| 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] Vardeman & Gezelter, in progress (2009). |
| 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 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 44 |
< |
* @file SimCreatorr.hpp |
| 44 |
> |
* @file SimCreator.hpp |
| 45 |
|
* @author tlin |
| 46 |
|
* @date 11/02/2004 |
| 46 |
– |
* @time 12:126am |
| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
|
|
| 54 |
|
#include "primitives/Molecule.hpp" |
| 55 |
|
#include "brains/SimInfo.hpp" |
| 56 |
|
#include "io/Globals.hpp" |
| 57 |
< |
#include "UseTheForce/ForceField.hpp" |
| 57 |
> |
#include "brains/ForceField.hpp" |
| 58 |
|
|
| 59 |
|
namespace OpenMD { |
| 60 |
|
|
| 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 |
< |
* 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 |
|
public: |
| 73 |
|
/** |
| 74 |
|
* Setup Simulation |
| 75 |
|
* @return a pointer to SimInfo |
| 76 |
< |
* @param mdfile the meta-data file name |
| 76 |
> |
* @param mdFileName the meta-data file name |
| 77 |
> |
* @param loadInitCoords should the initial coordinates be loaded from a file? |
| 78 |
|
*/ |
| 79 |
|
SimInfo* createSim(const std::string & mdFileName, bool loadInitCoords = true); |
| 80 |
|
|
| 82 |
|
|
| 83 |
|
/** |
| 84 |
|
* Parses the meta-data file |
| 85 |
< |
* @param mdfile |
| 86 |
< |
* @return 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 |
< |
Globals* parseFile(std::istream& rawMetaData, const std::string& mdFileName, int metaDataStartingLine); |
| 91 |
> |
Globals* parseFile(std::istream& rawMetaData, const std::string& mdFileName, int mdFileVersion, int metaDataStartingLine); |
| 92 |
|
|
| 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 |
|
|
| 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 OpenMD |
