This page was auto-generated from a Jupyter notebook: XeF2-preliminary/XeF2_highRes_wf.orb22_E1G.

About ePSdata

Cite this dataset.

Problems? Please raise any issues on Github.

XeF2 (4d pi, orb22-23 E1G/PG), 1-350eV Preliminary¶

06/04/20

Set-up¶

Load modules¶

[1]:

import sys
import os
from pathlib import Path
import numpy as np
import epsproc as ep
import xarray as xr

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', '')
dataPath = Path(dataFile).parent.as_posix()  # Use first file for job info, and set dir for scanning

[3]:

jobInfo = ep.headerFileParse(dataFile)
molInfo = ep.molInfoParse(dataFile)

*** Job info from file header.

 ePS XeF2_2020, batch XeF2_highRes_wf, orbital orb22_E1G
 XeF2 wavefn run, orb 22/23 ionization (Xe 4d, E1G/PG), sph grid. Inputs based on original 2019 calcs, now with chunking for higher E resolution.
 E=10.0:10.0:150.0 (15 points)


*** 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
dataSetXS = ep.readMatEle(fileBase = dataPath, recordType = 'CrossSection')
dataSetMatE = 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 dir
/home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G
Found 20 .out file(s)


*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E151.0_10.0_291.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E158.0_10.0_298.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E4.0_10.0_144.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E154.0_10.0_294.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E156.0_10.0_296.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E159.0_10.0_299.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E8.0_10.0_148.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E153.0_10.0_293.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E3.0_10.0_143.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E2.0_10.0_142.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E5.0_10.0_145.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E160.0_10.0_300.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E152.0_10.0_292.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E9.0_10.0_149.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E1.0_10.0_141.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E6.0_10.0_146.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E157.0_10.0_297.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E7.0_10.0_147.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E10.0_10.0_150.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E155.0_10.0_295.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 4 CrossSection segments.
Found 4 CrossSection segments (sets of results).
Processed 4 sets of CrossSection file segments, (0 blank)
*** ePSproc readMatEle(): scanning files for DumpIdy segments.

*** Scanning dir
/home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G
Found 20 .out file(s)


*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E151.0_10.0_291.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E158.0_10.0_298.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E4.0_10.0_144.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E154.0_10.0_294.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E156.0_10.0_296.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E159.0_10.0_299.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E8.0_10.0_148.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E153.0_10.0_293.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E3.0_10.0_143.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E2.0_10.0_142.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E5.0_10.0_145.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E160.0_10.0_300.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E152.0_10.0_292.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E9.0_10.0_149.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E1.0_10.0_141.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E6.0_10.0_146.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E157.0_10.0_297.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E7.0_10.0_147.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E10.0_10.0_150.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

*** Reading ePS output file:  /home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E155.0_10.0_295.0eV.inp.out
Expecting 15 energy points.
Expecting 3 symmetries.
Scanning CrossSection segments.
Expecting 45 DumpIdy segments.
Found 45 dumpIdy segments (sets of matrix elements).

Processing segments to Xarrays...
Processed 45 sets of DumpIdy file segments, (0 blank)

[5]:

# Stack multi-E Xarrays into single array.
# Keep results as list for compatibility with rest of code (otherwise will slice Xarray)
dataXS = [xr.combine_nested(dataSetXS, concat_dim = ['Eke']).sortby('Eke')]
dataMatE = [xr.combine_nested(dataSetMatE, concat_dim = ['Eke']).sortby('Eke')]

Job & molecule info¶

[6]:

ep.jobSummary(jobInfo, molInfo);


*** Job summary data
 ePS XeF2_2020, batch XeF2_highRes_wf, orbital orb22_E1G
 XeF2 wavefn run, orb 22/23 ionization (Xe 4d, E1G/PG), sph grid. Inputs based on original 2019 calcs, now with chunking for higher E resolution.
 E=10.0:10.0:150.0 (15 points)


Electronic structure input: '/home/paul/ePS_stuff/XeF2_2020/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 2 4 4 2 2 4 2 3 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 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0]
Ionizing orb sym:                ['PG']
Orb energy (eV):                 [-76.27895792]
Orb energy (H):                  [-2.8032]
Orb energy (cm^-1):              [-615231.28663731]
Threshold wavelength (nm):       16.25404984629001

*** 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-preliminary_XeF2_highRes_wf.orb22_E1G_10_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.

