Re: [Pw_forum] Quantum Espresso

2017-07-07 Thread Ubaid Mohd 
I tried with the same but it showing the problem after some iteration and I
enclosed my input file please have a look at that 

 iteration #  3 ecut=75.00 Ry beta=0.70
 Davidson diagonalization with overlap
 ethr =  5.28E-03,  avg # of iterations =  2.0

 negative rho (up, down):  3.835E-05 0.000E+00

 total cpu time spent up to now is 4472.4 secs

 total energy  = -34.18814464 Ry
 Harris-Foulkes estimate   = -34.19240349 Ry
 estimated scf accuracy<   0.00935740 Ry

 iteration #  4 ecut=75.00 Ry beta=0.70
 Davidson diagonalization with overlap
 c_bands:  1 eigenvalues not converged
 c_bands:  1 eigenvalues not converged
 c_bands:  1 eigenvalues not converged
 c_bands:  1 eigenvalues not converged

*Mohammad Ubaid*
*PhD Research Scholar*
*Department of Physics*
*Jamia Millia Islamia University*
*New Delhi - 110025*

On Thu, Jul 6, 2017 at 11:53 PM, Biswajit Santra  wrote:

> You can find many water crystal structure here http://aip.scitation.org/
> doi/suppl/10.1063/1.4824481
>
> However, you may not need it since you need isolated water molecule
> energy. A large cell of about 20-25 Angstrom length is typically sufficient
> to have negligible interactions with the periodic images.
>
> Best,
>
> Biswajit Santra
> Mobile: +1-609-227-9202
> http://www.princeton.edu/~bsantra/
>
> On Thu, Jul 6, 2017 at 12:07 PM, Ubaid Mohd  wrote:
>
>> Should I relax the isolated water molecule inside the cubical box?
>>
>> On 6 Jul 2017 5:17 pm, "Nicola Marzari"  wrote:
>>
>>> On 06/07/2017 13:39, Andrey Chibisov wrote:
>>> > Dear Mohammad,
>>> > You need to place the isolated water molecule in big cubic box (with
>>> the side about 15 Angstrom or bigger) and calculate the total energy. This
>>> will be the total energy of the isolated water molecule.
>>>
>>> Indeed! And you can monitor the length of the box to see when the total
>>> energy converges to the isolated limit (water has a dipole-dipole
>>> interaction with its periodic image).
>>>
>>> QE has also the option of using open boundary conditions, although I
>>> admit I'm not sure where they are implemented (certainly in environ,
>>> but maybe somewhere else).
>>>
>>> Last, if you use periodic boundary conditions, and want to be fussy,
>>> a bcc cell is considered the optimal traedoff - due to the fact that
>>> for a given volume it puts the periodic neighbors quite a bit farther
>>> (6-7%) than the cubic cell; not as much as the fcc cell, but compared
>>> to fcc you have only 8 rather than 12 neightbours.
>>>
>>> Probably noone in the history of simulations has tested this - so you
>>> could make a small paper out of it!
>>>
>>> nicola
>>>
>>>
>>> >
>>> > 06.07.2017, 15:30, "Ubaid Mohd" :
>>> >> Dear all,
>>> >> I am doing the calculations of water confinement between graphene
>>> sheets. I have done all the relaxation calculations. After relaxation I
>>> found the total energy of the graphene sheet, I also need  to find the
>>> total energy of the water molecule to get the total binding energy of the
>>> system.
>>> >> My question is, to find the total energy of the water molecule what
>>> should be the crystal structure of water and how I create the unit cell of
>>> water.
>>> >> Thanks in advance.
>>> >>
>>> >> Mohammad Ubaid
>>> >> PhD Research Scholar
>>> >> Department of Physics
>>> >> Jamia Millia Islamia University
>>> >> New Delhi - 110025
>>> >>
>>> >> On Mon, Jun 19, 2017 at 3:51 PM, Ubaid Mohd 
>>> wrote:
>>> >>> Thanks Sir
>>> >>>
>>> >>> Mohammad Ubaid
>>> >>> PhD Research Scholar
>>> >>> Department of Physics
>>> >>> Jamia Millia Islamia University
>>> >>> New Delhi - 110025
>>> >>>
>>> >>> Mohammad Ubaid
>>> >>> PhD Research Scholar
>>> >>> Department of Physics
>>> >>> Jamia Millia Islamia University
>>> >>> New Delhi - 110025
>>> >>>
>>> >>> On Mon, Jun 19, 2017 at 3:50 PM, Giovanni Cantele <
>>> giovanni.cant...@spin.cnr.it> wrote:
>>>  Users of this forum are usually kindly requested to provide their
>>> name and affiliation, when posting messages  ;-)
>>> 
>>>  The scf run reads the position in the input file, whichever run has
>>> come before. nscf read positions from outdir, if any
>>> 
>>>  Giovanni
>>> 
>>> > On 19 Jun 2017, at 12:14, Ubaid Mohd  wrote:
>>> >
>>> > Then only for scf run, following the relaxation run, whether we
>>> use initial coordinates or optimized coordinates
>>> >
>>> > On Mon, Jun 19, 2017 at 3:29 PM, Giovanni Cantele <
>>> giovanni.cant...@spin.cnr.it> wrote:
>>> >> Users of this forum are usually kindly requested to provide their
>>> name and affiliation, when posting messages!  ;-)
>>> >>
>>> >> If, after a relaxation run, you execute an nscf (e.g. for band
>>> structure or DOS )

