Dear researchers Thanks for your kind reply and suggestions. I will make the suggested modifications.
Thanks Kanak On Mon, Jul 27, 2015 at 4:00 PM, <[email protected]> wrote: > Send Pw_forum mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://pwscf.org/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: BFGS Relaxation (Lorenzo Paulatto) > 2. Re: Proper application of LDA+U only on specific orbital of a > particular atom (Tiana Davide) > 3. Re: BFGS Relaxation (ashkan shekaari) > 4. Re: How to calculate inverse participation ratio (IPR) using > espresso? (Stefano de Gironcoli) > 5. Re: BFGS Relaxation (Lorenzo Paulatto) > 6. Re: charge analysis (Jure Varlec) > 7. Re: BFGS Relaxation (ashkan shekaari) > 8. Re: BFGS Relaxation (ashkan shekaari) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 26 Jul 2015 10:29:59 +0200 > From: Lorenzo Paulatto <[email protected]> > Subject: Re: [Pw_forum] BFGS Relaxation > To: PWSCF Forum <[email protected]> > Message-ID: <1698107.M9CLjNTRp0@paulaxps> > Content-Type: text/plain; charset="iso-8859-1" > > On Saturday, July 25, 2015 07:28:34 PM Kanak Datta wrote: > > 1. I just wanted to know whether the cutoff values are ok or > not.......As I > > am from EEE background..I have very little knowledge on these things..... > > They are problably not, you have to test convergence. You can use the > initial > geometry (if it is not completely off) with a single k-point. As you > pseudos > are norm-conserving you do not need to set ecutrho: the default value of > 4*ecutwfc is ok. On the other hand a convergen ecutwfc is going to be > between > 40Ry and 120Ry, you'll see. As converged you can take 1mRy/atom, but if you > want to study other properties you've better check convergence of those > directly. > > > 2. Besides should the van der waals corrections be applied in relaxation > > part from the beginning? > > yes > > > -- > Dr. Lorenzo Paulatto > IdR @ IMPMC -- CNRS & Universit? Paris 6 > +33 (0)1 44 275 084 / skype: paulatz > http://www.impmc.upmc.fr/~paulatto/ > 23-24/4?16 Bo?te courrier 115 > 4 place Jussieu 75252 Paris C?dex 05 > > > > > ------------------------------ > > Message: 2 > Date: Sun, 26 Jul 2015 14:37:58 +0000 > From: Tiana Davide <[email protected]> > Subject: Re: [Pw_forum] Proper application of LDA+U only on specific > orbital of a particular atom > To: "[email protected]" <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > Simply Define it as a new atom type than apply to that type +U correction > ________________________________________ > From: [email protected] [[email protected]] on behalf > of [email protected] [[email protected]] > Sent: 26 July 2015 12:00 > To: [email protected] > Subject: Pw_forum Digest, Vol 96, Issue 25 > > Send Pw_forum mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://pwscf.org/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. BFGS Relaxation (Kanak Datta) > 2. Re: How to calculate orbital coefficient in QE? > (Giuseppe Mattioli) > 3. (no subject) (ashkan shekaari) > 4. Proper application of LDA+U only on specific orbital of a > particular atom (YousafMasood) > 5. Is vdw correction implemented in ph.x of QE 5.2 version? (Yin Li) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 25 Jul 2015 19:28:34 +0600 > From: Kanak Datta <[email protected]> > Subject: [Pw_forum] BFGS Relaxation > To: [email protected] > Message-ID: > < > capgf_qhrwtjpqy7hkeqp8mtojxwrdhtbean+a+rh9wghrnl...