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Scine::Swoose
2.1.0
This is the SCINE module Swoose.
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Scine::Swoose
2.1.0
This is the SCINE module Swoose.
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Class containing the parameters for SFAM's MM model obtained after parsing a SFAM parameter file. The angle and bond parameters are handled by the base class MMParameters. More...
#include <SfamParameters.h>
Public Member Functions | |
| bool | sanityCheck (const AtomTypesHolder &atomTypes) const |
| Checks whether the SFAM parameters are valid. | |
| std::vector< double > | getChargesForEachAtom (const AtomTypesHolder &atomTypes) const |
| Getter for the partial atomic charges for each atom. | |
| void | prepareC6Matrix (const AtomTypesHolder &atomTypes) |
| Resizes the C6 dispersion coefficient matrix to size NxN (N is number of distinct atom types). Furthermore, it creates a map which stores the indices of each atom type in the matrix. | |
| float | getC6 (int indexOfAtomTypeA, int indexOfAtomTypeB) const |
| Getter for the C6 dispersion coefficient with indices of atom types given. | |
| float | getC6 (const std::string &a, const std::string &b) const |
| Getter for the C6 dispersion coefficient for atoms with atom types a and b. | |
| std::vector< double > | getNonCovalentParameters () const |
| Getter for the non-covalent parameters a1, s8, a2, beta and the atomic charges scaling factor. | |
| void | setC6 (int indexOfAtomTypeA, int indexOfAtomTypeB, float c6) |
| Setter for the C6 dispersion coefficient with indices of atom types given. | |
| void | setC6 (const std::string &a, const std::string &b, float c6) |
| Setter for the C6 dispersion coefficient for atoms with atom types a and b. | |
| void | resetC6Matrix () |
| Resets the C6 matrix and the indices map. | |
| void | setNonCovalentParameters (std::vector< double > nonCovalentParameters) |
| Setter for the non-covalent parameters a1, s8, a2, beta and the atomic charges scaling factor. | |
| std::vector< Dihedral > | getMMDihedrals (std::string t1, std::string t2, std::string t3, std::string t4) const |
| Get MMDihedrals for the four atom types t1, t2, t3 and t4. (in principle there could be more than one (Fourier series)) | |
| ImproperDihedral | getMMImproperDihedral (std::string central, std::string t2, std::string t3, std::string t4) const |
| Get MMImproperDihedral for the four atom types t1, t2, t3 and t4. | |
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const std::map< std::string, int > & | getC6IndicesMap () const |
| Returns a const reference to the map containing the unique atom types of the system and their index in the c6 matrix. | |
| void | addCharge (std::string atomType, double charge) |
| void | addDihedral (DihedralType dihedralType, DihedralParameters dihedralParameters) |
| void | addImproperDihedral (ImproperDihedralType improperDihedralType, ImproperDihedralParameters improperDihedralParameters) |
| int | evaluateNumDistinctAtomTypes (const AtomTypesHolder &atomTypes) const |
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std::map< BondType, BondParameters > & | getBonds () |
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std::map< AngleType, AngleParameters > & | getAngles () |
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std::map< DihedralType, DihedralParameters > & | getDihedrals () |
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std::map< ImproperDihedralType, ImproperDihedralParameters > & | getImproperDihedrals () |
| std::map< std::string, double > & | getCharges () |
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const std::map< BondType, BondParameters > & | getBonds () const |
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const std::map< AngleType, AngleParameters > & | getAngles () const |
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const std::map< DihedralType, DihedralParameters > & | getDihedrals () const |
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const std::map < ImproperDihedralType, ImproperDihedralParameters > & | getImproperDihedrals () const |
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const std::map< std::string, double > & | getCharges () const |
 Public Member Functions inherited from Scine::MolecularMechanics::MMParameters | |
| virtual Bond | getMMBond (std::string t1, std::string t2) const |
| Get Bond for the two atom types t1 and t2. | |
| virtual Angle | getMMAngle (std::string t1, std::string t2, std::string t3) const |
| Get Angle for the three atom types t1, t2 and t3. | |
| virtual void | addBond (BondType bondType, BondParameters bondParameters) |
| Adds a bond to the bonds_ container. | |
| virtual void | addAngle (AngleType angleType, AngleParameters angleParameters) |
| Adds an angle to the angles_ container. | |
Additional Inherited Members | |
| Protected Attributes inherited from Scine::MolecularMechanics::MMParameters | |
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std::map< BondType, BondParameters > | bonds_ |
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std::map< AngleType, AngleParameters > | angles_ |
Class containing the parameters for SFAM's MM model obtained after parsing a SFAM parameter file. The angle and bond parameters are handled by the base class MMParameters.
1.8.5 
