Xtb contribution#711
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pmrv
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pmrv
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Thanks for the contribution! I've left some nits below, but looks generally good.
| def from_hdf(self, hdf=None, group_name=None): | ||
| super(FitsnapJob, self).from_hdf(hdf=hdf, group_name=group_name) | ||
| super(FitsnapJob, self).from_hdf(hdf=hdf, group_name=group_name) No newline at end of file |
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I didn't see this in the original PR, but this shouldn't be necessary if you're just calling super() anyway. Is there something weird going on, that made it necessary? If so we should look closer to the source.
| from xtb.ase.calculator import XTB | ||
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| @contextlib.contextmanager | ||
| def make_temp_directory(prefix=None): |
| outstring = '{}\n\n'.format(len(ase_atoms)) | ||
| for atom in ase_atoms: | ||
| outstring += '{} {} {} {}\n'.format(atom.symbol, | ||
| atom.position[0], | ||
| atom.position[1], | ||
| atom.position[2]) | ||
| outstring = outstring.strip('\n') | ||
| return outstring |
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Using StringIO and ase_atoms.write() should work as well, or are you specifically trying to surpress the cell dimensions in the output?
| if (self['output'] is not None) and ('xtb' in self['output'].list_groups()) and \ | ||
| (self.resultsdf.shape[0] == 0): | ||
| self.resultsdf = pd.read_hdf(self.project_hdf5.file_name, | ||
| key=self.job_name+'/output/xtb') No newline at end of file |
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I think writing/reading dataframes directly to hdf should work, but disregard if you've tried that.
| ase_atoms.get_total_energy() | ||
| except: | ||
| pass | ||
| if len(ase_atoms.calc.results) > 0: |
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Should set the job.status.aborted in the else clause.
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Added xTB calculator.