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/* |
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* Copyright (c) 2006 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/recenter/recenterCmd.h" |
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#include "brains/Thermo.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/DumpReader.hpp" |
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#include "io/DumpWriter.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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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 inputFileName; |
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std::string outputFileName; |
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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 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 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 creator; |
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SimInfo* info = creator.createSim(inputFileName, false); |
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DumpReader reader(info, inputFileName); |
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// very important step: |
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info->update(); |
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|
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outputFileName = args_info.output_arg; |
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|
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if (!outputFileName.compare(inputFileName)) { |
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sprintf(painCave.errMsg, "Input and Output File names should be different!"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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DumpWriter* writer = new DumpWriter(info, 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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int nFrames = reader.getNFrames(); |
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Vector3d COM; |
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Vector3d pos; |
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SimInfo::MoleculeIterator i; |
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Molecule::IntegrableObjectIterator j; |
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Molecule * mol; |
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StuntDouble * sd; |
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Thermo thermo(info); |
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|
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for (int istep = 0; istep < nFrames; istep++) { |
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reader.readFrame(istep); |
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COM = thermo.getCom(); |
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for( mol = info->beginMolecule(i); mol != NULL; |
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mol = info->nextMolecule(i) ) { |
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|
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for( sd = mol->beginIntegrableObject(j); sd != NULL; |
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sd = mol->nextIntegrableObject(j) ) { |
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|
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pos = sd->getPos(); |
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sd->setPos(pos - COM); |
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|
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} |
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} |
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writer->writeDump(); |
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} |
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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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simError(); |
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return 0; |
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} |
