| 45 |
|
#include "UseTheForce/ForceFieldFactory.hpp" |
| 46 |
|
#include "io/OptionSectionParser.hpp" |
| 47 |
|
#include "io/DirectionalAtomTypesSectionParser.hpp" |
| 48 |
+ |
#include "io/BaseAtomTypesSectionParser.hpp" |
| 49 |
|
#include "io/AtomTypesSectionParser.hpp" |
| 50 |
|
#include "io/LennardJonesAtomTypesSectionParser.hpp" |
| 51 |
|
#include "io/ChargeAtomTypesSectionParser.hpp" |
| 65 |
|
//set default force field filename |
| 66 |
|
setForceFieldFileName("Shapes.frc"); |
| 67 |
|
|
| 67 |
– |
//The ordering of section parsers is important |
| 68 |
– |
//DirectionalAtomTypesSectionParser should be before |
| 69 |
– |
//AtomTypesSectionParser since these two section parsers will actually |
| 70 |
– |
//create "real" AtomTypes (AtomTypesSectionParser will create AtomType |
| 71 |
– |
//and DirectionalAtomTypesSectionParser will create DirectionalAtomType |
| 72 |
– |
//which is a subclass of AtomType, therefore it should come first). Other |
| 73 |
– |
//AtomTypes Section Parser will not create the "real" AtomType, they only |
| 74 |
– |
//add and set some attribute of the AtomType. Thus the ordering of these |
| 75 |
– |
//are not important. AtomTypesSectionParser should be added before other atom |
| 76 |
– |
//type section parsers. Make sure they are added after |
| 77 |
– |
//DirectionalAtomTypesSectionParser and AtomTypesSectionParser. The order |
| 78 |
– |
//of BondTypesSectionParser, BendTypesSectionParser and |
| 79 |
– |
//TorsionTypesSectionParser are not important. |
| 68 |
|
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
| 69 |
< |
spMan_.push_back(new ShapeAtomTypesSectionParser()); |
| 70 |
< |
spMan_.push_back(new DirectionalAtomTypesSectionParser()); |
| 69 |
> |
spMan_.push_back(new ShapeAtomTypesSectionParser(forceFieldOptions_)); |
| 70 |
> |
spMan_.push_back(new BaseAtomTypesSectionParser()); |
| 71 |
|
spMan_.push_back(new AtomTypesSectionParser()); |
| 72 |
+ |
spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); |
| 73 |
|
spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); |
| 74 |
< |
spMan_.push_back(new ChargeAtomTypesSectionParser()); |
| 75 |
< |
spMan_.push_back(new MultipoleAtomTypesSectionParser()); |
| 76 |
< |
spMan_.push_back(new StickyAtomTypesSectionParser()); |
| 77 |
< |
spMan_.push_back(new BondTypesSectionParser()); |
| 78 |
< |
spMan_.push_back(new BendTypesSectionParser()); |
| 79 |
< |
spMan_.push_back(new TorsionTypesSectionParser()); |
| 74 |
> |
spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_)); |
| 75 |
> |
spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_)); |
| 76 |
> |
spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_)); |
| 77 |
> |
spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_)); |
| 78 |
> |
spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_)); |
| 79 |
> |
spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_)); |
| 80 |
|
|
| 81 |
|
} |
| 82 |
|
|
| 96 |
|
AtomType* at; |
| 97 |
|
|
| 98 |
|
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
| 99 |
+ |
// useBase sets the responsibilities, and these have to be done |
| 100 |
+ |
// after the atomTypes and Base types have all been scanned: |
| 101 |
+ |
|
| 102 |
+ |
std::vector<AtomType*> ayb = at->allYourBase(); |
| 103 |
+ |
if (ayb.size() > 1) { |
| 104 |
+ |
for (int j = ayb.size()-1; j > 0; j--) { |
| 105 |
+ |
|
| 106 |
+ |
ayb[j-1]->useBase(ayb[j]); |
| 107 |
+ |
|
| 108 |
+ |
} |
| 109 |
+ |
} |
| 110 |
|
at->makeFortranAtomType(); |
| 111 |
|
} |
| 112 |
|
|
| 121 |
|
} |
| 122 |
|
|
| 123 |
|
|
| 124 |
< |
// double SHAPES_FF::getRcutFromAtomType(AtomType* at){ |
| 124 |
> |
// RealType SHAPES_FF::getRcutFromAtomType(AtomType* at){ |
| 125 |
|
// } |
| 126 |
|
} //end namespace oopse |
| 127 |
|
|
