[Pw_forum] GPU14.03 compiling error

[Filippo Spiga]

Patches has to be regenerated or it is simply possible to skip to compile one 
file that works only with the SVN version of the code. I will fix this issue 
during this weekend. I apologize for the trouble

F

On Apr 3, 2014, at 11:18 AM, ???  wrote:

> dear all,
> happy to see that GPU 14.03 has been released, so
> i tried to compile it for calculation.
> i just followed the instructions in the README file and added few
> manual DFLAGS and make.
> but during the process, it failed with such an error:
> Fatal error: cannot open mudule file 'mp_bands.mod' for reading.
> i cannot figure out its reasons.
> need  your help
> thanks.
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--
Mr. Filippo SPIGA, M.Sc.
http://www.linkedin.com/in/filippospiga ~ skype: filippo.spiga

?Nobody will drive us out of Cantor's paradise.? ~ David Hilbert

*
Disclaimer: "Please note this message and any attachments are CONFIDENTIAL and 
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[Pw_forum] Fwd: Ag.pbe-dn-rrkjus_psl.0.1.UPF

[fatih.er...@adu.edu.tr]

Dear Andrea and Filipe, 

Thanks for your helps. As i understand this PP is suitable for only Ag 
surfaces. 

Sincerely yours. 

Fatih 

- Original Message -





- Original Message -

From: "Filipe Camargo Dalmatti Alves Lima"  
To: dalcorso at sissa.it, "PWSCF Forum"  
Sent: Friday, April 4, 2014 3:56:29 PM 
Subject: Re: [Pw_forum] Ag.pbe-dn-rrkjus_psl.0.1.UPF 

Dear Faith, 

This paper has been published using Ag surfaces and QE pseudopotentials: 
Structure and Molecule?Substrate Interaction in a Co-octaethyl Porphyrin 
Monolayer on the Ag(110) Surface 
http://pubs.acs.org/doi/abs/10.1021/jp2011233 

It might help you designing your own system. 

Best, 

Filipe 




On Fri, Apr 4, 2014 at 9:23 AM, Andrea Dal Corso < dalcorso at sissa.it > 
wrote: 


As far as I know, this Ag PP is working, and should be fine for Ag 
surfaces. 

Andrea 


On Fri, 2014-04-04 at 13:15 +0300, fatih.ersan at adu.edu.tr wrote: 
> Dear A. Dal Corso: 
> 
> I want to use Ag atoms for my study, when i'm searching suitable 
> pseudo-potentials(pp), i met Ag.pbe-dn-rrkjus_psl.0.1.UPF which has 
> config='[Kr] 4d9.5 5s1.5 5p0.0'electronic configurations. Is your scope to 
> generate this potential to examine catalytic activities or something like 
> this? Can i use this PP to adsorb on any sheet? Could you help me for me to 
> understand? 
> 
> Best wishes 
> 
> Fatih 
> ___ 
> Pw_forum mailing list 
> Pw_forum at pwscf.org 
> http://pwscf.org/mailman/listinfo/pw_forum 

-- 
Andrea Dal Corso Tel. 0039-040-3787428 
SISSA, Via Bonomea 265 Fax. 0039-040-3787249 
I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it 


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-- 
_ 
Filipe Camargo Dalmatti Alves Lima 
PhD Student 
University of S?o Paulo, Physics Institute, Materials Physics Department, 
Nanomol Group, Brazil. 
Phones: (11) 3091-6881 (USP) 
(11) 97408-2755 (Vivo) 

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[Pw_forum] Problem with PDOS of ionic crystals

[Alexander G. Kvashnin]

3A%2F%2Fwww.ntcstm.troitsk.ru%2F&sn=>142190,
>> Central'naya St. 7a, Troitsk, Moscow Region,
>> Russia=*
>>
>>
>>
>>
>> Dear Alexander,
>>
>> inside the pdos output file you should find, for EACH eigenvalue at EACH
>> k-point the decomposition of
>> the wave function, together with the sum of the square modulus of the
>> expansion coefficients.
>>
>> What you should notice is that, while for occupied states |psi|^2 =
>> 1.000, the coefficient square moduli do
>> not sum up to 1, as you move to high energy unoccupied states.
>>
>> Should the basis set used for the projection be orthogonal and complete,
>> that should not occur. However,
>> the code, as far as I remember, is only able to project onto the atomic
>> orbitals included in the pseudo potentials.
>>
>> Therefore, while the bands, even though unoccupied, are correctly (at DFT
>> level!) computed, the projection onto
>> the atomic orbitals might not be enough because would require atomic
>> orbitals (e.g. d states) not included
>> in the pseudo. The result is that the sum of the partial dos is LESS than
>> the (correct) total DOS.
>>
>> Giovanni
>>
>> --
>>
>> Giovanni Cantele, PhD
>> CNR-SPIN
>> c/o Dipartimento di Fisica
>> Universita' di Napoli "Federico II"
>> Complesso Universitario M. S. Angelo - Ed. 6
>> Via Cintia, I-80126, Napoli, Italy
>> e-mail: giovanni.cantele at spin.cnr.it
>> Phone: +39 081 676910
>> Skype contact: giocan74
>>
>> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
>> Web page: http://people.na.infn.it/~cantele
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> e-mail: giovanni.cantele at spin.cnr.it
> Phone: +39 081 676910
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>
>
> ___
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>



