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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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#include <algorithm> |
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|
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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 "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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std::vector<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 outputFileName; |
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|
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Lattice *simpleLat; |
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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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const double rhoConvertConst = 1.661; |
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double density; |
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double particleRadius; |
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|
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Mat3x3d hmat; |
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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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|
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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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/* get lattice type */ |
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latticeType = "FCC"; |
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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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sprintf(painCave.errMsg, "No input .md file name was specified" |
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"on the command line"); |
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painCave.isFatal = 1; |
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cmdline_parser_print_help(); |
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simError(); |
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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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latticeConstant = args_info.latticeCnst_arg; |
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particleRadius = args_info.radius_arg; |
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Globals* simParams = oldInfo->getSimParams(); |
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|
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/* Create nanoparticle */ |
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shapedLatticeSpherical nanoParticle(latticeConstant, latticeType, |
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particleRadius); |
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|
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/* Build a lattice and get lattice points for this lattice constant */ |
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vector<Vector3d> sites = nanoParticle.getSites(); |
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vector<Vector3d> orientations = nanoParticle.getOrientations(); |
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|
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std::cout <<"nSites: " << sites.size() << std::endl; |
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|
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/* Get number of lattice sites */ |
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int nSites = sites.size(); |
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|
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std::vector<Component*> components = simParams->getComponents(); |
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std::vector<RealType> molFractions; |
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std::vector<RealType> molecularMasses; |
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std::vector<int> nMol; |
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nComponents = components.size(); |
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|
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if (nComponents == 1) { |
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molFractions.push_back(1.0); |
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} else { |
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if (args_info.molFraction_given == nComponents) { |
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for (int i = 0; i < nComponents; i++) { |
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molFractions.push_back(args_info.molFraction_arg[i]); |
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} |
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} else if (args_info.molFraction_given == nComponents-1) { |
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RealType remainingFraction = 1.0; |
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for (int i = 0; i < nComponents-1; i++) { |
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molFractions.push_back(args_info.molFraction_arg[i]); |
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remainingFraction -= molFractions[i]; |
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} |
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molFractions.push_back(remainingFraction); |
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} else { |
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sprintf(painCave.errMsg, "nanoparticleBuilder can't figure out molFractions " |
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"for all of the components in the <MetaData> block."); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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RealType totalFraction = 0.0; |
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|
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/* Do some simple sanity checking*/ |
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|
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for (int i = 0; i < nComponents; i++) { |
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if (molFractions.at(i) < 0.0) { |
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sprintf(painCave.errMsg, "One of the requested molFractions was" |
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" less than zero!"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (molFractions.at(i) > 1.0) { |
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sprintf(painCave.errMsg, "One of the requested molFractions was" |
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" greater than one!"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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totalFraction += molFractions.at(i); |
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} |
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if (abs(totalFraction - 1.0) > 1e-6) { |
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sprintf(painCave.errMsg, "The sum of molFractions was not close enough to 1.0"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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int remaining = nSites; |
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for (int i=0; i < nComponents-1; i++) { |
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nMol.push_back(int((RealType)nSites * molFractions.at(i))); |
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remaining -= nMol.at(i); |
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} |
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nMol.push_back(remaining); |
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|
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|
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|
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// recompute actual mol fractions and perform final sanity check: |
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|
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int totalMolecules = 0; |
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RealType totalMass = 0.0; |
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for (int i=0; i < nComponents; i++) { |
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molFractions[i] = (RealType)(nMol.at(i))/(RealType)nSites; |
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totalMolecules += nMol.at(i); |
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molecularMasses.push_back(getMolMass(oldInfo->getMoleculeStamp(i), |
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oldInfo->getForceField())); |
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totalMass += (RealType)(nMol.at(i)) * molecularMasses.at(i); |
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} |
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RealType avgMass = totalMass / (RealType) totalMolecules; |
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|
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if (totalMolecules != nSites) { |
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sprintf(painCave.errMsg, "Computed total number of molecules is not equal " |
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"to the number of lattice sites!"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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vector<int> ids; |
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for (int i = 0; i < sites.size(); i++) ids.push_back(i); |
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/* Random particle is the default case*/ |
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if (!args_info.ShellRadius_given){ |
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/* do the iPod thing, Shuffle da vector */ |
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std::random_shuffle(ids.begin(), ids.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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sprintf(painCave.errMsg, "Number of .md components " |
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"does not match the number of shell radius specifications"); |
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painCave.isFatal = 1; |
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simError(); |
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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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outputFileName = args_info.output_arg; |
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|
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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, outputFileName, nMol); |
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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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SimCreator newCreator; |
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SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
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|
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|
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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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int l = 0; |
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|
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for (int i = 0; i < nComponents; i++){ |
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locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
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NewInfo->getForceField()); |
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for (int n = 0; n < nMol.at(i); n++) { |
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mol = NewInfo->getMoleculeByGlobalIndex(l); |
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locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
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l++; |
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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)= 2.0*particleRadius; |
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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) = 2.0*particleRadius; |
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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) = 2.0*particleRadius; |
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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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writer = new DumpWriter(NewInfo, outputFileName); |
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|
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if (writer == NULL) { |
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sprintf(painCave.errMsg, "Error in creating dumpwrite object "); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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writer->writeDump(); |
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|
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// deleting the writer will put the closing at the end of the dump file |
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|
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delete writer; |
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|
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// cleanup a by calling sim error..... |
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sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
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"generated.\n", outputFileName.c_str()); |
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painCave.isFatal = 0; |
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simError(); |
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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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std::vector<int> nMol) { |
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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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int i = 0; |
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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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if(i<nMol.size()){ |
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sprintf(buffer, "\tnMol = %i;", nMol.at(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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|
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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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|
