Re: [Pw_forum] kpoints for transmission calculations and complex band structures?
Dear Fang, Unfornately I don't have any experience with the systems you are investigating, but I'll add my comments that might provide you some insights. The answer for your question is simple but will require some effort to accomplish it: you must test your system and make sure the properties are converged. Convergence means the following: As you increase a given parameter that you are tracking, the results are not changing anymore. In order to achieve that for your systems, I would recommend two things: 1) Look for the literature and check the parameters they used the same systems. 2) Do a series of tests increasing the parameters at a point that the properties you are investigating are not changing anymore. We all know that for some systems these tests might be prohibitive (this is why the step 1 is so important). In that case, go for the best grid you can simulate and honestly note that on the reports. Just to remember you, if the DOS and total energy are converged, your tests for band structure can be only NSCF. But please MAKE A BACKUP of your ".save" folder (if you are using the wf_collect=.true.) because the NSCF messes up with the restart. I hope you find at least part of these insights useful. Best regards, Filipe On Sun, Sep 6, 2015 at 8:31 AM, Yue-Wen Fang <yuewen.f...@gmail.com> wrote: > Dear all, > > For a junction, e.g. Fe/MgO/Fe MTJ with a=b=2.8, c = 34 angstrom, a > general DOS calculation usually require a kgrid as 11*11*1, however, could > anyone tell me how many kpoints do I need to set for it in transmission > calculation and complex band structure calculation, respectively? > > Thank you in advance! > > Bests > Fang > > -- > > > Yue-Wen FANG, PhD candidate > Key Laboratory of Polar Materials and Devices, Ministry of Education > <http://clpm.ecnu.edu.cn/> > East China Normal University <http://english.ecnu.edu.cn/> > > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- _ Dr. Filipe Camargo Dalmatti Alves Lima Pos-Doc at Materials Physics Department. University of São Paulo, Physics Institute, Brazil. Phones:+55 (11) 3091-6881 (USP) +55 (11) 97408-2755 (Cellphone - Vivo) ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] DOS Calculation
Dear Kanak, Are you using Windows? I would suggest you delete the outdir line because there are a lot of specials characters that might be sources of errors. As default, the result will be written in the same folder you execute the calculation. Best, Filipe On Thu, Sep 10, 2015 at 8:34 AM, Kanak Datta <kanakee...@gmail.com> wrote: > Dear researchers > > I am facing problems in DOS calculation. I wanted to run the given example > in reference. I ran example 02 for this. The example is on bulk Ni. I ran > scf-> nscf and then went for dos. > > > outdir='D:\QuantumEspresso\Quantum ESPRESSO 64-bit 5.1.2-mpich2\ni' > prefix='ni' > fildos='ni.dos', > Emin=5.0, Emax=25.0, DeltaE=0.1 > / > > I used dos.x package for this. However I am getting the following error: > > Error in routine dos (1): > reading dos namelist > > I can't figure out what's wrong. Can you help? > Thanks in advance. > > Sincerely yours > Kanak > EEE, BUET > > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- _ Dr. Filipe Camargo Dalmatti Alves Lima Pos-Doc at Materials Physics Department. University of São Paulo, Physics Institute, Brazil. Phones:+55 (11) 3091-6881 (USP) +55 (11) 97408-2755 (Cellphone - Vivo) ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] regarding the stability of system
Dear sir, You cannot compare Fermi energy if you do not align the vacuum level of systems. Professor Baroni et al., if I remember correctly, have shown this in one of his works. In terms of energy formation, this paper below (and citing references) might help you: (Sorry, I am sending this email through my phone, couldn't change big size fonts) Also, other works of the professor Lucy Vitoria C. Assali discuss with very good details the energy formation of materials. Best regards, Filipe Intrinsic uncertainty on *ab initio* phase diagram and compound formation energy calculations: BCC Mo–Fe as a test case http://onlinelibrary.wiley.com/doi/10.1002/pssb.201248386/abstract On Thursday, November 6, 2014, mohaddeseh abbasnejad <m.abbasne...@gmail.com> wrote: > > Dear experts, > > In my calculations, I have studied four different configurations of > system. Based on the calculated energy, the stable configuration (lowest > value of energy) has larger Fermi energy and the highest value of energy > (less stable one) is related to the lowest Fermi energy. However, I have > read that increasing the Fermi energy in the system is expected to decrease > the stability. I was wondering if you would help me on which parameter > should be considered to determine the stability. > Thanks in advance. > > Regards, > M.Abbasnejad > -- > - > > Mohaddeseh Abbasnejad, > Room No. 323, Department of Physics, > University of Tehran, North Karegar Ave., > Tehran, P.O. Box: 14395-547- IRAN > Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781 > Cellphone: +98 917 731 7514 > E-Mail: m.abbasne...@gmail.com > <javascript:_e(%7B%7D,'cvml','m.abbasne...@gmail.com');> > Website: http://physics.ut.ac.ir > > ------------- > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of São Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Plotting HOMO, LUMO wavefunction
Plot_num = 7 for wavefunction. This script was written in python. All it asks are the parameters you wrote in the input file provided in quantum espresso and options for pp.x. You must edit this file by hand using an editor of your preference. The prof. Kulik's script should make you life easier, as the python would do the hard job for you. If it is not helping you, I am attaching an example of input to be used on pp.x prefix ='SAME_PREFIX_YOU_USE_ON_.IN_FILE', filplot = 'name of the output file. For each kpoint and kband there should be a DIFFERENTE NAME. Otherwise it will overwrite', plot_num = 7, #to plot wavefunctions. Are you using norm. conserving PPs? kpoint = 1,# If you are using monkhorst pack, you should first run a nscf calculation specifying the kpoints you are interested. Remember to backup your .save folder. kband = 4, # band you are plotting. Remember that bands = (number of electrons) / 2. If you have spin polarized you should check the up and down electrons. / nfile= 1, filepp(1)='add a name here', weight(1)= 1.0, iflag= 3, output_format=6, # cube format fileout='wavefunction.X.Y.Z.cube' / all you need to do is prepare this file for your needs and run pp.x best regards, On Tue, Nov 4, 2014 at 6:44 PM, Arpan Kundu <arpankund...@gmail.com> wrote: > Hi Filipe, > > Thanks a lot for your reply. The problem I am facing in plotting the > wavefunction is setting the appropriate parameters in pp.x. In the pp.x > manual, below are the options for plot_num. Which option should I select to > produce molecular orbitals? Also, I dont understand the method discussed > in the link that you provided: > http://hjklol.mit.edu/content/visualizing-molecular-orbitals . Where do I > edit the variables mentioned in the variables.py file ? > > > 0 = electron (pseudo-)charge density > >1 = total potential V_bare + V_H + V_xc > >2 = local ionic potential V_bare > >3 = local density of states at e_fermi > (number of states per volume, in bohr^3, > per energy unit, in Ry) > >4 = local density of electronic entropy > >5 = STM images > Tersoff and Hamann, PRB 31, 805 (1985) > >6 = spin polarization (rho(up)-rho(down)) > >7 = contribution of a selected wavefunction to the > (pseudo-)charge density. For norm-conserving PPs, > |psi|^2 (psi=selected wavefunction). Noncollinear case: > contribution of the given state to the charge or > to the magnetization along the direction indicated > by spin_component (0 = charge, 1 = x, 2 = y, 3 = z ) > > > > On Tue, Nov 4, 2014 at 8:00 AM, Filipe Camargo Dalmatti Alves Lima < > fl...@if.usp.br> wrote: > >> It might be a case that you should fine tuning the software you use to >> plot the wavefunction. >> >> I usually export as .cube and load the orbitals using the jmol for high >> quality image. >> >> Try typing these commands on the jmol console: >> >> load 'FILE.cube' >> background white >> isosurface NICKNAME_1 cutoff 0.009 color deepskyblue file '' >> isosurface NICKNAME_2 cutoff -0.0009 color red file '' >> >> As you can see, I can define different cutoff to drawn the "positive" and >> "negative" parts of the wavefunction. >> When you consider the figure is what you want, then type >> >> write povray 'ANYNAME.pov' >> >> It will generate a very good high quality image. >> >> I hope it helps you finding what you want. >> >> You might also consider study a very good tutorial (IMHO) provided by >> professor Heather Kulik, from MIT, at the link below: >> http://hjklol.mit.edu/content/visualizing-molecular-orbitals >> >> Best, >> >> Filipe >> >> >> >> >> >> >> >> >> On Sat, Nov 1, 2014 at 7:33 PM, Lorenzo Paulatto < >> lorenzo.paula...@impmc.upmc.fr> wrote: >> >>> On 10/31/2014 10:39 PM, Arpan Kundu wrote: >>> > Hi users, >>> > >>> > I want to plot the HOMO, LUMO wavefunction of H2O in QE. But the pp.x >>> > plots the charge density instead of the exact wavefunction. I mean the >>> > wavefunction should have a positive part and a negative part. But when >>> > I plot pp.x with a plot_num=7, it plots the contribution of the >>> > wavefunction to the charge density and it is mostly positive. Thanks a >>> > lot for your help. >>> > >>> > >>> Hi Arpan, >>> the manual of PP is only a couple of pages long, it's better to read it >>> to the end: >>> < >>> http://www.quantum-esp
Re: [Pw_forum] Plotting HOMO, LUMO wavefunction
It might be a case that you should fine tuning the software you use to plot the wavefunction. I usually export as .cube and load the orbitals using the jmol for high quality image. Try typing these commands on the jmol console: load 'FILE.cube' background white isosurface NICKNAME_1 cutoff 0.009 color deepskyblue file '' isosurface NICKNAME_2 cutoff -0.0009 color red file '' As you can see, I can define different cutoff to drawn the "positive" and "negative" parts of the wavefunction. When you consider the figure is what you want, then type write povray 'ANYNAME.pov' It will generate a very good high quality image. I hope it helps you finding what you want. You might also consider study a very good tutorial (IMHO) provided by professor Heather Kulik, from MIT, at the link below: http://hjklol.mit.edu/content/visualizing-molecular-orbitals Best, Filipe On Sat, Nov 1, 2014 at 7:33 PM, Lorenzo Paulatto < lorenzo.paula...@impmc.upmc.fr> wrote: > On 10/31/2014 10:39 PM, Arpan Kundu wrote: > > Hi users, > > > > I want to plot the HOMO, LUMO wavefunction of H2O in QE. But the pp.x > > plots the charge density instead of the exact wavefunction. I mean the > > wavefunction should have a positive part and a negative part. But when > > I plot pp.x with a plot_num=7, it plots the contribution of the > > wavefunction to the charge density and it is mostly positive. Thanks a > > lot for your help. > > > > > Hi Arpan, > the manual of PP is only a couple of pages long, it's better to read it > to the end: > < > http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PP.html#idp42384 > > > > kind regards > > -- > Dr. Lorenzo Paulatto > IdR @ IMPMC -- CNRS & Université Paris 6 > +33 (0)1 44 275 084 / skype: paulatz > http://www-int.impmc.upmc.fr/~paulatto/ > 23-24/4é16 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05 > > _______ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of São Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] (no subject)
This value is comparable to the number of electrons your pseudopotential has in the valence region. You might look inside of that pseudopotentials your are using to figure out the number of electrons. for example, the carbon pseudopotential (C.pbe-van_ak.UPF): Since the Z valence is 4, which means the Lowdin charges would show something around 4. Regards, Filipe I'm attaching below a Head example of a pseudopotential: Generated using Vanderbilt code, version 7 3 4 Author: unknownGeneration date:435 Automatically converted from original format 0The Pseudo was generated with a Non-Relativistic Calculation 1.000E+00Local Potential cutoff radius nl pn l occ RcutRcut US E pseu 2S 2 0 2.00 10.000 1.100 -1.00978244769 2P 2 1 2.00 10.000 1.100 -0.38870429969 0 Version Number CElement US Ultrasoft pseudopotential F Nonlinear Core Correction SLA PW PBE PBEPBE Exchange-Correlation functional 4.000 Z valence -10.72515811861 Total energy 0.000 0.000 Suggested cutoff for wfc and rho 1 Max angular momentum component 721 Number of points in mesh 24 Number of Wavefunctions, Number of Projectors Wavefunctions nl l occ 2S 0 2.00 2P 1 2.00 On Fri, Oct 17, 2014 at 11:04 AM, <khadije.khal...@gmail.com> wrote: > Dear All, > > I used projwfc.x to produce PDOS and lowdin charges but all of total > charges are positive as below. > I don’t know if my output is correct or I should do another calculations > to reach the final output. Based on my knowledge sum of the charges of all > atoms have to be equal to zero. > > Any suggestion is really appreciated. > Best, > Raha > > Lowdin Charges: > > > > Atom # 1: total charge = 5.2613, s, p, d, f = 1.3179 3.9435 > 0. > > Atom # 2: total charge = 3.7891, s, p, d, f = 0.9298 2.8593 > 0. > > Atom # 3: total charge = 5.2572, s, p, d, f = 1.3342 3.9230 > 0. > > Atom # 4: total charge = 3.7551, s, p, d, f = 0.8776 2.8776 > 0. > > Atom # 5: total charge = 3.9309, s, p, d, f = 0.8966 3.0342 > 0. > > Atom # 6: total charge = 3.6735, s, p, d, f = 0.8623 2.8112 > 0. > > Atom # 7: total charge = 5.4134, s, p, d, f = 1.2207 4.1927 > 0. > > Atom # 8: total charge = 0.6575, s, p, d, f = 0.6575 0. > 0. > > Atom # 9: total charge = 0.6583, s, p, d, f = 0.6583 0. > 0. > > Atom # 10: total charge = 5.2284, s, p, d, f = 1.3715 3.8570 > 0. > > Atom # 11: total charge = 3.8796, s, p, d, f = 0.9485 2.9311 > 0. > > Atom # 12: total charge = 4.7730, s, p, d, f = 1.1758 3.5972 > 0. > > Atom # 13: total charge = 7.0943, s, p, d, f = 1.8605 5.2338 > 0. > > Atom # 14: total charge = 5.7094, s, p, d, f = 1.6089 4.1005 > 0. > > Atom # 15: total charge = 5.7361, s, p, d, f = 1.6353 4.1008 > 0. > > Atom # 16: total charge = 11.1441, s, p, d, f = 1.0202 0.5294 > 9.5945 > > Atom # 17: total charge = 11.1219, s, p, d, f = 1.0086 0.5286 > 9.5847 > > Spilling Parameter: 0.0104 > > Khadije Khalili > PhD student of Solid State Physics > University of Mazandaan > Babolsar, Iran > > Sent from Windows Mail > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of São Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] convert to cif file
Open babel can do it for you. First all you need is to create a .xyz file then convert to PDB format. > After this, you just need do add an extra line with the crystal cell. > > I am pretty sure you can create your own shell script using sed, , awk, > grep and open babel. The algorithm, could be something like this: > > - find nat flag on pwscf input. ( can be done with grep) > - copy only the number (can be done using awk and defining = as delimiter ) > - write this number in a new file with cat or sed. > - jump 1 line in the file (fixed format xyz issues) > - find the flag ATOMIC_POSITIONS and copy all lines until K_POINTS flag > (can be done using sed) > - write it in your new xyz file. > - run open babel to convert the format. > Now the trick part might be the cell parameters since there are lot of > different ways to define your cell. I would say this step can't be fully > automated without tons of efforts to recognize and follow specific rules > for each case (ibrav type. angles, etc). If you use only a single way to > define your cells, use the same ideas as above and write a new line in your > file with the cell size. > > If you try to develop the script I can help you fixing the bugs/issues on > it and in the end you will learn how to make a new script. :-) > > Let me know if you need further assistance. > > Regards, > Filipe > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140903/0a54bfe9/attachment.html
[Pw_forum] Bugs found when compiling QE 5.1 on BGP
e DO loop does not match the END PARALLEL DO directive, or no directive matches the END PARALLEL DO directive. To eliminate these errors, we disabled omp at those lines by deleting the omp commands. However, we would prefer to use the full capacity of omp, and we are unsure if we may accidentally interfere other aspects of the code by removing this. Regards, Filipe and Paul Whitford -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140822/b21a677e/attachment.html
[Pw_forum] Relax calculation
The relax option does NOT optimize the lattice constants. (useful when you want to relax impurities of molecules) The vc-relax option optimize the lattice constants. (useful only you have crystalline system) Now it depends what you want to do: Do you have just a crystal? I should say vc-relax is enough. Do you have a slab with a molecule attached into the surface? I would first vc-relax the surface alone; I would insert the molecule, then I would optimize the geometry using relax option. If I had just a single molecule, I would create a very large box and just relax the structure. In order to be sure that your simulation is ok you must always check the convergence parameters: total energy, k-point mesh, DOS, forces, etc... all the time. Also, keep in mind the convergence depends on the property you want to investigate. Is there anything in particular that you have an issue? Regards, Filipe On Fri, Apr 25, 2014 at 6:14 PM, Sohail Ahmad wrote: > I am using QE 5.0.2 and I have a very basic question. > To optimise the structure of a material, i started with known experimental > lattice constants and calculated energy vs lattice to know the optimised > lattice constants. > > Now i wish to apply the strain > so i increased lattice constant 'a' by 2% (let us say) > > now i need to relax (i believe) to get optimised coordinates before > proceeding further and wish to know force and stress as well. > > So my question is i should consider it as 'relax' or "vc relax" > if relax then following should work but unfortunately no > tprnfor = .TRUE. > tstress = .TRUE. > ion_dynamics = 'bfgs' > If i donot consider force and stress, then it gives me final coordinates > > Is the above step true in this particular set of problems of strain > application or should i use variable cell. > i am little confused. > So > > - > > *Sohail Ahmad* > King Khalid University > Abha, Saudi Arabia > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140426/cf248cfd/attachment.html
[Pw_forum] The relax problem
By looking at the total forces. There is a part in the output that will show the forces on the atoms and the total force of the system. You can grep the output using this command: cat $youroutput | grep "total force" (or something like that, I don't remember the captcha exactly). This number should decrease along the time. If the total force reach the threshold condition, the calculation will stop. Otherwise it can also stop after lots of tries and it will complain saying that the convergence didn't achieved the mininum. For further info, the criteria for the force can be seen below: *etot_conv_thr* REAL Default: 1.0D-4 convergence threshold on total energy (a.u) for ionic minimization: the convergence criterion is satisfied when the total energy changes less than etot_conv_thr between two consecutive scf steps. Note that etot_conv_thr is extensive, like the total energy. See also forc_conv_thr - both criteria must be satisfied *forc_conv_thr* REAL Default: 1.0D-3 convergence threshold on forces (a.u) for ionic minimization: the convergence criterion is satisfied when all components of all forces are smaller than forc_conv_thr. See also etot_conv_thr (note that the latter is extensive, forc_conv_thr is not) - both criteria must be satisfied source: http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#id3119460 Regards, Filipe On Tue, Apr 22, 2014 at 10:04 PM, yjunwei2012 wrote: > Dear manchugh? > Thank you for your reply! I still have some problems and need your > help. When we relax the system, how can we judge the relax result is > successful or fail? and is there have some big different aspects between > relax and vc-relax? Thank you again! > > Best wishes! > JWY > > > > 2014-04-23 > -- > yjunwei2012 > -- > **manchugh at iitk.ac.in > *?*2014-04-23 05:04 > *???*Re: [Pw_forum] The relax problem > **"PWSCF Forum" > *???* > > Dear JWY > > Your output file still has the same number of atoms. There is no problem > with your system. You can see the missing atoms in the image you sent by > using "Number of units drawn" option in Modify tab of xcrysden. > > Thank you > Manjusha > Ph.D student > IIT Kanpur > India > > > Hello dear QE users, > > >I have used the 'calculation=relax' to calculation a 48 atomes' system, > > and I compare the structure data(after relax) with the one from input > > file(before relax),I find that there has a big difference. Then I > > import the two structures to Xcrysden, the result as the above two > > pictures show that, I do not understand why and wonder if some problems > > with symmetry? I am not sure. > > I look forward to your suggestion! Thank you! > > > > Best wishes! > > JWY > > > > 2014-04-22 > > > > > > > > yjunwei2012___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140422/f069fe8c/attachment.html
[Pw_forum] kpint.x
Do you want to plot the band structure? The answer might be the Xcrysden. ( http://www.xcrysden.org/ <http://www.xcrysden.org/>) It can help you build the k point path to calculate the bands. The procedure to achiev it is: 1) Run a SCF calculation and make sure the electronic properties are converged. 2) Run a NSCF restarting from the SCF you made and use the k point path suggested by Xcrysden. or Do you want to know the number o K points generated by the Monkhorst-Pack? Check the Monkhorst pack original article: http://journals.aps.org/prb/abstract/10.1103/PhysRevB.13.5188 Regards, Filipe On Mon, Apr 21, 2014 at 5:34 PM, Halima Zaari wrote: > Dear quantum espresso users and developers > can you give me a help to use k_point.x to generate a path from the > number of k_point > for expample in the case of 4*4*4 how i can find the direction of k_vector > thank you in advance > > -- > H.ZAARI > PhD Student in laboratory of magnetism and physics of high energy > Faculty of Sciences in Rabat - Morocco > Email: > * halimazaari at gmail.com * > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- _____ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140422/3aa36c36/attachment.html
[Pw_forum] Fwd: au111 surface
4796914 0.719331555Au >>3.326200204 2.202685361 0.719334648 >> Au 3.478788201 1.670372948 >> 0.051951374Au 3.865644556 2.412608619 >>0.051953914Au 4.175978091 >> 3.185452798 0.051947555Au 2.759515725 >>2.097309245 0.051954205 >> Au 3.133871517 2.883011335 >> 0.051949504Au 3.504225226 3.675472063 >>0.051948273Au 2.091449270 >> 2.593809644 0.051950705Au 2.407897276 >>3.365285757 0.051948060 >> Au 2.790900569 4.112185484 >> 0.051947893End final >> coordinates >> Any help will be appreciated. -- >> >> Khadije KhaliliPh.D >> Student of Solid-State PhysicsDepartment of >> PhysicsUniversity of >> MazandaranBabolsar, Irankh.khalili at stu.umz.ac.ir >> >> >> >> -Inline Attachment Follows- >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > Khadije Khalili > Ph.D Student of Solid-State Physics > Department of Physics > University of Mazandaran > Babolsar, Iran > kh.khalili at stu.umz.ac.ir > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140421/854311e3/attachment.html
[Pw_forum] pp.x with gamma-only calculations
Have you tried to run a NSCF (this calculations uses the restart wavefunction you made previously with the SCF) calculation with the K-point you want to plot? Usually this is the method I use to plot charge density. Run SCF with a M.H. grid good enough to ensure that my result is reliable. Run a NSCF with specific K-points I want to plot the charge density. (Since Monkhorst grid does not always include the k-points I want to analyze) I hope it will help you Regards, Filipe On Thu, Apr 10, 2014 at 9:19 AM, Juan J. Mel?ndez wrote: > Dear all: > > I want to get the charge density for a defective supercell, and it seems > to me that pp.x does not implement any ?gamma-only? tricks. Is this right? > If so, is there any way to overcome this (without recalculating, of course)? > > Thanks in advance > > Juanjo > > Juan J. Mel?ndez > 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: melendez at unex.es > Web: http://materiales.unex.es/miembros/personal/jj-melendez/Index.html > > > -- ><http://www.avast.com/> > > Este mensaje no contiene virus ni malware porque la protecci?n de avast! > Antivirus <http://www.avast.com/> est? activa. > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140410/6a5c4fca/attachment.html
[Pw_forum] Ag.pbe-dn-rrkjus_psl.0.1.UPF
Dear Faith, This paper has been published using Ag surfaces and QE pseudopotentials: Structure and Molecule-Substrate Interaction in a Co-octaethyl Porphyrin Monolayer on the Ag(110) Surface http://pubs.acs.org/doi/abs/10.1021/jp2011233 It might help you designing your own system. Best, Filipe On Fri, Apr 4, 2014 at 9:23 AM, Andrea Dal Corso wrote: > As far as I know, this Ag PP is working, and should be fine for Ag > surfaces. > > Andrea > > > On Fri, 2014-04-04 at 13:15 +0300, fatih.ersan at adu.edu.tr wrote: > > Dear A. Dal Corso: > > > > I want to use Ag atoms for my study, when i'm searching suitable > pseudo-potentials(pp), i met Ag.pbe-dn-rrkjus_psl.0.1.UPF which has > config='[Kr] 4d9.5 5s1.5 5p0.0'electronic configurations. Is your scope to > generate this potential to examine catalytic activities or something like > this? Can i use this PP to adsorb on any sheet? Could you help me for me to > understand? > > > > Best wishes > > > > Fatih > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > -- > Andrea Dal CorsoTel. 0039-040-3787428 > SISSA, Via Bonomea 265 Fax. 0039-040-3787249 > I-34136 Trieste (Italy) e-mail: dalcorso at sissa.it > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140404/e6d929d0/attachment.html
[Pw_forum] Gibbs Free energy
I found it: QHA (Quasi Harmonic Approximation): utilities for the calculation of projected density of states (PDOS) and of the free energy in the Quasi-Harmonic Approximation (to be used in conjunction with PHonon). sorry for ask. On Fri, Apr 4, 2014 at 9:11 AM, Filipe Camargo Dalmatti Alves Lima < flima at if.usp.br> wrote: > Dear Patrik, > > Just a curious question: what is QHA? > > Thanks, > > Filipe > > > On Fri, Apr 4, 2014 at 8:28 AM, Saied Md Pratik > wrote: > >> Hi All >> After running QHA (implemented in Quantum espresso) I have got >> E_internal,F_vibration, Specific heat (C_v), Entropy etc. Does F_vibration >> correspond to Helmholtz free energy? If so, Can anybody please tell me >> that how can I calculate Gibbs free energy? >> Thanks in advance. >> Pratik >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > _ > Filipe Camargo Dalmatti Alves Lima > PhD Student > University of S?o Paulo, Physics Institute, Materials Physics Department, > Nanomol Group, Brazil. > Phones: (11) 3091-6881 (USP) > (11) 97408-2755 (Vivo) > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140404/91422629/attachment.html
[Pw_forum] About Zero Forces
Have you already tried to use vc-relax instead of relax? vc-relax = variable cell relaxation. relax = internal coordinates relaxation. I would say you have nothing to optimize in terms of internal coordinates: you are using a high simmetry crystal that is written in terms of the lattice parameter. Regards, Filipe On Wed, Apr 2, 2014 at 7:03 AM, Mutlu COLAKOGULLARI wrote: > > Hello People, > > I want to relax CoPt bulk material. It has face-centered tetragonal (tP4) > structural type. The relaxation is always finisihing after 1 scf cycle and > 0 bfgs step. The forces are always zero. I mean the system is not relaxing. > I googled the problem and I tried something in input, nevertheless I failed > for every try. What am I doing something wrong? Do you have any suggestion > or comment or web page? > I am using svn version with latest updates. > Here is my input file: > > > calculation = 'relax', > restart_mode = 'from_scratch', > pseudo_dir= '/home/mutlusan/Desktop/CoPt/pseudos', > outdir= '/home/mutlusan/Desktop/CoPt/outdir.CoPt', > prefix= 'CoPt', > tprnfor = .true. > tstress = .true. > wf_collect= .true. > !etot_conv_thr = 1.0D-12, > !forc_conv_thr = 1.0D-11 , > nstep = 300 , >disk_io = 'low' > / > >ibrav = 6, > celldm(1)= 7.182849031 !a=3.801 A > celldm(3)= 0.979479084 !c=3.723 A > ntyp = 2, > nat = 4, > ecutwfc = 85, > ecutrho = 850, > occupations = 'smearing' > smearing = 'mv' > degauss = 0.01 > nspin=2 > starting_magnetization(1)=0.5 > / > > conv_thr = 1.0d-8, > diagonalization = 'david' > diago_david_ndim = 8 > mixing_mode = 'plain' > mixing_beta = 0.7 > mixing_ndim = 8 > / > > > ! upscale=100, > ion_dynamics = "bfgs", > bfgs_ndim = 8 > / > !CELL_PARAMETERS > ! 7.182849031 0.00 0.00 > ! 0.00 7.182849031 0.00 > ! 0.00 0.00 7.0355450393 > ATOMIC_SPECIES > Co58.9332 Co.pbe-sp-van.UPF > Pt 195.0800 Pt.pbe-n-van.UPF > ATOMIC_POSITIONS (crystal) > Co 0.00.00.0 > Co 0.50.50.0 > Pt 0.50.00.5 > Pt 0.00.50.5 > K_POINTS automatic > 8 8 8 1 1 1 > > I have attached the output file. > > with my best wishes, > > Mutlu. > __ > Mutlu COLAKOGULLARI > Phone : +90 (284) 235 1179 (ext: 1207) > Address : Trakya University >Sciences Faculty, Department of Physics, >Balkan Campus, (22100) Merkez - Edirne - TURKEY > Home page: http://goo.gl/DNXfNC > ______________ > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140402/4895dc7f/attachment.html
[Pw_forum] Reg: How to know the mode name and due to which atom it is happening?
It is because you did not finish all the steps to analyse the data. I got a similar problem before and I remember it is possible to obtain a file that has as the vectors of the modes that can be viewed in the xcrysden. Unfortunately I don't run simulations phonon simulations anymore, I couldn't remember everything I did in the past. I am pasting a manual section that explains it in details. (I also change the color to red the point I think might solve your issue.) 4.2 Calculation of interatomic force constants in real space First, dynamical matrices are calculated and saved for a suitable uniform grid of *q*-vectors (only those in the Irreducible Brillouin Zone of the crystal are needed). Although this can be done one *q*-vector at the time, a simpler procedure is to specify variable ldisp=.true. and to set variables nq1, nq2,nq3 to some suitable Monkhorst-Pack grid, that will be automatically generated, centered at [image: $ \bf q$] = 0 . Second, code q2r.x reads the dynamical matrices produced in the preceding step and Fourier-transform them, writing a file of Interatomic Force Constants in real space, up to a distance that depends on the size of the grid of *q*-vectors. Input documentation in the header of PHonon/PH/q2r.f90. *Program matdyn.x may be used to produce phonon modes and frequencies at any q using the Interatomic Force Constants file as input. Input documentation in the header of PHonon/PH/matdyn.f90.* See Example 02 for a complete calculation of phonon dispersions in AlAs. source: http://www.quantum-espresso.org/wp-content/uploads/Doc/ph_user_guide/node1.html I hope it will solve your issue. Best regards, Filipe On Tue, Apr 1, 2014 at 8:49 AM, Peram sreenivasa reddy < peramsreenivas at gmail.com> wrote: > Dear xirainbow, > > Thank you very much for your replay. > > In that case.dyn1 file also it is giving same only as in the case.ph.out > file. > > Please give me more clarification. > > Thanking you. > > > > On Tue, Apr 1, 2014 at 3:15 PM, xirainbow wrote: > >> You can find the answer at the end of *.dyn* files. >> >> On Mon, Mar 31, 2014 at 11:10 PM, Peram sreenivasa reddy >> wrote: >> > Dear Pwscf, >> > >> > In my phonon calculations i got one imaginary mode in gamma to X >> direction. >> > I want to know which mode it is? and due to which atom it is happening? >> > >> > I checked the case.ph.out file. In this file it is given like below. >> > >> > Mode symmetry, O_h (m-3m) point group: >> > omega( 1 - 3) =-16.6 [cm-1] --> T_1u G_15 G_4- I >> > omega( 4 - 6) =122.3 [cm-1] --> T_1u G_15 G_4- I >> > omega( 7 - 9) =145.0 [cm-1] --> T_2g G_25' G_5+ R >> > omega( 10 - 12) =258.5 [cm-1] --> T_1u G_15 G_4- I >> > >> > Here i am attaching the case.agr file >> > >> > Here all acoustic modes are given with same frequency. How can know that >> > particular mode name. >> > >> > >> > My system is X2YZ type. How can i know this imaginary mode is due to >> which >> > atom. I plotted partial phonon density of states also. But all atoms are >> > giving same contribution in this acoustic mode region. >> > >> > Thank you in advance. >> > >> > >> > >> > ___ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://pwscf.org/mailman/listinfo/pw_forum >> >> >> >> -- >> >> Hui Wang >> School of physics, Henan University of Science and Technology, Henan, >> China >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140401/f6b7ce75/attachment.html
[Pw_forum] QE + EPW
I would compare the make.sys file you had in the version 5.x and 4.0.3. You
might be able to figure out which flags are different and maybe it can fix
your problem.
After changing the make.sys backup it and try to compile again.
Warning: Everytime you ran ./configure it will override the make.sys.
Good luck,
Filipe
On Friday, March 7, 2014, yelena
>
wrote:
> Dear everyone,
> I'm trying to install EPW. EPW works with version 4.0.3 of QE, so I
> decided to make separate install QE 4.0.3 for EPW and leave my current
> 5.0.3 install for other calculations.
> I'm aware you don't provide support for obsolete versions but I've been
> having problems with 4.0.3 installation and I was hoping someone could
> help me.
> After ./configure everything looks ok (paralel env. detected...) but
> after make all I get
>
>
> read_upf_v2.f90:437.16-34:
>
>ALLOCATE( upf%nn(upf%nwfc), upf%nn(upf%nwfc), &
> 1 2
> Error: Allocate-object at (1) also appears at (2)
> make[1]: *** [read_upf_v2.o] Error 1
>
>
> Is there any suggestion how could i fix it?
> Best regards,
> J. Pesic
> PhD Student, Center for Solid State Physics and New Materials,
> IPB, Serbia
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
_
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:(11) 3091-6881 (USP)
(11) 97408-2755 (Vivo)
--
_
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:(11) 3091-6881 (USP)
(11) 97408-2755 (Vivo)
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[Pw_forum] Matlab call pw.x
Do you have mpi installed in machine?
type it in terminal:
locate mpirun
it should give you something like:
/usr/local/openmpi/bin/mpirun
/usr/local/openmpi/share/man/man1/mpirun.1
Regardless your linux provides a mpirun by default, I suggest you to
install it by yourself:
http://www.open-mpi.org/
You'll have more control over the settings.
I.M.H.O.: you should use the matlab to write files you need, then run the
job in terminal.
Best,
On Fri, Mar 7, 2014 at 1:30 PM, Lijuan He wrote:
> Dear everyone,
>
> I am trying to use Matlab to call pw.x but it does not work. My command
> line is
> system('~/espresso/bin/pw.x< ~/debug/H2+H.in >H2+H.out'). I know it
> probably because I need to first run mpi then call pw.x. But I cannot find
> the mpi. Anyone knows how to do this. Thanks very much.
>
> Best,
> Lijuan He
> Ph.D student in Georgia Tech
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
_____
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:(11) 3091-6881 (USP)
(11) 97408-2755 (Vivo)
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[Pw_forum] Fwd: Basic Relax Calculation issues
Dear Zarah,
Have you ever considered that you may want the cell relaxation in this
case? (vc-relax)
It will optimize the cell parameter in order to minimize the total energy.
You'll see that the system might have lots of interactions.
If you want to explore defects in crystals or surfaces, relaxing the
internal coordinates are essential since you are breaking the symmetry in
some way: by having impurities; surface interaction; vacancy defects and
etc. If it is the case you want to explore, you will need to use a
supercell approach. Remember: crystals are built based on symmetry rules.
If you are really curious, you might try to change the cell symmetry just
to observe how the internal coordinations behave (just increase z by 0.2).
It may not converge, but you will see a lot interactions.
Best regards,
Filipe
On Friday, February 28, 2014, Zarah Baiyee wrote:
> Hi All,
>
> I am a new user to Quantum Espresso, therefore this may be a bit trivial
> but I any help would be very welcome.
>
> I am attempting a relax calculation using espresso version 5.0.2, for the
> geometry optimisation of a perovskite structure. For the input below, the
> calculation runs, however does not compute any forces and convergence
> without geometry optimisation to the original structure, with 0 bfgs steps.
> I am able to perform an expected relaxation if alter the initial atomic
> positions to asymmetric: (i.e.) an oxygen molecule from: O (0.500 0.5
> 0.0) to O(0.499 0.5 0.0).
>
> Please may someone shed some light on to why this is the case, and if
> there is anything wrong with my input.
>
> Thanks
>
> Zarah
> Zbaiyee at gmail.com <javascript:_e(%7B%7D,'cvml','Zbaiyee at gmail.com');>
>
>
> calculation = "relax",
> prefix = "CO",
> pseudo_dir = "/Users/zarahbaiyee/espresso-5.0.2/pseudo",
> outdir = "/Users/zarahbaiyee/tmp",
> forc_conv_thr = 1.0D-5
> /
>
> ibrav = 0,
> nat = 5,
> ntyp = 3,
> ecutwfc = 60,
> ecutrho = 420,
> /
>
> conv_thr= 1.D-7,
> mixing_beta = 0.7D0,
> electron_maxstep = 400
> /
>
> /
> CELL_PARAMETERS bohr
> 7.60 0.0 0.0
> 0.0 7.60 0.0
> 0.0 0.0 7.60
> ATOMIC_SPECIES
> Ba 137.32 Ba.pbe-mt_fhi.UPF
> Fe 55.84 Fe.pbe-mt_fhi.UPF
> O 15.99 O.pbe-kjpaw.UPF
> ATOMIC_POSITIONS {crystal}
> Ba 0.000 0.0 0.0 0 0 0
> Fe 0.500 0.5 0.5
> O 0.000 0.5 0.5
> O 0.500 0.0 0.5
> O 0.500 0.5 0.0
> K_POINTS {automatic}
> 9 9 9 0 0 0
>
>
--
_
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:(11) 3091-6881 (USP)
(11) 97408-2755 (Vivo)
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[Pw_forum] convergence is hard to achieve using PAW
Dear Ganjar, Question zero: did you achiev a convergence using ultrasoft pseudopotentials using this input? If your answer is yes, the rest of the email might not help you... I think you misunderstood the option ibrav=0. As you may see in the input data description, when you select ibrav=0, it is written you should set only A or celldm(1). If it is the case you have A, B and C and right angles, it means you cell is orthorombic (ibrav=8). Of course you may use ibrav=0, however, I am not sure if the code understand A, B and C. Maybe, you should write B and C in terms of A value into the cell_parameter card. I am not an expert using ibrav=0 (I have never used, to be honest), sorry if I told you something you already had checked. If your input is ok, you should be able to measure the atom-atom distances and be sure they are the expected ones. My guess is that you will figure out that the cell is smaller than you want: the program is just ignoring the B and C parameters. I have already had problems setting wrong cell parameters, resulting in no convergence. I hope it helped, Best regards, Filipe Dalmatti Lima PhD Candidate University of S?o Paulo, Physics Institute, Materials Physics Department, Brazil. On Monday, March 3, 2014, Ganjar Kurniawan wrote: > Dear QE users > > This is the first time I use the PAW pseudopotential. I have calculated > the system using the PAW pseudopotential, but the convergence is very hard > to achieve. I treat the system as insulator (according to the experiment) > and I have tried to vary the mixing beta value from 0.7 until 0.2 (the > latest which I give with the difference is 0.1 gradually) but the latest > result become worst than the before. > > The question is whats wrong with my input?? > how about the value of ecutrho I have given?? > > What I must to do?? > > input and output file are attached > > I hope your advice please.. > > Thank you > > Best Regard > > Ganjar Kurniawan > Bandung Institute of Technology > > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 97408-2755 (Vivo) -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140306/1967d736/attachment.html
[Pw_forum] (no subject)
Dear Mokhavat, The band gap from DFT is a non reliable quantity. This is why people uses GW approach: to have a better band gap value. In other words, don't trust DFT gap. In your specific case I'm not sure how to answer since I have never used the bands.x before. Em 12/05/2013 06:54, "shiva mokhavat" escreveu: > > dear users > I am working on GaP compound.I found that experimental studies show 2.35 ev width for it's band gap. when I run bands.x the gap widht is 2.20 ev, but when I run dos.x the gap width is 1.45 ev.I used tetrahedra for nscf in dos, but use smearig for band. I attached my input files. I use espresso 4.3 > could anyone help me in this? > thanks > > ___ > 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/20130512/731436e6/attachment.html
[Pw_forum] Fermi energy reference point shift from 0 to -2
Hi, It is normal, the Fermi energy shows the energy of highest occupied electron and it does not necessary is exactly on zero. You can shift All energies by an additive constant without no problem. For one single system it is ok to shift the energies by an additive constant. (Like add +2.0508 to move the Fermi level to zero) and it is not changing the physics of the result, just the way you are presenting. However, BE CAREFUL! It dos not mean that you can align two different systems using this method. >From the QE website: * * *?The value of the Fermi energy (as well as of any energy, for that matter) depends upon the reference level. What you are referring to is probably the ?Fermi energy referred to the vacuum level? (i.e. the work function). In order to obtain that, you need to know what the vacuum level is, which cannot be said from a bulk calculation only?>* (Stefano Baroni, Sept. 2008). http://www.quantum-espresso.org/?page_id=364 Best regards, Filipe Lima - PhD Student - University of S?o Paulo, Brazil. On 04/04/2013, at 22:30, Shamsu Abubakar wrote: Thank you Mr. Robert for your kind response. I will include the verbosity='high' and repeat the calculations. However, you made mention that, when i plotted the DOS there is need to shift my Fermi level to zero; that i did not understand very well. My question is, How to shift my Fermi to zero?. Secondly, I always see my Fermi energy at the end of my scf calculation.'' the Fermi energy is -2.0508'', before total energy line. Does it mean -2.0508 is my actual Fermi energy? because the zero point in the DOS graph is just a reference point. Lastly, for my plotting software, i used Qtiplot. Usually, after my ./dos.x input and output, i take my 'dos' directly to plot my DOS. Therefore, I don't know if you or someone can help with some guide about it. Once again thank you and Best regards. Shamsu Abubakar Postgraduate student Department of Physics University Putra Malaysia -- *From:* Robert Hembree *To:* 'Shamsu Abubakar' ; 'PWSCF Forum' < pw_forum at pwscf.org> *Sent:* Friday, 5 April 2013, 1:17 *Subject:* RE: [Pw_forum] Fermi energy reference point shift from 0 to -2 Dear Shamsu Your input file and parameters are fine. When you plot the DOS you need to shift your Fermi level to zero if you want the gap to show up at zero. Add the line verbosity = ?high? to the control part of your input file and run pw.x again. Then you can grep your output file less scf.out | grep ?Fermi energy? You should get a line that looks like this: the Fermi energy is-1.6709 ev When you plot your DOS, for instance in gnuplot you would now plot plot ?Graph01.dos? ($1-(-1.6709)):2 w l and you should see your plot with the bandgap and dispersion at zero. When you do these calculations the Fermi level will rarely show up at exactly zero. Robert *From:* pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] *On Behalf Of *Shamsu Abubakar *Sent:* Wednesday, April 03, 2013 8:23 PM *To:* pw_forum at pwscf.org *Subject:* [Pw_forum] Fermi energy reference point shift from 0 to -2 Dear Q.E Users. I have a system of 4x4 graphene supercell, comprising 32 carbon atoms. I sucessfully run all the calculations i.e scf,nscf and other postprocessing such as DOS and PDOS. But the main problem i'm facing currently is on the density of state. Usually, i consider zero to be my fermi reference energy point in my ./dos.x input file, forexample,from -10 and 10 as my Emin and Emax respectivily. For pristine graphene,i expect to always see the dispersion at the zero vicinity, showing a semi metallic behavior, but surprisingly, its always moving away from zero to around -2, in the valence band side which i knew is unsual for pristine graphene. However, when i combine graphene with GaAs nanostructure, most of the interesting properties interms of orbitals contributions (PDOS), also resides on similar point -2. That is some of the contributions that are supposed to be seen at the vicinity of the fermi level, now moved to another point -2. Also, i consider changing the smearing from marzari-vanderbilt to Fermi- Dirac, but similar properties were observed. I decided to consider only 1x1, and 2x2 graphene supercell alone, still similar properties i observed also. In fact, i even consider changing my pseudopotential from pw91 to pbe.rrkjus still no progress. My problem now, i don't know what really causes these shift from 0 to -2. I attached one of my graphene scf input file for your verification and advice. title = 'Graphene monolayer01', prefix = 'Graph01', calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home//???/espresso-4.1.2/bin/' , pseudo_dir = '/home//???/???/espresso-4.1.2/upf_files/' , tstress = .true. , tprnfor = .true. , / ibrav
[Pw_forum] ecutwfc convergence
Dear Yusuf, I agree with everyone has said to you, but I just want to comment: "When the cutoff is enough?" I think this is your question, right? The best way to learn it is by testing your system with different parameters. For example: if you think that you need the best total energy description you should create a series of test varying the cutoff and testing the Total Energy. So, For a system you will run X simulations using different cutoffs 20 ry (200 ry), 25 ry (250 ry), 30 (300), 40 (400), 60 (600), ... (Remember charge density description (ecutrho) should change as you increase the kinect energy cutoff) For instance, lets pretend you obtained the following total energies: using 20 Ry = -20 eV using 25 Ry = -22 eV using 30 Ry = -22.501 eV using 40 Ry = -22.623 eV using 60 Ry = -22.625 eV In a perfect world as much ecutwfc is higher better would be your result. (if it does not happening, probably you are doing something wrong, like a poor k point description, etc) But do you need the best possible? In my example, there is a 2 eV difference by between 20 Ry and 25 Ry, so, it might not be a good idea use 20 Ry. However, comparing 30 and 40 ry, you have ~0.1 eV difference. Is this enough for the property that you are looking for? In some cases it could be enough, in others it won't. If you are looking at conformational changes that are around 0.5 eV probably you will need to increase your ecutwfc. You can use this procedure in all properties that you are interested in. In DOS case, you might compare if the DOS are changing as the cutoff increases. In summary: - The parameters that you choose are not changing the physics of your results. - They have a good relationship between correctness/computational time. - They are reasonable when you compare your work with the literature. - Your tests should be (relatively) fast since you don't want waste your machine time. That's it, I hope it will help you. Also, I hope I didn't make any mistake in my comment! :) Best regards, -- _____ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 8249-4628 (TIM) On Wed, Sep 26, 2012 at 9:44 AM, Eduardo Ariel Menendez Proupin < eariel99 at gmail.com> wrote: > Dear Yusuf > The cutoff depends on the pseudopotential that you use, not just on the > atom. Different pseudopotentials for the same atoms have different cutoff. > Also, some properties requiere higher cutoffs than others. For example, > forces and relative energies need lower cutoff than total energy and > stress. Using higher values does not harm, just take longer time and more > computer resources. Some programs include recommended cutoffs in the > pseudopotential, but the user is still responsible of testing it. > > If you want a starting parameter for graphene, use > C.pz-vbc.UPF with ecutwfc = 60.0 , > or > C.pbe-rrkjus.UPF with ecutwfc = 30.0 and ecutrho = 180.0 > > > the above work reasonably well to relax the structures with fixed cell, and > to get the bands and DOS. I fou want to calculate elastic properties or LDA+U > or PBE+U, or calculate conductance, etc, etc, these cutoffs may be too low. > Yo need to do tests increasing the values until you see no change in the > property that you want to calculate. > > If you plan to adsorb other atoms (e.g. oxygen) on the graphene, then > determine cutoffs that are valid for the full system and do all the > calculations with the same parameters. > > > > Dear Manasaje > > The system is graphene with 32 carbon atoms. The cutoff is not specified in > the pseudo and I need it before proceeding to other SCF and nscf calculations > and believe, cutoff is a property of an atom in question. So can I still go > ahead with the atoms in the unit cell. Thank you for your quick response > Yusuf > > > __ > __ > From: Eduardo Ariel Menendez Proupin <http://www.democritos.it/mailman/listinfo/pw_forum>> > To: pw_forum at pwscf.org <http://www.democritos.it/mailman/listinfo/pw_forum> > Sent: Wednesday, September 26, 2012 7:18 PM > Subject: Re: [Pw_forum] ecutwfc convergence > > > Dear Yusufm > > ecutwfc and ecutrho depend only on the hardest of the pseudopotentials used > for the atoms in the molecule or the crystal. If your molecule is C32 and > have no other elements, you can make tests with a C2 (which does not exists, > I guess), and the cutoffs for C32. > > Anyway, if your are going to calculate something that it is not the total > energy or the DOS, let's say, the phonons, or the Raman spectrum, it is > reasonable that you test the effect of the cutoff first on C2 and then on C32. >
[Pw_forum] how to calculate and plot HOMO or LUMO isosurface
Dear Giuseppe, Your are right, I am a physicist! Also, I completely forgot about the O2 fundamental state. Thank you for reply and for your correction! :-) Best regards all, Filipe On Wed, Jul 25, 2012 at 8:42 AM, Franklin Zhan wrote: > Many thanks to you guys. I learned a lot today. > > > Best regards, > -- > Franklin Zhan > > Ph.D student > School of Mechanical and Aerospace Engineering, > Nanyang Technological University, Singapore. > > > > > > > Date: Wed, 25 Jul 2012 13:15:01 +0200 > > From: carlo.nervi at unito.it > > > To: pw_forum at pwscf.org > > Subject: Re: [Pw_forum] how to calculate and plot HOMO or LUMO isosurface > > > > Il 25/07/2012 12.41, Franklin Zhan ha scritto: > > > ...However, O2 molecule is not magnetic material, thus I do not > > > know why we need to take the spin polarization into consideration. > > > > You have to review some chemistry... > > Try to have a look here: > > > > http://www.youtube.com/watch?v=Isd9IEnR4bw > > > > Carlo Nervi > > > > -- > > > > Prof. Carlo Nervi carlo.nervi at unito.it Tel! :+39 0116707507/8 > > > Fax: +39 0116707855 - Dipartimento di Chimica, via > > P. Giuria 7, 10125 Torino, Italy. http://lem.ch.unito.it/ > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > _______ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 8249-4628 (TIM) -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120725/4f5926cb/attachment.htm
[Pw_forum] self consistent calculation
Dear Ahmad,
The option nbnd is related to the number of electrons that you have in your
system.
