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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. 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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* 2. 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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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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* Created by Kelsey M. Stocker on 2/9/12. |
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* @author Kelsey M. Stocker |
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* |
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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 "shapedLatticeRod.hpp" |
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#include "shapedLatticeEllipsoid.hpp" |
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#include "nanorodBuilderCmd.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 OpenMD; |
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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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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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MoLocator* locator; |
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int nComponents; |
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double latticeConstant; |
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std::vector<double> lc; |
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|
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RealType rodRadius; |
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RealType rodLength; |
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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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|
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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.latticeConstant_arg; |
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rodRadius = args_info.radius_arg; |
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rodLength = args_info.length_arg; |
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Globals* simParams = oldInfo->getSimParams(); |
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|
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vector<Vector3d> sites; |
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vector<Vector3d> orientations; |
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|
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if (args_info.ellipsoid_flag) { |
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shapedLatticeEllipsoid nanoEllipsoid(latticeConstant, latticeType, |
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rodLength, rodRadius); |
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sites = nanoEllipsoid.getSites(); |
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orientations = nanoEllipsoid.getOrientations(); |
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} else { |
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|
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/* Create nanorod */ |
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shapedLatticeRod nanoRod(latticeConstant, latticeType, |
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rodRadius, rodLength); |
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/* Build a lattice and get lattice points for this lattice constant */ |
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sites = nanoRod.getSites(); |
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orientations = nanoRod.getOrientations(); |
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} |
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|
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std::vector<int> vacancyTargets; |
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vector<bool> isVacancy; |
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|
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Vector3d myLoc; |
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RealType myR; |
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|
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for (int i = 0; i < sites.size(); i++) |
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isVacancy.push_back(false); |
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|
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// cerr << "checking vacancyPercent" << "\n"; |
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if (args_info.vacancyPercent_given) { |
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// cerr << "vacancyPercent given" << "\n"; |
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if (args_info.vacancyPercent_arg < 0.0 || args_info.vacancyPercent_arg > 100.0) { |
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sprintf(painCave.errMsg, "vacancyPercent was set to a non-sensical value."); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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RealType vF = args_info.vacancyPercent_arg / 100.0; |
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// cerr << "vacancyPercent = " << vF << "\n"; |
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RealType vIR; |
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RealType vOR; |
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if (args_info.vacancyInnerRadius_given) { |
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vIR = args_info.vacancyInnerRadius_arg; |
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} else { |
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vIR = 0.0; |
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} |
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if (args_info.vacancyOuterRadius_given) { |
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vOR = args_info.vacancyOuterRadius_arg; |
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} else { |
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vOR = rodRadius; |
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} |
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if (vIR >= 0.0 && vOR <= rodRadius && vOR >= vIR) { |
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|
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for (int i = 0; i < sites.size(); i++) { |
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myLoc = sites[i]; |
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myR = myLoc.length(); |
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if (myR >= vIR && myR <= vOR) { |
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vacancyTargets.push_back(i); |
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} |
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} |
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std::random_shuffle(vacancyTargets.begin(), vacancyTargets.end()); |
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|
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int nTargets = vacancyTargets.size(); |
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vacancyTargets.resize((int)(vF * nTargets)); |
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|
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|
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sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n" |
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"\tsites between %lf and %lf.", (int) vacancyTargets.size(), |
