Re: [QE-users] Can QE calculate the exchange energy and correlation energy separately?
In order to separate exchange and correlation energies, one has to modify the code, because the two contributions are separately computed but immediately summed, Paolo On Sat, Nov 24, 2018 at 1:05 PM Gui Wei <201707021...@cqu.edu.cn> wrote: > Hi > Recently, I found out in an article that the author calculated the Pauli > repulsion between graphene and Ni(111),the calculations were carried out > with the VASP software package.And I know exchange energy is associated > with the Pauli exclusion principle,so can I think that the value of Pauli > exclusion is equal to the exchange energy's?If my point of view is correct, > how could I calculate it with QE6.3? > > https://pubs.acs.org/doi/10.1021/jp210667f > > > Wei gui > School of Mechanical Engineering，Chongqing University, China > ___ > users mailing list > users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- 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 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] High symmetry point overlap problem.
Hello, check the coordinates of the point in cartesian axes (just multiply the points in crystal axes by the matrix of the inverse lattice) and check the length of each segment of the path. It is likely that the fourth on is much longer than the others. I recommend using a number of points proportional to the length of each segment. This can be done in 3 lines in gnu/octave (or matlab, if you like the bling) k=[0.821428571428571 0.339285714285 0.0 0.0 0.0 0.5 0.5 0.5 0.5 0.0 0.5 0.0 0.0 0.0 0.5 0.0 0.0 ] b=[ 2.281217 -1.317061 0.344551 0.00 2.634122 0.344551 -2.281217 -1.317061 0.344551] kk=k*b norm(kk(1:4,:)-kk(2:5,:),2,"rows") Of course, it would be better if the code worked in every case, but even the best algorithm to spot high-symmetry points breaks down with some a sufficiently extreme case. On 1/17/19 7:15 PM, Vasilios Passias wrote: Hello. After running a band calculation for Bismuth Selenide, I encountered a problem with the high symmetry points: two distinct high symmetry points, K and \Gamma, have the same x-coordinate value (i.e. the value on the horizontal axis on bandstructure plot) : image.png The k-space path I used was Γ→A→Γ→K→M. I have the band input here: // / calculation = 'bands',/ / restart_mode = 'from_scratch',/ / pseudo_dir = '/home/passias2/qe-6.3/pseudo/',/ /// // / ibrav = 4,/ / celldm(1) = 7.81969,/ / celldm(3) = 6.92122,/ / nat = 15,/ / ntyp = 2,/ / ecutwfc = 300.0,/ / ecutrho = 1200.0,/ / nbnd = 130/ /// // / conv_thr = 1.0d-8,/ / mixing_beta = 0.1/ /// /ATOMIC_SPECIES/ / Bi 208.980 Bi.pbe-dn-kjpaw_psl.1.0.0.UPF/ / Se 78.971 Se.pbe-n-kjpaw_psl.0.2.UPF/ / / /ATOMIC_POSITIONS crystal/ / Se 0.00 0.00 0.00/ / Bi 0.33 0.67 0.066/ / Se 0.67 0.33 0.127/ / Se 0.00 0.00 0.206/ / Bi 0.33 0.67 0.267/ / Se 0.67 0.33 0.333/ / Bi 0.00 0.00 0.399/ / Se 0.33 0.67 0.46/ / Se 0.67 0.33 0.539/ / Bi 0.00 0.00 0.6/ / Se 0.33 0.67 0.666/ / Bi 0.67 0.33 0.732/ / Se 0.00 0.00 0.793/ / Se 0.33 0.67 0.872/ / Bi 0.67 0.33 0.933/ / / /K_POINTS crystal_b/ / 5/ / 0.0 0.0 0.0 30/ / 0.0 0.0 0.5 30/ / 0.0 0.0 0.0 30/ / 0.7 -0. 0.0 30/ / 0.5 0.0 0.0 30/ / / Could this error be from choosing a point outside of the irreducible Brillouin zone? Thank you for your time. / / ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users -- Lorenzo Paulatto - Paris ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Question on CPMD
