[QE-users] HOWTO build QE for Windows by cygwin64
Hi I had extended my CASTEP Windows build manual by Quantum Espresso chapters, so it works now for both codes ... The manual is designed for total beginners with code compilation (a lot of screen-shots) ... You can download it as PDF from this link: https://ulozto.cz/tamhle/uJrACumzRbe3#!ZGp3ZQR2ZwEwLJH5AJZ3BTZ1AzZmAmAyLyWFJyEwAyt5nmEuZj== Use the turtle icon for free non protected download ... I was unfortunately (trying very hard) not able to make a stable QE 7.1 parallel build (OpenMP nor MPI) after a lot of work and experiments. OpenMP works with older QE sources, MPI gives the same error with all QE versions ... So only serial version works for QE 7.1 The HOWTO mentions how to reproduce the OpenMP and MPI QE crashes Michal Husak UCT Prague ___ 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] Building Qunatum Espresso Windows binary by cygwin64 HOWTO ...
Hi I had made for CASTEP code users a detailed manual, how to create a Windows CASTEP binary form source code by the help of cygwin64 environment ... Almost the same approach can be used for building Windows Quantum Espresso (with some addition notice included as PS in the manual) ... The manual is for CASTEP, but all steps related to the cygwin64 environment setup are identical ... If anybody is interested in the procedure (for CASTEP, QE required to change a few things as described in QE readme) the link for download is: https://ulozto.cz/tamhle/RfzKA50fM7Mf/name/Nahrano-5-1-2023-v-10-44-48?view=gallery&sort=exif_date#!ZGAvZwR2ATRkAwIvA2Z4AQWvMTWvBJMAA003FaycA0SKpTWwAN== Michal Husak UCT Prague ___ 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] Again Fatal error in PMPI_Comm_free
Hi I had recompiled QE for a sueprocmputer using Intel Fortran ... Ale tests (including MPI version) pass through without any errors ... When I run QE on some real data I get (1 node 128 MPI parallelization) : Fatal error in PMPI_Comm_free: Invalid communicator, error stack: This issue was already mentioned by Mr. Yang LIU in relation to single / multiple type of atom calculation ... Solution was to run pw.x -ndiag 1 With -ndiag 1 the error was handled on my side as well ... But I do work with multiple atoms from beginning so it can not be the same problem ... Any idea what can be wrong ? Michal Husak UCT Prague ___ 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] m4 command missing - 7.1 QE does not compile libfox
Hi I had just found an interesting difference between QE 7.0 and QE 7.1 QE 7.1 require m4 command (C preprocesor) presence to be able to compile libfox . This command is sometimes not installed as default (eg. in cygwin64) ... Adding m4 to environment installation solves the issue ... Michal ___ 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] Proper setup for organometalic system ....
Hi alll I was up to now working with fully organic system - so I handled then with fixed occupany ... I was working with: OCCUAPTIONS: fixed I need to work now with organometalic systems - they contain group like e.g. Fe O6 (iron coordinated by 6 oxygen + organic parts) ... I belive it is still an insulator, but the fixed occupancy lead to non-converging SCF (oscillating between 2 states) ... Can anybody tell me what everything do i need to change in the setup to handle organometalic compounds ? Is simple following modification everything I need to do ?: OCCUAPTIONS: smearing Michal Husak UCT Prague ... ___ 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] Defining C diamond structure cp.x
