<div dir="ltr">Re: 5. how to espress fractional coordinates in quantum espresso<br> input (Ridwan Agbaoye)<div><br></div><div>Ridwan, </div><div>Just set verbosity='high' in scf calculation, and check scf.out. You will find co-ordinates all form you need. Besure to multiply with alat unit. By the way quantum espresso also support fractiona co-ordinates. Make sure you use unit 'crystal' for atomic position card. </div><div><br></div><div>Thanks. </div><div>Mohsin, LSU. </div><div>USA.<br><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Feb 11, 2016 at 5:00 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:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">Send Pw_forum mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. CHOOSING SMEARING PARAMETER (Omamuyovwi Akemu)<br>
2. supercell question (Sarah Alpine)<br>
3. Re: supercell question (James Johns)<br>
4. Re: supercell question (<a href="mailto:omamuyovwiakemu@yahoo.com">omamuyovwiakemu@yahoo.com</a>)<br>
5. how to espress fractional coordinates in quantum espresso<br>
input (Ridwan Agbaoye)<br>
6. Re: Charge analysis in QE (Yang, Chi-Ta)<br>
7. Regarding the installation problem in running configure.<br>
(Tushar Gupta)<br>
8. Re: how to espress fractional coordinates in quantum espresso<br>
input (stefano de gironcoli)<br>
9. Re: Regarding the installation problem in running configure.<br>
(Surender)<br>
10. Re: Regarding the installation problem in running configure.<br>
(Tushar Gupta)<br>
11. units of charge density and potential plots from pp.x plotted<br>
by Xrysden (meysam pazoki)<br>
12. Query in band structure calculation (nirav msc)<br>
13. Re: units of charge density and potential plots from pp.x<br>
plotted by Xrysden (Paolo Giannozzi)<br>
14. Re: Regarding the installation problem in running configure.<br>
(Surender)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 10 Feb 2016 12:51:12 +0000 (UTC)<br>
From: Omamuyovwi Akemu <<a href="mailto:omamuyovwiakemu@yahoo.com">omamuyovwiakemu@yahoo.com</a>><br>
Subject: [Pw_forum] CHOOSING SMEARING PARAMETER<br>
To: "<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>" <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:306397425.1630523.1455108672547.JavaMail.yahoo@mail.yahoo.com">306397425.1630523.1455108672547.JavaMail.yahoo@mail.yahoo.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear QE Users,<br>
?I read the article on how to choose smearing parameter involving a superimposed plot of various K-Points of Force against Smearing- THEOS Main/Electronic Temperature<br>
| ? |<br>
| ? | | ? | ? | ? | ? | ? |<br>
| THEOS Main/Electronic TemperatureI often get asked questions about electronic temperature and smearing, and so I decided to put here a few notes - detailed background reading can also be found in m... |<br>
| |<br>
| View on <a href="http://theossrv1.epfl.ch" rel="noreferrer" target="_blank">theossrv1.epfl.ch</a> | Preview by Yahoo |<br>
| |<br>
| ? |<br>
<br>
<br>
Please how can one deduce the error on the forces that? can be tolerated in a material since choosing a smearing involves error in the forces within tolerance?<br>
I have also been following papers on surface energy and realise that most papers used broadening of 0.02 for full-potential and pseudopotential approach. Pls can one use the same approach for calculations involves surface or it applies only to ensemble DFT only?<br>
<br>
I kindly request that give me the connection (or an article as above) in choosing nr3 with respect to K-point and ecutrho. I have read comments from the pw-forum but still having issues with the subject.Thank you for the anticipated comments.<br>
<br>
Jolayemi Omamuyovwi Rita( Mrs)Research Student,<br>
University of Benin,<br>
Nigeria.<br>
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Message: 2<br>
Date: Wed, 10 Feb 2016 06:17:43 -0800<br>
From: Sarah Alpine <<a href="mailto:sarahalpine1@gmail.com">sarahalpine1@gmail.com</a>><br>
Subject: [Pw_forum] supercell question<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<CAJr6meCRx2YfjBFH0O5SZyQ3QGwUKTGuutEd0y9OrQkdU=<a href="mailto:p4EA@mail.gmail.com">p4EA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Users,<br>
<br>
I would really appreciate some advice, please. I would like to model<br>
6-7 layers of copper, and 2-3 layers of titanium dioxide. Since it is a<br>
