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define runner cannot run properly if the coord file only contains one atom. #38

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WentongZhou opened this issue Apr 24, 2023 · 1 comment

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@WentongZhou
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WentongZhou commented Apr 24, 2023

I just ran the codes below to generate control files. Most of them work perfectly, but if the coord only contains one atom, it reports errors.
os.system(f'x2t coord.xyz > coord')
dp_b = get_define_template(ridft_path)
dp_b['charge'] = 1
dr_b = DefineRunner(parameters=dp_b)
dr_b.run_full()

the error is
turbomoleio.input.define.DefineExpectError: Expect could not find the pattern: ['ENTER THE MOLECULAR CHARGE*']. The job was alive.

the coord file is as below:
$coord
-8.60844330793820 7.57371620497213 -8.58652437452286 li
$user-defined bonds
$end

@davidwaroquiers
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Hello @WentongZhou

Thank you for opening this issue. Indeed, the DefineRunner currently does not work for just one atom. We currently don't have the resources to adapt it so that it works with one atom but if'd like to contribute and make a PR, we'd be happy to review it.

Best

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