| 43 |
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#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" |
| 47 |
|
#include "UseTheForce/ForceFieldFactory.hpp" |
| 48 |
+ |
#include "io/BaseAtomTypesSectionParser.hpp" |
| 49 |
|
#include "io/DirectionalAtomTypesSectionParser.hpp" |
| 50 |
|
#include "io/AtomTypesSectionParser.hpp" |
| 51 |
+ |
#include "io/BaseAtomTypesSectionParser.hpp" |
| 52 |
|
#include "io/LennardJonesAtomTypesSectionParser.hpp" |
| 53 |
|
#include "io/ChargeAtomTypesSectionParser.hpp" |
| 54 |
|
#include "io/MultipoleAtomTypesSectionParser.hpp" |
| 55 |
|
#include "io/StickyAtomTypesSectionParser.hpp" |
| 56 |
+ |
#include "io/StickyPowerAtomTypesSectionParser.hpp" |
| 57 |
+ |
#include "io/GayBerneAtomTypesSectionParser.hpp" |
| 58 |
|
#include "io/BondTypesSectionParser.hpp" |
| 59 |
|
#include "io/BendTypesSectionParser.hpp" |
| 60 |
|
#include "io/TorsionTypesSectionParser.hpp" |
| 61 |
+ |
#include "io/OptionSectionParser.hpp" |
| 62 |
|
#include "UseTheForce/ForceFieldCreator.hpp" |
| 63 |
|
|
| 64 |
|
namespace oopse { |
| 65 |
|
|
| 66 |
< |
DUFF::DUFF(){ |
| 66 |
> |
DUFF::DUFF(){ |
| 67 |
|
|
| 68 |
|
//set default force field filename |
| 69 |
|
setForceFieldFileName("DUFF2.frc"); |
| 70 |
|
|
| 71 |
< |
//the order of adding section parsers are important |
| 72 |
< |
//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since |
| 67 |
< |
//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create |
| 68 |
< |
//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass |
| 69 |
< |
//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the |
| 70 |
< |
//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not |
| 71 |
< |
//important. AtomTypesSectionParser should be added before other atom type section parsers. |
| 72 |
< |
//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser. |
| 73 |
< |
//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are |
| 74 |
< |
//not important. |
| 75 |
< |
spMan_.push_back(new DirectionalAtomTypesSectionParser()); |
| 71 |
> |
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
| 72 |
> |
spMan_.push_back(new BaseAtomTypesSectionParser()); |
| 73 |
|
spMan_.push_back(new AtomTypesSectionParser()); |
| 74 |
< |
spMan_.push_back(new LennardJonesAtomTypesSectionParser()); |
| 75 |
< |
spMan_.push_back(new ChargeAtomTypesSectionParser()); |
| 76 |
< |
spMan_.push_back(new MultipoleAtomTypesSectionParser()); |
| 77 |
< |
spMan_.push_back(new StickyAtomTypesSectionParser()); |
| 78 |
< |
spMan_.push_back(new BondTypesSectionParser()); |
| 79 |
< |
spMan_.push_back(new BendTypesSectionParser()); |
| 80 |
< |
spMan_.push_back(new TorsionTypesSectionParser()); |
| 74 |
> |
spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); |
| 75 |
> |
spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); |
| 76 |
> |
spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_)); |
| 77 |
> |
spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_)); |
| 78 |
> |
spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_)); |
| 79 |
> |
spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_)); |
| 80 |
> |
spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_)); |
| 81 |
> |
spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_)); |
| 82 |
> |
spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_)); |
| 83 |
> |
spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_)); |
| 84 |
|
|
| 85 |
< |
} |
| 85 |
> |
} |
| 86 |
|
|
| 87 |
< |
void DUFF::parse(const std::string& filename) { |
| 87 |
> |
void DUFF::parse(const std::string& filename) { |
| 88 |
|
ifstrstream* ffStream; |
| 89 |
+ |
bool hasGBtypes; |
| 90 |
+ |
|
| 91 |
|
ffStream = openForceFieldFile(filename); |
| 92 |
|
|
| 93 |
|
spMan_.parse(*ffStream, *this); |
| 95 |
|
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 96 |
|
AtomType* at; |
| 97 |
|
|
| 98 |
< |
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
| 99 |
< |
at->makeFortranAtomType(); |
| 98 |
> |
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 99 |
> |
at = atomTypeCont_.nextType(i)) { |
| 100 |
> |
// useBase sets the responsibilities, and these have to be done |
| 101 |
> |
// after the atomTypes and Base types have all been scanned: |
| 102 |
> |
|
| 103 |
> |
std::vector<AtomType*> ayb = at->allYourBase(); |
| 104 |
> |
if (ayb.size() > 1) { |
| 105 |
> |
for (int j = ayb.size()-1; j > 0; j--) { |
| 106 |
> |
|
| 107 |
> |
ayb[j-1]->useBase(ayb[j]); |
| 108 |
> |
|
| 109 |
> |
} |
| 110 |
> |
} |
| 111 |
> |
at->makeFortranAtomType(); |
| 112 |
|
} |
| 113 |
|
|
| 114 |
< |
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
| 115 |
< |
at->complete(); |
| 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 |
< |
} |
| 126 |
> |
int isError = 0; |
| 127 |
|
|
| 128 |
+ |
if (hasGBtypes) { |
| 129 |
+ |
completeGBFF(&isError); |
| 130 |
+ |
} |
| 131 |
+ |
|
| 132 |
+ |
delete ffStream; |
| 133 |
+ |
|
| 134 |
+ |
} |
| 135 |
+ |
|
| 136 |
+ |
DUFF::~DUFF(){ |
| 137 |
+ |
destroyLJTypes(); |
| 138 |
+ |
destroyStickyTypes(); |
| 139 |
+ |
destroyGayBerneTypes(); |
| 140 |
+ |
} |
| 141 |
|
} //end namespace oopse |
