CDTK.Tools.WaterModel module
- CDTK.Tools.WaterModel.angle_bending_potential(theta, mode='TIP4P/2005f')[source]
Construct angle bending potential for intramolecular angle bending
- CDTK.Tools.WaterModel.coulomb_potential(r, q_i, q_j)[source]
Construct Coulomb potential
r - distance [a.u.] q_i,q_j - charges [a.u.]
return Coulomb potential
- CDTK.Tools.WaterModel.get_m_site_xyz(r_xyz, mode='TIP4P/2005f')[source]
Return M-site coordinates for given water molecule
The M site is located along the bisector of the dihedral angle, coplanar with the molecule
Parameters: r_xyz - H2O xyz coordinates, ordered as OHH mode - water model to be applied [default: TIP4P/2005f]
- CDTK.Tools.WaterModel.lennard_jones_gradient(r_vec, mode='SPC')[source]
Calculate analytical gradient from Lennard-Jones type interaction
F_LJ = 4 * eps * ( 12*(sigma / r)**12 - 6*(sigma / r)**6) * e_r / r
Parameters: r_vec - vector between atoms mode - water model [default: SPC]
Returns: Analytical gradient
- CDTK.Tools.WaterModel.lennard_jones_potential(r, mode='SPC')[source]
Construct Lennard-Jones potential
V_LJ = 4 * eps * ( (sigma / r)**12 - (sigma / r)**6)
Parameters: r - distance between atoms mode - Water model [default: SPC]
Returns: Lennart-Jones potential