From wyanchao at gmail.com Tue Jan 2 06:58:23 2007 From: wyanchao at gmail.com (wang yanchao) Date: Tue, 2 Jan 2007 13:58:23 +0800 Subject: [Pw_forum] ask question Message-ID: <55639d30701012158l5add33dfh9a0778b7708b528f@mail.gmail.com> dear users: When I caculate the phonon of the k-point(not gamma),according to linear response theory, it should be apply perturbations. But I donot know how to added it and where it to be added? I have read the code which to caculate scf ,nscf and phonon, I think perturbations should be added in nscf,because in code of scf(nscf) there is a subroutine "move ion",but in nscf ,the "switch" is "-1". but the condition to call subroutine of "move ion" is that the value of "iswitch" is bigger "0".Now I am confused. If someone know it ,please tell me .thank you in advance. -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070102/933cbd81/attachment.htm From baroni at sissa.it Tue Jan 2 15:23:47 2007 From: baroni at sissa.it (Stefano Baroni) Date: Tue, 2 Jan 2007 15:23:47 +0100 Subject: [Pw_forum] ask question In-Reply-To: <55639d30701012158l5add33dfh9a0778b7708b528f@mail.gmail.com> References: <55639d30701012158l5add33dfh9a0778b7708b528f@mail.gmail.com> Message-ID: Dear Wang Yanchao, "phonon" applies calculates the response of the system to the displacement of individual ions. In case you have not already done so, you may find interesting to take a glance at the theory such as explained, e.g. in Rev. Mod. Phys. 73, 515 - 562 (2001). Happy New Year - Stefano Baroni On Jan 2, 2007, at 6:58 AM, wang yanchao wrote: > dear users: > When I caculate the phonon of the k-point(not gamma),according > to linear response theory, it should be apply perturbations. But I > donot know how to added it and where it to be added? > I have read the code which to caculate scf ,nscf and phonon, I > think perturbations should be added in nscf,because in code of scf > (nscf) there is a subroutine "move ion",but in nscf ,the "switch" > is "-1". but the condition to call subroutine of "move ion" is > that the value of "iswitch" is bigger "0".Now I am confused. If > someone know it ,please tell me .thank you in advance. > --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070102/c29a54ef/attachment.htm From naromero at gmail.com Thu Jan 4 02:17:09 2007 From: naromero at gmail.com (Nichols A. Romero) Date: Wed, 3 Jan 2007 20:17:09 -0500 Subject: [Pw_forum] MD simulations of polar liquids Message-ID: <6ac064b60701031717g143ff04bgc1bf3a4c944d8362@mail.gmail.com> Hi, This is a question regarding the NVT MD simulation of a polar liquid, i.e. a molecular fluid with a dipole moment (e.g. water, nitromethane, etc.) When dealing with a polar slab, there are dipole corrections to consider. This comes from a net dipole moment. Is there a similar issue with the NVT MD simulation of a polar liquid? My co-works here (Army Research Lab) have told me that there are such issues with there classical (non-DFT) simulation but that the corrections become smaller as one increases the system size. Does anyone no of such discussion at the DFT level which may be found in the literature? Bests, -- Nichols A. Romero, Ph.D. 1613 Denise Dr. Apt. D Forest Hill, MD 21050 443-567-8328 (C) 410-306-0709 (O) -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070103/4237137f/attachment.htm From tangney at civet.berkeley.edu Thu Jan 4 08:56:09 2007 From: tangney at civet.berkeley.edu (Paul Tangney) Date: Wed, 3 Jan 2007 23:56:09 -0800 (PST) Subject: [Pw_forum] MD simulations of polar liquids In-Reply-To: <20070104063806.6567.30260.Mailman@democritos.sissa.it> References: <20070104063806.6567.30260.Mailman@democritos.sissa.it> Message-ID: Hi Nichols, Dipole corrections to what quantity ? There is now a large literature on macroscopic polarization in the context of DFT (Resta, Vanderbilt and others) but if I understand your problem correctly, it is not necessary for you to delve into this. Slabs with net dipole moments under periodic boundary conditions are problematic because, in a slab calculation, you don't generally want the periodic images to 'see' each other, but a slab with a strong moment interacts with its images. If a dipole approximation is valid (if the spatial separation of charges is small compared to your unit cell) the dipole-dipole interaction decays with 1/r^5. For a bulk liquid, the problem should be much less serious because it is less ordered and there is no vacuum. There shouldn't be any strong multipole moments and any moments that do exist should be well screened and transient. Finite size effects are *much* *much* more serious for simple classical MD - particularly when only point-charge electrostatics are included. The reason is that, even in strongly ionic materials such as NaCl, water or silica, very simple electronic screening mechanisms (such as screening from polarizable atoms) are sufficient to kill electrostatic interactions within a few nanometers..and usually within 1 nm. On the other hand, finite size effects in MD with simple classical potentials are large because the only screening is from the ions themselves and occurs on ionic time scales. As a result, some physical properties (e.g. thermal expansion) require 1000 to 10000 atoms for convergence while the same property with DFT is converged with 50 to 100 atoms. I have been waving my hands while typing this - I'm going by my experience but these issues are poorly controlled, and should be investigated more thoroughly. Hopefully somebody will have the time some day. Best regards, Paul > Hi, > > This is a question regarding the NVT MD simulation of a polar liquid, i.e. a > molecular fluid with a dipole moment (e.g. water, nitromethane, etc.) > > When dealing with a polar slab, there are dipole corrections to consider. > This comes from a net dipole moment. Is there a similar issue with the NVT > MD simulation of a polar liquid? My co-works here (Army Research Lab) have > told me that there are such issues with there classical (non-DFT) simulation > but that the corrections become smaller as one increases the system size. > > Does anyone no of such discussion at the DFT level which may be found in > the literature? > > Bests, > -- ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo Paul Tangney Theory of Nanostructured Materials Facility The Molecular Foundry Lawrence Berkeley National Lab. E-mail: PTTangney at lbl.gov 1 Cyclotron Road, Bldg 67 Phone: (510) 495-2769 Berkeley, CA 94720 ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo From giannozz at nest.sns.it Thu Jan 4 11:38:42 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 4 Jan 2007 11:38:42 +0100 Subject: [Pw_forum] ph.x v3.2 on NEC SX-8 In-Reply-To: References: Message-ID: <13FAF5BC-0BB8-41C8-95F8-7ED13E789F59@nest.sns.it> On Dec 28, 2006, at 23:00 , wlyim at puccini.che.pitt.edu wrote: > the NEC executables pass a larger "nrxx" value, 22200 in NEC vs 20736 > in Intel, given that nr1=24,nr2=24,nr3=36. So in NEC, some zero "zeta" > were passed to dmxc_spin subroutine which led to "divide by zero" > error > at line 1192 in Modules/functionals.f90. this is very unlikely. At line 1192 there is a division by rho (= rho up + rho down), but rho > small = 1.d-30 (there is a check at the beginning of the function). There is also a division by another quantity (dz) that is never smaller than 1.d-6 by construction. You may try to increase the value of "small" to something less small, e.g. 1.d-10 Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From wlyim at puccini.che.pitt.edu Thu Jan 4 12:17:58 2007 From: wlyim at puccini.che.pitt.edu (wlyim at puccini.che.pitt.edu) Date: Thu, 4 Jan 2007 06:17:58 -0500 (EST) Subject: [Pw_forum] ph.x v3.2 on NEC SX-8 In-Reply-To: <13FAF5BC-0BB8-41C8-95F8-7ED13E789F59@nest.sns.it> Message-ID: On Thu, 4 Jan 2007, Paolo Giannozzi wrote: > > On Dec 28, 2006, at 23:00 , wlyim at puccini.che.pitt.edu wrote: > > > the NEC executables pass a larger "nrxx" value, 22200 in NEC vs 20736 > > in Intel, given that nr1=24,nr2=24,nr3=36. So in NEC, some zero "zeta" > > were passed to dmxc_spin subroutine which led to "divide by zero" > > error > > at line 1192 in Modules/functionals.f90. > > this is very unlikely. At line 1192 there is a division by rho > (= rho up + rho down), but rho > small = 1.d-30 (there is a check > at the beginning of the function). There is also a division by another > quantity (dz) that is never smaller than 1.d-6 by construction. > You may try to increase the value of "small" to something less > small, e.g. 1.d-10 I've checked, from ir=20737 to 22200, dz is zero. I've also tried to add a line in functionals.f90: zeta = (rhoup - rhodw) / rhotot if (zeta <= small) return ! added line ph.x can continue but give wrong result. > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Dr. Wai-Leung Yim Institut fuer Reine und Angewandte Chemie, Theoretische Chemie, Carl von Ossiezky Universtaet Oldenburg, 26129 Oldenburg, Germany Email: wlyim at puccini.che.pitt.edu Phone: +49-441-798-3950 (office) +49-441-798-5102 (home) Fax: +49-441-798-3964 From giannozz at nest.sns.it Thu Jan 4 12:44:48 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 4 Jan 2007 12:44:48 +0100 Subject: [Pw_forum] ph.x v3.2 on NEC SX-8 In-Reply-To: References: Message-ID: On Jan 4, 2007, at 12:17 , wlyim at puccini.che.pitt.edu wrote: >> There is also a division by another quantity (dz) that is never >> smaller >> than 1.d-6 by construction. actually I misinterpreted the definition of dz: dz is never LARGER then 1.d-6 by construction. You can simply set dz to a fixed value: 1.d-6, or 1.d-4 . Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From lawrence_lee_lee at yahoo.com.hk Thu Jan 4 12:56:05 2007 From: lawrence_lee_lee at yahoo.com.hk (Lawrence Lee) Date: Thu, 4 Jan 2007 19:56:05 +0800 (CST) Subject: [Pw_forum] difference between molecular dynamics of PW and that of CPMD Message-ID: <830379.42691.qm@web54407.mail.yahoo.com> Dear sir / madam, I am a new user of pwscf. I know that pw can do molecular dynamics. What is the difference between that and CPMD? Besides, do you know how to restart the run in pw.x? For example, if I have made a run of 400 steps with dt = 20 atomic time unit, but now I find it insufficient. I need the run to have 2000 steps, say. Do I have any method to proceed the run without doing it from the first step again? Lawrence. _______________________________________ YM - ???? ??????????????????????????????????????????? http://messenger.yahoo.com.hk -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070104/f365bc2a/attachment.htm From wlyim at puccini.che.pitt.edu Thu Jan 4 14:00:51 2007 From: wlyim at puccini.che.pitt.edu (wlyim at puccini.che.pitt.edu) Date: Thu, 4 Jan 2007 08:00:51 -0500 (EST) Subject: [Pw_forum] ph.x v3.2 on NEC SX-8 In-Reply-To: Message-ID: On Thu, 4 Jan 2007, Paolo Giannozzi wrote: > On Jan 4, 2007, at 12:17 , wlyim at puccini.che.pitt.edu wrote: > > >> There is also a division by another quantity (dz) that is never > >> smaller > >> than 1.d-6 by construction. > > actually I misinterpreted the definition of dz: dz is never LARGER then > 1.d-6 by construction. You can simply set dz to a fixed value: 1.d-6, or > 1.d-4 . > Dear Prof. Giannozzi, I tried your suggestion and set dz = 1.d-6 in functionals.f90: dz = min (1.d-6, 1.d-4 * abs (zeta) ) if (dz <= small) dz = 1.d-6 ! added line call xc_spin (rho, zeta - dz, ex, ec, vxupm, vxdwm, vcupm, vcdwm) call xc_spin (rho, zeta + dz, ex, ec, vxupp, vxdwp, vcupp, vcdwp) I hope I added it at the right point. Unfortunately, ph.x still gave wrong results: q = ( 0.000000000 0.000000000 0.000000000 ) ************************************************************************** omega( 1) = -40.084193 [THz] = -1337.073655 [cm-1] omega( 2) = -39.071262 [THz] = -1303.285663 [cm-1] omega( 3) = -39.071262 [THz] = -1303.285663 [cm-1] omega( 4) = -38.838931 [THz] = -1295.535888 [cm-1] omega( 5) = -38.070039 [THz] = -1269.888241 [cm-1] omega( 6) = -38.070039 [THz] = -1269.888241 [cm-1] ************************************************************************** ph-2.1.4, complied with INTEL and LINUX64 flags and internal FFTW, gave the results below (which is reasonable): q = ( 0.000000000 0.000000000 0.000000000 ) ************************************************************************** omega( 1) = -0.439781 [THz] = -14.669624 [cm-1] omega( 2) = 0.344752 [THz] = 11.499781 [cm-1] omega( 3) = 0.344752 [THz] = 11.499781 [cm-1] omega( 4) = 3.590255 [THz] = 119.758805 [cm-1] omega( 5) = 3.590255 [THz] = 119.758805 [cm-1] omega( 6) = 7.870822 [THz] = 262.544104 [cm-1] ************************************************************************** Is there any benchmark test on NEC machine for the latest version of espresso? Best regards, William -- Dr. Wai-Leung Yim Institut fuer Reine und Angewandte Chemie, Theoretische Chemie, Carl von Ossiezky Universtaet Oldenburg, 26129 Oldenburg, Germany Email: wlyim at puccini.che.pitt.edu Phone: +49-441-798-3950 (office) +49-441-798-5102 (home) Fax: +49-441-798-3964 From akohlmey at cmm.chem.upenn.edu Thu Jan 4 16:29:16 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 4 Jan 2007 10:29:16 -0500 (EST) Subject: [Pw_forum] ph.x v3.2 on NEC SX-8 In-Reply-To: Message-ID: On Thu, 4 Jan 2007 wlyim at puccini.che.pitt.edu wrote: WY> ************************************************************************** WY> WY> Is there any benchmark test on NEC machine for the latest version of WY> espresso? william, there are a bunch of examples for all kinds of calculations in the example subdirectory. those are regularly tested on a few platforms. please try a few of those (see the README files for descriptions) and see if they work reasonably. this might help to identify the source of the problem. cheers, axel. WY> WY> Best regards, WY> William WY> WY> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From ihsanas at yahoo.com Thu Jan 4 16:36:05 2007 From: ihsanas at yahoo.com (احسان عريقات) Date: Thu, 4 Jan 2007 07:36:05 -0800 (PST) Subject: [Pw_forum] average.x Message-ID: <537449.31818.qm@web52308.mail.yahoo.com> Hi I want to calculate the work function for slab ,Iread every thing abuot it in the fourm and made pp.x and average .x but I have some questions please answer me :1- what is the difference between column 1 and 2 in the output of average.x 2- In which units the potentials in the output of average.x is it Ryd 3-What is the difference between planner average and macroscopic average ,how we can calculate planner average . 4-Regfering to J.phy.condens.matter 11(1999),2689-2696 ,how can I choose the mean electrostatic potential as areference for Efermi and macroscopic potential . please answer me ,thanks. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From akohlmey at cmm.chem.upenn.edu Thu Jan 4 17:12:31 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 4 Jan 2007 11:12:31 -0500 (EST) Subject: [Pw_forum] difference between molecular dynamics of PW and that of CPMD In-Reply-To: <830379.42691.qm@web54407.mail.yahoo.com> Message-ID: On Thu, 4 Jan 2007, Lawrence Lee wrote: LL> Dear sir / madam, hi lawrence, LL> I am a new user of pwscf. I know that pw can do molecular dynamics. LL> What is the difference between that and CPMD? please be a bit more precise. do you refer to the CPMD package or the CPMD method (as implemented in cp.x )? in the first case you have two packages that implement first principles calculations using DFT and plane wave basis sets with pseudopotentials. due to differences in the interests of the developers, those two packages (quantum espresso and CPMD) have different strenghts and weaknesses. those can be mostly deduced from looking at the descriptions of the input file syntax (plus a few undocumented features, for which you have to read the source code ;-) ). in the second case you have to distinguish between the born-oppenheimer MD in pw.x, where the ground state wavefunction is fully computed in each MD step, and car-parrinello MD in cp.x where, starting from a ground state wavefunction, the wavefunction for subsequent steps is propagated along the trajectory of the atoms by means of an extenden lagrangian scheme (i.e. it is not exactly the ground state wavefunction, but 'oszillates around it'). strictly speaking, CP-dynamics are also using the born-oppenheimer approximation, but BO-MD vs CP-MD is the established nomenclature. historically, CP-MD used to be much more efficient than BO-MD, even though you have to use an about 5 times shorter time step, but more efficient diagonalization and extrapolation and the availability of more cpu power make BO-MD competitive. on top of that, CP-dynamics put a number of restrictions on the system you want to investigate (it needs a band gap, your atom dynamics is modified by the fictitious electron dynamics). LL> Besides, do you know how to restart the run in pw.x? For example, if LL> I have made a run of 400 steps with dt = 20 atomic time unit, but LL> now I find it insufficient. I need the run to have 2000 steps, say. LL> Do I have any method to proceed the run without doing it from the LL> first step again? have you tried using restart_mode='restart' instead of 'from_scratch' ?? axel. LL> LL> Lawrence. LL> LL> _______________________________________ LL> YM - ???u?T?? LL> ?N???A?S???W???A?A???B?????i?H?d?U?T?????A?A???A?W?????N?????Y?????A???????????N?????C LL> http://messenger.yahoo.com.hk -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From ding at sissa.it Thu Jan 4 16:59:28 2007 From: ding at sissa.it (Xunlei Ding) Date: Thu, 04 Jan 2007 16:59:28 +0100 Subject: [Pw_forum] average.x In-Reply-To: <537449.31818.qm@web52308.mail.yahoo.com> References: <537449.31818.qm@web52308.mail.yahoo.com> Message-ID: <459D2460.9040709@sissa.it> Suppose your input is like this -----------------------------input like this----------- 1 out.dat 1 400 //// number of points 3 //// 3 means along z direction 2.351833 //// window size ---------------------------------------------------------- ????? ?????? wrote: >Hi >I want to calculate the work function for slab ,Iread >every thing abuot it in the fourm and made pp.x and >average .x but I have some questions please answer me >:1- what is the difference between column 1 and 2 in >the output of average.x > > There are 3 columns in the output: column1 is the z direction (in bohr), column2 is the planner average and column3 is the average of column2 (the average of every n points in column2, n is determined by the "window size"). >2- In which units the potentials in the output of >average.x is it Ryd > > Yes. >3-What is the difference between planner average and >macroscopic average ,how we can calculate planner >average . > >4-Regfering to J.phy.condens.matter >11(1999),2689-2696 ,how can I choose the mean >electrostatic potential as areference for Efermi and >macroscopic potential . please answer me ,thanks. > >__________________________________________________ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > > From akohlmey at cmm.chem.upenn.edu Thu Jan 4 17:23:02 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 4 Jan 2007 11:23:02 -0500 (EST) Subject: [Pw_forum] average.x In-Reply-To: <537449.31818.qm@web52308.mail.yahoo.com> Message-ID: On Thu, 4 Jan 2007, ????? ?????? wrote: ??> Hi hi ??, ??> I want to calculate the work function for slab ,Iread ??> every thing abuot it in the fourm and made pp.x and ??> average .x but I have some questions please answer me ??> :1- what is the difference between column 1 and 2 in ??> the output of average.x please have a look at the corresponding sourcecode in the file average.f90. it is pretty well documented. ??> 2- In which units the potentials in the output of ??> average.x is it Ryd if you read the sourcecode, you'll see that this program does not care about units. so output units will be the same as what you put into it. ??> 3-What is the difference between planner average and ??> macroscopic average ,how we can calculate planner ??> average . see under 1). ??> 4-Regfering to J.phy.condens.matter ??> 11(1999),2689-2696 ,how can I choose the mean ??> electrostatic potential as areference for Efermi and you get a good approximation of the mean electrostatic potential by taking the average of the potential over all grid points (which should be equivalent to the average over all planar averages). axel ??> macroscopic potential . please answer me ,thanks. ??> ??> __________________________________________________ ??> Do You Yahoo!? ??> Tired of spam? Yahoo! Mail has the best spam protection around ??> http://mail.yahoo.com ??> _______________________________________________ ??> Pw_forum mailing list ??> Pw_forum at pwscf.org ??> http://www.democritos.it/mailman/listinfo/pw_forum ??> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From Xiangqian.Hu at duke.edu Thu Jan 4 18:22:19 2007 From: Xiangqian.Hu at duke.edu (xqhu@duke.edu) Date: Thu, 4 Jan 2007 12:22:19 -0500 Subject: [Pw_forum] How does PWSCF deal with charged solids? Message-ID: <03d501c73024$e3715600$e29a0398@HLHXQ> Hi, guys, Recently, I have been working on some charged solids (like diamond). I think the Makov-Payne correction only is used for isolated molecules. So I just wonder how PWSCF deals with charged solids? I calculated diamond with one more electron per unit cell through PWSCF. Is the total energy correct? Thank you very much. Xiangqian -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070104/094f8d83/attachment.htm From wyxpwscf at yahoo.com Sat Jan 6 09:07:06 2007 From: wyxpwscf at yahoo.com (Yuanxu WANG) Date: Sat, 6 Jan 2007 00:07:06 -0800 (PST) Subject: [Pw_forum] Raman Intensity Message-ID: <49614.56506.qm@web58311.mail.re3.yahoo.com> Dear ALL, I have a question. PWSCF can output Raman susceptibility tensors. How to calculate the Raman Intensity from these Raman susceptibility. Best WANG Yuanxu __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070106/a204ef10/attachment.htm From ezadshojaee at hotmail.com Sat Jan 6 10:27:54 2007 From: ezadshojaee at hotmail.com (Ezad Shojaee) Date: Sat, 06 Jan 2007 09:27:54 +0000 Subject: [Pw_forum] NaN Message-ID: hi i am performing phonon calculation by a Grid and i have "NaN" in one of the modes of a point in grid , so the dynamical matrix in that point is "NaN'" too what's the problem and what should i do ? thanx for any comment _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ From shaposh at isp.nsc.ru Sat Jan 6 14:36:29 2007 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Sat, 6 Jan 2007 19:36:29 +0600 Subject: [Pw_forum] parallel pw.x memory requirements Message-ID: <200701061936.29752.shaposh@isp.nsc.ru> Hi, according to manual, pw.x scf R&G parallelization should scale well in respect with memory requirement (i.e., total memory required should not increase much with the number of threads and should decrease per CPU almost linearly ) However, what i have noticed, the amount of memory used per CPU does not decrease more than 2 times. For example, running on 8-node SMP machine with 8 threads consume 4 times more memory comparing with one only thread ( with 1 pool, procs/pool=8 ) Is this expected behavior? Can somebody clarify this? Best Regards, Alexander Shaposhnikov From amit76.india at gmail.com Sat Jan 6 17:16:24 2007 From: amit76.india at gmail.com (Amit Kumar) Date: Sat, 6 Jan 2007 21:46:24 +0530 Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1296 - 13 msgs In-Reply-To: <20070104172301.7555.51742.Mailman@democritos.sissa.it> References: <20070104172301.7555.51742.Mailman@democritos.sissa.it> Message-ID: Respected Users, Wishing you all a happy new year first. I have two questions regarding pwscf input. Let us assume I have a surface unit cell of 1 Angstrom with one valence electron. So the electron density is order of 10^16 per cm^2. Right??? Now if I want to add extra 10^13 electrons in the system then is the 'nelec'' correct input flag??? I know "nelec" can be non integer in pwscf but my little confusion whether the value nelec = 1.0001 is valid one like nelec=1 or 2 ???? Is there any other way to add extra surface electron in the 2D system in pwscf??? Another question is when I use Example No. 7 of pwscf package with the flag filelph = "al.elph" switch on, I'm not getting any al.elph file where all the el-ph matrix elements are supposed to written. Looking forward to your useful comments.. Regards, Amit -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070106/4c0608f4/attachment.htm From shaposh at isp.nsc.ru Sat Jan 6 18:13:37 2007 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Sat, 6 Jan 2007 23:13:37 +0600 Subject: [Pw_forum] Parallelization of diaghg Message-ID: <200701062313.38105.shaposh@isp.nsc.ru> Hi, yet another parallelization issue. As far as i understand, subroutine cdiaghg for davidson diagonalization is not parallelized by default (in recent versions) and this is for good, as enabling parallel algorithm ('david + para ') only increases computation time (almost always for me). Profiling shows this routine takes 1/2 -2/3 exec times for big jobs running in parallel on 8-core dual Xeon clovertown 2.66GHz machine, so some working parallelization algorithm could give sizeable performance boost. I'd like to hear any comments from respected developers concerning this issue. Best Regards, Alexander Shaposhnikov From akohlmey at cmm.chem.upenn.edu Sat Jan 6 21:09:45 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 6 Jan 2007 15:09:45 -0500 Subject: [Pw_forum] parallel pw.x memory requirements In-Reply-To: <200701061936.29752.shaposh@isp.nsc.ru> References: <200701061936.29752.shaposh@isp.nsc.ru> Message-ID: <7b6913e90701061209v232c4e2kf64f863232dff0ba@mail.gmail.com> On 1/6/07, Alexander Shaposhnikov wrote: > Hi, > according to manual, pw.x scf R&G parallelization should scale well in respect > with memory requirement (i.e., total memory required should not increase > much with the number of threads and should decrease per CPU almost linearly ) please note, that this depends a _lot_ on the system size at hand and that with any distributed memory parallelization scheme, you have to have some replicated data and some additional overhead for managing the distributed data. so the above statement is only true for very large systems. > However, what i have noticed, the amount of memory used per CPU does not > decrease more than 2 times. For example, running on 8-node SMP machine with 8 > threads consume 4 times more memory comparing with one only thread ( with 1 > pool, procs/pool=8 ) please tell us how you determined the memory consumption. on unix machines with memory management, there are multiple 'sizes', i.e. the address spaces size, the resident set size, the data segment size and shared memory. those numbers can differ quite a bit. also, if you're running shared memory parallelization, the MPI library may allocate additional blocks of memory that is shared between all processes simply for communication purposes. in some cases (SGI ccNUMA machines with default settings, each MPI thread maps the _complete_ address space of all other threads, i.e. the total (virtual) memory use increases quadratical with the number of threads + serial overhead). > Is this expected behavior? Can somebody clarify this? hope that helps, axel. > > Best Regards, > Alexander Shaposhnikov > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Sat Jan 6 21:19:50 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 6 Jan 2007 15:19:50 -0500 Subject: [Pw_forum] Parallelization of diaghg In-Reply-To: <200701062313.38105.shaposh@isp.nsc.ru> References: <200701062313.38105.shaposh@isp.nsc.ru> Message-ID: <7b6913e90701061219l7ebf35ffj86c589ac1914839e@mail.gmail.com> On 1/6/07, Alexander Shaposhnikov wrote: > Hi, > > yet another parallelization issue. As far as i understand, subroutine cdiaghg > for davidson diagonalization is not parallelized > by default (in recent versions) and this is for good, as enabling parallel > algorithm ('david + para ') only increases computation time (almost always for > me). > Profiling shows this routine takes 1/2 -2/3 exec times for big jobs running > in parallel on 8-core dual Xeon clovertown 2.66GHz machine, so some working > parallelization algorithm could give sizeable performance boost. well, on the other hand you have to consider the problem of memory contention, which must be a huge problem on a machine like yours. i suggest, you first do a test by starting a series of 1, 2, 3, 4,...,8 identical and not too small serial calculations simultaneously and compare the wall time of those jobs to get an impression of how much of a performance improvement from this kind of machine is maximally possible (this is an ideally parallel problem with no communication). i have not previous experience with that kind of hardware, but extrapolating from woodcrest performance numbers and the fact, that your cpus are for all practical purposes two woodcrest cpus glued on one socket, i'd expect that you'd see a significant performance degradation when running 8 processes. i would not be surprised if the optimum would be to use only two thirds or even half the cores for larger problems. cheers, axel. > > I'd like to hear any comments from respected developers concerning this issue. > > Best Regards, > Alexander Shaposhnikov > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From shaposh at isp.nsc.ru Sat Jan 6 21:50:39 2007 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Sun, 7 Jan 2007 02:50:39 +0600 Subject: [Pw_forum] Parallelization of diaghg In-Reply-To: <7b6913e90701061219l7ebf35ffj86c589ac1914839e@mail.gmail.com> References: <200701062313.38105.shaposh@isp.nsc.ru> <7b6913e90701061219l7ebf35ffj86c589ac1914839e@mail.gmail.com> Message-ID: <200701070250.39882.shaposh@isp.nsc.ru> On Sunday 07 January 2007 02:19, Axel Kohlmeyer wrote: > On 1/6/07, Alexander Shaposhnikov wrote: > > Hi, > > > > yet another parallelization issue. As far as i understand, subroutine > > cdiaghg for davidson diagonalization is not parallelized > > by default (in recent versions) and this is for good, as enabling > > parallel algorithm ('david + para ') only increases computation time > > (almost always for me). > > Profiling shows this routine takes 1/2 -2/3 exec times for big jobs > > running in parallel on 8-core dual Xeon clovertown 2.66GHz machine, so > > some working parallelization algorithm could give sizeable performance > > boost. > > well, on the other hand you have to consider the problem of memory > contention, which must be a huge problem on a machine like yours. > > i suggest, you first do a test by starting a series of 1, 2, 3, > 4,...,8 identical > and not too small serial calculations simultaneously and compare the wall > time of those jobs to get an impression of how much of a performance > improvement from this kind of machine is maximally possible (this is > an ideally parallel problem with no communication). i have not previous > experience with that kind of hardware, but extrapolating from woodcrest > performance numbers and the fact, that your cpus are for all practical > purposes two woodcrest cpus glued on one socket, i'd expect that you'd > see a significant performance degradation when running 8 processes. > i would not be surprised if the optimum would be to use only two thirds > or even half the cores for larger problems. The SMP speedup for relatively large pw.x jobs (like scf calc. of 192 atom ZrO2 supercell with 50 ecut) is ~4.5. As i said, the cdiaghg does not parallelize and takes ~1/3 exec time of the whole 8-cpu job. Consider it could be efficiently run in parallel to get, say, 2X speedup on 8cpus - I could achieve ~5.5X total SMP speedup. Thats the difference. On the other hand, memory contention is indeed huge problem for cp/cpmd codes, so this Xeon machine is barely faster than dual Opteron 280 2.4GHz (4cores) for cpmd. For pw.x , however, it is ~2.5 faster for large jobs -and could be made even better with some working diaghg parallelization algorithm. > cheers, > axel. Best Regards, Alexander Shaposhnikov From akohlmey at cmm.chem.upenn.edu Sat Jan 6 22:03:21 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 6 Jan 2007 16:03:21 -0500 Subject: [Pw_forum] Parallelization of diaghg In-Reply-To: <200701070250.39882.shaposh@isp.nsc.ru> References: <200701062313.38105.shaposh@isp.nsc.ru> <7b6913e90701061219l7ebf35ffj86c589ac1914839e@mail.gmail.com> <200701070250.39882.shaposh@isp.nsc.ru> Message-ID: <7b6913e90701061303m50247040p20d886421c2437bc@mail.gmail.com> On 1/6/07, Alexander Shaposhnikov wrote: > > > The SMP speedup for relatively large pw.x jobs (like scf calc. of 192 atom > ZrO2 supercell with 50 ecut) is ~4.5. As i said, the cdiaghg does not > parallelize and takes ~1/3 exec time of the whole 8-cpu job. Consider it > could be efficiently run in parallel to get, say, 2X speedup on 8cpus - I > could achieve ~5.5X total SMP speedup. > Thats the difference. > > On the other hand, memory contention is indeed huge problem for cp/cpmd codes, > so this Xeon machine is barely faster than dual Opteron 280 2.4GHz (4cores) > for cpmd. For pw.x , however, it is ~2.5 faster for large jobs -and could be > made even better with some working diaghg parallelization algorithm. hmmmm.... what version of pw.x are you referring to? at least in version 3.2 there should be a parallel diagonalization that is used in pw.x (subroutine cdiagonalize in Modules/ptoolkit.f90). as far as i understand, this is not easy to parallelize, so there is an estimator that checks, whether the serial or the parallel algorithm would be more efficient. cheers, axel. > > > cheers, > > axel. > > Best Regards, > Alexander Shaposhnikov > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From shaposh at isp.nsc.ru Sat Jan 6 23:49:08 2007 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Sun, 7 Jan 2007 04:49:08 +0600 Subject: [Pw_forum] Parallelization of diaghg In-Reply-To: <7b6913e90701061303m50247040p20d886421c2437bc@mail.gmail.com> References: <200701062313.38105.shaposh@isp.nsc.ru> <200701070250.39882.shaposh@isp.nsc.ru> <7b6913e90701061303m50247040p20d886421c2437bc@mail.gmail.com> Message-ID: <200701070449.08675.shaposh@isp.nsc.ru> On Sunday 07 January 2007 03:03, Axel Kohlmeyer wrote: > hmmmm.... what version of pw.x are you referring to? > at least in version 3.2 there should be a parallel diagonalization > that is used in pw.x (subroutine cdiagonalize in Modules/ptoolkit.f90). > as far as i understand, this is not easy to parallelize, so there > is an estimator that checks, whether the serial or the parallel algorithm > would be more efficient. recent cvs. with diagonalization='david +para', the code almost always chooses parallel algorithm but this always increases total computation time, both on Intel and AMD SMP machines. So i guess the default 'david ' with serial diaghg is the best choice currently. By the way, i have found that diago_david_ndim=2 gives better times and also saves alot of memory comparing with default =4. Best Regards, Alexander Shaposhnikov > cheers, > axel. > From akohlmey at cmm.chem.upenn.edu Sun Jan 7 01:11:42 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Sat, 06 Jan 2007 19:11:42 -0500 Subject: [Pw_forum] need hints for running pw.x on BG/L Message-ID: <45A03ABE.6030808@cmm.chem.upenn.edu> hi everybody, does anybody have some experience with running pw.x on a BG/L and could send me a few do's and don'ts? i just managed to get (most) of the current QE-CVS compiled and cp.x (with plain CP-dynamics) working (quite nicely actually), but pw.x is still a bit picky and keeps crashing on me in the middle of total energy calculations without any error output. i'll keep playing around with different inputs and settings, but would appreciate any help. thanks, axel. -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From wyanchao at gmail.com Sun Jan 7 01:06:47 2007 From: wyanchao at gmail.com (wang yanchao) Date: Sun, 7 Jan 2007 08:06:47 +0800 Subject: [Pw_forum] ask question Message-ID: <55639d30701061606p2adafa3fq48d3a2c9bdd31dd@mail.gmail.com> dear Stefano: Thank you for your reply! I have read the paper which you suggest and get a lot ! Now I want to know how to displace the ion in pwscf code,in other word,which subroutine is called to do this task ? which ion displace when there are many ions in this system? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070107/c8eff464/attachment.htm From baroni at sissa.it Sun Jan 7 08:50:15 2007 From: baroni at sissa.it (Stefano Baroni) Date: Sun, 7 Jan 2007 08:50:15 +0100 Subject: [Pw_forum] ask question In-Reply-To: <55639d30701061606p2adafa3fq48d3a2c9bdd31dd@mail.gmail.com> References: <55639d30701061606p2adafa3fq48d3a2c9bdd31dd@mail.gmail.com> Message-ID: <67A58276-9B8E-4D2B-8DC5-B80007B3E6FC@sissa.it> On Jan 7, 2007, at 1:06 AM, wang yanchao wrote: > dear Stefano: > Thank you for your reply! I have read the paper which you > suggest and get a lot ! Now I want to know how to displace the ion > in pwscf code,in other word,which subroutine is called to do this > task ? phq_setup.f90 > which ion displace when there are many ions in this system? all of them S. --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070107/2115de4e/attachment.htm From giannozz at nest.sns.it Mon Jan 8 11:06:39 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 8 Jan 2007 11:06:39 +0100 Subject: [Pw_forum] parallel pw.x memory requirements In-Reply-To: <200701061936.29752.shaposh@isp.nsc.ru> References: <200701061936.29752.shaposh@isp.nsc.ru> Message-ID: On Jan 6, 2007, at 14:36 , Alexander Shaposhnikov wrote: > [...] what i have noticed, the amount of memory used per CPU > does not decrease more than 2 times. For example, running on > 8-node SMP machine with 8 threads consume 4 times more > memory comparing with one only thread ( with 1 pool, procs/pool=8 ) > Is this expected behavior? Can somebody clarify this? there is a "scalable" memory: - arrays containing quantities on either the real-space grid or the plane-wave basis set. These are distributed across processors (exception: in some cases, a single array as large as the entire real-space grid is used). and a "nonscalable" memory: - most remaining arrays. These not distributed but replicated. (or they exist only on the master process). Note that arrays with dimensions Nstates*Nstates (still) belong to this category - the code itself, libraries, etc Right now the amount of "nonscalable" memory is not so small, say > 200Mb, so the code will take a sizable amount of memory no matter how many processors you use. Work is in progress to reduce it to the strict minimum, in view of usage of massively parallel machines with not-so-much memory per processor. Meanwhile you can reduce the values of fixed dimensions (in Modules/parameters.f90) from their default value, especially those: ntypx, ndmx, nbrx . Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Mon Jan 8 12:26:59 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 8 Jan 2007 12:26:59 +0100 Subject: [Pw_forum] Parallelization of diaghg In-Reply-To: <200701070449.08675.shaposh@isp.nsc.ru> References: <200701062313.38105.shaposh@isp.nsc.ru> <200701070250.39882.shaposh@isp.nsc.ru> <7b6913e90701061303m50247040p20d886421c2437bc@mail.gmail.com> <200701070449.08675.shaposh@isp.nsc.ru> Message-ID: <70013D48-C39B-4545-9AE4-FEF2F0C5C369@nest.sns.it> On Jan 6, 2007, at 23:49 , Alexander Shaposhnikov wrote: > By the way, i have found that diago_david_ndim=2 gives better > times and also saves alot of memory comparing with default =4. it saves a lot of memory by reducing the workspace where auxiliary vectors (H-e)psi are stored during the diagonalization. This typically leads to a slight increase in execution times, because each time the workspace is filled one has to recalculate a new estimate of the eigenvectors. Maybe in your case the advantage of a reduced memory footprint more than compensate the cost of such operation (which has to be done anyway when the diagonalization is converged). Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From ezadshojaee at hotmail.com Mon Jan 8 18:23:57 2007 From: ezadshojaee at hotmail.com (Ezad Shojaee) Date: Mon, 08 Jan 2007 17:23:57 +0000 Subject: [Pw_forum] NaN in phonon Message-ID: hi i tried to perform ph.x by a grid and at the 10th point, i have NaN in the 15th mode, so is seems that the code is in a cycle and does not continue what should i do according to the long time it has take for the 9 points before?!! what's the problem? is there anyway to force the code to continue and use the interatomic force constants of other points ? thanx for any hint _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ From giannozz at nest.sns.it Mon Jan 8 18:56:33 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 8 Jan 2007 18:56:33 +0100 Subject: [Pw_forum] questions on molecular dynamics example In-Reply-To: References: <20061228063758.32036.28560.Mailman@democritos.sissa.it> Message-ID: <96787C8C-C714-42CD-A123-B4ACBF31B72E@nest.sns.it> On Dec 28, 2006, at 18:21 , Eduardo Ariel Menendez P wrote: > I think that wfc_extrapolation acts only for the first self-consistent > iteration at any ionic configuration [...] > pot_extrapolation influences the guess for the potential, then it > has a > direct influence on the number of iterations needed for self- > consistency. in principle correct, but since the first diagonalization is often performed with a rather large threshold, the output wavefunction will often have enough "memory" of the input one to influence self-consistency (according to Murphy's law, in a negative way). The ideal combination would be extrapolation of the wavefunctions + extrapolation of the potential + a wise choice of the diagonalization threshold; of course if the ionic steps are small enough Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From rudrabnrj at gmail.com Tue Jan 9 14:14:56 2007 From: rudrabnrj at gmail.com (Rudra) Date: Tue, 9 Jan 2007 18:44:56 +0530 Subject: [Pw_forum] calculating magnetic moment Message-ID: <2e36f8e50701090514o56da09a2rbc73311b8d2ef9fa@mail.gmail.com> hello friends, i want to calculate magnetic moment of atoms in a cluster.can I use pwscf for this purpose?and how? plz let me now thanking you -- rudra Please, if possible, don't send me MS Word or PowerPoint attachments ---------- Why?See: http://www.gnu.org/philosophy/no-word-attachments.html have a nice time -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070109/a7f77f34/attachment.htm From giannozz at nest.sns.it Tue Jan 9 14:23:29 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 9 Jan 2007 14:23:29 +0100 Subject: [Pw_forum] NaN in phonon In-Reply-To: References: Message-ID: On Jan 8, 2007, at 18:23 , Ezad Shojaee wrote: > i tried to perform ph.x by a grid and at the 10th point, i have NaN in > the 15th mode, so is seems that the code is in a cycle and does not > continue what should i do according to the long time it has take for > the 9 points before?!! what's the problem? NaN = Not a Number = serious trouble. It is impossible to say what the problem is on the basis of the above information alone Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From prasenjit.jnc at gmail.com Tue Jan 9 14:29:23 2007 From: prasenjit.jnc at gmail.com (Prasenjit Ghosh) Date: Tue, 9 Jan 2007 18:59:23 +0530 Subject: [Pw_forum] calculating magnetic moment In-Reply-To: <2e36f8e50701090514o56da09a2rbc73311b8d2ef9fa@mail.gmail.com> References: <2e36f8e50701090514o56da09a2rbc73311b8d2ef9fa@mail.gmail.com> Message-ID: <627e0ffa0701090529s2391e55br8e1e5f4b12ef26d@mail.gmail.com> Hi Rudra, you can do spin polarized cal. by setting nspin=2 in & system card. The code prints out the total magnetism for the system in mu_B/cell. If you want to find out the magnetic moment on each atom, use projwfc.x executable. At the end of the o/p file it prints out the polarization on each atom. Hope that helps. Prasenjit. On 1/9/07, Rudra wrote: > > hello friends, > i want to calculate magnetic moment of atoms in a cluster.can I use pwscf > for this purpose?and how? > plz let me now > thanking you > > -- > rudra Please, > if possible, don't send me MS Word or PowerPoint attachments > ---------- > Why?See: http://www.gnu.org/philosophy/no-word-attachments.html > have a nice time -- PRASENJIT GHOSH, Ph. D STUDENT, THEORETICAL SCIENCES UNIT, JNCASR, BANGALORE-560064, INDIA. PHONE: OFFICE : +91-80-22082835/34 MOBILE: +91-9880519401 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070109/195292fe/attachment.htm From naromero at gmail.com Tue Jan 9 15:15:27 2007 From: naromero at gmail.com (Nichols A. Romero) Date: Tue, 9 Jan 2007 09:15:27 -0500 Subject: [Pw_forum] calculating the stress tensor In-Reply-To: <58695.203.200.55.101.1152790667.squirrel@webmail3.ictp.trieste.it> References: <6ac064b60607101018q6dbf8148j95009e109ba60f41@mail.gmail.com> <58695.203.200.55.101.1152790667.squirrel@webmail3.ictp.trieste.it> Message-ID: <6ac064b60701090615s3b7818bbl204900f5bbc1c405@mail.gmail.com> Sandro, I am replying to this old e-mail now because the funds have become available to do some work in this area. I looked in Paolo Focher's thesis and there are some very helpful equations, so thank you. However, the eqn.'s are limited to LDA. Does anyone know where I could find the relevant equation(s) for the GGA functional contribution to the stress tensor? I imagine it should not be that different from LDA, but I want to be sure. On 7/13/06, Scandolo Sandro wrote: > > A number of useful formulae can be found in Paolo Focher's thesis (1994) > (dowloadable from http://www.sissa.it/cm/phd.php ), as well as in a > subsequent publication: > > Paolo Focher and Guido L. Chiarotti > Ab-initio Molecular Dynamics simulations of structural phase transitions > in ``Progress in Computational Physics of Matter'', eds. L. Reatto and F. > Manghi, p. 1-42, World Scientific, Singapore, (1995). > > (I can fax you the relevant pages of the latter when I'm back to Trieste, > late August). > > Best regards, > Sandro > > > > Hi, > > > > I and another post-doc are working on implementing a non-local > > functional into PWSCF. It is of the general form: > > E_xc[n(r)] = \int dr dr' n(r) phi(r,r') n(r') > > > > where n(r) and phi(r,r') are the charge density and a kernel, > > respectively. > > > > Forces require calculating V_xc which is analytically complicated, but > > has already been done. The next quantity that we want to compute is > > the stress tensor. > > > > Does any happen to have any notes on calculating the stress tensor in > > a PW basis set? > > > > I looked at the original paper on calculating the stress: > > > > O. H. Nielsen and R. M. Martin, Phys. Rev. Lett. 50, 697 (1983). > > > > Eqn. 3 contains the V_xc (mu_xc in their notation) and it also > > contains epsilon_xc which is the exchange-correlation energy per > > particle which cannot be easily written down in a closed analytic form > > for a non-local functional (I think). Otherwise, I don't see any > > higher derivatives of E_xc in the the expression for the stress. > > > > Does anyone have any useful references? > > > > Thanks, > > -- > > Nichols A. Romero, Ph.D. > > 1613 Denise Dr. Apt. D > > Forest Hill, MD 21050 > > 443-567-8328 (C) > > 410-306-0709 (O) > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Nichols A. Romero, Ph.D. 1613 Denise Dr. Apt. D Forest Hill, MD 21050 443-567-8328 (C) 410-306-0709 (O) -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070109/e3b74c62/attachment.htm From giannozz at nest.sns.it Tue Jan 9 15:23:28 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 9 Jan 2007 15:23:28 +0100 Subject: [Pw_forum] How does PWSCF deal with charged solids? In-Reply-To: <03d501c73024$e3715600$e29a0398@HLHXQ> References: <03d501c73024$e3715600$e29a0398@HLHXQ> Message-ID: <52B4FF99-8990-4DF6-B05D-6077512F4D63@nest.sns.it> On Jan 4, 2007, at 18:22 , xqhu at duke.edu wrote: > Recently, I have been working on some charged solids (like diamond). > I think the Makov-Payne correction only is used for isolated > molecules. > So I just wonder how PWSCF deals with charged solids? by (implicitly) adding a neutralizing background, i.e. calculating the G=0 energy terms as for a neutral system > I calculated diamond with one more electron per unit cell through > PWSCF. Is the total energy correct? it depends on what you mean by "correct". The total energy of a charged system is infinite for an infinite system. The calculated energy should ideally give information on the energy required to add or remove 1 electron to the system, not 10^23 electrons. For an isolated system, the calculated energy will eventually converge, for larger and larger supercells, to the energy of the charged system, but the convergence is exceedingly slow. The Makov-Payne correction does a decent job in this case. More refined (and expensive) approaches use a modified Coulomb interaction and enlarged supercells to solve the Poisson equation. For a true crystal, there isn't much one can do: you cannot (for instance) calculate the ionization potential or the electronic affinity by just making the difference between the calculated total energies for different charge states. A case in which energies for charged systems can be useful (with some care) is the relative stability of charge states for defects in semiconductors. For instance: E_f(-) = E(crystal:defect+e) - E(crystal) - E(defect) - \mu E_f(0) = E(crystal:defect) - E(crystal) - E(defect) where \mu is the energy of an electron from an electron reservoir, i.e. the Fermi energy of the crystal, inside the gap. A comparison of various charge states yields the relative stability with respect to the position of the Fermi energy (something that depends on the impurities that are present in the semiconductor). Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From lawrence_lee_lee at yahoo.com.hk Tue Jan 9 18:42:26 2007 From: lawrence_lee_lee at yahoo.com.hk (Lawrence Lee) Date: Wed, 10 Jan 2007 01:42:26 +0800 (CST) Subject: [Pw_forum] nosym=.true. in molecular dynamics by PWSCF Message-ID: <989518.49761.qm@web54402.mail.yahoo.com> Dear all, Is it really necessary that when using PWSCF to do molecular dynamics, the following: nosym=.true. had to be used? If yes, why? Lawrence _______________________________________ YM - ???? ??????????????????????????????????????????? http://messenger.yahoo.com.hk -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070110/92f22e23/attachment.htm From vranjan at ncsu.edu Tue Jan 9 22:06:29 2007 From: vranjan at ncsu.edu (Vivek Ranjan) Date: Tue, 9 Jan 2007 16:06:29 -0500 (EST) Subject: [Pw_forum] compilation problem Message-ID: <55378.152.14.74.117.1168376789.squirrel@webmail.ncsu.edu> Hello, I am trying to compile the latest (CVS) version of pwscf on IBM SP4 machine. I get the following error message. ( cd clib ; if test "make" = "" ; then make TLDEPS= all ; else make TLDEPS= all ; fi ) xlc_r -q64 -O2 -D__AIX -D__XLF -D__ESSL -D__MASS -D__MPI -D__PARA -I../include -c c_mkdir.c "c_mkdir.c", line 42.5: 1506-033 (S) Function F77_FUNC_ is not valid. Function cannot return a function. "c_mkdir.c", line 49.41: 1506-045 (S) Undeclared identifier length. "c_mkdir.c", line 51.19: 1506-045 (S) Undeclared identifier dirname. "c_mkdir.c", line 62.11: 1506-1332 (W) A function with return type "int(*)(const char*,const int*)" may not return a value of type "int". make: 1254-004 The error code from the last command is 1. Stop. make: 1254-004 The error code from the last command is 2. Stop. Any comments/suggestions ? Thanks in advance, Vivek From halim_said04 at yahoo.fr Tue Jan 9 22:20:48 2007 From: halim_said04 at yahoo.fr (halim said) Date: Tue, 9 Jan 2007 22:20:48 +0100 (CET) Subject: [Pw_forum] problem compiling espresso-3.2 in SGI origin machine Message-ID: <657096.96960.qm@web23304.mail.ird.yahoo.com> Dear Axel and Paolo, I am compiling espress-3.2 code in SGI origin machine, when I am taping ./configure every thing is fine. but when I am taping gmake all, there are some errors appear, how to deal with this problem in order to success for compiling the code. Below I am attaching configure and the errors which appeared after gmake Your help and support are highly appreciate. Regards, Halim ----------------------------------------------------------------------------------------------------- espresso-3.2>./configure checking build system type... mips-sgi-irix6.5 checking architecture... mips checking for f90... f90 checking for suffix of executables... checking for suffix of object files... o checking whether f90 accepts -g... yes checking for mpif90... no checking for f90... f90 checking whether f90 accepts -g... yes setting F90... f90 setting MPIF90... f90 checking for cc... cc checking whether cc accepts -g... yes checking for cc option to accept ANSI C... none needed setting CC... cc checking how to run the C preprocessor... cc -E checking for egrep... grep -E checking for ANSI C header files... yes checking for int *... yes checking size of int *... 4 checking malloc.h usability... yes checking malloc.h presence... yes checking for malloc.h... yes checking for struct mallinfo.arena... yes setting FFLAGS... -mips4 -64 -O2 -r10000 -r8 setting F90FLAGS... $(FFLAGS) setting FFLAGS_NOOPT... -mips4 -64 -O0 setting CFLAGS... -mips4 -64 -O2 -r10000 setting CPP... cpp setting CPPFLAGS... -P -traditional setting LD... f90 setting LDFLAGS... -mips4 -64 setting AR... ar setting ARFLAGS... ruv setting ARFLAGS_DYNAMIC...ruv checking whether make sets $(MAKE)... yes checking for Fortran libraries of f77... -L/usr/lib32/mips4/r10000 -L/usr/lib32/mips4 -L/usr/lib32 -lftn -lm checking for Fortran name-mangling scheme... lower case, underscore, no extra underscore checking for library containing dgemm... -lcomplib.sgimath setting BLAS_LIBS... -lcomplib.sgimath setting LAPACK_LIBS... ../flib/lapack.a setting FFT_LIBS... setting MASS_LIBS... checking for library containing mpi_init... -lmpi setting MPI_LIBS... -lmpi checking for library containing mpi_init... (cached) -lmpi setting DFLAGS... -D__COMPLIB -D__ORIGIN -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA setting IFLAGS... -I../include setting FDFLAGS... $(DFLAGS) checking for ranlib... echo setting RANLIB... echo -------------------------------------------------------------------- The following libraries have been found: BLAS_LIBS=-lcomplib.sgimath LAPACK_LIBS=../flib/lapack.a FFT_LIBS= MPI_LIBS=-lmpi Parallel environment detected successfully. Configured for compilation of parallel executables. configure: success --------------------------------------------------------------------------------------------------- espresso.3-2> gmake all gmake[1]: Leaving directory `/h2/home/espresso-3.2/iotk' ( cd Modules ; if test "gmake" = "" ; then make TLDEPS= all ; \ else gmake TLDEPS= all ; fi ) gmake[1]: Entering directory `/h2/home/espresso-3.2/Modules' f90 -mips4 -64 -O2 -r10000 -r8 -ftpp -macro_expand -D__COMPLIB -D__ORIGIN -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../CPV -c io_global.f90 This product's license is for 2 CPU's; Your system has 7 CPU's MODULE bfgs_module ^ f90-855 f90: ERROR BFGS_MODULE, File = bfgs_module.f90, Line = 9, Column = 8 The compiler has detected errors in module "BFGS_MODULE". No module information file will be created for this module. IF ( ( grad(:) .dot. step(:) ) > 0.D0 ) THEN ^ f90-318 f90: ERROR GDIIS_STEP, File = bfgs_module.f90, Line = 464, Column = 26 The operator "dot" has not been declared as a user defined operator. step(:) = - ( inv_hess(:,:) .times. grad(:) ) ^ f90-318 f90: ERROR GDIIS_STEP, File = bfgs_module.f90, Line = 469, Column = 42 f90: MIPSpro Fortran 90 Version 7.3 (f52) Mon Jan 8, 2007 11:53:12 f90: 1008 source lines f90: 3 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s) cf90: "explain cf90-message number" gives more information about each message gmake[1]: *** [bfgs_module.o] Error 2 gmake[1]: Leaving directory `/h2/home/espresso-3.2/Modules' gmake: *** [mods] Error 2 __________________________________________________ Do You Yahoo!? En finir avec le spam? Yahoo! Mail vous offre la meilleure protection possible contre les messages non sollicit?s http://mail.yahoo.fr Yahoo! Mail -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070109/43442c60/attachment.htm From akohlmey at cmm.chem.upenn.edu Tue Jan 9 22:43:49 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 9 Jan 2007 16:43:49 -0500 (EST) Subject: [Pw_forum] problem compiling espresso-3.2 in SGI origin machine In-Reply-To: <657096.96960.qm@web23304.mail.ird.yahoo.com> Message-ID: On Tue, 9 Jan 2007, halim said wrote: HS> Dear Axel and Paolo, HS> HS> I am compiling espress-3.2 code in SGI origin machine, when I am taping be prepared to suffer. SGI origins have inflicted a lot of pain on me at times. good thing, they are more or less obsolete these days... HS> ./configure HS> HS> every thing is fine. configure does next to no consistency checking on the fortran side, so a completed configure does not have much meaning except that it is required. simply using and adapting an existing make.sys template is no longer sufficient. HS> but when I am taping gmake all, HS> HS> there are some errors appear, how to deal with this problem in order HS> to success for compiling the code. HS> HS> Below I am attaching configure and the errors which appeared after gmake HS> HS> Your help and support are highly appreciate. HS> HS> Regards, HS> HS> Halim HS> HS> [...] HS> -------------------------------------------------------------------- HS> HS> The following libraries have been found: HS> BLAS_LIBS=-lcomplib.sgimath HS> LAPACK_LIBS=../flib/lapack.a HS> FFT_LIBS= HS> MPI_LIBS=-lmpi HS> Parallel environment detected successfully. HS> Configured for compilation of parallel executables. HS> configure: success ok. looking normal up to here... HS> espresso.3-2> gmake all HS> gmake[1]: Leaving directory `/h2/home/espresso-3.2/iotk' HS> ( cd Modules ; if test "gmake" = "" ; then make TLDEPS= all ; \ HS> else gmake TLDEPS= all ; fi ) HS> gmake[1]: Entering directory `/h2/home/espresso-3.2/Modules' HS> f90 -mips4 -64 -O2 -r10000 -r8 -ftpp -macro_expand -D__COMPLIB -D__ORIGIN -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../CPV -c io_global.f90 HS> This product's license is for 2 CPU's; Your system has 7 CPU's hmmmmmm.... looks like you need to pay SGI some more money. ;-) but that should apply only at run-time. HS> HS> MODULE bfgs_module HS> ^ HS> f90-855 f90: ERROR BFGS_MODULE, File = bfgs_module.f90, Line = 9, Column = 8 HS> The compiler has detected errors in module "BFGS_MODULE". No module information file will be created for this module. HS> HS> IF ( ( grad(:) .dot. step(:) ) > 0.D0 ) THEN HS> ^ HS> f90-318 f90: ERROR GDIIS_STEP, File = bfgs_module.f90, Line = 464, Column = 26 HS> The operator "dot" has not been declared as a user defined operator. ok. this means that either the sgi compiler is not sufficiently fortran 95 compliant or, that the prerequisite module basic_algebra_routines.f90 has not been compiled correctly. please do a 'gmake clean ; gmake all' to make sure that you are not continuing from a previous broken compile. please also make sure that Modules/make.depend contains the line: bfgs_module.o : basic_algebra_routines.o and if that does not help, i'd try to change F90 = f90 MPIF90 = f90 LD = f90 to F90 = f95 MPIF90 = f95 LD = f95 in make.sys axel. HS> HS> step(:) = - ( inv_hess(:,:) .times. grad(:) ) HS> ^ HS> f90-318 f90: ERROR GDIIS_STEP, File = bfgs_module.f90, Line = 469, Column = 42 HS> HS> f90: MIPSpro Fortran 90 Version 7.3 (f52) Mon Jan 8, 2007 11:53:12 HS> f90: 1008 source lines HS> f90: 3 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s) HS> cf90: "explain cf90-message number" gives more information about each message HS> gmake[1]: *** [bfgs_module.o] Error 2 HS> gmake[1]: Leaving directory `/h2/home/espresso-3.2/Modules' HS> gmake: *** [mods] Error 2 HS> HS> HS> HS> __________________________________________________ HS> Do You Yahoo!? HS> En finir avec le spam? Yahoo! Mail vous offre la meilleure protection possible contre les messages non sollicit?s HS> http://mail.yahoo.fr Yahoo! Mail -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Tue Jan 9 22:19:43 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 9 Jan 2007 16:19:43 -0500 Subject: [Pw_forum] compilation problem In-Reply-To: <55378.152.14.74.117.1168376789.squirrel@webmail.ncsu.edu> References: <55378.152.14.74.117.1168376789.squirrel@webmail.ncsu.edu> Message-ID: <7b6913e90701091319x4fa21dadmbe3b33ccd6315d82@mail.gmail.com> On 1/9/07, Vivek Ranjan wrote: > Hello, > > I am trying to compile the latest (CVS) version of pwscf on IBM SP4 > machine. I get the following error message. > > > ( cd clib ; if test "make" = "" ; then make TLDEPS= all ; else > make TLDEPS= all ; fi ) > xlc_r -q64 -O2 -D__AIX -D__XLF -D__ESSL -D__MASS -D__MPI -D__PARA > -I../include -c c_mkdir.c > "c_mkdir.c", line 42.5: 1506-033 (S) Function F77_FUNC_ is not valid. > Function cannot return a function. > "c_mkdir.c", line 49.41: 1506-045 (S) Undeclared identifier length. > "c_mkdir.c", line 51.19: 1506-045 (S) Undeclared identifier dirname. > "c_mkdir.c", line 62.11: 1506-1332 (W) A function with return type > "int(*)(const char*,const int*)" may not return a value of type "int". > make: 1254-004 The error code from the last command is 1. > > > Stop. > make: 1254-004 The error code from the last command is 2. > > > Stop. > > > Any comments/suggestions ? did you (re-)run configure? axel. > > Thanks in advance, > Vivek > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Tue Jan 9 21:31:00 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 9 Jan 2007 15:31:00 -0500 Subject: [Pw_forum] nosym=.true. in molecular dynamics by PWSCF In-Reply-To: <989518.49761.qm@web54402.mail.yahoo.com> References: <989518.49761.qm@web54402.mail.yahoo.com> Message-ID: <7b6913e90701091231m1c743cb4o34a745802b477647@mail.gmail.com> On 1/9/07, Lawrence Lee wrote: > Dear all, > > Is it really necessary that when using PWSCF to do molecular dynamics, the > following: > > nosym=.true. > > had to be used? If yes, why? please look at the documentation of the nosym flag! pw.x tries to minimize the number of k-points needed by eliminating symmetry equivalent ones. those can be quite a few, if you have a very symmetric starting structure. as soon as you move atoms, however, those k-points may no longer be equivalent, but the code assumes that the number of k-points does not change during a calculation. similarly point group symmetries are used to speed up the calculation in several places. cheers, axel. > > Lawrence > > _______________________________________ > YM - ???? > ??????????????????????????????????????????? > http://messenger.yahoo.com.hk -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From chaohao2002 at 163.com Wed Jan 10 02:16:08 2007 From: chaohao2002 at 163.com (Chaohao Hu) Date: Wed, 10 Jan 2007 09:16:08 +0800 Subject: [Pw_forum] How to eliminate imaginary frequencies in phonon calculations Message-ID: <200701100916087344221@163.com> Dear Pwscf users, A few days ago, I performed phonon calculations for two proposed structure of Na2BeH4. In my calculated results, there are no imaginary frequencies in the structure with low symmetry, but it appeared in another structure with orthorhombic symmetry. although I performed "vc-relax" calculation on it at 0.0 GPa, they can not be eliminated at all after finishing the phonon calculation. How to solve this problem? Does it mean that the high-symmetry structure is not stable if these imaginary frequencies exist indeed. What's the other criterions that can evaluate the thermal stability of a certain system? My input file and output file for phdos are enclosed as a compressed file here. I hope you can give me some useful hints. Thanks in advance. Best regards, C.H. 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MW%R-USO=V_[30;Q]]=<_OSMIWUU?F1U.S>G[CP?QX3,"/T?SA]__\=L_??O[ M[_YX]7_>W>^EE[`/+5Z^FU)ZE M5^=0]2B]6H+U)REZ&W&X?_0M&>I\QY\-]AS9.=@YKN<;_C2%SZE``@^WV7_\ MZD!\AU]Z;OT4RQ:]/'^^/[#6IX^C[[$=$O3T^?/?'Y)\#/"D[,5S"O%JQI#U M^!N"/,?QI,Q(*M,4A\6QA\_+*8KCYX<['?_^-S=?/9TM-\XF#M,,S\+AFVMF MU9]=WW,4.\S7?M`V$Y"',ZG?18.WZ)33\).K&5F MUT"0[?"JZIQ=Y1SFU8SF*64SGE),36F;=N1-$["F&D[W/L0Y.O_NE?R M;[_[TU[#K[\\WGW:V_:[_]S;1US5*[_:#O]]_:_NQ"_7Y;I Dear all, Since the displacive phase transition is second order, why some first order transitions are considered to be induced by the displacive instabilities? would you please give me some advices or some reference papers about this? best regards __________________________________________________ ??????????????? http://cn.mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070109/953bb581/attachment.htm From prasad.surendra at gmail.com Wed Jan 10 06:57:25 2007 From: prasad.surendra at gmail.com (surendra prasad) Date: Wed, 10 Jan 2007 11:27:25 +0530 Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1300 - 8 msgs In-Reply-To: <20070109212201.11320.13366.Mailman@democritos.sissa.it> References: <20070109212201.11320.13366.Mailman@democritos.sissa.it> Message-ID: Dear Sirs, I am a faculty member in the department of physics, Banaras Hindu University (B. H. U.), Varanasi. I want to initiate some works in the field of material modelling. i am having some queries. By using quantum espresso, is it possible to find *fits *for interatomic potential for the iron-chromiun (Fe-Cr) systems or any other systems. i will highly appreciate if anyone can clearify my doubts. Regards ---surendra Surendra Prasad, Department of Physics, Centre of Advanced Studies, B. H. U., Varanasi - 221005. -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070110/277d32cb/attachment.htm From ezadshojaee at hotmail.com Wed Jan 10 10:39:27 2007 From: ezadshojaee at hotmail.com (Ezad Shojaee) Date: Wed, 10 Jan 2007 09:39:27 +0000 Subject: [Pw_forum] NaN in Phonon Message-ID: hi dear Mr. Giannozzi , this is my input file for ph.x : &inputph tr2_ph=1.0d-12, prefix='...', ldisp=.true., nq1=4, nq2=4, nq3=4 amass(1)=..., amass(2)=..., outdir='....', fildyn='....', recover=.true. / in my case , in the 10th point in the grid , there are 18 irriducable representations and the code gave NaN in the 15th representation in the first iteration, then continued the 16-17-18th representations and converged normally so this is where it seems to be in a round : Representation # 18 mode # 18 Self-consistent Calculation iter # 12 total cpu time : 1952.6 secs av.it.: 1.0 thresh= 0.405E-07 alpha_mix = 0.700 |ddv_scf|^2 = 0.164E-12 End of self-consistent calculation Convergence has been achieved Number of q in the star = 4 List of q in the star: 1 0.500000000 0.000000000 0.000000000 2 -0.500000000 0.000000000 0.000000000 3 0.000000000 0.500000000 0.000000000 4 0.000000000 -0.500000000 0.000000000 what's your opinion ? _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ From halim_said04 at yahoo.fr Wed Jan 10 13:46:46 2007 From: halim_said04 at yahoo.fr (halim said) Date: Wed, 10 Jan 2007 13:46:46 +0100 (CET) Subject: [Pw_forum] problem compiling espresso-3.2 in SGI origin machine In-Reply-To: Message-ID: <20070110124647.85726.qmail@web23309.mail.ird.yahoo.com> Dear Axel, Thank you for your reply and for the advices that you gave me, I would like to say that I checked all what you said me, I checked Modules/make.depend contains the line: bfgs_module.o : basic_algebra_routines.o and it exists But infortunately I don't have f95, I have just f90, and the problem is still the same, I could not run with success the code, is there please other way in order to solve this problem, Thank you in advances for your help. Regards, Halim Axel Kohlmeyer a ?crit : On Tue, 9 Jan 2007, halim said wrote: HS> Dear Axel and Paolo, HS> HS> I am compiling espress-3.2 code in SGI origin machine, when I am taping be prepared to suffer. SGI origins have inflicted a lot of pain on me at times. good thing, they are more or less obsolete these days... HS> ./configure HS> HS> every thing is fine. configure does next to no consistency checking on the fortran side, so a completed configure does not have much meaning except that it is required. simply using and adapting an existing make.sys template is no longer sufficient. HS> but when I am taping gmake all, HS> HS> there are some errors appear, how to deal with this problem in order HS> to success for compiling the code. HS> HS> Below I am attaching configure and the errors which appeared after gmake HS> HS> Your help and support are highly appreciate. HS> HS> Regards, HS> HS> Halim HS> HS> [...] HS> -------------------------------------------------------------------- HS> HS> The following libraries have been found: HS> BLAS_LIBS=-lcomplib.sgimath HS> LAPACK_LIBS=../flib/lapack.a HS> FFT_LIBS= HS> MPI_LIBS=-lmpi HS> Parallel environment detected successfully. HS> Configured for compilation of parallel executables. HS> configure: success ok. looking normal up to here... HS> espresso.3-2> gmake all HS> gmake[1]: Leaving directory `/h2/home/espresso-3.2/iotk' HS> ( cd Modules ; if test "gmake" = "" ; then make TLDEPS= all ; \ HS> else gmake TLDEPS= all ; fi ) HS> gmake[1]: Entering directory `/h2/home/espresso-3.2/Modules' HS> f90 -mips4 -64 -O2 -r10000 -r8 -ftpp -macro_expand -D__COMPLIB -D__ORIGIN -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH -I../CPV -c io_global.f90 HS> This product's license is for 2 CPU's; Your system has 7 CPU's hmmmmmm.... looks like you need to pay SGI some more money. ;-) but that should apply only at run-time. HS> HS> MODULE bfgs_module HS> ^ HS> f90-855 f90: ERROR BFGS_MODULE, File = bfgs_module.f90, Line = 9, Column = 8 HS> The compiler has detected errors in module "BFGS_MODULE". No module information file will be created for this module. HS> HS> IF ( ( grad(:) .dot. step(:) ) > 0.D0 ) THEN HS> ^ HS> f90-318 f90: ERROR GDIIS_STEP, File = bfgs_module.f90, Line = 464, Column = 26 HS> The operator "dot" has not been declared as a user defined operator. ok. this means that either the sgi compiler is not sufficiently fortran 95 compliant or, that the prerequisite module basic_algebra_routines.f90 has not been compiled correctly. please do a 'gmake clean ; gmake all' to make sure that you are not continuing from a previous broken compile. please also make sure that Modules/make.depend contains the line: bfgs_module.o : basic_algebra_routines.o and if that does not help, i'd try to change F90 = f90 MPIF90 = f90 LD = f90 to F90 = f95 MPIF90 = f95 LD = f95 in make.sys axel. HS> HS> step(:) = - ( inv_hess(:,:) .times. grad(:) ) HS> ^ HS> f90-318 f90: ERROR GDIIS_STEP, File = bfgs_module.f90, Line = 469, Column = 42 HS> HS> f90: MIPSpro Fortran 90 Version 7.3 (f52) Mon Jan 8, 2007 11:53:12 HS> f90: 1008 source lines HS> f90: 3 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s) HS> cf90: "explain cf90-message number" gives more information about each message HS> gmake[1]: *** [bfgs_module.o] Error 2 HS> gmake[1]: Leaving directory `/h2/home/espresso-3.2/Modules' HS> gmake: *** [mods] Error 2 HS> HS> HS> HS> __________________________________________________ HS> Do You Yahoo!? HS> En finir avec le spam? Yahoo! Mail vous offre la meilleure protection possible contre les messages non sollicit?s HS> http://mail.yahoo.fr Yahoo! Mail -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum __________________________________________________ Do You Yahoo!? En finir avec le spam? Yahoo! Mail vous offre la meilleure protection possible contre les messages non sollicit?s http://mail.yahoo.fr Yahoo! Mail -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070110/022774ac/attachment.htm From baroni at sissa.it Wed Jan 10 14:35:23 2007 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 10 Jan 2007 14:35:23 +0100 Subject: [Pw_forum] about the displacive instabilities In-Reply-To: <20070109075444.49217.qmail@web15611.mail.cnb.yahoo.com> References: <20070109075444.49217.qmail@web15611.mail.cnb.yahoo.com> Message-ID: <5CADC870-85F0-46CD-A24D-5F8C6BB1DDB1@sissa.it> Hi, Li Yan. This is a good question which, I am sure, has been addressed many times in many places. There are for sure a number of textbook references. The only one that occurs to me by heart is unfortunately in French [N. Boccara, Symmetries brisees (Hermann, Paris, 1976)]. Any textbook dealing with Landau's theory of phase transitions would do. The literature in the field looks often more complicated than it actually should. You may want to take a glance at a pair of old papers of mine where your issue is addressed using minimum theoretical background. NARDELLI MB, BARONI S, GIANNOZZI P HIGH-PRESSURE LOW-SYMMETRY PHASES OF CESIUM-HALIDES PHYSICAL REVIEW B 51 (13): 8060-8068 APR 1 1995 NARDELLI MB, BARONI S, GIANNOZZI P PHONON SOFTENING AND HIGH-PRESSURE LOW-SYMMETRY PHASES OF CESIUM IODIDE PHYSICAL REVIEW LETTERS 69 (7): 1069-1072 AUG 17 1992 Hope you will find something useful in them. If not, I will try to write a short explanation, but for this you will have to wait for me to find 1-2 hours of spare time, which is not going to be tomorrow ... Cheers - Stefano On Jan 9, 2007, at 8:54 AM, li yan wrote: > Dear all, > Since the displacive phase transition is second order, why > some first order transitions are considered to be induced by the > displacive instabilities? would you please give me some advices or > some reference papers about this? > > best regards > __________________________________________________ > ??????????????? > http://cn.mail.yahoo.com --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070110/38841172/attachment.htm From sagars_daya at yahoo.co.in Wed Jan 10 17:10:35 2007 From: sagars_daya at yahoo.co.in (daya sagar) Date: Wed, 10 Jan 2007 16:10:35 +0000 (GMT) Subject: [Pw_forum] Can anyone explain my errors in vasp Message-ID: <643582.91164.qm@web8314.mail.in.yahoo.com> Hi, My name is Dayasagar. I have been using VASP to do abinitio DFT simulations of GaN NWs with 225 eV encut and vacuum = 2.6nm along X and Y directions. Can anyone please explain me the following error. My Run went on till 37th ionic iteration and showed the following error. ------------------------------------------------------------------------------------------------------------------- DAV: 35 -0.439193918571E+05 0.19144E+06 -0.24729E+05 19376 0.953E+02 0.234E+02 DAV: 36 -0.274732624636E+06 -0.23081E+06 -0.27733E+06 16696 0.116E+04 0.196E+02 DAV: 37 -0.972624721307E+05 0.17747E+06 -0.31438E+05 19200 0.120E+03 0.255E+02 forrtl: Permission denied getRegFromUnwindContext: Can't get Gr0 from UnwindContext, using 0 forrtl: severe (9): permission to access file denied, unit 8, file /m/utl0214/daya/gan/nanowires/100-axis/44ga-56n-dia2.0nm/vacuum-30/OUTCAR Image PC Routine Line Source vasp.4.6.26_ipf_m 4000000000727E80 Unknown Unknown Unknown vasp.4.6.26_ipf_m 4000000000726F90 Unknown Unknown Unknown vasp.4.6.26_ipf_m 40000000006BB120 Unknown Unknown Unknown vasp.4.6.26_ipf_m 400000000062DAC0 Unknown Unknown Unknown vasp.4.6.26_ipf_m 400000000062EA30 Unknown Unknown Unknown vasp.4.6.26_ipf_m 400000000064CC00 Unknown Unknown Unknown vasp.4.6.26_ipf_m 4000000000618340 Unknown Unknown Unknown vasp.4.6.26_ipf_m 40000000004F29B0 Unknown Unknown Unknown vasp.4.6.26_ipf_m 400000000007CCF0 Unknown Unknown Unknown vasp.4.6.26_ipf_m 4000000000005DD0 Unknown Unknown Unknown libc.so.6.1 2000000000DF3430 Unknown Unknown Unknown vasp.4.6.26_ipf_m 40000000000057C0 Unknown Unknown Unknown FATAL ERROR on MPI node 4 (ipf232): GM send to MPI node 0 (ipf235 [00:60:dd:48:cb:55]) failed: status 17 (target port was closed) the peer process has not started, has exited or is dead Small/Ctrl message completion error! mpiexec: Warning: accept_abort_conn: MPI_Abort from IP 10.16.1.84, killing all. mpiexec: killall: caught signal 15 (Terminated). mpiexec: kill_tasks: killing all tasks. wait_tasks: waiting for ipf235 ipf235 ipf234 ipf234 ipf232 ipf232 ipf231 ipf231 FATAL ERROR on MPI node 2 (ipf234): GM send to MPI node 0 (ipf235 [00:60:dd:48:cb:55]) failed: status 17 (target port was closed) the peer process has not started, has exited or is dead Small/Ctrl message completion error! mpiexec: process_kill_event: evt 18 task 0 on ipf235. mpiexec: process_kill_event: evt 19 task 1 on ipf235. mpiexec: process_kill_event: evt 20 task 2 on ipf234. mpiexec: process_kill_event: evt 24 task 6 on ipf231. mpiexec: process_kill_event: evt 25 task 7 on ipf231. mpiexec: process_kill_event: evt 21 task 3 on ipf234. mpiexec: process_obit_event: evt 14 task 6 on ipf231 stat 265. mpiexec: process_obit_event: evt 16 task 7 on ipf231 stat 265. mpiexec: process_kill_event: evt 22 task 4 on ipf232. mpiexec: process_kill_event: evt 23 task 5 on ipf232. wait_tasks: waiting for ipf235 ipf235 ipf234 ipf234 ipf232 ipf232 mpiexec: process_obit_event: evt 12 task 4 on ipf232 stat 255. mpiexec: process_obit_event: evt 17 task 5 on ipf232 stat 265. mpiexec: process_obit_event: evt 13 task 2 on ipf234 stat 265. mpiexec: process_obit_event: evt 15 task 3 on ipf234 stat 265. wait_tasks: waiting for ipf235 ipf235 -------------------------------------------------------------------------------------------------------------------- Thanks. Regards, Daya Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070110/37e0cd1a/attachment.htm From akohlmey at cmm.chem.upenn.edu Wed Jan 10 20:39:50 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 10 Jan 2007 14:39:50 -0500 Subject: [Pw_forum] Can anyone explain my errors in vasp In-Reply-To: <643582.91164.qm@web8314.mail.in.yahoo.com> References: <643582.91164.qm@web8314.mail.in.yahoo.com> Message-ID: <45A54106.1010505@cmm.chem.upenn.edu> daya sagar wrote: > Hi, > > My name is Dayasagar. I have been using VASP to do abinitio DFT please note, that this is a forum for the quantum espresso package, see http://www.quantum-espresso.org/ (you might want to check it out). ;-) > simulations of GaN NWs with 225 eV encut and vacuum = 2.6nm along X and > Y directions. Can anyone please explain me the following error. > My Run went on till 37th ionic iteration and showed the following error. > ------------------------------------------------------------------------------------------------------------------- > DAV: 35 -0.439193918571E+05 0.19144E+06 -0.24729E+05 19376 > 0.953E+02 0.234E+02 > DAV: 36 -0.274732624636E+06 -0.23081E+06 -0.27733E+06 16696 > 0.116E+04 0.196E+02 > DAV: 37 -0.972624721307E+05 0.17747E+06 -0.31438E+05 19200 > 0.120E+03 0.255E+02 here's the origin of your problem (and it has nothing to do with VASP): > forrtl: Permission denied > getRegFromUnwindContext: Can't get Gr0 from UnwindContext, using 0 > forrtl: severe (9): permission to access file denied, unit 8, file well, it looks as it you are either running out disk quota or your write access to your disk has been disabled. axel. > /m/utl0214/daya/gan/nanowires/100-axis/44ga-56n-dia2.0nm/vacuum-30/OUTCAR > Image PC Routine Line Source > vasp.4.6.26_ipf_m 4000000000727E80 Unknown Unknown Unknown > vasp.4.6.26_ipf_m 4000000000726F90 Unknown Unknown Unknown > vasp.4.6.26_ipf_m 40000000006BB120 Unknown Unknown Unknown > vasp.4.6.26_ipf_m 400000000062DAC0 Unknown Unknown Unknown > vasp.4.6.26_ipf_m 400000000062EA30 Unknown Unknown Unknown > vasp.4.6.26_ipf_m 400000000064CC00 Unknown Unknown Unknown > vasp.4.6.26_ipf_m 4000000000618340 Unknown Unknown Unknown > vasp.4.6.26_ipf_m 40000000004F29B0 Unknown Unknown Unknown > vasp.4.6.26_ipf_m 400000000007CCF0 Unknown Unknown Unknown > vasp.4.6.26_ipf_m 4000000000005DD0 Unknown Unknown Unknown > libc.so.6.1 2000000000DF3430 Unknown Unknown Unknown > vasp.4.6.26_ipf_m 40000000000057C0 Unknown Unknown Unknown > FATAL ERROR on MPI node 4 (ipf232): GM send to MPI node 0 (ipf235 > [00:60:dd:48:cb:55]) failed: status 17 (target port was closed) the peer > process has not started, has exited or is dead > Small/Ctrl message completion error! > mpiexec: Warning: accept_abort_conn: MPI_Abort from IP 10.16.1.84, > killing all. > mpiexec: killall: caught signal 15 (Terminated). > mpiexec: kill_tasks: killing all tasks. > wait_tasks: waiting for ipf235 ipf235 ipf234 ipf234 ipf232 ipf232 ipf231 > ipf231 > FATAL ERROR on MPI node 2 (ipf234): GM send to MPI node 0 (ipf235 > [00:60:dd:48:cb:55]) failed: status 17 (target port was closed) the peer > process has not started, has exited or is dead > Small/Ctrl message completion error! > mpiexec: process_kill_event: evt 18 task 0 on ipf235. > mpiexec: process_kill_event: evt 19 task 1 on ipf235. > mpiexec: process_kill_event: evt 20 task 2 on ipf234. > mpiexec: process_kill_event: evt 24 task 6 on ipf231. > mpiexec: process_kill_event: evt 25 task 7 on ipf231. > mpiexec: process_kill_event: evt 21 task 3 on ipf234. > mpiexec: process_obit_event: evt 14 task 6 on ipf231 stat 265. > mpiexec: process_obit_event: evt 16 task 7 on ipf231 stat 265. > mpiexec: process_kill_event: evt 22 task 4 on ipf232. > mpiexec: process_kill_event: evt 23 task 5 on ipf232. > wait_tasks: waiting for ipf235 ipf235 ipf234 ipf234 ipf232 ipf232 > mpiexec: process_obit_event: evt 12 task 4 on ipf232 stat 255. > mpiexec: process_obit_event: evt 17 task 5 on ipf232 stat 265. > mpiexec: process_obit_event: evt 13 task 2 on ipf234 stat 265. > mpiexec: process_obit_event: evt 15 task 3 on ipf234 stat 265. > wait_tasks: waiting for ipf235 ipf235 > -------------------------------------------------------------------------------------------------------------------- > > Thanks. > > Regards, > Daya > > > Send free SMS to your Friends on Mobile from your Yahoo! Messenger. > Download Now! http://messenger.yahoo.com/download.php > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Wed Jan 10 22:25:25 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 10 Jan 2007 16:25:25 -0500 Subject: [Pw_forum] problem compiling espresso-3.2 in SGI origin machine In-Reply-To: <20070110124647.85726.qmail@web23309.mail.ird.yahoo.com> References: <20070110124647.85726.qmail@web23309.mail.ird.yahoo.com> Message-ID: <45A559C5.3020407@cmm.chem.upenn.edu> halim said wrote: > Dear Axel, > > Thank you for your reply and for the advices that you gave me, I would > like to say that I checked all what you said