ESjob class - electronic structure file handling & ePS job creation

12/02/22

Demo for basic electronic structure file IO and creation of ePS jobs based on inputs.

Currently tested for Gamess and Molden IO only.
Uses CCLIB on the backend, so should be easily extendable to other CCLIB-supported cases.

Imports

[1]:

# Import main package
# import epsman as em

# For ePS job creation with electronic structure handling, use elecStructure.ESjob
from epsman.elecStructure.ESjob import ESjob

[2]:

# For testing, set the module path and test file.
import inspect
from pathlib import Path

modDir = Path(inspect.getfile(ESjob)).parent
testFilePath = modDir/'fileTest'  # Default module test files, these are included with Github repo.

Class creation

Basic file handling for Gamess Log files is implemented.

Setup minimally via ESjob(fileName = electronic structure file).
If job settings are already set, they will be used, otherwise set full paths here with fileBase = full path.
This creates an empty base object too, but this can be ignored for electronic structure file handling only.

Further details:

The file is handled via the an EShandler class object.
All methods are available as self.esData.method()
File parsing and conversion is via CCLIB, a full list of compatible electronic structure packages & data IO can be found in the CCLIB docs.
Only Gamess (US) files have been tested so far, which are further converted to Molden format for ePS (although recent versions of ePS can also read Gamess files directly).

[3]:

# Basic file handling for Gamess Log files is implemented.
job = ESjob(fileName = 'xe_SPKrATZP_rel.log', fileBase = testFilePath)

# Note an empty object can also be created.
# job = ESjob()

Set host = None
Set user = None
Set IP = None
Set password = None
Set mol = None
Set orb = None
Set batch = None
Set jobNote = None
Set elecStructure = None
Set genFile = None
Set jobSettings = None
Skipping setJobPaths() until job settings defined, run setJob() to set.
Set elecStructure = xe_SPKrATZP_rel.log

Set input file as /home/eps/github/epsman/epsman/elecStructure/fileTest/xe_SPKrATZP_rel.log, use self.setFiles to change.
Set output file as /home/eps/github/epsman/epsman/elecStructure/fileTest/xe_SPKrATZP_rel.molden, use self.setMoldenFile to override.

*** Read file /home/eps/github/epsman/epsman/elecStructure/fileTest/xe_SPKrATZP_rel.log with CCLIB, data set to self.data.
Read 1 atoms and 68 MOs
***Warning: inconsistent dim mapping, some Gamess or ePS dims unmapped. Check PD table for details.
*** Set orbPD data to self.orbPD, set group data to self.orbGrps

Found input file Point Group: {'Name': 'DNH', 'NAXIS': '8', 'ORDER': '32'}.
Mapped PGs: Gamess (DNH, 8)  > ePS (DAh) dim mapping.
Found 68 orbitals, in 45 groups.
Found 7 orb symmetries: ['A1g' 'A2u' 'E1u' 'E1g' 'E2g' 'E3u' 'E2u']
Assigned 54 electrons to 27 orbitals/19 orbital groups.

Occupied orbitals table:

/home/eps/.conda/envs/epsman-demo/lib/python3.7/site-packages/numpy/core/numeric.py:2378: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  return bool(asarray(a1 == a2).all())