dear LIANG, when you run in the NVE you should have something like this: if I am not wrong: ekinc is the kinetic energy of the electrons etot is the total potential energy (calculated with DFT) econs is the energy that to make a good simulation you want to make as constant as possible, but it will oscillate because electrons have a mass and a kinetic energy, so it will never be constant. econt is the constant of motion of the CP lagrangian, and this must always remain approximately constant, within the integration error of the verlet algorithm. If it is not constant your simulation is not good and you have to change some parameters. best regards, Riccardo Bertossa SISSA On 17/01/19 15:54, LEUNG Clarence wrote: Dear QE users, From CPMD, we can get EKINC ETOT ENTHAL ECONS and ECONT of the system. Which one is the total energy of the system? ETOT? or Ekinc + Etot ? or Etot - Ekinc ? Thanks. LIANG Xiongyi City University of Hong Kong ___ users mailing list 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] gfortran vs intel lead to different results of electron-phonon coupling by ph.x
Hi everyone, Using the same input files (from one of the tutorials, step-by-step), I got different output files of dynamical matrices when using different intel compilators (Intel 13, Intel 15 and Intel 16). Only the results using GNU gfortran are correct. In all calculations, there is no significant error of freqs. In turn, all scf calculations (intel and gnu) also work fine. Intel 15, QE 6.3 q = ( 0.0 0.0 0.0 ) ** freq ( 1) = 0.485694 [THz] = 16.201000 [cm-1] ( 0.833379 0.00 -0.410303 0.00 0.370314 0.00 ) freq ( 2) = 0.485694 [THz] = 16.201000 [cm-1] ( -0.037325 0.00 0.626695 0.00 0.778370 0.00 ) freq ( 3) = 0.485694 [THz] = 16.201000 [cm-1] ( -0.551441 0.00 -0.662499 0.00 0.506960 0.00 ) Intel 16, QE 6.3 q = ( 0.0 0.0 0.0 ) ** freq ( 1) = 0.485682 [THz] = 16.200616 [cm-1] ( -0.635098 0.00 0.108968 0.00 0.764707 0.00 ) freq ( 2) = 0.485682 [THz] = 16.200616 [cm-1] ( -0.688313 0.00 -0.529109 0.00 -0.496255 0.00 ) freq ( 3) = 0.485682 [THz] = 16.200616 [cm-1] ( 0.350537 0.00 -0.841528 0.00 0.411040 0.00 ) Intel 15, QE 6.2.1 q = ( 0.0 0.0 0.0 ) ** freq ( 1) = 0.485689 [THz] = 16.200826 [cm-1] ( 0.164642 0.00 0.968532 0.00 -0.186653 0.00 ) freq ( 2) = 0.485689 [THz] = 16.200826 [cm-1] ( 0.014161 0.00 0.186894 0.00 0.982278 0.00 ) freq ( 3) = 0.485689 [THz] = 16.200826 [cm-1] ( -0.986252 0.00 0.164367 0.00 -0.017055 0.00 ) The gfortran results are correct and the same like ones in the tutorial: q = ( 0.0 0.0 0.0 ) ** freq ( 1) = 0.486780 [THz] = 16.237227 [cm-1] ( 0.550619 0.00 0.765144 0.00 -0.333726 0.00 ) freq ( 2) = 0.486780 [THz] = 16.237227 [cm-1] ( 0.063986 0.00 0.359925 0.00 0.930784 0.00 ) freq ( 3) = 0.486780 [THz] = 16.237227 [cm-1] ( -0.832301 0.00 0.533862 -0.00 -0.149223 0.00 ) Default compilations (We use Intel Xeon E5-2670): DFLAGS = -D__FFTW3 -D__MPI -D__SCALAPACK MPIF90 = mpif90 F90 = ifort CC = icc F77 = ifort CPP = cpp CPPFLAGS = -P -traditional $(DFLAGS) $(IFLAGS) CFLAGS = -O3 $(DFLAGS) $(IFLAGS) F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(CUDA_F90FLAGS) $(IFLAGS) $(MODFLAGS) FFLAGS = -O2 -assume byterecl -g -traceback FFLAGS_NOOPT = -O0 -assume byterecl -g -traceback LD = mpif90 LDFLAGS = -static-intel LD_LIBS = BLAS_LIBS = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core BLAS_LIBS_SWITCH = external LAPACK_LIBS = LAPACK_LIBS_SWITCH = external SCALAPACK_LIBS = -lmkl_scalapack_lp64 -lmkl_blacs_openmpi_lp64 FFT_LIBS = -lfftw3 Everything run on 1 processor. Any suggestions? Tnak you in advance. Arena Konta The Institute of Thermophysics in Novosibirsk Scientific Center ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] High symmetry point overlap problem.
