<div dir="ltr"><div class="gmail_default" style="color:rgb(153,0,255)">Dear everyone,</div><div class="gmail_default" style="color:rgb(153,0,255)"><br></div><div class="gmail_default" style="color:rgb(153,0,255)">I am trying to visualize charge density in 3D using XCrysden but there are some issues. With iflag = 3, output_format = 3, I got .xsf file which xcrysden seems to understand and executes the unit cell. As I was trying to visualize charge density through data grid manipulations, it won't respond. In particular, whatever isovalue I choose to put in, it says "Specified isovalue is out of range" and xcrysden is frozen ultimately.</div><div class="gmail_default" style="color:rgb(153,0,255)"><br></div><div class="gmail_default" style="color:rgb(153,0,255)">Even if I was able to do pp.x calculations to get .xsf file, plotrho.x calculation was unsuccessful saying "At line 42 of file plotrho.f90 (unit = 1, file = 'si.rho001.xsf')Fortran runtime error: Bad integer for item 1 in list input".</div><div><br></div><div class="gmail_default" style="color:rgb(153,0,255)"><br></div><div class="gmail_default" style="color:rgb(153,0,255)">I am not sure what exactly is going on. If anyone could help me out, that would be awesome..</div><div class="gmail_default" style="color:rgb(153,0,255)"><br></div><div class="gmail_default" style="color:rgb(153,0,255)">Attached are the input files.</div><div class="gmail_default" style="color:rgb(153,0,255)"><br></div><div class="gmail_default" style="color:rgb(153,0,255)">Thank you so much.</div><div class="gmail_default" style="color:rgb(153,0,255)"><br></div><div class="gmail_default" style="color:rgb(153,0,255)"><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div style="text-align:center"><b style="color:rgb(0,0,255);font-size:large"><i><font face="arial black, sans-serif">Vijay Khanal</font></i></b></div><div><div><div><div style="text-align:center"><span style="color:rgb(0,0,255);font-family:monospace,monospace;font-size:12.8000001907349px">Department of Physics</span></div><div style="text-align:center"><font color="#0000ff" face="monospace, monospace">University of Nevada, Reno</font></div><div style="text-align:center"><font color="#0000ff" face="monospace, monospace">Phone:(1-<b><u>775-440-7036)</u></b></font></div><div style="text-align:center"><br></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Fri, Mar 25, 2016 at 8:30 PM, Vijay Khanal <span dir="ltr"><<a href="mailto:vj.khanal20@gmail.com" target="_blank">vj.khanal20@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="color:#9900ff">Dear QE users,</div><div class="gmail_default" style="color:#9900ff"><br></div><div class="gmail_default" style="color:#9900ff">Being a novice user, I am not entirely sure why would we like to do <b>nscf </b>calculations even if we have <b>scf </b>and <b>relax</b> calculations. Looks like we need nscf for post-processing of Bandstructure calculations, but there should definitely be more genuine reasons for doing that, I believe. Could you please clarify it for me?</div><div class="gmail_default" style="color:#9900ff"><br></div><div class="gmail_default" style="color:#9900ff">Thank you.</div><div class="gmail_default" style="color:#9900ff"><br></div><div class="gmail_default" style="color:#9900ff">Respectfully,</div><div class="gmail_default" style="color:#9900ff">Vijay Khanal.</div><div class="gmail_default" style="color:#9900ff"><br></div><div class="gmail_default" style="color:#9900ff"><br></div></div><div class="gmail_extra"><span class=""><br clear="all"><div><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div style="text-align:center"><b style="color:rgb(0,0,255);font-size:large"><i><font face="arial black, sans-serif">Vijay Khanal</font></i></b></div><div><div><div><div style="text-align:center"><span style="color:rgb(0,0,255);font-family:monospace,monospace;font-size:12.8000001907349px">Department of Physics</span></div><div style="text-align:center"><font color="#0000ff" face="monospace, monospace">University of Nevada, Reno</font></div><div style="text-align:center"><font color="#0000ff" face="monospace, monospace">Phone:(1-<b><u><a href="tel:775-440-7036" value="+17754407036" target="_blank">775-440-7036</a>)</u></b></font></div><div style="text-align:center"><br></div></div></div></div></div></div></div></div></div></div></div>
<br></span><div><div class="h5"><div class="gmail_quote">On Wed, Mar 23, 2016 at 4:00 AM, <span dir="ltr"><<a href="mailto:pw_forum-request@pwscf.org" target="_blank">pw_forum-request@pwscf.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Pw_forum mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: The format of potential file in example Al100<br>