			syms	Occ	OccN	degen	OrbGrpOcc	Gamess	ePS
E	iOrbGrp	OrbN
-34724.875681	1	1	A1g	True	2	1	2	A1G	SG
-5506.008795	2	2	A1g	True	2	1	2	A1G	SG
-4937.337107	3	3	A2u	True	2	1	2	A2U	A2U
	4	4	E1u	True	2	2	4	E1U	PU
	4	5	E1u	True	2	2	4	E1U	PU
-1169.749415	5	6	A1g	True	2	1	2	A1G	SG
-981.237103	6	7	A2u	True	2	1	2	A2U	A2U
	7	8	E1u	True	2	2	4	E1U	PU
	7	9	E1u	True	2	2	4	E1U	PU
-700.203360	9	10	E1g	True	2	2	4	E1G	PG
	9	11	E1g	True	2	2	4	E1G	PG
	8	12	A1g	True	2	1	2	A1G	SG
	10	13	E2g	True	2	2	4	E2G	DG
	10	14	E2g	True	2	2	4	E2G	DG
-229.247756	11	15	A1g	True	2	1	2	A1G	SG
-166.824838	12	16	A2u	True	2	1	2	A2U	A2U
	13	17	E1u	True	2	2	4	E1U	PU
	13	18	E1u	True	2	2	4	E1U	PU
-72.521062	14	19	A1g	True	2	1	2	A1G	SG
	15	20	E1g	True	2	2	4	E1G	PG
	15	21	E1g	True	2	2	4	E1G	PG
	16	22	E2g	True	2	2	4	E2G	DG
	16	23	E2g	True	2	2	4	E2G	DG
-27.472614	17	24	A1g	True	2	1	2	A1G	SG
-12.421997	18	25	A2u	True	2	1	2	A2U	A2U
	19	26	E1u	True	2	2	4	E1U	PU
	19	27	E1u	True	2	2	4	E1U	PU

Note the outputs here:

OrbN is the orbital numbering from the electronic structure file, usually corresponding to doubly-occupied orbitals as given by OccN.
iOrbGrp renumbers including degereacies, which matches the internal ordering in ePolyScat. Occupation is given by OrbGrpOcc.
Energies in eV.
degen is the orbital degeneracy.
syms lists the symmetries returned by CCLIB.
If reading a Gamess file, Gamess lists the symmteries in the usual format.
If a point group was found, ePS lists the equivalent ePS symmetry label for the group; the full list can be found at https://epolyscat.droppages.com/SymmetryLabels. Note that this mapping is set by epsman.sym.convertSyms.convertSymsGamessePS(), and can be set manually if incorrect. (TO TEST)

Attribs are also stored in the class…

[4]:

job.elecStructure

[4]:

'xe_SPKrATZP_rel.log'

[5]:

# The ESclass.EShandler class is used on the backend, and can be accessed as .esData
job.esData

[5]:

<epsman.elecStructure.ESclass.EShandler at 0x7f49d0f9f8d0>

[6]:

# Point group set
job.esData.PG

[6]:

'DAh'

[7]:

# Point group info - this lists the members with ePolyScat labels
job.esData.PGinfo

[7]:

{'ePSlabels': ['SG',
  'A2G',
  'B1G',
  'B2G',
  'PG',
  'DG',
  'FG',
  'GG',
  'SU',
  'A2U',
  'B1U',
  'B2U',
  'PU',
  'DU',
  'FU',
  'GU'],
 'ePSnote': ['D', 'infinity', 'h']}

[8]:

# Full symmetry mapping details - this lists input symmetries and mapping to ePS labels (currently only Gamess > ePS mapping supported)
job.esData.orbPD.attrs['PGmap']

[8]:

	Gamess	ePS	GDims
1	A1G	SG	13.0
2	A1U	SU	0.0
3	A2G	A2G	0.0
4	A2U	A2U	9.0
5	B1G	B1G	0.0
6	B1U	B1U	0.0
7	B2G	B2G	0.0
8	B2U	B2U	0.0
9	E1G	PG	5.0
10	E1U	PU	9.0
11	E2G	DG	5.0
12	E2U	DU	2.0
13	E3G	FG	0.0
14	E3U	FU	2.0
15		GU	NaN
16		GG	NaN

[9]:

# CCLIB data object is also accessible as .data
job.esData.data

[9]:

<cclib.parser.data.ccData_optdone_bool at 0x7f49d0eebb10>

Update/change master file

Just set a new file name and/or path.

This may also be required if the ESjob class is initialised without a file set.

