Re: [QE-users] Doubt regarding vc relax and relax - Reg
I am a crystallographer using QE for crystal structure verification. If I do not know sure the lattice parameters (I work e.g. on structure prediction), I must do vc-relax ... If I know the lattice parameters experimentaly and I want to study something on a crystal with this parameter known (eg.calculate optical properies, ssNMR) I run relax only ... Michal From: users on behalf of singaravelan T R Sent: Sunday, April 18, 2021 1:42:14 PM To: users@lists.quantum-espresso.org Subject: [QE-users] Doubt regarding vc relax and relax - Reg Dear all, Thanks for the reply. From the reply. I understood that if I am very sure about lattice parameter from experimental XRD. Then I can proceed with relax. If I am unsure about lattice parameter then I should proceed with vc-relax. Is that correct? with thanks, Singaravelan T R ___ 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] ?????? Re?? Error happens after setting max_seconds in turbo_davidson.x
Dear Iurri, With ecut = 40, the restart files can be writtensuccessfully for both QE6.5 and QE6.7. ButI afraid I have to set ecut as 80 as this is the value leads to the convergece of "band edge". If do the turbo davidson calculation with ecut = 40, the result will be out of accuracy as this calculation is based on both occupied and unoccupied states, won't it? The problem is that the restart file cannot be written once ecut=80 used in scf calculation (even using QE6.7). Do you have any suggestion to solve this restart file problem without affecting the accuracy of the result. Thanks. Best, Weijie Zhou Weijie Zhou PhD student University of Leeds UK ---- ??: "Iurii TIMROV" http://people.epfl.ch/265334 From: users http://people.epfl.ch/265334 From: users https://drive.google.com/drive/folders/1djSkUZ2MkF0nKNntQgZJ8wt3b3IpmHs-?usp=sharing I am sure there is enough space and time for writing data for restart files after double check. Best, Weijie Zhou Weijie Zhou PhD student University of Leeds UK -- -- ??: "Iurii TIMROV" https://www.quantum-espresso.org/forum In particular: - which version of QE do you use? - provide all input and output files (so that we can reproduce your problem) Moreover: - make sure you have enough disc space to write the data for restart - make sure that the code has enough time to write the data to disc (i.e. compare max_seconds with the total time of the job) Once all this is clarified, the QE developers can have a closer look at your problem. HTH Iurii -- Dr. Iurii TIMROV Senior Research Scientist Theory and Simulation of Materials (THEOS) Swiss Federal Institute of Technology Lausanne (EPFL) CH-1015 Lausanne, Switzerland +41 21 69 34 881 http://people.epfl.ch/265334 From: 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] Re： ReĢš ReĢš Error happens after setting max_seconds in turbo_davidson.x
Dear Kazume NISHIDATE, t says that the QE6.7 does not recognize the XML file written by the QE6.5. You should start over from the beginning using the QE6.7. Yes, you are right. This problem has been solved. Thanks for your solution. Best, Weijie Zhou Weijie Zhou PhD student University of Leeds UK --原始邮件-- 发件人: "Quantum ESPRESSO users Forum" 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] QE calculation on AWS
Hello users, I am performing Slab relaxation and neb calculation including 40+ atoms. Currently I am running calculation on ComputeCanada server, but it has some issues so am switching to AWS EC2 service. I would like assistance in choosing which instance best suites and reduces the calculation time for running such big QE calculation. Please suggest me with good options if any other possible. Thank You Regards, Rutika ___ 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] ReĢš ReĢš Error happens after setting max_seconds in turbo_davidson.x