workfunction (Giovanni Cantele)<br>
2. citing PSLibrary (Merlin Meheut)<br>
3. Re: citing PSLibrary (Giuseppe Mattioli)<br>
4. Re: negative occupations in DFT+U for nonmagnetic<br>
semiconductor (Mostafa Youssef)<br>
5. Re: Specifying initial velocities in MD (Ilya Ryabinkin)<br>
6. General question on restarted calculation (Cameron Foss)<br>
7. vc_relax calc. stopped converging (Vishal Gupta)<br>
8. TiO2, ZO2 and BaTiO3 nanoclusters (Andrey Chibisov)<br>
9. RE : Regarding PDOS (efi dwi indari)<br>
10. Band Diagram: Regarding (Suresh A)<br>
11. xmgrace installation problem (Vijay Khanal)<br>
12. Re: xmgrace installation problem (Mike Atambo)<br>
13. Re: xmgrace installation problem (Giovanni Cantele)<br>
14. Re: Band Diagram: Regarding (Giovanni Cantele)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 22 Mar 2016 12:37:04 +0100<br>
From: Giovanni Cantele <<a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a>><br>
Subject: Re: [Pw_forum] The format of potential file in example Al100<br>
workfunction<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:26AEF445-16EF-4CA1-B471-2F5AA4AEC056@spin.cnr.it" target="_blank">26AEF445-16EF-4CA1-B471-2F5AA4AEC056@spin.cnr.it</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
L3:<br>
WRITE (iunplot, '(3f20.10,i6)') gcutm, dual, ecutwfc<br>
<br>
ecutwfc = input variable, kinetic energy cutoff (Ry) for wave functions<br>
<br>
dual = ecutrho/ecutwfc, where ecutrho=kinetic energy cutoff (Ry) for charge density and potential<br>
<br>
by default dual=4, this can be easily obtained by representing the charge density in terms of the Fourier expansions of the Kohn-Sham orbitals,<br>
dual should be set >4 only if not norm conserving pseudo potentials are used in the calculation<br>
<br>
<br>
gcutm : ecutrho/(2 pi/a)^2, cut-off for |G|^2<br>
<br>
<br>
L4:<br>
WRITE (iunplot, '(i4,3x,a2,3x,f5.2)') &<br>
(nt, atm (nt), zv (nt), nt=1, ntyp)<br>
<br>
so, in your case, atomic species nt=1 has symbol atm(nt)=Al with valence zv(nt)=3 because the pseudo you use to represent that atom (Al) is built using three electrons in the valence<br>
<br>
Giovanni<br>
<br>
<br>
<br>
> On 22 Mar 2016, at 03:50, Yue-Wen Fang <<a href="mailto:yuewen.fang@gmail.com" target="_blank">yuewen.fang@gmail.com</a>> wrote:<br>
><br>
> Dear Prof. Giovanni,<br>
><br>
> Thanks for your answer. I read it and average.f90, but still don't know the specific meaning of L3 and 3.00 in L4. Could you help explain them?<br>
><br>
> Thanks for your time.<br>
><br>
><br>
> L1: 18 18 120 18 18 120 4 1<br>
> L2: 6 5.42350901 0.00000000 6.36396103 0.00000000 0.00000000 0.00000000<br>
> L3: 74.<a href="tel:5076722547" value="+15076722547" target="_blank">5076722547</a>(gcutm) 4.0000000000(dual) 25.000000000(ecuwfc) 11<br>
> L4: 1 Al 3.00(zv?)<br>
> L5: 1 0.000000000 0.000000000 4.242640687 1<br>
> L6: 2 0.500000000 0.500000000 3.535533906 1<br>
> L7: 3 0.000000000 0.000000000 2.828427125 1<br>
> L8: 4 0.500000000 0.500000000 2.121320344 1<br>
><br>
> Bests<br>
> Fang<br>
><br>
> 2016-03-15 18:42 GMT+08:00 Giovanni Cantele <<a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a> <mailto:<a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a>>>:<br>
> see PP/src/write_io_header.f90<br>
><br>
> Giovanni<br>
><br>
>> On 15 Mar 2016, at 09:05, Yue-Wen Fang <<a href="mailto:yuewen.fang@gmail.com" target="_blank">yuewen.fang@gmail.com</a> <mailto:<a href="mailto:yuewen.fang@gmail.com" target="_blank">yuewen.fang@gmail.com</a>>> wrote:<br>
>><br>
>> Dear users,<br>
>><br>
>> In the example of the workfunction for Al(100), we can get a file "Al100.pot" after executing pp.x after runing pp.x<br>
>><br>
>> The header part in the file is shown below (L1, L2... denote the line numbers):<br>
>><br>
>> L1: 18 18 120 18 18 120 4 1<br>
>> L2: 6 5.42350901 0.00000000 6.36396103 0.00000000 0.00000000 0.00000000<br>
>> L3: 74.<a href="tel:5076722547" value="+15076722547" target="_blank">5076722547</a> 4.0000000000 25.0000000000 11<br>
>> L4: 1 Al 3.00<br>
>> L5: 1 0.000000000 0.000000000 4.242640687 1<br>
>> L6: 2 0.500000000 0.500000000 3.535533906 1<br>
>> L7: 3 0.000000000 0.000000000 2.828427125 1<br>
>> L8: 4 0.500000000 0.500000000 2.121320344 1<br>
>><br>
>> Could anyone explain the meaning of this part? I didn't find the code in pwscf which generates the header part.<br>
>><br>
>> Actually I can guess some of them like FFT grid and coordinates, but I'm not sure for each number shown above. I appreciate experienced users' giving a hand. Many thanks.<br>
>><br>
>> Bests<br>
>> Fang<br>
>> --<br>
>> ------------------------------------------------------------------------------------------------------------<br>
