CDTK.Tools.TaylorAPES module

CDTK.Tools.TaylorAPES.atomic_masses(atomicSymbols)

Return atomic masses from periodic table for each coordinate [A.U.]

atomicSymbols - list of atomic symbols

CDTK.Tools.TaylorAPES.calc_coefficients(gs, Lx, X0, h, save='', ix1=None, ix2=None, gap=None, grad=None, curv=None, verbose=False, mcscf=True)

Calculate all coefficients for a Taylor series expansion at a given evaluation point

Gap, gradient (kappa_i) and curvatures (gamma_i,j) calculated in Cartesian normal mode coordinates (cnmc)

gs - GamessUSInterface object with options set for MCSCF calculation Lx - cartesian normal modes X0 - evaluation point [Angstrom] h - step size save - save coefficients in given path after completing one outer loop (default: don’t) ix1 - pass row index (i) where the coefficients should be calculated (default: calculate all coefficients) ix2 - pass column index (j) where the coefficients should be calculated (default: calculate all coefficients) verbose - print runtime information if True (default: False) gap,grad,curv - np arrays can be passed mcscf - if TRUE, use MCSCF level of theory for calculating the PES. If FALSE, use Koopmans (default: TRUE)

CDTK.Tools.TaylorAPES.calc_coeffs_cross(gs, Lx, X0, i, j, h)

Calculate the second order cross Taylor coefficient along Lx[i],Lx[j]

gs - GamessUSInterface object for MCSCF calculation Lx - Normal mode array with normal modes in rows X0 - ground state equilibrium geometry [Angstrom] i, j - Normal mode indices h - step size

CDTK.Tools.TaylorAPES.calc_coeffs_cross_koopmans(gs, Lx, X0, i, j, h)

Calculate the second order cross Taylor coefficient along Lx[i],Lx[j] CI singles level of theory

gs - GamessUSInterface object for CIS calculation Lx - Normal mode array with normal modes in rows X0 - ground state equilibrium geometry [Angstrom] i, j - Normal mode indices h - step size

CDTK.Tools.TaylorAPES.calc_coeffs_diag(gs, Lx, X0, i, h, gap=None)

Calculate the first and second Taylor coefficients for displacements along Lx[i]

gs - GamessUSInterface object for MCSCF calculation Lx - Normal mode array with normal modes in rows X0 - ground state equilibrium geometry [Angstrom] i - Normal mode index h - step size gap - Energies of electronic states at the center as np array (optional)

CDTK.Tools.TaylorAPES.calc_coeffs_diag_koopmans(gs, Lx, X0, i, h, gap=None)

Calculate the first and second Taylor coefficients for displacements along Lx[i] Koopmans level of theory

gs - GamessUSInterface object for CIS calculation Lx - Normal mode array with normal modes in rows X0 - ground state equilibrium geometry [Angstrom] i - Normal mode index h - step size gap - Energies of electronic states at the center as np array (optional)

CDTK.Tools.TaylorAPES.cda_crossterm(a, b, c, d, h)

Cross term by central difference approximation

a - f[X0 + h e_i + h e_j] b - f[X0 + h e_i - h e_j] c - f[X0 - h e_i + h e_j] d - f[X0 - h e_i - h e_j] h - step size

CDTK.Tools.TaylorAPES.cda_curvature(a, b, c, d, e, h)

Curvature @X0 by central difference approximation

a - f[X0 + 2h] b - f[X0 + h] c - f[X0] d - f[X0 - h] e - f[X0 - 2h] h - step size

CDTK.Tools.TaylorAPES.cda_gradient(a, b, h)

Gradient @ X0 by central difference approximation

a - f[X0 + h] b - f[X0 - h] h - step size

CDTK.Tools.TaylorAPES.coeffs_x_to_q_mfw(a, mu, w)

Transform coefficient vector / matrix a from cartesian to mass and frequency weighted coordinates

a.x to alpha.Q x.g.x to Q.gamma.Q

a - object to be transformed mu - reduced masses w - frequencies

CDTK.Tools.TaylorAPES.main(argv)

python TaylorAPES.py –opfile=opfile, –title=title, –step=step, –inputpath=inputpath

opfile - name of the MCTDH operator file title - MCTDH operator title step - step size in coefficient calculation inputpath - path with gamess options and initial geometry

Calculate Taylor coefficients with gamess options given in inputpath X0 (equilibrium geometry) and Hessian (cartesian) may be given in inputpath. Else, will be calculated from X0_guess.dat (xyz initial coordinates in inputpath). Saves MCTDH operator file in inputpath/opfile.

CDTK.Tools.TaylorAPES.nm_translate(X0, Lx, dist)

Calculate coordinates for translation along normal modes.

X0 - initial position Lx - vector of cartesian normal modes dist - vector of distances

CDTK.Tools.TaylorAPES.parse_gamess_options(path, p, func=[])

Parse GAMESS options from a text file Format: parameter=value

CDTK.Tools.TaylorAPES.shift_energies_zero(e)

” Shift array of energies such that the lowest one is zero

e - array of energies

CDTK.Tools.TaylorAPES.write_coefficients(fname, grad, curv, ix, comment='')

Write the coefficients given in grad, curv [ix] to fname

CDTK.Tools.TaylorAPES.write_mctdh_op(opfile, freq, gap, grad, curv, title)

Write an MCTDH operator file for Taylor model Hamiltonian opfile - target file name freq - eigenfrequencies of normal modes gap - for each electronic state, energy gap (scalar) grad - for each electronic state, gradient (vector) curv - for each electronic state, curvature (matrix)