import numpy as np
# Package fns.
from epsproc.basicPlotters import molPlot
from epsproc.util.conversion import (conv_ev_atm, conv_ev_nm)
#*************** Summary & display functions
# Print some jobInfo stuff & plot molecular structure
[docs]def jobSummary(jobInfo = None, molInfo = None, tolConv = 1e-2):
"""
Print some jobInfo stuff & plot molecular structure. (Currently very basic.)
Parameters
------------
jobInfo : dict, default = None
Dictionary of job data, as generated by :py:function:`epsproc.IO.headerFileParse()` from source ePS output file.
molInfo : dict, default = None
Dictionary of molecule data, as generated by :py:func:`epsproc.IO.molInfoParse()` from source ePS output file.
tolConv : float, default = 1e-2
Used to check for convergence in ExpOrb outputs, which defines single-center expansion of orbitals.
Returns
-------
JobInfo : list
orbInfo : dict
Properties of ionizing orbital, as determined from (jobInfo, molInfo).
History
-------
20/09/20 v2 Added orbInfo dict, and use this to hold all orbital related outputs for return. May break old codes (pre v1.2.6-dev).
Moved orbInfo to a separate function.
"""
# orbInfo = {}
# Pull job summary info
if jobInfo is not None:
print('\n*** Job summary data')
[print(line.strip('#')) for line in jobInfo['comments'][0:4]]
print(f"\nElectronic structure input: {jobInfo['Convert'][0].split()[1].strip()}")
print(f"Initial state occ:\t\t {jobInfo['OrbOccInit']}")
print(f"Final state occ:\t\t {jobInfo['OrbOcc']}")
print(f"IPot (input vertical IP, eV):\t\t {jobInfo['IPot']}")
# Log orbOcc
# orbInfo['OrbOccInit'] = jobInfo['OrbOccInit']
# orbInfo['OrbOccFinal'] = jobInfo['OrbOcc']
# Additional orb info
print("\n*** Additional orbital info (SymProd)")
# orbInfo['iList'] = jobInfo['OrbOccInit'] - jobInfo['OrbOcc']
iList = jobInfo['OrbOccInit'] - jobInfo['OrbOcc']
print(f"Ionizing orb:\t\t\t {iList}")
if molInfo is not None:
# Get orbGrp for event
# orbInfo['iOrbGrp'] = np.flatnonzero(orbInfo['iList']) + 1
orbX, orbInfo = getOrbInfo(jobInfo, molInfo)
# Find entries in orbTableX
# orbInfo['orbSym'] = np.unique(molInfo['orbTable'].where(molInfo['orbTable'].coords['OrbGrp'] == orbInfo['iOrbGrp'], drop = True).coords['Sym'])
print(f"Ionizing orb sym:\t\t {orbInfo['orbSym']}")
# orbInfo['orbIP'] = np.unique(molInfo['orbTable'].where(molInfo['orbTable'].coords['OrbGrp'] == orbInfo['iOrbGrp'], drop = True).sel(props = 'E'))
# orbInfo['orbIPH'] = np.unique(molInfo['orbTable'].where(molInfo['orbTable'].coords['OrbGrp'] == orbInfo['iOrbGrp'], drop = True).sel(props = 'EH'))
print(f"Orb energy (eV):\t\t {orbInfo['orbIP']}")
print(f"Orb energy (H):\t\t\t {orbInfo['orbIPH']}")
# orbInfo['orbIPnm'] = conv_ev_nm(orbInfo['orbIP'])
# orbInfo['orbIPcm'] = 1/orbInfo['orbIPnm']*1e7
# orbInfo['threshold'] = np.abs(orbInfo['orbIPnm'])[0]
print(f"Orb energy (cm^-1):\t\t {orbInfo['orbIPcm']}")
print(f"Threshold wavelength (nm):\t {orbInfo['threshold']}")
# Check ExpOrb outputs...
ind = (molInfo['orbTable'][:,8].values < 1-tolConv) + (molInfo['orbTable'][:,8].values > 1+tolConv)
if ind.any():
print(f"\n*** Warning: some orbital convergences outside single-center expansion convergence tolerance ({tolConv}):")
print(molInfo['orbTable'][ind, [0, 8]].values)
# Display structure
if molInfo is not None:
print('\n*** Molecular structure\n')
molPlot(molInfo)
# return jobInfo # Why bother? - but left for back-compatibility for now... had plans to do more with this?
# 20/09/20 Added orbInfo return, to allow further use of values determined above
return jobInfo, orbInfo
# Pull orbital-specific properties for job.
[docs]def getOrbInfo(jobInfo, molInfo):
"""
Pull orbital information for job from (jobInfo, molInfo) structures and return as Xarray.
20/09/20 v1 Adapted from routines in jobSummary().
"""
# Init dict.
orbInfo = {}
try:
# Find which orb is ionized using ePS orb numbering.
orbInfo['OrbOccInit'] = jobInfo['OrbOccInit']
orbInfo['OrbOccFinal'] = jobInfo['OrbOcc']
orbInfo['iList'] = jobInfo['OrbOccInit'] - jobInfo['OrbOcc']
# Get orbGrp for event
orbInfo['iOrbGrp'] = np.flatnonzero(orbInfo['iList']) + 1
# Find entries in orbTableX
orbX = molInfo['orbTable'].where(molInfo['orbTable'].coords['OrbGrp'] == orbInfo['iOrbGrp'], drop = True)
# Set orb properties to structure - mainly just taking relevant entries from orbTable, but will make for easier reference later.
orbInfo['orbN'] = orbX.orb.data[0]
orbInfo['orbSym'] = np.unique(molInfo['orbTable'].where(molInfo['orbTable'].coords['OrbGrp'] == orbInfo['iOrbGrp'], drop = True).coords['Sym'])
orbInfo['orbIP'] = np.unique(molInfo['orbTable'].where(molInfo['orbTable'].coords['OrbGrp'] == orbInfo['iOrbGrp'], drop = True).sel(props = 'E'))
orbInfo['orbIPH'] = np.unique(molInfo['orbTable'].where(molInfo['orbTable'].coords['OrbGrp'] == orbInfo['iOrbGrp'], drop = True).sel(props = 'EH'))
orbInfo['orbIPnm'] = conv_ev_nm(orbInfo['orbIP'])
orbInfo['orbIPcm'] = 1/orbInfo['orbIPnm']*1e7
orbInfo['threshold'] = np.abs(orbInfo['orbIPnm'])[0]
return orbX, orbInfo
except:
print("*** getOrbInfo Failed to get orbital info, returning empty.")
return None, None
# Print (LM) and symmetry sets with Pandas tables
[docs]def lmSymSummary(data):
"""Display summary info data tables.
Works nicely in a notebook cell, with Pandas formatted table... but not from function?
For a more sophisticated Pandas conversion, see :py:func:`epsproc.util.conversion.multiDimXrToPD`
"""
print('\n*** Index summary\n')
test = data.Sym.to_pandas()
print('Symmetry sets')
print(test.unstack())
test = data.LM.to_pandas()
print('\n(L,M) sets')
print(test.unstack().T)