[ase-users] Fwd: EIQMMM with turbomole stops

Daria Tombolelli tombolelli.daria at gmail.com
Sun Nov 10 13:14:12 CET 2019 

Dear Ivan,

I will do that for sure but I don't have available the newest version of
turbomole unfortunately. We are using 6.2 and 6.3 (mainly 6.2).

I will send you feedback on the test ASAP.

Best,
Daria

On Sun, 10 Nov 2019, 12:08 Kondov, Ivan (SCC) <ivan.kondov at kit.edu> wrote:

> Dear Daria,
>
> i just tested the qmmm module from the most recent ASE release with the
> most recent Turbomole 7.3.1 and it worked. Would you please install the
> most recent release of ASE (without your modifications!) and run the
> turbomole tests supplied with ASE:
>
> ase test  --jobs=0 --calculators=turbomole turbomole
>
> You should get (together with some more output):
>
> ========== Summary ==========
> Number of tests     7
> Passes:             7
> Failures:           0
> Errors:             0
> Skipped:            0
> =============================
> Test suite passed!
>
>
> 1) If the supplied tests work with the non-modified ASE release then you
> should not modify ase/calculators/turbomole.py.
> There might be another reason for the error that you get. Please send to
> me a minimal script reproducing the error so that I can debug.
>
> 2) If you get failures or errors from the tests then please repeat the
> test with the '--verbose' flag, i.e.
>
> ase test  --verbose --jobs=0 --calculators=turbomole turbomole
>
> Then please collect the output on the screen and send it to me as an
> attachment file.
>
> Best regards,
> Ivan
>
>
>
>
>
>
>
> Von: ase-users-bounces at listserv.fysik.dtu.dk <
> ase-users-bounces at listserv.fysik.dtu.dk> im Auftrag von Daria Tombolelli
> via ase-users <ase-users at listserv.fysik.dtu.dk>
> Gesendet: Montag, 4. November 2019 12:10
> An: Asmus Ougaard Dohn
> Cc: ase-users at listserv.fysik.dtu.dk
> Betreff: Re: [ase-users] Fwd: EIQMMM with turbomole stops
>
>
> Hi,
>
>
> Thank you for your reply.
>
>
> For some reason turbomole was not able to read the charges file (pc.txt)
> because in the file it was written:
>
>
> $point_charges nocheck list
>
>  I changed it in the ase/calculators/turbomole.py in the function
> set_point_charged
> > pcfile.write('$pointcharges\n')
>
>  Might be that the version of Turbomole is the problem?
>
>
> Best,
> Daria
>
>
>
>
> On Mon, 4 Nov 2019 at 10:18, Asmus Ougaard Dohn <asod at hi.is> wrote:
>
>
> Hello Daria,
>
>
> It looks like the point charge file generated by ASE is not read in
> properly by turbomole. Have you had a look at it?
>
>
> Best,
>
>
> Asmus
>
> From: ase-users-bounces at listserv.fysik.dtu.dk <
> ase-users-bounces at listserv.fysik.dtu.dk> on behalf of Daria Tombolelli
> via ase-users <ase-users at listserv.fysik.dtu.dk>
> Sent: Monday, November 4, 2019 8:11 AM
> To: ase-users at listserv.fysik.dtu.dk <ase-users at listserv.fysik.dtu.dk>
> Subject: [ase-users] Fwd: EIQMMM with turbomole stops
>
>
>
>
>
>
>
> Hi all,
>
>
> I am running some test for turbomole with ASE, to run QM/MM calculations
> of a water dimer, that I took from here:
> https://gitlab.com/ase/ase/blob/master/ase/test/turbomole/turbomole_qmmm.py
>
>
> When using calculators from line 26 to 30
>         EIQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(), interaction),
>    EIQMMM([3, 4, 5], Turbomole(**qm_par), TIP3P(), interaction,
>     vacuum=3.0),         EIQMMM([0, 1, 2], Turbomole(**qm_par), TIP3P(),
> interaction,                vacuum=3.0)]
>
>
> I get this error:
>
>
> TM command: "define" successfully executed
> TM command: "kdg" successfully executed
> TM command: "kdg" successfully executed
