NWChem: copy over newest data inputs and outputs before running 7.0

[berquist]

The first part of #1131, which just adds the new test data. It is not tested yet because at least geometry optimization results in a hard crash. A separate PR will add entries to testdata and whatever fixes are necessary to get the tests passing. Another PR after that will clean up the old NWChem versions and move them to regressions.

** basicNWChem7.0/dvb_gopt_hf.out: Customized restricted single point HF unittest ***
[NWChem /home/eric/development/cclib_berquist/data/NWChem/basicNWChem7.0/dvb_gopt_hf.out ERROR] Encountered error when parsing.
[NWChem /home/eric/development/cclib_berquist/data/NWChem/basicNWChem7.0/dvb_gopt_hf.out ERROR] Last line read:   no constraints, skipping    0.0000000000000000

Traceback (most recent call last):
  File "/home/eric/.pyenv/versions/miniconda3-4.7.12/envs/cclib_berquist_37/lib/python3.7/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/eric/.pyenv/versions/miniconda3-4.7.12/envs/cclib_berquist_37/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/eric/development/cclib_berquist/test/test_data.py", line 337, in <module>
    test_all(parsers, modules, terse=args.terse, silent=args.silent, loglevel=loglevel, summary=True, visual_tests=True)
  File "/home/eric/development/cclib_berquist/test/test_data.py", line 302, in test_all
    errors_or_failures = data_suite.testall()
  File "/home/eric/development/cclib_berquist/test/test_data.py", line 183, in testall
    datatype=test.datatype if hasattr(test, 'datatype') else None
  File "/home/eric/development/cclib_berquist/test/test_data.py", line 115, in getdatafile
    data = logfile.parse()
  File "/home/eric/development/cclib_berquist/cclib/parser/logfileparser.py", line 321, in parse
    self.extract(inputfile, line)
  File "/home/eric/development/cclib_berquist/cclib/parser/nwchemparser.py", line 124, in extract
    assert "maximum gradient threshold" in line
AssertionError

[berquist]

A separate PR will add entries to testdata and whatever fixes are necessary to get the tests passing.

I did need to make one small code change to get the slightly newer vibrational frequency output working, which was already there in some form for 7.0.

[codecov[bot]]

Codecov Report

Base: 87.84% // Head: 87.77% // Decreases project coverage by -0.06% :warning:

Coverage data is based on head (9a09d71) compared to base (8e6892a). Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1133      +/-   ##
==========================================
- Coverage   87.84%   87.77%   -0.07%     
==========================================
  Files          69       64       -5     
  Lines       13492    13435      -57     
==========================================
- Hits        11852    11793      -59     
- Misses       1640     1642       +2     

Impacted Files	Coverage Δ
cclib/parser/nwchemparser.py	96.54% <100.00%> (-0.29%)	:arrow_down:
cclib/parser/gaussianparser.py	95.38% <0.00%> (-0.13%)	:arrow_down:
cclib/parser/data.py	80.80% <0.00%> (ø)
cclib/__init__.py
cclib/method/__init__.py
cclib/bridge/__init__.py
cclib/parser/__init__.py
cclib/io/__init__.py
cclib/parser/psi4parser.py	97.53% <0.00%> (+0.16%)	:arrow_up:
... and 1 more

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[langner]

A separate PR will add entries to testdata and whatever fixes are necessary to get the tests passing.

I did need to make one small code change to get the slightly newer vibrational frequency output working, which was already there in some form for 7.0.

Was something failing there before?

[berquist]

It looks like the output file from the calculation I ran is just...missing a huge chunk in the middle (all of SCF) and gets cut off in a weird location. It was failing because of an unnecessary check if the SCF energy was there before parsing ZPVE, and it wasn't. I've just tried rerunning it again and...it's still missing. Maybe something is wrong with my NWChem copy...

[shivupa]

It looks like the output file from the calculation I ran is just...missing a huge chunk in the middle (all of SCF) and gets cut off in a weird location. It was failing because of an unnecessary check if the SCF energy was there before parsing ZPVE, and it wasn't. I've just tried rerunning it again and...it's still missing. Maybe something is wrong with my NWChem copy...

What file was this for specifically? I ran dvb_sp_hf.out and I didn't see anything missing in the diff wrt your output and wrt to nwchem6.5

[amandadumi]

This pull request in general looks great, thanks! Though, I want to make sure I understand. Shiv's files and yours produce the same output, so the nwchem parser was changed at 1148 to account for this variation in output by removing the unnecessary check on the SCF energy?

[berquist]

This pull request in general looks great, thanks! Though, I want to make sure I understand. Shiv's files and yours produce the same output, so the nwchem parser was changed at 1148 to account for this variation in output by removing the unnecessary check on the SCF energy?

Yes

[mkhorton]

Hi! We're seeing this error when trying to parse NWChem 7.0.2 output logs with cclib 1.7.2, was this resolved or do you have any advice? Thank you!

[berquist]

Hi Matt, this wasn't resolved, so thanks for the reminder. I'll try and get to it in the next day or two unless you already have a patch.

[mkhorton]

Amazing, thanks for the update @berquist! :)