diff --git a/modules/mol/mm/src/topology.cc b/modules/mol/mm/src/topology.cc index e4771197da32383b39b18022d92a724dd31fd11b..0c4076e43401e7523d1e41b54079f2da00d218d9 100644 --- a/modules/mol/mm/src/topology.cc +++ b/modules/mol/mm/src/topology.cc @@ -513,7 +513,7 @@ void Topology::GetHarmonicDistanceRestraintParameters(uint index, uint& atom_one } -void Topology::SetHarmonicBondParameters(uint index, const Real& bond_length, const Real& force_constant){ +void Topology::SetHarmonicBondParameters(uint index, const Real bond_length, const Real force_constant){ if(index >= harmonic_bonds_.size()){ throw ost::Error("Provided index exceeds number of harmonic bonds present in topology!"); } @@ -521,7 +521,7 @@ void Topology::SetHarmonicBondParameters(uint index, const Real& bond_length, co harmonic_bonds_[index].second[1] = force_constant; } -void Topology::SetHarmonicAngleParameters(uint index, const Real& angle, const Real& force_constant){ +void Topology::SetHarmonicAngleParameters(uint index, const Real angle, const Real force_constant){ if(index >= harmonic_angles_.size()){ throw ost::Error("Provided index exceeds number of harmonic angles present in topology!"); } @@ -529,7 +529,7 @@ void Topology::SetHarmonicAngleParameters(uint index, const Real& angle, const R harmonic_angles_[index].second[1] = force_constant; } -void Topology::SetUreyBradleyAngleParameters(uint index, const Real& angle, const Real& angle_force_constant, const Real& bond_length, const Real& bond_force_constant){ +void Topology::SetUreyBradleyAngleParameters(uint index, const Real angle, const Real angle_force_constant, const Real bond_length, const Real bond_force_constant){ if(index >= urey_bradley_angles_.size()){ throw ost::Error("Provided index exceeds number of urey_bradley angles present in topology!"); } @@ -539,7 +539,7 @@ void Topology::SetUreyBradleyAngleParameters(uint index, const Real& angle, cons urey_bradley_angles_[index].second[3] = bond_force_constant; } -void Topology::SetPeriodicDihedralParameters(uint index, const int& multiplicity, const Real& phase, const Real& force_constant){ +void Topology::SetPeriodicDihedralParameters(uint index, const int multiplicity, const Real phase, const Real force_constant){ if(index >= periodic_dihedrals_.size()){ throw ost::Error("Provided index exceeds number of periodic dihedrals present in topology!"); } @@ -548,7 +548,7 @@ void Topology::SetPeriodicDihedralParameters(uint index, const int& multiplicity periodic_dihedrals_[index].second[2] = force_constant; } -void Topology::SetPeriodicImproperParameters(uint index, const int& multiplicity, const Real& phase, const Real& force_constant){ +void Topology::SetPeriodicImproperParameters(uint index, const int multiplicity, const Real phase, const Real force_constant){ if(index >= periodic_impropers_.size()){ throw ost::Error("Provided index exceeds number of periodic impropers present in topology!"); } @@ -557,7 +557,7 @@ void Topology::SetPeriodicImproperParameters(uint index, const int& multiplicity periodic_impropers_[index].second[2] = force_constant; } -void Topology::SetHarmonicImproperParameters(uint index, const Real& angle, const Real& force_constant){ +void Topology::SetHarmonicImproperParameters(uint index, const Real angle, const Real force_constant){ if(index >= harmonic_impropers_.size()){ throw ost::Error("Provided index exceeds number of harmonic impropers present in topology!"); } @@ -565,7 +565,7 @@ void Topology::SetHarmonicImproperParameters(uint index, const Real& angle, cons harmonic_impropers_[index].second[1] = force_constant; } -void Topology::SetCMapParameters(uint index, const int& dimension, const std::vector<Real>& map){ +void Topology::SetCMapParameters(uint index, const int dimension, const std::vector<Real>& map){ if(index >= cmaps_.size()){ throw ost::Error("Provided index exceeds number of cmaps present in topology!"); } @@ -575,7 +575,7 @@ void Topology::SetCMapParameters(uint index, const int& dimension, const std::ve cmaps_[index].second = map; } -void Topology::SetLJPairParameters(uint index, const Real& sigma, const Real& epsilon){ +void Topology::SetLJPairParameters(uint index, const Real sigma, const Real epsilon){ if(index >= lj_pairs_.size()){ throw ost::Error("Provided index exceeds number of lj pairs present in topology!"); } @@ -583,7 +583,7 @@ void Topology::SetLJPairParameters(uint index, const Real& sigma, const Real& ep lj_pairs_[index].second[1] = epsilon; } -void Topology::SetDistanceConstraintParameters(uint index, const Real& distance){ +void Topology::SetDistanceConstraintParameters(uint index, const Real distance){ if(index >= distance_constraints_.size()){ throw ost::Error("Provided index exceeds number of distance_constraints present in topology!"); } diff --git a/modules/mol/mm/src/topology.hh b/modules/mol/mm/src/topology.hh index bc2f2bdcf6e365f98a97a665aaaf79bb6b2cc18c..35c0a251cf3d3bf6c5ee64ec4fc40534008c50c3 100644 --- a/modules/mol/mm/src/topology.hh +++ b/modules/mol/mm/src/topology.hh @@ -181,23 +181,26 @@ public: void GetHarmonicDistanceRestraintParameters(uint index, uint& atom_one, uint& atom_two, Real& length, Real& force_constant) const; - void SetHarmonicBondParameters(uint index, const Real& bond_length, const Real& force_constant); + void SetHarmonicBondParameters(uint index, const Real bond_length, const Real force_constant); - void SetHarmonicAngleParameters(uint index, const Real& angle, const Real& force_constant); + void SetHarmonicAngleParameters(uint index, const Real angle, const Real force_constant); - void SetUreyBradleyAngleParameters(uint index, const Real& angle, const Real& angle_force_constant, const Real& bond_length, const Real& bond_force_constant); + void SetUreyBradleyAngleParameters(uint index, const Real angle, const Real angle_force_constant, + const Real bond_length, const Real bond_force_constant); - void SetPeriodicDihedralParameters(uint index, const int& multiplicity, const Real& phase, const Real& force_constant); + void SetPeriodicDihedralParameters(uint index, const int multiplicity, + const Real phase, const Real force_constant); - void SetPeriodicImproperParameters(uint index, const int& multiplicity, const Real& phase, const Real& force_constant); + void SetPeriodicImproperParameters(uint index, const int multiplicity, const Real phase, + const Real force_constant); - void SetHarmonicImproperParameters(uint index, const Real& angle, const Real& force_constant); + void SetHarmonicImproperParameters(uint index, const Real angle, const Real force_constant); - void SetCMapParameters(uint index, const int& dimension, const std::vector<Real>& map); + void SetCMapParameters(uint index, const int dimension, const std::vector<Real>& map); - void SetLJPairParameters(uint index, const Real& sigma, const Real& epsilon); + void SetLJPairParameters(uint index, const Real sigma, const Real epsilon); - void SetDistanceConstraintParameters(uint index, const Real& distance); + void SetDistanceConstraintParameters(uint index, const Real distance); void SetHarmonicPositionRestraintParameters(uint index, const geom::Vec3& ref_position, Real k, Real x_scale = 1.0, Real y_scale = 1.0, Real z_scale = 1.0);