# | Line 53 | Line 53 | |
---|---|---|
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 669 | Line 669 | namespace oopse { | |
669 | // set the useRF logical | |
670 | useRF = 0; | |
671 | useSF = 0; | |
672 | + | useSP = 0; |
673 | ||
674 | ||
675 | if (simParams_->haveElectrostaticSummationMethod()) { | |
676 | std::string myMethod = simParams_->getElectrostaticSummationMethod(); | |
677 | toUpper(myMethod); | |
678 | if (myMethod == "REACTION_FIELD"){ | |
679 | < | useRF=1; |
679 | > | useRF = 1; |
680 | } else if (myMethod == "SHIFTED_FORCE"){ | |
681 | useSF = 1; | |
682 | } else if (myMethod == "SHIFTED_POTENTIAL"){ | |
# | Line 783 | Line 784 | namespace oopse { | |
784 | fInfo_.SIM_uses_SF = useSF; | |
785 | fInfo_.SIM_uses_SP = useSP; | |
786 | fInfo_.SIM_uses_BoxDipole = useBoxDipole; | |
786 | – | |
787 | – | if( myMethod == "REACTION_FIELD") { |
788 | – | |
789 | – | if (simParams_->haveDielectric()) { |
790 | – | fInfo_.dielect = simParams_->getDielectric(); |
791 | – | } else { |
792 | – | sprintf(painCave.errMsg, |
793 | – | "SimSetup Error: No Dielectric constant was set.\n" |
794 | – | "\tYou are trying to use Reaction Field without" |
795 | – | "\tsetting a dielectric constant!\n"); |
796 | – | painCave.isFatal = 1; |
797 | – | simError(); |
798 | – | } |
799 | – | } |
800 | – | |
787 | } | |
788 | ||
789 | void SimInfo::setupFortranSim() { | |
# | Line 1073 | Line 1059 | namespace oopse { | |
1059 | int sm = UNDAMPED; | |
1060 | RealType alphaVal; | |
1061 | RealType dielectric; | |
1062 | < | |
1062 | > | |
1063 | errorOut = isError; | |
1078 | – | alphaVal = simParams_->getDampingAlpha(); |
1079 | – | dielectric = simParams_->getDielectric(); |
1064 | ||
1065 | if (simParams_->haveElectrostaticSummationMethod()) { | |
1066 | std::string myMethod = simParams_->getElectrostaticSummationMethod(); | |
# | Line 1093 | Line 1077 | namespace oopse { | |
1077 | if (myMethod == "SHIFTED_FORCE") { | |
1078 | esm = SHIFTED_FORCE; | |
1079 | } else { | |
1080 | < | if (myMethod == "REACTION_FIELD") { |
1080 | > | if (myMethod == "REACTION_FIELD") { |
1081 | esm = REACTION_FIELD; | |
1082 | + | dielectric = simParams_->getDielectric(); |
1083 | + | if (!simParams_->haveDielectric()) { |
1084 | + | // throw warning |
1085 | + | sprintf( painCave.errMsg, |
1086 | + | "SimInfo warning: dielectric was not specified in the input file\n\tfor the reaction field correction method.\n" |
1087 | + | "\tA default value of %f will be used for the dielectric.\n", dielectric); |
1088 | + | painCave.isFatal = 0; |
1089 | + | simError(); |
1090 | + | } |
1091 | } else { | |
1092 | // throw error | |
1093 | sprintf( painCave.errMsg, | |
# | Line 1121 | Line 1114 | namespace oopse { | |
1114 | if (myScreen == "DAMPED") { | |
1115 | sm = DAMPED; | |
1116 | if (!simParams_->haveDampingAlpha()) { | |
1117 | < | //throw error |
1117 | > | // first set a cutoff dependent alpha value |
1118 | > | // we assume alpha depends linearly with rcut from 0 to 20.5 ang |
1119 | > | alphaVal = 0.5125 - rcut_* 0.025; |
1120 | > | // for values rcut > 20.5, alpha is zero |
1121 | > | if (alphaVal < 0) alphaVal = 0; |
1122 | > | |
1123 | > | // throw warning |
1124 | sprintf( painCave.errMsg, | |
1125 | "SimInfo warning: dampingAlpha was not specified in the input file.\n" | |
1126 | < | "\tA default value of %f (1/ang) will be used.\n", alphaVal); |
1126 | > | "\tA default value of %f (1/ang) will be used for the cutoff of\n\t%f (ang).\n", alphaVal, rcut_); |
1127 | painCave.isFatal = 0; | |
1128 | simError(); | |
1129 | + | } else { |
1130 | + | alphaVal = simParams_->getDampingAlpha(); |
1131 | } | |
1132 | + | |
1133 | } else { | |
1134 | // throw error | |
1135 | sprintf( painCave.errMsg, | |
# | Line 1436 | Line 1438 | namespace oopse { | |
1438 | return angularMomentum; | |
1439 | } | |
1440 | ||
1441 | < | |
1441 | > | StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) { |
1442 | > | return IOIndexToIntegrableObject.at(index); |
1443 | > | } |
1444 | > | |
1445 | > | void SimInfo::setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v) { |
1446 | > | IOIndexToIntegrableObject= v; |
1447 | > | } |
1448 | > | |
1449 | > | /* |
1450 | > | void SimInfo::setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v) { |
1451 | > | assert( v.size() == nAtoms_ + nRigidBodies_); |
1452 | > | sdByGlobalIndex_ = v; |
1453 | > | } |
1454 | > | |
1455 | > | StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) { |
1456 | > | //assert(index < nAtoms_ + nRigidBodies_); |
1457 | > | return sdByGlobalIndex_.at(index); |
1458 | > | } |
1459 | > | */ |
1460 | }//end namespace oopse | |
1461 |
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