Re: [Pw_forum] phosphorene monolayer
Dear Gautam,
it is not a problem to start from the experimental bulk structure since the
monolayer structure is not that different.
You should visualize your input file with Xcrysden. You would see that you
don't have the correct geometry to start with.
Best,
Dario
On Thu, Oct 5, 2017 at 11:24 PM, Gautam Gaddemane
wrote:
> Thank you so much Vahid. I have a question though..how did you get the
> initial CELL_PARAMETERS ? I obtained the initial cell and atomic parameters
> from bulk.
>
> GAUTAM GADDEMANE
> DEPARTMENT OF MATERIALS SCIENCE AND ENGINEERING
> UNIVERSITY OF TEXAS AT DALLAS
>
> On Thu, Oct 5, 2017 at 4:19 PM, Vahid Askarpour wrote:
>
>> Hi Gautam,
>>
>> The following relaxation input worked for me:
>>
>> BP
>> 2D
>> &control
>> calculation='vc-relax'
>> restart_mode='from_scratch',
>> prefix='BP'
>> pseudo_dir='./'
>> verbosity='high'
>> tprnfor=.true.
>> tstress=.true.
>> etot_conv_thr=1.0e-06
>> forc_conv_thr=1.0e-05
>> /
>> &system
>> ibrav=0,
>> nat= 4, ntyp= 1
>> ecutwfc = 50, ecutrho=200,
>> occupations = 'fixed' ,
>> /
>> &electrons
>> diagonalization='cg'
>> conv_thr = 1.0e-12
>> mixing_beta = 0.7
>> electron_maxstep = 500
>> mixing_mode = 'plain'
>> /
>> &IONS
>> ion_dynamics = 'bfgs'
>> pot_extrapolation='atomic'
>> wfc_extrapolation='atomic'
>> /
>> &CELL
>> cell_dynamics = 'bfgs'
>> wmass=0.002
>> cell_factor=2.0
>> cell_dofree='xyz'
>> /
>> ATOMIC_SPECIES
>> P 30.97376 P.pbesol-n-kjpaw_psl.0.1.UPF
>>
>> K_POINTS {automatic}
>> 14 12 1 0 0 0
>>
>> CELL_PARAMETERS (angstrom)
>>4.429539231 0.0 0.0
>>0.0 3.279402120 0.0
>>0.0 0.0 31.941846246
>>
>> ATOMIC_POSITIONS (crystal)
>> P0.001152971 0.0 0.015264978
>> P0.335395312 0.49800 0.015264292
>> P0.501101273 0.49800 0.081335135
>> P0.835350444 0.0 0.081335495
>>
>> Best,
>>
>> Vahid
>>
>> Vahid Askarpour
>> Department of Physics and Atmospheric Science
>> Dalhousie University,
>> Halifax, NS, Canada
>>
>> > On Oct 5, 2017, at 4:45 PM, Gautam Gaddemane
>> wrote:
>> >
>> > Dear All,
>> >
>> > I am trying to calculate the bands tructure for monolayer phosphorene
>> and I am just a week old in using quantum espresso.
>> > From the bulk unit cell I prepared an input file to relax the structure
>> but I was not able to get a good lattice constant nor a good band gap. It
>> would be very helpful if someone would guide me in this procedure.
>> > I have attahced the file I used to relax in this email
>> >
>> >
>> > &CONTROL
>> > calculation='vc-relax',
>> > outdir='./',
>> > prefix='calc',
>> > pseudo_dir='./',
>> > verbosity='high',
>> > /
>> >
>> > &SYSTEM
>> > ibrav=0,
>> > celldm(1)= 8.276999830d0
>> > nat=4,
>> > ntyp=1,
>> > ecutwfc=60,
>> > ecutrho=360,
>> > input_dft='lda',
>> > occupations='smearing',
>> > smearing='mv',
>> > degauss=0.005d0,
>> > /
>> >
>> > &ELECTRONS
>> > conv_thr=1d-06,
>> > mixing_beta=0.7d0,
>> > /
>> > &IONS
>> > ion_dynamics='bfgs'
>> > /
>> >
>> > &CELL
>> > cell_dynamics='bfgs'
>> > cell_dofree='2Dshape'
>> > /
>> > ATOMIC_SPECIES
>> > P 30.973800d0 P.pw-mt_fhi.UPF
>> >
>> > ATOMIC_POSITIONS {crystal}
>> >
>> > P 0.09004 0.0 0.050195117
>> > P 0.90967 0.0 0.949804902
>> > P 0.59033 0.5 0.949804902
>> > P 0.40996 0.5 0.050195117
>> >
>> > K_POINTS {automatic}
>> >
>> > 12 12 1 0 0 0
>> >
>> > CELL_PARAMETERS {alat}
>> >
>> > 1.0.0.
>> > 0.0.7511415530000.
>> > 0.0. 4.680365292
>> >
>> >
>> > thank you
>> > Gautam
>> >
>> > GAUTAM GADDEMANE
>> > DEPARTMENT OF MATERIALS SCIENCE AND ENGINEERING
>> > UNIVERSITY OF TEXAS AT DALLAS
>> > ___
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>>
>>
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Re: [Pw_forum] phosphorene monolayer
Dear Gautam,
The values you get are not completely impossible.
Try with PBE, since there are for sure a couple of calculations in the
literature to compare with.
For example
https://journals.aps.org/prb/abstract/10.1103/PhysRevB.90.085402
Best,
Dario
On Thu, Oct 5, 2017 at 10:31 PM, Gautam Gaddemane
wrote:
> 4.45 A and 3.26 A and a band gap of 0.67eV.
