| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
| 8 |
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* |
| 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 |
< |
* |
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* 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 |
|
* |
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< |
* 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 |
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* distribution. |
| 28 |
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* 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 |
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* such damages. |
| 31 |
+ |
* |
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+ |
* 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
| 42 |
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|
| 43 |
|
/** |
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< |
* @file SimCreatorr.hpp |
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> |
* @file SimCreator.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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|
| 50 |
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#ifndef BRAINS_SIMCREATOR_HPP |
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#define BRAINS_SIMCREATOR_HPP |
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|
| 53 |
< |
|
| 53 |
> |
#include <iostream> |
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#include "primitives/Molecule.hpp" |
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#include "brains/SimInfo.hpp" |
| 56 |
– |
#include "types/MakeStamps.hpp" |
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|
#include "io/Globals.hpp" |
| 57 |
< |
#include "UseTheForce/ForceField.hpp" |
| 57 |
> |
#include "brains/ForceField.hpp" |
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|
|
| 59 |
< |
// this routine is defined in BASS_interface.cpp |
| 61 |
< |
//another OOPS |
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< |
extern void set_interface_stamps( MakeStamps* ms, Globals* g ); |
| 59 |
> |
namespace OpenMD { |
| 60 |
|
|
| 64 |
– |
namespace oopse { |
| 65 |
– |
|
| 61 |
|
/** |
| 62 |
|
* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp" |
| 63 |
< |
* The only responsibility of SimCreator is to parse the meta-data file and create a SimInfo |
| 64 |
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* instance based on the information returned by parser. |
| 63 |
> |
* |
| 64 |
> |
* The only responsibility of SimCreator is to parse the meta-data |
| 65 |
> |
* file and create a SimInfo instance based on the information |
| 66 |
> |
* returned by parser. |
| 67 |
|
*/ |
| 68 |
|
class SimCreator { |
| 69 |
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public: |
| 73 |
|
/** |
| 74 |
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* Setup Simulation |
| 75 |
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* @return a pointer to SimInfo |
| 76 |
< |
* @param mdfile the meta-data file name |
| 76 |
> |
* @param mdFileName the meta-data file name |
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> |
* @param loadInitCoords should the initial coordinates be loaded from a file? |
| 78 |
|
*/ |
| 79 |
|
SimInfo* createSim(const std::string & mdFileName, bool loadInitCoords = true); |
| 80 |
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|
| 82 |
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|
| 83 |
|
/** |
| 84 |
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* Parses the meta-data file |
| 85 |
< |
* @param mdfile |
| 86 |
< |
* @param stamps |
| 87 |
< |
* @param simParams |
| 85 |
> |
* @param mdFileName the meta-data file name |
| 86 |
> |
* @param rawMetaData the raw meta-data stream |
| 87 |
> |
* @param mdFileVersion the version of code used to create the meta-data file |
| 88 |
> |
* @param metaDataStartingLine the starting line of the meta-data block |
| 89 |
> |
* @return a pointer to the simulation parameters in a #Globals object |
| 90 |
|
*/ |
| 91 |
< |
void parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams); |
| 91 |
> |
Globals* parseFile(std::istream& rawMetaData, const std::string& mdFileName, int mdFileVersion, int metaDataStartingLine); |
| 92 |
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|
| 93 |
|
|
| 94 |
|
/** create the molecules belong to current processor*/ |
| 95 |
|
virtual void createMolecules(SimInfo* info); |
| 96 |
|
|
| 97 |
+ |
/** |
| 98 |
+ |
* Figure out the data storage layout based on what kinds of |
| 99 |
+ |
* objects are being simulated |
| 100 |
+ |
*/ |
| 101 |
+ |
int computeStorageLayout(SimInfo* info); |
| 102 |
+ |
|
| 103 |
|
/** |
| 104 |
< |
* Sets the global index for atoms, rigidbodies and cutoff groups and fill up |
| 105 |
< |
* globalGroupMembership and globalMolMembership arrays which map atoms' |
| 106 |
< |
* global index to the global index of the groups (or molecules) they belong to. |
| 107 |
< |
* These array are never changed during the simulation. |
| 104 |
> |
* Sets the global index for atoms, rigidbodies and cutoff groups |
| 105 |
> |
* and fill up globalGroupMembership and globalMolMembership |
| 106 |
> |
* arrays which map atoms' global index to the global index of the |
| 107 |
> |
* groups (or molecules) they belong to. These array are never |
| 108 |
> |
* changed during the simulation. |
| 109 |
|
*/ |
| 110 |
|
void setGlobalIndex(SimInfo* info); |
| 111 |
|
|
| 112 |
|
void gatherParameters(SimInfo *info, const std::string& mdfile); |
| 106 |
– |
|
| 113 |
|
|
| 108 |
– |
/** Extracts the molecules stamps and adds them into SimInfo class */ |
| 109 |
– |
void compList(MakeStamps* stamps, Globals* simParams, |
| 110 |
– |
std::vector<std::pair<MoleculeStamp*, int> >& moleculeStamps) ; |
| 111 |
– |
|
| 114 |
|
/** |
| 115 |
|
* Divide the molecules among the processors |
| 116 |
|
*/ |
| 118 |
|
void divideMolecules(SimInfo* info); |
| 119 |
|
|
| 120 |
|
/** Load initial coordinates */ |
| 121 |
< |
void loadCoordinates(SimInfo* info); |
| 121 |
> |
void loadCoordinates(SimInfo* info, const std::string& mdFileName); |
| 122 |
|
|
| 123 |
|
std::string mdFileName_; //save the meta-data file name which may be used later |
| 124 |
+ |
|
| 125 |
|
}; |
| 126 |
|
|
| 127 |
< |
} //end namespace oopse |
| 127 |
> |
} //end namespace OpenMD |
| 128 |
|
#endif //BRAINS_SIMCREATOR_HPP |
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|
