Re: [QE-users] NEB with variable cell?
Hi Andrii, I also have been playing around with the same issue on NEB. Here is the thread where I asked a similar question, perhaps it will help you: https://www.mail-archive.com/users@lists.quantum-espresso.org/msg36422.html In my case I decided to average the cell parameters of the starting and final images and use that as my foundation to conduct neb. Since I was most interested in exploring the mechanism of photoisomerization which was concentrated around a particular set of atoms I don't believe it has posed a problem. So I guess my point is that the best course of action will simply depend on what you are intending to illustrate via neb. At least that's my two cents, perhaps someone else has a better idea! Apoorv Cavendish Laboratory, University of Cambridge On 2020-10-17 15:40, Andrii Shyichuk wrote: Dear Users, I have two structures (A and B), on which I want to do a NEB calculation, using them as the initial and the final images. The problem is: they differ in their cell size by about 1%. My options: 1. Do NEB with lattice vectors from structure A, then another NEB with vectors from structure B, and then another one with the average vectors. That, obviously, would be an approximation, and I will see how bad it is from the results. 2. Do manual frozen "NEB", where I simply interpolate structure A into structure B in N steps and just do SCFs. Not a NEB per se, but that's something. 3. Interpolate A cell vectors into B cell vectors in N steps, and do atomic position relaxations at each set of vectors. Not sure if the moving atoms will move the way I expect them to move. 4. Get the reaction path from option 1, and then do vc-relax at each step, freezing the moving atoms at the path. However, constraints in PW do not work with vc-relax, as I can see from the manual. Thus, what I can do is option 3 with constraints. So, what would you do? What do people usually do in situations like this? Thank you in advance. Best regards. Andrii Shyichuk Faculty of Chemistry, University of Wrocław, Poland. ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] NEB images with different cell parameters possible?
Sorry for not being clearer, the 'excited' state in our case is actually a metastable state, i.e. a stable state on its own that has undergone photoisomerisation via broadband light. I figured there wasn't variable cell neb. I thought to simply average the cell parameters and use them to conduct neb. I guess the geometries shouldn't be too affected by the slight change in cell parameters, and neb isn't too thrown off by that. Apoorv On 2019-09-06 16:00, Paolo Giannozzi wrote: Some time ago there was a project of variable-cell NEB, but it went nowhere. Anyway: here the problem is not variable-cell NEB but a NEB between an initial configuration in the ground state and a final one in the excited state, if I understand correctly. This is just plain impossible. Paolo On Fri, Sep 6, 2019 at 11:21 AM Giuseppe Mattioli wrote: Dear Apoorv Jain AFAIK, variable cell NEB is not implemented in QE (yet). HTH Giuseppe "A. Jain" ha scritto: Hi All, I would like to conduct an neb study on my system (ruthenium based crystals) where photoisomerisation takes place. We would like to investigate the mechanism of photoisomerisation. However the ground state and irradiated states (geometries obtained via accurate xrd experiments) have very slightly different cell parameters due to the magnitude of the photoisomerisation. The Ground State values are :Axis (Ang): A=8.3891, B=12.5019, C=13.1614. Angles (deg): a=99.481, b=98.613, c=90.27. Excited state: Axis (Ang): A=8.4845, B=12.4241, C=13.3243. Angles (deg): a=101.456, b=98.732, c=91.001. As you can see the values effectively only change by 1%. So I would like to know if is it possible to conduct neb on images whose cell parameters also change, ie I would use the ground state as the starting image and the excited state as the final image? I expect the answer is no. If not, has anybody come across a similar problem or has any suggestions for how I could approach this issue? Thank you for your help. Apoorv Jain (PhD Student) Department of Physics, University of Cambridge ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso [1]) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users [2] GIUSEPPE MATTIOLI CNR - ISTITUTO DI STRUTTURA DELLA MATERIA Via Salaria Km 29,300 - C.P. 10 I-00015 - Monterotondo Scalo (RM) Mob (*preferred*) +39 373 7305625 Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso [1]) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users [2] -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 Links: -- [1] http://www.max-centre.eu/quantum-espresso [2] https://lists.quantum-espresso.org/mailman/listinfo/users ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] NEB images with different cell parameters possible?
Hi All, I would like to conduct an neb study on my system (ruthenium based crystals) where photoisomerisation takes place. We would like to investigate the mechanism of photoisomerisation. However the ground state and irradiated states (geometries obtained via accurate xrd experiments) have very slightly different cell parameters due to the magnitude of the photoisomerisation. The Ground State values are :Axis (Ang): A=8.3891, B=12.5019, C=13.1614. Angles (deg): a=99.481, b=98.613, c=90.27. Excited state: Axis (Ang): A=8.4845, B=12.4241, C=13.3243. Angles (deg): a=101.456, b=98.732, c=91.001. As you can see the values effectively only change by 1%. So I would like to know if is it possible to conduct neb on images whose cell parameters also change, ie I would use the ground state as the starting image and the excited state as the final image? I expect the answer is no. If not, has anybody come across a similar problem or has any suggestions for how I could approach this issue? Thank you for your help. Apoorv Jain (PhD Student) Department of Physics, University of Cambridge ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] dvscf file from a grid ph.x run
Thanks a lot Thomas. This helps a lot. Thanks, Ankit Jain From: Dr. Thomas Brumme Sent: Wednesday, July 10, 2019 9:23:54 AM To: Quantum ESPRESSO users Forum; Ankit Jain Subject: Re: [QE-users] dvscf file from a grid ph.x run Dear Ankit, this discussion might help: https://www.mail-archive.com/users@lists.quantum-espresso.org/msg33771.html Regards Thomas Zitat von Ankit Jain : > Dear users, > > > I have been trying to collect and merge .dvscf files from a grid > example of ph.x and combine these files into a single file (like it > was created from serial single job). > > > So far I have little success on this. I searched on the mailing list > and it seems that the similar question was asked earlier: > > > https://www.mail-archive.com/users@lists.quantum-espresso.org/msg29613.html > > > The suggestion from this earlier question was to write a small > fortran script capable of reading and combining these binary files. > I am wondering if such utility already exists or if not, if someone > can point to piece of source code where these files are written so > that I can attempt to read and combine these files. > > > Thank You, > > Ankit Jain > > Denmark Technical University -- Dr. rer. nat. Thomas Brumme Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry Leipzig University Phillipp-Rosenthal-Strasse 31 04103 Leipzig Tel: +49 (0)341 97 36456 email: thomas.bru...@uni-leipzig.de ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] dvscf file from a grid ph.x run
