Re: [QE-users] hp.x - appropriate way to handle single dopant
Dear Dr. HOUARI, Thank you for your reply. I did not correct the band gap in any system. I am hoping if I apply some U parameter to Zn-3d, Co-3d and maybe to S-3p, I can capture the physics better. In this pursuit, some V parameter might also be an option. But this is not the problem I am facing. I am facing problem on how to obtain these U and V values. For undoped, periodic system, we can get the value using hp.x with simple unit cell. But the problem is for aperiodic doped system like the one I have. As you said, the calculated U from the 8 atoms ZnS unit cell is probably okay to use for 64 atoms supercell. But if I dope the unit cell (to get the U value of Co), this system (25% doping) is much different than the 64 atoms supercell (3.125% doping). And when I am trying to run hp.x directly for the 64 atoms (U applied only to the single Co), only a single iteration of 1 q point takes an hour using 2240 CPUs. So, it would take weeks to complete a calculation! I am hoping maybe I can calculate the U parameter separately for Co unit cell (i.e., Co-HCP) and then maybe for Zn and S from ZnS unit cell. But I have no rationale to support that it should work. And also the inter-site parameters cannot be obtained following this. Sincerely, Abdul On 5/21/2024 7:03 PM, Abdesalem Houari wrote: Dear Abdul Muhaymen, You say that your results are fine, except the band gap ! How did you correct it in pure ZnS, before Co-doping ? The most commun way in DFT is hybrid functionals (like HSE 06), which obviously are very demanding in computational cost. So the DFT+U (+V) could be a nice alternative. Here I think you might need on-site U not only for Co, but also for Zn (and as you said may be S). Since ZnS is a band insulator and covalent compound, the inter-site V could play an important role. In principle U and V parameters are neither transferable nor universal, but in your case ( calculated U from 8 atoms unit cell to use in 64 atoms supercell), Iguess it should be OK ! Best regards = Dr. Abdesalem HOUARI --- Department of physics, Theoretical Physics Laboratory University of Bejaia-06000. Algeria. E-mail: abdeslam.hou...@univ-bejaia.dz & habds...@yahoo.fr https://sites.google.com/site/houariabdeslam/homepage === On Tuesday, 21 May 2024 at 04:17:30 am GMT+1, Abdul Muhaymin via users wrote: Hello all, I am investigating single TM dopant in wide band gap semiconductors such as Co in ZnS. I am using a 64 atoms supercell where I replaced one of the Zn atom with a Co atom. I tested several convergence with respect to the supercell size. My results seem fine except the band gap. Now I want to apply the U correction to that Co-3d (and maybe to S-2p). For this, is it possible to use the unit cell (8 atoms) and run hp.x to get the U values? Or do I have to run hp.x with the large supercell (2*2*2 unit cell=64 atoms)? Also, at the beginning of our studies, during the structural relaxation phase, we first found our lattice parameter for the host semiconductor from multiple scf calculations and subsequently running an eos analysis (ev.x). Then we ran relax calculation but not vc-relax. We keep this lattice parameter constant and when introducing new dopants, we only vary the atomic positions (calculation='relax'). In this case, when running hp.x, could we replace the vc-relax calculation with relax calculation to self-consistently get the U values? Thanks, Abdul Muhaymin Graduate (MS) student, Materials Science and Nanotechnology Bilkent University, Ankara. ___ 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] hp.x - appropriate way to handle single dopant
Hello all, I am investigating single TM dopant in wide band gap semiconductors such as Co in ZnS. I am using a 64 atoms supercell where I replaced one of the Zn atom with a Co atom. I tested several convergence with respect to the supercell size. My results seem fine except the band gap. Now I want to apply the U correction to that Co-3d (and maybe to S-2p). For this, is it possible to use the unit cell (8 atoms) and run hp.x to get the U values? Or do I have to run hp.x with the large supercell (2*2*2 unit cell=64 atoms)? Also, at the beginning of our studies, during the structural relaxation phase, we first found our lattice parameter for the host semiconductor from multiple scf calculations and subsequently running an eos analysis (ev.x). Then we ran relax calculation but not vc-relax. We keep this lattice parameter constant and when introducing new dopants, we only vary the atomic positions (calculation='relax'). In this case, when running hp.x, could we replace the vc-relax calculation with relax calculation to self-consistently get the U values? Thanks, Abdul Muhaymin Graduate (MS) student, Materials Science and Nanotechnology Bilkent University, Ankara. ___ 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] Difference between data file saved inside outdir
Hello all, After a spin-polarized scf calculation, I have several files such as wfcup#.hdf5, wfcdw#hdf5 etc in in outdir/prefix.save. The number of the files are equal to the 2*number of k points. However, after nscf calculation, I am getting more data files in the outdir (not in outdir/prefix.save). I have N number of prefix.wfc* files where N is the number of processor I used. What is the difference between these two type of files? Are they both wavefunction? If I delete them, will there be any problem? Sincerely, Abdul Muhaymin, Graduate student, Bilkent University, Ankara. ___ 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] which data files need to be saved for assuring reproducibility?
