[QE-users] Si Band Calculation
Paolo Giannozzi
p.giannozzi at gmail.com
Wed Apr 24 22:27:35 CEST 2019
Jason, if the code says "error opening xml data file", either the data
file is not there, or it is there but not readable or it is corrupted. Your
version of QE is old and nobody has the time (nor the possibility) to
figure out what happens and why. You might locate where the error is issued
(with "grep 'error opening xml data file' */*f90 */*/*f90"), print there
the full file name and issue a command as in "CALL shell ('/bin/ls -l
'//filename)".
Please also note that the directory name reprinted by the code: /scratch/
382082.sunbird.chem.wisc.edu/silicon.save looks like
a temporary directory created by the batch queue.
Paolo
On Mon, Apr 22, 2019 at 5:29 AM JASON M SCHEELER <jscheeler at wisc.edu> wrote:
> Hi Oleksander,
>
> Thanks for the response. To perform calculations I connect to the
> supercomputing cluster here at my university through an ssh client.
> Whenever I do a calculation, an output file (which I believe is the xml
> data file you are referring to, right?) automatically gets generated in the
> output directory. Right before performing the bands calculation, I double
> checked that the xml file generated from the scf calculation is in the
> directory and I still get the same error message. Any other suggestions on
> what could be causing this error?
>
> Regards,
> Jason
>
> On Thu, Apr 18, 2019 at 5:05 PM Oleksandr Motornyi <
> oleksandr.motornyi at polytechnique.edu> wrote:
>
>> HI Jason,
>>
>> How do you launch your calculation? Do you use a bash script or do it by
>> hand? Are you sure that between scf and bands calculation outdir was not
>> erased for whatever reason? If yes you can then check by yourself that the
>> xml data file indeed exists in the outdir, as every time I experienced this
>> error it meant that there was some mismatch that did not allow the code to
>> find xml file or it was not in the outdir.
>>
>> Best regards,
>>
>> Oleksandr
>>
>> On 18/04/19 23:10, JASON M SCHEELER wrote:
>>
>> Hi Dominik,
>>
>> I didn't specify in my previous message, but the two files do indeed have
>> the same outdir parameter. Any other suggestions on what I could do to get
>> the calculation to work?
>>
>> Jason
>>
>> On Thu, Apr 18, 2019 at 12:59 PM <dv009200 at fh-muenster.de> wrote:
>>
>>> Hi Jason,
>>>
>>> What is your outdir parameter? Is it also the same or have you not
>>> defined
>>> it?
>>>
>>> Regards
>>>
>>> Dominik
>>>
>>>
>>> > Hi all,
>>> >
>>> > I am a new user to QE and I have set out to do some band structure
>>> > calculations on transition metal dichalcogenides (TMDCs). However,
>>> because
>>> > I'm new to QE, I want to start out with some basic calculations to get
>>> my
>>> > feet wet so I can work up to the more-challenging TMDC calculations.
>>> So,
>>> > I've attempted to try scf and bands calculations for Silicon. I can get
>>> > the Si scf calculation to converge, however, when I try the bands
>>> > calculation I get the following error message:
>>> >
>>> > Error in routine pw_readfile (1):
>>> > error opening xml data file
>>> >
>>> > After reading the forums, I've realized this error comes up (1) when a
>>> > bands calculation is attempted prior to an scf calculation, and (2)
>>> when
>>> > the prefix of the scf and bands input files are not the same. I have
>>> > satisfied both of these parameters and still get the error above. I'm
>>> not
>>> > sure what else to try to remedy this problem and get my bands
>>> calculation
>>> > to work. Any help on this problem would be greatly appreciated! Below
>>> are
>>> > the input files for the scf and bands calculation, as well as the
>>> output
>>> > file for the bands calculation where I get the error message. Thanks in
>>> > advance for your time and consideration.
>>> >
>>> > Jason Scheeler
>>> > PhD Student
>>> > University of Wisconsin-Madison
>>> >
>>> > scf input: si_scf.inp
>>> > &control
>>> > calculation = 'scf'
>>> > restart_mode='from_scratch',
>>> > prefix='silicon',
>>> > tstress = .true.
>>> > tprnfor = .true.
