[Pw_forum] Pw_forum Digest, Vol 103, Issue 10
K.M. Mohsin
mohsin.eee at gmail.com
Fri Feb 12 02:27:17 CET 2016
Re: 5. how to espress fractional coordinates in quantum espresso
input (Ridwan Agbaoye)
Ridwan,
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.
Thanks.
Mohsin, LSU.
USA.
On Thu, Feb 11, 2016 at 5:00 AM, <pw_forum-request at pwscf.org> wrote:
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> Today's Topics:
>
> 1. CHOOSING SMEARING PARAMETER (Omamuyovwi Akemu)
> 2. supercell question (Sarah Alpine)
> 3. Re: supercell question (James Johns)
> 4. Re: supercell question (omamuyovwiakemu at yahoo.com)
> 5. how to espress fractional coordinates in quantum espresso
> input (Ridwan Agbaoye)
> 6. Re: Charge analysis in QE (Yang, Chi-Ta)
> 7. Regarding the installation problem in running configure.
> (Tushar Gupta)
> 8. Re: how to espress fractional coordinates in quantum espresso
> input (stefano de gironcoli)
> 9. Re: Regarding the installation problem in running configure.
> (Surender)
> 10. Re: Regarding the installation problem in running configure.
> (Tushar Gupta)
> 11. units of charge density and potential plots from pp.x plotted
> by Xrysden (meysam pazoki)
> 12. Query in band structure calculation (nirav msc)
> 13. Re: units of charge density and potential plots from pp.x
> plotted by Xrysden (Paolo Giannozzi)
> 14. Re: Regarding the installation problem in running configure.
> (Surender)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 10 Feb 2016 12:51:12 +0000 (UTC)
> From: Omamuyovwi Akemu <omamuyovwiakemu at yahoo.com>
> Subject: [Pw_forum] CHOOSING SMEARING PARAMETER
> To: "pw_forum at pwscf.org" <pw_forum at pwscf.org>
> Message-ID:
> <306397425.1630523.1455108672547.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear QE Users,
> ?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
> | ? |
> | ? | | ? | ? | ? | ? | ? |
> | 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... |
> | |
> | View on theossrv1.epfl.ch | Preview by Yahoo |
> | |
> | ? |
>
>
> 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?
> 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?
>
> 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.
>
> Jolayemi Omamuyovwi Rita( Mrs)Research Student,
> University of Benin,
> Nigeria.
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> ------------------------------
>
> Message: 2
> Date: Wed, 10 Feb 2016 06:17:43 -0800
> From: Sarah Alpine <sarahalpine1 at gmail.com>
> Subject: [Pw_forum] supercell question
> To: pw_forum at pwscf.org
> Message-ID:
> <CAJr6meCRx2YfjBFH0O5SZyQ3QGwUKTGuutEd0y9OrQkdU=
> p4EA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Users,
>
> I would really appreciate some advice, please. I would like to model
> 6-7 layers of copper, and 2-3 layers of titanium dioxide. Since it is a
> film, I also need to add vacuum to this supercell. I am starting out with
> just the copper; I wrote the coordinates of the unit cell, how do I create
> 6-7 layers for the supercell with vacuum rather than create a crystall out
> of the unit cell?
