| 44 |
|
#include "UseTheForce/DarkSide/lj_interface.h" |
| 45 |
|
#include "UseTheForce/DarkSide/sticky_interface.h" |
| 46 |
|
#include "UseTheForce/ForceFieldFactory.hpp" |
| 47 |
< |
#include "io/DirectionalAtomTypesSectionParser.hpp" |
| 47 |
> |
#include "io/BaseAtomTypesSectionParser.hpp" |
| 48 |
|
#include "io/AtomTypesSectionParser.hpp" |
| 49 |
– |
#include "io/LennardJonesAtomTypesSectionParser.hpp" |
| 50 |
– |
#include "io/ChargeAtomTypesSectionParser.hpp" |
| 51 |
– |
#include "io/MultipoleAtomTypesSectionParser.hpp" |
| 49 |
|
#include "io/EAMAtomTypesSectionParser.hpp" |
| 53 |
– |
#include "io/StickyAtomTypesSectionParser.hpp" |
| 54 |
– |
#include "io/BondTypesSectionParser.hpp" |
| 55 |
– |
#include "io/BendTypesSectionParser.hpp" |
| 56 |
– |
#include "io/TorsionTypesSectionParser.hpp" |
| 50 |
|
#include "io/OptionSectionParser.hpp" |
| 51 |
|
#include "UseTheForce/ForceFieldCreator.hpp" |
| 52 |
|
#include "utils/simError.h" |
| 58 |
|
setForceFieldFileName("EAM.frc"); |
| 59 |
|
|
| 60 |
|
//the order of adding section parsers are important |
| 61 |
< |
//DirectionalAtomTypesSectionParser should be added before AtomTypesSectionParser Since |
| 69 |
< |
//These two section parsers will actually create "real" AtomTypes (AtomTypesSectionParser will create |
| 70 |
< |
//AtomType and DirectionalAtomTypesSectionParser will creat DirectionalAtomType which is a subclass |
| 71 |
< |
//of AtomType, therefore it should come first). Other AtomTypes Section Parser will not create the |
| 72 |
< |
//"real" AtomType, they only add and set some attribute of the AtomType. Thus their order are not |
| 73 |
< |
//important. AtomTypesSectionParser should be added before other atom type section parsers. |
| 74 |
< |
//Make sure they are added after DirectionalAtomTypesSectionParser and AtomTypesSectionParser. |
| 75 |
< |
//The order of BondTypesSectionParser, BendTypesSectionParser and TorsionTypesSectionParser are |
| 76 |
< |
//not important. |
| 61 |
> |
//OptionSectionParser must come first to set options for other parsers |
| 62 |
|
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
| 63 |
< |
spMan_.push_back(new DirectionalAtomTypesSectionParser()); |
| 63 |
> |
spMan_.push_back(new BaseAtomTypesSectionParser()); |
| 64 |
|
spMan_.push_back(new AtomTypesSectionParser()); |
| 65 |
< |
spMan_.push_back(new EAMAtomTypesSectionParser()); |
| 81 |
< |
|
| 82 |
< |
|
| 65 |
> |
spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_)); |
| 66 |
|
} |
| 67 |
|
|
| 68 |
|
void EAM_FF::parse(const std::string& filename) { |
| 75 |
|
AtomType* at; |
| 76 |
|
|
| 77 |
|
for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
| 78 |
+ |
// useBase sets the responsibilities, and these have to be done |
| 79 |
+ |
// after the atomTypes and Base types have all been scanned: |
| 80 |
+ |
|
| 81 |
+ |
std::vector<AtomType*> ayb = at->allYourBase(); |
| 82 |
+ |
if (ayb.size() > 1) { |
| 83 |
+ |
for (int j = ayb.size()-1; j > 0; j--) { |
| 84 |
+ |
|
| 85 |
+ |
ayb[j-1]->useBase(ayb[j]); |
| 86 |
+ |
|
| 87 |
+ |
} |
| 88 |
+ |
} |
| 89 |
|
at->makeFortranAtomType(); |
| 90 |
|
} |
| 91 |
|
|
| 97 |
|
} |
| 98 |
|
|
| 99 |
|
|
| 100 |
< |
double EAM_FF::getRcutFromAtomType(AtomType* at){ |
| 101 |
< |
double rcut = 0.0; |
| 100 |
> |
RealType EAM_FF::getRcutFromAtomType(AtomType* at){ |
| 101 |
> |
RealType rcut = 0.0; |
| 102 |
|
if (at->isEAM()) { |
| 103 |
|
GenericData* data = at->getPropertyByName("EAM"); |
| 104 |
|
if (data != NULL) { |