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vIR, vOR); |
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painCave.isFatal = 0; |
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simError(); |
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|
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isVacancy.clear(); |
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for (int i = 0; i < sites.size(); i++) { |
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bool vac = false; |
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for (int j = 0; j < vacancyTargets.size(); j++) { |
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if (i == vacancyTargets[j]) vac = true; |
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} |
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isVacancy.push_back(vac); |
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} |
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|
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} else { |
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sprintf(painCave.errMsg, "Something is strange about the vacancy\n" |
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"\tinner or outer radii. Check their values."); |
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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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/* Get number of lattice sites */ |
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int nSites = sites.size() - vacancyTargets.size(); |
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|
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// cerr << "sites.size() = " << sites.size() << "\n"; |
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// cerr << "nSites = " << nSites << "\n"; |
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// cerr << "vacancyTargets = " << vacancyTargets.size() << "\n"; |
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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> shellRadii; |
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std::vector<RealType> molecularMasses; |
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std::vector<int> nMol; |
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std::map<int, int> componentFromSite; |
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nComponents = components.size(); |
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// cerr << "nComponents = " << nComponents << "\n"; |
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|
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if (args_info.molFraction_given && args_info.shellRadius_given) { |
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sprintf(painCave.errMsg, "Specify either molFraction or shellRadius " |
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"arguments, but not both!"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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if (nComponents == 1) { |
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molFractions.push_back(1.0); |
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shellRadii.push_back(rodRadius); |
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} else if (args_info.molFraction_given) { |
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if ((int)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 ((int)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, "nanorodBuilder 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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} else if ((int)args_info.shellRadius_given) { |
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if ((int)args_info.shellRadius_given == nComponents) { |
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for (int i = 0; i < nComponents; i++) { |
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shellRadii.push_back(args_info.shellRadius_arg[i]); |
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} |
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} else if ((int)args_info.shellRadius_given == nComponents-1) { |
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for (int i = 0; i < nComponents-1; i++) { |
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shellRadii.push_back(args_info.shellRadius_arg[i]); |
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} |
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shellRadii.push_back(rodRadius); |
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} else { |
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sprintf(painCave.errMsg, "nanorodBuilder can't figure out the\n" |
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"\tshell radii 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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} else { |
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sprintf(painCave.errMsg, "You have a multi-component <MetaData> block,\n" |
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"\tbut have not specified either molFraction or shellRadius arguments."); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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if (args_info.molFraction_given) { |
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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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// recompute actual mol fractions and perform final sanity check: |
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|
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int totalMolecules = 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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} |
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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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} else { |
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|
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for (int i = 0; i < shellRadii.size(); i++) { |
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if (shellRadii.at(i) > rodRadius + 1e-6 ) { |
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sprintf(painCave.errMsg, "One of the shellRadius values exceeds the rod Radius."); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (shellRadii.at(i) <= 0.0 ) { |
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sprintf(painCave.errMsg, "One of the shellRadius values is smaller than zero!"); |
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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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vector<int> ids; |
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if ((int)args_info.molFraction_given){ |
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// cerr << "molFraction given 2" << "\n"; |
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sprintf(painCave.errMsg, "Creating a randomized spherically-capped nanorod."); |
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painCave.isFatal = 0; |
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simError(); |
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/* Random rod is the default case*/ |
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|
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for (int i = 0; i < sites.size(); i++) |
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if (!isVacancy[i]) ids.push_back(i); |
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|