film, I also need to add vacuum to this supercell. I am starting out with<br>
just the copper; I wrote the coordinates of the unit cell, how do I create<br>
6-7 layers for the supercell with vacuum rather than create a crystall out<br>
of the unit cell?<br>
Thanks,<br>
Sarah<br>
<br>
&control<br>
calculation='scf'<br>
pseudo_dir = '../espresso/pseudo/',<br>
outdir='./TMP/'<br>
prefix='copper001'<br>
/<br>
&system<br>
ibrav = 6, celldm(1) =7.56, celldm(3)=5.0, nat= 10, ntyp= 1,<br>
ecutwfc = 30.0, ecutrho = 240.0<br>
occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02<br>
/<br>
&electrons<br>
diagonalization='david'<br>
conv_thr = 1.0e-7<br>
mixing_beta = 0.7<br>
/<br>
ATOMIC_SPECIES<br>
Cu 63.55 Cu.pbe-nd-rrkjus.UPF<br>
ATOMIC_POSITIONS alat<br>
Cu 0.0 0.0 1.0<br>
Cu 0.5 0.5 1.0<br>
Cu 0.5 0.0 0.5<br>
Cu 0.0 0.5 0.5<br>
Cu 0.0 0.0 0.0<br>
Cu 0.5 0.5 0.0<br>
Cu 0.5 0.0 -0.5<br>
Cu 0.0 0.5 -0.5<br>
Cu 0.0 0.0 -1.0<br>
Cu 0.5 0.5 -1.0<br>
K_POINTS (automatic)<br>
8 8 8 1 1 0<br>
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Message: 3<br>
Date: Wed, 10 Feb 2016 08:35:47 -0600<br>
From: James Johns <<a href="mailto:jjohns@umn.edu">jjohns@umn.edu</a>><br>
Subject: Re: [Pw_forum] supercell question<br>
To: <a href="mailto:sarahalpine1@gmail.com">sarahalpine1@gmail.com</a>, <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<CAPyBSaw6YvaiCj=<a href="mailto:Fw9AoMoBe-ecSbFp%2BzOZshWPspoHH9tvbbg@mail.gmail.com">Fw9AoMoBe-ecSbFp+zOZshWPspoHH9tvbbg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Sara,<br>
It looks like you made a supercell with 5 layers in your input, and a<br>
vacuum of 3*7.56 bohr. I loaded it up in xcrysden just to check, so I'm<br>
not sure what the trouble is. If you wanted to increase the number of<br>
layers, you could continue to add copper atoms to your atomic positions at<br>
z=1.5, 2, 2.5 etc as. You could increase the size of your vacuum by<br>
increasing celldm(3) as well. As long as you keep your atomic positions in<br>
alat you should be good to go.<br>
Let me know if that helps,<br>
James<br>
<br>
On Wed, Feb 10, 2016 at 8:17 AM, Sarah Alpine <<a href="mailto:sarahalpine1@gmail.com">sarahalpine1@gmail.com</a>><br>
wrote:<br>
<br>
> Dear Users,<br>
><br>
> I would really appreciate some advice, please. I would like to model<br>
> 6-7 layers of copper, and 2-3 layers of titanium dioxide. Since it is a<br>
> film, I also need to add vacuum to this supercell. I am starting out with<br>
> just the copper; I wrote the coordinates of the unit cell, how do I create<br>
> 6-7 layers for the supercell with vacuum rather than create a crystall out<br>
> of the unit cell?<br>
> Thanks,<br>
> Sarah<br>
><br>
> &control<br>
> calculation='scf'<br>
> pseudo_dir = '../espresso/pseudo/',<br>
> outdir='./TMP/'<br>
> prefix='copper001'<br>
> /<br>
> &system<br>
> ibrav = 6, celldm(1) =7.56, celldm(3)=5.0, nat= 10, ntyp= 1,<br>
> ecutwfc = 30.0, ecutrho = 240.0<br>
> occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02<br>
> /<br>
> &electrons<br>
> diagonalization='david'<br>
> conv_thr = 1.0e-7<br>
> mixing_beta = 0.7<br>
> /<br>
> ATOMIC_SPECIES<br>
> Cu 63.55 Cu.pbe-nd-rrkjus.UPF<br>
> ATOMIC_POSITIONS alat<br>
> Cu 0.0 0.0 1.0<br>
> Cu 0.5 0.5 1.0<br>
> Cu 0.5 0.0 0.5<br>
> Cu 0.0 0.5 0.5<br>
> Cu 0.0 0.0 0.0<br>
> Cu 0.5 0.5 0.0<br>
> Cu 0.5 0.0 -0.5<br>
> Cu 0.0 0.5 -0.5<br>
> Cu 0.0 0.0 -1.0<br>
> Cu 0.5 0.5 -1.0<br>
> K_POINTS (automatic)<br>
> 8 8 8 1 1 0<br>
><br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">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>
<br>
--<br>
James E. Johns<br>
Assistant Professor<br>
Department of Chemistry<br>
University of Minnesota<br>
207 Pleasant St.<br>
Minneapolis, MN 55455<br>
<a href="http://www.chem.umn.edu/groups/johns/index.html" rel="noreferrer" target="_blank">http://www.chem.umn.edu/groups/johns/index.html</a><br>
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Message: 4<br>
Date: Wed, 10 Feb 2016 09:10:55 -0800<br>
From: "<a href="mailto:omamuyovwiakemu@yahoo.com">omamuyovwiakemu@yahoo.com</a>" <<a href="mailto:omamuyovwiakemu@yahoo.com">omamuyovwiakemu@yahoo.com</a>><br>
Subject: Re: [Pw_forum] supercell question<br>