>
> GAUTAM GADDEMANE
> DEPARTMENT OF MATERIALS SCIENCE AND ENGINEERING
> UNIVERSITY OF TEXAS AT DALLAS
>
> On Thu, Oct 5, 2017 at 3:28 PM, Matthieu Fortin-Deschênes <
> matthieu.fortin-desche...@polymtl.ca> wrote:
>
>> What values of lattice parameters and band gap did you get? With LDA
>> you expect some differences compared to experimental values.
>>
>> Matthieu
>>
>> Gautam Gaddemane a écrit :
>>
>> > Dear All,
>> >
>> > I am trying to calculate the bands tructure for monolayer phosphorene
>> and I
>> > am just a week old in using quantum espresso.
>> >> From the bulk unit cell I prepared an input file to relax the
>> structure but
>> > I was not able to get a good lattice constant nor a good band gap. It
>> would
>> > be very helpful if someone would guide me in this procedure.
>> > I have attahced the file I used to relax in this email
>> >
>> >
>> > &CONTROL
>> > calculation='vc-relax',
>> > outdir='./',
>> > prefix='calc',
>> > pseudo_dir='./',
>> > verbosity='high',
>> > /
>> >
>> > &SYSTEM
>> > ibrav=0,
>> > celldm(1)= 8.276999830d0
>> > nat=4,
>> > ntyp=1,
>> > ecutwfc=60,
>> > ecutrho=360,
>> > input_dft='lda',
>> > occupations='smearing',
>> > smearing='mv',
>> > degauss=0.005d0,
>> > /
>> >
>> > &ELECTRONS
>> > conv_thr=1d-06,
>> > mixing_beta=0.7d0,
>> > /
>> > &IONS
>> > ion_dynamics='bfgs'
>> > /
>> >
>> > &CELL
>> > cell_dynamics='bfgs'
>> > cell_dofree='2Dshape'
>> > /
>> > ATOMIC_SPECIES
>> > P 30.973800d0 P.pw-mt_fhi.UPF
>> >
>> > ATOMIC_POSITIONS {crystal}
>> >
>> > P 0.09004 0.0 0.050195117
>> > P 0.90967 0.0 0.949804902
>> > P 0.59033 0.5 0.949804902
>> > P 0.40996 0.5 0.050195117
>> >
>> > K_POINTS {automatic}
>> >
>> > 12 12 1 0 0 0
>> >
>> > CELL_PARAMETERS {alat}
>> >
>> > 1.0.0.
>> > 0.0.7511415530000.
>> > 0.0. 4.680365292
>> >
>> >
>> > thank you
>> > Gautam
>> >
>> > GAUTAM GADDEMANE
>> > DEPARTMENT OF MATERIALS SCIENCE AND ENGINEERING
>> > UNIVERSITY OF TEXAS AT DALLAS
>>
>>
>>
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[Pw_forum] Postdoc in Bremen/Nancy
Dear Users and Developers, We are looking for a postdoc that has some programming background and is interested in doing method development within QE (see below). Best, Dario Rocca Applications are invited for a three-year DFG-funded postdoctoral position under the supervision of Dr. Balint Aradi and Prof. Peter Deak at the University of Bremen (Germany) and of Dr. Dario Rocca and Dr. Sébastien Lebègue at the University of Lorraine (Nancy, France). The position is available immediately. The recruited postdoc will work on ab initio simulations of photocatalytic charge transfer processes on the TiO2 surface. A crucial part of the project is the development of a general and self-consistent charge correction scheme for low dimensional periodic systems. This part of the project will be guided by the University of Lorraine where the applicant must spend the first 6 months of the project. The methodological development will have to be implemented into the plane-wave code Quantum Espresso. The postdoc will then move to the University of Bremen and, parallel with testing different stages of the development, will investigate the photocatalytic oxidation of CO and reduction of NO2 on the anatase (101) surface, with special emphasis on electron- and hole-scavenging by O2 and H2O, respectively. Candidates should have completed a PhD in physics, chemistry or materials science, and should have a background in the theory of electronic structure calculations. Since the project will involve an extensive part of method development, good programming skills are necessary. Experience with solid state calculations and plane-wave codes is necessary. The working language is English. Interested candidates should send a copy of their CV (including a list of publications and references) to Peter Deak (email: deak at uni-bremen.de), and to Dr. Dario Rocca (email: dario.rocca at univ-lorraine.fr), simultaneously. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Regarding vc-relax calculations
Dear Mohaddesh, you should look the options of the variable cell_dofree Best, Dario Rocca On Tue, Apr 4, 2017 at 8:30 AM, mohaddeseh abbasnejad < m.abbasne...@gmail.com> wrote: > Dear experts, > > Hello, > > I was wondering if there is any option to fix one or two of the cell > parameters during vc-relax calculation? > Thanks in advance. > > Regards, > Mohaddeseh > > - > > 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 <+98%2021%206111%208634> & Fax No.: +98 21 > 8800 4781 <+98%2021%208800%204781> > Cellphone: +98 917 731 7514 <+98%20917%20731%207514> > E-Mail: m.abbasne...@gmail.com > Website: http://physics.ut.ac.ir > > - > > ___ > 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] folder corresponding to outdir is empty
Dear Kajal, try by removing disk_io = 'none' Best, Dario Rocca On Wed, Mar 8, 2017 at 9:35 PM, Kajal Jindal wrote: > Dear pwscf users, > > I am trying to calculate the band structure of BFO. The scf calculation > runs successfully. However, the folder corresponding to outdir is empty > after scf calculation. So, i am unable to proceed with bands calculation. > Output file of bands calculation stops with the following error: > > Error in routine pw_readfile(1): > Error opening xml datafile. > > I am attaching the scf input and output files along. > > Kindly suggest the problem. > > Regards, > Kajal Jindal, > University of Delhi > 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
Re: [Pw_forum] Error in routine phq_readin (5010)
Dear Sunetra, you input file works for me with QE 6.0 I just get the following warning Message from routine phq_readin: iverbosity is obsolete, use "verbosity" instead Best, Dario Rocca On Fri, Feb 24, 2017 at 8:54 AM, Sunetra Das wrote: > 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 > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Calculation of transition dipole moment
