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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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#include <map> |
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#include <fstream> |
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#include "config.h" |
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#include "nanorodBuilderCmd.h" |
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//#include "GeometryBuilder.hpp" |
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#ifdef HAVE_CGAL |
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#include "GeometryBuilder.hpp" |
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#endif |
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#include "GeometryFactory.hpp" |
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#include "Geometry.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 std; |
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using namespace oopse; |
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void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
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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 main(int argc, char *argv []) { |
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//register force fields |
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registerForceFields(); |
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|
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//register force fields |
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registerForceFields(); |
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registerLattice(); |
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|
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gengetopt_args_info args_info; |
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std::string latticeType; |
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std::string inputFileName; |
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std::string outPrefix; |
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std::string outMdFileName; |
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std::string outInitFileName; |
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std::string outGeomFileName; |
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Lattice *simpleLat; |
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int numMol; |
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double latticeConstant; |
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std::vector<double> lc; |
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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 rodLength; |
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double rodDiameter; |
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int nx, ny, nz; |
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Mat3x3d hmat; |
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MoLocator *locator; |
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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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DumpWriter *writer; |
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|
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// parse command line arguments |
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if (cmdline_parser(argc, argv, &args_info) != 0) |
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exit(1); |
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// Check for lib CGAL, if we don't have it, we should exit.... |
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#ifndef HAVE_CGAL |
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std::cerr << "nanoRodBuilder requires libCGAL to function, please rebuild OOPSE with libCGAL." |
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<< std::endl; |
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exit(1); |
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#endif |
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|
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|
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//get lattice type |
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latticeType = UpperCase(args_info.latticetype_arg); |
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gengetopt_args_info args_info; |
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std::string latticeType; |
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std::string inputFileName; |
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std::string outPrefix; |
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std::string outMdFileName; |
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std::string outInitFileName; |
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std::string outGeomFileName; |
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BaseLattice *simpleLat; |
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int numMol; |
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double latticeConstant; |
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std::vector<double> lc; |
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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 rodLength; |
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double rodDiameter; |
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int nx, |
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ny, |
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nz; |
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Mat3x3d hmat; |
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MoLocator *locator; |
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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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int curMolIndex; |
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DumpWriter *writer; |
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//get input file name |
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if (args_info.inputs_num) |
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inputFileName = args_info.inputs[0]; |
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else { |
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std::cerr << "You must specify a input file name.\n" << std::endl; |
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cmdline_parser_print_help(); |
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exit(1); |
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} |
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|
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//parse md file and set up the system |
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SimCreator oldCreator; |
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SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
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|
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if (oldInfo->getNMoleculeStamp()> 1) { |
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std::cerr << "can not build nanorod with more than one components" |
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<< std::endl; |
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exit(1); |
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} |
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|
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//get mass of molecule. |
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|
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mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