Dear users, I have been trying to collect and merge .dvscf files from a grid example of ph.x and combine these files into a single file (like it was created from serial single job). So far I have little success on this. I searched on the mailing list and it seems that the similar question was asked earlier: https://www.mail-archive.com/users@lists.quantum-espresso.org/msg29613.html The suggestion from this earlier question was to write a small fortran script capable of reading and combining these binary files. I am wondering if such utility already exists or if not, if someone can point to piece of source code where these files are written so that I can attempt to read and combine these files. Thank You, Ankit Jain Denmark Technical University ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] PWCOND: NAN/ SIGSEGV
Hello Subrata, setting 'ulimit -u unlimited' does not help. Thanks, Ankit Jain On 31 Aug 2018, at 11.17, Subrata Jana mailto:subrata.j...@niser.ac.in>> wrote: Hi, This error was also observed when a different version of a compiler was loaded than that used to compile the code. Suggested was to rebuild everything and please try this: ftp://ftp.iitb.ac.in/LDP/en/solrhe/ch06s10.html With Regards, SJ -- SUBRATA JANA Research Scholar School of Physical Sciences National Institute of Science Education and Research (NISER), Bhubaneswar PO- Bhimpur-Padanpur, Via- Jatni, District:- Khurda PIN – 752050, Odisha, INDIA On Fri, Aug 31, 2018 at 2:14 PM, Ankit Jain mailto:aj...@fysik.dtu.dk>> wrote: Dear All, I am new to PWCOND calculations and I created my input files following the provided examples. I am trying to do conductance calculation for Metal-conductor-metal system. I am running into SIGSEGV error. Things I tried: - running in serial vs parallel and on larger memory machines (16 cpus with 128 gb memory). - changing ikind in the pwcond.in<http://pwcond.in/> input from 1 to 2 as my right and left lead are same material. - setting ikind =2, and bdr = 40 in the input to pwcond.x (40 is my system size in the z-direction) - setting ikind=2 and bdl =10 and bds = 30 in the pwcond.x input file. In this case, program does not crash but returns NAN as non-zero value of transmittance. My scf.in<http://scf.in/>, pwcond.in<http://pwcond.in/>, scf.out and pwcond.out files are attached. The program (pwcond.x) dies with the following error: forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLineSource pwcond.x 00BA019D Unknown Unknown Unknown libpthread-2.17.s 7F841B50D6D0 Unknown Unknown Unknown libiomp5.so7F841A2F4595 Unknown Unknown Unknown libiomp5.so7F841A2F42D4 Unknown Unknown Unknown libiomp5.so7F841A2F5F16 Unknown Unknown Unknown libiomp5.so7F841A2F6215 Unknown Unknown Unknown libiomp5.so7F841A2F6137 Unknown Unknown Unknown libiomp5.so7F841A2F60EF Unknown Unknown Unknown libiomp5.so7F841A2F918F Unknown Unknown Unknown libiomp5.so7F841A2F8F3D Unknown Unknown Unknown libiomp5.so7F841A2ED4A3 Unknown Unknown Unknown libiomp5.so7F841A2EFD9E Unknown Unknown Unknown pwcond.x 00BE1FAA Unknown Unknown Unknown pwcond.x 00418405 compbs_ 439 compbs.f90 pwcond.x 00425A75 do_cond_ 520 do_cond.f90 pwcond.x 0042096F MAIN__ 22 condmain.f90 pwcond.x 0040E2EE Unknown Unknown Unknown libc-2.17.so<http://libc-2.17.so/> 7F841B153445 __libc_start_main Unknown Unknown pwcond.x 0040E1E9 Unknown Unknown Unknown Thank You, Ankit Jain Postdoctroal Scholar, DTU Physics, Denmark. ___ users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] PWCOND: NAN/ SIGSEGV
Dear All, I am new to PWCOND calculations and I created my input files following the provided examples. I am trying to do conductance calculation for Metal-conductor-metal system. I am running into SIGSEGV error. Things I tried: - running in serial vs parallel and on larger memory machines (16 cpus with 128 gb memory). - changing ikind in the pwcond.in input from 1 to 2 as my right and left lead are same material. - setting ikind =2, and bdr = 40 in the input to pwcond.x (40 is my system size in the z-direction) - setting ikind=2 and bdl =10 and bds = 30 in the pwcond.x input file. In this case, program does not crash but returns NAN as non-zero value of transmittance. My scf.in, pwcond.in, scf.out and pwcond.out files are attached. The program (pwcond.x) dies with the following error: forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PCRoutineLineSource pwcond.x 00BA019D Unknown Unknown Unknown libpthread-2.17.s 7F841B50D6D0 Unknown Unknown Unknown libiomp5.so7F841A2F4595 Unknown Unknown Unknown libiomp5.so7F841A2F42D4 Unknown Unknown Unknown libiomp5.so7F841A2F5F16 Unknown Unknown Unknown libiomp5.so7F841A2F6215 Unknown Unknown Unknown libiomp5.so7F841A2F6137 Unknown Unknown Unknown libiomp5.so7F841A2F60EF Unknown Unknown Unknown libiomp5.so7F841A2F918F Unknown Unknown Unknown libiomp5.so7F841A2F8F3D Unknown Unknown Unknown libiomp5.so7F841A2ED4A3 Unknown Unknown Unknown libiomp5.so7F841A2EFD9E Unknown Unknown Unknown pwcond.x 00BE1FAA Unknown Unknown Unknown pwcond.x 00418405 compbs_ 439 compbs.f90 pwcond.x 00425A75 do_cond_ 520 do_cond.f90 pwcond.x 0042096F MAIN__ 22 condmain.f90 pwcond.x 0040E2EE Unknown Unknown Unknown libc-2.17.so 7F841B153445 __libc_start_main Unknown Unknown pwcond.x 0040E1E9 Unknown Unknown Unknown Thank You, Ankit Jain Postdoctroal Scholar, DTU Physics, Denmark. scf.in Description: scf.in scf.out Description: scf.out pwcond.in Description: pwcond.in pwcond.out Description: pwcond.out ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[Pw_forum] k-mesh vs q-mesh
Hi All, I have a query regarding selecting the size of q-grids to use when trying to obtain phonon dispersion. Obviously there is a difference between k-mesh and q-mesh as they are used to calculate different properties, as referenced in this thread from 2012: http://qe-forge.org/pipermail/pw_forum/2012-January/097425.html. However my question is, how do we know the quality of a q-mesh that we have selected? Is that simply from the phonon dispersion and asking matdyn to calculated frequencies at a phonon point not in the grid then checking to see how well it fits, or is there another way where complete phonon frequencies do not have to be calculated to determine the quality of a q-mesh? Also adding onto that, when selecting a q-mesh how does one go about it? Is it ok to simply use the same grid size as that of the k-mesh (if not, how come?) and can the size of the k-mesh used give any clues as to what size q-mesh to use? Best, Apoorv Jain PhD Student Department of Chemical Engineering and Biotechnology University of Cambridge ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] q2r not reading matdyn
My input file ph.x is also given below. phonons of water-tos dark amass(1)=101.07! ru amass(2)=32.065! s amass(3)=15.999! o amass(4)=14.007! n amass(5)=12.011! c amass(6)=1.008 ! h outdir='./out/q#' tr2_ph=1.0d-12, prefix='h2o_tosylate_dark_ph' epsil=.false. recover=.true. start_q=#q last_q=#q ldisp=.true. nq1=2, nq2=2, nq3=2 / I have used a 2x2x2 mesh for both the k-points in pw.x and q-points in ph.x. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Multiple bond lengths and angles on xcrysden