> TM command: "sdg" successfully executed
> TM command: "sdg" successfully executed
> TM command: "sdg" successfully executed
> TM command: "kdg" successfully executed
> Traceback (most recent call last):
>   File "turbomole_qmmm.py", line 44, in <module>
>     E.append(dimer.get_potential_energy())
>   File
> "/net/work/tombolelli/QMML/ase_env/lib64/python3.6/site-packages/ase/atoms.py",
> line 671, in get_potential_energy
>     energy = self._calc.get_potential_energy(self)
>   File
> "/net/work/tombolelli/QMML/ase_env/lib64/python3.6/site-packages/ase/calculators/calculator.py",
> line 618, in get_potential_energy
>     energy = self.get_property('energy', atoms)
>   File
> "/net/work/tombolelli/QMML/ase_env/lib64/python3.6/site-packages/ase/calculators/calculator.py",
> line 668, in get_property
>     self.calculate(atoms, [name], system_changes)
>   File
> "/net/work/tombolelli/QMML/ase_env/lib64/python3.6/site-packages/ase/calculators/qmmm.py",
> line 191, in calculate
>     qmenergy = self.qmatoms.get_potential_energy()
>   File
> "/net/work/tombolelli/QMML/ase_env/lib64/python3.6/site-packages/ase/atoms.py",
> line 671, in get_potential_energy
>     energy = self._calc.get_potential_energy(self)
>   File
> "/net/work/tombolelli/QMML/ase_env/lib64/python3.6/site-packages/ase/calculators/turbomole.py",
> line 1949, in get_potential_energy
>     execute(self.calculate_energy)
>   File
> "/net/work/tombolelli/QMML/ase_env/lib64/python3.6/site-packages/ase/calculators/turbomole.py",
> line 71, in execute
>     raise err
>   File
> "/net/work/tombolelli/QMML/ase_env/lib64/python3.6/site-packages/ase/calculators/turbomole.py",
> line 69, in execute
>     raise RuntimeError(message)
> RuntimeError: TM command "dscf" execution failed with error:
>  dscf ended abnormally
> program stopped.
>
> See file ASE.TM.dscf.out for details.
>
>
>
> The last lines of the TM command: ASE.TM.dscf.out are:
>
>
>  1e-integrals will be neglected if expon. factor < 0.175893E-09
>
>  i/o-error : input variable is not real
>
>
>  WARNING : <rdebbs> could not read properly from string
> nocheck list
>
>
>  i/o-error : input variable is not real
>
>
>  WARNING : <rdebbs> could not read properly from string
> nocheck list
>
>
>  i/o-error : input variable is not real
>
>
>  WARNING : <rdebbs> could not read properly from string
> nocheck list
>
>
>  i/o-error : input variable is not real
>
>
>  WARNING : <rdebbs> could not read properly from string
> nocheck list
>
>
>  <ptchrd> : input error while reading point charges
>
>
>  MODTRACE: no modules on stack
>
>  fatal erro in ptchrd.
>  dscf ended abnormally
>
>
>
> What could the problem be?
>
>
> Best regards,
> Daria
>
>
> --
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Dr. Daria Tombolelli
> Technische Universität Berlin
> Fakultät II
> Institut für Chemie
> Sekretariat PC 14
> Straße des 17. Juni 135
> 10623 Berlin
>
> E-Mail: daria.tombolelli(at)tu-berlin.de
>
>
>
>
>
> Researchgate
>
> Raum: SE-RH 108
>
> wiss. Mitarbeiterin in der Arbeitsgruppe Prof. Dr. M. Mroginski
> http://www.modeling.tu-berlin.de
>
>
>
>
>
>
>
>
>
>
>  --
>
>
>
>
>
>
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>
>
>
>
>
> Dr. Daria Tombolelli
> Technische Universität Berlin
> Fakultät II
> Institut für Chemie
> Sekretariat PC 14
> Straße des 17. Juni 135
> 10623 Berlin
>
> E-Mail: daria.tombolelli(at)tu-berlin.de
>
>
>
>
>
> Researchgate
>
> Raum: SE-RH 108
>
> wiss. Mitarbeiterin in der Arbeitsgruppe Prof. Dr. M. Mroginski
> http://www.modeling.tu-berlin.de
>
>
>
>
>
>
>
>
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