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std::random_shuffle(ids.begin(), ids.end()); |
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|
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} else{ |
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sprintf(painCave.errMsg, "Creating an fcc nanorod."); |
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painCave.isFatal = 0; |
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simError(); |
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|
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// RealType smallestSoFar; |
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int myComponent = -1; |
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nMol.clear(); |
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nMol.resize(nComponents); |
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|
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// cerr << "shellRadii[0] " << shellRadii[0] << "\n"; |
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// cerr << "rodRadius " << rodRadius << "\n"; |
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|
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for (int i = 0; i < sites.size(); i++) { |
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myLoc = sites[i]; |
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myR = myLoc.length(); |
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// smallestSoFar = rodRadius; |
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// cerr << "vac = " << isVacancy[i]<< "\n"; |
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|
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if (!isVacancy[i]) { |
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|
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|
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// for (int j = 0; j < nComponents; j++) { |
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// if (myR <= shellRadii[j]) { |
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// if (shellRadii[j] <= smallestSoFar) { |
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// smallestSoFar = shellRadii[j]; |
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// myComponent = j; |
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// } |
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// } |
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// } |
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myComponent = 0; |
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componentFromSite[i] = myComponent; |
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nMol[myComponent]++; |
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// cerr << "nMol for myComp(" << myComponent<<") = " << nMol[myComponent] << "\n"; |
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} |
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} |
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} |
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// cerr << "nMol = " << nMol.at(0) << "\n"; |
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|
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outputFileName = args_info.output_arg; |
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|
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//creat new .md file on fly which corrects the number of molecule |
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|
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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; |
| 404 |
|
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SimCreator newCreator; |
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SimInfo* NewInfo = newCreator.createSim(outputFileName, false); |
| 407 |
|
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// Place molecules |
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Molecule* mol; |
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SimInfo::MoleculeIterator mi; |
| 411 |
mol = NewInfo->beginMolecule(mi); |
| 412 |
|
| 413 |
int l = 0; |
| 414 |
|
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for (int i = 0; i < nComponents; i++){ |
| 416 |
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
| 417 |
NewInfo->getForceField()); |
| 418 |
|
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// cerr << "nMol = " << nMol.at(i) << "\n"; |
| 420 |
if (!args_info.molFraction_given) { |
| 421 |
for (int n = 0; n < sites.size(); n++) { |
| 422 |
if (!isVacancy[n]) { |
| 423 |
if (componentFromSite[n] == i) { |
| 424 |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 425 |
locator->placeMol(sites[n], orientations[n], mol); |
| 426 |
l++; |
| 427 |
} |
| 428 |
} |
| 429 |
} |
| 430 |
} else { |
| 431 |
for (int n = 0; n < nMol.at(i); n++) { |
| 432 |
mol = NewInfo->getMoleculeByGlobalIndex(l); |
| 433 |
locator->placeMol(sites[ids[l]], orientations[ids[l]], mol); |
| 434 |
l++; |
| 435 |
} |
| 436 |
} |
| 437 |
} |
| 438 |
|
| 439 |
//fill Hmat |
| 440 |
hmat(0, 0)= 10.0*rodRadius; |
| 441 |
hmat(0, 1) = 0.0; |
| 442 |
hmat(0, 2) = 0.0; |
| 443 |
|
| 444 |
hmat(1, 0) = 0.0; |
| 445 |
hmat(1, 1) = 10.0*rodRadius; |
| 446 |
hmat(1, 2) = 0.0; |
| 447 |
|
| 448 |
hmat(2, 0) = 0.0; |
| 449 |
hmat(2, 1) = 0.0; |
| 450 |
hmat(2, 2) = 5.0*rodLength + 2.0*rodRadius; |
| 451 |
|
| 452 |
//set Hmat |
| 453 |
NewInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
| 454 |
|
| 455 |
|
| 456 |
//create dumpwriter and write out the coordinates |
| 457 |
writer = new DumpWriter(NewInfo, outputFileName); |
| 458 |
|
| 459 |
if (writer == NULL) { |
| 460 |
sprintf(painCave.errMsg, "Error in creating dumpwriter object "); |
| 461 |
painCave.isFatal = 1; |
| 462 |
simError(); |
| 463 |
} |
| 464 |
|
| 465 |
writer->writeDump(); |
| 466 |
|
| 467 |
// deleting the writer will put the closing at the end of the dump file |
| 468 |
|
| 469 |
delete writer; |
| 470 |
|
| 471 |
// cleanup a by calling sim error..... |
| 472 |
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " |
| 473 |
"generated.\n", outputFileName.c_str()); |
| 474 |
painCave.isFatal = 0; |
| 475 |
simError(); |
| 476 |
return 0; |
| 477 |
} |
| 478 |
|
| 479 |
void createMdFile(const std::string&oldMdFileName, |
| 480 |
const std::string&newMdFileName, |
| 481 |
std::vector<int> nMol) { |
| 482 |
ifstream oldMdFile; |
| 483 |
ofstream newMdFile; |
| 484 |
const int MAXLEN = 65535; |
| 485 |
char buffer[MAXLEN]; |
| 486 |
|
| 487 |
//create new .md file based on old .md file |
| 488 |
oldMdFile.open(oldMdFileName.c_str()); |
| 489 |
newMdFile.open(newMdFileName.c_str()); |
| 490 |
oldMdFile.getline(buffer, MAXLEN); |
| 491 |
|
| 492 |
int i = 0; |
| 493 |
while (!oldMdFile.eof()) { |
| 494 |
|
| 495 |
//correct molecule number |
| 496 |
if (strstr(buffer, "nMol") != NULL) { |
| 497 |
if(i<nMol.size()){ |
| 498 |
sprintf(buffer, "\tnMol = %i;", nMol.at(i)); |
| 499 |
newMdFile << buffer << std::endl; |
| 500 |
i++; |
| 501 |
} |
| 502 |
} else |
| 503 |
newMdFile << buffer << std::endl; |
| 504 |
|
| 505 |
oldMdFile.getline(buffer, MAXLEN); |
| 506 |
} |
| 507 |
|
| 508 |
oldMdFile.close(); |
| 509 |
newMdFile.close(); |
| 510 |
|
| 511 |
if (i != nMol.size()) { |
| 512 |
sprintf(painCave.errMsg, "Couldn't replace the correct number of nMol\n" |
| 513 |
"\tstatements in component blocks. Make sure that all\n" |
| 514 |
"\tcomponents in the template file have nMol=1"); |
| 515 |
painCave.isFatal = 1; |
| 516 |
simError(); |
| 517 |
} |
| 518 |
|
| 519 |
} |
| 520 |
|