To: "<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>" <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:1455124255.15494.YahooMailAndroidMobile@web121805.mail.ne1.yahoo.com">1455124255.15494.YahooMailAndroidMobile@web121805.mail.ne1.yahoo.com</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
Dear Sarah,<br>
<br>
The length of the cell along the z- direction should indicate the thickness of the slab plus vacuum.<br>
<br>
Rita<br>
<br>
Sent from Yahoo Mail on Android<br>
<br>
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<br>
Message: 5<br>
Date: Wed, 10 Feb 2016 17:25:06 +0000 (UTC)<br>
From: Ridwan Agbaoye <<a href="mailto:agbaoyeridwan@yahoo.com">agbaoyeridwan@yahoo.com</a>><br>
Subject: [Pw_forum] how to espress fractional coordinates in quantum<br>
espresso input<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:279416066.1798607.1455125106596.JavaMail.yahoo@mail.yahoo.com">279416066.1798607.1455125106596.JavaMail.yahoo@mail.yahoo.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Good day everybody?<br>
I want to do some calculations on a crystal whose atomic coordinates are given in fractional coordinates<br>
How do I convert the fractional coordinates to quantum espresso unit of atomic coordinates?<br>
Which flag do I need to use is it (crystal), (alat), (Bohr) or (angstrom)<br>
I appreciate everyone support towards answering questions to educate pwscf users?<br>
Agbaoye Ridwan OlamideFederal University of Agriculture, AbeokutaM.Sc. (in view)<br>
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Message: 6<br>
Date: Wed, 10 Feb 2016 17:35:56 +0000<br>
From: "Yang, Chi-Ta" <<a href="mailto:chita-yang@uiowa.edu">chita-yang@uiowa.edu</a>><br>
Subject: Re: [Pw_forum] Charge analysis in QE<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:BN3PR0401MB12035EAF900485FF3DA9AEE28ED70@BN3PR0401MB1203.namprd04.prod.outlook.com">BN3PR0401MB12035EAF900485FF3DA9AEE28ED70@BN3PR0401MB1203.namprd04.prod.outlook.com</a>><br>
<br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear Giuseppe,<br>
<br>
I tried to check the new cartesian coordinates with xcrysden, but could not open and gave me error message - Error: wrong # args: should be"pwInputPreset file". I checked the structure with xyz file ,and found that the structure with new coordinates expands. The distances between atoms are almost twice longer than the original ones. I am not sure if bader charge is reasonable upon this.<br>
<br>
Please see below the first 5 coordinates of my system from original QE.in to final bader ACF file.<br>
<br>
Thanks,<br>
Chi-Ta<br>
UI<br>
<br>
------------------------------------------------------------------------------------<a href="http://original.in" rel="noreferrer" target="_blank">original.in</a><br>
CELL_PARAMETERS {angstrom}<br>
5.698943615 0.0000000000 0.0000000000<br>
-4.2742077111 7.4031449178 0.0000000000<br>
0.0000000000 0.0000000000 32.000000000<br>
ATOMIC_POSITIONS {angstrom}<br>
Li 1.409999974 0.814063944 4.686666946<br>
Li -0.000000069 1.628127888 9.373333892<br>
Li -0.000000011 3.256255557 4.686666946<br>
Li -1.409999949 4.070319174 9.373333892<br>
Li -1.410000059 5.698447280 4.686666946<br>
<br>
<br>
--------------------------------------------------------------------------------------<a href="http://pp.in" rel="noreferrer" target="_blank">pp.in</a> fileplot<br>
75 120 432 75 120 432 66 5<br>
0 10.76944268 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000<br>
1.00000000000000 0.000000000000000E+000 0.000000000000000E+000<br>
-0.749999999973679 1.29903810564372 0.000000000000000E+000<br>
0.000000000000000E+000 0.000000000000000E+000 5.61507573364542<br>
1410.1585948767 12.0000000000 40.0000000000 0<br>
1 Li 3.00<br>
2 Ni 10.00<br>
3 Mn 15.00<br>
4 Co 9.00<br>
5 O 6.00<br>
1 0.252079033 0.141015163 0.817121712 1<br>
2 0.005082174 0.280355405 1.656190248 1<br>
3 0.006369515 0.579747049 0.813824987 1<br>
4 -0.249162597 0.719321092 1.657458257 1<br>
5 -0.247504790 1.007537235 0.811527088 1<br>
<br>
<br>
------------------------------------------------------------------------------------------cube<br>
Cubfile created from PWScf calculation<br>
Total SCF Density<br>
66 0.000000 0.000000 0.000000<br>
75 0.143593 0.000000 0.000000<br>
120 -0.067309 0.116583 0.000000<br>
432 0.000000 0.000000 0.139980<br>
3 3.000000 2.714751 1.518655 8.799945<br>
3 3.000000 0.054732 3.019271 17.836246<br>
