[QE-users] 3d-rho resolution
Dear users and developers, I am trying to generate more and less accurate electron density cubes (to study how some properties, extracted from cubes, depend on their resolution) but fail somewhere. Here is the pp.x input: prefix = myinput filplot = myinput.rho plot_num = 0 / nfile = 1 filepp(1) = myinput.rho iflag = 3 output_format = 6 !e1(1) = 1, e1(2) = 0, e1(3) = 0 !e2(1) = 0, e2(2) = 1, e2(3) = 0 !e3(1) = 0, e3(2) = 0, e3(3) = 1 x0(1) = 0, x0(2) = 0, x0(3) = 0 nx = 1000, ny = 1000, nz = 1000 fileout = myinput.cube / Regardless of nx, ny, and nz (e.g. 50, 50, 50 vs 1000, 1000, 1000) I get the same outputs. What should I change to generate cubes with different resolutions? Parameters in SCF are very accurate, so my guess: It is pp.x input lines. not pw.x parameters. Thank you in advance! -- Best wishes, Al., phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] pp.x: iflag=1 for the plot_number=0
Dear users and developers, Is it possible to plot 1D-distribution of the charge density with pp.x? Looks like for plot_number=0 ifrag cannot be anything than 3. With the following input only myinput.rho is generated. (I tried the latest QE version.) prefix = myinput filplot = myinput.rho plot_num = 0 / nfile = 1 filepp(1) = myinput.rho iflag = 1 e1(1) = 0, e1(2) = 0, e1(3) = 1 ! z-direction along the cell x0(1) = 0, x0(2) = 0, x0(3) = 0 ! origin nx = 500 fileout = myinput.1d-rho / Thank you for any comment/suggestions/help! -- Best wishes, Al, phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] high-temperature vc-md
Dear users and developers, Are there any tricks for running an NPT ensemble with pw.x (vc-md) for high-temperatures? I do not have problems with 300-350-400K (reaching minimum Etot+Ekin fluctuations after a reasonable amount of steps) but cannot reach it for 600K. Below I show the basic input parameters used. Thank you for any suggestions! restart_mode = 'restart' calculation = 'vc-md' nstep = 1000 dt = 60 ! 3fs, 1/10 of the highest vibration T ! verbosity = 'high' wf_collect = .true. pseudo_dir = '.' / [all good] nosym = .True. / [all defaut] / ion_velocities = 'default' tempw = 600 ion_dynamics = 'beeman' pot_extrapolation = 'atomic' ! 1st, 2nd order from prev step, no gain wfc_extrapolation = 'none' ! 1st, 2nd order from prev step, no gain ! remove_rigid_rot = .True. trick for not big enough supercells ion_temperature = 'rescaling' tolp = 10 nraise = 1 refold_pos = .True. / cell_dynamics = 'pr' ! Parrinello-Rahman, also Wentzcovitch 'w' is avail ! wmass - fictitious cell mass, see default for 'pr' or 'w' cell_factor = 2 / ATOMIC_SPECIES ... ATOMIC_POSITIONS crystal ... K_POINTS automatic [converged grid tested to give accurate cell stresses] -- Best wishes, Al., phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] nscf with Hubbard
Dear users and developers, Are there any specific tricks for nscf with Hubbard corrections? Strangely it takes a comparable amount of resources as scf. E.g. scf for 4 4 4 grid (for a huge cell) takes just a bit less time as scf for 2 2 2 -> nscf 4 4 4. I am using the simplest correction (lda_plus_u_kind = 1) in qe-6.4 (because I want to finish project with one version, not the most new). Thank you! -- Best wishes, Al., phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] epsilon.x jdos
Dear users and developers, Can please someone share an example of inputs for jdos calculation? Whatever I try (for both pw.x input and epsilon.x input) in output I see: Performing jdos calculation... jdos : 0.00s CPU 0.00s WALL ( 1 calls) epsilon : 2.06s CPU 2.36s WALL Thank you! -- Best wishes, Al., phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] open_grid for epsilon.x
Dear users and developers, Did anybody succeed with the oped_grid.x code for LDA/GGA/vdw functionals? I want to use epsilon.x for a big system (for which I do not have enough computational resources to switch-off the symmetry for k-grid in scf calculation), I am trying open_grid.x and the code does not seem to work. Thank you. -- Best wishes, Al., phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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] mixing distances
Dear Giuseppe, Thank you a lot for your reply! Will play with NaCl pair and different levels of theory, looks like a fun system to understand theory better. I do agree that the initial question is not well-defined. To limit the topic to a semiconductor slab (for simplicity let it be symmetrical relative to (xy) plane, i.e. no dipole is entering the vacuum above/below the slab) and a neutral molecule: How can I be sure that an distance L (between slab and a molecule, let it be 10 Angstrom) plane wave DFT code sees them as two non-interacting systems? -- Best wishes, Al., phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] mixing distances
Dear QE community, Please suggest what is the "sensitivity" of PW DFT: What is the maximum real distance where wavefunctions of the subsystems mix in a way seen by PW DFT? What is the best way to verify it? My experience, if objects are separated by > 7 Angstrom, their wavefunctions do not mix. E.g. if dos1 of system1 and dos2 of system2 (calculated separately for isolated system1 and isolated system2) ideally overlap with the dos of system1+system2 (calculated as a whole), can I conclude that systems are electronically decoupled? Thank you a lot in advance. -- Best wishes, Al., phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] phonon bands shift
Dear Nicola, Thank you for your reply! I used your email to show more examples (I see this feature in a few high symmetry systems and in one good paper). May I please ask you to have a look (email topic "phonon")? I would hugely appreciate your help. I was thinking to calculate a set of high-symmetry points in Brillouin zone using qplot=.True. and than use them for q2r and bands, but the problem is that it (probably) cannot be done as a uniform grid is needed for q2r. Am I incorrect? I tried raising and lowering q-grid, using supercells (e.g. ibrav=8 instead of ibrav=9), calculating separate q's, switching off the symmetry, etc. -- Best wishes, Al., phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] q2r with qplot
Apologies for the typo: ph.x input ... ldisp = .True., qplot = .True. ... / 5 0.5 0.5 0.5 1 !1st 0.25 0.25 0.25 1 0.0 0.0 0.0 1 !2nd 0.25 0.25 0.0 1 0.5 0.5 0.0 1 !3rd -- Best wishes, Al., phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] q2r with qplot
