[Pw_forum] Pw_forum Digest, Vol 110, Issue 28

Thu Sep 29 08:33:06 CEST 2016

Dear Mighfar Imam,
                            Thank you very much for your kind reply.

Best regards,
 Neha Bothra,
 Ph.D student,
 JNCASR,
  Bengaluru, India.

On Wed, Sep 28, 2016 at 3:30 PM, <pw_forum-request at pwscf.org> wrote:

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> Today's Topics:
>
>    1. supercell and vacuum (Lorenzo Pedrazzetti)
>    2. how to consider disordered crystal structure (Neha Bothra)
>    3. Re: supercell and vacuum (Stefano de Gironcoli)
>    4. Re: supercell and vacuum (Stefano de Gironcoli)
>    5. Re: supercell and vacuum (Dae Kwang Jun)
>    6. Re: supercell and vacuum (Jess Wellendorff)
>    7. Re: Lower limit of target pressure (Subhodip Chatterjee)
>    8. Re: Lower limit of target pressure (Paolo Giannozzi)
>    9. Re: how to consider disordered crystal structure (mimam at ictp.it)
>   10. Re: Lower limit of target pressure (Subhodip Chatterjee)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 28 Sep 2016 04:51:58 +0000
> From: Lorenzo Pedrazzetti <lorenzo.pedrazzetti at polimi.it>
> Subject: [Pw_forum] supercell and vacuum
> To: "pw_forum at pwscf.org" <pw_forum at pwscf.org>
> Message-ID: <44rkccrstkwm9yx3mi51kmyg.1475038291492 at email.android.com>
> Content-Type: text/plain; charset="utf-8"
>
> Goodmorning qe community,
> I created an interface metal/semic by using virtual nanolab; when I come
> to check my structure with xcrysden I notice that, when vacuum is added
> enlarging the corresponding CELL_PARAMETERS component, all my atoms move
> along that direction, effectively expanding the cell instead of introducing
> vacuum layers.
> Where do I mess up? I thought the system is such that fixed celldm () and
> ATOMIC_POSITIONS all atoms should not move anymore.
> Thanks, have a nice day.
>
> Sent from my ASUS
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> ------------------------------
>
> Message: 2
> Date: Wed, 28 Sep 2016 10:35:14 +0530
> From: Neha Bothra <neha3bothra at gmail.com>
> Subject: [Pw_forum] how to consider disordered crystal structure
> To: pw_forum at pwscf.org
> Message-ID:
>         <CAC2yGDD6uCotMqc086By2yip46wZ0kMxGt5mgfYvSz4FHqU+ug at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear All,
>             I am trying to make a structure of *CeAgGa3 compound* from the
> following cif file in which *two different atoms have same configurations*.
> But I don't know how to do it? Can any one help?
>
> The coordinations are as follows:
>  Ce                 0.00000000    0.00000000    0.00000000
>  Ga                 0.00000000    2.16475000    2.70417500
>  Ag                 0.00000000    2.16475000    2.70417500
>  Ga                 0.00000000    0.00000000    4.17200119
>
> Thank you in advance for any helps regarding my request.
>
> Best regards,
> Neha Bothra,
> Ph.D student,
> JNCASR,
> Bengaluru, India.
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> ------------------------------
>
> Message: 3
> Date: Wed, 28 Sep 2016 08:18:01 +0200
> From: Stefano de Gironcoli <degironc at sissa.it>
> Subject: Re: [Pw_forum] supercell and vacuum
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <02A42E67-8ADB-45C6-8FDA-4CF6D45C4D9A at sissa.it>
> Content-Type: text/plain; charset="us-ascii"
>
> Looks like a problem in how you 'add vacuum' In your virtual nanolab step.
> Difficult to say without further information.
>
> stefano
> (sent from my phone)
>
> > On 28 Sep 2016, at 06:51, Lorenzo Pedrazzetti <
> lorenzo.pedrazzetti at polimi.it> wrote:
> >
> > Goodmorning qe community,
> > I created an interface metal/semic by using virtual nanolab; when I come
> to check my structure with xcrysden I notice that, when vacuum is added
> enlarging the corresponding CELL_PARAMETERS component, all my atoms move
> along that direction, effectively expanding the cell instead of introducing
> vacuum layers.
> > Where do I mess up? I thought the system is such that fixed celldm ()
> and ATOMIC_POSITIONS all atoms should not move anymore.
> > Thanks, have a nice day.
