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/* |
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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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* 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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* 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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* 3. Redistributions in binary form must reproduce the above copyright |
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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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* 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] Vardeman & Gezelter, in progress (2009). |
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*/ |
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/** |
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* @file SimCreatorr.hpp |
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* @author tlin |
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* @date 11/02/2004 |
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* @time 12:126am |
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* @version 1.0 |
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*/ |
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/** |
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* @file SimCreatorr.hpp |
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* @author tlin |
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* @date 11/02/2004 |
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* @time 12:126am |
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* @version 1.0 |
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*/ |
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#ifndef BRAINS_SIMCREATOR_HPP |
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#define BRAINS_SIMCREATOR_HPP |
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#include <iostream> |
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#include "primitives/Molecule.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "types/MakeStamps.hpp" |
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#include "io/Globals.hpp" |
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#include "UseTheForce/ForceField.hpp" |
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// this routine is defined in BASS_interface.cpp |
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//another OOPS |
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extern void set_interface_stamps( MakeStamps* ms, Globals* g ); |
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namespace OpenMD { |
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namespace oopse { |
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/** |
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* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp" |
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* The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo |
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* instance based on the information returned by parser. |
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*/ |
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class SimCreator { |
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public: |
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/** |
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* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp" |
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* The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo |
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* instance based on the information returned by parser. |
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*/ |
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class SimCreator { |
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public: |
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virtual ~SimCreator() {} |
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virtual ~SimCreator() {} |
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/** |
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* Setup Simulation |
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* @return a pointer to SimInfo |
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* @param mdfile the meta-data file name |
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*/ |
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SimInfo* createSim(const std::string & mdFileName, bool loadInitCoords = true); |
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/** |
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* Setup Simulation |
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* @return a pointer to SimInfo |
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* @param mdfile the meta-data file name |
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*/ |
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SimInfo* createSim(const std::string & mdFileName, bool loadInitCoords = true); |
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private: |
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private: |
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/** |
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* Parses the meta-data file |
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* @param mdfile |
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* @param stamps |
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* @param simParams |
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*/ |
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void parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams); |
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/** |
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* Parses the meta-data file |
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* @param mdfile |
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* @return simParams |
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*/ |
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Globals* parseFile(std::istream& rawMetaData, const std::string& mdFileName, int metaDataStartingLine); |
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/** create the molecules belong to current processor*/ |
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virtual void createMolecules(SimInfo* info); |
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/** create the molecules belong to current processor*/ |
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virtual void createMolecules(SimInfo* info); |
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/** |
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* Sets the global index for atoms, rigidbodies and cutoff groups and fill up |
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* globalGroupMembership and globalMolMembership arrays which map atoms' |
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* global index to the global index of the groups (or molecules) they belong to. |
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* These array are never changed during the simulation. |
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*/ |
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void setGlobalIndex(SimInfo* info); |
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/** |
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* Sets the global index for atoms, rigidbodies and cutoff groups and fill up |
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* globalGroupMembership and globalMolMembership arrays which map atoms' |
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* global index to the global index of the groups (or molecules) they belong to. |
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* These array are never changed during the simulation. |
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*/ |
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void setGlobalIndex(SimInfo* info); |
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void gatherParameters(SimInfo *info, const std::string& mdfile); |
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void gatherParameters(SimInfo *info, const std::string& mdfile); |
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/** Extracts the molecules stamps and adds them into SimInfo class */ |
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void compList(MakeStamps* stamps, Globals* simParams, |
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std::vector<std::pair<MoleculeStamp*, int> >& moleculeStamps) ; |
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/** |
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* Divide the molecules among the processors |
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*/ |
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/** |
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* Divide the molecules among the processors |
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*/ |
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void divideMolecules(SimInfo* info); |
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void divideMolecules(SimInfo* info); |
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/** Load initial coordinates */ |
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void loadCoordinates(SimInfo* info); |
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/** Load initial coordinates */ |
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void loadCoordinates(SimInfo* info, const std::string& mdFileName); |
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std::string mdFileName_; //save the meta-data file name which may be used later |
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}; |
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std::string mdFileName_; //save the meta-data file name which may be used later |
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}; |
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} //end namespace oopse |
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} //end namespace OpenMD |
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#endif //BRAINS_SIMCREATOR_HPP |
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