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear researchers > > For BFGS relaxation of bilayer WS2..I have been using the following code... > &CONTROL > calculation = 'relax', > restart_mode = 'from_scratch', > outdir = 'D:\QuantumEspresso\Quantum ESPRESSO 64-bit > 5.1.2-mpich2\WS2Bilayer\outdir', > prefix = 'WS2Bilayer', > / > &SYSTEM > ibrav = 0, > a = 1.86, > nat = 6, > ntyp = 2, > occupations = 'smearing', > smearing = 'methfessel-paxton', > degauss = 0.001, > nspin=2, > ecutwfc = 20, > ecutrho = 160, > nbnd = 30, > starting_magnetization=0.6, > / > > &ELECTRONS > conv_thr = 1.0d-5, > mixing_mode = 'plain', > mixing_beta = 0.7, > diagonalization = 'david', > diago_full_acc = .true. > / > &IONS > ion_dynamics = 'bfgs', > pot_extrapolation = 'second_order', > wfc_extrapolation = 'second_order', > upscale = 100, > / > CELL_PARAMETERS > 1.5 0.8660254038 0.00000 > 1.5 -0.8660254038 0.00000 > 0.0000 0.00000 15.0 > ATOMIC_SPECIES > W 183.84 W.pbe-hgh.UPF > S 32.066 S.pbe-hgh.UPF > ATOMIC_POSITIONS (angstrom) > S 0.000000000 0.000000000 5.15 > S 0.000000000 0.000000000 2 > W 1.818653348 0.000000000 3.575 > S 0.000000000 0.000000000 8.6 > S 0.000000000 0.000000000 10.175 > W 1.818653348 0.000000000 11.75 > K_POINTS {automatic} > 24 24 1 0 0 0 > > > 1. I just wanted to know whether the cutoff values are ok or not.......As I > am from EEE background..I have very little knowledge on these things..... > 2. Besides should the van der waals corrections be applied in relaxation > part from the beginning? > > Thanks in advance. > > Sincerely yours > kanak > BUET > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150725/3bc8e388/attachment-0001.html > > ------------------------------ > > Message: 2 > Date: Sat, 25 Jul 2015 16:10:34 +0200 > From: Giuseppe Mattioli <[email protected]> > Subject: Re: [Pw_forum] How to calculate orbital coefficient in QE? > To: PWSCF Forum <[email protected]> > Message-ID: > < > 20150725161034.horde.nud3mhkwxed1dia0i0ng...@webmail.sic.rm.cnr.it> > Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes > > > Dear Reza > > Please add always your scientific affiliation beside your name to your > posts to this forum. > > Regarding your question, a single Kohn-Sham orbital corresponds to > each eigenvalue. If you want to know the projection of the KS orbitals > on the lowdin atomic-centered basis set (i.e., the atomic > contributions to all the KS orbitals) you should post-process your > pw.x calculation by using projwfc.x (see the corresponding manual for > details). > > HTH > > Giuseppe > > Giuseppe Mattioli > ISM-CNR > Italy > > Quoting reza vatan <[email protected]>: > > > Dear all, > > > > When I run PWSCF for a system, QE just gives me the eigenvalues for each > k > > point but not the orbital (or wavefunction) coefficients of those > > eigenvalues. I used the "wf_collect=.true." in my input file (attached > > file) but still no wavefuction coefficient. Does anyone here know how I > can > > get the coefficients? > > > > Thanks in advances. > > > > Best, > > Reza. > > > -- > ******************************************************** > - 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: <[email protected]> > > > > ------------------------------ > > Message: 3 > Date: Sat, 25 Jul 2015 21:40:07 +0430 > From: ashkan shekaari <[email protected]> > Subject: [Pw_forum] (no subject) > To: pw_forum <[email protected]> > Message-ID: > < > cagchc0vkuzem6ee8dvihz35wbvggiz9scb1h9cvr0q5kgfb...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear users > For a cp run, how one can tune parameters such as emass , emass cutoff, > fnosep, fnoseh? > > Kind regards > Ashkan Shekaari > Tell: +98 933 459 7122; +98 921 346 7384 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150725/af53b2ea/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Sun, 26 Jul 2015 02:31:20 +0900 > From: YousafMasood <[email protected]> > Subject: [Pw_forum] Proper application of LDA+U only on specific > orbital of a particular atom > To: " QE Forum " <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150726/fb3a1f7c/attachment-0001.html > > ------------------------------ > > Message: 5 > Date: Sun, 26 Jul 2015 09:00:18 +0100 > From: "Yin Li" <[email protected]> > Subject: [Pw_forum] Is vdw correction implemented