Error in Structural Optimization of BeO.

[lim520]

Dear Dr.Jochym

I was trying to optimize the structure for BeO and was encountering following errors.

In [12]:

print "Stress tensor (Voigt notation, GPa):\n", cryst.get_stress()/GPa

Print also the forces (eV/A)

print "\nForces on atoms (eV/A)"

print "======================"

print cryst.get_forces()

---

ValueError Traceback (most recent call last)

in () ----> 1 print "Stress tensor (Voigt notation, GPa):\n", cryst.get_stress()/GPa 2 3 # Print also the forces (eV/A) 4 5 print "\nForces on atoms (eV/A)" /home/ras256/nipy/lib/python2.7/site-packages/ase/atoms.pyc in get_stress(self, voigt) 701 raise RuntimeError('Atoms object has no calculator.') 702 --> 703 stress = self._calc.get_stress(self) 704 shape = stress.shape 705 /home/ras256/nipy/lib/python2.7/site-packages/ase/calculators/calculator.pyc in get_stress(self, atoms) 353 354 def get_stress(self, atoms=None): --> 355 return self.get_property('stress', atoms).copy() 356 357 def get_dipole_moment(self, atoms=None): /home/ras256/nipy/lib/python2.7/site-packages/ase/calculators/calculator.pyc in get_property(self, name, atoms) 381 if name not in self.results: 382 try: --> 383 self.calculate(atoms, [name], system_changes) 384 except Exception: 385 self.reset() /home/ras256/nipy/lib/python2.7/site-packages/qeutil/**init**.pyc in calculate(self, atoms, properties, system_changes) 140 141 self.command=self.build_command(properties,self.parameters) --> 142 self.run_calculation(atoms, properties, system_changes) 143 144 # if {'energy','stress'} & set(properties) : /home/ras256/nipy/lib/python2.7/site-packages/qeutil/**init**.pyc in run_calculation(self, atoms, properties, system_changes) 377 raise RuntimeError('%s returned an error: %d' % 378 (self.name, errorcode)) --> 379 self.read_results() 380 381 /home/ras256/nipy/lib/python2.7/site-packages/qeutil/**init**.pyc in read_results(self) 408 if ln.find('JOB DONE.')>-1 : 409 # Job is done we can read the output --> 410 r=read_quantumespresso_textoutput(fn) 411 self.results['energy']=r['etotal']/Rydberg 412 s=array(r['stress'])\* 1e-1 \* ase.units.GPa /home/ras256/nipy/lib/python2.7/site-packages/qeutil/qeio.pyc in read_quantumespresso_textoutput(filename, verbose) 282 number = len(CAUGHT_LINES) 283 for n in range(number): --> 284 Results['kpts'].append([float(get_number(el)) for el in CAUGHT_LINES[n].split()[4:7]]) 285 Results['kpts_wk'].append([float(CAUGHT_LINES[n].split()[9])]) 286 ValueError: could not convert string to float: e Stress tensor (Voigt notation, GPa): Please look in to this and help me. With regards Linu M

[jochym]

Have you checked if the relevant calculations converged and produced correct output in the calculation directory. The error looks like a problem with the data left after the calculation. Check the .out and CRASH files. To really debug this I would need access to the .out files for the calculation (even better to a whole calculation directory).

[lim520]

Thank you for your reply. I have checked the calculations and i see no crash file in the directory. I have emailed you the relevant files. Please have a look.

[lim520]

Dear Dr Jochym

Please find the attached files

With regards Linu Malakkal

On Fri, Mar 21, 2014 at 5:32 AM, Paweł T. Jochym notifications@github.comwrote:

Have you checked if the relevant calculations converged and produced correct output in the calculation directory. The error looks like a problem with the data left after the calculation. Check the .out and CRASH files. To really debug this I would need access to the .out files for the calculation (even better to a whole calculation directory).

— Reply to this email directly or view it on GitHubhttps://github.com/jochym/qe-util/issues/2#issuecomment-38267989 .

[jochym]

W dniu 21.03.2014 21:55, lim520 pisze:

Dear Dr Jochym

Please find the attached files

Dear Linu !

I have found some time to look over the out files from your calculation. It looks like the calculation never finished properly. There is no final concluding line and the output is broken mid-iteration. This is an immediate reason for the error message.

Try to find out why the calculation stopped. Check the queuing system output files for the clues. If you got lost you can send me the output and I will try to help.

I have noticed you have closed the issue on github. Was it intentional or accidental? If you would like to keep working on it just re-open the issue.

Regards, P.

Paweł T. Jochym Institute of Nuclear Physics, PAN Cracow, Poland