Figure and data processing for Topical Review: Extracting Molecular Frame Photoionization Dynamics from Experimental Data - MFPADs only

18/07/22

This document illustrates the use of the Photoelectron Metrology Toolkit (PEMtk) for analysis of matrix element fitting results, plus some additional plotting routines. Results and figures are as reported in the manuscript Topical Review: Extracting Molecular Frame Photoionization Dynamics from Experimental Data [1], available via Authorea.

Full data and code (current version) available via Figshare, DOI: 10.6084/m9.figshare.20293782.

For general info, see the PEMtk analysis routines docs.

Plotting backend via Plotly Surface plots, see https://plot.ly/python/3d-subplots

saveFigs = False

Read data

# dataSet = "matE_fittingAgg_Ref_230422_c.ncf"
dataSet = 'matE_fittingAgg_Ref_240422_DS_c.ncf'

import xarray as xr
dataIn = xr.open_dataset(dataSet, engine="h5netcdf")  # OK!
dataIn

<xarray.Dataset>
Dimensions:  (Cont: 2, Eke: 51, Targ: 1, Total: 2, Type: 2, mu: 3, l: 6, m: 3,
              it: 1)
Coordinates:
  * Cont     (Cont) object 'PU' 'SU'
    Ehv      (Eke) float64 17.4 18.4 19.4 20.4 21.4 ... 63.4 64.4 65.4 66.4 67.4
  * Eke      (Eke) float64 0.1 1.1 2.1 3.1 4.1 5.1 ... 46.1 47.1 48.1 49.1 50.1
    SF       (Eke) complex128 (2.1560627+3.741674j) ... (4.4127053+1.8281945j)
  * Targ     (Targ) object 'SG'
  * Total    (Total) object 'PU' 'SU'
  * Type     (Type) object 'L' 'V'
  * it       (it) int64 1
  * l        (l) int64 1 3 5 7 9 11
  * m        (m) int64 -1 0 1
  * mu       (mu) int64 -1 0 1
Data variables:
    comp     (Eke, mu, l, m, Cont, Targ, Total) complex128 (nan+nanj) ... (na...
    compC    (Eke, mu, l, m, Cont, Targ, Total) complex128 (nan+nanj) ... (na...
    orb5     (Eke, mu, it, Type, l, m, Cont, Targ, Total) complex128 (nan+nan...

xarray.Dataset

• Dimensions:
  • Cont: 2
  • Eke: 51
  • Targ: 1
  • Total: 2
  • Type: 2
  • mu: 3
  • l: 6
  • m: 3
  • it: 1
• Coordinates: (11)
  • Cont
    (Cont)
    object
    'PU' 'SU'

    array(['PU', 'SU'], dtype=object)

  • Ehv
    (Eke)
    float64
    ...

    array([17.4, 18.4, 19.4, 20.4, 21.4, 22.4, 23.4, 24.4, 25.4, 26.4, 27.4, 28.4,
           29.4, 30.4, 31.4, 32.4, 33.4, 34.4, 35.4, 36.4, 37.4, 38.4, 39.4, 40.4,
           41.4, 42.4, 43.4, 44.4, 45.4, 46.4, 47.4, 48.4, 49.4, 50.4, 51.4, 52.4,
           53.4, 54.4, 55.4, 56.4, 57.4, 58.4, 59.4, 60.4, 61.4, 62.4, 63.4, 64.4,
           65.4, 66.4, 67.4])

  • Eke
    (Eke)
    float64
    0.1 1.1 2.1 3.1 ... 48.1 49.1 50.1

    array([ 0.1,  1.1,  2.1,  3.1,  4.1,  5.1,  6.1,  7.1,  8.1,  9.1, 10.1, 11.1,
           12.1, 13.1, 14.1, 15.1, 16.1, 17.1, 18.1, 19.1, 20.1, 21.1, 22.1, 23.1,
           24.1, 25.1, 26.1, 27.1, 28.1, 29.1, 30.1, 31.1, 32.1, 33.1, 34.1, 35.1,
           36.1, 37.1, 38.1, 39.1, 40.1, 41.1, 42.1, 43.1, 44.1, 45.1, 46.1, 47.1,
           48.1, 49.1, 50.1])

  • SF
    (Eke)
    complex128
    ...

    array([2.156063+3.741674j, 2.223752+3.62778j , 2.289441+3.523691j,
           2.353297+3.428077j, 2.415466+3.339846j, 2.476074+3.258095j,
           2.535234+3.182067j, 2.593044+3.111125j, 2.649593+3.044725j,
           2.70496 +2.982404j, 2.759217+2.923758j, 2.812427+2.868442j,
           2.864649+2.816151j, 2.915936+2.766619j, 2.966336+2.719613j,
           3.015894+2.674923j, 3.06465 +2.632367j, 3.112643+2.591779j,
           3.159908+2.553012j, 3.206475+2.515935j, 3.252376+2.480428j,
           3.297638+2.446382j, 3.342287+2.413701j, 3.386348+2.382296j,
           3.429842+2.352086j, 3.472792+2.322996j, 3.515217+2.29496j ,
           3.557137+2.267915j, 3.598568+2.241804j, 3.639527+2.216575j,
           3.68003 +2.192179j, 3.720093+2.16857j , 3.759728+2.145709j,
           3.798951+2.123556j, 3.837772+2.102075j, 3.876204+2.081233j,
           3.914259+2.060999j, 3.951948+2.041343j, 3.989281+2.02224j ,
           4.026267+2.003663j, 4.062917+1.985589j, 4.099239+1.967995j,
           4.135243+1.950861j, 4.170935+1.934167j, 4.206324+1.917894j,
           4.241419+1.902025j, 4.276225+1.886543j, 4.31075 +1.871434j,
           4.345001+1.856682j, 4.378984+1.842273j, 4.412705+1.828194j])