-- 
*Sincerely yours,*

*Alexander G. Kvashnin *


*=PhD Student Moscow
Institute of Physics and Technology  http://mipt.ru/
<http://s.wisestamp.com/links?url=http%3A%2F%2Fmipt.ru%2F&sn=>*
*141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia*





*Junior research scientistTechnological Institute for Superhard and Novel
Carbon Materialshttp://www.tisnum.ru/
<http://s.wisestamp.com/links?url=http%3A%2F%2Fwww.tisnum.ru%2F&sn=>
<http://s.wisestamp.com/links?url=http%3A%2F%2Fwww.ntcstm.troitsk.ru%2F&sn=>142190,
Central'naya St. 7a, Troitsk, Moscow Region,
Russia=*
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[Pw_forum] projected band structure and Fermi surface calculation

[Pietro Bonfa']

Dear Dr. Peng Chen,

you are right, thanks. I will change to code according to your
suggestion as soon as I can.

Best regards,
Pietro Bonfa'

On 04/02/2014 07:41 PM, Peng Chen wrote:
> Dear Bonfa',
> 
> Thank you for providing the code, it is really helpful. I think the
> codes "  if nspin > 1 : ..." need to be changed for the noncollinear
> case. In this case, nspin=4, but there is no spin component part in the
> xml file. 
> 
> 
> 
> 
> On Tue, Apr 1, 2014 at 3:22 PM, Pietro Bonfa'  > wrote:
> 
> Dear Dr. Peng Chen,
> 
> I made a very simple python script that parses projwfc.x xml output (a
> file that is called atomic_proj.xml in the outdir directory) and writes
> atomic orbital contributions to the eigenfunction at each kpoint (and
> eigenvalues too).
> I uploaded it here: https://gitorious.org/qe-stuff/aopbs/
> 
> You can use it to produce the kind of figures attached (Fe orbitals in
> simple cubic Fe).
> I used this script just for debugging purposes and never for data
> analysis. Please check if it gives reliable outputs before using it.
> 
> To get the figure attached you need to run a band structure calculation
> and then use the projwfc.x postprocessing tool.
> My script is very badly documented but it should easy to understand.
> 
> If you find errors please let me know.
> 
> Best regards,
> Pietro Bonfa'
> 
> 
> 
> On 03/31/2014 09:43 PM, Peng Chen wrote:
> > Dear QE users,
> >
> > Is it possible to project band structure onto atoms like projected
> DOS?
> > Eg. for the slab calculation, I am interested in how much the first
> > layer atoms contributes to the surface band. For the heretostructure 1
> > monolayer A+substrate B, I am wondering how much A atoms contribute to
> > the interface band structure. I tried k-resolved DOS, but the result
> > image is too fuzzy to identify the bands. Any suggestions are greatly
> > appreciated!
> >
> > Another problem is related to Fermi surface calculation. Can I
> calculate
> > Fermi surface for a slab? I followed example08, but always get error:
> >  Error in routine irrek_nc (1):
> >  Internal problem with k points
> > I think the only difference is that bulk is used in example08.
> >
> >
> > ___
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> > http://pwscf.org/mailman/listinfo/pw_forum
> >
> 
> 
> --
> Pietro Bonfa' - PhD student
> Dipartimento di Fisica e Scienze della Terra "Macedonio Melloni"
> Viale delle Scienze 7A
> 43124 Parma - Italy
> 
> ___
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> http://pwscf.org/mailman/listinfo/pw_forum
> 
> 
> 
> 
> ___
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> http://pwscf.org/mailman/listinfo/pw_forum
> 


-- 
Pietro Bonfa' - PhD student
Dipartimento di Fisica e Scienze della Terra "Macedonio Melloni"
Viale delle Scienze 7A
43124 Parma - Italy

[Pw_forum] Gibbs Free energy

[Saied Md Pratik]

Hi All
  After running QHA (implemented in Quantum espresso) I have got
E_internal,F_vibration, Specific heat (C_v), Entropy etc. Does F_vibration
correspond to Helmholtz free energy? If so, Can anybody  please tell me
that how can I calculate Gibbs free energy?
  Thanks in advance.
  Pratik
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[Pw_forum] Gibbs Free energy

[Paolo Giannozzi]

On Fri, 2014-04-04 at 16:58 +0530, Saied Md Pratik wrote:

>   After running QHA (implemented in Quantum espresso) I have got
> E_internal,F_vibration, Specific heat (C_v), Entropy etc. Does
> F_vibration correspond to Helmholtz free energy? 

it is the vibrational contribution to the Helmholtz free energy

> If so, Can anybody  please tell me  that how can I calculate Gibbs
> free energy?