Hello. After running a band calculation for Bismuth Selenide, I encountered a problem with the high symmetry points: two distinct high symmetry points, K and \Gamma, have the same x-coordinate value (i.e. the value on the horizontal axis on bandstructure plot) : [image: image.png] The k-space path I used was Γ→A→Γ→K→M. I have the band input here: ** * calculation = 'bands',* * restart_mode = 'from_scratch',* * pseudo_dir = '/home/passias2/qe-6.3/pseudo/',* */* ** * ibrav = 4,* * celldm(1) = 7.81969,* * celldm(3) = 6.92122,* * nat = 15,* * ntyp = 2,* * ecutwfc = 300.0,* * ecutrho = 1200.0,* * nbnd = 130* */* ** * conv_thr = 1.0d-8,* * mixing_beta = 0.1* */* *ATOMIC_SPECIES* * Bi 208.980 Bi.pbe-dn-kjpaw_psl.1.0.0.UPF* * Se 78.971 Se.pbe-n-kjpaw_psl.0.2.UPF* *ATOMIC_POSITIONS crystal* * Se 0.00 0.00 0.00* * Bi 0.33 0.67 0.066* * Se 0.67 0.33 0.127* * Se 0.00 0.00 0.206* * Bi 0.33 0.67 0.267* * Se 0.67 0.33 0.333* * Bi 0.00 0.00 0.399* * Se 0.33 0.67 0.46* * Se 0.67 0.33 0.539* * Bi 0.00 0.00 0.6* * Se 0.33 0.67 0.666* * Bi 0.67 0.33 0.732* * Se 0.00 0.00 0.793* * Se 0.33 0.67 0.872* * Bi 0.67 0.33 0.933* *K_POINTS crystal_b* * 5* * 0.0 0.0 0.0 30* * 0.0 0.0 0.5 30* * 0.0 0.0 0.0 30* * 0.7 -0. 0.0 30* * 0.5 0.0 0.0 30* Could this error be from choosing a point outside of the irreducible Brillouin zone? Thank you for your time. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Question on CPMD
Dear QE users, From CPMD, we can getEKINC ETOT ENTHAL ECONS and ECONT of the system. Which one is the total energy of the system? ETOT? or Ekinc + Etot ? or Etot - Ekinc ? Thanks. LIANG Xiongyi City University of Hong Kong ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Error during compilation
Dear Redwan doing troubleshooting at distance is quite cumbersome. If you do make clean and then make libfox what do you get ? regards Pietro Delugas SISSA - Trieste MAX - European Center of Excellence On Thu, Jan 17, 2019 at 12:13 PM Redwan Sajjad wrote: > Paolo > > Thanks for the reply. I did *make clean* and then *make all*, I got the > exact same error message regarding > FoX. The FoX folder under qe-6.3 is empty. I am running Mac OS Sierra High > and gfortran 6.3.0. > > > /Redwan > > On 17 Jan, 2019, at 4:16 PM, Paolo Giannozzi > wrote: > > On Thu, Jan 17, 2019 at 6:04 AM Redwan Sajjad > wrote: > >> >> Then it terminates with the message Can’t open module file >> ‘m_common_io.mod’. >> > > the compilation of FoX hasn't been successful: "make clean", then > recompile and look carefully for error messages > > Paolo > > >> Thanks. >> >> -- >> Redwan >> >> >> On 17 Jan, 2019, at 8:22 AM, Redwan Sajjad >> wrote: >> >> Hello >> >> While compiling (make all) QE on Mac OS (Sierra High), I am getting the >> following error >> *clang: error: no such file or directory* >> followed by a path where the QE folder is located. There are several >> lines of the same errors containing different paths. >> >> >> Thank you. >> >> >> -- >> Redwan N. Sajjad >> Bangladesh University of Engineering and Technology. >> Dhaka-1000, Bangladesh. >> >> >> ___ >> users mailing list >> users@lists.quantum-espresso.org >> https://lists.quantum-espresso.org/mailman/listinfo/users > > > > -- > 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 > > ___ > users mailing list > 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 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Error during compilation
On Thu, Jan 17, 2019 at 12:13 PM Redwan Sajjad wrote: Thanks for the reply. I did *make clean* and then *make all*, I got the > exact same error message regarding > FoX. > which error message? this one? > Then it terminates with the message Can’t open module file >> ‘m_common_io.mod’. >> > it just means that FoX has not been correctly compiled, it doesn't explain why. There must be a message explaining why it wasn't compiled. Please also try the patched 6.3 version in qe-6.3-backports: https://github.com/QEF/q-e/tree/qe-6.3-backports Paolo -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] How to apply force to the atoms using cp.x
Dear Lu Hailin You may use a variable-cell dynamics (i.e., 'VC-RELAX', 'VC-CP', 'VC-CP-WF') with press=whatever in KBar and cell_dofree=z. HTH Giuseppe Lu Hailin <415005...@qq.com> ha scritto: Dear all, How can I apply a vertical force to the atoms to model an applied pressure using Quantum Espresso 6.1. version on Linux, the value of which was varied from 500 MPa to 5 GPa . I find that the code '"ATOMIC_FORCES"may make it,but the Ha/a.u. units is not MPa or GPa. Any help would be appreciated. Thank you! Best regards, -- KBar LU Hailin, Graduate Student State Key Laboratory of Mechanical Transmission, Chongqing University Chongqing 400044, China Tel: (+86) 18362360286 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: ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] positions at EPFL
Dear QE Users, this is a brief note to mention that we have several positions (7) for postdocs/phds/software engineers - on the development side, on high-throughput with QE, on AiiDA and Materials Cloud - all info at http://theossrv1.epfl.ch/Main/Openings nicola -- Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL Director, National Centre for Competence in Research NCCR MARVEL, EPFL http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] [SUSPECTED SPAM-Ironport] Geometry of Transition state
Dear Giuseppe, Thank you so much for your guide. BR, Parisa On Thu, 17/01/2019 10:37 AM, Giuseppe Mattioli wrote: > Dear Parisa > You can use CI-NEB. Look into the documentation of the neb.x code and examples > HTH > Giuseppe > > PARISA ALAMDARI " target="_blank"> ha scritto: > > > Dear QS users, > > I used constraint calulation using pw.x to find transition state in > > a reaction. Is there any way to maximize the energy of this > > estimated TS? > > Thanks for your guides, > > Best Regards, > > Parisa > > AUT, Iran > > > > -- > > This email was Anti Virus checked by Security Gateway. > > > > 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: " target="_blank"> > > ___ > users mailing list > users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > -- > This email was Anti Virus checked by Security Gateway. > ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] How to apply force to the atoms using cp.x
Dear all, How can I apply a vertical force to the atoms to model an applied pressure using Quantum Espresso 6.1. version on Linux, the value of which was varied from 500 MPa to 5 GPa . I find that the code '"ATOMIC_FORCES"may make it,but the Ha/a.u. units is not MPa or GPa. Any help would be appreciated. Thank you! Best regards, -- LU Hailin, Graduate Student State Key Laboratory of Mechanical Transmission, Chongqing University Chongqing 400044, China Tel: (+86) 18362360286___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Error during compilation