Dear Huy Pham, I don't know if this is the easiest way but you could use the turboTDDFT code https://arxiv.org/pdf/1402.0486.pdf If you use the davidson diagonalization and the option no_hxc=.true. you will obtain as output some oscillator strengths which are proportional to the transition dipole moments between Kohn-Sham valence and conduction states. You will need to verify the units. If no_hxc=.false. you obtain a similar quantity at the TDDFT level. In this case conduction (and valence) bands are mixed together by Hartree-xc effects in the TDDFT kernel. Best, Dario On Wed, Feb 15, 2017 at 1:19 AM, Huy Pham wrote: > Dear QE users, > > I want to calculate the transition dipole moment between conduction and > valence bands for an isolated molecule using QE. I searched the forum but > didn't find much information. > Can anyone give me some suggestions? > > Thanks, > Huy > > -- > Huy Pham, PhD > Postdoctoral Researcher > Department of Chemistry and Biochemistry > University of California, San Diego > 9500 Gilman Drive > Urey Hall 4205 > La Jolla, CA 92093 > E-mail: > pchuy1...@gmail.com > > > ___ > 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] Re : Learning TDDFT calculation in Atomic label (CH4 molecule) using turbo_lanczos.x and turbo_davidson.x
Dear Prem, I was trying in different way to converge scf calculation in case of carbon > dimer without "smearing". First I converge the system using "smearing" then > again I performed the scf calculation by changing the "restart_mode" from > "from_scratch" to "restart". In this condition, the scf calculation for > carbon dimer is converging & also turbo_davidson.x is possible. Do you > think, this is a right approach ?? > At equilibrium distance I would guess that this dimer has a finite gap and smearing shouldn't be necessary. At large interatomic distances the gap will go to 0 and you might need a smearing to converge. Are you interested in large interatomic distances? Your procedure is not too clear but as far as I understand you perform a calculation with a smearing and then you restart it removing the smearing. I'm surprised you don't get an error message. I think that as long as the ground state calculation converges without smearing you can safely use the turbo-tddft code. > > > Also I have observed that if I am using hybrid functional, the system is > converging normally (keeping the restart_mode = from_scratch & without > "smearing"). > As Iurii said it is possible that the hybrid functional increases the value of the gap and the smearing is not anymore necessary. However, if you keep increasing the interatomic distance you will have the same problem > > > Can I compute the absorption spectra for a molecule having triplet ground > state using turbo_davidson.x or turbo_lanczos.x ?? > I don't think so since triplet states require spin polarized calculations and the structure of the TDDFT Liouvillian is different in the case of triple states. You should first of all compute the PBE and hybrid gap for you system. If your C2 is at equilibrium it should not have a ~0 gap Best, Dario Rocca > > > > > > > > > > > > Thanks & regards, > Prem Sen > Ph.D. Student, > IIT Bombay, > Mumbai,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
Re: [Pw_forum] all-electrons calculations
Dear Farah, You don't need any additional flag, just select PAW pseudopotentials for your calculation. Not all the the functionalities of QE can be used with PAW Best, Dario Rocca On Sat, Jan 28, 2017 at 4:18 PM, FARAH MARSUSI wrote: > Dear All, > > I could not find any documentation regarding paw method and descriptions > of its input flags in QE. Would be very grateful, if introduce any. > > > Best regards, > > F. Marsusi, > > > Amirkabir University of Technology. > > ___ > 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] Help
Dear Hassan, Did you have a good reason to change pseudopotentials? If you don't, your way of proceeding is not the most "elegant" but still legitimate. There are certain approximations and properties which are significantly more affected by the pseudopotential (an optical gap approximated at the PBE level is probably weakly affected by the pseudopotential while at the Bethe-Salpeter equation level of theory the effect is likely to be more important). If you do not find the expected result you might try using the pseudopotentials consistently. Still the pseudopotential should not change the physics of your problem, and, in case it does, I would not trust the final result Best, Dario On Sun, Jan 15, 2017 at 3:17 AM, HASSAN AHMOUM wrote: > Dear users, > > I did a study on the crystallin electronics and thermoelectric and > magnetic properties using ultrasoft pseudopotential and for the optical > properties I used norme-conserving pseudopotential, my question now is: > do I have the right to publish all these results knowing that I changed > the type of pseudopotential to study optical properties? > > for optical properties i used the cristallin structure founded in the case > of ultrasoft, do i have right to do this too?, or i should do optimized > again with norme-conserving pseudopotential( we all know that i will get > different value of lattice parameter --> different properties). > > and another thing, the electrical gap is superior than optical gap,in the > reality it's opposite. > > any adive please > > > > > > > > > > *--- > Hassan AHMOUMEquipe Physique de la Matière Condensée et Modélisation > des sysèmes. (EPMCMS).Laboratoire Physique des Matériaux et Modélisation > des Systèmes (LP2MS).Université Moulay Ismail- Faculté des Sciences de > Meknès.BP 11201, Zitoune Meknès-MarocTel. +212 603-73-05-96* > > ___ > 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 CONVERTER
Dera Imani if you have correctly chosen the upf format in the input file the last step that you are missing is to run extract.sh to extract the pseudopotential from the .out file Best, Dario Rocca On Thu, Dec 1, 2016 at 4:46 PM, Himani Mishra wrote: > Dear sir, > > I have generated a fully relativistic pseudo potential using oncvpsp code > and got results in the form of .out file format. Here I am facing problem > as I am not able to convert my pseudopotential to .UPF format. Kindly help > me with this. > > Regards, > Himani Mishra > RSE2016002 > IIIT Allahabad > > ___ > 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] Unit-cell and Super-cell bandgap difference