> Thanks,
> Sarah
>
> &control
> calculation='scf'
> pseudo_dir = '../espresso/pseudo/',
> outdir='./TMP/'
> prefix='copper001'
> /
> &system
> ibrav = 6, celldm(1) =7.56, celldm(3)=5.0, nat= 10, ntyp= 1,
> ecutwfc = 30.0, ecutrho = 240.0
> occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02
> /
> &electrons
> diagonalization='david'
> conv_thr = 1.0e-7
> mixing_beta = 0.7
> /
> ATOMIC_SPECIES
> Cu 63.55 Cu.pbe-nd-rrkjus.UPF
> ATOMIC_POSITIONS alat
> Cu 0.0 0.0 1.0
> Cu 0.5 0.5 1.0
> Cu 0.5 0.0 0.5
> Cu 0.0 0.5 0.5
> Cu 0.0 0.0 0.0
> Cu 0.5 0.5 0.0
> Cu 0.5 0.0 -0.5
> Cu 0.0 0.5 -0.5
> Cu 0.0 0.0 -1.0
> Cu 0.5 0.5 -1.0
> K_POINTS (automatic)
> 8 8 8 1 1 0
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> ------------------------------
>
> Message: 3
> Date: Wed, 10 Feb 2016 08:35:47 -0600
> From: James Johns <jjohns at umn.edu>
> Subject: Re: [Pw_forum] supercell question
> To: sarahalpine1 at gmail.com, pw_forum at pwscf.org
> Message-ID:
> <CAPyBSaw6YvaiCj=
> Fw9AoMoBe-ecSbFp+zOZshWPspoHH9tvbbg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Sara,
> It looks like you made a supercell with 5 layers in your input, and a
> vacuum of 3*7.56 bohr. I loaded it up in xcrysden just to check, so I'm
> not sure what the trouble is. If you wanted to increase the number of
> layers, you could continue to add copper atoms to your atomic positions at
> z=1.5, 2, 2.5 etc as. You could increase the size of your vacuum by
> increasing celldm(3) as well. As long as you keep your atomic positions in
> alat you should be good to go.
> Let me know if that helps,
> James
>
> On Wed, Feb 10, 2016 at 8:17 AM, Sarah Alpine <sarahalpine1 at gmail.com>
> wrote:
>
> > Dear Users,
> >
> > I would really appreciate some advice, please. I would like to model
> > 6-7 layers of copper, and 2-3 layers of titanium dioxide. Since it is a
> > film, I also need to add vacuum to this supercell. I am starting out with
> > just the copper; I wrote the coordinates of the unit cell, how do I
> create
> > 6-7 layers for the supercell with vacuum rather than create a crystall
> out
> > of the unit cell?
> > Thanks,
> > Sarah
> >
> > &control
> > calculation='scf'
> > pseudo_dir = '../espresso/pseudo/',
> > outdir='./TMP/'
> > prefix='copper001'
> > /
> > &system
> > ibrav = 6, celldm(1) =7.56, celldm(3)=5.0, nat= 10, ntyp= 1,
> > ecutwfc = 30.0, ecutrho = 240.0
> > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.02
> > /
> > &electrons
> > diagonalization='david'
> > conv_thr = 1.0e-7
> > mixing_beta = 0.7
> > /
> > ATOMIC_SPECIES
> > Cu 63.55 Cu.pbe-nd-rrkjus.UPF
> > ATOMIC_POSITIONS alat
> > Cu 0.0 0.0 1.0
> > Cu 0.5 0.5 1.0
> > Cu 0.5 0.0 0.5
> > Cu 0.0 0.5 0.5
> > Cu 0.0 0.0 0.0
> > Cu 0.5 0.5 0.0
> > Cu 0.5 0.0 -0.5
> > Cu 0.0 0.5 -0.5
> > Cu 0.0 0.0 -1.0
> > Cu 0.5 0.5 -1.0
> > K_POINTS (automatic)
> > 8 8 8 1 1 0
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
> >
>
>
>
> --
> James E. Johns
> Assistant Professor
> Department of Chemistry
> University of Minnesota
> 207 Pleasant St.
> Minneapolis, MN 55455
> http://www.chem.umn.edu/groups/johns/index.html
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> ------------------------------
>
> Message: 4
> Date: Wed, 10 Feb 2016 09:10:55 -0800
> From: "omamuyovwiakemu at yahoo.com" <omamuyovwiakemu at yahoo.com>
> Subject: Re: [Pw_forum] supercell question
> To: "pw_forum at pwscf.org" <pw_forum at pwscf.org>
> Message-ID:
> <
> 1455124255.15494.YahooMailAndroidMobile at web121805.mail.ne1.yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Sarah,
>
> The length of the cell along the z- direction should indicate the
> thickness of the slab plus vacuum.
