# | Line 53 | Line 53 | |
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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" | |
# | Line 599 | Line 600 | namespace oopse { | |
600 | //setup fortran force field | |
601 | /** @deprecate */ | |
602 | int isError = 0; | |
603 | + | |
604 | + | setupCutoff(); |
605 | ||
606 | setupElectrostaticSummationMethod( isError ); | |
607 | setupSwitchingFunction(); | |
# | Line 610 | Line 613 | namespace oopse { | |
613 | painCave.isFatal = 1; | |
614 | simError(); | |
615 | } | |
613 | – | |
614 | – | |
615 | – | setupCutoff(); |
616 | ||
617 | calcNdf(); | |
618 | calcNdfRaw(); | |
# | Line 1073 | Line 1073 | namespace oopse { | |
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()) { | |
# | Line 1121 | Line 1120 | namespace oopse { | |
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 | } | |
# | Line 1436 | Line 1441 | namespace oopse { | |
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 |
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