Dear Vipul, the difference (0.4 eV) in energy between the cell and the supercell is sizeable.You should try to understand this problem first of all. To compare you don't need to relax. If you relax two equivalent systems (cell and 2x2x2 supercell) you should obtain consistent results, namely that the supercell has double the lattice parameter of the cell Best Dario On Mon, Nov 28, 2016 at 6:08 AM, Vipul Shivaji Ghemud < vi...@physics.unipune.ac.in> wrote: > Thank you Dario, I'll take a run with same k-mesh. The energy of supercell > is 0.4eV less than the 8times that of unit cell. I have just taken scf > (without relax) > > > Dear Vipul, > > There could be two main explanations for your results: > > -A problem with the k-points you use to compute the bandstrucure: the > > > grid > > for the cell and supercell must be consistent > > -An error in the supercell. Try comparing total energies: does the > > supercell have 8 times the total energy of the cell? > > Best, > > Dario Rocca > > > On Fri, Nov 25, 2016 at 7:47 AM, Vipul Shivaji Ghemud < > > vi...@physics.unipune.ac.in> wrote: > > > I have been using 8*8*8 for unit cell and 4*4*4 for supercell as my > > supercell is 2*2*2 unit cell. > > > > > Dear Vipul, > > > how many k-points did you use for the cell and for the supercell > > > Best > > > Dario > > > > > On Thu, Nov 24, 2016 at 6:23 AM, Vipul Shivaji Ghemud < > > > vi...@physics.unipune.ac.in> wrote: > > > > > Hi all, > > > I am working on a system of 9atoms in a unit-cell having bandgap of > > 3.5eV; > > > but I am considering the super-cell(4 unit-cells) then the bandgap is > > > reduced by ~0.45eV for HSE06. The bandgaps are similar with GGA. Is it > > due > > > to the exchnage-correlation contribution of the increased number of > > > electrons in the system, as the code QE considers unit-cell and > > super-cell > > > both a a single system? It's a bulk cubic system. I am facing similar > > > problem with other systems also. > > > -- > Vipul S. Ghemud > Ph.D. student. > Dept of Physics, > SPPU, Ganeshkhind, > Pune- 411007. > > > ___ > 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] blyp
Dear Ashkan, For pseudopotential generation take a look at these notes by Paolo Giannozzi http://www.quantum-espresso.org/wp-content/uploads/Doc/pseudo-gen.pdf I you don't have very good reasons to use BLYP you could try PBE instead Best, Dario Rocca On Thu, Nov 24, 2016 at 5:27 PM, ashkan shekaari wrote: > Dear Dario, > > Thank you so much for your quick response. But how could I generate a blyp > pseudo potential for Mo? There does not exist such a file in QE download > page. > > On Nov 24, 2016 7:16 PM, "dario rocca" wrote: > >> Dear Ashkan >> not necessary but strongly recommended >> Best, >> Dario Rocca >> >> On Thu, Nov 24, 2016 at 2:08 PM, ashkan shekaari >> wrote: >> >>> Dear experts, >>> >>> is it necessary to use blyp pseudopotentials when input_dft is set to >>> blyp? >>> *--* >>> *Regards,* >>> *Ashkan Shekaari* >>> *Plasma Physics Research Center* >>> *Science and Research Branch* >>> *I A U, 14778-93855 Tehran, Iran.* >>> >>> ___ >>> 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] Unit-cell and Super-cell bandgap difference
Dear Vipul, There could be two main explanations for your results: -A problem with the k-points you use to compute the bandstrucure: the grid for the cell and supercell must be consistent -An error in the supercell. Try comparing total energies: does the supercell have 8 times the total energy of the cell? Best, Dario Rocca On Fri, Nov 25, 2016 at 7:47 AM, Vipul Shivaji Ghemud < vi...@physics.unipune.ac.in> wrote: > I have been using 8*8*8 for unit cell and 4*4*4 for supercell as my > supercell is 2*2*2 unit cell. > > > Dear Vipul, > > how many k-points did you use for the cell and for the supercell > > Best > > Dario > > > On Thu, Nov 24, 2016 at 6:23 AM, Vipul Shivaji Ghemud < > > vi...@physics.unipune.ac.in> wrote: > > > Hi all, > > I am working on a system of 9atoms in a unit-cell having bandgap of > 3.5eV; > > but I am considering the super-cell(4 unit-cells) then the bandgap is > > reduced by ~0.45eV for HSE06. The bandgaps are similar with GGA. Is it > due > > to the exchnage-correlation contribution of the increased number of > > electrons in the system, as the code QE considers unit-cell and > super-cell > > both a a single system? It's a bulk cubic system. I am facing similar > > problem with other systems also. > > > > > > > > -- > > Vipul S. Ghemud > > Ph.D. student. > > Dept of Physics, > > SPPU, Ganeshkhind, > > Pune- 411007. > > > > > > > -- > Vipul S. Ghemud > Ph.D. student. > Dept of Physics, > SPPU, Ganeshkhind, > Pune- 411007. > > > ___ > 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] blyp
Dear Ashkan not necessary but strongly recommended Best, Dario Rocca On Thu, Nov 24, 2016 at 2:08 PM, ashkan shekaari wrote: > Dear experts, > > is it necessary to use blyp pseudopotentials when input_dft is set to blyp? > *--* > *Regards,* > *Ashkan Shekaari* > *Plasma Physics Research Center* > *Science and Research Branch* > *I A U, 14778-93855 Tehran, Iran.* > > ___ > 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] Unit-cell and Super-cell bandgap difference
Dear Vipul, how many k-points did you use for the cell and for the supercell Best Dario On Thu, Nov 24, 2016 at 6:23 AM, Vipul Shivaji Ghemud < vi...@physics.unipune.ac.in> wrote: > Hi all, > I am working on a system of 9atoms in a unit-cell having bandgap of 3.5eV; > but I am considering the super-cell(4 unit-cells) then the bandgap is > reduced by ~0.45eV for HSE06. The bandgaps are similar with GGA. Is it due > to the exchnage-correlation contribution of the increased number of > electrons in the system, as the code QE considers unit-cell and super-cell > both a a single system? It's a bulk cubic system. I am facing similar > problem with other systems also. > > > > -- > Vipul S. Ghemud > Ph.D. student. > Dept of Physics, > SPPU, Ganeshkhind, > Pune- 411007. > > > ___ > 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] nscf calculation
Dear Q.J. Wang, No, it is not possible. In a nscf calculation you need to "fix" your Hamiltonian which is determined from a previous scf calculation. Best, Dario Rocca On Tue, Nov 1, 2016 at 2:06 PM, Q.J.Wang wrote: > Dear QE developer, > I want to know whether QE can perform a nscf calculation without a scf > calculation? > > > > -- > Best regards > > Q.J.Wang > > XiangTan University > > > > > ___ > 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] Estimate time for relaxing bigger unit cells?
