| 1 |
< |
/* |
| 1 |
> |
/* |
| 2 |
|
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
|
* |
| 4 |
|
* The University of Notre Dame grants you ("Licensee") a |
| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
< |
/** |
| 44 |
< |
* @file SimCreatorr.hpp |
| 45 |
< |
* @author tlin |
| 46 |
< |
* @date 11/02/2004 |
| 47 |
< |
* @time 12:126am |
| 48 |
< |
* @version 1.0 |
| 49 |
< |
*/ |
| 43 |
> |
/** |
| 44 |
> |
* @file SimCreator.hpp |
| 45 |
> |
* @author tlin |
| 46 |
> |
* @date 11/02/2004 |
| 47 |
> |
* @time 12:126am |
| 48 |
> |
* @version 1.0 |
| 49 |
> |
*/ |
| 50 |
|
|
| 51 |
|
#ifndef BRAINS_SIMCREATOR_HPP |
| 52 |
|
#define BRAINS_SIMCREATOR_HPP |
| 53 |
|
|
| 54 |
< |
|
| 54 |
> |
#include <iostream> |
| 55 |
|
#include "primitives/Molecule.hpp" |
| 56 |
|
#include "brains/SimInfo.hpp" |
| 56 |
– |
#include "types/MakeStamps.hpp" |
| 57 |
|
#include "io/Globals.hpp" |
| 58 |
< |
#include "UseTheForce/ForceField.hpp" |
| 58 |
> |
#include "brains/ForceField.hpp" |
| 59 |
|
|
| 60 |
< |
// this routine is defined in BASS_interface.cpp |
| 61 |
< |
//another OOPS |
| 62 |
< |
extern void set_interface_stamps( MakeStamps* ms, Globals* g ); |
| 60 |
> |
namespace OpenMD { |
| 61 |
|
|
| 62 |
< |
namespace oopse { |
| 62 |
> |
/** |
| 63 |
> |
* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp" |
| 64 |
> |
* |
| 65 |
> |
* The only responsibility of SimCreator is to parse the meta-data |
| 66 |
> |
* file and create a SimInfo instance based on the information |
| 67 |
> |
* returned by parser. |
| 68 |
> |
*/ |
| 69 |
> |
class SimCreator { |
| 70 |
> |
public: |
| 71 |
|
|
| 72 |
< |
/** |
| 67 |
< |
* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp" |
| 68 |
< |
* The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo |
| 69 |
< |
* instance based on the information returned by parser. |
| 70 |
< |
*/ |
| 71 |
< |
class SimCreator { |
| 72 |
< |
public: |
| 72 |
> |
virtual ~SimCreator() {} |
| 73 |
|
|
| 74 |
< |
virtual ~SimCreator() {} |
| 75 |
< |
|
| 76 |
< |
/** |
| 77 |
< |
* Setup Simulation |
| 78 |
< |
* @return a pointer to SimInfo |
| 79 |
< |
* @param mdfile the meta-data file name |
| 80 |
< |
*/ |
| 81 |
< |
SimInfo* createSim(const std::string & mdFileName, bool loadInitCoords = true); |
| 74 |
> |
/** |
| 75 |
> |
* Setup Simulation |
| 76 |
> |
* @return a pointer to SimInfo |
| 77 |
> |
* @param mdfile the meta-data file name |
| 78 |
> |
*/ |
| 79 |
> |
SimInfo* createSim(const std::string & mdFileName, bool loadInitCoords = true); |
| 80 |
|
|
| 81 |
< |
private: |
| 81 |
> |
private: |
| 82 |
|
|
| 83 |
< |
/** |
| 84 |
< |
* Parses the meta-data file |
| 85 |
< |
* @param mdfile |
| 86 |
< |
* @param stamps |
| 87 |
< |
* @param simParams |
| 88 |
< |
*/ |
| 91 |
< |
void parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams); |
| 83 |
> |
/** |
| 84 |
> |
* Parses the meta-data file |
| 85 |
> |
* @param mdfile |
| 86 |
> |
* @return simParams |
| 87 |
> |
*/ |
| 88 |
> |
Globals* parseFile(std::istream& rawMetaData, const std::string& mdFileName, int mdFileVersion, int metaDataStartingLine); |
| 89 |
|
|
| 90 |
|
|
| 91 |
< |
/** create the molecules belong to current processor*/ |
| 92 |
< |
virtual void createMolecules(SimInfo* info); |
| 91 |
> |
/** create the molecules belong to current processor*/ |
| 92 |
> |
virtual void createMolecules(SimInfo* info); |
| 93 |
|
|
| 94 |
< |
/** |
| 95 |
< |
* Sets the global index for atoms, rigidbodies and cutoff groups and fill up |
| 96 |
< |
* globalGroupMembership and globalMolMembership arrays which map atoms' |
| 97 |
< |
* global index to the global index of the groups (or molecules) they belong to. |
| 98 |
< |
* These array are never changed during the simulation. |
| 99 |
< |
*/ |
| 100 |
< |
void setGlobalIndex(SimInfo* info); |
| 94 |
> |
/** |
| 95 |
> |
* Figure out the data storage layout based on what kinds of |
| 96 |
> |
* objects are being simulated |
| 97 |
> |
*/ |
| 98 |
> |
int computeStorageLayout(SimInfo* info); |
| 99 |
> |
|
| 100 |
> |
/** |
| 101 |
> |
* Sets the global index for atoms, rigidbodies and cutoff groups |
| 102 |
> |
* and fill up globalGroupMembership and globalMolMembership |
| 103 |
> |
* arrays which map atoms' global index to the global index of the |
| 104 |
> |
* groups (or molecules) they belong to. These array are never |
| 105 |
> |
* changed during the simulation. |
| 106 |
> |
*/ |
| 107 |
> |
void setGlobalIndex(SimInfo* info); |
| 108 |
|
|
| 109 |
< |
void gatherParameters(SimInfo *info, const std::string& mdfile); |
| 106 |
< |
|
| 109 |
> |
void gatherParameters(SimInfo *info, const std::string& mdfile); |
| 110 |
|
|
| 111 |
< |
/** Extracts the molecules stamps and adds them into SimInfo class */ |
| 112 |
< |
void compList(MakeStamps* stamps, Globals* simParams, |
| 113 |
< |
std::vector<std::pair<MoleculeStamp*, int> >& moleculeStamps) ; |
| 111 |
< |
|
| 112 |
< |
/** |
| 113 |
< |
* Divide the molecules among the processors |
| 114 |
< |
*/ |
| 111 |
> |
/** |
| 112 |
> |
* Divide the molecules among the processors |
| 113 |
> |
*/ |
| 114 |
|
|
| 115 |
< |
void divideMolecules(SimInfo* info); |
| 115 |
> |
void divideMolecules(SimInfo* info); |
| 116 |
|
|
| 117 |
< |
/** Load initial coordinates */ |
| 118 |
< |
void loadCoordinates(SimInfo* info); |
| 117 |
> |
/** Load initial coordinates */ |
| 118 |
> |
void loadCoordinates(SimInfo* info, const std::string& mdFileName); |
| 119 |
|
|
| 120 |
< |
std::string mdFileName_; //save the meta-data file name which may be used later |
| 122 |
< |
}; |
| 120 |
> |
std::string mdFileName_; //save the meta-data file name which may be used later |
| 121 |
|
|
| 122 |
< |
} //end namespace oopse |
| 122 |
> |
}; |
| 123 |
> |
|
| 124 |
> |
} //end namespace OpenMD |
| 125 |
|
#endif //BRAINS_SIMCREATOR_HPP |
| 126 |
|
|
