[ase-users] Fwd: EIQMMM with turbomole stops

Sun Nov 10 13:57:56 CET 2019

Dear Daria,

Versions 6.2 and 6.3 are very old that might not have the keyword $point_charges or the keyword is supported but has different parameters. The turbomole calculator was substantially extended two or three years ago with turbomole versions 6.6 and 7.0. On the turbomole website there is no documenation for 6.2 and 6.3 and these versions seem to be unsupported. Therefore, I would recommend that you use turbomole >= 6.6 if you want to use it with ASE. Alternatively (not recommended) you can make own local modifications in the turbomole calculator to make it work.

Best regards,
Ivan

Von: Daria Tombolelli <tombolelli.daria at gmail.com>
Gesendet: Sonntag, 10. November 2019 13:14
An: Kondov, Ivan (SCC)
Cc: ase-users at listserv.fysik.dtu.dk; Asmus Ougaard Dohn
Betreff: Re: [ase-users] Fwd: EIQMMM with turbomole stops

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

 -- 

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