| 53 |
|
#include "brains/SimInfo.hpp" |
| 54 |
|
#include "math/Vector3.hpp" |
| 55 |
|
#include "primitives/Molecule.hpp" |
| 56 |
+ |
#include "primitives/StuntDouble.hpp" |
| 57 |
|
#include "UseTheForce/fCutoffPolicy.h" |
| 58 |
|
#include "UseTheForce/DarkSide/fElectrostaticSummationMethod.h" |
| 59 |
|
#include "UseTheForce/DarkSide/fElectrostaticScreeningMethod.h" |
| 600 |
|
//setup fortran force field |
| 601 |
|
/** @deprecate */ |
| 602 |
|
int isError = 0; |
| 603 |
+ |
|
| 604 |
+ |
setupCutoff(); |
| 605 |
|
|
| 606 |
|
setupElectrostaticSummationMethod( isError ); |
| 607 |
|
setupSwitchingFunction(); |
| 613 |
|
painCave.isFatal = 1; |
| 614 |
|
simError(); |
| 615 |
|
} |
| 613 |
– |
|
| 614 |
– |
|
| 615 |
– |
setupCutoff(); |
| 616 |
|
|
| 617 |
|
calcNdf(); |
| 618 |
|
calcNdfRaw(); |
| 1073 |
|
int sm = UNDAMPED; |
| 1074 |
|
RealType alphaVal; |
| 1075 |
|
RealType dielectric; |
| 1076 |
< |
|
| 1076 |
> |
|
| 1077 |
|
errorOut = isError; |
| 1078 |
– |
alphaVal = simParams_->getDampingAlpha(); |
| 1078 |
|
dielectric = simParams_->getDielectric(); |
| 1079 |
|
|
| 1080 |
|
if (simParams_->haveElectrostaticSummationMethod()) { |
| 1120 |
|
if (myScreen == "DAMPED") { |
| 1121 |
|
sm = DAMPED; |
| 1122 |
|
if (!simParams_->haveDampingAlpha()) { |
| 1123 |
< |
//throw error |
| 1123 |
> |
// first set a cutoff dependent alpha value |
| 1124 |
> |
// we assume alpha depends linearly with rcut from 0 to 20.5 ang |
| 1125 |
> |
alphaVal = 0.5125 - rcut_* 0.025; |
| 1126 |
> |
// for values rcut > 20.5, alpha is zero |
| 1127 |
> |
if (alphaVal < 0) alphaVal = 0; |
| 1128 |
> |
|
| 1129 |
> |
// throw warning |
| 1130 |
|
sprintf( painCave.errMsg, |
| 1131 |
|
"SimInfo warning: dampingAlpha was not specified in the input file.\n" |
| 1132 |
< |
"\tA default value of %f (1/ang) will be used.\n", alphaVal); |
| 1132 |
> |
"\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_); |
| 1133 |
|
painCave.isFatal = 0; |
| 1134 |
|
simError(); |
| 1135 |
|
} |
| 1441 |
|
return angularMomentum; |
| 1442 |
|
} |
| 1443 |
|
|
| 1444 |
< |
|
| 1444 |
> |
StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) { |
| 1445 |
> |
return IOIndexToIntegrableObject.at(index); |
| 1446 |
> |
} |
| 1447 |
> |
|
| 1448 |
> |
void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) { |
| 1449 |
> |
IOIndexToIntegrableObject= v; |
| 1450 |
> |
} |
| 1451 |
> |
|
| 1452 |
> |
/* |
| 1453 |
> |
void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) { |
| 1454 |
> |
assert( v.size() == nAtoms_ + nRigidBodies_); |
| 1455 |
> |
sdByGlobalIndex_ = v; |
| 1456 |
> |
} |
| 1457 |
> |
|
| 1458 |
> |
StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) { |
| 1459 |
> |
//assert(index < nAtoms_ + nRigidBodies_); |
| 1460 |
> |
return sdByGlobalIndex_.at(index); |
| 1461 |
> |
} |
| 1462 |
> |
*/ |
| 1463 |
|
}//end namespace oopse |
| 1464 |
|
|