Dear QE-community, Can please someone suggest the input for q2r.x for the following case: ph.x input ... ldisp = .False., qplot = .True. ... / 5 0.5 0.5 0.5 1 !1st 0.25 0.25 0.25 1 0.0 0.0 0.0 1 !2nd 0.25 0.25 0.0 1 0.5 0.5 0.0 1 !3rd How to feed them q2r.x? I want to continue with the phonon bands exactly in between (0.5 0.5 0.5) - (0.0 0.0 0.0) - (0.5 0.5 0.0) using the calculation for five q-points, but am stuck with the q2r input. I tried this (and other options) but it did not work: ... / 1 1 1 5 file.G1 file.G2 file.G3 file.G4 file.G5 I will be very happy with the hints. Thank you! -- Best wishes, Al., phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] ldos for a sphere
Dear users and developers, I am wondering if there is a functionality in QE that would allow to integrate dos [not for the parallelepiped boxes with n_proj_boxes in projwfc.x but] for the spheres? Something like described for vasp in doi:10.1038/nature11812 where they obtained dos around point X (please see p5 of SI, 2nd part of the page). Thanks in advance, Al. -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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] raman with phcg
Dear Paolo, Input is the same as described in the 1st message - see .../PHonon/example12 (qe-6.7) - exactly the same - modified for SiH4 put the middle of the ibrav = 1 with A = 20.0 - with lraman = .True., deltatau = 0.01. First one terminates okay, but results do not look nice, and the same (as in other 2 cases) erroe appears: " *** Starting Conjugate Gradient minimization *** *** Conjugate Gradient minimization not converged after 50 iterations residual norm |Ax-b|^2 : 0.2455E+00 *** pol. # 1 : 50 iterations *** Conjugate Gradient minimization not converged after 50 iterations residual norm |Ax-b|^2 : 0.2697E+00 *** pol. # 2 : 50 iterations *** Conjugate Gradient minimization not converged after 50 iterations residual norm |Ax-b|^2 : 0.2214E-01 *** pol. # 3 : 50 iterations ATOMIC_POSITIONS Si0.000.000.00 H 0.12853074400.12853074400.1285307440 H-0.1285307440 -0.12853074400.1285307440 H-0.12853074400.1285307440 -0.1285307440 H 0.1285307440 -0.1285307440 -0.1285307440 dielectric constantpolarizability (A^3) 22.258419 -0.015166 -0.013281 0.133927E+02 -0.772596E-01 -0.676541E-01 -0.021430 22.246210 -0.039084 -0.109170E+00 0.133917E+02 -0.199103E+00 0.026548 0.038463 22.274244 0.135239E+00 0.195939E+00 0.133939E+02 z*( 1) -4.3411 -0.0029 -0.1075 -0.0073 -4.34850.1224 0.0366 -0.0246 -4.2874 z*( 2)0.8033 -0.4537 -0.4544 -0.45810.7774 -0.4578 -0.4751 -0.47800.8034 z*( 3)0.8033 -0.45370.4544 -0.45810.77740.4578 0.47510.47800.8034 z*( 4)0.80330.4537 -0.4544 0.45810.77740.4578 -0.47510.47800.8034 z*( 5)0.80330.45370.4544 0.45810.7774 -0.4578 0.4751 -0.47800.8034 *** Starting Conjugate Gradient minimization *** d2ion: alpha = 0.50 *** mode # 1 : using asr *** mode # 2 : using asr *** mode # 3 : using asr *** Conjugate Gradient minimization not converged after 50 iterations residual norm |Ax-b|^2 : 0.3928E-03 *** mode # 4 : 50 iterations *** Conjugate Gradient minimization not converged after 50 iterations residual norm |Ax-b|^2 : 0.3821E-03 *** mode # 5 : 50 iterations *** Conjugate Gradient minimization not converged after 50 iterations residual norm |Ax-b|^2 : 0.3925E-03 *** mode # 6 : 50 iterations *** mode # 7 : using symmetry *** mode # 8 : using symmetry *** mode # 9 : using symmetry *** mode # 10 : using symmetry *** mode # 11 : using symmetry *** mode # 12 : using symmetry *** mode # 13 : using symmetry *** mode # 14 : using symmetry *** mode # 15 : using symmetry Symmetry violation sum_ij |D_ij-D_ji| : 3.158358 ASR violation sum_i |D_ij| : 2.908104 diagonalizing the dynamical matrix ... ** omega( 1) =-41.789471 [THz] =*** [cm-1] omega( 2) =-41.747411 [THz] =*** [cm-1] omega( 3) =-41.067104 [THz] =*** [cm-1] omega( 4) =-41.026620 [THz] =*** [cm-1] omega( 5) =-40.999019 [THz] =*** [cm-1] omega( 6) =-40.464473 [THz] =*** [cm-1] omega( 7) =-40.425285 [THz] =*** [cm-1] omega( 8) =-40.404738 [THz] =*** [cm-1] omega( 9) = -0.002473 [THz] = -0.082484 [cm-1] omega( 10) = -0.01 [THz] = -0.21 [cm-1] omega( 11) = 0.006516 [THz] = 0.217342 [cm-1] omega( 12) = 44.041877 [THz] =1469.078889 [cm-1] omega( 13) = 44.042544 [THz] =1469.101146 [cm-1] omega( 14) = 44.051925 [THz] =1469.414038 [cm-1] omega( 15) = 46.311307 [THz] =1544.778927 [cm-1] " On Mon, Jun 13, 2022 at 8:29 PM Paolo Giannozzi wrote: > On 13/06/2022 15:47, Aleksandra Oranskaia wrote: > > > I found out that even without Raman cross sections, phcg gives some > > troubles with CG minimization [...] > *** Conjugate Gradient > minimization not converged after 50 > iterations > > hard to say anything sensible, with so little information available > > 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 > -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are no
[QE-users] path length in neb
Dear QE users and developers, Can please someone explain to me how initial path length is being calculated? Or point where it is done in the source code? Say, we have A-B molecule where A and B are its subparts (first image). NEB1: - B is rotated by +90 degrees about the axis that goes through the A-B bond (intermediate image) - B is rotated by +90 degrees more (last image) NEB2: - A is rotated by -90 and B is rotated by +90 degrees (last image). For balanced motion, NEB2 is more reasonable choice, and indeed its initial (as well as optimized) path length is smaller than that for NEB1 (number of images are equal). I would be happy to understand from the mathematical perspective why initial path length differs for NEB1 and NEB2. Thank you! -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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] raman with phcg
Dear Paolo, Thank you for your reply. I found out that even without Raman cross sections, phcg gives some troubles with CG minimization (did not find how to fix it, with ph.x same input works ok): "G-vector sticks info sticks: dense smooth PW G-vecs:dense smooth PW Sum1585158539741655416555161 Reading collected, re-writing distributed wavefunctions *** Starting Conjugate Gradient minimization *** *** Conjugate Gradient minimization not converged after 50 iterations " Do I understand correctly, that Raman might not work in phcg.x but in ph.x there are more chances to succeed? (I was testing phcg.x assuming it might be faster than ph.x for molecules). -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] raman with phcg
Dear user and developers of QE, Can someone please explain what is the meaning of this error and how to fix it? Input is the same as in PHonon/example12 (qe-6.7) with putting SiH4 in the middle of the ibrav = 1 with A = 20.0, plus setting lraman = .True., deltatau = 0.01. Error in output: ... Starting calculation of Raman coefficients NEW-OLD atomic charge density approx. for the potential negative rho (up, down): 1.334E-06 0.000E+00 Generating pointlists ... new r_m : 0.0409 (alat units) 1.1598 (a.u.) for type1 new r_m : 0.0409 (alat units) 1.1598 (a.u.) for type2 %% Error in routine make_pointlists (1): inconsistent sizes %% -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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] Bands with ESM
