Hi Timrov Iurii, I have fixed the links so that anyone who has them can see the content. Thank you for your feedback.
Best, Hien Vo Graduate Student @ The Chemistry Department The University of Chicago From: Timrov Iurii Sent: Thursday, August 13, 2020 1:22 PM To: Quantum ESPRESSO users Forum Subject: Re: [QE-users] Relaxing magnetic structures Dear Hien Vo, Unfortunately I do not have access to your files (access denied). > I was concerned about this too, but I’m trying to relax the structure for > computing phonons by the finite displacement, so would larger values be ok in > this case? >From my experience, forc_conv_thr=1.0D-5 and etot_conv_thr=1.0D-6 should be a >safe choice. Bum maybe others can also comment on this. > The k-point mesh I used is 8x6x8 which (after symmetry), gives 130 k-points > for the 20-atom unit cell. In the 2nd link (my results for convergence > tests), I did check degauss against different k-point meshes. I’m using this > value so that my results are comparable to past work done in the group. Do > you think I should change it? Ok. If the convergence w.r.t. k-mesh and smearing was checked, then it should be fine. > I’m using this U since it was computed by a postdoc in the group and we’re > trying to maintain consistency so that my results and hers are comparable. Ok Greetings, Iurii -- Dr. Iurii Timrov Postdoctoral Researcher STI - IMX - THEOS and NCCR - MARVEL Swiss Federal Institute of Technology Lausanne (EPFL) CH-1015 Lausanne, Switzerland +41 21 69 34 881 http://people.epfl.ch/265334 From: users <[email protected]> on behalf of Hien Vo <[email protected]> Sent: Thursday, August 13, 2020 5:50:17 PM To: Quantum ESPRESSO users Forum Subject: Re: [QE-users] Relaxing magnetic structures Hi Timrov Iurii, Thank you so much for replying to me! I’ve included my affiliation at the bottom of this email. >What is not clear to me is why you have a different starting_magnetization in >the final SCF run. Why not using the same starting_magnetization? There might >be different minima, and by using different starting_magnetization you can end >up in different minima. Not sure that this is what happens in your case though. I think I was being unclear here. The final scf was done as part of the vc-relax routine. I’m including a link to my output here : https://drive.google.com/drive/folders/1JgEJWZVYAbLJI3w_OsSxAUhZQDA5JuLR?usp=sharing . Since the relaxation took quite some time I had to split it into 2 runs, the second run is in the 0.7-2.out file. At the end when it runs the final scf run at the relaxed structure, the program picks starting_magnetization = -0.69 and 0.69, while originally my input is -0.7 and 0.7. I think it’s fine that the program picks another starting_magnetization, just wish it gave me a lower P. > As far as I know, typically, the differences in the pressure between the > final step of vc-relax and the final SCF run is due to the not-large-enough > cutoff (check the pw_forum archive for more discussions about this). But in > your case you have 100/800 Ry which are already seem to be large, but I do > not know if these are "good" cutoffs for the pseudos that you use. So I am > not sure that this is the source of the problem in your case, but maybe it is > worth checking. So before doing these calculations I checked the convergence on a 10-atom cell. The results are here: https://drive.google.com/file/d/1dZRt-5dzDAibgV49Z4nX3QQKt04TA3hR/view?usp=sharing . I think it looks fine? >These are extremely small. I would use values not smaller than this: >forc_conv_thr=1.0D-5, >etot_conv_thr=1.0D-6, >and in many cases even larger values should be OK, like this >forc_conv_thr=1.0D-4, >etot_conv_thr=1.0D-5 I was concerned about this too, but I’m trying to relax the structure for computing