Hi As i had mentioned we intensively work on a graphical user interface for QE targeted primary on crystallographic data processing (CIF input) This is in put for pw.x (not cp.x). I hope this is not a problem ... Functional Diamond input file for QE generated by our code CheckCif-DFT follows ... As you see: No ibraw experiments necessary, QE automatically chose correct ibraw from the space_group = 227 line ... Only 1 atom position required: ATOMIC_POSITIONS crystal_sg C 0 0 0 This is I belive the diamond description with should be preferred, because it reflects you need to operate only with 1 atom (everything else is space-group generated) ... Please keep in mind QE will internally transform the F cell to P cell (to speed up the calcluation) and it doe snot transform the results back to the F cell ... So e.g. lattice energy will be 4x less (P cell) thna in F cell ... The input performs vc-relax lattice optimziation, please modifiy the pseudo_dit and outdit to amke it working ... ### ## Generated by CheckCif-DFT ## ### &CONTROL pseudo_dir = 'M:/MyProject/C#2017/Fnukal/bakalarka - 25.2.2022/CheckCif-DFT/CheckCif-DFT/bin/Debug/qe/pseudo/' outdir = 'M:/MyProject/C#2017/Fnukal/bakalarka - 25.2.2022/Examples/DIAMOND_AMS_DATA/out/' prefix = 'aiida' calculation = 'vc-relax' etot_conv_thr = 1.00d-03 forc_conv_thr = 1.00d-02 tprnfor = .true. tstress = .true. disk_io = 'none' / &SYSTEM space_group = 227 A = 3.56679 B = 3.56679 C = 3.56679 cosBC = 0 cosAC = 0 cosAB = 0 nat = 1 ntyp = 1 ecutrho = 5.5000d+02 ecutwfc = 5.5000d+01 occupations = 'fixed' vdw_corr = 'Grimme-D3' / &ELECTRONS conv_thr = 1.d-07 / &IONS ion_dynamics = 'bfgs' / &CELL cell_dynamics = 'bfgs' / ATOMIC_SPECIES C 12.0106 C.pbe-n-rrkjus_psl.1.0.0.UPF ATOMIC_POSITIONS crystal_sg C 0 0 0 K_POINTS automatic 2 2 2 0 0 0 ___ 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] Non consistent C->P, P->C cell transformation generated by Quantum Espresso
Hi When the input to QE is done through space group number, the centered space groups (C,I,F) in conventional cells are automatically transferred by QE to primitive cell P (to speed up the calculation) ... We need to transfer the QE result back to the original conventional cell (to be able to compare the data from standard CIF file with QE results) ... I will be easy if QE will use always the same matrix for C->P transformation ... Unfortunately this is not the case QE use different matrix like: 0.5 -0.5 0 0.5 0.5 0 0 0 1 than it use 0.5 0.5 0 0.5 -0.5 0 0 0 1 e.t.c. Is there any way how to easy decipher form QE output what transformation was done with the input data (what matrix did QE chosen for the given C->P transformation) ? It is a pity QE does not list the transformation was done, nor what matrix was chosen ... Can this be done e.g. by calculating the transformation matrix between the P cell parameters and original C conventional parameters (we hope at lest the transfer of cell to Cartesian vector is done always identically) ? Michal Husak ___ 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] Quantum espresso 7.0 Windows binary ....
I had see the new Qunatum Espresso WWW ... On the Download section disappeared all links to binary files for any platform ... I know that for the Windows was a link to old QE 6.4.1 , but it was at least something for users not experienced enough to make a build ... Questions: 1) Does anybody have experiences/manual how to build QE 7.0 for Windows (giving optimal performance = Intel MKL + Microsoft MPI) ? 2) Are there any planes to put on the QE WWW an "official" Windows binary ? I am able to create a Windows QE binary myself (by cygwin64 environment), but the performance and stability is not so good as the 6.4.1 build made by somebody, who understand the rebuilding better than I do ... So I belive to have some optimized Windows binary made by some expert will be strongly appreciated by all users ... Michal Husak UCT Prague ___ 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] QE automatically converge centered cell to primitive ?