3 3.000000 0.068596 6.243553 8.764442<br>
3 3.000000 -2.683342 7.746687 17.849902<br>
3 3.000000 -2.665489 10.850615 8.739694<br>
<br>
<br>
------------------------------------------------------------------------------------------------bader<br>
# X Y Z CHARGE MIN DIST ATOMIC VOL<br>
--------------------------------------------------------------------------------<br>
1 2.7147510 1.5186550 8.7999450 2.0988754 1.2593539 20.4268562<br>
2 0.0547320 3.0192710 17.8362460 2.1011053 1.2504756 20.1011325<br>
3 0.0685960 6.2435530 8.7644420 2.0990261 1.2389623 20.4596629<br>
4 -2.6833420 7.7466870 17.8499020 2.1025553 1.2311932 19.5598220<br>
5 -2.6654890 10.8506150 8.7396940 2.0998684 1.2281964 20.4315428<br>
<br>
<br>
<br>
<br>
<br>
________________________________________<br>
From: <a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a> <<a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a>> on behalf of Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><br>
Sent: Tuesday, February 9, 2016 9:01 AM<br>
To: PWSCF Forum<br>
Subject: Re: [Pw_forum] Charge analysis in QE<br>
<br>
Dear Chi-Ta<br>
<br>
> ".cube" shows a new set of cartesian coordinates based on fileout,<br>
> which is different from my original cartesian coordinates.<br>
<br>
Check whether the refolding of coordinates into your supercell<br>
possibly made by pw.x or pp.x yielded a different but equivalent set<br>
of cartesian coordinates.<br>
<br>
> Is it normal to have a new set of cartesian coordinates? In this<br>
> case, will it affect bader charge?<br>
<br>
It is in cube files, and no, it does not affect the results of Bader analysis.<br>
<br>
HTH<br>
<br>
Giuseppe<br>
<br>
Quoting "Yang, Chi-Ta" <<a href="mailto:chita-yang@uiowa.edu">chita-yang@uiowa.edu</a>>:<br>
<br>
> Dear Giuseppe,<br>
><br>
> Thanks for your replay. I tried bader charge analysis, but have a<br>
> concern about it.<br>
> I used cartesian coordinates in my pw.x input file. I noticed that<br>
> the coordinate systems in the output files of pp.x (fileout and.cube<br>
> ) are different.<br>
><br>
> "fileout" shows crystal coordinates<br>
><br>
> ".cube" shows a new set of cartesian coordinates based on fileout,<br>
> which is different from my original cartesian coordinates.<br>
><br>
> Is it normal to have a new set of cartesian coordinates? In this<br>
> case, will it affect bader charge?<br>
><br>
> Thanks a lot,<br>
> Chi-Ta Yang<br>
> University of Iowa<br>
><br>
> ________________________________________<br>
> From: <a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a> <<a href="mailto:pw_forum-bounces@pwscf.org">pw_forum-bounces@pwscf.org</a>> on<br>
> behalf of Giuseppe Mattioli <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><br>
> Sent: Monday, February 8, 2016 9:50 AM<br>
> To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
> Subject: Re: [Pw_forum] Charge analysis in QE<br>
><br>
> Dear Chi-Ta Yang<br>
><br>
>> For the charge analysis in QE, is it fine to use the charge values<br>
>> from the .out files?<br>
><br>
> No, it is a fast on-the-fly calculation. You can post-process your<br>
> results a) with projwfc.x to obtain Lowdin charges or b) with pp.x<br>
> to export the<br>
> total charge density as a .cube file and then with an external tool<br>
> you find here (<a href="http://theory.cm.utexas.edu/henkelman/code/bader" rel="noreferrer" target="_blank">http://theory.cm.utexas.edu/henkelman/code/bader</a>) to<br>
> calculate the<br>
> Bader charges from the cube files. Better results are obtained by<br>
> using denser FFT grids than default ones and by using NC or PAW PPs<br>
> in the case of<br>
> the Bader tool.<br>
><br>
> HTH<br>
> Giuseppe<br>
><br>
> On Monday, February 08, 2016 03:26:32 PM Yang, Chi-Ta wrote:<br>
>> Dear All,<br>
>><br>
>><br>
>> For the charge analysis in QE, is it fine to use the charge values<br>
>> from the .out files? (below)<br>
>><br>
>> If yes, do you recommend to use high K point for a better quality<br>
>> of these values or other recommendations? What kind of charge is<br>
>> this (ex:<br>
>> bader...) ?<br>
>><br>
>><br>
>><br>
>> Magnetic moment per site:<br>
>> atom: 1 charge: 2.1845 magn: 0.1742 constr: 0.0000<br>
>> atom: 2 charge: 2.1716 magn: 0.1740 constr: 0.0000<br>
>> atom: 3 charge: 2.1820 magn: 0.1742 constr: 0.0000<br>
