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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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*/ |
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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 "applications/simpleBuilder/simpleBuilderCmd.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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|
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void createMdFile(const std::string&oldMdFileName, |
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const std::string&newMdFileName, |
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int nMol); |
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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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Lattice *simpleLat; |
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RealType latticeConstant; |
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std::vector<RealType> lc; |
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const RealType rhoConvertConst = 1.661; |
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RealType density; |
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int nx, ny, nz; |
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Mat3x3d hmat; |
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MoLocator *locator; |
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std::vector<Vector3d> latticePos; |
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std::vector<Vector3d> latticeOrt; |
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int nMolPerCell; |
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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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density = args_info.density_arg; |
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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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simpleLat = LatticeFactory::getInstance()->createLattice(latticeType); |
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|
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if (simpleLat == NULL) { |
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sprintf(painCave.errMsg, "Lattice Factory can not create %s lattice\n", |
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latticeType.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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nMolPerCell = simpleLat->getNumSitesPerCell(); |
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|
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//get the number of unit cells in each direction: |
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|
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nx = args_info.nx_arg; |
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|
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if (nx <= 0) { |
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sprintf(painCave.errMsg, "The number of unit cells in the x direction " |
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"must be greater than 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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ny = args_info.ny_arg; |
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|
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if (ny <= 0) { |
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sprintf(painCave.errMsg, "The number of unit cells in the y direction " |
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"must be greater than 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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nz = args_info.nz_arg; |
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|
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if (nz <= 0) { |
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sprintf(painCave.errMsg, "The number of unit cells in the z direction " |
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"must be greater than 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 nSites = nMolPerCell * nx * ny * nz; |
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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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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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|
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SimCreator oldCreator; |
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SimInfo* oldInfo = oldCreator.createSim(inputFileName, false); |
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|
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// Calculate lattice constant (in Angstroms) |
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|
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RealType avgMass = MoLocator::getMolMass(oldInfo->getMoleculeStamp(0), |
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oldInfo->getForceField()); |
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|
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latticeConstant = pow(rhoConvertConst * nMolPerCell * avgMass / density, |
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(RealType)(1.0 / 3.0)); |
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|
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// Set the lattice constant |
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|
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lc.push_back(latticeConstant); |
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simpleLat->setLatticeConstant(lc); |
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|
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// Calculate the lattice sites and fill the lattice vector. |
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|
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// Get the standard orientations of the cell sites |
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|
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latticeOrt = simpleLat->getLatticePointsOrt(); |
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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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for(int i = 0; i < nx; i++) { |
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for(int j = 0; j < ny; j++) { |
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for(int k = 0; k < nz; k++) { |
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|
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// Get the position of the cell sites |
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|
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simpleLat->getLatticePointsPos(latticePos, i, j, k); |
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|
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for(int l = 0; l < nMolPerCell; l++) { |
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sites.push_back(latticePos[l]); |
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orientations.push_back(latticeOrt[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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outputFileName = args_info.output_arg; |
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|
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// create a new .md file on the fly which corrects the number of molecules |
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|
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createMdFile(inputFileName, outputFileName, nSites); |
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|
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delete oldInfo; |
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|
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// We need to read in the new SimInfo object, then Parse the |
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// md file and set up the system |
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|
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SimCreator newCreator; |
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SimInfo* newInfo = newCreator.createSim(outputFileName, false); |
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|
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// fill Hmat |
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|
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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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|
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newInfo->getSnapshotManager()->getCurrentSnapshot()->setHmat(hmat); |
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|
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// place the molecules |
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|
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Molecule* mol; |
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locator = new MoLocator(newInfo->getMoleculeStamp(0), |
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newInfo->getForceField()); |
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for (int n = 0; n < nSites; n++) { |
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mol = newInfo->getMoleculeByGlobalIndex(n); |
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locator->placeMol(sites[n], orientations[n], mol); |
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} |
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|
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// Create DumpWriter and write out the coordinates |
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|
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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 DumpWriter"); |
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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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sprintf(painCave.errMsg, "A new OpenMD 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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painCave.severity = OPENMD_INFO; |
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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, |
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const std::string&newMdFileName, |
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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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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, "\t\tnMol = %d;", nMol); |
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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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|
