src Directory Reference

Files
file	ao_basis.py
	This module implements the functions that constructs atomic orbital basis by n Gaussian Type Orbitals (nGTO)
file	create_input_g09.py
file	create_input_gms.py
file	create_input_qe.py
file	defaults.py
	This module implements the functions that set up default parameters for different types of simulations.
file	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.
file	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.
file	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.
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.
file	extract_qe.py
file	hamiltonian_el.py
	This module defines the functions that return time-averaged energy and the Non-Adiabatic couplings (NACs).
file	hamiltonian_vib.py
	This module implements the function which creates and updates ham_vib vibronic hamiltonian object.
file	include_mm.py
	This module defines a function initializing "Hamiltonian" objects for MM part.
file	main.py
	This module sets initial parameters from GAMESS output, creates initial system, and executes runMD script.
file	md.py
	This module implements functions setting initial system and executing NA-MD calculation.
file	misc.py
	This module implements a function reducing matrix sizes according to active_space.
file	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)>.
file	overlap.py
	This module implements the functions that calculates the overlap matrixes of atomic and molecular orbitals with different time steps.
file	path_libra_lib.py
	This module defines the function which makes paths to the libra libraries.
file	print_results.py
	This module implements the functions which print out the results of NA-MD calculation.
file	reorder_matrices.py
	This module implements a function that reorders elements of density matrices or energy ones according to a permutation "perm".
file	spin_indx.py
file	states.py
	This module defines the function which creates a list of ground and excited states.
file	test_tsh3c.py
file	unavoided_tmp.py
file	unittest_Libra-X.py
file	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.
file	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.
file	x_to_libra_qe.py