>> Yue-Wen FANG, PhD candidate<br>
>> East China Normal University? <<a href="http://english.ecnu.edu.cn/" rel="noreferrer" target="_blank">http://english.ecnu.edu.cn/</a>><br>
>><br>
>><br>
>><br>
>> _______________________________________________<br>
>> Pw_forum mailing list<br>
>> <a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a> <mailto:<a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a>><br>
>> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a> <<a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a>><br>
> --<br>
><br>
> Giovanni Cantele, PhD<br>
> CNR-SPIN<br>
> c/o Dipartimento di Fisica<br>
> Universita' di Napoli "Federico II"<br>
> Complesso Universitario M. S. Angelo - Ed. 6<br>
> Via Cintia, I-80126, Napoli, Italy<br>
> e-mail: <a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a> <mailto:<a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a>><br>
> Phone: <a href="tel:%2B39%20081%20676910" value="+39081676910" target="_blank">+39 081 676910</a><br>
> Skype contact: giocan74<br>
><br>
> ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" rel="noreferrer" target="_blank">http://www.researcherid.com/rid/A-1951-2009</a> <<a href="http://www.researcherid.com/rid/A-1951-2009" rel="noreferrer" target="_blank">http://www.researcherid.com/rid/A-1951-2009</a>><br>
> Web page: <a href="http://people.na.infn.it/~cantele" rel="noreferrer" target="_blank">http://people.na.infn.it/~cantele</a> <<a href="http://people.na.infn.it/~cantele" rel="noreferrer" target="_blank">http://people.na.infn.it/~cantele</a>><br>
><br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a> <mailto:<a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a>><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a> <<a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a>><br>
><br>
><br>
><br>
> --<br>
> ------------------------------------------------------------------------------------------------------------<br>
> Yue-Wen FANG, PhD candidate<br>
> East China Normal University? <<a href="http://english.ecnu.edu.cn/" rel="noreferrer" target="_blank">http://english.ecnu.edu.cn/</a>><br>
><br>
><br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
<br>
--<br>
<br>
Giovanni Cantele, PhD<br>
CNR-SPIN<br>
c/o Dipartimento di Fisica<br>
Universita' di Napoli "Federico II"<br>
Complesso Universitario M. S. Angelo - Ed. 6<br>
Via Cintia, I-80126, Napoli, Italy<br>
e-mail: <a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a><br>
Phone: <a href="tel:%2B39%20081%20676910" value="+39081676910" target="_blank">+39 081 676910</a><br>
Skype contact: giocan74<br>
<br>
ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" rel="noreferrer" target="_blank">http://www.researcherid.com/rid/A-1951-2009</a><br>
Web page: <a href="http://people.na.infn.it/~cantele" rel="noreferrer" target="_blank">http://people.na.infn.it/~cantele</a><br>
<br>
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Message: 2<br>
Date: Tue, 22 Mar 2016 12:23:34 +0000<br>
From: Merlin Meheut <<a href="mailto:merlin.meheut@gmail.com" target="_blank">merlin.meheut@gmail.com</a>><br>
Subject: [Pw_forum] citing PSLibrary<br>
To: <a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<<a href="mailto:CAOZRYoC2-NTt63LKbjCwf5BzUoqVqs0PxLoLod7P4QdkA%2B1pJg@mail.gmail.com" target="_blank">CAOZRYoC2-NTt63LKbjCwf5BzUoqVqs0PxLoLod7P4QdkA+1pJg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear PWSCF users,<br>
<br>
I have made important use of some pseudopotentials present in the<br>
PSLibrary, and I would like to describe them in a publication. More<br>
precisely, I used the pseudopotentials Mg.blyp-spn-rrkjus_psl.1.0.0.UPF,<br>
K.blyp-spn-rrkjus_psl.1.0.0.UPF, and Li.blyp-sl-rrkjus_psl.1.0.0.UPF.<br>
<br>
Do you have any advice on how to describe them, and/or on how to cite the<br>
PSLIbrary (version 1.0.0)?<br>
<br>
Thank you very much for any advice,<br>
<br>
Best regards,<br>
<br>
Merlin Meheut<br>
<br>
--<br>
Merlin M?heut<br>
adresse labo:<br>
GET - OMP - Universit? Paul Sabatier<br>
14 avenue Edouard Belin<br>
31400 Toulouse<br>
FRANCE<br>
tel: <a href="tel:%28%2B33%29%205%2061%2033%2026%2017" value="+33561332617" target="_blank">(+33) 5 61 33 26 17</a><br>
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<br>
Message: 3<br>
Date: Tue, 22 Mar 2016 13:49:05 +0100<br>
From: Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>><br>
Subject: Re: [Pw_forum] citing PSLibrary<br>
To: <a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a><br>
Message-ID: <4817076.5OUG813eSe@amore2><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
<br>
Dear Merlin<br>
<br>