Dear QE users, I'm trying to view a crystal structure in xcrysden that I have structurally optimized with and without cell relaxation. I would like to compare the bond angles and lengths outputted from the two runs. Is there any way to get xcrysden to output the all the bond angles and lengths rather than me having to do it manually using the 'distance' tab? Better yet can that be done in a post processing suite on QE? Thanks, Apoorv Apoorv Jain Department of Chemical Engineering and Biotechnology University of Cambridge ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Bader analysis: CRITIC2
Thank You Dr. Alberto for clarifying my doubts and for the suggestion on using pp.x with plot_num=21. I am currently US PP and I guess as such my best option is to follow this convoluted procedure. I will follow your suggestions and will try to do the analysis with critic2. Thanks again for your time and response. Thank You, Ankit Jain Postdoctoral Researcher, Stanford University On Wed, Jul 26, 2017 at 12:32 AM, Alberto Otero de la Roza < aoterodelar...@gmail.com> wrote: > Hi Ankit, > > > 1. If I am extracting the right charge density from QE using pp.x in > > step 2? I am extracting electron (pseudo)-charge density > > Yes, plot_num=0 is the correct valence pseudo-charge density. > > > 2. If I am specifying right valence electrons in step 3 with zpsp > keyword, > > especially for Cl, should it be be 7 or 17? > > That depends on how many electrons your pseudopotentials represent. 7 > for Cl sounds about right unless you are doing pretty hardcore stuff > (pun intended). But you shouldn't take my word for it - you can get > the ZPSP by summing the number of valence electrons in the first few > lines of the UPF file (column "occ"). > > > Also I need to specify total_density (rho_with_core.cube in above > > case) as the argument to integrable? > > Your second input should be: > > crystal rho_with_core.cube > load rho_with_core.cube id rhoae > load rho_without_core.cube id rhoval > integrable rhoval > yt > > The point is that you want to integrate rho_without_core (which sums > to the correct number of electrons) in the basins of rho_with_core > (which has maxima at the nuclear positions). Also, if you are using > PAW and a recent version of QE (6.x), you don't need this convoluted > process - a more "correct" version of the rho_with_core.cube can be > obtained with plot_num = 21. > > Best, > > Alberto > > --- > Dr. Alberto Otero de la Roza > Department of Chemistry, > University of British Columbia, Okanagan > Kelowna, British Columbia, Canada V1V 1V7 > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Bader analysis: CRITIC2
Dear all, I have been trying to calculate the bader charges using the approach suggested at: http://qe-forge.org/pipermail/pw_forum/2017-May/112779.html but I am stuck with few questions and is wondering if someone could help me this. The steps I am following are as follow: 1. Do pw.x scf run 2. Do pp.x run with plot_num=0 to get electron (pseudo-)charge density and save in file rho_without_core.cube 3. do critic2 run with: crystal rho_without_core.cube load rho_without_core.cube core id rho zpsp Cl 7 C 4 H 1 rid file rho_with_core.cube field rho crystal rho_with_core.cube load rho_with_core.cube id rhoval integrable rhoval yt My questions are: 1. If I am extracting the right charge density from QE using pp.x in step 2? I am extracting electron (pseudo)-charge density 2. If I am specifying right valence electrons in step 3 with zpsp keyword, especially for Cl, should it be be 7 or 17? Also I need to specify total_density (rho_with_core.cube in above case) as the argument to integrable? Thank You, Ankit Jain Stanford University. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Postdoctoral Fellowship in Computational Materials Science for Renewable Fuels and Feedstocks
Dear Subscribers to QE Mailing List We welcome applications for the position below at University of Toronto ( http://light.utoronto.ca). *Postdoctoral Fellowship in Computational Materials Science for Renewable Fuels and Feedstocks* *Description*: We invite applications to a postdoctoral fellowship pursuing the goal of CO2 reduction to valuable fuels and feedstocks. The incumbent will bring expertise in atomistic simulations for modeling heterogeneous catalysis, ultimately to eluciate and then predict and optimize electrocatalytic reactions such as CO2RR with the aid of *ab initio* simulations. *Requirements*: - familiarity with Linux operating system and high-performance cluster environments - ab-initio modeling - DFT software packages such as VASP, Quantum Espresso, CP2K - ability to work in collaboration with experimentalists to advance combined computational/ experimental efforts on new catalyst design. *- proven experience and sucess in computational studies of heterogeneous catalystis.* How to apply: - please send your detailed CV listing your past publications, and names of three referees, to ted.sarg...@utoronto.ca by Jan 15, 2017 *For more information on the research group:* Please see http://light.utoronto.ca Sample publications: [1] A. Bernstein, E. H. Sargent, A. Aspuru-Guzik, …. M. Molina, "Renewables need a grand-challenge strategy," *Nature*, DOI:10.1038/538030a, 2016. [2] B. Zhang, … A. Vojvodic, E. H. Sargent, "Homogeneously dispersed, multimetal oxygen-evolving catalysts," *Science*, vol. 352, pp. 333-337. [3] M. Liu, … S. O. Kelley, E. H. Sargent, "Enhanced electrocatalytic CO2 reduction via field-induced reagent concentration," *Nature*, doi:10.1038/nature19060, 2016. [4] C. R. Kagan, Efrat Lifshitz, E. H. Sargent, D. V. Talapin, "Building devices from colloidal quantum dots," *Science*, 10.1126/science.aac5523, 2016. [5] Z. Ning, E. H. Sargent, "Quantum-dot-in-perovskite solids," *Nature*, vol. 523, pp. 324-328, 2015. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] ph.x Grid for dvscf
Dear QE developers and users, I am trying to do el-ph calculations on large system and is using grid-scheme for parallelization. So far, I am able to use grid scheme successfully for dynamical matrix calculations. I am wondering if I could use the grid scheme for dvscf calculations as well? I need dvscf files for my further calculations for each q-point. Thanks You, Ankit Jain Postdoctoral Fellow University of Toronto ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Fwd: Phonon dispersion from using matdyn.x