>
> Rita
>
> Sent from Yahoo Mail on Android
>
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> ------------------------------
>
> Message: 5
> Date: Wed, 10 Feb 2016 17:25:06 +0000 (UTC)
> From: Ridwan Agbaoye <agbaoyeridwan at yahoo.com>
> Subject: [Pw_forum] how to espress fractional coordinates in quantum
> espresso input
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <279416066.1798607.1455125106596.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Good day everybody?
> I want to do some calculations on a crystal whose atomic coordinates are
> given in fractional coordinates
> How do I convert the fractional coordinates to quantum espresso unit of
> atomic coordinates?
> Which flag do I need to use is it (crystal), (alat), (Bohr) or (angstrom)
> I appreciate everyone support towards answering questions to educate pwscf
> users?
> Agbaoye Ridwan OlamideFederal University of Agriculture, AbeokutaM.Sc. (in
> view)
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> ------------------------------
>
> Message: 6
> Date: Wed, 10 Feb 2016 17:35:56 +0000
> From: "Yang, Chi-Ta" <chita-yang at uiowa.edu>
> Subject: Re: [Pw_forum] Charge analysis in QE
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <
> BN3PR0401MB12035EAF900485FF3DA9AEE28ED70 at BN3PR0401MB1203.namprd04.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear Giuseppe,
>
> 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.
>
> Please see below the first 5 coordinates of my system from original QE.in
> to final bader ACF file.
>
> Thanks,
> Chi-Ta
> UI
>
>
> ------------------------------------------------------------------------------------
> original.in
> CELL_PARAMETERS {angstrom}
> 5.698943615 0.0000000000 0.0000000000
> -4.2742077111 7.4031449178 0.0000000000
> 0.0000000000 0.0000000000 32.000000000
> ATOMIC_POSITIONS {angstrom}
> Li 1.409999974 0.814063944 4.686666946
> Li -0.000000069 1.628127888 9.373333892
> Li -0.000000011 3.256255557 4.686666946
> Li -1.409999949 4.070319174 9.373333892
> Li -1.410000059 5.698447280 4.686666946
>
>
>
> --------------------------------------------------------------------------------------
> pp.in fileplot
> 75 120 432 75 120 432 66 5
> 0 10.76944268 0.00000000 0.00000000 0.00000000
> 0.00000000 0.00000000
> 1.00000000000000 0.000000000000000E+000 0.000000000000000E+000
> -0.749999999973679 1.29903810564372 0.000000000000000E+000
> 0.000000000000000E+000 0.000000000000000E+000 5.61507573364542
> 1410.1585948767 12.0000000000 40.0000000000 0
> 1 Li 3.00
> 2 Ni 10.00
> 3 Mn 15.00
> 4 Co 9.00
> 5 O 6.00
> 1 0.252079033 0.141015163 0.817121712 1
> 2 0.005082174 0.280355405 1.656190248 1
> 3 0.006369515 0.579747049 0.813824987 1
> 4 -0.249162597 0.719321092 1.657458257 1
> 5 -0.247504790 1.007537235 0.811527088 1
>
>
>
> ------------------------------------------------------------------------------------------cube
> Cubfile created from PWScf calculation
> Total SCF Density
> 66 0.000000 0.000000 0.000000
> 75 0.143593 0.000000 0.000000
> 120 -0.067309 0.116583 0.000000
> 432 0.000000 0.000000 0.139980
> 3 3.000000 2.714751 1.518655 8.799945
> 3 3.000000 0.054732 3.019271 17.836246
> 3 3.000000 0.068596 6.243553 8.764442
> 3 3.000000 -2.683342 7.746687 17.849902
> 3 3.000000 -2.665489 10.850615 8.739694
>
>
>
> ------------------------------------------------------------------------------------------------bader
