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void
DirectRegion.init(Atom[] atoms,
double[] polarizability,
double[][][] globalMultipole,
double[][] cartMultipolePhi,
AtomicDoubleArray3D field,
AtomicDoubleArray3D fieldCR,
boolean generalizedKirkwoodTerm,
GeneralizedKirkwood generalizedKirkwood,
EwaldParameters ewaldParameters,
double dielectric,
double[][][] inducedDipole,
double[][][] inducedDipoleCR,
double[][] directDipole,
double[][] directDipoleCR,
double[][] directField,
double[][] directFieldCR)
void
InducedDipoleFieldReduceRegion.init(Atom[] atoms,
double[][][] inducedDipole,
double[][][] inducedDipoleCR,
boolean generalizedKirkwoodTerm,
GeneralizedKirkwood generalizedKirkwood,
EwaldParameters ewaldParameters,
double dielectric,
double[][] cartesianDipolePhi,
double[][] cartesianDipolePhiCR,
AtomicDoubleArray3D field,
AtomicDoubleArray3D fieldCR)
void
InducedDipoleFieldRegion.init(Atom[] atoms,
Crystal crystal,
boolean[] use,
int[] molecule,
double[] ipdamp,
double[] thole,
double[][][] coordinates,
RealSpaceNeighborParameters realSpaceNeighborParameters,
double[][][] inducedDipole,
double[][][] inducedDipoleCR,
boolean reciprocalSpaceTerm,
ReciprocalSpace reciprocalSpace,
LambdaMode lambdaMode,
EwaldParameters ewaldParameters,
AtomicDoubleArray3D field,
AtomicDoubleArray3D fieldCR,
PMETimings pmeTimings)
void
OPTRegion.init(int currentOptOrder,
Atom[] atoms,
double[] polarizability,
double[][][] inducedDipole,
double[][][] inducedDipoleCR,
double[][] cartesianDipolePhi,
double[][] cartesianDipolePhiCR,
AtomicDoubleArray3D field,
AtomicDoubleArray3D fieldCR,
boolean generalizedKirkwoodTerm,
GeneralizedKirkwood generalizedKirkwood,
EwaldParameters ewaldParameters,
double dielectric)
void
PCGSolver.init(Atom[] atoms,
double[][][] coordinates,
double[] polarizability,
double[] ipdamp,
double[] thole,
boolean[] use,
Crystal crystal,
double[][][] inducedDipole,
double[][][] inducedDipoleCR,
double[][] directDipole,
double[][] directDipoleCR,
AtomicDoubleArray3D field,
AtomicDoubleArray3D fieldCR,
EwaldParameters ewaldParameters,
double dieletric,
ParallelTeam parallelTeam,
IntegerSchedule realSpaceSchedule,
long[] realSpaceSCFTime)
void
PermanentFieldRegion.init(Atom[] atoms,
Crystal crystal,
double[][][] coordinates,
double[][][] globalMultipole,
double[][][] inducedDipole,
double[][][] inducedDipoleCR,
int[][][] neighborLists,
ScaleParameters scaleParameters,
boolean[] use,
int[] molecule,
double[] ipdamp,
double[] thole,
int[][] ip11,
int[][] mask12,
int[][] mask13,
int[][] mask14,
LambdaMode lambdaMode,
boolean reciprocalSpaceTerm,
ReciprocalSpace reciprocalSpace,
EwaldParameters ewaldParameters,
PCGSolver pcgSolver,
IntegerSchedule permanentSchedule,
RealSpaceNeighborParameters realSpaceNeighborParameters,
AtomicDoubleArray3D field,
AtomicDoubleArray3D fieldCR,
PMETimings pmeTimings)
void
RealSpaceEnergyRegion.init(Atom[] atoms,
Crystal crystal,
ExtendedSystem extendedSystem,
boolean esvTerm,
double[][][] coordinates,
MultipoleType.MultipoleFrameDefinition[] frame,
int[][] axisAtom,
double[][][] globalMultipole,
double[][][] titrationMultipole,
double[][][] tautomerMultipole,
double[][][] inducedDipole,
double[][][] inducedDipoleCR,
boolean[] use,
int[] molecule,
int[][] ip11,
int[][] mask12,
int[][] mask13,
int[][] mask14,
int[][] mask15,
boolean[] isSoft,
double[] ipdamp,
double[] thole,
RealSpaceNeighborParameters realSpaceNeighborParameters,
boolean gradient,
boolean lambdaTerm,
boolean nnTerm,
LambdaMode lambdaMode,
Polarization polarization,
EwaldParameters ewaldParameters,
ScaleParameters scaleParameters,
AlchemicalParameters alchemicalParameters,
long[] realSpaceEnergyTime,
AtomicDoubleArray3D grad,
AtomicDoubleArray3D torque,
AtomicDoubleArray3D lambdaGrad,
AtomicDoubleArray3D lambdaTorque,
SharedDouble shareddEdLambda,
SharedDouble sharedd2EdLambda2)
void
SORRegion.init(Atom[] atoms,
double[] polarizability,
double[][][] inducedDipole,
double[][][] inducedDipoleCR,
double[][] directDipole,
double[][] directDipoleCR,
double[][] cartesianDipolePhi,
double[][] cartesianDipolePhiCR,
AtomicDoubleArray3D field,
AtomicDoubleArray3D fieldCR,
boolean generalizedKirkwoodTerm,
GeneralizedKirkwood generalizedKirkwood,
EwaldParameters ewaldParameters)