From p.giannozzi at gmail.com Fri Apr 3 22:17:00 2020 From: p.giannozzi at gmail.com (Paolo Giannozzi) Date: Fri, 3 Apr 2020 22:17:00 +0200 Subject: [QE-developers] Units in PP Message-ID: Can anybody help completing the table here? https://gitlab.com/QEF/q-e/-/issues/174 (See also https://gitlab.com/QEF/q-e/-/merge_requests/858) Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ttduyle at gmail.com Wed Apr 8 21:38:33 2020 From: ttduyle at gmail.com (Duy Le) Date: Wed, 8 Apr 2020 15:38:33 -0400 Subject: [QE-developers] Phase of wave-function Message-ID: Dear developers, After reading many threads about the subject, and lot of testing, I still not very confident in handling the phases of wave functions. I would appreciate if you could help me with the following: 1. Do all wave-functions (of all bands) of a given k-point have the same phase? In other words, is psi(k, ib1) psi(k, ib2)* gauge invariant? 2. I want also to calculate psi(k, ib1) psi(k2, ib2)*. How should it be done so the random phases of wfc do not affect the result? 3. Could you please tell me if there is any part of the PWSCF code that deals with phase of wave function so I can learn how it is done? Thank you very much. Be safe! Duy Le University of Central Florida -------------- next part -------------- An HTML attachment was scrubbed... URL: From degironc at sissa.it Wed Apr 8 22:06:09 2020 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 8 Apr 2020 22:06:09 +0200 Subject: [QE-developers] Phase of wave-function In-Reply-To: References: Message-ID: On 08/04/20 21:38, Duy Le wrote: > Dear developers, > > After reading many threads about the subject, and lot of testing, I > still not very confident in handling the phases of wave functions. I > would appreciate?if you could help me with the following: > > 1. Do all wave-functions (of all bands) of a given k-point have the > same phase? In other words, is psi(k, ib1) psi(k, ib2)* gauge invariant? no. the phase of an eigenvector is determined by the diagonalization routine. The safe assumption is that it's basically random, and for degenerate eigenvalues you can assume a random (unitary) rotation inside the degenerate manifold.? this is why in molecular dynamics simulations when you want to extrapolate the starting wavfunctions of a given time step from previous ones, before performing the extrapolation, you need to align the two (or more) wfc subspaces. basically you compute W= and built the unitary rotation that best align the two wfc sets from SVD of W ->? U? then build? |psi'(t')> = |psi(t')> U as the set at t' best aligned to the wfc at t. check routine?? extrapolate_wfcs?? in file update_pot.f90 in PW/src > 2. I want also to calculate psi(k, ib1) psi(k2, ib2)*. How should it > be done so the random phases of wfc do not affect the result? similarly random phases should be assumed ( in addition to the exp(+ikr) phase from the Bloch vector) so you better work with the periodic part of the wavefuncitons u(k) you can compute? the matrix of the overlap of the periodic part of the wfcs at the two kpoints? W = < psi(k1)| exp(i(k1-k2)r)|psi(k2)>=,? extract the best unitary transformation from that and play with it in order to align wfcs at different k's. this is one of the basic operation that Wannier 90 code peforms. > 3. Could you please tell me if there is any part of the PWSCF code > that deals with phase of wave function so I can learn how it is done? see above best stefano > > Thank you very much. Be safe! > > Duy Le > University of Central Florida > > _______________________________________________ > developers mailing list > developers at lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From paulatz at gmail.com Wed Apr 8 22:20:39 2020 From: paulatz at gmail.com (Lorenzo Paulatto) Date: Wed, 8 Apr 2020 22:20:39 +0200 Subject: [QE-developers] Phase of wave-function In-Reply-To: References: Message-ID: <8459d1b6-f939-f723-959b-5e65fdacf0f6@gmail.com> I'll add something on Stefano answer that I find useful when working on this kind of problems: an observable quantity cannot depend on the random phase. If you want to compute and expression that depends on the phase it means that 1) it is not an observable 2) you did a mistake 3) both. If you fall in (1) it could be that when you sum over all k-points ad/or occupied bands the phases cancel out. This is annoying, but inevitable. And it actually allows you to check that your calculations are correct. This also mean that you cannot combine wavefunctions-relate quantities at the same k-point/bands that come from different pw calculations, as the phases may not cancel out any more (typically a problem when trying to implement a restart without wavefunctions). I.e. if you want to compute ) you have to be sure that O|psi> has been computed with the same |psi> as > On 08/04/20 21:38, Duy Le wrote: >> Dear developers, >> >> After reading many threads about the subject, and lot of testing, I >> still not very confident in handling the phases of wave functions. I >> would appreciate?if you could help me with the following: >> >> 1. Do all wave-functions (of all bands) of a given k-point have the >> same phase? In other words, is psi(k, ib1) psi(k, ib2)* gauge invariant? > > no. the phase of an eigenvector is determined by the diagonalization > routine. The safe assumption is that it's basically random, and for > degenerate eigenvalues you can assume a random (unitary) rotation inside > the degenerate manifold.? this is why in molecular dynamics simulations > when you want to extrapolate the starting wavfunctions of a given time > step from previous ones, before performing the extrapolation, you need > to align the two (or more) wfc subspaces. > > basically you compute W= and built the unitary rotation > that best align the two wfc sets from SVD of W ->? U? then build > |psi'(t')> = |psi(t')> U as the set at t' best aligned to the wfc at t. > > check routine?? extrapolate_wfcs?? in file update_pot.f90 in PW/src > >> 2. I want also to calculate psi(k, ib1) psi(k2, ib2)*. How should it >> be done so the random phases of wfc do not affect the result? > > similarly random phases should be assumed ( in addition to the exp(+ikr) > phase from the Bloch vector) so you better work with the periodic part > of the wavefuncitons u(k) > > you can compute? the matrix of the overlap of the periodic part of the > wfcs at the two kpoints? W = < psi(k1)| > exp(i(k1-k2)r)|psi(k2)>=,? extract the best unitary > transformation from that and play with it in order to align wfcs at > different k's. this is one of the basic operation that Wannier 90 code > peforms. > >> 3. Could you please tell me if there is any part of the PWSCF code >> that deals with phase of wave function so I can learn how it is done? > > see above > > best > > stefano > >> >> Thank you very much. Be safe! >> >> Duy Le >> University of Central Florida >> >> _______________________________________________ >> developers mailing list >> developers at lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/developers > > _______________________________________________ > developers mailing list > developers at lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/developers > -- Lorenzo Paulatto - Paris From ttduyle at gmail.com Wed Apr 8 23:52:45 2020 From: ttduyle at gmail.com (Duy Le) Date: Wed, 8 Apr 2020 17:52:45 -0400 Subject: [QE-developers] Phase of wave-function In-Reply-To: <8459d1b6-f939-f723-959b-5e65fdacf0f6@gmail.com> References: <8459d1b6-f939-f723-959b-5e65fdacf0f6@gmail.com> Message-ID: Thank you very much, Stefano and Lorenzo, for the helpful information. W.r.t Lorenzo's points, I think I understood it correctly. Indeed, it is not an observable: X(k1,k2, ib1, ib2) = Integral_r Intergral_r' { psi( k1, ib1) psi(k1, ib2)* f(r-r') psi( k2, ib1)* psi(k2, ib2)} dr dr' however, eigenvalues