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DOI Creative Commons Attribution-NonCommercial-ShareAlike 4.0 (CC BY-NC-SA 4.0)

ePSproc: xef2 wavefn run, orb 12 ioinzation (Iodine 3d, A1G/SG), 1-60eV

Job details

  • ePS xef2, batch xef2_1.0-60.1eV, orbital orb12_A1G

  • xef2 wavefn run on AntonJr, orb 12 ioinzation (Iodine 3d, A1G/SG), sph/ grid

  • E=1.0:2.5:60.1 (24 points)

  • Tue Feb 12 19:42:57 EST 2019

Set-up

Load modules

[1]:
import sys
import os
import numpy as np
import epsproc as ep

from datetime import datetime as dt
timeString = dt.now()
* pyevtk not found, VTK export not available.
* plotly not found, plotly plots not available.

Load data

[2]:
# File path only, from env var DATAFILE
# dataPath = os.getcwd()
dataFile = os.environ.get('DATAFILE', '')
[3]:
jobInfo = ep.headerFileParse(dataFile)
molInfo = ep.molInfoParse(dataFile)
*** Job info from file header.

 ePS xef2, batch xef2_1.0-60.1eV, orbital orb12_A1G
 xef2 wavefn run on AntonJr, orb 12 ioinzation (Iodine 3d, A1G/SG), sph/ grid
 E=1.0:2.5:60.1 (24 points)
 Tue Feb 12 19:42:57 EST 2019

*** Found orbitals
1   1 Ene =   -1276.2548 Spin =Alpha Occup =   2.000000
2   2 Ene =    -202.4761 Spin =Alpha Occup =   2.000000
3   3 Ene =    -181.5792 Spin =Alpha Occup =   2.000000
4   4 Ene =    -181.5770 Spin =Alpha Occup =   2.000000
5   5 Ene =    -181.5770 Spin =Alpha Occup =   2.000000
6   6 Ene =     -43.1198 Spin =Alpha Occup =   2.000000
7   7 Ene =     -36.1973 Spin =Alpha Occup =   2.000000
8   8 Ene =     -36.1881 Spin =Alpha Occup =   2.000000
9   9 Ene =     -36.1881 Spin =Alpha Occup =   2.000000
10  10 Ene =     -26.3038 Spin =Alpha Occup =   2.000000
11  11 Ene =     -26.3038 Spin =Alpha Occup =   2.000000
12  12 Ene =     -25.8711 Spin =Alpha Occup =   2.000000
13  13 Ene =     -25.8673 Spin =Alpha Occup =   2.000000
14  14 Ene =     -25.8673 Spin =Alpha Occup =   2.000000
15  15 Ene =     -25.8578 Spin =Alpha Occup =   2.000000
16  16 Ene =     -25.8578 Spin =Alpha Occup =   2.000000
17  17 Ene =      -8.5562 Spin =Alpha Occup =   2.000000
18  18 Ene =      -6.2727 Spin =Alpha Occup =   2.000000
19  19 Ene =      -6.2547 Spin =Alpha Occup =   2.000000
20  20 Ene =      -6.2547 Spin =Alpha Occup =   2.000000
21  21 Ene =      -2.8143 Spin =Alpha Occup =   2.000000
22  22 Ene =      -2.8032 Spin =Alpha Occup =   2.000000
23  23 Ene =      -2.8032 Spin =Alpha Occup =   2.000000
24  24 Ene =      -2.7810 Spin =Alpha Occup =   2.000000
25  25 Ene =      -2.7810 Spin =Alpha Occup =   2.000000
26  26 Ene =      -1.5681 Spin =Alpha Occup =   2.000000
27  27 Ene =      -1.5619 Spin =Alpha Occup =   2.000000
28  28 Ene =      -1.0877 Spin =Alpha Occup =   2.000000
29  29 Ene =      -0.7372 Spin =Alpha Occup =   2.000000
30  30 Ene =      -0.6738 Spin =Alpha Occup =   2.000000
31  31 Ene =      -0.6738 Spin =Alpha Occup =   2.000000
32  32 Ene =      -0.6426 Spin =Alpha Occup =   2.000000
33  33 Ene =      -0.6426 Spin =Alpha Occup =   2.000000
34  34 Ene =      -0.5518 Spin =Alpha Occup =   2.000000
35  35 Ene =      -0.4994 Spin =Alpha Occup =   2.000000
36  36 Ene =      -0.4994 Spin =Alpha Occup =   2.000000

*** Found atoms
Z = 54 ZS = 54 r =   0.0000000000   0.0000000000   0.0000000000
Z =  9 ZS =  9 r =   0.0000000000   0.0000000000  -1.9373220000
Z =  9 ZS =  9 r =   0.0000000000   0.0000000000   1.9373220000
[4]:
# Scan file(s) for various data types...

