[QE-users] Possible error in documentation of matdyn.x (v 7.3.1)
Dear developers, I think that there is an error in the documentation of matdyn.x. While in the documentation it is written that the matdyn.eig file contains the phonon eigenvectors and matdyn.modes contains the displacements (eigenvectors divided by the square root of the mass), however, if one looks at the subroutine "write_eigenvectors", the eigenvectors are divided by the sqrt of mass., while in the "writemodes" subroutine, the normalized eigenvectors of the dynamical matrix are written. With regards, Prasenjit IISER Pune ___ 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] Error in Phonon calculation while considering DFT-D3 corrections
Thanks Ivan for the clarification. Does setting the dftd3_threebody=.false. implies that it would produce the same results as dft-d2? With regards, Prasenjit From: "icarnimeo" To: "users" Sent: Monday, August 19, 2024 3:25:15 PM Subject: Re: [QE-users] Error in Phonon calculation while considering DFT-D3 corrections Dear Sayandeep, Prasenjit the Grimme D3 correction IS implemented in QE (pw.x, d3hess.x, ph.x). Only the three body term of D3 in ph.x is not implemented. For this reason phonon calculations should be run with dftd3_threebody=.false. I was able to run the d3hess program with the input provided in the emails in this thread without any problems. The only (minor) issue I could notice is that the ATOMIC_SPECIES card was empty, and it should be filled with the pseudo specification. Best, IC ___ 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 ___ 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] Error in Phonon calculation while considering DFT-D3 corrections
Dear Sayandeep, What this message means is that phonons with DFT-D3 correction is not implemented in QE. I do not know whether this has been implemented in the latest version. May be the developers can comment. If it is not implemented, you cannot compute the phonons with DFPT. However, you can use the finite displacement/frozen phonon method to compute the phonons. Hope this helps. With regards, Prasenjit IISER Pune From: "Sayandeep GHOSH" To: "users" Sent: Tuesday, August 13, 2024 8:12:32 PM Subject: [QE-users] Error in Phonon calculation while considering DFT-D3 corrections Hello all, Currently I was trying to calculate the phonon for kagome materials. Hence, I have to consider the DFT-D3 correction. >From what I've gathered from the d3hess.x documentation, the process to >include dispersion effects on vibrational frequencies should be as follows: 1. Perform a relaxation or SCF calculation. 2. Run d3hess.x. 3. Run ph.x. However, I was getting the following error in the second step. The error message is as follows: %% task # 12 from pbcgdisp : error # 1 Atom displacement not implemented with the threebody term %% I incorporated the changes which was discussed in the following [ https://www.mail-archive.com/users@lists.quantum-espresso.org/msg44417.html | Re: [QE-users] Phonon calculation with DFT-D3 correction (mail-archive.com) ] Please find the input for scf calculation (scf.in) &CONTROL calculation = 'scf', restart_mode = 'from_scratch' prefix = 'CVS', outdir = './output', verbosity = 'high' tstress = .true. tprnfor = .true. etot_conv_thr = 1.0D-12 forc_conv_thr = 1.0D-7 / &SYSTEM ibrav = 4 celldm(1) = 10.636266035055442 celldm(3) = 1.66503783444 nat = 9 ntyp = 3 ecutwfc = 37 ecutrho = 148 occupations = 'smearing', smearing = 'gaussian', degauss = 0.0015, vdw_corr = 'grimme-d3', dftd3_threebody = .false. / &ELECTRONS electron_maxstep = 200 conv_thr = 1.D-6 / ATOMIC_SPECIES ATOMIC_POSITIONS (crystal) Cs -0.00 0.00 0.50 V 0.50 0.00 -0.00 V -0.00 0.50 0.00 V 0.50 0.50 0.00 Sb 0.666870 0.333430 0.7485578106 Sb 