>> atom: 4 charge: 2.1826 magn: 0.1743 constr: 0.0000<br>
>> atom: 5 charge: 2.1711 magn: 0.1739 constr: 0.0000<br>
>> atom: 6 charge: 2.1841 magn: 0.1741 constr: 0.0000<br>
>> atom: 7 charge: 7.3535 magn: 1.9625 constr: 0.0000<br>
>> atom: 8 charge: 7.3507 magn: 2.0039 constr: 0.0000<br>
>><br>
>> Thanks a lot,<br>
>> Chi-Ta Yang<br>
>> University of Iowa<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 + 39 06 90672836 - Fax +39 06 90672316<br>
> E-mail: <<a href="mailto:giuseppe.mattioli@ism.cnr.it">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>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">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>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">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>
********************************************************<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)<br>
Tel <a href="tel:%2B%2039%2006%2090672836" value="+390690672836">+ 39 06 90672836</a> - Fax <a href="tel:%2B39%2006%2090672316" value="+390690672316">+39 06 90672316</a><br>
E-mail: <<a href="mailto:giuseppe.mattioli@ism.cnr.it">giuseppe.mattioli@ism.cnr.it</a>><br>
<a href="http://www.ism.cnr.it/en/staff/giuseppe-mattioli/" rel="noreferrer" target="_blank">http://www.ism.cnr.it/en/staff/giuseppe-mattioli/</a><br>
ResearcherID: F-6308-2012<br>
<br>
<br>
_______________________________________________<br>
Pw_forum mailing list<br>
<a href="mailto:Pw_forum@pwscf.org">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>
<br>
Message: 7<br>
Date: Thu, 11 Feb 2016 00:13:28 +0530<br>
From: Tushar Gupta <<a href="mailto:tushar108gupta@gmail.com">tushar108gupta@gmail.com</a>><br>
Subject: [Pw_forum] Regarding the installation problem in running<br>
configure.<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID:<br>
<<a href="mailto:CAKpvqC%2B-4WecEss1a1dBj3qc8qLQTReOo9%2B63o65nrp8oCh9Kw@mail.gmail.com">CAKpvqC+-4WecEss1a1dBj3qc8qLQTReOo9+63o65nrp8oCh9Kw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear all,<br>
<br>
I am a novice to this field of computational studies and i am trying to<br>
install quantum espresso version 5.3.0 in linux so as I run the<br>
configuration file I am getting an error which says unable to find a<br>
fftw3.f file. I am unable to figure out what to do next.<br>
I will be even more grateful if any body could suggest me a good reference<br>
so that I can clear my basics in this field of computational studies<br>
particularly with this quantum espresso.<br>
Please try to respond in a simplest manner possible.<br>
<br>
<br>
Thanks and Regards:<br>
*Tushar Gupta.*<br>
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<br>
Message: 8<br>
Date: Wed, 10 Feb 2016 19:56:10 +0100<br>
From: stefano de gironcoli <<a href="mailto:degironc@sissa.it">degironc@sissa.it</a>><br>
Subject: Re: [Pw_forum] how to espress fractional coordinates in<br>
quantum espresso input<br>
To: <a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a><br>
Message-ID: <<a href="mailto:56BB87CA.2040700@sissa.it">56BB87CA.2040700@sissa.it</a>><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
On 10/02/2016 18:25, Ridwan Agbaoye wrote:<br>
> Good day everybody<br>
><br>
> I want to do some calculations on a crystal whose atomic coordinates<br>
> are given in fractional coordinates<br>
><br>
> How do I convert the fractional coordinates to quantum espresso unit<br>
> of atomic coordinates<br>
><br>
you don't need to convert them<br>
> Which flag do I need to use is it (crystal), (alat), (Bohr) or (angstrom)<br>
><br>
choosing the "crystal" option the coordinates are interpreted as<br>
fractional coordinates<br>
<br>
stefano<br>
<br>
> I appreciate everyone support towards answering questions to educate<br>
> pwscf users<br>
><br>
> Agbaoye Ridwan Olamide<br>
> Federal University of Agriculture, Abeokuta<br>
> M.Sc. (in view)<br>
><br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">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>
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<br>
Message: 9<br>
Date: Thu, 11 Feb 2016 02:19:43 +0530<br>
From: "Surender" <<a href="mailto:surender_kumar@iitb.ac.in">surender_kumar@iitb.ac.in</a>><br>
Subject: Re: [Pw_forum] Regarding the installation problem in running<br>
configure.<br>