# For dir scan
# dataXS = ep.readMatEle(fileBase = dataPath, recordType = 'CrossSection')
# dataMatE = ep.readMatEle(fileBase = dataPath, recordType = 'DumpIdy')

# For single file
dataXS = ep.readMatEle(fileIn = dataFile, recordType = 'CrossSection')
dataMatE = ep.readMatEle(fileIn = dataFile, recordType = 'DumpIdy')

*** ePSproc readMatEle(): scanning files for CrossSection segments.

*** Scanning file(s)
['/mnt/femtobackSSHFS/FemtoShare/Results/ePolyScat_stuff/xef2/xef2_1.0-60.1eV/xef2_1.0-60.1eV_orb12_A1G.inp.out']

*** Reading ePS output file:  /mnt/femtobackSSHFS/FemtoShare/Results/ePolyScat_stuff/xef2/xef2_1.0-60.1eV/xef2_1.0-60.1eV_orb12_A1G.inp.out
Expecting 24 energy points.
Expecting 2 symmetries.
Scanning CrossSection segments.
Expecting 3 CrossSection segments.
Found 3 CrossSection segments (sets of results).
Processed 3 sets of CrossSection file segments, (0 blank)
*** ePSproc readMatEle(): scanning files for DumpIdy segments.

*** Scanning file(s)
['/mnt/femtobackSSHFS/FemtoShare/Results/ePolyScat_stuff/xef2/xef2_1.0-60.1eV/xef2_1.0-60.1eV_orb12_A1G.inp.out']

*** Reading ePS output file:  /mnt/femtobackSSHFS/FemtoShare/Results/ePolyScat_stuff/xef2/xef2_1.0-60.1eV/xef2_1.0-60.1eV_orb12_A1G.inp.out
Expecting 24 energy points.
Expecting 2 symmetries.
Scanning CrossSection segments.
Expecting 48 DumpIdy segments.
Found 48 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 48 sets of DumpIdy file segments, (0 blank)

Job & molecule info

[5]:
ep.jobSummary(jobInfo, molInfo);

*** Job summary data
 ePS xef2, batch xef2_1.0-60.1eV, orbital orb12_A1G
 xef2 wavefn run on AntonJr, orb 12 ioinzation (Iodine 3d, A1G/SG), sph/ grid
 E=1.0:2.5:60.1 (24 points)
 Tue Feb 12 19:42:57 EST 2019

Electronic structure input: '/home/paul/ePS_stuff/xef2/electronic_structure/xef2_SPKrATZP_rel_geom_v2.molden'
Initial state occ:               [2 2 2 4 2 2 4 2 2 2 4 4 2 2 4 2 4 4 2 2 2 2 4 4 2 4]
Final state occ:                 [2 2 2 4 2 2 4 2 2 1 4 4 2 2 4 2 4 4 2 2 2 2 4 4 2 4]
IPot (input vertical IP, eV):            12.35

*** Additional orbital info (SymProd)
Ionizing orb:                    [0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
Ionizing orb sym:                ['SG']
Orb energy (eV):                 [-703.98848886]
Orb energy (H):                  [-25.8711]
Orb energy (cm^-1):              [-5678050.13578627]
Threshold wavelength (nm):       1.7611679645049914

*** Warning: some orbital convergences outside single-center expansion convergence tolerance (0.01):
[[10.          0.81998167]
 [11.          0.80599244]
 [26.          0.9860914 ]
 [27.          0.98404896]]

*** Molecular structure

../_images/XeF2_xef2_1.0-60.1eV_orb12_A1G_9_1.png

1-photon ePS Cross-Sections

Plot 1-photon cross-sections and \(beta_2\) parameters (for an unaligned ensemble) from ePS calculations. These are taken directly from the ePS output file, CrossSection segments. See the ePS manual, ``GetCro` command, for further details <https://www.chem.tamu.edu/rgroup/lucchese/ePolyScat.E3.manual/GetCro.html>`__.

Cross-sections by symmetry & type

Types correspond to:

  • ‘L’: length gauge results.

  • ‘V’: velocity gauge results.

  • ‘M’: mixed gauge results.

Symmetries correspond to allowed ionizing transitions for the molecular point group (IRs typically corresponding to (x,y,z) polarization geometries), see the ePS manual for a list of symmetries. Symmetry All corresponds to the sum over all allowed sets of symmetries.

