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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, 24107 (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 <iostream> |
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#include <fstream> |
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#include <string> |
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|
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#include "applications/hydrodynamics/HydroCmd.h" |
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#include "applications/hydrodynamics/HydrodynamicsModel.hpp" |
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#include "applications/hydrodynamics/HydrodynamicsModelCreator.hpp" |
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#include "applications/hydrodynamics/HydrodynamicsModelFactory.hpp" |
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#include "applications/hydrodynamics/AnalyticalModel.hpp" |
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#include "applications/hydrodynamics/BeadModel.hpp" |
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#include "applications/hydrodynamics/RoughShell.hpp" |
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#include "applications/hydrodynamics/ShapeBuilder.hpp" |
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#include "brains/Register.hpp" |
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#include "brains/SimCreator.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "utils/StringUtils.hpp" |
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#include "utils/simError.h" |
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#include "utils/MemoryUtils.hpp" |
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using namespace OpenMD; |
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|
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struct SDShape{ |
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StuntDouble* sd; |
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Shape* shape; |
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}; |
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void registerHydrodynamicsModels(); |
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void writeHydroProps(std::ostream& os); |
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|
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int main(int argc, char* argv[]){ |
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//register force fields |
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registerForceFields(); |
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registerHydrodynamicsModels(); |
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|
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gengetopt_args_info args_info; |
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std::string dumpFileName; |
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std::string mdFileName; |
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std::string prefix; |
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|
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//parse the command line option |
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if (cmdline_parser (argc, argv, &args_info) != 0) { |
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exit(1) ; |
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} |
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|
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//get the dumpfile name and meta-data file name |
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if (args_info.input_given){ |
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dumpFileName = args_info.input_arg; |
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} else { |
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std::cerr << "Does not have input file name" << std::endl; |
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exit(1); |
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} |
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|
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if (args_info.output_given){ |
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prefix = args_info.output_arg; |
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} else { |
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prefix = getPrefix(dumpFileName); |
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} |
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std::string outputFilename = prefix + ".diff"; |
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|
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//parse md file and set up the system |
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SimCreator creator; |
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SimInfo* info = creator.createSim(dumpFileName, true); |
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|
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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Molecule::IntegrableObjectIterator ii; |
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StuntDouble* integrableObject; |
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Mat3x3d identMat; |
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identMat(0,0) = 1.0; |
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identMat(1,1) = 1.0; |
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identMat(2,2) = 1.0; |
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|
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Globals* simParams = info->getSimParams(); |
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RealType temperature; |
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RealType viscosity; |
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|
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if (simParams->haveViscosity()) { |
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viscosity = simParams->getViscosity(); |
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} else { |
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sprintf(painCave.errMsg, "viscosity must be set\n"); |
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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 (simParams->haveTargetTemp()) { |
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temperature = simParams->getTargetTemp(); |
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} else { |
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sprintf(painCave.errMsg, "target temperature must be set\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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std::map<std::string, SDShape> uniqueStuntDoubles; |
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|
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for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
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for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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if (uniqueStuntDoubles.find(integrableObject->getType()) == uniqueStuntDoubles.end()) { |
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|
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integrableObject->setPos(V3Zero); |
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integrableObject->setA(identMat); |
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if (integrableObject->isRigidBody()) { |
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RigidBody* rb = static_cast<RigidBody*>(integrableObject); |
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rb->updateAtoms(); |
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} |
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|
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SDShape tmp; |
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tmp.shape = ShapeBuilder::createShape(integrableObject); |
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tmp.sd = integrableObject; |
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uniqueStuntDoubles.insert(std::map<std::string, SDShape>::value_type(integrableObject->getType(), tmp)); |
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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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std::map<std::string, SDShape>::iterator si; |
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for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) { |
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HydrodynamicsModel* model; |
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Shape* shape = si->second.shape; |
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StuntDouble* sd = si->second.sd;; |
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if (args_info.model_given) { |
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model = HydrodynamicsModelFactory::getInstance()->createHydrodynamicsModel(args_info.model_arg, sd, info); |
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} else if (shape->hasAnalyticalSolution()) { |
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model = new AnalyticalModel(sd, info); |
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} else { |
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model = new BeadModel(sd, info); |
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} |
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|
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model->init(); |
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|
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std::ofstream ofs; |
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std::stringstream outputBeads; |
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outputBeads << prefix << "_" << model->getStuntDoubleName() << ".xyz"; |
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ofs.open(outputBeads.str().c_str()); |
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model->writeBeads(ofs); |
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ofs.close(); |
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|
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//if beads option is turned on, skip the calculation |
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if (!args_info.beads_flag) { |
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model->calcHydroProps(shape, viscosity, temperature); |
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std::ofstream outputDiff; |
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outputDiff.open(outputFilename.c_str()); |
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model->writeHydroProps(outputDiff); |
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outputDiff.close(); |
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} |
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|
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delete model; |
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} |
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|
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|
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//MemoryUtils::deletePointers(shapes); |
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delete info; |
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|
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} |
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|
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void registerHydrodynamicsModels() { |
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HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<RoughShell>("RoughShell")); |
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HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<BeadModel>("BeadModel")); |
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HydrodynamicsModelFactory::getInstance()->registerHydrodynamicsModel(new HydrodynamicsModelBuilder<AnalyticalModel>("AnalyticalModel")); |
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|
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} |