me, > I checked Modules/make.depend > contains the line: > > bfgs_module.o : basic_algebra_routines.o and it exists > > But infortunately I don't have f95, I have just f90, and the problem is > still the same, I could not run with success the code, is there please > other way in order to solve this problem, the f95 suggestion was just a wild guess (it has worked for me on an IBM AIX machine once). for further debugging, i'd need access to such an SGI Origin in order to narrow down the problem and ideally find a workaround or a solution. to be frank, i don't think a machine like this is worth the effort anymore. one option you can try, is to install the g95 compiler from http://ftp.g95.org, it is supposed to work with QE on x86-linux, but... axel. > > Thank you in advances for your help. > > Regards, > > Halim > > */Axel Kohlmeyer /* a ?crit : > > On Tue, 9 Jan 2007, halim said wrote: > > HS> Dear Axel and Paolo, > HS> > HS> I am compiling espress-3.2 code in SGI origin machine, when I am > taping > > be prepared to suffer. SGI origins have inflicted a lot of > pain on me at times. good thing, they are more or less > obsolete these days... > > HS> ./configure > HS> > HS> every thing is fine. > > configure does next to no consistency checking on the fortran > side, so a completed configure does not have much meaning > except that it is required. simply using and adapting > an existing make.sys template is no longer sufficient. > > HS> but when I am taping gmake all, > HS> > HS> there are some errors appear, how to deal with this problem in order > HS> to success for compiling the code. > HS> > HS> Below I am attaching configure and the errors which appeared > after gmake > HS> > HS> Your help and support are highly appreciate. > HS> > HS> Regards, > HS> > HS> Halim > HS> > HS> > > [...] > > HS> -------------------------------------------------------------------- > HS> > HS> The following libraries have been found: > HS> BLAS_LIBS=-lcomplib.sgimath > HS> LAPACK_LIBS=../flib/lapack.a > HS> FFT_LIBS= > HS> MPI_LIBS=-lmpi > HS> Parallel environment detected successfully. > HS> Configured for compilation of parallel executables. > HS> configure: success > > ok. looking normal up to here... > > HS> espresso.3-2> gmake all > HS> gmake[1]: Leaving directory `/h2/home/espresso-3.2/iotk' > HS> ( cd Modules ; if test "gmake" = "" ; then make TLDEPS= all ; \ > HS> else gmake TLDEPS= all ; fi ) > HS> gmake[1]: Entering directory `/h2/home/espresso-3.2/Modules' > HS> f90 -mips4 -64 -O2 -r10000 -r8 -ftpp -macro_expand -D__COMPLIB > -D__ORIGIN -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA > -I../include -I./ -I../Modules -I../iotk/src -I../PW -I../PH > -I../CPV -c io_global.f90 > > > HS> This product's license is for 2 CPU's; Your system has 7 CPU's > > > hmmmmmm.... looks like you need to pay SGI some more money. ;-) > but that should apply only at run-time. > > HS> > HS> MODULE bfgs_module > HS> ^ > HS> f90-855 f90: ERROR BFGS_MODULE, File = bfgs_module.f90, Line = > 9, Column = 8 > HS> The compiler has detected errors in module "BFGS_MODULE". No > module information file will be created for this module. > HS> > HS> IF ( ( grad(:) .dot. step(:) ) > 0.D0 ) THEN > HS> ^ > HS> f90-318 f90: ERROR GDIIS_STEP, File = bfgs_module.f90, Line = > 464, Column = 26 > HS> The operator "dot" has not been declared as a user defined operator. > > ok. this means that either the sgi compiler is not sufficiently > fortran 95 compliant or, that the prerequisite module > basic_algebra_routines.f90 has not been compiled correctly. > > please do a 'gmake clean ; gmake all' to make sure that you > are not continuing from a previous broken compile. > please also make sure that Modules/make.depend > contains the line: > > bfgs_module.o : basic_algebra_routines.o > > and if that does not help, i'd try to change > > F90 = f90 > MPIF90 = f90 > LD = f90 > > to > > F90 = f95 > MPIF90 = f95 > LD = f95 > > in make.sys > > > axel. > > HS> > HS> step(:) = - ( inv_hess(:,:) .times. grad(:) ) > HS> ^ > HS> f90-318 f90: ERROR GDIIS_STEP, File = bfgs_module.f90, Line = > 469, Column = 42 > HS> > HS> f90: MIPSpro Fortran 90 Version 7.3 (f52) Mon Jan 8, 2007 11:53:12 > HS> f90: 1008 source lines > HS> f90: 3 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s) > HS> cf90: "explain cf90-message number" gives more information about > each message > HS> gmake[1]: *** [bfgs_module.o] Error 2 > HS> gmake[1]: Leaving directory `/h2/home/espresso-3.2/Modules' > HS> gmake: *** [mods] Error 2 > HS> > HS> > HS> > HS> __________________________________________________ > HS> Do You Yahoo!? > HS> En finir avec le spam? Yahoo! Mail vous offre la meilleure > protection possible contre les messages non sollicit?s > HS> http://mail.yahoo.fr Yahoo! Mail > > -- > ======================================================================= > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ======================================================================= > If you make something idiot-proof, the universe creates a better idiot. > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > __________________________________________________ > Do You Yahoo!? > En finir avec le spam? Yahoo! Mail vous offre la meilleure protection > possible contre les messages non sollicit?s > http://mail.yahoo.fr Yahoo! Mail > -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From sanjeev0302 at rediffmail.com Thu Jan 11 05:00:21 2007 From: sanjeev0302 at rediffmail.com (Sanjeev Kumar Gupta) Date: 11 Jan 2007 04:00:21 -0000 Subject: [Pw_forum] Can anyone explain my errors in vasp Message-ID: <20070111040021.1747.qmail@webmail58.rediffmail.com> ? Dear Daya, This is forum for Quantum-Expresso user. Sorry, for your help, but if you search on google for VASP, then you can also find porum for search. It is avilable. Regards s K Gupta On Thu, 11 Jan 2007 Axel Kohlmeyer wrote : >daya sagar wrote: >>Hi, >> >> My name is Dayasagar. I have been using VASP to do abinitio DFT > >please note, that this is a forum for the quantum espresso package, >see http://www.quantum-espresso.org/ (you might want to check it out). ;-) > >>simulations of GaN NWs with 225 eV encut and vacuum = 2.6nm along X and Y directions. Can anyone please explain me the following error. >>My Run went on till 37th ionic iteration and showed the following error. >>------------------------------------------------------------------------------------------------------------------- >>DAV: 35 -0.439193918571E+05 0.19144E+06 -0.24729E+05 19376 0.953E+02 0.234E+02 >>DAV: 36 -0.274732624636E+06 -0.23081E+06 -0.27733E+06 16696 0.116E+04 0.196E+02 >>DAV: 37 -0.972624721307E+05 0.17747E+06 -0.31438E+05 19200 0.120E+03 0.255E+02 > >here's the origin of your problem (and it has nothing to do with VASP): > >>forrtl: Permission denied >>getRegFromUnwindContext: Can't get Gr0 from UnwindContext, using 0 >>forrtl: severe (9): permission to access file denied, unit 8, file > >well, it looks as it you are either running out disk quota or >your write access to your disk has been disabled. > >axel. > > >>/m/utl0214/daya/gan/nanowires/100-axis/44ga-56n-dia2.0nm/vacuum-30/OUTCAR >>Image PC Routine Line Source >>vasp.4.6.26_ipf_m 4000000000727E80 Unknown Unknown Unknown >>vasp.4.6.26_ipf_m 4000000000726F90 Unknown Unknown Unknown >>vasp.4.6.26_ipf_m 40000000006BB120 Unknown Unknown Unknown >>vasp.4.6.26_ipf_m 400000000062DAC0 Unknown Unknown Unknown >>vasp.4.6.26_ipf_m 400000000062EA30 Unknown Unknown Unknown >>vasp.4.6.26_ipf_m 400000000064CC00 Unknown Unknown Unknown >>vasp.4.6.26_ipf_m 4000000000618340 Unknown Unknown Unknown >>vasp.4.6.26_ipf_m 40000000004F29B0 Unknown Unknown Unknown >>vasp.4.6.26_ipf_m 400000000007CCF0 Unknown Unknown Unknown >>vasp.4.6.26_ipf_m 4000000000005DD0 Unknown Unknown Unknown >>libc.so.6.1 2000000000DF3430 Unknown Unknown Unknown >>vasp.4.6.26_ipf_m 40000000000057C0 Unknown Unknown Unknown >>FATAL ERROR on MPI node 4 (ipf232): GM send to MPI node 0 (ipf235 [00:60:dd:48:cb:55]) failed: status 17 (target port was closed) the peer process has not started, has exited or is dead >>Small/Ctrl message completion error! >>mpiexec: Warning: accept_abort_conn: MPI_Abort from IP 10.16.1.84, killing all. >>mpiexec: killall: caught signal 15 (Terminated). >>mpiexec: kill_tasks: killing all tasks. >>wait_tasks: waiting for ipf235 ipf235 ipf234 ipf234 ipf232 ipf232 ipf231 ipf231 >>FATAL ERROR on MPI node 2 (ipf234): GM send to MPI node 0 (ipf235 [00:60:dd:48:cb:55]) failed: status 17 (target port was closed) the peer process has not started, has exited or is dead >>Small/Ctrl message completion error! >>mpiexec: process_kill_event: evt 18 task 0 on ipf235. >>mpiexec: process_kill_event: evt 19 task 1 on ipf235. >>mpiexec: process_kill_event: evt 20 task 2 on ipf234. >>mpiexec: process_kill_event: evt 24 task 6 on ipf231. >>mpiexec: process_kill_event: evt 25 task 7 on ipf231. >>mpiexec: process_kill_event: evt 21 task 3 on ipf234. >>mpiexec: process_obit_event: evt 14 task 6 on ipf231 stat 265. >>mpiexec: process_obit_event: evt 16 task 7 on ipf231 stat 265. >>mpiexec: process_kill_event: evt 22 task 4 on ipf232. >>mpiexec: process_kill_event: evt 23 task 5 on ipf232. >>wait_tasks: waiting for ipf235 ipf235 ipf234 ipf234 ipf232 ipf232 >>mpiexec: process_obit_event: evt 12 task 4 on ipf232 stat 255. >>mpiexec: process_obit_event: evt 17 task 5 on ipf232 stat 265. >>mpiexec: process_obit_event: evt 13 task 2 on ipf234 stat 265. >>mpiexec: process_obit_event: evt 15 task 3 on ipf234 stat 265. >>wait_tasks: waiting for ipf235 ipf235 >>-------------------------------------------------------------------------------------------------------------------- >> >>Thanks. >> >>Regards, >>Daya >> >> >>Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php >> > >-- ======================================================================= >Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania >Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 >tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 >======================================================================= >If you make something idiot-proof, the universe creates a better idiot. >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum ==================================================== Sanjeev Kumar Gupta Junior Research Fellow (DAE-BRNS) Computational Condensed Matter Physics Lab.(CCMP) Department of Physics, Faculty of Science, The M.S.University of Baroda, Vadodara - 390 002. Ph.No: +91-265-279 5339 (O) extn: 30-25 mobile:09374616019 Email: sanjeev0302 at rediffmail.com sanjeev0302 at yahoo.co.in skgupta-phy at msubaroda.ac.in ==================================================== Residential Address- Dr. Vikram Sarabhai Hall, Room No.-95, Boys' Hostel,M.S.University Campus, Pratapgunj,Vadodara-390 002,Gujarat,INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070111/5f246dd1/attachment.htm From rudrabnrj at gmail.com Thu Jan 11 06:20:02 2007 From: rudrabnrj at gmail.com (Rudra) Date: Thu, 11 Jan 2007 10:50:02 +0530 Subject: [Pw_forum] error Message-ID: <2e36f8e50701102120k65d30bdn2b3fdb8c230d8bdc@mail.gmail.com> friends, i am workin in noncolin magnetism and gave my file as: ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, ecutwfc =18.0 ,nelec=1 starting_magnetization(1)=.5, noncolin=.true. / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 this is ending with the error: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from atomic_wfc_nc : error # 1 too many wfcs can anyone tell me the possible origin? thanks in advance -- rudra Please, if possible, don't send me MS Word or PowerPoint attachments ---------- Why?See: http://www.gnu.org/philosophy/no-word-attachments.html have a nice time -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070111/201744ca/attachment.htm From rudrabnrj at gmail.com Thu Jan 11 11:49:36 2007 From: rudrabnrj at gmail.com (Rudra) Date: Thu, 11 Jan 2007 16:19:36 +0530 Subject: [Pw_forum] Can anyone explain my errors in vasp In-Reply-To: <20070111040021.1747.qmail@webmail58.rediffmail.com> References: <20070111040021.1747.qmail@webmail58.rediffmail.com> Message-ID: <2e36f8e50701110249v7629a86k63626e120bb2568d@mail.gmail.com> if u r a registrer vasp user then join vasp forum instead On 11 Jan 2007 04:00:21 -0000, Sanjeev Kumar Gupta < sanjeev0302 at rediffmail.com> wrote: > > > Dear Daya, > This is forum for Quantum-Expresso user. Sorry, for your help, but if you > search on google for VASP, then you can also find porum for search. It is > avilable. > Regards > s K Gupta > > On Thu, 11 Jan 2007 Axel Kohlmeyer wrote : > > >daya sagar wrote: > >>Hi, > >> > >> My name is Dayasagar. I have been using VASP to do abinitio DFT > > > >please note, that this is a forum for the quantum espresso package, > >see http://www.quantum-espresso.org/ (you might want to check it out). > ;-) > > > >>simulations of GaN NWs with 225 eV encut and vacuum = 2.6nm along X and > Y directions. Can anyone please explain me the following error. > >>My Run went on till 37th ionic iteration and showed the following error. > > >>------------------------------------------------------------------------------------------------------------------- > >>DAV: 35 -0.439193918571E+05 0.19144E+06 -0.24729E+05 19376 > 0.953E+02 0.234E+02 > >>DAV: 36 -0.274732624636E+06 -0.23081E+06 -0.27733E+06 16696 > 0.116E+04 0.196E+02 > >>DAV: 37 -0.972624721307E+05 0.17747E+06 -0.31438E+05 19200 > 0.120E+03 0.255E+02 > > > >here's the origin of your problem (and it has nothing to do with VASP): > > > >>forrtl: Permission denied > >>getRegFromUnwindContext: Can't get Gr0 from UnwindContext, using 0 > >>forrtl: severe (9): permission to access file denied, unit 8, file > > > >well, it looks as it you are either running out disk quota or > >your write access to your disk has been disabled. > > > >axel. > > > > > >>/m/utl0214/daya/gan/nanowires/100-axis/44ga-56n-dia2.0nm > /vacuum-30/OUTCAR > >>Image PC Routine Line > Source > >>vasp.4.6.26_ipf_m 4000000000727E80 Unknown Unknown > Unknown > >>vasp.4.6.26_ipf_m 4000000000726F90 Unknown Unknown > Unknown > >>vasp.4.6.26_ipf_m 40000000006BB120 Unknown Unknown > Unknown > >>vasp.4.6.26_ipf_m 400000000062DAC0 Unknown Unknown > Unknown > >>vasp.4.6.26_ipf_m 400000000062EA30 Unknown Unknown > Unknown > >>vasp.4.6.26_ipf_m 400000000064CC00 Unknown Unknown > Unknown > >>vasp.4.6.26_ipf_m 4000000000618340 Unknown Unknown > Unknown > >>vasp.4.6.26_ipf_m 40000000004F29B0 Unknown Unknown > Unknown > >>vasp.4.6.26_ipf_m 400000000007CCF0 Unknown Unknown > Unknown > >>vasp.4.6.26_ipf_m 4000000000005DD0 Unknown Unknown > Unknown > >>libc.so.6.1 2000000000DF3430 Unknown Unknown > Unknown > >>vasp.4.6.26_ipf_m 40000000000057C0 Unknown Unknown > Unknown > >>FATAL ERROR on MPI node 4 (ipf232): GM send to MPI node 0 (ipf235 > [00:60:dd:48:cb:55]) failed: status 17 (target port was closed) the peer > process has not started, has exited or is dead > >>Small/Ctrl message completion error! > >>mpiexec: Warning: accept_abort_conn: MPI_Abort from IP 10.16.1.84, > killing all. > >>mpiexec: killall: caught signal 15 (Terminated). > >>mpiexec: kill_tasks: killing all tasks. > >>wait_tasks: waiting for ipf235 ipf235 ipf234 ipf234 ipf232 ipf232 ipf231 > ipf231 > >>FATAL ERROR on MPI node 2 (ipf234): GM send to MPI node 0 (ipf235 > [00:60:dd:48:cb:55]) failed: status 17 (target port was closed) the peer > process has not started, has exited or is dead > >>Small/Ctrl message completion error! > >>mpiexec: process_kill_event: evt 18 task 0 on ipf235. > >>mpiexec: process_kill_event: evt 19 task 1 on ipf235. > >>mpiexec: process_kill_event: evt 20 task 2 on ipf234. > >>mpiexec: process_kill_event: evt 24 task 6 on ipf231. > >>mpiexec: process_kill_event: evt 25 task 7 on ipf231. > >>mpiexec: process_kill_event: evt 21 task 3 on ipf234. > >>mpiexec: process_obit_event: evt 14 task 6 on ipf231 stat 265. > >>mpiexec: process_obit_event: evt 16 task 7 on ipf231 stat 265. > >>mpiexec: process_kill_event: evt 22 task 4 on ipf232. > >>mpiexec: process_kill_event: evt 23 task 5 on ipf232. > >>wait_tasks: waiting for ipf235 ipf235 ipf234 ipf234 ipf232 ipf232 > >>mpiexec: process_obit_event: evt 12 task 4 on ipf232 stat 255. > >>mpiexec: process_obit_event: evt 17 task 5 on ipf232 stat 265. > >>mpiexec: process_obit_event: evt 13 task 2 on ipf234 stat 265. > >>mpiexec: process_obit_event: evt 15 task 3 on ipf234 stat 265. > >>wait_tasks: waiting for ipf235 ipf235 > > >>-------------------------------------------------------------------------------------------------------------------- > >> > >>Thanks. > >> > >>Regards, > >>Daya > >> > >> > >>Send free SMS to your Friends on Mobile from your Yahoo! Messenger. > Download Now! http://messenger.yahoo.com/download.php > >> > > > >-- > ======================================================================= > >Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > > Center for Molecular Modeling -- University of Pennsylvania > >Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > >tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > >======================================================================= > >If you make something idiot-proof, the universe creates a better idiot. > >_______________________________________________ > >Pw_forum mailing list > >Pw_forum at pwscf.org > >http://www.democritos.it/mailman/listinfo/pw_forum > > ==================================================== > Sanjeev Kumar Gupta > Junior Research Fellow (DAE-BRNS) > Computational Condensed Matter Physics Lab.(CCMP) > Department of Physics, Faculty of Science, > The M.S.University of Baroda, Vadodara - 390 002. > Ph.No: +91-265-279 5339 (O) extn: 30-25 > mobile:09374616019 > Email: sanjeev0302 at rediffmail.com > sanjeev0302 at yahoo.co.in > skgupta-phy at msubaroda.ac.in > ==================================================== > > Residential Address- > > Dr. Vikram Sarabhai Hall, > Room No.-95, Boys' Hostel,M.S.University Campus, > Pratapgunj,Vadodara-390 002,Gujarat,INDIA > > > -- rudra Please, if possible, don't send me MS Word or PowerPoint attachments ---------- Why?See: http://www.gnu.org/philosophy/no-word-attachments.html have a nice time -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070111/cbada8ed/attachment.htm From emenendez at macul.ciencias.uchile.cl Fri Jan 12 14:18:00 2007 From: emenendez at macul.ciencias.uchile.cl (Eduardo Ariel Menendez P) Date: Fri, 12 Jan 2007 10:18:00 -0300 (CLST) Subject: [Pw_forum] question on the pressure in molecular dynamics Message-ID: Hi everybody, I have a doubt concernig the pressure reported by pw or cp in a molecular dynamics run. The stress tensor and its trace (the pressure) reported in molecular dynamics by pwscf and other quantum codes is a static pressure. In a molecular dinamics simulation, if I want the "real" pressure, I must add dp=(N/V) k_B T, N being the number of atoms and V the volume of the cell, and T the instantaneous temperature or its meand value. In other words, the pressure of a non ideal gas (or liquid) is P=(N/V) k_B T + virial term (do not worry about the exact expression), then I understand that the pressure given by the codes is equivalent to the virial term. Is this correct? I found strange that nobody mentions it. Therefore, I understand that to have the "real" pressure I must add (N/V)k_B T to the pressure reported by pw or cp. Please, correct me if I am wrong. Next level of question. If I do Parrinello-Rahman dynamics with a Nose thermostast, what is the pressure specified by the keyword press ? Does it include the thermal pressure? I see that there is also a Nose thermostast for the cell. What is its importance? Is it neccessary to use this cell thermostat for the NPT ensemble? Thanks Eduardo From jess.kondor at gmail.com Fri Jan 12 18:16:08 2007 From: jess.kondor at gmail.com (Jess Kondor) Date: Fri, 12 Jan 2007 18:16:08 +0100 Subject: [Pw_forum] Ba ultrasoft psp Message-ID: <9d7293e10701120916m46f21712t9c9393429afedad9@mail.gmail.com> Hello everyone, Does anybody have a good Ba ultrasoft pseudopotential in LDA approximation? I generated one from vanderbilt library, but I feel did something wrong - using it together with Ti and O from pwscf web-site on simple test I cannot get convergence more than 1.d-10 (moreover, on the last scf steps warning 'some eigenvalues do not converge' appears' - not a good sign according manual). Regards, JK -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070112/1bff6e10/attachment.htm From napolesd at cactus.iico.uaslp.mx Fri Jan 12 21:30:47 2007 From: napolesd at cactus.iico.uaslp.mx (Jose Manuel Napoles Duarte) Date: Fri, 12 Jan 2007 14:30:47 -0600 (CST) Subject: [Pw_forum] cohesive energy of C60 Message-ID: Dear pwscf users, I am trying to do a test pwscf calculation of fullerene C60 in a FCC bravais lattice. I have the reference of Saito and Oshiyama (PRL 66 ,2637 (1991)) and that of Troullier and Martins (PRB 46,1754 (1992)) where both groups found a cohesive energy of 1.6 eV. However in a preliminar result I have found the following energy for fcc c60 with lattice parameter (a_0)= 26.7248 a.u. (equivalent to a_0= 14.142 Angstrom): > grep ! c60fccgeom10.out ! total energy = -683.97694515 ryd and for the isolated molecule: grep ! c60damp.out No symmetry! ! total energy = -683.91687200 ryd ! total energy = -683.91692937 ryd ! total energy = -683.91700216 ryd ! total energy = -683.91706827 ryd ! total energy = -683.91702891 ryd ! total energy = -683.91705256 ryd ! total energy = -683.91706654 ryd ! total energy = -683.91708083 ryd ! total energy = -683.91707390 ryd ! total energy = -683.91708201 ryd ! total energy = -683.91708245 ryd ! total energy = -683.91708268 ryd ! total energy = -683.91708291 ryd ! total energy = -683.91708326 ryd ! total energy = -683.91708337 ryd ! total energy = -683.91708436 ryd ! total energy = -683.91708405 ryd ! total energy = -683.91708381 ryd ! total energy = -683.91708464 ryd ! total energy = -683.91708457 ryd ! total energy = -683.91708430 ryd So giving a cohesive energy of 0.81410756 eV which I guess is about 1/2 of the energy reported in the references given above. I really don`t understend what is happening. The C60 molecule is set such that each axis crosses a double bond at the midpoint. Below is the input file for the fcc-C60. For the isolated molecule I first do a damped dynamics optimization. thanks J. M. Napoles PhD student Instituto de Investigacion en Comunicacion Optica Universidad Autonoma de San Luis Potosi San Luis Potosi, Mexico / &control calculation='scf' restart_mode='from_scratch' prefix='C60fccgeom' pseudo_dir=' ' outdir=' ' / &system ibrav=2, nat=60, ntyp=1,celldm(1)=26.7247738 ecutwfc = 50.0, ecutrho = 300.0 occupations='smearing', smearing='methfessel-paxton', degauss=0.005 / &electrons conv_thr = 1.0d-6 mixing_beta = 0.5 / ATOMIC_SPECIES C 12.0107 C.pz-rrkjus.UPF ATOMIC_POSITIONS {angstrom} C 1.407368348 -1.169270087 -2.996352523 C 1.155000914 -2.998721394 1.414231172 C -2.569868573 0.727048774 2.278942600 C -1.407369748 1.169270123 2.996354503 C -2.572934630 -0.708858874 2.281123936 C -1.168248777 -2.993711628 1.413850706 C -1.154999556 2.998716434 -1.414235192 C 2.569873218 -0.727045947 -2.278934183 C -3.443475569 -0.684030397 0.000528040 C -2.285795345 -2.567271017 -0.714319855 C -1.411460082 -1.163183560 -2.996790774 C 2.569183053 -0.719996621 2.281933017 C 2.572942818 0.708860996 -2.281117431 C 0.691950027 -0.006743425 -3.441895530 C 0.712638046 -2.278049679 2.574700204 C -0.712641482 2.278048778 -2.574700904 C -0.691960543 0.006744382 3.441896564 C 2.275044288 -2.577090608 -0.713619986 C -2.275043517 2.577094390 0.713619895 C -1.412387498 -1.153994791 2.999932296 C -0.723266366 -2.274967859 2.574471677 C 2.572243493 0.715908748 2.279712906 C -3.001182866 -1.404764735 -1.159915160 C 1.155438733 -3.003036722 -1.404638851 C -2.572239887 -0.715911865 -2.279718564 C 1.412386937 1.153998869 -2.999931150 C -2.995166398 1.414092648 -1.164264062 C 0.722467030 2.282840618 2.567674821 C -0.007446490 -3.440967562 0.696724153 C 3.440539698 -0.698842016 0.001593642 C -3.440541125 0.698844548 -0.001591405 C -1.167819674 -2.998024268 -1.404977765 C -0.722472878 -2.282835618 -2.567674762 C 2.995170011 -1.414092306 1.164257891 C 0.723259638 2.274974525 -2.574473179 C -1.155437472 3.003038299 1.404638985 C 3.001187729 1.404761625 1.159913217 C 1.167819111 2.998024849 1.404975960 C 2.995521908 -1.417677189 -1.158979906 C 1.168247528 2.993715403 -1.413852038 C 0.007444736 3.440964394 -0.696728588 C -3.001537554 -1.401174161 1.163337969 C 1.406467715 -1.160078807 3.000371626 C -0.690908691 -0.003781257 -3.442111538 C -2.286027765 -2.565072224 0.721571219 C 3.001546058 1.401171970 -1.163329086 C -1.406469268 1.160075629 -3.000369224 C 0.690898738 0.003779607 3.442113424 C -2.274832893 2.574892089 -0.722292146 C 2.286031105 2.565069342 -0.721567056 C 0.007232021 3.443069261 0.686129858 C 2.285800339 2.567266719 0.714321873 C 1.411455172 1.163183237 2.996789095 C -2.569178195 0.719996609 -2.281934935 C 3.443475635 0.684027870 -0.000523865 C -2.995519741 1.417679476 1.158987181 C 2.274836356 -2.574893690 0.722285126 C 0.713422702 -2.285919833 -2.567457257 C -0.713428440 2.285919456 2.567457625 C -0.007232083 -3.443071526 -0.686134267 K_POINTS {automatic} 6 6 6 0 0 0 From niuli1978 at yahoo.com.cn Sat Jan 13 06:04:33 2007 From: niuli1978 at yahoo.com.cn (li niu) Date: Sat, 13 Jan 2007 13:04:33 +0800 (CST) Subject: [Pw_forum] projected phonon DOS Message-ID: <144640.67920.qm@web15011.mail.cnb.yahoo.com> Dear PWSCF user, I can calculate the total phonon DOS and now I want to calculate projected phonon DOS with tetrahedra (associated with specific atom or vibrational mode in the unit cell). I searched the pw_forum archive but did not find anything useful. The projwfc.x program can be used to calculate only electronic projected DOS. I wonder if someone have written a code for calculating it , or how should I make a subroutine to do it ? thanks! Li Niu Harbin institute of technology, China --------------------------------- Mp3???-??????? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070113/60db74d6/attachment.htm From lanhaiping at gmail.com Sat Jan 13 06:58:28 2007 From: lanhaiping at gmail.com (lan haiping) Date: Sat, 13 Jan 2007 13:58:28 +0800 Subject: [Pw_forum] Question about Example10 Message-ID: Hi All, Happy new year ! I have a question about berry phase calculation for born effetive charge implemented in espresso. I just run a series calculation with the script of example10 by modifying parameters , while i can not obtain satisfactory results for O sites. Actually, I could obtain born effective tensor of Pb site about 3.9 -3.92 e whenever i increase ecutoffrho , conv_thr or use denser kmesh.. But the born effective tensor of O sites , i.e . the three diagonal elements are not consistent with the result of Zhong et al (PRL.72.3618). The values i obtained are -1.98 , -5.85, -1.90e respectively for 3 different directions. The procedure for me to calculate this quantity of O sites is really followed that of Pb in Example10. Would you please give me some hints for this problem ? Regards hai-ping -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070113/18028247/attachment.htm From giannozz at nest.sns.it Sat Jan 13 12:16:44 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sat, 13 Jan 2007 12:16:44 +0100 Subject: [Pw_forum] cohesive energy of C60 In-Reply-To: References: Message-ID: <471405C9-D1F3-40D0-B13F-18CC80EBB66B@nest.sns.it> On Jan 12, 2007, at 21:30 , Jose Manuel Napoles Duarte wrote: > I am trying to do a test pwscf calculation of fullerene C60 in a FCC > bravais lattice. I have the reference of Saito and Oshiyama (PRL 66, > 2637 (1991)) and that of Troullier and Martins (PRB 46,1754 (1992)) > where both groups found a cohesive energy of 1.6 eV. However in a > preliminar result I have found [...] a cohesive energy of > 0.81410756 eV what a waste of digits, for a value > which I guess is about 1/2 of the energy reported in the references > given above and is physically meaningless (solid C60 is bonded by van der Waals forces). Anyway: try to make a calculation as similar as possible to the one of Troullier and Martins: same cell, same k-points, no smearing (C60 is an insulator), pseudopotentials as similar as possible (ultrasoft are nice because they allow you to use a small cutoff, but if you don't, they are just a hassle). First of all, however, check that the calculation for the "isolated" molecule is performed using exactly the same cutoff, same pseudopotential, etc, and that the cell is large enough. Years ago I made a large number of calculations on C60 systems. I don't remember having checked the cohesive energy, but everything else I got was quite the same as in the TM paper Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Sun Jan 14 11:10:07 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sun, 14 Jan 2007 11:10:07 +0100 Subject: [Pw_forum] Question about Example10 In-Reply-To: References: Message-ID: On Jan 13, 2007, at 6:58 , lan haiping wrote: > I have a question about berry phase calculation for born effetive > charge implemented in espresso. [...] I could obtain born > effective tensor of Pb site > about 3.9 -3.92 e whenever i increase ecutoffrho , conv_thr or use > denser > kmesh. But the born effective tensor of O sites , i.e . the three > diagonal > elements are not consistent with the result of Zhong et al (PRL. > 72.3618). > The values i obtained are -1.98 , -5.85, -1.90e respectively for > 3 different > directions. did you try linear response? If you get the same result, that's it P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From lanhaiping at gmail.com Sun Jan 14 17:06:15 2007 From: lanhaiping at gmail.com (lan haiping) Date: Mon, 15 Jan 2007 00:06:15 +0800 Subject: [Pw_forum] Question about Example10 In-Reply-To: References: Message-ID: thank you, Paolo. I will try ph.x to test this result.. Regards, Hai-Ping On 1/14/07, Paolo Giannozzi wrote: > > > On Jan 13, 2007, at 6:58 , lan haiping wrote: > > > I have a question about berry phase calculation for born effetive > > charge implemented in espresso. [...] I could obtain born > > effective tensor of Pb site > > about 3.9 -3.92 e whenever i increase ecutoffrho , conv_thr or use > > denser > > kmesh. But the born effective tensor of O sites , i.e . the three > > diagonal > > elements are not consistent with the result of Zhong et al (PRL. > > 72.3618). > > The values i obtained are -1.98 , -5.85, -1.90e respectively for > > 3 different > > directions. > > did you try linear response? If you get the same result, that's it > P. > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070115/0ab71dd3/attachment.htm From stewart at cnf.cornell.edu Mon Jan 15 04:13:38 2007 From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu) Date: Sun, 14 Jan 2007 22:13:38 -0500 Subject: [Pw_forum] processing large charge_density and spin_density xml files In-Reply-To: <7b6913e90701091231m1c743cb4o34a745802b477647@mail.gmail.com> References: <989518.49761.qm@web54402.mail.yahoo.com> <7b6913e90701091231m1c743cb4o34a745802b477647@mail.gmail.com> Message-ID: <20070115031338.92344.qmail@mail.spidergraphics.com> Hi everyone, I have been looking at a fairly large system (160 atoms) with a nanowire between two (111) leads in PWscf. I have converged the system, but now I would like to plot out the charge density. I have the xml files for charge density and spin density. However, I am running into insufficient virtual memory complaints when running pp.x, even when I run the parallel version. Does anyone know if it is possible to read the xml files directly with some visualization packages (XCrysDens). The xml files are fairly large (58 MB), so I may be running into file size limit problems. Is it always necessary to run pp.x and then generate plot output? I have been using version 3.1.1 for these calculations. Thanks, Derek ################################ Derek Stewart, Ph. D. Scientific Computation Associate 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From ezadshojaee at hotmail.com Mon Jan 15 08:07:06 2007 From: ezadshojaee at hotmail.com (Ezad Shojaee) Date: Mon, 15 Jan 2007 07:07:06 +0000 Subject: [Pw_forum] NaN in Phonon Message-ID: hi dear Mr. Giannozzi , this is my input file for ph.x : &inputph tr2_ph=1.0d-12, prefix='...', ldisp=.true., nq1=4, nq2=4, nq3=4 amass(1)=..., amass(2)=..., outdir='....', fildyn='....', recover=.true. / in my case , in the 10th point in the grid , there are 18 irriducable representations and the code gave NaN in the 15th representation in the first iteration, then continued the 16-17-18th representations and converged normally so this is where it seems to be in a round : Representation # 18 mode # 18 Self-consistent Calculation iter # 12 total cpu time : 1952.6 secs av.it.: 1.0 thresh= 0.405E-07 alpha_mix = 0.700 |ddv_scf|^2 = 0.164E-12 End of self-consistent calculation Convergence has been achieved Number of q in the star = 4 List of q in the star: 1 0.500000000 0.000000000 0.000000000 2 -0.500000000 0.000000000 0.000000000 3 0.000000000 0.500000000 0.000000000 4 0.000000000 -0.500000000 0.000000000 what's your opinion ? _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum _________________________________________________________________ Don't just search. Find. Check out the new MSN Search! http://search.msn.com/ From peterwiney at gmail.com Mon Jan 15 20:27:37 2007 From: peterwiney at gmail.com (Peter Winey) Date: Mon, 15 Jan 2007 14:27:37 -0500 Subject: [Pw_forum] a question about a calculation on a relatively large system Message-ID: Dear all, I am trying to do a structural relaxation on a relatively large system, which has 240 atoms in one unit cell. I know it may sound crazy, but the crystal contains only C and H atoms, so I thought that my cluster might be able to handle it. Indeed, I was able to run pwscf structural relaxation calculations. The 1st iteration finished ok. However, at the end of the 2nd iteration (which also finished ok), after the program printed out: ------------------------------------------ ... number of scf cycles = 2 number of bfgs steps = 1 energy old = - 2084.xxx energy new = - 2086.xxx CASE: energy_new < energy_old ------------------------------------------ The run stopped without giving any information expect saying that "mpi stopped without calling mpi_finalize" or sth like that. I repeated the calculation and it always stopped at the same place. It is wierd since I had no problem before when running smaller systems (say, 150 atoms). Could some one give me a hint on what could be the reason? Is it related to the system size? If so, I have no idea why the pw.x program is able to finish the first and the second iteration, but does not continue... Thanks in advance for any suggestions that you may have! -Peter ******************************************** Peter Winey, Ph.D., DuPont peterwiney at gmail.com ******************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070115/1a0cbac2/attachment.htm From naivebamboo at hotmail.com Tue Jan 16 06:16:49 2007 From: naivebamboo at hotmail.com (naivebamboo Huang) Date: Tue, 16 Jan 2007 00:16:49 -0500 Subject: [Pw_forum] The choice of Acoustic Sum Rule for crystal Message-ID: Dear PWscf users, I am trying to calculate the phonon eigen modes of Bi2Te3 crystal at gamma point. The fraction of one Te atom has two different reported values in the literature (x1=0.792, x2=0.7905). I want to know which value is more appropriate. I calculated the energy of the cell and found the configure with x=0.7905 has a very slightly lower energy(0.001% lower, does this mean the well is flat?). I also calculated the frequency. Both of the configurations give 14 positive frequencies and 1 negative frequency (totally 15 modes). I just thought this may be due to the acoustic sum rule. I impose asr='simple' and used dynmat.x to get the frequency. Only x=0.792 gives 12 positive frequencies and 3 zero frequency. But if I set asr='crystal', both configures can produce 12 positive frequencies and 3 zero frequency. After checking with the gamma point of experimental dispersion curve at 300 K, the configure x=0.792 and asr='crystal' give the best results. My questions are (1) which ASR should I use, since the different ASR give different frequencies (10% difference for x=0.792 configure) (2) how can I trust the results I calculated? Does the positive eigen frequency indicate a stable structure? I guessed at 300 K, the frequencies should be different from those of the relax structure. Thanks very much Baoling _________________________________________________________________ The MSN Entertainment Guide to Golden Globes is here. Get all the scoop. http://tv.msn.com/tv/globes2007/?icid=nctagline2 From yuwen_66 at yahoo.com Tue Jan 16 10:37:23 2007 From: yuwen_66 at yahoo.com (W. YU) Date: Tue, 16 Jan 2007 01:37:23 -0800 (PST) Subject: [Pw_forum] misunderstanding on code to determine Fermi energy Message-ID: <89790.45524.qm@web51013.mail.yahoo.com> Dear PW users, I read some of the codes from PW to determine the Fermi energy - namely sumkg,efermig and other related ones. I can't understand something here. In function sumkg(et,nbnd,nks,wk,degauss,ngauss,e,is,isk), the parameter 'isk' could be 1 or 2 to determine the spin components: 1 for up and 2 for down. Then the function calculate the number of states at a given energy e. If I am right, 'is' could also be 1 or 2 to choose spin component for calculating states. This way, the total number of states seems for one spin only (i.e. roughly half of nelec). But in function efermig, the so calculated number of states is compared with nelec. So I know I must have some misunderstanding in this. Could anybody clear my mind? Thanks! W. YU ____________________________________________________________________________________ Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 From umari at democritos.it Tue Jan 16 11:27:39 2007 From: umari at democritos.it (umari at democritos.it) Date: Tue, 16 Jan 2007 11:27:39 +0100 Subject: [Pw_forum] Re: a question about a calculation on a relatively large system Message-ID: <20070116112739.nm9oatk2iobos8gg@mail.democritos.it> Dear Peter, If you have to deal with large systems in a supercell sampled only at the gamma point, you could perform ionic relaxation using the CPV code cp.x. For this task you should peform a damped molecular dynamics, using either a Car-Parrinello or a Born-Oppenheimer scheme, (the latter should be used for metallic systems). It works fine with large systems up to hundreds of atoms. Best regards, Paolo Umari ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From giannozz at nest.sns.it Tue Jan 16 11:32:43 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 16 Jan 2007 11:32:43 +0100 Subject: [Pw_forum] ph.x v3.2 on NEC SX-8 In-Reply-To: References: Message-ID: <325F5EE3-9948-4475-AC50-6A4A48EF378B@nest.sns.it> On Jan 4, 2007, at 14:00 , wlyim at puccini.che.pitt.edu wrote: > Unfortunately, ph.x still gave wrong results [...] Is there any > benchmark test on NEC machine for the latest version of espresso? there are examples (examples 2, 5, 6 notably), that have been reported to work with Nec sx-8. Do they work for you? P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Tue Jan 16 11:37:54 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 16 Jan 2007 11:37:54 +0100 Subject: [Pw_forum] problem in relaxation by using bfgs In-Reply-To: <2fb18d9f0612220020x36188117g36a386607ebfb157@mail.gmail.com> References: <2fb18d9f0612220020x36188117g36a386607ebfb157@mail.gmail.com> Message-ID: <85295439-6D82-46E8-8A2B-9EB4A4600AC1@nest.sns.it> On Dec 22, 2006, at 9:20 , Javad hashemifar wrote: > I am trying to relax a tetragonal interface supercell at different > values of vertical lattice parameter (celldm(3)). I am using > calculation=relax and the namelist IONS is as follows: > > ion_dynamic = bfgs > bfgs_ndim = 3, > pot_extrapolation = "second_order", > wfc_extrapolation = "second_order", > > [...] For some values of celldm(3) every thing is OK and the system > relax well and both etot_conv_thr and forc_conv_thr satisfies. But in > some other values of celldm(3) the calculation stops with the > following error: > > from checkallsym : error # 1 > some of the original symmetry operations not satisfied we tried your test and actually there is a problem, but we don't know what the problem is. Could you please verify if the error happens also if you remove the line bfgs_ndim = 3 ? Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Tue Jan 16 11:40:10 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 16 Jan 2007 11:40:10 +0100 Subject: [Pw_forum] error In-Reply-To: <2e36f8e50701102120k65d30bdn2b3fdb8c230d8bdc@mail.gmail.com> References: <2e36f8e50701102120k65d30bdn2b3fdb8c230d8bdc@mail.gmail.com> Message-ID: On Jan 11, 2007, at 6:20 , Rudra wrote: > > i am workin in noncolin magnetism and gave my file as: > ibrav= 2, celldm(1) =10.20, nat= 2, ntyp= 1, > ecutwfc =18.0 ,nelec=1 > starting_magnetization(1)=.5, > noncolin=.true. > / > &electrons > mixing_beta = 0.7 > conv_thr = 1.0d-8 > > this is ending with the error: > from atomic_wfc_nc : error # 1 > too many wfcs please provide a test job Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Tue Jan 16 11:50:45 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 16 Jan 2007 11:50:45 +0100 Subject: [Pw_forum] a question about a calculation on a relatively large system In-Reply-To: References: Message-ID: <421493EA-D152-4912-8B08-705AB755EEEC@nest.sns.it> On Jan 15, 2007, at 20:27 , Peter Winey wrote: > I am trying to do a structural relaxation on a relatively large > system, > which has 240 atoms in one unit cell [...] at the end of the 2nd > iteration > (which also finished ok), after the program printed out: > ------------------------------------------ > ... > number of scf cycles = 2 > number of bfgs steps = 1 > energy old = - 2084.xxx > energy new = - 2086.xxx > CASE: energy_new < energy_old > ------------------------------------------ > The run stopped without giving any information expect saying that "mpi > stopped without calling mpi_finalize" or sth like that. one frequent reason for silent crashes is an out-of-memory condition, but it doesn't look likely in this case. What kind of options have you used for structural relaxation? P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Tue Jan 16 11:53:38 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 16 Jan 2007 11:53:38 +0100 Subject: [Pw_forum] NaN in Phonon In-Reply-To: References: Message-ID: On Jan 15, 2007, at 8:07 , Ezad Shojaee wrote: > dear Mr. Giannozzi please address to the forum. Effective now, I will ignore all messages directly addressed to myself. > what's your opinion ? my opinion is that in order to have a nonzero (although small) possibility to see your problem addresed, you must submit enough data to allow it to be reproduced --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Tue Jan 16 12:11:53 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 16 Jan 2007 12:11:53 +0100 Subject: [Pw_forum] processing large charge_density and spin_density xml files In-Reply-To: <20070115031338.92344.qmail@mail.spidergraphics.com> References: <989518.49761.qm@web54402.mail.yahoo.com> <7b6913e90701091231m1c743cb4o34a745802b477647@mail.gmail.com> <20070115031338.92344.qmail@mail.spidergraphics.com> Message-ID: <2E533143-674D-45CA-8206-66000F780E76@nest.sns.it> On Jan 15, 2007, at 4:13 , stewart at cnf.cornell.edu wrote: > [...] I am running into insufficient virtual memory complaints when > running pp.x, even when I run the parallel version. this is very strange: pp.x shouldn't require more memory than the scf calculation. Actually it should require much less memory. Try to locate where it complains. > Does anyone know if it is possible to read the xml files directly with > some visualization packages (XCrysDens). The xml files are fairly > large (58 MB) 58 Mb doesn't look to me that large > Is it always necessary to run pp.x and then generate plot output? as of now, it is. In the future, it would be highly desirable to be able to parse directly the xml file with a browser and a web application, but this is not going to happen soon enough to solve your problem Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From matteo at umn.edu Tue Jan 16 16:41:30 2007 From: matteo at umn.edu (Matteo Cococcioni) Date: 16 Jan 2007 09:41:30 -0600 Subject: [Pw_forum] The choice of Acoustic Sum Rule for crystal In-Reply-To: References: Message-ID: Dear Baoling, I will try to address some of your questions. On Jan 15 2007, naivebamboo Huang wrote: >Dear PWscf users, > I am trying to calculate the phonon eigen modes of Bi2Te3 crystal > at gamma point. The fraction of one Te atom has two different reported > values in the literature (x1=0.792, x2=0.7905). This sounds pretty obscure to me: what is the fraction of one Te atom? are you considering two different compositions? I want to know which > value is more appropriate. I calculated the energy of the cell and found > the configure with x=0.7905 has a very slightly lower energy(0.001% > lower, does this mean the well is flat?). I also calculated the > frequency. Both of the configurations give 14 positive frequencies and 1 > negative frequency (totally 15 modes). I just thought this may be due to > the acoustic sum rule. I impose asr='simple' and used dynmat.x to get the > frequency. Only x=0.792 gives 12 positive frequencies and 3 zero > frequency. But if I set asr='crystal', both configures can produce 12 > positive frequencies and 3 zero frequency. After checking with the gamma > point of experimental dispersion curve at 300 K, the configure x=0.792 > and asr='crystal' give the best results. My questions are > (1) which ASR should I use, since the different ASR give >different frequencies (10% difference for x=0.792 configure) Here is the explanation I have found in dynmat.f90: ! asr character indicates the type of Acoustic Sum Rule imposed ! - 'no': no Acoustic Sum Rules imposed (default) ! - 'simple': previous implementation of the asr used ! (3 translational asr imposed by correction of ! the diagonal elements of the dynamical matrix) ! - 'crystal': 3 translational asr imposed by optimized ! correction of the dyn. matrix (projection). ! - 'one-dim': 3 translational asr + 1 rotational asr ! imposed by optimized correction of the dyn. mat. (the ! rotation axis is the direction of periodicity; it ! will work only if this axis considered is one of ! the cartesian axis). ! - 'zero-dim': 3 translational asr + 3 rotational asr ! imposed by optimized correction of the dyn. mat. ! Note that in certain cases, not all the rotational asr ! can be applied (e.g. if there are only 2 atoms in a ! molecule or if all the atoms are aligned, etc.). ! In these cases the supplementary asr are cancelled ! during the orthonormalization procedure (see below). ! Finally, in all cases except 'no' a simple correction ! on the effective charges is performed (same as in the ! previous implementation). It sounds to me like: asr = 'simple' should work in most cases; probably 'crystal' is more accurate and works better. However I would expect that only the frequencies close to 0 will differ. Corrections on the others should be small. > (2) how can I trust the results I calculated? Does the positive >eigen frequency indicate a stable structure? I guessed at 300 K, the >frequencies should be different from those of the relax structure. > I would say yes. If frequencies are positive as in your case I would trust the crystal is in a local minimum at least. You could even check comparing the energy of the relaxed ionic configuration (at which I guess you are computing phonons) with that obtained imposing the distorsion pattern of one of the vibrational mode you want to check and making sure the former is lower than the latter. At 300K in principle you should take into account thermal expansion (e.g. with the quasi harmonic approximation) and compute phonons from the finite T free energy. I wouldn't expect however a very large difference from the 0K result you are considering. Hope this helps. Matteo >Thanks very much > >Baoling > >_________________________________________________________________ >The MSN Entertainment Guide to Golden Globes is here. Get all the scoop. >http://tv.msn.com/tv/globes2007/?icid=nctagline2 > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science University of Minnesota 151 Amundson Hall 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From peterwiney at gmail.com Tue Jan 16 17:19:12 2007 From: peterwiney at gmail.com (Peter Winey) Date: Tue, 16 Jan 2007 11:19:12 -0500 Subject: [Pw_forum] a question about a calculation on a relatively large system In-Reply-To: <421493EA-D152-4912-8B08-705AB755EEEC@nest.sns.it> References: <421493EA-D152-4912-8B08-705AB755EEEC@nest.sns.it> Message-ID: Thanks for the heads-up! The system is a molecular crystal. I monitored the memory usage, which was fine. My input file is like the following: &control calculation='relax' restart_mode='from_scratch', wf_collect=.true., prefix='pwscf', pseudo_dir = '/home/winey/pseudo', outdir='.', forc_conv_thr = 0.001 tprnfor=.true. / &system ibrav = 8 celldm(1) = 16.223 celldm(2) = 3.2124 celldm(3) = 1.1942 nat=248, ntyp=2, ecutwfc = 30.0, occupations='fixed', / &electrons conv_thr = 1.0d-8 mixing_beta = 0.3 / &ions upscale=10 / ATOMIC_SPECIES C 12.0107 C.pbe-van_ak.UPF H 1.00794 H.pbe-van_ak.UPF K_POINTS {gamma} ATOMIC_POSITIONS {crystal} C .... ... H ... ... -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070116/c5778b11/attachment.htm From akohlmey at cmm.chem.upenn.edu Tue Jan 16 17:52:32 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 16 Jan 2007 11:52:32 -0500 (EST) Subject: [Pw_forum] processing large charge_density and spin_density xml files In-Reply-To: <20070115031338.92344.qmail@mail.spidergraphics.com> Message-ID: On Sun, 14 Jan 2007 stewart at cnf.cornell.edu wrote: DS> Hi everyone, hi derek. happy new year. DS> I have been looking at a fairly large system (160 atoms) with a nanowire DS> between two (111) leads in PWscf. I have converged the system, but now I DS> would like to plot out the charge density. I have the xml files for charge DS> density and spin density. However, I am running into insufficient virtual DS> memory complaints when running pp.x, even when I run the parallel version. hmm, you are running binaries compiled with intel fortran, right? did you try increasing the stack size (using 'ulimit -s')? what is the exact error message? could you try generating a core dump (run 'ulimit -c unlimited', then pw.x as usual), then 'idb pw.x core.XXXX' and on the idb prompt type 'where' to generate a stack trace, so we can see where it crashes. DS> Does anyone know if it is possible to read the xml files directly with some DS> visualization packages (XCrysDens). The xml files are fairly large (58 MB), DS> so I may be running into file size limit problems. Is it always necessary DS> to run pp.x and then generate plot output? if the stack size 'trick' does not help, you can think about reducing the number of grid points used for plotting. in CPMD using half the grid in each direction (i.e. 1/8th of the data!) is the default and usually is quite sufficient to get very nice pictures. you should be able to set the output grid in pp.x, but if that still is not sufficient, you might want to try as a matter of last resort an NSCF calculation from a converged potential/wavefunction with a smaller real space density cutoff (and thus grid) and use that to get the output. cheers, axel. DS> DS> I have been using version 3.1.1 for these calculations. DS> DS> Thanks, DS> DS> Derek DS> DS> DS> ################################ DS> Derek Stewart, Ph. D. DS> Scientific Computation Associate DS> 250 Duffield Hall DS> Cornell Nanoscale Facility (CNF) DS> Ithaca, NY 14853 DS> stewart (at) cnf.cornell.edu DS> (607) 255-2856 DS> _______________________________________________ DS> Pw_forum mailing list DS> Pw_forum at pwscf.org DS> http://www.democritos.it/mailman/listinfo/pw_forum DS> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From akohlmey at cmm.chem.upenn.edu Tue Jan 16 18:08:27 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 16 Jan 2007 12:08:27 -0500 (EST) Subject: [Pw_forum] Ba ultrasoft psp In-Reply-To: <9d7293e10701120916m46f21712t9c9393429afedad9@mail.gmail.com> Message-ID: On Fri, 12 Jan 2007, Jess Kondor wrote: JK> Hello everyone, jess, JK> Does anybody have a good Ba ultrasoft pseudopotential in LDA approximation? JK> I generated one from vanderbilt library, but I feel did something wrong - in case nobody responded yet and just as a caveat for everybody else. there is one thing that i noticed when re-creating pseudopotentials with the parameters from the vanderbilt library: many of these parameter sets are rather old and it appears that the polynomial fitting algorithm has been changed since, so that some fine-tuning is required for heavier elements. you can tell from looking at the output file from the pseudopotential generation, as it contains warnings about negative densities. adding constraints to the polynomial fitting to eliminate them or bring those as close to zero as possible improves in my experience those potentials massively. without they seem ok in minimal tests, but as soon as you start looking at more sensitive properties, the potentials start generating inconsistent results. JK> using it together with Ti and O from pwscf web-site on simple test I cannot JK> get convergence more than 1.d-10 (moreover, on the last scf steps warning JK> 'some eigenvalues do not converge' appears' - not a good sign according JK> manual). jess, if you're still interested, please let me know. it is rather straightforward to add a few constraints and redo the potential. i can do this for you, if you would be willing to run a few tests (eg. lattice constant, bulk modulus etc.,) also for a couple other functionals, so that - if tested ok - they could be added to the pseudopotential library... cheers, axel. JK> JK> Regards, JK> JK JK> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From matteo at umn.edu Tue Jan 16 19:14:01 2007 From: matteo at umn.edu (Matteo Cococcioni) Date: 16 Jan 2007 12:14:01 -0600 Subject: [Pw_forum] The choice of Acoustic Sum Rule for crystal In-Reply-To: References: Message-ID: Dear Baoling, I probably missed the point in the previous email. You probably meant that you are considering two different atomic positions for Te atoms along one direction at least. You are finding very close energies for the two positions, but they seem to be close too (depends on the cell parameter which you don't provide). Did you relax the structure? are they two local minima which you get with different initial structures (I don't think so) or one of them is slightly unstable towards the other? what are the atomic forces on each of them? What is the energy of a configuration with intermediate position of the Te atom? hope this helps, Matteo On Jan 15 2007, naivebamboo Huang wrote: >Dear PWscf users, > I am trying to calculate the phonon eigen modes of Bi2Te3 crystal > at gamma point. The fraction of one Te atom has two different reported > values in the literature (x1=0.792, x2=0.7905). I want to know which > value is more appropriate. I calculated the energy of the cell and found > the configure with x=0.7905 has a very slightly lower energy(0.001% > lower, does this mean the well is flat?). I also calculated the > frequency. Both of the configurations give 14 positive frequencies and 1 > negative frequency (totally 15 modes). I just thought this may be due to > the acoustic sum rule. I impose asr='simple' and used dynmat.x to get the > frequency. Only x=0.792 gives 12 positive frequencies and 3 zero > frequency. But if I set asr='crystal', both configures can produce 12 > positive frequencies and 3 zero frequency. After checking with the gamma > point of experimental dispersion curve at 300 K, the configure x=0.792 > and asr='crystal' give the best results. My questions are > (1) which ASR should I use, since the different ASR give >different frequencies (10% difference for x=0.792 configure) > (2) how can I trust the results I calculated? Does the positive >eigen frequency indicate a stable structure? I guessed at 300 K, the >frequencies should be different from those of the relax structure. > >Thanks very much > >Baoling > >_________________________________________________________________ >The MSN Entertainment Guide to Golden Globes is here. Get all the scoop. >http://tv.msn.com/tv/globes2007/?icid=nctagline2 > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Matteo Cococcioni Department of Chemical Engineering and Materials Science University of Minnesota 151 Amundson Hall 421 Washington Av. SE Minneapolis, MN 55455 Tel. +1 612 624 9056 Fax +1 612 626 7246 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% From naivebamboo at hotmail.com Tue Jan 16 22:33:37 2007 From: naivebamboo at hotmail.com (naivebamboo Huang) Date: Tue, 16 Jan 2007 16:33:37 -0500 Subject: [Pw_forum] The choice of Acoustic Sum Rule for crystal In-Reply-To: Message-ID: Dear Matteo, Thanks very much. Yes, they are fractional coordinates of one Te atom (Te1 atom), that is, atomic position in the unit cell. I am sorry for the confusion. What I mean is that the energies of the two positions seems to change little comparing to their position change. The lattice constant is 10.45 angstrom, and so the difference of the position is not small. I think this is due to the weak Te1-Te1 interaction (van der Waals interaction). I tried to relax the structure use vc-relaxation, but meet an error during the optimization. I am trying to work it out now. The configure with x=0.7905 is the relaxed structure that other people get use the same pseudopotential. The frequencies I got from PWscf are attached. You can see mode 4 of the two configures are much different. Also, if ASR changes from 'simple' to 'crystal', 10% difference appears (for all the modes). Is this acceptable? Since the frequencies are all positive, I just guess they are at least local minimal configures. The configure with x=0.792, though energy is higher, reproduces the measured modes best. I don't know which result I should trust. Thanks Baoling x=0.7905 total energy =-382.4400695 Ry x=0.792 total energy =-382.43346308 Ry (however, x=0.792 reproduces the measured bond lengths of Te-Bi, Te-Te ) x=0.7905 ( ASR='crystal') # mode [cm-1] [THz] IR 1 0.00 0.0000 0.0000 2 0.00 0.0000 0.0000 3 0.00 0.0000 0.0000 4 11.81 0.3541 0.0000 5 79.89 2.3950 0.0000 6 79.89 2.3950 0.0000 7 84.52 2.5339 0.0000 8 84.52 2.5339 0.0000 9 101.25 3.0353 0.0000 10 128.73 3.8593 0.0000 11 142.63 4.2760 0.0000 12 150.50 4.5118 0.0000 13 150.50 4.5118 0.0000 14 153.94 4.6148 0.0000 15 153.94 4.6148 0.0000 x=0.792 (ASR='crystal') # mode [cm-1] [THz] IR 1 0.00 0.0000 0.0000 2 0.00 0.0000 0.0000 3 0.00 0.0000 0.0000 4 36.49 1.0941 0.0000 5 75.48 2.2627 0.0000 6 75.48 2.2627 0.0000 7 83.00 2.4884 0.0000 8 83.00 2.4884 0.0000 9 100.00 2.9978 0.0000 10 111.66 3.3476 0.0000 11 138.25 4.1446 0.0000 12 141.25 4.2346 0.0000 13 141.25 4.2346 0.0000 14 167.48 5.0210 0.0000 15 167.48 5.0210 0.0000 x=0.792 (ASR='simple') # mode [cm-1] [THz] IR 1 0.00 0.0000 0.0000 2 0.00 0.0000 0.0000 3 0.00 0.0000 0.0000 4 53.43 1.6017 0.0000 5 56.12 1.6825 0.0000 6 56.12 1.6825 0.0000 7 69.99 2.0982 0.0000 8 69.99 2.0982 0.0000 9 98.14 2.9421 0.0000 10 98.14 2.9421 0.0000 11 113.40 3.3997 0.0000 12 113.40 3.3997 0.0000 13 114.78 3.4411 0.0000 14 131.36 3.9381 0.0000 15 145.97 4.3760 0.0000 >From: Matteo Cococcioni >Reply-To: pw_forum at pwscf.org >To: pw_forum at pwscf.org >Subject: Re: [Pw_forum] The choice of Acoustic Sum Rule for crystal >Date: 16 Jan 2007 12:14:01 -0600 > > >Dear Baoling, > >I probably missed the point in the previous email. You probably meant that >you are considering two different atomic positions for Te atoms along one >direction at least. You are finding very close energies for the two >positions, but they seem to be close too (depends on the cell parameter >which you don't provide). Did you relax the structure? are they two local >minima which you get with different initial structures (I don't think so) >or one of them is slightly unstable towards the other? what are the atomic >forces on each of them? What is the energy of a configuration with >intermediate position of the Te atom? > >hope this helps, > >Matteo > > > >On Jan 15 2007, naivebamboo Huang wrote: > >>Dear PWscf users, >> I am trying to calculate the phonon eigen modes of Bi2Te3 crystal >>at gamma point. The fraction of one Te atom has two different reported >>values in the literature (x1=0.792, x2=0.7905). I want to know which value >>is more appropriate. I calculated the energy of the cell and found the >>configure with x=0.7905 has a very slightly lower energy(0.001% lower, >>does this mean the well is flat?). I also calculated the frequency. Both >>of the configurations give 14 positive frequencies and 1 negative >>frequency (totally 15 modes). I just thought this may be due to the >>acoustic sum rule. I impose asr='simple' and used dynmat.x to get the >>frequency. Only x=0.792 gives 12 positive frequencies and 3 zero >>frequency. But if I set asr='crystal', both configures can produce 12 >>positive frequencies and 3 zero frequency. After checking with the gamma >>point of experimental dispersion curve at 300 K, the configure x=0.792 and >>asr='crystal' give the best results. My questions are >> (1) which ASR should I use, since the different ASR give >>different frequencies (10% difference for x=0.792 configure) >> (2) how can I trust the results I calculated? Does the positive >>eigen frequency indicate a stable structure? I guessed at 300 K, the >>frequencies should be different from those of the relax structure. >> >>Thanks very much >> >>Baoling >> >>_________________________________________________________________ >>The MSN Entertainment Guide to Golden Globes is here. Get all the scoop. >>http://tv.msn.com/tv/globes2007/?icid=nctagline2 >> >>_______________________________________________ >>Pw_forum mailing list >>Pw_forum at pwscf.org >>http://www.democritos.it/mailman/listinfo/pw_forum >> > >-- >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >Matteo Cococcioni >Department of Chemical Engineering and Materials Science >University of Minnesota >151 Amundson Hall >421 Washington Av. SE >Minneapolis, MN 55455 >Tel. +1 612 624 9056 Fax +1 612 626 7246 >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum _________________________________________________________________ Find sales, coupons, and free shipping, all in one place! ?MSN Shopping Sales & Deals http://shopping.msn.com/content/shp/?ctid=198,ptnrid=176,ptnrdata=200639 From eminekb at yahoo.com Wed Jan 17 06:11:53 2007 From: eminekb at yahoo.com (e kb) Date: Tue, 16 Jan 2007 21:11:53 -0800 (PST) Subject: [Pw_forum] The choice of Acoustic Sum Rule for crystal In-Reply-To: Message-ID: <487333.95246.qm@web34801.mail.mud.yahoo.com> Dear Baoling, I am not an experienced user, but I want to comment a little on your case. In these two position configurations, the energy difference is not as small as you think, I guess, sth like 90 meV. (why to compare in percentages??) so 0.792 is not the global minimum. If I were you, I would find my own equilibrium position configuration first. At least you have a good initial guess, 0.7905, which is found by using the same pseudopotential. You can search around it and find yours - which i guess would not be so far away from 0.7905. Then at your result, make a "converged" phonon calculation, using several asr schemes if you want, and later you can post your mail to the group with the title 'The choice of ASR'. But for now, I am not sure that this is your problem. Again, you dont have to take this seriously, I am just a newbie. Emine Kucukbenli naivebamboo Huang wrote: Dear Matteo, Thanks very much. Yes, they are fractional coordinates of one Te atom (Te1 atom), that is, atomic position in the unit cell. I am sorry for the confusion. What I mean is that the energies of the two positions seems to change little comparing to their position change. The lattice constant is 10.45 angstrom, and so the difference of the position is not small. I think this is due to the weak Te1-Te1 interaction (van der Waals interaction). I tried to relax the structure use vc-relaxation, but meet an error during the optimization. I am trying to work it out now. The configure with x=0.7905 is the relaxed structure that other people get use the same pseudopotential. The frequencies I got from PWscf are attached. You can see mode 4 of the two configures are much different. Also, if ASR changes from 'simple' to 'crystal', 10% difference appears (for all the modes). Is this acceptable? Since the frequencies are all positive, I just guess they are at least local minimal configures. The configure with x=0.792, though energy is higher, reproduces the measured modes best. I don't know which result I should trust. Thanks Baoling x=0.7905 total energy =-382.4400695 Ry x=0.792 total energy =-382.43346308 Ry (however, x=0.792 reproduces the measured bond lengths of Te-Bi, Te-Te ) x=0.7905 ( ASR='crystal') # mode [cm-1] [THz] IR 1 0.00 0.0000 0.0000 2 0.00 0.0000 0.0000 3 0.00 0.0000 0.0000 4 11.81 0.3541 0.0000 5 79.89 2.3950 0.0000 6 79.89 2.3950 0.0000 7 84.52 2.5339 0.0000 8 84.52 2.5339 0.0000 9 101.25 3.0353 0.0000 10 128.73 3.8593 0.0000 11 142.63 4.2760 0.0000 12 150.50 4.5118 0.0000 13 150.50 4.5118 0.0000 14 153.94 4.6148 0.0000 15 153.94 4.6148 0.0000 x=0.792 (ASR='crystal') # mode [cm-1] [THz] IR 1 0.00 0.0000 0.0000 2 0.00 0.0000 0.0000 3 0.00 0.0000 0.0000 4 36.49 1.0941 0.0000 5 75.48 2.2627 0.0000 6 75.48 2.2627 0.0000 7 83.00 2.4884 0.0000 8 83.00 2.4884 0.0000 9 100.00 2.9978 0.0000 10 111.66 3.3476 0.0000 11 138.25 4.1446 0.0000 12 141.25 4.2346 0.0000 13 141.25 4.2346 0.0000 14 167.48 5.0210 0.0000 15 167.48 5.0210 0.0000 x=0.792 (ASR='simple') # mode [cm-1] [THz] IR 1 0.00 0.0000 0.0000 2 0.00 0.0000 0.0000 3 0.00 0.0000 0.0000 4 53.43 1.6017 0.0000 5 56.12 1.6825 0.0000 6 56.12 1.6825 0.0000 7 69.99 2.0982 0.0000 8 69.99 2.0982 0.0000 9 98.14 2.9421 0.0000 10 98.14 2.9421 0.0000 11 113.40 3.3997 0.0000 12 113.40 3.3997 0.0000 13 114.78 3.4411 0.0000 14 131.36 3.9381 0.0000 15 145.97 4.3760 0.0000 --------------------------------- Access over 1 million songs - Yahoo! Music Unlimited. -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070116/ca605b20/attachment.htm From giannozz at nest.sns.it Wed Jan 17 09:02:26 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 17 Jan 2007 09:02:26 +0100 Subject: [Pw_forum] misunderstanding on code to determine Fermi energy In-Reply-To: <89790.45524.qm@web51013.mail.yahoo.com> References: <89790.45524.qm@web51013.mail.yahoo.com> Message-ID: On Jan 16, 2007, at 10:37 , W. YU wrote: > In function sumkg(et,nbnd,nks,wk,degauss,ngauss,e,is,isk), > the parameter 'isk' could be 1 or 2 to determine the spin > components: 1 for up and 2 for down. Then the function > calculate the number of states at a given energy e. > > If I am right, 'is' could also be 1 or 2 to choose > spin component for calculating states. This way, the > total number of states seems for one spin only (i.e. > roughly half of nelec). But in function efermig, the > so calculated number of states is compared with nelec. these routines are used in two different cases: - in an ordinary calculation of the Fermi energy, sumkg is called by efermig with nelec = number of electrons, is=0 - in a calculation of constrained occupancies with a given magnetization, sumkg is called by efermig with 1) nelec = number of electrons up, is=1 and 2) nelec = number of electrons down, is=2 . The two results are stored into two Fermi energies, one for spin up, one for spin down. You have to go up in the calling tree to understand how this is done. Admittedly it could be done in a less obscure way Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From yuwen_66 at yahoo.com Wed Jan 17 11:34:46 2007 From: yuwen_66 at yahoo.com (W. YU) Date: Wed, 17 Jan 2007 02:34:46 -0800 (PST) Subject: [Pw_forum] RE: misunderstanding on code to determine Fermi energy Message-ID: <241335.51155.qm@web51008.mail.yahoo.com> Dear Paolo, Thank you very much for explaining it to me. By trying to printout values, I also found the tricky thing of the k point weight add up to 2.0000. This fact also partially answered my question. Best regards, W. YU ____________________________________________________________________________________ Looking for earth-friendly autos? Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center. http://autos.yahoo.com/green_center/ From yuwen_66 at yahoo.com Wed Jan 17 11:36:09 2007 From: yuwen_66 at yahoo.com (W. YU) Date: Wed, 17 Jan 2007 02:36:09 -0800 (PST) Subject: [Pw_forum] RE: misunderstanding on code to determine Fermi energy Message-ID: <353553.75143.qm@web51007.mail.yahoo.com> Dear Paolo, Thank you very much for explaining it to me. By trying to printout values, I also found the tricky thing of the k point weight add up to 2.0000. This fact also partially answered my question. Best regards, W. YU ____________________________________________________________________________________ Sucker-punch spam with award-winning protection. Try the free Yahoo! Mail Beta. http://advision.webevents.yahoo.com/mailbeta/features_spam.html From marzari at MIT.EDU Wed Jan 17 12:32:47 2007 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 17 Jan 2007 06:32:47 -0500 Subject: [Pw_forum] The choice of Acoustic Sum Rule for crystal In-Reply-To: References: Message-ID: <45AE095F.20201@mit.edu> The difference for the high frequency modes between the two sum rules is somewhat suspicious. I would try to increase the k-point sampling, and see if this improves agreement. Also, make sure that your sfc, nscf and phonon calculations are all well converged. Tighten the tolerances for all, and see if anything changes. nicola naivebamboo Huang wrote: > Dear Matteo, > Thanks very much. Yes, they are fractional coordinates of one Te atom > (Te1 atom), that is, atomic position in the unit cell. I am sorry for > the confusion. What I mean is that the energies of the two positions > seems to change little comparing to their position change. The lattice > constant is 10.45 angstrom, and so the difference of the position is not > small. I think this is due to the weak Te1-Te1 interaction (van der > Waals interaction). I tried to relax the structure use vc-relaxation, > but meet an error during the optimization. I am trying to work it out > now. The configure with x=0.7905 is the relaxed structure that other > people get use the same pseudopotential. The frequencies I got from > PWscf are attached. > You can see mode 4 of the two configures are much different. Also, > if ASR changes from 'simple' to 'crystal', 10% difference appears (for > all the modes). Is this acceptable? Since the frequencies are all > positive, I just guess they are at least local minimal configures. The > configure with x=0.792, though energy is higher, reproduces the measured > modes best. I don't know which result I should trust. > > Thanks > > Baoling > > x=0.7905 total energy =-382.4400695 Ry > x=0.792 total energy =-382.43346308 Ry (however, x=0.792 > reproduces the measured bond lengths of Te-Bi, Te-Te ) > > x=0.7905 ( ASR='crystal') > # mode [cm-1] [THz] IR > 1 0.00 0.0000 0.0000 > 2 0.00 0.0000 0.0000 > 3 0.00 0.0000 0.0000 > 4 11.81 0.3541 0.0000 > 5 79.89 2.3950 0.0000 > 6 79.89 2.3950 0.0000 > 7 84.52 2.5339 0.0000 > 8 84.52 2.5339 0.0000 > 9 101.25 3.0353 0.0000 > 10 128.73 3.8593 0.0000 > 11 142.63 4.2760 0.0000 > 12 150.50 4.5118 0.0000 > 13 150.50 4.5118 0.0000 > 14 153.94 4.6148 0.0000 > 15 153.94 4.6148 0.0000 > > x=0.792 (ASR='crystal') > # mode [cm-1] [THz] IR > 1 0.00 0.0000 0.0000 > 2 0.00 0.0000 0.0000 > 3 0.00 0.0000 0.0000 > 4 36.49 1.0941 0.0000 > 5 75.48 2.2627 0.0000 > 6 75.48 2.2627 0.0000 > 7 83.00 2.4884 0.0000 > 8 83.00 2.4884 0.0000 > 9 100.00 2.9978 0.0000 > 10 111.66 3.3476 0.0000 > 11 138.25 4.1446 0.0000 > 12 141.25 4.2346 0.0000 > 13 141.25 4.2346 0.0000 > 14 167.48 5.0210 0.0000 > 15 167.48 5.0210 0.0000 > > x=0.792 (ASR='simple') > # mode [cm-1] [THz] IR > 1 0.00 0.0000 0.0000 > 2 0.00 0.0000 0.0000 > 3 0.00 0.0000 0.0000 > 4 53.43 1.6017 0.0000 > 5 56.12 1.6825 0.0000 > 6 56.12 1.6825 0.0000 > 7 69.99 2.0982 0.0000 > 8 69.99 2.0982 0.0000 > 9 98.14 2.9421 0.0000 > 10 98.14 2.9421 0.0000 > 11 113.40 3.3997 0.0000 > 12 113.40 3.3997 0.0000 > 13 114.78 3.4411 0.0000 > 14 131.36 3.9381 0.0000 > 15 145.97 4.3760 0.0000 > >> From: Matteo Cococcioni >> Reply-To: pw_forum at pwscf.org >> To: pw_forum at pwscf.org >> Subject: Re: [Pw_forum] The choice of Acoustic Sum Rule for crystal >> Date: 16 Jan 2007 12:14:01 -0600 >> >> >> Dear Baoling, >> >> I probably missed the point in the previous email. You probably meant >> that you are considering two different atomic positions for Te atoms >> along one direction at least. You are finding very close energies for >> the two positions, but they seem to be close too (depends on the cell >> parameter which you don't provide). Did you relax the structure? are >> they two local minima which you get with different initial structures >> (I don't think so) or one of them is slightly unstable towards the >> other? what are the atomic forces on each of them? What is the energy >> of a configuration with intermediate position of the Te atom? >> >> hope this helps, >> >> Matteo >> >> >> >> On Jan 15 2007, naivebamboo Huang wrote: >> >>> Dear PWscf users, >>> I am trying to calculate the phonon eigen modes of Bi2Te3 >>> crystal at gamma point. The fraction of one Te atom has two different >>> reported values in the literature (x1=0.792, x2=0.7905). I want to >>> know which value is more appropriate. I calculated the energy of the >>> cell and found the configure with x=0.7905 has a very slightly lower >>> energy(0.001% lower, does this mean the well is flat?). I also >>> calculated the frequency. Both of the configurations give 14 positive >>> frequencies and 1 negative frequency (totally 15 modes). I just >>> thought this may be due to the acoustic sum rule. I impose >>> asr='simple' and used dynmat.x to get the frequency. Only x=0.792 >>> gives 12 positive frequencies and 3 zero frequency. But if I set >>> asr='crystal', both configures can produce 12 positive frequencies >>> and 3 zero frequency. After checking with the gamma point of >>> experimental dispersion curve at 300 K, the configure x=0.792 and >>> asr='crystal' give the best results. My questions are >>> (1) which ASR should I use, since the different ASR give >>> different frequencies (10% difference for x=0.792 configure) >>> (2) how can I trust the results I calculated? Does the >>> positive eigen frequency indicate a stable structure? I guessed at >>> 300 K, the frequencies should be different from those of the relax >>> structure. >>> >>> Thanks very much >>> >>> Baoling >>> >>> _________________________________________________________________ >>> The MSN Entertainment Guide to Golden Globes is here. Get all the >>> scoop. http://tv.msn.com/tv/globes2007/?icid=nctagline2 >>> >>> _______________________________________________ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> -- >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> Matteo Cococcioni >> Department of Chemical Engineering and Materials Science >> University of Minnesota >> 151 Amundson Hall >> 421 Washington Av. SE >> Minneapolis, MN 55455 >> Tel. +1 612 624 9056 Fax +1 612 626 7246 >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > _________________________________________________________________ > Find sales, coupons, and free shipping, all in one place! MSN Shopping > Sales & Deals > http://shopping.msn.com/content/shp/?ctid=198,ptnrid=176,ptnrdata=200639 > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From niuli1978 at yahoo.com.cn Wed Jan 17 13:28:37 2007 From: niuli1978 at yahoo.com.cn (li niu) Date: Wed, 17 Jan 2007 20:28:37 +0800 (CST) Subject: [Pw_forum] Raman spectra of amorphous materials Message-ID: <572915.45357.qm@web15001.mail.cnb.yahoo.com> Dear all, My question is: can PWSCF code be used to calculate Raman spectrum of amorphous materials? How to do ?Any help would be appreciate much! best regards! niuli --------------------------------- Mp3???-??????? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070117/ff0cb9cf/attachment.htm From marzari at MIT.EDU Wed Jan 17 13:57:34 2007 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 17 Jan 2007 07:57:34 -0500 Subject: [Pw_forum] Raman spectra of amorphous materials In-Reply-To: <572915.45357.qm@web15001.mail.cnb.yahoo.com> References: <572915.45357.qm@web15001.mail.cnb.yahoo.com> Message-ID: <45AE1D3E.2000109@mit.edu> See Paolo Umari phd: http://library.epfl.ch/theses/?nr=2774 li niu wrote: > Dear all, > > My question is: can PWSCF code be used to calculate Raman > spectrum of amorphous materials? How to do ?Any help would > be appreciate much! > best regards! > > niuli > > ------------------------------------------------------------------------ > Mp3???-??????? > -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From emenendez at macul.ciencias.uchile.cl Wed Jan 17 15:00:52 2007 From: emenendez at macul.ciencias.uchile.cl (Eduardo Ariel Menendez P) Date: Wed, 17 Jan 2007 11:00:52 -0300 (CLST) Subject: [Pw_forum] question on the pressure in molecular dynamics In-Reply-To: <6ac064b60701170635o56e0c0feydb4c40a783518075@mail.gmail.com> References: <6ac064b60701170635o56e0c0feydb4c40a783518075@mail.gmail.com> Message-ID: Hi, Let me insist in this question, as I have had no answer yet. > > Hi everybody, > I have a doubt concernig the pressure reported by pw or cp in a molecular > dynamics run. The stress tensor and its trace (the pressure) reported in > molecular > dynamics by pwscf and other > quantum codes is a static pressure. In a > molecular dinamics simulation, > if I want the "real" pressure, I must add > dp=(N/V) k_B T, N being the number of atoms and V the volume of the > cell, and T the instantaneous temperature or its meand value. > > In other words, the pressure of a non ideal gas (or liquid) is > > P=(N/V) k_B T + virial term (do not worry about the exact expression), > > then I understand that the pressure given by the codes is equivalent to > the virial term. > Is this correct? I found strange that nobody mentions it. > > Therefore, I understand that to have the "real" pressure I must add > (N/V)k_B T to the pressure reported by pw or cp. Please, correct me if I > am > wrong. > > Next level of question. If I do Parrinello-Rahman dynamics with a Nose > thermostast, what is the pressure specified by the keyword press ? Does > it include the thermal pressure? > I see that there is also a Nose thermostast for the cell. What is its > importance? Is it neccessary to use this cell thermostat for the NPT > ensemble? > Later I saw in the CP source that there is a subroutine 'add_thermal_stress', (which seems better than just 'add_thermal_press'), cpr_mod.f90: subroutine add_thermal_stress( stress, pmass, omega, h, vels, nsp, na ) However, I found no CALL to this subroutine. Then my doubt increased. Eduardo From naromero at gmail.com Wed Jan 17 16:00:33 2007 From: naromero at gmail.com (Nichols A. Romero) Date: Wed, 17 Jan 2007 10:00:33 -0500 Subject: [Pw_forum] MD simulations of polar liquids In-Reply-To: References: <20070104063806.6567.30260.Mailman@democritos.sissa.it> Message-ID: <6ac064b60701170700p44ca2c6drd2cecc99133e56c6@mail.gmail.com> Thanks to Paul Tangney for a very comprehensive and useful explanation. I believe that you are absolute right wrt to the issues to the electrostatic issues that arise in DFT vs. classical MD calculations. I would like to expand upon the issue that I am running into in the hopes that somebody on the list may have an idea. I am studying liquid nitromethane in a VERY small unit cell. There are only 8 nitromethane molecules. Already a problematic systems because the predominat interaction is vdW. It is also at a very low density. I run an NVT simulation for about 8 ps. I wrote a seperate program that takes each nitromethane molecular and calculation the translational kinetic energy, rotation kinetic energy of the molecular (I recalculate the moment of inertia at each step) and outputs a temperature based on those quantities, e.g. T_trans=KE_trans/(3*N_mol) Anyhow, if the system is properly equilibrated, I would think that the average T_trans and T_rot would be equal to the imposed temperature by the thermostat. However, I am finding that it is lower by 20-40% lower. My only ideas are that: 1. That this system requires ALOT more time to equilibrate. 