[7]:

# 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-preliminary_XeF2_highRes_wf.orb22_E1G_13_0.png

\(\beta_{2}\) by symmetry & type¶

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

[8]:

# Repeat for betas
for data in dataXS:
    daPlot = data.sel(XC='BETA')
    daPlot.plot.line(x='Eke', col='Type')

../_images/XeF2-preliminary_XeF2_highRes_wf.orb22_E1G_15_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>`__.

[9]:

# Set threshold for significance, only matrix elements with abs values > thres % will be plotted
thresPlot = 0.1

[10]:

# 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 = thresPlot, thresType = 'pc', figsize = (15,10))

    # Plot phases, with unwrap
    daPlot, daPlotpd, legendList, gFig = ep.lmPlot(data, thres = thresPlot, thresType = 'pc', figsize = (15,10), pType='phaseUW')

/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/xarray/core/nputils.py:215: RuntimeWarning: All-NaN slice encountered
  result = getattr(npmodule, name)(values, axis=axis, **kwargs)

Plotting data XeF2_highRes_wf.orb22_E1G_E151.0_10.0_291.0eV.inp.out, pType=a, thres=2.828909780457982, with Seaborn

/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/xarray/core/nputils.py:215: 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_highRes_wf.orb22_E1G_E151.0_10.0_291.0eV.inp.out, pType=phaseUW, thres=2.828909780457982, with Seaborn

../_images/XeF2-preliminary_XeF2_highRes_wf.orb22_E1G_18_4.png

../_images/XeF2-preliminary_XeF2_highRes_wf.orb22_E1G_18_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.

[11]:

# Set threshold
thresCalc = 1e-3

# Set pol geoms - these correspond to (z,x,y) in molecular frame (relative to principle/symmetry axis)
eAngs = ep.setPolGeoms()

[12]:

# 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 = thresCalc,
                             SFflag = True, verbose = 0))  # Run for all Eke, selected gauge only

[13]:

# 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', '/home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E10.0_10.0_150.0eV.inp.out_BLM-L_2020-04-02_08-49-15.nc']

/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/xarray/backends/h5netcdf_.py:211: FutureWarning: complex dtypes are supported by h5py, but not part of the NetCDF API. You are writing an HDF5 file that is not a valid NetCDF file! In the future, this will be an error, unless you set invalid_netcdf=True.
  self.ds.attrs[key] = value
/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/xarray/backends/h5netcdf_.py:285: FutureWarning: complex dtypes are supported by h5py, but not part of the NetCDF API. You are writing an HDF5 file that is not a valid NetCDF file! In the future, this will be an error, unless you set invalid_netcdf=True.
  nc4_var.attrs[k] = v

[14]:

# 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 = thresPlot,
                                                   plotDims = ('Labels','l','m'),
                                                   figsize = (15,10))

/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/xarray/core/nputils.py:215: RuntimeWarning: All-NaN slice encountered
  result = getattr(npmodule, name)(values, axis=axis, **kwargs)

Plotting data XeF2_highRes_wf.orb22_E1G_E151.0_10.0_291.0eV.inp.out, pType=a, thres=0.12970378447436834, with Seaborn

../_images/XeF2-preliminary_XeF2_highRes_wf.orb22_E1G_23_2.png

../_images/XeF2-preliminary_XeF2_highRes_wf.orb22_E1G_23_3.png

Error & consistency checks¶

[15]:

