from:"ashkan shekaari"

Re: [Pw_forum] GPU

2017-07-13 Thread ashkan shekaari

Dear Yasser,

Thank you so much for your quick response.

Regards,
Ashkan

*Ashkan Shekaari*
Plasma Physics Research Center
Science and Research Branch
I A U, 14778-93855 Tehran, Iran.

On Thu, Jul 13, 2017 at 4:18 PM, Yasser Fowad AlWahedi <yaalwah...@pi.ac.ae>
wrote:

> Dear Ashkan
>
> The current version of QE-GPU (5.4) should support  Fermi till Kepler
> architectures. The card should have decent double precision performance.
> Examples are Tesla series K20, K20x, K40 and K80 all have good double
> precision performance.
>
> If you are purchasing for a workstation, then buy a GPU having a
> fan/blower based cooling solution. Stay away from passively cooled cards
> (e.g. Tesla K80).
>
> If you have limited budget then kepler based Titan , Titan Z and Titan
> black should have decent double precision performance but at lower costs.
>
> Yasser Al Wahedi
> Assistant Professor
> Khalifa University of Science and Technology
>
> Get Outlook for Android <https://aka.ms/ghei36>
>
>
>
> From: ashkan shekaari
> Sent: Friday, 14 July, 00:01
> Subject: [Pw_forum] GPU
> To: pw_forum
>
>
> Dear experts,
>
> Does anyone know what type of nvidia graphic cards is suitable for
> calculating with quda_enabled quantum espresso?
>
> I mean what are the minimum specifications a given cuda-supported graphic
> card must have to be suitable for computing with quantum espresso?
>
>
> 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] GPU

2017-07-13 Thread ashkan shekaari

Dear experts,

Does anyone know what type of nvidia graphic cards is suitable for
calculating with quda_enabled quantum espresso?
I mean what are the minimum specifications a given cuda-supported graphic
card must have to be suitable for computing with quantum espresso?

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] 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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Re: [Pw_forum] supercell band structure

2017-05-18 Thread ashkan shekaari

You should take band unfolding into consideration. For example, for a unit
cell if we have
Kpoints
x  y  z  n
...

for a 2×2 super cell we should write
Kpoints
2x 2y  2z  n

2×2 Super cell > bz is multiplied by 1/2 > kpoints must be
multiplied by 2 to neutralize such a change.

On May 18, 2017 1:45 AM, "Pietro Bonfa'"  wrote:

> Dear Mohammadreza Hosseini,
>
> are you talking about band folding? I wrote a small utility to unfold
> the band structure of supercells long time ago. It's in a git repository
> hosted on qe-forge.org (project name is unfold).
>
> Kind regards,
> Pietro Bonfa'
>
> On 05/15/2017 11:16 AM, Mohammadreza Hosseini wrote:
> >
> >
> > 
> > From: Mohammadreza Hosseini
> > Sent: Sunday, May 14, 2017 1:43 AM
> > To: pw_forum@pwscf.org
> > Subject: Re: Pw_forum Digest, Vol 118, Issue 12
> >
> > Dear All
> >
> > I am calculating the band structure of phagraphyne. First we computed
> for primitive unit cell and then for the 2X2 supercell. Although the bulk
> structure is same the band structure is different. What is the problem ?
> Should parameters be optimized again for supercell?
> >
> > Mohammadreza Hosseini
> > Tarbiat modares uiversity
> > 
> > From: pw_forum-boun...@pwscf.org  on behalf
> of pw_forum-requ...@pwscf.org 
> > Sent: Saturday, May 13, 2017 10:00 PM
> > To: pw_forum@pwscf.org
> > Subject: Pw_forum Digest, Vol 118, Issue 12
> >
> > Send Pw_forum mailing list submissions to
> > pw_forum@pwscf.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://pwscf.org/mailman/listinfo/pw_forum
> > or, via email, send a message with subject or body 'help' to
> > pw_forum-requ...@pwscf.org
> >
> > You can reach the person managing the list at
> > pw_forum-ow...@pwscf.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Pw_forum digest..."
> >
> >
> > Today's Topics:
> >
> >1. Re: how to determine the symmetry of a given phonon mode  in
> >   quantum espresso (Lorenzo Paulatto)
> >2. Re: Gipaw - Magnetic susceptibility (Davide Ceresoli)
> >
> >
> > --
> >
> > Message: 1
> > Date: Sat, 13 May 2017 15:08:04 +0200
> > From: Lorenzo Paulatto 
> > Subject: Re: [Pw_forum] how to determine the symmetry of a given
> > phonon mode in quantum espresso
> > To: PWSCF Forum 
> > Message-ID: <1728518.gkaUiGcZ5e@paulaxps>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > On Friday, 12 May 2017 23:44:33 CEST Mihiri Hewa bosthanthirige wrote:
> >> Hi,
> >> I am graduate student at Clemson university, currently working with
> Quantum
> >> Espresso. I would like to know how to determine the symmetry of a given
> >> phonon mode in quantum espresso.
> >
> > Hello,
> > it is printed in the output of phonon at the end of the calculation,
> i.e.:
> > ...
> > End of self-consistent calculation
> >
> >
> > --
> > Dr. Lorenzo Paulatto
> > IdR @ IMPMC -- CNRS & Universit? Paris 6
> > +33 (0)1 44 275 084 / skype: paulatz
> > http://www.impmc.upmc.fr/~paulatto/
> > 23-24/4?16 Bo?te courrier 115,
> > 4 place Jussieu 75252 Paris C?dex 05
> > -- next part --
> > An HTML attachment was scrubbed...
> > URL: http://pwscf.org/pipermail/pw_forum/attachments/20170513/
> 0ddc04ba/attachment-0001.html
> >
> > --
> >
> > Message: 2
> > Date: Sat, 13 May 2017 16:09:02 +0200
> > From: Davide Ceresoli 
> > Subject: Re: [Pw_forum] Gipaw - Magnetic susceptibility
> > To: PWSCF Forum 
> > Message-ID: <6933968b-d5f1-fb6b-c518-e47ca4ce6...@cnr.it>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> > Dear Alan,
> >  I think that there is no problem in doing a G=0 response
> > with a shifted mesh. The response is at G=0, hence it couples
> > wfcs at the same k. The susceptibility depends a lot on k-points
> > sampling and if your system has a vanishing band gap, convergence
> > can be a nightmare.
> > By default the macroscopic shape is diagonal:
> >nmr_macroscopic_shape(:,:) = 0.d0
> >nmr_macroscopic_shape(1,1) = 2.d0 / 3.d0
> >nmr_macroscopic_shape(2,2) = 2.d0 / 3.d0
> >nmr_macroscopic_shape(3,3) = 2.d0 / 3.d0
> > You can change the component (demagnetizing field) in the input file.
> >
> > Good luck for your calculations!
> >
> > Best,
> >  Davide
> >
> >
> >
> > On 05/12/2017 07:47 PM, Ambrozio wrote:
> >> Dear QE users and Developers,
> >>
> >> I'm working with NMR calculations in Gipaw. Recently I did some
> shielding
> >> calculations and I have some questions regarding the magnetic
> susceptibility.
> >> The article from developers Mauri et

Re: [Pw_forum] QE for aqueous solution?

2017-05-06 Thread ashkan shekaari

Dear Mattioli,
You are right and I strongly agree with you DFT is capable of providing a
universally-agreed on framework to deal with the temperature dependence of
liquid water via the CPMD technique. What I am trying to say is that
simulating an aqueous solution by a triclinic Bravais lattice--as is
demonstrated in the example--is not but a simple, imprecise approximation.
And no one can provide a better, more precise picture within QE.

Regards,
Ashkan

*Ashkan Shekaari*
Plasma Physics Research Center
Science and Research Branch
I A U, 14778-93855 Tehran, Iran.

On Sat, May 6, 2017 at 1:27 PM, ashkan shekaari <sheka...@gmail.com> wrote:

> To the best of my knowledge, David could examine only the atomic structure
> of the solute using high-performance computer clusters supposing that the
> solute is made of not a large number of atoms and he has to write on his
> own several codes in order to obtain the temperature dependence of some
> phase transition indicators such as mean-square displacements and the
> Lindemann index.
>
> Regards,
> Ashkan
>
> *Ashkan Shekaari*
> Plasma Physics Research Center
> Science and Research Branch
> I A U, 14778-93855 Tehran, Iran.
>
> On Sat, May 6, 2017 at 1:17 PM, ashkan shekaari <sheka...@gmail.com>
> wrote:
>
>> Actually, I have recently published a paper on melting behavior of some
>> graphene quantum dots containing 6 and 10 atoms, but I had to write on my
>> own more than 800 program lines in bash and fortran for such small-sized
>> structures to get my desired results. And it is based on such an experience
>> that I believe QE is not that sophisticated in DFMD calculations of large,
>> non-solid, molecular structures. Even if you are a highly-experienced
>> programmer, you cannot get the desired results conclusively as the number
>> of atoms increases to form a solution.
>>
>> Regards,
>> Ashkan
>>
>> *Ashkan Shekaari*
>> Plasma Physics Research Center
>> Science and Research Branch
>> I A U, 14778-93855 Tehran, Iran.
>>
>> On Sat, May 6, 2017 at 1:00 PM, ashkan shekaari <sheka...@gmail.com>
>> wrote:
>>
>>> Dear Mattioli,
>>>
>>> Water is not a crystal and therefore it cannot be treated as a periodic
>>> structure. The aforementioned example provides only a naive picture of
>>> water as an aqueous compartment leading to a crude approximation of the
>>> given system as well. Moreover, QE is not best suited for DFMD simulations
>>> of large, nonperiodic, liquid systems.
>>>
>>> Regards,
>>> Ashkan
>>>
>>> *Ashkan Shekaari*
>>> Plasma Physics Research Center
>>> Science and Research Branch
>>> I A U, 14778-93855 Tehran, Iran.
>>>
>>> On Sat, May 6, 2017 at 12:21 PM, Giuseppe Mattioli <
>>> giuseppe.matti...@ism.cnr.it> wrote:
>>>
>>>>
>>>> Dear David and Ashkan
>>>>
>>>> > You cannot simulate the system as periodic. You have to use a large
>>>> super
>>>> > cell with vacuum spaces along the three spatial directions. Moreover,
>>>> you
>>>> > can simulate the solution only via importing a large number of atomic
>>>> > positions of the order of 25000 at least, which does not seem to be
>>>> > feasible by QE even in case of using random generators unless you
>>>> have a
>>>> > supercomputer facility.
>>>>
>>>> This comments are misleading, if not wrong in some cases.
>>>> First of all you can for sure perform ab initio molecular dynamics
>>>> (aimd) simulations of a water solution in a periodic box, and you do
>>>> not need a huge number of atoms. One of the cp.x examples provides
>>>> starting points, see here
>>>> /Your_Path_To_Espresso_6.1/Examples/CPV/example04
>>>>
>>>> >> Does anyone know of examples, benchmarks, or recommendations?  Would
>>>> the
>>>> >> X.blyp-van.ak pseudopotentials be appropriate?  Any guidance or
>>>> advice
>>>> >> about parameter settings for this application would be much
>>>> appreciated
>>>>
>>>> Yes, you can use ultrasoft pseudopotentials such as X.blyp-van.ak.
>>>> They used to be old and well-tested vanderbilt ultrasoft
>>>> pseudopotentials generated many years ago by Axel Kohlmeyer (ak). But
>>>> if you are not familiar with this terminology (ultrasoft,
>>>> norm-conserving, van, mt, rrkj, paw, ...) you should start with some
>>>> t

Re: [Pw_forum] QE for aqueous solution?

2017-05-06 Thread ashkan shekaari

To the best of my knowledge, David could examine only the atomic structure
of the solute using high-performance computer clusters supposing that the
solute is made of not a large number of atoms and he has to write on his
own several codes in order to obtain the temperature dependence of some
phase transition indicators such as mean-square displacements and the
Lindemann index.

Regards,
Ashkan

*Ashkan Shekaari*
Plasma Physics Research Center
Science and Research Branch
I A U, 14778-93855 Tehran, Iran.

On Sat, May 6, 2017 at 1:17 PM, ashkan shekaari <sheka...@gmail.com> wrote:

> Actually, I have recently published a paper on melting behavior of some
> graphene quantum dots containing 6 and 10 atoms, but I had to write on my
> own more than 800 program lines in bash and fortran for such small-sized
> structures to get my desired results. And it is based on such an experience
> that I believe QE is not that sophisticated in DFMD calculations of large,
> non-solid, molecular structures. Even if you are a highly-experienced
> programmer, you cannot get the desired results conclusively as the number
> of atoms increases to form a solution.
>
> Regards,
> Ashkan
>
> *Ashkan Shekaari*
> Plasma Physics Research Center
> Science and Research Branch
> I A U, 14778-93855 Tehran, Iran.
>
> On Sat, May 6, 2017 at 1:00 PM, ashkan shekaari <sheka...@gmail.com>
> wrote:
>
>> Dear Mattioli,
>>
>> Water is not a crystal and therefore it cannot be treated as a periodic
>> structure. The aforementioned example provides only a naive picture of
>> water as an aqueous compartment leading to a crude approximation of the
>> given system as well. Moreover, QE is not best suited for DFMD simulations
>> of large, nonperiodic, liquid systems.
>>
>> Regards,
>> Ashkan
>>
>> *Ashkan Shekaari*
>> Plasma Physics Research Center
>> Science and Research Branch
>> I A U, 14778-93855 Tehran, Iran.
>>
>> On Sat, May 6, 2017 at 12:21 PM, Giuseppe Mattioli <
>> giuseppe.matti...@ism.cnr.it> wrote:
>>
>>>
>>> Dear David and Ashkan
>>>
>>> > You cannot simulate the system as periodic. You have to use a large
>>> super
>>> > cell with vacuum spaces along the three spatial directions. Moreover,
>>> you
>>> > can simulate the solution only via importing a large number of atomic
>>> > positions of the order of 25000 at least, which does not seem to be
>>> > feasible by QE even in case of using random generators unless you have
>>> a
>>> > supercomputer facility.
>>>
>>> This comments are misleading, if not wrong in some cases.
>>> First of all you can for sure perform ab initio molecular dynamics
>>> (aimd) simulations of a water solution in a periodic box, and you do
>>> not need a huge number of atoms. One of the cp.x examples provides
>>> starting points, see here
>>> /Your_Path_To_Espresso_6.1/Examples/CPV/example04
>>>
>>> >> Does anyone know of examples, benchmarks, or recommendations?  Would
>>> the
>>> >> X.blyp-van.ak pseudopotentials be appropriate?  Any guidance or advice
>>> >> about parameter settings for this application would be much
>>> appreciated
>>>
>>> Yes, you can use ultrasoft pseudopotentials such as X.blyp-van.ak.
>>> They used to be old and well-tested vanderbilt ultrasoft
>>> pseudopotentials generated many years ago by Axel Kohlmeyer (ak). But
>>> if you are not familiar with this terminology (ultrasoft,
>>> norm-conserving, van, mt, rrkj, paw, ...) you should start with some
>>> tutorial on pseudopotentials, because you must be sure to use
>>> converged plane-wave and density cutoffs for a given set of
>>> pseudopotentials.
>>>
>>> There is a very large number of options that must be set in the cp.x
>>> input. I cannot review them here. But there are also tons of
>>> literature on aimd simulations of water solutions, and you will easily
>>> find something that will help to choice a lot of parameters (box
>>> dimensions, NVT, NVP, NVE dynamics, thermostats, ...)
>>>
>>> > Indeed, QE is not best suited for MD simulations and I strongly
>>> recommend
>>> > the gromacs package.
>>>
>>> Of course Ashkan might be right on a couple of points: if you have
>>> very big molecules weakly interacting with the solvent, and you are
>>> interested in the morphology of the solute only, then you have to
>>> perform very long md simulations and to use a large number of wat

Re: [Pw_forum] QE for aqueous solution?

2017-05-06 Thread ashkan shekaari

Actually, I have recently published a paper on melting behavior of some
graphene quantum dots containing 6 and 10 atoms, but I had to write on my
own more than 800 program lines in bash and fortran for such small-sized
structures to get my desired results. And it is based on such an experience
that I believe QE is not that sophisticated in DFMD calculations of large,
non-solid, molecular structures. Even if you are a highly-experienced
programmer, you cannot get the desired results conclusively as the number
of atoms increases to form a solution.

Regards,
Ashkan

*Ashkan Shekaari*
Plasma Physics Research Center
Science and Research Branch
I A U, 14778-93855 Tehran, Iran.