You may increase this number without increase the number of k-points.
Usually you should request nbnd equal the number of valence electrons
divided by 2 (plus more bands if you want unoccupied states, I would
suggest add +4 bands at least).
Best regards,
--
_
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:(11) 3091-6881 (USP)
(11) 8249-4628 (TIM)
On Wed, Jul 18, 2012 at 11:41 AM, Sohail Ahmad wrote:
> Dear Users
>
> I run scf and nscf and calculated band structure and DOS succesfully for
> Molybdenum Disulphide (valence electron =36) in a 4x4x4 with nbnd =20
> but the problem in band structure i couldnot see sufficient no. of bands
>
> Then i tried to repeat the same in 12x12x12 with nbnd=30 but the program
> failed to run
>
> Should i try for lesser mesh for scf and do bigger mesh for nscf
>
>
> calculation = 'scf',
> restart_mode = 'from_scratch',
> prefix = 'MoSb1',
> pseudo_dir = '/home/sandeep/espresso-4.2.1/pseudo',
> outdir = './OUT',
> /
>
> ibrav = 4, celldm(1) = 6.0281946, celldm(3) = 3.89, nat = 6, ntyp = 2,
> ecutwfc = 70,
> ecutrho = 300,
> nbnd = 30,
> occupations = 'smearing', smearing = 'gaussian', degauss = 0.001,
> nspin = 2,
> starting_magnetization(1) = 0.1d0,
> /
>
> mixing_beta = 0.3,
> conv_thr = 1.0d-9,
> /
> ATOMIC_SPECIES
> Mo 95.96 Mo.pw91-n-van.UPF
> S 32.06 S.pw91-van_ak.UPF
> ATOMIC_POSITIONS {crystal}
> Mo 0. 0.6667 0.2500
> Mo 0.6667 0. 0.7500
> S 0. 0.6667 0.6200
> S 0.6667 0. 0.1200
> S 0.6667 0. -0.6200
> S 0. 0.6667 -0.1200
> K_POINTS AUTOMATIC
> 12 12 12 1 1 1
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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[Pw_forum] A question about the Ph.x code.
Dear Claudio, When I set epsil=.true., I receive this error: %% from phq_readin : error # 1 no elec. field with metals %% I think it is happening because I am using typical configuration to converge metallic systems (occupations='smearing',smearing='gaussian', degauss=0.008,) Otherwise, I can't achieve the scf convergence. Best regards, -- _ Filipe Camargo Dalmatti Alves Lima PhD Student University of S?o Paulo, Physics Institute, Materials Physics Department, Nanomol Group, Brazil. Phones:(11) 3091-6881 (USP) (11) 8249-4628 (TIM) On Wed, Jul 18, 2012 at 8:42 AM, Claudio Perottoni wrote: > Dear Filipe, > > Try setting epsil=.true. in your input file. > > Regards, > > Claudio > > > On 17-Jul-12 20:45, Filipe Camargo Dalmatti Alves Lima wrote: >> Dear QE users, >> >> I am having a problem regarding the ph.x /dynmat codes, >> >> I am investigating an oxide cluster containing metal ions using a >> supercell approach (at least 6A of vaccum in all directions). >> I couldn't converge the system without the "smearing" option (which is >> normally used to treat metal systems) even though my system has a gap. >> Due to the supercell approach, I have chosen only gamma k-point. >> >> When I submit the ph.x, it finishes without any error or warning message. >> However, when I calculate the dynmat to extract the results, it >> doesn't show me the IR activity >> >> I have attached below a part of the dynmat result. >> >> Do you know any hints am I doing wrongly? I am using the QE version >> 5.0, US-PP and PBE Exc. >> >> Thank you for your attention, >> This is my first time investigating IR properties. >> (I studied the examples within the QE folder and the tutorials in the >> QE website. ) >> >> Best regards, >> >> Filipe Camargo Dalmatti Alves Lima >> PhD Student >> University of S?o Paulo, Physics Institute, Materials Physics >> Department, Nanomol Group, Brazil. >> >> >> >> ...Force constants read >> ...epsilon and Z* not read (not found on file) >> A direction for q was not specified:TO-LO splitting will be absent >> Max |d(i,j)-d*(j,i)| = 0.058265 >> Max |d(i,j)-d*(j,i)|/|d(i,j)|: 189.4604% >> >> Polarizability (A^3 units) >> multiply by 1.00 for Clausius-Mossotti correction >> 0.000.000.00 >> 0.000.000.00 >> 0.000.000.00 >> >> IR activities are in (D/A)^2/amu units >> >> # mode [cm-1][THz] IR >> 1 -214.16 -6.42020. >> 2 -177.79 -5.33000. >> 3 -148.87 -4.46310. >> 4 -123.72 -3.70900. >> 5 -110.65 -3.31730. >> 6-94.07 -2.82010. >> 7-88.21 -2.64450. >> 8-84.06 -2.52000. >> 9-76.63 -2.29740. >> 10-75.77 -2.27170. >> 11-68.21 -2.04490. >> ... >> ## my ph.x input # >> >> >>tr2_ph=1.0d-14, >>prefix='NbO_opt', >>amass(1)=15.99, >>amass(2)=92.92, >>epsil=.false., >>trans=.true., >>fildyn='NbO_opt.dyn', >>niter_ph=100, >>recover=.true., >> / >> 0.0 0.0 0.0 >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- > ** > Dr. Cl?udio A. Perottoni > > Universidade de Caxias do Sul > Centro de Ci?ncias Exatas e Tecnologia > Rua Francisco Get?lio Vargas, 1130 > 95070-560 Caxias do Sul - RS - Brazil > Phone: +55 54 3218 2607 > http://www.ucs.br/ccet/defq/caperott/ > ** > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