2. That initially all the energy must be getting locked into intramolecular vibrations. Ideas anyone? On 1/4/07, Paul Tangney wrote: > > > Hi Nichols, > > Dipole corrections to what quantity ? > > There is now a large literature on macroscopic polarization > in the context of DFT (Resta, Vanderbilt and others) but if > I understand your problem correctly, it is not necessary for > you to delve into this. > > Slabs with net dipole moments under periodic boundary > conditions are problematic because, in a slab calculation, > you don't generally want the periodic images to 'see' each other, but > a slab with a strong moment interacts with its images. > If a dipole approximation is valid (if the spatial separation > of charges is small compared to your unit cell) the dipole-dipole > interaction decays with 1/r^5. > > For a bulk liquid, the problem should be much less serious because > it is less ordered and there is no vacuum. > There shouldn't be any strong multipole moments and any moments that > do exist should be well screened and transient. > > Finite size effects are *much* *much* more serious for simple > classical MD - particularly when only point-charge electrostatics > are included. The reason is that, even in strongly ionic materials > such as NaCl, water or silica, very simple electronic screening mechanisms > (such as screening from polarizable atoms) are sufficient > to kill electrostatic interactions within a few nanometers..and usually > within 1 nm. On the other hand, finite size effects in MD with simple > classical potentials are large because the only screening is from > the ions themselves and occurs on ionic time scales. > As a result, some physical properties (e.g. thermal expansion) require > 1000 to 10000 atoms for convergence while the same property with > DFT is converged with 50 to 100 atoms. > > I have been waving my hands while typing this - I'm going by > my experience but these issues are poorly controlled, and > should be investigated more thoroughly. > Hopefully somebody will have the time some day. > > Best regards, > > Paul > > > Hi, > > > > This is a question regarding the NVT MD simulation of a polar liquid, > i.e. a > > molecular fluid with a dipole moment (e.g. water, nitromethane, etc.) > > > > When dealing with a polar slab, there are dipole corrections to > consider. > > This comes from a net dipole moment. Is there a similar issue with the > NVT > > MD simulation of a polar liquid? My co-works here (Army Research Lab) > have > > told me that there are such issues with there classical (non-DFT) > simulation > > but that the corrections become smaller as one increases the system > size. > > > > Does anyone no of such discussion at the DFT level which may be found in > > the literature? > > > > Bests, > > > > -- > ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo > Paul Tangney > Theory of Nanostructured Materials Facility > The Molecular Foundry > Lawrence Berkeley National Lab. E-mail: PTTangney at lbl.gov > 1 Cyclotron Road, Bldg 67 Phone: (510) 495-2769 > Berkeley, CA 94720 > ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Nichols A. Romero, Ph.D. 1613 Denise Dr. Apt. D Forest Hill, MD 21050 443-567-8328 (C) 410-306-0709 (O) -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070117/10ad35ca/attachment.htm From degironc at sissa.it Wed Jan 17 18:10:43 2007 From: degironc at sissa.it (degironc) Date: Wed, 17 Jan 2007 18:10:43 +0100 Subject: [Pw_forum] question on the pressure in molecular dynamics In-Reply-To: References: <6ac064b60701170635o56e0c0feydb4c40a783518075@mail.gmail.com> Message-ID: <45AE5893.1060803@sissa.it> If you want the real pressure you should do a real (so to speak) dynamics in a variable cell. In such a case the system will be evoluted according to a Parrinello-Raman or Wentzcovitch extended Lagrangian and the system (after equilibration) will fluctuate around the pressure specified in the input [variable press in the &CEL namelist]. Hope it helps, Stefano de Gironcoli Eduardo Ariel Menendez P wrote: >Hi, >Let me insist in this question, as I have had no answer yet. > > > > > Hi everybody, > > I have a doubt concernig the pressure reported by pw or cp in a molecular > > dynamics run. The stress tensor and its trace (the pressure) reported in > > molecular > > dynamics by pwscf and other > > quantum codes is a static pressure. In a > > molecular dinamics simulation, > > if I want the "real" pressure, I must add > > dp=(N/V) k_B T, N being the number of atoms and V the volume of the > > cell, and T the instantaneous temperature or its meand value. > > > > In other words, the pressure of a non ideal gas (or liquid) is > > > > P=(N/V) k_B T + virial term (do not worry about the exact expression), > > > > then I understand that the pressure given by the codes is equivalent to > > the virial term. > > Is this correct? I found strange that nobody mentions it. > > > > Therefore, I understand that to have the "real" pressure I must add > > (N/V)k_B T to the pressure reported by pw or cp. Please, correct me if I > > am > > wrong. > > > > Next level of question. If I do Parrinello-Rahman dynamics with a Nose > > thermostast, what is the pressure specified by the keyword press ? Does > > it include the thermal pressure? > > I see that there is also a Nose thermostast for the cell. What is its > > importance? Is it neccessary to use this cell thermostat for the NPT > > ensemble? > > >Later I saw in the CP source that there is a subroutine >'add_thermal_stress', (which seems better than just 'add_thermal_press'), > >cpr_mod.f90: subroutine add_thermal_stress( stress, pmass, omega, h, vels, nsp, na ) > >However, I found no CALL to this subroutine. Then my doubt increased. > > >Eduardo > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From akohlmey at cmm.chem.upenn.edu Wed Jan 17 18:30:33 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 17 Jan 2007 12:30:33 -0500 (EST) Subject: [Pw_forum] MD simulations of polar liquids In-Reply-To: <6ac064b60701170700p44ca2c6drd2cecc99133e56c6@mail.gmail.com> Message-ID: On Wed, 17 Jan 2007, Nichols A. Romero wrote: NR> I am studying liquid nitromethane in a VERY small unit cell. There are only NR> 8 nitromethane molecules. NR> Already a problematic systems because the predominat interaction is vdW. It NR> is also at a very low density. NR> I run an NVT simulation for about 8 ps. I wrote a seperate program that NR> takes each nitromethane molecular NR> and calculation the translational kinetic energy, rotation kinetic energy of NR> the molecular (I recalculate NR> the moment of inertia at each step) and outputs a temperature based on those NR> quantities, e.g. T_trans=KE_trans/(3*N_mol) NR> NR> Anyhow, if the system is properly equilibrated, I would think that the NR> average T_trans and T_rot would be equal NR> to the imposed temperature by the thermostat. However, I am finding that it NR> is lower by 20-40% lower. My only NR> ideas are that: NR> 1. That this system requires ALOT more time to equilibrate. NR> 2. That initially all the energy must be getting locked into intramolecular NR> vibrations. to get equipartitioning of the kinetic energy between all degrees of freedom, you will have to run individual thermostats on all of them (so-called massive nose-hoover chains). the transfer between rotational and translational degrees of freedom is generally slow and in smaller systems even more so. if you start from a classical pre-equilibration it is quite likely that you will provide a high excitation of the vibrational modes, due to bond lengths being different. rotations (i.e. orientation) should be less critical, particularly at lower density. please note, that using massive thermostatting will improve ergodicity, but also modifies your dynamics significantly (= win some, lose some ;-). also, and that may be even more important here, with only 8 molecules each molecule will 'see' the _same_ molecule on the 'both sides' in each direction, due to PBC. which should - to some degree - force all rotations to be somewhat synchronized across the whole 'crystal'. i have not looked at anything that small, but you can should be able to verify the impact of that effect from classical MD, where equilibration is not a problem. cheers, axel. NR> NR> Ideas anyone? -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From marzari at MIT.EDU Wed Jan 17 18:42:57 2007 From: marzari at MIT.EDU (Nicola Marzari) Date: Wed, 17 Jan 2007 12:42:57 -0500 Subject: [Pw_forum] question on the pressure in molecular dynamics In-Reply-To: <45AE5893.1060803@sissa.it> References: <6ac064b60701170635o56e0c0feydb4c40a783518075@mail.gmail.com> <45AE5893.1060803@sissa.it> Message-ID: <45AE6021.6010205@mit.edu> Another way of saying this: two supercells containing the same partincles in the same positions, but with different velocities (e.g. in one case zero, in the other very large) will have the same instantaneous stress, but will have different average pressures, and in a constant pressure molecular dynamics will lead to different average volumes. nicola degironc wrote: > If you want the real pressure you should do a real (so to speak) > dynamics in a variable cell. > In such a case the system will be evoluted according to a > Parrinello-Raman or Wentzcovitch > extended Lagrangian and the system (after equilibration) will fluctuate > around the pressure > specified in the input [variable press in the &CEL namelist]. > Hope it helps, > Stefano de Gironcoli > > Eduardo Ariel Menendez P wrote: > >> Hi, >> Let me insist in this question, as I have had no answer yet. >> >> > >> > Hi everybody, >> > I have a doubt concernig the pressure reported by pw or cp in a >> molecular >> > dynamics run. The stress tensor and its trace (the pressure) >> reported in >> > molecular >> > dynamics by pwscf and other >> > quantum codes is a static pressure. In a >> > molecular dinamics simulation, >> > if I want the "real" pressure, I must add >> > dp=(N/V) k_B T, N being the number of atoms and V the volume of the >> > cell, and T the instantaneous temperature or its meand value. >> > >> > In other words, the pressure of a non ideal gas (or liquid) is >> > >> > P=(N/V) k_B T + virial term (do not worry about the exact expression), >> > >> > then I understand that the pressure given by the codes is equivalent to >> > the virial term. >> > Is this correct? I found strange that nobody mentions it. >> > >> > Therefore, I understand that to have the "real" pressure I must add >> > (N/V)k_B T to the pressure reported by pw or cp. Please, correct me >> if I >> > am >> > wrong. >> > >> > Next level of question. If I do Parrinello-Rahman dynamics with a Nose >> > thermostast, what is the pressure specified by the keyword press ? >> Does >> > it include the thermal pressure? >> > I see that there is also a Nose thermostast for the cell. What is its >> > importance? Is it neccessary to use this cell thermostat for the NPT >> > ensemble? >> > >> Later I saw in the CP source that there is a subroutine >> 'add_thermal_stress', (which seems better than just 'add_thermal_press'), >> >> cpr_mod.f90: subroutine add_thermal_stress( stress, pmass, omega, h, >> vels, nsp, na ) >> >> However, I found no CALL to this subroutine. Then my doubt increased. >> >> >> Eduardo ----------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu From ceresoli at sissa.it Wed Jan 17 18:36:33 2007 From: ceresoli at sissa.it (Davide Ceresoli) Date: Wed, 17 Jan 2007 18:36:33 +0100 Subject: [Pw_forum] question on the pressure in molecular dynamics In-Reply-To: References: <6ac064b60701170635o56e0c0feydb4c40a783518075@mail.gmail.com> Message-ID: <45AE5EA1.70208@sissa.it> Dear Eduardo, you are totally right regarding the pressure. At finite temperature, even at constant volume, you must add the kinetic contribution to the pressure. This contribution always tends to "expand" the solid and for high enough temperature, it may become important. I've looked at the Andersen and Parrinello-Rahman papers, and the kinetic term is always present in the formulas. The "external" pressure you apply on the system must to balance both the kinetic term and the virial term. So, the kinetic term is correctly taken into account in the P-R equations of motion, in the code. Could be that this contribution (which averages to P_kin = (N/V) k_B T) is not printed in output. Regards, Davide Eduardo Ariel Menendez P wrote: > Hi, > Let me insist in this question, as I have had no answer yet. > > > > > Hi everybody, > > I have a doubt concernig the pressure reported by pw or cp in a molecular > > dynamics run. The stress tensor and its trace (the pressure) reported in > > molecular > > dynamics by pwscf and other > > quantum codes is a static pressure. In a > > molecular dinamics simulation, > > if I want the "real" pressure, I must add > > dp=(N/V) k_B T, N being the number of atoms and V the volume of the > > cell, and T the instantaneous temperature or its meand value. > > > > In other words, the pressure of a non ideal gas (or liquid) is > > > > P=(N/V) k_B T + virial term (do not worry about the exact expression), > > > > then I understand that the pressure given by the codes is equivalent to > > the virial term. > > Is this correct? I found strange that nobody mentions it. > > > > Therefore, I understand that to have the "real" pressure I must add > > (N/V)k_B T to the pressure reported by pw or cp. Please, correct me if I > > am > > wrong. > > > > Next level of question. If I do Parrinello-Rahman dynamics with a Nose > > thermostast, what is the pressure specified by the keyword press ? Does > > it include the thermal pressure? > > I see that there is also a Nose thermostast for the cell. What is its > > importance? Is it neccessary to use this cell thermostat for the NPT > > ensemble? > > > Later I saw in the CP source that there is a subroutine > 'add_thermal_stress', (which seems better than just 'add_thermal_press'), > > cpr_mod.f90: subroutine add_thermal_stress( stress, pmass, omega, h, vels, nsp, na ) > > However, I found no CALL to this subroutine. Then my doubt increased. > > > Eduardo > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From degironc at sissa.it Wed Jan 17 23:10:09 2007 From: degironc at sissa.it (degironc) Date: Wed, 17 Jan 2007 23:10:09 +0100 Subject: [Pw_forum] a question about a calculation on a relatively large system In-Reply-To: References: Message-ID: <45AE9EC1.30000@sissa.it> What happens if you restart the calculation (restart_mode='restart' in &CONTROL namelist) ? does it go on or does it stop at the same point ? stefano Peter Winey wrote: > Dear all, > > I am trying to do a structural relaxation on a relatively large > system, which > has 240 atoms in one unit cell. > > I know it may sound crazy, but the crystal contains only C and H atoms, > so I thought that my cluster might be able to handle it. > > Indeed, I was able to run pwscf structural relaxation calculations. > The 1st > iteration finished ok. However, at the end of the 2nd iteration (which > also > finished ok), after the program printed out: > ------------------------------------------ > ... > number of scf cycles = 2 > number of bfgs steps = 1 > energy old = - 2084.xxx > energy new = - 2086.xxx > CASE: energy_new < energy_old > ------------------------------------------ > The run stopped without giving any information expect saying that "mpi > stopped without calling mpi_finalize" or sth like that. > > I repeated the calculation and it always stopped at the same place. > It is wierd since I had no problem before when running smaller systems > (say, 150 atoms). > > Could some one give me a hint on what could be the reason? Is it related > to the system size? If so, I have no idea why the pw.x program is able to > finish the first and the second iteration, but does not continue... > > Thanks in advance for any suggestions that you may have! > > -Peter > > ******************************************** > Peter Winey, Ph.D., DuPont > peterwiney at gmail.com > ******************************************** From eyvaz_isaev at yahoo.com Thu Jan 18 02:45:18 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 17 Jan 2007 17:45:18 -0800 (PST) Subject: [Pw_forum] Sorry Message-ID: <287637.69114.qm@web60321.mail.yahoo.com> Dear all, My apologies for not replying, I am quite busy, but hopefully in few days I will be able to answer to your questions and send the QHA code. Very bests, Eyvaz. ____________________________________________________________________________________ It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar. http://tools.search.yahoo.com/toolbar/features/mail/ -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070117/98209c9c/attachment.htm From yuwen_66 at yahoo.com Thu Jan 18 03:30:12 2007 From: yuwen_66 at yahoo.com (W. YU) Date: Wed, 17 Jan 2007 18:30:12 -0800 (PST) Subject: [Pw_forum] Free energy w.r.t. T and QHA Message-ID: <757074.21103.qm@web51013.mail.yahoo.com> Dear PW users, I have found that any code capable of phonon calculation (including PWscf-phonon)) would calculate the curve of F as a function of T under the framework of qausi-harmonic approximation (QHA). My question is: Is this calculation (F as a function of T)of any real significance? Since under QHA, free energy F is a funciton of temperature T and volume V. In a real situation, the system volume would change with temperature T, so does the phonon spectrum. Thus, in calculation of F(T) curve, we need phonon spectrum at each specific T which is sure different under QHA. This is for sure not the practice done by any codes. F is simply calculated with only a specific set of spectra (usually the spectra at static equilibrium geometry). It is understandable if this sort of calculation neglects the thermal expansion, but we will end up with harmonic approxiation then. Yes, from my own experience, the changes of phonon spectrum are small w.r.t. volume, but at least in principle it should be accounted for. Anybody interested? plase give some comments,thanks! W. YU ____________________________________________________________________________________ Need Mail bonding? Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users. http://answers.yahoo.com/dir/?link=list&sid=396546091 From degironc at sissa.it Thu Jan 18 09:26:40 2007 From: degironc at sissa.it (degironc) Date: Thu, 18 Jan 2007 09:26:40 +0100 Subject: [Pw_forum] Free energy w.r.t. T and QHA In-Reply-To: <757074.21103.qm@web51013.mail.yahoo.com> References: <757074.21103.qm@web51013.mail.yahoo.com> Message-ID: <45AF2F40.5050203@sissa.it> In order to calculate the static equilibrium one calculates the energy E(a) as a function of the structural parameters (these can be just the lattice parameter for simple elementary solids or include several internal coordinates for more complex solids or surface coordinates if you look to surfaces) and search for the minimum. This however does not contain in any way the effect of temperature, not even the Zero-Point Energy. In QHA you do the same thing. You calculate the free-energy, F(T,a), as a function of the structural parameters and search for the minimum. This provides you with a reasonable approximation of structural thermal effects (that is thermal expansion) if you are well below melting point. You can the estimate thermal effect on vibrational, elastic and electronic properties as well ... to the extent they are associated with the stuctural change and not to "truly anharmonic effects" beyound QHA. You may find interesting/clarifying to have a look to M.Lazzeri, and S.deGironcoli, Phys. Rev. B65, 245402 (2002),"A first principles study of the thermal expansion of Be (1 0 1_bar 0)" M.Lazzeri, and S.deGironcoli, Phys. Rev. Lett. 81, 2096 (1998), "Ab-Initio Study of Be (0001) Surface Thermal Expansion" hope this helps, stefano W. YU wrote: >Dear PW users, > >I have found that any code capable of phonon >calculation (including PWscf-phonon)) would calculate >the curve of F as a function of T under the framework >of qausi-harmonic approximation (QHA). > >My question is: Is this calculation (F as a function >of T)of any real significance? Since under QHA, free >energy F is a funciton of temperature T and volume V. >In a real situation, the system volume would change >with temperature T, so does the phonon spectrum. Thus, >in calculation of F(T) curve, we need phonon spectrum >at each specific T which is sure different under QHA. >This is for sure not the practice done by any codes. F >is simply calculated with only a specific set of >spectra (usually the spectra at static equilibrium >geometry). It is understandable if this sort of >calculation neglects the thermal expansion, but we >will end up with harmonic approxiation then. > >Yes, from my own experience, the changes of phonon >spectrum are small w.r.t. volume, but at least in >principle it should be accounted for. > >Anybody interested? plase give some comments,thanks! > >W. YU > > > > > > >____________________________________________________________________________________ >Need Mail bonding? >Go to the Yahoo! Mail Q&A for great tips from Yahoo! Answers users. >http://answers.yahoo.com/dir/?link=list&sid=396546091 >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From yuwen_66 at yahoo.com Thu Jan 18 10:00:53 2007 From: yuwen_66 at yahoo.com (W. YU) Date: Thu, 18 Jan 2007 01:00:53 -0800 (PST) Subject: [Pw_forum] RE: Free energy w.r.t. T and QHA Message-ID: <649062.74666.qm@web51004.mail.yahoo.com> Dear Stefano, Thank you very much for your explanations. Maybe I didn't make myself clear enough! I understand the general processures of a QHA calculation, but what really bothers me is that many DFT code with phonon functionality simply calculates F-T relationship at a SPECIFIC volume and made a F-T curve. Of course, there is nothing wrong in doing so if no real situation is considered since F IS a function of T and V (or other structural parameters). But this is in fact incorrect when thermal expansion is concerned in the spirit of QHA. Then in order to make a F-T curve, phonon spectrum has to be found at each equilibrium geometry under the given T instead of the single set of spectra. Hope I have made it clearer this time! Thanks W. YU ____________________________________________________________________________________ Get your own web address. Have a HUGE year through Yahoo! Small Business. http://smallbusiness.yahoo.com/domains/?p=BESTDEAL From degironc at sissa.it Thu Jan 18 10:15:24 2007 From: degironc at sissa.it (degironc) Date: Thu, 18 Jan 2007 10:15:24 +0100 Subject: [Pw_forum] RE: Free energy w.r.t. T and QHA In-Reply-To: <649062.74666.qm@web51004.mail.yahoo.com> References: <649062.74666.qm@web51004.mail.yahoo.com> Message-ID: <45AF3AAC.9020503@sissa.it> Sorry but I don't understand... the root of the QHA is the assumption that phonon spectra depend on the structure but not on the temperature (other than for the dependenceof the structure on T). That is: QHA assumes that omega(a,T) is actually omega(a(T)) and calculates a(T) and all derived properties with the procedure I recalled previously. This is obviously an approximation to reality and these is the reason for the A in QHA. stefano W. YU wrote: >Dear Stefano, > >Thank you very much for your explanations. > >Maybe I didn't make myself clear enough! > >I understand the general processures of a QHA >calculation, but what really bothers me is that many >DFT code with phonon functionality simply calculates >F-T relationship at a SPECIFIC volume and made a F-T >curve. Of course, there is nothing wrong in doing so >if no real situation is considered since F IS a >function of T and V (or other structural parameters). >But this is in fact incorrect when thermal expansion >is concerned in the spirit of QHA. Then in order to >make a F-T curve, phonon spectrum has to be found at >each equilibrium geometry under the given T instead of >the single set of spectra. > >Hope I have made it clearer this time! Thanks > >W. YU > > > > > > >____________________________________________________________________________________ >Get your own web address. >Have a HUGE year through Yahoo! Small Business. >http://smallbusiness.yahoo.com/domains/?p=BESTDEAL >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From chen_shao_hua197 at yahoo.com.tw Thu Jan 18 10:44:36 2007 From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=) Date: Thu, 18 Jan 2007 17:44:36 +0800 (CST) Subject: [Pw_forum] how to use lambda.x to get Eliashberg coefficient "alpha^2F(w)"? Message-ID: <733398.82831.qm@web73005.mail.tp2.yahoo.com> Dear members, The "User's Guide" have mentioned that one can use lambda.x to get Eliashberg coefficient "alpha^2F(w)". But I don't see this procedure in Examples directory. Can anyone tell me how to use lambda.x to get it ? Thank you very much !! max ___________________________________________________ ??????? ? ???????????????? http://messenger.yahoo.com.tw/ From giannozz at nest.sns.it Thu Jan 18 11:38:57 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 18 Jan 2007 11:38:57 +0100 Subject: [Pw_forum] how to use lambda.x to get Eliashberg coefficient "alpha^2F(w)"? In-Reply-To: <733398.82831.qm@web73005.mail.tp2.yahoo.com> References: <733398.82831.qm@web73005.mail.tp2.yahoo.com> Message-ID: On Jan 18, 2007, at 10:44 , ? ?? wrote: > The "User's Guide" have mentioned that one can use > lambda.x to get Eliashberg coefficient "alpha^2F(w)". > But I don't see this procedure in Examples directory. > Can anyone tell me how to use lambda.x to get it ? the lambda.x code is actually obsolete. It uses a file format that is no longer there. It should be easily adapted to the new format (or vice versa) but there is an alternative way to calculate the Eliashberg function, used in example 7. Such procedure is mostly undocumented and UNTESTED. Whoever wants to calculate electron-phonon coefficients should 1) know what he/she is doing, 2) carefully test that the results make sense Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From yuwen_66 at yahoo.com Thu Jan 18 13:11:37 2007 From: yuwen_66 at yahoo.com (W. YU) Date: Thu, 18 Jan 2007 04:11:37 -0800 (PST) Subject: [Pw_forum] Free energy w.r.t. T and QHA Message-ID: <97527.16167.qm@web51003.mail.yahoo.com> Dear Stefano and all, I am sorry that I couldn't make my question clear. Maybe someone who trys to read the small code called 'fqha' in the pwtools directory would know what I am trying to elaborate. I have no idea who wrote it but I think it does a similar work (that is, given a single phonon dos, calculate F at different T). The author must have some reasons in mind for doing this! W. YU ____________________________________________________________________________________ Be a PS3 game guru. Get your game face on with the latest PS3 news and previews at Yahoo! Games. http://videogames.yahoo.com/platform?platform=120121 From baroni at sissa.it Thu Jan 18 14:35:48 2007 From: baroni at sissa.it (Stefano Baroni) Date: Thu, 18 Jan 2007 14:35:48 +0100 Subject: [Pw_forum] Free energy w.r.t. T and QHA In-Reply-To: <97527.16167.qm@web51003.mail.yahoo.com> References: <97527.16167.qm@web51003.mail.yahoo.com> Message-ID: <433FE3E0-2138-4055-AC50-1CC8CCB5B323@sissa.it> On Jan 18, 2007, at 1:11 PM, W. YU wrote: > Dear Stefano and all, > > I am sorry that I couldn't make my question clear. > > Maybe someone who trys to read the small code called > 'fqha' in the pwtools directory would know what I am > trying to elaborate. maybe someone who tries to read a textbook on the QHA (Landau and Lifchitz's Statistical Physics could be an excellent choice) would know how the QHA works ... > I have no idea who wrote it but I think it does a > similar work (that is, given a single phonon dos, > calculate F at different T). The author must have some > reasons in mind for doing this! sure, he/she does! Stefano Baroni --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070118/0b893868/attachment.htm From babazade at gmail.com Thu Jan 18 15:36:14 2007 From: babazade at gmail.com (Amin Babazadeh) Date: Thu, 18 Jan 2007 18:06:14 +0330 Subject: [Pw_forum] electrical conductivity Message-ID: dear users I will appreciate if someone tell me how i can calculate electrical conductivity in espresso? thanks a lot sincerely yours -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070118/200998c6/attachment.htm From smogunov at sissa.it Thu Jan 18 16:03:55 2007 From: smogunov at sissa.it (Alexandre Smogunov) Date: Thu, 18 Jan 2007 16:03:55 +0100 Subject: [Pw_forum] electrical conductivity In-Reply-To: References: Message-ID: <1169132635.45af8c5bb99f1@webmail.sissa.it> Dear Amin What is implemented in ESPRESSO (in the PWCOND subdirectory) is the calculation of the ballistic conductance in nanocontacts which is actually proportinal to the total electron transmission at the Fermi energy (Landauer-Buttiker formula). The system you set up is {metal lead+scatterer+metal lead} then you run pw.x to calculate the self-consistent potential and use further pwcond.x to solve the scattering problem and to calculate transmission and reflection coefficients. regards, Alexander Smogunov Quoting Amin Babazadeh : > dear users > I will appreciate if someone tell me how i can calculate electrical > conductivity in espresso? > thanks a lot > sincerely yours > > -- > AMIN > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From emenendez at macul.ciencias.uchile.cl Thu Jan 18 16:12:41 2007 From: emenendez at macul.ciencias.uchile.cl (Eduardo Ariel Menendez P) Date: Thu, 18 Jan 2007 12:12:41 -0300 (CLST) Subject: [Pw_forum] Re: Free energy w.r.t. T and QHA In-Reply-To: <20070118133601.2280.41690.Mailman@democritos.sissa.it> References: <20070118133601.2280.41690.Mailman@democritos.sissa.it> Message-ID: > > > >My question is: Is this calculation (F as a function > >of T)of any real significance? Since under QHA, free > >energy F is a funciton of temperature T and volume V. I don't know if this is the goal of fqha or if it is useful, but thermodynamics books state that -dF/dT at constant volume is the entropy. > >In a real situation, the system volume would change > >with temperature T, so does the phonon spectrum. Thus, > >in calculation of F(T) curve, we need phonon spectrum > >at each specific T which is sure different under QHA. After you read the foundations of QHA in Laundau&Lihshits or in Ashcroft&Mermin, consider the following method 1) For a certain volume you calculate the phonon DOS. 2) With phonon DOS you (fqha.f90) calculate F(V,T), i.e. the free energy at this volume and at the temperature T that you want. 3) Repeat 1 and 2 for other volumes. You will have a different phonon DOS for each volume (just do it and look). Note that here you have gone beyond the QHA, because you are calculating with DFT. The same would happen if you use classical interatomic potentials like Lennard-Jones or Buckingham. However, if you use only spring-like interatomic potentials, then you obtain the same phonon DOS for any volume. In other words, if you use realistic potentials or DFT, the elastic constants (the second derivative of the energy funtion) depend on the volume. 4) If you did that, now you have a table of values of the function F(V,T). If you want the thermal expansion, consider that the pressure is P=-dF/dV at constant T. Let f(V)=F(V,T) for any particular T. Solving (numerically) P=-df/dV you get V for this temperature. Repeating this for different temperatures you get a table of the function V(T) for this particular pressure. 5) If you want the equation of state, just calculate P=-dF/dV for all the T, then you have P(V,T). It is laborious, maybe you can automate it. Regards Eduardo From sanjeev0302 at rediffmail.com Thu Jan 18 19:36:42 2007 From: sanjeev0302 at rediffmail.com (Sanjeev Kumar Gupta) Date: 18 Jan 2007 18:36:42 -0000 Subject: [Pw_forum] Force constant Message-ID: <20070118183642.24425.qmail@webmail73.rediffmail.com> Dear Espresso users !! I will appreciate if someone tell me how I can calculate Force constant and Raman Spectra in espresso?. Can we calculate IR or Raman active mode also? Presently i am at STEP_4, in FONONI calculation. I am very thankful to all group member of Quantum-Espresso Scientist. Thanks a lot !! Sincerely yours Sanjeev Gupta ? ==================================================== Sanjeev Kumar Gupta Junior Research Fellow (DAE-BRNS) Computational Condensed Matter Physics Lab.(CCMP) Department of Physics, Faculty of Science, The M.S.University of Baroda, Vadodara - 390 002. Ph.No: +91-265-279 5339 (O) extn: 30-25 mobile:09374616019 Email: sanjeev0302 at rediffmail.com sanjeev0302 at yahoo.co.in skgupta-phy at msubaroda.ac.in ==================================================== Residential Address- Dr. Vikram Sarabhai Hall, Room No.-95, Boys' Hostel,M.S.University Campus, Pratapgunj,Vadodara-390 002,Gujarat,INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070118/aeccfe99/attachment.htm From hushujun at mail.sdu.edu.cn Fri Jan 19 04:40:42 2007 From: hushujun at mail.sdu.edu.cn (Shujun Hu) Date: Fri, 19 Jan 2007 11:40:42 +0800 Subject: [Pw_forum] Parallel error on the cluster Message-ID: <369178042.18730@mail.sdu.edu.cn> Dear Drs, When i start a parallel job on the 4 nodes pc cluster using the command: mpiexec -n 8 pw.x -npool 4 zno-pw.out & The following error information is given: [root at node01 7.05]# ############################################################ ############################################################ # UNRECOVERABLE ERROR (ierr=-1) # ERROR IN: iotk_scan_dat (iotk_dat.spp:723) # CVS Revision: 1.3 # Dat not found name=PSEUDO_DIR ################################################################################ ######################################## aborting job: while the following command is OK: mpiexec -n 4 pw.x -npool 2 zno-pw.out & The version of code is the newest PWSCF-3.2. However, the old version 3.1 can run correctly by using both the above commands to start the job. I donnt know why. I am waiting for your help. Best wishes. Shujun Hu Following is the input file: &CONTROL title = zno , calculation = 'relax' , restart_mode = 'scratch' , wf_collect = .true. , outdir = '/home/neshque/work/7.05/temp/' , pseudo_dir = '/home/neshque/work/PSEUDOPOTENTIAL/' , prefix = zno , disk_io = 'minimal' , verbosity = 'high' , nstep = 5000 , tstress = .true. , tprnfor = .true. , dt = 50 , forc_conv_thr = 5.0D-3 , etot_conv_thr = 1.0D-4 , / &SYSTEM ibrav = 1, celldm(1) = 15.1181, nat = 38, ntyp = 3 , ecutwfc = 40 , ecutrho = 200 , nosym = .false. , nbnd = 190, occupations = 'tetrahedra' , degauss = 0.005 , smearing = 'methfessel-paxton' , nspin = 2 , starting_magnetization(3) = 3, lda_plus_u = .false. , / &ELECTRONS electron_maxstep = 500, conv_thr = 1E-5 , startingpot = 'file' , startingwfc = 'atomic' , mixing_mode = 'plain' , mixing_beta = 0.4 , diagonalization = 'david' , diago_thr_init = 1E-3 , / &IONS ion_dynamics = 'damp' , / ATOMIC_SPECIES Zn 65.38000 Zn.pbe-van.UPF O 15.99940 O.pbe-rrkjus.UPF Co 58.9332 Co.pbe-nd-rrkjus.UPF ATOMIC_POSITIONS angstrom Zn 0.000 0.000 0.000 O 2.189 5.891 2.912 Zn 6.567 1.674 0.736 O 5.135 3.347 1.472 Zn 5.891 2.912 5.119 O 0.837 0.368 3.679 Zn 5.633 0.334 3.342 O 7.565 3.648 4.477 Zn 6.212 6.124 5.244 O 2.075 4.751 7.514 Zn 1.044 2.441 0.407 O 3.119 7.192 7.921 Zn 3.859 6.589 1.886 O 6.868 4.679 6.793 Co 2.777 3.773 5.728 O 4.933 1.327 5.274 Zn 0.779 7.786 5.861 O 6.974 5.742 1.422 Zn 4.477 4.768 7.684 O 4.684 6.841 4.411 Zn 1.447 6.471 0.708 O 2.682 2.816 4.159 Zn 3.980 7.796 5.958 O 0.612 6.117 5.175 Zn 3.458 2.578 1.781 O 5.615 0.147 1.472 Zn 0.189 1.891 2.909 O 4.458 4.577 5.772 Zn 7.713 5.130 3.303 O 1.746 1.459 6.589 Zn 7.037 6.372 7.717 O 1.139 3.393 1.931 Zn 4.435 4.351 3.512 O 5.509 7.088 6.879 Zn 0.400 2.400 5.600 O 2.320 1.040 1.600 Zn 2.480 0.960 4.160 O 4.080 1.680 7.760 K_POINTS automatic 4 4 4 1 1 1 From hushujun at mail.sdu.edu.cn Fri Jan 19 05:03:15 2007 From: hushujun at mail.sdu.edu.cn (Shujun Hu) Date: Fri, 19 Jan 2007 12:03:15 +0800 Subject: [Pw_forum] Please delete the Message "Parallel error on the cluster" Message-ID: <369179395.22966@mail.sdu.edu.cn> Dear Drs, I am very sorry for causing the trouble. I have found the answer. Please delete the Message "Parallel error on the cluster" and this one. Best wishes. Shujun Hu From konstantin_kudin at yahoo.com Fri Jan 19 06:02:33 2007 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Thu, 18 Jan 2007 21:02:33 -0800 (PST) Subject: [Pw_forum] vc-relax with PW In-Reply-To: <369179395.22966@mail.sdu.edu.cn> Message-ID: <270754.37761.qm@web57713.mail.re3.yahoo.com> Hi all, This is a public announcement coupled with a request for qualified help, so if you are NOT interested, please disregard. I added some constraints on cell coordinates for vc-relax to the CVS, so that one can optimize only a subset of those. Here is an example of cell_dynamics='damp-w' : input lattice vectors (alat, hexagonal cell, vacuum in Z) 1.000000 0.000000 0.000000 -0.500000 0.866025 0.000000 0.000000 0.000000 1.250000 first step stress: total stress (Ry/bohr**3) (kbar) P= -15.58 0.00066135 0.00012844 0.00000009 97.29 18.89 0.01 0.00012844 -0.00097768 -0.00000005 18.89 -143.82 -0.01 0.00000009 -0.00000005 -0.00000129 0.01 -0.01 -0.19 The old code would update to: 1.000003703 0.000000719 0.000000001 -0.500001229 0.866019900 0.000000000 0.000000001 0.000000000 1.249999991 The new code with constraints can do this: 1.000003703 0.000000000 0.000000000 -0.500000614 0.866019900 0.000000000 0.000000000 0.000000000 1.250000000 So only x1, x2, and y2 are updated. What is interesting is that it looks like the fully unconstrained code is somewhat rotating the lattice vectors (note the +delta_y1 and -delta_x2). If somebody understands what the VC code actually does, please take a look. Kostya ____________________________________________________________________________________ Do you Yahoo!? Everyone is raving about the all-new Yahoo! Mail beta. http://new.mail.yahoo.com From akohlmey at cmm.chem.upenn.edu Fri Jan 19 17:56:50 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Fri, 19 Jan 2007 11:56:50 -0500 (EST) Subject: [Pw_forum] Please delete the Message "Parallel error on the cluster" In-Reply-To: <369179395.22966@mail.sdu.edu.cn> Message-ID: On Fri, 19 Jan 2007, Shujun Hu wrote: SH> SH> Dear Drs, SH> I am very sorry for causing the trouble. I have found the answer. Please delete SH> the Message "Parallel error on the cluster" and this one. interesting request. however, you have to get used to the fact that everything that is posted in forums like this one, will survive _much_ longer than you think. if you have an somewhat uncommon name like me, it is amazing to see what comes up if you search in a web search engine for it. e.g. i found e-mails i sent to the linux kernel mailing list over 10 years ago. nobody expected at that time, that these mails would be archived on multiple servers all around the world. it is also a good lesson to see, how fast one forgets that everybody is a beginner and thus makes beginner's mistakes at some point. ;-) cheers, axel. SH> SH> Best wishes. SH> SH> Shujun Hu SH> SH> SH> _______________________________________________ SH> Pw_forum mailing list SH> Pw_forum at pwscf.org SH> http://www.democritos.it/mailman/listinfo/pw_forum SH> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From babazade at gmail.com Sat Jan 20 07:30:09 2007 From: babazade at gmail.com (Amin Babazadeh) Date: Sat, 20 Jan 2007 10:00:09 +0330 Subject: [Pw_forum] electrical conductivity In-Reply-To: <1169132635.45af8c5bb99f1@webmail.sissa.it> References: <1169132635.45af8c5bb99f1@webmail.sissa.it> Message-ID: Dear Dr.Alexandre Thanks a lot for your recommendation.But i have one more question.would you please give some references for theory of calculation of transmission coefficient by using scattering.I read your paper (Complex band structure with ultrasoft pseudopotential:fcc Ni ...) and it was so helpful for understanding the theory of calculating complex band structure.but now i am interesting to know how we can use the complex band structure to find transmission coefficient. sincerely yours On 1/18/07, Alexandre Smogunov wrote: > > Dear Amin > What is implemented in ESPRESSO (in the PWCOND subdirectory) > is the calculation of the ballistic conductance in nanocontacts which > is actually proportinal to the total electron transmission at the Fermi > energy (Landauer-Buttiker formula). > The system you set up is {metal lead+scatterer+metal lead} then > you run pw.x to calculate the self-consistent potential and use further > pwcond.x to solve the scattering problem and to calculate transmission and > reflection coefficients. > > regards, Alexander Smogunov > > Quoting Amin Babazadeh : > > > dear users > > I will appreciate if someone tell me how i can calculate electrical > > conductivity in espresso? > > thanks a lot > > sincerely yours > > > > -- > > AMIN > > > > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070120/e2b2dae3/attachment.htm From smogunov at sissa.it Sat Jan 20 09:39:17 2007 From: smogunov at sissa.it (Alexandre Smogunov) Date: Sat, 20 Jan 2007 09:39:17 +0100 Subject: [Pw_forum] electrical conductivity In-Reply-To: References: <1169132635.45af8c5bb99f1@webmail.sissa.it> Message-ID: <1169282357.45b1d535aafa0@webmail.sissa.it> Dear Amin For theory and computational procedure you can look at our papers: PRB 70, 045417 (2004); PRB 73, 075418 (2006). In our method we follow closely to the method of Choi and Ihm described in details in PRB 59, 2267 (1999). Recent extension of our method to spin-orbit coupling is given in PRB 74, 045429 (2006). For practical examples you can have look at example12 and example22 of ESPRESSO package. Good luck and feel free to ask any questions, Alexander. Phys. Rev. B 74, 045429 (2006) Quoting Amin Babazadeh : > Dear Dr.Alexandre > Thanks a lot for your recommendation.But i have one more question.would you > please give some references for theory of calculation of transmission > coefficient by using scattering.I read your paper (Complex band structure > with ultrasoft pseudopotential:fcc Ni ...) and it was so