Dal Corso, A. Comput. Mater. Sci. 2014, 95, 337?350.<br>
<br>
HTH<br>
Giuseppe<br>
<br>
On Tuesday, March 22, 2016 12:23:34 PM Merlin Meheut wrote:<br>
> Dear PWSCF users,<br>
><br>
> I have made important use of some pseudopotentials present in the<br>
> PSLibrary, and I would like to describe them in a publication. More<br>
> precisely, I used the pseudopotentials Mg.blyp-spn-rrkjus_psl.1.0.0.UPF,<br>
> K.blyp-spn-rrkjus_psl.1.0.0.UPF, and Li.blyp-sl-rrkjus_psl.1.0.0.UPF.<br>
><br>
> Do you have any advice on how to describe them, and/or on how to cite the<br>
> PSLIbrary (version 1.0.0)?<br>
><br>
> Thank you very much for any advice,<br>
><br>
> Best regards,<br>
><br>
> Merlin Meheut<br>
<br>
********************************************************<br>
- Article premier - Les hommes naissent et demeurent<br>
libres et ?gaux en droits. Les distinctions sociales<br>
ne peuvent ?tre fond?es que sur l'utilit? commune<br>
- Article 2 - Le but de toute association politique<br>
est la conservation des droits naturels et<br>
imprescriptibles de l'homme. Ces droits sont la libert?,<br>
la propri?t?, la s?ret? et la r?sistance ? l'oppression.<br>
********************************************************<br>
<br>
Giuseppe Mattioli<br>
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
v. Salaria Km 29,300 - C.P. 10<br>
I 00015 - Monterotondo Stazione (RM), Italy<br>
Tel <a href="tel:%2B%2039%2006%2090672836" value="+390690672836" target="_blank">+ 39 06 90672836</a> - Fax <a href="tel:%2B39%2006%2090672316" value="+390690672316" target="_blank">+39 06 90672316</a><br>
E-mail: <<a href="mailto:giuseppe.mattioli@ism.cnr.it" target="_blank">giuseppe.mattioli@ism.cnr.it</a>><br>
<a href="http://www.ism.cnr.it/english/staff/mattiolig" rel="noreferrer" target="_blank">http://www.ism.cnr.it/english/staff/mattiolig</a><br>
ResearcherID: F-6308-2012<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Tue, 22 Mar 2016 14:28:37 +0000<br>
From: Mostafa Youssef <<a href="mailto:myoussef@mit.edu" target="_blank">myoussef@mit.edu</a>><br>
Subject: Re: [Pw_forum] negative occupations in DFT+U for nonmagnetic<br>
semiconductor<br>
To: "<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>" <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:0AE34FFC1339F64387D182A8D7E4D99B6D18A9DB@OC11EXPO32.exchange.mit.edu" target="_blank">0AE34FFC1339F64387D182A8D7E4D99B6D18A9DB@OC11EXPO32.exchange.mit.edu</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Thank you for the clarification, Prof. de Gironcoli. I think I misinterpreted the meaning of the matrix elements.<br>
<br>
Best Regards,<br>
Mostafa<br>
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Message: 5<br>
Date: Tue, 22 Mar 2016 10:30:44 -0400<br>
From: Ilya Ryabinkin <<a href="mailto:igryabinkin@gmail.com" target="_blank">igryabinkin@gmail.com</a>><br>
Subject: Re: [Pw_forum] Specifying initial velocities in MD<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAHcT10qrp7Et0KTgeKUjh7nZYN=<a href="mailto:SJ7pRqg7j0PD9zvmRv3GRXA@mail.gmail.com" target="_blank">SJ7pRqg7j0PD9zvmRv3GRXA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=UTF-8<br>
<br>
Well, I figured it out by myself... Here is a short tutorial for those<br>
who might be interested.<br>
<br>
All below is pertinent to QE 5.2.1.<br>
There is an undocumented feature allowing one to specify initial velocities.<br>
<br>
1. Add to the input list<br>
&IONS<br>
ion_velocities = 'from_input'<br>
/<br>
<br>
2. Add a new input card "ATOMIC_VELOCITIES".<br>
<br>
Here is the quotation from the source code (read_card_f90):<br>
! ATOMIC_VELOCITIES<br>
!<br>
! read velocities (in atomic units) from standard input<br>
!<br>
! Syntax:<br>
!<br>
! ATOMIC_VELOCITIES<br>
! label(1) Vx(1) Vy(1) Vz(1)<br>
! ....<br>
! label(n) Vx(n) Vy(n) Vz(n)<br>
!<br>
! Example:<br>
!<br>
! ???<br>
!<br>
! Where:<br>
!<br>
! label (character(len=4)) atomic label<br>
! Vx(:), Vy(:) and Vz(:) (REAL) x, y and z velocity components of<br>
! the ions<br>
!<br>
<br>
<br>
Two caveats:<br>
Caveat #1. Velocities are given in bohr/1Rut, not in atomic units as<br>
the source says!<br>
<br>
Caveat #2. If there are no frozen atoms in a cell, the center-of-mass<br>
velocity will be subtracted from<br>
the given velocities leading to a different value of the initial<br>
kinetic energy. If any of atomic coordinate is<br>
frozen, the velocities are assigned as given.<br>
<br>
<br>
--<br>
*******************************************************<br>
Ilya Ryabinkin<br>
Postdoctoral Scholar<br>
Physical and Environmental Sciences<br>
University of Toronto Scarborough<br>
<a href="http://www.utsc.utoronto.ca/~aizmaylov/Members.html" rel="noreferrer" target="_blank">http://www.utsc.utoronto.ca/~aizmaylov/Members.html</a><br>