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|
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//creat lattice |
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simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
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|
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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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|
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latticeConstant = args_info.latticeCnst_arg; |
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rodLength = args_info.length_arg; |
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rodDiameter = args_info.width_arg; |
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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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|
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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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//creat Molocator |
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locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
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|
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/* |
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Assume we are carving nanorod out of a cublic block of material and that |
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the shape the material will fit within that block.... |
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The model in geometry builder assumes the long axis is in the y direction and the x-z plane is the |
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diameter of the particle. |
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*/ |
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// Number of Unit Cells in Length first |
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ny = (int)(rodLength/latticeConstant); |
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// Number of unit cells in Width |
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nx = (int)(rodDiameter/latticeConstant); |
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nz = (int)(rodDiameter/latticeConstant); |
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// Create geometry for nanocrystal |
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#ifdef HAVE_CGAL |
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GeometryBuilder *myGeometry; |
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// GeometryBuilder myGeometry(rodLength,rodDiameter); |
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if (args_info.twinnedCrystal_flag){ |
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myGeometry = new GeometryBuilder(rodLength,rodDiameter); |
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} |
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else{ |
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myGeometry = new GeometryBuilder(rodLength,rodDiameter); |
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} |
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if (args_info.genGeomview_given){ |
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if (args_info.genGeomview_flag){ |
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outGeomFileName = getPrefix(inputFileName.c_str()) + ".off"; |
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myGeometry->dumpGeometry(outGeomFileName); |
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} |
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} |
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#endif |
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/* |
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We have to build the system first to figure out how many molecules |
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there are then create a md file and then actually build the |
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system. |
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*/ |
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|
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//place the molecules |
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// parse command line arguments |
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if (cmdline_parser(argc, argv, &args_info) != 0) |
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exit(1); |
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|
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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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numMol = 0; |
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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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//if (oldInfo->getNGlobalMolecules() != numMol) { |
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|
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|
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|
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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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|
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for(int l = 0; l < numMolPerCell; l++) { |
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//get lattice type |
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latticeType = UpperCase(args_info.latticetype_arg); |
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|
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if (!LatticeFactory::getInstance()->hasLatticeCreator(latticeType)) { |
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std::cerr << latticeType << " is an invalid lattice type" << std::endl; |
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std::cerr << LatticeFactory::getInstance()->toString() << std::endl; |
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exit(1); |
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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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numMol++; |
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} |
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#else |
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numMol++; |
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#endif |
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} |
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} |
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} |
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} |
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|
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//get input file name |
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if (args_info.inputs_num) |
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inputFileName = args_info.inputs[0]; |
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else { |
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std::cerr << "You must specify a input file name.\n" << std::endl; |
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cmdline_parser_print_help(); |
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exit(1); |
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} |
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|
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// needed for writing out new md file. |
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|
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outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
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outMdFileName = outPrefix + ".md"; |