> # X Y Z CHARGE MIN DIST ATOMIC
> VOL
>
> --------------------------------------------------------------------------------
> 1 2.7147510 1.5186550 8.7999450 2.0988754 1.2593539
> 20.4268562
> 2 0.0547320 3.0192710 17.8362460 2.1011053 1.2504756
> 20.1011325
> 3 0.0685960 6.2435530 8.7644420 2.0990261 1.2389623
> 20.4596629
> 4 -2.6833420 7.7466870 17.8499020 2.1025553 1.2311932
> 19.5598220
> 5 -2.6654890 10.8506150 8.7396940 2.0998684 1.2281964
> 20.4315428
>
>
>
>
>
> ________________________________________
> From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf
> of Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
> Sent: Tuesday, February 9, 2016 9:01 AM
> To: PWSCF Forum
> Subject: Re: [Pw_forum] Charge analysis in QE
>
> Dear Chi-Ta
>
> > ".cube" shows a new set of cartesian coordinates based on fileout,
> > which is different from my original cartesian coordinates.
>
> Check whether the refolding of coordinates into your supercell
> possibly made by pw.x or pp.x yielded a different but equivalent set
> of cartesian coordinates.
>
> > Is it normal to have a new set of cartesian coordinates? In this
> > case, will it affect bader charge?
>
> It is in cube files, and no, it does not affect the results of Bader
> analysis.
>
> HTH
>
> Giuseppe
>
> Quoting "Yang, Chi-Ta" <chita-yang at uiowa.edu>:
>
> > Dear Giuseppe,
> >
> > Thanks for your replay. I tried bader charge analysis, but have a
> > concern about it.
> > I used cartesian coordinates in my pw.x input file. I noticed that
> > the coordinate systems in the output files of pp.x (fileout and.cube
> > ) are different.
> >
> > "fileout" shows crystal coordinates
> >
> > ".cube" shows a new set of cartesian coordinates based on fileout,
> > which is different from my original cartesian coordinates.
> >
> > Is it normal to have a new set of cartesian coordinates? In this
> > case, will it affect bader charge?
> >
> > Thanks a lot,
> > Chi-Ta Yang
> > University of Iowa
> >
> > ________________________________________
> > From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on
> > behalf of Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
> > Sent: Monday, February 8, 2016 9:50 AM
> > To: pw_forum at pwscf.org
> > Subject: Re: [Pw_forum] Charge analysis in QE
> >
> > Dear Chi-Ta Yang
> >
> >> For the charge analysis in QE, is it fine to use the charge values
> >> from the .out files?
> >
> > No, it is a fast on-the-fly calculation. You can post-process your
> > results a) with projwfc.x to obtain Lowdin charges or b) with pp.x
> > to export the
> > total charge density as a .cube file and then with an external tool
> > you find here (http://theory.cm.utexas.edu/henkelman/code/bader) to
> > calculate the
> > Bader charges from the cube files. Better results are obtained by
> > using denser FFT grids than default ones and by using NC or PAW PPs
> > in the case of
> > the Bader tool.
> >
> > HTH
> > Giuseppe
> >
> > On Monday, February 08, 2016 03:26:32 PM Yang, Chi-Ta wrote:
> >> Dear All,
> >>
> >>
> >> For the charge analysis in QE, is it fine to use the charge values
> >> from the .out files? (below)
> >>
> >> If yes, do you recommend to use high K point for a better quality
> >> of these values or other recommendations? What kind of charge is
> >> this (ex:
> >> bader...) ?
