Manipulating individual excitation pathways#

Individual abstract pathways#

Pathway represents an individual excitation pathway (a double-sided Feynman diagram) not associated with any specific molecular vibrational mode. It can be instantiated with a leaf node of rotsim2d.pathways.KetBra excitation tree:

In [1]: import rotsim2d.pathways as pw

In [2]: import rotsim2d.dressedleaf as dl

In [3]: import molspecutils.molecule as mol

In [4]: from pprint import pprint

In [5]: kb1 = pw.KetBra(mol.DiatomState(nu=0, j=1), mol.DiatomState(nu=0, j=1))

In [6]: kb1 = pw.multi_excite(kb1, light_names=['omg1', 'omg2', 'omg3'],
   ...:                       parts=['ket', 'both', 'both'])
   ...: 

In [7]: kb1 = pw.readout(kb1)

In [8]: pw1 = dl.Pathway(kb1.leaves[0])

In [9]: pw1.pprint()
diagram:
<-|0,1><0,1|  
->|1,0><0,1|  
<-|0,1><0,1|  
->|1,0><0,1|  
  |0,1><0,1|  
Pathway label: PPP
R-class: R5
G-factor label: PRP
G-factors: (0.06415002990995841, -0.1111111111111111, 0.1434438276373117)
Total side: 1
4-fold amplitude: 8.52651414328119e+101j
Experimental label: Ground-state hole-burning
Colors: 1
Coherence during waiting time: False

Pathway label classifies the transitions induced by each light interaction by a sequence of three letters: P, Q or R. The transition label and the G-factor label are defined in 1. R-class (R1..R8) is the label used in Hamm and Zanni book 2. The experimental label is explained in the linked diagram, which classifies all symmetric top SII pathways that start with P-branch excitation.

A list of all pathways in a given excitation tree can be obtained by using the class method Pathway.from_kb_tree():

In [10]: pws1 = dl.Pathway.from_kb_tree(kb1)

In [11]: pprint(pws1[:2])
[Pathway(leaf=Ketbra(DiatomState(nu=0, j=1), DiatomState(nu=0, j=1))),
 Pathway(leaf=Ketbra(DiatomState(nu=0, j=1), DiatomState(nu=0, j=1)))]

With Pathway.from_kb_list() we can obtain a list pathways from a list of excitation trees:

In [12]: js = (0, 1, 2, 3)

In [13]: kbs = pw.gen_pathways(js, meths=[pw.only_SII, pw.only_twocolor],
   ....:                       rotor='symmetric', kiter_func='range(j+1)')
   ....: 

Such potentially long list of pathways can be classified by 2D peaks they generate and printed out for easier inspection:

In [14]: pws1_by_peaks = dl.split_by_peaks(pws1)

In [15]: dl.print_dl_dict(pws1_by_peaks, fields=['trans_label', 'tw_coherence', 'js'])
('|0,1><1,0|', '|0,1><1,0|')
    Pathway(trans_label=PPP, tw_coherence=False, js=(1, 0, 1, 0))
    Pathway(trans_label=PP(P), tw_coherence=False, js=(1, 0, 1, 0))
    Pathway(trans_label=P2R2R, tw_coherence=True, js=(1, 0, 1, 0))
    Pathway(trans_label=P(P)P, tw_coherence=False, js=(1, 0, 1, 0))
    Pathway(trans_label=P(P)(P), tw_coherence=False, js=(1, 0, 1, 0))
    Pathway(trans_label=P(R)(R), tw_coherence=True, js=(1, 2, 1, 0))
('|0,1><1,0|', '|0,1><1,2|')
    Pathway(trans_label=PPR, tw_coherence=False, js=(1, 2, 1, 0))
    Pathway(trans_label=PP(R), tw_coherence=False, js=(1, 2, 1, 0))
    Pathway(trans_label=P2R2P, tw_coherence=True, js=(1, 2, 1, 0))
    Pathway(trans_label=P(R)P, tw_coherence=True, js=(1, 2, 1, 0))
('|0,1><1,0|', '|1,0><2,1|')
    Pathway(trans_label=P2R(P), tw_coherence=True, js=(1, 0, 1, 0))
    Pathway(trans_label=P(P)2R, tw_coherence=False, js=(1, 0, 1, 0))
    Pathway(trans_label=P(P)(2R), tw_coherence=False, js=(1, 0, 1, 0))
    Pathway(trans_label=P(R)(2P), tw_coherence=True, js=(1, 2, 1, 0))
('|0,1><1,0|', '|1,2><2,1|')
    Pathway(trans_label=P2R(R), tw_coherence=True, js=(1, 2, 1, 0))
    Pathway(trans_label=P(R)2R, tw_coherence=True, js=(1, 2, 1, 0))
('|0,1><1,2|', '|0,1><1,0|')
    Pathway(trans_label=RRP, tw_coherence=False, js=(1, 0, 1, 2))
    Pathway(trans_label=RR(P), tw_coherence=False, js=(1, 0, 1, 2))
    Pathway(trans_label=R2P2R, tw_coherence=True, js=(1, 0, 1, 2))
    Pathway(trans_label=R(P)R, tw_coherence=True, js=(1, 0, 1, 2))
('|0,1><1,2|', '|0,1><1,2|')
    Pathway(trans_label=RRR, tw_coherence=False, js=(1, 2, 1, 2))
    Pathway(trans_label=RR(R), tw_coherence=False, js=(1, 2, 1, 2))
    Pathway(trans_label=RPP, tw_coherence=True, js=(1, 2, 3, 2))
    Pathway(trans_label=R2P2P, tw_coherence=True, js=(1, 2, 1, 2))
    Pathway(trans_label=R2R2R, tw_coherence=True, js=(1, 2, 3, 2))
    Pathway(trans_label=R(P)(P), tw_coherence=True, js=(1, 0, 1, 2))
    Pathway(trans_label=R(R)R, tw_coherence=False, js=(1, 2, 1, 2))
    Pathway(trans_label=R(R)(R), tw_coherence=False, js=(1, 2, 1, 2))
('|0,1><1,2|', '|0,3><1,2|')
    Pathway(trans_label=RP(R), tw_coherence=True, js=(1, 2, 3, 2))
    Pathway(trans_label=R(R)P, tw_coherence=False, js=(1, 2, 3, 2))
    Pathway(trans_label=R(R)(P), tw_coherence=False, js=(1, 2, 3, 2))
('|0,1><1,2|', '|1,0><2,1|')
    Pathway(trans_label=R2P(P), tw_coherence=True, js=(1, 0, 1, 2))
    Pathway(trans_label=R(P)2P, tw_coherence=True, js=(1, 0, 1, 2))
('|0,1><1,2|', '|1,2><2,1|')
    Pathway(trans_label=R2P(R), tw_coherence=True, js=(1, 2, 1, 2))
    Pathway(trans_label=R(P)(2R), tw_coherence=True, js=(1, 0, 1, 2))
    Pathway(trans_label=R(R)2P, tw_coherence=False, js=(1, 2, 1, 2))
    Pathway(trans_label=R(R)(2P), tw_coherence=False, js=(1, 2, 1, 2))
('|0,1><1,2|', '|1,2><2,3|')
    Pathway(trans_label=R2R(R), tw_coherence=True, js=(1, 2, 3, 2))
    Pathway(trans_label=R(R)2R, tw_coherence=False, js=(1, 2, 3, 2))
    Pathway(trans_label=R(R)(2R), tw_coherence=False, js=(1, 2, 3, 2))

tw_coherence tells whether the system is in a coherence state or population state between second and third pulse. fields argument determines what information is printed for each pathway. Valid field names are defined in Pathway.fields.

Pathways associated with vibrational modes#

To associate a pathway with some concrete vibrational mode, we need an instance of a class implementing the molspecutils.molecule.VibrationalMode interface. Two such classes are molspecutils.molecule.COAlchemyMode and molspecutils.molecule.CH3ClAlchemyMode. Let’s use the latter:

In [16]: from molspecutils.molecule import CH3ClAlchemyMode

In [17]: import rotsim2d.visual as vis

In [18]: ch3cl_mode = CH3ClAlchemyMode()
Using database directory /home/docs/.cache/happier/db
sqlite3 database not found: /home/docs/.cache/happier/db/CH3Cl_nu3_1.sqlite3
HITRAN data not found, fetching with HAPI
HAPI version: 1.1.0.7
To get the most up-to-date version please check http://hitran.org/hapi
ATTENTION: Python versions of partition sums from TIPS-2017 are available at http://hitran.org/suppl/TIPS/
           To use them in HAPI ver. 1.1.0.7, use partitionFunction parameter of the absorptionCoefficient_ routine.

           It is free to use HAPI. If you use HAPI in your research or software development,
           please cite it using the following reference:
           R.V. Kochanov, I.E. Gordon, L.S. Rothman, P. Wcislo, C. Hill, J.S. Wilzewski,
           HITRAN Application Programming Interface (HAPI): A comprehensive approach
           to working with spectroscopic data, J. Quant. Spectrosc. Radiat. Transfer 177, 15-30 (2016)
           DOI: 10.1016/j.jqsrt.2016.03.005
Using /home/docs/.cache/happier/db


Data is fetched from http://hitran.org

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END DOWNLOAD
                     Lines parsed: 110462
PROCESSED
Converting from HITRAN to sqlite3

In [19]: kbs = pw.gen_pathways(range(1, 10), meths=[pw.only_SII, pw.only_twocolor],
   ....:                       rotor='symmetric', kiter_func='range(j if j<10 else 10)')
   ....: 

In [20]: dressed_pws = dl.DressedPathway.from_kb_list(kbs, ch3cl_mode, 296.0)

In [21]: peaks = dl.Peak2DList.from_dp_list(dressed_pws, tw=1.0e-12, angles=[0.0]*4)

In [22]: vis.plot2d_scatter(peaks)
Out[22]: 
{'ax': <AxesSubplot:>,
 'axcbar': <AxesSubplot:>,
 'fig': <Figure size 640x480 with 2 Axes>,
 'sc': <matplotlib.collections.PathCollection at 0x7f21503483d0>}

As before, we can filter the excitation tree with functions from rotsim2d.pathways. We can also investigate the polarization dependence and waiting time dependence by changing angles and tw arguments of Peak2DList.from_dp_list(). plot2d_scatter() is a convenience functions for plotting a list of 2D peaks.

1: G.Kowzan, T. K. Allison, Theory of rotationally-resolved two-dimensional infrared spectroscopy, arXiv:XXXX, (2022)
2: P.Hamm, M. Zanni,”Concepts and methods of 2D infrared spectroscopy”. Cambridge University Press, 2011.

rotsim2d documentation

Manipulating individual excitation pathways

Contents

Manipulating individual excitation pathways#

Individual abstract pathways#

Pathways associated with vibrational modes#