phonons by the finite displacement, so would larger values be ok in this case? >> degauss=0.0036, >This is also very small. Which k point mesh do you use? You did not specify. The k-point mesh I used is 8x6x8 which (after symmetry), gives 130 k-points for the 20-atom unit cell. In the 2nd link (my results for convergence tests), I did check degauss against different k-point meshes. I’m using this value so that my results are comparable to past work done in the group. Do you think I should change it? >> Hubbard_U(2)=3 >> Hubbard_U(3)=3 >It seems you are using an empirical U or maybe you took from literature. >Please note that it is possible to compute U for your system from first >principles using the HP code of QE. If you are >interested, have a look at >this paper: https://journals.aps.org/prb/abstract/10.1103/PhysRevB.98.085127 I’m using this U since it was computed by a postdoc in the group and we’re trying to maintain consistency so that my results and hers are comparable. Best, Hien Vo Graduate Student @ The Chemistry Department The University of Chicago From: Timrov Iurii Sent: Thursday, August 13, 2020 3:30 AM To: [email protected] Subject: Re: [QE-users] Relaxing magnetic structures Dear Hien Vo, First of all, do not forget to add your affiliation when posting to the pw_forum. Also, it is useful to specify which version of QE was used. Check the posting guidelines here: https://www.quantum-espresso.org/forum > What I notice is the vc-relax would get P to 0 but the final scf calculation > at the relaxed structure would give me a large P using a different > starting_magnetization from the one I used for the input. What is not clear to me is why you have a different starting_magnetization in the final SCF run. Why not using the same starting_magnetization? There might be different minima, and by using different starting_magnetization you can end up in different minima. Not sure that this is what happens in your case though. As far as I know, typically, the differences in the pressure between the final step of vc-relax and the final SCF run is due to the not-large-enough cutoff (check the pw_forum archive for more discussions about this). But in your case you have 100/800 Ry which are already seem to be large, but I do not know if these are "good" cutoffs for the pseudos that you use. So I am not sure that this is the source of the problem in your case, but maybe it is worth checking. Some comments about your input parameters: > forc_conv_thr=1.0D-6, > etot_conv_thr=1.4D-9, These are extremely small. I would use values not smaller than this: forc_conv_thr=1.0D-5, etot_conv_thr=1.0D-6, and in many cases even larger values should be OK, like this forc_conv_thr=1.0D-4, etot_conv_thr=1.0D-5 > degauss=0.0036, This is also very small. Which k point mesh do you use? You did not specify. > Hubbard_U(2)=3 > Hubbard_U(3)=3 It seems you are using an empirical U or maybe you took from literature. Please note that it is possible to compute U for your system from first principles using the HP code of QE. If you are interested, have a look at this paper: https://journals.aps.org/prb/abstract/10.1103/PhysRevB.98.085127 > La 138.9055 La.pbe-spfn-kjpaw_psl.1.0.0.UPF > Co1 58.9332 Co.pbe-spn-kjpaw_psl.0.3.1.UPF > Co2 58.9332 Co.pbe-spn-kjpaw_psl.0.3.1.UPF > O 16.00 O.pbe-n-kjpaw_psl.1.0.0.UPF This is your choice to use these pseudos. Just for the reference, I suggest to have a look here: https://www.materialscloud.org/discover/sssp/table/efficiency Cheers, Iurii -- Dr. Iurii Timrov Postdoctoral Researcher STI - IMX - THEOS and NCCR - MARVEL Swiss Federal Institute of Technology Lausanne (EPFL) CH-1015 Lausanne, Switzerland +41 21 69 34 881 http://people.epfl.ch/265334 From: users <[email protected]> on behalf of Hien Vo <[email