> >>
> >>
> >>
> >> Magnetic moment per site:
> >> atom: 1 charge: 2.1845 magn: 0.1742 constr:
> 0.0000
> >> atom: 2 charge: 2.1716 magn: 0.1740 constr:
> 0.0000
> >> atom: 3 charge: 2.1820 magn: 0.1742 constr:
> 0.0000
> >> atom: 4 charge: 2.1826 magn: 0.1743 constr:
> 0.0000
> >> atom: 5 charge: 2.1711 magn: 0.1739 constr:
> 0.0000
> >> atom: 6 charge: 2.1841 magn: 0.1741 constr:
> 0.0000
> >> atom: 7 charge: 7.3535 magn: 1.9625 constr:
> 0.0000
> >> atom: 8 charge: 7.3507 magn: 2.0039 constr:
> 0.0000
> >>
> >> Thanks a lot,
> >> Chi-Ta Yang
> >> University of Iowa
> >
> > ********************************************************
> > - Article premier - Les hommes naissent et demeurent
> > libres et ?gaux en droits. Les distinctions sociales
> > ne peuvent ?tre fond?es que sur l'utilit? commune
> > - Article 2 - Le but de toute association politique
> > est la conservation des droits naturels et
> > imprescriptibles de l'homme. Ces droits sont la libert?,
> > la propri?t?, la s?ret? et la r?sistance ? l'oppression.
> > ********************************************************
> >
> > Giuseppe Mattioli
> > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> > v. Salaria Km 29,300 - C.P. 10
> > I 00015 - Monterotondo Stazione (RM), Italy
> > Tel + 39 06 90672836 - Fax +39 06 90672316
> > E-mail: <giuseppe.mattioli at ism.cnr.it>
> > http://www.ism.cnr.it/english/staff/mattiolig
> > ResearcherID: F-6308-2012
> >
> > _______________________________________________
> > Pw_forum mailing list
> > 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
>
>
> --
> ********************************************************
> - Article premier - Les hommes naissent et demeurent
> libres et ?gaux en droits. Les distinctions sociales
> ne peuvent ?tre fond?es que sur l'utilit? commune
> - Article 2 - Le but de toute association politique
> est la conservation des droits naturels et
> imprescriptibles de l'homme. Ces droits sont la libert?,
> la propri?t?, la s?ret? et la r?sistance ? l'oppression.
> ********************************************************
>
> Giuseppe Mattioli
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> v. Salaria Km 29,300 - C.P. 10
> I 00015 - Monterotondo Stazione (RM)
> Tel + 39 06 90672836 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
> ResearcherID: F-6308-2012
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 11 Feb 2016 00:13:28 +0530
> From: Tushar Gupta <tushar108gupta at gmail.com>
> Subject: [Pw_forum] Regarding the installation problem in running
> configure.
> To: pw_forum at pwscf.org
> Message-ID:
> <
> CAKpvqC+-4WecEss1a1dBj3qc8qLQTReOo9+63o65nrp8oCh9Kw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear all,
>
> I am a novice to this field of computational studies and i am trying to
> install quantum espresso version 5.3.0 in linux so as I run the
> configuration file I am getting an error which says unable to find a
> fftw3.f file. I am unable to figure out what to do next.
> I will be even more grateful if any body could suggest me a good reference
> so that I can clear my basics in this field of computational studies
> particularly with this quantum espresso.
> Please try to respond in a simplest manner possible.
