ADF parser API

Imports to get the resource files

from vibrav.base import resource
from vibrav.util.open_files import uncompress_file
import os

Uncompress the resource file to read.

decomp = uncompress_file(resource('adf-ethane-ts-freq.t21.ascii.xz'))

Read the ASCII formatted ADF TAPE21 file

from vibrav.adf import Tape21

Read the atom and frequency tables.

ed = Tape21(decomp)

Parse the frequency data frame

The r_mass column is calculated on the fly when parsing the mass-weighted normal modes with the formula,

\[\mu_i = \left(\sum_k^{3N}l_{CARTk,i}^2\right)^{-1} = \left(\sum_k^{3N}\left(\frac{l_{MWC k,i}}{\sqrt{m_k}}\right)^2\right)^{-1} = N_i^2\]

The reason that we must use the ASCII formatted TAPE21 file from ADF rather than the output is that ADF prints the non-mass-weighted normalized cartesians with three decimals of precision. Looking at the equation shown above the \(l_{CARTk,i}\) matrix elements are indeed non-mass-weighted cartesian normal modes. However, they are not normalized and the information of the reduced masses can still be extracted.

To calculate the reduced masses the program will need the latest developers version of both the exa and exatomic packages.

ed.parse_frequency(cart=True)
ed.frequency

	dx	dy	dz	frequency	freqdx	r_mass	symbol	label	ir_int	frame
frequency
0	2.413489e-16	-1.291217e-15	-0.003898	-239.036547	0	1.008159	C	0	0	0
1	-6.154398e-16	2.740316e-16	0.003898	-239.036547	0	1.008159	C	1	0	0
2	-6.876806e-02	4.021443e-01	-0.014579	-239.036547	0	1.008159	H	2	0	0
3	3.826512e-01	-1.415172e-01	-0.014579	-239.036547	0	1.008159	H	3	0	0
4	-3.138831e-01	-2.606270e-01	-0.014579	-239.036547	0	1.008159	H	4	0	0
...	...	...	...	...	...	...	...	...	...	...
139	-2.142217e-02	1.661105e-04	0.002568	3044.853587	17	1.100672	H	3	0	0
140	2.947483e-01	-3.633216e-01	-0.180326	3044.853587	17	1.100672	H	4	0	0
141	8.272322e-02	-2.807390e-01	0.112829	3044.853587	17	1.100672	H	5	0	0
142	1.433751e-01	1.971820e-01	0.093630	3044.853587	17	1.100672	H	6	0	0
143	5.269408e-01	-9.430460e-02	-0.206459	3044.853587	17	1.100672	H	7	0	0

144 rows × 10 columns

Parse the atom data frame

ed.parse_atom()
ed.atom

	symbol	set	label	x	y	z	Z	frame
atom
0	C	0	0	0.000000	0.000000	1.450715	6.0	0
1	C	1	1	0.000000	0.000000	-1.450715	6.0	0
2	H	2	2	1.905940	0.346368	2.224450	1.0	0
3	H	3	3	-0.653007	-1.823777	2.224450	1.0	0
4	H	4	4	-1.252933	1.477409	2.224450	1.0	0
5	H	5	5	-0.653007	1.823777	-2.224450	1.0	0
6	H	6	6	-1.252933	-1.477409	-2.224450	1.0	0
7	H	7	7	1.905940	-0.346368	-2.224450	1.0	0

Remove the uncompressed resource file

os.remove(decomp)