Lammps output

[samwaseda]

No description provided.

[jan-janssen]

Be careful before merging, as this depends on pymatgen

[jan-janssen]

I implemented pymatgen in conda-forge conda-forge/staged-recipes#8888 so we could merge it now, still as pymatgen is restricted to Python > 3.5 and windows is not supported this would also restrict the availability of pyiron.

[jan-janssen]

The tests fail with:

======================================================================
FAIL: test_lammps_water (lammps.test_lammps.TestLammps)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/pyiron/pyiron/tests/lammps/test_lammps.py", line 132, in test_lammps_water
    self.assertTrue(all([node in hdf_nodes for node in nodes]))
AssertionError: False is not true
----------------------------------------------------------------------

[coveralls]

Pull Request Test Coverage Report for Build 2024

• 28 of 31 (90.32%) changed or added relevant lines in 2 files are covered.
• 52 unchanged lines in 3 files lost coverage.
• Overall coverage decreased (-0.3%) to 69.158%

---

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
pyiron/lammps/base.py	23	26	88.46%

Files with Coverage Reduction	New Missed Lines	%
pyiron/base/job/generic.py	1	60.94%
pyiron/lammps/control.py	1	58.52%
pyiron/base/pyio/parser.py	50	64.86%

Totals
Change from base Build 1999:	-0.3%
Covered Lines:	12250
Relevant Lines:	17713

---

💛 - Coveralls

[jan-janssen]

While I was able to fix the bug above I now get the following error only for Python 2:

======================================================================
ERROR: test_lammps_water (lammps.test_lammps.TestLammps)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/pyiron/pyiron/tests/lammps/test_lammps.py", line 127, in test_lammps_water
    self.job_water.run()
  File "pyiron/base/job/generic.py", line 593, in run
    self._run_if_collect()
  File "pyiron/base/job/generic.py", line 1133, in _run_if_collect
    self.collect_output()
  File "pyiron/lammps/interactive.py", line 371, in collect_output
    super(LammpsInteractive, self).collect_output()
  File "pyiron/lammps/base.py", line 284, in collect_output
    self.collect_output_log(file_name="log.lammps", cwd=self.working_directory)
  File "pyiron/lammps/base.py", line 370, in collect_output_log
    delim_whitespace=True) for llst, llen in zip(l_start, l_end)]
TypeError: initial_value must be unicode or None, not str
----------------------------------------------------------------------

[jan-janssen]

The test on windows fail with the following error message:

700======================================================================
701ERROR: test_lammps_water (lammps.test_lammps.TestLammps)
702----------------------------------------------------------------------
703Traceback (most recent call last):
704  File "C:\projects\pyiron\tests\lammps\test_lammps.py", line 125, in test_lammps_water
705    self.job_water.run()
706  File "pyiron\base\job\generic.py", line 593, in run
707    self._run_if_collect()
708  File "pyiron\base\job\generic.py", line 1133, in _run_if_collect
709    self.collect_output()
710  File "pyiron\lammps\interactive.py", line 371, in collect_output
711    super(LammpsInteractive, self).collect_output()
712  File "pyiron\lammps\base.py", line 287, in collect_output
713    self.collect_output_log(file_name="log.lammps", cwd=self.working_directory)
714  File "pyiron\lammps\base.py", line 365, in collect_output_log
715    self.collect_errors(file_name)
716  File "pyiron\lammps\base.py", line 345, in collect_errors
717    error = extract_data_from_file(file_name, tag="ERROR", num_args=1000)
718  File "pyiron\base\pyio\parser.py", line 71, in extract_data_from_file
719    with open(file_name) as infile:
720IOError: [Errno 22] invalid mode ('r') or filename: u'C:/projects/pyiron/tests/lammps/lammps/lammps_water_hdf5/lammps_water/C:/projects/pyiron/tests/lammps/lammps/lammps_water_hdf5/lammps_water/log.lammps'
721
722----------------------------------------------------------------------
723Ran 347 tests in 74.929s

@sudarsan-surendralal Can you take a look at this?