[Pw_forum] gipaw calculation with DFT+U missing prefix.hub files
Jia Chen
jiachenchem at gmail.com
Fri Sep 1 17:11:46 CEST 2017
Thank you very much!
On Fri, Sep 1, 2017 at 9:20 AM, Paolo Giannozzi <paolo.giannozzi at uniud.it>
wrote:
> Oh, I see: it happens when there is a single k-point, because in that case
> atomic wavefunctions are just kept in memory and never saved to a buffer.
> Quick-and-dirty solution: in PW/src/orthoatwfc.f90, remove the line
> IF ( nks > 1 ) &
> just before the line
> CALL save_buffer (wfcU, nwordwfcU, iunhub, ik)
>
> Paolo
>
> On Thu, Aug 31, 2017 at 6:52 PM, Jia Chen <jiachenchem at gmail.com> wrote:
>
>> Great, thank you very much. I copy my input file below. It will be very
>> helpful if you can tell anything is incorrect. Appreciate it.
>> ===================================
>> &control
>> calculation = 'scf',
>> restart_mode = 'from_scratch',
>> nstep = 5000,
>> max_seconds = 84000,
>> wf_collect = .TRUE.
>> outdir = './'
>> pseudo_dir = './'
>> /
>> &system
>> ibrav = 0,
>> nat = 32,
>> ntyp = 4,
>> ecutwfc = 100.D0, ! wave function cutoff
>> occupations ='smearing'
>> degauss =0.002
>> nspin = 1
>> spline_ps = .true.
>> lda_plus_u = .TRUE.
>> lda_plus_u_kind = 0
>> Hubbard_U(1) =5.0
>> !Hubbard_J(1,1) = 0.5
>> starting_magnetization(1)=0.0
>> /
>>
>> &electrons
>> electron_maxstep = 200
>> conv_thr = 1.D-8
>> mixing_mode = 'plain'
>> mixing_beta = 0.2D0
>> /
>> &ions
>> /
>>
>> &cell
>> !cell_dynamics = 'bfgs'
>> !press = 0.00
>> /
>>
>> CELL_PARAMETERS {angstrom}
>> 7.0009999275 0.0000000000 0.0000000000
>> 0.0000000000 10.3559999466 0.0000000000
>> -2.5006805806 <(500)%20680-5806> 0.0000000000 7.
>> 9845650713 <(984)%20565-0713>
>>
>> ATOMIC_SPECIES
>> Co 1.00 Co.pbe-sp-mt_gipaw.UPF
>> K 1.00 K.pbe-tm-semi-gipaw-xy.UPF
>> N 1.00 N.pbe-tm-new-gipaw-dc.UPF
>> C 1.00 C.pbe-tm-new-gipaw-dc.UPF
>>
>>
>> ATOMIC_POSITIONS {Angstrom}
>> Co 0.000000000 5.177999973 0.000000000
>> Co -1.250340290 0.000000000 3.992282536
>> K 3.203347102 7.930935236 1.002222654
>> K 1.296972208 2.425064711 6.982342536
>> K 2.547312498 2.752935263 2.990060000
>> K 1.953006849 7.603064684 4.994505071
>> K 0.000000000 0.000000000 0.000000000
>> K -1.250340290 5.177999973 3.992282536
>> C 0.772793234 5.709262659 1.656797219
>> C 3.727526180 4.646737288 6.327767971
>> C 4.977866470 0.531262686 2.335485436
>> C -0.477547019 9.824737261 5.649079636
>> C 5.430639095 4.620847312 0.905449658
>> C -0.930319681 5.735152634 7.079115532
>> C 0.320020609 9.798847286 3.086832997
>> C 4.180298842 0.557152661 4.897732075
>> C 0.767450404 3.443370093 0.227560105
>> C 3.732869202 6.912630162 7.757004803
>> C 4.983209418 8.621369758 3.764722505
>> C -0.482889937 1.734629880 4.219842804
>> N 1.250821945 6.012693810 2.634107989
>> N 3.249497685 4.343306137 5.350456844
>> N 4.499837901 0.834693837 1.358174546
>> N 0.000481581 9.521306110 6.626390763
>> N 4.491633074 4.281170320 1.449198582
>> N 0.008686519 6.074829627 6.535366370
>> N 1.259026809 9.459170293 2.543083834
>> N 3.241292747 0.896829654 5.441481237
>> N 1.260714400 2.488546784 0.387251417
>> N 3.239605156 7.867453162 7.597313654
>> N 4.489945446 7.666546758 3.605031118
>> N 0.010374109 2.689453189 4.379533953
>> K_POINTS automatic
>> 1 1 1 0 0 0
>>
>>
>> On Thu, Aug 31, 2017 at 8:50 AM, Davide Ceresoli <davide.ceresoli at cnr.it>
>> wrote:
>>
>>> I will also do some tests, but I'm busy in the next few days.
>>> D.
>>>
>>> On 08/31/2017 07:54 AM, Paolo Giannozzi wrote:
>>> > Unfortunately there isn't much that can be done unless the problem you
>>> mention
>>> > is reproduced
>>> >
>>> > On Wed, Aug 30, 2017 at 11:42 PM, Jia Chen <jiachenchem at gmail.com
>>> > <mailto:jiachenchem at gmail.com>> wrote:
>>> >
>>> > what happened to me on four different machines when nspin = 1 is
>>> that
>>> > prefix.hub files were created, but they are empty. One machine is
>>> Cori of
>>> > nersc, and QE was the compiled by staffs there.