Dear Tomas, Since you need to relax several 64 atoms cells the best estimate is to relax it once to be sure that it converges and to have an accurate estimate of the time. However, consider that a 64 atoms cell close to equilibrium might converge much more rapidly than a cell far from equilibrium. A calculation involves several different mathematical operations with different scaling. When the system is big the operations with the worst scaling dominate. When the system is small instead even an operation with a good scaling can take an important percentage of the total computer time. I'm not sure I would try to guess the time for 64 atoms from a 8 atoms cell. Best, Dario On Fri, Oct 14, 2016 at 5:04 PM, Rojas Solorzano, Tomas wrote: > Dear QE community, > > > I am looking for a way to get a rough estimate of the time for a > relaxation of a 64 atoms unit cell based on the time that takes a 8 atom > unit cell of the same system. I am supposed to request for an allocation in > the cluster and for my project will need to relax several unit cells of > that size. > > I am aware of the formula in the documentation to estimate the > SCF calculations but I though there might be tips for the relaxation. My > initial try was to relax the 64 unit cell for a few hours and estimate it > by comparing to the small one, but I am not sure how. > > > Regards and Thank you!. > > > Tomas R > > Ohio University > > ___ > 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] testing HSE for BCC Fe
Ciao Nicola, I agree that 'time-to-accurate-solution' is the goal. However, when you have a variable as in Vasp PRECFOCK= Low | Medium | Fast | Normal | Accurate that allows you to do a HF calculation in 10 hours if PREFOCK=Low and in an infinite time if PREFOCK=Accurate, I see the time saving part but the accuracy can be hardly tested. And it makes also hard to do a comparison of performance and results with other codes. Best, Dario On Fri, Sep 9, 2016 at 11:55 AM, Nicola Marzari wrote: > On 09/09/2016 11:37, dario rocca wrote: > > -If you changed the default values of some variables such as Precfock or > > Nkred in Vasp the computational parameters are not anymore the same in > > Vasp and QE. > > > Ciao Dario, > > > all true, but at the end what counts for a expert in DFT but not in > computational implementations is "time-to-accurate-solution". > > This latter requires time in itself to establish (i.e. what are the > parameters > that give me a converged result - say, for non symmetric configurations, > with forces that are converged to .XXX eV/A), but for a DFT > scientist that is a user of codes, rather than a developer of codes, > the question above (let's call it TASK "time-to-accurate-solution > knowing own CPU budget") is a very important one. > > nic > > > -- > 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 > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] testing HSE for BCC Fe
Dear Daniel I said "surprisingly" huge because I compared to the VASP code with the > same parameters (Ecutoff, NKpoints, Nq) and with the HSE functional. > Indeed, with the VASP code during one night on my computer I got a few tens > of iterations compared to one with QE :(. > With exactly the same parameters the computational time (on one processor) should be comparable. There are two important points you should consider to make a comparison: -Different type of methodology: Using EXX with Ultrasoft pseudopotentials a very large number of augmentation charges are computed. As already suggested setting tqr=.true. should solve this problem. -If you changed the default values of some variables such as Precfock or Nkred in Vasp the computational parameters are not anymore the same in Vasp and QE. Best, Dario > From my point of view, I compare 2 pseudopotential-based methods for the > same parameters which I can control via the input file : my question would > then more preferably be "which default parameter should I modify to make > the QE calculation time similar to the VASP one ?" > > Best wishes, > > Daniel > > > > > > > Le 2016-09-09 09:47, Stefano de Gironcoli a écrit : > > Please read the literature about hybrid functionals in plane waves; > understand why the computational time is, not unexpectedly, huge and start > think about it. > If you come up with some smart idea on how to reduce the computational > time without compromising accuracy (as for the ACE transformation recently > proposed by Lin Lin and implemented in the latest QE version) let us know > Best, > stefano > (sent from my phone) > > On 09 Sep 2016, at 09:30, Daniel Stoeffler unistra.fr> wrote: > > > > Hello, > > As a new QE user, I do some tests with the HSE Functional for BCC > ferromagnetic Fe with a cell containing 2 atoms (because a want to go to > CoFe after that). > > My input file is : > > &control > title='Fe CC HSE', > calculation = 'scf', > prefix = 'Fe_CC_HSE', > pseudo_dir='./', > verbosity = 'high' > / > &system > ibrav = 6, > celldm(1) = 5.45, > celldm(3) = 1.0, > nat = 2, > ntyp = 1, > nspin = 2, > occupations='smearing', smearing='gauss', degauss=0.01, > starting_magnetization(1) = 1.0, > ecutwfc = 33, > input_dft='HSE', > report = 5 > / > &electrons > mixing_beta = 0.7 > / > > ATOMIC_SPECIES > Fe 55.845 Fe.pbe-sp-van.UPF > > ATOMIC_POSITIONS (crystal) > Fe 0.000 0.000 0.000 > Fe 0.500 0.500 0.500 > > K_POINTS (automatic) > 