Hi We had entered inside QE a structure described by fractional coordinates (asymmetric unit cell) and space group (C 2/c ) From the output we see QE had itself transformed the structure to another space group and unit cell (probably P 2/c triclinic system) to get speed of calculation Question: - does QE anywhere mention, this transformation was done ? - does it anywhere give the used transformation matrix ? We simply need to reconstruct from the QE the atom positions corresponding to the original CIF data Michal Husak UCT Prague ___ 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] libxc needed for this functional - QE bulid with libxc
Paolo , you are right ... It is required to add all 3 option in the ./configure to make the build correct --with-libxc(yes|no) Use libXC for some XC functionals (default: no) --with-libxc-prefix=DIR Directory where libxc was installed. --with-libxc-include=DIR Directory where libxc Fortran headers were installed. It is not clear from the help, that only adding: --with-libxc-prefix=DIR is not sufficient ... I had generated now pw.x 3x bigger than standard pw.x accepting the SCAN functional ... Michal The final binary differs from the one build without libxc so the libxc linking was hopefully successful ... it wasn't: Error in routine set_dft_from_name (2): libxc needed for this functional Paolo ___ 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] libxc needed for this functional - QE bulid with libxc
Hi I had successfully compiled libxc and than recompiled QE 6.8 with the --with-libxc-include=\opt\etsf option of the ./configure The final binary differs from the one build without libxc so the libxc linking was hopefully successful ... After requesting SCAN functional I sill get following message: %% Error in routine set_dft_from_name (2): libxc needed for this functional %% How is it possible with QE build with the libxc ? Any idea what to check ? Michal ___ 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] there are process with no planes
I am trying to run QE 6.8 on a supercomputer node with 128 cores ... I use pure MPI parallelization Run on 16 and 32 cores works OK ... Run on 64+ cores ends with following error: Error in routine fft_type_set (6): there are processes with no planes. Use pencil decomposition (-pd .true.) Can anybody explain what it means ? Is my system to simple to it can not feed all cores ? Where can I enter the -pd .true. option ? Michal Husak UCT Prague ___ 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] Error in routine good_fft_order (1):
Hi I had recompiled QE 6.7 and 6.8 with cygwin under Windows ... If I run the result on a test data i get for both the message below short after startup ... Any suggestion what to do ? Related question - does anybody have pre-compiled Windows binary of QE, preferably with SCAN functional support (with libxc added) ? Michal Husak UCT Prague %% Error in routine good_fft_order (1): invalid np %% stopping ... ___ 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] Non standard space groups usage with Qunatum Espresso
Hi The Quantum Espresso makes possible to enter structure, by the help of space group. Namely eg: space_group = 19 . ATOMIC_POSITIONS crystal_sg C 0.56050 0.14143 0.60159 Unfortunately the CIF description of structures often use non-standard space group settings. Typicaly: space_group = 14 is standardly described as P 21/c But it can be P 21/n, P 21/b,P 21/a ... etc ... (totaly 1 standard and 8 non-standard setting) The non-standard settings can be identified only through Herman-Mogen symbol, not by Space Group number ... So what is the optimal solution for non -standard space group setting ? a) transfer structure to standard space group setting b) do not use space gropu and generate all atoms in the unit celll by external software c) support symmetry input by HermanMogen symbols (not only 230 grpusp but cca 500 possibel descriptions) in future QE versions ? Michal UCT Prague ___ 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] Rcompilation of QE 6.7 by Cygwin 64 - result does not work ...
Hi I had recompiled QE 6.7 under Cygwin 64 with gl fortran ... (Windows 7 ) ... Compilation and installation worked without any error ... Than I had tried to process a simple l-alanin test input witch works OK with Windows 7 6.4 QE binaries. Otutup with error message follow bellow Error in routine good_fft_order (1): invalid np Any idea what is wrong ? Can enybody eventualy offer 6.7 QE binary compiled for Microsoft MPI with added link to the XC library (I nedd SCAN fucntional working) ... Michal Michal@Krtek /cygdrive/f/qe_projects/test_cygwin64/LALA_space_group $ pw.x < LALA_scf.in Program PWSCF v.6.7MaX starts on 16Apr2021 at 15:19:45 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017); URL http://www.quantum-espresso.org";, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/quote Parallel version (MPI), running on 1 processors MPI processes distributed on 1 nodes Waiting for input... Reading input from standard input Current dimensions of program PWSCF are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 4 Max angular momentum in pseudopotentials (lmaxx) = 3 file C.pbe-n-kjpaw_psl.1.0.0.UPF: wavefunction(s) 2S 2P renormalized file O.pbe-n-kjpaw_psl.0.1.UPF: wavefunction(s) 2P renormalized Subspace diagonalization in iterative solution of the eigenvalue problem: a serial algorithm will be used %% Error in routine good_fft_order (1): invalid np %% stopping ... -- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- Michal@Krtek /cygdrive/f/qe_projects/test_cygwin64/LALA_space_group $ ___ 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] How to quess computational expenses for small organic molecular crystals (PBE0 functional) ...