in ph.x of QE 5.2 > version? > To: pw_forum <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="us-ascii" > > Dear QE developers, > > It is an exciting news that QE 5.2 has been released. I wonder whether in > this new version I can involve vdw-correction in phonon calculation. > Thank you very much in advance! > > Best Regards, > Yin > > > > Dr. Yin Li > Research Associate > Department of Biophysics,Medical School, University of Pecs, > No.12 Szigeti Street, Pecs, H-7624, HUNGARY > Phone: +36-72-535271/36271 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150726/157c35ed/attachment-0001.html > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > > End of Pw_forum Digest, Vol 96, Issue 25 > **************************************** > > > > ------------------------------ > > Message: 3 > Date: Sun, 26 Jul 2015 21:50:20 +0430 > From: ashkan shekaari <[email protected]> > Subject: Re: [Pw_forum] BFGS Relaxation > To: pw_forum <[email protected]> > Message-ID: > <CAGchC0sWEFBPGPxyXdobiQmXEkw+Jf6oCn8_n9Q= > [email protected]> > Content-Type: text/plain; charset="utf-8" > > Dear kanak > Ecutwfc is too small. Find the optimal value. Set ecutrho = 5*ecutwfc. > Set mixing mode local TF because of inhomogenity. > Set conv thr of order 10^-9set dt= 20 > > Kind regards > Ashkan Shekaari > Tell: +98 933 459 7122; +98 921 346 7384 > On Jul 25, 2015 5:59 PM, "Kanak Datta" <[email protected]> wrote: > > > Dear researchers > > > > For BFGS relaxation of bilayer WS2..I have been using the following > code... > > &CONTROL > > calculation = 'relax', > > restart_mode = 'from_scratch', > > outdir = 'D:\QuantumEspresso\Quantum ESPRESSO 64-bit > > 5.1.2-mpich2\WS2Bilayer\outdir', > > prefix = 'WS2Bilayer', > > / > > &SYSTEM > > ibrav = 0, > > a = 1.86, > > nat = 6, > > ntyp = 2, > > occupations = 'smearing', > > smearing = 'methfessel-paxton', > > degauss = 0.001, > > nspin=2, > > ecutwfc = 20, > > ecutrho = 160, > > nbnd = 30, > > starting_magnetization=0.6, > > / > > > > &ELECTRONS > > conv_thr = 1.0d-5, > > mixing_mode = 'plain', > > mixing_beta = 0.7, > > diagonalization = 'david', > > diago_full_acc = .true. > > / > > &IONS > > ion_dynamics = 'bfgs', > > pot_extrapolation = 'second_order', > > wfc_extrapolation = 'second_order', > > upscale = 100, > > / > > CELL_PARAMETERS > > 1.5 0.8660254038 0.00000 > > 1.5 -0.8660254038 0.00000 > > 0.0000 0.00000 15.0 > > ATOMIC_SPECIES > > W 183.84 W.pbe-hgh.UPF > > S 32.066 S.pbe-hgh.UPF > > ATOMIC_POSITIONS (angstrom) > > S 0.000000000 0.000000000 5.15 > > S 0.000000000 0.000000000 2 > > W 1.818653348 0.000000000 3.575 > > S 0.000000000 0.000000000 8.6 > > S 0.000000000 0.000000000 10.175 > > W 1.818653348 0.000000000 11.75 > > K_POINTS {automatic} > > 24 24 1 0 0 0 > > > > > > 1. I just wanted to know whether the cutoff values are ok or not.......As > > I am from EEE background..I have very little knowledge on these > things..... > > 2. Besides should the van der waals corrections be applied in relaxation > > part from the beginning? > > > > Thanks in advance. > > > > Sincerely yours > > kanak > > BUET > > > > _______________________________________________ > > Pw_forum mailing list > > [email protected] > > http://pwscf.org/mailman/listinfo/pw_forum > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150726/df1d2f46/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Sun, 26 Jul 2015 19:25:25 +0200 > From: Stefano de Gironcoli <[email protected]> > Subject: Re: [Pw_forum] How to calculate inverse participation ratio > (IPR) using espresso? > To: PWSCF Forum <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=us-ascii > > I guess what you may look at is the integral of |psi|^4 over your cell. > There should be a post-processing tool computing local density of states > (basically |psi|^2) that could be easily modified for your purpose > > stefano > (sent from