Hello Vincenzo, Thanks for your suggestions again. 1,2) Is using (10 10 10) or ( 4 4 4) a good idea for a 2D system? My system is non-periodic in z direction and that is why I am using (10 10 1) qgrid. 3) I tried asr as well but I still get negative frequencies. So I switched it off just to remove one extra debugging parameter in the input file. Thanks, Ankit Jain On Mon, Sep 1, 2014 at 1:25 AM, Vincenzo Verdolino < vincenzo.verdolino at gmail.com> wrote: > So in this case it's obvious that is a q mash issue. I would try as it > follows: > > 1)make an homogeneous mash (10 10 10) > 2)did you check the combination 4 4 4? That should be already enough > 3)is there a particular reason why you are not using any acoustic sum > rules corrections?? > > relaxations looks fine > > V > > > On Mon, Sep 1, 2014 at 2:37 AM, ankit jain > wrote: > >> Hello Vincenzo, >> >> Thanks for your reply again. >> >> As you suggested, I did phonon calculation using ph.x at one of the >> negative frequency (according to matdyn.x) point. ph.x produce all >> positive frequencies for this point. Does this mean that there is something >> wring in the way I am using matdyn.x for interpolating frequencies? >> >> Also, you are right that my system is 2D system with free surface. I have >> vacuum in the z-direction to avoid any interaction. I also used only one >> k-point to sample the z-direction. I have fully relaxed the structure using >> multiple steps of vc-relax and relax (repeating them couple of times). I >> am attaching my pw.out file with this mail to get the idea of forces and >> stress. >> >> Thanks, >> ANkit Jain >> >> >> On Sun, Aug 31, 2014 at 2:57 PM, Vincenzo Verdolino < >> vincenzo.verdolino at gmail.com> wrote: >> >>> Hi Ankit Jain, >>> >>> Germanium >>> >>> tr2_ph=1.0d-18 >>> ldisp=.true. >>> nq1=10 >>> nq2=10 >>> nq3=1 >>> prefix='GEPH_dfpt' >>> outdir='/scratch' >>> fildyn='./dfpt_10x/ge.dyn' >>> / >>> >>> >>> this activate a dispersive phonon calculation. If you switch the ldisp >>> flag to .false. , if you unset nq1, nq2 and nq3 (you just neglect those) >>> and if you specify q1 q2 and q3 at the very end of the input file (after >>> the final slash /) you can calculate the frequencies at that q point. Ex. >>> >>> Germanium >>> >>> tr2_ph=1.0d-18 >>> prefix='GEPH_dfpt' >>> outdir='/scratch' >>> fildyn='./dfpt_10x/ge.dyn' >>> / >>> 1.0 0.0 0.0 >>> >>> I suggest you to pick one q point where you found imaginary frequencies >>> (from your frequencies output file) and just run ph.x < ph.in on it. >>> >>> However I have to tell you that I am not familiar with phonon >>> calculation on surfaces which I believe it's what you are doing right now. >>> Am I correct? i see that your cell is stretched along "z" and you >>> k-sampling is highly non-homogeneous. This may dramatically effects your >>> phonon calculation. One last thing...did you relax through a vc-relax job >>> or is that a pseudo-crystal experimental structure? >>> >>> >>> >>> On Sun, Aug 31, 2014 at 7:28 PM, ankit jain >> > wrote: >>> >>>> Hello Vincenzo, >>>> >>>> Thanks a lot for your reply. >>>> >>>> >>>> "First thing that i would try is to check if phonon calculations at a >>>> q point where matdyn gives you negative is correct or not" >>>> How would I check this? >>>> >>>> Also I am using tr2_ph = 1e-18 in the ph.in and conv_thr=1.0d-12 in >>>> the pw.in file. >>>> My kgrid is 14*12*1 in the pw.in file. >>>> >>>> Thanks, >>>> Ankit Jain >>>> >>>> >>>> >>>> On Sun, Aug 31, 2014 at 1:13 PM, Vincenzo Verdolino < >>>> vincenzo.verdolino at gmail.com> wrote: >>>> >>>>> Dear, >>>>> >>>>> I have similar issues so i am not sure to be able to help you. First >>>>> thing that i would try is to check if phonon calculations at a q point >>>>> where matdyn gives you negative is correct or not. If yes that means that >>>>> you k-samplin is good enough and it is only a matter of q mash for the >>>>> FFT. >>>>> Another check should be on the scf thras
[Pw_forum] Fwd: Phonon dispersion from using matdyn.x
Hello Vincenzo, Thanks for your reply again. As you suggested, I did phonon calculation using ph.x at one of the negative frequency (according to matdyn.x) point. ph.x produce all positive frequencies for this point. Does this mean that there is something wring in the way I am using matdyn.x for interpolating frequencies? Also, you are right that my system is 2D system with free surface. I have vacuum in the z-direction to avoid any interaction. I also used only one k-point to sample the z-direction. I have fully relaxed the structure using multiple steps of vc-relax and relax (repeating them couple of times). I am attaching my pw.out file with this mail to get the idea of forces and stress. Thanks, ANkit Jain On Sun, Aug 31, 2014 at 2:57 PM, Vincenzo Verdolino < vincenzo.verdolino at gmail.com> wrote: > Hi Ankit Jain, > > Germanium > > tr2_ph=1.0d-18 > ldisp=.true. > nq1=10 > nq2=10 > nq3=1 > prefix='GEPH_dfpt' > outdir='/scratch' > fildyn='./dfpt_10x/ge.dyn' > / > > > this activate a dispersive phonon calculation. If you switch the ldisp > flag to .false. , if you unset nq1, nq2 and nq3 (you just neglect those) > and if you specify q1 q2 and q3 at the very end of the input file (after > the final slash /) you can calculate the frequencies at that q point. Ex. > > Germanium > > tr2_ph=1.0d-18 > prefix='GEPH_dfpt' > outdir='/scratch' > fildyn='./dfpt_10x/ge.dyn' > / > 1.0 0.0 0.0 > > I suggest you to pick one q point where you found imaginary frequencies > (from your frequencies output file) and just run ph.x < ph.in on it. > > However I have to tell you that I am not familiar with phonon calculation > on surfaces which I believe it's what you are doing right now. Am I > correct? i see that your cell is stretched along "z" and you k-sampling is > highly non-homogeneous. This may dramatically effects your phonon > calculation. One last thing...did you relax through a vc-relax job or is > that a pseudo-crystal experimental structure? > > > > On Sun, Aug 31, 2014 at 7:28 PM, ankit jain > wrote: > >> Hello Vincenzo, >> >> Thanks a lot for your reply. >> >> >> "First thing that i would try is to check if phonon calculations at a q >> point where matdyn gives you negative is correct or not" >> How would I check this? >> >> Also I am using tr2_ph = 1e-18 in the ph.in and conv_thr=1.0d-12 in the >> pw.in file. >> My kgrid is 14*12*1 in the pw.in file. >> >> Thanks, >> Ankit Jain >> >> >> >> On Sun, Aug 31, 2014 at 1:13 PM, Vincenzo Verdolino < >> vincenzo.verdolino at gmail.com> wrote: >> >>> Dear, >>> >>> I have similar issues so i am not sure to be able to help you. First >>> thing that i would try is to check if phonon calculations at a q point >>> where matdyn gives you negative is correct or not. If yes that means that >>> you k-samplin is good enough and it is only a matter of q mash for the FFT. >>> Another check should be on the scf thrashold in ph.in input file >>> >>> >>> Let me know >>> >>> Sent from my iPhone >>> >>> > On 31/ago/2014, at 17:03, ankit jain >>> wrote: >>> > >>> > >>> > Hello QE developers and users, >>> > >>> > Recently, I am trying to calculate phonon dispersion of a 2D material >>> using pw.x, ph.x, q2r.x and matdyn.x but I am getting very strange results. >>> > >>> > In my calculations the phonon frequencies reported by ph.x are all >>> real for all non-gamma phonon q-points. But, when I use matdyn.x to >>> calculate phonon frequencies at other points (other than the one for which >>> ph.x calculated frequencies), I get negative (imaginary) frequencies. And >>> these negative frequencies are present for non-gamma points as can be seen >>> in attached frequency file. >>> > >>> > I am having difficulty in understanding these results and hoping >>> someone could help. >>> > >>> > Thank You, >>> > Ankit Jain >>> > PhD Candidate >>> > IIT India >>> > >>> > >>> > >>> > >>> > >>> > >>> > ___ >>> > Pw_forum mailing list >>> > Pw_forum at pwscf.org >>> > http://pwscf.org/mailman/listinfo/pw_forum >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140831/567d8c65/attachment.html -- next part -- A non-text attachment was scrubbed... Name: pw.out Type: application/octet-stream Size: 28666 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140831/567d8c65/attachment.obj
[Pw_forum] Fwd: Phonon dispersion from using matdyn.x
Hello Vincenzo, Thanks a lot for your reply. "First thing that i would try is to check if phonon calculations at a q point where matdyn gives you negative is correct or not" How would I check this? Also I am using tr2_ph = 1e-18 in the ph.in and conv_thr=1.0d-12 in the pw.in file. My kgrid is 14*12*1 in the pw.in file. Thanks, Ankit Jain On Sun, Aug 31, 2014 at 1:13 PM, Vincenzo Verdolino < vincenzo.verdolino at gmail.com> wrote: > Dear, > > I have similar issues so i am not sure to be able to help you. First thing > that i would try is to check if phonon calculations at a q point where > matdyn gives you negative is correct or not. If yes that means that you > k-samplin is good enough and it is only a matter of q mash for the FFT. > Another check should be on the scf thrashold in ph.in input file > > > Let me know > > Sent from my iPhone > > > On 31/ago/2014, at 17:03, ankit jain > wrote: > > > > > > Hello QE developers and users, > > > > Recently, I am trying to calculate phonon dispersion of a 2D material > using pw.x, ph.x, q2r.x and matdyn.x but I am getting very strange results. > > > > In my calculations the phonon frequencies reported by ph.x are all real > for all non-gamma phonon q-points. But, when I use matdyn.x to calculate > phonon frequencies at other points (other than the one for which ph.x > calculated frequencies), I get negative (imaginary) frequencies. And these > negative frequencies are present for non-gamma points as can be seen in > attached frequency file. > > > > I am having difficulty in understanding these results and hoping someone > could help. > > > > Thank You, > > Ankit Jain > > PhD Candidate > > IIT India > > > > > > > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140831/b4ade94d/attachment.html
[Pw_forum] Fwd: Phonon dispersion from using matdyn.x
Hello QE developers and users, Recently, I am trying to calculate phonon dispersion of a 2D material using pw.x, ph.x, q2r.x and matdyn.x but I am getting very strange results. In my calculations the phonon frequencies reported by ph.x are all real for all non-gamma phonon q-points. But, when I use matdyn.x to calculate phonon frequencies at other points (other than the one for which ph.x calculated frequencies), I get negative (imaginary) frequencies. And these negative frequencies are present for non-gamma points as can be seen in attached frequency file. I am having difficulty in understanding these results and hoping someone could help. Thank You, Ankit Jain PhD Candidate IIT India -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140831/de8d7368/attachment.html -- next part -- A non-text attachment was scrubbed... Name: pw.in Type: application/octet-stream Size: 601 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140831/de8d7368/attachment.obj -- next part -- A non-text attachment was scrubbed... Name: ph.in Type: application/octet-stream Size: 150 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140831/de8d7368/attachment-0001.obj -- next part -- A non-text attachment was scrubbed... Name: q2r.in Type: application/octet-stream Size: 96 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140831/de8d7368/attachment-0002.obj -- next part -- A non-text attachment was scrubbed... Name: matdyn.in Type: application/octet-stream Size: 374 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140831/de8d7368/attachment-0003.obj -- next part -- A non-text attachment was scrubbed... Name: frequency Type: application/octet-stream Size: 1006 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140831/de8d7368/attachment-0004.obj
[Pw_forum] calculation of lifetime due to anharmonic 3rd order IFC
Hello Prasad, I agree. I have gone through d3.x input file and mailing list and it looks like it calculates 3rd order FCs using DFPT calculations and it needs one of the three q-points involved to be the Gamma point. Typically, DFPT force constants are expensive and therefore people use finite-difference on DFT supercell forces to calculate the 3rd order FCs. For phonon-phonon lifetime, I am not aware of any implementation in QE code. Thanks, Ankit Jain On Thu, Jun 19, 2014 at 7:06 AM, Prasad Matukumilli < prasadchoudary at gmail.com> wrote: > Dear Mr.Sridhar, > > D3.x gives 3rd order IFCs, after that to arrive at lifetimes, is there any > script or tool for that part? > I know this issue has been posted repeatedly in this forum but I am unable > to find any answer. > > Best regards, > ** > Prasad Matukumilli > Research Scholar, > Advanced Technology Development Centre, > Indian Institute of Technology (IIT) > Kharagpur - 721302, India > ** > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140619/6da58220/attachment.html
[Pw_forum] Phonon Dispersion using matdyn.x
Dear QE developers and users, I am using ph.x, q2r.x, and matdyn.x to calculate a phonon dispersion of a one-dimensional polymer (I am using vacuum in other two directions). I am using a phonon qgrid of 1*1*6 for the calculation of dispersion from ph.x. Later using q2r.x and matdyn.x, I am calculation phonon dispersion for 1*1*20 phonon qgrid. My problem is that for the phonon qgrid of 1*1*6, I get non-negative frequencies at all of the irreducible phonon q points, but when I use matdyn.x to calculate phonon frequencies on 1*1*20, some of my acoustic modes frequencies are negative for non-gamma points! For instance, if my irreducible qpoints are 0.0, 0.1,0.3,0.5 (let say), then I get non-negative frequencies from ph.x for all four of these q points (which is right), but when I use matdyn.x to intepolate the frequencies, I get negative frequencies for lowest frequency acoustic phonons with q-points less than 0.1. I am using NORMCONS PP, electron k-grid = 1*1*12, with ecutwfc = 100 Ry, conv_thr=1.0d-12, tr2_ph = 1.0d-14, zasr/asr='one-dim' I am attaching my pw.in, ph.in, q2r.in and matdyn.in files with this mail. Thanks, Ankit Jain IIT Indore, India -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140418/6d89fdae/attachment.html -- next part -- A non-text attachment was scrubbed... Name: matdyn.in Type: application/octet-stream Size: 167 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140418/6d89fdae/attachment.obj -- next part -- A non-text attachment was scrubbed... Name: ph.in Type: application/octet-stream Size: 185 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140418/6d89fdae/attachment-0001.obj -- next part -- A non-text attachment was scrubbed... Name: pw.in Type: application/octet-stream Size: 875 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140418/6d89fdae/attachment-0002.obj -- next part -- A non-text attachment was scrubbed... Name: q2r.in Type: application/octet-stream Size: 94 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140418/6d89fdae/attachment-0003.obj
[Pw_forum] negative phonon frequencies for 1-D polymer chain