G=F+PV

"Even within physics, I see an important death. Thermodynamics,
essential to so much thinking in biology, is a dying language." 
Harness the Hubris: Useful Things Physicists Could Do in Biology
V. Adrian Parsegian, Physics Today, June 1997

P.
>   Thanks in advance.
> 
>   Pratik
> 
> ___
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-- 
 Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
 Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
 Phone +39-0432-558216, fax +39-0432-558222 

[Pw_forum] Problem with PDOS of ionic crystals

[Alexander G. Kvashnin]

S than
> the (correct) total DOS.
>
> Giovanni
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> e-mail: giovanni.cantele at spin.cnr.it
> Phone: +39 081 676910
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>
>
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[Pw_forum] Problem with PDOS of ionic crystals

[Giovanni Cantele]

s I remember, is only able to project onto the atomic 
> orbitals included in the pseudo potentials.
> 
> Therefore, while the bands, even though unoccupied, are correctly (at DFT 
> level!) computed, the projection onto
> the atomic orbitals might not be enough because would require atomic orbitals 
> (e.g. d states) not included
> in the pseudo. The result is that the sum of the partial dos is LESS than the 
> (correct) total DOS.
> 
> Giovanni
> 
> -- 
> 
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> e-mail: giovanni.cantele at spin.cnr.it
> Phone: +39 081 676910
> Skype contact: giocan74
> 
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
> 
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
> 
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

-- 

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cantele at spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele

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[Pw_forum] Ag.pbe-dn-rrkjus_psl.0.1.UPF

[Andrea Dal Corso]

As far as I know, this Ag PP is working, and should be fine for Ag
surfaces. 

Andrea


On Fri, 2014-04-04 at 13:15 +0300, fatih.ersan at adu.edu.tr wrote:
> Dear A. Dal Corso:
> 
> I want to use Ag atoms for my study, when i'm searching suitable 
> pseudo-potentials(pp), i met Ag.pbe-dn-rrkjus_psl.0.1.UPF which has 
> config='[Kr] 4d9.5 5s1.5 5p0.0'electronic configurations. Is your scope to 
> generate this potential to examine catalytic activities or something like 
> this? Can i use this PP to adsorb on any sheet? Could you help me for me to 
> understand?
> 
> Best wishes
> 
> Fatih
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

-- 
Andrea Dal CorsoTel. 0039-040-3787428
SISSA, Via Bonomea 265  Fax. 0039-040-3787249
I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it

[Pw_forum] Incorrect magnetic moment from PWSCF

[anyy zsj]

Thank you for your reply!


The results I used to compare are values given in Bohr mag/cell as
output of PWSCF. However, the obtained value is always higher compare
to literature. Actually, I can reproduce the results with vasp code.
So the only problem seems to be the pseudopotential. The
pseudopotential I employed is *.pbe-mt_fhi.UPF. Is there some problem
with these potentials? Or is there PAW pseudopotential for PWSCF to
use?




2014-04-04 0:29 GMT+08:00 Ari P Seitsonen :
>
>
> Dear An,
>
>   Could you please tell some more details: How do you evaluate the magnetic 
> moment (total moment of the cell, per atom Ti atom, from projected density of 
> states, from L?wdin analysis, ..., is the system ferromagnetic, 
> anti-ferromagnetic, ...), a good reference to the earlier literature, and 
> possibly the full input, with atomic coordinates so that we others could try 
> to reproduce the problem, if needed.
>
>   Based on this partial input it is somewhat difficult to judge, as we don't 
> know which pseudo potentials/PAW dataset you are using etc.
>
> Greetings from Zurich,
>
>apsi
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>   Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
>   Institut f?r Chemie der Universit?t Z?rich, CH-8057 Z?rich
>   Tel: +41 44 63 54 497  /  Mobile: +41 79 71 90 935
>
>
>
> On Thu, 3 Apr 2014, anyy zsj wrote:
>
>> Hello everyone:
>> Recently I calculated the magnetic moment of a system which has a
>> hexagonal lattice. However, the results obtained from PWSCF
>> calculations are always bigger than that from literatures (about 2
>> times bigger). I tried many parameters such starting_magnetism and
>> tot_magnetism but still cannot get the correct results. Please give me
>> some advice about this. Thank you!
>> Below is my input file with norm-conserved pseudopotentials:
>>
>> &control
>>calculation = 'scf'
>>restart_mode='from_scratch'
>>prefix='Ti2C'
>>pseudo_dir = './'
>>outdir = './'
>> /
>> &system
>>ibrav = 4
>>a = 4.20
>> c = 20.2
>> nat = 3
>>ntyp = 2
>>ecutwfc = 50.0
>>   occupations = 'smearing'
>>smearing = 'm-p'
>>degauss = 0.001
>>   nspin=2,
>>starting_magnetization(1)= 0.2
>> /
>> &electrons
>>electron_maxstep = 5000
>>diagonalization='david'
>>mixing_mode = 'plain'
>>mixing_beta = 0.7
>> /
>>
>>
>> An
>> Postdoc
>> Peking University
>> ___
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>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
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[Pw_forum] Ag.pbe-dn-rrkjus_psl.0.1.UPF

[fatih.er...@adu.edu.tr]

Dear A. Dal Corso:

I want to use Ag atoms for my study, when i'm searching suitable 
pseudo-potentials(pp), i met Ag.pbe-dn-rrkjus_psl.0.1.UPF which has 
config='[Kr] 4d9.5 5s1.5 5p0.0'electronic configurations. Is your scope to 
generate this potential to examine catalytic activities or something like this? 
Can i use this PP to adsorb on any sheet? Could you help me for me to 
understand?