# 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-preliminary_XeF2_highRes_wf.orb22_E1G_25_0.png

[16]:

# 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 = thresCalc,
                             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'

[17]:

# 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', '/home/paul/ePS_stuff/XeF2_2020/XeF2_highRes_wf/orb22_E1G/XeF2_highRes_wf.orb22_E1G_E10.0_10.0_150.0eV.inp.out_BLM-V_2020-04-02_08-49-15.nc']

/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/xarray/backends/h5netcdf_.py:211: FutureWarning: complex dtypes are supported by h5py, but not part of the NetCDF API. You are writing an HDF5 file that is not a valid NetCDF file! In the future, this will be an error, unless you set invalid_netcdf=True.
  self.ds.attrs[key] = value
/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/xarray/backends/h5netcdf_.py:285: FutureWarning: complex dtypes are supported by h5py, but not part of the NetCDF API. You are writing an HDF5 file that is not a valid NetCDF file! In the future, this will be an error, unless you set invalid_netcdf=True.
  nc4_var.attrs[k] = v

[18]:

# 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 = thresPlot,
                                                   plotDims = ('Labels','l','m'),
                                                   figsize = (15,10))

Plotting data XeF2_highRes_wf.orb22_E1G_E151.0_10.0_291.0eV.inp.out, pType=a, thres=0.12977838864678504, with Seaborn

../_images/XeF2-preliminary_XeF2_highRes_wf.orb22_E1G_28_1.png

../_images/XeF2-preliminary_XeF2_highRes_wf.orb22_E1G_28_2.png

[19]:

# 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) > thresCalc:
        # 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 = thresPlot,
                                                       plotDims = ('Labels','l','m'),
                                                       figsize = (15,10))

Differences, L vs. V gauge BLMs
Max difference in BLMs (L-V): 0 (0.23460029341235752-1.053003400409692e-17j)
Plotting data (No filename), pType=a, thres=0.023460029341235755, with Seaborn

/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/xarray/core/nputils.py:215: RuntimeWarning: All-NaN slice encountered
  result = getattr(npmodule, name)(values, axis=axis, **kwargs)

../_images/XeF2-preliminary_XeF2_highRes_wf.orb22_E1G_29_2.png

../_images/XeF2-preliminary_XeF2_highRes_wf.orb22_E1G_29_3.png

[20]:

# 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=thresCalc, dims = 'Eke')
    BLMplot.imag.squeeze().plot.line(x='Eke', col='Euler');

Machine tolerance:  2.220446049250313e-16
Max imaginary value: 0 0.6353212079680562

/home/paul/anaconda3/envs/ePSproc-v1.2/lib/python3.7/site-packages/xarray/core/nputils.py:215: RuntimeWarning: All-NaN slice encountered
  result = getattr(npmodule, name)(values, axis=axis, **kwargs)

../_images/XeF2-preliminary_XeF2_highRes_wf.orb22_E1G_30_2.png

Version info¶

Original job details¶

[21]:

print(jobInfo['ePolyScat'][0])
print('Run: ' + jobInfo['Starting'][0].split('at')[1])

ePolyScat Version E3
Run:  2020-03-25  11:26:23.191 (GMT -0400)

ePSproc details¶

[22]:

templateVersion = '0.0.7'
templateDate = '30/03/20'

[23]:

%load_ext version_information

[24]:

%version_information epsproc, xarray

[24]:

Software	Version
Python	3.7.6 64bit [GCC 7.3.0]
IPython	7.12.0
OS	Linux 4.15.0 66 generic x86_64 with debian stretch sid
epsproc	1.2.5
xarray	0.15.0
Thu Apr 02 14:18:28 2020 EDT

[25]:

print('Run: {}'.format(timeString.strftime('%Y-%m-%d_%H-%M-%S')))
host = !hostname
print('Host: {}'.format(host[0]))

Run: 2020-04-02_08-49-15
Host: AntonJr

[ ]: