Re: [Pw_forum] Pseudopotential for indium
Dear Nicola, Yes, indium is metallic. The parameters I use to treat it are: occupations= 'smearing', smearing = 'cold', degauss= 0.02, There are 13 valence electrons in indium and 34 Kohn-Sham states. I have checked the band occupations for all the k-points; at least the two uppermost bands are empty, in most case even more. Here are the results of my tests. Exp. : 3.2449 x 3.2449 x 4.9420 angstroms -- K-points | Ecut/Ry | Ecutrho/Ry | PSP | Fntal | cell parameters -- 8x8x8=40 120 1200 PAW nrel PBE3.2168 x 5.3095 8x8x8=40 150600NC nrel PBE3.2213 x 5.3194 8x8x8=40 50500 PAW rel+SOPZ3.0786 x 5.0095 8x8x8=40 120 1200 PAW rel+SOPZ3.1032 x 5.0938 12x12x12=126 50500 PAW rel+SOPZ3.1692 x 4.7429 16x16x16=288 50500 PAW rel+SOPZ3.1340 x 4.8412 12x12x12=126 120 1200 PAW rel+SOPZ3.2094 x 4.7811 16x16x16=288 120 1200 PAW rel+SOPZ3.1647 x 4.9076 The best result is the last one. So the PAW of In is very hard (!) and need a huge amount of k-points… This is the first time I see this problem with a PAW PSP of the library… Thank you all for your hints. Pascal Pascal Boulet — Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email : pascal.bou...@univ-amu.fr Le 7 déc. 2017 à 17:35, Nicola Marzari a écrit : > > Thanks Pascal - this is metallic, > and you are using smearing, correct? Something like 0.02 Ry, and > Marzari-Vanderbilt cold smearing? > > Also, how many electrons does your pseudo have? Do you have enough bands > (i.e. are the top ones empty)? > > nicola > > > > On 07/12/2017 14:23, Pascal Boulet wrote: >> Dear Nicola, >> You are right I also noticed that the ‘pseudo' state energies match very >> well the AE ones. >> Regarding the alloys Vegard’s law should hold according to experimental >> data. We are indeed using supercells. >> I am currently running tests on pure indium. As mentioned by Paolo, the mass >> is irrelevant in the results for static calculations (as expected!). I have >> preliminary results with relativistic+SO calculation that are a bit better: >> 3.0786 x 3.0786 x 5.0095 >> Recall: >> exp.: 3.2449 x 3.2449 x 4.9420 >> previous calc.: 3.2168 x 3.2168 x 5.3095 >> This is obtained with Ecut=50 Ry Ecutrho=500 Ry, 8x8x8 kpts=40 kpts >> With these parameters c improves substantially (1.4% off) but a and c worsen >> a bit (5% off). >> I am running a test with more kpts first. In a second step I will increase >> Ecut and Ecutrho and will report to the forum. >> Pascal >> Pascal Boulet >> — >> /Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY/ >> Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen - >> F-13013 Marseille - FRANCE >> Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 >> Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email : >> pascal.bou...@univ-amu.fr <mailto:pascal.bou...@univ-amu.fr> >> Le 6 déc. 2017 à 23:24, Nicola Marzari > <mailto:nicola.marz...@epfl.ch>> a écrit : >>> >>> Dear Pascal, >>> >>> >>> the comparison with all-electron calculations looks good to me - see >>> here for tests and for the other pseudos: >>> http://materialscloud.org/sssp/results/In_conv_patt.png >>> >>> Comparing with expts is more delicate - c/a with PBE is >>> quite a bit off e.g. in ferroelectric perovskites. >>> >>> Re the alloy, how are you constructing the intermediate concentrations? >>> Supercells? (Vegard law should hold) >>> >>> nicola >>> >>> On 06/12/2017 23:03, Paolo Giannozzi wrote: >>>> You mean: the value 49.0 here? >>>> ATOMIC_SPECIES >>>> In 49.0 In.pbe-dn-kjpaw_psl.1.0.0.UPF >>>> Iit is used only by molecular dynamics, not by structural optimization. >>>> >>>> I don't remember In to be an especially nasty element, at least for >>>> simple III-V compounds like InAs. I would examine the effect of a denser >>>> k-point grid, and of spin-orbit >>>> >>>> Paolo
Re: [Pw_forum] Pseudopotential for indium
Dear Nicola, You are right I also noticed that the ‘pseudo' state energies match very well the AE ones. Regarding the alloys Vegard’s law should hold according to experimental data. We are indeed using supercells. I am currently running tests on pure indium. As mentioned by Paolo, the mass is irrelevant in the results for static calculations (as expected!). I have preliminary results with relativistic+SO calculation that are a bit better: 3.0786 x 3.0786 x 5.0095 Recall: exp.: 3.2449 x 3.2449 x 4.9420 previous calc.: 3.2168 x 3.2168 x 5.3095 This is obtained with Ecut=50 Ry Ecutrho=500 Ry, 8x8x8 kpts=40 kpts With these parameters c improves substantially (1.4% off) but a and c worsen a bit (5% off). I am running a test with more kpts first. In a second step I will increase Ecut and Ecutrho and will report to the forum. Pascal Pascal Boulet — Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email : pascal.bou...@univ-amu.fr Le 6 déc. 2017 à 23:24, Nicola Marzari a écrit : > > Dear Pascal, > > > the comparison with all-electron calculations looks good to me - see > here for tests and for the other pseudos: > http://materialscloud.org/sssp/results/In_conv_patt.png > > Comparing with expts is more delicate - c/a with PBE is > quite a bit off e.g. in ferroelectric perovskites. > > Re the alloy, how are you constructing the intermediate concentrations? > Supercells? (Vegard law should hold) > > nicola > > On 06/12/2017 23:03, Paolo Giannozzi wrote: >> You mean: the value 49.0 here? >> ATOMIC_SPECIES >> In 49.0 In.pbe-dn-kjpaw_psl.1.0.0.UPF >> Iit is used only by molecular dynamics, not by structural optimization. >> >> I don't remember In to be an especially nasty element, at least for >> simple III-V compounds like InAs. I would examine the effect of a denser >> k-point grid, and of spin-orbit >> >> Paolo >> >> >> On Wed, Dec 6, 2017 at 10:46 PM, Saif Ullah > <mailto:kiterunn...@gmail.com>> wrote: >> >>Dear Boulet, >> >>I think I found where the error is. You are using the atomic number >>of In instead of its atomic mass. >> >>Regards >>Saif >>Department of physics, UFJF, Brazil >> >> >> >>On Wed, Dec 6, 2017 at 6:45 PM, Pascal Boulet >>mailto:pascal.bou...@univ-amu.fr>> wrote: >> >>Thanks Lorenzo for the suggestion. I have tried with Ecut=120 Ry >>and Ecutrho=1200 Ry. I get a slightly better result (but c is >>still very bad): >>3.2168 x 3.2168 x 5.3095 >> >>as compared with: >>exp.: 3.2449 x 3.2449 x 4.9420 angström >>previous calc.: 3.2715 x 3.2715 x 5.4541 angström >> >> >>Best, >> >>Pascal Boulet >>— >>/Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY/ >>Aix-Marseille University - ST JEROME - Avenue Escadrille >>Normandie Niemen - F-13013 Marseille - FRANCE >>Tél: +33(0)4 13 55 18 10 - Fax >>: +33(0)4 13 55 18 50 >>Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos >><http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos> - >>Email : pascal.bou...@univ-amu.fr <mailto:pascal.bou...@univ-amu.fr> >> >> >> >> >>Le 6 déc. 2017 à 18:54, Lorenzo Paulatto ><mailto:paul...@gmail.com>> a écrit : >> >>> Hello, >>>can you try with a much higher cutoff (100 Ry or more) and see >>>if the lattice parameter improves? I've noticed that sometimes >>>pslibrary pseudos are much a harder than they look, especially >>>when converging stress >>> >>>Cheers >>> >>>-- >>>Lorenzo Paulatto >>>Written on a virtual keyboard with real fingers >>> >>>On Dec 6, 2017 18:32, "Pascal Boulet" >>>mailto:pascal.bou...@univ-amu.fr>> >>>wrote: >>> >>>Dear all, >>> >>>We are working on some In-containing semiconductors >>>M(1-x)In(x)L. M is supposed to be a smaller atom than In. >>>We are facing the problem that when we vary x from 0 to 1 >>>
Re: [Pw_forum] Pseudopotential for indium
The amazing thing is that I get more or less the same result with HGH NC pseudopotential of QE website library with Ecut=150 Ry and Ecutrho=600 Ry: 3.2213 x 3.2213 x 5.3194 Best, Pascal Boulet — Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email : pascal.bou...@univ-amu.fr Le 6 déc. 2017 à 18:54, Lorenzo Paulatto a écrit : > Hello, > can you try with a much higher cutoff (100 Ry or more) and see if the lattice > parameter improves? I've noticed that sometimes pslibrary pseudos are much a > harder than they look, especially when converging stress > > Cheers > > -- > Lorenzo Paulatto > Written on a virtual keyboard with real fingers > > On Dec 6, 2017 18:32, "Pascal Boulet" wrote: > Dear all, > > We are working on some In-containing semiconductors M(1-x)In(x)L. M is > supposed to be a smaller atom than In. We are facing the problem that when we > vary x from 0 to 1 the cell parameters is decreasing instead of increasing. > Although this may happen, it should not be the case here since ‘pure’ ML has > a smaller cell parameter than ‘pure’ InL. > > We have run some calculations on crystal indium using the PSL library pseudo > potentials (both PAW and USPP). one of the calculated cell parameters are > miles away from the experimental ones: > exp.: 3.2449 x 3.2449 x 4.9420 angström > calc.: 3.2715 x 3.2715 x 5.4541 angström > > Does anyone have tested the In pseudo potentials of the PSL library or faced > this problem with indium? > > Thank you for your help and time. > > Best regards > > PS1. here are some information from the input file: > > calculation= 'vc-relax’, > etot_conv_thr = 1d-7, > forc_conv_thr = 5d-5, > ibrav = 0, >nat= 2, > ntyp = 1, > ecutwfc= 45.d0, > ecutrho= 450.d0, > nbnd = 18 > &ELECTRONS > conv_thr = 1d-8, > &CELL > press_conv_thr = 0.01d0, > cell_factor= 1.5, > ATOMIC_SPECIES > In 49.0 In.pbe-dn-kjpaw_psl.1.0.0.UPF > K_POINTS automatic > 8 8 4 1 1 1 > CELL_PARAMETERS angstroms > 3.2449 0. 0. > 0. 3.2449 0. > 0. 0. 4.9420 > ATOMIC_POSITIONS crystal > In 0.0.0. > In 0.50000.50000.5000 > > PS2. And some from the output: > > bfgs converged in 18 scf cycles and 15 bfgs steps > (criteria: energy < 1.0E-07 Ry, force < 5.0E-05Ry/Bohr, cell < > 1.0E-02kbar) > CELL_PARAMETERS (angstrom) >3.271466870 0.0 0.00000 >0.0 3.271466870 0.0 >0.0 0.0 5.454067219 > !total energy =-821.46750731 Ry > total stress (Ry/bohr**3) (kbar) P=0.30 > > Pascal Boulet > — > Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY > Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen - > F-13013 Marseille - FRANCE > Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 > Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email : > pascal.bou...@univ-amu.fr > > > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Pseudopotential for indium
Thanks Lorenzo for the suggestion. I have tried with Ecut=120 Ry and Ecutrho=1200 Ry. I get a slightly better result (but c is still very bad): 3.2168 x 3.2168 x 5.3095 as compared with: exp.: 3.2449 x 3.2449 x 4.9420 angström previous calc.: 3.2715 x 3.2715 x 5.4541 angström Best, Pascal Boulet — Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email : pascal.bou...@univ-amu.fr Le 6 déc. 2017 à 18:54, Lorenzo Paulatto a écrit : > Hello, > can you try with a much higher cutoff (100 Ry or more) and see if the lattice > parameter improves? I've noticed that sometimes pslibrary pseudos are much a > harder than they look, especially when converging stress > > Cheers > > -- > Lorenzo Paulatto > Written on a virtual keyboard with real fingers > > On Dec 6, 2017 18:32, "Pascal Boulet" wrote: > Dear all, > > We are working on some In-containing semiconductors M(1-x)In(x)L. M is > supposed to be a smaller atom than In. We are facing the problem that when we > vary x from 0 to 1 the cell parameters is decreasing instead of increasing. > Although this may happen, it should not be the case here since ‘pure’ ML has > a smaller cell parameter than ‘pure’ InL. > > We have run some calculations on crystal indium using the PSL library pseudo > potentials (both PAW and USPP). one of the calculated cell parameters are > miles away from the experimental ones: > exp.: 3.2449 x 3.2449 x 4.9420 angström > calc.: 3.2715 x 3.2715 x 5.4541 angström > > Does anyone have tested the In pseudo potentials of the PSL library or faced > this problem with indium? > > Thank you for your help and time. > > Best regards > > PS1. here are some information from the input file: > > calculation= 'vc-relax’, > etot_conv_thr = 1d-7, > forc_conv_thr = 5d-5, > ibrav = 0, >nat= 2, > ntyp = 1, > ecutwfc= 45.d0, > ecutrho= 450.d0, > nbnd = 18 > &ELECTRONS > conv_thr = 1d-8, > &CELL > press_conv_thr = 0.01d0, > cell_factor= 1.5, > ATOMIC_SPECIES > In 49.0 In.pbe-dn-kjpaw_psl.1.0.0.UPF > K_POINTS automatic > 8 8 4 1 1 1 > CELL_PARAMETERS angstroms > 3.2449 0. 0. > 0. 3.2449 0. > 0. 0. 4.9420 > ATOMIC_POSITIONS crystal > In 0.0.0. > In 0.50000.50000.5000 > > PS2. And some from the output: > > bfgs converged in 18 scf cycles and 15 bfgs steps > (criteria: energy < 1.0E-07 Ry, force < 5.0E-05Ry/Bohr, cell < > 1.0E-02kbar) > CELL_PARAMETERS (angstrom) >3.271466870 0.0 0.00000 >0.0 3.271466870 0.0 >0.0 0.0 5.454067219 > !total energy =-821.46750731 Ry > total stress (Ry/bohr**3) (kbar) P=0.30 > > Pascal Boulet > — > Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY > Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen - > F-13013 Marseille - FRANCE > Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 > Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email : > pascal.bou...@univ-amu.fr > > > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Pseudopotential for indium
Dear all, We are working on some In-containing semiconductors M(1-x)In(x)L. M is supposed to be a smaller atom than In. We are facing the problem that when we vary x from 0 to 1 the cell parameters is decreasing instead of increasing. Although this may happen, it should not be the case here since ‘pure’ ML has a smaller cell parameter than ‘pure’ InL. We have run some calculations on crystal indium using the PSL library pseudo potentials (both PAW and USPP). one of the calculated cell parameters are miles away from the experimental ones: exp.: 3.2449 x 3.2449 x 4.9420 angström calc.: 3.2715 x 3.2715 x 5.4541 angström Does anyone have tested the In pseudo potentials of the PSL library or faced this problem with indium? Thank you for your help and time. Best regards PS1. here are some information from the input file: calculation= 'vc-relax’, etot_conv_thr = 1d-7, forc_conv_thr = 5d-5, ibrav = 0, nat= 2, ntyp = 1, ecutwfc= 45.d0, ecutrho= 450.d0, nbnd = 18 &ELECTRONS conv_thr = 1d-8, &CELL press_conv_thr = 0.01d0, cell_factor= 1.5, ATOMIC_SPECIES In 49.0 In.pbe-dn-kjpaw_psl.1.0.0.UPF K_POINTS automatic 8 8 4 1 1 1 CELL_PARAMETERS angstroms 3.2449 0. 0. 0. 3.2449 0. 0. 0. 4.9420 ATOMIC_POSITIONS crystal In 0.0.0. In 0.50000.50000.5000 PS2. And some from the output: bfgs converged in 18 scf cycles and 15 bfgs steps (criteria: energy < 1.0E-07 Ry, force < 5.0E-05Ry/Bohr, cell < 1.0E-02kbar) CELL_PARAMETERS (angstrom) 3.271466870 0.0 0.0 0.0 3.271466870 0.0 0.0 0.0 5.454067219 !total energy =-821.46750731 Ry total stress (Ry/bohr**3) (kbar) P= 0.30 Pascal Boulet — Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email : pascal.bou...@univ-amu.fr ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Physical meaning of two imaginary phonon frequencies at NEB saddle point and Transition State Theory
Hello, My guess: you have to remove one of the imaginary frequencies (most probably the smallest one) by following the corresponding eigenvector (=moving the atoms accordingly). Then, you will have to make sure that the transition state connects the reactants and products you are interested in. HTH, Pascal Pascal Boulet — Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email : pascal.bou...@univ-amu.fr Le 13 nov. 2017 à 12:44, JAY Antoine a écrit : > Dear all, > I have been using NEB to obtain the Delta E and phonon DOS at > begining/end/saddle point to properly evaluate the vibrationnal entropy > contribution in the transition state theory. > Commonly, one frequency in "negative" at the saddle point, the one that is > "responssible" of the transition and the following of its eigen vector from > the initial state give the minimum energy path. > However, when two phonon frequencies are "negatives" at the saddle point, > that means that at least 3 energy minima are link together to the same > saddle point. > The transition state theory cannot be applied there as the preexponential > term is the ratio of the 3N-3 phonon frequencies of initial state over the > 3N-4 frequencies of the saddle point, giving the dimension of a time (state > life time) > Using 3N-5 frequencies without the two negatives ones would not have a > physical meaning for the initial partition function. > > Any idea on how to treat such a problem to evaluate the transition rate would > be appreciated. > > Best regards. > > Antoine Jay ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] How to calculate Mean Square Displacement (MSD)
Hello, Yes, you should account for periodic boundaries and fold back images. Details and algorithms can be found in: Computer Simulation of Liquids'' by M.P. Allen and D. Tildesley Clarendon Press Oxford 1987. Best, Pascal Boulet — Professor in computational chemistry - DEPARTEMENT OF CHEMISTRY Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email : pascal.bou...@univ-amu.fr Le 30 oct. 2017 à 08:29, Nam Tran a écrit : > Dear QE experts, > > I am trying to evaluate MSD for my simulation. > My problem is that when an atom exits the simulation cell. > I do not know whether I should consider the distance with atom that goes > about outside the box (a) or its image (b). Please check the image below > (Blue is the original position t=0, red is the position at time t) > > > Best Regards > Nam Tran > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Big Bugs in PDOS calculations for Quantum Espresso 5.1
Hello, I may be wrong but your input file looks strange: you have an isolated molecule (CO) but you specify 6 as a Bravais lattice and a mesh of k-points. I would choose ibrav=0, kpoint=gamma, assume_isolated=… , and a big box to be sure the molecule is isolated. Perhaps you will get better results with these options…(?) HTH, Pascal - Pascal Boulet - Professor - DEPARTEMENT OF CHEMISTRY Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email : pascal.bou...@univ-amu.fr Le 10 oct. 2017 à 03:37, Jibiao Li a écrit : > > Dear QE developers, > > Here I am reporting a big bug in Quantum Espresso. QE 6.1 and 5.1 yield > completely different pdos for a simple CO molecule. The results from QE 5.1 > are completely wrong, because 2px and 2py associated with 1pi orbitals should > not be splitted into three levels. These outcomes are impossible for DFT > calculations. The results from QE 6.1 is also unsatisfying;the 2pz states > should not be populated at a deep level below -28 eV? > > Best > > Jibiao Li > > Yangtze Normal Univeristy, China > > CO.pw.inp > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '/home/jibiao/Calc/CO_Fe100/T/' , > pseudo_dir = '/home/jibiao/Codes/pseudo/' , > prefix = 'CO' , > tstress = .true. , > tprnfor = .true. , > / > &SYSTEM >ibrav = 6, >celldm(1) = 10.847032278, >celldm(3) = 3.28, > nat = 2, > ntyp = 2, > ecutwfc = 29 , > ecutrho = 180 , > occupations = 'smearing' , > degauss = 0.05D0 , > smearing = 'methfessel-paxton' , > exxdiv_treatment = 'gygi-baldereschi' , > / > &ELECTRONS > mixing_beta = 0.2D0 , > diagonalization = 'david' , > / > ATOMIC_SPECIES > C 12.01000 C.pbe-van_ak.UPF > O 15.99900 O.pbe-van_ak.UPF > ATOMIC_POSITIONS angstrom > C 2.870022.869767.634009081 > O 2.870222.869898.812254230 > K_POINTS automatic > 4 4 1 0 0 0 > > CO.projwfc.in > > &PROJWFC > prefix = 'CO' , > outdir = '/home/jibiao/Calc/CO_Fe100/T/' , > ngauss = 0 , > degauss = 0.01470 , > DeltaE = 0.02 , > / > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Parallelism
Dear all, We have a rather big system (a=b=c= 20 angs) of 646 atoms, 2160 states. We are running it at the Gamma point with PBE functional (no hybrid). Here are our settings: We use 6*12=72 processors. Task groups = 1 We set nr1s, nr2s and nr3s to 216, so that 72 is a divisor of 216, as suggest in the manual (we are using USPP, ecut=48 Ry, ecutRho=10*ecut). FFTs are performed on a 6*6 grid (option ndiag=36). The job runs for 1 hour (I set this limit for the test in the queuing system) but QE cannot perform even the 1st step of the SCF cycle (last lines of output = iteration # 1 ecut=48.00 Ry beta=0.20 Davidson diagonalization with overlap). Are the above settings wrong? Or should we just use more processors? Could the openmp option be useful in this case? Thank you for your hints, Best, Pascal - Pascal Boulet - Professor - DEPARTEMENT OF CHEMISTRY Aix-Marseille University - ST JEROME - Avenue Escadrille Normandie Niemen - F-13013 Marseille - FRANCE Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/infos - Email : pascal.bou...@univ-amu.fr ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Quantum Espresso
Hello, 1. Use VESTA to cut a cluster out of the crystalline structure of the bulk Al. Use Google to find some tutorials on how to use VESTA for that purpose. 2. Use QE tutorials to make the input file for your particular case. It should be easy, but you have to do your homework. Best, Pascal - Pascal Boulet - MCF HDR, Resp. L2 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/annuaire - Email : pascal.bou...@univ-amu.fr Le 10 juil. 2017 à 15:32, Shishir Timilsena a écrit : > i am new to quantum espresso.. > > On Mon, Jul 10, 2017 at 6:56 PM, Giovanni Cantele > wrote: > 1) please provide name and affiliation, when posting messages > > 2) generally speaking, it is difficult that people might provide just the > input file(s) you need, much more likely instead to > get help about more specific issues > > 3) in the case someone has worked on the same system you are planning to deal > with, the question should be more precise. > Even going to the old literature on metal clusters (literature that you can > easily find and read), e.g. > https://journals.aps.org/prl/pdf/10.1103/PhysRevLett.67.224 , > for a given number of atoms, metal clusters > might (and usually do) have isomers. So the input relative to which isomer of > which Al_n cluster you are interested in? > > Maybe the right route is to identify the system, look at the possible issues > arising in a typical DFT calculation with that system > (there should be and extensive literature on the subject), try to perform > simple calculations (e.g. with small number of atoms, I would > try Al4 of the above mentioned paper), and then move to more complex > calculations. You need to build a supercell. Are you familiar with supercell > calculations? If not, try to use google to find Quantum-ESPRESSO related > tutorials. > > Giovanni > > >> On 10 Jul 2017, at 14:55, Shishir Timilsena wrote: >> >> can anyone send me the input file for aluminum cluster ??? >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > -- > > Giovanni Cantele, PhD > CNR-SPIN > c/o Dipartimento di Fisica > Universita' di Napoli "Federico II" > Complesso Universitario M. S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > e-mail: giovanni.cant...@spin.cnr.it > Phone: +39 081 676910 > Skype contact: giocan74 > > ResearcherID: http://www.researcherid.com/rid/A-1951-2009 > Web page: http://people.fisica.unina.it/~cantele > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Quantum Espresso
Hello, 1. Use VESTA to cut a cluster out of the crystalline structure of the bulk Al. Use Google to find some tutorials on how to use VESTA for that purpose. 2. Use QE tutorials to make the input file for your particular case. It should be easy, but you have to do your homework. Best, Pascal - Pascal Boulet - MCF HDR, Resp. L2 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/annuaire - Email : pascal.bou...@univ-amu.fr Le 10 juil. 2017 à 15:32, Shishir Timilsena a écrit : > i am new to quantum espresso.. > > On Mon, Jul 10, 2017 at 6:56 PM, Giovanni Cantele > wrote: > 1) please provide name and affiliation, when posting messages > > 2) generally speaking, it is difficult that people might provide just the > input file(s) you need, much more likely instead to > get help about more specific issues > > 3) in the case someone has worked on the same system you are planning to deal > with, the question should be more precise. > Even going to the old literature on metal clusters (literature that you can > easily find and read), e.g. > https://journals.aps.org/prl/pdf/10.1103/PhysRevLett.67.224 , > for a given number of atoms, metal clusters > might (and usually do) have isomers. So the input relative to which isomer of > which Al_n cluster you are interested in? > > Maybe the right route is to identify the system, look at the possible issues > arising in a typical DFT calculation with that system > (there should be and extensive literature on the subject), try to perform > simple calculations (e.g. with small number of atoms, I would > try Al4 of the above mentioned paper), and then move to more complex > calculations. You need to build a supercell. Are you familiar with supercell > calculations? If not, try to use google to find Quantum-ESPRESSO related > tutorials. > > Giovanni > > >> On 10 Jul 2017, at 14:55, Shishir Timilsena wrote: >> >> can anyone send me the input file for aluminum cluster ??? >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > -- > > Giovanni Cantele, PhD > CNR-SPIN > c/o Dipartimento di Fisica > Universita' di Napoli "Federico II" > Complesso Universitario M. S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > e-mail: giovanni.cant...@spin.cnr.it > Phone: +39 081 676910 > Skype contact: giocan74 > > ResearcherID: http://www.researcherid.com/rid/A-1951-2009 > Web page: http://people.fisica.unina.it/~cantele > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] building surfaces using gdis
Hello, You can try with VESTA: http://jp-minerals.org/vesta/en/ HTH Pascal - Pascal Boulet - MCF HDR, Resp. L2 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/annuaire - Email : pascal.bou...@univ-amu.fr Le 19 mai 2017 à 10:11, Winfred Mulwa a écrit : > Dear all > I am trying to build surfaces using gdis and it shows i am not getting there. > Kindly, is there any one with an idea on how to go about it?? > Kind regards > Dr. Mulwa Winfred. > Computational Material Science, > University of Eldoret, > Kenya. > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Figure of merit(ZT)
Hello, I guess nobody can answer you. You give no information about how you calculate these data: codes, technical conditions of calculations… How do you get ZT? What do you mean by with or without occupation? What is "k-mesh": number of k-points? Also, please give your affiliation, so we know whom we are discussing with. Best regards Pascal - Pascal Boulet - MCF HDR, Resp. L2 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/annuaire - Email : pascal.bou...@univ-amu.fr Le 10 mai 2017 à 16:04, ade wale a écrit : > Dear all, > There is inconsistence in my ZT value for SrTiO3, when its pure 60atoms > (0.61 @ 800K with k-mesh of 1200, 0.57 @800k with k-mesh of 12) which is > very high compare to Pr doping 8% according to literature(0.21, 0.23 @ > 800K,670K respectively) all without using occupation, even with occupation > its too high(0.95 @800K with k-mesh of 12). > >But, my own Pr doping 8%(0.22, 0.24, 0.38 @ 750K, 800K,1150K > respectively, > with k-mesh of 45) with occupation. > Please what can I do. > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Symmetry recognition
Dear all, Thank you for your answers. I am trying to reproduce it with a smaller system… I indeed restart from an incomplete calculation. Pascal Le 23 févr. 2017 à 21:45, Paolo Giannozzi a écrit : > Of course there is a reason, but not necessarily a good one. If you > are "restarting from an incomplete calculation", I guess that the code > overwrites the input coordinates with the current ones. The symmetry > should be the same, but sometimes numerical noise breaks the symmetry. > It is impossible to say more without an example. > > Paolo > > On Thu, Feb 23, 2017 at 8:56 AM, Pascal Boulet > wrote: >> Dear all, >> >> I am running a structural optimization with QE 6.0. The structure is >> orthorhombic, ibrav=8, with 8 symmetry elements. The first run did not >> converge so I have to restart it. But as I restart it, the number of >> symmetry is now 4, there is a descent of symmetry. I shall say that I use >> the space_group option with COORDINATES crystal_sg. But the problem remains >> if I put all the coordinates (unsurprisingly). >> >> Is there a reason for this, and can I avoid this? >> >> Thank you >> Best regards >> Pascal >> >> - >> Pascal Boulet - MCF HDR, Resp. L2 MPCI - DEPARTEMENT CHIMIE >> Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - >> 13013 Marseille >> Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 >> Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/annuaire - Email : >> pascal.bou...@univ-amu.fr >> >> >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Symmetry recognition
Dear all, I am running a structural optimization with QE 6.0. The structure is orthorhombic, ibrav=8, with 8 symmetry elements. The first run did not converge so I have to restart it. But as I restart it, the number of symmetry is now 4, there is a descent of symmetry. I shall say that I use the space_group option with COORDINATES crystal_sg. But the problem remains if I put all the coordinates (unsurprisingly). Is there a reason for this, and can I avoid this? Thank you Best regards Pascal - Pascal Boulet - MCF HDR, Resp. L2 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://madirel.univ-amu.fr/pages_web_BOULET_PASCAL/annuaire - Email : pascal.bou...@univ-amu.fr ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] problem about inputfile
Hello, There is a $ instead of & before IONS, maybe… Pascal Le 1 janv. 2017 à 16:16, Nasim Ha a écrit : > I want run pw.x but it stopped with this eroor : Error in routine > read_cards_pw (1): > atomic position info missing > I insert inputfile. > -- > N.H.Jazi > PhD student of Physics. > Physics Department,Central Tehran Branch,Islamic Azad > University,Tehran,88074907,Iran. > <2polyaniline.pw-in>___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] regarding convergence of system
Hello, At first glance: 1.The mixing parameter is probably to high: try 0.2 instead of 0.7. 2.Do you need electron smearing? Is it a metal? If not, I would first try occupation=‘fixed’ together with nbnd=n (number of orbitals valence+conduction) and remove smearing and degauss keywords. 3. This an oxide, you might need DFT+U… I do not know for sure. At 2nd glance: please give your affiliation! HTH, Pascal - Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Le 4 oct. 2016 à 12:15, Amita Sihag a écrit : > Dear all > I am trying to converge a supercell(2*2*1) of LaCoO3. The system is not > converged even after 500 iterations and 6 days. It is not achieving > convergence after so long.Please suggest the necessary. It will be a great > help.I am posting the input file of system > > &CONTROL >title = 'LaCoO3' , > prefix = 'LaCoO3' > calculation = 'vc-relax' , > max_seconds = 1.0d+7 , > restart_mode = 'from_scratch' > outdir = > '/home/SSM_grp/amitasihag/LaCoO3/221/nonmagnetic/out' , > pseudo_dir = './' , > / > &SYSTEM >ibrav = 0, > celldm(1)= 1.89 , > nat = 40, > ntyp = 3, > ecutwfc = 30 , > ecutrho = 300 , > occupations = 'smearing' , > smearing = 'gaussian' , > degauss = 0.020 > / > &ELECTRONS > electron_maxstep = 1500 , > conv_thr = 1.0d-4 , > mixing_mode = 'plain' , > mixing_beta = 0.7 , > diagonalization = 'david' , > > / > &IONS > / > &CELL > / > CELL_PARAMETERS alat > 11.145365372 -0.712543576 -0.511263360 >4.817125474 10.076876074 -0.512591875 >2.406770662 1.411311463 4.846536018 > > ATOMIC_SPECIES >La 138.91 La.pbe-nsp-van.UPF >Co 58.933 Co.pbe-sp-van.UPF >O15.999 O.pbe-van_ak.UPF > ATOMIC_POSITIONS alat > La 2.570235772 1.475769989 1.203980885 > La 5.043826568 6.594009649 0.701404953 > La 8.208023646 1.169121254 0.739924489 > La 10.540444808 6.193518050 0.672086391 > La 7.828816665 4.582125889 3.150594320 > La 10.161237827 9.606522686 3.082756222 > La 13.325435071 4.181634280 3.121275751 > La 15.799025866 9.299873941 2.618699819 > Co 0.0 0.0 0.0 > Co 2.408562737 5.038438038 -0.256295937 > Co 5.572682687 -0.356271788 -0.255631680 > Co 7.981245423 4.682166250 -0.511927617 > Co 5.193223752 3.052636419 2.165050529 > Co 7.602625127 8.080210085 1.913608150 > Co 10.766636570 2.695433772 1.909072328 > Co 13.176037945 7.723007437 1.657629949 > O6.992683749 5.929956840 3.249477607 > O9.402656127 10.967922022 2.996121010 > O 12.568245646 5.570689038 2.997441518 > O 14.982978449 10.597343273 2.736823953 > O3.386282547 0.178300388 1.085856789 > O5.801015207 5.204954323 0.825239239 > O8.966605535 -0.192278403 0.826559701 > O 11.376577768 4.845686479 0.573203119 > O7.789346679 3.623570534 4.584043374 > O 10.199663612 8.717912060 4.247900859 > O 13.363561035 3.352073083 4.210598832 > O 15.771782625 8.288580019 4.090623371 > O2.597478896 2.487063627 -0.267942599 > O5.005700775 7.423571164 -0.387918090 > O8.169597743 2.057731597 -0.425220079 > O 10.579914964 7.152073724 -0.761362624 > O8.554085222 4.145085667 2.016871101 > O 11.033664829 9.142012963 1.654431985 > O 14.196470737 3.749360741 1.656499814 > O 16.536162443 8.824852211 1.505548708 > O1.833099424 1.950791650 2.317132061 > O4.172791165 7.026283196 2.166180951 > O7.335596976 1.633630902 2.168248787 > O9.815176618 6.630558274 1.805809668 > K_POINTS automatic > 2 2 4 0 0 0 > > Thank you > Amita > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Skutterudite
Hello, Here is a paper reference from which you can get the crystal data. Pascal Le 24 sept. 2016 à 00:40, Taiwo Oginni a écrit : > -- Forwarded message -- > From: "Taiwo Oginni" > Date: Sep 23, 2016 16:22 > Subject: Skutterudite > To: > Cc: > > Pls can someone help me with atomic positions of skutterudite compound > especially CoSb3,thanks. > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum - Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] restarting a nscf run
Dear all, Just a simple question. I have run a nscf calculation that was stopped by the queuing system because it exceeded the allocated time. If I resubmit it, is it going to continue or start over? Thank you. Best regards Pascal -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Hugoniot Calculation...
Hello, that’s the kind of question you have to solve in the first place with your supervisor (what needs be calculated, etc.), eventually with the help of QE manual. Best regards Pascal Le 5 juin 2016 à 17:04, Ramon Valencia a écrit : > Dear pwscf users, > > I would like to know how calculate the Hugoniot curve using pwscf (MD > calculation) step by step. > > Thank you in advance. > > Rezor... > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] error: nb less than number of procs
Thanks for the answer. We have decreased the number of procs and it works. Pascal Le 24 mai 2016 à 14:24, Paolo Giannozzi a écrit : > nb is related to the number of bands, not necessarily equal to it. Anyway: it > means that linear-algebra operations such as conventional diagonalization or > iterative orthonormalization are parallelized on too many processors (-nd N) > > Paolo > > On Tue, May 24, 2016 at 11:23 AM, Pascal Boulet > wrote: > Dear all, > > we have a crash with the message: error in routine blk2cyc_redist(1): nb less > than the number of proc. > > What is nb? Is it the number of electronic bands (nbnd)? > > Best regards > Pascal > > -- > Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE > Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - > 13013 Marseille > Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 > Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr > Afin de respecter l'environnement, merci de n'imprimer cet email que si > nécessaire. > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > > > -- > Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > _______ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] error: nb less than number of procs
Dear all, we have a crash with the message: error in routine blk2cyc_redist(1): nb less than the number of proc. What is nb? Is it the number of electronic bands (nbnd)? Best regards Pascal -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Error in routine read_namelists (5010):
Hello, « reading namelist control » means there is a wrong (not existing,…) or misspelled keyword in the CONTROL namelist. Check carefully your input against the website manual, and you will find your mistake… Best regards Pascal Le 22 mai 2016 à 22:30, Korichi Khadija a écrit : > hello > I am new to Quantum Espresso and when I run pw.x of the scrpit below , > > &control > calculation='scf' > restart_mode='from_scratch', > pseudo_dir='/home/Julnar/software/espresso-4.3.2/pseudo', > outdir='/scratch/' > prefix='lead' > tmp_dir='/home/Julnar/software/espresso-4.3.2/S3DE/iotk/tmp' > > / > &system > ibrav = 6, > celldm(1) = 7.5416, > celldm(3) = 0.98655, > nat= 5, > ntyp= 3, > nspin = 2, > starting_magnetization(2)=1.0, > ecutwfc = 37.0, > ecutrho = 370.0 > occupations='smearing', > smearing='methfessel-paxton', > degauss=0.01 > / > &electrons > conv_thr = 1.0e-8 > mixing_beta = 0.1 > / > ATOMIC_SPECIES > Sr 87.62 Sr.pw91-nsp-van.UPF > Ru 101.10 Ru.pw91-n-van.UPF > O 16.00 O.pw91-van_ak.UPF > ATOMIC_POSITIONS > Sr0 0 0 > O 0.5 0.5 0 > Ru0.5 0.5 0.494 > O 0.5 0 0.494 > O 0 0.5 0.494 > K_POINTS (automatic) > 10 10 10 1 1 1 > > *** > > I am getting the following error: > > > > 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); > 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 > Waiting for input... > Reading input from standard input > > > %% > Error in routine read_namelists (5010): > reading namelist control > %%%%%%%% > > > > Please may someone shed some light on to why this is the case, and if there > is anything wrong with my input. ? > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Relativistic pseudopotential for Zr
Hello, You can find various flavors of relativistic pseudo potentials for Zr (and S) in the pslibrary. See http://www.quantum-espresso.org/pseudopotentials/pslibrary/ HTH, Pascal Le 11 mai 2016 à 21:23, Sohail Ahmad a écrit : > Dear QE users > I wish to study spin orbit effect in ZrS2. > Unfortunately, relativistic pseudopotential is not available for Zr on QE > website. > Can we use scalar relativistic for Zr and fully relativistic for S for SOC > calculation? > Can anyone provide me fully relativistic pseudopotential for Zr? > Best Wishes > - > Dr. Sohail Ahmad > King Khalid University > Abha, Saudi Arabia > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] (no subject)
Hello, Yes, peak one up in the table at https://en.wikipedia.org/wiki/Hexagonal_crystal_system and go to http://www.cryst.ehu.es to get symmetry operations. Pascal Le 6 janv. 2016 à 07:42, Nasrin zekavat falak a écrit : > > > Hi dear > pleaz ,Full symmetry of the hexagonal structure to send me. > Thank you. > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Convergence Not Acheived
Hello, It should not be a problem to converge this structure... I suggest you to try this first: mixing_beta = 0.2 For HGH type of pseudopotentials you may need to use a much higher cut-off energy to get reliable results (between 80 and 120 Ry, to be tested). HTH Pascal Le 13 déc. 2015 à 00:52, Mofrad, Amir Mehdi (MU-Student) a écrit : > Dear all Quantum Espresso users and developers, > > I want to do a geometry optimization on Sodalite. My problem is that > apparently after 100 iterations it does not converge and the run stops. I > attach my both input file and output file. Any help would be unconditionally > appreciated. > > Best, > > Amir M. Mofrad > University of Missouri > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] add vacuum
Hello, you can relax the cell in the directions of the slab using keyword cell_do_free. HTH Pascal Le 11 déc. 2015 à 09:33, Jaret Qi a écrit : > Hello QE users, > I need to add vacuum along the z-direction to study E-field effect using > saw-like potential. In this case do I need to do vc-relax or relax will be > enough? > > Thank you in advance, > Jaret > ASU > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] adding vacuum
So, I think in this case you should also relax the z-axis: The system tends to fill the vacuum by moving atoms since it cannot adapt the cell parameter. Pascal Le 16 nov. 2015 à 21:49, Jaret Qi a écrit : > To make it clear, I am not adding vacuum to isolate my system like in > graphene where we make the z-axis large enough to make it graphene not > graphite. My system is a (001) interface between semi-metallic and > semiconductor, so i am trying to minimize the interaction along the interface > which is along the z-axis and study some properties and match it with > experimental results. I need a reasonable vacuum so I began with 4A. > > > > > > On Monday, November 16, 2015 1:31 PM, Nicola Marzari > wrote: > > > On 16/11/2015 21:17, Jaret Qi wrote: > > but that will cost time! > > you are right! just keep the 4 angstroms, no one will notice. > > (actually, skip the calculations altogether, and make up some > plausible numbers in your paper - that will be even faster). > > nicola > > > > > > > > > On Monday, November 16, 2015 9:26 AM, Pascal Boulet > > wrote: > > > > > > Hello, > > > > 4 angstroms wide seems to be very small for the vacuum. As a rule of > > thumb you should use at least 2.5 times the thickness of your slab. This > > is what we observed in the calculations of semiconductor slabs. This has > > to be tested. > > > > Pascal > > > > Le 16 nov. 2015 à 16:40, Jaret Qi > <mailto:jare...@yahoo.com>> a écrit : > > > >> Hello all, > >> I am trying to minimize the interaction between my system and its > >> periodic images. To do so, I introduced a layer of vacuum along the > >> z-axis by increasing the lattice vector along the z-axis by 4A. At the > >> same time, I fixed it by using this parameter: cell_dofree='2Dxy', > >> But I have noticed atoms that are close to the vacuum move along the > >> z-axis and vacuum is decreasing, is this wrong or I should use > >> different cell_dofree? > >> note:relaxation still ongoing, not relaxed yet. > >> > >> > >> JARET, > >> ASU > >> ___ > >> Pw_forum mailing list > >> Pw_forum@pwscf.org <mailto:Pw_forum@pwscf.org> > >> http://pwscf.org/mailman/listinfo/pw_forum > > > > -- > > Pascal Boulet /- MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE/ > > Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie > > Niemen - 13013 Marseille > > Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 > > Site : http://allos.up.univ-mrs.fr/pascal - Email : > > pascal.bou...@univ-amu.fr <mailto:pascal.bou...@univ-amu.fr> > > /Afin de respecter l'environnement, merci de n'imprimer cet email que si > > nécessaire./ > > > > > > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > -- > Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL > Director, National Centre for Competence in Research NCCR MARVEL, EPFL > http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project > > > -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] adding vacuum
Hello, 4 angstroms wide seems to be very small for the vacuum. As a rule of thumb you should use at least 2.5 times the thickness of your slab. This is what we observed in the calculations of semiconductor slabs. This has to be tested. Pascal Le 16 nov. 2015 à 16:40, Jaret Qi a écrit : > Hello all, > I am trying to minimize the interaction between my system and its periodic > images. To do so, I introduced a layer of vacuum along the z-axis by > increasing the lattice vector along the z-axis by 4A. At the same time, I > fixed it by using this parameter: cell_dofree='2Dxy', > But I have noticed atoms that are close to the vacuum move along the z-axis > and vacuum is decreasing, is this wrong or I should use different cell_dofree? > note:relaxation still ongoing, not relaxed yet. > > > JARET, > ASU > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Error in Calculus of bands
Hello, This question has been answered many times. Search on the QE forum (see 1st page of QE website). Best regards Pascal Le 21 sept. 2015 à 22:00, Yenner Bentarcurt a écrit : > Dear all user of Quantum espresso > I'm running a calculus of bands structure of the maghemite ( space group 212) > and this fails and > the following error is reported > .. >Band Structure Calculation > Davidson diagonalization with overlap > > %% > Error in routine cdiaghg (761): > S matrix not positive definite > %% > > stopping ... > - > > The input used is > > &CONTROL > calculation = 'bands' , > wf_collect = .true. , > > / > &SYSTEM > ibrav = 1, > celldm(1) = 16.1229, > nat = 53, >ntyp = 2, > ecutwfc = 40 , > ecutrho = 800 , >nbnd = 380, > ... > / > &ELECTRONS >. > / > ATOMIC_SPECIES > Fe 55.84500 Fe.pbe-sp-van_ak.UPF >O 15.99940 O.pbe-van_ak.UPF > ATOMIC_POSITIONS bohr > Fe 2.2029671501.738169599 10.054652074 > Fe 13.9287261229.970672948 13.794011253 > . > K_POINTS > 21 > 0.50.50.5 1.0 > 0.40.40.4 2.0 > 0.30.30.3 3.0 > 0.20.20.2 4.0 > 0.10.10.1 5.0 > 0.00.00.0 6.0 > 0.10.00.0 7.0 > 0.20.00.0 8.0 > 0.30.00.0 9.0 > 0.40.00.0 10.0 > 0.50.00.0 11.0 > 0.50.10.0 12.0 > 0.50.20.0 13.0 > 0.50.30.0 14.0 > 0.50.40.0 15.0 > 0.50.50.0 16.0 > 0.40.40.0 17.0 > 0.30.30.0 18.0 > 0.20.20.0 19.0 > 0.10.10.0 20.0 > 0.00.00.0 21.0 > > > Being all for now, I await a reply > > Yenner > PhD Student > Central University of Venezuela > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Effective parallel implementation?
0.337592989 0.921446502 >> Sb 0.157106996 0.0 0.168796495 >> Sb 0.157106996 0.0 0.668796480 >> Sb 0.842893004 0.0 0.331203520 >> Sb 0.842893004 0.0 0.831203520 >> Sb 0.157106996 0.0 0.331203520 >> Sb 0.157106996 0.0 0.831203520 >> Sb 0.842893004 0.0 0.168796495 >> Sb 0.842893004 0.0 0.668796480 >> Sb 0.337592989 0.157106996 0.0 >> Sb 0.337592989 0.157106996 0.5 >> Sb 0.662407041 0.842893004 0.0 >> Sb 0.662407041 0.842893004 0.5 >> Sb 0.662407041 0.157106996 0.0 >> Sb 0.662407041 0.157106996 0.5 >> Sb 0.337592989 0.842893004 0.0 >> Sb 0.337592989 0.842893004 0.5 >> Sb 0.5 0.837592959 0.328553498 >> Sb 0.5 0.837592959 0.828553498 >> Sb 0.5 0.162407011 0.171446502 >> Sb 0.5 0.162407011 0.671446502 >> Sb 0.5 0.162407011 0.328553498 >> Sb 0.5 0.162407011 0.828553498 >> Sb 0.5 0.837592959 0.171446502 >> Sb 0.5 0.837592959 0.671446502 >> Sb 0.657106996 0.5 0.418796480 >> Sb 0.657106996 0.5 0.918796480 >> Sb 0.342893004 0.5 0.081203505 >> Sb 0.342893004 0.50000 0.581203520 >> Sb 0.657106996 0.5 0.081203505 >> Sb 0.657106996 0.5 0.581203520 >> Sb 0.342893004 0.5 0.418796480 >> Sb 0.342893004 0.5 0.918796480 >> Sb 0.837592959 0.657106996 0.25000 >> Sb 0.837592959 0.657106996 0.75000 >> Sb 0.162407011 0.342893004 0.25000 >> Sb 0.162407011 0.342893004 0.75000 >> Sb 0.162407011 0.657106996 0.25000 >> Sb 0.162407011 0.657106996 0.75000 >> Sb 0.837592959 0.342893004 0.25000 >> Sb 0.837592959 0.342893004 0.75000 >> U 0.0 0.0 0.0 >> U 0.0 0.0 0.5 >> K_POINTS automatic >> 4 4 2 0 0 0 >> > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Calculating cell constants in different tempretures
Hello, Vc-relax is useful for relaxing the cell parameters and atomic positions at zero kelvin. For finite temperature simulation you have to choose ‘vc-md’ for the calculation, beeman for ions (which is the default), ‘pr' or ‘w' for the cell dynamics and the appropriate temperature for ions (see tempw and ion_temperature). These are the basic keywords to start. HTH Pascal Le 26 août 2015 à 09:25, reza vatan a écrit : > Dear QE Users: > > I want to calculate the lattice constant of crystalline Si in different > temperatures. I tried "vc-relax" calculations with ion_temperature = > "rescaling" and tempw = 100D0 options, but it didn't work. So I just wanted > to know if any one here could help me regarding this problem? > > Any comments would be highly appreciated. > > Many thanks, > Reza Vatan, > Electerical Engineering Department, > Arizona State University > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Displaying charge density difference
Hi ozan, to try to give you an answer one has to know between what and what you want to calculate the difference. Cheers. Pascal > > From: Ozan Dernek > Sent: Tue Aug 25 16:33:02 CEST 2015 > To: > Subject: [Pw_forum] Displaying charge density difference > > > Hi, > I want to display the difference of charge densities of a bimetallic > structure by using VMD. > But the .cube file has only the charge density information. Is it possible to > obtain charge density difference by using weight flag or should I do separate > calculations ? (For both cases an explanation about how to do them will be > much appreciated.) > > Cheers, > Ozan > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Calculation of Physical quantity using pw.x executable.
Dear Sapna, Easy answer: have a look at the numerous examples given in the QE distribution. Run the examples, learn the logic of the keywords. Best regards Pascal Le 10 août 2015 à 07:49, sapna bondwal a écrit : > > Dear all, > > I want someone to give me the gist of all properties that can be calculated > and all physical quantities that can be obtained by using pw.x executable. > I am interested in nanosystems. I have seen supercell approach written in > every paper but I want to make it clear what it actually is? How do we use > it for doing structural optimization of nanosystem? I expect some simple > examples which can clarify the basic approach. > -- > > Sapna Bondwal > Research Scholar > IIT ROORKEE > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Can I obtain IR spectrum from CPMD trajectory in Quantum Espresso?
Thank you Giuseppe for your answer. Best, Pascal Le 29 juil. 2015 à 23:26, Giuseppe Mattioli a écrit : > > Dear Pascal > If I remember well, you can obtain the cell dipole trajectory by > adding assume_isolated='mp' to your cp.x molecular dynamics input of a > system contained in a cubic cell (mp is defined for cubic cells only). > But the system should be really "isolated" (e.g., a molecule with its > center of mass always near to the center of the box) or you may have > jumps in the dipole due to PBC which should result in noise when you > FFT the dipole autocorrelation function. In my experience (an isolated > Co-oxo cluster), it was the only way to obtain an IR spectrum in a > DFT+U framework (DFPT still does not work together with DFT+U). It > should be also useful in the case of vdw corrections implemented in > cp.x. > HTH > Giuseppe > > Quoting Pascal Boulet : > >> Thank you Paolo and Nicola for your answer. >> >> Best >> Pascal >> >> Le 29 juil. 2015 à 18:16, Paolo Giannozzi a écrit : >> >>> From the FFTs of the atomic velocity autocorrelation function you >>> can extract phonon frequencies, but you do not get "true" spectra >>> >>> Paolo >>> >>> On Wed, Jul 29, 2015 at 6:08 PM, Pascal Boulet >>> wrote: >>> Hello, >>> >>> Isn’t it possible to get IR spectra from the FFTs of the atomic >>> velocity autocorrelation function? >>> >>> Pascal >>> >>> Le 29 juil. 2015 à 17:58, Nicola Marzari a écrit : >>> >>>> >>>> Dear Yin, >>>> >>>> >>>> you need to calculate at every time step the total dipole in the unit >>>> cell, and then do the fourier transform of the autocorrelation - see e.g. >>>> here: http://journals.aps.org/prl/pdf/10.1103/PhysRevLett.81.1235 or many >>>> other papers published on the topic. >>>> >>>> Note that if you do Car-Parrinello MD, rather than Born-Oppenhimer MD, >>>> the vibrational frequencies can be slightly softened due to the fact >>>> that the ions are dressed (and slowed down) by the coefficients of the >>>> plane waves. The smaller the fictitious mass, the small the effect. >>>> >>>> Now, I'm not sure how to write the polarization at every time step - >>>> maybe others can comment or add to the documentation. For PWSCF >>>> you'd switch on lberry, but I'm not sure if you can do it during an >>>> md (if now, maybe switch on lelfield, and then keep the applied field >>>> equal to zero). >>>> >>>> In CP I suppose you could switch tefield on, but still have zero >>>> applied field. >>>> >>>> Any other suggestion? Also, I think that tefield in CP and in PWSCF >>>> mean different things - shall we switch the name in CP to lelfield? >>>> >>>>nicola >>>> >>>> >>>> >>>> On 29/07/2015 15:56, liyinc...@gmail.com wrote: >>>>> Dear Quantum Espresso developers, >>>>> >>>>> I want to obtain IR spectra of crystals at room temperature. Considering >>>>> the temperature effect, I decided to use CPMD. I wonder whether it is >>>>> possible to get IR spectra from CPMD trajectory in Quantum Espresso? >>>>> What's more, can I involve vdw-correction in CPMD? If yes, can IR >>>>> spectra be calculated in the presence of vdw-correction? >>>>> >>>>> Thank you very much! >>>>> >>>>> Best Regards, >>>>> ---- >>>>> Dr. Yin Li >>>>> Department of Biophysics,Medical School, University of Pecs, >>>>> No.12 Szigeti Street, Pecs, H-7624, HUNGARY >>>>> Phone: +36-72-535271/36271 >>>>> >>>>> >>>>> ___ >>>>> Pw_forum mailing list >>>>> Pw_forum@pwscf.org >>>>> http://pwscf.org/mailman/listinfo/pw_forum >>>>> >>>> >>>> -- >>>> -- >>>> Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL >>>> Director, National Centre for Competence in Research NCCR MARVEL, EPFL >>>
Re: [Pw_forum] Can I obtain IR spectrum from CPMD trajectory in Quantum Espresso?
Thank you Paolo and Nicola for your answer. Best Pascal Le 29 juil. 2015 à 18:16, Paolo Giannozzi a écrit : > From the FFTs of the atomic velocity autocorrelation function you can extract > phonon frequencies, but you do not get "true" spectra > > Paolo > > On Wed, Jul 29, 2015 at 6:08 PM, Pascal Boulet > wrote: > Hello, > > Isn’t it possible to get IR spectra from the FFTs of the atomic velocity > autocorrelation function? > > Pascal > > Le 29 juil. 2015 à 17:58, Nicola Marzari a écrit : > >> >> Dear Yin, >> >> >> you need to calculate at every time step the total dipole in the unit >> cell, and then do the fourier transform of the autocorrelation - see e.g. >> here: http://journals.aps.org/prl/pdf/10.1103/PhysRevLett.81.1235 or many >> other papers published on the topic. >> >> Note that if you do Car-Parrinello MD, rather than Born-Oppenhimer MD, >> the vibrational frequencies can be slightly softened due to the fact >> that the ions are dressed (and slowed down) by the coefficients of the >> plane waves. The smaller the fictitious mass, the small the effect. >> >> Now, I'm not sure how to write the polarization at every time step - >> maybe others can comment or add to the documentation. For PWSCF >> you'd switch on lberry, but I'm not sure if you can do it during an >> md (if now, maybe switch on lelfield, and then keep the applied field >> equal to zero). >> >> In CP I suppose you could switch tefield on, but still have zero >> applied field. >> >> Any other suggestion? Also, I think that tefield in CP and in PWSCF >> mean different things - shall we switch the name in CP to lelfield? >> >> nicola >> >> >> >> On 29/07/2015 15:56, liyinc...@gmail.com wrote: >>> Dear Quantum Espresso developers, >>> >>> I want to obtain IR spectra of crystals at room temperature. Considering >>> the temperature effect, I decided to use CPMD. I wonder whether it is >>> possible to get IR spectra from CPMD trajectory in Quantum Espresso? >>> What's more, can I involve vdw-correction in CPMD? If yes, can IR >>> spectra be calculated in the presence of vdw-correction? >>> >>> Thank you very much! >>> >>> Best Regards, >>> >>> Dr. Yin Li >>> Department of Biophysics,Medical School, University of Pecs, >>> No.12 Szigeti Street, Pecs, H-7624, HUNGARY >>> Phone: +36-72-535271/36271 >>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> -- >> -- >> Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL >> Director, National Centre for Competence in Research NCCR MARVEL, EPFL >> http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > -- > Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE > Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - > 13013 Marseille > Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 > Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr > Afin de respecter l'environnement, merci de n'imprimer cet email que si > nécessaire. > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > > > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Can I obtain IR spectrum from CPMD trajectory in Quantum Espresso?
Hello, Isn’t it possible to get IR spectra from the FFTs of the atomic velocity autocorrelation function? Pascal Le 29 juil. 2015 à 17:58, Nicola Marzari a écrit : > > Dear Yin, > > > you need to calculate at every time step the total dipole in the unit > cell, and then do the fourier transform of the autocorrelation - see e.g. > here: http://journals.aps.org/prl/pdf/10.1103/PhysRevLett.81.1235 or many > other papers published on the topic. > > Note that if you do Car-Parrinello MD, rather than Born-Oppenhimer MD, > the vibrational frequencies can be slightly softened due to the fact > that the ions are dressed (and slowed down) by the coefficients of the > plane waves. The smaller the fictitious mass, the small the effect. > > Now, I'm not sure how to write the polarization at every time step - > maybe others can comment or add to the documentation. For PWSCF > you'd switch on lberry, but I'm not sure if you can do it during an > md (if now, maybe switch on lelfield, and then keep the applied field > equal to zero). > > In CP I suppose you could switch tefield on, but still have zero > applied field. > > Any other suggestion? Also, I think that tefield in CP and in PWSCF > mean different things - shall we switch the name in CP to lelfield? > > nicola > > > > On 29/07/2015 15:56, liyinc...@gmail.com wrote: >> Dear Quantum Espresso developers, >> >> I want to obtain IR spectra of crystals at room temperature. Considering >> the temperature effect, I decided to use CPMD. I wonder whether it is >> possible to get IR spectra from CPMD trajectory in Quantum Espresso? >> What's more, can I involve vdw-correction in CPMD? If yes, can IR >> spectra be calculated in the presence of vdw-correction? >> >> Thank you very much! >> >> Best Regards, >> >> Dr. Yin Li >> Department of Biophysics,Medical School, University of Pecs, >> No.12 Szigeti Street, Pecs, H-7624, HUNGARY >> Phone: +36-72-535271/36271 >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > -- > -- > Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL > Director, National Centre for Competence in Research NCCR MARVEL, EPFL > http://theossrv1.epfl.ch/Main/Contact http://nccr-marvel.ch/en/project > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Problem with relaxing large system
Dear Nkosinathi, Strictly speaking, your calculation does not crash: it ends up after the maximum number of SCF steps is reached. I had a look at the structure and I have a few remarks. 1. Is it normal that the Al-Al distances are 2.8 angstroms long? It seems a bit of a large distance to me, but I may be wrong. 2. For ultrasoft pseudopotential I would suggest to use 10*ecutwfc for the charge density cutoff (see ecutrho). 3. It is possible that your system is metallic. Do you use electron smearing in your calculation? If not I would try it (see smearing=‘cold' and degauss=0.02). 4. It is very unlikely that the water molecules are aligned the way they are in the input. They should form hydrogen bonds together and interactions with the solid. This may also explain why the density is hard to converge: the input coordinates are probably very far from the " solution ". If you can " improve " the starting structure it would facilitate the converge. Hope this help a bit, Best regards Pascal Le 17 juil. 2015 à 09:17, Nkosinathi Malaza a écrit : > Dear All, > > I need assistance with relaxing the system of Al and H2O, the system has 123 > atoms with ESM=bc3. The input file runs until it crashes, what can be the > problem? > > I have attached the output file. > > Kind regards > > N. Malaza > Wits University > Johannesburg > South Africa > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Pascal Boulet - MCF HDR, Resp. L1 MPCI - DEPARTEMENT CHIMIE Aix-Marseille Université - ST JEROME - Avenue Escadrille Normandie Niemen - 13013 Marseille Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50 Site : http://allos.up.univ-mrs.fr/pascal - Email : pascal.bou...@univ-amu.fr Afin de respecter l'environnement, merci de n'imprimer cet email que si nécessaire. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Cygwin - Make pw Error
Hi, gfortran does not understand -pthread: it is not in its list of arguments. You have to remove it. Pascal Le 2 févr. 2015 à 20:27, hossein daneshpajooh a écrit : > I know, but I have added all packages related to pthread, still not working! > and if problem is from libiotk I don't know how to solve it. > Now dear Paolo what do you suggest to try? > > > > > >gfortran -g -pthread -o iotk_print_kinds.x iotk_print_kinds.o > > libiotk.a > > >gfortran: error: unrecognized command line option ‘-pthread’ > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum Pascal Boulet -- pascal.bou...@univ-amu.fr Aix-Marseille University MADIREL Laboratory Avenue Normandie-Niemen F-13397 Marseille Cedex 20 Tel.: +33 413.55.18.10 Fax: +33 413.55.18.50 http://allos.up.univ-mrs.fr/pascal/ ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] residual forces along z-dimension after vc-relax
Hello,
With these small residual forces I would say that your structure is well
converged.
Pascal
Le 16 janv. 2015 à 19:42, Anna Kuznetsova a écrit :
> Dear users,
>
> I am trying to achieve the perfect relaxation of hexagonal unit cell in
> orthorhombic coordinates, however, I still see quite substantial residual
> forces along z-dimension. Doing finer k-mesh sampling does not help with the
> issue.
> I am quite sure that the coordinates of atoms in each layer are correct, so I
> was expecting that vc-relax will result only in the change in the unit cell
> dimensions, but not the changes of atomic positions inside it.
>
> Please, give me some hints of what could be wrong in my input to help me
> achieve full relaxation of the unit cell.
>
>
> Input (also attached):
>
> &CONTROL
> calculation = "vc-relax",
> pseudo_dir = "/u/annakuz/espresso/pseudo",
> outdir = "/lustre/work1/annakuz/tmp4",
> /
> &SYSTEM
> ibrav = 8,
> celldm(1) = 5.781869696282005, celldm(2) = 1.732050807568878, celldm(3)
> = 1.632993161855452,
> nat = 8,
> ntyp= 2,
> ecutwfc = 80,
> ecutrho = 700,
> occupations='smearing', smearing='gauss', degauss=0.03
> /
> &ELECTRONS
> conv_thr= 1.D-12
> /
> &IONS
> /
> &CELL
> /
> ATOMIC_SPECIES
> Si 28.0855 Si.pz-n-kjpaw_psl.0.1.UPF
> C 12.0107 C.pz-n-kjpaw_psl.0.1.UPF
> ATOMIC_POSITIONS {crystal}
> Si 0.00 0.00 0.00
> C0.00 0.00 0.375
> Si 0.50 0.50 0.00
> C0.50 0.50 0.375
> Si 0.50 0.16667 0.5
> C0.50 0.16667 0.875
> Si 1.00 0.7 0.5
> C1.00 0.7 0.875
>
> K_POINTS automatic
> 15 8 9 1 1 1
>
>
> Output is attached but here is the final result of relaxation showing forces
> still present in z-direction:
>
>
> convergence has been achieved in 31 iterations
> Forces acting on atoms (Ry/au):
> atom1 type 1 force = 0. -0.00370.00011491
> atom2 type 2 force = 0.0.0026 -0.00011491
> atom3 type 1 force = 0. -0.00370.00011493
> atom4 type 2 force = 0.0.0030 -0.00011491
> atom5 type 1 force = 0.0.00370.00011498
> atom6 type 2 force = 0. -0.0029 -0.00011498
> atom7 type 1 force = 0.0.00360.00011495
> atom8 type 2 force = 0. -0.0027 -0.00011497
> Total force = 0.000325 Total SCF correction = 0.00
>
> entering subroutine stress ...
> total stress (Ry/bohr**3) (kbar) P= -0.09
> -0.0088 0. 0. -0.13 0.00 0.00
>0. -0.0088 0. 0.00 -0.13 0.00
>0. 0. 0.0001 0.00 0.00 0.00
>
> bfgs converged in 3 scf cycles and 2 bfgs steps
> (criteria: energy < 0.10E-03, force < 0.10E-02, cell < 0.50E+00)
> End of BFGS Geometry Optimization
> Final enthalpy =-250.0275444323 Ry
> Begin final coordinates
> new unit-cell volume =547.64431 a.u.^3 (81.15251 Ang^3 )
>
> CELL_PARAMETERS (alat= 5.78186970)
>0.998918439 0.0 0.0
>0.0 1.730177232 0.0
>0.0 0.0 1.639355189
> ATOMIC_POSITIONS (crystal)
> Si 0.0 -0.00091 -0.000421399
> C0.0 -0.3 0.375421398
> Si 0.5 0.49909 -0.000421402
> C0.5 0.49991 0.375421397
> Si 0.5 0.16758 0.499578593
> C0.5 0.16675 0.875421409
> Si 1.0 0.66758 0.499578597
> C1.0 0.66671 0.875421408
> End final coordinates
>
> Thank you for help!
> --
> Best regards,
> Anna
> <2h_sic_pz_vcrelax5.rx.out><2h_sic_pz_vcrelax5.rx.in>___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
___
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Re: [Pw_forum] Avoiding vacuum and obtaining a periodic relaxed structure
Hello Naseem,
I had a look at your structure with xcrysden. The structure has some
overlapping atoms which probably causes the crash. You have to rebuild the
structure properly before you can go on.
Best regards
Pascal
Le 15 janv. 2015 à 11:59, Naseem Hassan a écrit :
> Dear Pascal Boulet,
>
> Thanks for the guidance. You answer is the first ever answer I received on
> QE. I selected C-C bond length around 1.5 Angstrom. And tried to execute the
> vc-relax using latest version of QE but I got some error. As I can see from
> the error I should increase the Cell factor (Increasing cell vectors to my
> understanding ?). I am presenting my input and Error file below for your kind
> review. Might be you can suggest me something to modify input file for the
> improved calculations and to eliminate the error.
>
> Input file is
>
> &control
> calculation='vc-relax'
> restart_mode='from_scratch'
> pseudo_dir = '/share/QE_pseudo'
> outdir='./'
> prefix='Graphane'
> forc_conv_thr=1.0D-4
> nstep=3000
> /
> &system
> ibrav= 0
> nat= 24, ntyp= 2
> ecutwfc =60.0
> occupations='smearing'
> degauss=0.002
> /
> &electrons
> scf_must_converge = .false.
> mixing_mode='plain'
> /
> &ions
> ion_dynamics = 'damp'
> ! ion_temperature='not_controlled'
> /
> &cell
> cell_dynamics = 'damp-pr'
> ! ion_temperature='not_controlled'
> /
> CELL_PARAMETERS {angstrom}
> 10.000 0. 0.000
> 0.00 10.00 0.000
> 0. 0. 10.0
> ATOMIC_SPECIES
> H 1.0079 H.pw-mt_fhi.UPF
> C 12.0111 C.pw-mt_fhi.UPF
> ATOMIC_POSITIONS {angstrom}
> C5.367107970 4.716603635 1.053018481
> C6.255850131 5.148617707 2.197431688
> C5.604070962 5.956723221 3.300642187
> C5.221138074 5.110436404 4.489234599
> C4.929412403 5.933432549 5.718863005
> C4.751718300 5.084706368 6.956077606
> C5.325054303 5.689729332 8.206876709
> C4.097184203 4.164227727 4.168731293
> H6.706474032 4.257638763 2.659887322
> H4.344006686 3.515258124 3.319860376
> H3.854647824 3.519241858 5.021187742
> H3.190910142 4.727029043 3.904250319
> H3.696251345 4.818294626 7.110426161
> H4.348967601 4.517546557 1.417990955
> H5.731392495 3.757052353 0.655098847
> H7.101013257 5.709772742 1.774202810
> H6.288921269 6.743142271 3.648137411
> H4.714167633 6.481058689 2.916034182
> H6.110659580 4.502596625 4.738962908
> H4.050783951 6.573507244 5.541152210
> H5.775952152 6.619568616 5.878615758
> H4.786163229 6.607591885 8.486624196
> H6.356503452 6.007847752 7.983988564
> H5.270145007 4.125317908 6.789870671
> K_POINTS {automatic}
> 3 3 1 0 0 0
>
>
> and the Error show in output file is as follow
>
>
> Error in routine scale_h (1):
> Not enough space allocated for radial FFT: try restarting with a larger
> cell_factor.
>
>
> %%
> Error in routine scale_h (1):
>
>
> %%
>
>
> %%
>
>
> %%
> Error in routine scale_h (1):
> Error in routine scale_h (1):
> Not enough space allocated for radial FFT: try restarting with a larger
> cell_factor.
> Error in routine scale_h (1):
> Not enough space allocated for radial FFT: try restarting with a larger
> cell_factor.
>
> %%
>
> %%
>
> Error in routine scale_h (1):
> Not enough space allocated for radial FFT: try restarting with a larger
> cell_factor.
>
> %%
> Not enough space allocated for radial FFT: try restarting with a larger
> cell_factor.
>
> %%
>
> Error in routine scale_h (1):
>
Re: [Pw_forum] Avoiding vacuum and obtaining a periodic relaxed structure
Hello,
My brute force suggestion:
1. Select a chemically consistent axis so that the bond length is around 1.5
angstrom.
2. Optimize the cell parameters and atomic positions using vc-relax
Pascal
Le 14 janv. 2015 à 09:16, Naseem Hassan a écrit :
> Dear All
>
> I have made a structure similar to propylene using chemcraft. Then I picked
> the Cartesian coordinates and made an input file for relaxation. But I am not
> sure How long a Cell vector I should select along z-axis (along the Carbon
> chain). I want this structure to be periodic along the chain only. I selected
> 9 and 10 Angstrom of lattice vector along Z-axis and obtained C-C distance 5
> and 6 Angstrom (Approx) respectively. It seems with 10 Angstrom a little
> vacuum is added and C-C bonds are elongated more. if I give small lattice
> vector (say 7 Ang) then C-C bond shrinks. How to obtain an optimized C-C bond
> length ? What is proper method of avoiding vacuum and obtaining a perfect
> periodic relaxed structure.
>
> Kindly have a look at the input file.
>
> &control
> calculation='relax'
> restart_mode='from_scratch'
> pseudo_dir = '/share/QE_pseudo'
> outdir='./'
> prefix='Graphane'
> forc_conv_thr=1.0D-4
> nstep=3000
> /
> &system
> ibrav= 0
> nat= 24, ntyp= 2
> ecutwfc =60.0
> occupations='smearing'
> degauss=0.002
> /
> &electrons
> scf_must_converge = .false.
> mixing_mode='plain'
> /
> &ions
> ion_dynamics = 'damp'
> ! ion_temperature='not_controlled'
> /
> CELL_PARAMETERS {angstrom}
> 10.000 0. 0.000
> 0.00 10.00 0.000
> 0. 0. 10.0
> ATOMIC_SPECIES
> H 1.0079 H.pw-mt_fhi.UPF
> C 12.0111 C.pw-mt_fhi.UPF
> ATOMIC_POSITIONS {angstrom}
> C5.367107970 4.716603635 1.053018481
> C6.255850131 5.148617707 2.197431688
> C5.604070962 5.956723221 3.300642187
> C5.221138074 5.110436404 4.489234599
> C4.929412403 5.933432549 5.718863005
> C4.751718300 5.084706368 6.956077606
> C5.325054303 5.689729332 8.206876709
> C4.097184203 4.164227727 4.168731293
> H6.706474032 4.257638763 2.659887322
> H4.344006686 3.515258124 3.319860376
> H3.854647824 3.519241858 5.021187742
> H3.190910142 4.727029043 3.904250319
> H3.696251345 4.818294626 7.110426161
> H4.348967601 4.517546557 1.417990955
> H5.731392495 3.757052353 0.655098847
> H7.101013257 5.709772742 1.774202810
> H6.288921269 6.743142271 3.648137411
> H4.714167633 6.481058689 2.916034182
> H6.110659580 4.502596625 4.738962908
> H4.050783951 6.573507244 5.541152210
> H5.775952152 6.619568616 5.878615758
> H4.786163229 6.607591885 8.486624196
> H6.356503452 6.007847752 7.983988564
> H5.270145007 4.125317908 6.789870671
> K_POINTS {automatic}
> 3 3 1 0 0 0
> Many thanks
> Naseem
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Pascal Boulet
--
pascal.bou...@univ-amu.fr
Aix-Marseille University
MADIREL Laboratory
Avenue Normandie-Niemen
F-13397 Marseille Cedex 20
Tel.: +33 413.55.18.10
Fax: +33 413.55.18.50
http://allos.up.univ-mrs.fr/pascal/
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[Pw_forum] Restarting on the geometry only
Dear all, I am working on a big structure (384 atoms). I have optimized the atomic positions and cell parameters at the Gamma point. Now that's done, I would like to run a SCF calculation with more k-points. The 'restart' option fails with error message:read_rho_xml : error > dimensions do not matchI guess it is caused by the change in the number of k-points in the input file (?). Please correct if I am wrong. How can I restart on the geometry only? Should I change something in the code? If so, could you tell me what to change and where? Thank in advancePascal >-----Pascal Boulet Aix-Marseille University MADIREL Laboratory Avenue Normandie-Niemen 13397 Marseille Cedex 20 Email: pascal.bou...@univ-amu.fr Tel. +33 413 55 18 10 Fax +33 413 55 18 50___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] TB09 metaGGA
Dear Juanjo, As far as I know, metaGGAs are like GGAs for gaps: there are not accurate. For getting good gaps you have to switch to hybrid functionals or GW formalism (not implemented in QE though). Depending on what you want to do, of course, and if you know the gap value you may try this: optimize with a standard GGA functional, run a nscf calculation and if the gap is not totally closed up then operate a rigid band shifting for further properties calculations. This is a bit brute force... If you do not know the gap value: run a hybrid single point calculation on the GGA optimized structure. As Yves said, there are not so many options... Pascal "Juanjo Meléndez" wrote:Dear Yves Thanks a lot for your comments. Unfortunately, I need a good description ofgaps to calculate optical absorption, and hybrid functionals are prohibitive forthe supercells that I need to use. That is why I started to try withmetaGGA. I will have a look to the paper you mention (which I did not know, by theway, thanks!) for more ideas... Take care Juanjo From: Yves Ferro Sent: Friday, October 31, 2014 10:20 AMTo: PWSCF Forum Subject: Re: [Pw_forum] TB09 metaGGA DearJuanjo, From what I can remember:- the meta-GGA kinetic terms are notsaved in order to restart a nscf, at least up to the 5.0 version,- the tools for building meta-GGA PPs are not availablein QE.However, I'm not sure using meta-GGA pseudos will solveyour problem. Meta-GGA are known to have numerical instabilities such as theones you met, in particular when then electronic density drop to a very lowlevel as probably in your ionic crystal LiF, on the contrary with Si and C thatform covalent structures. You can have a look to this paper you probablyknow:E.R. Johnson, JCP 131, 0341112009 I don't believe a cure to you problem exists at themoment, except by changing the functional to a GGA one. Best regards, Yves. Le 31 oct. 2014 à 09:26, Juanjo Meléndez a écrit : Hi Pascal Thanks for replying. I agree with you that building a PP consistent with the metaGGA functional would solve most of the instability problems. But I do not have *any* experience building PPs (which, by the way, seems to be not trivial to me, even less trivial for metaGGA), so I followed http://dx.doi.org/10.1016/j.cpc.2013.02.020 and tried the trick. I was just wondering if any general strategy for convergence exists. Regarding point 2, I asked one of the authors of the aforementioned paper and he declared not the have seen such a problem before, so I guess that the kinetic terms are not responsible. I have overcome the problem by using a dense kpoints path already in scf calculations and calculating the bands without the standard intermediate nscf run, but it would be nice if the developers could have a look and check. Again, thank you very much for your interest. Juanjo Juan J. Meléndez Associate Professor Department of Physics · University of Extremadura Avda. de Elvas, s/n 06006 Badajoz (Spain) Phone: +34 924 28 96 55 Fax: +34 924 28 96 51 Email: melen...@unex.es Web: http://materiales.unex.es/miembros/personal/jj-melendez/Index.html From: Pascal BOULET Sent: Thursday, October 30, 2014 7:15 PM To: PWSCF Forum Subject: Re: [Pw_forum] TB09 metaGGA hello, I have never tried meta-GGA functionals with QE, so I am guessing. For point 1, one possible reason is the inadequacy between the pseudo potential and the functional. I guess you have build a special pseudopotential for this functional. Point 2: Could it be because the meta-GGA kinetic terms are not saved in the checkpoint file and hence not readable when doing the nscf? Pascal "Juanjo Meléndez" wrote: Hi all I am starting to work with metaGGA functionals in QE (v.5.1 + libXc), following Èric Germaneau and colleagues’ work (http://dx.doi.org/10.1016/j.cpc.2013.02.020).I know that metaGGA is little tested, but I would be pleased if somebodycould answer a couple of questions: 1) Convergence is quite tricky. Up to know, I got some results in simple systems using a very small mixing_beta (within 0.01–0.05), not too many bands (just one or two conduction bands, never converged for more bands) and restarting from a previously fully converged calculation. I got results only for carbon, silicon and germanium, never got any convergence for any binary simple compound (like LiF). Does anyone have additional hints for metaGGA calculations to converge? 2) In addition, I get something wrong with nscfcalculations. After convergence of a scf run, I get a list of bands at eachk-point, as usual –nothing strange here. Then I made a path of k-points toget the band structure and run a nscf calculation. This finishes fine aswell, but the bands are not only different from those from the scfcalculations,
Re: [Pw_forum] TB09 metaGGA
hello, I have never tried meta-GGA functionals with QE, so I am guessing. For point 1, one possible reason is the inadequacy between the pseudo potential and the functional. I guess you have build a special pseudopotential for this functional. Point 2: Could it be because the meta-GGA kinetic terms are not saved in the checkpoint file and hence not readable when doing the nscf? Pascal "Juanjo Meléndez" wrote:Hi all I am starting to work with metaGGA functionals in QE (v. 5.1+ libXc), following Èric Germaneau and colleagues’ work (http://dx.doi.org/10.1016/j.cpc.2013.02.020).I know that metaGGA is little tested, but I would be pleased if somebody couldanswer a couple of questions: 1) Convergence is quite tricky. Up to know, I got someresults in simple systems using a very small mixing_beta (within 0.01–0.05), nottoo many bands (just one or two conduction bands, never converged for more bands) and restarting from a previously fully converged calculation. I got results only for carbon, silicon and germanium, never got any convergence forany binary simple compound (like LiF). Does anyone have additional hints formetaGGA calculations to converge? 2) In addition, I get something wrong with nscf calculations.After convergence of a scf run, I get a list of bands at each k-point, as usual–nothing strange here. Then I made a path of k-points to get the band structureand run a nscf calculation. This finishes fine as well, but the bands are notonly different from those from the scf calculations, but also unrealisticallyhigh. I am attaching the input and output files for both the scf and nscf runs,as well as a couple of eigenval.xml files taken after nscf. Does anybody knowhow to manage this? Or could this be a bug in the code? Thanks a lot in advance Take care Juanjo Juan J.Meléndez Associate Professor Department of Physics · University ofExtremadura Avda. de Elvas, s/n 06006 Badajoz (Spain) Phone: +34 924 28 9655 Fax: +34 924 28 96 51 Email: melen...@unex.es Web: http://materiales.unex.es/miembros/personal/jj-melendez/Index.html “All thosewho look stupid actually are, as also are half of those who do not look like”(F. de Quevedo) Este mensaje no contiene virus ni malware porque la protección de avast! Antivirus está activa. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum >----- Pascal Boulet Aix-Marseille University MADIREL Laboratory Avenue Normandie-Niemen 13397 Marseille Cedex 20 Email: pascal.bou...@univ-amu.fr Tel. +33 413 55 18 10 Fax +33 413 55 18 50___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] SCF input file for 2D graphene sheet