Best wishes

Fatih

[Pw_forum] Problem with PDOS of ionic crystals

[Alexander G. Kvashnin]

I am sorry, I forgot to attached my calculated DOS. Here I attached a
picture with my obtained DOS, where you can see that there is no
contributions from both Na and Cl to the conduction band region.

* --*

*Sincerely yours,*
*Alexander G. Kvashnin *


*=PhD Student Moscow
Institute of Physics and Technology  http://mipt.ru/
<http://s.wisestamp.com/links?url=http%3A%2F%2Fmipt.ru%2F&sn=>*
*141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia*





*Junior research scientistTechnological Institute for Superhard and Novel
Carbon Materialshttp://www.tisnum.ru/
<http://s.wisestamp.com/links?url=http%3A%2F%2Fwww.tisnum.ru%2F&sn=>
<http://s.wisestamp.com/links?url=http%3A%2F%2Fwww.ntcstm.troitsk.ru%2F&sn=>142190,
Central'naya St. 7a, Troitsk, Moscow Region,
Russia=*


On 4 April 2014 12:43, Alexander G. Kvashnin  wrote:

> Dear QE users,
>
> I tried to calculate PDOS for simple cubic NaCl structure. I performed an
> optimization vc-relax with 6x6x6 k-points, than I made scf calculations,
> nscf calculations and after that I ran projwfc to plot PDOS.
> My question is why when I plotted DOS_Na+DOS_Cl it differs from the total
> DOS for whole system, specially in conduction band?
>
> Here is my nscf file and input file for projfwc:
>
>  &control
> calculation='nscf'
> restart_mode='restart',
> tstress = .true.
> tprnfor = .true.
> prefix='nacl',
> pseudo_dir = '.',
> outdir='.',
> nstep = 200
>  /
>  &system
> nosym = .false.,
>  ibrav = 1,
>  nat = 4,
>  ntyp = 2,
>  ecutwfc = 30,
>  celldm(1) = 10.750047341391399,
>  occupations = 'tetrahedra',
>  /
>  &electrons
> conv_thr =  1.0d-8
> mixing_beta = 0.7
> electron_maxstep = 300
>  /
> ATOMIC_SPECIES
>  Na22.9897Na.pbe-sp-van_ak.UPF
>  Cl35.4527Cl.pbe-n-van.UPF
> ATOMIC_POSITIONS  crystal
> Na  -0.5  -0.5   0.0
> Na  -0.5   0.0  -0.5
> Cl  -0.5   0.0   0.0
> Cl  -0.5  -0.5  -0.5
> Cl   0.0  -0.5   0.0
> Cl   0.0   0.0  -0.5
> Na   0.0   0.0   0.0
> Na   0.0  -0.5  -0.5
> K_POINTS automatic
>  6 6 6  0 0 0
>
>  &inputpp
> outdir='./'
> prefix='nacl'
> ngauss=1, degauss=0.02
> DeltaE=0.05
> Emin=-15.0, Emax=15.0,
> filpdos='nacl.k'
>  /
>
>
> Any suggestion are welcome!
> Thank you in advance!
>
> * --*
>
> *Sincerely yours,*
> *Alexander G. Kvashnin *
>
>
> *=PhD Student Moscow
> Institute of Physics and Technology  http://mipt.ru/
> <http://s.wisestamp.com/links?url=http%3A%2F%2Fmipt.ru%2F&sn=>*
> *141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia*
>
>
>
>
>
> *Junior research scientistTechnological Institute for Superhard and Novel
> Carbon Materialshttp://www.tisnum.ru/
> <http://s.wisestamp.com/links?url=http%3A%2F%2Fwww.tisnum.ru%2F&sn=>
> <http://s.wisestamp.com/links?url=http%3A%2F%2Fwww.ntcstm.troitsk.ru%2F&sn=>142190,
> Central'naya St. 7a, Troitsk, Moscow Region,
> Russia=====*
>
>
>
>
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[Pw_forum] Problem with PDOS of ionic crystals

[Alexander G. Kvashnin]

Dear QE users,

I tried to calculate PDOS for simple cubic NaCl structure. I performed an
optimization vc-relax with 6x6x6 k-points, than I made scf calculations,
nscf calculations and after that I ran projwfc to plot PDOS.
My question is why when I plotted DOS_Na+DOS_Cl it differs from the total
DOS for whole system, specially in conduction band?

Here is my nscf file and input file for projfwc:

 &control
calculation='nscf'
restart_mode='restart',
tstress = .true.
tprnfor = .true.
prefix='nacl',
pseudo_dir = '.',
outdir='.',
nstep = 200
 /
 &system
nosym = .false.,
 ibrav = 1,
 nat = 4,
 ntyp = 2,
 ecutwfc = 30,
 celldm(1) = 10.750047341391399,
 occupations = 'tetrahedra',
 /
 &electrons
conv_thr =  1.0d-8
mixing_beta = 0.7
electron_maxstep = 300
 /
ATOMIC_SPECIES
 Na22.9897Na.pbe-sp-van_ak.UPF
 Cl35.4527Cl.pbe-n-van.UPF
ATOMIC_POSITIONS  crystal
Na  -0.5  -0.5   0.0
Na  -0.5   0.0  -0.5
Cl  -0.5   0.0   0.0
Cl  -0.5  -0.5  -0.5
Cl   0.0  -0.5   0.0
Cl   0.0   0.0  -0.5
Na   0.0   0.0   0.0
Na   0.0  -0.5  -0.5
K_POINTS automatic
 6 6 6  0 0 0

 &inputpp
outdir='./'
prefix='nacl'
ngauss=1, degauss=0.02
DeltaE=0.05
Emin=-15.0, Emax=15.0,
filpdos='nacl.k'
 /


Any suggestion are welcome!
Thank you in advance!
 *--*

*Sincerely yours,*
*Alexander G. Kvashnin *


*=PhD Student Moscow
Institute of Physics and Technology  http://mipt.ru/
<http://s.wisestamp.com/links?url=http%3A%2F%2Fmipt.ru%2F&sn=>*
*141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia*





*Junior research scientistTechnological Institute for Superhard and Novel
Carbon Materialshttp://www.tisnum.ru/
<http://s.wisestamp.com/links?url=http%3A%2F%2Fwww.tisnum.ru%2F&sn=>
<http://s.wisestamp.com/links?url=http%3A%2F%2Fwww.ntcstm.troitsk.ru%2F&sn=>142190,
Central'naya St. 7a, Troitsk, Moscow Region,
Russia=====*
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[Pw_forum] Incorrect magnetic moment from PWSCF

[Ari P Seitsonen]

Hi,

   FAQ-answer would be:

http://qe-forge.org/gf/project/pslibrary/

   If those do not help, please write again, with a complete input and the 
external reference.

 Greetings,

apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
   Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
   Institut f?r Chemie der Universit?t Z?rich, CH-8057 Z?rich
   Tel: +41 44 63 54 497  /  Mobile: +41 79 71 90 935


On Fri, 4 Apr 2014, anyy zsj wrote:

> Thank you for your reply!
>
>
> The results I used to compare are values given in Bohr mag/cell as
> output of PWSCF. However, the obtained value is always higher compare
> to literature. Actually, I can reproduce the results with vasp code.
> So the only problem seems to be the pseudopotential. The
> pseudopotential I employed is *.pbe-mt_fhi.UPF. Is there some problem
> with these potentials? Or is there PAW pseudopotential for PWSCF to
> use?
>
>
>
>
> 2014-04-04 0:29 GMT+08:00 Ari P Seitsonen :
>>
>>
>> Dear An,
>>
>>   Could you please tell some more details: How do you evaluate the magnetic 
>> moment (total moment of the cell, per atom Ti atom, from projected density 
>> of states, from L?wdin analysis, ..., is the system ferromagnetic, 
>> anti-ferromagnetic, ...), a good reference to the earlier literature, and 
>> possibly the full input, with atomic coordinates so that we others could try 
>> to reproduce the problem, if needed.
>>
>>   Based on this partial input it is somewhat difficult to judge, as we don't 
>> know which pseudo potentials/PAW dataset you are using etc.
>>
>> Greetings from Zurich,
>>
>>apsi
>>
>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>>   Ari Paavo Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
>>   Institut f?r Chemie der Universit?t Z?rich, CH-8057 Z?rich
>>   Tel: +41 44 63 54 497  /  Mobile: +41 79 71 90 935
>>
>>
>>
>> On Thu, 3 Apr 2014, anyy zsj wrote:
>>
>>> Hello everyone:
>>> Recently I calculated the magnetic moment of a system which has a
>>> hexagonal lattice. However, the results obtained from PWSCF
>>> calculations are always bigger than that from literatures (about 2
>>> times bigger). I tried many parameters such starting_magnetism and
>>> tot_magnetism but still cannot get the correct results. Please give me
>>> some advice about this. Thank you!
>>> Below is my input file with norm-conserved pseudopotentials:
>>>
>>> &control
>>>calculation = 'scf'
>>>restart_mode='from_scratch'
>>>prefix='Ti2C'
>>>pseudo_dir = './'
>>>outdir = './'
>>> /
>>> &system
>>>ibrav = 4
>>>a = 4.20
>>> c = 20.2
>>> nat = 3
>>>ntyp = 2
>>>ecutwfc = 50.0
>>>   occupations = 'smearing'
>>>smearing = 'm-p'
>>>degauss = 0.001
>>>   nspin=2,
>>>starting_magnetization(1)= 0.2
>>> /
>>> &electrons
>>>electron_maxstep = 5000
>>>diagonalization='david'
>>>mixing_mode = 'plain'
>>>mixing_beta = 0.7
>>> /
>>>
>>>
>>> An
>>> Postdoc
>>> Peking University
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>

[Pw_forum] Solved! The parallel problem!