> >
> > Sent from my ASUS
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
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> ------------------------------
>
> Message: 4
> Date: Wed, 28 Sep 2016 08:21:16 +0200
> From: Stefano de Gironcoli <degironc at sissa.it>
> Subject: Re: [Pw_forum] supercell and vacuum
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <33895D6F-F2FE-47A4-BB1C-1788DF460902 at sissa.it>
> Content-Type: text/plain; charset="us-ascii"
>
> Are your atomic positions given in alat or crystal setting ? Understand
> the difference between the two options
>
> stefano
> (sent from my phone)
>
> > On 28 Sep 2016, at 06:51, Lorenzo Pedrazzetti <
> lorenzo.pedrazzetti at polimi.it> wrote:
> >
> > Goodmorning qe community,
> > I created an interface metal/semic by using virtual nanolab; when I come
> to check my structure with xcrysden I notice that, when vacuum is added
> enlarging the corresponding CELL_PARAMETERS component, all my atoms move
> along that direction, effectively expanding the cell instead of introducing
> vacuum layers.
> > Where do I mess up? I thought the system is such that fixed celldm ()
> and ATOMIC_POSITIONS all atoms should not move anymore.
> > Thanks, have a nice day.
> >
> > Sent from my ASUS
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
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> ------------------------------
>
> Message: 5
> Date: Wed, 28 Sep 2016 15:21:42 +0900
> From: Dae Kwang Jun <jdaekwang at gmail.com>
> Subject: Re: [Pw_forum] supercell and vacuum
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>         <CAC+GeGrRzYxtQYNJO0++eirXqdC=8CdqVdAXPKTnrQ+XK=rLpQ at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Wednesday, 28 September 2016, Stefano de Gironcoli <degironc at sissa.it>
> wrote:
>
> > Looks like a problem in how you 'add vacuum' In your virtual nanolab
> step.
> > Difficult to say without further information.
> >
> > stefano
> > (sent from my phone)
> >
> > On 28 Sep 2016, at 06:51, Lorenzo Pedrazzetti <
> > lorenzo.pedrazzetti at polimi.it
> > <javascript:_e(%7B%7D,'cvml','lorenzo.pedrazzetti at polimi.it');>> wrote:
> >
> > Goodmorning qe community,
> > I created an interface metal/semic by using virtual nanolab; when I come
> > to check my structure with xcrysden I notice that, when vacuum is added
> > enlarging the corresponding CELL_PARAMETERS component, all my atoms move
> > along that direction, effectively expanding the cell instead of
> introducing
> > vacuum layers.
> > Where do I mess up? I thought the system is such that fixed celldm () and
> > ATOMIC_POSITIONS all atoms should not move anymore.
> > Thanks, have a nice day.
> >
> > Sent from my ASUS
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org <javascript:_e(%7B%7D,'cvml','Pw_forum at pwscf.org');>
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
> > Dear Lorenzo
>
> It is possible that you are using fractional coordinates.  Try checking the
> settings and the units.
>
> Sincerely,
>
> Dae Kwang Jun
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> ------------------------------
>
> Message: 6
> Date: Wed, 28 Sep 2016 08:23:17 +0200
> From: Jess Wellendorff <jess.wellendorff at quantumwise.com>
> Subject: Re: [Pw_forum] supercell and vacuum
> To: pw_forum at pwscf.org
> Message-ID: <820da64d-1b95-85a5-2ebc-7da6cf2c2d93 at quantumwise.com>
> Content-Type: text/plain; charset="windows-1252"
>
> Dear Lorenzo.
>
> If this is indeed a problem related to Virtual NanoLab, I will be happy
> to try to help you out. Could you give more details on what you did in
> VNL? And preferably also attach the generated PWscf input file.
>
> --
> Jess Wellendorff
> Scientific Specialist
> QuantumWise A/S
> Fruebjergvej 3, Postbox 4
> 2100 Copenhagen, Denmark
> Web:   www.quantumwise.com
> Email: jess.wellendorff at quantumwise.com
> Tel:   +45 69901888
> --
>
>
>
> On 09/28/2016 08:18 AM, Stefano de Gironcoli wrote:
> > Looks like a problem in how you 'add vacuum' In your virtual nanolab
> > step. Difficult to say without further information.
> >
> > stefano
> > (sent from my phone)
> >
> > On 28 Sep 2016, at 06:51, Lorenzo Pedrazzetti
> > <lorenzo.pedrazzetti at polimi.it <mailto:lorenzo.pedrazzetti at polimi.it>>
> > wrote:
> >
> >> Goodmorning qe community,
> >> I created an interface metal/semic by using virtual nanolab; when I
> >> come to check my structure with xcrysden I notice that, when vacuum
> >> is added enlarging the corresponding CELL_PARAMETERS component, all
> >> my atoms move along that direction, effectively expanding the cell
> >> instead of introducing vacuum layers.
> >> Where do I mess up? I thought the system is such that fixed celldm ()
> >> and ATOMIC_POSITIONS all atoms should not move anymore.
> >> Thanks, have a nice day.
> >>
> >> Sent from my ASUS
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
> >> http://pwscf.org/mailman/listinfo/pw_forum
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
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> ------------------------------
>
> Message: 7
> Date: Wed, 28 Sep 2016 13:12:51 +0530
> From: Subhodip Chatterjee <subhopcqc at gmail.com>
> Subject: Re: [Pw_forum] Lower limit of target pressure
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>         <CAAuJ=OTfRzBLnwDhPbq6_xcW1ypur9dhEghqTHeSUxvDB_LSyg@
> mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Paolo,
>
> I want to add few more informations.
>
> After the vc-relax calculation, the magnitude of pressure is  -*0.02 kbar*.
>
> And what I mentioned in my last post (i.e. *3.61 kbar*) is the pressure
> after the final SCF calculation.
>
> It will be a big help if you can guide me to solve this issue.
>
> Best regards
> Subhodip
>
> On Mon, Sep 26, 2016 at 11:24 AM, Subhodip Chatterjee <subhopcqc at gmail.com
> >
> wrote:
>
> > INPUT
> >
> > *press = 0.001*
> > *press_conv_thr = 0.0001*
> >
> > OUTPUT
> > *P (kbar) = 3.61*
> >
> > Best regards
> > Subhodip
> >
> > On Sat, Sep 24, 2016 at 7:15 PM, Paolo Giannozzi <p.giannozzi at gmail.com>
> > wrote:
> >
> >> "A lot" = how much? the default tolerance on pressure convergence is 0.5
> >> KBar
> >>
> >>
> >> Paolo
> >>
> >> On Sat, Sep 24, 2016 at 8:39 AM, Subhodip Chatterjee <
> subhopcqc at gmail.com
> >> > wrote:
> >>
> >>> Dear PWSCF developers,
> >>>
> >>> Is there any restriction in the code for the "press" (target pressure)
> >>> input?
> >>>
> >>> I successfully get my vc-relax calculations converged to desired
> >>> pressure values as high as several terapascal, however, when I set a
> low
> >>> enough value, e.g. 1 bar (i.e. press = 0.001), the final pressure in
> the
> >>> output differs a lot!
> >>>
> >>> Best regards
> >>> Subhodip
> >>>
> >>> --
> >>> *Subhodip Chatterjee*
> >>>
> >>> *Senior Research Fellow*
> >>>
> >>> *Department of Chemistry*
> >>> *University of Calcutta*
> >>> *Kolkata, India*
> >>>
> >>> _______________________________________________
> >>> Pw_forum mailing list
> >>> Pw_forum at 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 at pwscf.org
> >> http://pwscf.org/mailman/listinfo/pw_forum
> >>
> >
> >
> >
> > --
> > *Subhodip Chatterjee*
> >
> > *Senior Research Fellow*
> >
> > *Department of Chemistry*
> > *University of Calcutta*
> > *Kolkata, India*
> >
>
>
>
> --
> *Subhodip Chatterjee*
>
> *Senior Research Fellow*
>
> *Department of Chemistry*
> *University of Calcutta*
> *Kolkata, India*
> -------------- next part --------------
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> ------------------------------
>
> Message: 8
> Date: Wed, 28 Sep 2016 09:58:14 +0200
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> Subject: Re: [Pw_forum] Lower limit of target pressure
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>         <CAPMgbCvKb+z0LYRvC21+UmJbKvpsMjFNwMJc6OcbBdyuQcYpwg
> @mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> You already solved the "issue":  the variable-cell optimization is done
> with the plane-wave basis set for the starting cell, while the last step is
> done with the plane-wave basis set for the final cell. The two differ by a
> little bit (unless the cutoff is so high to guarantee perfect convergence
> in both cases). Search for "Pulay stress"in the literature.
>
> Paolo
>
> On Wed, Sep 28, 2016 at 9:42 AM, Subhodip Chatterjee <subhopcqc at gmail.com>
> wrote:
>
> > Dear Paolo,
> >
> > I want to add few more informations.
> >
> > After the vc-relax calculation, the magnitude of pressure is  -*0.02
> kbar*
> > .
> >
> > And what I mentioned in my last post (i.e. *3.61 kbar*) is the pressure
> > after the final SCF calculation.
> >
> > It will be a big help if you can guide me to solve this issue.
