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#include <string> |
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#include <map> |
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#include <fstream> |
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#include <algorithm> |
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#include "config.h" |
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#include "shapedLatticeSpherical.hpp" |
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#include "nanoparticleBuilderCmd.h" |
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#include "sphericalNanoparticle.hpp" |
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#include "lattice/LatticeFactory.hpp" |
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#include "utils/MoLocator.hpp" |
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#include "lattice/Lattice.hpp" |
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using namespace oopse; |
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void createMdFile(const std::string&oldMdFileName, |
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const std::string&newMdFileName, |
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int numMol); |
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int components,int* numMol); |
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int main(int argc, char *argv []) { |
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Lattice *simpleLat; |
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int numMol; |
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MoLocator* locator; |
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int* numMol; |
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int nComponents; |
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double latticeConstant; |
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std::vector<double> lc; |
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double mass; |
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double mass; |
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const double rhoConvertConst = 1.661; |
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double density; |
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double particleRadius; |
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Mat3x3d hmat; |
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MoLocator *locator; |
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sphericalNanoparticle *nanoparticle; |
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std::vector<Vector3d> latticePos; |
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std::vector<Vector3d> latticeOrt; |
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int numMolPerCell; |
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SimCreator oldCreator; |
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SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
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nShells = 0; |
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if (args_info.coreShellRadius_given){ |
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nShells = args_info.coreShellRadius_given; |
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} |
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nComponents = oldInfo->getNMoleculeStamp(); |
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/* Check to see if we have enough components to build that many shells. */ |
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if (nShells){ |
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if (oldInfo->getNMoleculeStamp() != nShells) { |
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std::cerr << "Not enough components present in MD file to build specified number of shells" |
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<< std::endl; |
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exit(1); |
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} |
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} |
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//creat lattice |
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simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
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if (simpleLat == NULL) { |
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std::cerr << "Error in creating lattice" << std::endl; |
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exit(1); |
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} |
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numMolPerCell = simpleLat->getNumSitesPerCell(); |
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/*calculate lattice constant (in Angstrom) |
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latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
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1.0 / 3.0);*/ |
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latticeConstant = pow(rhoConvertConst * numMolPerCell * mass / density, |
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1.0 / 3.0);*/ |
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latticeConstant = args_info.latticeCnst_arg; |
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particleRadius = args_info.radius_arg; |
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particleDiameter = 2.0 * particleRadius; |
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Globals* simParams = oldInfo->getSimParams(); |
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/* set lattice constant */ |
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lc.push_back(latticeConstant); |
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simpleLat->setLatticeConstant(lc); |
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/* Find out how many different components in this simualtion */ |
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nComponents =simParams->getNComponents(); |
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/*determine the output file names*/ |
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if (args_info.output_given){ |
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outInitFileName = args_info.output_arg; |
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}else{ |
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outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
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} |
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std::cout <<"Before build shaped lattice. "<<std::endl; |
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/* create Molocators */ |
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locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
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/* create a new spherical nanoparticle */ |
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nanoparticle = new sphericalNanoparticle(particleRadius,latticeConstant); |
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/* Build a nanoparticle to see how many sites are there */ |
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numSites = new int[nComponents] |
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int numSites = nanoparticle.getNMol(simpleLat); |
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/* Create nanoparticle */ |
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shapedLatticeSpherical nanoParticle(latticeConstant,latticeType,particleRadius); |
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std::cout <<"Before build getPoints. "<<std::endl; |
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/* Build a lattice and get lattice points for this lattice constant */ |
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vector<Vector3d> nanoParticleSites = nanoParticle.getPoints(); |
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/* Get number of lattice sites */ |
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numSites = nanoParticleSites.size(); |
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//std::cout <<"numSites are %d "<<numSites<<std::endl; |
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// std::cout <<"nComponents are %d "<<nComponents<<std::endl; |
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numMol = new int[nComponents]; |
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/* Random particle is the default case*/ |
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if (!args_info.ShellRadius_given){ |
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std::cout << "Creating a random nanoparticle" << std::endl; |
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/* Check to see if we have enough components */ |
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if (nComponents != args_info.molFraction_given + 1){ |
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if (nComponents != args_info.molFraction_given && nComponents != 1){ |
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std::cerr << "Number of components does not equal molFraction occurances." << std::endl; |
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exit 1; |
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exit(1); |
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} |
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/* Build the mole fractions and number of molecules of each type */ |
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int totComponents = 0; |
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for (int i = 0;i<nComponents-2;i++){ /* Figure out Percent for each component */ |
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for (int i = 0;i<nComponents-1;i++){ /* Figure out Percent for each component */ |
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numMol[i] = int((double)numSites * args_info.molFraction_arg[i]); |