Hello Andrea, I am not using 5.0.3 patch to QE 5.0.2 right now and I guess this is the issue. I will try using it today and will see how things go. Thanks a lot, Ankit Jain On Mon, Apr 14, 2014 at 3:24 AM, Andrea Dal Corso wrote: > Did you apply the 5.0.3 patch to QE 5.0.2? Without the patch, the phonon > code gives wrong frequencies for some q points. > > HTH, > > Andrea > > > On Mon, 2014-04-14 at 01:19 -0400, ankit jain wrote: > > Hello Sanjeev, > > > > The pseudopotentials I am using are > > H.pz-vbc.UPF< > http://www.quantum-espresso.org/wp-content/uploads/upf_files/H.pz-vbc.UPF> > > and C.pz-vbc.UPF< > http://www.quantum-espresso.org/wp-content/uploads/upf_files/C.pz-vbc.UPF> > > > > > > Pseudopotential type: NORMCONS > > Method: Von Barth-Car (direct fit) > > Functional type: Perdew-Zunger (LDA) exch-corr > > scalar relativistic > > > > > > I have tried kgrid of 1*1*6 and 1*1*12, but both give negative > frequencies. > > > > > > > > On Mon, Apr 14, 2014 at 12:18 AM, Sanjeev Gupta > > wrote: > > > > > what is kind of pseudopotential? > > > How much k-point? > > > > > > > > > wishes > > > sanjeev > > > > > > > > > On Sun, Apr 13, 2014 at 9:25 AM, Ankit >wrote: > > > > > >> Hello QE developers and users, > > >> > > >> I am trying to calculate phonon dispersion using ph.x and matdyn.x > > >> routines of QE and I am stuck woth negative frequencies for a while > now. > > >> > > >> I have a 1-D chain of polyethylene which has 6 atoms in the unit-cell. > > >> The polymer chain is aligned in z-direction and I have added vacuum on > > >> x- and y- direction. I did the structure relaxation and I am getting > > >> total force after relaxtion as 0.20, which I guess is sufficiently > > >> small. > > >> > > >> After relaxation, when I am trying to calculate phonon dispersion > using > > >> ph.x and matdyn.x I am getting netting frequencies for some of the > > >> phonon modes. I searched online and on QE mailing list and tried > couple > > >> of different things: > > >> > > >> 1. The negative frequencies are appearing for non-gamma point as well, > > >> so I guess its not a ASR issue. Anyway, I am using ASR but even after > > >> this I am getting negative frequencies. > > >> 2. I reduced my tr2_ph and conv_thr to 1.0d-14 and 1.0d-15 which I > guess > > >> are very small as suggested on QE FAQs. > > >> 3. I checked phonon mode shapes for modes with negative frequencies > and > > >> they do not look like rotational mode. > > >> 4. I tried changing number of k points from 6 to 12 in z direction but > > >> this is also not the cause. > > >> > > >> I am really stuck here and not sure about the cause of negative > > >> frequencies. With vc-relax, my structure is getting relaxed which I > > >> guess means my structure is stable. But then I am not sure why I am > > >> getting negative frequencies. > > >> > > >> I really appreciate any help or suggestions. > > >> > > >> Thanks, > > >> > > >> Ankit Jain > > >> IIT Indore, > > >> Indore, > > >> India > > >> > > >> > > >> ___ > > >> Pw_forum mailing list > > >> Pw_forum at pwscf.org > > >> http://pwscf.org/mailman/listinfo/pw_forum > > >> > > > > > > > > > > > > -- > > > With Best Regards, > > > > > > > > > Dr. Sanjeev Kumar Gupta > > > Fulbright Post-Doctoral Scholar > > > Dept. of Physics > > > Michigan Technological University > > > 1400 Townsend Drive, Houghton > > > MI 49931, USA > > > > > > > > > ___ > > > Pw_forum mailing list > > > Pw_forum at pwscf.org > > > http://pwscf.org/mailman/listinfo/pw_forum > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > -- > Andrea Dal CorsoTel. 0039-040-3787428 > SISSA, Via Bonomea 265 Fax. 0039-040-3787249 > I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140414/78d9f1e6/attachment.html
[Pw_forum] negative phonon frequencies for 1-D polymer chain
Hello Prasenjit, Please find the output file for vc-relax attached. I had rerun my calculations so this file has slightly different coordinate from what is reported in pw.in. Thanks, Ankit Jain On Mon, Apr 14, 2014 at 2:12 AM, Sanjeev Gupta wrote: > good. > can you take one more test to change the pseudo and see. May be I am > wrong but see. > > > > > > > On Sun, Apr 13, 2014 at 11:02 PM, ankit jain gmail.com>wrote: > >> I have tried acoustic sum rule and it does not change negative >> frequencies. >> I have rerun calculations with several different parameters and seems to >> have modified my vc-relax output file. I am re-running it and will send it >> as soon as it is done. >> >> >> On Mon, Apr 14, 2014 at 1:51 AM, Prasenjit Ghosh > > wrote: >> >>> Did you try using the acoustic sum rule and see whether the imaginary >>> frequencies are still there? Also can I have a look at the vc-relax output >>> file? >>> >>> Prasenjit >>> >>> >>> On 14 April 2014 11:10, ankit jain wrote: >>> >>>> Hello Prasenjit, >>>> >>>> I am getting negative phonon frequencies for non-gamma points also. >>>> After structure optimization, the total force is 0.20 Ry/au and >>>> pressure is -0.24 kbar. >>>> >>>> I am using ecutwfc of 100 Ry, which is converged with respect to the >>>> total energy of the system. I am not able to do convergence with respect to >>>> phonon modes as some modes have negative frequencies. Is there a way to do >>>> ecutwfc convergence for phonon modes without calculating phonon >>>> frequencies? >>>> >>>> I am atatching my pw.in, ph.in pw.out and ph.out files (which I forgot >>>> to attch in my original mail) here. >>>> >>>> Thanks, >>>> ANkit Jain >>>> >>>> >>>> On Mon, Apr 14, 2014 at 1:29 AM, Prasenjit Ghosh < >>>> prasenjit.jnc at gmail.com> wrote: >>>> >>>>> For which q-point are you getting the imaginary modes? If it is at >>>>> gamma, then it may be related to the instability in the structure, if it >>>>> is >>>>> at other q-points, may be lattice parameter is not properly optimized. How >>>>> large is the stress you are getting at the end of the vc-relax calculation >>>>> (when the code recalculates the total energy, stress and forces with the >>>>> optimized lattice parameters & atomic positions). Also have you checked >>>>> the >>>>> convergence of the phonon modes with ecutwfc because typically the phonons >>>>> converge much slowly with the size of the basis set than other parameters? >>>>> >>>>> With regards, >>>>> >>>>> Prasenjit >>>>> >>>>> >>>>> On 13 April 2014 21:55, Ankit wrote: >>>>> >>>>>> Hello QE developers and users, >>>>>> >>>>>> I am trying to calculate phonon dispersion using ph.x and matdyn.x >>>>>> routines of QE and I am stuck woth negative frequencies for a while >>>>>> now. >>>>>> >>>>>> I have a 1-D chain of polyethylene which has 6 atoms in the unit-cell. >>>>>> The polymer chain is aligned in z-direction and I have added vacuum on >>>>>> x- and y- direction. I did the structure relaxation and I am getting >>>>>> total force after relaxtion as 0.20, which I guess is sufficiently >>>>>> small. >>>>>> >>>>>> After relaxation, when I am trying to calculate phonon dispersion >>>>>> using >>>>>> ph.x and matdyn.x I am getting netting frequencies for some of the >>>>>> phonon modes. I searched online and on QE mailing list and tried >>>>>> couple >>>>>> of different things: >>>>>> >>>>>> 1. The negative frequencies are appearing for non-gamma point as well, >>>>>> so I guess its not a ASR issue. Anyway, I am using ASR but even after >>>>>> this I am getting negative frequencies. >>>>>> 2. I reduced my tr2_ph and conv_thr to 1.0d-14 and 1.0d-15 which I >>>>>> guess >>>>>> are very small as suggested on QE FAQs. >>>>>> 3. I checked phonon mode
[Pw_forum] negative phonon frequencies for 1-D polymer chain
