| 6 |
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* 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 |
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* 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" |
| 47 |
|
#include "io/AtomTypesSectionParser.hpp" |
| 48 |
+ |
#include "io/BaseAtomTypesSectionParser.hpp" |
| 49 |
|
#include "io/LennardJonesAtomTypesSectionParser.hpp" |
| 50 |
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#include "io/ChargeAtomTypesSectionParser.hpp" |
| 51 |
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#include "io/MultipoleAtomTypesSectionParser.hpp" |
| 58 |
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#include "io/OptionSectionParser.hpp" |
| 59 |
|
#include "UseTheForce/ForceFieldCreator.hpp" |
| 60 |
|
|
| 61 |
< |
namespace oopse { |
| 61 |
> |
namespace OpenMD { |
| 62 |
|
|
| 63 |
|
DUFF::DUFF(){ |
| 64 |
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|
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//set default force field filename |
| 66 |
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setForceFieldFileName("DUFF2.frc"); |
| 67 |
|
|
| 69 |
– |
//The order of adding section parsers is important. |
| 70 |
– |
//OptionSectionParser must come first to set options for other parsers |
| 71 |
– |
//DirectionalAtomTypesSectionParser should be added before |
| 72 |
– |
//AtomTypesSectionParser, and these two section parsers will actually |
| 73 |
– |
//create "real" AtomTypes (AtomTypesSectionParser will create AtomType and |
| 74 |
– |
//DirectionalAtomTypesSectionParser will create DirectionalAtomType, which |
| 75 |
– |
//is a subclass of AtomType and should come first). Other AtomTypes Section |
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– |
//Parser will not create the "real" AtomType, they only add and set some |
| 77 |
– |
//attribute of the AtomType. Thus their order are not important. |
| 78 |
– |
//AtomTypesSectionParser should be added before other atom type section |
| 79 |
– |
//parsers. Make sure they are added after DirectionalAtomTypesSectionParser |
| 80 |
– |
//and AtomTypesSectionParser. The order of BondTypesSectionParser, |
| 81 |
– |
//BendTypesSectionParser and TorsionTypesSectionParser are not important. |
| 68 |
|
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
| 69 |
< |
spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); |
| 69 |
> |
spMan_.push_back(new BaseAtomTypesSectionParser()); |
| 70 |
|
spMan_.push_back(new AtomTypesSectionParser()); |
| 71 |
+ |
spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); |
| 72 |
|
spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); |
| 73 |
|
spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_)); |
| 74 |
|
spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_)); |
| 83 |
|
|
| 84 |
|
void DUFF::parse(const std::string& filename) { |
| 85 |
|
ifstrstream* ffStream; |
| 86 |
+ |
|
| 87 |
|
ffStream = openForceFieldFile(filename); |
| 88 |
|
|
| 89 |
|
spMan_.parse(*ffStream, *this); |
| 93 |
|
|
| 94 |
|
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 95 |
|
at = atomTypeCont_.nextType(i)) { |
| 96 |
< |
at->makeFortranAtomType(); |
| 97 |
< |
} |
| 96 |
> |
// useBase sets the responsibilities, and these have to be done |
| 97 |
> |
// after the atomTypes and Base types have all been scanned: |
| 98 |
|
|
| 99 |
< |
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 100 |
< |
at = atomTypeCont_.nextType(i)) { |
| 101 |
< |
at->complete(); |
| 99 |
> |
std::vector<AtomType*> ayb = at->allYourBase(); |
| 100 |
> |
if (ayb.size() > 1) { |
| 101 |
> |
for (int j = ayb.size()-1; j > 0; j--) { |
| 102 |
> |
|
| 103 |
> |
ayb[j-1]->useBase(ayb[j]); |
| 104 |
> |
|
| 105 |
> |
} |
| 106 |
> |
} |
| 107 |
|
} |
| 108 |
|
|
| 116 |
– |
int isError = 0; |
| 117 |
– |
|
| 109 |
|
delete ffStream; |
| 119 |
– |
|
| 110 |
|
} |
| 111 |
|
|
| 112 |
< |
DUFF::~DUFF(){ |
| 123 |
< |
destroyLJTypes(); |
| 124 |
< |
destroyStickyTypes(); |
| 125 |
< |
destroyGayBerneTypes(); |
| 126 |
< |
} |
| 127 |
< |
} //end namespace oopse |
| 112 |
> |
} //end namespace OpenMD |