As was found out by Prof. Minoru, the problem was in the diagonalization algorithm: 'cg' (instead of 'david') solved the convergence. -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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] Bands with ESM (Otani Minoru)
Dear Minoru, Thank you again for the response! I tried increasing the ecutwfc (with ecutrho accordingly) though I had been using safe 'converged' values, decreasing conv_thr, adding more vacuum, nothing worked yet. If you do not mind I will send you the email (from this (very nice!) paper: https://arxiv.org/pdf/2012.10090.pdf) with the preudopotentials and inputs. Maybe you would see the source of a trouble. Thank you, -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] Bands with ESM (Otani Minoru)
Dear Minoru,
First of all, many thanks for your attention and reply.
Secondly, I was playing around the issue: both NSCF (calculation = 'bands'
or 'nscf') failed at the very 1st k-point ("Error in routine c_bands (1):
too many bands are not converged"). Particularly for my structure
bands/pdos were easily plotted without ESM (I am testing simple MoS2 with
H2O above).
Can I please ask you to try bands and pdos visualization for Any system
under your hand with bc1/bc2/bc3 (e.g. Al(001) from the examples)?
Hope to hear from you,
Al.
--
Best wishes,
Alex (she/her/hers),
phd candidate in chemical sciences
'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman)
https://cpms.kaust.edu.sa/
--
This message and its contents, including attachments are intended solely
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Re: [QE-users] gamma_gamma
Issue is still not understood :( -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] Bands with ESM
Dear users and developers of QE, Is it technically possible to calculate NSCF (calculation = 'bands') for the case with esm_bc = 'bc1'? I am getting "Error in routine c_bands (1): too many bands are not converged" at the very 1st k-point. The goal is to plot band structure for the cases with 'bc2' and 'bc3' (for 'bc1' one can easily plot bands with saw-tooth method), but I am not sure this is possible. I will very much appreciate any advice. Thank you! -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] gamma_gamma
Dear QE users and developers, I would be very grateful if someone were kind to help me with very basics about the oxygen atom and its 6 valence electrons (pbe pseudopotential). Doing SCF with gamma and occupations = 'from_input' (1. 1. 1. 1. 0. 0. 0. 0. | 1. 1. 0. 0. 0. 0. 0. 0.) I got total energy -32.69566577 Ry, and occupations = 'smearing' (that in output were printed as: 1. 1. 1. 1. 0. 0. 0. 0. | 1. 1/3 1/3 1/3 0. 0. 0. 0.) i got total energy -32.66588752 Ry. With all-electron numerical orbital FHI-aims I obtained the same picture with 400meV difference in favor of the 1st case. Question1: Is that a physical result? Should not be the 2nd case lower in energy? Doing SCF with 1 1 1 'k-grid' and occupations = 'from_input' (1. 1. 1. 1. 0. 0. 0. 0. | 1. 1. 0. 0. 0. 0. 0. 0.) I got total energy -32.66511579 Ry, and occupations = 'smearing' (that in output were printed as: 1. 1. 1. 1. 0. 0. 0. 0. | 1. 1/3 1/3 1/3 0. 0. 0. 0.) i got total energy -32.66588710 Ry. Question2: Why do the results differ from gamma treatment? Question3: Why was it possible to converge (1. 1. 1. 1. 0. 0. 0. 0. | 1. 1. 0. 0. 0. 0. 0. 0.) and not possible to converge the same systems with (1. 1. 1. 1. 0. 0. 0. 0. | 1. 0. 1. 0. 0. 0. 0. 0.) or (1. 1. 1. 1. 0. 0. 0. 0. | 1. 0. 0. 1. 0. 0. 0. 0.)? Sorry for shallow questions, Hope to hear from you, Al. --- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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] restarting the calculation
Dear Lorenzo, When I asked this question I thought about restarting the calculation from the one with forced occupations = 'from_input' letting the system choose its desired spin multiplicity with occupations = 'smearing'. Will play around with this. Thank you a lot for the help! -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] restarting the calculation
Hello dear users and developers of QE! Can please somebody advise on how to restart the calculation when you successfully finish SCF calculation but want to re-run it with higher precision starting with the previously generated wavefunctions? I tried restarting_mode = 'restart' but as I understand it works either for structural relaxations or non-complete SCF when max_sexonds was used. What am I missing? Thank you! -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples ___ 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
[QE-users] Probable bug in additional_kpoints.f90 subroutine
Thank you for the corrections! Where can I get the updated files (additional_kpoints.f90, plotband.f90, ...?) ? -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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] new qe superfeatures
Can please somebody explain how "additional k points" work? For example, for 2 2 2 in nqx, 6 6 6 in dft and additional points in crystal_b: 3 0.0 0.0 0.0 20 0.5 0.0 0.0 20 0.5 0.5 0.5 1 How many points will be calculated and how? I would highly appreciate any comments/explanations. Thank you! --- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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] possible bug in bands calculation
Please cancel this shame, I got the source of an error. On Mon, Jan 24, 2022 at 8:25 PM Aleksandra Oranskaia < aleksandra.oransk...@kaust.edu.sa> wrote: > Hi! > > I see some weirdness that would highly appreciate help with or comments. > > This is bands pathway for ibrav = 7: > K_POINTS crystal_b > 8 > 0.0 0.0 0.0 50 !G > 0.5 0.0 0.0 50 !M > 0.5 0.0 0.5 50 !L > 0.0 0.0 0.0 50 !G > 0.5 0.5 0.0 50 !K > 0.5 0.5 0.5 50 !H > 0.0 0.0 0.0 50 !G > 0.0 0.0 0.5 1 !A > > From bands.x output: > Reading collected, re-writing distributed wavefunctions > high-symmetry point: 0. 0. 0. x coordinate 0. > high-symmetry point: 0.5000 0.2887 0. x coordinate 0.5774 > high-symmetry point: 0.5000 0.2887 0.1648 x coordinate 0.7421 > high-symmetry point: 0. 0. 0. x coordinate 1.3425 > high-symmetry point: 0.5000 0.8660 0. x coordinate 2.3425 > high-symmetry point: 0.5000 0.8660 0.1648 x coordinate 2.5073 > high-symmetry point: 0. 0. 0. x coordinate 2.5073 > high-symmetry point: 0. 0. 0.1648 x coordinate 2.6720 > > I am not sure prelast point should be like this and not 3.2508, 3.6856. > > This result was obtained by 6.4 and 6.8 versions. > > -- > Best wishes, > Alex (she/her/hers), > phd candidate in chemical sciences > 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) > https://cpms.kaust.edu.sa/ > -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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