Paolo Thanks for the reply. I did *make clean* and then *make all*, I got the exact same error message regarding FoX. The FoX folder under qe-6.3 is empty. I am running Mac OS Sierra High and gfortran 6.3.0. /Redwan On 17 Jan, 2019, at 4:16 PM, Paolo Giannozzi wrote: On Thu, Jan 17, 2019 at 6:04 AM Redwan Sajjad wrote: > > Then it terminates with the message Can’t open module file > ‘m_common_io.mod’. > the compilation of FoX hasn't been successful: "make clean", then recompile and look carefully for error messages Paolo > Thanks. > > -- > Redwan > > > On 17 Jan, 2019, at 8:22 AM, Redwan Sajjad wrote: > > Hello > > While compiling (make all) QE on Mac OS (Sierra High), I am getting the > following error > *clang: error: no such file or directory* > followed by a path where the QE folder is located. There are several lines > of the same errors containing different paths. > > > Thank you. > > > -- > Redwan N. Sajjad > Bangladesh University of Engineering and Technology. > Dhaka-1000, Bangladesh. > > > ___ > users mailing list > users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- 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 ___ users mailing list 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
Re: [QE-users] Error during compilation
On Thu, Jan 17, 2019 at 6:04 AM Redwan Sajjad wrote: > > Then it terminates with the message Can’t open module file > ‘m_common_io.mod’. > the compilation of FoX hasn't been successful: "make clean", then recompile and look carefully for error messages Paolo > Thanks. > > -- > Redwan > > > On 17 Jan, 2019, at 8:22 AM, Redwan Sajjad wrote: > > Hello > > While compiling (make all) QE on Mac OS (Sierra High), I am getting the > following error > *clang: error: no such file or directory* > followed by a path where the QE folder is located. There are several lines > of the same errors containing different paths. > > > Thank you. > > > -- > Redwan N. Sajjad > Bangladesh University of Engineering and Technology. > Dhaka-1000, Bangladesh. > > > ___ > users mailing list > users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- 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 ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Geometry of Transition state
Dear Parisa, I used the PWneb package which implement the Nudged Elastic Band (NEB) method to explore the Potential energy surface (PES) looking for a TS. You can start looking the package information https://www.quantum-espresso.org/Doc/neb_user_guide.pdf https://www.quantum-espresso.org/Doc/INPUT_NEB.html HTH Regards G. Il giorno gio 17 gen 2019 alle ore 10:28 PARISA ALAMDARI < p.alamd...@aut.ac.ir> ha scritto: > Dear QS users, > I used constraint calulation using pw.x to find transition state in a > reaction. Is there any way to maximize the energy of this estimated TS? > Thanks for your guides, > Best Regards, > Parisa > AUT, Iran > > -- > This email was Anti Virus checked by Security Gateway. > > ___ > users mailing list > users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users -- *** Guido Menichetti Post-Doc researcher in Solid State Physics Istituto Italiano di Tecnologia Graphene Labs: Theory and technology of 2D materials Address: Via Morego, 30, 16163 Genova Email: guido.meniche...@iit.it guido.meniche...@df.unipi.it menichetti.gu...@gmail.com ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Geometry of Transition state
Dear QS users, I used constraint calulation using pw.x to find transition state in a reaction. Is there any way to maximize the energy of this estimated TS? Thanks for your guides, Best Regards, Parisa AUT, Iran -- This email was Anti Virus checked by Security Gateway. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