To: "PWSCF Forum" <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:0c7955c07afd4427b4cce9eec1d03935.squirrel@gpo.iitb.ac.in">0c7955c07afd4427b4cce9eec1d03935.squirrel@gpo.iitb.ac.in</a>><br>
Content-Type: text/plain;charset=utf-8<br>
<br>
Hi Tushar,<br>
<br>
You didn't mentions your OS so I assume its Ubuntu and you have already<br>
installed "libfftw3-dev" package. Now you can try the following, first<br>
find out the location of "fftw3.f" and then add it to your IFLAGS in<br>
"make.sys" file. For Ubuntu 12.04 LTS this file is located in<br>
"/usr/include/". After adding to IFLAGS, it should look like<br>
<br>
IFLAGS = -I../include -I/usr/include/<br>
<br>
If above doesn't work, then try to copy the file into FFTXlib folder<br>
located in your main QE directory and have look at the discussion<br>
<a href="http://www.mail-archive.com/pw_forum%40pwscf.org/msg27600.html" rel="noreferrer" target="_blank">http://www.mail-archive.com/pw_forum%40pwscf.org/msg27600.html</a><br>
<br>
HTH<br>
Surender Kumar<br>
<br>
> Dear all,<br>
><br>
> I am a novice to this field of computational studies and i am trying to<br>
> install quantum espresso version 5.3.0 in linux so as I run the<br>
> configuration file I am getting an error which says unable to find a<br>
> fftw3.f file. I am unable to figure out what to do next.<br>
> I will be even more grateful if any body could suggest me a good reference<br>
> so that I can clear my basics in this field of computational studies<br>
> particularly with this quantum espresso.<br>
> Please try to respond in a simplest manner possible.<br>
><br>
><br>
> Thanks and Regards:<br>
> *Tushar Gupta.*<br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">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>
<br>
------------------------------<br>
<br>
Message: 10<br>
Date: Thu, 11 Feb 2016 11:20:35 +0530<br>
From: Tushar Gupta <<a href="mailto:tushar108gupta@gmail.com">tushar108gupta@gmail.com</a>><br>
Subject: Re: [Pw_forum] Regarding the installation problem in running<br>
configure.<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAKpvqCLZkZA1k5REn-aUHY6xHr69YTcHta2ZXOXV=<a href="mailto:pugMVDepQ@mail.gmail.com">pugMVDepQ@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi surender<br>
my OS is centOS.<br>
<br>
Thanks.<br>
Tushar<br>
<br>
*Tushar Gupta.*<br>
<br>
On Thu, Feb 11, 2016 at 2:19 AM, Surender <<a href="mailto:surender_kumar@iitb.ac.in">surender_kumar@iitb.ac.in</a>> wrote:<br>
<br>
> Hi Tushar,<br>
><br>
> You didn't mentions your OS so I assume its Ubuntu and you have already<br>
> installed "libfftw3-dev" package. Now you can try the following, first<br>
> find out the location of "fftw3.f" and then add it to your IFLAGS in<br>
> "make.sys" file. For Ubuntu 12.04 LTS this file is located in<br>
> "/usr/include/". After adding to IFLAGS, it should look like<br>
><br>
> IFLAGS = -I../include -I/usr/include/<br>
><br>
> If above doesn't work, then try to copy the file into FFTXlib folder<br>
> located in your main QE directory and have look at the discussion<br>
> <a href="http://www.mail-archive.com/pw_forum%40pwscf.org/msg27600.html" rel="noreferrer" target="_blank">http://www.mail-archive.com/pw_forum%40pwscf.org/msg27600.html</a><br>
><br>
> HTH<br>
> Surender Kumar<br>
><br>
> > Dear all,<br>
> ><br>
> > I am a novice to this field of computational studies and i am trying to<br>
> > install quantum espresso version 5.3.0 in linux so as I run the<br>
> > configuration file I am getting an error which says unable to find a<br>
> > fftw3.f file. I am unable to figure out what to do next.<br>
> > I will be even more grateful if any body could suggest me a good<br>
> reference<br>
> > so that I can clear my basics in this field of computational studies<br>
> > particularly with this quantum espresso.<br>
> > Please try to respond in a simplest manner possible.<br>
> ><br>
> ><br>
> > Thanks and Regards:<br>
> > *Tushar Gupta.*<br>
> > _______________________________________________<br>
> > Pw_forum mailing list<br>
> > <a href="mailto:Pw_forum@pwscf.org">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>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">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>
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------------------------------<br>
<br>
