| 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 |
|
|
| 50 |
|
#include "io/BondTypesSectionParser.hpp" |
| 51 |
|
#include "io/BendTypesSectionParser.hpp" |
| 52 |
|
#include "io/TorsionTypesSectionParser.hpp" |
| 53 |
+ |
#include "io/InversionTypesSectionParser.hpp" |
| 54 |
|
#include "io/OptionSectionParser.hpp" |
| 55 |
|
#include "UseTheForce/ForceFieldCreator.hpp" |
| 56 |
|
|
| 57 |
< |
namespace oopse { |
| 57 |
> |
namespace OpenMD { |
| 58 |
|
|
| 59 |
|
Amber_FF::Amber_FF(){ |
| 60 |
|
|
| 64 |
|
//The order of adding section parsers is important. |
| 65 |
|
|
| 66 |
|
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
| 66 |
– |
|
| 67 |
|
spMan_.push_back(new BaseAtomTypesSectionParser()); |
| 68 |
|
spMan_.push_back(new AtomTypesSectionParser()); |
| 69 |
|
spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); |
| 71 |
|
spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_)); |
| 72 |
|
spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_)); |
| 73 |
|
spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_)); |
| 74 |
< |
|
| 74 |
> |
spMan_.push_back(new InversionTypesSectionParser(forceFieldOptions_)); |
| 75 |
|
} |
| 76 |
|
|
| 77 |
|
void Amber_FF::parse(const std::string& filename) { |
| 78 |
|
ifstrstream* ffStream; |
| 79 |
|
|
| 80 |
|
ffStream = openForceFieldFile(filename); |
| 81 |
– |
|
| 81 |
|
spMan_.parse(*ffStream, *this); |
| 82 |
|
|
| 83 |
|
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 85 |
|
|
| 86 |
|
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 87 |
|
at = atomTypeCont_.nextType(i)) { |
| 88 |
< |
at->makeFortranAtomType(); |
| 88 |
> |
|
| 89 |
> |
// useBase sets the responsibilities, and these have to be done |
| 90 |
> |
// after the atomTypes and Base types have all been scanned: |
| 91 |
> |
|
| 92 |
> |
std::vector<AtomType*> ayb = at->allYourBase(); |
| 93 |
> |
if (ayb.size() > 1) { |
| 94 |
> |
for (int j = ayb.size()-1; j > 0; j--) { |
| 95 |
> |
|
| 96 |
> |
ayb[j-1]->useBase(ayb[j]); |
| 97 |
> |
|
| 98 |
> |
} |
| 99 |
> |
} |
| 100 |
> |
at->makeFortranAtomType(); |
| 101 |
|
} |
| 102 |
|
|
| 103 |
|
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 104 |
|
at = atomTypeCont_.nextType(i)) { |
| 105 |
|
at->complete(); |
| 106 |
|
} |
| 107 |
< |
|
| 107 |
> |
|
| 108 |
|
delete ffStream; |
| 109 |
|
|
| 110 |
|
} |
| 112 |
|
Amber_FF::~Amber_FF(){ |
| 113 |
|
destroyLJTypes(); |
| 114 |
|
} |
| 115 |
< |
} //end namespace oopse |
| 115 |
> |
} //end namespace OpenMD |