[yjunwei2012]

Hello dear QE users,
  I have solved the QE + openmpi parallel problem, The reason for the 
problem as follows,
though I install openmpi and QE, I did not add the openmpi bin to the bashrc, 
so in fact I compile the QE without openmpi, as show in the ouput file ,it is 
still a serial version.
  Now, I recompile the QE after openmpi is OK. It is Parallel version (MPI).
  Thank you for your attention!
  Best wishes!
  JWY 

2014-04-04



yjunwei2012
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[Pw_forum] Problem with PDOS of ionic crystals

[Giovanni Cantele]

On 04 Apr 2014, at 10:43, Alexander G. Kvashnin  wrote:

> Dear QE users,
> 
> I tried to calculate PDOS for simple cubic NaCl structure. I performed an 
> optimization vc-relax with 6x6x6 k-points, than I made scf calculations, nscf 
> calculations and after that I ran projwfc to plot PDOS. 
> My question is why when I plotted DOS_Na+DOS_Cl it differs from the total DOS 
> for whole system, specially in conduction band?
> 
> Here is my nscf file and input file for projfwc:
> 
>  &control
> calculation='nscf'
> restart_mode='restart',
> tstress = .true.
> tprnfor = .true.
> prefix='nacl',
> pseudo_dir = '.',
> outdir='.',
> nstep = 200 
>  /
>  &system
> nosym = .false.,
>  ibrav = 1,
>  nat = 4,
>  ntyp = 2,
>  ecutwfc = 30,
>  celldm(1) = 10.750047341391399,
>  occupations = 'tetrahedra',
>  /
>  &electrons
> conv_thr =  1.0d-8
> mixing_beta = 0.7
> electron_maxstep = 300
>  /
> ATOMIC_SPECIES
>  Na22.9897Na.pbe-sp-van_ak.UPF
>  Cl35.4527Cl.pbe-n-van.UPF
> ATOMIC_POSITIONS  crystal
> Na  -0.5  -0.5   0.0
> Na  -0.5   0.0  -0.5
> Cl  -0.5   0.0   0.0
> Cl  -0.5  -0.5  -0.5
> Cl   0.0  -0.5   0.0
> Cl   0.0   0.0  -0.5
> Na   0.0   0.0   0.0
> Na   0.0  -0.5  -0.5
> K_POINTS automatic 
>  6 6 6  0 0 0
> 
>  &inputpp
> outdir='./'
> prefix='nacl'
> ngauss=1, degauss=0.02
> DeltaE=0.05
> Emin=-15.0, Emax=15.0,
> filpdos='nacl.k'
>  /
> 
> 
> Any suggestion are welcome!
> Thank you in advance!
>  --
> Sincerely yours,
> Alexander G. Kvashnin 
> =
> PhD Student 
> Moscow Institute of Physics and Technology  http://mipt.ru/
> 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia
> 
> Junior research scientist
> Technological Institute for Superhard 
> and Novel Carbon Materials
> http://www.tisnum.ru/
> 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia
> = 
> 



Dear Alexander,

inside the pdos output file you should find, for EACH eigenvalue at EACH 
k-point the decomposition of
the wave function, together with the sum of the square modulus of the expansion 
coefficients.

What you should notice is that, while for occupied states |psi|^2 = 1.000, the 
coefficient square moduli do
not sum up to 1, as you move to high energy unoccupied states.

Should the basis set used for the projection be orthogonal and complete, that 
should not occur. However,
the code, as far as I remember, is only able to project onto the atomic 
orbitals included in the pseudo potentials.

Therefore, while the bands, even though unoccupied, are correctly (at DFT 
level!) computed, the projection onto
the atomic orbitals might not be enough because would require atomic orbitals 
(e.g. d states) not included
in the pseudo. The result is that the sum of the partial dos is LESS than the 
(correct) total DOS.

Giovanni

-- 

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cantele at spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele

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[Pw_forum] Ag.pbe-dn-rrkjus_psl.0.1.UPF

[Filipe Camargo Dalmatti Alves Lima]

Dear Faith,

This paper has been published using Ag surfaces and QE pseudopotentials:
Structure and Molecule-Substrate Interaction in a Co-octaethyl Porphyrin
Monolayer on the Ag(110) Surface
http://pubs.acs.org/doi/abs/10.1021/jp2011233

It might help you designing your own system.

Best,

Filipe




On Fri, Apr 4, 2014 at 9:23 AM, Andrea Dal Corso  wrote:

> As far as I know, this Ag PP is working, and should be fine for Ag
> surfaces.
>
> Andrea
>
>
> On Fri, 2014-04-04 at 13:15 +0300, fatih.ersan at adu.edu.tr wrote:
> > Dear A. Dal Corso:
> >
> > I want to use Ag atoms for my study, when i'm searching suitable
> pseudo-potentials(pp), i met Ag.pbe-dn-rrkjus_psl.0.1.UPF which has
> config='[Kr] 4d9.5 5s1.5 5p0.0'electronic configurations. Is your scope to
> generate this potential to examine catalytic activities or something like
> this? Can i use this PP to adsorb on any sheet? Could you help me for me to
> understand?
> >
> > Best wishes
> >
> > Fatih
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> Andrea Dal CorsoTel. 0039-040-3787428
> SISSA, Via Bonomea 265  Fax. 0039-040-3787249
> I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
_
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:(11) 3091-6881  (USP)
    (11) 97408-2755 (Vivo)
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[Pw_forum] Gibbs Free energy

[Filipe Camargo Dalmatti Alves Lima]

I found it:

QHA (Quasi Harmonic Approximation): utilities for the calculation of
projected density of states (PDOS) and of the free energy in the
Quasi-Harmonic Approximation (to be used in conjunction with PHonon).

sorry for ask.


On Fri, Apr 4, 2014 at 9:11 AM, Filipe Camargo Dalmatti Alves Lima <
flima at if.usp.br> wrote:

> Dear Patrik,
>
> Just a curious question: what is QHA?
>
> Thanks,
>
> Filipe
>
>
> On Fri, Apr 4, 2014 at 8:28 AM, Saied Md Pratik  > wrote:
>
>> Hi All
>>   After running QHA (implemented in Quantum espresso) I have got
>> E_internal,F_vibration, Specific heat (C_v), Entropy etc. Does F_vibration
>> correspond to Helmholtz free energy? If so, Can anybody  please tell me
>> that how can I calculate Gibbs free energy?
>>   Thanks in advance.
>>   Pratik
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
> _
> Filipe Camargo Dalmatti Alves Lima
> PhD Student
> University of S?o Paulo, Physics Institute, Materials Physics Department,
> Nanomol Group, Brazil.
> Phones:(11) 3091-6881  (USP)
> (11) 97408-2755 (Vivo)
>



-- 
_
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:(11) 3091-6881  (USP)
(11) 97408-2755 (Vivo)
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[Pw_forum] Gibbs Free energy

[Filipe Camargo Dalmatti Alves Lima]

Dear Patrik,

Just a curious question: what is QHA?

Thanks,

Filipe


On Fri, Apr 4, 2014 at 8:28 AM, Saied Md Pratik
wrote:

> Hi All
>   After running QHA (implemented in Quantum espresso) I have got
> E_internal,F_vibration, Specific heat (C_v), Entropy etc. Does F_vibration
> correspond to Helmholtz free energy? If so, Can anybody  please tell me
> that how can I calculate Gibbs free energy?
>   Thanks in advance.
>   Pratik
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
_
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:(11) 3091-6881  (USP)
(11) 97408-2755 (Vivo)
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[Pw_forum] QE v.5.0.2: the openmpi parallel problem

[yjunwei2012]

Dear Giovanni,
Thank you for your reply, I am checking my environment and config.log file!
  Best wishes!

2014-04-04



yjunwei2012



Giovanni Cantele 
?2014-04-03 23:37
???Re: [Pw_forum] QE v.5.0.2: the openmpi parallel problem
"PWSCF Forum"
???



On 03 Apr 2014, at 17:01, yjunwei2012  wrote:


Dear all user:
   When I run a example (ecut.40.in) with openmpi,the run command in terminal 
as this: mpirun -np 8 pw.x  ecuttest.40.out. To my surprise, in the 
output file, the same information show 8 times, though the cpu is 100%.
I do not know whether the QE5.0.2 have a parallel version, if no, how can I 
make my QE5.0.2 run parallel jobs? I have installed 
gcc4.4.7,gcc-c++,gcc-gfortran ,openmpi-1.6.5 and QE5.0.2 on the centos6.5.
Thank you very much!

JWY

2014-04-03



yjunwei2012
___
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum
Of course, QE ANY.VERSION does run in parallel. However, it seems that the 
compilation of the parallel executable did fail
in your case. Indeed, you can read in your output ?Serial version?. That could 
explain the strange 8-times-replicated output,
due to the fact that you run 8 tasks of the SAME serial executable, rather than 
split a parallel executable into 8 tasks!!


You should first verify your installation, e.g. if a parallel environment was 
detected. At this purpose, check 
espresso-5.0.2/install/config.log


Giovanni


-- 

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cantele at spin.cnr.it
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: http://people.na.infn.it/~cantele
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[Pw_forum] QE v.5.0.2: the openmpi parallel problem

[yjunwei2012]

Dear Lorenzo,
Thank you for your help,this is my make.sys file!
  Best wishes! 

2014-04-04



yjunwei2012



Lorenzo Paulatto 
?2014-04-03 23:19
???Re: [Pw_forum] QE v.5.0.2: the openmpi parallel problem
"PWSCF Forum"
???