my phone) > > > On 24 Jul 2015, at 02:12, reza vatan <[email protected]> wrote: > > > > Dear all, > > > > I obtained the DOS plot (the attachment) of a-Si generated by a > supercell containing 64 atom using QE. For finding mobility edge in my DOS > plot, I'm willing to calculate the inverse participation ratio of the > electronic states in the plot as a measure of localization. I'm wondering > if there is any way to calculate IPR using Espresso output files. > > > > Any suggestion would be highly appreciated. > > > > Thanks in advance. > > > > Best, > > Reza > > <dos.png> > > _______________________________________________ > > Pw_forum mailing list > > [email protected] > > http://pwscf.org/mailman/listinfo/pw_forum > > > > ------------------------------ > > Message: 5 > Date: Sun, 26 Jul 2015 22:33:22 +0200 > From: Lorenzo Paulatto <[email protected]> > Subject: Re: [Pw_forum] BFGS Relaxation > To: PWSCF Forum <[email protected]> > Message-ID: <13697678.1KnueQC9tk@paulaxps> > Content-Type: text/plain; charset="iso-8859-1" > > On Sunday, July 26, 2015 09:50:20 PM ashkan shekaari wrote: > > Dear kanak > > Ecutwfc is too small. Find the optimal value. Set ecutrho = 5*ecutwfc. > > Dear Ashkan, > this is not the first time that I see you giving this advice. Do you have > any > specific reason for choosing a factor 5? > Kanak only has norm-conserving pseudos, which normally do not require any > more > than the default value: ecutrho=4*ecutwfc. Using 5 instead of 4 would > require > an interpolation at every scf step, which takes cpu time and memory. > > > Set mixing mode local TF because of inhomogenity. > > Set conv thr of order 10^-9set dt= 20 > > dt is not used by BFGS > > kind regards > > -- > Dr. Lorenzo Paulatto > IdR @ IMPMC -- CNRS & Universit? Paris 6 > +33 (0)1 44 275 084 / skype: paulatz > http://www.impmc.upmc.fr/~paulatto/ > 23-24/4?16 Bo?te courrier 115 > 4 place Jussieu 75252 Paris C?dex 05 > > > > > ------------------------------ > > Message: 6 > Date: Mon, 27 Jul 2015 09:17:10 +0200 > From: Jure Varlec <[email protected]> > Subject: Re: [Pw_forum] charge analysis > To: <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="US-ASCII" > > Dear Raj kamal, > > In order to calculate Bader charges, you need to do three steps: > > - Do an scf calculation using pw.x. > - Use pp.x to extract the charge density and put it into a CUBE file. > Use the same prefix and outdir as for pw.x and use iflag = 3 and > output_format = 6 to generate the CUBE file. > - Use the program linked below to compute Bader or Vornoi charges. > > http://theory.cm.utexas.edu/henkelman/code/bader/ > > Regards, > > Jure Varlec > National Institute of Chemistry > Ljubljana > > > On Sat, 25 Jul 2015 06:18:51 +0530 > Raj kamal <[email protected]> wrote: > > > dear QE experts, > > i need to calculate badar charge or charge > > analysis calculation for my lithium intercalated graphene system .i > > tried lot to learn about this i couldnt much info .kindly please > > anyone send me clear description of input and output of any system of > > charge analysis.thanks in advance. > > > > > > ------------------------------ > > Message: 7 > Date: Mon, 27 Jul 2015 11:56:36 +0430 > From: ashkan shekaari <[email protected]> > Subject: Re: [Pw_forum] BFGS Relaxation > To: pw_forum <[email protected]> > Message-ID: > < > cagchc0sytbh-bxsu26u8twydcwsl6hfcxucd17gykaxcrkv...