| 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" |
| 68 |
|
//set default force field filename |
| 69 |
|
setForceFieldFileName("DUFF2.frc"); |
| 70 |
|
|
| 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. |
| 71 |
|
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
| 72 |
< |
spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); |
| 72 |
> |
spMan_.push_back(new BaseAtomTypesSectionParser()); |
| 73 |
|
spMan_.push_back(new AtomTypesSectionParser()); |
| 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_)); |
| 97 |
|
|
| 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 |
|
|
