomCounter); |
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} |
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shesActualSizetoMe++; |
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} |
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} |
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// shellLocate.placeMol(pos, A, moleculeVector,shellAtomCount); |
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for (i=0;i<9;i++) simnfo->Hmat[i] = 0; |
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simnfo->Hmat[0] = 1; |
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simnfo->Hmat[4] = 1; |
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simnfo->Hmat[8] = 1; |
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// set up the SimInfo object |
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simnfo = new SimInfo(); |
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simnfo->n_atoms = nAtoms; |
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sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
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sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
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simnfo->atoms = atoms; |
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// set up the writer and write out |
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writer = new DumpWriter( simnfo ); |
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writer->writeFinal(0.0); |
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// clean up |
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delete[] myLattice; |
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return hasError; |
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} |
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// Begin Builder routines-------------------------------> |
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/* Builds a standard core-shell nanoparticle. |
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*/ |
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void nanoBuilder::buildWithCoreShell(double dist, double pos[3]){ |
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if ( dist <= particleRadius ){ |
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moleculeVector.push_back(myMol); |
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if (dist <= coreRadius){ |
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coreAtomCount =+ nCoreModelAtoms; |
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moleculeVector[moleculeCount].pos[0] = pos[0]; |
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moleculeVector[moleculeCount].pos[1] = pos[1]; |
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moleculeVector[moleculeCount].pos[2] = pos[2]; |
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moleculeVector[moleculeCount].myStamp = coreStamp; |
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moleculeVector[moleculeCount].isCore = 1; |
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moleculeVector[moleculeCount].isShell = 0; |
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} |
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// Place shell |
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else{ |
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shellAtomCount =+ nShellModelAtoms; |
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moleculeVector[moleculeCount].pos[0] = pos[0]; |
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moleculeVector[moleculeCount].pos[1] = pos[1]; |
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moleculeVector[moleculeCount].pos[2] = pos[2]; |
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moleculeVector[moleculeCount].myStamp = shellStamp; |
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moleculeVector[moleculeCount].isCore = 0; |
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moleculeVector[moleculeCount].isShell = 1; |
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} |
417 |
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moleculeCount++; |
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} |
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} |
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/* |
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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 |
|
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|
429 |
|
|
moleculeVector.push_back(myMol); |
430 |
|
|
if (dist <= coreRadius){ |
431 |
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|
432 |
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|
coreAtomCount =+ nCoreModelAtoms; |
433 |
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moleculeVector[moleculeCount].pos[0] = pos[0]; |
434 |
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|
moleculeVector[moleculeCount].pos[1] = pos[1]; |
435 |
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|
moleculeVector[moleculeCount].pos[2] = pos[2]; |
436 |
|
|
moleculeVector[moleculeCount].myStamp = coreStamp; |
437 |
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|
moleculeVector[moleculeCount].isCore = 1; |
438 |
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|
moleculeVector[moleculeCount].isShell = 0; |
439 |
|
|
|
440 |
|
|
if ((dist >= coreRadius - vacancyRadius/2.0) && |
441 |
|
|
(dist <= coreRadius + vacancyRadius/2.0)){ |
442 |
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|
|
443 |
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|
vacancyInterface.push_back(moleculeCount); |
444 |
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|
nInterface++; |
445 |
|
|
} |
446 |
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} else { |
447 |
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// Place shell |
448 |
|
|
shellAtomCount =+ nShellModelAtoms; |
449 |
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moleculeVector[moleculeCount].pos[0] = pos[0]; |
450 |
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|
moleculeVector[moleculeCount].pos[1] = pos[1]; |
451 |
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|
moleculeVector[moleculeCount].pos[2] = pos[2]; |
452 |
|
|
moleculeVector[moleculeCount].myStamp = shellStamp; |
453 |
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|
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 |
|
|
|