Re: [Pw_forum] equation of state fitting
Thank You all for your kind help and suggestions. I would further like to clarify a few more things from the suggestions received. Dear Dr. Michael Mehl, Quoting you from your reply, "You must have minimum energy structure for your crystal structure at that volume. This means minimizing the energy with respect to all atomic positions and all lattice parameters: b/a, c/a, etc., while keeping the volume fixed." I have to keep the volume of my structure fixed during the structural optimization? Is it the equilibrium volume obtained from the equation of fitting, that I have to keep fixed, while varying the other structural parameters? As you said the equilibrium lattice parameter comes very close to the experimental value given in the tutorial, but the bulk modulus value deviates beyond the 10% range in case of all the equations of state, specially for the Keane equation it deviates hugely while for the 2nd order Birch equation the deviation is the least. From the output data obtained after the fittings, the 'E_diff' values (that is the difference between the calculated total energy data and the fitted data at a given lattice parameter) are of the order of 10^-4 Ry and in case of the 2nd order Birch equation all the E_diff values are nil. Dear Dr. Alberto, Thank you for the link to the article. I will follow your suggestions and try again. Dear Dr. Lorenzo, Yes sir, the structure obtained is satisfactory and the equilibrium lattice parameter is also very close to the experimental value. I have already tested the convergence of the energy with respect to the ecutwfc value, as was instructed in the tutorial. So I should keep on increasing the parameter and check every time if the experimental value is getting reproduced and stick to that ecutwfc value? Please correct me if I am wrong. I will also try the 2nd method suggested by you. Thank you again to all of you. Regards, Sunetra Das. On 16 August 2017 at 23:07, Lorenzo Paulatto wrote: > On 16/08/17 18:36, Sunetra Das wrote: > > those equation fitting match the given experimental value, not even > > close. > > Dear Sunetra, > Is your structure satisfactory? Can you reproduce the experimental > geometry and volume? > > If not, you won't be ablt to get a good bulk modulus. > > If yes, try increasing the ecutwfc quite a bit, or run your calculations > at constant number of plane waves, which if I remember correctly means > changing ecutwfc ~ alat^-2 > > hth > > -- > Dr. Lorenzo Paulatto > IdR @ IMPMC -- CNRS & Université Paris 6 > phone: +33 (0)1 442 79822 / skype: paulatz > www: http://www-int.impmc.upmc.fr/~paulatto/ > mail: 23-24/423 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 > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] equation of state fitting
Dear QE users, I would like to know if there are any other equation of state that we can use to fit the 'etot vs alat' graph to find out the equilibrium lattice constant. I have been following the QE tutorials to learn the basics where it has been demonstrated how to fit a etot vs alat graph using the four given equations of state. But none of the obtained equilibrium bulk modulus values from those equation fitting match the given experimental value, not even close. How to improve the fitting of the equations or is there any other equation I can use to fit the obtained data? I am new to QE, any suggestion is highly appreciated. Thank you. Regards, Sunetra Das Assistant Professor, MMC College, Kolkata, WB, India. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] How to calculate band structure of a doped system
Dear Manu, Thank you very much for your help. Regards, Sunetra Das. On 17 June 2017 at 09:38, Manu Hegde wrote: > https://www-amdis.iaea.org/Workshops/ICTP2012/Paolo. > Giannozzi-Lecture-QE-ICTP-2012-01-26.pdf > > On Sat, Jun 17, 2017 at 12:03 AM, Sunetra Das > wrote: > >> Dear Manu, >> >> Can you please share the link for the tutorial on formation energy you >> mentioned in the earlier email? I am unable to find the one you are >> suggesting. It would be of great help. >> >> Thank you. >> >> Regards, >> >> Sunetra Das. >> Department of Physics, >> MMC College, Kolkata, India. >> >> ___ >> 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] How to calculate band structure of a doped system
Dear Manu, Can you please share the link for the tutorial on formation energy you mentioned in the earlier email? I am unable to find the one you are suggesting. It would be of great help. Thank you. Regards, Sunetra Das. Department of Physics, MMC College, Kolkata, India. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Error in routine potinit (1): starting and expected charges differ
00.0 1.0 0.470000.00.0 1.0 0.440000.00.0 1.0 0.410000.00.0 1.0 0.380000.00.0 1.0 0.350000.00.0 1.0 0.320000.00.0 1.0 0.290000.00.0 1.0 0.250000.00.0 1.0 0.220000.00.0 1.0 0.190000.00.0 1.0 0.150000.00.0 1.0 0.120000.00.0 1.0 0.10.00.0 1.0 0.080000.00.0 1.0 0.050000.00.0 1.0 0.030000.00.0 1.00000 0.00.00.0 1.0 Can anybody please point out where lies the fault in my input file? Thank you. Regards, Sunetra Das. Assistant Professor, Department of Physics MMC College, Kolkata, India. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Structural optimization
Hello Everybody, I am new to QE and trying to learn structural optimization. Are the two terms 'structural relaxation' and 'structural optimization' synonymous ? If yes, then is it meaningful to carry out any structural optimization on an unit cell only or is it more meaningful to optimize the supercell structure? My system has a 4x4 supercell structure of 32 atoms. Also can anybody please guide me through the correct sequence of steps to optimize a structure? Should I carry out a 'relax' calculation and follow it by a 'vc-relax' and then finally a 'scf' calculation? Or can I do a 'vc-relax' in the very first go without any 'relax' calculation? Is it mandatory to mention the 'dt' parameter for a 'vc-relax' run? Kindly help. Regards, Sunetra Das Assistant Professor, Maharaja Manindra Chandra College, Kolkata, India. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Error in routine phq_readin (5010)
Hello all, I am trying to run the ph.x code for my system in espress0-5.0.3, but the code stops with the following error code: * %% Error in routine phq_readin (5010): reading inputph namelist %%* Following is my input: *phonon &INPUTPH outdir = './tmp' , prefix = 'In4' , ldisp = .true., dvscf_star%pat = .true. , recover = .false. , qplot = .false. , q2d = .false. , q_in_band_form = .true. , amass(1) = 114.82, iverbosity = 1, tr2_ph = 1e-10 ,alpha_mix(1) = 0.7 , nk1 = 31 , nk2 = 31 , nk3 = 1 , k1 = 0 , k2 = 0 , k3 = 0 , nq1 = 5 , nq2 = 5 , nq3 = 1 , /1.0 0.0 0.0 * Can anyone please help me with the above error message ? Thanks you. Sunetra. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Topic 8
Thank you for your help, Mr. Jing Yang. On 24 February 2017 at 16:30, wrote: > Send Pw_forum mailing list submissions to > pw_forum@pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://pwscf.org/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-requ...@pwscf.org > > You can reach the person managing the list at > pw_forum-ow...@pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > >1. Re: Silicon 111 surface (Giovanni Cantele) >2. ESM Example (Al slab with bc2) and Otani/Sugino example > (Louis Fry-Bouriaux) >3. Re: Symmetry recognition (Louis Fry-Bouriaux) >4. Re: Symmetry recognition (Paolo Giannozzi) >5. Re: Symmetry recognition (Louis Fry-Bouriaux) >6. Re: Symmetry recognition (Paolo Giannozzi) >7. (no subject) (Sunetra Das) >8. Charge is wrong error (Sunetra Das) >9. Re: Charge is wrong error (Jing Yang) > 10. basis set module PROJWFC (alberto) > 11. Re: About output of PDOS calculations of CeO2 (Giuseppe Mattioli) > 12. Re: basis set module PROJWFC (Lorenzo Paulatto) > > > -- > > Message: 1 > Date: Thu, 23 Feb 2017 12:19:23 +0100 > From: Giovanni Cantele > Subject: Re: [Pw_forum] Silicon 111 surface > To: PWSCF Forum > Message-ID: <46431764-885c-414f-8833-8087fe3e2...@spin.cnr.it> > Content-Type: text/plain; charset="utf-8" > > Hi, > this is the reply to the message you sent me, it is better for me to > continue di discussion on PW_forum, being a way > to share doubts, mistakes, problems with many other people that might help! > > You can build your Si(111) surface with any tool (by hand, using VNL, any > other builder), but this tool will do just what > you ask it to do, so before using the tool you ALWAYS need basic > understanding. In this respect, I also suggest to look > to the extensive documentation of Quantum-ESPRESSO and to the tutorials > that are freely available in the web. > > Coming to your problem, Quantum-ESPRESSO, as you know, is based on plane > waves, as such can only handle > systems that are periodic in all three directions. If you need to simulate > something that is periodic in only two, one or no > direction in space (a surface, a 1D wire, a cluster/molecule/quantum dot > respectively) you use the supercell approach. > > Let?s consider the case of a surface and let?s choose x and y as > directions parallel to the surface, such that the z direction is orthogonal > to it (you can make a different choice, of course). > > 1) In the x-y plane you have to identify the surface unit cell, spanned by > two vectors a1 and a2 that describe the surface periodicity. > Beware the choice of a1 and a2: they