I will try changing the pseudopotential and repeat the calculations. I will report back to you as sson as my calculations are finish (will probably take a day to finish structure relaxation). On Mon, Apr 14, 2014 at 2:12 AM, Sanjeev Gupta wrote: > good. > can you take one more test to change the pseudo and see. May be I am > wrong but see. > > > > > > > On Sun, Apr 13, 2014 at 11:02 PM, ankit jain gmail.com>wrote: > >> I have tried acoustic sum rule and it does not change negative >> frequencies. >> I have rerun calculations with several different parameters and seems to >> have modified my vc-relax output file. I am re-running it and will send it >> as soon as it is done. >> >> >> On Mon, Apr 14, 2014 at 1:51 AM, Prasenjit Ghosh > > wrote: >> >>> Did you try using the acoustic sum rule and see whether the imaginary >>> frequencies are still there? Also can I have a look at the vc-relax output >>> file? >>> >>> Prasenjit >>> >>> >>> On 14 April 2014 11:10, ankit jain wrote: >>> >>>> Hello Prasenjit, >>>> >>>> I am getting negative phonon frequencies for non-gamma points also. >>>> After structure optimization, the total force is 0.20 Ry/au and >>>> pressure is -0.24 kbar. >>>> >>>> I am using ecutwfc of 100 Ry, which is converged with respect to the >>>> total energy of the system. I am not able to do convergence with respect to >>>> phonon modes as some modes have negative frequencies. Is there a way to do >>>> ecutwfc convergence for phonon modes without calculating phonon >>>> frequencies? >>>> >>>> I am atatching my pw.in, ph.in pw.out and ph.out files (which I forgot >>>> to attch in my original mail) here. >>>> >>>> Thanks, >>>> ANkit Jain >>>> >>>> >>>> On Mon, Apr 14, 2014 at 1:29 AM, Prasenjit Ghosh < >>>> prasenjit.jnc at gmail.com> wrote: >>>> >>>>> For which q-point are you getting the imaginary modes? If it is at >>>>> gamma, then it may be related to the instability in the structure, if it >>>>> is >>>>> at other q-points, may be lattice parameter is not properly optimized. How >>>>> large is the stress you are getting at the end of the vc-relax calculation >>>>> (when the code recalculates the total energy, stress and forces with the >>>>> optimized lattice parameters & atomic positions). Also have you checked >>>>> the >>>>> convergence of the phonon modes with ecutwfc because typically the phonons >>>>> converge much slowly with the size of the basis set than other parameters? >>>>> >>>>> With regards, >>>>> >>>>> Prasenjit >>>>> >>>>> >>>>> On 13 April 2014 21:55, Ankit wrote: >>>>> >>>>>> Hello QE developers and users, >>>>>> >>>>>> I am trying to calculate phonon dispersion using ph.x and matdyn.x >>>>>> routines of QE and I am stuck woth negative frequencies for a while >>>>>> now. >>>>>> >>>>>> I have a 1-D chain of polyethylene which has 6 atoms in the unit-cell. >>>>>> The polymer chain is aligned in z-direction and I have added vacuum on >>>>>> x- and y- direction. I did the structure relaxation and I am getting >>>>>> total force after relaxtion as 0.20, which I guess is sufficiently >>>>>> small. >>>>>> >>>>>> After relaxation, when I am trying to calculate phonon dispersion >>>>>> using >>>>>> ph.x and matdyn.x I am getting netting frequencies for some of the >>>>>> phonon modes. I searched online and on QE mailing list and tried >>>>>> couple >>>>>> of different things: >>>>>> >>>>>> 1. The negative frequencies are appearing for non-gamma point as well, >>>>>> so I guess its not a ASR issue. Anyway, I am using ASR but even after >>>>>> this I am getting negative frequencies. >>>>>> 2. I reduced my tr2_ph and conv_thr to 1.0d-14 and 1.0d-15 which I >>>>>> guess >>>>>> are very small as suggested on QE FAQs. >>>>>> 3. I checked phonon mode
[Pw_forum] negative phonon frequencies for 1-D polymer chain
I have tried acoustic sum rule and it does not change negative frequencies. I have rerun calculations with several different parameters and seems to have modified my vc-relax output file. I am re-running it and will send it as soon as it is done. On Mon, Apr 14, 2014 at 1:51 AM, Prasenjit Ghosh wrote: > Did you try using the acoustic sum rule and see whether the imaginary > frequencies are still there? Also can I have a look at the vc-relax output > file? > > Prasenjit > > > On 14 April 2014 11:10, ankit jain wrote: > >> Hello Prasenjit, >> >> I am getting negative phonon frequencies for non-gamma points also. After >> structure optimization, the total force is 0.20 Ry/au and pressure is >> -0.24 kbar. >> >> I am using ecutwfc of 100 Ry, which is converged with respect to the >> total energy of the system. I am not able to do convergence with respect to >> phonon modes as some modes have negative frequencies. Is there a way to do >> ecutwfc convergence for phonon modes without calculating phonon frequencies? >> >> I am atatching my pw.in, ph.in pw.out and ph.out files (which I forgot >> to attch in my original mail) here. >> >> Thanks, >> ANkit Jain >> >> >> On Mon, Apr 14, 2014 at 1:29 AM, Prasenjit Ghosh > > wrote: >> >>> For which q-point are you getting the imaginary modes? If it is at >>> gamma, then it may be related to the instability in the structure, if it is >>> at other q-points, may be lattice parameter is not properly optimized. How >>> large is the stress you are getting at the end of the vc-relax calculation >>> (when the code recalculates the total energy, stress and forces with the >>> optimized lattice parameters & atomic positions). Also have you checked the >>> convergence of the phonon modes with ecutwfc because typically the phonons >>> converge much slowly with the size of the basis set than other parameters? >>> >>> With regards, >>> >>> Prasenjit >>> >>> >>> On 13 April 2014 21:55, Ankit wrote: >>> >>>> Hello QE developers and users, >>>> >>>> I am trying to calculate phonon dispersion using ph.x and matdyn.x >>>> routines of QE and I am stuck woth negative frequencies for a while now. >>>> >>>> I have a 1-D chain of polyethylene which has 6 atoms in the unit-cell. >>>> The polymer chain is aligned in z-direction and I have added vacuum on >>>> x- and y- direction. I did the structure relaxation and I am getting >>>> total force after relaxtion as 0.20, which I guess is sufficiently >>>> small. >>>> >>>> After relaxation, when I am trying to calculate phonon dispersion using >>>> ph.x and matdyn.x I am getting netting frequencies for some of the >>>> phonon modes. I searched online and on QE mailing list and tried couple >>>> of different things: >>>> >>>> 1. The negative frequencies are appearing for non-gamma point as well, >>>> so I guess its not a ASR issue. Anyway, I am using ASR but even after >>>> this I am getting negative frequencies. >>>> 2. I reduced my tr2_ph and conv_thr to 1.0d-14 and 1.0d-15 which I guess >>>> are very small as suggested on QE FAQs. >>>> 3. I checked phonon mode shapes for modes with negative frequencies and >>>> they do not look like rotational mode. >>>> 4. I tried changing number of k points from 6 to 12 in z direction but >>>> this is also not the cause. >>>> >>>> I am really stuck here and not sure about the cause of negative >>>> frequencies. With vc-relax, my structure is getting relaxed which I >>>> guess means my structure is stable. But then I am not sure why I am >>>> getting negative frequencies. >>>> >>>> I really appreciate any help or suggestions. >>>> >>>> Thanks, >>>> >>>> Ankit Jain >>>> IIT Indore, >>>> Indore, >>>> India >>>> >>>> >>>> ___ >>>> Pw_forum mailing list >>>> Pw_forum at pwscf.org >>>> http://pwscf.org/mailman/listinfo/pw_forum >>>> >>> >>> >>> >>> -- >>> PRASENJIT GHOSH, >>> IISER Pune, >>> Dr. Homi Bhabha Road, Pashan >>> Pune, Maharashtra 411008, India >>> >>> Phone: +91 (20) 2590 8203 >>> Fax: +91 (20) 2589 9790 >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > PRASENJIT GHOSH, > IISER Pune, > Dr. Homi Bhabha Road, Pashan > Pune, Maharashtra 411008, India > > Phone: +91 (20) 2590 8203 > Fax: +91 (20) 2589 9790 > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140414/5d160019/attachment.html