helpful for > understanding the theory of calculating complex band structure.but now i am > interesting to know how we can use the complex band structure to find > transmission coefficient. > sincerely yours > > > On 1/18/07, Alexandre Smogunov wrote: > > > > Dear Amin > > What is implemented in ESPRESSO (in the PWCOND subdirectory) > > is the calculation of the ballistic conductance in nanocontacts which > > is actually proportinal to the total electron transmission at the Fermi > > energy (Landauer-Buttiker formula). > > The system you set up is {metal lead+scatterer+metal lead} then > > you run pw.x to calculate the self-consistent potential and use further > > pwcond.x to solve the scattering problem and to calculate transmission and > > reflection coefficients. > > > > regards, Alexander Smogunov > > > > Quoting Amin Babazadeh : > > > > > dear users > > > I will appreciate if someone tell me how i can calculate electrical > > > conductivity in espresso? > > > thanks a lot > > > sincerely yours > > > > > > -- > > > AMIN > > > > > > > > > > > > > ---------------------------------------------------------------- > > SISSA Webmail https://webmail.sissa.it/ > > Powered by Horde http://www.horde.org/ > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > -- > AMIN > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From babazade at gmail.com Sat Jan 20 20:13:16 2007 From: babazade at gmail.com (Amin Babazadeh) Date: Sat, 20 Jan 2007 22:43:16 +0330 Subject: [Pw_forum] electrical conductivity In-Reply-To: <1169282357.45b1d535aafa0@webmail.sissa.it> References: <1169132635.45af8c5bb99f1@webmail.sissa.it> <1169282357.45b1d535aafa0@webmail.sissa.it> Message-ID: Dear Dr.Alexandre Thanks a lot for your help. best the wishes Amin On 1/20/07, Alexandre Smogunov wrote: > > Dear Amin > For theory and computational procedure you can look at our papers: > PRB 70, 045417 (2004); PRB 73, 075418 (2006). > In our method we follow closely to the method of Choi and Ihm > described in details in PRB 59, 2267 (1999). > Recent extension of our method to spin-orbit coupling is given in > PRB 74, 045429 (2006). > For practical examples you can have look at example12 and example22 > of ESPRESSO package. > Good luck and feel free to ask any questions, > Alexander. > > > > Phys. Rev. B 74, 045429 (2006) > > Quoting Amin Babazadeh : > > > Dear Dr.Alexandre > > Thanks a lot for your recommendation.But i have one more question.wouldyou > > please give some references for theory of calculation of transmission > > coefficient by using scattering.I read your paper (Complex band > structure > > with ultrasoft pseudopotential:fcc Ni ...) and it was so helpful for > > understanding the theory of calculating complex band structure.but now i > am > > interesting to know how we can use the complex band structure to find > > transmission coefficient. > > sincerely yours > > > > > > On 1/18/07, Alexandre Smogunov wrote: > > > > > > Dear Amin > > > What is implemented in ESPRESSO (in the PWCOND subdirectory) > > > is the calculation of the ballistic conductance in nanocontacts which > > > is actually proportinal to the total electron transmission at the > Fermi > > > energy (Landauer-Buttiker formula). > > > The system you set up is {metal lead+scatterer+metal lead} then > > > you run pw.x to calculate the self-consistent potential and use > further > > > pwcond.x to solve the scattering problem and to calculate transmission > and > > > reflection coefficients. > > > > > > regards, Alexander Smogunov > > > > > > Quoting Amin Babazadeh : > > > > > > > dear users > > > > I will appreciate if someone tell me how i can calculate electrical > > > > conductivity in espresso? > > > > thanks a lot > > > > sincerely yours > > > > > > > > -- > > > > AMIN > > > > > > > > > > > > > > > > > > > ---------------------------------------------------------------- > > > SISSA Webmail https://webmail.sissa.it/ > > > Powered by Horde http://www.horde.org/ > > > > > > _______________________________________________ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > > > > -- > > AMIN > > > > > > > ---------------------------------------------------------------- > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070120/8efd8803/attachment.htm From lanhaiping at gmail.com Sun Jan 21 10:10:15 2007 From: lanhaiping at gmail.com (lan haiping) Date: Sun, 21 Jan 2007 17:10:15 +0800 Subject: [Pw_forum] Question about Example10 In-Reply-To: References: Message-ID: Dear Paolo, I then test this result with ph.x code. The born effetive charge tensors obtained are greatly consistent with published results in Zhong et al (PRL.72.3618) , for O sites (-5.81,-2.57,- 2.57) , for Pb sites (3.92,3.92,3.92) (all are diagonal elements of E-U tensors). I then recalculated with Berry Phase method, and still cannot find satisfactory results for O sites. A typical resulted tensor is (-5.84, -1.90 ,-1.98). Would you please give some comments ? regards, h.p On 1/14/07, Paolo Giannozzi wrote: > > > On Jan 13, 2007, at 6:58 , lan haiping wrote: > > > I have a question about berry phase calculation for born effetive > > charge implemented in espresso. [...] I could obtain born > > effective tensor of Pb site > > about 3.9 -3.92 e whenever i increase ecutoffrho , conv_thr or use > > denser > > kmesh. But the born effective tensor of O sites , i.e . the three > > diagonal > > elements are not consistent with the result of Zhong et al (PRL. > > 72.3618). > > The values i obtained are -1.98 , -5.85, -1.90e respectively for > > 3 different > > directions. > > did you try linear response? If you get the same result, that's it > P. > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070121/03a88def/attachment.htm From shevgaonkar at gmail.com Tue Jan 23 08:57:24 2007 From: shevgaonkar at gmail.com (Prashant Shevgaonkar) Date: Tue, 23 Jan 2007 13:27:24 +0530 Subject: [Pw_forum] bug in atlas Message-ID: <141aec2e0701222357v3c2c1186xab1fe0643e9c04a1@mail.gmail.com> Atlas has recently (20Nov06) reported an error in computation of complex GEMM (C = A*B +C) for the special case B = Atransp. ( http://sourceforge.net/mailarchive/forum.php?thread_id=31031975&forum_id=434) How serious is this error and would this affect pwscf calculations? ------------------------------------------------------------------ Prashant Shevgaonkar, Chemical Engineering Department, Vishwakarma Institute of Technology, Pune, India 411 037 Email: shevgaonkar at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070123/ecceb4d5/attachment.htm From jhashemifar at gmail.com Tue Jan 23 11:43:48 2007 From: jhashemifar at gmail.com (Javad hashemifar) Date: Tue, 23 Jan 2007 11:43:48 +0100 Subject: [Pw_forum] problem in DOS Message-ID: <2fb18d9f0701230243t1e6d5e10wdd009b84ad06503b@mail.gmail.com> Dear Espresso users During DOS calculation I encountered a strange problem. When I run dos.x < inputfile it seems that the program doesn't do any thing. First I thought that probably dos.x did not realize the input file but when I modified some of the parameters in the input file, dos.x got error. After further check I found that the same problem occures for pp.x while there is no problem for pw.x in both scf and nscf calculation. Let me to note that we have installed pwscf in parallel version using the MPI libraries. I will appreciate your kind helps and comments. Javad Hashemifar From jhashemifar at gmail.com Tue Jan 23 11:59:31 2007 From: jhashemifar at gmail.com (Javad hashemifar) Date: Tue, 23 Jan 2007 11:59:31 +0100 Subject: [Pw_forum] problem in relaxation by using bfgs In-Reply-To: <85295439-6D82-46E8-8A2B-9EB4A4600AC1@nest.sns.it> References: <2fb18d9f0612220020x36188117g36a386607ebfb157@mail.gmail.com> <85295439-6D82-46E8-8A2B-9EB4A4600AC1@nest.sns.it> Message-ID: <2fb18d9f0701230259nc3f2b3pfd29c30e30e5c590@mail.gmail.com> Many thanks Dr Giannozzi for your kind attention. I found that if I use bfgs_ndim = 2 then the mentioned problem will not appear at all. If you find any reason behind this error please keep us (users) informed. Kind regards Javad Hashemifar On 1/16/07, Paolo Giannozzi wrote: > > On Dec 22, 2006, at 9:20 , Javad hashemifar wrote: > > > I am trying to relax a tetragonal interface supercell at different > > values of vertical lattice parameter (celldm(3)). I am using > > calculation=relax and the namelist IONS is as follows: > > > > ion_dynamic = bfgs > > bfgs_ndim = 3, > > pot_extrapolation = "second_order", > > wfc_extrapolation = "second_order", > > > > [...] For some values of celldm(3) every thing is OK and the system > > relax well and both etot_conv_thr and forc_conv_thr satisfies. But in > > some other values of celldm(3) the calculation stops with the > > following error: > > > > from checkallsym : error # 1 > > some of the original symmetry operations not satisfied > > we tried your test and actually there is a problem, but we don't > know what the problem is. Could you please verify if the error > happens also if you remove the line > bfgs_ndim = 3 > ? Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ====================================== Seyed Javad Hashemifar, Ph.D. [current:] Tel:+49-203-3794743 Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran --------------------------------------------------------------------------- From giannozz at nest.sns.it Tue Jan 23 12:15:53 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 23 Jan 2007 12:15:53 +0100 Subject: [Pw_forum] problem in DOS In-Reply-To: <2fb18d9f0701230243t1e6d5e10wdd009b84ad06503b@mail.gmail.com> References: <2fb18d9f0701230243t1e6d5e10wdd009b84ad06503b@mail.gmail.com> Message-ID: <7CBA77C7-0252-407A-B04E-F8FFD16DE688@nest.sns.it> On Jan 23, 2007, at 11:43 , Javad hashemifar wrote > When I run dos.x < inputfile it seems that the program doesn't do > any thing [...] we have installed pwscf in parallel version using the > MPI libraries. does it happen in parallel execution or also in serail execution? does "dos.x -inp inputfile" work? Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From lawrence_lee_lee at yahoo.com.hk Tue Jan 23 12:16:29 2007 From: lawrence_lee_lee at yahoo.com.hk (Lawrence Lee) Date: Tue, 23 Jan 2007 19:16:29 +0800 (CST) Subject: [Pw_forum] About Pseudo-Potential generation Message-ID: <531837.68363.qm@web54509.mail.yahoo.com> Dear all, I have serveral questions about PP generation. Please forgive me if there are any stupid question as I am a new in this field. (1) Comparing Rabe-Rappe-Kaxiras-Joannopoulos and Troullier-Martin pseudization, it seems that the former is simpler. But actually which one is better? Do each of them have their particular advantages. (2) What's the difference between using one channel as the local PP and pseudizing the all electron potential. (3) Sometimes, one will use fractional occupation such as [Ne]3s1.5 for Mg. Why's that? (4) If I want to do high pressure calculation later, does it mean that I must use a small core radius. Thanks for helping me! Lawrence _______________________________________ YM - ???? ??????????????????????????????????????????? http://messenger.yahoo.com.hk -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070123/7243f1bc/attachment.htm From giannozz at nest.sns.it Tue Jan 23 12:19:13 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 23 Jan 2007 12:19:13 +0100 Subject: [Pw_forum] Question about Example10 In-Reply-To: References: Message-ID: On Jan 21, 2007, at 10:10 , lan haiping wrote: > Dear Paolo you didn't read my recommandation not to address messages to me, did you? > The born effetive charge tensors obtained are greatly consistent > with published results in Zhong et al (PRL.72.3618) , for O sites > (-5.81,-2.57,-2.57) , for Pb sites (3.92,3.92,3.92) (all are > diagonal elements of E-U tensors). > > I then recalculated with Berry Phase method, and still cannot find > satisfactory results for O sites. A typical resulted tensor is > (-5.84, -1.90,-1.98). actually, results from Berry phase and from linear response methods coincide only at k-point convergence Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From jhashemifar at gmail.com Tue Jan 23 12:27:15 2007 From: jhashemifar at gmail.com (Javad hashemifar) Date: Tue, 23 Jan 2007 12:27:15 +0100 Subject: [Pw_forum] problem in DOS In-Reply-To: <7CBA77C7-0252-407A-B04E-F8FFD16DE688@nest.sns.it> References: <2fb18d9f0701230243t1e6d5e10wdd009b84ad06503b@mail.gmail.com> <7CBA77C7-0252-407A-B04E-F8FFD16DE688@nest.sns.it> Message-ID: <2fb18d9f0701230327x684a2996h4391a59b52e73a74@mail.gmail.com> Thanks for your reply. It happens in both parallel and serial execution. In fact I tested several possibilities: running in parallel on the same number of nodes that pw.x ran, running in serial after a parallel ran of pw.x, running a serial after a serial ran of pw.x, and in all cases the same problem happens. We are using the latest version of Espresso (released on Nov. 2006) Bests Javad Hashemifar On 1/23/07, Paolo Giannozzi wrote: > > On Jan 23, 2007, at 11:43 , Javad hashemifar wrote > > > When I run dos.x < inputfile it seems that the program doesn't do > > any thing [...] we have installed pwscf in parallel version using the > > MPI libraries. > > does it happen in parallel execution or also in serail execution? > does "dos.x -inp inputfile" work? > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ====================================== Seyed Javad Hashemifar, Ph.D. [current:] Tel:+49-203-3794743 Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran --------------------------------------------------------------------------- From jhashemifar at gmail.com Tue Jan 23 14:02:49 2007 From: jhashemifar at gmail.com (Javad hashemifar) Date: Tue, 23 Jan 2007 14:02:49 +0100 Subject: [Pw_forum] problem in DOS In-Reply-To: <2fb18d9f0701230327x684a2996h4391a59b52e73a74@mail.gmail.com> References: <2fb18d9f0701230243t1e6d5e10wdd009b84ad06503b@mail.gmail.com> <7CBA77C7-0252-407A-B04E-F8FFD16DE688@nest.sns.it> <2fb18d9f0701230327x684a2996h4391a59b52e73a74@mail.gmail.com> Message-ID: <2fb18d9f0701230502ue061c81oc2724c2d09932ef6@mail.gmail.com> Sorry, I forgot to say that "dos.x -inp inputfile" command also did not work! Javad Hashemifar On 1/23/07, Javad hashemifar wrote: > Thanks for your reply. > It happens in both parallel and serial execution. In fact I tested > several possibilities: running in parallel on the same number of nodes > that pw.x ran, running in serial after a parallel ran of pw.x, running > a serial after a serial ran of pw.x, and in all cases the same problem > happens. > We are using the latest version of Espresso (released on Nov. 2006) > > Bests > Javad Hashemifar > > On 1/23/07, Paolo Giannozzi wrote: > > > > On Jan 23, 2007, at 11:43 , Javad hashemifar wrote > > > > > When I run dos.x < inputfile it seems that the program doesn't do > > > any thing [...] we have installed pwscf in parallel version using the > > > MPI libraries. > > > > does it happen in parallel execution or also in serail execution? > > does "dos.x -inp inputfile" work? > > > > Paolo > > --- > > Paolo Giannozzi, Democritos and University of Udine, Italy > > > > > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > ====================================== > Seyed Javad Hashemifar, Ph.D. > [current:] > Tel:+49-203-3794743 Fax:+49-203-3794742 > Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen > 47048 Dusiburg, Germany > [permanent:] > Tel: +98-311-3912375 Fax: +98-311-3912376 > Physics Department, Isfahan University of Technology > 84156 Isfahan, Iran > --------------------------------------------------------------------------- > -- ====================================== Seyed Javad Hashemifar, Ph.D. [current:] Tel:+49-203-3794743 Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran --------------------------------------------------------------------------- From giannozz at nest.sns.it Tue Jan 23 14:35:11 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 23 Jan 2007 14:35:11 +0100 Subject: [Pw_forum] problem in DOS In-Reply-To: <2fb18d9f0701230502ue061c81oc2724c2d09932ef6@mail.gmail.com> References: <2fb18d9f0701230243t1e6d5e10wdd009b84ad06503b@mail.gmail.com> <7CBA77C7-0252-407A-B04E-F8FFD16DE688@nest.sns.it> <2fb18d9f0701230327x684a2996h4391a59b52e73a74@mail.gmail.com> <2fb18d9f0701230502ue061c81oc2724c2d09932ef6@mail.gmail.com> Message-ID: On Jan 23, 2007, at 14:02 , Javad hashemifar wrote: > Sorry, I forgot to say that "dos.x -inp inputfile" command also > did not work! does it work in at least some cases (for instance, example 8)? if not, it may be something related to your compiler or libraries. If it does, please provide a test job for a case that doesn't work Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From lanhaiping at gmail.com Tue Jan 23 15:09:00 2007 From: lanhaiping at gmail.com (lan haiping) Date: Tue, 23 Jan 2007 22:09:00 +0800 Subject: [Pw_forum] Question about Example10 In-Reply-To: References: Message-ID: :), thank you ! Actually, I read your recommandation about mailing-list. And i do reply the mail to the forum, not directly to you ! Thank you for your suggestion. I then test it , and report to the forum . Best wishes, Hai-Ping On 1/23/07, Paolo Giannozzi wrote: > > On Jan 21, 2007, at 10:10 , lan haiping wrote: > > > Dear Paolo > > you didn't read my recommandation not to address messages to me, > did you? > > > The born effetive charge tensors obtained are greatly consistent > > with published results in Zhong et al (PRL.72.3618) , for O sites > > (-5.81,-2.57,-2.57) , for Pb sites (3.92,3.92,3.92) (all are > > diagonal elements of E-U tensors). > > > > I then recalculated with Berry Phase method, and still cannot find > > satisfactory results for O sites. A typical resulted tensor is > > (-5.84, -1.90,-1.98). > > actually, results from Berry phase and from linear response methods > coincide only at k-point convergence > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070123/d28e773d/attachment.htm From jhashemifar at gmail.com Tue Jan 23 16:14:51 2007 From: jhashemifar at gmail.com (Javad hashemifar) Date: Tue, 23 Jan 2007 16:14:51 +0100 Subject: [Pw_forum] problem in DOS In-Reply-To: References: <2fb18d9f0701230243t1e6d5e10wdd009b84ad06503b@mail.gmail.com> <7CBA77C7-0252-407A-B04E-F8FFD16DE688@nest.sns.it> <2fb18d9f0701230327x684a2996h4391a59b52e73a74@mail.gmail.com> <2fb18d9f0701230502ue061c81oc2724c2d09932ef6@mail.gmail.com> Message-ID: <2fb18d9f0701230714q9370995wc98e4de61d9d03b@mail.gmail.com> No, it seems that it does not work for any case even for example 8. Would you please give some comments about possible compiler or library problems and the way it should be solved. Many thanks in advance Javad Hashemifar On 1/23/07, Paolo Giannozzi wrote: > > On Jan 23, 2007, at 14:02 , Javad hashemifar wrote: > > > Sorry, I forgot to say that "dos.x -inp inputfile" command also > > did not work! > > does it work in at least some cases (for instance, example 8)? > if not, it may be something related to your compiler or libraries. > If it does, please provide a test job for a case that doesn't work > > Paolo > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ====================================== Seyed Javad Hashemifar, Ph.D. [current:] Tel:+49-203-3794743 Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran --------------------------------------------------------------------------- From akohlmey at cmm.chem.upenn.edu Tue Jan 23 17:01:30 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 23 Jan 2007 11:01:30 -0500 (EST) Subject: [Pw_forum] problem in DOS In-Reply-To: <2fb18d9f0701230714q9370995wc98e4de61d9d03b@mail.gmail.com> Message-ID: On Tue, 23 Jan 2007, Javad hashemifar wrote: please try running in serial to make sure your input is correct. with some MPI implementations (e.g. MPICH and derived), you do not see any error output, since the connection is terminated before that text can be forwarded. axel. JH> No, it seems that it does not work for any case even for example 8. JH> Would you please give some comments about possible compiler or library JH> problems and the way it should be solved. JH> JH> Many thanks in advance JH> Javad Hashemifar JH> JH> On 1/23/07, Paolo Giannozzi wrote: JH> > JH> > On Jan 23, 2007, at 14:02 , Javad hashemifar wrote: JH> > JH> > > Sorry, I forgot to say that "dos.x -inp inputfile" command also JH> > > did not work! JH> > JH> > does it work in at least some cases (for instance, example 8)? JH> > if not, it may be something related to your compiler or libraries. JH> > If it does, please provide a test job for a case that doesn't work JH> > JH> > Paolo JH> > --- JH> > Paolo Giannozzi, Democritos and University of Udine, Italy JH> > JH> > JH> > _______________________________________________ JH> > Pw_forum mailing list JH> > Pw_forum at pwscf.org JH> > http://www.democritos.it/mailman/listinfo/pw_forum JH> > JH> JH> JH> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From konstantin_kudin at yahoo.com Tue Jan 23 17:26:22 2007 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Tue, 23 Jan 2007 08:26:22 -0800 (PST) Subject: [Pw_forum] bug in atlas In-Reply-To: <141aec2e0701222357v3c2c1186xab1fe0643e9c04a1@mail.gmail.com> Message-ID: <401563.17335.qm@web57709.mail.re3.yahoo.com> Dear Prashant, The question you are asking should be straightforward to figure out on your own. Just grep through the source code (it is GPL and is available), find all the instances of complex GEMM, and find those that utilize the special case. Then you can report your findings back to the list. Regards, Kostya --- Prashant Shevgaonkar wrote: > Atlas has recently (20Nov06) reported an error in computation of > complex > GEMM (C = A*B +C) for the special case B = Atransp. > ( > http://sourceforge.net/mailarchive/forum.php?thread_id=31031975&forum_id=434) > How serious is this error and would this affect pwscf calculations? > > ------------------------------------------------------------------ > Prashant Shevgaonkar, > Chemical Engineering Department, > Vishwakarma Institute of Technology, > Pune, India 411 037 > Email: shevgaonkar at gmail.com > ____________________________________________________________________________________ Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited From akohlmey at cmm.chem.upenn.edu Tue Jan 23 18:17:57 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 23 Jan 2007 12:17:57 -0500 (EST) Subject: [Pw_forum] bug in atlas In-Reply-To: <401563.17335.qm@web57709.mail.re3.yahoo.com> Message-ID: On Tue, 23 Jan 2007, Konstantin Kudin wrote: KK> Dear Prashant, KK> KK> The question you are asking should be straightforward to figure out on KK> your own. Just grep through the source code (it is GPL and is KK> available), find all the instances of complex GEMM, and find those that KK> utilize the special case. KK> KK> Then you can report your findings back to the list. good idea! and very useful, too. but sadly, that is only (the easy) half of the job. you also have to check the LAPACK subroutines that QE uses for the use of that problematic call, which is a bit messy since there are quite a few cross-calls from within lapack, so best is to check all of it. cheers, axel. KK> KK> Regards, KK> Kostya KK> KK> KK> --- Prashant Shevgaonkar wrote: KK> KK> > Atlas has recently (20Nov06) reported an error in computation of KK> > complex KK> > GEMM (C = A*B +C) for the special case B = Atransp. KK> > ( KK> > KK> http://sourceforge.net/mailarchive/forum.php?thread_id=31031975&forum_id=434) KK> > How serious is this error and would this affect pwscf calculations? KK> > KK> > ------------------------------------------------------------------ KK> > Prashant Shevgaonkar, KK> > Chemical Engineering Department, KK> > Vishwakarma Institute of Technology, KK> > Pune, India 411 037 KK> > Email: shevgaonkar at gmail.com KK> > KK> KK> KK> KK> KK> ____________________________________________________________________________________ KK> Yahoo! Music Unlimited KK> Access over 1 million songs. KK> http://music.yahoo.com/unlimited KK> _______________________________________________ KK> Pw_forum mailing list KK> Pw_forum at pwscf.org KK> http://www.democritos.it/mailman/listinfo/pw_forum KK> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From mverissi at ictp.it Tue Jan 23 19:49:19 2007 From: mverissi at ictp.it (Marcos Verissimo Alves) Date: Tue, 23 Jan 2007 19:49:19 +0100 (CET) Subject: [Pw_forum] bug in atlas In-Reply-To: References: <401563.17335.qm@web57709.mail.re3.yahoo.com> Message-ID: <40372.10.50.40.120.1169578159.squirrel@webmail3.ictp.trieste.it> Hi all, I have performed a parallel calculation for relaxing a dithiol, and the results came out fine. Now I want to plot |psi|^2 of the band immediately above the Fermi level (the LUMO). I am running pp.x with the following input: &inputpp prefix = 'dithiol_relax' outdir = './' filplot = 'dithiol_relax_pp' plot_num = 7 kpoint = 0.000 0.000 0.000 kband = 14 lsign=.false. / &plot iflag = 3 output_format = 5 fileout = 'dithiol.lumo.xsf' / I suspect the problem is in the "kpoint" entry. I have already tried setting it to "Gamma", "1", and last as shown above, but with no success. I am obtaining the following error: Program POST-PROC v.3.0 starts ... Today is 23Jan2007 at 19:33:29 Parallel version (MPI) Number of processors in use: 4 R & G space division: proc/pool = 4 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from postproc : error # 18 reading inputpp namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... What is wrong in the inputpp section? Marcos -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Condensed Matter and Statistical Physics Sector International Centre for Theoretical Physics Trieste, Italy -------- I have become so addicted to vi that I try to exit OpenOffice by typing :wq! From mverissi at ictp.it Tue Jan 23 20:03:48 2007 From: mverissi at ictp.it (Marcos Verissimo Alves) Date: Tue, 23 Jan 2007 20:03:48 +0100 (CET) Subject: [Pw_forum] Problem in pp.x Message-ID: <40382.10.50.40.120.1169579028.squirrel@webmail3.ictp.trieste.it> Sorry for repeating the e-mail, but the subject was not correct... I have performed a parallel calculation for relaxing a dithiol, and the results came out fine. Now I want to plot |psi|^2 of the band immediately above the Fermi level (the LUMO). I am running pp.x with the following input: &inputpp prefix = 'dithiol_relax' outdir = './' filplot = 'dithiol_relax_pp' plot_num = 7 kpoint = 0.000 0.000 0.000 kband = 14 lsign=.false. / &plot iflag = 3 output_format = 5 fileout = 'dithiol.lumo.xsf' / I suspect the problem is in the "kpoint" entry. I have already tried setting it to "Gamma", "1", and last as shown above, but with no success. I am obtaining the following error: Program POST-PROC v.3.0 starts ... Today is 23Jan2007 at 19:33:29 Parallel version (MPI) Number of processors in use: 4 R & G space division: proc/pool = 4 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from postproc : error # 18 reading inputpp namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... What is wrong in the inputpp section? Marcos -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Condensed Matter and Statistical Physics Sector International Centre for Theoretical Physics Trieste, Italy -------- I have become so addicted to vi that I try to exit OpenOffice by typing :wq! _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Condensed Matter and Statistical Physics Sector International Centre for Theoretical Physics Trieste, Italy -------- I have become so addicted to vi that I try to exit OpenOffice by typing :wq! From akohlmey at cmm.chem.upenn.edu Wed Jan 24 01:13:01 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 23 Jan 2007 19:13:01 -0500 (EST) Subject: [Pw_forum] Problem in pp.x In-Reply-To: <40382.10.50.40.120.1169579028.squirrel@webmail3.ictp.trieste.it> Message-ID: On Tue, 23 Jan 2007, Marcos Verissimo Alves wrote: hi marcos, greetings from snowy philly! MVA> Sorry for repeating the e-mail, but the subject was not correct... MVA> MVA> I have performed a parallel calculation for relaxing a dithiol, and the MVA> results came out fine. Now I want to plot |psi|^2 of the band immediately MVA> above the Fermi level (the LUMO). I am running pp.x with the following MVA> input: MVA> MVA> &inputpp MVA> prefix = 'dithiol_relax' MVA> outdir = './' MVA> filplot = 'dithiol_relax_pp' MVA> plot_num = 7 MVA> kpoint = 0.000 0.000 0.000 this kind of input does not make sense in a namelist. i suppose the kpoint value refers to the 'index' number of the k-point in your previous calculation. ciao, axel. ps: our group just got a (new) post doc from bazil... ;-) MVA> kband = 14 MVA> lsign=.false. MVA> / MVA> &plot MVA> iflag = 3 MVA> output_format = 5 MVA> fileout = 'dithiol.lumo.xsf' MVA> / MVA> MVA> I suspect the problem is in the "kpoint" entry. I have already tried MVA> setting it to "Gamma", "1", and last as shown above, but with no success. MVA> I am obtaining the following error: MVA> MVA> Program POST-PROC v.3.0 starts ... MVA> Today is 23Jan2007 at 19:33:29 MVA> MVA> Parallel version (MPI) MVA> MVA> Number of processors in use: 4 MVA> R & G space division: proc/pool = 4 MVA> MVA> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MVA> from postproc : error # 18 MVA> reading inputpp namelist MVA> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% MVA> MVA> stopping ... MVA> MVA> What is wrong in the inputpp section? MVA> MVA> Marcos MVA> MVA> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From yupiaofei at mail.sdu.edu.cn Wed Jan 24 03:59:07 2007 From: yupiaofei at mail.sdu.edu.cn (yupiaofei(SDU)) Date: Wed, 24 Jan 2007 10:59:07 +0800 Subject: [Pw_forum] Hi, how to generate the pseudopotentials of I element? References: <366523921.07863@mail.sdu.edu.cn> Message-ID: <369607624.12719@mail.sdu.edu.cn> for example, i want to generate the pseudopotentials of I elements? What should i do? This is USPP of I used in CASTEP. Can we obtain some help from these datas? Ultrasoft potential generated using the setting suggested by Prof. Lee group (I_sml_01). ============================================================ | pseudopotential report: version 7.2.1 date 6-11-1998 | ------------------------------------------------------------ | I ceperley-alder exchange-corr | | z = 53. zv = 7. exfact = .00000 | | etot = -23.02217 | | index orbital occupation energy | | 1 500 2.00 -1.30 | | 2 510 5.00 -.53 | | keyps = 3 ifpcor = 0 | | rinner = 1.60 for L= 1 | | rinner = 1.60 for L= 2 | | rinner = 1.60 for L= 3 | | new generation scheme: | | nbeta = 4 kkbeta = 645 rcloc = 2.0000 | | ibeta l epsilon rcut | | 1 0 -1.30 2.00 | | 2 0 .00 2.00 | | 3 1 -.53 2.00 | | 4 1 .00 2.00 | | lloc = 2 eloc = .000 | | ifqopt = 3 nqf = 8 qtryc = 10.000 | | all electron calculation used koelling-harmon equation | | ************logarithmic mesh************ | ============================================================ Convergence test ---------------- I2 dimer, orthorombic cell, a=6.05, b=5.95, c=6.00 Angstrom, LDA Fractional coordinates: (0.71102 0.72156 0.71658) and (0.44630 0.45485 0.44986) ============================================================= Ecut Etot dE Force on atom 1 (eV) (eV) (eV/atom) (eV/A) ------------------------------------------------------------- 150 (COARSE) -628.946 0.225 -0.82947 -0.98877 -0.42398 175 (MEDIUM) -628.985 0.206 -0.69620 -0.68307 -0.60302 200 -629.167 0.115 -0.72123 -0.71046 -0.62692 210 (FINE) -629.231 0.083 -1.11127 -0.71342 -0.63400 230 -629.325 0.036 -0.92169 -0.94618 -1.05568 240 (PRECISE) -629.348 0.024 -0.95878 -0.89582 -0.93315 280 -629.376 0.010 -0.95180 -0.90413 -0.92772 320 -629.383 0.006 -0.95300 -0.90585 -0.92960 400 -629.395 0.001 -0.96039 -0.92010 -0.95487 450 -629.395 0.000 -0.96071 -0.92041 -0.95521 800 -629.396 -0.94534 -0.90747 -0.92607 ============================================================= From akohlmey at cmm.chem.upenn.edu Wed Jan 24 04:34:00 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 23 Jan 2007 22:34:00 -0500 (EST) Subject: [Pw_forum] Hi, how to generate the pseudopotentials of I element? In-Reply-To: <369607624.12719@mail.sdu.edu.cn> Message-ID: On Wed, 24 Jan 2007, yupiaofei(SDU) wrote: YP> for example, i want to generate the pseudopotentials of I elements? What should i do? YP> YP> This is USPP of I used in CASTEP. Can we obtain some help from these datas? those are parameters for a vanderbilt uspp. it should be rather straightforward to recreate the potential with the vanderbilt code and then convert them to UPF with uspp2upf.x. regardless of how well the reproduction of those parameters work, i would recommend to do careful transferability tests. axel. YP> YP> Ultrasoft potential generated using the setting YP> suggested by Prof. Lee group (I_sml_01). YP> YP> ============================================================ YP> | pseudopotential report: version 7.2.1 date 6-11-1998 | YP> ------------------------------------------------------------ YP> | I ceperley-alder exchange-corr | YP> | z = 53. zv = 7. exfact = .00000 | YP> | etot = -23.02217 | YP> | index orbital occupation energy | YP> | 1 500 2.00 -1.30 | YP> | 2 510 5.00 -.53 | YP> | keyps = 3 ifpcor = 0 | YP> | rinner = 1.60 for L= 1 | YP> | rinner = 1.60 for L= 2 | YP> | rinner = 1.60 for L= 3 | YP> | new generation scheme: | YP> | nbeta = 4 kkbeta = 645 rcloc = 2.0000 | YP> | ibeta l epsilon rcut | YP> | 1 0 -1.30 2.00 | YP> | 2 0 .00 2.00 | YP> | 3 1 -.53 2.00 | YP> | 4 1 .00 2.00 | YP> | lloc = 2 eloc = .000 | YP> | ifqopt = 3 nqf = 8 qtryc = 10.000 | YP> | all electron calculation used koelling-harmon equation | YP> | ************logarithmic mesh************ | YP> ============================================================ YP> YP> Convergence test YP> ---------------- YP> I2 dimer, orthorombic cell, a=6.05, b=5.95, c=6.00 Angstrom, LDA YP> Fractional coordinates: YP> (0.71102 0.72156 0.71658) and (0.44630 0.45485 0.44986) YP> YP> ============================================================= YP> Ecut Etot dE Force on atom 1 YP> (eV) (eV) (eV/atom) (eV/A) YP> ------------------------------------------------------------- YP> 150 (COARSE) -628.946 0.225 -0.82947 -0.98877 -0.42398 YP> 175 (MEDIUM) -628.985 0.206 -0.69620 -0.68307 -0.60302 YP> 200 -629.167 0.115 -0.72123 -0.71046 -0.62692 YP> 210 (FINE) -629.231 0.083 -1.11127 -0.71342 -0.63400 YP> 230 -629.325 0.036 -0.92169 -0.94618 -1.05568 YP> 240 (PRECISE) -629.348 0.024 -0.95878 -0.89582 -0.93315 YP> 280 -629.376 0.010 -0.95180 -0.90413 -0.92772 YP> 320 -629.383 0.006 -0.95300 -0.90585 -0.92960 YP> 400 -629.395 0.001 -0.96039 -0.92010 -0.95487 YP> 450 -629.395 0.000 -0.96071 -0.92041 -0.95521 YP> 800 -629.396 -0.94534 -0.90747 -0.92607 YP> ============================================================= YP> ??????????????????????????????????????????j)b? b?????+?o????????i?????zj ?+h????f??f??X??)???p??+ YP> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From wmbmacam at lg.ehu.es Wed Jan 24 09:50:50 2007 From: wmbmacam at lg.ehu.es (=?UTF-8?B?TWlndWVsIE1hcnTDrW5leiBDYW5hbGVz?=) Date: Wed, 24 Jan 2007 09:50:50 +0100 Subject: [Pw_forum] Debye temp, phonon DOS and sum rules. Message-ID: <45B71DEA.8080305@lg.ehu.es> Dear People, To save you from reading a boring tale, I'll put my questions first and the long boring tale later. My questions are: 1) Is trying to calculate the Debye temperature from the phonon DOS too na?ve? 2) What are the practical differences between simple and crystal asr? Could be translated to: What does "optimized corrections of the IFC" in pwtools/qwr.f90 mean? 3) Is the hoop I'm seeing at around 17cm-1 a van Hove singularity I haven't covered in my dispersion curves or something more profound? Thanks a lot for your patiente and attention. I am currently interested in calculating some Debye temperatures for some materials. How would I calculate it? The way that strikes more obvious to me is calculating the phonon density of states. Remembering that as w->0 g(w) should be proportional to w2, one could fit a parabola to the curve and then associate the parameters to the Debye density of states. Once you know c, T_d comes inmediately. Here I find the first issue: at q->0, w doesn't ->0 (unless you have an infinite k-point grid). I thought that, when calculating the interatomic force constants, one can impose sum rules so that when q->0 the forces will vanish and w->0. After checking convergence (Na.pz-n-vbc.UPF PP, up to 45 Ry and meshes of 10, 12, 14, 16 and 20 20 20 k point grids), I've calculated the phonon dos with asr=no, simple and crystal (both in matdyn and q2r). There was no difference (at first sight, less than 1% above 17cm-1), except in the w->0 regime. This was expected. It seems to me that at large omegas, asr=crystal is closer to asr=no than simple asr. Anyway, in all three cases, there appeared a weird jump in g(w) at around 15 cm-1. It doesn't seem to be due to a van Hove singularity, though. I've mapped the phonon dispersion curve (as seen in Phys. Rev. 128 1112 (1962)) and the first \nabla w(k)=0 appears at roughly 29 cm-1. Thanks again for your infinite patiente and attention, Miguel -- ---------------------------------------- Miguel Mart?nez Canales Dto. F?sica de la Materia Condensada UPV/EHU Facultad de Ciencia y Tecnolog?a Apdo. 644 48080 Bilbao (Spain) Fax: +34 94 601 3500 Tlf: +34 94 601 5437 ---------------------------------------- "The problem with Renault is that they dont have the skills to convince FIA that the mass damper is just a brake cooler." Annonymous From giannozz at nest.sns.it Wed Jan 24 14:57:56 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 24 Jan 2007 14:57:56 +0100 Subject: [Pw_forum] Problem in pp.x In-Reply-To: <40382.10.50.40.120.1169579028.squirrel@webmail3.ictp.trieste.it> References: <40382.10.50.40.120.1169579028.squirrel@webmail3.ictp.trieste.it> Message-ID: On Jan 23, 2007, at 20:03 , Marcos Verissimo Alves wrote: > I suspect the problem is in the "kpoint" entry. I have already tried > setting it to "Gamma", "1" "1" is good: "kpoint=1" > What is wrong in the inputpp section? nothing is wrong. Try in serial execution. Most likely is the usual problem with input redirection in parallel execution (a problem of mpi libraries, not of the code) P. --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Wed Jan 24 15:05:37 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 24 Jan 2007 15:05:37 +0100 Subject: [Pw_forum] About Pseudo-Potential generation In-Reply-To: <531837.68363.qm@web54509.mail.yahoo.com> References: <531837.68363.qm@web54509.mail.yahoo.com> Message-ID: <614E0571-32CA-46D9-A812-C9B1C3CFCBDC@nest.sns.it> On Jan 23, 2007, at 12:16 , Lawrence Lee wrote: > (1) Comparing Rabe-Rappe-Kaxiras-Joannopoulos and Troullier-Martin > pseudization, it seems that the former is simpler. But actually > which one > is better? my impression is that RRKJ yields softer potentials than TM, but TM always works, RRKJ often fails to produce a potential > (2) > What's the difference between using one channel as the local PP > and pseudizing the all electron potential. one channel less to be treated as nonlocal > (3) > Sometimes, one will use fractional occupation such as [Ne]3s1.5 for > Mg. > Why's that? computational convenience, more freedom in choosing the reference configuration > (4) > If I want to do high pressure calculation later, does it mean that > I must use > a small core radius. preferrably, yes. The notes on pseudopotential generation that come with the documentation of the atomic code contain several answers to frequent questions on pseudopotentials Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From babazade at gmail.com Thu Jan 25 06:15:36 2007 From: babazade at gmail.com (Amin Babazadeh) Date: Thu, 25 Jan 2007 08:45:36 +0330 Subject: [Pw_forum] nuclear charge change Message-ID: Dear users Would you please tell me that how i can change nuclear charge in quantum espresso code.We know that the nuclear charge in H(hydrogen) is 1 (Z=1) but in my calculation it should be .5 (Z=.5) or 1.5 (Z=1.5) but i don't how to do it in espresso. I will appreciate if helps me sincerely yours -- AMIN -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070125/fb342522/attachment.htm From akohlmey at cmm.chem.upenn.edu Thu Jan 25 06:25:21 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Thu, 25 Jan 2007 00:25:21 -0500 (EST) Subject: [Pw_forum] nuclear charge change In-Reply-To: Message-ID: On Thu, 25 Jan 2007, Amin Babazadeh wrote: AB> Dear users AB> Would you please tell me that how i can change nuclear charge in quantum AB> espresso code.We know that the nuclear charge in H(hydrogen) is 1 (Z=1) but AB> in my calculation it should be .5 (Z=.5) or 1.5 (Z=1.5) but i don't how AB> to do it in espresso. dear amin, you will have to create special pseudopotentials for that. this is not an entirely unusual case, so perhaps somebody here on the list has potentials for that case and can help you out. cheers, axel. AB> I will appreciate if helps me AB> sincerely yours AB> AB> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From Jeremie.Teyssier at physics.unige.ch Thu Jan 25 09:24:15 2007 From: Jeremie.Teyssier at physics.unige.ch (jeremie) Date: Thu, 25 Jan 2007 09:24:15 +0100 Subject: [Pw_forum] Zr, Y and Lu NC pseudo Message-ID: <000001c7405a$336ca160$ade021c0@PORTABLE> Dear all I am intensively trying to build (or convert) pseudo potentials of Zr, Y and Lu to make phonon calculations. Unfortunately, all the PP?s I got, gave weird band structures, very far from what I got with US PPS. As anybody these PPS files or a reliable way to check if a PP is ok or not before trying it in a very long calculation? Thanks for your help. J?r?mie Jeremie Teyssier DPMC 24 quai Ernest Ensermet CH-1211 Geneve 4 SUISSE tel: (41) 22 379 65 78 fax: (41) 22 379 68 69 web: http://optics.unige.ch/jeremie/home_jeremie.