[QE-users] possible bug in bands calculation
Hi! I see some weirdness that would highly appreciate help with or comments. This is bands pathway for ibrav = 7: K_POINTS crystal_b 8 0.0 0.0 0.0 50 !G 0.5 0.0 0.0 50 !M 0.5 0.0 0.5 50 !L 0.0 0.0 0.0 50 !G 0.5 0.5 0.0 50 !K 0.5 0.5 0.5 50 !H 0.0 0.0 0.0 50 !G 0.0 0.0 0.5 1 !A >From bands.x output: Reading collected, re-writing distributed wavefunctions high-symmetry point: 0. 0. 0. x coordinate 0. high-symmetry point: 0.5000 0.2887 0. x coordinate 0.5774 high-symmetry point: 0.5000 0.2887 0.1648 x coordinate 0.7421 high-symmetry point: 0. 0. 0. x coordinate 1.3425 high-symmetry point: 0.5000 0.8660 0. x coordinate 2.3425 high-symmetry point: 0.5000 0.8660 0.1648 x coordinate 2.5073 high-symmetry point: 0. 0. 0. x coordinate 2.5073 high-symmetry point: 0. 0. 0.1648 x coordinate 2.6720 I am not sure prelast point should be like this and not 3.2508, 3.6856. This result was obtained by 6.4 and 6.8 versions. -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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] new qe superfeatures
Dear Prof Lorenzo (Paulatto), I summarized the messages above and sent to the email shown in your reply (paulatz at googlemail), please check your spam folder if you have not received it. Thank you for helping! -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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] new qe superfeatures
Further comment on a bug (looks like not very bad one): Ok, numbering of k-points differs from reference (where bands dispersion happens between 507-578): the range has to be 9-80 for plotband. Unfortunately, bands.x fails "two consecutive same k, exiting" without writing plottable file. Hope to hear from you soon and thanks/sorry for the attention. -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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] new qe superfeatures
Yep it is a bug (i asked smart people to run the example). In reference folder the address for the pseudos was: /home/paulatto/espresso/pseudo/ so probably 'paulatto' is the developer to contact. Can please somebody share his/her full name or contacts? -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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] new qe superfeatures
I have a feeling that there is something wrong in exx bands procedure: - PP/examples/exx_scf_bands_example/reference contains output made with qe-6.6 (even in qe-7.0 release); however, public release of 6.6 does not have this functionality with additional k points for exx bands - 1st step scf of this example done with 6.7 or 6.8 differs from the reference: info on k-points in the beginning of the output is displayed correctly (and I got why later on 507-578 k-points are plotted), but later on something goes wrong - this is the last point in output (must be k=0.0 0.0 0.0!) k =-0.3000 0.7000 0.5000 ( 346 PWs) bands (ev): -0.9483 1.3600 5.3099 6.4907 11.0460 11.1308 13.3137 16.0597 occupation numbers 0. 0. 0. 0. 0. 0. 0. 0. highest occupied, lowest unoccupied level (ev): 6.28729.1448 !total energy = -16.27044038 Ry estimated scf accuracy< 1.8E-12 Ry convergence has been achieved in 1 iterations Please, run this example with publicly available qe version and confirm that your output matches the reference. -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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] new qe superfeatures
Thanks for the reply on the 2nd question.
Regarding the 1st one:
I found the example in PP folder, it worked.
I tried the same calculation with spin-orbit coupling but got an error:
%%
Error in routine fft_type_set (6):
there are processes with no planes. Use pencil decomposition (-pd .true.)
%%
Are exx bands impossible with soc or I need to somehow recompile the code
with "-pd .true."?
Also would be happy to know what is the meaning of the 2nd line in plotband
input in the example ("-10 20 507 578")?
--
Best wishes,
Alex (she/her/hers),
phd candidate in chemical sciences
'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman)
https://cpms.kaust.edu.sa/
--
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[QE-users] new qe superfeatures
Hello dear users and developers, 1) I just noticed a new feature with additional k-points for getting exx band dispersions. I am a bit confused: previously one had to use wannier90 trick for exx bands ( https://mattermodeling.stackexchange.com/questions/1176/calculating-hse06-band-structures-on-quantum-espresso) as the bands require nscf calculations that were not doable with hybrid functionals in qe. If now exx bands are possible to plot without the trick - can any basic example be provided? Please. 2) Among new features "pdos in local basis" is mentioned. What exactly is meant here? Is any example available? Many thanks for your response! -- Best wishes, Alex (she/her/hers), phd candidate in chemical sciences 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman) https://cpms.kaust.edu.sa/ -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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
[QE-users] neb - first_last_opt
Dear developers, One of the very useful features of NEB does not work as it is supposed (?): if one sets 'first_last_opt = False' in input -- (s)he will anyway find 'first_last_opt=T' in output. I tried to go to .../qe-6.7/NEB/src and look at how it is written (plus i compared it with the previous qe version: did not see changes). If I am not mistaken this option indeed is supposed to freeze initial and final configuration. As I am not sure how to correct the source code (without breaking it) - I will highly appreciate any advice. Thanks in adcance, Alex (phd student, KAUST). -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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
[QE-users] dft+u+v with spin-orbit
Dear users and developers, Is it technically possible to mk calculations for dft+u+v accounting for spin-orbit coupling (using qe-6.7 compiled for u-correction for l=1)? Using u and v values obtained by hp.x (with scalar relativistic pseudos) and these lines (for fully relativistic preudos): lda_plus_u = .True. lda_plus_u_kind = 2 U_projection_type = 'ortho-atomic' Hubbard_parameters = 'file' lspinorb = .true. noncolin = .true. ? I am getting this error (preudos are ok for calculations with no Hubbard correction, they describe electrons on desired l level): Error in routine offset_atom_wfc (1): wrong offset: your pseudopotential file for atomic species 1 likely does not contain the needed atomic wavefunctions -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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
[QE-users] neb bug?