>
>
> Thanks and Regards:
> *Tushar Gupta.*
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> ------------------------------
>
> Message: 8
> Date: Wed, 10 Feb 2016 19:56:10 +0100
> From: stefano de gironcoli <degironc at sissa.it>
> Subject: Re: [Pw_forum] how to espress fractional coordinates in
> quantum espresso input
> To: pw_forum at pwscf.org
> Message-ID: <56BB87CA.2040700 at sissa.it>
> Content-Type: text/plain; charset="windows-1252"
>
> On 10/02/2016 18:25, Ridwan Agbaoye wrote:
> > Good day everybody
> >
> > I want to do some calculations on a crystal whose atomic coordinates
> > are given in fractional coordinates
> >
> > How do I convert the fractional coordinates to quantum espresso unit
> > of atomic coordinates
> >
> you don't need to convert them
> > Which flag do I need to use is it (crystal), (alat), (Bohr) or (angstrom)
> >
> choosing the "crystal" option the coordinates are interpreted as
> fractional coordinates
>
> stefano
>
> > I appreciate everyone support towards answering questions to educate
> > pwscf users
> >
> > Agbaoye Ridwan Olamide
> > Federal University of Agriculture, Abeokuta
> > M.Sc. (in view)
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
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> ------------------------------
>
> Message: 9
> Date: Thu, 11 Feb 2016 02:19:43 +0530
> From: "Surender" <surender_kumar at iitb.ac.in>
> Subject: Re: [Pw_forum] Regarding the installation problem in running
> configure.
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID: <0c7955c07afd4427b4cce9eec1d03935.squirrel at gpo.iitb.ac.in>
> Content-Type: text/plain;charset=utf-8
>
> Hi Tushar,
>
> You didn't mentions your OS so I assume its Ubuntu and you have already
> installed "libfftw3-dev" package. Now you can try the following, first
> find out the location of "fftw3.f" and then add it to your IFLAGS in
> "make.sys" file. For Ubuntu 12.04 LTS this file is located in
> "/usr/include/". After adding to IFLAGS, it should look like
>
> IFLAGS = -I../include -I/usr/include/
>
> If above doesn't work, then try to copy the file into FFTXlib folder
> located in your main QE directory and have look at the discussion
> http://www.mail-archive.com/pw_forum%40pwscf.org/msg27600.html
>
> HTH
> Surender Kumar
>
> > Dear all,
> >
> > I am a novice to this field of computational studies and i am trying to
> > install quantum espresso version 5.3.0 in linux so as I run the
> > configuration file I am getting an error which says unable to find a
> > fftw3.f file. I am unable to figure out what to do next.
> > I will be even more grateful if any body could suggest me a good
> reference
> > so that I can clear my basics in this field of computational studies
> > particularly with this quantum espresso.
> > Please try to respond in a simplest manner possible.
> >
> >
> > Thanks and Regards:
> > *Tushar Gupta.*
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
>
> ------------------------------
>
> Message: 10
> Date: Thu, 11 Feb 2016 11:20:35 +0530
> From: Tushar Gupta <tushar108gupta at gmail.com>
> Subject: Re: [Pw_forum] Regarding the installation problem in running
> configure.
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAKpvqCLZkZA1k5REn-aUHY6xHr69YTcHta2ZXOXV=
> pugMVDepQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi surender
> my OS is centOS.
>
> Thanks.
> Tushar
>
> *Tushar Gupta.*
>
> On Thu, Feb 11, 2016 at 2:19 AM, Surender <surender_kumar at iitb.ac.in>
> wrote:
>
> > Hi Tushar,
> >
> > You didn't mentions your OS so I assume its Ubuntu and you have already
> > installed "libfftw3-dev" package. Now you can try the following, first
> > find out the location of "fftw3.f" and then add it to your IFLAGS in
> > "make.sys" file. For Ubuntu 12.04 LTS this file is located in
> > "/usr/include/". After adding to IFLAGS, it should look like
> >
> > IFLAGS = -I../include -I/usr/include/
> >
> > If above doesn't work, then try to copy the file into FFTXlib folder
> > located in your main QE directory and have look at the discussion
> > http://www.mail-archive.com/pw_forum%40pwscf.org/msg27600.html
> >
> > HTH
> > Surender Kumar
> >
> > > Dear all,
> > >
> > > I am a novice to this field of computational studies and i am trying to
> > > install quantum espresso version 5.3.0 in linux so as I run the
> > > configuration file I am getting an error which says unable to find a
> > > fftw3.f file. I am unable to figure out what to do next.