Hi I need to get a guess for computational cost for small organic crystalline system + PBE0 functional ... I had run multiple scf of different similar system on identical HW (24 core node) ... From my understanding, the computational time should be approximately proportional to N^3 The N should be number of electrons handled by the calculations ... The question is what should be used as N: 1) I belive it should be the number of valance electrons calculated for asymmetric unit cell content. e.g. for crystalline urea (C N2 O1 H4) crystallizing in P -4 21 m (4 molecule in unit cell) the N shoudl be1*4+2*5+1*6+4*1 = 24. It should be not 4*24 because the code utilize symmetry not to calculate symmetrically dependent molecules ... The N should not include non-valence electrons, become they are effectively handed by pseudo-potentials ... 2) I belive the k-points should be include in form Nkpoits * N^3 to get a complexity guess, because each k-point is just an additional calculation of a N^3 system ... Unfortunately my result show I am wrong ... I get up to 50x discrepancy in calculation cost than guess from 1) and 2) assumption ... The starting structures should be OK according geometry (good X-ray result). I perform only single point energy calculation ... Any related idea ? Michal ___ 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] How does pw.x make the cell choice for space group No.12 with unique axis b ?
You should describe your structure by the space group setting. IBRAW and Wickoff position will be handled automatically + you can copy the coordinates directly form the CIF Dear QE experts, I find it confusing in the description Wyckoff position specifications in the card ATOMIC_POSITIONS. https://www.quantum-espresso.org/Doc/INPUT_PW.html For space group No.12 under the convention unique axis b, there are three cell choices. The Wyckoff position 4i has different forms for the three choices, namely (according to ITA) UNIQUE AXIS b, CELL CHOICE 1 4i x,0,z ; x+1/2,1/2,z ; xb,0,zb ; xb+1/2,1/2,zb UNIQUE AXIS b, CELL CHOICE 2 4i x,0,z ; x,1/2,z+1/2 ; xb,0,zb ; xb,1/2,zb+1/2 UNIQUE AXIS b, CELL CHOICE 3 4i x,0,z ; x+1/2,1/2,z+1/2 ; xb,0,zb ; xb+1/2,1/2,zb+1/2 (xb means x-bar) If I am to write the ATOMIC_POSITIONS card, how should I specify the parameters x and z? How do I know that pw.x takes CELL CHOICE 1/2/3 ? Thank you for your help. Best regards, Yunlong Lian ___ 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] Sub optimal performance on 32 core AMD machine
I had purchased a new PC with 2x 16 core AMD EPYC processors . 64 cores with hyper threading ... I was hoping my QM programs (Quantum Espresso, CASTEP) will run on the new system faster, than on my old 4 core i7 Intel machine (8 year old) To my great surprise, the opposite is almost true :-(. My main task is scf and geometry optimization of middle sized organic molecular crystals (abut 100 C,H,N per unit cell) ... I was playing with OpenMPI/OpenMP setup changes ... I was playing with the secret MKL_DEBUG_CPU_TYPE=5 parameter (responsible for slow run of Intel MKL compiled code on AMD) ... Nothing helps, the best speed is obteined when I use only 4 cores (OpenMPI or OpenMP - results similar) ... Using 16 or 32 cores gives almost no benefit ... The CPU load for run on 1/4/816/32 coresponds to the nubmer of CPU set = they try to do something ... Any idea what I should check, try optimize ? Maybe the bottleneck is memory access, not CPU power (I have 128 GB almost not used RAM) ? Michal Husak UCT Prague ___ 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] Incorrect identification+generations of atoms in specialpositions (space_group options used).