*******************************************************<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Tue, 22 Mar 2016 16:29:20 -0400<br>
From: Cameron Foss <<a href="mailto:cjfoss@umass.edu" target="_blank">cjfoss@umass.edu</a>><br>
Subject: [Pw_forum] General question on restarted calculation<br>
To: <a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<CANUcA0PcWSystyeUB0RqfUD=b=<a href="mailto:1xqTcB1j1mNk5fBRJvpkc72g@mail.gmail.com" target="_blank">1xqTcB1j1mNk5fBRJvpkc72g@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hello all,<br>
<br>
I have had mixed results with restarted calculations when calculating<br>
phonons in TMD MoSe2. Particularly, a dispersion obtained from an<br>
interrupted simulation that was restarted (after an unplanned stop)<br>
returned an 'ok' dispersion despite having some negative frequencies in the<br>
ZA branch (the ZA being the characteristic quadratic flexural phonon mode<br>
in 2D materials). This 'ok' dispersion was calculated on a 6x6x4 MP grid<br>
size. In an attempt to refine the simulation and avoid numerical errors, I<br>
increased the MP grid size to 17x17x1 (in literature a 2D grid size<br>
definition has been used to generate the dispersion of other 2D materials<br>
like MoS2) and implemented controlled stops within walltime limits to avoid<br>
unplanned interruptions in the simulation. Another change between the old<br>
and new simulation was the fact that I isolated the monolayer in the middle<br>
of the unit cell rather than resting at the bottom (I have provided both<br>
input scripts). The dispersion obtained from this latter simulation was<br>
practically nonsense as if the input file defined a highly unstable<br>
structure despite the convergence of relaxation calculations. In short the<br>
first interrupted simulation on a more coarse MP grid yield far better<br>
results than the isolated denser grid simulation. Is there any insight as<br>
to what possible errors that may have occurred? or is it possible that I<br>
did not trace the BZ appropriately as a result of the height offset? (I did<br>
attempt to trace along the z-direction at the Gamma and K points and their<br>
values were accurate and invariant of z despite the rest of the dispersion<br>
being completely incorrect)<br>
<br>
%% the first input file that gave an ok dispersion %%<br>
Phonons in MoSe2<br>
&control<br>
calculation='scf'<br>
restart_mode='from_scratch',<br>
!pseudo_dir='directory where pseudopotentials are stored/',<br>
!outdir='directory where large files are written/'<br>
pseudo_dir='/home/cjfoss/espresso-5.1/pseudo/',<br>
outdir='/oasis/scratch/cjfoss/temp_project/out'<br>
prefix='mose2PH',<br>
/<br>
&system<br>
ibrav=4, celldm(1)=6.2134195, celldm(3)=8,<br>
nat=3, ntyp=2, ecutwfc =140<br>
/<br>
&electrons<br>
conv_thr = 1.0d-14<br>
mixing_beta = 0.7<br>
/<br>
ATOMIC_SPECIES<br>
Mo 95.94 Mo.pw-mt_fhi.UPF<br>
Se 78.96 Se.pw-mt_fhi.UPF<br>
ATOMIC_POSITIONS alat<br>
Se 0.000000000 0.000000000 0.000000000<br>
Mo 0.500000000 0.288675135 0.493465193<br>
Se 0.000000000 0.000000000 0.986930347<br>
K_POINTS automatic<br>
6 6 4 1 1 1<br>
<br>
<br>
%% the second input file that gave bad results %%<br>
Phonons in MoSe2<br>
&control<br>
calculation='scf'<br>
restart_mode='from_scratch',<br>
!pseudo_dir='directory where pseudopotentials are stored/',<br>
!outdir='directory where large files are written/'<br>
pseudo_dir='/home/cjfoss/espresso-5.1/pseudo/',<br>
outdir='/home/cjfoss/espresso-5.1/2dout'<br>
prefix='mose2PH_v7',<br>
/<br>
&system<br>
ibrav=4, celldm(1)=6.2134195, celldm(3)=8,<br>
nat=3, ntyp=2, ecutwfc =140<br>
/<br>
&electrons<br>
conv_thr = 1.0d-12<br>
mixing_beta = 0.7<br>
/<br>
ATOMIC_SPECIES<br>
Mo 95.94 Mo.pw-mt_fhi.UPF<br>
Se 78.96 Se.pw-mt_fhi.UPF<br>
ATOMIC_POSITIONS alat<br>
Se 0.000000000 0.000000000 3.000000000<br>
Mo 0.500000000 0.288675135 3.493465193<br>
Se 0.000000000 0.000000000 3.986930347<br>
K_POINTS automatic<br>
17 17 1 1 1 1<br>
<br>
%% note the main differences are the MP grid size and the z-direction<br>
offset.<br>
<br>
Any insight is welcome!<br>
<br>
Best regards,<br>
Cameron<br>
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Message: 7<br>
Date: Wed, 23 Mar 2016 07:16:33 +0530<br>
From: Vishal Gupta <<a href="mailto:vishal.gupta@iitrpr.ac.in" target="_blank">vishal.gupta@iitrpr.ac.in</a>><br>
Subject: [Pw_forum] vc_relax calc. stopped converging<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CANAZiL-+ZKJGtUfG-+mhqGQ2EO3rUVpsjfzQGGs=<a href="mailto:HndFEeaGXw@mail.gmail.com" target="_blank">HndFEeaGXw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi all,<br>