> > > I will be even more grateful if any body could suggest me a good
> > reference
> > > so that I can clear my basics in this field of computational studies
> > > particularly with this quantum espresso.
> > > Please try to respond in a simplest manner possible.
> > >
> > >
> > > Thanks and Regards:
> > > *Tushar Gupta.*
> > > _______________________________________________
> > > Pw_forum mailing list
> > > 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: 11
> Date: Wed, 10 Feb 2016 10:08:10 +0100
> From: meysam pazoki <meysam.pazoki at gmail.com>
> Subject: [Pw_forum] units of charge density and potential plots from
> pp.x plotted by Xrysden
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAJjG5pLkyC=
> xRox+3Jj2R5DMAfE6EVPA6hKN3BKS91OXkhCfGg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi All!
>
> I have a short question about the units of charge density and potential
> plots of Xrysden (output of PP.X) > are they in the units of e/a03 and
> Hartree respectively?
> I need this for reply to referee and appreciate your reply and help to me.
> I attached one example of charge density plots of my calcs in Xcrysden.
>
> Thanks in Advance
> Best REgards
> /Meysam
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> ------------------------------
>
> Message: 12
> Date: Thu, 11 Feb 2016 06:43:27 +0000 (UTC)
> From: nirav msc <nirav_physics85 at yahoo.com>
> Subject: [Pw_forum] Query in band structure calculation
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <1265835901.1928535.1455173008034.JavaMail.yahoo at mail.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear QE Users,
> 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'
> ??? restart_mode='from_scratch',
> ??? tstress = .true.
> ??? tprnfor = .true.
> ??? prefix='Fe0.75Ni0.25',
> ??? wf_collect=.true.,??? pseudo_dir = '/usr/share/espresso/pseudo/', ?
> outdir='/tmp/'
> ?/
> ?&system
> ??? ibrav= 6, celldm(1)= 7, celldm(3)=2.828, nat=4,ntyp=2,
> ??? ecutwfc =70, ecutrho= 700, occupations='smearing',
> smearing='marzari-vanderbilt', degauss=0.01
> ??? nspin=2, starting_magnetization(1)=0.1, starting_magnetization(2)=0.1
> ? /
> ?&electrons
> ??? conv_thr =? 1.0d-5, mixing_beta = 0.1, electron_maxstep=200
> ?/
> ATOMIC_SPECIES
> ?Fe? 55.845? Fe.pbe-nd-rrkjus.UPF
> ?Ni? 58.6934 Ni.pbe-nd-rrkjus.UPF
> ATOMIC_POSITIONS
> Fe 0.00 0.00 0.50
> Fe 0.50 0.50 0.25
> Fe 0.50 0.50 0.75
> Ni 0.00 0.00 0.00
> K_POINTS [automatic]
> 4 4 4 1 1 1
>
> Your help will be highly appreciated. Thanks & Regards
> N Pandya?
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> ------------------------------
>
> Message: 13
> Date: Thu, 11 Feb 2016 08:34:03 +0100
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> Subject: Re: [Pw_forum] units of charge density and potential plots
> from pp.x plotted by Xrysden
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAPMgbCs=xciASF99XM6ZqhmgLc8Z=
> eTYjZAf0owKNMhgh-Mhvg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> >From the top section of the input documentation file PW/Doc/INPUT_PW.*:
>
> All quantities whose dimensions are not explicitly specified are in
> RYDBERG ATOMIC UNITS. Charge is "number" charge (i.e. not multiplied
> by e); potentials are in energy units (i.e. they are multiplied by
> e)
>
> Paolo
>
> On Wed, Feb 10, 2016 at 10:08 AM, meysam pazoki <meysam.pazoki at gmail.com>
> wrote:
>
> > Hi All!
> >
> > I have a short question about the units of charge density and potential
> > plots of Xrysden (output of PP.X) > are they in the units of e/a03 and
> > Hartree respectively?