might be deduced from the bulk > crystals or be more complicated if the surface > is along special directions or if it undergoes some reconstruction. > > In the case of Si(111) you should first decide if you want to choose the > minimal cell, or if you want to consider complex reconstruction > (that is structures where one or more surface unit cells are gathered to > build more complex structures) The minimal cell is obtained > by considering the 111 plane of Si and trying to understand the > periodicity vectors within that plane. The complex reconstruction are > instead > obtained once you know how many cells are gathered along the a1 and a2 > directions. For example, in the case of Si(111), whose structure > had been long debated many years ago, it can undergo a 7x7 reconstruction > (with a very large surface unit cell). You can find details wherever, > for example this is one of the Google search results: > http://nanowiz.tripod.com/sisteps/si111.htm <http://nanowiz.tripod.com/ > sisteps/si111.htm> > > > 2) once the surface unit cell is identified, you must decide how many > planes you want to consider in the direction (z-axis) orthogonal to the > surface. > In this case beware the fact that as you move in along z, you might meet > one or more planes that are not equivalent to the 1st one. In other words, > the second plane might not be obtained simply through a rigid shift along > z of the 1st one, but there might be 2 or more planes before one equivalent > to the first one is found > > > 3) at this point you have the minimal number of atomic coordinates that, > replicated along a1 and a2 reproduce a slab, that is, a Si(111) surface > composed > by a certain number of planes. How to choose a3 (this is one of the issues &
[Pw_forum] Charge is wrong error
Hello everybody I am getting wrong charge error as given below, in my output file: * WARNING: integrated charge= 6.02151254, expected= 6. %% Error in routine electrons (1): charge is wrong %% stopping ...* I have checked the FAQ section of QE website where the solution is given as to use a gaussian smearing. I am using a gaussian smearing for my metallic system, still the error. I am using QE version 5.0.3. Also the error occurs after several iterations. I am copying my input file contents below: * &CONTROL calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = './tmp' , pseudo_dir = '/home/sunetra/Desktop/In_qe/' , prefix = 'In_vc-relax' , lkpoint_dir = .true. , verbosity = 'high' , tstress = .true. , tprnfor = .true. , forc_conv_thr = 1.0D-2 , etot_conv_thr = 10.0D-10 , / &SYSTEM ibrav = 0, nat = 2,ntyp = 1, ecutwfc = 30 ,nbnd = 10, occupations = 'smearing' , degauss = 0.06 , smearing = 'gaussian' , input_dft = 'PBE' , / &ELECTRONSelectron_maxstep = 3000, scf_must_converge = .true. ,conv_thr = 1D-10 , mixing_beta = 0.7 , mixing_mode = 'plain' ,mixing_ndim = 8 , diagonalization = 'cg' ,diago_cg_maxiter = 3000 , / &ions / &cell /CELL_PARAMETERS Angstrom 4.9536653100.00.0 2.476832660 4.290000.0 0.00.0 20.0 ATOMIC_SPECIES In 114.81800 In.pbe-hgh.UPF ATOMIC_POSITIONS Angstrom In 2.4768326601.430000.0 In 4.9536653102.86000 0.0K_POINTS automatic 31 31 1 0 0 0 * Kindly can anyone please guide me in this matter? Thank you. Regards, Sunetra Das ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] (no subject)
Hello everybody I am getting wrong charge error as given below, in my output file: * WARNING: integrated charge= 6.02151254, expected= 6. %% Error in routine electrons (1): charge is wrong %% stopping ...* I have checked the FAQ section of QE website where the solution is given as to use a gaussian smearing. I am using a gaussian smearing for my metallic system, still the error. I am copying my input file contents below: * &CONTROL calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = './tmp' , pseudo_dir = '/home/sunetra/Desktop/In_qe/' , prefix = 'In_vc-relax' , lkpoint_dir = .true. , verbosity = 'high' , tstress = .true. , tprnfor = .true. , forc_conv_thr = 1.0D-2 , etot_conv_thr = 10.0D-10 , / &SYSTEM ibrav = 0, nat = 2,ntyp = 1, ecutwfc = 30 ,nbnd = 10, occupations = 'smearing' , degauss = 0.06 , smearing = 'gaussian' , input_dft = 'PBE' , / &ELECTRONSelectron_maxstep = 3000, scf_must_converge = .true. ,conv_thr = 1D-10 , mixing_beta = 0.7 , mixing_mode = 'plain' ,mixing_ndim = 8 , diagonalization = 'cg' ,diago_cg_maxiter = 3000 , / &ions / &cell /CELL_PARAMETERS Angstrom 4.9536653100.00.0 2.476832660 4.290000.0 0.00.0 20.0 ATOMIC_SPECIES In 114.81800 In.pbe-hgh.UPF ATOMIC_POSITIONS Angstrom In 2.4768326601.430000.0 In 4.953665310 2.860000.0K_POINTS automatic 31 31 1 0 0 0 * Kindly guide me in this matter. Thank you. Regards, Sunetra Das ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
