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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 |
| 10 |
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* publication of scientific results based in part on use of the |
| 11 |
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* program. An acceptable form of acknowledgement is citation of |
| 12 |
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* the article in which the program was described (Matthew |
| 13 |
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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 |
| 15 |
< |
* 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. |
| 11 |
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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 |
| 14 |
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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 |
| 33 |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
| 35 |
+ |
* |
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+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [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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/** |
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#ifndef BRAINS_SIMCREATOR_HPP |
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#define BRAINS_SIMCREATOR_HPP |
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|
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< |
|
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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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|
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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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|
| 64 |
– |
namespace oopse { |
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– |
|
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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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> |
* The only responsibility of SimCreator is to parse the meta-data |
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> |
* file and create a SimInfo instance based on the information |
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> |
* 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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* 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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> |
* @return simParams |
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*/ |
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void parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams); |
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> |
Globals* parseFile(std::istream& rawMetaData, const std::string& mdFileName, int metaDataStartingLine); |
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|
| 89 |
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|
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/** create the molecules belong to current processor*/ |
| 91 |
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virtual void createMolecules(SimInfo* info); |
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< |
|
| 92 |
> |
|
| 93 |
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/** |
| 94 |
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* Sets the global index for atoms, rigidbodies and cutoff groups and fill up |
| 95 |
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* globalGroupMembership and globalMolMembership arrays which map atoms' |
| 96 |
< |
* global index to the global index of the groups (or molecules) they belong to. |
| 97 |
< |
* These array are never changed during the simulation. |
| 94 |
> |
* Sets the global index for atoms, rigidbodies and cutoff groups |
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> |
* and fill up globalGroupMembership and globalMolMembership |
| 96 |
> |
* arrays which map atoms' global index to the global index of the |
| 97 |
> |
* groups (or molecules) they belong to. These array are never |
| 98 |
> |
* changed during the simulation. |
| 99 |
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*/ |
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void setGlobalIndex(SimInfo* info); |
| 101 |
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|
| 102 |
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void gatherParameters(SimInfo *info, const std::string& mdfile); |
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– |
|
| 103 |
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|
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– |
/** Extracts the molecules stamps and adds them into SimInfo class */ |
| 109 |
– |
void compList(MakeStamps* stamps, Globals* simParams, |
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– |
std::vector<std::pair<MoleculeStamp*, int> >& moleculeStamps) ; |
| 111 |
– |
|
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/** |
| 105 |
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* Divide the molecules among the processors |
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*/ |
| 108 |
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void divideMolecules(SimInfo* info); |
| 109 |
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|
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/** Load initial coordinates */ |
| 111 |
< |
void loadCoordinates(SimInfo* info); |
| 111 |
> |
void loadCoordinates(SimInfo* info, const std::string& mdFileName); |
| 112 |
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|
| 113 |
|
std::string mdFileName_; //save the meta-data file name which may be used later |
| 114 |
+ |
|
| 115 |
|
}; |
| 116 |
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|
| 117 |
< |
} //end namespace oopse |
| 117 |
> |
} //end namespace OpenMD |
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|
#endif //BRAINS_SIMCREATOR_HPP |
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|