[Pw_forum] negative phonon frequencies for 1-D polymer chain
Hello Prasenjit, I am getting negative phonon frequencies for non-gamma points also. After structure optimization, the total force is 0.20 Ry/au and pressure is -0.24 kbar. I am using ecutwfc of 100 Ry, which is converged with respect to the total energy of the system. I am not able to do convergence with respect to phonon modes as some modes have negative frequencies. Is there a way to do ecutwfc convergence for phonon modes without calculating phonon frequencies? I am atatching my pw.in, ph.in pw.out and ph.out files (which I forgot to attch in my original mail) here. Thanks, ANkit Jain On Mon, Apr 14, 2014 at 1:29 AM, Prasenjit Ghosh wrote: > For which q-point are you getting the imaginary modes? If it is at gamma, > then it may be related to the instability in the structure, if it is at > other q-points, may be lattice parameter is not properly optimized. How > large is the stress you are getting at the end of the vc-relax calculation > (when the code recalculates the total energy, stress and forces with the > optimized lattice parameters & atomic positions). Also have you checked the > convergence of the phonon modes with ecutwfc because typically the phonons > converge much slowly with the size of the basis set than other parameters? > > With regards, > > Prasenjit > > > On 13 April 2014 21:55, Ankit wrote: > >> Hello QE developers and users, >> >> I am trying to calculate phonon dispersion using ph.x and matdyn.x >> routines of QE and I am stuck woth negative frequencies for a while now. >> >> I have a 1-D chain of polyethylene which has 6 atoms in the unit-cell. >> The polymer chain is aligned in z-direction and I have added vacuum on >> x- and y- direction. I did the structure relaxation and I am getting >> total force after relaxtion as 0.20, which I guess is sufficiently >> small. >> >> After relaxation, when I am trying to calculate phonon dispersion using >> ph.x and matdyn.x I am getting netting frequencies for some of the >> phonon modes. I searched online and on QE mailing list and tried couple >> of different things: >> >> 1. The negative frequencies are appearing for non-gamma point as well, >> so I guess its not a ASR issue. Anyway, I am using ASR but even after >> this I am getting negative frequencies. >> 2. I reduced my tr2_ph and conv_thr to 1.0d-14 and 1.0d-15 which I guess >> are very small as suggested on QE FAQs. >> 3. I checked phonon mode shapes for modes with negative frequencies and >> they do not look like rotational mode. >> 4. I tried changing number of k points from 6 to 12 in z direction but >> this is also not the cause. >> >> I am really stuck here and not sure about the cause of negative >> frequencies. With vc-relax, my structure is getting relaxed which I >> guess means my structure is stable. But then I am not sure why I am >> getting negative frequencies. >> >> I really appreciate any help or suggestions. >> >> Thanks, >> >> Ankit Jain >> IIT Indore, >> Indore, >> India >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > PRASENJIT GHOSH, > IISER Pune, > Dr. Homi Bhabha Road, Pashan > Pune, Maharashtra 411008, India > > Phone: +91 (20) 2590 8203 > Fax: +91 (20) 2589 9790 > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140414/04a29159/attachment.html -- next part -- A non-text attachment was scrubbed... Name: ph.in Type: application/octet-stream Size: 185 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140414/04a29159/attachment.obj -- next part -- A non-text attachment was scrubbed... Name: ph.out Type: application/octet-stream Size: 123825 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140414/04a29159/attachment-0001.obj -- next part -- A non-text attachment was scrubbed... Name: pw.in Type: application/octet-stream Size: 767 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140414/04a29159/attachment-0002.obj -- next part -- A non-text attachment was scrubbed... Name: pw.out Type: application/octet-stream Size: 14629 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140414/04a29159/attachment-0003.obj
[Pw_forum] negative phonon frequencies for 1-D polymer chain
Hello Sanjeev, The pseudopotentials I am using are H.pz-vbc.UPF<http://www.quantum-espresso.org/wp-content/uploads/upf_files/H.pz-vbc.UPF> and C.pz-vbc.UPF<http://www.quantum-espresso.org/wp-content/uploads/upf_files/C.pz-vbc.UPF> Pseudopotential type: NORMCONS Method: Von Barth-Car (direct fit) Functional type: Perdew-Zunger (LDA) exch-corr scalar relativistic I have tried kgrid of 1*1*6 and 1*1*12, but both give negative frequencies. On Mon, Apr 14, 2014 at 12:18 AM, Sanjeev Gupta wrote: > what is kind of pseudopotential? > How much k-point? > > > wishes > sanjeev > > > On Sun, Apr 13, 2014 at 9:25 AM, Ankit wrote: > >> Hello QE developers and users, >> >> I am trying to calculate phonon dispersion using ph.x and matdyn.x >> routines of QE and I am stuck woth negative frequencies for a while now. >> >> I have a 1-D chain of polyethylene which has 6 atoms in the unit-cell. >> The polymer chain is aligned in z-direction and I have added vacuum on >> x- and y- direction. I did the structure relaxation and I am getting >> total force after relaxtion as 0.20, which I guess is sufficiently >> small. >> >> After relaxation, when I am trying to calculate phonon dispersion using >> ph.x and matdyn.x I am getting netting frequencies for some of the >> phonon modes. I searched online and on QE mailing list and tried couple >> of different things: >> >> 1. The negative frequencies are appearing for non-gamma point as well, >> so I guess its not a ASR issue. Anyway, I am using ASR but even after >> this I am getting negative frequencies. >> 2. I reduced my tr2_ph and conv_thr to 1.0d-14 and 1.0d-15 which I guess >> are very small as suggested on QE FAQs. >> 3. I checked phonon mode shapes for modes with negative frequencies and >> they do not look like rotational mode. >> 4. I tried changing number of k points from 6 to 12 in z direction but >> this is also not the cause. >> >> I am really stuck here and not sure about the cause of negative >> frequencies. With vc-relax, my structure is getting relaxed which I >> guess means my structure is stable. But then I am not sure why I am >> getting negative frequencies. >> >> I really appreciate any help or suggestions. >> >> Thanks, >> >> Ankit Jain >> IIT Indore, >> Indore, >> India >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > With Best Regards, > > > Dr. Sanjeev Kumar Gupta > Fulbright Post-Doctoral Scholar > Dept. of Physics > Michigan Technological University > 1400 Townsend Drive, Houghton > MI 49931, USA > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140414/e244fc34/attachment.html
