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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 |
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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 |
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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," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
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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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* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 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 |
| 30 |
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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: |
| 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). |
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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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/** |
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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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#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 "io/Globals.hpp" |
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< |
#include "UseTheForce/ForceField.hpp" |
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> |
#include "brains/ForceField.hpp" |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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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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* @param mdfile |
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* @return simParams |
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*/ |
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< |
Globals* parseFile(const std::string mdFileName); |
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> |
Globals* parseFile(std::istream& rawMetaData, const std::string& mdFileName, int mdFileVersion, int metaDataStartingLine); |
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|
| 90 |
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|
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/** create the molecules belong to current processor*/ |
| 92 |
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virtual void createMolecules(SimInfo* info); |
| 93 |
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|
| 94 |
+ |
/** |
| 95 |
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* Figure out the data storage layout based on what kinds of |
| 96 |
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* objects are being simulated |
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*/ |
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+ |
int computeStorageLayout(SimInfo* info); |
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+ |
|
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/** |
| 101 |
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* Sets the global index for atoms, rigidbodies and cutoff groups and fill up |
| 102 |
< |
* globalGroupMembership and globalMolMembership arrays which map atoms' |
| 103 |
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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. |
| 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 |
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> |
* changed during the simulation. |
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*/ |
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void setGlobalIndex(SimInfo* info); |
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|
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|
void divideMolecules(SimInfo* info); |
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|
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/** Load initial coordinates */ |
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< |
void loadCoordinates(SimInfo* info); |
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> |
void loadCoordinates(SimInfo* info, const std::string& mdFileName); |
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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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+ |
|
| 122 |
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}; |
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|
| 124 |
< |
} //end namespace oopse |
| 124 |
> |
} //end namespace OpenMD |
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#endif //BRAINS_SIMCREATOR_HPP |
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|