Dear C. Conesa I was afraid I am faced exactly with the same problem you mentioned in your contribution ... But had identified 2 problems on my side instead : 1) I forget to use uniqueb = .true. => incorrect identification of special positions 2) after correcting mistake 1) I had used incorrect CIF with multiple inclusion of the same atoms (CSD Mercury Bug/Future related to molecules completed by symmetry operations). If you can E-mail me directly (hus...@vscht.cz) your CIF file, + QE inoput file with potentials in /potential sub directory I can try to analyze your problem ( I am primary a crystallographer teaching symmetry operations e.t.c.) ... Michal nguage: es-ES Dear all, Last 11th of september I sent a similar question, but the answer, provided by Paolo Giannozzi, did not clarify much. I can say that in that occasion I was using qe-6.5. Should I use qe -6.6? Regards, José C. Conesa ___ 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] Incorrect identification+generations of atoms inspecialpositions (space_group options used).
Problem solved on my side ... I apology for disturbing :-). The CSD Mercury software added to the CIF file from some reason some symmetry generated atoms ... It probably try to save the whole molecule (1/2 generated by mirror operation) = create incorrect cif with duplicated atoms positions ... So e.g. one O atoms was found in the file 2x (but with different x,y,z so manual identification was complex)... It error was clear from total number of symmetry independent atoms in the CIF (correct 40 , incorrect 73) ... I can confirm QE had correctly identified the Zn, S, C placed on the mirror operation symmetry and it did not generated them 4x, but correctly 2x It tells me atom 7 and 150 overlap, 7 should be O -0.503 0.4513 0.3517 As for 150 I don’t know, not very easy to spot in a short time. Pietro ___ 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] Incorrect identification+generations of atoms in specialpositions (space_group options used).
Hi Pietro I use 6.4.1 (the latest one for witch Windows binary are available for download from QE listed WWW). The whole non functional input follows. If you can check this, it will be very helpful. Michal &CONTROL calculation = 'scf' etot_conv_thr = 1.46d-03 forc_conv_thr = 1.00d-04 outdir = './out/' prefix = 'aiida' pseudo_dir = './pseudo/' tprnfor = .true. tstress = .true. verbosity = 'high' / &SYSTEM ecutrho = 4.80d+02 ecutwfc = 6.00d+01 uniqueb = .true. space_group = 11 ! 1 21/m 1 A = 6.1103 B = 20.6990 C = 11.7877 cosBC = 0 ! alpha cosAC = -0.092405345 ! beta cosAB = 0 ! gamma nat = 73 ntyp = 6 occupations = 'fixed' / &ELECTRONS conv_thr = 2.92d-08 electron_maxstep = 80 mixing_beta = 4.00d-01 / ATOMIC_SPECIES C 12.011 C.pbe-n-kjpaw_psl.1.0.0.UPF H 1.00794 H.pbe-rrkjus_psl.1.0.0.UPF N 14.0067 N.pbe-n-radius_5.UPF O 15.9994 O.pbe-n-kjpaw_psl.0.1.UPF S 32.066 s_pbe_v1.4.uspp.F.UPF Zn 65.39 Zn_pbe_v1.uspp.F.UPF ATOMIC_POSITIONS crystal_sg Zn 0.37830 0.2500 0.24657 S 0.8360 0.2500 0.58850 S 0.87002 0.2500 -0.03294 O -0.1486 0.54916 0.09311 O -0.503 0.4513 0.3517 N 0.5387 0.2500 0.3965 N 0. 