of X(k1,k2) matrix are observable. >From my tests with different pwscf runs (with different # cores to generate random phases), the matrix elements are phase-dependent (except for the diagonal one, where phase is canceled out) and their eigenvalues are not phase dependent, which is what I want. It could be because the matrix goes over the whole BZ, the results are gauge invariant. Since I am not very confident with the phase, I want to get some comment from developers, and indeed they are very helpful. Duy Le University of Central Florida On Wed, Apr 8, 2020 at 4:21 PM Lorenzo Paulatto wrote: > I'll add something on Stefano answer that I find useful when working on > this kind of problems: an observable quantity cannot depend on the > random phase. If you want to compute and expression that depends on the > phase it means that 1) it is not an observable 2) you did a mistake 3) > both. > > If you fall in (1) it could be that when you sum over all k-points ad/or > occupied bands the phases cancel out. This is annoying, but inevitable. > And it actually allows you to check that your calculations are correct. > > This also mean that you cannot combine wavefunctions-relate quantities > at the same k-point/bands that come from different pw calculations, as > the phases may not cancel out any more (typically a problem when trying > to implement a restart without wavefunctions). I.e. if you want to > compute ) you have to be sure that O|psi> has been computed > with the same |psi> as > good work > > > > On 4/8/20 10:06 PM, Stefano de Gironcoli wrote: > > > > On 08/04/20 21:38, Duy Le wrote: > >> Dear developers, > >> > >> After reading many threads about the subject, and lot of testing, I > >> still not very confident in handling the phases of wave functions. I > >> would appreciate if you could help me with the following: > >> > >> 1. Do all wave-functions (of all bands) of a given k-point have the > >> same phase? In other words, is psi(k, ib1) psi(k, ib2)* gauge invariant? > > > > no. the phase of an eigenvector is determined by the diagonalization > > routine. The safe assumption is that it's basically random, and for > > degenerate eigenvalues you can assume a random (unitary) rotation inside > > the degenerate manifold. this is why in molecular dynamics simulations > > when you want to extrapolate the starting wavfunctions of a given time > > step from previous ones, before performing the extrapolation, you need > > to align the two (or more) wfc subspaces. > > > > basically you compute W= and built the unitary rotation > > that best align the two wfc sets from SVD of W -> U then build > > |psi'(t')> = |psi(t')> U as the set at t' best aligned to the wfc at t. > > > > check routine extrapolate_wfcs in file update_pot.f90 in PW/src > > > >> 2. I want also to calculate psi(k, ib1) psi(k2, ib2)*. How should it > >> be done so the random phases of wfc do not affect the result? > > > > similarly random phases should be assumed ( in addition to the exp(+ikr) > > phase from the Bloch vector) so you better work with the periodic part > > of the wavefuncitons u(k) > > > > you can compute the matrix of the overlap of the periodic part of the > > wfcs at the two kpoints W = < psi(k1)| > > exp(i(k1-k2)r)|psi(k2)>=, extract the best unitary > > transformation from that and play with it in order to align wfcs at > > different k's. this is one of the basic operation that Wannier 90 code > > peforms. > > > >> 3. Could you please tell me if there is any part of the PWSCF code > >> that deals with phase of wave function so I can learn how it is done? > > > > see above > > > > best > > > > stefano > > > >> > >> Thank you very much. Be safe! > >> > >> Duy Le > >> University of Central Florida > >> > >> _______________________________________________ > >> developers mailing list > >> developers at lists.quantum-espresso.org > >> https://lists.quantum-espresso.org/mailman/listinfo/developers > > > > _______________________________________________ > > developers mailing list > > developers at lists.quantum-espresso.org > > https://lists.quantum-espresso.org/mailman/listinfo/developers > > > > -- > Lorenzo Paulatto - Paris > _______________________________________________ > developers mailing list > developers at lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/developers > -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.z at outlook.com Thu Apr 9 12:18:34 2020 From: a.z at outlook.com (ZHUNG Andio) Date: Thu, 9 Apr 2020 10:18:34 +0000 Subject: [QE-developers] Suggesting to add Natural Bond Orbital (NBO) analysis and Solid State Adaptive Natural Density Partitioning (SSAdNDP) to Quantum Espresso package Message-ID: Hello? Dear Sir/Madam. Thanks great for your contribution for Quantum Espresso. Natural Bond Orbital (NBO) analysis and Solid State Adaptive Natural Density Partitioning (SSAdNDP) are used to to obtain the density matrix and search bond but it only works with VASP code. Could add these two methods to Quantum Espresso package? For details, please visit the website: http://ion.chem.usu.edu/~boldyrev/ssadndp.php Yours Sincerely? Andio Zhung -------------- next part -------------- An HTML attachment was scrubbed... URL: From zcanyu at yahoo.com Fri Apr 10 11:22:06 2020 From: zcanyu at yahoo.com (Canyu Zhong) Date: Fri, 10 Apr 2020 17:22:06 +0800 Subject: [QE-developers] Could you get NEB, TD-DFT and Phonon implemented into Burai References: <000201d60f19$88103190$983094b0$.ref@yahoo.com> Message-ID: <000201d60f19$88103190$983094b0$@yahoo.com> Hello, Sir/Madam. The tool Burrai 1.3 is compitable for windows but the module about NEB, TD-DFT and Phonon has not been implemented. Could you get it done? Yours Sincerely? Andio Zhung -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 17951 bytes Desc: not available URL: From p.giannozzi at gmail.com Mon Apr 20 08:51:28 2020 From: p.giannozzi at gmail.com (Paolo Giannozzi) Date: Mon, 20 Apr 2020 08:51:28 +0200 Subject: [QE-developers] Pseudopotential utilities Message-ID: Hi all I am moving the utilities for pseudopotential processing and conversion from "upftools/" into the library of pseudopotential code, currently under development. Has anybody any information about the status and usefulness of the following codes? - interpolate.x - the UPF <=> CASINO converters - the HGH2QE converter Note that I am planning to remove support for old PP formats in QE and to leave only converters. Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 -------------- next part -------------- An HTML attachment was scrubbed... URL: From degironc at sissa.it Mon Apr 20 09:20:39 2020 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 20 Apr 2020 09:20:39 +0200 Subject: [QE-developers] Pseudopotential utilities In-Reply-To: References: Message-ID: Hi Paolo, I think interpolate.x is useful for building virtual atoms. It is not a very common task so i'm not sure it works in all cases but it has its use. stefano On 20/04/20 08:51, Paolo Giannozzi wrote: > Hi all > > I am moving the utilities for pseudopotential processing and > conversion from "upftools/" into the library of pseudopotential code, > currently under development. > Has anybody any information about the status and usefulness of the > following codes? > - interpolate.x > - the UPF <=> CASINO converters > - the HGH2QE converter > Note that I am planning to remove support for old PP formats in QE and > to leave only converters. > > Paolo > -- > 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 > > > _______________________________________________ > developers mailing list > developers at lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/developers -------------- next part -------------- An HTML attachment was scrubbed... URL: From sopan.dol at gmail.com Sat Apr 25 11:54:58 2020 From: sopan.dol at gmail.com (Swapnasopan Datta) Date: Sat, 25 Apr 2020 15:24:58 +0530 Subject: [QE-developers] URGENT Help Required Message-ID: Dear Sir/Ma'am, I would like to work on a project for which I propose to use Quantum Espresso. The project is to test the binding efficacy of a proposed drug candidate. I would like to run a simulation involving a sugar moiety and a long chain fatty acid. One of the hydroxyl groups is supposed to form a chemical bond with the carboxylic end of the lipid. I would like to find how stable this product would be. I would like to tell you that I have a Microsoft Windows Operating System only and I shall have to run the QE software on it. I am an experimentalist by training and am not familiar with most of the software jargon. Please help me to 1. Download the Windows 10 version of QE, 2. Install it, and 3. Run it successfully to solve the problem. I need your help urgently for this project. Please provide clear, step-by-step instructions. Thanking you in anticipation. Yours truly Swapnasopan -------------- next part -------------- An HTML attachment was scrubbed... URL: From ajay at laas.fr Tue Apr 28 09:09:25 2020 From: ajay at laas.fr (Antoine Jay) Date: Tue, 28 Apr 2020 09:09:25 +0200 Subject: [QE-developers] Warning in LAXlib Message-ID: <2931-5ea7d680-7-3863fb80@175747884> Dear developers, Here is a small warning when compiling LAXlib: mp_diag.f90:41:37: ?? LOGICAL, SAVE :: lax_is_initialized = .false.????????????????????????????????? 1 Warning: Legacy Extension: Duplicate SAVE attribute specified at (1) The SAVE is not needed as it is already written under the 'IMPLICITE NONE' Friendly, Antoine Jay -------------- next part -------------- An HTML attachment was scrubbed... URL: From ccz11 at a.baumlqye.club Mon Apr 27 16:29:05 2020 From: ccz11 at a.baumlqye.club (trade) Date: Mon, 27 Apr 2020 22:29:05 +0800 Subject: [QE-developers] =?utf-8?q?=5BSPAM=5D_developers=40lists=2Equantum?= =?utf-8?b?LWVzcHJlc3NvLm9yZ+S4gOWll+mrmOaViOWGs+etluS6uumCruS7tg==?= =?utf-8?b?5Y+R6YCB57O757uf77yM5Yqp5Yqb55ar5oOF6auY5pWI5byA5Y+R?= Message-ID: <202004272229050585667@a.baumlqye.club> 疫情当前，今年=;外贸如何做，客户å=14;何开发？ 很多行业都遭受=;疫情打击，如何过ę=93;寒冬？ 那么危中有机，=;现在很多外贸公司ī=92;策略，通过防疫用=1697;来度过这段艰难的&=#26102;间，主营行业都ࣦ=8;于维护老客户和放 =531;开发的节奏，静等&#=30123;情后主营行业回暖=和爆发，毕竟全球༙=6;求依旧存在。 非=;常好。 那么我们作为专=;业提供外贸客户开Ö=57;系统来说。 首先我们可以帮=;助您找到各行业，ī=78;至需求防疫用品国=2806;海量客户，迅速找=到采购人进行合作Ӎ=0;抢占先机。 而主营行业，也=;同样可以进行，与ê=58;户优先建立联系维=5252;好关系，甚至疫情&=#26399;间就进行采购细节=;洽谈，等待后续合Ë=16;。 为此我们还提供=;两种邮件开发模式z=90;短期简单需求，Ĕ=04;如现在做防疫用品=0986;口，快速联系即可&=#23545;接上，可以群发。=;每天1~3万封邮件。&=024;对主营行业，需要&#=31215;累沉淀，需要持续=营销，支持EDM邮件精=0934;营销的方式。 疫情当下，线上ą=59;大势所趋，通过线=9978;外贸系统，加快国&=#22806;开发，询盘自然也=;就少不了。 感兴趣的朋友，Ē=26;迎联系 QQ：2755365043 &nbs=p; 微信/电话：18038068680 &#=26041;生 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Qrrrr_7173.jpg" Type: image/png Size: 38281 bytes Desc: not available URL: From yadavdk072 at gmail.com Tue Apr 28 08:09:00 2020 From: yadavdk072 at gmail.com (Dinesh Yadav) Date: Tue, 28 Apr 2020 11:54:00 +0545 Subject: [QE-developers] problem in making .eig file in wannier90 Message-ID: Dear QE experts, I am using wannier90 via quantum espresso. Since my compound is hexagonal, I choose k point 9 9 3 in SCF calculation and I chose kmesh 4 4 4 from kmesh.pl tools. After running SCF and nscf calculation I proceed for wannier calculation with mp_grid 4 4 4, Post-processing commands runs successfully and .nnkp file also generated but as I run pw2wannier command no any mmn, amn and .eig forms which terminate my calculation with this error. Wannier mode is: standalone ----------------- *** Reading nnkp ----------------- Checking info from wannier.nnkp file - Real lattice is ok - Reciprocal lattice is ok Something wrong! numk= 64 iknum= 256 So please kindly suggest me to eliminate such error in wannier90. Thank you!! Sudeep Jnawali CDP, TU, Nepal -------------- next part -------------- An HTML attachment was scrubbed... URL: