Nonadiabatic vibrational spectrum simulation package

Originate from NADVIBS.X by Michael Schuurman 2007

NadVibS.exe:

• Diagonalize diabatic vibronic Hamiltonian
• Determine Franck-Condon overlap
• Generate input file for BROOKLYN to calculate spin-orbit fine structure

modify.py:

• Renormalize, rescale, invert, shift the spectrum
• Throw out the lines with 0 intensity

plot.py:

• Plot the simulated line spectrum
• Plot continuous spectrum

Python scripts are simple: use -h argument to show help message

To run NadVibS, use command: mpirun -hostfile hostfile -np #CPU NadVibSDirectory/NadVibS.exe -m MemoryInMB -o OutputDirectory > log

NadVibS requires 2 input files: nadvibs.in & basis.in, an example is provided. nadvibs.in will be automatically generated by SurfGenBound (see https://github.com/YifanShenSZ/SurfGenBound for details). However, user has to take care of the FORTRAN namelist file basis.in:

• restart = 0, new job; else, restart
• niter = number of lanczos iterations to be performed
• basis = number of basis functions for each vibrational mode
• initstate = the initial vibrational state of the precursor (specified by the quanta of each precursor normal mode)
• nstates = number of electronic states
• ordr = order of the expansion for diabatic hamiltonian
• natoms = number of atoms in molecule
• nmodes = number of vibrational modes
• nirreps = number of irreducible representations in point group symmetry
• npirr = number of normal modes in each irreducible representation
• shiftref = 0, do not use new origin; else, use new origin
• bconv = (default 0) -lg( convergence tolerence for eigen value )
• idroots = (default 0) how many of the lead contributors to a vibronic level to identify
• soroots = (default 0) number of roots to compute spin orbit parameters
• reorthog = (default 0) >0, request re-orthogonalization; >1, exact dot products are to be used to monitor lanczos vector orthogonality
• chkorthog = (default 100) every how many iterations compute exact dot products if using recurrence
• nseg = (default 1) number of segements to divide lanczos vector into
• ztoler = (default 1d-20) Any coefficient less ztoler is set to 0
• maxdisk = (default 1000) maximum amount of disk available for use (in MB)
• weights = (default 1) initial weights of the electronic states

Global Arrays 5.4 or later

1. M. S. Schuurman, R. A. Young, D. R. Yarkony 2007 Chem. Phys.
2. M. S. Schuurman, D. Yarkony 2008 J. Chem. Phys.