0.2500 0.1203 N 0.1723 0.32744 0.24257 N -0.2534 0.54195 0.17640 N -0.3909 0.49661 0.32605 C 0.6628 0.2500 0.4774 C 0.6876 0.2500 0.0565 C 0.0542 0.33986 0.3306 H 0.0712 0.3127 0.3936 C -0.0898 0.39033 0.3324 H -0.1703 0.3965 0.3947 C -0.1145 0.43227 0.24017 C 0.0033 0.41927 0.1484 H -0.0113 0.4456 0.0842 C 0.1430 0.36680 0.1531 H 0.2207 0.3585 0.0905 C -0.2567 0.48945 0.2472 C -0.4264 0.58903 0.2024 C -0.4780 0.56359 0.3210 C -0.6128 0.57937 0.1075 H -0.6679 0.5360 0.1105 H -0.5579 0.5867 0.0348 H -0.7292 0.6094 0.1176 C -0.3382 0.65732 0.1980 H -0.3119 0.6677 0.1211 H -0.2031 0.6605 0.2462 H -0.4437 0.6869 0.2240 C -0.3517 0.59922 0.4198 H -0.1986 0.6008 0.4076 H -0.3693 0.5769 0.4897 H -0.4077 0.6424 0.4242 C -0.7202 0.56226 0.3416 H -0.7356 0.5461 0.4168 H -0.7984 0.5346 0.2864 H -0.7794 0.6052 0.3346 O -0.1486 -0.04916 0.09311 O -0.503 0.0487 0.3517 N 0.1723 0.17256 0.24257 N -0.2534 -0.04195 0.17640 N -0.3909 0.00339 0.32605 C 0.0542 0.16014 0.3306 H 0.0712 0.1873 0.3936 C -0.0898 0.10967 0.3324 H -0.1703 0.1035 0.3947 C -0.1145 0.06773 0.24017 C 0.0033 0.08073 0.1484 H -0.0113 0.0544 0.0842 C 0.1430 0.13320 0.1531 H 0.2207 0.1415 0.0905 C -0.2567 0.01055 0.2472 C -0.4264 -0.08903 0.2024 C -0.4780 -0.06359 0.3210 C -0.6128 -0.07937 0.1075 H -0.6679 -0.0360 0.1105 H -0.5579 -0.0867 0.0348 H -0.7292 -0.1094 0.1176 C -0.3382 -0.15732 0.1980 H -0.3119 -0.1677 0.1211 H -0.2031 -0.1605 0.2462 H -0.4437 -0.1869 0.2240 C -0.3517 -0.09922 0.4198 H -0.1986 -0.1008 0.4076 H -0.3693 -0.0769 0.4897 H -0.4077 -0.1424 0.4242 C -0.7202 -0.06226 0.3416 H -0.7356 -0.0461 0.4168 H -0.7984 -0.0346 0.2864 H -0.7794 -0.1052 0.3346 K_POINTS automatic 6 2 3 0 0 0 Hi which version of the code are you using ? with qe-6.6 using your parameters I got two positions site n. atom positions (alat units) 1 Zn tau( 1) = ( 0.4873906 2.5406690 1.4472625 ) 2 Zn tau( 2) = ( 0.3343454 0.8468897 0.4736359 ) With alat = 11.5468 a.u. alat = 11.5468 a.u. ibrav=-12 hope it helps greetings - Pietro Sent from <https://go.microsoft.com/fwlink/?LinkId=550986>Mail for Windows 10 From: <mailto:michal.hu...@vscht.cz>Michal Husak Sent: Thursday, November 12, 2020 10:34 AM To: <mailto:users@lists.quantum-espresso.org>users@lists.quantum-espresso.org Subject: [QE-users] Incorrect identification+generations of atoms in specialpositions (space_group options used). I ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Incorrect identification+generations of atoms in special positions (space_group options used).
I had carefully checked this mailing list and I had found several topic related to the same issue - QE generates multiple atoms for atoms in special positions. Not solved in any answer. What I mean: General position: x,y,z crystallographic position, atom not on a symmetry element (e.g. for spac egropu number 11, P21/m , 4 atoms are generated). Special position: eg 2e x,z, (for space group 11, 2 atoms should be generated). Atom is on the mirror element. I had a structure described by CIF information in following way: _symmetry_Int_Tables_number 11 _cell_length_a 6.1103(2) _cell_length_b 20.6990(10) _cell_length_c 11.7877(5) _cell_angle_alpha90.00 _cell_angle_beta 95.302(3) _cell_angle_gamma90.00 Zn 0.37830 0.2500 0.24657 The Zn is on the mirror This can be transferred to QE input: space_group = 11 uniqueb = .true. A = 6.1103 B = 20.6990 C = 11.7877 cosAB = 0 cosAC = -0.092405345 cosBC = 0 And: ATOMIC_POSITIONS crystal_sg Zn 2e 0.37830 0.24657 Or Zn 0.37830 0.2500 0.24657 Both input generate error = overlapped atoms. What is wrong ? Michal ___ 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