[Pw_forum] Confusion about silicon phonon dispersion along K-X path

2017-07-07 Thread balabi 






Dear developers,    I am calculating silicon phonon dispersion, however, I got confused about the dispersion along K-X.    I found there are apparently different results on the web. Some are the same with my calculation, most are not.    My result along k-path "Γ - K - X - Γ - L" is here:     https://pasteboard.co/GzWanr4.png    The only result that is the same with me is on QuantumWise page :     http://quantumwise.com/about-us/item/836-silicon-phonon-bandstructure    However, most of the results that I googled is quite different along K-X, for example    http://exciting-code.org/phonon-properties-in-diamond-structure-crystals    or paper    DOI: 10.1103/PhysRevB.87.165201     in which the author claimed they calculate the phonon by QE        I notice that the length of K-X is not the same in two different result.     Besides the same problem exists for similar structure like AlAs etc. But I don't know what is going wrong here? Which is the right result? Thank you for helping.best regards            





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[Pw_forum] weekly snapshots

2017-07-07 Thread Mahmoud Payami Shabestari 
Hi Everybody,
I was looking for the weekly snapshots of QE, but found that it is not 
updated for a few months.
I do not know where can I access releases later than espresso-r13450.

Best regards
M. Payami
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[Pw_forum] Dead Link on Webpage Concerning Parallel Performance

2017-07-07 Thread Robert Molt 
Good evening,

On the FAQ for parallel execution, there is a reference to section 3 of 
the User Guide. This link seems to be dead, as it redirects elsewhere 
(which does not seem to be the User Guide). The top of the page also 
states "Page Not Found."


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[Pw_forum] Fermi level related query

2017-07-07 Thread Anindya Bose 
Dear Sir,
I would like to know that where can I get the information regarding fermi
energy in quantum espresso files(eg.scf,nscf,bands). I am facing a trouble
with it.Please help.I will be waiting for the response.

Thanks and regards,
Anindya Bose
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Re: [Pw_forum] q-grid

2017-07-07 Thread Lorenzo Paulatto 
 > Dear experts,
 >
 > Is *nq1=2, nq2=2, nq3=2* enough for a phonon calculation of a bulk 
system?