  • Targ
    (Targ)
    object
    'SG'

    array(['SG'], dtype=object)

  • Total
    (Total)
    object
    'PU' 'SU'

    array(['PU', 'SU'], dtype=object)

  • Type
    (Type)
    object
    'L' 'V'

    array(['L', 'V'], dtype=object)

  • it
    (it)
    int64
    1

    array([1])

  • l
    (l)
    int64
    1 3 5 7 9 11

    array([ 1,  3,  5,  7,  9, 11])

  • m
    (m)
    int64
    -1 0 1

    array([-1,  0,  1])

  • mu
    (mu)
    int64
    -1 0 1

    array([-1,  0,  1])

• Data variables: (3)
  • comp
    (Eke, mu, l, m, Cont, Targ, Total)
    complex128
    ...

    array([[[[[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]],
    
    
    
             ...,
    
    
    
             [[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]]],
    
    
    
    
            ...,
    
    
    
    
            [[[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]],
    
    
    
             ...,
    
    
    
             [[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]]]],
    
    
    
    
    
           ...,
    
    
    
    
    
           [[[[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]],
    
    
    
             ...,
    
    
    
             [[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]]],
    
    
    
    
            ...,
    
    
    
    
            [[[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]],
    
    
    
             ...,
    
    
    
             [[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]]]]])

  • compC
    (Eke, mu, l, m, Cont, Targ, Total)
    complex128
    ...

    array([[[[[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]],
    
    
    
             ...,
    
    
    
             [[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]]],
    
    
    
    
            ...,
    
    
    
    
            [[[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]],
    
    
    
             ...,
    
    
    
             [[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]]]],
    
    
    
    
    
           ...,
    
    
    
    
    
           [[[[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]],
    
    
    
             ...,
    
    
    
             [[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]]],
    
    
    
    
            ...,
    
    
    
    
            [[[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]],
    
    
    
             ...,
    
    
    
             [[[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]],
    
    
              ...,
    
    
              [[[nan+nanj, nan+nanj]],
    
               [[nan+nanj, nan+nanj]]]]]]])

  • orb5
    (Eke, mu, it, Type, l, m, Cont, Targ, Total)
    complex128
    ...

    Cont :

    SU

    E :

    0.1

    Ehv :

    15.68

    Lmax :

    11

    QNs :

    ['m', 'l', 'mu', 'ip', 'it', 'Value']

    SF :

    (2.1560627+3.741674j)

    Targ :

    SG

    Total :

    SU

    dataType :

    matE

    file :

    n2_3sg_0.1-50.1eV_A2.inp.out

    fileBase :

    D:\code\github\ePSproc\data\photoionization\n2_multiorb

    fileList :

    n2_3sg_0.1-50.1eV_A2.inp.out

    jobLabel :

    3sg-1

    array([[[[[[[[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[-1.775708e+00+6.347477e-01j,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]],
    
    
    
               ...,
    
    
    
               [[[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]]],
    
    
    
    
              [[[[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[-1.940346e+00+6.946600e-01j,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]],
    
    
    
               ...,
    
    
    
               [[[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]]]]],
    
    
    
    
    
    
            ...,
    
    
    
    
    
    
            [[[[[[[-1.775708e+00+6.347477e-01j,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]],
    
    
    
               ...,
    
    
    
               [[[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]]],
    
    
    
    
              [[[[[-1.940346e+00+6.946600e-01j,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]],
    
    
    
               ...,
    
    
    
               [[[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]]]]]],
    
    
    
    
    
    
    
           ...,
    
    
    
    
    
    
    
           [[[[[[[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[-4.273165e-01-6.962661e-01j,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]],
    
    
    
               ...,
    
    
    
               [[[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[ 8.921339e-06-4.697151e-06j,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]]],
    
    
    
    
              [[[[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[-4.160651e-01-6.449011e-01j,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]],
    
    
    
               ...,
    
    
    
               [[[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]]]]],
    
    
    
    
    
    
            ...,
    
    
    
    
    
    
            [[[[[[[-4.273165e-01-6.962661e-01j,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]],
    
    
    
               ...,
    
    
    
               [[[[ 8.921339e-06-4.697151e-06j,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]]],
    
    
    
    
              [[[[[-4.160651e-01-6.449011e-01j,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]],
    
    
    
               ...,
    
    
    
               [[[[ 5.366789e-06-2.484258e-06j,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]],
    
    
                ...,
    
    
                [[[          nan         +nanj,
                             nan         +nanj]],
    
                 [[          nan         +nanj,
                             nan         +nanj]]]]]]]]])

• Attributes: (0)

# Restack for MFPAD plotter
from epsproc.util.listFuncs import dataTypesList

refDims = dataTypesList()['matE']['def']
dataStacked = dataIn.stack(refDims(sType='sDict'))
dataStacked
       # for k,v in dataSet.items():
       #      label = f'{key}_{k}'
       #      data.data[label] = {dType:v}

OMP: Info #273: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.

* sparse not found, sparse matrix forms not available.
* natsort not found, some sorting functions not available.