Hello Cam, you should not set celldm(3) to 0. QE works with 3D periodic models. So if you are interested in graphene sheet, you have to find the c length so that the graphene sheet does not interact with its images in the c direction. c=10-15 angs should do the job but you have to check this. BTW, if you intend to relax the structure, the c parameter should be fixed. Use the cell_dofree keyword for this, as you mentioned. Best regardsPascal Cameron Foss wrote:Hello all, I have looked through a lot of the forum and have yet to find anything that helps with this question. However, if I am wrong where should I look for the answer to this? I am trying to run a scf simulation of a 2D graphene sheet of carbon atoms. Graphite is an hexagonal structure and uses ibrav=4, I have tried using this and setting celldm(3)=0, to indicate no height component, but that doesn't work. I have also tried indicating a free lattice (ibrav=0) and setting c=0, and setting the CELL_PARAMETERS card vectors to only having 2D components (ie the z-components are set to 0). However, that too has errors when I try running the pw.x code or loading the file in XCrySDen.? (NOTE: I have been playing with QE-5.1 for only the past few weeks and am using XCrySDen to visualize the generated unit cells.)? Particularly the error I get from XCrySDen in the terminal is: Num of Atoms =0, Num of Frames =0. I have also looked at the cell_dofree variable in the CELL card. but setting that to xy does not seem to work either, which I would suspect since I still have to define ?a height to the structure.?Are any of these approaches a viable way of getting just a 2D structure of graphene and I might be missing something? Or should i be going about this in another way?? Best,Cam ___ Pw_forum mailing list Pw_forum at pwscf.org http://pwscf.org/mailman/listinfo/pw_forum >----- Pascal Boulet Aix-Marseille University MADIREL Laboratory Avenue Normandie-Niemen 13397 Marseille Cedex 20 Email: pascal.boulet at univ-amu.fr Tel. +33 413 55 18 10 Fax +33 413 55 18 50 -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140628/52a95f9f/attachment.html
[Pw_forum] question on parallelism on bands
Thank you Paolo for your quick answer. Pascal > > From: Paolo Giannozzi > Sent: Mon May 26 13:28:21 CEST 2014 > To: PWSCF Forum > Subject: Re: [Pw_forum] question on parallelism on bands > > > On Mon, 2014-05-26 at 12:00 +0200, pascal boulet wrote: > > > I have to run calculations on a rather big system: 35.9x35.9x71.8 bohr, > > 384 atoms, 1280 bands and few k-points (at most 6). I would like to > > parallelize the calculations on the bands > > unless you are using hybrid functionals, there isn't a real advantage > in "band" parallelization for pw.x. > > > but I am not familiar with this. I have up to 50x12=600 procs at disposal. > > I envisage to use 144 procs and the following options for pw.x: > > -bands 12 -ntg 12 -ndiag 64 > > > Would you say these are more or less adequate parameters ? > > I would say no: too few processors for plane wave parallelization. > > Paolo > > > Thank you for your help, > > Pascal > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum >- Pascal Boulet Aix-Marseille University MADIREL Laboratory Avenue Normandie-Niemen 13397 Marseille Cedex 20 Email: pascal.boulet at univ-amu.fr Tel. +33 413 55 18 10 Fax +33 413 55 18 50
[Pw_forum] question on parallelism on bands
Dear all, I have to run calculations on a rather big system: 35.9x35.9x71.8 bohr, 384 atoms, 1280 bands and few k-points (at most 6). I would like to parallelize the calculations on the bands but I am not familiar with this. I have up to 50x12=600 procs at disposal. I envisage to use 144 procs and the following options for pw.x: -bands 12 -ntg 12 -ndiag 64 Would you say these are more or less adequate parameters ? Thank you for your help, Pascal -- next part -- A non-text attachment was scrubbed... Name: pascal_boulet.vcf Type: text/x-vcard Size: 413 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20140526/c53ee45c/attachment.vcf
[Pw_forum] DFT-DF
Hello, It's probably due to a FORTRAN writing format which is incompatible with the size of the real number (above 100?) that should be written. You can check this by comparing the format in the FORTRAN code (look in the corresponding *F90 file of PWSCF) and the value of the coefficient which should be stored somewhere in a file (perhaps in a *.F90 FORTRAN file as well). Pascal mohammad moaddeli wrote:Dear all users, I set london=.true. in the PW input file and the output is:== Program PWSCF v.5.0.2 (svn rev. 9656) starts on 19May2014 at? 9:47:57? 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); ? URL http://www.quantum-espresso.org";, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/quote.php Parallel version (MPI), running on 8 processors R & G space division:? proc/nbgrp/npool/nimage =?? 8 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 Waiting for input... Reading input from standard input - Parameters for Dispersion Correction: - ?? atom? VdW radius?? C_6 ??? C? 2.744 60.710 ??? Au 3.349??? *** Subspace diagonalization in iterative solution of the eigenvalue problem: a serial algorithm will be used Parallelization info sticks:?? dense? smooth PW G-vecs:??? dense?? smooth? PW Min 287 287 85??? 27529??? 27529??? 4417 Max 288 288 86??? 27534??? 27534??? 4424 Sum??? 2297??? 2297??? 687?? 220247?? 220247?? 35371 bravais-lattice index =??? 8 lattice parameter (alat)? =?? 4.6391? a.u. unit-cell volume? =??? 3112.5884 (a.u.)^3 number of atoms/cell? =?? 13 number of atomic types??? =??? 2 number of electrons?? =??? 59.00 number of Kohn-Sham states=?? 36 kinetic-energy cutoff =? 65.? Ry charge density cutoff = 260.? Ry convergence threshold =? 1.0E-08 mixing beta?? =?? 0.3000 number of iterations used =??? 8? plain mixing Exchange-correlation? = BLYP ( 1 3 1 3 0) EXX-fraction? =??? 0.00 nstep =? 200 ==I do not know why the value of C_6 parameter of Au is just a * symbol ??? Any help will be appreciated, mmShahid Chamran University ___ Pw_forum mailing list Pw_forum at pwscf.org http://pwscf.org/mailman/listinfo/pw_forum >----- Pascal Boulet Aix-Marseille University MADIREL Laboratory Avenue Normandie-Niemen 13397 Marseille Cedex 20 Email: pascal.boulet at univ-amu.fr Tel. +33 413 55 18 10 Fax +33 413 55 18 50 -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140519/8155ccc0/attachment.html
[Pw_forum] QE MD trajectory
Hello, It does NOT matter whether you refold or not the coordinates since you have to calculate the smallest distance between atoms (eventually using periodic images) to get MSD. Pascal Prateek Mehta wrote:Hi all, I am using pwscf to perform MD. I was wondering if the atomic positions in the output file are the unfolded coordinates or are they refolded back into the periodic cell. I see there is a flag "refold_pos" which is specified as false in a default MD run. I ask because I want to calculate the mean square displacements. Prateek ___ Pw_forum mailing list Pw_forum at pwscf.org http://pwscf.org/mailman/listinfo/pw_forum >----- Pascal Boulet Aix-Marseille University MADIREL Laboratory Avenue Normandie-Niemen 13397 Marseille Cedex 20 Email: pascal.boulet at univ-amu.fr Tel. +33 413 55 18 10 Fax +33 413 55 18 50 -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140514/f7bfc9d7/attachment.html
[Pw_forum] atoms overlapped
Dear Tommaso The atom coordinates are crystal not angstrom. In addition there should be no atoms at position 100, 010. Etc... Hope this help Pascal > > From: Tommaso Francese > Sent: Wed Apr 30 14:15:22 CEST 2014 > To: > Subject: [Pw_forum] atoms overlapped > > > Dear all QE users, > i?m trying to make a scf calculation of a cubic zirconia. I verified the > structure with xcrysden, and it seems to be correct. But when i run the code, > it turns out that there is an overlapping of atomic positions. Here i attach > the code i used, can anyone help me? > Thanks in advance!!! > Tommaso Francese, Universit? C? Foscari di Venezia > > > &CONTROL > calculation = 'scf' , > restart_mode = 'from_scratch' , > outdir = '/home/***/QE/espresso-5.0.2/tmp/' , > pseudo_dir = '/home/***/upf_files/' , > prefix = 'zrcubic' , > disk_io = 'high' , > / > &SYSTEM >ibrav = 1, >A = 5.1454 , >B = 5.1454 , >C = 5.1454 , >cosAB = 0 , >cosAC = 0 , >cosBC = 0 , > nat = 22, > ntyp = 2, > ecutwfc = 30 , > ecutrho = 120 , > nbnd = 80, >input_dft = 'B3LYP' , > occupations = 'fixed' , > exxdiv_treatment = 'gygi-baldereschi' , > / > &ELECTRONS > conv_thr = 1.0D-4 , > mixing_mode = 'plain' , > mixing_beta = 0.7 , > diagonalization = 'david' , > diago_full_acc = .true. , > / > ATOMIC_SPECIES >Zr 91.22400 Zr.pz-mt_fhi.UPF > O 15.99900 O.pz-mt_fhi.UPF > ATOMIC_POSITIONS angstroms >Zr 0.00.00.0 >Zr 0.00.01.0 >Zr 0.01.00.0 >Zr 0.01.01.0 >Zr 1.00.00.0 >Zr 1.00.01.0 >Zr 1.01.00.0 >Zr 1.01.01.0 >Zr 0.00.50.5 >Zr 1.00.50.5 >Zr 0.50.00.5 >Zr 0.51.00.5 >Zr 0.50.50.0 >Zr 0.50.51.0 > O 0.250000.250000.25000 > O 0.750000.750000.75000 > O 0.750000.750000.25000 > O 0.250000.250000.75000 > O 0.750000.250000.75000 > O 0.250000.750000.25000 > O 0.250000.750000.75000 > O 0.750000.250000.25000 > K_POINTS automatic > 4 4 4 1 1 1 >
[Pw_forum] citing Quantum ESPRESSO
That's very strange! We have recently published a paper in this journal and had no question about this. We cited QE as follows: P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, D. Ceresoli, G.L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso, S. de Gironcoli, S. Fabris, G. Fratesi, R. Gebauer, U. Gerstmann, C. Gougoussis, A. Kokalj, M. Lazzeri, L. Martin-Samos, N. Marzari, F. Mauri, R. Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, S. Scandolo, G. Sclauzero, A.P. Seitsonen, A. Smogunov, P. Umari, and R.M. Wentzcovitch, J. Phys.: Condens. Matter. 21, 2009 (395502). It might be that your are in trouble because of the way you mentioned QE in your article or because you mentioned the website in the citation which shows a .org extension (?). Regards, Pascal > > From: Paolo Giannozzi > Sent: Fri Mar 28 10:28:09 CET 2014 > To: PWSCF Forum > Subject: Re: [Pw_forum] citing Quantum ESPRESSO > > > On Wed, 2014-03-26 at 15:31 +0400, Dmitry Pshenay-Severin wrote: > > > I was puzzled by the editors of Journal of Electronic Materials > > so are we. The trademarks are registered by a non-profit organization: > Quantum Espresso Foundation, 5A Colville Road, W38BL London. It is not > "the manufacturer", though. Have you tried to explain to the editors > that their request does not make sense for most open-source software? > > Paolo > > > , that asked me to add "the manufacturer name and geographic location > > for all brand names cited in the article. Some examples are Quantum > > Espresso... Following these brand names in parentheses, should be the > > full company names and the city and state where the companies are > > located." > > I have cited the package as was suggested on your site: > > > > > > "Quantum ESPRESSO [ref]" > > > > > > > > [ref] P. Giannozzi, S. Baroni, N. Bonini et al. J.Phys.:Condens.Matter > > 21, 395502 (2009); http://www.quantum-espresso.org. > > > > > > Could you, please, help me to properly add manufacturer name, the city > > and state of its location. > > > > > > Best regards, > > Dmitry > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum >- Pascal Boulet Aix-Marseille University MADIREL Laboratory Avenue Normandie-Niemen 13397 Marseille Cedex 20 Email: pascal.boulet at univ-amu.fr Tel. +33 413 55 18 10 Fax +33 413 55 18 50
[Pw_forum] weird error when computing phonons
Dear all, I have been calculating the phonons (QE 5.0.2) on a 6x6x6(=28) grid of q-points. There are 15 irreps and 5 atoms in the structure. Everything has gone fine until q-point 22, but q-point 23 has failed with error message: Error in routine phq_setup (1): problem with modes file I have tried to "recover" the calculations but without success. Hence, I am now calculating q-points 23-28 with the start-q/last-q option, and it seems to work (so far: 2nd irrep of q-point 23 in under way). Have you ever encounted such a problem? Thank you for your help. Best regards Pascal >----- Pascal Boulet Aix-Marseille University MADIREL Laboratory Avenue Normandie-Niemen 13397 Marseille Cedex 20 Email: pascal.boulet at univ-amu.fr Tel. +33 413 55 18 10 Fax +33 413 55 18 50
[Pw_forum] Help
Hello, It seems that the answer is in the error message: you cannot combine structural optimization with full LDA+U. And as far I know, it is also true for optimization + SOC: they are NOT compatible. So you should better first optimize your structure with a "standard" method and then switch on LDA+U and SOC. HTH pascal Shahid Sattar wrote:Dear QE Fellows, I am trying to apply LDA+U+SOC Scheme on Mn-doped silicon system (Magnetism is also incorporated).?I am using version espresso-5.0.2.?After running till first scf cycle (couple of?iterations), when it comes to write the forces acting and coordinates of relaxed system, the calculation is crashed with the following error: ?%% ? ? ?Error in routine force_hub (1): ? ? ? forces in full LDA+U scheme are not yet implemented ?%% ? ? ?stopping ... ... Can somebody check the input and suggest some solution?? Thank you in advance. Below is the input: - &control ? ? calculation='relax', ? ? restart_mode='from_scratch', ? ? prefix='sil', ? ?! verbosity='high', ? ?! tprnfor=.true. ? ? pseudo_dir = '/home/sattar', ? ? etot_conv_thr=1.0d-4, ? ? ? ? ? ! Total Energy conf. for ionic min. ? ? forc_conv_thr=1.0d-3, ? ? ? ? ? ! Force conv for ion min. ? ?! tstress=.true. ? ? nstep=150, ? ? outdir='tmp/', ?/ &system ? ? ibrav = 4, ? ? a=15.44, b=15.44, c=25, ? ? cosab=-0.5, cosbc=0.0, cosac=0.0 ? ? nat=34, ntyp= 3, ? ? ecutwfc = 40,ecutrho=350, ? ? occupations='smearing', smearing='fd', degauss=0.01 ? ? nspin =4, ? ? starting_magnetization(1)= 0.0 ? ? starting_magnetization(2)= 0.5 ? ? lda_plus_u = .true. ? ? lda_plus_u_kind = 1 ? ? lspinorb=.true., ? ? noncolin=.true., ? ? Hubbard_U(2) = 4.0, ? ? Hubbard_J=0.0 ? ? nosym = .FALSE. ?/ ?&electrons ? ? mixing_beta = 0.3, ? ? conv_thr = ?1.0d-7, ? ? electron_maxstep=300, ?/ &CELL ? ? cell_dynamics='bfgs', ?/ &IONS ? ? ion_dynamics='bfgs', / ATOMIC_SPECIES Si ?28.086 ?Si.pbe-n-rrkjus_psl.0.1.UPF Mn 54.938 ?Mn.rel-pbe-spn-rrkjus_psl.0.2.3.UPF ATOMIC_POSITIONS (angstrom) Si Mn ;;; ;;; ;;; ;;; ;;; K_POINTS AUTOMATIC 4 4 1 0 0 0 --? Kind Regards, *Shahid Sattar* Ph. D. Student Material Science and Engineering (MSE) KAUST _______ Pw_forum mailing list Pw_forum at pwscf.org http://pwscf.org/mailman/listinfo/pw_forum >- Pascal Boulet Aix-Marseille University MADIREL Laboratory Avenue Normandie-Niemen 13397 Marseille Cedex 20 Email: pascal.boulet at univ-amu.fr Tel. +33 413 55 18 10 Fax +33 413 55 18 50 -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140227/aeb98abb/attachment.html