Dear Weijie, It says that the QE6.7 does not recognize the XML file written by the QE6.5. You should start over from the beginning using the QE6.7. > 2021/04/19 5:28、飘 <508682...@qq.com>のメール: > > Error in routine read_xml_file (4): > fatal error reading xml file > best regards kazume NISHIDATE 敬具 西館数芽 nisid...@iwate-u.ac.jp kazume.nishid...@gmail.com ___ 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] Re?? Re?? Error happens after setting max_seconds in turbo_davidson.x
Dear Iurii, Thanks for your reply. I modified my input followed with your suggestion but ecut is set as 40 (30 cannot make convergence), and ran the calculation using QE6.5. It made restart file successfully. It seems that large memory contributed to big value of ecut leads to the problem. But in scf calculation, ecut of 40 is not good one as it lead to highest occupied/lowest unoccupied shitfed to 5.2276/5.4369 from4.8298/5.6383 (ecut 80). Besides, I tried to use QE6.7 with ecut 80, and other parameters for input files are same with yours. But new error occured when running turbo_davidson.x giving the error as Reading xml data from directory: ../../../tmp_Mo8O26_davidson_size20_e-4_nosmearing_QE6.7/Mo_O.save/ Message from routine qes_read:magnetizationType: do_magnetization: wrong number of occurrences Message from routine qexsd_readschema : error reading output_obj of xsd data file %% %% %% Error in routine read_xml_file (4): fatal error reading xml file %% Do you have any clue about this error? The inputoutput files for this calcualtion could be accessed in https://drive.google.com/drive/folders/1lJTr7WdcOf73Bk36fSxP-yHZk52iDqGS?usp=sharing; Thanks, Weijie Zhou Weijie Zhou PhD student University of Leeds UK ---- ??: "Iurii TIMROV" http://people.epfl.ch/265334 From: users http://people.epfl.ch/265334 From: users https://drive.google.com/drive/folders/1djSkUZ2MkF0nKNntQgZJ8wt3b3IpmHs-?usp=sharing I am sure there is enough space and time for writing data for restart files after double check. Best, Weijie Zhou Weijie Zhou PhD student University of Leeds UK -- -- ??: "Iurii TIMROV" https://www.quantum-espresso.org/forum In particular: - which version of QE do you use? - provide all input and output files (so that we can reproduce your problem) Moreover: - make sure you have enough disc space to write the data for restart - make sure that the code has enough time to write the data to disc (i.e. compare max_seconds with the total time of the job) Once all this is clarified, the QE developers can have a closer look at your problem. HTH Iurii -- Dr. Iurii TIMROV Senior Research Scientist Theory and Simulation of Materials (THEOS) Swiss Federal Institute of Technology Lausanne (EPFL) CH-1015 Lausanne, Switzerland +41 21 69 34 881 http://people.epfl.ch/265334 From: 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] Projected Band structure
Dear QE users, As suggested i have gone through the example files of PP in quantum espresso. But still i am not able to understand to generate projected bands although i have tried for it but i have got lowdin charges instead. I will be thankful for the help in this regard. regards Mayuri Mayuri Bora INSPIRE Fellow Advanced Functional Material Laboratory Tezpur University Napaam http://www.tezu.ernet.in/afml/ * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. ___ 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] Doubt regarding vc relax and relax - Reg