On Sat, May 6, 2017 at 1:00 PM, ashkan shekaari <sheka...@gmail.com> wrote:

> Dear Mattioli,
>
> Water is not a crystal and therefore it cannot be treated as a periodic 
> structure.
> The aforementioned example provides only a naive picture of water as an
> aqueous compartment leading to a crude approximation of the given system as
> well. Moreover, QE is not best suited for DFMD simulations of large,
> nonperiodic, liquid systems.
>
> Regards,
> Ashkan
>
> *Ashkan Shekaari*
> Plasma Physics Research Center
> Science and Research Branch
> I A U, 14778-93855 Tehran, Iran.
>
> On Sat, May 6, 2017 at 12:21 PM, Giuseppe Mattioli <
> giuseppe.matti...@ism.cnr.it> wrote:
>
>>
>> Dear David and Ashkan
>>
>> > You cannot simulate the system as periodic. You have to use a large
>> super
>> > cell with vacuum spaces along the three spatial directions. Moreover,
>> you
>> > can simulate the solution only via importing a large number of atomic
>> > positions of the order of 25000 at least, which does not seem to be
>> > feasible by QE even in case of using random generators unless you have a
>> > supercomputer facility.
>>
>> This comments are misleading, if not wrong in some cases.
>> First of all you can for sure perform ab initio molecular dynamics
>> (aimd) simulations of a water solution in a periodic box, and you do
>> not need a huge number of atoms. One of the cp.x examples provides
>> starting points, see here
>> /Your_Path_To_Espresso_6.1/Examples/CPV/example04
>>
>> >> Does anyone know of examples, benchmarks, or recommendations?  Would
>> the
>> >> X.blyp-van.ak pseudopotentials be appropriate?  Any guidance or advice
>> >> about parameter settings for this application would be much appreciated
>>
>> Yes, you can use ultrasoft pseudopotentials such as X.blyp-van.ak.
>> They used to be old and well-tested vanderbilt ultrasoft
>> pseudopotentials generated many years ago by Axel Kohlmeyer (ak). But
>> if you are not familiar with this terminology (ultrasoft,
>> norm-conserving, van, mt, rrkj, paw, ...) you should start with some
>> tutorial on pseudopotentials, because you must be sure to use
>> converged plane-wave and density cutoffs for a given set of
>> pseudopotentials.
>>
>> There is a very large number of options that must be set in the cp.x
>> input. I cannot review them here. But there are also tons of
>> literature on aimd simulations of water solutions, and you will easily
>> find something that will help to choice a lot of parameters (box
>> dimensions, NVT, NVP, NVE dynamics, thermostats, ...)
>>
>> > Indeed, QE is not best suited for MD simulations and I strongly
>> recommend
>> > the gromacs package.
>>
>> Of course Ashkan might be right on a couple of points: if you have
>> very big molecules weakly interacting with the solvent, and you are
>> interested in the morphology of the solute only, then you have to
>> perform very long md simulations and to use a large number of water
>> molecules, and this might be costly and time-consuming if performed at
>> an aimd level. If you want to study proton exchanges, reactions,
>> dipole dynamics, ... you need aimd. You surely know whether your
>> scientific task strictly requires aimd rather than model-potential md.
>>
>> HTH
>> Giuseppe
>>
>> Quoting ashkan shekaari <sheka...@gmail.com>:
>>
>> > Indeed, QE is not best suited for MD simulations and I strongly
>> recommend
>> > the gromacs package.
>>
>> > You cannot simulate the system as periodic. You have to use a large
>> super
>> > cell with vacuum spaces along the three spatial directions. Moreover,
>> you
>> > can simulate the solution only via importing a large number of atomic
>> > positions of the order of 25000 at least, which does not seem to be
>> > feasible by QE even

Re: [Pw_forum] QE for aqueous solution?

2017-05-06 Thread ashkan shekaari

Dear Mattioli,

Water is not a crystal and therefore it cannot be treated as a
periodic structure.
The aforementioned example provides only a naive picture of water as an
aqueous compartment leading to a crude approximation of the given system as
well. Moreover, QE is not best suited for DFMD simulations of large,
nonperiodic, liquid systems.

Regards,
Ashkan

*Ashkan Shekaari*
Plasma Physics Research Center
Science and Research Branch
I A U, 14778-93855 Tehran, Iran.

On Sat, May 6, 2017 at 12:21 PM, Giuseppe Mattioli <
giuseppe.matti...@ism.cnr.it> wrote:

>
> Dear David and Ashkan
>
> > You cannot simulate the system as periodic. You have to use a large super
> > cell with vacuum spaces along the three spatial directions. Moreover, you
> > can simulate the solution only via importing a large number of atomic
> > positions of the order of 25000 at least, which does not seem to be
> > feasible by QE even in case of using random generators unless you have a
> > supercomputer facility.
>
> This comments are misleading, if not wrong in some cases.
> First of all you can for sure perform ab initio molecular dynamics
> (aimd) simulations of a water solution in a periodic box, and you do
> not need a huge number of atoms. One of the cp.x examples provides
> starting points, see here
> /Your_Path_To_Espresso_6.1/Examples/CPV/example04
>
> >> Does anyone know of examples, benchmarks, or recommendations?  Would the
> >> X.blyp-van.ak pseudopotentials be appropriate?  Any guidance or advice
> >> about parameter settings for this application would be much appreciated
>
> Yes, you can use ultrasoft pseudopotentials such as X.blyp-van.ak.
> They used to be old and well-tested vanderbilt ultrasoft
> pseudopotentials generated many years ago by Axel Kohlmeyer (ak). But
> if you are not familiar with this terminology (ultrasoft,
> norm-conserving, van, mt, rrkj, paw, ...) you should start with some
> tutorial on pseudopotentials, because you must be sure to use
> converged plane-wave and density cutoffs for a given set of
> pseudopotentials.
>
> There is a very large number of options that must be set in the cp.x
> input. I cannot review them here. But there are also tons of
> literature on aimd simulations of water solutions, and you will easily
> find something that will help to choice a lot of parameters (box
> dimensions, NVT, NVP, NVE dynamics, thermostats, ...)
>
> > Indeed, QE is not best suited for MD simulations and I strongly recommend
> > the gromacs package.
>
> Of course Ashkan might be right on a couple of points: if you have
> very big molecules weakly interacting with the solvent, and you are
> interested in the morphology of the solute only, then you have to
> perform very long md simulations and to use a large number of water
> molecules, and this might be costly and time-consuming if performed at
> an aimd level. If you want to study proton exchanges, reactions,
> dipole dynamics, ... you need aimd. You surely know whether your
> scientific task strictly requires aimd rather than model-potential md.
>
> HTH
> Giuseppe
>
> Quoting ashkan shekaari <sheka...@gmail.com>:
>
> > Indeed, QE is not best suited for MD simulations and I strongly recommend
> > the gromacs package.
>
> > You cannot simulate the system as periodic. You have to use a large super
> > cell with vacuum spaces along the three spatial directions. Moreover, you
> > can simulate the solution only via importing a large number of atomic
> > positions of the order of 25000 at least, which does not seem to be
> > feasible by QE even in case of using random generators unless you have a
> > supercomputer facility.
> >
> > On May 6, 2017 9:09 AM, "D J Anick" <david.an...@rcn.com> wrote:
> >
> >> Hello plane wavers,
> >>
> >> I am interested in using QE for a molecular dynamics simulation of an
> >> aqueous solution containing a solute, modeling it as a 3-D periodic
> cell.
> >> Principal questions would be about solvation shell geometries,
> distribution
> >> of configurations adopted by the solute, and H-bond duration /
> stability.
> >>
> >> Does anyone know of examples, benchmarks, or recommendations?  Would the
> >> X.blyp-van.ak pseudopotentials be appropriate?  Any guidance or advice
> >> about parameter settings for this application would be much appreciated.
> >>
> >> Thank you in advance,
> >> David Anick
> >> david.anick###rcn.com
> >> ___
> >> Pw_forum mailing list
> >> Pw_forum@pwscf.org
> >> http://pwscf.org/mailman

Re: [Pw_forum] QE for aqueous solution?

2017-05-05 Thread ashkan shekaari

Indeed, QE is not best suited for MD simulations and I strongly recommend
the gromacs package.

On May 6, 2017 9:09 AM, "D J Anick"  wrote:

> Hello plane wavers,
>
> I am interested in using QE for a molecular dynamics simulation of an
> aqueous solution containing a solute, modeling it as a 3-D periodic cell.
> Principal questions would be about solvation shell geometries, distribution
> of configurations adopted by the solute, and H-bond duration / stability.
>
> Does anyone know of examples, benchmarks, or recommendations?  Would the
> X.blyp-van.ak pseudopotentials be appropriate?  Any guidance or advice
> about parameter settings for this application would be much appreciated.
>
> Thank you in advance,
> David Anick
> david.anick###rcn.com
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Re: [Pw_forum] QE for aqueous solution?

2017-05-05 Thread ashkan shekaari

You cannot simulate the system as periodic. You have to use a large super
cell with vacuum spaces along the three spatial directions. Moreover, you
can simulate the solution only via importing a large number of atomic
positions of the order of 25000 at least, which does not seem to be
feasible by QE even in case of using random generators unless you have a
supercomputer facility.

On May 6, 2017 9:09 AM, "D J Anick"  wrote:

> Hello plane wavers,
>
> I am interested in using QE for a molecular dynamics simulation of an
> aqueous solution containing a solute, modeling it as a 3-D periodic cell.
> Principal questions would be about solvation shell geometries, distribution
> of configurations adopted by the solute, and H-bond duration / stability.
>
> Does anyone know of examples, benchmarks, or recommendations?  Would the
> X.blyp-van.ak pseudopotentials be appropriate?  Any guidance or advice
> about parameter settings for this application would be much appreciated.
>
> Thank you in advance,
> David Anick
> david.anick###rcn.com
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Re: [Pw_forum] convergence can't achieved with QE6.0.2 and 5.4.0

2017-05-05 Thread ashkan shekaari

Change mixing beta to 0.7
increase ecutwfc
Use rrkjus pseudopotential

On May 5, 2017 12:56 PM, "Paolo Giannozzi"  wrote:

> On Fri, May 5, 2017 at 9:26 AM, Q.J.Wang  wrote:
>
> > I use QE6.0 to relax a slab structure,  the total force can't converge,
> > however, when I use the old version QE5.0.2, it works well. The input
> file
>
> ... is incomplete, so unusable. Please provide a complete input and an
> output for 5.0.2 and for 6.0
>
> Paolo
> --
> 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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Re: [Pw_forum] Convergence problem with Pb180Se180 Cluster optimization

2017-04-21 Thread ashkan shekaari

Dear Naren,
Increase ecut. Use more intense kpoint mesh.

On Apr 21, 2017 4:50 PM, "Giuseppe Mattioli" 
wrote:

>
> Dear Naren
> Your calculation is very expensive, and calculations of 0D objects in a
> plane-wave/PBC framework are often prone to convergence issues. This said,
> you
> can try to
>
> 1) perform a simple calculation of the PbSe unit cell with the same
> pseudopotentials. Are there similar convergence problems? You are using hgh
> that
> are norm-conserving pseudopotentials (NCPP) and they could require a
> richer pw basis set. I would not be surprised if, after proper convergence
> tests
> performed on the unit cell, you ended up with ecutwfc=70~80 Ry. There is
> no need to specify ecutrho, anyway. It is fixed to a default ecutwfc*4 value
> in the case of NCPP.
>
> 2) lower mixing_beta, even down to very small values such as 0.05~0.01.
> Sometimes it helps to reach convergence (slowly but steady).
>
> It is impossible to say more without looking at you cluster, but if it is
> simply cut out from the bulk along low-index directions (e.g., a cube) you
> have to deal with a mess of surface dangling bonds that want to play nasty
> charge displacements between occupied and unoccupied electronic levels,
> even inducing a metallic character in your cluster. People used to
> saturate such dangling bonds with pseudo-H atoms (H atoms having formal
> charge
> lower or higher than 1.0, depending on the formal valence of the saturated
> atom). If you don't want to saturate the surface you must keep into account
> the possibility that the cluster surface reconstruct, and you should
> anticipate reconstruction trends by lplacing the atoms nearer to the
> expected
> final positions. It could be a very difficult task, look at the
> instructive story of the Si 7x7 reconstruction in this movie!
>
> https://www.youtube.com/watch?v=BXdC0NhAMBY
>
> HTH
> Giuseppe
>
> On Friday, April 21, 2017 04:06:06 AM Narendranath Ghosh wrote:
> > Dear all!
> >
> >
> >
> > I am currently trying to optimizing a Pb180Se180 cluster using  QE.
> >
> > But after 83 iterations it didnâ€™t get converged.
> >
> > *Input  *
> >
> > calculation='relax',
> >
> >   outdir='/staging/op/NAREN_USC/PbSe_360_FINAL_based_Pb68Se68/OUTPUT',
> >
> >   prefix='PbSe-360',
> >
> >   pseudo_dir='/staging/op/NAREN_USC/PbSe_360_FINAL_based_
> Pb68Se68/pseudo',
> >
> >   verbosity='low',
> >
> > /
> >
> >
> >
> > 
> >
> >   ibrav=0,
> >
> >   celldm(1)=90.7068539791d0,
> >
> >   nat=360,
> >
> >   ntyp=2,
> >
> >   ecutwfc=30.0d0,
> >
> >   ecutrho=120.0d0,
> >
> >   input_dft='PBE',
> >
> >   occupations='smearing',
> >
> >   smearing='gaussian',
> >
> >   degauss=0.002000d0,
> >
> > /
> >
> > 
> >
> >   diagonalization='david',
> >
> >   mixing_mode='plain',
> >
> >   mixing_beta=0.700d0,
> >
> > /
> >
> > 
> >
> > /
> >
> > ATOMIC_SPECIES
> >
> >  Pb 207.20d0 Pb.pbe-hgh.UPF
> >
> >  Se 78.96d0  Se.pbe-hgh.UPF
> >
> >
> >
> > ATOMIC_POSITIONS {alat}
> >
> >   Pb   0.483110d0   0.474050d0   0.499930d0
> >
> >   Se   0.519080d0   0.527870d0   0.598110d0
> >
> >   Se   0.590190d0   0.471260d0   0.215480d0
> >
> > â€¦â€¦â€¦â€¦â€¦â€¦â€¦â€¦â€¦â€¦â€¦â€¦â€¦â€¦â€¦â€¦â€¦â€¦â€¦â€¦
> â€¦â€¦â€¦â€¦.
> >
> > K_POINTS {gamma}
> >
> >
> >
> > CELL_PARAMETERS {alat}
> >
> >   1.d0  0.d0  0.d0
> >
> >   0.d0  1.d0  0.d0
> >
> >   0.d0  0.d0  1.d0
> >
> >
> >
> >
> >
> > *Output*
> >
> > iteration # 81 ecut=30.00 Ry beta=0.70
> >
> >  Davidson diagonalization with overlap
> >
> >  WARNING: 9 eigenvalues not converged in regterg
> >
> >  ethr =  4.62E-04,  avg # of iterations = 21.0
> >
> >
> >
> >  total cpu time spent up to now is92680.3 secs
> >
> >
> >
> >  total energy  =2098.58547221 Ry
> >
> >  Harris-Foulkes estimate   =  -16225.87153481 Ry
> >
> >  estimated scf accuracy<  209398.02191142 Ry
> >
> >
> >
> >  iteration # 82 ecut=30.00 Ry beta=0.70
> >
> >  Davidson diagonalization with overlap
> >
> >  WARNING: 5 eigenvalues not converged in regterg
> >
> >  c_bands:  5 eigenvalues not converged
> >
> >  ethr =  4.62E-04,  avg # of iterations = 20.0
> >
> >
> >
> >  total cpu time spent up to now is95793.4 secs
> >
> >
> >
> >  total energy  =1914.32044477 Ry
> >
> >  Harris-Foulkes estimate   =  -18801.41916562 Ry
> >
> >  estimated scf accuracy<  243341.55571758 Ry
> >
> >
> >
> >  iteration # 83 ecut=30.00 Ry beta=0.70
> >
> >  Davidson diagonalization with overlap
> >
> >  WARNING:   138 eigenvalues not converged in regterg
> >
> >  ethr =  4.62E-04,  avg # of iterations = 27.0
> >
> >
> >
> >  total cpu time spent up to now is99442.6 secs
> >
> >
> >
> >  total energy  =

Re: [Pw_forum] Problem in CPMD simulation

2017-02-12 Thread ashkan shekaari

Try repeating the calculations without setting electron_temperature.
use ion_temperature = 'rescaling', without fnosep.