7 7 7 0 0 0 > > Surprisingly, the computation time is huge as writen into the output file : > > === > > iteration # 9 ecut=33.00 Ry beta=0.70 > Davidson diagonalization with overlap > ethr = 5.49E-08, avg # of iterations = 2.3 > > Magnetic moment per site: > atom:1charge: 14.4350magn:2.6346constr: > 0. > atom:2charge: 14.4351magn:2.6343constr: > 0. > > total cpu time spent up to now is7.2 secs > > End of self-consistent calculation > > convergence has been achieved in 9 iterations > > EXX: now go back to refine exchange calculation > > total cpu time spent up to now is 4239.4 secs > > Self-consistent Calculation > > iteration # 1 ecut=33.00 Ry beta=0.70 > Davidson diagonalization with overlap > ethr = 5.49E-08, avg # of iterations = 4.9 > > total cpu time spent up to now is52490.2 secs > > iteration # 2 ecut=33.00 Ry beta=0.70 > Davidson diagonalization with overlap > > === > > So, the calculation takes 7 seconds for converging with PBE, 1h10min for > calculating the EXX term and 14h35min for the first HSE iteration. Is this > correct ? And if so, please, could you try to explain me how to reduce the > computation time. Thanks in advance. > > Best wishes, > > Daniel > > > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > > ___ > Pw_forum mailing > listPw_forum@pwscf.orghttp://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] Error in turbu_spectrum.x
Dear Ullah, I use Gnuplot or Xmgrace but it's a matter of taste. Just be careful that the first column contains text Best, Dario On Fri, Aug 19, 2016 at 3:23 AM, Ullah, Habib wrote: > Hi, > > Thanks Dario, and I solved the issue. Actually, in the case of CH4, I > generated only five Lanczos iteration when open the CH4.tddfpt-st-out. > > Lanczos iteration:5 Pol:1 > > lr_apply_liouvillian: not applying interaction > > alpha(0005)= 0.000E+00 > > beta (0005)= 0.121609176647445E+02 > > gamma(0005)= 0.121609176647445E+02 > > z1= 1 0.000E+00 0.000E+00 > > End of Lanczos iterations > > Finished linear response calculation... > > But for the Benzene, I generated 1500, and got Benzene.plot by execution > of turbo_spectrum.x. Which software will be best for plotting? I tried with > excel but could not plot. > > Kind regards > > Habib > > *From:* pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] *On > Behalf Of *Ullah, Habib > *Sent:* 19 August 2016 0:13 > > *To:* PWSCF Forum > *Subject:* Re: [Pw_forum] Error in turbu_spectrum.x > > > > Dear Dario, > > Thanks for yor reply, actually for the first time I am doing this > simulations, please kindly have a look on the attached snapshot of my > directory. I think, I did not generate at least 450 Lanczos iterations, I > don’t have an idea how to do? But first I run the PW.x, successfully > followed by turbo_lanczos.x (stage one) and then again the stage 2, and > finally, got error in the turbo_spectrum.x. > > Kind Regards > > *Habib Ullah* > > Ph.D Student in Renewable Energy, > > Environment and Sustainability Institute, > > College of Engineering, Mathematics and Physical Science, > > University of Exeter, > > Penryn Campus, Penryn, TR10 9FE, UK > > phone; +44(0)1326259320 > Phone +44 (0) 7540652183 > > Email; hu...@exeter.ac.uk > > web; http://emps.exeter.ac.uk/renewable-energy/staff/hu203 > > > > *From:* pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org > ] *On Behalf Of *dario rocca > *Sent:* 18 August 2016 11:05 PM > *To:* PWSCF Forum > *Subject:* Re: [Pw_forum] Error in turbu_spectrum.x > > > > Dear Ullah, > > you are mentioning an error in the postprocessing. Did you generate at > least 450 Lanczos iterations with the turbo_lanczos.x code? > > Best, > > Dario > > > > On Thu, Aug 18, 2016 at 2:49 PM, Ullah, Habib wrote: > > Dear All, > > I'm doing simulation for the absorption spectrum of CH4 using; > turbo_spectrum.x. I read the paper provided in the TDDFPT section of QE > (turboTDDFT - a code for the simulation of molecular spectra using the > Liouville-Lanczos approach to time-dependent density-functional > perturbation theory). However, I am getting an error in the running of > turbo_spectrum.x (see output below). > Parallel version (MPI), running on 7 processors > R & G space division: proc/nbgrp/npool/nimage = 7 > > Reading 5 Lanczos steps for direction 1 > 450 steps will be considered > > %%% > %%% > Error in routine tddfpt_calculate_spectrum (1): > Error in Itermax0 > %%% > %%% > > I read the forum but could not found similar issue that is why posting. > My input is! > &lr_input > prefix='ch4', > outdir='/home/ISAD/hu203/habib/espresso-5.0.3/TDDFPT/Examples/CH4/', > itermax=1 > itermax0=450 > extrapolation="osc" > epsil=0.01 > end=3.50d0 > increment=0.001d0 > start=0.0d0 > ipol=4 > / > > > ___ > 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] Error in turbu_spectrum.x
