@@ -92,7 +92,7 @@ void Input::reader(const std::string & filename) {
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int nAtoms = int (spheresInput.size () / 4 );
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for (int i = 0 ; i < nAtoms; ++i) {
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Eigen::Vector3d center;
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- center << spheresInput[j], spheresInput[j + 1 ], spheresInput[j + 2 ];
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+ center = ( Eigen::Vector3d () << spheresInput[j], spheresInput[j + 1 ], spheresInput[j + 2 ]). finished () ;
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Sphere sph (center, spheresInput[j + 3 ]);
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spheres_.push_back (sph);
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j += 4 ;
@@ -216,6 +216,16 @@ void Input::reader(const PCMInput & host_input) {
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derivativeOutsideType_ = detail::derivativeTraits (" DERIVATIVE" );
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epsilonStaticOutside_ = host_input.outside_epsilon ;
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epsilonDynamicOutside_ = host_input.outside_epsilon ;
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+ // Initialize interface parameters with bogus values
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+ epsilonStatic1_ = 0.0 ;
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+ epsilonDynamic1_ = 0.0 ;
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+ epsilonStatic2_ = 0.0 ;
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+ epsilonDynamic2_ = 0.0 ;
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+ center_ = 0.0 ;
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+ width_ = 0.0 ;
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+ origin_ = std::vector<double >(3 , 0.0 );
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+ profileType_ = 0 ;
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+ maxL_ = 0 ;
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} else { // This part must be reviewed!! Some data members are not initialized...
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// Just initialize the solvent object in this class
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hasSolvent_ = true ;
@@ -232,6 +242,7 @@ void Input::reader(const PCMInput & host_input) {
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epsilonStaticOutside_ = solvent_.epsStatic ;
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epsilonDynamicOutside_ = solvent_.epsDynamic ;
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}
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+
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integratorType_ = " COLLOCATION" ;
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integratorScaling_ = 1.07 ;
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@@ -256,7 +267,7 @@ void Input::initMolecule() {
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Eigen::VectorXd charges = Eigen::VectorXd::Zero (nuclei);
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int j = 0 ;
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for (int i = 0 ; i < nuclei; ++i) {
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- centers.col (i) << geometry_[j], geometry_[j + 1 ], geometry_[j + 2 ];
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+ centers.col (i) = ( Eigen::Vector3d () << geometry_[j], geometry_[j + 1 ], geometry_[j + 2 ]). finished () ;
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charges (i) = geometry_[j + 3 ];
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j += 4 ;
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}
@@ -338,7 +349,7 @@ GreenData Input::outsideStaticGreenParams() const {
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retval.epsilon2 = epsilonStatic2_;
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retval.center = center_;
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retval.width = width_;
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- retval.origin << origin_[0 ], origin_[1 ], origin_[2 ];
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+ retval.origin = ( Eigen::Vector3d () << origin_[0 ], origin_[1 ], origin_[2 ]). finished () ;
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retval.maxL = maxL_;
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}
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return retval;
@@ -352,7 +363,7 @@ GreenData Input::outsideDynamicGreenParams() const {
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retval.epsilon2 = epsilonDynamic2_;
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retval.center = center_;
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retval.width = width_;
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- retval.origin << origin_[0 ], origin_[1 ], origin_[2 ];
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+ retval.origin = ( Eigen::Vector3d () << origin_[0 ], origin_[1 ], origin_[2 ]). finished () ;
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retval.maxL = maxL_;
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}
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return retval;
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