[10]:

# If the file doesn't exist an error will be printed.
job.setMasterESfile(fileName = 'xe_SPKrATZP_rel_copy.log')

Set elecStructure = xe_SPKrATZP_rel_copy.log

Set input file as /home/eps/github/epsman/epsman/elecStructure/fileTest/xe_SPKrATZP_rel_copy.log, use self.setFiles to change.
Set output file as /home/eps/github/epsman/epsman/elecStructure/fileTest/xe_SPKrATZP_rel_copy.molden, use self.setMoldenFile to override.
Could not import `openbabel`, fallback mechanism might not work.

*** Read file /home/eps/github/epsman/epsman/elecStructure/fileTest/xe_SPKrATZP_rel_copy.log with CCLIB, data set to self.data.
*** Error: File /home/eps/github/epsman/epsman/elecStructure/fileTest/xe_SPKrATZP_rel_copy.log not found or empty.

Molden file creation demo

This is set by self.checkLocalESfiles()
- This will check for a Molden version of the file and sync to host (if set).
A call to self.esData.writeMoldenFile2006() directly will write a new Molden file from the Gamess .log file.

[11]:

# If a Gamess file is set, the molden version will be checked & can be created if missing
# For testing use <github repo>/tests (set in .gitignore)
testPath = modDir.parent.parent/'tests'
testPath.mkdir(exist_ok=True)

# Reset master file to use for testing
job.setMasterESfile(fileName = 'xe_SPKrATZP_rel.log')

Set elecStructure = xe_SPKrATZP_rel.log

Set input file as /home/eps/github/epsman/epsman/elecStructure/fileTest/xe_SPKrATZP_rel.log, use self.setFiles to change.
Set output file as /home/eps/github/epsman/epsman/elecStructure/fileTest/xe_SPKrATZP_rel.molden, use self.setMoldenFile to override.

*** Read file /home/eps/github/epsman/epsman/elecStructure/fileTest/xe_SPKrATZP_rel.log with CCLIB, data set to self.data.
Read 1 atoms and 68 MOs
***Warning: inconsistent dim mapping, some Gamess or ePS dims unmapped. Check PD table for details.
*** Set orbPD data to self.orbPD, set group data to self.orbGrps

Found input file Point Group: {'Name': 'DNH', 'NAXIS': '8', 'ORDER': '32'}.
Mapped PGs: Gamess (DNH, 8)  > ePS (DAh) dim mapping.
Found 68 orbitals, in 45 groups.
Found 7 orb symmetries: ['A1g' 'A2u' 'E1u' 'E1g' 'E2g' 'E3u' 'E2u']
Assigned 54 electrons to 27 orbitals/19 orbital groups.

Occupied orbitals table:

/home/eps/.conda/envs/epsman-demo/lib/python3.7/site-packages/numpy/core/numeric.py:2378: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  return bool(asarray(a1 == a2).all())

			syms	Occ	OccN	degen	OrbGrpOcc	Gamess	ePS
E	iOrbGrp	OrbN
-34724.875681	1	1	A1g	True	2	1	2	A1G	SG
-5506.008795	2	2	A1g	True	2	1	2	A1G	SG
-4937.337107	3	3	A2u	True	2	1	2	A2U	A2U
	4	4	E1u	True	2	2	4	E1U	PU
	4	5	E1u	True	2	2	4	E1U	PU
-1169.749415	5	6	A1g	True	2	1	2	A1G	SG
-981.237103	6	7	A2u	True	2	1	2	A2U	A2U
	7	8	E1u	True	2	2	4	E1U	PU
	7	9	E1u	True	2	2	4	E1U	PU
-700.203360	9	10	E1g	True	2	2	4	E1G	PG
	9	11	E1g	True	2	2	4	E1G	PG
	8	12	A1g	True	2	1	2	A1G	SG
	10	13	E2g	True	2	2	4	E2G	DG
	10	14	E2g	True	2	2	4	E2G	DG
-229.247756	11	15	A1g	True	2	1	2	A1G	SG
-166.824838	12	16	A2u	True	2	1	2	A2U	A2U
	13	17	E1u	True	2	2	4	E1U	PU
	13	18	E1u	True	2	2	4	E1U	PU
-72.521062	14	19	A1g	True	2	1	2	A1G	SG
	15	20	E1g	True	2	2	4	E1G	PG
	15	21	E1g	True	2	2	4	E1G	PG
	16	22	E2g	True	2	2	4	E2G	DG
	16	23	E2g	True	2	2	4	E2G	DG
-27.472614	17	24	A1g	True	2	1	2	A1G	SG
-12.421997	18	25	A2u	True	2	1	2	A2U	A2U
	19	26	E1u	True	2	2	4	E1U	PU
	19	27	E1u	True	2	2	4	E1U	PU