Dear Ullah, you are mentioning an error in the postprocessing. Did you generate at least 450 Lanczos iterations with the turbo_lanczos.x code? Best, Dario On Thu, Aug 18, 2016 at 2:49 PM, Ullah, Habib wrote: > Dear All, > > I'm doing simulation for the absorption spectrum of CH4 using; > turbo_spectrum.x. I read the paper provided in the TDDFPT section of QE > (turboTDDFT - a code for the simulation of molecular spectra using the > Liouville-Lanczos approach to time-dependent density-functional > perturbation theory). However, I am getting an error in the running of > turbo_spectrum.x (see output below). > Parallel version (MPI), running on 7 processors > R & G space division: proc/nbgrp/npool/nimage = 7 > > Reading 5 Lanczos steps for direction 1 > 450 steps will be considered > > > %% > Error in routine tddfpt_calculate_spectrum (1): > Error in Itermax0 > > %% > > I read the forum but could not found similar issue that is why posting. > My input is! > &lr_input > prefix='ch4', > outdir='/home/ISAD/hu203/habib/espresso-5.0.3/TDDFPT/Examples/CH4/', > itermax=1 > itermax0=450 > extrapolation="osc" > epsil=0.01 > end=3.50d0 > increment=0.001d0 > start=0.0d0 > ipol=4 > / > > > ___ > 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] "scf" calculation with "PBE0" hybrid functional
Dear Narendra, While a PBE calculation requires a single FFT for the density the PBE0 calculation requires N_bands*N_bands FFTs for the co-density. In your case if nspin=1 you would have about 47000 FFTs for a single EXX evaluation. Despite the number of processors, the number of bands might be the bottleneck of your calculation. I don't know if an efficient band parallelization is available for the EXX in QE but it could help. Best, Dario On Mon, Aug 8, 2016 at 1:39 PM, Narendranath Ghosh wrote: > Dear Dario > I could not complete my last PBE0 "scf" job containing 434 > atoms (CNT+Fullerene). The job could not stop but still running without > writing any more in the output file. These lines are written in the output > 34 hours ago .I have tried it twice but I found same thing. > > EXX: now go back to refine exchange calculation > > total cpu time spent up to now is42069.2 secs > > Self-consistent Calculation > > iteration # 1 ecut=30.00 Ry beta=0.45 > Davidson diagonalization with overlap > > I could not understand what's happening.I have used 24 node with 384 > processors.I have alter ecut, cell length, beta values nothing happened. > > Please suggest any idea... > > > > On Sun, Aug 7, 2016 at 10:53 AM, dario rocca wrote: > >> I will let the MD experts to reply to this question :) >> >> On Sat, Aug 6, 2016 at 2:49 AM, Narendranath Ghosh < >> ghosh.nare...@gmail.com> wrote: >> >>> Dear Dario >>> >>> Thank you very much for your valuable suggestion. As my systems are >>> quite large and require high computational resources , I decided to compare >>> one of my result with that of PBE0. >>> >>> One problem that I am facing now "after successfully optimized the >>> (CNT+Fullerene) systems now I am looking for to get 5 picosecond "md" >>> trajectory". >>> In QE which flags allowed one to get *MD trajectories * *with NVE >>> ensemble. *I find some idea from http://qe-forge.org/piper >>> mail/pw_forum/2009-June/087573.html. But that is not clear to me. >>> >>> Please suggest any idea. >>> >>> Thank you again >>> >>> *Narendra Nath Ghosh* >>> >>> *Research Associate* >>> >>> *University of Gour Banga* >>> >>> *Department of Computational Physics * >>> >>> *Malda-732102* >>> >>> *India* >>> >>> On Sat, Aug 6, 2016 at 10:48 AM, dario rocca wrote: >>> >>>> Dear Narendra, >>>> If you do a PBE calculation with norm-conserving, ultrasoft, and PAW >>>> pseudopotentials very likely you will get very similar results (but it >>>> depends >>>> also on the quality of the pseudopotential, the property under >>>> consideration, etc.). >>>> In the case of PBE0 the type of pseudopotential will have a stronger >>>> effect on the final result. >>>> For purely esthetic reasons, if your previous calculations didn't take >>>> too long you could redo them with norm-conserving pseudopotentials and >>>> confirm that the results are indeed the same. >>>> Otherwise I don't see anything wrong in comparing, for example, a gap >>>> obtained at PBE level with US pseudos and a gap obtained at PBE0 >>>> level with NC pseudos. >>>> Best, >>>> Dario >>>> >>>> >>>> >>>> On Fri, Aug 5, 2016 at 3:44 PM, Narendranath Ghosh < >>>> ghosh.nare...@gmail.com> wrote: >>>> >>>>> Dear Dario >>>>> >>>>> Thank you very much for your support.It works well and some of the >>>>> jobs have been finished successfully. >>>>> >>>>> But one thing in my mind. In my whole calculations , I used PBE with >>>>> ultrasoft pseudopotentials. But to do "scf" calculations with PBE0 >>>>> "hybrid" >>>>> functional I have to use "Norm conserving pseudopotential". So how >>>>> can I compare these two results. >>>>> >>>>> Please suggest any idea. >>>>> >>>>> Thank you again >>>>> >>>>> *Narendra Nath Ghosh* >>>>> >>>>> *Research Associate* >>>>> >>>>> *University of Gour Banga* >>>>> >>>>> *Department of Computational Physics * >>>>>
Re: [Pw_forum] "scf" calculation with "PBE0" hybrid functional