Hi dear users and developers, I am calculating neb (from qe-6.4.1) for a system of 54 electrons, asking for 34 bands (i.e. that qe considers 68 wfc). Every few steps calculation crashes with: %% Error in routine read_wfc (29): cannot open restart file /scratch/./...save/wfc81 for reading %% Is that a bug? If not, what info should i get from this kind of crash? PS When replying please instruct on how I should reply back on a specific topic. Thank you! Al. -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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
[QE-users] C3 symm
Dear developers of QE, I am 99% sure that QE-6.4.1 does not recognize D3h, C3v point groups. After playing with big clusters, I checked it on NH3 molecule: QE assigned NH3 to C2v. If I am not mistaken, it is possible to fix it easily? Huge thanks in advance. Best, Al. -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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] NEB images with different cell parameters
Hi Apoorv, You can use external code for vcneb like Uspex-9.4.4 in interface with QE. (In my opinion it does not make lots of sense to study photoisomerization with ground state dft, i would rather think of post hf methods to explore pes of the first excited state(s)) Anyhow could you please share the details of ‘accurate xrd’ experiment where people obtained lattice constants of photoexcited material? -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ 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] vc-relax for orthorhombic systems
Dear Giuseppe and Lorenzo, Thank you both for sharing your knowledge, I truly appreciate all your comments and will think on them. Let me reply: to Giuseppe: > Why do you need to be so tightly close to experimental lattice parameters? Yes, I do try to validate setups for using them in evolutionary crystallography methods (A.Oganov methods) that are based on large scale optimizations (for them one needs settings as “cheap” as possible, but still reasonably correct). In general, I would always trust functional/pseudopotentials that give close to experimental structural parameters (I try to use as a reference low temperature XRD for lattice constants, like obtained at 5K) as well as band gaps (as reasonable as DFT can do it, I also check them using higher levels of theory that are too expensive for optimizations). Fixing experimental lattice constants introduce artifice forces/stresses, so I avoid this approach when possible. to Lorenzo: > Also, keep in mind that vc-relax is done at fixed number of plane-waves, not > constant cutoff. You should always repeat it starting from the final > configuration and Could you please rewrite the last sentence? > Correcting for the lack of VdW interaction with a simple Grimme-D2 method > could be enough to get a better agreement. Thanks for the suggestion, I did tested all vdw corrections (for PBE and PBEsol) and majority of vdw functionals (btw, for my systems D2 gave crazy numbers). to everybody: 3 days in a row I was testing everything that my imagination allowed to and came up to a conclusion that with soft materials, with orthorhombic cells of > 20 atoms there are TOO many degrees of freedom to expect vc-relax to give good numbers for cell parameters. Within the same third decimal digit in total energy (-.xxX Ry) one might came to slightly(?!) different cells depending on starting points and general logic of relaxation (say, you start from orthorhombic space group doing relax and for a corresponding ibrav continue with vc-relax Or you start from the closest tetragonal space group and continue with xyz vc-relax). I will also do a few variable-cell NEB (coupled with QE for ab initio part) between the orthorhombic and tetragonal systems, maybe it will help me more to better understand the problem. PS I have a full right to be wrong I am learning and will be thankful for any feedback ;-) Best, Alex. ___ Aleksandra Oranskaia (M.Sc.) ChemS PhD student, KAUST Phone: +966 50 1335254 > On Apr 8, 2019, at 1:00 PM, users-requ...@lists.quantum-espresso.org wrote: > > Send users mailing list submissions to > users@lists.quantum-espresso.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.quantum-espresso.org/mailman/listinfo/users > or, via email, send a message with subject or body 'help' to > users-requ...@lists.quantum-espresso.org > > You can reach the person managing the list at > users-ow...@lists.quantum-espresso.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of users digest..." > > > Today's Topics: > > 1. Re: Compilation on a server ends with error 1 (Fabio Costa) > 2. Pseudopotential type is different in the website description > and in the file (Rajesh Raju) > 3. Re: Compilation on a server ends with error 1 > (Pietro Davide Delugas) > 4. Ab-Initio Thermal Transport (Arihant Bhandari) > 5. (no subject) (as gj) > 6. Re-use of charge density don't give exactely the sameresult > in scf (JAY Antoine) > 7. Re: Re-use of charge density don't give exactely the same > result in scf (Pietro Delugas) > 8. Re: Re-use of charge density don't give exactely the same > result in scf (Pietro Delugas) > 9. Re: Re-use of charge density don't give exactely the same > result in scf (Paolo Giannozzi) > 10. Re: vc-relax for orthorhombic systems (Aleksandra Oranskaia) > 11. Re: vc-relax for orthorhombic systems (Lorenzo Paulatto) > 12. Re: vc-relax for orthorhombic systems (Giuseppe Mattioli) > > > -- > > Message: 1 > Date: Sun, 7 Apr 2019 23:53:39 + > From: Fabio Costa > To: Quantum Espresso users Forum > Subject: Re: [QE-users] Compilation on a server ends with error 1 > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Paolo and Pietro > > Thanks for the assistance, and sorry for the late reply on your advice. > > I contacted the system administrator, and he explained to me that as there > are several other applications running under this old gfortran version, and > because of that he could not just issue "sudo apt update gfortran", on the
Re: [QE-users] vc-relax for orthorhombic systems