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|
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//creat new .md file on fly which corrects the number of molecule |
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createMdFile(inputFileName, outMdFileName, numMol); |
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|
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if (oldInfo != NULL) |
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delete oldInfo; |
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|
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|
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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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|
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SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false); |
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|
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// This was so much fun the first time, lets do it again. |
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|
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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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|
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//parse md file and set up the system |
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SimCreator oldCreator; |
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SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
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|
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if (oldInfo->getNMoleculeStamp()> 1) { |
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std::cerr << "can not build nanorod with more than one components" |
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<< std::endl; |
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exit(1); |
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} |
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|
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//get mass of molecule. |
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|
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mass = getMolMass(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
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|
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//creat lattice |
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simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
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|
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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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|
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numMolPerCell = simpleLat->getNumSitesPerCell(); |
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|
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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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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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|
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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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|
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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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} |
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|
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|
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latticeConstant = args_info.latticeCnst_arg; |
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rodLength = args_info.length_arg; |
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rodDiameter = args_info.width_arg; |
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|
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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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|
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|
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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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//creat Molocator |
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locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
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|
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/* |
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< |
Assume we are carving nanorod out of a cublic block of material and that |
| 335 |
< |
the shape the material will fit within that block.... |
| 336 |
< |
The model in geometry builder assumes the long axis is in the y direction and the x-z plane is the |
| 337 |
< |
diameter of the particle. |
| 338 |
< |
*/ |
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// Number of Unit Cells in Length first |
| 340 |
< |
ny = (int)(rodLength/latticeConstant); |
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// Number of unit cells in Width |
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nx = (int)(rodDiameter/latticeConstant); |
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nz = (int)(rodDiameter/latticeConstant); |
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|
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|
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|
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// Create geometry for nanocrystal |
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//GeometryBuilder myGeometry(rodLength,rodDiameter); |
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|
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/* |
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We have to build the system first to figure out how many molecules there are |
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< |
then create a md file and then actually build the system. |
| 353 |
< |
*/ |
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|
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//place the molecules |
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|
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curMolIndex = 0; |
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|
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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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|
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|
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/* |
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void BaseLattice::getLatticePointsPos(std::vector<Vector3d>& latticePos, int nx, int ny, int nz){ |
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|
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latticePos.resize(nCellSites); |
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|
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for( int i=0;i < nCellSites;i++){ |
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|
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latticePos[i][0] = origin[0] + cellSitesPos[i][0] + cellLen[0] * (double(nx) - 0.5); |
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latticePos[i][1] = origin[1] + cellSitesPos[i][1] + cellLen[1] * (double(ny) - 0.5); |
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latticePos[i][2] = origin[2] + cellSitesPos[i][2] + cellLen[2] * (double(nz) - 0.5); |
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} |
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|