> > I need this for reply to referee and appreciate your reply and help to
> me.
> > I attached one example of charge density plots of my calcs in Xcrysden.
> >
> > Thanks in Advance
> > Best REgards
> > /Meysam
> >
> > _______________________________________________
> > 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
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> ------------------------------
>
> Message: 14
> Date: Thu, 11 Feb 2016 15:47:55 +0530
> From: "Surender" <surender_kumar at iitb.ac.in>
> Subject: Re: [Pw_forum] Regarding the installation problem in running
> configure.
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID: <8248cc6f5959facf55ad6b969e04ce42.squirrel at gpo.iitb.ac.in>
> Content-Type: text/plain;charset=utf-8
>
> Hi
> Even for CentOS the procedure is same, first locate fftw3.f file by running
> locate fftw3.f (in terminal)
>
> === sample output ====
> /export/apps/fftw3/intel/float/include/fftw3.f
> /export/apps/intel/Compiler/11.1/069/mkl/include/fftw/fftw3.f
> /export/apps/intel/Compiler/11.1/073/mkl/include/fftw/fftw3.f
>
> So my fftw3.f is located in /export/apps/fftw3/intel/float/include (if
> available, you can try the intel version as well), now change your IFLAGS
> in make.sys file and it should look like
>
> IFLAGS = -I../include -I/export/apps/fftw3/intel/float/include
>
> And if it doesn't work the copy and paste the fftw3.f file in FFTXlib
> folder in espresso-5.3.0. If you can't locate fftw3.f then you will have
> to ask your sysadmin either to locate or install the same.
>
> Surender Kumar
>
> PS : Both options worked for me (Cluster with CentOS release 5.4)
>
> > Hi surender
> > my OS is centOS.
> >
> > Thanks.
> > Tushar
> >
> > *Tushar Gupta.*
> >
> > On Thu, Feb 11, 2016 at 2:19 AM, Surender <surender_kumar at iitb.ac.in>
> > wrote:
> >
> >> Hi Tushar,
> >>
> >> You didn't mentions your OS so I assume its Ubuntu and you have already
> >> installed "libfftw3-dev" package. Now you can try the following, first
> >> find out the location of "fftw3.f" and then add it to your IFLAGS in
> >> "make.sys" file. For Ubuntu 12.04 LTS this file is located in
> >> "/usr/include/". After adding to IFLAGS, it should look like
> >>
> >> IFLAGS = -I../include -I/usr/include/
> >>
> >> If above doesn't work, then try to copy the file into FFTXlib folder
> >> located in your main QE directory and have look at the discussion
> >> http://www.mail-archive.com/pw_forum%40pwscf.org/msg27600.html
> >>
> >> HTH
> >> Surender Kumar
> >>
> >> > Dear all,
> >> >
> >> > I am a novice to this field of computational studies and i am trying
> >> to
> >> > install quantum espresso version 5.3.0 in linux so as I run the
> >> > configuration file I am getting an error which says unable to find a
> >> > fftw3.f file. I am unable to figure out what to do next.
> >> > I will be even more grateful if any body could suggest me a good
> >> reference
> >> > so that I can clear my basics in this field of computational studies
> >> > particularly with this quantum espresso.
> >> > Please try to respond in a simplest manner possible.
> >> >
> >> >
> >> > Thanks and Regards:
> >> > *Tushar Gupta.*
> >> > _______________________________________________
> >> > Pw_forum mailing list
> >> > 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
> >>
> > _______________________________________________
> > Pw_forum mailing list
> > 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
>
> End of Pw_forum Digest, Vol 103, Issue 10
> *****************************************
>
--
K. M. MOHSIN
Graduate Research Assistant,
Dept. of Electrical and Computer Engineering,
Louisiana State University, Baton Rouge, LA. U.S.A.
Phone : +1 (832) 868 8371
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