With my best regards,
Ashkan

*Ashkan Shekaari*
Plasma Physics Research Center
Science and Research Branch
I A U, 14778-93855 Tehran, Iran.

On Sun, Feb 12, 2017 at 2:12 AM, Debdipto Acharya <
debdipto.acha...@gmail.com> wrote:

> Dear QE developers,
>
> I am trying to do a CPMD simulation of water chain on graphene oxide
> nanosheet. First I have done the electron minimization step. Then I have
> performed CPMD simulation. But the fictitious kinetic energy of the
> electrons keep increasing during the dynamics. So I have tried by quenching
> the electrons from time to time. For this I performed two congugate
> gradient iteration (electron_dynamics 'cg') before switching back to verlet
> dynamics for the electrons. But this step stopped  with an unexpected
> error. The input and output files are attached with the mail.  I have also
> tried to run BOMD simulation for this system. And I am getting the same
> error. Instead of ifort, if I use gfortran, the problem goes away. But with
> gfortran the speed of the calculation is 3-4 times slower than with ifort.
>
> Thanks for your kind response in advance
>
> Regards
> Debdipto Acharya
> Prof. Shobhana Narasimhan's Lab,
> Theoretical Sciences Unit,
> JNCASR,
> Bangalore, India
>
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[Pw_forum] URGENT

2017-02-04 Thread ashkan shekaari

Dear experts,
Is temperature applied to a given system through the equipartition theorem
in a CPMD simulation?

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] Cpmd

2017-02-04 Thread ashkan shekaari

Dear experts,
How does the cp code import temperature for example for a 6-atom system
such as atomic clusters? I mean temperature is meaningful when the number
of atoms is of the order of the Avogadro number. Does it apply a kind of
periodic boundary condition as what is used in classical MD, generating
many copies of the given system in a periodic fashion?
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[Pw_forum] URGENT

2017-01-08 Thread ashkan shekaari

Dear experts,

In dealing with charged unit cells, what kind of scheme is applied in
quantum espresso to reduce periodic-image errors?


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] CPMD

2017-01-05 Thread ashkan shekaari

Dear experts,


Once a CPMD simulation at zero pressure, constant volume, and at a finite
temperature (say, T=70 K) is performed (temperature is kept constant by
rescaling the nuclear degrees of freedom), what kind of MD (NVE, or, NPT)
is going to be used?




Regards,
Ashkan

*Ashkan Shekaari*
Plasma Physics Research Center
Science and Research Branch
I A U, 14778-93855 Tehran, Iran.
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Re: [Pw_forum] problem about inputfile

2017-01-01 Thread ashkan shekaari

ATOMIC_POSITIONS, not ATOMIC_*POSITITONS*

Regards,
Ashkan

*Ashkan Shekaari*
Plasma Physics Research Center
Science and Research Branch
I A U, 14778-93855 Tehran, Iran.

On Sun, Jan 1, 2017 at 7:29 PM, Pascal Boulet <pascal.bou...@univ-amu.fr>
wrote:

> Hello,
>
> There is a $ instead of & before IONS, maybe…
>
> Pascal
>
> Le 1 janv. 2017 à 16:16, Nasim Ha <nasim.h1...@gmail.com> a écrit :
>
> > I want run pw.x but it stopped with this eroor : Error in routine
> > read_cards_pw (1):
> > atomic position info missing
> > I insert inputfile.
> > --
> > N.H.Jazi
> > PhD student of Physics.
> > Physics Department,Central Tehran Branch,Islamic Azad
> > University,Tehran,88074907,Iran.
> > <2polyaniline.pw-in>___
> > Pw_forum mailing list
> > Pw_forum@pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
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>
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[Pw_forum] URGENT

2016-12-24 Thread ashkan shekaari

Dear experts,
Is it sensible performing CPMD simulations in a time duration of about 300
fs?
How should such a parameter be determined?


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] time-in-CPMD

2016-12-23 Thread ashkan shekaari

Dear Nicola Marzari,
Is it sensible to perform a CPMD simulation in a time duration of about 300
fs?
How such a parameter should be determined?


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] URGENT

2016-12-20 Thread ashkan shekaari

Dear experts,

Should the total energy computed in a cp run be equal to that computed in a
scf run?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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[Pw_forum] CP

2016-12-20 Thread ashkan shekaari

Dear experts,
In CP simulations, how one could determine the effective electron mass in
CP Lagrangian?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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[Pw_forum] melt

2016-12-17 Thread ashkan shekaari

Dear experts,
Is it sensible trying to calculate the melting point of a semiconducting
material by applying CPMD on its unit cell, or, one has to apply MD
simulations on a large super cell of the material containing thousands of
atoms?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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Re: [Pw_forum] Number of iterations

2016-12-14 Thread ashkan shekaari

You are running out of RAM. No way, but check if the below works:
Increase your swap and run your operating system in text mode.

On Dec 14, 2016 11:20 PM, "fataneh bostan afroz" 
wrote:

> Dear All
> I perform   calculation of 'vc-relax',  using GGA+U
> The calculation is cut after 8  iteration because of shortage of RAM
> Can I determine  lower than 8  iteration for 'vc-relax',
> please guide me
> thank you
>
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[Pw_forum] 0

2016-12-09 Thread ashkan shekaari

Dear experts,

For the case of ibrav=0, how one could name high-symmetry points in the BZ?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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Re: [Pw_forum] kp

2016-11-28 Thread ashkan shekaari

Dear Giovanni,
Thank you so much for your explanatory response. So, as I understood, there
is no way to calculate band structure for a molecule and this is
nonsensical. Is it true?

On Nov 29, 2016 1:46 AM, <meisam@gmail.com> wrote:

> Just to add that plain wave is not a good approximation to reproduce
> molecular orbitals.
>
> Mortaza A
>
> PhD of Physics
> Ulm University, Germany
>
> On 28 Nov 2016, at 21:43, Giovanni Cantele <giovanni.cant...@spin.cnr.it>
> wrote:
>
> if you try to ask the question: "what the k-point mesh is for?" you can
> easily understand
> that a k-point mesh is for the Brillouin zone (BZ) sampling, that is,
> perform sums over k-points
> that approximate, with a required level of accuracy, the integral over the
> whole BZ. This is
> because in a crystal, the energy E(K) depends on the k vectors, and the
> same holds for the
> wave functions. However, when you build for example a cubic supercell
> including vacuum to
> simulate a molecule, you are actually dealing with a fictitious cubic
> crystal where the repeated
> units are sufficiently far apart from each other to not interact.
>
> Absence of interaction means flat (atomic-like) energy levels, that do not
> have dependence
> on the k vector. That is, the E(K) dispersion that you get in the case of
> a molecule, provided
> you include a sufficient vacuum space in your supercell, does not depend
> on k. If this is
> the case, you can use only the gamma point (a larger grid means large but
> useless
> computational time, because you are summing over eigenvalues at different
> k-points that
> are all the same!) for self consistency and BZ path is not needed, because
> if you select any
> path you should get flat, k-independent bands
>
> Giovanni
>
>
> On 28 Nov 2016, at 18:12, ashkan shekaari <sheka...@gmail.com> wrote:
>
> Dear experts,
>
> Is it necessary using kpoint mesh when we are dealing with molecules?
>
> In the case of a molecule in cubic vacuum, what path in BZ should be
> selected?
> *--*
> *Regards,*
> *Ashkan Shekaari*
> *Plasma Physics Research Center*
> *Science and Research Branch*
> *I A U, 14778-93855 Tehran, Iran.*
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[Pw_forum] kp

2016-11-28 Thread ashkan shekaari

Dear experts,

Is it necessary using kpoint mesh when we are dealing with molecules?

In the case of a molecule in cubic vacuum, what path in BZ should be
selected?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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[Pw_forum] BLYP

2016-11-28 Thread ashkan shekaari

Dear experts,

Is it sensible to use input_dft=b3lyp with blyp pseudopotentials?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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[Pw_forum] P. G. Parameters

2016-11-26 Thread ashkan shekaari

Dear Paolo Giannozzi,

Thank you so much for your quick response. I was wondering if you could
kindly inform me how one could determine the pseudopotential generation
parameters *ener*, *rcut*, and *rcutus* for a given atom?

*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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[Pw_forum] PP

2016-11-26 Thread ashkan shekaari

Dear experts,

Within the file Mo.pbe-spn-rrkjus_psl.0.2.UPF it is seen that tm=.true.
which means the PP has been generated using the TM method, but as its name
explains, the file has been generated using RRKJ method. Which one is
correct?
*--*

*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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Re: [Pw_forum] blyp

2016-11-24 Thread ashkan shekaari

Dear Dario,

Thank you so much for your quick response. But how could I generate a blyp
pseudo potential for Mo? There does not exist such a file in QE download
page.

On Nov 24, 2016 7:16 PM, "dario rocca" <roc...@gmail.com> wrote:

> Dear Ashkan
> not necessary but strongly recommended
> Best,
> Dario Rocca
>
> On Thu, Nov 24, 2016 at 2:08 PM, ashkan shekaari <sheka...@gmail.com>
> wrote:
>
>> Dear experts,
>>
>> is it necessary to use blyp pseudopotentials when input_dft is set to
>> blyp?
>> *--*
>> *Regards,*
>> *Ashkan Shekaari*
>> *Plasma Physics Research Center*
>> *Science and Research Branch*
>> *I A U, 14778-93855 Tehran, Iran.*
>>
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[Pw_forum] blyp

2016-11-24 Thread ashkan shekaari

Dear experts,

is it necessary to use blyp pseudopotentials when input_dft is set to blyp?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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[Pw_forum] MF

2016-11-18 Thread ashkan shekaari

Dear experts,

Does setting
  lspinorb=true
  noncolin=true
  fixed_magnetization
  constraint_magnetization
apply a magnetic field to the system under study?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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[Pw_forum] val

2016-11-17 Thread ashkan shekaari

Dear Giovanni,

As my last question, how could I determine the valence shell for a given
atom such as Mo?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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[Pw_forum] valence

2016-11-17 Thread ashkan shekaari

DEAR EXPERTS,

For a given atom such as Mo, which shells are considered by Q. E. as the
valence?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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Re: [Pw_forum] SPIN

2016-11-17 Thread ashkan shekaari

Dear Giovanni Cantele,

Thank you so much for the detailed response. As my last question, what is
the exact difference between starting magnetization and total magnetization?

*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*

On Thu, Nov 17, 2016 at 2:16 PM, Giovanni Cantele <
giovanni.cant...@spin.cnr.it> wrote:

> No, it is not necessary if you do not expect that the system under study
> has a magnetisation.
> See here:
> http://www.quantum-espresso.org/wp-content/uploads/Doc/pw_
> user_guide/node10.html#SECTION00043030
>
> In practice, for solids where NO internal or external magnetic field is
> not present,
> time-reversal symmetry applies. This has the consequence that
>
> E(k,up) = E(-k,down)
>
> so for a non-magnetic solid, even in the presence of spin-orbit coupling,
> it is possible that the spin-up and spin-down
> densities are the same and the total magnetisation zero. Non-magnetic
> solids then can divided into
> systems with (spatial) inversion symmetry and systems where this symmetry
> does not apply.
>
> The former have the additional constraint that E(k,
> any_spin)=E(-k,any_spin) that, combined with the previous equation,
> produces double SPIN degenerate bands (so each state AT GIVEN is at least
> double degenerate). Germanium is an example.
>
> The latter show a lifting of this double SPIN degeneracy, like in the case
> of GaAs. The spin degeneracy is recovered ONLY
> for those k-points for which k and -k are equivalent (thus differing by
> only a reciprocal lattice vector). Gamma point is an example.
>
> Giovanni
>
>
> On 16 Nov 2016, at 22:17, ashkan shekaari <sheka...@gmail.com> wrote:
>
> Dear experts,
>
> Is starting magnetization necessary to have a full spin-orbit coupling?
>
> What value should it take on?
> *--*
> *Regards,*
> *Ashkan Shekaari*
> *Plasma Physics Research Center*
> *Science and Research Branch*
> *I A U, 14778-93855 Tehran, Iran.*
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>
> --
>
> 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.cant...@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] SPIN

2016-11-16 Thread ashkan shekaari

Dear experts,

Is starting magnetization necessary to have a full spin-orbit coupling?

What value should it take on?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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[Pw_forum] Soc

2016-11-15 Thread ashkan shekaari

Dear experts,

1- Is adding
 lspinorb=true
 noncolin=true
enough to have a full spin orbit coupling?

2- Regardless of SOI, what are the other kinds of interaction Q.E. is able
to compute for a given system such as monolayer MoS2?
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[Pw_forum] Hpsi

2016-11-15 Thread ashkan shekaari

Dear Nicola Marzari,

If I want to add a term to the Hamiltonian of a given system, which
line/lines of h_psi.f90 must be modified and how?
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[Pw_forum] Urgent

2016-11-15 Thread ashkan shekaari

Dear Paolo Giannozzi,

If I want to add a term to the Hamiltonian of a given system, which
line/lines of h_psi.f90 must be modified and how?
*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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Re: [Pw_forum] A Cutting-edge Question !!!

2016-11-14 Thread ashkan shekaari

Dear Dr. Paulatto,
Thank you so much for your quick response. I was wondering if you could
possibly inform me which line must be modified.

On Nov 14, 2016 2:05 PM, "Lorenzo Paulatto" <lorenzo.paula...@impmc.upmc.fr>
wrote:

> On Monday, November 14, 2016 1:59:12 PM CET ashkan shekaari wrote:
> > Dear Matteo,
> > Thank you so much for your explanatory response.
> >
> > The very essence of my question is as follows:
> > If I want to add a term or a constant to the Hamiltonian of a given
> system,
> > which subroutine or code (*.f90) must be modified?
>
>
> PW/src/h_psi.f90
>
> but it may be harder than you expect
>
> kind regards
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Université Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www:   http://www-int.impmc.upmc.fr/~paulatto/
> mail:  23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05
>
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Re: [Pw_forum] A Cutting-edge Question !!!

2016-11-14 Thread ashkan shekaari

Dear Matteo,
Thank you so much for your explanatory response.

The very essence of my question is as follows:
If I want to add a term or a constant to the Hamiltonian of a given system,
which subroutine or code (*.f90) must be modified?

On Nov 14, 2016 12:02 PM, "Matteo Cococcioni" <mat...@umn.edu> wrote:

> Dear Ashkan,
>
> I'm not sure I understand your question completely, but will attempt an
> answer.
>
> First thing to keep in mind is that QE (as any other DFT code) works with
> the Kohn-Sham single particle Hamiltonian (is that what you are looking
> for?), whose eigenstates are the ones that allow you to construct the
> ground state charge density of a system and to evaluate its total energy.
> Due to the Bloch theorem (i.e. to the translational invariance of
> crystalline solids) this Hamiltonian is block-diagonal on the k-points
> (crystal momentum of electrons). Also, QE uses an expansion of Kohn-Sham
> wavefunctions on a plane-wave basis set. So, each of these blocks of the
> Hamiltonian is npw x npw where npw is the number of plane-waves used in the
> expansion of the wavefunctions of that specific k-point. QE performs an
> iterative diagonalization of each block that is involves computing the
> action of the Hamiltonian onto the current wavefunction H |psi>. This is
> done in a routine called h_psi which is the driver to compute various parts
> of the Hamiltonian and to operate it on the wavefunction. So I guess you
> can look inside that routine in order to find what you need.
>
> Best regards,
>
> Matteo
>
> On Sun, Nov 13, 2016 at 11:24 PM, ashkan shekaari <sheka...@gmail.com>
> wrote:
>
>> Dear experts,
>>
>> How, could one derive the Hamiltonian of a given system resulting in
>> energy eigenvalues (band structure) *through the modules or subroutines*
>> included in Q. E. integrated suite?
>>
>> Is there anyway for this end?
>>
>> For example, if I provide an input scf file, how could I figure out what
>> Hamiltonian will be used in my calculations?
>>
>> How could I make a change in the Hamiltonian of a system by manipulating
>> subroutines (not the input file)?
>>
>>
>> *--*
>> *Regards,*
>> *Ashkan Shekaari*
>> *Plasma Physics Research Center*
>> *Science and Research Branch*
>> *I A U, 14778-93855 Tehran, Iran.*
>>
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[Pw_forum] A Cutting-edge Question !!!

2016-11-13 Thread ashkan shekaari

Dear experts,

How, could one derive the Hamiltonian of a given system resulting in energy
eigenvalues (band structure) *through the modules or subroutines* included
in Q. E. integrated suite?