No, is usually is not.

kind regards


-- 
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Université Paris 6
phone: +33 (0)1 442 79822 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/423 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05
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[Pw_forum] Allowed symmetries in GIPAW

2017-07-07 Thread J. Nelson 
Dear all QE users,

I am using QE-6.1.

The user guide for GIPAW explains that 'symmetry operations that do not 
map cartesian axes are not allowed (i.e. 120 deg. rotations)'.

Does this mean that the Cartesian rotation matrices for each symmetry 
operation - e.g.:

   isym =  4 180 deg rotation - cart. axis [1,0,0]

  cryst.   s( 4) = ( 0  1  0  )
   ( 1  0  0  )
   ( 0  0 -1  )

  cart.s( 4) = (  1.000  0.000  0.000 )  [<--this matrix 
here]
   (  0.000 -1.000  0.000 )
   (  0.000  0.000 -1.000 )

need to be diagonal for the symmetry operation to be compatible with 
GIPAW? Are symmetry operations with an associated fractional translation 
allowed?


Many thanks,

Joseph Nelson
TCM Group
Cavendish Laboratory
University of Cambridge
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[Pw_forum] q-grid

2017-07-07 Thread ashkan shekaari 
Dear experts,

Is *nq1=2, nq2=2, nq3=2* enough for a phonon calculation of a bulk system?

Regards,
Ashkan

*Ashkan Shekaari*
Plasma Physics Research Center
Science and Research Branch
I A U, 14778-93855 Tehran, Iran.
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[Pw_forum] Relaxation of florine adsorption in graphene sheet

2017-07-07 Thread nipesh dulal 
Dear all QE users

i am doing adsorption of halogens molecule in graphene sheet but in case of
florine molecule in parallel oreintation site there comes of no convergence
in 200 iterations also. here is the input file i have used


calculation='relax'
restart_mode='from_scratch'
prefix='florine_pb_relax'
outdir='/home/quantumespresso/Downloads/graphene/florine/plane_bridge',
pseudo_dir = '/home/quantumespresso/Downloads/graphene/pseudopotentials',
tstress=.true.
tprnfor=.true.
verbosity='high'
forc_conv_thr=1.0d-3
etot_conv_thr=1.0d-4
/

ibrav=4
celldm(1)=13.95
celldm(3)=2.71
nat=20
ntyp=2
ecutwfc=45.0
ecutrho=450
occupations='smearing'
smearing='mv'
degauss=0.002
vdw_corr='dft-d'
/

diagonalization='david'
mixing_mode='plain'
electron_maxstep = 250
mixing_beta=0.6
conv_thr = 1.0D-8
/

ion_dynamics='bfgs'
/

ATOMIC_SPECIES
C 12.011 C.pbe-rrkjus.UPF
F 18.99 F.pbe-n-rrkjus_psl.0.1.UPF

ATOMIC_POSITIONS (angstrom)
C 0.001400942  -0.001453110   0.61554
C 1.231769902   0.708444719  -0.000164578
C 2.461445114  -0.001453346   0.61603
C 3.692208579   0.708052777   0.000149947
C -1.229013376   2.129353884   0.000149939
C 0.001751031   2.838869744   0.63271
C 1.231423642   2.128967448  -0.000163848
C 2.461792428   2.838870669   0.63165
C 4.922433860  -0.001636920   0.46712
C 6.153356720   0.708055695   0.000150032
C 3.691861453   2.129361584   0.000149967
C 4.922782755   2.839054473   0.47035
C -2.459588312   4.260366023   0.000130489
C -1.228895707   4.970349561   0.000108927
C 0.001082483   4.260080304   0.000108924
C 1.231770589   4.970065828   0.000131168
C 2.461771791   4.260080654   0.000108986
C 3.692437760   4.970346822   0.000108951
F 1.231555657   2.178219256   3.259341253
F 1.231547759   0.659338334   3.259346502


K_POINTS {automatic}
5 5 1 0 0 0

With Best Regrads
Nipesh Dulal
Tribhuwan university
Kathmandu,Nepal
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