Hello users, I have done some calculations using QE (used pw.x, dos.x, bands.x, pp.x). I want to make sure that my results are reproducible. In this case, which data files should I keep forever? So far I am keeping all the data files in the outdir directory. I noticed that inside the outdir, I have another prefix.save directory where I have several files in .hdf5 format for up and down wave functions (wfcup*.hdf5 and wfcdw*.hdf5). I guess these are the wave function which I will keep. But I also see that in some outdir, I have N number of prefix.wfc* files where N is the number of processor I used. These files are generated not after relax or scf calculation I guess but after nscf calculation or dos.x post-processing, probably. What is the difference between these two type of files? and which ones should be stored forever to assure reproducibility? I am using version 7.2 for calculation using 56 cores and 7.3 for post-processing (dos.x/pp.x) using 10 cores. Sincerely, Abdul Muhaymin, Graduate student, Institute of nanotechnology and material science, National nanotechnology research center, Bilkent University, Ankara. ___ 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] pw.x - choosing starting_magnetization value for specific expected total magnetization
Thanks Guido. I understand this starting_magnetization switch now. I wasn't using DFT+U since I first wanted to see what happens without any U correction and planned to use U correction later. But this is a good suggestion to set a near 0 U value to have the occupation matrix in the output. I will try this. Thank you Sincerely, Abdul On 2/21/24 18:37, Abdul Muhaymin wrote: Hello QE users, As I understood that thestarting_magnetization is used to break the spin symmetry and can affect the solution. When I did a simple calculation changing starting_magnetization, it always converged to the same ground state. However, I noticed that for other structures, this is not the case. Since there are many local minima, the starting_magnetization value determines on what magnetic solution the calculation converges to. So my question is then how we should choose it? For example, I am trying to simulate a Cu dopant in ZnS. Since Cu2+ has 9 electron in its 3d subshell, a neutral dopant then only has 1 unpaired electron. So, should I expect 1 Bohr mag/cell? When I set tot_charge=-1 to simulate a charged defect, I got everything as 0. as expected since there will be no unpaired electron. But simulating the neutral dopant, I am getting 0.00 total and absolute magnetization. Inspecting the projwfc.x output, I see that the dopant atom has 0.0018 polarization. Why is this the case? Why not the polarization is 1.00 or close to 1? My second question is how I can correctly convert my expected magnetization to starting magnetization value. For example, if I expect the magnetization per cell to be 3 Bohr magneton, what should I choose as the starting_magnetization? It seems total magnetization, absolute magnetization, polarization etc. are in Bohr magneton unit but not the starting_magnetization. I cannot choose starting_magnetization = 3 since it should be between -1 to +1. So, how to choose starting_magnetization in this case? Sincerely, Abdul Muhaymin, Graduate(MS) Student, Institute of Materials Science and Nanotechnology, Bilkent University, Ankara ___ 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] pw.x - choosing starting_magnetization value for specific expected total magnetization
Hello QE users, As I understood that thestarting_magnetization is used to break the spin symmetry and can affect the solution. When I did a simple calculation changing starting_magnetization, it always converged to the same ground state. However, I noticed that for other structures, this is not the case. Since there are many local minima, the starting_magnetization value determines on what magnetic solution the calculation converges to. So my question is then how we should choose it? For example, I am trying to simulate a Cu dopant in ZnS. Since Cu2+ has 9 electron in its 3d subshell, a neutral dopant then only has 1 unpaired electron. So, should I expect 1 Bohr mag/cell? When