protected]> Sent: Wednesday, August 12, 2020 7:39:07 PM To: [email protected] Subject: [QE-users] Relaxing magnetic structures Hello QE community, I’m trying to relax a-type afm LaCoO3 using the vc-relax option and I can’t seem to get P close to 0. What I notice is the vc-relax would get P to 0 but the final scf calculation at the relaxed structure would give me a large P using a different starting_magnetization from the one I used for the input. I’m including my input here (I’m calculating phonons with these so I’m trying to reduce the force and stress as much as possible) as well as relevant output from the run before final scf calculation and also the final scf calculation. Any tips would be greatly appreciated! INPUT: &CONTROL calculation='vc-relax', tprnfor=.TRUE., forc_conv_thr=1.0D-6, etot_conv_thr=1.4D-9, max_seconds=64800 / &SYSTEM ibrav=12, celldm(1)=10.284016,celldm(2)=1.43711648,celldm(3)=1.011898,celldm(4)=-0.025604, nat=20,ntyp=4, occupations='smearing',degauss=0.0036, ecutwfc=100,ecutrho=800, nspin=2,starting_magnetization(2)=-0.7,starting_magnetization(3)=0.7, lda_plus_u=.TRUE. Hubbard_U(2)=3 Hubbard_U(3)=3 / &ELECTRONS electron_maxstep=3000 mixing_beta=0.05D conv_thr=1.4D-9 / &IONS trust_radius_ini=0.2 trust_radius_max=0.5 / &CELL / ATOMIC_SPECIES La 138.9055 La.pbe-spfn-kjpaw_psl.1.0.0.UPF Co1 58.9332 Co.pbe-spn-kjpaw_psl.0.3.1.UPF Co2 58.9332 Co.pbe-spn-kjpaw_psl.0.3.1.UPF O 16.00 O.pbe-n-kjpaw_psl.1.0.0.UPF ATOMIC_POSITIONS (crystal) La 0.50000 0.25000 0.00000 La 0.50000 0.75000 0.00000 La 0.00000 0.75000 0.50000 La 0.00000 0.25000 0.50000 Co2 0.00000 0.00000 0.00000 Co1 0.00000 0.50000 0.00000 Co1 0.50000 0.50000 0.50000 Co2 0.50000 0.00000 0.50000 O 0.00000 0.25000 0.06296 O 0.00000 0.75000 0.93704 O 0.28148 0.96852 0.21852 O 0.71852 0.03148 0.78148 O 0.21852 0.03148 0.71852 O 0.78148 0.96852 0.28148 O 0.71852 0.53148 0.21852 O 0.28148 0.46852 0.78148 O 0.78148 0.46852 0.71852 O 0.21852 0.53148 0.28148 O 0.50000 0.75000 0.56296 O 0.50000 0.25000 0.43704 OUTPUT OF RUN BEFORE FINAL SCF: Forces acting on atoms (cartesian axes, Ry/au): atom 1 type 1 force = 0.00000012 -0.00000087 -0.00000173 atom 2 type 1 force = -0.00000012 0.00000087 0.00000173 atom 3 type 1 force = -0.00000012 0.00000087 -0.00000173 atom 4 type 1 force = 0.00000012 -0.00000087 0.00000173 atom 5 type 3 force = 0.00000000 0.00000000 0.00000000 atom 6 type 2 force = -0.00000000 0.00000000 0.00000000 atom 7 type 2 force = 0.00000000 -0.00000000 -0.00000000 atom 8 type 3 force = -0.00000000 -0.00000000 0.00000000 atom 9 type 4 force = 0.00000005 -0.00000028 0.00000287 atom 10 type 4 force = -0.00000005 0.00000028 -0.00000287 atom 11 type 4 force = 0.00000119 0.00000007 -0.00000115 atom 12 type 4 force = -0.00000119 -0.00000007 0.00000115 atom 13 type 4 force = -0.00000119 -0.00000007 -0.00000115 atom 14 type 4 force = 0.00000119 0.00000007 0.00000115 atom 15 type 4 force = -0.00000118 -0.00000098 -0.00000108 atom 16 type 4 force = 0.00000118 0.00000098 0.00000108 atom 17 type 4 force = 0.00000118 0.00000098 -0.00000108 atom 18 type 4 force = -0.00000118 -0.00000098 0.00000108 atom 19 type 4 force = -0.00000005 0.00000028 0.00000287 atom 20 type 4 force = 0.00000005 -0.00000028 -0.00000287 Computing stress (Cartesian axis) and pressure total stress (Ry/bohr**3) (kbar) P= -0.00 0.00000000 0.00000000 0.00000000 0.00 0.00 0.00 0.00000000 -0.00000002 0.00000000 0.00 -0.00 0.00 0.00000000 0.00000000 -0.00000000 0.00 0.00 -0.00 Message from routine bfgs: history already reset at previous step: stopping bfgs converged in 30 scf cycles and 29 bfgs steps (criteria: energy < 1.4E-09 Ry, force < 1.0E-06Ry/Bohr, cell < 5.0E-01kbar) End of BFGS Geometry Optimization Final enthalpy = -3840.8280670928 Ry Begin final coordinates new unit-cell volume = 1540.07698 a.u.