Right now I am testing some desperate approaches like increasing k-points, decreasing mixing_beta together with trust_radii to force systems to change sightly fro step to step in vc-relax, etc. I also thought that more precise calculation of stresses (in vc-relx routine) might help, does anyone have experience with parameters involved in stress calculations like ecfixed, qcutz, q2sigma? Best, Alex. ___ Aleksandra Oranskaia (M.Sc.) ChemS PhD student, KAUST Phone: +966 50 1335254 > On Apr 6, 2019, at 1:00 PM, users-requ...@lists.quantum-espresso.org wrote: > > Send users mailing list submissions to > users@lists.quantum-espresso.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.quantum-espresso.org/mailman/listinfo/users > or, via email, send a message with subject or body 'help' to > users-requ...@lists.quantum-espresso.org > > You can reach the person managing the list at > users-ow...@lists.quantum-espresso.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of users digest..." > > > Today's Topics: > > 1. vc-relax for orthorhombic systems (Aleksandra Oranskaia) > > > ------ > > Message: 1 > Date: Fri, 5 Apr 2019 19:39:39 +0300 > From: Aleksandra Oranskaia > To: Quantum Espresso users Forum > Subject: [QE-users] vc-relax for orthorhombic systems > Message-ID: <8fca3967-9817-4748-b8d3-34ec6f029...@kaust.edu.sa> > Content-Type: text/plain; charset="iso-8859-1" > > Dear QE users and developers, > > 1 When dealing with orthorhombic systems, I start with space_group > super-tight relaxation of the atomic positions (keeping right balance in > force and scf accuracy, increasing ecutrho plus 100 Ry than my system > actually requires, etc), continue with vc-relax using dofree = ibrav (and > press_thr = 0.0), and Always obtain at least one lattice constant screwed up > (with an error like +/- 0.1 A as compared to the experimental constant). > I tried 1000 setups for a few systems (varying functionals, vdw corrections, > different pseudo libraries, etc) and have a feeling that sth is not right > with vc-relax: for other than orthorhombic systems the results match the > experimental lattice constants with an acceptable error. > > 2 I was wondering how vc-relax work for big orthorhombic unit cells. I took > alpha-S8 (space group 70, so 128 atoms turn into 32 within ibrav = 10 with 8 > symmetry elements) and am not satisfied with any lattice constants: on PBEsol > level, error in volume is <1% as compared to the experimental unit cell, but > lattice constants are like 10.602 (exp: 10.465), 12.937 (exp: 12.866), 24.286 > (exp: 24.486) A that do not look acceptable at all :-( > > I would hugely appreciate any comments, > > > Thanks, > Alex. > ___ > Aleksandra Oranskaia (M.Sc.) > ChemS PhD student, KAUST > Phone: +966 50 1335254 > > > > > > > > -- > > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > -- next part -- > An HTML attachment was scrubbed... > URL: > <http://lists.quantum-espresso.org/pipermail/users/attachments/20190405/7ab54d9a/attachment-0001.html> > > -- > > Subject: Digest Footer > > ___ > users mailing list > users@lists.quantum-espresso.org > https://lists.quantum-espresso.org/mailman/listinfo/users > > -- > > End of users Digest, Vol 141, Issue 6 > * -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] vc-relax for orthorhombic systems
Dear QE users and developers, 1 When dealing with orthorhombic systems, I start with space_group super-tight relaxation of the atomic positions (keeping right balance in force and scf accuracy, increasing ecutrho plus 100 Ry than my system actually requires, etc), continue with vc-relax using dofree = ibrav (and press_thr = 0.0), and Always obtain at least one lattice constant screwed up (with an error like +/- 0.1 A as compared to the experimental constant). I tried 1000 setups for a few systems (varying functionals, vdw corrections, different pseudo libraries, etc) and have a feeling that sth is not right with vc-relax: for other than orthorhombic systems the results match the experimental lattice constants with an acceptable error. 2 I was wondering how vc-relax work for big orthorhombic unit cells. I took alpha-S8 (space group 70, so 128 atoms turn into 32 within ibrav = 10 with 8 symmetry elements) and am not satisfied with any lattice constants: on PBEsol level, error in volume is <1% as compared to the experimental unit cell, but lattice constants are like 10.602 (exp: 10.465), 12.937 (exp: 12.866), 24.286 (exp: 24.486) A that do not look acceptable at all :-( I would hugely appreciate any comments, Thanks, Alex. ___ Aleksandra Oranskaia (M.Sc.) ChemS PhD student, KAUST Phone: +966 50 1335254 -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] default nbnd
Hello dear users and developers of QE, Could please someone advice which lines to change in the source code for nbnd to add by default not 20%, but 30% empty bands? I need it for using QE for the evolutionary crystallography algorithm which depends on generating and optimizing large set of structures (of different composition), and particularly my systems are metallic or narrow band gap semiconductors that for good convergence need ~ 30% empty states. Thanks in advance, Best, Alex. ___ Aleksandra Oranskaia (M.Sc.) ChemS PhD student, KAUST Phone: +966 50 1335254 -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] HSE06 restart
Hello dear developers of QE, Could you please share any hints on restarting HSE06 calculations? I usually put > 30min more in job submission scripts than I set max_seconds in QE input, but it still does not help. >From all my HSE06 jobs only twice the output of the stopped job was written >correctly and only once the job successfully restarted, in all dozen cases I >was loosing core-hours from my project allocation :-( I would appreciate any advice on this issue. Thanks in advance, Alex. ___ Aleksandra Oranskaia (M.Sc.) ChemS PhD student, KAUST Phone: +966 50 1335254 -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] differently complied QE
Hello Nicola, [hope I am correctly using the forum and my messages reach you] I tried GNU and Intel compilations, both on two very different workstations, all for 6.2.1 and 6.3 versions, for the same inputs with the tightened parameters. In all the cases lattice constant is the same up to the 4th decimal (i.e, they all were like 3.458). However, on our University Supercomputer (Cray XC40, admin installation) I am getting the result that differs (being like 3.453). 3.458 vs 3.453 is like 3.46 vs 3.45 that probably is not cool at all. Could you please suggest any “benchmark” vc-relax input to check if cray compilation on the supercomputer is correct? Thanks in advance, Alex. ___ Aleksandra Oranskaia (M.Sc.) ChemS PhD student, KAUST Phone: +966 50 1335254 > On Jan 8, 2019, at 2:49 AM, Aleksandra Oranskaia > wrote: > > Thank you for the respond! > > I was confused with the difference, because if the 3rd digit is “arbitrary” > (depends on libraries, compilers, hardware, etc.) than there is no sense in > reporting lattice constants in papers with this accuracy; however, it is a > common practice. > > I used: > conv_thr=1.d-8 > tot_conv_thr=1.d-6 > forc_conv_thr=1.d-6 > cell_dofree=‘volume’ (for the cubic cell) > > I will try to increase conv_thr and press_conv_thr, as well as to compare gnu > and intel compillations, and reply back. > > > Best, > Alex. > > ___ > Aleksandra Oranskaia (M.Sc.) > ChemS PhD student, KAUST > Phone: +966 50 1335254 > > >> On Jan 8, 2019, at 2:39 AM, Nicola Marzari > <mailto:nicola.marz...