| 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 |
|
} |
| 614 |
– |
|
| 615 |
– |
|
| 616 |
– |
setupCutoff(); |
| 616 |
|
|
| 617 |
|
calcNdf(); |
| 618 |
|
calcNdfRaw(); |
| 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"){ |
| 784 |
|
fInfo_.SIM_uses_SF = useSF; |
| 785 |
|
fInfo_.SIM_uses_SP = useSP; |
| 786 |
|
fInfo_.SIM_uses_BoxDipole = useBoxDipole; |
| 787 |
– |
|
| 788 |
– |
if( myMethod == "REACTION_FIELD") { |
| 789 |
– |
|
| 790 |
– |
if (simParams_->haveDielectric()) { |
| 791 |
– |
fInfo_.dielect = simParams_->getDielectric(); |
| 792 |
– |
} else { |
| 793 |
– |
sprintf(painCave.errMsg, |
| 794 |
– |
"SimSetup Error: No Dielectric constant was set.\n" |
| 795 |
– |
"\tYou are trying to use Reaction Field without" |
| 796 |
– |
"\tsetting a dielectric constant!\n"); |
| 797 |
– |
painCave.isFatal = 1; |
| 798 |
– |
simError(); |
| 799 |
– |
} |
| 800 |
– |
} |
| 801 |
– |
|
| 787 |
|
} |
| 788 |
|
|
| 789 |
|
void SimInfo::setupFortranSim() { |
| 1059 |
|
int sm = UNDAMPED; |
| 1060 |
|
RealType alphaVal; |
| 1061 |
|
RealType dielectric; |
| 1062 |
< |
|
| 1062 |
> |
|
| 1063 |
|
errorOut = isError; |
| 1079 |
– |
alphaVal = simParams_->getDampingAlpha(); |
| 1080 |
– |
dielectric = simParams_->getDielectric(); |
| 1064 |
|
|
| 1065 |
|
if (simParams_->haveElectrostaticSummationMethod()) { |
| 1066 |
|
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
| 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, |
| 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, |