^3 ( 228.21586 Ang^3 ) density = 7.15506 g/cm^3 CELL_PARAMETERS (alat= 10.28401600) 0.992999501 0.012644330 0.000000000 -0.018068355 1.404995305 0.000000000 0.000000000 0.000000000 1.014750287 ATOMIC_POSITIONS (crystal) La 0.499998392 0.250000173 -0.003228188 La 0.500001608 0.749999827 0.003228188 La 0.000001608 0.749999827 0.496771812 La -0.000001608 0.250000173 0.503228188 Co2 0.000000000 0.000000000 0.000000000 Co1 -0.000000000 0.500000000 0.000000000 Co1 0.500000000 0.500000000 0.500000000 Co2 0.500000000 0.000000000 0.500000000 O 0.000000937 0.250000107 0.072799662 O -0.000000937 0.749999893 0.927200338 O 0.250055043 0.962702639 0.249942716 O 0.749944957 0.037297361 0.750057284 O 0.249944957 0.037297361 0.749942716 O 0.750055043 0.962702639 0.250057284 O 0.749947635 0.537297843 0.249945383 O 0.250052365 0.462702157 0.750054617 O 0.750052365 0.462702157 0.749945383 O 0.249947635 0.537297843 0.250054617 O 0.499999063 0.749999893 0.572799662 O 0.500000937 0.250000107 0.427200338 End final coordinates OUTPUT FROM FINAL SCF RUN: A final scf calculation at the relaxed structure. The G-vectors are recalculated for the final unit cell Results may differ from those at the preceding step. Parallelization info -------------------- sticks: dense smooth PW G-vecs: dense smooth PW Min 938 469 129 58844 20811 2997 Max 939 471 130 58845 20812 2999 Sum 9385 4699 1291 588445 208113 29981 bravais-lattice index = 12 lattice parameter (alat) = 10.2840 a.u. unit-cell volume = 1540.0770 (a.u.)^3 number of atoms/cell = 20 number of atomic types = 4 number of electrons = 184.00 number of Kohn-Sham states= 110 kinetic-energy cutoff = 100.0000 Ry charge density cutoff = 800.0000 Ry convergence threshold = 2.3E-11 mixing beta = 0.0500 number of iterations used = 8 plain mixing Exchange-correlation = SLA PW PBX PBC ( 1 4 3 4 0 0) celldm(1)= 10.213861 celldm(2)= 1.416338 celldm(3)= 1.019956 celldm(4)= -0.007299 celldm(5)= 0.000000 celldm(6)= 0.000000 ….. atomic species valence mass pseudopotential La 11.00 138.90550 La( 1.00) Co1 17.00 58.93320 Co( 1.00) Co2 17.00 58.93320 Co( 1.00) O 6.00 16.00000 O ( 1.00) Starting magnetic structure atomic species magnetization La -0.000 Co1 -0.069 Co2 0.069 O 0.000 ….. Forces acting on atoms (cartesian axes, Ry/au): atom 1 type 1 force = -0.00001228 0.00097281 0.00036384 atom 2 type 1 force = 0.00001228 -0.00097281 -0.00036384 atom 3 type 1 force = 0.00001228 -0.00097281 0.00036384 atom 4 type 1 force = -0.00001228 0.00097281 -0.00036384 atom 5 type 3 force = 0.00000000 0.00000000 0.00000000 atom 6 type 2 force = 0.00000000 0.00000000 0.00000000 atom 7 type 2 force = 0.00000000 0.00000000 -0.00000000 atom 8 type 3 force = 0.00000000 0.00000000 0.00000000 atom 9 type 4 force = 0.00000007 -0.00000556 0.00123004 atom 10 type 4 force = -0.00000007 0.00000556 -0.00123004 atom 11 type 4 force = -0.00000878 0.00068623 0.00000095 atom 12 type 4 force = 0.00000878 -0.00068623 -0.00000095 atom 13 type 4 force = 0.00000878 -0.00068623 0.00000095 atom 14 type 4 force = -0.00000878 0.00068623 -0.00000095 atom 15 type 4 force = 0.00000535 -0.00045735 0.00000063 atom 16 type 4 force = -0.00000535 0.00045735 -0.00000063 atom 17 type 4 force = -0.00000535 0.00045735 0.00000063 atom 18 type 4 force = 0.00000535 -0.00045735 -0.00000063 atom 19 type 4 force = -0.00000007 0.00000556 0.00123004 atom 20 type 4 force = 0.00000007 -0.00000556 -0.00123004 Total force = 0.003618 Total SCF correction = 0.000003 Computing stress (Cartesian axis) and pressure total stress (Ry/bohr**3) (kbar) P= 5.83 0.00004353 0.00000056 0.00000000 6.40 0.08 0.00 0.00000056 0.00002911 0.00000000 0.08 4.28 0.00 0.00000000 0.00000000 0.00004631 0.00 0.00 6.81 Best, Hien Vo
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