On 04/03/2014 05:01 PM, yjunwei2012 wrote:

I do not know whether the QE5.0.2 have a parallel version, if no, how can I 
make my QE5.0.2 run parallel jobs? I have installed 
gcc4.4.7,gcc-c++,gcc-gfortran ,openmpi-1.6.5 and QE5.0.2 on the centos6.5. 
Thank you very much!




It does have a parallel version, but did you compile it correctly? Please send 
us your make.sys file (rename it to something else, as .sys files are often 
blocked) so we can double-check this.

kind regards

-- 
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Universit? Paris 6
+33 (0)1 44 275 084 / skype: paulatz
http://www-int.impmc.upmc.fr/~paulatto/
23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
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[Pw_forum] (no subject)

[薛诗川]

when compiling GPU 14.03, there is an error that i cannot figure out:
---
data_structure_gpu.f90(18): error #7002: Error in opening the compiled
module file. Check INCLUDE paths.   [MP_BANDS]
USE mp_bands,   ONLY : me_bgrp, nproc_bgrp, root_bgrp, intra_bgrp_comm
-

is it my compiler's problem?
why does it ask me to check include path?
have u come across such problems and how u solved it?
thanks in advance

and below is my compiling log.txt
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ar: creating libphigemm.a
iotk_stream.f90(42): warning #6843: A dummy argument with an explicit 
INTENT(OUT) declaration is not given an explicit value.   [VAL]
subroutine iotk_stream_read_LOGICAL1(unit,header,val,setpos,getpos,noval,ierr)
-^
iotk_stream.f90(406): warning #6843: A dummy argument with an explicit 
INTENT(OUT) declaration is not given an explicit value.   [VAL]
subroutine iotk_stream_read_INTEGER1(unit,header,val,setpos,getpos,noval,ierr)
-^
iotk_stream.f90(770): warning #6843: A dummy argument with an explicit 
INTENT(OUT) declaration is not given an explicit value.   [VAL]
subroutine iotk_stream_read_REAL1(unit,header,val,setpos,getpos,noval,ierr)
--^
iotk_stream.f90(861): warning #6843: A dummy argument with an explicit 
INTENT(OUT) declaration is not given an explicit value.   [VAL]
subroutine iotk_stream_read_REAL2(unit,header,val,setpos,getpos,noval,ierr)
--^
iotk_stream.f90(1134): warning #6843: A dummy argument with an explicit 
INTENT(OUT) declaration is not given an explicit value.   [VAL]
subroutine iotk_stream_read_COMPLEX1(unit,header,val,setpos,getpos,noval,ierr)
-^
iotk_stream.f90(1225): warning #6843: A dummy argument with an explicit 
INTENT(OUT) declaration is not given an explicit value.   [VAL]
subroutine iotk_stream_read_COMPLEX2(unit,header,val,setpos,getpos,noval,ierr)
-^
iotk_stream.f90(1498): warning #6843: A dummy argument with an explicit 
INTENT(OUT) declaration is not given an explicit value.   [VAL]
subroutine iotk_stream_read_CHARACTER1(unit,header,val,setpos,getpos,noval,ierr)
---^
iotk_attr+COMPLEX2_0.f90(131): remark #8291: Recommended relationship between 
field width 'W' and the number of fractional digits 'D' in this edit descriptor 
is 'W>=D+7'.
read(string(pos+1:pos1-1),"(G100.95)",iostat=iostat) tmpreal
-^
iotk_attr+COMPLEX1_0.f90(131): remark #8291: Recommended relationship between 
field width 'W' and the number of fractional digits 'D' in this edit descriptor 
is 'W>=D+7'.
read(string(pos+1:pos1-1),"(G100.95)",iostat=iostat) tmpreal
-^
iotk_attr+REAL2_0.f90(129): remark #8291: Recommended relationship between 
field width 'W' and the number of fractional digits 'D' in this edit descriptor 
is 'W>=D+7'.
read( string(pos+1:pos1-1), "(G100.95)",iostat=iostat) val(index)
---^
iotk_attr+REAL1_0.f90(129): remark #8291: Recommended relationship between 
field width 'W' and the number of fractional digits 'D' in this edit descriptor 
is 'W>=D+7'.
read( string(pos+1:pos1-1), "(G100.95)",iostat=iostat) val(index)
---^
ar: creating libiotk.a
make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make 
rule.
make[3]: warning: jobserver unavailable: using -j1.  Add `+' to parent make 
rule.
kind.f90(38): remark #8291: Recommended relationship between field width 'W' 
and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
WRITE( stdout,'(/,T2,A,T78,A,2(/,T2,A,T75,I6),3(/,T2,A,T67,E14.8))') &
^
kind.f90(44): remark #8291: Recommended relationship between field width 'W' 
and the number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
WRITE( stdout,'(/,T2,A,T78,A,2(/,T2,A,T75,I6),3(/,T2,A,T67,E14.8))') &
^
bfgs_module.f90(934): remark #8291: Recommende