[Pw_forum] Geometry optimization generates same coordinates
Hello, You have to increase the number of geometry optimization steps! 1 is definitely not enough. As you can see at the end PW says: The maximum number of steps has been reached. There are a few points I shall raise: * If I am right, your are using ultrasoft PP. Are you sure you need that large a cutoff energy? have you made convergence tests? * You are mixing UPP with PAW. Not sure it is wise... * Obviously the geometry is very far from equilibrium: see Total force = 647.681262 and P= 1879.85. According to the job title you are adsorbing a PAH on graphene. If this is right, your starting structure is nonsense. The distance between the PAH and the surface is only 0.06 angstrom! As you can see the first displacements PW is doing is to enlarge the distance between the PAH and the surface. Pascal > > From: jbobak > Sent: Fri Jan 31 17:41:03 CET 2014 > To: PWSCF Forum > Subject: Re: [Pw_forum] Geometry optimization generates same coordinates > > > Hi, > > Thank you so much for the quick response. I believe the coordinates are > exactly the same. My output is copied below. It is long, but I'm still too > new at this to know which parts are most important for you. > > Thank you again, > Julia > > Program PWSCF v.5.0.2 (svn rev. 9656) starts on 24Jan2014 at 2:10:51 > > 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); > URL http://www.quantum-espresso.org";, > in publications or presentations arising from this work. More details at > http://www.quantum-espresso.org/quote.php > > Parallel version (MPI), running on32 processors > R & G space division: proc/nbgrp/npool/nimage = 32 > > 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 > Waiting for input... > Reading input from standard input >file C.pbe-rrkjus.UPF: wavefunction(s) 2S 2P renormalized > > Subspace diagonalization in iterative solution of the eigenvalue > problem: > scalapack distributed-memory algorithm (size of sub-group: 4* 4 procs) > > > Parallelization info > > sticks: dense smooth PW G-vecs:dense smooth PW > Min1136 568147 26287192934 12287 > Max1138 569148 26288492991 12291 > Sum 36367 18193 4729 8412137 2975069 393245 > > > Title: > TetraceneOnGraphene > > > bravais-lattice index =0 > lattice parameter (alat) = 33.1600 a.u. > unit-cell volume = 47365.8630 (a.u.)^3 > number of atoms/cell = 158 > number of atomic types=2 > number of electrons = 596.00 > number of Kohn-Sham states= 298 > kinetic-energy cutoff = 60. Ry > charge density cutoff = 480. Ry > convergence threshold = 1.0E-08 > mixing beta = 0.7000 > number of iterations used =8 plain mixing > Exchange-correlation = SLA PW PBX PBC ( 1 4 3 4 0) > EXX-fraction =0.00 > nstep =1 > > > celldm(1)= 33.16 celldm(2)= 0.00 celldm(3)= 0.00 > celldm(4)= 0.00 celldm(5)= 0.00 celldm(6)= 0.00 > > crystal axes: (cart. coord. in units of alat) >a(1) = ( 1.00 0.00 0.00 ) >a(2) = ( 0.50 0.866025 0.00 ) >a(3) = ( 0.00 0.00 1.50 ) > > reciprocal axes: (cart. coord. in units 2 pi/alat) >b(1) = ( 1.00 -0.577350 0.00 ) >b(2) = ( 0.00 1.154701 0.00 ) >b(3) = ( 0.00 0.00 0.67 ) > > > PseudoPot. # 1 for C read from file: > /global/software/espresso-5.0.3-intel-ompi/pseudo/C.pbe-rrkjus.UPF > MD5 check sum: 00fb224312de0c5b6853bd333518df6f > Pseudo is Ultrasoft, Zval = 4.0 > Generated by new atomic code, or converted to UPF format > Using radial grid of 627 points, 4 beta functions with: > l(1) = 0 > l(2) = 0 > l(3) = 1 > l(4) = 1 > Q(r) pseudized with 0 coefficients > > > PseudoPot. # 2 for H read from file: > /global/software/espresso-5.0.3-intel-ompi/pseudo/H.pbe-kjpaw.UPF > MD5 check sum: b6732a8c2b51919c45a22ac3ed50cb01 > Pseudo is Projector augmented-wave, Zval = 1.0 > Generated using "atomic" code by
[Pw_forum] HgTe
Dear Sara, Both pseudos may/should be correct. If they are "well-behaved" pseudos, they should give the same results (unless the 6s26p0.55d9.55f0 pseudo has been designed for a special purpose). Anyway, in any circumstances you have to check the validity of the pseudo. Pascal sara barati wrote: Dear all I Want to calculate structrul properties of? HgTe with espresso .For thise I convert pseudopotentials ?80-Hg-GGA.fhi and 52-Te-GGA .fhi from abinit with upftools. I use 6s26p05d105f0?valance orbitals for Hg. But in some pseudopotentials for Hg in espresso these orbitals are 6s26p0.55d9.55f0. Which one is correct? could anyone help me with this? I attached the converted file to this email.___ Pw_forum mailing list Pw_forum at pwscf.org http://pwscf.org/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130626/8943829e/attachment.html
[Pw_forum] Not converging scf calculation
One more thing: are you sure the cell parameters you give are in the right units w.r.t. PW defaults (angstrom/Bohr)? You should check this too. regards, P. Le 28/04/2013 11:01, Ker Park a ?crit : > Hello all, > > I am doing scf calculation for bulk MoS2, but it never reaches > convergence. > I tried up to 300 Ry for 'ecut' though, the total energies were around > 250 Ry and fluctuated randomly (energies were even positive). I am > copying my 'scf.in' file below. Please generously provide any > suggestions. The crystal structure is Hexagonal structure with a basis > of 6 atoms (I think). I checked a lot of times, but my structure setup > could be wrong. I am also copying the addresses where the crystal > structure is shown. Please let me know if my structure could be simpler. > > Many thanks, > Kerr > > http://www.drilube.co.jp/english/product/molybdenum.html > > http://nsfafresh.org/wiki/index.php?title=MoS2 > > http://www.machinerylubrication.com/Read/861/solid-film-lubricants > > > -- > > > !MoS2 scf.in > &control > calculation='scf' > restart_mode='from_scratch', > !pseudo_dir='directory where pseudopotentials are stored/', > !outdir='directory where large files are written/' > pseudo_dir='../../pseudo', > outdir='./output100' > prefix='PH', > / > &system > ibrav=4, celldm(1)=5.9715, celldm(3)=3.8905, > nat=6, ntyp=2, ecutwfc =300 > / > &electrons > conv_thr = 1.0d-8 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Mo 95.94Mo.pw-mt_fhi.UPF > S 32.065 S.pw-mt_fhi.UPF > ATOMIC_POSITIONS alat > Mo 0 0 0 > S 2.9858 1.7238 2.9971 > S 0 0 8.6190 > Mo 2.9858 1.7238 11.6161 > S 0 0 14.6133 > S 1.5800 0.9122 20.2352 > K_POINTS automatic > 4 4 4 0 0 0 > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- A non-text attachment was scrubbed... Name: pascal_boulet.vcf Type: text/x-vcard Size: 413 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20130428/39cfb28d/attachment.vcf
[Pw_forum] Electronic band structures for primitive and conventional unit cells
Thank you all for your responds. We indeed knew about the folding of the BZ when using conventional cells, but we overlook the possibility that X point becomes Gamma point. Best regards, Pascal Le 18/03/2013 23:30, Yun Wang a ?crit : > Dear Pascal, > > What you found is related to the Brillouin zone folding. You can > find more details in Roarld Hoffmann's book: Solids and surfaces. The > band structure using the primitive cell is correct. > > Cheers, > Yun > > On Mon, Mar 18, 2013 at 9:05 PM, pascal boulet > mailto:pascal.boulet at univ-amu.fr>> wrote: > > Dear all, > > We are facing a problem with differences in electronic band > structures when we use primitive or conventional unit cells. > > The structure we are dealing with is Mg2Si for which the primitive > UC is: > ATOMIC_POSITIONS crystal > Si 0.0 0.0 0.0 > Mg 0.25000 0.25000 0.25000 > Mg 0.75000 0.75000 0.75000 > > The cubic space group is 225, a=12.0421785 bohr and Mg2Si is FCC. > > The rest of the input is (I make it short): > K_POINTS crystal > 120 > 0.500.250.751.0 > 0.500.260.741.0 > 0.500.270.731.0 > etc. > calculation = 'bands', > celldm(1) =12.0421785, > nat = 3, > ibrav = 2, > > > If we use this UC we get a indirect band gap (G-X), which is > correct. If we now use the conventional UC (12 atoms in the cube) > we get a direct band gap at Gamma. In this case, we are using the > following input file : > calculation = 'bands', > celldm(1) = 1, > nat = 12, > ibrav = 0, > > K_POINTS crystal > 126 > .0 .0 .0 1. > .020 .020 .020 1. > .040 .040 .040 1. > .060 .060 .060 1. > .080 .080 .080 1. > .100 .100 .100 1. > .120 .120 .120 1. > etc. > > CELL_PARAMETERS > 12.03517200 0.0 0.0 > 0.0 12.03517200 0.0 > 0.0 0.0 12.03517200 > ATOMIC_POSITIONS crystal > Si0.00.00.0 > Si0.50.50.0 > Si0.00.50.5 > Si0.50.00.5 > Mg0.25 0.25 0.25 > Mg0.75 0.75 0.75 > Mg0.25 0.25 0.75 > Mg0.25 0.75 0.25 > Mg0.75 0.25 0.25 > Mg0.25 0.75 0.75 > Mg0.75 0.25 0.75 > Mg0.75 0.75 0.25 > > Could you please tell us what we are doing wrong in the second > calculation? > > Thank you for your response. > > Best regards, > Pascal > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org> > http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > > Dr. Yun Wang > Research Fellow > Centre for Clean Environment and Energy > Griffith School of Environment > Gold Coast Campus, Griffith University > QLD 4222, Australia > Tel:(61-7) 5552 8456 > Fax:(61-7) 5552 8067 > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- A non-text attachment was scrubbed... Name: pascal_boulet.vcf Type: text/x-vcard Size: 413 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20130319/5c4ee287/attachment.vcf
[Pw_forum] Electronic band structures for primitive and conventional unit cells
Dear all, We are facing a problem with differences in electronic band structures when we use primitive or conventional unit cells. The structure we are dealing with is Mg2Si for which the primitive UC is: ATOMIC_POSITIONS crystal Si 0.0 0.0 0.0 Mg 0.25000 0.25000 0.25000 Mg 0.75000 0.75000 0.75000 The cubic space group is 225, a=12.0421785 bohr and Mg2Si is FCC. The rest of the input is (I make it short): K_POINTS crystal 120 0.500.250.751.0 0.500.260.741.0 0.500.270.731.0 etc. calculation = 'bands', celldm(1) =12.0421785, nat = 3, ibrav = 2, If we use this UC we get a indirect band gap (G-X), which is correct. If we now use the conventional UC (12 atoms in the cube) we get a direct band gap at Gamma. In this case, we are using the following input file : calculation = 'bands', celldm(1) = 1, nat = 12, ibrav = 0, K_POINTS crystal 126 .0 .0 .0 1. .020 .020 .020 1. .040 .040 .040 1. .060 .060 .060 1. .080 .080 .080 1. .100 .100 .100 1. .120 .120 .120 1. etc. CELL_PARAMETERS 12.03517200 0.0 0.0 0.0 12.03517200 0.0 0.0 0.0 12.03517200 ATOMIC_POSITIONS crystal Si0.00.00.0 Si0.50.50.0 Si0.00.50.5 Si0.50.00.5 Mg0.25 0.25 0.25 Mg0.75 0.75 0.75 Mg0.25 0.25 0.75 Mg0.25 0.75 0.25 Mg0.75 0.25 0.25 Mg0.25 0.75 0.75 Mg0.75 0.25 0.75 Mg0.75 0.75 0.25 Could you please tell us what we are doing wrong in the second calculation? Thank you for your response. Best regards, Pascal -- next part -- A non-text attachment was scrubbed... Name: pascal_boulet.vcf Type: text/x-vcard Size: 413 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20130318/c029ace8/attachment.vcf
[Pw_forum] question on parallelism options and scaling factor
Thanks Giovanni for your suggestion. I will send the scaling tests a sson as possible. Regards Pascal Le 06/02/2013 10:24, Giovanni Pizzi a ?crit : > Dear Pascal, > since you have more than one k-point, you could try to have each pool > within one node, so that only inter-pool communication occurs over > infiniband; for instance if you have 4 k-points you may try to use 4 > pools on 4 nodes (or possibly 2 pools on 2 nodes, or 4 pools on 2 > nodes, etc). > This kind of parallelization should scale pretty well, if your system > allows it (i.e. you have enough kpoints and your system fits in RAM). > Then, you can try to optimize the parallelization using the other > parallelization options. > > If you manage to do some scaling tests using the pools, could you > please report your results on this mailing list? > > Thanks, and best regards, > > Giovanni Pizzi > > > On 02/05/2013 10:12 PM, pascal boulet wrote: >> Dear all, >> >> I have a basic question about parallelism and scaling factor. >> >> First, I am running calculations on a cubic system with 58 atoms >> (alat=19.5652 a.u.), 540 electrons (324 KS states) and few k-points >> (4x4x4 grid=4 k-points), on 32 cores (4 nodes) but I can submit on many >> more. >> >> I guess the best thing to do is to parallelize the calculation on the >> bands but maybe also on the FFTs. We have an infiniband interconnection >> network between the nodes. >> >> What would you suggest as values for image/pools/ntg/bands ? >> >> I have made a SCF test calculation on 16 and 32 cores. For the SCF cycle >> (13 steps) I get the following timing: >> For 16 cores: total cpu time spent up to now is22362.4 secs >> For 32 cores: total cpu time spent up to now is17932.6 secs >> >> The speedup is "only" 25%. I would have expected a better speedup for >> such a small number of cores. Am i wrong? What is your experience? >> >> (For additional information, if helpful: QE 5.0.1 has been compiled with >> openMPI, intel 12.1 and FFTW 3.2.2.) >> >> thank you for your answers. >> >> Regards >> Pascal >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > -- > Giovanni Pizzi > Post-doctoral Research Scientist > EPFL STI IMX THEOS > MXC 340 (B?timent MXC) > Station 12 > CH-1015 Lausanne (Switzerland) > Phone: +41 21 69 31124 > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- next part -- A non-text attachment was scrubbed... Name: pascal_boulet.vcf Type: text/x-vcard Size: 413 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20130206/9c16fe3c/attachment.vcf
[Pw_forum] question on parallelism options and scaling factor
