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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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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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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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|
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#include <cstdlib> |
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#include <cstdio> |
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#include <cstring> |
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#include <cmath> |
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#include <iostream> |
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#include <string> |
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#include <map> |
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#include <fstream> |
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|
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#include "config.h" |
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|
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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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#include "brains/Register.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "brains/SimCreator.hpp" |
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#include "io/DumpWriter.hpp" |
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#include "math/Vector3.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "utils/StringUtils.hpp" |
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|
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using namespace std; |
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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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|
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int main(int argc, char *argv []) { |
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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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|
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|
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|
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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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|
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|
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|
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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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int nShells; /* Number of shells in nanoparticle*/ |
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int numSites; |
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|
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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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|
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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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|
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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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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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|
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nComponents = oldInfo->getNMoleculeStamp(); |
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|
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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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|
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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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|
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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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|
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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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|
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|
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|
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|
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|
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/* create Molocators */ |
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locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
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|
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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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|
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|
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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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std::cerr << "Number of components does not equal molFraction occurances." << std::endl; |
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exit 1; |
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} |
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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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numMol[i] = int((double)numSites * args_info.molFraction_arg[i]); |
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totComponents += numMol[i]; |
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} |
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numMol[nComponents-1] = numSites - totComponents; |
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|
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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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|
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|
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|
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} |
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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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// 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, numcomponents,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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|
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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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|
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//fill Hmat |
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hmat(0, 0)= nx * latticeConstant; |
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hmat(0, 1) = 0.0; |
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hmat(0, 2) = 0.0; |
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|
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hmat(1, 0) = 0.0; |
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hmat(1, 1) = ny * latticeConstant; |
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hmat(1, 2) = 0.0; |
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|
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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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|
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//set Hmat |
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NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
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|
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|
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//create dumpwriter and write out the coordinates |
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NewInfo->setFinalConfigFileName(outInitFileName); |
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writer = new DumpWriter(NewInfo); |
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|
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if (writer == NULL) { |
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std::cerr << "error in creating DumpWriter" << std::endl; |
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exit(1); |
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} |
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|
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writer->writeDump(); |
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std::cout << "new initial configuration file: " << outInitFileName |
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<< " is generated." << std::endl; |
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|
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//delete objects |
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|
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//delete oldInfo and oldSimSetup |
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|
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if (NewInfo != NULL) |
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delete NewInfo; |
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|
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if (writer != NULL) |
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delete writer; |
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delete simpleLat; |
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cmdline_parser_free(&args_info); |
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return 0; |
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} |
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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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ifstream oldMdFile; |
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ofstream newMdFile; |
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const int MAXLEN = 65535; |
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char buffer[MAXLEN]; |
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|
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//create new .md file based on old .md file |
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oldMdFile.open(oldMdFileName.c_str()); |
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newMdFile.open(newMdFileName.c_str()); |
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|
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oldMdFile.getline(buffer, MAXLEN); |
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|
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while (!oldMdFile.eof()) { |
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|
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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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} else |
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newMdFile << buffer << std::endl; |
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|
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oldMdFile.getline(buffer, MAXLEN); |
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} |
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|
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oldMdFile.close(); |
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newMdFile.close(); |
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} |
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|