Message: 11<br>
Date: Wed, 10 Feb 2016 10:08:10 +0100<br>
From: meysam pazoki <<a href="mailto:meysam.pazoki@gmail.com">meysam.pazoki@gmail.com</a>><br>
Subject: [Pw_forum] units of charge density and potential plots from<br>
pp.x plotted by Xrysden<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAJjG5pLkyC=<a href="mailto:xRox%2B3Jj2R5DMAfE6EVPA6hKN3BKS91OXkhCfGg@mail.gmail.com">xRox+3Jj2R5DMAfE6EVPA6hKN3BKS91OXkhCfGg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi All!<br>
<br>
I have a short question about the units of charge density and potential<br>
plots of Xrysden (output of PP.X) > are they in the units of e/a03 and<br>
Hartree respectively?<br>
I need this for reply to referee and appreciate your reply and help to me.<br>
I attached one example of charge density plots of my calcs in Xcrysden.<br>
<br>
Thanks in Advance<br>
Best REgards<br>
/Meysam<br>
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<br>
Message: 12<br>
Date: Thu, 11 Feb 2016 06:43:27 +0000 (UTC)<br>
From: nirav msc <<a href="mailto:nirav_physics85@yahoo.com">nirav_physics85@yahoo.com</a>><br>
Subject: [Pw_forum] Query in band structure calculation<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<<a href="mailto:1265835901.1928535.1455173008034.JavaMail.yahoo@mail.yahoo.com">1265835901.1928535.1455173008034.JavaMail.yahoo@mail.yahoo.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear QE Users,<br>
I tried to calculate band structure of Z1 phase of Fe3Ni by using procedure mentioned in QE example in which I am getting very few bands below the fermi level in valance band. Is this type of band structure normal or it shows abnormality or any error in calculation? scf file of present calculation is given below and image of band structure is also attached herewith. Kindly provide your suggestions for the same.&control??? calculation='scf'<br>
??? restart_mode='from_scratch',<br>
??? tstress = .true.<br>
??? tprnfor = .true.<br>
??? prefix='Fe0.75Ni0.25',<br>
??? wf_collect=.true.,??? pseudo_dir = '/usr/share/espresso/pseudo/', ? outdir='/tmp/'<br>
?/<br>
?&system<br>
??? ibrav= 6, celldm(1)= 7, celldm(3)=2.828, nat=4,ntyp=2,<br>
??? ecutwfc =70, ecutrho= 700, occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01<br>
??? nspin=2, starting_magnetization(1)=0.1, starting_magnetization(2)=0.1<br>
? /<br>
?&electrons<br>
??? conv_thr =? 1.0d-5, mixing_beta = 0.1, electron_maxstep=200<br>
?/<br>
ATOMIC_SPECIES<br>
?Fe? 55.845? Fe.pbe-nd-rrkjus.UPF<br>
?Ni? 58.6934 Ni.pbe-nd-rrkjus.UPF<br>
ATOMIC_POSITIONS<br>
Fe 0.00 0.00 0.50<br>
Fe 0.50 0.50 0.25<br>
Fe 0.50 0.50 0.75<br>
Ni 0.00 0.00 0.00<br>
K_POINTS [automatic]<br>
4 4 4 1 1 1<br>
<br>
Your help will be highly appreciated. Thanks & Regards<br>
N Pandya?<br>
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<br>
Message: 13<br>
Date: Thu, 11 Feb 2016 08:34:03 +0100<br>
From: Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com">p.giannozzi@gmail.com</a>><br>
Subject: Re: [Pw_forum] units of charge density and potential plots<br>
from pp.x plotted by Xrysden<br>
To: PWSCF Forum <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID:<br>
<CAPMgbCs=xciASF99XM6ZqhmgLc8Z=<a href="mailto:eTYjZAf0owKNMhgh-Mhvg@mail.gmail.com">eTYjZAf0owKNMhgh-Mhvg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
>From the top section of the input documentation file PW/Doc/INPUT_PW.*:<br>
<br>
All quantities whose dimensions are not explicitly specified are in<br>
RYDBERG ATOMIC UNITS. Charge is "number" charge (i.e. not multiplied<br>
by e); potentials are in energy units (i.e. they are multiplied by<br>
e)<br>
<br>
Paolo<br>
<br>
On Wed, Feb 10, 2016 at 10:08 AM, meysam pazoki <<a href="mailto:meysam.pazoki@gmail.com">meysam.pazoki@gmail.com</a>><br>
wrote:<br>
<br>
> Hi All!<br>
><br>
> I have a short question about the units of charge density and potential<br>
> plots of Xrysden (output of PP.X) > are they in the units of e/a03 and<br>
> Hartree respectively?<br>
> I need this for reply to referee and appreciate your reply and help to me.<br>
> I attached one example of charge density plots of my calcs in Xcrysden.<br>
><br>
> Thanks in Advance<br>
> Best REgards<br>
> /Meysam<br>
><br>
> _______________________________________________<br>
> Pw_forum mailing list<br>