Dear Paolo, Thank you for your quick answer. All the best, Pascal Le 06/02/2013 10:17, Paolo Giannozzi a ?crit : > On Feb 5, 2013, at 22:12 , pascal boulet wrote: > >> I guess the best thing to do is to parallelize the calculation on >> the bands > "band" parallelization is currently implemented only for some > specific cases. > Same for "image" parallelization. > > There is no quick and easy answer to your question. Your calculation is > relatively small, so you should likely exploit k-point (-npool 4) and > FFT > parallelization, using a few processors. How many it depends upon the > size of your FFT grids. Here some explanations: > http://www.fisica.uniud.it/%7Egiannozz/QE-Tutorial/tutorial_para.pdf > See also the general user guide, chapter 3: > http://www.quantum-espresso.org/wp-content/uploads/Doc/user_guide/ > and the user guide for PWscf, sec. 4.4 and 4.5: > http://www.quantum-espresso.org/wp-content/uploads/Doc/pw_user_guide/ > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- next part -- A non-text attachment was scrubbed... Name: pascal_boulet.vcf Type: text/x-vcard Size: 413 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20130206/dba1bdf2/attachment.vcf
[Pw_forum] question on parallelism options and scaling factor
Dear all, I have a basic question about parallelism and scaling factor. First, I am running calculations on a cubic system with 58 atoms (alat=19.5652 a.u.), 540 electrons (324 KS states) and few k-points (4x4x4 grid=4 k-points), on 32 cores (4 nodes) but I can submit on many more. I guess the best thing to do is to parallelize the calculation on the bands but maybe also on the FFTs. We have an infiniband interconnection network between the nodes. What would you suggest as values for image/pools/ntg/bands ? I have made a SCF test calculation on 16 and 32 cores. For the SCF cycle (13 steps) I get the following timing: For 16 cores: total cpu time spent up to now is22362.4 secs For 32 cores: total cpu time spent up to now is17932.6 secs The speedup is "only" 25%. I would have expected a better speedup for such a small number of cores. Am i wrong? What is your experience? (For additional information, if helpful: QE 5.0.1 has been compiled with openMPI, intel 12.1 and FFTW 3.2.2.) thank you for your answers. Regards Pascal -- next part -- A non-text attachment was scrubbed... Name: pascal_boulet.vcf Type: text/x-vcard Size: 413 bytes Desc: not available Url : http://pwscf.org/pipermail/pw_forum/attachments/20130205/ee0e4031/attachment.vcf
[Pw_forum] general question on materials physics
Thank you Stefano for your precisions. Best regards Pascal -- Dr. pascal Boulet, computational chemist University of Aix-Marseille I Laboratoire Chimie Provence, UMR 6264 Group of Theoretical Chemistry Avenue Normandie-Niemen 13397 Marseille Cedex 20 France ** Tel. (+33) (0)413.55.18.10 Fax. (+33) (0)491.55.18.50 ** http://www.lc-provence.fr https://sites.google.com/a/univ-provence.fr/pb-comput-chem %%
[Pw_forum] general question on materials physics
I think that I've just found the answer: the SC is heavily doped! P. -- Dr. pascal Boulet, computational chemist University of Aix-Marseille I Laboratoire Chimie Provence, UMR 6264 Group of Theoretical Chemistry Avenue Normandie-Niemen 13397 Marseille Cedex 20 France ** Tel. (+33) (0)413.55.18.10 Fax. (+33) (0)491.55.18.50 ** http://www.lc-provence.fr https://sites.google.com/a/univ-provence.fr/pb-comput-chem %%
[Pw_forum] general question on materials physics
Dear all, Sorry to bother you with this silly question but it puzzles me a bit! In a recent article, I have seen a DOS in which the Fermi level is located in the conduction band. So, it seems to me that the materials is metallic. But there is clearly a band gap of about 2 eV. I always thought that for metals the gap was closed. Is there a contradiction in the paper or am I wrong? Thank you for your answer. Best Pascal -- Dr. pascal Boulet, computational chemist University of Aix-Marseille I Laboratoire Chimie Provence, UMR 6264 Group of Theoretical Chemistry Avenue Normandie-Niemen 13397 Marseille Cedex 20 France ** Tel. (+33) (0)413.55.18.10 Fax. (+33) (0)491.55.18.50 ** http://www.lc-provence.fr https://sites.google.com/a/univ-provence.fr/pb-comput-chem %%
[Pw_forum] general question on openMP
Dear all, I am not familiar with the openMP parallelization. I would like to know in what circumstances openMP is worth being used? Same question for MPI+openMP. Thank you for your help. Best regards Pascal
[Pw_forum] Pressure-induced phase transition
Dear Amin, Regarding your question: And how can I use phonon calculations to help me find the phase transition? I've heard about some "mode softening", but I am not sure how it can be used in this context? When pressure changes you may observe that one or several phonon modes are softening, meaning, their frequencies are decreasing, eventually becoming imaginary in values. To see this you have to calculate the phonon dispersion band, that is, the phonon modes over the whole Brillouin zone (BZ), not just at the gamma point. If for some pressure you observe a negative (or more correctly imaginary) frequency at a particular q-point of the BZ, it means that the system undergoes an instability and is likely to transform into another structure. This you can see in the following paper: Phys. Rev. B, 78, 100102(R), 2008 in Figure 3b where the phonon softening is observed at the X q-point. Regards Pascal * Anglais - d?tect? * Anglais * Fran?ais * Anglais * Fran?ais
[Pw_forum] problem with symmetry recognition
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Vic, Stefano and Giuseppe, Thank you for your help and sorry for this lengthy post. Following Stefano's comment I need to provide ALL the atomic positions, which I did not do! I gave only the positions in the primitive unit cell (UC). But then, if I provide all the positions (I guess in the full UC) why should QE fill the others? In addition, I did some calculations on Mg2Si (FCC, 12 atoms in the full UC) by providing only the 3 atoms of the primitive UC. QE found 48 symmetry elements, which is correct, and the optimized cell parameters seemed OK. So, still, is it wrong? I have just tried Mn4Si7 with the full UC (44 atoms) and QE found 8 symmetry operations which is correct. I also checked with the Bilbao Jmol applet that my structure is correct. BTW, I also noticed something that looks strange to me. The coordinates reported by QE in the output are not those I give in the input: X and Y are the same but not Z which is scaled by c/a. So, for me, the distance between the atoms is changed in the Z direction(?). That could explain why the SCF converge is so difficult...(?) See the second set of coordinates I copied from QE output, below. For those who are interested, I provide here all the positions (cell parameters: celldm(1)=10.46100d0,celldm(3)=3.17100d0, ibrav=6). The atom positions with more digits are those of the atoms in the reduced UC (I generated all the positions with the Bilbao website). Input file: ATOMIC_POSITIONS crystal Si 0.1627 0.6791 0.1815 Si 0.837300 0.320900 0.181500 Si 0.679100 0.837300 0.818500 Si 0.320900 0.162700 0.818500 Si 0.162700 0.320900 0.681500 Si 0.837300 0.679100 0.681500 Si 0.679100 0.162700 0.318500 Si 0.320900 0.837300 0.318500 Si 0.1933 0.1507 0.1129 Si 0.806700 0.849300 0.112900 Si 0.150700 0.806700 0.887100 Si 0.849300 0.193300 0.887100 Si 0.193300 0.849300 0.612900 Si 0.806700 0.150700 0.612900 Si 0.150700 0.193300 0.387100 Si 0.849300 0.806700 0.387100 Si 0.3436 0.2279 0.5409 Si 0.656400 0.772100 0.540900 Si 0.227900 0.656400 0.459100 Si 0.772100 0.343600 0.459100 Si 0.343600 0.772100 0.040900 Si 0.656400 0.227900 0.040900 Si 0.227900 0.343600 0.959100 Si 0.772100 0.656400 0.959100 Si 0.333 0.333 0.2500 Si 0.667 0.667 0.2500 Si 0.333 0.667 0.7500 Si 0.667 0.333 0.7500 Mn 0. 0.5000 0.0625 Mn 0.50 0.00 0.937500 Mn 0.00 0.50 0.562500 Mn 0.50 0.00 0.437500 Mn 0. 0.5000 0.3125 Mn 0.50 0.00 0.687500 Mn 0.00 0.50 0.812500 Mn 0.50 0.00 0.187500 Mn 0.5000 0.5000 0.1250 Mn 0.50 0.50 0.875000 Mn 0.50 0.50 0.625000 Mn 0.50 0.50 0.375000 Mn 0. 0. 0. Mn 0.00 0.00 0.50 Mn 0. 0. 0.2500 Mn 0.00 0.00 0.75 - From output file: [...] 8 Sym.Ops. (no inversion) Cartesian axes site n. atom positions (alat units) 1 Si tau( 1) = ( 0.1627000 0.6791000 0.5755365 ) 2 Si tau( 2) = ( 0.8373000 0.3209000 0.5755365 ) 3 Si tau( 3) = ( 0.6791000 0.8373000 2.5954635 ) 4 Si tau( 4) = ( 0.3209000 0.1627000 2.5954635 ) 5 Si tau( 5) = ( 0.1627000 0.3209000 2.1610365 ) 6 Si tau( 6) = ( 0.8373000 0.6791000 2.1610365 ) 7 Si tau( 7) = ( 0.6791000 0.1627000 1.0099635 ) 8 Si tau( 8) = ( 0.3209000 0.8373000 1.0099635 ) 9 Si tau( 9) = ( 0.1933000 0.1507000 0.3580059 ) 10 Si tau( 10) = ( 0.8067000 0.8493000 0.3580059 ) 11 Si tau( 11) = ( 0.1507000 0.8067000 2.8129941 ) 12 Si tau( 12) = ( 0.8493000 0.1933000 2.8129941 ) 13 Si tau( 13) = ( 0.1933000 0.8493000 1.9435059 ) 14 Si tau( 14) = ( 0.8067000 0.1507000 1.9435059 ) 15 Si tau( 15) = ( 0.1507000 0.1933000 1.2274941 ) 16 Si tau( 16) = ( 0.8493000 0.8067000 1.2274941 ) 17 Si tau( 17) = ( 0.3436000 0.2279000 1.7151939 ) 18 Si tau( 18) = ( 0.6564000 0.7721000 1.7151939 ) 19 Si tau( 19) = ( 0.2279000 0.6564000 1.4558061 ) 20 Si tau( 20) = ( 0.7721000 0.3436000 1.4558061 ) 21 Si tau( 21) = ( 0.3436000 0.7721000 0.1296939 ) 22 Si tau( 22) = ( 0.6564000 0.2279000 0.1296939 ) 23 Si tau( 23) = ( 0.2279000 0.3436000 3.0413061 ) 24 Si tau( 24) = ( 0.7721000 0.6564000 3.0413061 ) 25 Si tau( 25) = ( 0.33
[Pw_forum] problem with symmetry recognition
Dear all, I am struggling to make QE recognize the symmetry of a solid compound. The group number is 116, it is a tetragonal primitive structure with 9 atoms in the primitive unit cell. In the input file I give the reduced coordinates I obtained from the Pearson database. I tried the following structure descriptions: alat = 1., ibrav = 0 CELL_PARAMETERS cubic 10.461 0. 0. 0. 10.461 0. 0. 0. 33.172 then: celldm(1)=10.461, celldm(3)=3.171, ibrav=6 No way! The idea is to optimize the cell parameters, so I would like QE to retain the crystal symmetry. Does anybody have an idea what could be wrong? Thank you Pascal * Anglais - d?tect? * Anglais * Fran?ais * Anglais * Fran?ais
[Pw_forum] optimized cell parameters with pw version 4.2.1 versus 4.3.1
Hello again, Please, forget my previous message: I did not noticed there is a final SCF cycle at the optimized structure! Sorry for that. regards Pascal
[Pw_forum] optimized cell parameters with pw version 4.2.1 versus 4.3.1
Dear all, I am optimizing the cell parameters of some compounds. With pw.x version 4.2.1 the optimized parameters are given at the end of the output. It seems that it is not the case with version 4.3.1, even with verbosity='high'. Is it possible to reactivate the priniting of the optimized parameters? Regards Pascal
[Pw_forum] CP simulation with ensemble-dft algorithm
Dear Nicola, I confirm that I have no problem to converge the density with the ensemble-DFT algorithm. I am working on silver nanoparticules. With a small one (13 atoms only) the convergence is reach within 10 cycles. I am going to try with a bigger one soon (38 atoms). Regards Pascal * * Anglais * Fran?ais * Anglais * Fran?ais
[Pw_forum] CP simulation with ensemble-dft algorithm
Dear Giovanni, Humm... hard to say because the data are not printed in the output file. Here is what I get, for instance: nfiekinc temph temppetot enthal econs econtvnhh xnhh0vnhp xnhp0 nfi temppE -T.S-mu.nbsp +K_p #Iter Step20 0 -502.49200 -502.62143 -502.62143 6 cg_sub: missed minimum, case 1, iteration 1 cg_sub: missed minimum, case 1, iteration 2 cg_sub: missed minimum, case 1, iteration 3 cg_sub: missed minimum, case 1, iteration 4 cg_sub: missed minimum, case 1, iteration 5 NOTE: eigenvalues are not computed without ortho Occupations : 2.00 2.00 2.00 2.00 2.00 2.00 1.99 1.99 1.99 1.98 1.97 1.95 1.94 1.89 1.83 1.77 1.58 1.33 1.999884 1.999793 ... 0.001473 0.000546 0.000502 0.000278 0.000134 0.79 0.33 0.19 0.00 nfi temppE -T.S-mu.nbsp +K_p #Iter Step21 0 -502.49200 -502.62143 -502.62143 6 < etc. So, there is nothing about ekinc, temph, tempp, ... However, the data "nfiekinc temph temppetot enthal econs econtvnhh xnhh0vnhp xnhp0" look like those given in the file xxx.evp (except for one missing column). If this is right, then in this file ekinc = 0. during the whole simulation. That's strange! So, I guess there is something wrong somewhere in my input. Pascal > Date: Fri, 17 Jun 2011 10:27:09 +0200 (CEST) > From: Giovanni La Penna > Subject: Re: [Pw_forum] CP simulation with ensemble-dft algorithm > To: PWSCF Forum > Message-ID: > Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII > > > Dear Pascal, > > The input shows that you are trying to > carry the system to 627 K starting with > random velocities and a time-step of 20 au (about 0.5 fs). > I expect a huge Kel after a few time-steps, due > to huge current atomic velocities, not manageable > with the given time-step. > Please, tell me (us) if this won't happen. > > Giovanni La Penna > > * * Anglais * Fran?ais * Anglais * Fran?ais
[Pw_forum] CP simulation with ensemble-dft algorithm
Thank you Paolo and Changru: it works fine now. Pascal
[Pw_forum] CP simulation with ensemble-dft algorithm
Dear all,
It seems that my first post was completely unreadable (html). Sorry for
that. Here is the content.
I am trying to run a CP simulation (cp.x) of a molecule in contact with
a small metallic cluster of atoms.
First here is the input file of my test job:
&CONTROL
title = 'MD',
calculation = 'cp',
dt= 20.d0,
isave = 5,
nstep = 10,
etot_conv_thr = 5.d-7,
prefix= 'test',
pseudo_dir= '/opt/espresso-4.3.1/pseudo',
restart_mode = 'from_scratch',
verbosity = 'high',
iprint= 1
/
&SYSTEM
ibrav = 0,
celldm(1) = 34.015084,
nat = 4,
ntyp= 2,
ecutwfc = 25.,
ecutrho = 200.,
occupations = 'ensemble',
smearing= 'fd',
degauss = 0.02,
input_dft = 'PBE',
nbnd= 30,
assume_isolated = 'makov-payne'
/
&ELECTRONS
conv_thr= 5.d-7,
mixing_beta = 0.4d0,
startingwfc = 'random',
tcg = .TRUE.,
electron_velocities = 'zero',
electron_temperature = 'nose',
fnosee = 300.,
ekincw = 0.001,
orthogonalization = 'Gram-Schmidt'
/
&IONS
ion_dynamics= 'verlet',
ion_temperature = 'nose',
ion_velocities = 'random',
remove_rigid_rot = .TRUE.,
tempw = 623.d0,
ndega = -6,
nhpcl = 1,
fnosep = 24.,
/
ATOMIC_SPECIES
Ag 107.8682 Ag.pbe-d-rrkjus.UPF
N14.0067N.pbe-rrkjus.UPF
ATOMIC_POSITIONS angstrom
Ag 6.467294548 12.585619859 10.268802850
Ag 6.293658753 10.453834050 12.214668134
N4.165456080 10.433924294 8.842653616
N3.807795851 10.451920023 9.956290174
CELL_PARAMETERS {cubic}
1. 0. 0.
0. 1. 0.
0. 0. 1.
If I run the above input file, I get the following error message:
%%
from ions_print_info : error # 1
tcap and tnosep both true
%%
What is the meaning of the variables tcap and tnosep?
It seems they are not adjustable variables through the input file since
they are not referenced in the manual. Indeed, if I set tcap=.false. in
the input file I get the following:
%%
from read_namelists : error #19
reading namelist ions
%%
So, is there any contradiction in my input file?
Thank you for your help
Best regards
Pascal
[Pw_forum] CP simulation with ensemble-dft algorithm
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