| 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). |
| 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 |
| 47 |
|
* @time 12:126am |
| 55 |
|
#include "primitives/Molecule.hpp" |
| 56 |
|
#include "brains/SimInfo.hpp" |
| 57 |
|
#include "io/Globals.hpp" |
| 58 |
< |
#include "UseTheForce/ForceField.hpp" |
| 58 |
> |
#include "brains/ForceField.hpp" |
| 59 |
|
|
| 60 |
|
namespace OpenMD { |
| 61 |
|
|
| 85 |
|
* @param mdfile |
| 86 |
|
* @return simParams |
| 87 |
|
*/ |
| 88 |
< |
Globals* parseFile(std::istream& rawMetaData, const std::string& mdFileName, int metaDataStartingLine); |
| 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); |
| 93 |
+ |
|
| 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 |