0.333130 0.666270 0.2514421894 Sb 0.333130 0.666270 0.7485578106 Sb 0.666870 0.333430 0.2514421894 Sb -0.00 0.00 0.00 K_POINTS automatic 9 9 4 0 0 0 ## And the input file for d3hess.x (d3hess.in) &INPUT prefix = 'CVS', outdir = './output', filhess = 'CVS.hess', step = 1.0d-3 / ### Could anyone help me figure out this error? Thanks in advance. Regards, Sayandeep Ghosh Laboratory for Chemistry of Novel Materials, Materials Research Institute, Université de Mons - UMONS Place du Parc, 20, B-7000 MONS (Belgium) ___ 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 ___ 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] Pencil decomposition
In the command line you should add the following: -pd .true. For eg. $/path_to_your_mpirun/mpirun -np 4 /path_to_your_qe/pw.x -pd .true. < name_of_input_file > name_of_output_file With regards, Prasenjit - Original Message - From: "Suraj P" To: "users" Sent: Monday, July 22, 2024 11:09:06 AM Subject: [QE-users] Pencil decomposition Dear QE users, Im getting an error when I have done vc-relax calcualtion for Ni2P hexagonal lattice asking me to use pencil decomposition. Under which cards and what comment should be written to eliminate this error. Im attaching the input and output files of the same. kindly have a look into these. Thanking you, Suraj Research student, IIT Kharagpur ___ 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 ___ 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] Phonon calculation with DFT-D3 correction
Alternatively, you can calculate using the frozen phonon method. Prasenjit IISER Pune From: "users" To: "users" Sent: Wednesday, May 15, 2024 3:49:18 AM Subject: Re: [QE-users] Phonon calculation with DFT-D3 correction ph.x currently does not support the three-body terms with the D3 dispersion correction. You can turn it off with the dftd3_threebody tag in pw.x, and follow the three step procedure you outlined in your email. If you want to include the three-body terms, you can use the supercell approach (e.g., phonopy) instead of DFPT with ph.x. Three-body terms tend to have a pretty small effect in my experience, but that's system-dependent, in principle, and you might want to test it. Refer to the original D3 papers for a discussion. Three-body terms are not used at all in VASP, for reference (but they're hidden in the source code). I also generally recommend using D3 with BJ damping or D3M/D3M-BJ instead of the standard "zero damping" D3. (dftd3_version flag in pw.x). Omar A. Ashour UC Berkeley On May 14, 2024, at 2:51 PM, Jing Lian Ng wrote: BQ_BEGIN Hello all, I am currently trying to perform phonon calculation with DFT-D3 correction. Based on what I read from d3hess.x documentation, I believe I can include dispersion effects on vibrational frequencies by: 1. Relax / Scf calculation 2. run d3hess.x 3. run ph.x However, I encounter an error on step2, with the error message being: %%% task # 28 from pbcgdisp : error # 1 Atom displacement not implemented with the threebody term %% My input file for scf is as follows: ## / &SYSTEM ntyp = 1 nat = 2 ibrav = 0 ecutwfc = 100 ecutrho = 400 vdw_corr = 'DFT-D3' / &ELECTRONS mixing_mode = 'plain' mixing_beta = 0.3 / &IONS / &CELL / ATOMIC_SPECIES H 1.008 H.upf CELL_PARAMETERS angstrom 5.216575 0.00 0.00 0.00 6.049260 0.00 -6.40884630521040 0.00 36.38325638013446 ## Can someone advise on what could be the possible error? Thanks! -- Best regards, Jing Lian Ng , PhD Student Wang Material Group The University of Texas at Austin | [ http://che.utexas.edu/ | McKetta Department of Chemical Engineering ] | [ https://wangmaterialsgroup.com/ | Wang Materials Group ] ___ 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 BQ_END ___ 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 ___ 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] ESM model with vacuum/metal boundary condition (bc3)