[12]:

# Make a copy & test
import shutil
shutil.copy(job.esData.fullPath.as_posix(), (testPath/job.elecStructure).as_posix())

# Set & read new file - note this does not create Molden file
job.setMasterESfile(fileName = job.elecStructure, fileBase = testPath)

Set elecStructure = xe_SPKrATZP_rel.log

Set input file as /home/eps/github/epsman/tests/xe_SPKrATZP_rel.log, use self.setFiles to change.
Set output file as /home/eps/github/epsman/tests/xe_SPKrATZP_rel.molden, use self.setMoldenFile to override.

*** Read file /home/eps/github/epsman/tests/xe_SPKrATZP_rel.log with CCLIB, data set to self.data.
Read 1 atoms and 68 MOs
***Warning: inconsistent dim mapping, some Gamess or ePS dims unmapped. Check PD table for details.
*** Set orbPD data to self.orbPD, set group data to self.orbGrps

Found input file Point Group: {'Name': 'DNH', 'NAXIS': '8', 'ORDER': '32'}.
Mapped PGs: Gamess (DNH, 8)  > ePS (DAh) dim mapping.
Found 68 orbitals, in 45 groups.
Found 7 orb symmetries: ['A1g' 'A2u' 'E1u' 'E1g' 'E2g' 'E3u' 'E2u']
Assigned 54 electrons to 27 orbitals/19 orbital groups.

Occupied orbitals table:

/home/eps/.conda/envs/epsman-demo/lib/python3.7/site-packages/numpy/core/numeric.py:2378: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  return bool(asarray(a1 == a2).all())

			syms	Occ	OccN	degen	OrbGrpOcc	Gamess	ePS
E	iOrbGrp	OrbN
-34724.875681	1	1	A1g	True	2	1	2	A1G	SG
-5506.008795	2	2	A1g	True	2	1	2	A1G	SG
-4937.337107	3	3	A2u	True	2	1	2	A2U	A2U
	4	4	E1u	True	2	2	4	E1U	PU
	4	5	E1u	True	2	2	4	E1U	PU
-1169.749415	5	6	A1g	True	2	1	2	A1G	SG
-981.237103	6	7	A2u	True	2	1	2	A2U	A2U
	7	8	E1u	True	2	2	4	E1U	PU
	7	9	E1u	True	2	2	4	E1U	PU
-700.203360	9	10	E1g	True	2	2	4	E1G	PG
	9	11	E1g	True	2	2	4	E1G	PG
	8	12	A1g	True	2	1	2	A1G	SG
	10	13	E2g	True	2	2	4	E2G	DG
	10	14	E2g	True	2	2	4	E2G	DG
-229.247756	11	15	A1g	True	2	1	2	A1G	SG
-166.824838	12	16	A2u	True	2	1	2	A2U	A2U
	13	17	E1u	True	2	2	4	E1U	PU
	13	18	E1u	True	2	2	4	E1U	PU
-72.521062	14	19	A1g	True	2	1	2	A1G	SG
	15	20	E1g	True	2	2	4	E1G	PG
	15	21	E1g	True	2	2	4	E1G	PG
	16	22	E2g	True	2	2	4	E2G	DG
	16	23	E2g	True	2	2	4	E2G	DG
-27.472614	17	24	A1g	True	2	1	2	A1G	SG
-12.421997	18	25	A2u	True	2	1	2	A2U	A2U
	19	26	E1u	True	2	2	4	E1U	PU
	19	27	E1u	True	2	2	4	E1U	PU