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Lorenzo > dt only works in cp MD . > Thanks so much for your attention. > > Kind regards > Ashkan Shekaari > Tell: +98 933 459 7122; +98 921 346 7384 > On Jul 27, 2015 1:04 AM, "Lorenzo Paulatto" < > [email protected]> > wrote: > > > On Sunday, July 26, 2015 09:50:20 PM ashkan shekaari wrote: > > > Dear kanak > > > Ecutwfc is too small. Find the optimal value. Set ecutrho = 5*ecutwfc. > > > > Dear Ashkan, > > this is not the first time that I see you giving this advice. Do you have > > any > > specific reason for choosing a factor 5? > > Kanak only has norm-conserving pseudos, which normally do not require any > > more > > than the default value: ecutrho=4*ecutwfc. Using 5 instead of 4 would > > require > > an interpolation at every scf step, which takes cpu time and memory. > > > > > Set mixing mode local TF because of inhomogenity. > > > Set conv thr of order 10^-9set dt= 20 > > > > dt is not used by BFGS > > > > kind regards > > > > -- > > Dr. Lorenzo Paulatto > > IdR @ IMPMC -- CNRS & Universit? Paris 6 > > +33 (0)1 44 275 084 / skype: paulatz > > http://www.impmc.upmc.fr/~paulatto/ > > 23-24/4?16 Bo?te courrier 115 > > 4 place Jussieu 75252 Paris C?dex 05 > > > > > > _______________________________________________ > > Pw_forum mailing list > > [email protected] > > http://pwscf.org/mailman/listinfo/pw_forum > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150727/6cc97b5e/attachment-0001.html > > ------------------------------ > > Message: 8 > Date: Mon, 27 Jul 2015 12:04:48 +0430 > From: ashkan shekaari <[email protected]> > Subject: Re: [Pw_forum] BFGS Relaxation > To: pw_forum <[email protected]> > Message-ID: > < > cagchc0uxymxvc8ljqka9d7rpnkjevogavo3u8-bruvhjzhi...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear kanak > Another thing > Set vdw_corr='grimme-d2' > In &system card to consider van deer Waals interaction between layers. It > works nice. > > Kind regards > Ashkan Shekaari > Tell: +98 933 459 7122; +98 921 346 7384 > On Jul 25, 2015 5:59 PM, "Kanak Datta" <[email protected]> wrote: > > > Dear researchers > > > > For BFGS relaxation of bilayer WS2..I have been using the following > code... > > &CONTROL > > calculation = 'relax', > > restart_mode = 'from_scratch', > > outdir = 'D:\QuantumEspresso\Quantum ESPRESSO 64-bit > > 5.1.2-mpich2\WS2Bilayer\outdir', > > prefix = 'WS2Bilayer', > > / > > &SYSTEM > > ibrav = 0, > > a = 1.86, > > nat = 6, > > ntyp = 2, > > occupations = 'smearing', > > smearing = 'methfessel-paxton', > > degauss = 0.001, > > nspin=2, > > ecutwfc = 20, > > ecutrho = 160, > > nbnd = 30, > > starting_magnetization=0.6, > > / > > > > &ELECTRONS > > conv_thr = 1.0d-5, > > mixing_mode = 'plain', > > mixing_beta = 0.7, > > diagonalization = 'david', > > diago_full_acc = .true. > > / > > &IONS > > ion_dynamics = 'bfgs', > > pot_extrapolation = 'second_order', > > wfc_extrapolation = 'second_order', > > upscale = 100, > > / > > CELL_PARAMETERS > > 1.5 0.8660254038 0.00000 > > 1.5 -0.8660254038 0.00000 > > 0.0000 0.00000 15.0 > > ATOMIC_SPECIES > > W 183.84 W.pbe-hgh.UPF > > S 32.066 S.pbe-hgh.UPF > > ATOMIC_POSITIONS (angstrom) > > S 0.000000000 0.000000000 5.15 > > S 0.000000000 0.000000000 2 > > W 1.818653348 0.000000000 3.575 > > S 0.000000000 0.000000000 8.6 > > S 0.000000000 0.000000000 10.175 > > W 1.818653348 0.000000000 11.75 > > K_POINTS {automatic} > > 24 24 1 0 0 0 > > > > > > 1. I just wanted to know whether the cutoff values are ok or not.......As > > I am from EEE background..I have very little knowledge on these > things..... > > 2. Besides should the van der waals corrections be applied in relaxation > > part from the beginning? > > > > Thanks in advance. > > > > Sincerely yours > > kanak > > BUET > > > > _______________________________________________ > > Pw_forum mailing list > > [email protected] > > http://pwscf.org/mailman/listinfo/pw_forum > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20150727/ac0d3875/attachment-0001.html > > ------------------------------ > > _______________________________________________ > Pw_forum mailing list > [email protected] > http://pwscf.org/mailman/listinfo/pw_forum > > End of Pw_forum Digest, Vol 96, Issue 26 > **************************************** >
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