Is there anyway for this end?

For example, if I provide an input scf file, how could I figure out what
Hamiltonian will be used in my calculations?

How could I make a change in the Hamiltonian of a system by manipulating
subroutines (not the input file)?


*--*
*Regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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[Pw_forum] WanT

2016-10-31 Thread ashkan shekaari

Dear all,

Does anyone have a sample input file for the code disentangle.x?

I was wondering if you could kindly help me provide such a file.
*--*
*Best,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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Re: [Pw_forum] Van der Waals interactions

2016-10-09 Thread ashkan shekaari

Dear Eliya,

you have to set vdw_corr value in  namelist.

*--*
*Best,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*

On Sun, Oct 9, 2016 at 4:20 PM, Eliya Asmani <eliya6...@gmail.com> wrote:

> Dear all
>
> I want to consider the Van der Waals (vdw) interactions in my
> calculations. I'm using LDA (with Perdew-Zunger parametrization) pseudo
> potential and also 5.2.1 version of quantum espresso.
>
> It is OK to use input_dft = 'vdw-df' in input file or another functionals can 
> be found in this file:
>
> "Modules/funct.f90"
>
> Thanks
>
> Eliya Asmani,
> Postdoctoral Researcher
> School of Physics, Institute for Research in Fundamental Sciences (IPM)
> Tehran, Iran
>
>
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Re: [Pw_forum] ibrav

2016-07-31 Thread ashkan shekaari

Dear mamba,

define as below:

ibrav=0
celldm(1)=a large value

and use CELL_PARAMETERS to define a large box containing the atoms

and to set a vacuum around the box large enough to eliminate the
periodicity.





*--*
*Best,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*

On Sun, Jul 31, 2016 at 3:17 AM, sandile mamba <sandilemam...@gmail.com>
wrote:

> Dear all
>
> I want to write an input file for a molecule with 95 atoms. It does not
> have a specific crystal structure. My question is, is it possible to have
> such an input file in quantum espresso.
>
> --
> Kind Regards From
>
> Mr Sandile Thulani Mamba
>
> UKZN Student
> Cell +268 7629 4865
> Cell +27 72 956 2380
>
>
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[Pw_forum] US

2016-06-03 Thread ashkan shekaari

Dear experts,

Is it necessary to take the kinetic energy cut-off for the charge density
and the potential 8-12 times larger than the energy cut-off for the wave
functions for the case of 2D-MoS2?

Doesn't a less value of about 4 times larger than the energy cut-off for
the wave functions work?

*--*
*Best,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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Re: [Pw_forum] uf

2016-06-01 Thread ashkan shekaari

Dear Ari,

Thank you so much. I've downloaded it but its examples do not work.

I am unfolding the bands on my own.

Best.

*--*
*Best,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*

On Tue, May 31, 2016 at 4:08 PM, Ari P Seitsonen <ari.p.seitso...@iki.fi>
wrote:

>
> Dear Ashkan,
>
>   I am aware of this:
>
> https://www.ifm.liu.se/theomod/compphys/band-unfolding/
>
> Greetings from Paris,
>
>apsi
>
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>   Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
> Ecole Normale Supérieure (ENS), Département de Chimie, Paris
> Mobile (F) : +33 789 37 24 25    (CH) : +41 79 71 90 935
>
>
>
> On Fri, 27 May 2016, ashkan shekaari wrote:
>
> Dear experts,
>> How could one unfold the folded band structure of a supercell?
>>
>> Is there a code for this purpose in QE?
>>
>> --
>> Best,
>> Ashkan Shekaari
>> Plasma Physics Research Center
>> Science and Research Branch
>> I A U, 14778-93855 Tehran, Iran.
>>
>
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[Pw_forum] uf

2016-05-27 Thread ashkan shekaari

Dear experts,

How could one unfold the folded band structure of a supercell?

Is there a code for this purpose in QE?

*--*
*Best,*
*Ashkan Shekaari*
*Plasma Physics Research Center*
*Science and Research Branch*
*I A U, 14778-93855 Tehran, Iran.*
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Re: [Pw_forum] ib

2016-05-25 Thread ashkan shekaari

Dear Paolo,

It seems that the THERMO_PW package does not work properly and has a
problem.

*--*
*All the best,*
*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, 14778-93855 Tehran, Iran.*

On Wed, May 25, 2016 at 9:49 PM, ashkan shekaari <sheka...@gmail.com> wrote:

> Dear Paolo,
>
> pw.x is OK. But thermo_pw.x results in the error. Is anything wrong with
> thermo_pw package?
>
> *--*
> *All the best,*
> *Ashkan Shekaari*
> *Plasma Physics Research Center, Science and Research Branch, *
> *I A U, 14778-93855 Tehran, Iran.*
>
> On Wed, May 25, 2016 at 9:46 PM, ashkan shekaari <sheka...@gmail.com>
> wrote:
>
>> Dear Paolo,
>>
>> This is my input file and I use thermo_pw.x.
>>
>> 
>>  calculation = 'scf'
>>  prefix='sc-0',
>>  tstress = .true.,
>>  tprnfor = .true.,
>>  pseudo_dir = '/home/ashkan/apps/5.3/espresso-5.3.0/pseudo',
>>  outdir='./'
>>  wf_collect= .true.,
>>  verbosity= 'high',
>> /
>> 
>>  ibrav = 4,
>>  a = 6.3220,
>>  b = 6.3220,
>>  c = 15.70,
>>  cosAB=-0.5,
>>  cosAC=0.0,
>>  cosBC=0.0,
>>  nat = 12,
>>  ntyp = 2,
>>  ecutwfc = 60.0,
>>  ecutrho = 200.0,
>>  occupations = 'smearing'
>>  smearing = 'm-p'
>>  degauss = 0.01
>> /
>> 
>>  mixing_beta = 0.7,
>>  conv_thr = 1.0d-10,
>>  mixing_mode = 'local-TF',
>> /
>>
>> ATOMIC_SPECIES
>> Mo 95.960 Mo.pbe-spn-rrkjus_psl.0.2.UPF
>> S  32.065 S.pbe-n-rrkjus_psl.0.1.UPF
>>
>> ATOMIC_POSITIONS (crystal)
>> Mo  0.000  0.000  0.000
>> Mo  0.500  0.000  0.000
>> Mo  0.501  0.502  0.000
>> Mo  0.001  0.502  0.000
>> S   0.167  0.335  0.1003800
>> S   0.167  0.335 -0.1003800
>> S   0.667  0.335  0.1003800
>> S   0.667  0.335 -0.1003800
>> S   0.169  0.837 -0.1003800
>> S   0.169  0.837  0.1003800
>> S   0.669  0.837 -0.1003800
>> S   0.669  0.837  0.1003800
>>
>> K_POINTS {automatic}
>> 22 22 1 0 0 0
>>
>> *--*
>> *All the best,*
>> *Ashkan Shekaari*
>> *Plasma Physics Research Center, Science and Research Branch, *
>> *I A U, 14778-93855 Tehran, Iran.*
>>
>> On Wed, May 25, 2016 at 9:45 PM, ashkan shekaari <sheka...@gmail.com>
>> wrote:
>>
>>> This is my input file and I use thermo_pw.x
>>>
>>> 
>>>  calculation = 'scf'
>>>  prefix='sc-0',
>>>  tstress = .true.,
>>>  tprnfor = .true.,
>>>  pseudo_dir = '/home/ashkan/apps/5.3/espresso-5.3.0/pseudo',
>>>  outdir='./'
>>>  wf_collect= .true.,
>>>  verbosity= 'high',
>>> /
>>> 
>>>  ibrav = 4,
>>>  a = 6.3220,
>>>  b = 6.3220,
>>>  c = 15.70,
>>>  cosAB=-0.5,
>>>  cosAC=0.0,
>>>  cosBC=0.0,
>>>  nat = 12,
>>>  ntyp = 2,
>>>  ecutwfc = 60.0,
>>>  ecutrho = 200.0,
>>>  occupations = 'smearing'
>>>  smearing = 'm-p'
>>>  degauss = 0.01
>>> /
>>> 
>>>  mixing_beta = 0.7,
>>>  conv_thr = 1.0d-10,
>>>  mixing_mode = 'local-TF',
>>> /
>>>
>>> ATOMIC_SPECIES
>>> Mo 95.960 Mo.pbe-spn-rrkjus_psl.0.2.UPF
>>> S  32.065 S.pbe-n-rrkjus_psl.0.1.UPF
>>>
>>> ATOMIC_POSITIONS (crystal)
>>> Mo  0.000  0.000  0.000
>>> Mo  0.500  0.000  0.000
>>> Mo  0.501  0.502  0.000
>>> Mo  0.001  0.5000002  0.000
>>> S   0.167  0.335  0.1003800
>>> S   0.167  0.335 -0.1003800
>>> S   0.667  0.335  0.1003800
>>> S   0.667  0.335 -0.1003800
>>> S   0.169  0.837 -0.1003800
>>> S   0.169  0.837  0.1003800
>>> S   0.669  0.837 -0.1003800
>>> S   0.669  0.837  0.1003800
>>>
>>> K_POINTS {automatic}
>>> 22 22 1 0 0 0
>>>
>>> *--*
>>> *All the best,*
>>> *Ashkan Shekaari*
>>> *Plasma Physics Research Center, Science and Research Branch, *
>>> *I A U, 14778-93855 Tehran, Iran.*
>>>
>>> On Wed, May 25, 2016 at 8:44 PM, Paolo Giannozzi <p.gianno...@gmail.com>
>>> wrote:
>>>
>>>> Hard to say, since you do not provide your input file but just a few
>>>> lines (which run without any error when inserted in another job)
>>>>
>>>

Re: [Pw_forum] ib

2016-05-25 Thread ashkan shekaari

Dear Paolo,

pw.x is OK. But thermo_pw.x results in the error. Is anything wrong with
thermo_pw package?

*--*
*All the best,*
*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, 14778-93855 Tehran, Iran.*

On Wed, May 25, 2016 at 9:46 PM, ashkan shekaari <sheka...@gmail.com> wrote:

> Dear Paolo,
>
> This is my input file and I use thermo_pw.x.
>
> 
>  calculation = 'scf'
>  prefix='sc-0',
>  tstress = .true.,
>  tprnfor = .true.,
>  pseudo_dir = '/home/ashkan/apps/5.3/espresso-5.3.0/pseudo',
>  outdir='./'
>  wf_collect= .true.,
>  verbosity= 'high',
> /
> 
>  ibrav = 4,
>  a = 6.3220,
>  b = 6.3220,
>  c = 15.70,
>  cosAB=-0.5,
>  cosAC=0.0,
>  cosBC=0.0,
>  nat = 12,
>  ntyp = 2,
>  ecutwfc = 60.0,
>  ecutrho = 200.0,
>  occupations = 'smearing'
>  smearing = 'm-p'
>  degauss = 0.01
> /
> 
>  mixing_beta = 0.7,
>  conv_thr = 1.0d-10,
>  mixing_mode = 'local-TF',
> /
>
> ATOMIC_SPECIES
> Mo 95.960 Mo.pbe-spn-rrkjus_psl.0.2.UPF
> S  32.065 S.pbe-n-rrkjus_psl.0.1.UPF
>
> ATOMIC_POSITIONS (crystal)
> Mo  0.000  0.000  0.000
> Mo  0.500  0.000  0.000
> Mo  0.501  0.502  0.000
> Mo  0.001  0.502  0.000
> S   0.167  0.335  0.1003800
> S   0.167  0.335 -0.1003800
> S   0.667  0.335  0.1003800
> S   0.667  0.335 -0.1003800
> S   0.169  0.837 -0.1003800
> S   0.169  0.837  0.1003800
> S   0.669  0.837 -0.1003800
> S   0.669  0.837  0.1003800
>
> K_POINTS {automatic}
> 22 22 1 0 0 0
>
> *--*
> *All the best,*
> *Ashkan Shekaari*
> *Plasma Physics Research Center, Science and Research Branch, *
> *I A U, 14778-93855 Tehran, Iran.*
>
> On Wed, May 25, 2016 at 9:45 PM, ashkan shekaari <sheka...@gmail.com>
> wrote:
>
>> This is my input file and I use thermo_pw.x
>>
>> 
>>  calculation = 'scf'
>>  prefix='sc-0',
>>  tstress = .true.,
>>  tprnfor = .true.,
>>  pseudo_dir = '/home/ashkan/apps/5.3/espresso-5.3.0/pseudo',
>>  outdir='./'
>>  wf_collect= .true.,
>>  verbosity= 'high',
>> /
>> 
>>  ibrav = 4,
>>  a = 6.3220,
>>  b = 6.3220,
>>  c = 15.70,
>>  cosAB=-0.5,
>>  cosAC=0.0,
>>  cosBC=0.0,
>>  nat = 12,
>>  ntyp = 2,
>>  ecutwfc = 60.0,
>>  ecutrho = 200.0,
>>  occupations = 'smearing'
>>  smearing = 'm-p'
>>  degauss = 0.01
>> /
>> 
>>  mixing_beta = 0.7,
>>  conv_thr = 1.0d-10,
>>  mixing_mode = 'local-TF',
>> /
>>
>> ATOMIC_SPECIES
>> Mo 95.960 Mo.pbe-spn-rrkjus_psl.0.2.UPF
>> S  32.065 S.pbe-n-rrkjus_psl.0.1.UPF
>>
>> ATOMIC_POSITIONS (crystal)
>> Mo  0.000  0.000  0.000
>> Mo  0.500  0.000  0.000
>> Mo  0.5000001  0.502  0.000
>> Mo  0.001  0.502  0.000
>> S   0.167  0.335  0.1003800
>> S   0.167  0.335 -0.1003800
>> S   0.667  0.335  0.1003800
>> S   0.667  0.335 -0.1003800
>> S   0.169  0.837 -0.1003800
>> S   0.169  0.837  0.1003800
>> S   0.669  0.837 -0.1003800
>> S   0.6666669  0.837  0.1003800
>>
>> K_POINTS {automatic}
>> 22 22 1 0 0 0
>>
>> *--*
>> *All the best,*
>> *Ashkan Shekaari*
>> *Plasma Physics Research Center, Science and Research Branch, *
>> *I A U, 14778-93855 Tehran, Iran.*
>>
>> On Wed, May 25, 2016 at 8:44 PM, Paolo Giannozzi <p.gianno...@gmail.com>
>> wrote:
>>
>>> Hard to say, since you do not provide your input file but just a few
>>> lines (which run without any error when inserted in another job)
>>>
>>> Paolo
>>>
>>> On Wed, May 25, 2016 at 5:51 PM, ashkan shekaari <sheka...@gmail.com>
>>> wrote:
>>>
>>>> Dear Paolo,
>>>>
>>>> I got the right input for super cell:
>>>>
>>>> 
>>>>  ibrav = 4,
>>>>  a = 6.3220,
>>>>  b = 6.3220,
>>>>  c = 15.70,
>>>>  cosAB=-0.5,
>>>>  cosAC=0.0,
>>>>  cosBC=0.0,
>>>>
>>>> but I have an error as below:
>>>>
>>>>  task # 1
>>>>  from input : error # 1
>>>>  do not specify both celldm and a,b,c!
>>>>
>>>> This is while I have not used celldm. Is anything wrong with the input
>>>> file?
>>>>
>>>>
>>>>
>>>&

Re: [Pw_forum] ib

2016-05-25 Thread ashkan shekaari

Dear Paolo,

This is my input file and I use thermo_pw.x.


 calculation = 'scf'
 prefix='sc-0',
 tstress = .true.,
 tprnfor = .true.,
 pseudo_dir = '/home/ashkan/apps/5.3/espresso-5.3.0/pseudo',
 outdir='./'
 wf_collect= .true.,
 verbosity= 'high',
/

 ibrav = 4,
 a = 6.3220,
 b = 6.3220,
 c = 15.70,
 cosAB=-0.5,
 cosAC=0.0,
 cosBC=0.0,
 nat = 12,
 ntyp = 2,
 ecutwfc = 60.0,
 ecutrho = 200.0,
 occupations = 'smearing'
 smearing = 'm-p'
 degauss = 0.01
/

 mixing_beta = 0.7,
 conv_thr = 1.0d-10,
 mixing_mode = 'local-TF',
/

ATOMIC_SPECIES
Mo 95.960 Mo.pbe-spn-rrkjus_psl.0.2.UPF
S  32.065 S.pbe-n-rrkjus_psl.0.1.UPF

