| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 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 |
< |
* |
| 18 |
< |
* 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 |
|
* |
| 12 |
< |
* 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 |
|
* distribution. |
| 28 |
|
* 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 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* 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, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
|
| 43 |
|
#include "UseTheForce/DUFF.hpp" |
| 44 |
– |
#include "UseTheForce/DarkSide/lj_interface.h" |
| 45 |
– |
#include "UseTheForce/DarkSide/sticky_interface.h" |
| 46 |
– |
#include "UseTheForce/DarkSide/gb_interface.h" |
| 44 |
|
#include "UseTheForce/ForceFieldFactory.hpp" |
| 45 |
|
#include "io/BaseAtomTypesSectionParser.hpp" |
| 46 |
|
#include "io/DirectionalAtomTypesSectionParser.hpp" |
| 58 |
|
#include "io/OptionSectionParser.hpp" |
| 59 |
|
#include "UseTheForce/ForceFieldCreator.hpp" |
| 60 |
|
|
| 61 |
< |
namespace oopse { |
| 61 |
> |
namespace OpenMD { |
| 62 |
|
|
| 63 |
|
DUFF::DUFF(){ |
| 64 |
|
|
| 83 |
|
|
| 84 |
|
void DUFF::parse(const std::string& filename) { |
| 85 |
|
ifstrstream* ffStream; |
| 89 |
– |
bool hasGBtypes; |
| 86 |
|
|
| 87 |
|
ffStream = openForceFieldFile(filename); |
| 88 |
|
|
| 104 |
|
|
| 105 |
|
} |
| 106 |
|
} |
| 111 |
– |
at->makeFortranAtomType(); |
| 107 |
|
} |
| 108 |
|
|
| 114 |
– |
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 115 |
– |
at = atomTypeCont_.nextType(i)) { |
| 116 |
– |
at->complete(); |
| 117 |
– |
} |
| 118 |
– |
|
| 119 |
– |
hasGBtypes = false; |
| 120 |
– |
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 121 |
– |
at = atomTypeCont_.nextType(i)) { |
| 122 |
– |
if (at->isGayBerne()) |
| 123 |
– |
hasGBtypes = true; |
| 124 |
– |
} |
| 125 |
– |
|
| 126 |
– |
int isError = 0; |
| 127 |
– |
|
| 128 |
– |
if (hasGBtypes) { |
| 129 |
– |
completeGBFF(&isError); |
| 130 |
– |
} |
| 131 |
– |
|
| 109 |
|
delete ffStream; |
| 133 |
– |
|
| 110 |
|
} |
| 111 |
|
|
| 112 |
< |
DUFF::~DUFF(){ |
| 137 |
< |
destroyLJTypes(); |
| 138 |
< |
destroyStickyTypes(); |
| 139 |
< |
destroyGayBerneTypes(); |
| 140 |
< |
} |
| 141 |
< |
} //end namespace oopse |
| 112 |
> |
} //end namespace OpenMD |