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070125/b50f4bc9/attachment.htm From giannozz at nest.sns.it Thu Jan 25 10:50:36 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 25 Jan 2007 10:50:36 +0100 Subject: [Pw_forum] Debye temp, phonon DOS and sum rules. In-Reply-To: <45B71DEA.8080305@lg.ehu.es> References: <45B71DEA.8080305@lg.ehu.es> Message-ID: On Jan 24, 2007, at 9:50 , Miguel Mart?nez Canales wrote: > 1) Is trying to calculate the Debye temperature from the phonon DOS > too na?ve? It should be possible; for sufficiently isotropic dispersions you might also try to estimate the coefficient c in w(q)=cq for q->0 > 2) What are the practical differences between simple and crystal asr? 'simple' asr consists in modifying the diagonal term only of the force constant matrix so that the sum over all atoms of the induced forces is zero. 'crystal' asr modifies the matrix in such a way to conserve the symmetry, I think. > Could be translated to: What does "optimized corrections of the IFC" > in pwtools/q2r.f90 mean? it means that you have to read the original reference, if any (try this: PRB 71, 205214 (2005) ) > 3) Is the hoop I'm seeing at around 17cm-1 a van Hove singularity I > haven't > covered in my dispersion curves or something more profound? hard to say, especially without seeing Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From lawrence_lee_lee at yahoo.com.hk Thu Jan 25 13:44:12 2007 From: lawrence_lee_lee at yahoo.com.hk (Lawrence Lee) Date: Thu, 25 Jan 2007 20:44:12 +0800 (CST) Subject: [Pw_forum] About Pseudo-Potential generation In-Reply-To: <614E0571-32CA-46D9-A812-C9B1C3CFCBDC@nest.sns.it> Message-ID: <352847.95305.qm@web54513.mail.yahoo.com> Dear Paolo, Thanks very much for your answering. But I still do not fully understand your answers about fractional occupation. In my example, some may use [Ne]3s1.5 for Mg. And you said that this is for computational convenience. Can you elaborate more on this point? By the way, if this config is used, should I correspondingly set zval=1.5 , instead of let it default? Thanks a lot! Lawrence _______________________________________ YM - ???? ??????????????????????????????????????????? http://messenger.yahoo.com.hk -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070125/87cda318/attachment.htm From wmbmacam at lg.ehu.es Thu Jan 25 17:59:35 2007 From: wmbmacam at lg.ehu.es (=?ISO-8859-1?Q?Miguel_Mart=EDnez_Canales?=) Date: Thu, 25 Jan 2007 17:59:35 +0100 Subject: [Pw_forum] Debye temp, phonon DOS and sum rules. In-Reply-To: References: <45B71DEA.8080305@lg.ehu.es> Message-ID: <45B8E1F7.1080908@lg.ehu.es> Dear Paolo, Thank you very much for your answers. I am particularly thankful for the reference to Nicola Marzari's paper. MMC> 3) Is the hoop I'm seeing at around 17cm-1 a van Hove singularity I MMC> haven't covered in my dispersion curves or something more profound? PG> hard to say, especially without seeing OK, as I've seen attachments sometimes fail, I'll later provide the first 21 files of my phdos. Anyway, I think I've found the issue. It was related to the nk's I was using to get the phonon density of states. It seems that a regular 6,6,6 or 8,8,8 mesh is not enough, although with that mesh the IFC seems to have converged. Using a 20,20,20 or higher mesh would yield a more logical behaviour. $ head -21 na.phdos -0.2601E-05 0.0000E+00 0.1000E+01 0.4175E-05 0.2000E+01 0.1670E-04 0.3000E+01 0.3758E-04 0.4000E+01 0.6680E-04 0.5000E+01 0.1044E-03 0.6000E+01 0.1503E-03 0.7000E+01 0.2046E-03 0.8000E+01 0.2672E-03 0.9000E+01 0.3382E-03 0.1000E+02 0.4175E-03 0.1100E+02 0.5052E-03 0.1200E+02 0.6012E-03 0.1300E+02 0.7056E-03 0.1400E+02 0.8183E-03 0.1500E+02 0.2017E-02 0.1600E+02 0.2252E-02 0.1700E+02 0.2474E-02 0.1800E+02 0.2683E-02 0.1900E+02 0.2880E-02 0.2000E+02 0.3064E-02 One can easily see the hop and the lack of parabolic behaviour above 14 cm^-1. On a side note, the difference between a 40 40 40 and a 12 12 12 phonon dos is like night and day. Is such difference to be expected? I suppose it's related to the way the phonon dos is computed within the code. Finally, it might interest you to know that fitting a parabola to the low w regime and using the pseudopotential's equilibrium lattice parametre, the Debye temperature is 152 K, very close to the value presented in Table 23.3 of Ashcroft's and Mermin's book. Thanks again, Miguel -- ---------------------------------------- Miguel Mart?nez Canales Dto. F?sica de la Materia Condensada UPV/EHU Facultad de Ciencia y Tecnolog?a Apdo. 644 48080 Bilbao (Spain) Fax: +34 94 601 3500 Tlf: +34 94 601 5437 ---------------------------------------- "If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas." George Bernard Shaw From giannozz at nest.sns.it Thu Jan 25 19:19:37 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 25 Jan 2007 19:19:37 +0100 Subject: [Pw_forum] Debye temp, phonon DOS and sum rules. In-Reply-To: <45B8E1F7.1080908@lg.ehu.es> References: <45B71DEA.8080305@lg.ehu.es> <45B8E1F7.1080908@lg.ehu.es> Message-ID: On Jan 25, 2007, at 17:59 , Miguel Mart?nez Canales wrote: > On a side note, the difference between a 40 40 40 and a 12 12 12 > phonon > dos is like night and day. Is such difference to be expected? maybe not like "day and night", but it takes quite a dense grid if you want to see a DOS with all the singularities as in textbooks > I suppose it's related to the way the phonon dos is computed within > the code. it is a rather straightforward tetrahedron method > Finally, it might interest you to know that fitting a parabola to > the low w > regime and using the pseudopotential's equilibrium lattice parametre, > the Debye temperature is 152 K, very close to the value presented in > Table 23.3 of Ashcroft's and Mermin's book. so now we know that Ashcroft's and Mermin's book is correct :-) Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From meheut at impmc.jussieu.fr Thu Jan 25 23:36:33 2007 From: meheut at impmc.jussieu.fr (meheut at impmc.jussieu.fr) Date: Thu, 25 Jan 2007 23:36:33 +0100 Subject: [Pw_forum] Acoustic branches Message-ID: <20070125233633.ex67mt5xoo48g088@www-ext.lmcp.jussieu.fr> Dear Drs, I would like to use pwscf to compute the acoustic branches only of the crystal. I already computed the complete phonon dispersion, but the acoustic branches are crossing with other modes. Do you think possible to disjoin the acoustic modes frequencies from the other modes? Best wishes. Merlin meheut From degironc at sissa.it Fri Jan 26 13:29:20 2007 From: degironc at sissa.it (degironc) Date: Fri, 26 Jan 2007 13:29:20 +0100 Subject: [Pw_forum] Acoustic branches In-Reply-To: <20070125233633.ex67mt5xoo48g088@www-ext.lmcp.jussieu.fr> References: <20070125233633.ex67mt5xoo48g088@www-ext.lmcp.jussieu.fr> Message-ID: <45B9F420.3020800@sissa.it> close to gamma the acoustic branches have linear dispersion. Away from gamma one should follow the modes that are connected to these three modes at gamma. If there is no symmetry these are just the three lowest branches. If there is some symmetry they can cross a few branches with different symmetry labels and should be possible to follow the acoustic ones comparing the eigenvectors. But I dont see any special meaning of acoustic modes far away from gamma. What are you looking for ? stefano meheut at impmc.jussieu.fr wrote: > Dear Drs, > > I would like to use pwscf to compute the acoustic branches only of the > crystal. I already computed the complete phonon dispersion, but the > acoustic branches are crossing with other modes. Do you think possible > to disjoin the acoustic modes frequencies from the other modes? > > Best wishes. > > Merlin meheut > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at nest.sns.it Fri Jan 26 13:40:55 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 26 Jan 2007 13:40:55 +0100 Subject: [Pw_forum] About Pseudo-Potential generation In-Reply-To: <352847.95305.qm@web54513.mail.yahoo.com> References: <352847.95305.qm@web54513.mail.yahoo.com> Message-ID: <484876A4-78AA-45AA-99A4-AE6EC62ABC9E@nest.sns.it> On Jan 25, 2007, at 13:44 , Lawrence Lee wrote: > In my example, some may use [Ne]3s1.5 for Mg. And you said that > this is > for computational convenience. Can you elaborate more on this point? see atomic_doc/pseudo-gen.tex > By the way, if this config is used, should I correspondingly set > zval=1.5 no, you shouldn't --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Fri Jan 26 13:51:50 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 26 Jan 2007 13:51:50 +0100 Subject: [Pw_forum] Zr, Y and Lu NC pseudo In-Reply-To: <000001c7405a$336ca160$ade021c0@PORTABLE> References: <000001c7405a$336ca160$ade021c0@PORTABLE> Message-ID: On Jan 25, 2007, at 9:24 , jeremie wrote: > I am intensively trying to build (or convert) pseudo potentials of > Zr, Y and Lu to make phonon calculations. Unfortunately, all the > PP?s I got, gave weird band structures, very far from what I got > with US PPS. if you have good US PP's, you can use them for phonon calculations. It is slightly trickier than with norm-conserving PP's (in particular you need very small convergence thresholds) but it should work > As anybody these PPS files or a reliable way to check if a PP is ok > or not before trying it in a very long calculation? see atomic_doc/pseudo-gen.tex. Basically, you can make checks in atoms (with the atomic code used to generate them) for different atomic configurations, or in simple crystals or molecules Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Fri Jan 26 14:26:58 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 26 Jan 2007 14:26:58 +0100 Subject: [Pw_forum] projected phonon DOS In-Reply-To: <144640.67920.qm@web15011.mail.cnb.yahoo.com> References: <144640.67920.qm@web15011.mail.cnb.yahoo.com> Message-ID: <16E2EF10-C652-4CA7-AC0C-97EE53B0372A@nest.sns.it> On Jan 13, 2007, at 6:04 , li niu wrote: > I can calculate the total phonon DOS and now I want to calculate > projected phonon DOS with tetrahedra (associated with specific atom > or vibrational mode in the unit cell). I searched the pw_forum > archive but did not find anything useful. you didn't search very carefully: http://www.democritos.it/pipermail/pw_forum/2005-August/002816.html Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From baroni at sissa.it Fri Jan 26 15:13:32 2007 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 26 Jan 2007 15:13:32 +0100 Subject: [Pw_forum] Acoustic branches In-Reply-To: <20070125233633.ex67mt5xoo48g088@www-ext.lmcp.jussieu.fr> References: <20070125233633.ex67mt5xoo48g088@www-ext.lmcp.jussieu.fr> Message-ID: Dear Merlin. It is not possible to caculate the acoustic branch only. In case the acoustic branches cross upper ("optic") branches, I think it would not even be meaningful to do so. Stefano On Jan 25, 2007, at 11:36 PM, meheut at impmc.jussieu.fr wrote: > > > Dear Drs, > > I would like to use pwscf to compute the acoustic branches only of the > crystal. I already computed the complete phonon dispersion, but the > acoustic branches are crossing with other modes. Do you think possible > to disjoin the acoustic modes frequencies from the other modes? > > Best wishes. > > Merlin meheut > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070126/5c2ff5d3/attachment.htm From merlin.meheut at impmc.jussieu.fr Fri Jan 26 16:16:16 2007 From: merlin.meheut at impmc.jussieu.fr (merlin.meheut at impmc.jussieu.fr) Date: Fri, 26 Jan 2007 16:16:16 +0100 Subject: [Pw_forum] Acoustic branches In-Reply-To: <45B9F420.3020800@sissa.it> References: <20070125233633.ex67mt5xoo48g088@www-ext.lmcp.jussieu.fr> <45B9F420.3020800@sissa.it> Message-ID: <20070126161616.k0ifqoecqsksk0s0@www.impmc.jussieu.fr> Dear Stefano, My point is to compute the so-called "acoustic contribution" to thermodynamical properties such as heat capacity or so. It is commonly used in empirical models calculations (such as Debye-Einstein models). Moreover, I am working with big structures, and I have some trouble obtaining good dispersion curves near Gamma, so I would like to extract information from the acoustic branches over the complete Brillouin zone. This is related to the point of calculating thermodynamic properties with only gamma frequencies, so that a model has to be set for the acoustic part ( because, as it goes to zero, it can create some singularities). I am not sure to be very clear myself, this is exploratory. To say it in a different way, experimentally we have information on optical frequencies (at gamma point) but not easily on what's below (except sound wave velocity but as I said before I have some trouble having a good curve at low q for acoustic modes ). The goal is to calculate the contribution of those frequencies on which we have no information by optical spectroscopy. Thanks in any case for your idea of "following the eigenvectors", this is probably the better one. Is there an easy way to do it? (I think I know the answer). Best wishes, Merlin Quoting degironc : > close to gamma the acoustic branches have linear dispersion. > Away from gamma one should follow the modes that are connected > to these three modes at gamma. If there is no symmetry these are just > the three lowest branches. If there is some symmetry they can cross > a few branches with different symmetry labels and should be possible > to follow the acoustic ones comparing the eigenvectors. > But I dont see any special meaning of acoustic modes far away from > gamma. > What are you looking for ? > > stefano > > meheut at impmc.jussieu.fr wrote: > >> Dear Drs, >> >> I would like to use pwscf to compute the acoustic branches only of the >> crystal. I already computed the complete phonon dispersion, but the >> acoustic branches are crossing with other modes. Do you think possible >> to disjoin the acoustic modes frequencies from the other modes? >> >> Best wishes. >> >> Merlin meheut >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From baroni at sissa.it Fri Jan 26 21:19:09 2007 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 26 Jan 2007 21:19:09 +0100 Subject: [Pw_forum] Acoustic branches In-Reply-To: <20070126161616.k0ifqoecqsksk0s0@www.impmc.jussieu.fr> References: <20070125233633.ex67mt5xoo48g088@www-ext.lmcp.jussieu.fr> <45B9F420.3020800@sissa.it> <20070126161616.k0ifqoecqsksk0s0@www.impmc.jussieu.fr> Message-ID: <65F435E4-3D03-45F6-A926-050702F5D3B4@sissa.it> Dear Merlin (this is another Stefano answering): On Jan 26, 2007, at 4:16 PM, merlin.meheut at impmc.jussieu.fr wrote: > Thanks in any case for your idea of "following the eigenvectors", > this is probably the better one. Is there an easy way to do it? (I > think I know the answer). one neat way would be to use Wannier functions (or their lattice equivalent). The idea of lattice Wannier functions has been popularized by Karin Rabe some 10 years ago (or so). Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070126/f8f7a436/attachment.htm From niuli1978 at yahoo.com.cn Sat Jan 27 04:18:15 2007 From: niuli1978 at yahoo.com.cn (li niu) Date: Sat, 27 Jan 2007 11:18:15 +0800 (CST) Subject: [Pw_forum] about the projected phonon DOS Message-ID: <967793.65449.qm@web15006.mail.cnb.yahoo.com> Dear Paolo, Thanks for your reply. I found this archive before I sent a mail to the pw_forum. http://www.democritos.it/pipermail/pw_forum/2005-August/002816.html However, I can not find PP/dost.f90 in the ESPRSSO-3.2 code. I understand that I should make a subroutine to do projected phonon DOS according to your attachment. Is that right? Can you give me some more hints on how to make this subroutine? Thanks! NiuLi --------------------------------- ??????-3.5G???20M?? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070127/bd2a52fd/attachment.htm From shaposh at isp.nsc.ru Sat Jan 27 08:39:53 2007 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Sat, 27 Jan 2007 13:39:53 +0600 Subject: [Pw_forum] Electron affinity calculation Message-ID: <200701271339.53346.shaposh@isp.nsc.ru> Hello ALL, I would like to calculate Electron Affinity in zirconia. The simplest idea is to put additional electron in the cell and calculate total energy difference.This, however, will not work as calculated bands energies and fermi level are not connected to vacuum level. So, the energy of the first conductive band, which is a good estimation of the electron affinity, is meaningless by itself. My question is, what is the established approach for the calculations of electron affinity for the plane wave band dft calculations? Best Regards, Alexander Shaposhnikov From baroni at sissa.it Sat Jan 27 08:54:24 2007 From: baroni at sissa.it (Stefano Baroni) Date: Sat, 27 Jan 2007 08:54:24 +0100 Subject: [Pw_forum] Electron affinity calculation In-Reply-To: <200701271339.53346.shaposh@isp.nsc.ru> References: <200701271339.53346.shaposh@isp.nsc.ru> Message-ID: On Jan 27, 2007, at 8:39 AM, Alexander Shaposhnikov wrote: Hi Sasha: > I would like to calculate Electron Affinity in zirconia. > The simplest idea is to put additional electron in the cell > and calculate total energy difference.This, however, will not > work as calculated bands energies and fermi level are not connected > to vacuum level. So, the energy of the first conductive band, which > is a good > estimation of the electron affinity, is meaningless by itself. right > My question is, what is the established approach for the > calculations of > electron affinity for the plane wave band dft calculations? I believe, you should first ask (and answer) the preliminary question: what makes " ... the first conduction band ... meaningful ..?.. " The answer does not depend on the theoretical approach (DFT), nor on the basis set (plane waves), but on nature: the surface. So, in order to calculate electron affinities in an extended system you have to simulate "the place the added electron comes from", i.e. the vacuum, and the interface between that place and the solid, i.e. a surface. Hope this clarifies a bit. Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070127/ffa08e5a/attachment.htm From shaposh at isp.nsc.ru Sat Jan 27 09:22:44 2007 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Sat, 27 Jan 2007 14:22:44 +0600 Subject: [Pw_forum] Electron affinity calculation In-Reply-To: References: <200701271339.53346.shaposh@isp.nsc.ru> Message-ID: <200701271422.44059.shaposh@isp.nsc.ru> Hello Dr. Baroni, Thank you, i was thinking about surface myself, good to know i was in the right direction! I will try to create slab surface model. Best Regards, Alexander Shaposhnkov On Saturday 27 January 2007 13:54, Stefano Baroni wrote: > On Jan 27, 2007, at 8:39 AM, Alexander Shaposhnikov wrote: > > My question is, what is the established approach for the > > calculations of > > electron affinity for the plane wave band dft calculations? > > I believe, you should first ask (and answer) the preliminary > question: what makes " ... the first conduction band ... > meaningful ..?.. " The answer does not depend on the theoretical > approach (DFT), nor on the basis set (plane waves), but on nature: > the surface. So, in order to calculate electron affinities in an > extended system you have to simulate "the place the added electron > comes from", i.e. the vacuum, and the interface between that place > and the solid, i.e. a surface. > > Hope this clarifies a bit. > > Stefano > > --- > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > Trieste > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From baroni at sissa.it Fri Jan 26 21:19:09 2007 From: baroni at sissa.it (Stefano Baroni) Date: Fri, 26 Jan 2007 21:19:09 +0100 Subject: [Pw_forum] Acoustic branches In-Reply-To: <20070126161616.k0ifqoecqsksk0s0@www.impmc.jussieu.fr> References: <20070125233633.ex67mt5xoo48g088@www-ext.lmcp.jussieu.fr> <45B9F420.3020800@sissa.it> <20070126161616.k0ifqoecqsksk0s0@www.impmc.jussieu.fr> Message-ID: <65F435E4-3D03-45F6-A926-050702F5D3B4@sissa.it> Dear Merlin (this is another Stefano answering): On Jan 26, 2007, at 4:16 PM, merlin.meheut at impmc.jussieu.fr wrote: > Thanks in any case for your idea of "following the eigenvectors", > this is probably the better one. Is there an easy way to do it? (I > think I know the answer). one neat way would be to use Wannier functions (or their lattice equivalent). The idea of lattice Wannier functions has been popularized by Karin Rabe some 10 years ago (or so). Stefano --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070126/f8f7a436/attachment-0001.htm From amit76.india at gmail.com Sun Jan 28 18:11:25 2007 From: amit76.india at gmail.com (Amit Kumar) Date: Sun, 28 Jan 2007 22:41:25 +0530 Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1325 - 4 msgs In-Reply-To: <20070127102803.10227.54450.Mailman@democritos.sissa.it> References: <20070127102803.10227.54450.Mailman@democritos.sissa.it> Message-ID: Respected Users, I'm getting following error in new version of pwscf code to calculate electron phonon coupling. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from elphsum : error # 1 q is not a vector in the dense grid %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% when I'm using only one special q point 0.6666667 0.0 0.0 ( Can anyone tell me is the above co-ordinates correct for Graphite K-POINT???? ) There is no error if I use the old version's scf nscf phonon nscf elec phonon method instead of using new version's la2F=.true. procedure with automatic k-point. How to get rid of this error in the new version???? Your kind help will be greatly appreciated. Regards Amit -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070128/b5af9413/attachment.htm From eyvaz_isaev at yahoo.com Sun Jan 28 22:49:30 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sun, 28 Jan 2007 13:49:30 -0800 (PST) Subject: [Pw_forum] QHA code Message-ID: <421674.1032.qm@web60314.mail.yahoo.com> Dear users, Few days ago I sent the QHA code to the forum, but it seems it was rejected due to a size reason. Now I am trying to submit it again. To me it would be nice if it distributed with the QE code. Besides, I feel I do not receive all messages sent to the forum. Bests, Eyvaz. ____________________________________________________________________________________ Food fight? Enjoy some healthy debate in the Yahoo! Answers Food & Drink Q&A. http://answers.yahoo.com/dir/?link=list&sid=396545367 -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070128/559a105c/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: QHA_distribution.tar.gz Type: application/x-gzip Size: 16273 bytes Desc: not available Url : /pipermail/attachments/20070128/559a105c/attachment.bin From rui_zhi_zhang at yahoo.com Mon Jan 29 03:35:55 2007 From: rui_zhi_zhang at yahoo.com (ruizhi zhang) Date: Sun, 28 Jan 2007 18:35:55 -0800 (PST) Subject: [Pw_forum] How to generate pseudo of atoms on a partially occupied position using virtual.x ? Message-ID: <443284.14658.qm@web39808.mail.mud.yahoo.com> Dear all： I want to study a system in which oxygen atoms are on a partially occupied position. So I need to generate a 'virtual' potential of oxygen using Virtual Crystal Approximation . As has been discussed in the forum, using virtual.x in upftools/ new pseudopotential = (1-x)V1+xV2 However, in my case V1 is pseudo of Oxygen and V2 is a vacancy, and I do not know how to deal with it. Can I generate a pseudo of Oxygen specifying the Z valance=0 ? (Maybe it is a stupid idea) and use this as the pseudo of vacancy? Thank you very much in advance. Best regards ruizhi zhang --------------------------------- 8:00? 8:25? 8:40? Find a flick in no time with theYahoo! Search movie showtime shortcut. -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070128/5c18099d/attachment.htm From jhashemifar at gmail.com Mon Jan 29 09:08:57 2007 From: jhashemifar at gmail.com (Javad hashemifar) Date: Mon, 29 Jan 2007 09:08:57 +0100 Subject: [Pw_forum] Problem in pp.x In-Reply-To: References: <40382.10.50.40.120.1169579028.squirrel@webmail3.ictp.trieste.it> Message-ID: <2fb18d9f0701290008w7b5ade08t9370d9e06f46e853@mail.gmail.com> Regarding the "input redirection" problem, I had similar problem few days ago during DOS and charge density calculations. After some consideration I found that this problem roots in the DFLAGS that I used for installation of Espresso. When I added -D__INTEL to these DFLAGS and installed it again, the problem was solved. Javad Hashemifar On 1/24/07, Paolo Giannozzi wrote: > > On Jan 23, 2007, at 20:03 , Marcos Verissimo Alves wrote: > > > I suspect the problem is in the "kpoint" entry. I have already tried > > setting it to "Gamma", "1" > > "1" is good: "kpoint=1" > > > What is wrong in the inputpp section? > > nothing is wrong. Try in serial execution. Most likely is the > usual problem with input redirection in parallel execution > (a problem of mpi libraries, not of the code) > > P. > --- > Paolo Giannozzi, Democritos and University of Udine, Italy > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- ====================================== Seyed Javad Hashemifar, Ph.D. [current:] Tel:+49-203-3794743 Fax:+49-203-3794742 Fachbereich Physik (AG Kratzer), Universitat Duisburg-Essen 47048 Dusiburg, Germany [permanent:] Tel: +98-311-3912375 Fax: +98-311-3912376 Physics Department, Isfahan University of Technology 84156 Isfahan, Iran --------------------------------------------------------------------------- From degironc at sissa.it Mon Jan 29 09:16:33 2007 From: degironc at sissa.it (degironc) Date: Mon, 29 Jan 2007 09:16:33 +0100 Subject: [Pw_forum] How to generate pseudo of atoms on a partially occupied position using virtual.x ? In-Reply-To: <443284.14658.qm@web39808.mail.mud.yahoo.com> References: <443284.14658.qm@web39808.mail.mud.yahoo.com> Message-ID: <45BDAD61.2010604@sissa.it> the simplest way to generate the pseudopotential you are want is to modify (it should be trivial) virtual.x code so that it accepts only one pseudo in input and multiplies it by x. However the quality of VCA depends on the assumption that the two mixed potentials are similar... It is unlikely that this is the case for an oxygen and a vacancy. The proper way to deal with vacancies is within the supercell aproach. What kind of properties are you interested in ? stefano ruizhi zhang wrote: > Dear all? > I want to study a system in which oxygen atoms are on a partially > occupied position. So I need to generate a 'virtual' potential of > oxygen using Virtual Crystal Approximation . As has been discussed in > the forum, using virtual.x in upftools/ > new pseudopotential = (1-x)V1+xV2 > However, in my case V1 is pseudo of Oxygen and V2 is a vacancy, and I > do not know how to deal with it. > Can I generate a pseudo of Oxygen specifying the Z valance=0 ? (Maybe > it is a stupid idea) and use this as the pseudo of vacancy? > Thank you very much in advance. > Best regards > ruizhi zhang > > ------------------------------------------------------------------------ > 8:00? 8:25? 8:40? Find a flick > in no time > with theYahoo! Search movie showtime shortcut. > From wierzbom at ts.infn.it Mon Jan 29 11:10:23 2007 From: wierzbom at ts.infn.it (Malgorzata Wierzbowska) Date: Mon, 29 Jan 2007 11:10:23 +0100 (CET) Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1325 - 4 msgs In-Reply-To: References: <20070127102803.10227.54450.Mailman@democritos.sissa.it> Message-ID: On Sun, 28 Jan 2007, Amit Kumar wrote: > Respected Users, > > I'm getting following error in new version of pwscf code to calculate > electron phonon coupling. > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from elphsum : error # 1 > q is not a vector in the dense grid > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > The above error and the question has been answered on pw-forum. The phonon grid q and the k-mesh for phonon calc. should be the subsets of the dense k-grid in the first scf calculations (i.e. scf-fit). Gosia > when I'm using only one special q point > > 0.6666667 0.0 0.0 > > ( Can anyone tell me is the above co-ordinates correct for Graphite > K-POINT???? ) > > There is no error if I use the old version's scf nscf phonon nscf elec > phonon method > instead of using new version's la2F=.true. procedure with automatic k-point. > > How to get rid of this error in the new version???? > Your kind help will be greatly appreciated. > > Regards > Amit > From giannozz at nest.sns.it Mon Jan 29 11:17:45 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 29 Jan 2007 11:17:45 +0100 Subject: [Pw_forum] QHA code In-Reply-To: <421674.1032.qm@web60314.mail.yahoo.com> References: <421674.1032.qm@web60314.mail.yahoo.com> Message-ID: On Jan 28, 2007, at 22:49 , Eyvaz Isaev wrote: > Few days ago I sent the QHA code to the forum, but it seems it was > rejected due to a size reason. Now I am trying to submit it again. To > me it would be nice if it distributed with the QE code. thank you! > Besides, I feel I do not receive all messages sent to the forum. you can easily verify this by checking the archive : http://www.democritos.it/pipermail/pw_forum/ Paolo --- Paolo Giannozzi, Democritos and University of Udine, Italy From giannozz at nest.sns.it Mon Jan 29 11:23:13 2007 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 29 Jan 2007 11:23:13 +0100 Subject: [Pw_forum] about the projected phonon DOS In-Reply-To: <967793.65449.qm@web15006.mail.cnb.yahoo.com> References: <967793.65449.qm@web15006.mail.cnb.yahoo.com> Message-ID: <74F89264-AF7A-4528-9E37-A3F664E4934E@nest.sns.it> On Jan 27, 2007, at 4:18 , li niu wrote: > I can not find PP/dost.f90 in the ESPRSSO-3.2 code. flib/dost.f90 --- Paolo Giannozzi, Democritos and University of Udine, Italy From eyvaz_isaev at yahoo.com Mon Jan 29 12:21:50 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Mon, 29 Jan 2007 03:21:50 -0800 (PST) Subject: [Pw_forum] How to generate pseudo of atoms on a partially occupied position using virtual.x ? In-Reply-To: <443284.14658.qm@web39808.mail.mud.yahoo.com> Message-ID: <946459.76524.qm@web60316.mail.yahoo.com> Hi, > I want to study a system in which oxygen atoms are > on a partially occupied position. So I need to > generate a 'virtual' potential of oxygen using > Virtual Crystal Approximation . As has been > discussed in the forum, using virtual.x in upftools/ > new pseudopotential = (1-x)V1+xV2 > However, in my case V1 is pseudo of Oxygen and V2 > is a vacancy, and I do not know how to deal with it. > > Can I generate a pseudo of Oxygen specifying the Z > valance=0 ? (Maybe it is a stupid idea) and use this > as the pseudo of vacancy? > I think you are out of lucky. Because there is no opprtunity in pseudopotentials to consider partially occupied positions. To deal with this problem you can use the EMTO code. Bests, Eyvaz. > Thank you very much in advance. > > Best regards > ruizhi zhang > > > --------------------------------- > 8:00? 8:25? 8:40? Find a flick in no time > with theYahoo! Search movie showtime shortcut. ____________________________________________________________________________________ Need a quick answer? Get one in minutes from people who know. Ask your question on www.Answers.yahoo.com From baroni at sissa.it Mon Jan 29 16:03:13 2007 From: baroni at sissa.it (Stefano Baroni) Date: Mon, 29 Jan 2007 16:03:13 +0100 Subject: [Pw_forum] How to generate pseudo of atoms on a partially occupied position using virtual.x ? In-Reply-To: <443284.14658.qm@web39808.mail.mud.yahoo.com> References: <443284.14658.qm@web39808.mail.mud.yahoo.com> Message-ID: <32C63B06-0B99-407B-9A3C-9000BFB545F5@sissa.it> Dear Ruizhi: the virtual crystal approximation is definitely not the way to go to study defective systems. The VCA applies to those cases where the different atoms in the disorder sublattices have rather similar properties. This not your case, where an atom is certainly not similar enough to "no atom". Cheers - Stefano Baroni On Jan 29, 2007, at 3:35 AM, ruizhi zhang wrote: > Dear all? > > I want to study a system in which oxygen atoms are on a partially > occupied position. So I need to generate a 'virtual' potential of > oxygen using Virtual Crystal Approximation . As has been discussed > in the forum, using virtual.x in upftools/ > new pseudopotential = (1-x)V1+xV2 > However, in my case V1 is pseudo of Oxygen and V2 is a vacancy, and > I do not know how to deal with it. > Can I generate a pseudo of Oxygen specifying the Z valance=0 ? > (Maybe it is a stupid idea) and use this as the pseudo of vacancy? > > Thank you very much in advance. > > Best regards > ruizhi zhang > > 8:00? 8:25? 8:40? Find a flick in no time > with theYahoo! Search movie showtime shortcut. --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070129/7b0799ed/attachment.htm From srijan.india at gmail.com Mon Jan 29 17:07:11 2007 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Mon, 29 Jan 2007 21:37:11 +0530 Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1325 - 4 msgs In-Reply-To: References: <20070127102803.10227.54450.Mailman@democritos.sissa.it> Message-ID: <3fcc7e670701290807p345b0b06wffbf9607811e1662@mail.gmail.com> Respected Users, Would you like to tell me what automatic (like 48 48 1) the dense k-point grid in the first scf calculations (i.e. scf-fit). I should use to get special q point > > 0.6666667 0.0 0.0 >as a the subsets of the scf-fit ???? Is there any definite rule except applying a trial and error method like 4 4 1, 6 6 1, 9 9 1, 38 38 1 etc. etc. ???? Your kind help will be greatly appreciated. Regards, Amit On 1/29/07, Malgorzata Wierzbowska wrote: > > On Sun, 28 Jan 2007, Amit Kumar wrote: > > > > Respected Users, > > > > I'm getting following error in new version of pwscf code to calculate > > electron phonon coupling. > > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > from elphsum : error # 1 > > q is not a vector in the dense grid > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > > > The above error and the question has been answered on pw-forum. > The phonon grid q and the k-mesh for phonon calc. should be > the subsets of the dense k-grid in the first scf calculations > (i.e. scf-fit). > > Gosia > > > > when I'm using only one special q point > > > > 0.6666667 0.0 0.0 > > > > ( Can anyone tell me is the above co-ordinates correct for Graphite > > K-POINT???? ) > > > > There is no error if I use the old version's scf nscf phonon nscf elec > > phonon method > > instead of using new version's la2F=.true. procedure with automatic > k-point. > > > > How to get rid of this error in the new version???? > > Your kind help will be greatly appreciated. > > > > Regards > > Amit > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070129/2f4ba92f/attachment.htm From wierzbom at ts.infn.it Mon Jan 29 17:28:25 2007 From: wierzbom at ts.infn.it (Malgorzata Wierzbowska) Date: Mon, 29 Jan 2007 17:28:25 +0100 (CET) Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1325 - 4 msgs In-Reply-To: <3fcc7e670701290807p345b0b06wffbf9607811e1662@mail.gmail.com> References: <20070127102803.10227.54450.Mailman@democritos.sissa.it> <3fcc7e670701290807p345b0b06wffbf9607811e1662@mail.gmail.com> Message-ID: On Mon, 29 Jan 2007, Srijan Kumar Saha wrote: > Respected Users, > > Would you like to tell me what automatic (like 48 48 1) > the dense k-point grid in the first scf calculations > (i.e. scf-fit). I should use > to get special q point >> >> 0.6666667 0.0 0.0 >> as a the subsets of the scf-fit ???? > Is there any definite rule except applying a trial and > error method like 4 4 1, 6 6 1, 9 9 1, 38 38 1 etc. etc. ???? > Your kind help will be greatly appreciated. > Regards, > Amit > If q=(2/3,0.0,0.0) your k-mesh for phonons and k-fit mesh should be modulo 3. So (4 4 1) and (38 38 1) are for sure bad. Meshes (6 6 1) and (9 9 1) are too small, although they would not give the error if your rare k-mesh (k-mesh for phonons) were modulo 3. Actually, for this kind of calculations you should ask for 3 meshes: k_fit, k_phonon, q_phonon. And always k_fit/(k_phonon + q_phonon) should be the integer number. Gosia > On 1/29/07, Malgorzata Wierzbowska wrote: >> >> On Sun, 28 Jan 2007, Amit Kumar wrote: >> >> >> > Respected Users, >> > >> > I'm getting following error in new version of pwscf code to calculate >> > electron phonon coupling. >> > >> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> > from elphsum : error # 1 >> > q is not a vector in the dense grid >> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> > >> >> The above error and the question has been answered on pw-forum. >> The phonon grid q and the k-mesh for phonon calc. should be >> the subsets of the dense k-grid in the first scf calculations >> (i.e. scf-fit). >> >> Gosia >> >> >> > when I'm using only one special q point >> > >> > 0.6666667 0.0 0.0 >> > >> > ( Can anyone tell me is the above co-ordinates correct for Graphite >> > K-POINT???? ) >> > >> > There is no error if I use the old version's scf nscf phonon nscf elec >> > phonon method >> > instead of using new version's la2F=.true. procedure with automatic >> k-point. >> > >> > How to get rid of this error in the new version???? >> > Your kind help will be greatly appreciated. >> > >> > Regards >> > Amit >> > >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > From srijan.india at gmail.com Mon Jan 29 17:39:40 2007 From: srijan.india at gmail.com (Srijan Kumar Saha) Date: Mon, 29 Jan 2007 22:09:40 +0530 Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1325 - 4 msgs In-Reply-To: References: <20070127102803.10227.54450.Mailman@democritos.sissa.it> <3fcc7e670701290807p345b0b06wffbf9607811e1662@mail.gmail.com> Message-ID: <3fcc7e670701290839k7fb250d0oe0d6f24c19db0601@mail.gmail.com> Dear Malgorzata , It's very nice to recieve your quick reply. Thank you very much my adorable friend. >>>>>>>And always k_fit/(k_phonon + q_phonon) should be the integer number. So if I use 48 48 1 for k_fit 24 24 1 for k_phonon and 2/3 0.0 0.0 for a special single q point (it's not automatic generated value) Then I think it will be fine , Right??? OK let me try. Regards, Amit On 1/29/07, Malgorzata Wierzbowska wrote: > > On Mon, 29 Jan 2007, Srijan Kumar Saha wrote: > > > > Respected Users, > > > > Would you like to tell me what automatic (like 48 48 1) > > the dense k-point grid in the first scf calculations > > (i.e. scf-fit). I should use > > to get special q point > >> > >> 0.6666667 0.0 0.0 > >> as a the subsets of the scf-fit ???? > > Is there any definite rule except applying a trial and > > error method like 4 4 1, 6 6 1, 9 9 1, 38 38 1 etc. etc. ???? > > Your kind help will be greatly appreciated. > > Regards, > > Amit > > > > If q=(2/3,0.0,0.0) your k-mesh for phonons and k-fit mesh > should be modulo 3. So (4 4 1) and (38 38 1) are for sure bad. > Meshes (6 6 1) and (9 9 1) are too small, although they would > not give the error if your rare k-mesh (k-mesh for phonons) were > modulo 3. > Actually, for this kind of calculations you should ask for > 3 meshes: k_fit, k_phonon, q_phonon. > And always k_fit/(k_phonon + q_phonon) should be the integer > number. > > Gosia > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070129/632a5fd4/attachment.htm From wierzbom at ts.infn.it Mon Jan 29 18:05:24 2007 From: wierzbom at ts.infn.it (Malgorzata Wierzbowska) Date: Mon, 29 Jan 2007 18:05:24 +0100 (CET) Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #1325 - 4 msgs In-Reply-To: <3fcc7e670701290839k7fb250d0oe0d6f24c19db0601@mail.gmail.com> References: <20070127102803.10227.54450.Mailman@democritos.sissa.it> <3fcc7e670701290807p345b0b06wffbf9607811e1662@mail.gmail.com> <3fcc7e670701290839k7fb250d0oe0d6f24c19db0601@mail.gmail.com> Message-ID: On Mon, 29 Jan 2007, Srijan Kumar Saha wrote: > > >>>>>>>And always k_fit/(k_phonon + q_phonon) should be the integer > number. > > So if I use 48 48 1 for k_fit > 24 24 1 for k_phonon and > > 2/3 0.0 0.0 for a special single q point (it's not > automatic generated value) > Then I think it will be fine , Right??? It should be right, I mean with respect to the error we spoke about. I guess that the z-value of points in (48 48 1) and (24 24 1) will be 0.0. Another problem is whether this grid is dense enough to get accurate results.... This you should test. I would put for scf-fit something like 64 or 72 if you have enough time for calculations. At the end scf-fit is a single scf, we do it only once. Later you can calculate more phonons with the same scf-fit