> >
> > Best regards
> > Subhodip
> >
> > On Mon, Sep 26, 2016 at 11:24 AM, Subhodip Chatterjee <
> subhopcqc at gmail.com
> > > wrote:
> >
> >> INPUT
> >>
> >> *press = 0.001*
> >> *press_conv_thr = 0.0001*
> >>
> >> OUTPUT
> >> *P (kbar) = 3.61*
> >>
> >> Best regards
> >> Subhodip
> >>
> >> On Sat, Sep 24, 2016 at 7:15 PM, Paolo Giannozzi <p.giannozzi at gmail.com
> >
> >> wrote:
> >>
> >>> "A lot" = how much? the default tolerance on pressure convergence is
> 0.5
> >>> KBar
> >>>
> >>>
> >>> Paolo
> >>>
> >>> On Sat, Sep 24, 2016 at 8:39 AM, Subhodip Chatterjee <
> >>> subhopcqc at gmail.com> wrote:
> >>>
> >>>> Dear PWSCF developers,
> >>>>
> >>>> Is there any restriction in the code for the "press" (target pressure)
> >>>> input?
> >>>>
> >>>> I successfully get my vc-relax calculations converged to desired
> >>>> pressure values as high as several terapascal, however, when I set a
> low
> >>>> enough value, e.g. 1 bar (i.e. press = 0.001), the final pressure in
> the
> >>>> output differs a lot!
> >>>>
> >>>> Best regards
> >>>> Subhodip
> >>>>
> >>>> --
> >>>> *Subhodip Chatterjee*
> >>>>
> >>>> *Senior Research Fellow*
> >>>>
> >>>> *Department of Chemistry*
> >>>> *University of Calcutta*
> >>>> *Kolkata, India*
> >>>>
> >>>> _______________________________________________
> >>>> Pw_forum mailing list
> >>>> Pw_forum at 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 at pwscf.org
> >>> http://pwscf.org/mailman/listinfo/pw_forum
> >>>
> >>
> >>
> >>
> >> --
> >> *Subhodip Chatterjee*
> >>
> >> *Senior Research Fellow*
> >>
> >> *Department of Chemistry*
> >> *University of Calcutta*
> >> *Kolkata, India*
> >>
> >
> >
> >
> > --
> > *Subhodip Chatterjee*
> >
> > *Senior Research Fellow*
> >
> > *Department of Chemistry*
> > *University of Calcutta*
> > *Kolkata, India*
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at 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
> -------------- next part --------------
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> ------------------------------
>
> Message: 9
> Date: Wed, 28 Sep 2016 11:31:58 +0200
> From: mimam at ictp.it
> Subject: Re: [Pw_forum] how to consider disordered crystal structure
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID:
>         <af3aa4b1138602980a4d205736dfcc91.squirrel at webmail.ictp.it>
> Content-Type: text/plain;charset=iso-8859-1
>
> I guess this is from a VASP input file.
> This is VASP's way of using virtual crystal approximation: It does not use
> a "virtual atom", rather puts the real atoms at the same position with
> weighted pseudopotentials in the INCAR file.
>
> HTH
> Mighfar
>
>
> > Dear All,
> >             I am trying to make a structure of *CeAgGa3 compound* from
> the
> > following cif file in which *two different atoms have same
> > configurations*.
> > But I don't know how to do it? Can any one help?
> >
> > The coordinations are as follows:
> >  Ce                 0.00000000    0.00000000    0.00000000
> >  Ga                 0.00000000    2.16475000    2.70417500
> >  Ag                 0.00000000    2.16475000    2.70417500
> >  Ga                 0.00000000    0.00000000    4.17200119
> >
> > Thank you in advance for any helps regarding my request.
> >
> > Best regards,
> > Neha Bothra,
> > Ph.D student,
> > JNCASR,
> > Bengaluru, India.
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
>
> --
> Mighfar Imam,
> Postdoc
> MRC, IISc, Bangalore.
>
>
>
>
> ------------------------------
>
> Message: 10
> Date: Wed, 28 Sep 2016 09:32:06 +0000
> From: Subhodip Chatterjee <subhopcqc at gmail.com>
> Subject: Re: [Pw_forum] Lower limit of target pressure
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
>         <CAAuJ=OQ7SrHBvEqDrmG2-1H+K+T3N=d4E2pwjAo_8M3da=p2Kw at mail.
> gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Paolo,
>
> Thanks for your reply. But the main problem is not solved, because none of
> the two values are appropriate with respect to the input, i.e. target
> pressure of 0.001 kbar with a pressure convergence threshold of 0.0001
> kbar!
>
> What changes in the input are needed to get the optimized geometry at 0.001
> kbar pressure?
>
> Best regards
> Subhodip
>
> --
> *Subhodip Chatterjee*
>
> *Senior Research Fellow*
>
> *Department of Chemistry*
> *University of Calcutta*
> *Kolkata, India*
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> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
> End of Pw_forum Digest, Vol 110, Issue 28
> *****************************************
>
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