> <a href="mailto:Pw_forum@pwscf.org">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>
<br>
--<br>
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>
Phone <a href="tel:%2B39-0432-558216" value="+390432558216">+39-0432-558216</a>, fax <a href="tel:%2B39-0432-558222" value="+390432558222">+39-0432-558222</a><br>
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<br>
Message: 14<br>
Date: Thu, 11 Feb 2016 15:47:55 +0530<br>
From: "Surender" <<a href="mailto:surender_kumar@iitb.ac.in">surender_kumar@iitb.ac.in</a>><br>
Subject: Re: [Pw_forum] Regarding the installation problem in running<br>
configure.<br>
To: "PWSCF Forum" <<a href="mailto:pw_forum@pwscf.org">pw_forum@pwscf.org</a>><br>
Message-ID: <<a href="mailto:8248cc6f5959facf55ad6b969e04ce42.squirrel@gpo.iitb.ac.in">8248cc6f5959facf55ad6b969e04ce42.squirrel@gpo.iitb.ac.in</a>><br>
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<br>
Hi<br>
Even for CentOS the procedure is same, first locate fftw3.f file by running<br>
locate fftw3.f (in terminal)<br>
<br>
=== sample output ====<br>
/export/apps/fftw3/intel/float/include/fftw3.f<br>
/export/apps/intel/Compiler/11.1/069/mkl/include/fftw/fftw3.f<br>
/export/apps/intel/Compiler/11.1/073/mkl/include/fftw/fftw3.f<br>
<br>
So my fftw3.f is located in /export/apps/fftw3/intel/float/include (if<br>
available, you can try the intel version as well), now change your IFLAGS<br>
in make.sys file and it should look like<br>
<br>
IFLAGS = -I../include -I/export/apps/fftw3/intel/float/include<br>
<br>
And if it doesn't work the copy and paste the fftw3.f file in FFTXlib<br>
folder in espresso-5.3.0. If you can't locate fftw3.f then you will have<br>
to ask your sysadmin either to locate or install the same.<br>
<br>
Surender Kumar<br>
<br>
PS : Both options worked for me (Cluster with CentOS release 5.4)<br>
<br>
> Hi surender<br>
> my OS is centOS.<br>
><br>
> Thanks.<br>
> Tushar<br>
><br>
> *Tushar Gupta.*<br>
><br>
> On Thu, Feb 11, 2016 at 2:19 AM, Surender <<a href="mailto:surender_kumar@iitb.ac.in">surender_kumar@iitb.ac.in</a>><br>
> wrote:<br>
><br>
>> Hi Tushar,<br>
>><br>
>> You didn't mentions your OS so I assume its Ubuntu and you have already<br>
>> installed "libfftw3-dev" package. Now you can try the following, first<br>
>> find out the location of "fftw3.f" and then add it to your IFLAGS in<br>
>> "make.sys" file. For Ubuntu 12.04 LTS this file is located in<br>
>> "/usr/include/". After adding to IFLAGS, it should look like<br>
>><br>
>> IFLAGS = -I../include -I/usr/include/<br>
>><br>
>> If above doesn't work, then try to copy the file into FFTXlib folder<br>
>> located in your main QE directory and have look at the discussion<br>
>> <a href="http://www.mail-archive.com/pw_forum%40pwscf.org/msg27600.html" rel="noreferrer" target="_blank">http://www.mail-archive.com/pw_forum%40pwscf.org/msg27600.html</a><br>
>><br>
>> HTH<br>
>> Surender Kumar<br>
>><br>
>> > Dear all,<br>
>> ><br>
>> > I am a novice to this field of computational studies and i am trying<br>
>> to<br>
>> > install quantum espresso version 5.3.0 in linux so as I run the<br>
>> > configuration file I am getting an error which says unable to find a<br>
>> > fftw3.f file. I am unable to figure out what to do next.<br>
>> > I will be even more grateful if any body could suggest me a good<br>
>> reference<br>
>> > so that I can clear my basics in this field of computational studies<br>
>> > particularly with this quantum espresso.<br>
>> > Please try to respond in a simplest manner possible.<br>
>> ><br>
>> ><br>
>> > Thanks and Regards:<br>
>> > *Tushar Gupta.*<br>
>> > _______________________________________________<br>
>> > Pw_forum mailing list<br>
>> > <a href="mailto:Pw_forum@pwscf.org">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>
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End of Pw_forum Digest, Vol 103, Issue 10<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><font style="font-family:verdana,helvetica,sans-serif;font-style:italic" size="2"><span style="font-weight:bold"><br>K. M. MOHSIN<br>
</span>Graduate Research Assistant,<br>Dept. of Electrical and Computer Engineering,<br>Louisiana State University, Baton Rouge, LA. U.S.A.<br>Phone : +1 (832) 868 8371</font><div style="display:inline"></div></div>
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