>>> > pseudo_dir = 'where psuedopotential files are kept',
>>> > /
>>> > &system
>>> > ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1,
>>> > ecutwfc =18.0,
>>> > /
>>> > &electrons
>>> > diagonalization='david'
>>> > mixing_mode = 'plain'
>>> > mixing_beta = 0.7
>>> > conv_thr = 1.0d-8
>>> > /
>>> > ATOMIC_SPECIES
>>> > Si 28.086 Si.pz-vbc.UPF
>>> > ATOMIC_POSITIONS
>>> > Si 0.00 0.00 0.00
>>> > Si 0.25 0.25 0.25
>>> > K_POINTS
>>> > 10
>>> > 0.1250000 0.1250000 0.1250000 1.00
>>> > 0.1250000 0.1250000 0.3750000 3.00
>>> > 0.1250000 0.1250000 0.6250000 3.00
>>> > 0.1250000 0.1250000 0.8750000 3.00
>>> > 0.1250000 0.3750000 0.3750000 3.00
>>> > 0.1250000 0.3750000 0.6250000 6.00
>>> > 0.1250000 0.3750000 0.8750000 6.00
>>> > 0.1250000 0.6250000 0.6250000 3.00
>>> > 0.3750000 0.3750000 0.3750000 1.00
>>> > 0.3750000 0.3750000 0.6250000 3.00
>>> >
>>> > si bands input: si_bands.inp
>>> > &control
>>> > calculation='bands'
>>> > pseudo_dir = ' where psuedopotential files are kept ',
>>> > prefix='silicon',
>>> > /
>>> > &system
>>> > ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1,
>>> > ecutwfc =18.0, nbnd = 8,
>>> > /
>>> > &electrons
>>> > diagonalization='david'
>>> > /
>>> > ATOMIC_SPECIES
>>> > Si 28.086 Si.pz-vbc.UPF
>>> > ATOMIC_POSITIONS alat
>>> > Si 0.00 0.00 0.00
>>> > Si 0.25 0.25 0.25
>>> > K_POINTS
>>> > 28
>>> > 0.0 0.0 0.0 1.0
>>> > 0.0 0.0 0.1 1.0
>>> > 0.0 0.0 0.2 1.0
>>> > 0.0 0.0 0.3 1.0
>>> > 0.0 0.0 0.4 1.0
>>> > 0.0 0.0 0.5 1.0
>>> > 0.0 0.0 0.6 1.0
>>> > 0.0 0.0 0.7 1.0
>>> > 0.0 0.0 0.8 1.0
>>> > 0.0 0.0 0.9 1.0
>>> > 0.0 0.0 1.0 1.0
>>> > 0.0 0.0 0.0 1.0
>>> > 0.0 0.1 0.1 1.0
>>> > 0.0 0.2 0.2 1.0
>>> > 0.0 0.3 0.3 1.0
>>> > 0.0 0.4 0.4 1.0
>>> > 0.0 0.5 0.5 1.0
>>> > 0.0 0.6 0.6 1.0
>>> > 0.0 0.7 0.7 1.0
>>> > 0.0 0.8 0.8 1.0
>>> >
>>> > si bands output: si_bands.log
>>> > Program PWSCF v.6.0 (svn rev. 13079) starts on 18Apr2019 at
>>> 10:29:38
>>> >
>>> > This program is part of the open-source Quantum ESPRESSO suite
>>> > for quantum simulation of materials; please cite
>>> > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502
>>> (2009);
>>> > URL http://www.quantum-espresso.org",
>>> > in publications or presentations arising from this work. More
>>> details
>>> > at
>>> > http://www.quantum-espresso.org/quote
>>> >
>>> > Serial version
>>> > Waiting for input...
>>> > Reading input from standard input
>>> >
>>> > Current dimensions of program PWSCF are:
>>> > Max number of different atomic species (ntypx) = 10
>>> > Max number of k-points (npk) = 40000
>>> > Max angular momentum in pseudopotentials (lmaxx) = 3
>>> >
>>> > Atomic positions and unit cell read from directory:
>>> > /scratch/382082.sunbird.chem.wisc.edu/silicon.save/<
>>> http://382082.sunbird.chem.wisc.edu/silicon.save/>
>>> >
>>> >
>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>> > Error in routine pw_readfile (1):
>>> > error opening xml data file
>>> >
>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>> >
>>> > stopping ...
>>> >
>>> > _______________________________________________
>>> > Quantum Espresso is supported by MaX (
>>> www.max-centre.eu/quantum-espresso)
>>> > users mailing list users at lists.quantum-espresso.org
>>> > https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>>
>>> _______________________________________________
>>> Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso
>>> )
>>> users mailing list users at lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>
>>
>> _______________________________________________
>> Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso)
>> users mailing list users at lists.quantum-espresso.orghttps://lists.quantum-espresso.org/mailman/listinfo/users
>>
>>
>> --
>> Oleksandr Motornyi
>> PhD candidate
>>
>> Laboratoire de Solides Irradies
>> Ecole Polytechnique (Palaiseau, France)
>>
>> _______________________________________________
>> Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso)
>> users mailing list users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
> _______________________________________________
> Quantum Espresso is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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