yifanshensz / nadvibs

Nonadiabatic vibrational spectrum simulation package

NadVibS

Nonadiabatic vibrational spectrum simulation package

Originate from NADVIBS.X by Michael Schuurman 2007

Featured utilities

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

Usage

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

Dependency

Global Arrays 5.4 or later

Reference:

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