ATOMIC_POSITIONS (crystal)
Mo  0.000  0.000  0.000
Mo  0.500  0.000  0.000
Mo  0.501  0.502  0.000
Mo  0.001  0.502  0.000
S   0.167  0.335  0.1003800
S   0.167  0.335 -0.1003800
S   0.667  0.335  0.1003800
S   0.667  0.335 -0.1003800
S   0.169  0.837 -0.1003800
S   0.169  0.837  0.1003800
S   0.669  0.837 -0.1003800
S   0.669  0.837  0.1003800

K_POINTS {automatic}
22 22 1 0 0 0

*--*
*All the best,*
*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, 14778-93855 Tehran, Iran.*

On Wed, May 25, 2016 at 9:45 PM, ashkan shekaari <sheka...@gmail.com> wrote:

> This is my input file and I use thermo_pw.x
>
> 
>  calculation = 'scf'
>  prefix='sc-0',
>  tstress = .true.,
>  tprnfor = .true.,
>  pseudo_dir = '/home/ashkan/apps/5.3/espresso-5.3.0/pseudo',
>  outdir='./'
>  wf_collect= .true.,
>  verbosity= 'high',
> /
> 
>  ibrav = 4,
>  a = 6.3220,
>  b = 6.3220,
>  c = 15.70,
>  cosAB=-0.5,
>  cosAC=0.0,
>  cosBC=0.0,
>  nat = 12,
>  ntyp = 2,
>  ecutwfc = 60.0,
>  ecutrho = 200.0,
>  occupations = 'smearing'
>  smearing = 'm-p'
>  degauss = 0.01
> /
> 
>  mixing_beta = 0.7,
>  conv_thr = 1.0d-10,
>  mixing_mode = 'local-TF',
> /
>
> ATOMIC_SPECIES
> Mo 95.960 Mo.pbe-spn-rrkjus_psl.0.2.UPF
> S  32.065 S.pbe-n-rrkjus_psl.0.1.UPF
>
> ATOMIC_POSITIONS (crystal)
> Mo  0.000  0.000  0.000
> Mo  0.500  0.000  0.000
> Mo  0.501  0.502  0.000
> Mo  0.001  0.502  0.000
> S   0.167  0.335  0.1003800
> S   0.167  0.335 -0.1003800
> S   0.667  0.335  0.1003800
> S   0.667  0.335 -0.1003800
> S   0.169  0.837 -0.1003800
> S   0.169  0.837  0.1003800
> S   0.669  0.837 -0.1003800
> S   0.669  0.837  0.1003800
>
> K_POINTS {automatic}
> 22 22 1 0 0 0
>
> *--*
> *All the best,*
> *Ashkan Shekaari*
> *Plasma Physics Research Center, Science and Research Branch, *
> *I A U, 14778-93855 Tehran, Iran.*
>
> On Wed, May 25, 2016 at 8:44 PM, Paolo Giannozzi <p.gianno...@gmail.com>
> wrote:
>
>> Hard to say, since you do not provide your input file but just a few
>> lines (which run without any error when inserted in another job)
>>
>> Paolo
>>
>> On Wed, May 25, 2016 at 5:51 PM, ashkan shekaari <sheka...@gmail.com>
>> wrote:
>>
>>> Dear Paolo,
>>>
>>> I got the right input for super cell:
>>>
>>> 
>>>  ibrav = 4,
>>>  a = 6.3220,
>>>  b = 6.3220,
>>>  c = 15.70,
>>>  cosAB=-0.5,
>>>  cosAC=0.0,
>>>  cosBC=0.0,
>>>
>>> but I have an error as below:
>>>
>>>  task #     1
>>>  from input : error # 1
>>>  do not specify both celldm and a,b,c!
>>>
>>> This is while I have not used celldm. Is anything wrong with the input
>>> file?
>>>
>>>
>>>
>>>
>>> *--*
>>> *All the best,*
>>> *Ashkan Shekaari*
>>> *Plasma Physics Research Center, Science and Research Branch, *
>>> *I A U, 14778-93855 Tehran, Iran.*
>>>
>>> On Wed, May 25, 2016 at 3:38 PM, ashkan shekaari <sheka...@gmail.com>
>>> wrote:
>>>
>>>> Or, what other quantities or namelists should be used?
>>>>
>>>> *--*
>>>> *All the best,*
>>>> *Ashkan Shekaari*
>>>> *Plasma Physics Research Center, Science and Research Branch, *
>>>> *I A U, 14778-93855 Tehran, Iran.*
>>>>
>>>> On Wed, May 25, 2016 at 3:32 PM, ashkan shekaari <sheka...@gmail.com>
>>>> wrote:
>>>>
>>>>> Could you please tell me how?
>>>>>
>>>>> For example for a 2*2 super cell of 2D-mos2 I have:
>>>>>
>>>>>  ibrav = 0,
>>>>>  celldm(1) = 5.9735,
&g

Re: [Pw_forum] ib

2016-05-25 Thread ashkan shekaari

This is my input file and I use thermo_pw.x


 calculation = 'scf'
 prefix='sc-0',
 tstress = .true.,
 tprnfor = .true.,
 pseudo_dir = '/home/ashkan/apps/5.3/espresso-5.3.0/pseudo',
 outdir='./'
 wf_collect= .true.,
 verbosity= 'high',
/

 ibrav = 4,
 a = 6.3220,
 b = 6.3220,
 c = 15.70,
 cosAB=-0.5,
 cosAC=0.0,
 cosBC=0.0,
 nat = 12,
 ntyp = 2,
 ecutwfc = 60.0,
 ecutrho = 200.0,
 occupations = 'smearing'
 smearing = 'm-p'
 degauss = 0.01
/

 mixing_beta = 0.7,
 conv_thr = 1.0d-10,
 mixing_mode = 'local-TF',
/

ATOMIC_SPECIES
Mo 95.960 Mo.pbe-spn-rrkjus_psl.0.2.UPF
S  32.065 S.pbe-n-rrkjus_psl.0.1.UPF

ATOMIC_POSITIONS (crystal)
Mo  0.000  0.000  0.000
Mo  0.500  0.000  0.000
Mo  0.501  0.502  0.000
Mo  0.001  0.502  0.000
S   0.167  0.335  0.1003800
S   0.167  0.335 -0.1003800
S   0.667  0.335  0.1003800
S   0.667  0.335 -0.1003800
S   0.169  0.837 -0.1003800
S   0.169  0.837  0.1003800
S   0.669  0.837 -0.1003800
S   0.669  0.837  0.1003800

K_POINTS {automatic}
22 22 1 0 0 0

*--*
*All the best,*
*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, 14778-93855 Tehran, Iran.*

On Wed, May 25, 2016 at 8:44 PM, Paolo Giannozzi <p.gianno...@gmail.com>
wrote:

> Hard to say, since you do not provide your input file but just a few lines
> (which run without any error when inserted in another job)
>
> Paolo
>
> On Wed, May 25, 2016 at 5:51 PM, ashkan shekaari <sheka...@gmail.com>
> wrote:
>
>> Dear Paolo,
>>
>> I got the right input for super cell:
>>
>> 
>>  ibrav = 4,
>>  a = 6.3220,
>>  b = 6.3220,
>>  c = 15.70,
>>  cosAB=-0.5,
>>  cosAC=0.0,
>>  cosBC=0.0,
>>
>> but I have an error as below:
>>
>>  task # 1
>>  from input : error # 1
>>  do not specify both celldm and a,b,c!
>>
>> This is while I have not used celldm. Is anything wrong with the input
>> file?
>>
>>
>>
>>
>> *--*
>> *All the best,*
>> *Ashkan Shekaari*
>> *Plasma Physics Research Center, Science and Research Branch, *
>> *I A U, 14778-93855 Tehran, Iran.*
>>
>> On Wed, May 25, 2016 at 3:38 PM, ashkan shekaari <sheka...@gmail.com>
>> wrote:
>>
>>> Or, what other quantities or namelists should be used?
>>>
>>> *--*
>>> *All the best,*
>>> *Ashkan Shekaari*
>>> *Plasma Physics Research Center, Science and Research Branch, *
>>> *I A U, 14778-93855 Tehran, Iran.*
>>>
>>> On Wed, May 25, 2016 at 3:32 PM, ashkan shekaari <sheka...@gmail.com>
>>> wrote:
>>>
>>>> Could you please tell me how?
>>>>
>>>> For example for a 2*2 super cell of 2D-mos2 I have:
>>>>
>>>>  ibrav = 0,
>>>>  celldm(1) = 5.9735,
>>>>
>>>> CELL_PARAMETERS (alat=  5.9735)
>>>>2.00   0.000.00
>>>>   -1.00   1.73    0.00
>>>>0.00   0.005.00
>>>>
>>>> ,but I wanna use ibrav=4.
>>>>
>>>> How these parameters should be changed?
>>>>
>>>> *--*
>>>> *All the best,*
>>>> *Ashkan Shekaari*
>>>> *Plasma Physics Research Center, Science and Research Branch, *
>>>> *I A U, 14778-93855 Tehran, Iran.*
>>>>
>>>> On Wed, May 25, 2016 at 3:22 PM, Paolo Giannozzi <p.gianno...@gmail.com
>>>> > wrote:
>>>>
>>>>> it is
>>>>>
>>>>> On Wed, May 25, 2016 at 12:48 PM, ashkan shekaari <sheka...@gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Dear experts,
>>>>>>
>>>>>> Is it possible to make a super cell without setting ibrav=0 ?
>>>>>> *--*
>>>>>> *All the best,*
>>>>>> *Ashkan Shekaari*
>>>>>> *Plasma Physics Research Center, Science and Research Branch, *
>>>>>> *I A U, 14778-93855 Tehran, Iran.*
>>>>>>
>>>>>> ___
>>>>>> Pw_forum mailing list
>>>>>> Pw_forum@pwscf.org
>>>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>>
>>>>> ___
>>>>> Pw_forum mailing list
>>>>> Pw_forum@pwscf.org
>>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>>
>>>>
>>>>
>>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
> 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
>
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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Re: [Pw_forum] ib

2016-05-25 Thread ashkan shekaari

Dear Paolo,

I got the right input for super cell:


 ibrav = 4,
 a = 6.3220,
 b = 6.3220,
 c = 15.70,
 cosAB=-0.5,
 cosAC=0.0,
 cosBC=0.0,

but I have an error as below:

 task # 1
 from input : error # 1
 do not specify both celldm and a,b,c!

This is while I have not used celldm. Is anything wrong with the input file?




*--*
*All the best,*
*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, 14778-93855 Tehran, Iran.*

On Wed, May 25, 2016 at 3:38 PM, ashkan shekaari <sheka...@gmail.com> wrote:

> Or, what other quantities or namelists should be used?
>
> *--*
> *All the best,*
> *Ashkan Shekaari*
> *Plasma Physics Research Center, Science and Research Branch, *
> *I A U, 14778-93855 Tehran, Iran.*
>
> On Wed, May 25, 2016 at 3:32 PM, ashkan shekaari <sheka...@gmail.com>
> wrote:
>
>> Could you please tell me how?
>>
>> For example for a 2*2 super cell of 2D-mos2 I have:
>>
>>  ibrav = 0,
>>  celldm(1) = 5.9735,
>>
>> CELL_PARAMETERS (alat=  5.9735)
>>2.00   0.000.00
>>   -1.00   1.730.00
>>0.00   0.005.00
>>
>> ,but I wanna use ibrav=4.
>>
>> How these parameters should be changed?
>>
>> *--*
>> *All the best,*
>> *Ashkan Shekaari*
>> *Plasma Physics Research Center, Science and Research Branch, *
>> *I A U, 14778-93855 Tehran, Iran.*
>>
>> On Wed, May 25, 2016 at 3:22 PM, Paolo Giannozzi <p.gianno...@gmail.com>
>> wrote:
>>
>>> it is
>>>
>>> On Wed, May 25, 2016 at 12:48 PM, ashkan shekaari <sheka...@gmail.com>
>>> wrote:
>>>
>>>> Dear experts,
>>>>
>>>> Is it possible to make a super cell without setting ibrav=0 ?
>>>> *--*
>>>> *All the best,*
>>>> *Ashkan Shekaari*
>>>> *Plasma Physics Research Center, Science and Research Branch, *
>>>> *I A U, 14778-93855 Tehran, Iran.*
>>>>
>>>> ___
>>>> Pw_forum mailing list
>>>> Pw_forum@pwscf.org
>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>
>>>
>>>
>>>
>>> --
>>> 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
>>>
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>
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Re: [Pw_forum] ib

2016-05-25 Thread ashkan shekaari

Or, what other quantities or namelists should be used?

*--*
*All the best,*
*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, 14778-93855 Tehran, Iran.*

On Wed, May 25, 2016 at 3:32 PM, ashkan shekaari <sheka...@gmail.com> wrote:

> Could you please tell me how?
>
> For example for a 2*2 super cell of 2D-mos2 I have:
>
>  ibrav = 0,
>  celldm(1) = 5.9735,
>
> CELL_PARAMETERS (alat=  5.9735)
>2.00   0.000.00
>   -1.00   1.730.00
>0.00   0.005.00
>
> ,but I wanna use ibrav=4.
>
> How these parameters should be changed?
>
> *--*
> *All the best,*
> *Ashkan Shekaari*
> *Plasma Physics Research Center, Science and Research Branch, *
> *I A U, 14778-93855 Tehran, Iran.*
>
> On Wed, May 25, 2016 at 3:22 PM, Paolo Giannozzi <p.gianno...@gmail.com>
> wrote:
>
>> it is
>>
>> On Wed, May 25, 2016 at 12:48 PM, ashkan shekaari <sheka...@gmail.com>
>> wrote:
>>
>>> Dear experts,
>>>
>>> Is it possible to make a super cell without setting ibrav=0 ?
>>> *--*
>>> *All the best,*
>>> *Ashkan Shekaari*
>>> *Plasma Physics Research Center, Science and Research Branch, *
>>> *I A U, 14778-93855 Tehran, Iran.*
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>>
>> --
>> 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
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
___
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Re: [Pw_forum] ib

2016-05-25 Thread ashkan shekaari

Could you please tell me how?

For example for a 2*2 super cell of 2D-mos2 I have:

 ibrav = 0,
 celldm(1) = 5.9735,

CELL_PARAMETERS (alat=  5.9735)
   2.00   0.000.00
  -1.00   1.730.00
   0.00   0.005.00

,but I wanna use ibrav=4.

How these parameters should be changed?

*--*
*All the best,*
*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, 14778-93855 Tehran, Iran.*

On Wed, May 25, 2016 at 3:22 PM, Paolo Giannozzi <p.gianno...@gmail.com>
wrote:

> it is
>
> On Wed, May 25, 2016 at 12:48 PM, ashkan shekaari <sheka...@gmail.com>
> wrote:
>
>> Dear experts,
>>
>> Is it possible to make a super cell without setting ibrav=0 ?
>> *--*
>> *All the best,*
>> *Ashkan Shekaari*
>> *Plasma Physics Research Center, Science and Research Branch, *
>> *I A U, 14778-93855 Tehran, Iran.*
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
> 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
>
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
___
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[Pw_forum] ib

2016-05-25 Thread ashkan shekaari

Dear experts,

Is it possible to make a super cell without setting ibrav=0 ?
*--*
*All the best,*
*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, 14778-93855 Tehran, Iran.*
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[Pw_forum] sc

2016-05-24 Thread ashkan shekaari

Dear experts,

I've calculated the band structure of a 2*2 super cell of MoS2 monolayer
but it is different from that of its unit cell. Is something wrong with my
calculation?

I've also accounted for the back folding effect so that I've changed the
k-points of the unit cell calculation:

0.00  0.00 0.00 50
0.50  0.00 0.00 37
0.66 -0.33 0.00 75
0.00  0.00 0.00 1

as follows:

0.00  0.00 0.00 50
1.00  0.00 0.00 37
1.32 -0.66 0.00 75
0.00  0.00 0.00 1


*--*
*All the best,*
*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, 14778-93855 Tehran, Iran.*


mos2-band.ps
Description: PostScript document
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Re: [Pw_forum] pdos

2016-05-07 Thread ashkan shekaari

Dear experts,

in quantum mechanics, the quantum number *m* is between *-l *and* l *:
-l<=m<=l

and so m=-1, 0, +1 for l=1. but in the output of a pdos calculation, values
of m

are seen as follows:

 state #   9: atom   1 (Mo ), wfc  5 (l=2 m= 1)
 state #  10: atom   1 (Mo ), wfc  5 (l=2 m= 2)
 state #  11: atom   1 (Mo ), wfc  5 (l=2 m= 3)
 state #  12: atom   1 (Mo ), wfc  5 (l=2 m= 4)
 state #  13: atom   1 (Mo ), wfc  5 (l=2 m= 5)

Is, for example,  (l=2 , m= 1) equivalent to m=-2 or

 (l=2 m= 1)-->  m=-2
 (l=2 m= 2)-->  m=-1
  (l=2 m= 3)-->  m=0
  (l=2 m= 4)-->  m=1
  (l=2 m= 5)-->  m=2

?

*--*
*All the best,*
*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, 14778-93855 Tehran, Iran.*

On Sun, May 8, 2016 at 12:06 AM, ashkan shekaari <sheka...@gmail.com> wrote:

> Dear experts,
>
> in quantum mechanics, the quantum number *m* is between *-l *and* l *:
> -l<=m<=l
>
> and so m=-1, 0, +1. but in the output of a pdos calculation, values of m
>
> are seen as follows:
>
>  state #   9: atom   1 (Mo ), wfc  5 (l=2 m= 1)
>  state #  10: atom   1 (Mo ), wfc  5 (l=2 m= 2)
>  state #  11: atom   1 (Mo ), wfc  5 (l=2 m= 3)
>  state #  12: atom   1 (Mo ), wfc  5 (l=2 m= 4)
>  state #  13: atom   1 (Mo ), wfc  5 (l=2 m= 5)
>
> Is, for example,  (l=2 , m= 1) equivalent to m=-2 or
>
>  (l=2 m= 1)-->  m=-2
>  (l=2 m= 2)-->  m=-1
>   (l=2 m= 3)-->  m=0
>   (l=2 m= 4)-->  m=1
>   (l=2 m= 5)-->  m=2
>
> ?
>
> *--*
> *All the best,*
> *Ashkan Shekaari*
> *Plasma Physics Research Center, Science and Research Branch, *
> *I A U, 14778-93855 Tehran, Iran.*
>
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[Pw_forum] pdos

2016-05-07 Thread ashkan shekaari

Dear experts,

in quantum mechanics, the quantum number *m* is between *-l *and* l *:
-l<=m<=l

and so m=-1, 0, +1. but in the output of a pdos calculation, values of m

are seen as follows:

 state #   9: atom   1 (Mo ), wfc  5 (l=2 m= 1)
 state #  10: atom   1 (Mo ), wfc  5 (l=2 m= 2)
 state #  11: atom   1 (Mo ), wfc  5 (l=2 m= 3)
 state #  12: atom   1 (Mo ), wfc  5 (l=2 m= 4)
 state #  13: atom   1 (Mo ), wfc  5 (l=2 m= 5)

Is, for example,  (l=2 , m= 1) equivalent to m=-2 or

 (l=2 m= 1)-->  m=-2
 (l=2 m= 2)-->  m=-1
  (l=2 m= 3)-->  m=0
  (l=2 m= 4)-->  m=1
  (l=2 m= 5)-->  m=2

?

*--*
*All the best,*
*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, 14778-93855 Tehran, Iran.*
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Re: [Pw_forum] VC_relax doesn't converge

2016-04-18 Thread ashkan shekaari

Dear Gupta,
Your ecutwfc is too small. Try with a larger value.

*--*
*All the best,*
*Ashkan Shekaari*
*Plasma Physics Research Center, **Science and Research Branch, *
*I A U, **14778-93855 Tehran, Iran.*
*0098 (933) 459 7122*

On Mon, Apr 18, 2016 at 9:47 PM, Vishal Gupta <vishal.gu...@iitrpr.ac.in>
wrote:

> Hi all,
> I've been running a vc_relax calculation on a 40 atom system. The
> calculation works fine for some cycles. The total force had come down to
> 0.06108. After some time. the force started increasing monotonically. Ive
> tried Gaussian broadening by using smearing=mv and tried degauss from 0.1
> to 4.0D0 but there isn't much change in the minimum of force. Also, I cant
> change K-points or Ecut as both of them are already at best values.
>  The input file is
>  /
>  
>ibrav = 0,
>  nat = 40,
> ntyp = 1,
>  ecutwfc = 12 ,
>   occupations ='smearing' ,
> smearing='mv'
> degauss = 0.05D0 ,
>
>  /
>  
>  mixing_beta = 0.3 ,
>  mixing_mode='TF' ,
>  diagonalization = 'david' ,
>  electron_maxstep = 200 ,
>  /
>
> [/]
> /
> 
> cell_dynamics= 'sd' ,
> cell_dofree='xy' ,
> /
>
> CELL_PARAMETERS angstrom
> 22.2653580478047960.0000.000
>  0.000   11.1312169797245100.000
>  0.0000.000   10.000
>
> P.S. Ive tried changing cell dynamics to 'damp-pr' , 'sd' and 'damp-w',
> but the same problem persists.
> Can anybody Please help me identifying the mistake ?
> Thank You.
> Best Regards,
> Vishal Gupta
>
> B.Tech. 3rd year Mechanical
> Indian Institute of Technology Ropar
> Rupnagar (140001), Punjab, India.
> Email :- vishal.gu...@iitrpr.ac.in
> RMML, IIT Ropar
> <https://sites.google.com/a/iitrpr.ac.in/ropar-mechanics-of-materials-laboratory/people>
>
>
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Re: [Pw_forum] PRoblem in reporting the Relaxed coordinates

2016-04-09 Thread ashkan shekaari

May I see your input file? (relax.in)

*--*
*Best regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, **14778-93855 Tehran, Iran.*
*Mobile: +98 (933) 459 7122*

On Sat, Apr 9, 2016 at 10:02 PM, ashkan shekaari <sheka...@gmail.com> wrote:

> May I see your input file? (relax.in)
>
> On Sat, Apr 9, 2016 at 10:00 PM, ashkan shekaari <sheka...@gmail.com>
> wrote:
>
>> Dear meysam,
>>
>> To the best of my knowledge, your atoms have not been relaxed because of
>> NaN values obtained in for example the Ti coordinates.
>>
>> On Sat, Apr 9, 2016 at 9:52 PM, meysam pazoki <meysam.paz...@gmail.com>
>> wrote:
>>
>>> Dear Quantum Espresso Users!
>>>
>>> My relaxation calculation(relax) is finished successfully,
>>> But, I cant read the relaxed coordinates for one the atoms in the
>>> scf.out file. It appears like this in the output file:
>>> Ti  ***     22.345
>>> CAn you comment on that how can i have the relaxed coordinates for this
>>> atom?
>>> I have a constraint for this atom.
>>>
>>> My Best Regards
>>> /Meysam
>>>
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>>
>>
>>
>> --
>> *Best regards,*
>> *Ashkan Shekaari*
>> *Plasma Physics Research Center, Science and Research Branch, *
>> *I A U, **14778-93855 Tehran, Iran.*
>> *Mobile: +98 (933) 459 7122*
>>
>
>
>
> --
> *Best regards,*
> *Ashkan Shekaari*
> *Plasma Physics Research Center, Science and Research Branch, *
> *I A U, **14778-93855 Tehran, Iran.*
> *Mobile: +98 (933) 459 7122*
>
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Re: [Pw_forum] PRoblem in reporting the Relaxed coordinates

2016-04-09 Thread ashkan shekaari

May I see your input file? (relax.in)

On Sat, Apr 9, 2016 at 10:00 PM, ashkan shekaari <sheka...@gmail.com> wrote:

> Dear meysam,
>
> To the best of my knowledge, your atoms have not been relaxed because of
> NaN values obtained in for example the Ti coordinates.
>
> On Sat, Apr 9, 2016 at 9:52 PM, meysam pazoki <meysam.paz...@gmail.com>
> wrote:
>
>> Dear Quantum Espresso Users!
>>
>> My relaxation calculation(relax) is finished successfully,
>> But, I cant read the relaxed coordinates for one the atoms in the scf.out
>> file. It appears like this in the output file:
>> Ti  ***     22.345
>> CAn you comment on that how can i have the relaxed coordinates for this
>> atom?
>> I have a constraint for this atom.
>>
>> My Best Regards
>> /Meysam
>>
>> ___
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>>
>
>
>
> --
> *Best regards,*
> *Ashkan Shekaari*
> *Plasma Physics Research Center, Science and Research Branch, *
> *I A U, **14778-93855 Tehran, Iran.*
> *Mobile: +98 (933) 459 7122*
>



-- 
*Best regards,*
*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, **14778-93855 Tehran, Iran.*
*Mobile: +98 (933) 459 7122*
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Re: [Pw_forum] PRoblem in reporting the Relaxed coordinates

2016-04-09 Thread ashkan shekaari

Dear meysam,

To the best of my knowledge, your atoms have not been relaxed because of
NaN values obtained in for example the Ti coordinates.

On Sat, Apr 9, 2016 at 9:52 PM, meysam pazoki <meysam.paz...@gmail.com>
wrote:

> Dear Quantum Espresso Users!
>
> My relaxation calculation(relax) is finished successfully,
> But, I cant read the relaxed coordinates for one the atoms in the scf.out
> file. It appears like this in the output file:
> Ti  ***     22.345
> CAn you comment on that how can i have the relaxed coordinates for this
> atom?
> I have a constraint for this atom.
>
> My Best Regards
> /Meysam
>
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*Plasma Physics Research Center, Science and Research Branch, *
*I A U, **14778-93855 Tehran, Iran.*
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Re: [Pw_forum] mos2

2016-04-07 Thread ashkan shekaari

Dear Ari,
Thank you so much for your great help.

On Wed, Apr 6, 2016 at 11:45 PM, Ari P Seitsonen <ari.p.seitso...@iki.fi>
wrote:

>
> Dear Ashkan,
>
>   First on your band structures, apparently you have aligned the zero of
> energy, on the vertical axis, somewhat differently. But overall, maybe they
> are correct. I guess that in the "super-cell" you refer the k points
> (Gamma, M, K) to the corresponding reciprocal lattice vectors, so that
> actually M_sc = 1/2 M_uc. And at K_sc you obtain the same gap as at K_uc,
> because the latter is actually K'_sc; shortly, K = (1/3,1/3,0) and K' =
> (-1/3,-1/3,0) = (2/3,2/3,0) (in units of the reciprocal lattice vectors),
> and since K_sc = 1/2 K_uc, also K'_sc = 1/2 K'_uc = K_sc. It might need a
> bit of drawing hexagons, before this become clear. :)
>
>   Back-folding, since in a super-cell your lattice vectors in real space
> are longer, in reciprocal space they are correspondingly shorter (let us
> call them b1_sc and b2_sc). And since you have the periodicity also in the
> reciprocal space, the Brillouin zone is smaller and you have for example
> many more "Gamma points", Gamma_sc, in the original Brillouin zone of the
> "unit cell". So for example in your case, 2x2, b1_sc = 1/2 b1_uc = M_uc. So
> you should obtain the same bands in the super-cell at the point Gamma_sc as
> M_uc. Thus I would see the bands at ca -1.6 and -2.1 eV at M_uc as the
> bands -1.3 and -1.7 eV at Gamma_sc. The band beginning at Gamma_uc and
> going toward 1/2 K_uc, that is also seen Gamma_sc-K_sc. And so on. But not
> only those, you see more bands because of the two two-dimensionality of
> your band structure.
>
>   But to start understanding back-folding I would start by looking at a
> band structure in one dimension: You can take for example a cos(k)
> function, which mimics the dispersion of the s-type band (one can look up
> in a solid-state book why so). When you double the real-space unit cell,
> you can divide the reciprocal unit cell, so you cut the band at mid-point
> between the minimum at Gamma and maximum at X (if that is 1/2 b, you
> reciprocal lattice vector, or if you want to call it "M") and "fold it
> back", going away from the 1/2 X point toward Gamma again but with the same
> energy dependence as before: e(k) = e(X-k). Thus you get two bands in the
> new Brillouin zone, and they have the same energy at the point 1/2 X. Or
> you can go through the exercise of having a super-cell consisting of two
> atoms in the real-space cell, and when you make the atoms as identical, the
> band structure will be as the one of the super-cell, naturally.
>
>   Well, this is certainly much more clearly explained in some text books
> or lecture notes. :)
>
> Greetings,
>
>apsi
>
> PS Indeed, I would also learn how to use a consistent alignment of
> energies in the case of periodic systems with a band gap. Hint: Either
> mid-gap or top of valence band as the reference
>
>
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>   Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
> Ecole Normale Supérieure (ENS), Département de Chimie, Paris
> Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935
>
>
> On Wed, 6 Apr 2016, ashkan shekaari wrote:
>
> Dear Ari,
>> I obtained the bands below via routine calculations (without
>> back-folding). Is something wrong with my calculations?
>>
>> What do you mean back-folding?
>>
>> On Wed, Apr 6, 2016 at 9:30 PM, Ari P Seitsonen <ari.p.seitso...@iki.fi>
>> wrote:
>>
>>   Dear Ashkan,
>>
>> Yes, due to back-folding - unless you perform the "back-folding".
>> Jonas Björk told me that they have a public code for doing this and it
>> should
>>   also work with QE (I have not tried it myself though, even if I
>> should have applied it recently - sorry Jonas!)
>>
>>   Greetings,
>>
>>  apsi
>>
>>
>> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>> Ari Paavo Seitsonen / ari.p.seitso...@iki.fi /
>> http://www.iki.fi/~apsi/
>>   Ecole Normale Supérieure (ENS), Département de Chimie, Paris
>>   Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935
>>
>>
>>   On Wed, 6 Apr 2016, ashkan shekaari wrote:
>>
>> Dear QE users,
>> Does the 2*2 supercell of mos2 monolayer have a different
>> band structure than that of the single unit cell?
>>
>>
>> --
>> Best regards,
>&g

Re: [Pw_forum] mos2

2016-04-06 Thread ashkan shekaari

Dear Ari,

I obtained the bands below via routine calculations (without back-folding).
Is something wrong with my calculations?

What do you mean back-folding?

On Wed, Apr 6, 2016 at 9:30 PM, Ari P Seitsonen <ari.p.seitso...@iki.fi>
wrote:

>
> Dear Ashkan,
>
>   Yes, due to back-folding - unless you perform the "back-folding". Jonas
> Björk told me that they have a public code for doing this and it should
> also work with QE (I have not tried it myself though, even if I should have
> applied it recently - sorry Jonas!)
>
> Greetings,
>
>apsi
>
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>   Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
> Ecole Normale Supérieure (ENS), Département de Chimie, Paris
> Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935
>
>
>
> On Wed, 6 Apr 2016, ashkan shekaari wrote:
>
> Dear QE users,
>> Does the 2*2 supercell of mos2 monolayer have a different band structure
>> than that of the single unit cell?
>>
>>
>> --
>> Best regards,
>> Ashkan Shekaari
>> Plasma Physics Research Center, Science and Research Branch,
>> I A U, 14778-93855 Tehran, Iran.
>> Mobile: +98 (933) 459 7122
>>
>
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>



-- 
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*Ashkan Shekaari*
*Plasma Physics Research Center, Science and Research Branch, *
*I A U, **14778-93855 Tehran, Iran.*
*Mobile: +98 (933) 459 7122*


supercell.ps
Description: PostScript document


unitcell.ps
Description: PostScript document
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[Pw_forum] mos2

2016-04-06 Thread ashkan shekaari

Dear QE users,

Does the 2*2 supercell of mos2 monolayer have a different band structure
than that of the single unit cell?


-- 
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*Plasma Physics Research Center, Science and Research Branch, *
*I A U, **14778-93855 Tehran, Iran.*
*Mobile: +98 (933) 459 7122*
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Re: [Pw_forum] MoS2 band

2016-03-15 Thread ashkan shekaari

Dear Thomas,
Thank you so much for doing me the favor.

•••
Best regards,
Ashkan Shekaari
•••
On Mar 15, 2016 8:25 PM, "Thomas Brumme" <thomas.bru...@mpsd.mpg.de> wrote:

> Dear Ashkan,
>
> using the k-path selection tool of XCrysDen I get the coordinates:
>
> 0.00  0.00  0.00  Gamma
> 0.50  0.00  0.00  M
> 0.66 -0.33  0.00  K
> 0.00  0.00  0.00  Gamma
>
> so a possible input for QE could be:
>
> K_POINTS crystal_b
> 4
>  0.00  0.00  0.00  50
>  0.50  0.00  0.00  37
>  0.66 -0.33  0.00  75
>  0.00  0.00  0.000000  1
>
> Regards
>
> Thomas
>
>
> On 03/15/2016 05:43 PM, ashkan shekaari wrote:
>
> Dear Thomas,
> Could you please tell me what is the true kpoint list on the path gamma K
> M gamma?
> I mean the coordinates of the points gamma, K, and M inn BZ.
>
> •••
> Best regards,
> Ashkan Shekaari
> •••
> On Mar 15, 2016 1:48 PM, "Thomas Brumme" <thomas.bru...@mpsd.mpg.de>
> wrote:
>
>> Dear Ashkan,
>>
>> Have you checked that you use the right k-point list in the band
>> structure calculation?
>> The K point seems to be wrong... The input file for the scf calculation
>> seems to be
>> correct even if you could probably use a smaller cutoff, which you
>> however need to check.
>>
>> Regards
>>
>> Thomas
>>
>> P.S.: Please add your affiliation.
>>
>> On 03/15/2016 07:09 AM, ashkan shekaari wrote:
>>
>> Dear all,
>>
>> I was trying to calculate the band structure of monolayer MoS2 according
>> to the input file below. Although the resulted band structure had a band
>> gap of about 1.9 eV, it didn't illustrate a direct type band gap at K
>> high symmetry point in Brillouin zone. I was wondering if something is
>> wrong with the input file?
>>
>> --
>> Thanks in advance,
>> Ashkan Shekaari
>>
>>
>>
>> ___
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>>
>>
>> --
>> Dr. rer. nat. Thomas Brumme
>> Max Planck Institute for the Structure and Dynamics of Matter
>> Luruper Chaussee 149
>> 22761 Hamburg
>>
>> Tel:  +49 (0)40 8998 6557
>>
>> email: thomas.bru...@mpsd.mpg.de
>>
>>
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>
>
> ___
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>
> --
> Dr. rer. nat. Thomas Brumme
> Max Planck Institute for the Structure and Dynamics of Matter
> Luruper Chaussee 149
> 22761 Hamburg
>
> Tel:  +49 (0)40 8998 6557
>
> email: thomas.bru...@mpsd.mpg.de
>
>
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Re: [Pw_forum] MoS2 band

2016-03-15 Thread ashkan shekaari

Dear Thomas,
Could you please tell me what is the true kpoint list on the path gamma K M
gamma?
I mean the coordinates of the points gamma, K, and M inn BZ.

•••
Best regards,
Ashkan Shekaari
•••
On Mar 15, 2016 1:48 PM, "Thomas Brumme" <thomas.bru...@mpsd.mpg.de> wrote:

> Dear Ashkan,
>
> Have you checked that you use the right k-point list in the band structure
> calculation?
> The K point seems to be wrong... The input file for the scf calculation
> seems to be
> correct even if you could probably use a smaller cutoff, which you however
> need to check.
>
> Regards
>
> Thomas
>
> P.S.: Please add your affiliation.
>
> On 03/15/2016 07:09 AM, ashkan shekaari wrote:
>
> Dear all,
>
> I was trying to calculate the band structure of monolayer MoS2 according
> to the input file below. Although the resulted band structure had a band
> gap of about 1.9 eV, it didn't illustrate a direct type band gap at K
> high symmetry point in Brillouin zone. I was wondering if something is
> wrong with the input file?
>
> --
> Thanks in advance,
> Ashkan Shekaari
>
>
>
> ___
> Pw_forum mailing 
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>
>
> --
> Dr. rer. nat. Thomas Brumme
> Max Planck Institute for the Structure and Dynamics of Matter
> Luruper Chaussee 149
> 22761 Hamburg
>
> Tel:  +49 (0)40 8998 6557
>
> email: thomas.bru...@mpsd.mpg.de
>
>
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[Pw_forum] MoS2 band

2016-03-15 Thread ashkan shekaari

Dear all,

I was trying to calculate the band structure of monolayer MoS2 according to
the input file below. Although the resulted band structure had a band gap
of about 1.9 eV, it didn't illustrate a direct type band gap at K high
symmetry point in Brillouin zone. I was wondering if something is wrong
with the input file?

-- 
Thanks in advance,
Ashkan Shekaari


0-scf.in
Description: Binary data


011.ps
Description: PostScript document
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[Pw_forum] Fwd: Msd

2015-08-10 Thread ashkan shekaari

Dear family
Does anybody know how QE computes mean square displacements?
By means of the below formula?

Kind regards
Ashkan Shekaari
-- Forwarded message --
From: "ashkan shekaari" <sheka...@gmail.com>
Date: Aug 10, 2015 8:08 PM
Subject: Msd
To: "Andrea Dal Corso" <dalco...@sissa.it>
Cc:

Dear Andrea
Do you know how mean square displacements are calculated in QE? Does QE use
the below formula?
Thanks in advance.

Kind regards
Ashkan Shekaari
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[Pw_forum] Cp

2015-08-09 Thread ashkan shekaari

Dear developers
Mean square displacement in the cp output file is written in terms of a.u.
. Does it mean the quantity has the length dimension? Or it is length^2?

Kind regards
Ashkan Shekaari
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[Pw_forum] Cp

2015-08-08 Thread ashkan shekaari

Dear developers
Why rescaling does not work for cell temperature in cp while it is
introduced as a permitted parameter?

Kind regards
Ashkan Shekaari
Tell: +98 933 459 7122; +98 921 346 7384
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[Pw_forum] Sp

2015-08-06 Thread ashkan shekaari

Dear users
Is the fine structure or Zeeman effect included in QE?

Kind regards
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[Pw_forum] K

2015-08-04 Thread ashkan shekaari

Dear users
Does the qe compute the constant k prime infinity of Keane eos? There is
not such quantity in output of ev.x

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[Pw_forum] Cp

2015-07-31 Thread ashkan shekaari

Dear Paolo Giannozzi
For a cp simulation, is a unit cell enough or I have to consider a
supercell?

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[Pw_forum] (no subject)

2015-07-27 Thread ashkan shekaari

Dear users
What is the difference between cell temperature and ion temperature in cp ?
Should I consider both of them for the purpose of increasing temperature of
a crystal?

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Re: [Pw_forum] BFGS Relaxation

2015-07-27 Thread ashkan shekaari

Dear kanak
Another thing
Set vdw_corr='grimme-d2'
In  card to consider van deer Waals interaction between layers. It
works nice.

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Ashkan Shekaari
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On Jul 25, 2015 5:59 PM, "Kanak Datta" <kanakee...@gmail.com> wrote:

> Dear researchers
>
> For BFGS relaxation of bilayer WS2..I have been using the following code...
> 
>   calculation = 'relax',
>  restart_mode = 'from_scratch',
>outdir = 'D:\QuantumEspresso\Quantum ESPRESSO 64-bit
> 5.1.2-mpich2\WS2Bilayer\outdir',
>prefix = 'WS2Bilayer',
> /
> 
>  ibrav = 0,
> a = 1.86,
> nat = 6,
> ntyp = 2,
> occupations = 'smearing',
> smearing = 'methfessel-paxton',
> degauss = 0.001,
> nspin=2,
> ecutwfc = 20,
> ecutrho = 160,
> nbnd = 30,
> starting_magnetization=0.6,
>  /
>
> 
> conv_thr = 1.0d-5,
> mixing_mode = 'plain',
> mixing_beta = 0.7,
> diagonalization = 'david',
> diago_full_acc = .true.
>  /
> 
> ion_dynamics  = 'bfgs',
> pot_extrapolation = 'second_order',
> wfc_extrapolation = 'second_order',
> upscale   = 100,
> /
> CELL_PARAMETERS
> 1.5 0.8660254038 0.0
> 1.5 -0.8660254038 0.0
> 0. 0.0 15.0
> ATOMIC_SPECIES
> W 183.84 W.pbe-hgh.UPF
> S 32.066 S.pbe-hgh.UPF
> ATOMIC_POSITIONS (angstrom)
> S   0.0  0.0   5.15
> S   0.0  0.0   2
> W   1.818653348  0.0   3.575
> S   0.0  0.0   8.6
> S   0.0  0.0   10.175
> W   1.818653348  0.0   11.75
> K_POINTS {automatic}
> 24 24 1   0 0 0
>
>
> 1. I just wanted to know whether the cutoff values are ok or not...As
> I am from EEE background..I have very little knowledge on these things.
> 2. Besides should the van der waals corrections be applied in relaxation
> part from the beginning?
>
> Thanks in advance.
>
> Sincerely yours
> kanak
> BUET
>
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Re: [Pw_forum] BFGS Relaxation

2015-07-27 Thread ashkan shekaari

Dear Lorenzo
dt only works in cp MD .
Thanks so much for your attention.

Kind regards
Ashkan Shekaari
Tell: +98 933 459 7122; +98 921 346 7384
On Jul 27, 2015 1:04 AM, "Lorenzo Paulatto" <lorenzo.paula...@impmc.upmc.fr>
wrote:

> On Sunday, July 26, 2015 09:50:20 PM ashkan shekaari wrote:
> > Dear kanak
> > Ecutwfc is too small. Find the optimal value. Set ecutrho = 5*ecutwfc.
>
> Dear Ashkan,
> this is not the first time that I see you giving this advice. Do you have
> any
> specific reason for choosing a factor 5?
> Kanak only has norm-conserving pseudos, which normally do not require any
> more
> than the default value: ecutrho=4*ecutwfc. Using 5 instead of 4 would
> require
> an interpolation at every scf step, which takes cpu time and memory.
>
> > Set mixing mode local TF because of inhomogenity.
> > Set conv thr of order 10^-9set dt= 20
>
> dt is not used by BFGS
>
> kind regards
>
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC -- CNRS & Université Paris 6
> +33 (0)1 44 275 084 / skype: paulatz
> http://www.impmc.upmc.fr/~paulatto/
> 23-24/4é16 Boîte courrier 115
> 4 place Jussieu 75252 Paris Cédex 05
>
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Re: [Pw_forum] BFGS Relaxation

2015-07-26 Thread ashkan shekaari

Dear kanak
Ecutwfc is too small. Find the optimal value. Set ecutrho = 5*ecutwfc.
Set mixing mode local TF because of inhomogenity.
Set conv thr of order 10^-9set dt= 20

Kind regards
Ashkan Shekaari
Tell: +98 933 459 7122; +98 921 346 7384
On Jul 25, 2015 5:59 PM, "Kanak Datta" <kanakee...@gmail.com> wrote:

> Dear researchers
>
> For BFGS relaxation of bilayer WS2..I have been using the following code...
> 
>   calculation = 'relax',
>  restart_mode = 'from_scratch',
>outdir = 'D:\QuantumEspresso\Quantum ESPRESSO 64-bit
> 5.1.2-mpich2\WS2Bilayer\outdir',
>prefix = 'WS2Bilayer',
> /
> 
>  ibrav = 0,
> a = 1.86,
> nat = 6,
> ntyp = 2,
> occupations = 'smearing',
> smearing = 'methfessel-paxton',
> degauss = 0.001,
> nspin=2,
> ecutwfc = 20,
> ecutrho = 160,
> nbnd = 30,
> starting_magnetization=0.6,
>  /
>
> 
> conv_thr = 1.0d-5,
> mixing_mode = 'plain',
> mixing_beta = 0.7,
> diagonalization = 'david',
> diago_full_acc = .true.
>  /
> 
> ion_dynamics  = 'bfgs',
> pot_extrapolation = 'second_order',
> wfc_extrapolation = 'second_order',
> upscale   = 100,
> /
> CELL_PARAMETERS
> 1.5 0.8660254038 0.0
> 1.5 -0.8660254038 0.0
> 0. 0.0 15.0
> ATOMIC_SPECIES
> W 183.84 W.pbe-hgh.UPF
> S 32.066 S.pbe-hgh.UPF
> ATOMIC_POSITIONS (angstrom)
> S   0.0  0.0   5.15
> S   0.0  0.0   2
> W   1.818653348  0.0   3.575
> S   0.0  0.0   8.6
> S   0.0  0.0   10.175
> W   1.818653348  0.0   11.75
> K_POINTS {automatic}
> 24 24 1   0 0 0
>
>
> 1. I just wanted to know whether the cutoff values are ok or not...As
> I am from EEE background..I have very little knowledge on these things.
> 2. Besides should the van der waals corrections be applied in relaxation
> part from the beginning?
>
> Thanks in advance.
>
> Sincerely yours
> kanak
> BUET
>
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[Pw_forum] (no subject)

2015-07-25 Thread ashkan shekaari

Dear users
For a cp run, how one can tune parameters such as emass , emass cutoff,
fnosep, fnoseh?

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Ashkan Shekaari
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[Pw_forum] Cp

2015-07-25 Thread ashkan shekaari

Dear qe users
I have a cp calculation which has error : max number of iterations exceeded.
What does it mean?

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Ashkan Shekaari
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[Pw_forum] (no subject)

2015-07-22 Thread ashkan shekaari

Dear we users
If I import van der Waals correction grimme dftd2 to relaxation of a
system, get relaxed position, then run a scf calculation without this
correction and then run a phonon calculation, is it a right calculation?
Or I have to consider the correction for all calculations?

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Re: [Pw_forum] Convergence issue in MoS2 super cell

2015-07-21 Thread ashkan shekaari

Dear mahendra
Do you use mixing mode=`local-TF`
?
If you deal with a mono layer you have to use that in  card

Set ecutrho 5 times of ecutwfc.

If these not work reduce mixing beta value.

Kind regards
Ashkan Shekaari
Tell: +98 933 459 7122; +98 921 346 7384
On Jul 21, 2015 8:51 PM, "Mahendra Jalkhediya" <
jalkhediya.mahen...@gmail.com> wrote:

> I am relaxing the MoS2 super cell with adatom containing 28 atoms (1 K
> atom, 9 Mo atoms, 18 S atoms ). I did simulation for vc-relax but the
> simulation result is :-"convergence NOT achieved after *** iterations:
> stopping". I tried it by changing different parameters but same problem
> is coming. Here i am attaching the input file. Please check where I am
> wrong.
>
> I tried it for " ecutwfc= 40, 70, 90 ecutrho= 400, 700, 900 cell_factor=
> 2.5, 3.5.
>
>
> Regards
> Mahendra Jalkhediya
> IIT Kanpur
>
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Re: [Pw_forum] (no subject)

2015-07-20 Thread ashkan shekaari

Dear Giannozzi
Is a mos2 bilayer an inhomogeneous system?

Kind regards
Ashkan Shekaari
Tell: +98 933 459 7122; +98 921 346 7384
On Jul 20, 2015 12:47 AM, "Paolo Giannozzi" <p.gianno...@gmail.com> wrote:

> A system with a strongly inhomogeneous charge density (e.g. a surface)
>
> Paolo
>
> On Sun, Jul 19, 2015 at 7:57 PM, ashkan shekaari <sheka...@gmail.com>
> wrote:
>
>> What is the meaning of highly inhomogeneous system?
>>
>> Kind regards
>> Ashkan Shekaari
>> Tell: +98 933 459 7122; +98 921 346 7384
>> On Jul 19, 2015 10:20 PM, "ashkan shekaari" <sheka...@gmail.com> wrote:
>>
>>> Dear users
>>> Can I use local-TF for mono layer and bilayer mos2?
>>>
>>> Kind regards
>>> Ashkan Shekaari
>>> Tell: +98 933 459 7122; +98 921 346 7384
>>>
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>
>
>
> --
> Paolo Giannozzi, Dept. Chemistry,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
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Re: [Pw_forum] (no subject)

2015-07-19 Thread ashkan shekaari

What is the meaning of highly inhomogeneous system?

Kind regards
Ashkan Shekaari
Tell: +98 933 459 7122; +98 921 346 7384
On Jul 19, 2015 10:20 PM, "ashkan shekaari" <sheka...@gmail.com> wrote:

> Dear users
> Can I use local-TF for mono layer and bilayer mos2?
>
> Kind regards
> Ashkan Shekaari
> Tell: +98 933 459 7122; +98 921 346 7384
>
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[Pw_forum] (no subject)

2015-07-19 Thread ashkan shekaari

Dear users
Can I use local-TF for mono layer and bilayer mos2?

Kind regards
Ashkan Shekaari
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[Pw_forum] (no subject)

2015-07-04 Thread ashkan shekaari

Dear users
Is it possible to make mos2 mono layer in a cubic lattice?

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[Pw_forum] (no subject)

2015-07-02 Thread ashkan shekaari

Dear users
I have a 3 atom unit cell and I am going to calculate the melting
temperature using the Lindemann criteria. In this criteria there is a mass
M and a r0 . but I have 3 atoms and 3 mean square displacements. What
should I do?

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[Pw_forum] (no subject)

2015-07-01 Thread ashkan shekaari

Dear users
Does the 4*4*4 q mesh result in values different from 4*4*1 for a monolayer?
Which is true or more exact?