[13]:

# self.checkLocalESfiles() will check for Molden file and also sync to host (if set)
job.checkLocalESfiles()

Written Molden2006 format file /home/eps/github/epsman/tests/xe_SPKrATZP_rel.molden
Set elecStructure = xe_SPKrATZP_rel.molden

*** Can't sync files, self.host or self.hostDefn[host][elecFile] not set.

[14]:

# self.esData.write* methods can also be called
job.esData.writeMoldenFile2006()

Written Molden2006 format file /home/eps/github/epsman/tests/xe_SPKrATZP_rel.molden

Create ePolyScat input from Gamess source

The main routine self.buildePSjob will attempt to execute all the build steps and, hopefully, produce useful output if it fails.

Minimally this needs an ionization channel defined (this is set according to the iOrbGrp numbers defined in the tables above), which will allow local job creation. However, if a host machine is not set, the final steps will fail.

[15]:

# Test with host not set...
job.buildePSjob(channel = 18)

*** Set ionization from orbital/channel 18.
Updated orb table...

Occupied orbitals by group:

	E	OrbN	syms	Occ	OccN	degen	OrbGrpOcc	Gamess	ePS	OrbGrpOccFinal
iOrbGrp
1	-34724.875681	1	A1g	True	2	1	2	A1G	SG	2
2	-5506.008795	2	A1g	True	2	1	2	A1G	SG	2
3	-4937.337107	3	A2u	True	2	1	2	A2U	A2U	2
4	-4937.337107	4	E1u	True	2	2	4	E1U	PU	4
5	-1169.749415	6	A1g	True	2	1	2	A1G	SG	2
6	-981.237103	7	A2u	True	2	1	2	A2U	A2U	2
7	-981.237103	8	E1u	True	2	2	4	E1U	PU	4
9	-700.203360	10	E1g	True	2	2	4	E1G	PG	4
8	-700.203360	12	A1g	True	2	1	2	A1G	SG	2
10	-700.203360	13	E2g	True	2	2	4	E2G	DG	4
11	-229.247756	15	A1g	True	2	1	2	A1G	SG	2
12	-166.824838	16	A2u	True	2	1	2	A2U	A2U	2
13	-166.824838	17	E1u	True	2	2	4	E1U	PU	4
14	-72.521062	19	A1g	True	2	1	2	A1G	SG	2
15	-72.521062	20	E1g	True	2	2	4	E1G	PG	4
16	-72.521062	22	E2g	True	2	2	4	E2G	DG	4
17	-27.472614	24	A1g	True	2	1	2	A1G	SG	2
18	-12.421997	25	A2u	True	2	1	2	A2U	A2U	1
19	-12.421997	26	E1u	True	2	2	4	E1U	PU	4


*** Building job test, orb18 (A2U/DAh), batch: test
Set mol = test
Set orb = orb18_A2U
Set batch = test
Generator file set: test.orb18_A2U.conf

*** Job paths set in self.hostDefn['None']:

*** Warning: can't find host 'None' in self.hostDefn.
Set self.ePSglobals for global job settings.
{'LMax': 30}
self.symList not set, running for defaults (all symmetry species).

*** Failed to build job, can't write gen file or create job tree - is the host set?
None

[15]:

False

In this example the build fails at file IO, since there is no host or paths defined. The ePSrecords generated can be found in two dictionaries, defining the calculation parameters and molecule settings. (For more on these settings, see the ePolyScat manual and sample jobs.)

