Example 2: Calculating the lifetime along a given mode: CO on Pd(111)

ATTENTION This example/functionality is broken and needs to be fixed

In this example we calculate a single lifetime and relaxation rate along a given vibrational normal mode for CO on Pd(111), namely the internal stretch mode. Example 3 shows how to calculate finite difference displacements along a normal mode.

In order to run this example you need to either run example 3 with FHI-aims or download the dataset from following URL and extract it in the example folder

Download Dataset

Code

#    This file is part of coolvib
#
#        coolvib is free software: you can redistribute it and/or modify
#        it under the terms of the GNU General Public License as published by
#        the Free Software Foundation, either version 3 of the License, or
#        (at your option) any later version.
#
#        coolvib is distributed in the hope that it will be useful,
#        but WITHOUT ANY WARRANTY; without even the implied warranty of
#        MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#        GNU General Public License for more details.
#
#        You should have received a copy of the GNU General Public License
#        along with coolvib.  If not, see <http://www.gnu.org/licenses/>.
"""
example 2: 
Calculating lifetime along a given mode displacement for 
CO on Pd(111) internal stretch calculated with FHI-Aims
"""
import numpy as np
from ase.io import read
import os, sys

import coolvib
from scipy import linalg as LA

#####DEFINE SYSTEM######

system = read('mode/mode_eq/geometry.in')
cell = system

model = coolvib.workflow_mode(system, code='aims')

finite_difference_incr = 0.0025

keywords = {
    'discretization_type' : 'gaussian',
    'discretization_broadening' : 0.01,
    'discretization_length' : 0.01,
    'max_energy' : 7,
    'temperature' : 300,
    'delta_function_type': 'gaussian',
    'delta_function_width': 0.60,
    'perturbing_energy' : 0.0,
        }

print 'workflow initialized and keywords set'

######READ QM INPUT DATA###

model.read_input_data(spin=False, 
        path='mode/', 
        prefix='mode', 
        filename='aims.out', 
        incr=finite_difference_incr)
print 'successfully read QM input data'

# model.calculate_spectral_function(mode='default', **keywords)
# print 'successfully calculated spectral_function'
# model.print_spectral_function('nacs-spectrum.out')
# model.calculate_friction_from_spectrum(**keywords)

print 'successfully calculated friction tensor'
model.calculate_friction(**keywords)

model.analyse_friction()

Detailed Explanation

All settings are equivalent to the tensor case in example 1. The only difference is that now there is only one spectral function and routines associated with calculating friction are called friction (rather than friction_tensor).