[ase-users] Fwd: EIQMMM with turbomole stops
Kondov, Ivan (SCC)
ivan.kondov at kit.edu
Sun Nov 10 12:08:08 CET 2019
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
--
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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