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*/ |
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|
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|
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|
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|
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numMol = 0; |
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< |
for(int i = 0; i < nx; i++) { |
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for(int j = 0; j < ny; j++) { |
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for(int k = 0; k < nz; k++) { |
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< |
//if (oldInfo->getNGlobalMolecules() != numMol) { |
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< |
|
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< |
|
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|
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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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|
| 235 |
< |
for(int l = 0; l < numMolPerCell; l++) { |
| 236 |
< |
/* |
| 237 |
< |
if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){ |
| 238 |
< |
numMol++; |
| 239 |
< |
} |
| 240 |
< |
*/ |
| 241 |
< |
numMol++; |
| 242 |
< |
} |
| 243 |
< |
} |
| 244 |
< |
} |
| 245 |
< |
} |
| 246 |
< |
|
| 247 |
< |
|
| 248 |
< |
// needed for writing out new md file. |
| 249 |
< |
|
| 250 |
< |
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
| 251 |
< |
outMdFileName = outPrefix + ".md"; |
| 252 |
< |
|
| 253 |
< |
//creat new .md file on fly which corrects the number of molecule |
| 254 |
< |
createMdFile(inputFileName, outMdFileName, numMol); |
| 255 |
< |
|
| 256 |
< |
if (oldInfo != NULL) |
| 257 |
< |
delete oldInfo; |
| 258 |
< |
|
| 259 |
< |
|
| 260 |
< |
// We need to read in new siminfo object. |
| 261 |
< |
//parse md file and set up the system |
| 262 |
< |
//SimCreator NewCreator; |
| 263 |
< |
|
| 264 |
< |
SimInfo* NewInfo = oldCreator.createSim(outMdFileName, false); |
| 265 |
< |
|
| 266 |
< |
// This was so much fun the first time, lets do it again. |
| 267 |
< |
|
| 268 |
< |
Molecule* mol; |
| 269 |
< |
SimInfo::MoleculeIterator mi; |
| 270 |
< |
mol = NewInfo->beginMolecule(mi); |
| 271 |
< |
|
| 272 |
< |
for(int i = 0; i < nx; i++) { |
| 273 |
< |
for(int j = 0; j < ny; j++) { |
| 274 |
< |
for(int k = 0; k < nz; k++) { |
| 275 |
< |
|
| 276 |
< |
//get the position of the cell sites |
| 277 |
< |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
| 278 |
< |
|
| 279 |
< |
for(int l = 0; l < numMolPerCell; l++) { |
| 280 |
< |
if (mol != NULL) { |
| 281 |
< |
/* |
| 282 |
< |
if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){ |
| 283 |
< |
locator->placeMol(latticePos[l], latticeOrt[l], mol); |
| 284 |
< |
} |
| 285 |
< |
*/ |
| 286 |
< |
locator->placeMol(latticePos[l], latticeOrt[l], mol); |
| 287 |
< |
} else { |
| 288 |
< |
std::cerr << std::endl; |
| 289 |
< |
} |
| 290 |
< |
mol = NewInfo->nextMolecule(mi); |
| 291 |
< |
} |
| 292 |
< |
} |
| 293 |
< |
} |
| 294 |
< |
} |
| 295 |
< |
|
| 296 |
< |
|
| 297 |
< |
|
| 298 |
< |
//fill Hmat |
| 299 |
< |
hmat(0, 0)= nx * latticeConstant; |
| 300 |
< |
hmat(0, 1) = 0.0; |
| 301 |
< |
hmat(0, 2) = 0.0; |
| 302 |
< |
|
| 303 |
< |
hmat(1, 0) = 0.0; |
| 304 |
< |
hmat(1, 1) = ny * latticeConstant; |
| 305 |
< |
hmat(1, 2) = 0.0; |
| 306 |
< |
|
| 307 |
< |
hmat(2, 0) = 0.0; |
| 308 |
< |
hmat(2, 1) = 0.0; |
| 309 |
< |
hmat(2, 2) = nz * latticeConstant; |
| 310 |
< |
|
| 311 |
< |
//set Hmat |
| 312 |
< |
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 313 |
< |
|
| 314 |
< |
|
| 315 |
< |
//create dumpwriter and write out the coordinates |
| 316 |
< |
NewInfo->setFinalConfigFileName(outInitFileName); |
| 317 |
< |
writer = new DumpWriter(NewInfo); |
| 318 |
< |
|
| 319 |
< |
if (writer == NULL) { |
| 320 |
< |
std::cerr << "error in creating DumpWriter" << std::endl; |
| 321 |
< |
exit(1); |
| 322 |
< |
} |
| 323 |
< |
|
| 324 |
< |
writer->writeDump(); |
| 325 |
< |
std::cout << "new initial configuration file: " << outInitFileName |
| 326 |
< |
<< " is generated." << std::endl; |
| 327 |
< |
|
| 328 |
< |
//delete objects |
| 329 |
< |
|
| 330 |
< |
//delete oldInfo and oldSimSetup |
| 331 |
< |
|
| 332 |
< |
if (NewInfo != NULL) |
| 333 |
< |
delete NewInfo; |
| 334 |
< |
|
| 335 |
< |
if (writer != NULL) |
| 336 |
< |
delete writer; |
| 337 |
< |
|
| 338 |
< |
return 0; |
| 315 |
> |
|
| 316 |
> |
//fill Hmat |
| 317 |
> |
hmat(0, 0)= nx * latticeConstant; |
| 318 |
> |
hmat(0, 1) = 0.0; |
| 319 |
> |
hmat(0, 2) = 0.0; |
| 320 |
> |
|
| 321 |
> |
hmat(1, 0) = 0.0; |
| 322 |
> |
hmat(1, 1) = ny * latticeConstant; |
| 323 |
> |
hmat(1, 2) = 0.0; |
| 324 |
> |
|
| 325 |
> |
hmat(2, 0) = 0.0; |
| 326 |
> |
hmat(2, 1) = 0.0; |
| 327 |
> |
hmat(2, 2) = nz * latticeConstant; |
| 328 |
> |
|
| 329 |
> |
//set Hmat |
| 330 |
> |
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 331 |
> |
|
| 332 |
> |
|
| 333 |
> |
//create dumpwriter and write out the coordinates |
| 334 |
> |
NewInfo->setFinalConfigFileName(outInitFileName); |
| 335 |
> |
writer = new DumpWriter(NewInfo); |
| 336 |
> |
|
| 337 |
> |
if (writer == NULL) { |
| 338 |
> |
std::cerr << "error in creating DumpWriter" << std::endl; |
| 339 |
> |
exit(1); |
| 340 |
> |
} |
| 341 |
> |
|
| 342 |
> |
writer->writeDump(); |
| 343 |
> |
std::cout << "new initial configuration file: " << outInitFileName |
| 344 |
> |
<< " is generated." << std::endl; |
| 345 |
> |
|
| 346 |
> |
//delete objects |
| 347 |
> |
|
| 348 |
> |
//delete oldInfo and oldSimSetup |
| 349 |
> |
|
| 350 |
> |
if (NewInfo != NULL) |
| 351 |
> |
delete NewInfo; |
| 352 |
> |
|
| 353 |
> |
if (writer != NULL) |
| 354 |
> |
delete writer; |
| 355 |
> |
delete simpleLat; |
| 356 |
> |
cmdline_parser_free(&args_info); |
| 357 |
> |
return 0; |
| 358 |
|
} |
| 359 |
|
|
| 360 |
|
void createMdFile(const std::string&oldMdFileName, const std::string&newMdFileName, |
| 361 |
|
int numMol) { |
| 362 |
< |
ifstream oldMdFile; |
| 363 |
< |
ofstream newMdFile; |
| 364 |
< |
const int MAXLEN = 65535; |
| 365 |
< |
char buffer[MAXLEN]; |
| 366 |
< |
|
| 367 |
< |
//create new .md file based on old .md file |
| 368 |
< |
oldMdFile.open(oldMdFileName.c_str()); |
| 369 |
< |
newMdFile.open(newMdFileName.c_str()); |
| 370 |
< |
|
| 362 |
> |
ifstream oldMdFile; |
| 363 |
> |
ofstream newMdFile; |
| 364 |
> |
const int MAXLEN = 65535; |
| 365 |
> |
char buffer[MAXLEN]; |
| 366 |
> |
|
| 367 |
> |
//create new .md file based on old .md file |
| 368 |
> |
oldMdFile.open(oldMdFileName.c_str()); |
| 369 |
> |
newMdFile.open(newMdFileName.c_str()); |
| 370 |
> |
|
| 371 |
> |
oldMdFile.getline(buffer, MAXLEN); |
| 372 |
> |
|
| 373 |
> |
while (!oldMdFile.eof()) { |
| 374 |
> |
|
| 375 |
> |
//correct molecule number |
| 376 |
> |
if (strstr(buffer, "nMol") != NULL) { |
| 377 |
> |
sprintf(buffer, "\tnMol = %i;", numMol); |
| 378 |
> |
newMdFile << buffer << std::endl; |
| 379 |
> |
} else |
| 380 |
> |
newMdFile << buffer << std::endl; |
| 381 |
> |
|
| 382 |
|
oldMdFile.getline(buffer, MAXLEN); |
| 383 |
< |
|
| 384 |
< |
while (!oldMdFile.eof()) { |
| 385 |
< |
|
| 386 |
< |
//correct molecule number |
| 357 |
< |
if (strstr(buffer, "nMol") != NULL) { |
| 358 |
< |
sprintf(buffer, "\tnMol = %i;", numMol); |
| 359 |
< |
newMdFile << buffer << std::endl; |
| 360 |
< |
} else |
| 361 |
< |
newMdFile << buffer << std::endl; |
| 362 |
< |
|
| 363 |
< |
oldMdFile.getline(buffer, MAXLEN); |
| 364 |
< |
} |
| 365 |
< |
|
| 366 |
< |
oldMdFile.close(); |
| 367 |
< |
newMdFile.close(); |
| 383 |
> |
} |
| 384 |
> |
|
| 385 |
> |
oldMdFile.close(); |
| 386 |
> |
newMdFile.close(); |
| 387 |
|
} |
| 388 |
|
|