Dear all, Thanks for the reply. From the reply. I understood that if I am very sure about lattice parameter from experimental XRD. Then I can proceed with relax. If I am unsure about lattice parameter then I should proceed with vc-relax. Is that correct? with thanks, Singaravelan T R ___ 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] Why magnetic system give zero magnetic moment for all atoms
Dear Jibiao Li IMHO, your system is not "obviously" magnetic as it has an even number of electrons that may be fully paired. If you want to calculate energy differences between different accessible spin states, you should also fix the tot_magnetization value of your system to meaningful values, e.g. 0, 2, ... PBE might not be the best functional to calculate such differences, anyway. You may want to read this old but very interesting paper to have an idea of theoretical limits of DFT i the case of small inorganic molecules chemisorbed by Fe (a most relevant biological topic!) https://pubs.acs.org/doi/10.1021/jp070549l HTH Giuseppe Quoting Jibiao Li : Dear All, I am performing spin polarized calcualtion with the developer version. My system is CO adsorpion on a single Fe atom embeded in a single sheet of graphene. Obviously this system is magetic. However, the calculation gives zero magnetic moments for all atoms (see below). Is it normal or is there anything wrong with my calculations ? negative rho (up, down): 1.127E-03 1.127E-03 Magnetic moment per site (integrated on atomic sphere of radius R) atom 1 (R=0.038) charge= 2.6752 magn= 0. atom 2 (R=0.038) charge= 0.9377 magn= -0. atom 3 (R=0.052) charge= 11.7120 magn= -0. atom 4 (R=0.044) charge= 2.4585 magn= -0. atom 5 (R=0.044) charge= 2.4585 magn= -0. atom 6 (R=0.044) charge= 2.4583 magn= 0. atom 7 (R=0.044) charge= 2.4583 magn= 0. atom 8 (R=0.038) charge= 0.9651 magn= 0. atom 9 (R=0.038) charge= 0.9693 magn= 0. atom 10 (R=0.038) charge= 0.9693 magn= 0. atom 11 (R=0.038) charge= 0.9701 magn= 0. atom 12 (R=0.038) charge= 0.9598 magn= -0. atom 13 (R=0.038) charge= 0.9701 magn= 0. atom 14 (R=0.038) charge= 0.9776 magn= 0. atom 15 (R=0.038) charge= 0.9562 magn= 0. atom 16 (R=0.038) charge= 0.9562 magn= 0. atom 17 (R=0.038) charge= 0.9838 magn= 0. atom 18 (R=0.038) charge= 0.9838 magn= 0. atom 19 (R=0.038) charge= 0.9907 magn= 0. atom 20 (R=0.038) charge= 0.9747 magn= 0. atom 21 (R=0.038) charge= 0.9625 magn= 0. atom 22 (R=0.038) charge= 0.9747 magn= 0. atom 23 (R=0.038) charge= 0.9647 magn= -0. atom 24 (R=0.038) charge= 0.9688 magn= 0. atom 25 (R=0.038) charge= 0.9688 magn= 0. atom 26 (R=0.038) charge= 0.9746 magn= -0. atom 27 (R=0.038) charge= 0.9623 magn= 0. atom 28 (R=0.038) charge= 0.9746 magn= -0. atom 29 (R=0.038) charge= 0.9904 magn= -0. atom 30 (R=0.038) charge= 0.9837 magn= -0. atom 31 (R=0.038) charge= 0.9837 magn= -0. atom 32 (R=0.038) charge= 0.9775 magn= -0. atom 33 (R=0.038) charge= 0.9567 magn= -0. atom 34 (R=0.038) charge= 0.9567 magn= -0. atom 35 (R=0.038) charge= 0.9703 magn= -0. atom 36 (R=0.038) charge= 0.9595 magn= -0. atom 37 (R=0.038) charge= 0.9703 magn= -0. total cpu time spent up to now is 4133.5 secs End of self-consistent calculation CONTROL calculation = 'relax' , restart_mode = 'from_scratch' , outdir = './' , pseudo_dir = '/home/jibiaoli/pseudo/' , prefix = '2d' , nstep = 199 , / SYSTEM ibrav = 8, celldm(1) = 23.59760901, celldm(2) = 0.592429525, celldm(3) = 1.5817524, nat = 37, ntyp = 4, ecutwfc = 49 , ecutrho = 511 , occupations = 'smearing' , degauss = 0.02D0 , smearing = 'gaussian' , nspin = 2, starting_magnetization(1) = -0.1, starting_magnetization(2) = 2.8, starting_magnetization(3) = -0.1, starting_magnetization(4) = 0, / ELECTRONS electron_maxstep = 299, mixing_beta = 0.2D0 , diagonalization = 