files in the tmp-directory. But all your chosen q-points should fit to above k-fit mesh. Wait a second... what is the point to use la2F if you have only one q-point? The whole project was ment to use q2r and matdyn in order to get many q-points from a few q-point calculations. So, once you make some tests on a single q-point with old style calculations for phonons, and you are sure about your phonon k-mesh, you should choose all phonons and calculate them in one run with the la2F. Maybe your phonon grid could be then 3 3 1 or 6 6 1.... Gosia > > > On 1/29/07, Malgorzata Wierzbowska wrote: >> >> On Mon, 29 Jan 2007, Srijan Kumar Saha wrote: >> >> >> > Respected Users, >> > >> > Would you like to tell me what automatic (like 48 48 1) >> > the dense k-point grid in the first scf calculations >> > (i.e. scf-fit). I should use >> > to get special q point >> >> >> >> 0.6666667 0.0 0.0 >> >> as a the subsets of the scf-fit ???? >> > Is there any definite rule except applying a trial and >> > error method like 4 4 1, 6 6 1, 9 9 1, 38 38 1 etc. etc. ???? >> > Your kind help will be greatly appreciated. >> > Regards, >> > Amit >> > >> >> If q=(2/3,0.0,0.0) your k-mesh for phonons and k-fit mesh >> should be modulo 3. So (4 4 1) and (38 38 1) are for sure bad. >> Meshes (6 6 1) and (9 9 1) are too small, although they would >> not give the error if your rare k-mesh (k-mesh for phonons) were >> modulo 3. >> Actually, for this kind of calculations you should ask for >> 3 meshes: k_fit, k_phonon, q_phonon. >> And always k_fit/(k_phonon + q_phonon) should be the integer >> number. >> >> Gosia >> >> >> > From shein at ihim.uran.ru Tue Jan 30 09:03:25 2007 From: shein at ihim.uran.ru (Igor R. Shein) Date: Tue, 30 Jan 2007 13:03:25 +0500 Subject: [Pw_forum] Plot phonon dispersion Message-ID: <45BEFBCD.6050200@ihim.uran.ru> How it is possible (for example - plotband....) from ****.freq to construct the postscript plot file for a phonon dispersion ? Igor Shein From yukihiro_okuno at fujifilm.co.jp Tue Jan 30 14:41:22 2007 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Tue, 30 Jan 2007 22:41:22 +0900 Subject: [Pw_forum] How to use upftools ( where is the manual about upftools) Message-ID: Dear PWscf usrs. I've just started to use PWscf. So, sorry such a basic question like below. I want to use pseudo-potential of Bi. But there are no Bi pseudo potential. So I want to use Vanderbilts's code to generate pseudo potential and convert to upf format by upftools. But I can't found the manual about upftools in PWscf directory. Where is the manual on upftools which I should read, ( I also use virtual crystal approximation so, I want to use virsual.x) and how to use vdb2upf.x Sincerely From akohlmey at cmm.chem.upenn.edu Tue Jan 30 17:53:37 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Tue, 30 Jan 2007 11:53:37 -0500 (EST) Subject: [Pw_forum] How to use upftools ( where is the manual about upftools) In-Reply-To: Message-ID: On Tue, 30 Jan 2007 yukihiro_okuno at fujifilm.co.jp wrote: YO> Dear PWscf usrs. YO> YO> I've just started to use PWscf. YO> So, sorry such a basic question like below. YO> YO> I want to use pseudo-potential of Bi. YO> But there are no Bi pseudo potential. YO> YO> So I want to use Vanderbilts's code to generate pseudo potential YO> and convert to upf format by upftools. YO> YO> But I can't found the manual about upftools in PWscf directory. dear yukihiro, the ultimate manual is always the source code. ;-) the usage of the upf converter programs is rather simple. just run, e.g.: ./uspp2upf.x bi_ps.uspp and you'll create: bi_ps.uspp.UPF you should edit the INFO section of the file to reflect the creation of the potential. however now a word of warning. the Bi potential parameters in the vanderbilt package seem to need a little tweaking with the current vanderbilt code to create a 'clean' pseudopotential. i have (rather recently) tried to tweak the parameters so that the potential looks clean, but i am still waiting for the confirmation that they were tested successfully (jess?). if you are willing to do the required careful tests yourself, just let me know and i can send you the upf files right away (i can't post them to the mailing list due to size limitations). YO> Where is the manual on upftools which I should read, YO> ( I also use virtual crystal approximation so, I want to use virsual.x) YO> and how to use vdb2upf.x for virtual.x the same is true than for uspp2upf.x. you can also those tools interactively without any arguments and they will ask for the required information. cheers, axel. YO> YO> Sincerely YO> YO> YO> YO> YO> YO> _______________________________________________ YO> Pw_forum mailing list YO> Pw_forum at pwscf.org YO> http://www.democritos.it/mailman/listinfo/pw_forum YO> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From eyvaz_isaev at yahoo.com Tue Jan 30 21:15:41 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 30 Jan 2007 12:15:41 -0800 (PST) Subject: [Pw_forum] Plot phonon dispersion Message-ID: <866734.14068.qm@web60325.mail.yahoo.com> Hi, How it is possible (for example - plotband....) from ****.freq to construct the postscript plot file for a phonon dispersion ? It is possible, as example, using my little program and script. Bests, Eyvaz. Igor Shein _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum ____________________________________________________________________________________ Never Miss an Email Stay connected with Yahoo! Mail on your mobile. Get started! http://mobile.yahoo.com/services?promote=mail From yukihiro_okuno at fujifilm.co.jp Wed Jan 31 06:57:02 2007 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Wed, 31 Jan 2007 14:57:02 +0900 Subject: [Pw_forum] On tne optimization error in PbTiO3 Message-ID: Dear PWscf Users. I'm now working the optimization of PbTiO3 But in the process of calculation, my calculation stopped with an error like below CASE: energy_new > energy_old new trust radius = 0.0000499856 bohr trust_radius < trust_radius_min resetting bfgs history %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from bfgs : error # 1 bfgs history already reset at previous step %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... What is wrong and how to treat such an erro? This is my input file &control calculation = 'relax', restart_mode = 'from_scratch', pseudo_dir = '/home/okuno/PWSCF/espresso-3.1.1/pseudo/', outdir = './', forc_conv_thr = 1.0D-5 / &system ibrav=6 celldm(1)=7.36203352272 celldm(3)=1.07 nat=5 ntyp=3 nbnd=25 ecutwfc=30.0 occupations = 'fixed' degauss=0.00 / &electrons conv_thr = 1e-7, mixing_beta=0.3, / &IONS ion_dynamics='bfgs' bfgs_ndim=3 pot_extrapolation = "second_order" wfc_extrapolation = "second_order" / ATOMIC_SPECIES Pb 207.2 Pb.vdb.UPF Ti 47.867 Ti.vdb.UPF O 15.9994 O.vdb.UPF ATOMIC_POSITIONS {crystal} Pb 0.000000000 0.000000000 0.000000000 Ti 0.500000000 0.500000000 0.534020000 O 0.000000000 0.500000000 0.611230000 O 0.500000000 0.000000000 0.611230000 O 0.500000000 0.500000000 0.103910000 K_POINTS {automatic} 4 4 4 1 1 1 From shein at ihim.uran.ru Wed Jan 31 10:00:02 2007 From: shein at ihim.uran.ru (Igor R. Shein) Date: Wed, 31 Jan 2007 12:00:02 +0300 Subject: [Pw_forum] Plot phonon dispersion In-Reply-To: <866734.14068.qm@web60325.mail.yahoo.com> References: <866734.14068.qm@web60325.mail.yahoo.com> Message-ID: <45C05A92.1070203@ihim.uran.ru> Hi, Eyvas, And as and on conditions it is possible to receive these programs? Igor Eyvaz Isaev ?????: > Hi, > > How it is possible (for example - plotband....) from ****.freq to > construct the postscript plot file for a phonon dispersion ? > > It is possible, as example, using my little program and script. > > Bests, > Eyvaz. > > > Igor Shein > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > ____________________________________________________________________________________ > Never Miss an Email > Stay connected with Yahoo! Mail on your mobile. Get started! > http://mobile.yahoo.com/services?promote=mail > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- PhD Igor R. Shein Leading researcher Insitute of the Solid State Chemistry Ural Branch Of the Russial Academy of Sciences Pervomaiskaya st. 91, 620041 Yekaterinburg, Russia Tel: +7 343 362 3387 Fax: +7 343 374 4495 From asen at gate.sinica.edu.tw Wed Jan 31 08:39:25 2007 From: asen at gate.sinica.edu.tw (A Sen) Date: Wed, 31 Jan 2007 15:39:25 +0800 Subject: [Pw_forum] About (7,3) nanowire coordinates In-Reply-To: <20070131063822.10271.42750.Mailman@democritos.sissa.it> References: <20070131063822.10271.42750.Mailman@democritos.sissa.it> Message-ID: <20070131073630.M25140@gate.sinica.edu.tw> Dear All, I would like to generate all of the 85 coordinates of the (7,3) Au chiral nanowire using PWScf, which has already been done a long ago by Dr. Andrea (Ref. Science, v291,pp290,2001). I would greatly appreciate if you could please provide me the input file for this. What would be the input file for the (6,0) nanowire as well? With best regards, Arijit -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070131/539a6e5d/attachment.htm From ezadshojaee at hotmail.com Wed Jan 31 09:32:18 2007 From: ezadshojaee at hotmail.com (Ezad Shojaee) Date: Wed, 31 Jan 2007 08:32:18 +0000 Subject: [Pw_forum] q not allowed Message-ID: hi trying phonon calculation, i used a small grid (331). but using q2r.x, the code has given " q not allowed" in the archive i saw this: >there is a mismatch between what the q2r.x code thinks q-points should be, >and what you provided. what should i do? so i have to forget this grid? how should i choose the grid not to have this error? my case is base-centered tetragonal thanx _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ From Vasile.Chis at physics.gu.se Wed Jan 31 10:21:37 2007 From: Vasile.Chis at physics.gu.se (Vasile Chis) Date: Wed, 31 Jan 2007 10:21:37 +0100 Subject: [Pw_forum] Induced charge density, phonon. Message-ID: <1170235297.26002.20.camel@zeeman.fy.chalmers.se> Dear users. I was wondering if I could get some help regarding the induced charge density at a surface due to a phonon at a specific q-point. The surface is based on the slab model. For a specific mode (surface mode) at a specific q-parallel-point (SBZ zone boundary) I would like to extract the induced charge density in real space along the slab z-axis, delta-n(R,z) where R=(x,y) (a point i the slab plane). I have tried with some lighter examples to use and try to understand the option in INPUT_PH namely fildrho. All this gave was a lot of zeros, regardless at which q-point this was done. Any explanations why? I've would be pleased for any ideas of how to access this problem and how to get the desired charge density in real space. Thank you in advance. Best regards Vasse -- ___________________________________ Vasile Chis, Ph.D Student Interface Modelling Group Department of Physics G?teborgs Universitet Fysikg?rden 6B S-412 96 G?teborg, SWEDEN tel :+46 (0) 31 7723338 mobile :+46 (0) 70 8348867 fax. :+46 (0) 31 7723367 email :Vasile.Chis at physics.gu.se ___________________________________ From eyvaz_isaev at yahoo.com Wed Jan 31 12:12:38 2007 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 31 Jan 2007 03:12:38 -0800 (PST) Subject: [Pw_forum] q not allowed In-Reply-To: Message-ID: <469265.71188.qm@web60324.mail.yahoo.com> Hi, > trying phonon calculation, i used a small grid > (331). but using q2r.x, the > code has given " q not allowed" > in the archive i saw this: > >there is a mismatch between what the q2r.x code > thinks q-points should be, > >and what you provided. Sorry, but quite stupid question: are these q-vectros you used in cartesian or wrt basis vescors? As far as I know q2r.x uses q-vectors in cartesian. Besides, it might be that you specified insufficent digits for q-vectors, so they do not coincide with those generated by q2r.x. > what should i do? so i have to forget this grid? how > should i choose the grid not to have this error? > my case is base-centered tetragonal The best way is using of the latest version of QE where you can specify nx,ny,nz in ph.in file so that the program ph.x generates q-vectors and then calculates dynamical matrices for thes q-points. The next step is FFT by means of q2r.x. See example 6. Bests, Eyvaz. > thanx > > _________________________________________________________________ > Express yourself instantly with MSN Messenger! > Download today it's FREE! > http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ____________________________________________________________________________________ No need to miss a message. Get email on-the-go with Yahoo! Mail for Mobile. Get started. http://mobile.yahoo.com/mail From degironc at sissa.it Wed Jan 31 12:37:45 2007 From: degironc at sissa.it (degironc) Date: Wed, 31 Jan 2007 12:37:45 +0100 Subject: [Pw_forum] On tne optimization error in PbTiO3 In-Reply-To: References: Message-ID: <45C07F89.5090509@sissa.it> In general calculated energies are a little noisy (due to insufficient scf accuracy and/or insufficient accuracy in the integration of the XC functional on the FFT real space grid). Moreover Energies and forces are slightly inconsistent (due to insufficient scf accuracy). Hence it is pointless to pretend a convergence in the relaxation below this noise level. When the history of the relaxation makes no sense the code reduce the size of the tipical step and restart the history, but if the step is so small that you are already digging below the noise level this does not help. By the way forc_conv_thr = 1.0D-5 is an extremey strict threshold. default value is 1.0d-3 and usually is alread fine. 1.0d-4 should be more than enough for any purpouse. stefano yukihiro_okuno at fujifilm.co.jp wrote: >Dear PWscf Users. > >I'm now working the optimization of PbTiO3 > >But in the process of calculation, my calculation > >stopped with an error like below > > CASE: energy_new > energy_old > > new trust radius = 0.0000499856 bohr > > trust_radius < trust_radius_min > > resetting bfgs history > > > >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from bfgs : error # 1 > bfgs history already reset at previous step > >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... > > >What is wrong and how to treat such an erro? > >This is my input file > >&control > calculation = 'relax', > restart_mode = 'from_scratch', > pseudo_dir = '/home/okuno/PWSCF/espresso-3.1.1/pseudo/', > outdir = './', > forc_conv_thr = 1.0D-5 > / > &system > ibrav=6 > celldm(1)=7.36203352272 > celldm(3)=1.07 > nat=5 > ntyp=3 > nbnd=25 > ecutwfc=30.0 > occupations = 'fixed' > degauss=0.00 > / > &electrons > conv_thr = 1e-7, > mixing_beta=0.3, > / >&IONS > ion_dynamics='bfgs' > bfgs_ndim=3 > pot_extrapolation = "second_order" > wfc_extrapolation = "second_order" >/ >ATOMIC_SPECIES > Pb 207.2 Pb.vdb.UPF > Ti 47.867 Ti.vdb.UPF > O 15.9994 O.vdb.UPF >ATOMIC_POSITIONS {crystal} >Pb 0.000000000 0.000000000 0.000000000 >Ti 0.500000000 0.500000000 0.534020000 >O 0.000000000 0.500000000 0.611230000 >O 0.500000000 0.000000000 0.611230000 >O 0.500000000 0.500000000 0.103910000 >K_POINTS {automatic} > 4 4 4 1 1 1 > > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From yukihiro_okuno at fujifilm.co.jp Wed Jan 31 14:54:28 2007 From: yukihiro_okuno at fujifilm.co.jp (yukihiro_okuno at fujifilm.co.jp) Date: Wed, 31 Jan 2007 22:54:28 +0900 Subject: [Pw_forum] Integrated DOS in dos.x output is not consistent in nelec Message-ID: Dear PWscf Users. I had calculated PbTiO3 dos by the following procedure, 1) I did scf calculation 2) then I increase KPOINTS and do non-scf run, 3) finally I had calculate total DOS by dos.x The all valence electron number nelec = 44 and the Fermi Enegy output which lay in the energy gap is ( in 2) process I set occupation='tetrahedra' ) the Fermi Enegy is 11.1368 eV But I see the output total DOS in 3) around Fermi Energy eV dos(E) Int dos(E) 10.850 0.0000E+00 0.3353E+02 10.900 0.0000E+00 0.3353E+02 10.950 0.0000E+00 0.3353E+02 11.000 0.0000E+00 0.3353E+02 11.050 0.0000E+00 0.3353E+02 11.100 0.0000E+00 0.3353E+02 11.150 0.0000E+00 0.3353E+02 11.200 0.0000E+00 0.3353E+02 11.250 0.0000E+00 0.3353E+02 11.300 0.0000E+00 0.3353E+02 11.350 0.0000E+00 0.3353E+02 11.400 0.0000E+00 0.3353E+02 11.450 0.0000E+00 0.3353E+02 11.500 0.0000E+00 0.3353E+02 The Integrated Dos around Fermi Enegy for the case of insulater it must be nelec/2 = 22 ( for non-spin polarized case) but, it seems different number 33.5333.... Why such a problem have happen? Sincerely, Yukihiro Okuno. With my input file are &control calculation = 'scf', restart_mode = 'from_scratch', pseudo_dir = '/home/okuno/PWSCF/espresso-3.1.1/pseudo/', outdir = './', prefix = "PbTiO3" / &system ibrav=6 celldm(1)=7.36203352272 celldm(3)=1.07 nat=5 ntyp=3 nbnd=26 ecutwfc=30.0 occupations = 'fixed' degauss=0.00 / &electrons conv_thr = 1e-12, mixing_beta=0.3, / ATOMIC_SPECIES Pb 207.2 Pb.vdb.UPF Ti 47.867 Ti.vdb.UPF O 15.9994 O.vdb.UPF ATOMIC_POSITIONS {crystal} Pb 0.000000000 0.000000000 -0.014724444 Ti 0.500000000 0.500000000 0.533084193 O 0.000000000 0.500000000 0.615412576 O 0.500000000 0.000000000 0.615412576 O 0.500000000 0.500000000 0.111205097 K_POINTS {automatic} 4 4 4 1 1 1 and process 2) for nscf run for DOS &control calculation = 'nscf', pseudo_dir = '/home/okuno/PWSCF/espresso-3.1.1/pseudo/', outdir = './', prefix = 'PbTiO3' / &system ibrav=6 celldm(1)=7.36203352272 celldm(3)=1.07 nat=5 ntyp=3 nbnd=26 ecutwfc=30.0 occupations = 'tetrahedra' / &electrons conv_thr = 1e-12, mixing_beta=0.3, / ATOMIC_SPECIES Pb 207.2 Pb.vdb.UPF Ti 47.867 Ti.vdb.UPF O 15.9994 O.vdb.UPF ATOMIC_POSITIONS {crystal} Pb 0.000000000 0.000000000 -0.014724444 Ti 0.500000000 0.500000000 0.533084193 O 0.000000000 0.500000000 0.615412576 O 0.500000000 0.000000000 0.615412576 O 0.500000000 0.500000000 0.111205097 K_POINTS {automatic} 8 8 8 1 1 1 and process 3) for dos.x input file is &inputpp outdir='/home/okuno/PWSCF/espresso-3.1.1/Work/PbTiO3', prefix='PbTiO3', fildos='PbTiO3.dos', Emin=-15.0, Emax=20.0, DeltaE=0.05 / From stewart at cnf.cornell.edu Wed Jan 31 15:28:00 2007 From: stewart at cnf.cornell.edu (stewart at cnf.cornell.edu) Date: Wed, 31 Jan 2007 09:28:00 -0500 Subject: [Pw_forum] About (7,3) nanowire coordinates In-Reply-To: <20070131073630.M25140@gate.sinica.edu.tw> References: <20070131063822.10271.42750.Mailman@democritos.sissa.it> <20070131073630.M25140@gate.sinica.edu.tw> Message-ID: <20070131142800.71006.qmail@mail.spidergraphics.com> Hi Arijit, The coordinates for the (7,3) Au nanowire are available on the Science website. Check under the supplemental data for the paper. This provides the positions in a_0 units as well as the forces on each atom. If you are unable to access this, let me know and I'll send them your way. Best regards, Derek A Sen writes: > Dear All, > > I would like to generate all of the 85 coordinates of the (7,3) Au chiral > > nanowire using PWScf, which has already been done a long ago by > > Dr. Andrea (Ref. Science, v291,pp290,2001). I would greatly > > appreciate if you could please provide me the input file for this. What would be > > the input file for the (6,0) nanowire as well? > > With best regards, > > Arijit ################################ Derek Stewart, Ph. D. Scientific Computation Associate 250 Duffield Hall Cornell Nanoscale Facility (CNF) Ithaca, NY 14853 stewart (at) cnf.cornell.edu (607) 255-2856 From akohlmey at cmm.chem.upenn.edu Wed Jan 31 15:37:09 2007 From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer) Date: Wed, 31 Jan 2007 09:37:09 -0500 (EST) Subject: [Pw_forum] On tne optimization error in PbTiO3 In-Reply-To: <45C07F89.5090509@sissa.it> Message-ID: On Wed, 31 Jan 2007, degironc wrote: hi, let me translate this into 'beginner speak': the problem here essentially boils down to: you cannot get more accuracy on one property, if you do not calculate the property it depends on accurate enough. if one changes a parameter, one has to check, what other parameters need to be changed as well. in case of geometry optimization. if you want to converge the geometry very accurately (as stefano pointed out, 1.0e-5 is extreme), you first have to make sure that you compute the forces on the atoms accurate enough. that accuracy depends primarily on the basis set size (plane wave energy cutoff) and the convergence parameter for single point energy. so you have to do a run of single point calculations where you print out the forces to find out how high you have to crank up the PW-cutoff and how tight you have to converge the wavefunction to get forces that accurate. the second point is the 'noise' from evaluating the xc-functionals (especially when you include gradient correction). and interpolated with splines, with a very coarse grid the forces may be pretty random. now, with ultra-soft pseudopotentials, the wavefunction cutoff needed to get a converged energy is rather low, but to avoid the noise from the xc-functional evaluation (and from the augmentation charges), you need a higher density cutoff (by default 4x the wavefunction cutoff). if you search the mailing archive you'll find that 30-40ry for the wavefunction cutoff and a factor of 10 for the density cutoff (i.e. 300-400ry) is a conservative choice. hope that helps, axel. SdG> In general calculated energies are a little noisy (due to insufficient SdG> scf accuracy and/or SdG> insufficient accuracy in the integration of the XC functional on the FFT SdG> real space grid). SdG> Moreover Energies and forces are slightly inconsistent (due to SdG> insufficient scf accuracy). SdG> Hence it is pointless to pretend a convergence in the relaxation below SdG> this noise level. SdG> When the history of the relaxation makes no sense the code reduce the SdG> size of the tipical SdG> step and restart the history, but if the step is so small that you are SdG> already digging below SdG> the noise level this does not help. SdG> SdG> By the way forc_conv_thr = 1.0D-5 is an extremey strict threshold. SdG> default value is 1.0d-3 and usually is alread fine. 1.0d-4 should be SdG> more than SdG> enough for any purpouse. SdG> SdG> stefano SdG> SdG> yukihiro_okuno at fujifilm.co.jp wrote: SdG> SdG> >Dear PWscf Users. SdG> > SdG> >I'm now working the optimization of PbTiO3 SdG> > SdG> >But in the process of calculation, my calculation SdG> > SdG> >stopped with an error like below SdG> > SdG> > CASE: energy_new > energy_old SdG> > SdG> > new trust radius = 0.0000499856 bohr SdG> > SdG> > trust_radius < trust_radius_min SdG> > SdG> > resetting bfgs history SdG> > SdG> > SdG> > SdG> >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% SdG> > from bfgs : error # 1 SdG> > bfgs history already reset at previous step SdG> > SdG> >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% SdG> > SdG> > stopping ... SdG> > SdG> > SdG> >What is wrong and how to treat such an erro? SdG> > SdG> >This is my input file SdG> > SdG> >&control SdG> > calculation = 'relax', SdG> > restart_mode = 'from_scratch', SdG> > pseudo_dir = '/home/okuno/PWSCF/espresso-3.1.1/pseudo/', SdG> > outdir = './', SdG> > forc_conv_thr = 1.0D-5 SdG> > / SdG> > &system SdG> > ibrav=6 SdG> > celldm(1)=7.36203352272 SdG> > celldm(3)=1.07 SdG> > nat=5 SdG> > ntyp=3 SdG> > nbnd=25 SdG> > ecutwfc=30.0 SdG> > occupations = 'fixed' SdG> > degauss=0.00 SdG> > / SdG> > &electrons SdG> > conv_thr = 1e-7, SdG> > mixing_beta=0.3, SdG> > / SdG> >&IONS SdG> > ion_dynamics='bfgs' SdG> > bfgs_ndim=3 SdG> > pot_extrapolation = "second_order" SdG> > wfc_extrapolation = "second_order" SdG> >/ SdG> >ATOMIC_SPECIES SdG> > Pb 207.2 Pb.vdb.UPF SdG> > Ti 47.867 Ti.vdb.UPF SdG> > O 15.9994 O.vdb.UPF SdG> >ATOMIC_POSITIONS {crystal} SdG> >Pb 0.000000000 0.000000000 0.000000000 SdG> >Ti 0.500000000 0.500000000 0.534020000 SdG> >O 0.000000000 0.500000000 0.611230000 SdG> >O 0.500000000 0.000000000 0.611230000 SdG> >O 0.500000000 0.500000000 0.103910000 SdG> >K_POINTS {automatic} SdG> > 4 4 4 1 1 1 SdG> > SdG> > SdG> >_______________________________________________ SdG> >Pw_forum mailing list SdG> >Pw_forum at pwscf.org SdG> >http://www.democritos.it/mailman/listinfo/pw_forum SdG> > SdG> > SdG> SdG> _______________________________________________ SdG> Pw_forum mailing list SdG> Pw_forum at pwscf.org SdG> http://www.democritos.it/mailman/listinfo/pw_forum SdG> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From ferretti.andrea at unimore.it Wed Jan 31 15:42:15 2007 From: ferretti.andrea at unimore.it (Andrea Ferretti) Date: Wed, 31 Jan 2007 15:42:15 +0100 (CET) Subject: [Pw_forum] Integrated DOS in dos.x output is not consistent in nelec In-Reply-To: References: Message-ID: Dear Yukihiro, > > The all valence electron number nelec = 44 > [....] > but, it seems different number 33.5333.... > > Why such a problem have happen? > > > &inputpp > outdir='/home/okuno/PWSCF/espresso-3.1.1/Work/PbTiO3', > prefix='PbTiO3', > fildos='PbTiO3.dos', > Emin=-15.0, Emax=20.0, DeltaE=0.05 > / > I suspect your problems are due to the values you specified for Emin=-15.0 or DeltaE=0.05 small numbers of electron from the DOS may be due to the fact Emin is not below the lowest eigenvalue (my suggestion is to avoid providing Emin except you really need it)... a second problem may be connected with the DeltaE value: since the integration of the DOS is performed on the output energy grid, a too coarse grid may result in wrong integration... ( note that the default value for DeltaE is 0.01 eV ) hope it helps andrea -- Andrea Ferretti National Research Center S3, CNR-INFM ( http://s3.infm.it ) Dipartimento di Fisica, Universita' di Modena e Reggio Emilia Via Campi 213/A I-41100 Modena, Italy Tel: +39 059 2055301 Fax: +39 059 374794 Skype: andrea_ferretti URL: http://www.nanoscience.unimo.it Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From shaposh at isp.nsc.ru Wed Jan 31 15:50:59 2007 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Wed, 31 Jan 2007 20:50:59 +0600 Subject: [Pw_forum] Electron affinity calculation In-Reply-To: <200701271422.44059.shaposh@isp.nsc.ru> References: <200701271339.53346.shaposh@isp.nsc.ru> <200701271422.44059.shaposh@isp.nsc.ru> Message-ID: <200701312050.59267.shaposh@isp.nsc.ru> I have tried several slab models and the first conduction band is still meaningless, i.e. much higher than it should be in real crystall. I have not tried to optimize the structures though. I guess, i have to 1. Optimize the structure. 2. Remove some electrons from the system, hoping to create surface charge. Am i right here? Best Regards, Alexander Shaposhnikov On Saturday 27 January 2007 14:22, Alexander Shaposhnikov wrote: > Hello Dr. Baroni, > > Thank you, i was thinking about surface myself, > good to know i was in the right direction! > I will try to create slab surface model. > > Best Regards, > Alexander Shaposhnkov > > On Saturday 27 January 2007 13:54, Stefano Baroni wrote: > > On Jan 27, 2007, at 8:39 AM, Alexander Shaposhnikov wrote: > > > My question is, what is the established approach for the > > > calculations of > > > electron affinity for the plane wave band dft calculations? > > > > I believe, you should first ask (and answer) the preliminary > > question: what makes " ... the first conduction band ... > > meaningful ..?.. " The answer does not depend on the theoretical > > approach (DFT), nor on the basis set (plane waves), but on nature: > > the surface. So, in order to calculate electron affinities in an > > extended system you have to simulate "the place the added electron > > comes from", i.e. the vacuum, and the interface between that place > > and the solid, i.e. a surface. > > > > Hope this clarifies a bit. > > > > Stefano > > > > --- > > Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - > > Trieste > > [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) > > > > Please, if possible, don't send me MS Word or PowerPoint attachments > > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From ceresoli at sissa.it Wed Jan 31 16:14:22 2007 From: ceresoli at sissa.it (Davide Ceresoli) Date: Wed, 31 Jan 2007 16:14:22 +0100 Subject: [Pw_forum] Electron affinity calculation In-Reply-To: <200701312050.59267.shaposh@isp.nsc.ru> References: <200701271339.53346.shaposh@isp.nsc.ru> <200701271422.44059.shaposh@isp.nsc.ru> <200701312050.59267.shaposh@isp.nsc.ru> Message-ID: <45C0B24E.7070400@sissa.it> Alexander Shaposhnikov wrote: > I have tried several slab models and the first conduction band > is still meaningless, i.e. much higher than it should be in real crystall. > I have not tried to optimize the structures though. Have you subtracted the value of the vacuum level from the edge of the conduction band? in a slab geometry the vacuum level is given by the average hartree potential in the vacuum region, in between the slab. HTH Davide From baroni at sissa.it Wed Jan 31 16:20:52 2007 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 31 Jan 2007 16:20:52 +0100 Subject: [Pw_forum] Electron affinity calculation In-Reply-To: <200701312050.59267.shaposh@isp.nsc.ru> References: <200701271339.53346.shaposh@isp.nsc.ru> <200701271422.44059.shaposh@isp.nsc.ru> <200701312050.59267.shaposh@isp.nsc.ru> Message-ID: On Jan 31, 2007, at 3:50 PM, Alexander Shaposhnikov wrote: > > I have tried several slab models and the first conduction band > is still meaningless, i.e. much higher than it should be in real > crystall. the absolute value of the energy levels are of course as meaningless as they are for a bulk calculation, and for the same reason: the average electrostatic potential of an infinite solid is ill defined (periodically repeated slabs do constitute an infinite, periodic, system). What you ought to look after is the position of individual energy levels *with respect to the value of the potential in the vacuum region*. > I have not tried to optimize the structures though. > > I guess, i have to > 1. Optimize the structure. fine > 2. Remove some electrons from the system, hoping to create surface > charge. I think that the value of the lumo energy with respect to the vacuum potential should be a fair estimate of the electron affinity you are looking for. S. --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070131/898aba84/attachment.htm From shaposh at isp.nsc.ru Wed Jan 31 17:09:45 2007 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Wed, 31 Jan 2007 22:09:45 +0600 Subject: [Pw_forum] Electron affinity calculation In-Reply-To: <45C0B24E.7070400@sissa.it> References: <200701271339.53346.shaposh@isp.nsc.ru> <200701312050.59267.shaposh@isp.nsc.ru> <45C0B24E.7070400@sissa.it> Message-ID: <200701312209.45892.shaposh@isp.nsc.ru> Why the average hartree potential? Shouldn't it be the total potential averaged in the median plane in-between the slabs? Best Regards, Alexander Shaposhnikov On Wednesday 31 January 2007 21:14, Davide Ceresoli wrote: > Alexander Shaposhnikov wrote: > > I have tried several slab models and the first conduction band > > is still meaningless, i.e. much higher than it should be in real > > crystall. I have not tried to optimize the structures though. > > Have you subtracted the value of the vacuum level from the edge > of the conduction band? in a slab geometry the vacuum level is > given by the average hartree potential in the vacuum region, > in between the slab. > > HTH > > Davide > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From ceresoli at sissa.it Wed Jan 31 17:37:15 2007 From: ceresoli at sissa.it (Davide Ceresoli) Date: Wed, 31 Jan 2007 17:37:15 +0100 Subject: [Pw_forum] Electron affinity calculation In-Reply-To: <200701312209.45892.shaposh@isp.nsc.ru> References: <200701271339.53346.shaposh@isp.nsc.ru> <200701312050.59267.shaposh@isp.nsc.ru> <45C0B24E.7070400@sissa.it> <200701312209.45892.shaposh@isp.nsc.ru> Message-ID: <45C0C5BB.7090709@sissa.it> Alexander Shaposhnikov wrote: > Why the average hartree potential? > Shouldn't it be the total potential averaged in the median plane > in-between the slabs? > All right. It's the electrostatic potential. I generally use plot_num = 11 (11=the V_bare + V_H potential) in postprocessing. From baroni at sissa.it Wed Jan 31 17:44:12 2007 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 31 Jan 2007 17:44:12 +0100 Subject: [Pw_forum] Electron affinity calculation In-Reply-To: <200701312209.45892.shaposh@isp.nsc.ru> References: <200701271339.53346.shaposh@isp.nsc.ru> <200701312050.59267.shaposh@isp.nsc.ru> <45C0B24E.7070400@sissa.it> <200701312209.45892.shaposh@isp.nsc.ru> Message-ID: because they tend to the same value far out in the vacuum, but the Hartree potential does so more fast than the total potential. can you tell why? SB On Jan 31, 2007, at 5:09 PM, Alexander Shaposhnikov wrote: > Why the average hartree potential? > Shouldn't it be the total potential averaged in the median plane > in-between the slabs? > > Best Regards, > Alexander Shaposhnikov > > > On Wednesday 31 January 2007 21:14, Davide Ceresoli wrote: >> Alexander Shaposhnikov wrote: >>> I have tried several slab models and the first conduction band >>> is still meaningless, i.e. much higher than it should be in real >>> crystall. I have not tried to optimize the structures though. >> >> Have you subtracted the value of the vacuum level from the edge >> of the conduction band? in a slab geometry the vacuum level is >> given by the average hartree potential in the vacuum region, >> in between the slab. >> >> HTH >> >> Davide >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20070131/ff7d86dd/attachment.htm From peterwiney at gmail.com Wed Jan 31 22:49:04 2007 From: peterwiney at gmail.com (Peter Winey) Date: Wed, 31 Jan 2007 16:49:04 -0500 Subject: [Pw_forum] a question about a calculation on a relatively large system In-Reply-To: <484321DC-4E72-449C-953A-0D74635C06C1@nest.sns.it> References: <421493EA-D152-4912-8B08-705AB755EEEC@nest.sns.it> <484321DC-4E72-449C-953A-0D74635C06C1@nest.sns.it> Message-ID: Dear all, Thanks a lot for all the expert advice! I tried cpv on my system and it worked fine! Well, I am still curious why pw.x did not work. It would be useful to identify whether or not it is due to the system size. A couple of things that I have tested: 1. Using "restart_mode='restart' ", the run stopped at the same point. 2. Using smaller ecutwfc did not help either. 3. Runing the job on an SGI and a PC cluster, no difference found In this case, I am not sure what to try next. The pw.x input file is as follows (sorry about its length). If someone can have a quick test run on it, I would really appreciate it. ---------------pw.x input file------------------------------- relax CxHy &control calculation='relax' restart_mode='from_scratch', wf_collect=.true., prefix='pwscf', pseudo_dir = '/usr/local/src/espresso-3.0/pseudo', outdir='.', forc_conv_thr = 0.001 tprnfor=.true. nstep =5000 / &system ibrav = 8 celldm(1) = 16.1666058323 celldm(2) = 3.06639392168 celldm(3) = 1.29421390999 nat=248, ntyp=2, ecutwfc = 30.0, occupations='fixed', / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / &ions upscale=10 / ATOMIC_SPECIES C 12.0107 C.pbe-van_ak.UPF H 1.00794 H.pbe-van_ak.UPF K_POINTS {gamma} ATOMIC_POSITIONS {crystal} C 0.9217 0.25 0.3256 C 0.5783 0.75 0.8256 C 0.0783 0.75 0.6744 C 0.4217 0.25 0.1744 C 0.0044 0.25 0.4345 C 0.4956 0.75 0.9345 C 0.9956 0.75 0.5655 C 0.5044 0.25 0.0655 C 0.0674 0.20162 0.4754 C 0.4326 0.79838 0.9754 C 0.9326 0.70162 0.5246 C 0.5674 0.29838 0.0246 C 0.9326 0.79838 0.5246 C 0.5674 0.20162 0.0246 C 0.0674 0.29838 0.4754 C 0.4326 0.70162 0.9754 C 0.068 0.15944 0.39951 C 0.432 0.84056 0.89951 C 0.932 0.65944 0.60049 C 0.568 0.34056 0.10049 C 0.932 0.84056 0.60049 C 0.568 0.15944 0.10049 C 0.068 0.34056 0.39951 C 0.432 0.65944 0.89951 C 0.0046 0.16377 0.2802 C 0.4954 0.83623 0.7802 C 0.9954 0.66377 0.7198 C 0.5046 0.33623 0.2198 C 0.9954 0.83623 0.7198 C 0.5046 0.16377 0.2198 C 0.0046 0.33623 0.2802 C 0.4954 0.66377 0.7802 C 0.9221 0.20631 0.2476 C 0.5779 0.79369 0.7476 C 0.0779 0.70631 0.7524 C 0.4221 0.29369 0.2524 C 0.0779 0.79369 0.7524 C 0.4221 0.20631 0.2524 C 0.9221 0.29369 0.2476 C 0.5779 0.70631 0.7476 C 0.0866 0.13154 0.1954 C 0.4134 0.86846 0.6954 C 0.9134 0.63154 0.8046 C 0.5866 0.36846 0.3046 C 0.9134 0.86846 0.8046 C 0.5866 0.13154 0.3046 C 0.0866 0.36846 0.1954 C 0.4134 0.63154 0.6954 C 0.0975 0.14886 0.0763 C 0.4025 0.85114 0.5763 C 0.9025 0.64886 0.9237 C 0.5975 0.35114 0.4237 C 0.9025 0.85114 0.9237 C 0.5975 0.14886 0.4237 C 0.0975 0.35114 0.0763 C 0.4025 0.64886 0.5763 C 0.0252 0.19708 0.0455 C 0.4748 0.80292 0.5455 C 0.9748 0.69708 0.9545 C 0.5252 0.30292 0.4545 C 0.9748 0.80292 0.9545 C 0.5252 0.19708 0.4545 C 0.0252 0.30292 0.0455 C 0.4748 0.69708 0.5455 C 0.93 0.22297 0.12521 C 0.57 0.77703 0.62521 C 0.07 0.72297 0.87479 C 0.43 0.27703 0.37479 C 0.07 0.77703 0.87479 C 0.43 0.22297 0.37479 C 0.93 0.27703 0.12521 C 0.57 0.72297 0.62521 C 0.1108 0.22313 0.95068 C 0.3892 0.77687 0.45068 C 0.8892 0.72313 0.04932 C 0.6108 0.27687 0.54932 C 0.8892 0.77687 0.04932 C 0.6108 0.22313 0.54932 C 0.1108 0.27687 0.95068 C 0.3892 0.72313 0.45068 C 0.1646 0.11297 0.39613 C 0.3354 0.88703 0.89613 C 0.8354 0.61297 0.60387 C 0.6646 0.38703 0.10387 C 0.8354 0.88703 0.60387 C 0.6646 0.11297 0.10387 C 0.1646 0.38703 0.39613 C 0.3354 0.61297 0.89613 C 0.2393 0.08719 0.4884 C 0.2607 0.91281 0.9884 C 0.7607 0.58719 0.5116 C 0.7393 0.41281 0.0116 C 0.7607 0.91281 0.5116 C 0.7393 0.08719 0.0116 C 0.2393 0.41281 0.4884 C 0.2607 0.58719 0.9884 C 0.3266 0.04374 0.4613 C 0.1734 0.95626 0.9613 C 0.6734 0.54374 0.5387 C 0.8266 0.45626 0.0387 C 0.6734 0.95626 0.5387 C 0.8266 0.04374 0.0387 C 0.3266 0.45626 0.4613 C 0.1734 0.54374 0.9613 C 0.3386 0.0266 0.3431 C 0.1614 0.9734 0.8431 C 0.6614 0.5266 0.6569 C 0.8386 0.4734 0.1569 C 0.6614 0.9734 0.6569 C 0.8386 0.0266 0.1569 C 0.3386 0.4734 0.3431 C 0.1614 0.5266 0.8431 C 0.2643 0.05242 0.2492 C 0.2357 0.94758 0.7492 C 0.7357 0.55242 0.7508 C 0.7643 0.44758 0.2508 C 0.7357 0.94758 0.7508 C 0.7643 0.05242 0.2508 C 0.2643 0.44758 0.2492 C 0.2357 0.55242 0.7492 C 0.177 0.09588 0.2738 C 0.323 0.90412 0.7738 C 0.823 0.59588 0.7262 C 0.677 0.40412 0.2262 C 0.823 0.90412 0.7262 C 0.677 0.09588 0.2262 C 0.177 0.40412 0.2738 C 0.323 0.59588 0.7738 C 0.2052 0.1385 0.9741 C 0.2948 0.8615 0.4741 C 0.7948 0.6385 0.0259 C 0.7052 0.3615 0.5259 C 0.7948 0.8615 0.0259 C 0.7052 0.1385 0.5259 C 0.2052 0.3615 0.9741 C 0.2948 0.6385 0.4741 C 0.2871 0.09507 0.9432 C 0.2129 0.90493 0.4432 C 0.7129 0.59507 0.0568 C 0.7871 0.40493 0.5568 C 0.7129 0.90493 0.0568 C 0.7871 0.09507 0.5568 C 0.2871 0.40493 0.9432 C 0.2129 0.59507 0.4432 C 0.3808 0.09512 0.8396 C 0.1192 0.90488 0.3396 C 0.6192 0.59512 0.1604 C 0.8808 0.40488 0.6604 C 0.6192 0.90488 0.1604 C 0.8808 0.09512 0.6604 C 0.3808 0.40488 0.8396 C 0.1192 0.59512 0.3396 C 0.3916 0.13816 0.7686 C 0.1084 0.86184 0.2686 C 0.6084 0.63816 0.2314 C 0.8916 0.36184 0.7314 C 0.6084 0.86184 0.2314 C 0.8916 0.13816 0.7314 C 0.3916 0.36184 0.7686 C 0.1084 0.63816 0.2686 C 0.3093 0.18228 0.7974 C 0.1907 0.81772 0.2974 C 0.6907 0.68228 0.2026 C 0.8093 0.31772 0.7026 C 0.6907 0.81772 0.2026 C 0.8093 0.18228 0.7026 C 0.3093 0.31772 0.7974 C 0.1907 0.68228 0.2974 C 0.2145 0.18316 0.89954 C 0.2855 0.81684 0.39954 C 0.7855 0.68316 0.10046 C 0.7145 0.31684 0.60046 C 0.7855 0.81684 0.10046 C 0.7145 0.18316 0.60046 C 0.2145 0.31684 0.89954 C 0.2855 0.68316 0.39954 H 0.1087 0.1988 0.5547 H 0.3913 0.8012 0.0547 H 0.8913 0.6988 0.4453 H 0.6087 0.3012 0.9453 H 0.8913 0.8012 0.4453 H 0.6087 0.1988 0.9453 H 0.1087 0.3012 0.5547 H 0.3913 0.6988 0.0547 H 0.2312 0.0989 0.5694 H 0.2688 0.9011 0.0694 H 0.7688 0.5989 0.4306 H 0.7312 0.4011 0.9306 H 0.7688 0.9011 0.4306 H 0.7312 0.0989 0.9306 H 0.2312 0.4011 0.5694 H 0.2688 0.5989 0.0694 H 0.3783 0.0258 0.5242 H 0.1217 0.9742 0.0242 H 0.6217 0.5258 0.4758 H 0.8783 0.4742 0.9758 H 0.6217 0.9742 0.4758 H 0.8783 0.0258 0.9758 H 0.3783 0.4742 0.5242 H 0.1217 0.5258 0.0242 H 0.3981 0.9969 0.3259 H 0.1019 0.0031 0.8259 H 0.6019 0.4969 0.6741 H 0.8981 0.5031 0.1741 H 0.6019 0.0031 0.6741 H 0.8981 0.9969 0.1741 H 0.3981 0.5031 0.3259 H 0.1019 0.4969 0.8259 H 0.2733 0.0403 0.1686 H 0.2267 0.9597 0.6686 H 0.7267 0.5403 0.8314 H 0.7733 0.4597 0.3314 H 0.7267 0.9597 0.8314 H 0.7733 0.0403 0.3314 H 0.2733 0.4597 0.1686 H 0.2267 0.5403 0.6686 H 0.28 0.0654 0.9919 H 0.22 0.9346 0.4919 H 0.72 0.5654 0.0081 H 0.78 0.4346 0.5081 H 0.72 0.9346 0.0081 H 0.78 0.0654 0.5081 H 0.28 0.4346 0.9919 H 0.22 0.5654 0.4919 H 0.4373 0.0653 0.8181 H 0.0627 0.9347 0.3181 H 0.5627 0.5653 0.1819 H 0.9373 0.4347 0.6819 H 0.5627 0.9347 0.1819 H 0.9373 0.0653 0.6819 H 0.4373 0.4347 0.8181 H 0.0627 0.5653 0.3181 H 0.4562 0.1377 0.6988 H 0.0438 0.8623 0.1988 H 0.5438 0.6377 0.3012 H 0.9562 0.3623 0.8012 H 0.5438 0.8623 0.3012 H 0.9562 0.1377 0.8012 H 0.4562 0.3623 0.6988 H 0.0438 0.6377 0.1988 H 0.3178 0.2116 0.7476 H 0.1822 0.7884 0.2476 H 0.6822 0.7116 0.2524 H 0.8178 0.2884 0.7524 H 0.6822 0.7884 0.2524 H 0.8178 0.2116 0.7524 H 0.3178 0.2884 0.7476 H 0.1822 0.7116 0.2476 -------------- next part -------------- An HTML attachment was scrubbed... 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