I've been running a vc_relax calculation on a 40 atom system. The<br>
calculation worked fine for some cycles. The total force had come down to<br>
0.108 and when the no of cycles was complete, I started another calculation<br>
with the final atomic positions and lattice parametres.<br>
In this new file, the force started increasing and it increased to 0.2 and<br>
now the iterations don't converge even in 400 steps.<br>
The CELL parameters are :-<br>
[&Ions/]<br>
/<br>
&CELL<br>
cell_dynamics= 'damp-w' ,<br>
cell_dofree='xy' ,<br>
/<br>
<br>
Please tell me where am I making the mistake.<br>
Thank You.<br>
Best Regards,<br>
Vishal Gupta<br>
<br>
B.Tech. 3rd year Mechanical<br>
Indian Institute of Technology Ropar<br>
Rupnagar (140001), Punjab, India.<br>
Email :- <a href="mailto:vishal.gupta@iitrpr.ac.in" target="_blank">vishal.gupta@iitrpr.ac.in</a><br>
RMML, IIT Ropar<br>
<<a href="https://sites.google.com/a/iitrpr.ac.in/ropar-mechanics-of-materials-laboratory/people" rel="noreferrer" target="_blank">https://sites.google.com/a/iitrpr.ac.in/ropar-mechanics-of-materials-laboratory/people</a>><br>
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Message: 8<br>
Date: Wed, 23 Mar 2016 12:23:22 +1000<br>
From: Andrey Chibisov <<a href="mailto:andreichibisov@yandex.ru" target="_blank">andreichibisov@yandex.ru</a>><br>
Subject: [Pw_forum] TiO2, ZO2 and BaTiO3 nanoclusters<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:1844551458699802@web27g.yandex.ru" target="_blank">1844551458699802@web27g.yandex.ru</a>><br>
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<br>
Message: 9<br>
Date: Wed, 23 Mar 2016 10:03:34 +0700<br>
From: efi dwi indari <<a href="mailto:efidwiindari@gmail.com" target="_blank">efidwiindari@gmail.com</a>><br>
Subject: [Pw_forum] RE : Regarding PDOS<br>
To: <a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<CAHN8SfnTEAdbwTsO28xSKsQJryGirtgDjO0qzs_8uccmhdgG=<a href="mailto:g@mail.gmail.com" target="_blank">g@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Mr. Sushant Kumar Behera,<br>
<br>
I use gnuplot. There is a nice tutorial at this following link :<br>
<a href="http://people.duke.edu/~hpgavin/gnuplot.html" rel="noreferrer" target="_blank">http://people.duke.edu/~hpgavin/gnuplot.html</a><br>
<br>
Hope it helps.<br>
<br>
Best Regards,<br>
<br>
Efi Dwi Indari<br>
Research Assistant Institut Teknologi Bandung<br>
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Message: 10<br>
Date: Wed, 23 Mar 2016 10:03:39 +0530<br>
From: Suresh A <<a href="mailto:suresh2007pgp19@gmail.com" target="_blank">suresh2007pgp19@gmail.com</a>><br>
Subject: [Pw_forum] Band Diagram: Regarding<br>
To: <a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<<a href="mailto:CAE_UR%2BWMxfq7eH0g%2BSWy5wi08_fYa1iDhKCK-eZud_qnKOkSYQ@mail.gmail.com" target="_blank">CAE_UR+WMxfq7eH0g+SWy5wi08_fYa1iDhKCK-eZud_qnKOkSYQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear All,<br>
Band structure is plotted using plotband.x executable in<br>
espresso. Can one use plotband.x to do other things like colouring band<br>
structures, differentiating specific band with different colour and making<br>
journal publication quality pictures?. If there is other software please<br>
direct me towards it.<br>
Thanks in advance<br>
With Regards,<br>
A.Suresh,<br>
Research Scholar,<br>
Madurai Kamaraj University,<br>
Madurai.<br>
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Message: 11<br>
Date: Tue, 22 Mar 2016 21:49:40 -0700<br>
From: Vijay Khanal <<a href="mailto:vj.khanal20@gmail.com" target="_blank">vj.khanal20@gmail.com</a>><br>
Subject: [Pw_forum] xmgrace installation problem<br>
To: pw_forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAJ+hQ2cOPmJG5jhVdtRaJo8Gik3MEMSnTtEZ7H=<a href="mailto:Xup85jK5sVQ@mail.gmail.com" target="_blank">Xup85jK5sVQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear everyone,<br>
<br>
I am a novice user of Quantum Espresso. I have been facing the following<br>
issue since the day I had tried to visualize the bandstructure of Silicon.<br>
<br>
I was trying to install xmgrace in my mac OSX Yosemite(10.10.5). Following<br>
the installation steps, looks like the dependency(MOTIF) is not installed.<br>
I tired installing it from<br>
<a href="http://www.ist-inc.com/motif/download/motif_files/openmotif-compat-2.1.32_IST.macosx10.5.dmg" rel="noreferrer" target="_blank">http://www.ist-inc.com/motif/download/motif_files/openmotif-compat-2.1.32_IST.macosx10.5.dmg</a>,<br>
it actually is installed; but then when I get back to xmgrace installation,<br>
it says "configure: error: M*tif has not been found". I tried with its<br>
source too (<br>
<a href="http://www.ist-inc.com/motif/download/motif_files/openmotif-2.1.32_IST.source.tar.gz" rel="noreferrer" target="_blank">http://www.ist-inc.com/motif/download/motif_files/openmotif-2.1.32_IST.source.tar.gz</a>),<br>
but couldn't do it. Please let me know how I can get rid of this issue.<br>
<br>
If there exists any easier alternative to xmgrace, that would be even<br>
better.<br>
<br>
Thank you so much for your time!<br>
<br>
<br>
Sincerely,<br>
Vijay Khanal<br>
*Vijay Khanal*<br>
Department of Physics<br>
University of Nevada, Reno<br>
Phone:(1-*<a href="tel:775-440-7036" value="+17754407036" target="_blank">775-440-7036</a>)*<br>
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<br>
Message: 12<br>
Date: Wed, 23 Mar 2016 09:17:31 +0000<br>
From: Mike Atambo <<a href="mailto:mikeat4999@gmail.com" target="_blank">mikeat4999@gmail.com</a>><br>
Subject: Re: [Pw_forum] xmgrace installation problem<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAEBLkK-LeNT1=<a href="mailto:mbFG8FifbkXLskJZ4YraQg5du1-LyuYODtTzQ@mail.gmail.com" target="_blank">mbFG8FifbkXLskJZ4YraQg5du1-LyuYODtTzQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Vijay,<br>
You may want to give more details (like the error when installing Motif)<br>
this will help other Mac users to spot your particular error,<br>
but, that said iv heard of something called brew for MAC users, try it,<br>
here are some instructions on stackoverflow:<br>
<a href="http://stackoverflow.com/a/28999461/1908184" rel="noreferrer" target="_blank">http://stackoverflow.com/a/28999461/1908184</a><br>
<br>
On Wed, Mar 23, 2016 at 5:50 AM Vijay Khanal <<a href="mailto:vj.khanal20@gmail.com" target="_blank">vj.khanal20@gmail.com</a>> wrote:<br>
<br>
> Dear everyone,<br>
><br>
> I am a novice user of Quantum Espresso. I have been facing the following<br>
> issue since the day I had tried to visualize the bandstructure of Silicon.<br>
><br>
> I was trying to install xmgrace in my mac OSX Yosemite(10.10.5). Following<br>
> the installation steps, looks like the dependency(MOTIF) is not installed.<br>
> I tired installing it from<br>
> <a href="http://www.ist-inc.com/motif/download/motif_files/openmotif-compat-2.1.32_IST.macosx10.5.dmg" rel="noreferrer" target="_blank">http://www.ist-inc.com/motif/download/motif_files/openmotif-compat-2.1.32_IST.macosx10.5.dmg</a>,<br>
> it actually is installed; but then when I get back to xmgrace installation,<br>
> it says "configure: error: M*tif has not been found". I tried with its<br>
> source too (<br>
> <a href="http://www.ist-inc.com/motif/download/motif_files/openmotif-2.1.32_IST.source.tar.gz" rel="noreferrer" target="_blank">http://www.ist-inc.com/motif/download/motif_files/openmotif-2.1.32_IST.source.tar.gz</a>),<br>
> but couldn't do it. Please let me know how I can get rid of this issue.<br>
><br>
> If there exists any easier alternative to xmgrace, that would be even<br>
> better.<br>
><br>
> Thank you so much for your time!<br>
><br>
><br>
> Sincerely,<br>
> Vijay Khanal<br>
> *Vijay Khanal*<br>
> Department of Physics<br>
> University of Nevada, Reno<br>
> Phone:(1-*<a href="tel:775-440-7036" value="+17754407036" target="_blank">775-440-7036</a>)*<br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
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<br>
Message: 13<br>
Date: Wed, 23 Mar 2016 10:34:16 +0100<br>
From: Giovanni Cantele <<a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a>><br>
Subject: Re: [Pw_forum] xmgrace installation problem<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:BA659F88-736C-4AEB-A660-50C74AC8187D@spin.cnr.it" target="_blank">BA659F88-736C-4AEB-A660-50C74AC8187D@spin.cnr.it</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
you can use gnu plot but else xmgrace.<br>
<br>
For Mac Os X the most straightforward way to install those packages in through macports, see instruction at<br>
<a href="https://www.macports.org" rel="noreferrer" target="_blank">https://www.macports.org</a> <<a href="https://www.macports.org/" rel="noreferrer" target="_blank">https://www.macports.org/</a>><br>
on how to install MacPOrts and, then, external packages.<br>
<br>
Giovanni<br>
<br>
<br>
> On 23 Mar 2016, at 05:49, Vijay Khanal <<a href="mailto:vj.khanal20@gmail.com" target="_blank">vj.khanal20@gmail.com</a>> wrote:<br>
><br>
> Dear everyone,<br>
><br>
> I am a novice user of Quantum Espresso. I have been facing the following issue since the day I had tried to visualize the bandstructure of Silicon.<br>
><br>