[19]:

# Global calculation settings
job.esData.ePSglobals

[19]:

{'LMax': 30}

[20]:

# Job settings
job.esData.ePSrecords

[20]:

OrderedDict([('elecStructure',
              PosixPath('/home/eps/github/epsman/tests/xe_SPKrATZP_rel.molden')),
             ('IP', 12.422),
             ('OrbOccInit', '2 2 2 4 2 2 4 4 2 4 2 2 4 2 4 4 2 2 4'),
             ('OrbOccTarget', '2 2 2 4 2 2 4 4 2 4 2 2 4 2 4 4 2 1 4'),
             ('InitSpinDeg', 1),
             ('TargSpinDeg', 2),
             ('SpinDeg', 1),
             ('InitSym', 'SG'),
             ('TargSym', 'A2U'),
             ('Ssym',
              '(SG SG SG SG SG SG SG SG SG SG SG SG SG SG SG SG A2G A2G A2G A2G A2G A2G A2G A2G A2G A2G A2G A2G A2G A2G A2G A2G B1G B1G B1G B1G B1G B1G B1G B1G B1G B1G B1G B1G B1G B1G B1G B1G B2G B2G B2G B2G B2G B2G B2G B2G B2G B2G B2G B2G B2G B2G B2G B2G PG PG PG PG PG PG PG PG PG PG PG PG PG PG PG PG DG DG DG DG DG DG DG DG DG DG DG DG DG DG DG DG FG FG FG FG FG FG FG FG FG FG FG FG FG FG FG FG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG GG SU SU SU SU SU SU SU SU SU SU SU SU SU SU SU SU A2U A2U A2U A2U A2U A2U A2U A2U A2U A2U A2U A2U A2U A2U A2U A2U B1U B1U B1U B1U B1U B1U B1U B1U B1U B1U B1U B1U B1U B1U B1U B1U B2U B2U B2U B2U B2U B2U B2U B2U B2U B2U B2U B2U B2U B2U B2U B2U PU PU PU PU PU PU PU PU PU PU PU PU PU PU PU PU DU DU DU DU DU DU DU DU DU DU DU DU DU DU DU DU FU FU FU FU FU FU FU FU FU FU FU FU FU FU FU FU GU GU GU GU GU GU GU GU GU GU GU GU GU GU GU GU)'),
             ('Csym',
              '(SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU SG A2G B1G B2G PG DG FG GG SU A2U B1U B2U PU DU FU GU)')])

Note that the default case sets all possible scattering and continuum symmetries for the point group set, which is not usually what one wants… setting self.symList directly will bypass the automatic setting.

To override this manually, self.esData.genSymList() can be used to generate pairs, or simply pass a list to job.esData.symList directly.

[26]:

# symList holds all (Scattering, Continuum) pairs as tuples.
# This can be set from lists with genSymList

# TODO: fix self.setSyms for this!
# TODO: add Ssym,Csym options to buildePSjob() method.

job.esData.genSymList(Ssym=['SG','A2G'],Csym=['SG','DG'])
job.esData.symList

[26]:

[('SG', 'SG'), ('SG', 'DG'), ('A2G', 'SG'), ('A2G', 'DG')]

Versions

[16]:

import scooby
scooby.Report(additional=['epsman', 'fabric', 'cclib'])

[16]:

Sat Feb 12 14:23:42 2022 EST
OS	Linux	CPU(s)	64	Machine	x86_64
Architecture	64bit	Environment	Jupyter
Python 3.7.10 (default, Feb 26 2021, 18:47:35) [GCC 7.3.0]
epsman	0.0.1	fabric	2.6.0	cclib	1.7
numpy	1.19.2	scipy	1.6.1	IPython	7.21.0
matplotlib	3.3.4	scooby	0.5.6
Intel(R) Math Kernel Library Version 2020.0.2 Product Build 20200624 for Intel(R) 64 architecture applications

[17]:

# Check current Git commit for local ePSproc version
from pathlib import Path
import epsman as em

!git -C {Path(em.__file__).parent} branch
!git -C {Path(em.__file__).parent} log --format="%H" -n 1

  master
* restructure160221
2cdcf0ebb27837e540886652f591c6a0246dc46b

[18]:

# Check current remote commits
!git ls-remote --heads git://github.com/phockett/epsman

21b4357a169baf9fa7887c68bd1cf8f92c59642c        refs/heads/master
2cdcf0ebb27837e540886652f591c6a0246dc46b        refs/heads/restructure160221

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