Cross-section units are MBarn.

[6]:
# Plot cross sections using Xarray functionality
# Set here to plot per file - should add some logic to combine files.
for data in dataXS:
    daPlot = data.sel(XC='SIGMA')
    daPlot.plot.line(x='Eke', col='Type')
../_images/XeF2_xef2_1.0-60.1eV_orb12_A1G_12_0.png

\(\beta_{2}\) by symmetry & type

Types & symmetries as per cross-sections. Normalized \(\beta_{2}\) paramters, dimensionless.

[7]:
# Repeat for betas
for data in dataXS:
    daPlot = data.sel(XC='BETA')
    daPlot.plot.line(x='Eke', col='Type')
../_images/XeF2_xef2_1.0-60.1eV_orb12_A1G_14_0.png

Dipole matrix elements

For 1-photon ionization. These are taken directly from ePS DumpIdy segments. See the ePS manual, ``DumpIdy` command, for further details <https://www.chem.tamu.edu/rgroup/lucchese/ePolyScat.E3.manual/DumpIdy.html>`__.

[8]:
# Set threshold for significance, only matrix elements with abs values > thres % will be plotted
thres = 0.1
[9]:
# Plot for each fie
for data in dataMatE:
    # Plot with sensible defaults - all dims with lmPlot()

    # Plot only values > theshold
    daPlot, daPlotpd, legendList, gFig = ep.lmPlot(data, thres = thres, thresType = 'pc', figsize = (15,10))

    # Plot phases, with unwrap
    daPlot, daPlotpd, legendList, gFig = ep.lmPlot(data, thres = thres, thresType = 'pc', figsize = (15,10), pType='phaseUW')
/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/xarray/core/nputils.py:223: RuntimeWarning: All-NaN slice encountered
  result = getattr(npmodule, name)(values, axis=axis, **kwargs)
Plotting data xef2_1.0-60.1eV_orb12_A1G.inp.out, pType=a, thres=10.1581107134, with Seaborn
/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/xarray/core/nputils.py:223: RuntimeWarning: All-NaN slice encountered
  result = getattr(npmodule, name)(values, axis=axis, **kwargs)
/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/numpy/lib/function_base.py:1520: RuntimeWarning: invalid value encountered in greater
  _nx.copyto(ddmod, pi, where=(ddmod == -pi) & (dd > 0))
/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/numpy/lib/function_base.py:1522: RuntimeWarning: invalid value encountered in less
  _nx.copyto(ph_correct, 0, where=abs(dd) < discont)
Plotting data xef2_1.0-60.1eV_orb12_A1G.inp.out, pType=phaseUW, thres=10.1581107134, with Seaborn
../_images/XeF2_xef2_1.0-60.1eV_orb12_A1G_17_4.png
../_images/XeF2_xef2_1.0-60.1eV_orb12_A1G_17_5.png

MFPADs

Calculated MF \(\beta\) parameters, using ePS dipole matrix elements. These are calculated by ep.mfblm(), as a function of energy and polarization geometry. See the ePSproc docs on ``ep.mfblm()` <https://epsproc.readthedocs.io/en/latest/modules/epsproc.MFBLM.html>`__ for further details, and this demo notebook.

[10]:
# Set pol geoms - these correspond to (z,x,y) in molecular frame (relative to principle/symmetry axis)
eAngs = ep.setPolGeoms()
[11]:
# Drop threshold for MF calcs
thres = 1e-3
# Calculate for each fie & pol geom
# TODO - file logic, and parallelize
BLM = []
for data in dataMatE:
    BLM.append(ep.mfblmEuler(data, selDims = {'Type':'L'}, eAngs = eAngs, thres = thres,
                             SFflag = True, verbose = 0))  # Run for all Eke, selected gauge only
[12]:
# Save BLM data - defaults to working dir and 'ep_timestamp' file
# TODO - testing for array/multiple file case
for data in BLM:
    fileName = dataFile + '_BLM-L_' + timeString.strftime('%Y-%m-%d_%H-%M-%S')
    ep.writeXarray(data, fileName = fileName)
['Written to h5netcdf format', '/mnt/femtobackSSHFS/FemtoShare/Results/ePolyScat_stuff/xef2/xef2_1.0-60.1eV/xef2_1.0-60.1eV_orb12_A1G.inp.out_BLM-L_2020-02-13_16-07-43.nc']
/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/h5netcdf/core.py:481: H5pyDeprecationWarning: other_ds.dims.create_scale(ds, name) is deprecated. Use ds.make_scale(name) instead.
  h5ds.dims.create_scale(h5ds, scale_name)
[13]:
# Normalize and plot results
for BLMplot in BLM:
    # Plot unnormalized B00 only, real part
    # This is/should be in units of MBarn (TBC).
#     BLMplot.where(np.abs(BLMplot) > thres, drop = True).real.squeeze().sel({'l':0, 'm':0}).plot.line(x='Eke', col='Euler');
    BLMplot.XS.real.squeeze().plot.line(x='Eke', col='Euler');