> I was trying to install xmgrace in my mac OSX Yosemite(10.10.5). Following the installation steps, looks like the dependency(MOTIF) is not installed. I tired installing it from <a href="http://www.ist-inc.com/motif/download/motif_files/openmotif-compat-2.1.32_IST.macosx10.5.dmg" rel="noreferrer" target="_blank">http://www.ist-inc.com/motif/download/motif_files/openmotif-compat-2.1.32_IST.macosx10.5.dmg</a> <<a href="http://www.ist-inc.com/motif/download/motif_files/openmotif-compat-2.1.32_IST.macosx10.5.dmg" rel="noreferrer" target="_blank">http://www.ist-inc.com/motif/download/motif_files/openmotif-compat-2.1.32_IST.macosx10.5.dmg</a>>, it actually is installed; but then when I get back to xmgrace installation, it says "configure: error: M*tif has not been found". I tried with its source too (<a href="http://www.ist-inc.com/motif/download/motif_files/openmotif-2.1.32_IST.source.tar.gz" rel="noreferrer" target="_blank">http://www.ist-inc.com/motif/download/motif_files/openmotif-2.1.32_IST.source.tar.gz</a> <<a href="http://www.ist-inc.com/motif/download/motif_files/openmotif-2.1.32_IST.source.tar.gz" rel="noreferrer" target="_blank">http://www.ist-inc.com/motif/download/motif_files/openmotif-2.1.32_IST.source.tar.gz</a>>), but couldn't do it. Please let me know how I can get rid of this issue.<br>
><br>
> If there exists any easier alternative to xmgrace, that would be even better.<br>
><br>
> Thank you so much for your time!<br>
><br>
><br>
> Sincerely,<br>
> Vijay Khanal<br>
> Vijay Khanal<br>
> Department of Physics<br>
> University of Nevada, Reno<br>
> Phone:<a href="tel:%281-775-440-7036" value="+17754407036" target="_blank">(1-775-440-7036</a>)<br>
><br>
> _______________________________________________<br>
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<br>
--<br>
<br>
Giovanni Cantele, PhD<br>
CNR-SPIN<br>
c/o Dipartimento di Fisica<br>
Universita' di Napoli "Federico II"<br>
Complesso Universitario M. S. Angelo - Ed. 6<br>
Via Cintia, I-80126, Napoli, Italy<br>
e-mail: <a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a><br>
Phone: <a href="tel:%2B39%20081%20676910" value="+39081676910" target="_blank">+39 081 676910</a><br>
Skype contact: giocan74<br>
<br>
ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" rel="noreferrer" target="_blank">http://www.researcherid.com/rid/A-1951-2009</a><br>
Web page: <a href="http://people.na.infn.it/~cantele" rel="noreferrer" target="_blank">http://people.na.infn.it/~cantele</a><br>
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Message: 14<br>
Date: Wed, 23 Mar 2016 10:36:59 +0100<br>
From: Giovanni Cantele <<a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a>><br>
Subject: Re: [Pw_forum] Band Diagram: Regarding<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org" target="_blank">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:CA65D738-231A-4608-9182-814733D4E715@spin.cnr.it" target="_blank">CA65D738-231A-4608-9182-814733D4E715@spin.cnr.it</a>><br>
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<br>
any software able to plot data files, like gnu plot, xmgrace, etc. is suitable for plotting high quality pictures, under Linux/MacOsX environments.<br>
<br>
Giovanni<br>
<br>
<br>
> On 23 Mar 2016, at 05:33, Suresh A <<a href="mailto:suresh2007pgp19@gmail.com" target="_blank">suresh2007pgp19@gmail.com</a>> wrote:<br>
><br>
> Dear All,<br>
> Band structure is plotted using plotband.x executable in espresso. Can one use plotband.x to do other things like colouring band structures, differentiating specific band with different colour and making journal publication quality pictures?. If there is other software please direct me towards it.<br>
> Thanks in advance<br>
> With Regards,<br>
> A.Suresh,<br>
> Research Scholar,<br>
> Madurai Kamaraj University,<br>
> Madurai.<br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org" target="_blank">Pw_forum@pwscf.org</a><br>
> <a href="http://pwscf.org/mailman/listinfo/pw_forum" rel="noreferrer" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br>
<br>
--<br>
<br>
Giovanni Cantele, PhD<br>
CNR-SPIN<br>
c/o Dipartimento di Fisica<br>
Universita' di Napoli "Federico II"<br>
Complesso Universitario M. S. Angelo - Ed. 6<br>
Via Cintia, I-80126, Napoli, Italy<br>
e-mail: <a href="mailto:giovanni.cantele@spin.cnr.it" target="_blank">giovanni.cantele@spin.cnr.it</a><br>
Phone: <a href="tel:%2B39%20081%20676910" value="+39081676910" target="_blank">+39 081 676910</a><br>
Skype contact: giocan74<br>
<br>
ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" rel="noreferrer" target="_blank">http://www.researcherid.com/rid/A-1951-2009</a><br>
Web page: <a href="http://people.na.infn.it/~cantele" rel="noreferrer" target="_blank">http://people.na.infn.it/~cantele</a><br>
<br>
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