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43 |
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#include "UseTheForce/DUFF.hpp" |
44 |
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#include "UseTheForce/DarkSide/lj_interface.h" |
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– |
#include "UseTheForce/DarkSide/charge_interface.h" |
46 |
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#include "UseTheForce/DarkSide/dipole_interface.h" |
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#include "UseTheForce/DarkSide/sticky_interface.h" |
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#include "UseTheForce/DarkSide/gb_interface.h" |
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#include "UseTheForce/ForceFieldFactory.hpp" |
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#include "io/DirectionalAtomTypesSectionParser.hpp" |
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#include "io/AtomTypesSectionParser.hpp" |
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#include "io/LennardJonesAtomTypesSectionParser.hpp" |
51 |
< |
#include "io/ElectrostaticAtomTypesSectionParser.hpp" |
51 |
> |
#include "io/ChargeAtomTypesSectionParser.hpp" |
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> |
#include "io/MultipoleAtomTypesSectionParser.hpp" |
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#include "io/StickyAtomTypesSectionParser.hpp" |
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+ |
#include "io/StickyPowerAtomTypesSectionParser.hpp" |
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#include "io/GayBerneAtomTypesSectionParser.hpp" |
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#include "io/BondTypesSectionParser.hpp" |
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#include "io/BendTypesSectionParser.hpp" |
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#include "io/TorsionTypesSectionParser.hpp" |
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+ |
#include "io/OptionSectionParser.hpp" |
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#include "UseTheForce/ForceFieldCreator.hpp" |
61 |
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|
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namespace oopse { |
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|
64 |
< |
DUFF::DUFF(){ |
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> |
DUFF::DUFF(){ |
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//set default force field filename |
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setForceFieldFileName("DUFF2.frc"); |
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< |
//the order of adding section parsers are important |
70 |
< |
//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since |
71 |
< |
//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create |
72 |
< |
//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass |
73 |
< |
//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the |
74 |
< |
//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not |
75 |
< |
//important. AtomTypesSectionParser should be added before other atom type section parsers. |
76 |
< |
//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser. |
77 |
< |
//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are |
78 |
< |
//not important. |
79 |
< |
spMan_.push_back(new DirectionalAtomTypesSectionParser()); |
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 |
76 |
> |
//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. |
82 |
> |
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
83 |
> |
spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); |
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spMan_.push_back(new AtomTypesSectionParser()); |
85 |
< |
spMan_.push_back(new LennardJonesAtomTypesSectionParser()); |
86 |
< |
spMan_.push_back(new ElectrostaticAtomTypesSectionParser()); |
87 |
< |
spMan_.push_back(new StickyAtomTypesSectionParser()); |
88 |
< |
spMan_.push_back(new BondTypesSectionParser()); |
89 |
< |
spMan_.push_back(new BendTypesSectionParser()); |
90 |
< |
spMan_.push_back(new TorsionTypesSectionParser()); |
85 |
> |
spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); |
86 |
> |
spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_)); |
87 |
> |
spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_)); |
88 |
> |
spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_)); |
89 |
> |
spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_)); |
90 |
> |
spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_)); |
91 |
> |
spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_)); |
92 |
> |
spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_)); |
93 |
> |
spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_)); |
94 |
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|
95 |
< |
} |
95 |
> |
} |
96 |
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|
97 |
< |
void DUFF::parse(const std::string& filename) { |
97 |
> |
void DUFF::parse(const std::string& filename) { |
98 |
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ifstrstream* ffStream; |
99 |
+ |
bool hasGBtypes; |
100 |
+ |
|
101 |
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ffStream = openForceFieldFile(filename); |
102 |
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|
103 |
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spMan_.parse(*ffStream, *this); |
105 |
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ForceField::AtomTypeContainer::MapTypeIterator i; |
106 |
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AtomType* at; |
107 |
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|
108 |
< |
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
109 |
< |
at->makeFortranAtomType(); |
108 |
> |
for (at = atomTypeCont_.beginType(i); at != NULL; |
109 |
> |
at = atomTypeCont_.nextType(i)) { |
110 |
> |
at->makeFortranAtomType(); |
111 |
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} |
112 |
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|
113 |
< |
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
114 |
< |
at->complete(); |
113 |
> |
for (at = atomTypeCont_.beginType(i); at != NULL; |
114 |
> |
at = atomTypeCont_.nextType(i)) { |
115 |
> |
at->complete(); |
116 |
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} |
117 |
+ |
|
118 |
+ |
hasGBtypes = false; |
119 |
+ |
for (at = atomTypeCont_.beginType(i); at != NULL; |
120 |
+ |
at = atomTypeCont_.nextType(i)) { |
121 |
+ |
if (at->isGayBerne()) |
122 |
+ |
hasGBtypes = true; |
123 |
+ |
} |
124 |
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|
125 |
< |
} |
125 |
> |
int isError = 0; |
126 |
|
|
127 |
+ |
if (hasGBtypes) { |
128 |
+ |
completeGBFF(&isError); |
129 |
+ |
} |
130 |
+ |
|
131 |
+ |
delete ffStream; |
132 |
+ |
|
133 |
+ |
} |
134 |
+ |
|
135 |
+ |
DUFF::~DUFF(){ |
136 |
+ |
destroyLJTypes(); |
137 |
+ |
destroyStickyTypes(); |
138 |
+ |
destroyGayBerneTypes(); |
139 |
+ |
} |
140 |
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} //end namespace oopse |