    # Plot values normalised by B00 - now set in calculation function
    # Plot results with lmPlot(), ordering by Euler sets
    # Version with (semi-manual) Euler grouping
    daPlot, daPlotpd, legendList, gFig = ep.lmPlot(BLMplot.swap_dims({'Euler':'Labels'}), SFflag = False, eulerGroup = True,
                                                   thresType = 'pc', thres = thres,
                                                   plotDims = ('Labels','l','m'),
                                                   figsize = (15,10))
Plotting data xef2_1.0-60.1eV_orb12_A1G.inp.out, pType=a, thres=0.001468340773845271, with Seaborn
../_images/XeF2_xef2_1.0-60.1eV_orb12_A1G_22_1.png
../_images/XeF2_xef2_1.0-60.1eV_orb12_A1G_22_2.png

Error & consistency checks

[14]:
# Check SF values
for data in dataMatE:
    # Plot values, single plot
    data.SF.pipe(np.abs).plot.line(x='Eke')
    data.SF.real.plot.line(x='Eke')
    data.SF.imag.plot.line(x='Eke')

    # Plot values, facet plot
#     data.SF.pipe(np.abs).plot.line(x='Eke', col='Sym')

../_images/XeF2_xef2_1.0-60.1eV_orb12_A1G_24_0.png
[15]:
# Compare calculated BLMs for L and V types (dafault above for L)

# Calculate for each fie & pol geom, and compare.
BLMv = []
BLMdiff = []
for n, data in enumerate(dataMatE):
    BLMv.append(ep.mfblmEuler(data, selDims = {'Type':'V'}, eAngs = eAngs, thres = thres,
                             SFflag = True, verbose = 0))  # Run for all Eke, selected gauge only

    BLMdiff.append(BLM[n] - BLMv[n])
    BLMdiff[n]['dXS'] = BLM[n].XS - BLMv[n].XS  # Set XS too, dropped in calc above

    BLMdiff[n].attrs['dataType'] = 'matE'
[16]:
# Save BLM data - defaults to working dir and 'ep_timestamp' file
# TODO - testing for array/multiple file case
for data in BLMv:
    fileName = dataFile + '_BLM-V_' + timeString.strftime('%Y-%m-%d_%H-%M-%S')
    ep.writeXarray(data, fileName = fileName)
['Written to h5netcdf format', '/mnt/femtobackSSHFS/FemtoShare/Results/ePolyScat_stuff/xef2/xef2_1.0-60.1eV/xef2_1.0-60.1eV_orb12_A1G.inp.out_BLM-V_2020-02-13_16-07-43.nc']
/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/h5netcdf/core.py:481: H5pyDeprecationWarning: other_ds.dims.create_scale(ds, name) is deprecated. Use ds.make_scale(name) instead.
  h5ds.dims.create_scale(h5ds, scale_name)
[17]:
# Normalize and plot results
for BLMplot in BLMv:
    # Plot unnormalized B00 only, real part
    # This is/should be in units of MBarn (TBC).
#     BLMplot.where(np.abs(BLMplot) > thres, drop = True).real.squeeze().sel({'l':0, 'm':0}).plot.line(x='Eke', col='Euler');
    BLMplot.XS.real.squeeze().plot.line(x='Eke', col='Euler');