Dear all, I am trying to perform calculations for a charged system with assume_isolated = "esm" and using a vacuum/metal boundary condition (esm_bc='bc3'). However, I am confused regarding how to choose the position offset for the start of the effective screening region (esm_w). Some preliminary calculations by varying esm_w suggests that the results (for eg. the electrostatic potential on the vacuum side, magnitude of the bias applied to the surface, etc.) strongly depends on the choice of the "esm_w" variable. Can anyone please suggest how to choose an optimal value of "esm_w"? Thanking you in advance. With regards, Prasenjit Ghosh IISER Pune ___ 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] using ESM with boundary condition "bc1" for charged slab
Thanks a lot Paolo for the clarification. With regards, Prasenjit - Original Message - From: "Paolo Giannozzi" To: "users" , "pghosh" Sent: Wednesday, February 14, 2024 9:46:36 PM Subject: Re: [QE-users] using ESM with boundary condition "bc1" for charged slab I inquired with the author of ESM and this is what he told me: "Since BC1 has no screening medium in the system, we need to keep charge neutral in the DFT cell. Otherwise, the total energy is diverging. In the earlier versions, the manual included a note for such charge neutrality condition, but for added safety, a routine to check this has been incorporated into the program. In an ESM-RISM calculation, even when using BC1, there is no need to impose the charge neutrality condition in the DFT cell, as the RISM part automatically generates a compensating charge to maintain the charge neutrality condition throughout the whole system." Paolo On 2/9/24 06:07, Ghosh, Prasenjit wrote: > > Non si ricevono spesso messaggi di posta elettronica da > pgh...@iiserpune.ac.in. Informazioni sul perché è importante > <https://secure-web.cisco.com/12AJuZ9ZsbH7OSSDaFdwYXUBzeEOCvjPihIc7H0WS6WY6Hx9lMBQkozsbXYvV0X-7Cjhn8W42VD0os00rHvSbmmrEi9OT0_ofj4puyNmirk20xRGg1Qm1khWm51fv0ofpaqoZddH-87afA2Pgm1MrQKy1gNaLOuKYcIYZntQvwvU0hMs5hfaS4PrRCLsZDsp9OCaIxO4vaVNWDkKq1Dp_SrxG2-wQtaH0xwsvLXOMFszwHv0gXQVQf0dCWZ2em23xQ-oZfJ4PKQBYOVwX1oRrNWqqqRlrpNBUua6pZDVF-W7DhIWS7oogHz5S4tLXZFMy/https%3A%2F%2Faka.ms%2FLearnAboutSenderIdentification> > > > Dear all, > > I am performing a calculation for a negatively charged slab using > assume_isolated = 'esm' > esm_bc = 'bc1' > > Till qe-7.0 the scf calculation proceeds. However, from version 7.1 the > calculation stops with the following error: > "cannot have charge, when ESM-BC1". > > This is the consequence of a check by the "esm_check" subroutine. What I > fail to understand is that this check is also present in qe-6.8, > however, there the calculation doesn't stop. > Am I missing something? > Also why is this stopped from version 7.1. Are there any issues in the > previous versions regarding the implementations of the same? I thought > that this is an effective way to perform charged slab calculations. > > Any help in clarifying this will be highly appreciated. > > With regards, > Prasenjit > > > ___ > 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 > (http://secure-web.cisco.com/1wg-Sn_ZUMtTyRMZsJKyKizaSqviZGjuik7-lGVJ130wHC5m66P1pvQ-ZUMUrYeXMA3qovdkUqGYUVjeTA3Mtg8obh8En3oN8CaZYpId-5ugTnWdq_I3lPum3Z5dVkPCsx--ir1MrwJldToxCEhBi8JOASttShakfuwRQsrHgG1vXd8luY3SSSwp3WjTDfNaWMAcQmKCxEWh5k67PcPvMMSqvvWl5Ky4RllnaHPcD1sveD9rSkht8dgXkN0Pths4Vvy0lzUAxnVmnPiJUJrWnnwkgrRp5-bL5nzsis57bBSuGRHvuKSB2q76txY6-ehxL/http%3A%2F%2Fwww.max-centre.eu) > 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, +39-0432-558216 ___ 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