>>> >
>>> > On Wed, Aug 30, 2017 at 4:15 PM, Paolo Giannozzi <
>>> p.giannozzi at gmail.com
>>> > <mailto:p.giannozzi at gmail.com>> wrote:
>>> >
>>> > It works for me on a simple test also for nspin=1
>>> >
>>> > Paolo
>>> >
>>> > On Wed, Aug 30, 2017 at 6:41 PM, Jia Chen <
>>> jiachenchem at gmail.com
>>> > <mailto:jiachenchem at gmail.com>> wrote:
>>> >
>>> > Thank you very much for this! The special something in my
>>> > calculation is npsin = 1, when it is 2, prefix.hub files
>>> were written.
>>> >
>>> > Cheers
>>> > Jia
>>> >
>>> > On Wed, Aug 30, 2017 at 3:02 AM, Paolo Giannozzi
>>> > <p.giannozzi at gmail.com <mailto:p.giannozzi at gmail.com>>
>>> wrote:
>>> >
>>> > I was actually confusing the *.hub files (containing
>>> atomic
>>> > wavefunctions) with the "occup" file, containing
>>> occupancies of
>>> > the Hubbard manifold. Anyway: files *hub are written
>>> at the end
>>> > of the run in normal conditions, so there must be
>>> something
>>> > special about your calculation
>>> >
>>> > Paolo
>>> >
>>> > On Wed, Aug 30, 2017 at 7:45 AM, Jia Chen <
>>> jiachenchem at gmail.com
>>> > <mailto:jiachenchem at gmail.com>> wrote:
>>> >
>>> > Dear Paolo Giannozzi,
>>> >
>>> > I used QE-6.1, and also tried QE-5.4. I checked
>>> prefix.save
>>> > directory, but didn't find prefix.hub files. Is
>>> writing
>>> > prefix.hub files an option can be activated? Thank
>>> you very
>>> > much?
>>> >
>>> > Cheers
>>> >
>>> > On Wed, Aug 30, 2017 at 1:32 AM, Paolo Giannozzi
>>> > <p.giannozzi at gmail.com <mailto:
>>> p.giannozzi at gmail.com>> wrote:
>>> >
>>> > It would help to know which version of the
>>> code you
>>> > used. In recent QE versions "prefix.hub" files
>>> have been
>>> > moved inside the "prefix.save/" directory.
>>> Maybe GIPAW
>>> > is trying to read them from the old location
>>> and the
>>> > empty files you see are just the result of a
>>> fortran
>>> > open of nonexistent files
>>> >
>>> > Paolo
>>> >
>>> > On Wed, Aug 30, 2017 at 5:24 AM, Jia Chen
>>> > <jiachenchem at gmail.com <mailto:
>>> jiachenchem at gmail.com>>
>>> > wrote:
>>> >
>>> > Dear All,
>>> >
>>> > I am not sure if this is a good place to
>>> ask this
>>> > question, but since gipaw depends on QE, I
>>> might try
>>> > my luck here. I am trying to do nmr
>>> calculation with
>>> > gipaw based on DFT+U. The calculation
>>> ended on a
>>> > error message of missing prefix.hub files.
>>> Pwscf
>>> > actually created prefix.hub files with
>>> DFT+U, but
>>> > those file are empty. I hope gipaw experts
>>> here can
>>> > help me with this issue. Appreciate it.
>>> >
>>> > Cheers
>>> > Jia Chen
>>> >
>>> > _____________________________
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>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > Paolo Giannozzi, Dip. Scienze Matematiche
>>> Informatiche e
>>> > Fisiche,
>>> > Univ. Udine, via delle Scienze 208, 33100
>>> Udine, Italy
>>> > Phone +39-0432-558216
>>> <tel:+39%200432%20558216>, fax
>>> > +39-0432-558222 <tel:+39%200432%20558222>
>>> >
>>> >
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>>> >
>>> > --
>>> > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche
>>> e Fisiche,
>>> > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>>> > Phone +39-0432-558216 <tel:+39%200432%20558216>, fax
>>> > +39-0432-558222 <tel:+39%200432%20558222>
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>>> >
>>> >
>>> > --
>>> > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e
>>> Fisiche,
>>> > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>>> > Phone +39-0432-558216 <tel:+39%200432%20558216>, fax
>>> +39-0432-558222
>>> > <tel:+39%200432%20558222>
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>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > 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
>>> >
>>>
>>> --
>>> +--------------------------------------------------------------+
>>> Davide Ceresoli
>>> CNR Institute of Molecular Science and Technology (CNR-ISTM)
>>> c/o University of Milan, via Golgi 19, 20133 Milan, Italy
>>> Email: davide.ceresoli at cnr.it
>>> Phone: +39-02-50314276, +39-347-1001570 (mobile)
>>> Skype: dceresoli
>>> Website: http://sites.google.com/site/dceresoli/
>>> +--------------------------------------------------------------+
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>>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
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>>
>
>
>
> --
> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216 <+39%200432%20558216>, fax +39-0432-558222
> <+39%200432%20558222>
>
>
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