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#include "UseTheForce/DarkSide/lj_interface.h" |
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#include "UseTheForce/DarkSide/sticky_interface.h" |
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#include "UseTheForce/ForceFieldFactory.hpp" |
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#include "io/OptionSectionParser.hpp" |
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#include "io/DirectionalAtomTypesSectionParser.hpp" |
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#include "io/BaseAtomTypesSectionParser.hpp" |
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#include "io/AtomTypesSectionParser.hpp" |
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#include "io/LennardJonesAtomTypesSectionParser.hpp" |
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#include "io/ChargeAtomTypesSectionParser.hpp" |
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#include "io/BendTypesSectionParser.hpp" |
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#include "io/TorsionTypesSectionParser.hpp" |
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#include "UseTheForce/ForceFieldCreator.hpp" |
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#include "UseTheForce/SHAPES_FF.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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|
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SHAPES_FF::SHAPES_FF(){ |
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//set default force field filename |
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setForceFieldFileName("EAM.frc"); |
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setForceFieldFileName("Shapes.frc"); |
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|
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//The order of adding section parsers are important |
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//DirectionalAtomTypesSectionParser should be added before |
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//The ordering of section parsers is important... |
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//OptionSectionParser must come first to set options for other parsers |
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//DirectionalAtomTypesSectionParser should be before |
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//AtomTypesSectionParser since these two section parsers will actually |
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//create "real" AtomTypes (AtomTypesSectionParser will create AtomType |
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//and DirectionalAtomTypesSectionParser will creat DirectionalAtomType |
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//and DirectionalAtomTypesSectionParser will create DirectionalAtomType |
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//which is a subclass of AtomType, therefore it should come first). Other |
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//AtomTypes Section Parser will not create the "real" AtomType, they only |
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//add and set some attribute of the AtomType. Thus their order are not |
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//important. AtomTypesSectionParser should be added before other atom |
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//add and set some attribute of the AtomType. Thus the ordering of these |
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//are not important. AtomTypesSectionParser should be added before other atom |
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//type section parsers. Make sure they are added after |
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//DirectionalAtomTypesSectionParser and AtomTypesSectionParser. The order |
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//of BondTypesSectionParser, BendTypesSectionParser and |
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//TorsionTypesSectionParser are not important. |
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|
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spMan_.push_back(new ShapeAtomTypesSectionParser()); |
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spMan_.push_back(new DirectionalAtomTypesSectionParser()); |
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> |
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
| 83 |
> |
spMan_.push_back(new ShapeAtomTypesSectionParser(forceFieldOptions_)); |
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> |
spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); |
| 85 |
> |
spMan_.push_back(new BaseAtomTypesSectionParser()); |
| 86 |
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spMan_.push_back(new AtomTypesSectionParser()); |
| 87 |
< |
spMan_.push_back(new LennardJonesAtomTypesSectionParser()); |
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< |
spMan_.push_back(new ChargeAtomTypesSectionParser()); |
| 89 |
< |
spMan_.push_back(new MultipoleAtomTypesSectionParser()); |
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< |
spMan_.push_back(new StickyAtomTypesSectionParser()); |
| 91 |
< |
spMan_.push_back(new BondTypesSectionParser()); |
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< |
spMan_.push_back(new BendTypesSectionParser()); |
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< |
spMan_.push_back(new TorsionTypesSectionParser()); |
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> |
spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); |
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> |
spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_)); |
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> |
spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_)); |
| 90 |
> |
spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_)); |
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> |
spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_)); |
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> |
spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_)); |
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> |
spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_)); |
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|
| 95 |
< |
} |
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|
| 95 |
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} |
| 96 |
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|
| 97 |
|
SHAPES_FF::~SHAPES_FF(){ |
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// We need to clean up the fortran side so we don't have bad things happen if |
| 99 |
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// we try to create a second EAM force field. |
| 100 |
< |
destroyEAMTypes(); |
| 100 |
> |
destroyShapeTypes(); |
| 101 |
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} |
| 102 |
< |
} //end namespace oopse |
| 103 |
< |
|
| 99 |
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void SHAPES_FF::parse(const std::string& filename) { |
| 102 |
> |
|
| 103 |
> |
void SHAPES_FF::parse(const std::string& filename) { |
| 104 |
|
ifstrstream* ffStream; |
| 105 |
|
ffStream = openForceFieldFile(filename); |
| 106 |
< |
|
| 106 |
> |
|
| 107 |
|
spMan_.parse(*ffStream, *this); |
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|
| 108 |
> |
|
| 109 |
|
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 110 |
|
AtomType* at; |
| 111 |
< |
|
| 111 |
> |
|
| 112 |
|
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
| 113 |
< |
at->makeFortranAtomType(); |
| 114 |
< |
} |
| 113 |
> |
// useBase sets the responsibilities, and these have to be done |
| 114 |
> |
// after the atomTypes and Base types have all been scanned: |
| 115 |
|
|
| 116 |
+ |
std::vector<AtomType*> ayb = at->allYourBase(); |
| 117 |
+ |
if (ayb.size() > 1) { |
| 118 |
+ |
for (int j = ayb.size()-1; j > 0; j--) { |
| 119 |
+ |
|
| 120 |
+ |
ayb[j-1]->useBase(ayb[j]); |
| 121 |
+ |
|
| 122 |
+ |
} |
| 123 |
+ |
} |
| 124 |
+ |
at->makeFortranAtomType(); |
| 125 |
+ |
} |
| 126 |
+ |
|
| 127 |
|
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
| 128 |
< |
at->complete(); |
| 128 |
> |
at->complete(); |
| 129 |
|
} |
| 130 |
|
|
| 131 |
+ |
int isError = 0; |
| 132 |
+ |
completeShapeFF(&isError); |
| 133 |
+ |
|
| 134 |
|
delete ffStream; |
| 135 |
< |
} |
| 136 |
< |
|
| 137 |
< |
|
| 138 |
< |
double SHAPES_FF::getRcutFromAtomType(AtomType* at){ |
| 139 |
< |
|
| 140 |
< |
} |
| 141 |
< |
|
| 124 |
< |
|
| 135 |
> |
} |
| 136 |
> |
|
| 137 |
> |
|
| 138 |
> |
// RealType SHAPES_FF::getRcutFromAtomType(AtomType* at){ |
| 139 |
> |
// } |
| 140 |
> |
} //end namespace oopse |
| 141 |
> |
|