    # Plot values normalised by B00 - now set in calculation function
    # Plot results with lmPlot(), ordering by Euler sets
    # Version with (semi-manual) Euler grouping
    daPlot, daPlotpd, legendList, gFig = ep.lmPlot(BLMplot.swap_dims({'Euler':'Labels'}), SFflag = False, eulerGroup = True,
                                                   thresType = 'pc', thres = thres,
                                                   plotDims = ('Labels','l','m'),
                                                   figsize = (15,10))
Plotting data xef2_1.0-60.1eV_orb12_A1G.inp.out, pType=a, thres=0.0014690955811964875, with Seaborn
../_images/XeF2_xef2_1.0-60.1eV_orb12_A1G_27_1.png
../_images/XeF2_xef2_1.0-60.1eV_orb12_A1G_27_2.png
[18]:
# Difference between 'L' and 'V' results
# NOTE - this currently drops XS

print('Differences, L vs. V gauge BLMs')

for BLMplot in BLMdiff:
    maxDiff = BLMplot.max()
    print(f'Max difference in BLMs (L-V): {0}', maxDiff.data)

    if np.abs(maxDiff) > thres:
        # Plot B00 only, real part
#         BLMplot.where(np.abs(BLMplot) > thres, drop = True).real.squeeze().sel({'l':0, 'm':0}).plot.line(x='Eke', col='Euler');
        BLMplot.dXS.real.squeeze().plot.line(x='Eke', col='Euler');

        # Plot values normalised by B00 - now set in calculation function
        # Plot results with lmPlot(), ordering by Euler sets
        # Version with (semi-manual) Euler grouping
        daPlot, daPlotpd, legendList, gFig = ep.lmPlot(BLMplot.swap_dims({'Euler':'Labels'}), SFflag = False, eulerGroup = True,
                                                       thresType = 'pc', thres = thres,
                                                       plotDims = ('Labels','l','m'),
                                                       figsize = (15,10))

Differences, L vs. V gauge BLMs
Max difference in BLMs (L-V): 0 (0.34692345160788+8.725762238127286e-17j)
Plotting data (No filename), pType=a, thres=0.00034692345160788, with Seaborn
../_images/XeF2_xef2_1.0-60.1eV_orb12_A1G_28_1.png
../_images/XeF2_xef2_1.0-60.1eV_orb12_A1G_28_2.png
[19]:
# Check imaginary components - should be around machine tolerance.
print('Machine tolerance: ', np.finfo(float).eps)
for BLMplot in BLM:
    maxImag = BLMplot.imag.max()
    print(f'Max imaginary value: {0}', maxImag.data)

#     BLMplot.where(np.abs(BLMplot) > thres, drop = True).imag.squeeze().plot.line(x='Eke', col='Euler');

    BLMplot = ep.matEleSelector(BLMplot, thres=thres, dims = 'Eke')
    BLMplot.imag.squeeze().plot.line(x='Eke', col='Euler');
Machine tolerance:  2.220446049250313e-16
Max imaginary value: 0 4.1933287884051097e-16
../_images/XeF2_xef2_1.0-60.1eV_orb12_A1G_29_1.png

Version info

Original job details

[20]:
print(jobInfo['ePolyScat'][0])
print('Run: ' + jobInfo['Starting'][0].split('at')[1])
ePolyScat Version E3
Run:  2019-02-12  20:54:33.594 (GMT -0500)

ePSproc details

[21]:
templateVersion = '0.0.6'
templateDate = '12/01/20'
[22]:
%load_ext version_information
[23]:
%version_information epsproc, xarray
[23]:
SoftwareVersion
Python3.7.5 64bit [GCC 7.3.0]
IPython7.9.0
OSLinux 5.0.0 36 generic x86_64 with debian buster sid
epsproc1.2.4
xarray0.14.0
Thu Feb 13 16:10:52 2020 EST
[24]:
print('Run: {}'.format(timeString.strftime('%Y-%m-%d_%H-%M-%S')))
host = !hostname
print('Host: {}'.format(host[0]))
Run: 2020-02-13_16-07-43
Host: jake

Cite this dataset

Hockett, Paul (2019). ePSproc: xef2 wavefn run, orb 12 ioinzation (Iodine 3d, A1G/SG), 1-60eV. Dataset on Zenodo. DOI: 10.5281/zenodo.3676893. URL: https://phockett.github.io/ePSdata/xef2_1.0-60.1eV/xef2_1.0-60.1eV_orb12_A1G.html

Bibtex:

@data{xef2 wavefn run, orb 12 ioinzation (Iodine 3d, A1G/SG), 1-60eV,
    title = {ePSproc: xef2 wavefn run, orb 12 ioinzation (Iodine 3d, A1G/SG), 1-60eV}
    author = {Hockett, Paul},
    doi = {10.5281/zenodo.3676893},
    publisher = {Zenodo},
    year = {2019},
    url = {https://phockett.github.io/ePSdata/xef2_1.0-60.1eV/xef2_1.0-60.1eV_orb12_A1G.html}
  }

See citation notes on ePSdata for further details.

DOI Creative Commons Attribution-NonCommercial-ShareAlike 4.0 (CC BY-NC-SA 4.0)