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std::cout<<numMol[i]<<std::endl; |
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totComponents += numMol[i]; |
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} |
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numMol[nComponents-1] = numSites - totComponents; |
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/* do the iPod thing, Shuffle da vector */ |
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std::random_shuffle(nanoParticleSites.begin(), nanoParticleSites.end()); |
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} else{ /*Handle core-shell with multiple components.*/ |
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std::cout << "Creating a core-shell nanoparticle." << std::endl; |
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if (nComponents != args_info.ShellRadius_given + 1){ |
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std::cerr << "Number of components does not equal ShellRadius occurances." << std::endl; |
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exit 1; |
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} |
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exit(1); |
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} |
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} |
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//get the orientation of the cell sites |
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//get the orientation of the cell sites |
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//for the same type of molecule in same lattice, it will not change |
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latticeOrt = simpleLat->getLatticePointsOrt(); |
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latticeOrt = nanoParticle.getPointsOrt(); |
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std::cout<<"Orientational vector Size: "<< std::endl; |
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std::cout<<latticeOrt.size()<< std::endl; |
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// needed for writing out new md file. |
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outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
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outMdFileName = outPrefix + ".md"; |
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outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
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outMdFileName = outPrefix + ".md"; |
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//creat new .md file on fly which corrects the number of molecule |
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createMdFile(inputFileName, outMdFileName, numcomponents,numMol); |
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//creat new .md file on fly which corrects the number of molecule |
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createMdFile(inputFileName, outMdFileName, nComponents,numMol); |
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if (oldInfo != NULL) |
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delete oldInfo; |
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// We need to read in new siminfo object. |
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//parse md file and set up the system |
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//SimCreator NewCreator; |
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SimCreator newCreator; |
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SimInfo* NewInfo = newCreator.createSim(outMdFileName, false); |
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SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false); |
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// This was so much fun the first time, lets do it again. |
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// Place molecules |
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Molecule* mol; |
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SimInfo::MoleculeIterator mi; |
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mol = NewInfo->beginMolecule(mi); |
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for(int i = -nx; i < nx; i++) { |
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for(int j = -ny; j < ny; j++) { |
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for(int k = -nz; k < nz; k++) { |
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//get the position of the cell sites |
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simpleLat->getLatticePointsPos(latticePos, i, j, k); |
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for(int l = 0; l < numMolPerCell; l++) { |
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#ifdef HAVE_CGAL |
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if (myGeometry->isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){ |
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#endif |
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if (mol != NULL) { |
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locator->placeMol(latticePos[l], latticeOrt[l], mol); |
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} else { |
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std::cerr<<"Error in placing molecule " << std::endl; |
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} |
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mol = NewInfo->nextMolecule(mi); |
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#ifdef HAVE_CGAL |
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} |
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#endif |
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} |
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} |
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} |
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int l = 0; |
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for (mol = NewInfo->beginMolecule(mi); mol != NULL; mol = NewInfo->nextMolecule(mi)) { |
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locator->placeMol(nanoParticleSites[l], latticeOrt[l], mol); |
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l++; |
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} |
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//fill Hmat |
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hmat(0, 0)= nx * latticeConstant; |
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hmat(0, 0)= latticeConstant; |
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hmat(0, 1) = 0.0; |
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hmat(0, 2) = 0.0; |
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hmat(1, 0) = 0.0; |
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hmat(1, 1) = ny * latticeConstant; |
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hmat(1, 1) = latticeConstant; |
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hmat(1, 2) = 0.0; |
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hmat(2, 0) = 0.0; |
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hmat(2, 1) = 0.0; |
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hmat(2, 2) = nz * latticeConstant; |
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hmat(2, 2) = latticeConstant; |
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//set Hmat |
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NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
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delete NewInfo; |
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if (writer != NULL) |
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delete writer; |
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delete simpleLat; |
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> |
delete writer; |
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cmdline_parser_free(&args_info); |
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return 0; |
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} |
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void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
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int components,int &nummol) { |
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> |
int components,int* numMol) { |
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ifstream oldMdFile; |
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ofstream newMdFile; |
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const int MAXLEN = 65535; |
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newMdFile.open(newMdFileName.c_str()); |
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oldMdFile.getline(buffer, MAXLEN); |
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> |
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> |
int i = 0; |
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while (!oldMdFile.eof()) { |
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//correct molecule number |
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if (strstr(buffer, "nMol") != NULL) { |
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< |
sprintf(buffer, "\tnMol = %i;", numMol); |
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< |
newMdFile << buffer << std::endl; |
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> |
if(i<components){ |
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> |
sprintf(buffer, "\tnMol = %i;", numMol[i]); |
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> |
newMdFile << buffer << std::endl; |
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> |
i++; |
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} |
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} else |
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newMdFile << buffer << std::endl; |
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