File List

Here is a list of all documented files with brief descriptions:

[detail level 12]

src
ao_basis.py	This module implements the functions that constructs atomic orbital basis by n Gaussian Type Orbitals (nGTO)
defaults.py	This module implements the functions that set up default parameters for different types of simulations
detect_g09.py	This module implements a function that detect columns showing gradients, molecular energies, molecular orbitals, and atomic basis information written in the Gaussian09 output file; also implements a function that shows the detected columns for debugging
detect_gms.py	This module implements a function that detect columns showing gradients, molecular energies, molecular orbitals, and atomic basis information written in the GAMESS output file; also implements a function that shows the detected columns for debugging
extract_g09.py	This module implements the functions that extract atomic forces , molecular energies, molecular orbitals, and atomic basis information written in Gaussian output file
extract_gms.py	This module implements the functions that extract atomic forces , molecular energies, molecular orbitals, and atomic basis information written in gamess output file
hamiltonian_el.py	This module defines the functions that return time-averaged energy and the Non-Adiabatic couplings (NACs)
hamiltonian_vib.py	This module implements the function which creates and updates ham_vib vibronic hamiltonian object
include_mm.py	This module defines a function initializing "Hamiltonian" objects for MM part
main.py	This module sets initial parameters from GAMESS output, creates initial system, and executes runMD script
md.py	This module implements functions setting initial system and executing NA-MD calculation
misc.py	This module implements a function reducing matrix sizes according to active_space
moment.py	This program implements the module that calculates and returns the dipole moment matrixes at given space coordinates r like <MO(t)| r |MO(t+dt)>
overlap.py	This module implements the functions that calculates the overlap matrixes of atomic and molecular orbitals with different time steps
path_libra_lib.py	This module defines the function which makes paths to the libra libraries
print_results.py	This module implements the functions which print out the results of NA-MD calculation
reorder_matrices.py	This module implements a function that reorders elements of density matrices or energy ones according to a permutation "perm"
states.py	This module defines the function which creates a list of ground and excited states
x_to_libra_g09.py	This module implements the functions that extract parameters from the gamess output file: atomic forces , molecular energies, molecular orbitals, and atomic basis information
x_to_libra_gms.py	This module implements the functions that extract parameters from the gamess output file: atomic forces , molecular energies, molecular orbitals, and atomic basis information