@epfl.ch>> wrote: >> >> >> Last - note that 3.458 and 3.453 are really close - so the accuracy you have >> now is good enough for research purposes. >> >> nicola >> >> >> >> On 08/01/2019 00:38, Nicola Marzari wrote: >>> Well, the numbers you get are not infinitely precise - there is >>> a threshold where you stop minimizing forces and cell geometry, >>> using forces and stresses that are not perfect because each SCF cycle is >>> not converged to infinite perfection. >>> Bottom line - try to tighten all the convergencies (scf convergence >>> at every cycle, and forces at every ionic relxations, and pressure...) >>> conv_thr for electrons >>> etot_conv_thr for ions >>> forc_conv_thr for ions >>> press_conv_thr for cell >>> are the variables to play with. I would make sure conv_thr is very tight >>> (10^-10 per atom, or even less) and then play with forc_ and press_ >>> nicola >>> On 07/01/2019 14:24, Aleksandra Oranskaia wrote: >>>> Hello dear users and developers of QE, >>>> >>>> I have recently noticed that one and the same QE version that was >>>> installed with different libraries, compilers, on different machines (with >>>> very different hardware) not only gives different total energies for the >>>> same inputs but also quite different optimized lattice constants (say, >>>> 3.458 versus 3.453 that does not seem no be acceptable). >>>> >>>> So the question is: how to know which installation accumulates some >>>> small(?) numerical problems? >>>> In standard QE pw examples there is no example with variable-cell >>>> relaxation done on “ideally” installed code, so there is no reference >>>> point to reproduce. >>>> >>>> >>>> >>>> Best, >>>> Alex. >>>> ___ >>>> Aleksandra Oranskaia (M.Sc.) >>>> ChemS PhD student, KAUST >>>> Phone: +966 50 1335254 >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> This message and its contents, including attachments are intended solely >>>> for the original recipient. If you are not the intended recipient or have >>>> received this message in error, please notify me immediately and delete >>>> this message from your computer system. Any unauthorized use or >>>> distribution is prohibited. Please consider the environment before >>>> printing this email. >>>> >>>> ___ >>>> users mailing list >>>> users@lists.quantum-espresso.org <mailto:users@lists.quantum-espresso.org> >>>> https://lists.quantum-espresso.org/mailman/listinfo/users >>>> >> >> >> -- >> ---
Re: [QE-users] differently complied QE
Thank you for the respond! I was confused with the difference, because if the 3rd digit is “arbitrary” (depends on libraries, compilers, hardware, etc.) than there is no sense in reporting lattice constants in papers with this accuracy; however, it is a common practice. I used: conv_thr=1.d-8 tot_conv_thr=1.d-6 forc_conv_thr=1.d-6 cell_dofree=‘volume’ (for the cubic cell) I will try to increase conv_thr and press_conv_thr, as well as to compare gnu and intel compillations, and reply back. Best, Alex. ___ Aleksandra Oranskaia (M.Sc.) ChemS PhD student, KAUST Phone: +966 50 1335254 > On Jan 8, 2019, at 2:39 AM, Nicola Marzari wrote: > > > Last - note that 3.458 and 3.453 are really close - so the accuracy you have > now is good enough for research purposes. > > nicola > > > > On 08/01/2019 00:38, Nicola Marzari wrote: >> Well, the numbers you get are not infinitely precise - there is >> a threshold where you stop minimizing forces and cell geometry, >> using forces and stresses that are not perfect because each SCF cycle is >> not converged to infinite perfection. >> Bottom line - try to tighten all the convergencies (scf convergence >> at every cycle, and forces at every ionic relxations, and pressure...) >> conv_thr for electrons >> etot_conv_thr for ions >> forc_conv_thr for ions >> press_conv_thr for cell >> are the variables to play with. I would make sure conv_thr is very tight >> (10^-10 per atom, or even less) and then play with forc_ and press_ >> nicola >> On 07/01/2019 14:24, Aleksandra Oranskaia wrote: >>> Hello dear users and developers of QE, >>> >>> I have recently noticed that one and the same QE version that was installed >>> with different libraries, compilers, on different machines (with very >>> different hardware) not only gives different total energies for the same >>> inputs but also quite different optimized lattice constants (say, 3.458 >>> versus 3.453 that does not seem no be acceptable). >>> >>> So the question is: how to know which installation accumulates some >>> small(?) numerical problems? >>> In standard QE pw examples there is no example with variable-cell >>> relaxation done on “ideally” installed code, so there is no reference point >>> to reproduce. >>> >>> >>> >>> Best, >>> Alex. >>> ___ >>> Aleksandra Oranskaia (M.Sc.) >>> ChemS PhD student, KAUST >>> Phone: +966 50 1335254 >>> >>> >>> >>> >>> >>> >>> >>> >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> ___ >>> users mailing list >>> users@lists.quantum-espresso.org >>> https://lists.quantum-espresso.org/mailman/listinfo/users >>> > > > -- > -- > 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 -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] differently complied QE
Thank you for the respond! I was confused with the difference, because if the 3rd digit is “arbitrary” (depends on libraries, compilers, hardware, etc.) than there is no sense in reporting lattice constants in papers with this accuracy; however, it is a common practice. I used: conv_thr=1.d-8 tot_conv_thr=1.d-6 forc_conv_thr=1.d-6 cell_dofree=‘volume’ (for the cubic cell) I will try to increase conv_thr and press_conv_thr, as well as to compare gnu and intel compillations, and reply back. Best, Alex. ___ Aleksandra Oranskaia (M.Sc.) ChemS PhD student, KAUST Phone: +966 50 1335254 > On Jan 8, 2019, at 2:39 AM, Nicola Marzari wrote: > > > Last - note that 3.458 and 3.453 are really close - so the accuracy you have > now is good enough for research purposes. > > nicola > > > > On 08/01/2019 00:38, Nicola Marzari wrote: >> Well, the numbers you get are not infinitely precise - there is >> a threshold where you stop minimizing forces and cell geometry, >> using forces and stresses that are not perfect because each SCF cycle is >> not converged to infinite perfection. >> Bottom line - try to tighten all the convergencies (scf convergence >> at every cycle, and forces at every ionic relxations, and pressure...) >> conv_thr for electrons >> etot_conv_thr for ions >> forc_conv_thr for ions >> press_conv_thr for cell >> are the variables to play with. I would make sure conv_thr is very tight >> (10^-10 per atom, or even less) and then play with forc_ and press_ >> nicola >> On 07/01/2019 14:24, Aleksandra Oranskaia wrote: >>> Hello dear users and developers of QE, >>> >>> I have recently noticed that one and the same QE version that was installed >>> with different libraries, compilers, on different machines (with very >>> different hardware) not only gives different total energies for the same >>> inputs but also quite different optimized lattice constants (say, 3.458 >>> versus 3.453 that does not seem no be acceptable). >>> >>> So the question is: how to know which installation accumulates some >>> small(?) numerical problems? >>> In standard QE pw examples there is no example with variable-cell >>> relaxation done on “ideally” installed code, so there is no reference point >>> to reproduce. >>> >>> >>> >>> Best, >>> Alex. >>> ___ >>> Aleksandra Oranskaia (M.Sc.) >>> ChemS PhD student, KAUST >>> Phone: +966 50 1335254 >>> >>> >>> >>> >>> >>> >>> >>> >>> This message and its contents, including attachments are intended solely >>> for the original recipient. If you are not the intended recipient or have >>> received this message in error, please notify me immediately and delete >>> this message from your computer system. Any unauthorized use or >>> distribution is prohibited. Please consider the environment before printing >>> this email. >>> >>> ___ >>> users mailing list >>> users@lists.quantum-espresso.org >>> https://lists.quantum-espresso.org/mailman/listinfo/users >>> > > > -- > -- > 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 -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] differently complied QE
Hello dear users and developers of QE, I have recently noticed that one and the same QE version that was installed with different libraries, compilers, on different machines (with very different hardware) not only gives different total energies for the same inputs but also quite different optimized lattice constants (say, 3.458 versus 3.453 that does not seem no be acceptable). So the question is: how to know which installation accumulates some small(?) numerical problems? In standard QE pw examples there is no example with variable-cell relaxation done on “ideally” installed code, so there is no reference point to reproduce. Best, Alex. ___ Aleksandra Oranskaia (M.Sc.) ChemS PhD student, KAUST Phone: +966 50 1335254 -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] phonons with vdW functional
I will be very thankful for any thoughts on this issue. Also if you know QE experts please kindly redirect the message. > On Nov 26, 2018, at 6:05 PM, Aleksandra Oranskaia > wrote: > > Hello dear users and developers of QE, > > I am trying to calculate phonons using very good structure (tightly > optimized, matching the experimental one, etc), but whatever I do the result > is: > > > %% > Error in routine cdiaghg (448): > S matrix not positive definite > > %% > > I varied: > - number of processors (with too large # of processors similar issues are > reported) > - ecutrho increasing it up to ecutwfc*15 > - different smearings schemes (the system is a narrow band gap semiconductor) > - different diagonalization procedures (from my personal experience: david > fail sometimes where cg saves the day) > - used nosym=.true. > > I would highly appreciate any thoughts on the nature of this mistake > happening in the very beginning of phonon calculation. > > > Best, > Alex. > ___ > Aleksandra Oranskaia (M.Sc.) > ChemS PhD student, KAUST > Phone: +966 50 1335254 > > > > > > -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] phonons with vdW functional
Hello dear users and developers of QE, I am trying to calculate phonons using very good structure (tightly optimized, matching the experimental one, etc), but whatever I do the result is: %% Error in routine cdiaghg (448): S matrix not positive definite %% I varied: - number of processors (with too large # of processors similar issues are reported) - ecutrho increasing it up to ecutwfc*15 - different smearings schemes (the system is a narrow band gap semiconductor) - different diagonalization procedures (from my personal experience: david fail sometimes where cg saves the day) - used nosym=.true. I would highly appreciate any thoughts on the nature of this mistake happening in the very beginning of phonon calculation. Best, Alex. ___ Aleksandra Oranskaia (M.Sc.) ChemS PhD student, KAUST Phone: +966 50 1335254 -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [Pw_forum] TiO2 001 Slab Convergence
Hi Will, 1 In your input I am confused with the combination of “relax” calculation and: cell_dynamics = 'bfgs', press=0.1d0, I do not know which calculation is eventually being done “relax” or “vc-relax”? If the second, I would doubt if it is correct to relax z-direction of the slab, especially accounting the pressure. I think that variable cell relaxation for the slab you might want to use cell_dofree = xy and treat z-parametr as a constant. 2 From my little experience, increasing amount of vacuum to 20A might drastically improve the convergence, especially if 10A of vacuum is added bilaterally behind and above the slab (the slab atoms are put in the middle of the cell). This is connected with the dipole cancellation routine. 3 What might also decrease the convergence time is the decreasing your ecutrho cutoff, say to to around 5*ecutwfc. In pw.x manual it is suggested to use (8-12)*ecutwfc for UPF, but in papers people often use (5-6)*ecutwfc. Just to find the convergence grounds, you could start with 5*ecutwfc and after the initial relaxation switch to a larger cutoff. It would be interesting to see the output. Anyway good luck with the convergence :) Alex. 1st yr PhD student in KAUST, KSC, PSE -- -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] NEB first_last_opt
Hello dear QE users, I have a question regarding pre-optimization of starting and ending points of NEB. Dealing with multi-scale simulation of a vacancy migration in a huge supercell (say, 350-400 atoms), should one make a pre-optimization of starting and ending points of a path? I tried both ways and came to the conclusion that pre-optimization pushes the system away from the minimum energy path (leading to the increased barriers), because pre-optimization implies too deep restructuring towards deeper minimums rather than the local minimums closest to the minimum energy pathway. In my opinion it is more physical if a migration corresponds to a minimum energy pathway AND minimum restructuring. If you would simulate vacancy migration in a huge supercell with NEB optimization, would you optimize starting and ending points? Why? Thanks in advance and hope to hear your opinions and reasonings, Regards, Alex. -- -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