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Ashkan Shekaari
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Re: [Pw_forum] Raman Spectra

2015-06-29 Thread ashkan shekaari

Dear amreen
Because of the elimination of the core in pseudopotential methods , these
methods are not accurate enough in optical properties.

Kind regards
Ashkan Shekaari
Tell: +98 933 459 7122; +98 921 346 7384
On Jun 25, 2015 6:43 PM, "ashkan shekaari" <sheka...@gmail.com> wrote:

> Dear
> Espresso is weak in optical area because of its pseudization method
>
> Kind regards
> Ashkan Shekaari
> Tell: +98 933 459 7122 ; +98 921 346 7384
> Website: http://fizx.blogfa.com
> Skype: ashkan-shekaari
> On Jun 18, 2015 9:32 AM, "Amreen Bano" <banoamree...@gmail.com> wrote:
>
>> Dear all,
>>
>> I am working on optical properties.
>> I have run dynmat.x file and obtained the output below:
>>
>> # mode   [cm-1][THz]  IR  Raman   depol.fact
>> 1   -487.60  -14.6178   37.7287   277.86090.6461
>> 2 -0.00   -0.0.334597.41700.7437
>> 3 -0.00   -0.0.  8113.29750.7291
>> 4 -0.00   -0.0. 25779.90200.7455
>> 5  0.000.0.  6417.84420.6634
>> 6  0.000.0.   171.70540.6246
>> 7  0.000.0. 29050.28080.7489
>> 8 56.801.70284.4068273118.78750.7446
>> 9160.494.8115   11.3630 55305.28850.7395
>>10223.346.69543.8373 91527.11270.7438
>>11327.829.82772.9918 21597.63730.7373
>>12351.66   10.54241.9769   1081889.82250.7431
>>13555.84   16.66373.8963 13013.88340.2450
>>14748.23   22.43159.1009  3164.22750.1576
>>15790.74   23.70595.1725   764.08950.5078.
>> With the 2nd and 5th column i can form raman spectra, but output contains
>> very few values which is giving abnormal plot.
>> how can i plot a correct and smooth plot for raman spectra.
>> please suggest me the correct path.
>>
>> --
>> Amreen Bano
>> Department of Physics,
>> Barkatullah University,
>> Bhopal-462 026
>> INDIA
>> +91-9993515955
>> banoamree...@gmail.com
>>
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[Pw_forum] Qha

2015-06-29 Thread ashkan shekaari

Dear qe users
I have calculated vibration energy and entropy and specific heat for a
single layer mos2 but I obtained NaN values for the first two quantities.
Does it mean I have obtained wrong values?

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Ashkan Shekaari
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Re: [Pw_forum] Raman Spectra

2015-06-25 Thread ashkan shekaari

Dear
Espresso is weak in optical area because of its pseudization method

Kind regards
Ashkan Shekaari
Tell: +98 933 459 7122 ; +98 921 346 7384
Website: http://fizx.blogfa.com
Skype: ashkan-shekaari
On Jun 18, 2015 9:32 AM, "Amreen Bano" <banoamree...@gmail.com> wrote:

> Dear all,
>
> I am working on optical properties.
> I have run dynmat.x file and obtained the output below:
>
> # mode   [cm-1][THz]  IR  Raman   depol.fact
> 1   -487.60  -14.6178   37.7287   277.86090.6461
> 2 -0.00   -0.0.334597.41700.7437
> 3 -0.00   -0.0.  8113.29750.7291
> 4 -0.00   -0.0. 25779.90200.7455
> 5  0.000.0.  6417.84420.6634
> 6  0.000.0.   171.70540.6246
> 7  0.000.0. 29050.28080.7489
> 8 56.801.70284.4068273118.78750.7446
> 9160.494.8115   11.3630 55305.28850.7395
>10223.346.69543.8373 91527.11270.7438
>11327.829.82772.9918 21597.63730.7373
>12351.66   10.54241.9769   1081889.82250.7431
>13555.84   16.66373.8963 13013.88340.2450
>14748.23   22.43159.1009  3164.22750.1576
>15790.74   23.70595.1725   764.08950.5078.
> With the 2nd and 5th column i can form raman spectra, but output contains
> very few values which is giving abnormal plot.
> how can i plot a correct and smooth plot for raman spectra.
> please suggest me the correct path.
>
> --
> Amreen Bano
> Department of Physics,
> Barkatullah University,
> Bhopal-462 026
> INDIA
> +91-9993515955
> banoamree...@gmail.com
>
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[Pw_forum] Ion

2015-06-10 Thread ashkan shekaari

Dear all
Does any one know is it possible to define ions in QE?

Best Regards
Ashkan Shekaari
Independent Condensed-Matter Researcher / Programmer
Tehran, Iran
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Re: [Pw_forum] Mos2

2015-06-10 Thread ashkan shekaari

Dear cantele
Thanks so much.
Can I import temperature in my band calculations? Somehow in input file.

Best Regards
Ashkan Shekaari
Independent Condensed-Matter Researcher / Programmer
Tehran, Iran
Tell: +98 933 459 7122 ; +98 921 346 7384
Website: http://fizx.blogfa.com
On Jun 10, 2015 2:50 PM, "Giovanni Cantele" <giovanni.cant...@spin.cnr.it>
wrote:

> maybe there is something wrong in your path, but this cannot be seen if
> you do not provide also
> the input file of the non self-consistent calculation (calculation=‘bands’
> or calculation=‘nscf’).
>
> However, possible coordinates of K are: (1/3,1/3,0), (2/3,-1/3,0), (1/3,
> -2/3,0), (-1/3,-1/3,0), (-2/3,1/3,0), (-1/3,2/3,0).
> So, it seems that for sure the coordinates of your K point are wrong.
> Moreover, the coordinates of the M point (that you do not provide)
> should be wrong as well, because it seems that also the band structure
> along M-Gamma has some issues.
>
> If you choose (2/3,-1/3,0), use (1/2,0,0) for M point.
>
> Giovanni
>
> On 10 Jun 2015, at 00:08, ashkan shekaari <sheka...@gmail.com> wrote:
>
> Dear all
> Why I can not obtain the true band structure?
> I mean I can not obtain the max of valence and min of conduction bands at
> K. Why?
> The band and scf.in are enclosed.
> I use the path gamma-K-M-gamma and (2/3,1/3,0) for K.
>
> Best Regards
> Ashkan Shekaari
> Independent Condensed-Matter Researcher / Programmer
> Tehran, Iran
> Tell: +98 933 459 7122 ; +98 921 346 7384
> Website: http://fizx.blogfa.com
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>
> --
>
> 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.cant...@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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Re: [Pw_forum] Mos2

2015-06-10 Thread ashkan shekaari

Dear kondrin
Does it mean my calculation is wrong?

Best Regards
Ashkan Shekaari
Independent Condensed-Matter Researcher / Programmer
Tehran, Iran
Tell: +98 933 459 7122 ; +98 921 346 7384
Website: http://fizx.blogfa.com
On Jun 10, 2015 2:01 PM, "MKondrin" <mkond...@hppi.troitsk.ru> wrote:

> ashkan shekaari wrote:
> >
> > Dear all
> > Why I can not obtain the true band structure?
> > I mean I can not obtain the max of valence and min of conduction bands
> > at K. Why?
> > The band and scf.in <http://scf.in> are enclosed.
> > I use the path gamma-K-M-gamma and (2/3,1/3,0) for K.
> >
> Hi!
>
> I am not sure but AFAIK band structure with direct gap at K-point is
> realized only at certain stacking of MoS2 sheets. In your input file
> only one sheet is described, so its stacking is determined by the space
> group. I suppose that in this case the best practice is to check that QE
> indeed found all symmetry operations (the number of Sym. Ops. is written
> in the beginning of output file -- at least it should be equal to the
> one you have in mind).
>
> Best regards,
>
> M. V. Kondrin (High Pressure Physics Institute RAS)
> >
> > Best Regards
> > Ashkan Shekaari
> > Independent Condensed-Matter Researcher / Programmer
> > Tehran, Iran
> > Tell: +98 933 459 7122 ; +98 921 346 7384
> > Website: http://fizx.blogfa.com
> >
> > 
> >
> > ___
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Re: [Pw_forum] How to disable parallel configuration

2015-06-09 Thread ashkan shekaari

Dear gather
The problem is not about your parallel config
This is because of your input file and I think the problem arises from tour
 card

Best Regards
Ashkan Shekaari
Independent Condensed-Matter Researcher / Programmer
Tehran, Iran
Tell: +98 933 459 7122 ; +98 921 346 7384
Website: http://fizx.blogfa.com
On Jun 8, 2015 12:54 PM, "Filippo Spiga" <spiga.fili...@gmail.com> wrote:

> Dear Gargee,
>
> Are you running QE-GPU on your laptop? Most likely it is not going to work
> or, if works, it is going to be slow anyway. GPU embedded in laptops are
> not powerful enough, QE-GPU works better with NVIDIA TESLA GPU (e.g. K20,
> K40 and K80). These cards are designed for compute workload.
>
> HTH
>
> Regards,
> Filippo
>
> On Jun 8, 2015, at 8:51 AM, Gargee Bhattacharyya <
> bhattacharyya.gar...@gmail.com> wrote:
> >
> > Sir ,
> >I am having error of following type
> >
> > MPI_ABORT was invoked on rank 0 in communication MPI_COMM_WORLD with
> error code 0. I am running my program from my laptop. I am trying to
> disable parallel configuration from the help of following link :
> >
> > https://github.com/fspiga/QE-GPU
> >
> > I shall be highly obliged if you help me to disable the parallel
> configuration in my laplop.
> >
> > 
> >   calculation='scf'
> >   restart_mode='from_scratch'
> >   tstress=.true.
> >   tprnfor=.true.
> >   prefix='ZnO'
> >   pseudo_dir='/home/iit/GARGEE/espresso-5.1.2/pseudo/',
> >   out_dir='home/iit/GARGEE/ZnO/',
> >   forc_conv_thr=1.D-4
> > /
> > 
> >   ibrav=4
> >   nat=4
> >   ntyp=2
> >   A=3.2495
> >   B=3.2495
> >   C=3.2495
> >   cosAB=0
> >   cosBC=0
> >   cosAC=-0.577
> >   ecutwfc=55
> >   ecutrho=440
> > /
> > 
> >   conv_thr=1.0e-10
> > /
> > 
> > /
> > 
> > /
> > _SPECIES
> >   Zn 65  Zn.pbe-van.UPF
> >O 16   O.pbe-van_ak.UPF
> > /
> > _POSITIONS(crystal)
> >   Zn  0.0   0.0   0.0
> >   Zn  0.333 0.666 0.5
> >   O   0.0   0.0   0.345
> >   O   0.333 0.666 0.845
> > K_POINTS automatic
> >   4 4 4 0 0 0
> >
> >
> > --
> > Yours sincerely
> >
> > Gargee Bhattacharyya
> > PhD Student
> > Materials Sciences & Engineering
> > Indian Institute of Technology, Indore
> > 
> > M.Tech (VLSI Design & Microelectronics Technology)
> > Department of ETCE
> > Jadavpur University
> > ___
> > Pw_forum mailing list
> > Pw_forum@pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> Mr. Filippo SPIGA, M.Sc.
> http://fspiga.github.io ~ 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 may be privileged or otherwise protected from disclosure. The contents
> are not to be disclosed to anyone other than the addressee. Unauthorized
> recipients are requested to preserve this confidentiality and to advise the
> sender immediately of any error in transmission."
>
>
>
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Re: [Pw_forum] Error in running pw.x for band structure with free lattice reg.,

2015-06-09 Thread ashkan shekaari

Dear muthu
If you use ibrav=0 ,you should specify _parameters in your input file
scf.in

Best Regards
Ashkan Shekaari
Independent Condensed-Matter Researcher / Programmer
Tehran, Iran
Tell: +98 933 459 7122 ; +98 921 346 7384
Website: http:// <http://fizx.blogfa.com>fizx.blogfa.com
You cannot use k points labels with ibrav=0. In order to plot the bands
of the 8 atoms cell, it is necessary to define the path in the cubic
Brillouin zone giving the coordinates of the k points.

HTH,

Andrea


On Sun, 2015-06-07 at 20:33 +0530, Muthu V wrote:
> Dear All QE Users
>
> I am trying to get band strucutre for Si crystal. i have edited the
example
> input file and used free lattce option (ibrav= 0 instead of ibrav= 2) with
> no of atoms is 8 instead of 2.
> while scf runs and gives sucessful result without any error. but when
> programme enters into band calculation it shows the following error
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *Program PWSCF v.5.1.1 starts on  7Jun2015 at 20:18:34  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
> <http://www.quantum-espresso.org>",  in publications or presentations
> arising from this work. More details at
> http://www.quantum-espresso.org/quote
> <http://www.quantum-espresso.org/quote> Parallel version (MPI),
running
> on 1 processors Waiting for input... Reading input from
> standard
> input

> Error in routine find_bz_type (1): Wrong
> ibrav

> stopping ...*
>
> With this email i have enclosed the script file i have used. How to
reslove
> this problem?
>
> Thank you
>
>
>
> *-*
>
> *Muthu V  *
>
>
>
>
>
> *Madurai Kamaraj University Madurai Tamil
> NaduIndia-*
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--
Andrea Dal CorsoTel. 0039-040-3787428
SISSA, Via Bonomea 265  Fax. 0039-040-3787249
I-34136 Trieste (Italy) e-mail: dalco...@sissa.it



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Re: [Pw_forum] pw.x error reading namelist ions

2015-06-09 Thread ashkan shekaari

Dear visual
Import the part  in your input file as below:

/

Best Regards
Ashkan Shekaari
Independent Condensed-Matter Researcher / Programmer
Tehran, Iran
Tell: +98 933 459 7122 ; +98 921 346 7384
Website: http://fizx.blogfa.com
On Jun 9, 2015 9:26 PM, "Ari P Seitsonen" <ari.p.seitso...@iki.fi> wrote:

>
> Dear Vishal Gupta,
>
>   Isn't it obvious: The namelist '' is indeed not present in your
> input; this is required, even if being empty, when doing "calculation =
> 'relax'".
>
> Greetings from Paris,
>
>apsi
>
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
>   Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
>   Ecole Normale Supérieure (ENS), Département de Chimie, Paris
>   Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935
>
>
> On Tue, 9 Jun 2015, Vishal Gupta wrote:
>
>  Hi,I am trying to run an input file from QE on High Performance Cluster
>> but it gives the following error :-
>> Error in routine  read_namelists (1):
>> reading namelist ions
>>
>> Input :-
>> 
>>  calculation = 'relax' ,
>>   pseudo_dir = '/home/vishalgupta/GB' ,
>>   prefix = 'Ni_exc1' ,
>>  /
>>  
>>ibrav = 2,
>>celldm(1) = 3.52,
>>  nat = 47,
>> ntyp = 1,
>>  ecutwfc = 20 ,
>>  /
>>  
>>  mixing_beta = 0.7 ,
>>  diagonalization = 'cg' ,
>>  /
>> ATOMIC_SPECIES
>>Ni   58.69340  Ni.pz-hgh.UPF
>> ATOMIC_POSITIONS alat
>>Ni 14.9340952194.978031740   10.0
>> ...
>> K_POINTS automatic
>>   6 6 6   0 0 0
>>
>> Output :-
>> MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
>> with errorcode 1.
>>
>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>> You may or may not see output from other processes, depending on
>> exactly when Open MPI kills them.
>> Parallel version (MPI), running on20 processors
>>  R & G space division:  proc/nbgrp/npool/nimage =  20
>>  Reading input from a.in
>> Error in routine  read_namelists (1):
>>   reading namelist ions
>>
>> THANK YOU
>> Vishal Gupta
>> B.Tech. 2nd year Mechanical
>> Indian Institute of Technology Ropar
>> Rupnagar (140001), Punjab, India.
>> Email :- vishal.gu...@iitrpr.ac.in
>>
>>
>>
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[Pw_forum] Mos2

2015-06-09 Thread ashkan shekaari

Dear all
Why I can not obtain the true band structure?
I mean I can not obtain the max of valence and min of conduction bands at
K. Why?
The band and scf.in are enclosed.
I use the path gamma-K-M-gamma and (2/3,1/3,0) for K.

Best Regards
Ashkan Shekaari
Independent Condensed-Matter Researcher / Programmer
Tehran, Iran
Tell: +98 933 459 7122 ; +98 921 346 7384
Website: http://fizx.blogfa.com


scf.in
Description: Binary data
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