'david' , / IONS ion_dynamics = 'bfgs' , / ATOMIC_SPECIES O 15.999 O.pbe-n-kjpaw_psl.1.0.0.UPF Fe 55.850 Fe.pbe-spn-kjpaw_psl.1.0.0.UPF N 14.007 N.pbe-n-kjpaw_psl.1.0.0.UPF C 12.010 C.pbe-n-kjpaw_psl.1.0.0.UPF ATOMIC_POSITIONS angstrom O 6.9340166756 3.6989245228 3.8528176290 C 6.9340166756 3.6989245228 2.6728176290 Fe 6.9340166756 3.6989245228 0.8728176290 N 5.6059434603 2.4072809825 0.8730142439 N 5.6059434603 4.9905680641 0.8730142439 N 8.2619454617 2.4072286380 0.8730110298 N 8.2619454617 4.9906204086 0.8730110298 C -0.0178633308 0.00 0.8730568507 C -0.0178354701 2.4770183342 0.8730574443 C -0.0178354701 4.9208307125 0.8730574443 C 2.0828914672 1.2436366562 0.8730559742 C 2.1294070947 3.6989245238 0.8730543580 C 2.0828914672 6.1542123905 0.8730559742 C 4.1515598342 0.00 0.8730547888 C 4.2422651536 2.4525822834 0.8730507905 C 4.2422651536 4.9452667633 0.8730507905 C 6.2369236427 1.2005616382 0.8730586550 C 6.2369236427 6.1972874084 0.8730586550 C 8.3173386913 0.00 0.8730685226 C 10.3713556874
Re: [QE-users] Doubt in performing vc relax and relax - Reg
You are wrong. During scf you do not change lattice parameters. Relax is used when you are sure about lattice parameters - eg. from X-ray diffraction. From: users on behalf of singaravelan T R Sent: Sunday, April 18, 2021 8:38:16 AM To: users@lists.quantum-espresso.org Subject: [QE-users] Doubt in performing vc relax and relax - Reg Dear all, I think vc - relax and relax are nearly the same things by following arguments. If wrong please correct me. In case of relax calculation, we check for atomic position optimization, and then separately do the lattice parameter vs total energy by running scf, Optimization. But in case of vc - relax we do both (lattice parameter and atomic position optimization) in a single go. I think that vc- relax is more suitable if we need to optimise a, c and also atomic position by running scf. And relax is suitable if we need to optimize a and atomic position alone. All these things are in context of bulk systems like silicon. with thanks, Singaravelan T R ___ 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] Why magnetic system give zero magnetic moment for all atoms
Dear All, I am performing spin polarized calcualtion with the developer version. My system is CO adsorpion on a single Fe atom embeded in a single sheet of graphene. Obviously this system is magetic. However, the calculation gives zero magnetic moments for all atoms (see below). Is it normal or is there anything wrong with my calculations ? negative rho (up, down): 1.127E-03 1.127E-03 Magnetic moment per site (integrated on atomic sphere of radius R) atom 1 (R=0.038) charge= 2.6752 magn= 0. atom 2 (R=0.038) charge= 0.9377 magn= -0. atom 3 (R=0.052) charge= 11.7120 magn= -0. atom 4 (R=0.044) charge= 2.4585 magn= -0. atom 5 (R=0.044) charge= 2.4585 magn= -0. atom 6 (R=0.044) charge= 2.4583 magn= 0. atom 7 (R=0.044) charge= 2.4583 magn= 0. atom 8 (R=0.038) charge= 0.9651 magn= 0. atom 9 (R=0.038) charge= 0.9693 magn= 0. atom 10 (R=0.038) charge= 0.9693 magn= 0. atom 11 (R=0.038) charge= 0.9701 magn= 0. atom 12 (R=0.038) charge= 0.9598 magn= -0. atom 13 (R=0.038) charge= 0.9701 magn= 0. atom 14 (R=0.038) charge= 0.9776 magn= 0. atom 15 (R=0.038) charge= 0.9562 magn= 0. atom 16 (R=0.038) charge= 0.9562 magn= 0. atom 17 (R=0.038) charge= 0.9838 magn= 0. atom 18 (R=0.038) charge= 0.9838 magn= 0. atom 19 (R=0.038) charge= 0.9907 magn= 0. atom 20 (R=0.038) charge= 0.9747 magn= 0. atom 21 (R=0.038) charge= 0.9625 magn= 0. atom 22 (R=0.038) charge= 0.9747 magn= 0. atom 23 (R=0.038) charge= 0.9647 magn= -0. atom 24 (R=0.038) charge= 0.9688 magn= 0. atom 25 (R=0.038) charge= 0.9688 magn= 0. atom 26 (R=0.038) charge= 0.9746 magn= -0. atom 27 (R=0.038) charge= 0.9623 magn= 0. atom 28 (R=0.038) charge= 0.9746 magn= -0. atom 29 (R=0.038) charge= 0.9904 magn= -0. atom 30 (R=0.038) charge= 0.9837 magn= -0. atom 31 (R=0.038) charge= 0.9837 magn= -0. atom 32 (R=0.038) charge= 0.9775 magn= -0. atom 33 (R=0.038) charge= 0.9567 magn= -0. atom 34 (R=0.038) charge= 0.9567 magn= -0. atom 35 (R=0.038) charge= 0.9703 magn= -0. atom 36 (R=0.038) charge= 0.9595 magn= -0. atom 37 (R=0.038) charge= 0.9703 magn= -0. total cpu time spent up to now is 4133.5 secs End of self-consistent calculation CONTROL calculation = 'relax' , restart_mode = 'from_scratch' , outdir = './' , pseudo_dir = '/home/jibiaoli/pseudo/' , prefix = '2d' , nstep = 199 , / SYSTEM ibrav = 8, celldm(1) = 23.59760901, celldm(2) = 0.592429525, celldm(3) = 1.5817524, nat = 37, ntyp = 4, ecutwfc = 49 , ecutrho = 511 , occupations = 'smearing' , degauss = 0.02D0 , smearing = 'gaussian' , nspin = 2, starting_magnetization(1) = -0.1, starting_magnetization(2) = 2.8, starting_magnetization(3) = -0.1, starting_magnetization(4) = 0, / ELECTRONS electron_maxstep = 299, mixing_beta = 0.2D0 , diagonalization = 'david' , / IONS ion_dynamics = 'bfgs' , / ATOMIC_SPECIES O 15.999 O.pbe-n-kjpaw_psl.1.0.0.UPF Fe 55.850 Fe.pbe-spn-kjpaw_psl.1.0.0.UPF N 14.007 N.pbe-n-kjpaw_psl.1.0.0.UPF C 12.010 C.pbe-n-kjpaw_psl.1.0.0.UPF ATOMIC_POSITIONS angstrom O 6.9340166756 3.6989245228 3.8528176290 C 6.9340166756 3.6989245228 2.6728176290 Fe 6.9340166756 3.6989245228 0.8728176290 N 5.6059434603 2.4072809825 0.8730142439 N 5.6059434603 4.9905680641 0.8730142439 N 8.2619454617 2.4072286380 0.8730110298 N 8.2619454617 4.9906204086 0.8730110298 C -0.0178633308 0.00 0.8730568507 C -0.0178354701 2.4770183342 0.8730574443 C -0.0178354701 4.9208307125 0.8730574443 C 2.0828914672 1.2436366562 0.8730559742 C 2.1294070947 3.6989245238 0.8730543580 C 2.0828914672 6.1542123905 0.8730559742 C 4.1515598342 0.00 0.8730547888 C 4.2422651536 2.4525822834 0.8730507905 C 4.2422651536 4.9452667633 0.8730507905 C 6.2369236427 1.2005616382 0.8730586550 C 6.2369236427 6.1972874084 0.8730586550 C 8.3173386913 0.00 0.8730685226 C 10.3713556874 1.2412551379 0.8730644966 C 10.3159798880 3.6989245238 0.8730564313 C 10.3713556874 6.1565939088 0.8730644966 C 1.3983816512 0.00 0.8730550420 C 1.3982497647 2.4770211151 0.8730548598 C 1.3982497647 4.9208279316 0.8730548598 C 3.4964768966 1.2412907830 0.8730582823 C 3.5518074884 3.6989245238 0.8730504409 C 3.4964768966 6.1565582637 0.8730582823 C 5.5504587549 0.00 0.8730644983 C 7.6308954080 1.2005515154 0.8730595405 C 7.6308954080 6.1972975312 0.8730595405 C 9.7162145171 0.00 0.8730613644 C 9.6256116280 2.4525476568 0.8730541166 C 9.6256116280 4.9453013898 0.8730541166 C 11.7849236132 1.2436057457 0.8730599352 C 11.7383344691 3.6989245238 0.8730590021 C 11.7849236132 6.1542433010
[QE-users] Doubt in performing vc relax and relax - Reg
Dear all, I think vc - relax and relax are nearly the same things by following arguments. If wrong please correct me. In case of relax calculation, we check for atomic position optimization, and then separately do the lattice parameter vs total energy by running scf, Optimization. But in case of vc - relax we do both (lattice parameter and atomic position optimization) in a single go. I think that vc- relax is more suitable if we need to optimise a, c and also atomic position by running scf. And relax is suitable if we need to optimize a and atomic position alone. All these things are in context of bulk systems like silicon. with thanks, Singaravelan T R ___ 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