I set tot_charge=-1 to simulate a charged defect, I got everything as 0. as expected since there will be no unpaired electron. But simulating the neutral dopant, I am getting 0.00 total and absolute magnetization. Inspecting the projwfc.x output, I see that the dopant atom has 0.0018 polarization. Why is this the case? Why not the polarization is 1.00 or close to 1? My second question is how I can correctly convert my expected magnetization to starting magnetization value. For example, if I expect the magnetization per cell to be 3 Bohr magneton, what should I choose as the starting_magnetization? It seems total magnetization, absolute magnetization, polarization etc. are in Bohr magneton unit but not the starting_magnetization. I cannot choose starting_magnetization = 3 since it should be between -1 to +1. So, how to choose starting_magnetization in this case? Sincerely, Abdul Muhaymin, Graduate(MS) Student, Institute of Materials Science and Nanotechnology, Bilkent University, Ankara ___ 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] pw.x - understanding magnetization
Hello QE users, I am trying to understand how to appropriately set the |starting_magnetization |value and how to interpret the output related to magnetization in the pw.x. I tested for a simple system (BCC Fe) with various |starting_magnetization |and observed that it doesn't matter. The |total energy, total magnetization, and absolute magnetization| values remain the same. So, does this mean any |starting_magnetization |value can be used? Secondly, when I observe the "|Magnetic moment per site (integrated on atomic sphere of radius R)|" values, and sum up all the magnetic moments, it doesn't match with the |total magnetization| or |absolute magnetization| which is reported at the end |(in Bohr mag/cell)|. The sum of magnetic moment per site is always less than the sum of total magnetization. What could be the reason for this? Is this because magnetic moment per site is integrated on atomic sphere of radius R where R < 1? Sincerely, Abdul Muhaymin, Graduate(MS) Student, Institute of Materials Science and Nanotechnology, Bilkent University, Ankara.___ 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] DFT-1/2 calculation using QE
Hello everyone, I saw that DFT-1/2 method can improve electronic properties (with some caveat) without increasing computational cost with respect to ordinary DFT. For VASP, there are programs available that can prepare the POTCAR for DFT-1/2 calculation. My question is does QE also have some program to modify the pseduopotential to run a DFT-1/2 calculation? In general I am interested on how to proceed with QE for DFT-1/2 calculation. I haven't found any material on this such as hands-on tutorial/sections in the QE schools. Any direction is greatly appreciated. Sincerely, Abdul Muhaymin Graduate student, Institute of Material Science and Nanotechnology, Bilkent University. ___ 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] error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory
Dear users, I am trying to run pw.x in a cluster (centos) that requires loading three modules: intel, impi, and quantum-espresso. Now, I am getting an error saying: `pw.x: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory`. According to the instruction I find in QE troubleshooting guide, I added the `export LD_LIBRARY_PATH=/lib64:"$LD_LIBRARY_PATH"` line in my script because libfftw3.so.3 exists in `/lib64/`. However, it still gives the same error. So, I ran a `ldd pw.x` command to check what happened, and I saw that: ... (truncated ) libmkl_scalapack_ilp64.so => /opt/intel/compilers_and_libraries_2019.4.243/linux/mkl/lib/intel64_lin/libmkl_scalapack_ilp64.so (0x7fe15c6ea000) libfftw3.so.3 => Not found ... (truncated) That means only libfftw3.so.3 is not linked. When I checked the value of $LD_LIBRARY_PATH, it successfully added the `/lib64` part but still I get the same error. What could be the reason for this error? Do I need to recompile QE? The version of QE running is 6.4.1. Thanks. Sincerely, Abdul Muhaymin Undergraduate – Bilkent University ___ 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