I will let the MD experts to reply to this question :) On Sat, Aug 6, 2016 at 2:49 AM, Narendranath Ghosh wrote: > Dear Dario > > Thank you very much for your valuable suggestion. As my systems are quite > large and require high computational resources , I decided to compare one > of my result with that of PBE0. > > One problem that I am facing now "after successfully optimized the > (CNT+Fullerene) systems now I am looking for to get 5 picosecond "md" > trajectory". > In QE which flags allowed one to get *MD trajectories * *with NVE > ensemble. *I find some idea from http://qe-forge.org/piper > mail/pw_forum/2009-June/087573.html. But that is not clear to me. > > Please suggest any idea. > > Thank you again > > *Narendra Nath Ghosh* > > *Research Associate* > > *University of Gour Banga* > > *Department of Computational Physics * > > *Malda-732102* > > *India* > > On Sat, Aug 6, 2016 at 10:48 AM, dario rocca wrote: > >> Dear Narendra, >> If you do a PBE calculation with norm-conserving, ultrasoft, and PAW >> pseudopotentials very likely you will get very similar results (but it >> depends >> also on the quality of the pseudopotential, the property under >> consideration, etc.). >> In the case of PBE0 the type of pseudopotential will have a stronger >> effect on the final result. >> For purely esthetic reasons, if your previous calculations didn't take >> too long you could redo them with norm-conserving pseudopotentials and >> confirm that the results are indeed the same. >> Otherwise I don't see anything wrong in comparing, for example, a gap >> obtained at PBE level with US pseudos and a gap obtained at PBE0 >> level with NC pseudos. >> Best, >> Dario >> >> >> >> On Fri, Aug 5, 2016 at 3:44 PM, Narendranath Ghosh < >> ghosh.nare...@gmail.com> wrote: >> >>> Dear Dario >>> >>> Thank you very much for your support.It works well and some of the >>> jobs have been finished successfully. >>> >>> But one thing in my mind. In my whole calculations , I used PBE with >>> ultrasoft pseudopotentials. But to do "scf" calculations with PBE0 "hybrid" >>> functional I have to use "Norm conserving pseudopotential". So how can >>> I compare these two results. >>> >>> Please suggest any idea. >>> >>> Thank you again >>> >>> *Narendra Nath Ghosh* >>> >>> *Research Associate* >>> >>> *University of Gour Banga* >>> >>> *Department of Computational Physics * >>> >>> *Malda-732102* >>> >>> *India* >>> >>> >>> On Thu, Aug 4, 2016 at 2:17 AM, dario rocca wrote: >>> >>>> Dear Narendranath, >>>> Your calculation has reached convergence if you read the message "EXX >>>> self-consistency reached". >>>> You can learn some details about the scf procedure with hybrid >>>> functionals in PW/examples/EXX_example. >>>> PBE0 and hybrid functional calculations are in general very expensive. >>>> I would suggest you run an example to see what to expect. >>>> You might also try to perform a calculation on your system with minimal >>>> computational parameters (very small cut-off, few/one k-points) just to see >>>> that your run can indeed terminate smoothly. Then I would look for a set of >>>> parameters which are a good compromise between computational time and the >>>> accuracy you need. >>>> You might also try to modify the parameter ecutfock to gain some speed. >>>> For sure a hybrid functional calculation on a CNT+Fullerene system >>>> might be rather challenging. >>>> Best, >>>> Dario >>>> >>>> On Wed, Aug 3, 2016 at 11:16 AM, Narendranath Ghosh < >>>> ghosh.nare...@gmail.com> wrote: >>>> >>>>> Dear all >>>>> >>>>>After optimizing a system "CNT+Fullerene" with >>>>> "PBE" I am trying to calculate "scf" calculation with "PBE0" hybrid >>>>> functional using NC Pseudopotential. >>>>> >>>>> In output file I found "*convergence has been achieved in 15 >>>>> iterations" *But the job was not finished even after more than one >>>>> week. I could not find any mistake in my input. >>>>> >>>>> >>>>> Please suggest any idea. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ___ >>>>> 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 >> > > > ___ > 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] "scf" calculation with "PBE0" hybrid functional
Dear Narendra, If you do a PBE calculation with norm-conserving, ultrasoft, and PAW pseudopotentials very likely you will get very similar results (but it depends also on the quality of the pseudopotential, the property under consideration, etc.). In the case of PBE0 the type of pseudopotential will have a stronger effect on the final result. For purely esthetic reasons, if your previous calculations didn't take too long you could redo them with norm-conserving pseudopotentials and confirm that the results are indeed the same. Otherwise I don't see anything wrong in comparing, for example, a gap obtained at PBE level with US pseudos and a gap obtained at PBE0 level with NC pseudos. Best, Dario On Fri, Aug 5, 2016 at 3:44 PM, Narendranath Ghosh wrote: > Dear Dario > > Thank you very much for your support.It works well and some of the jobs > have been finished successfully. > > But one thing in my mind. In my whole calculations , I used PBE with > ultrasoft pseudopotentials. But to do "scf" calculations with PBE0 "hybrid" > functional I have to use "Norm conserving pseudopotential". So how can I > compare these two results. > > Please suggest any idea. > > Thank you again > > *Narendra Nath Ghosh* > > *Research Associate* > > *University of Gour Banga* > > *Department of Computational Physics * > > *Malda-732102* > > *India* > > > On Thu, Aug 4, 2016 at 2:17 AM, dario rocca wrote: > >> Dear Narendranath, >> Your calculation has reached convergence if you read the message "EXX >> self-consistency reached". >> You can learn some details about the scf procedure with hybrid >> functionals in PW/examples/EXX_example. >> PBE0 and hybrid functional calculations are in general very expensive. I >> would suggest you run an example to see what to expect. >> You might also try to perform a calculation on your system with minimal >> computational parameters (very small cut-off, few/one k-points) just to see >> that your run can indeed terminate smoothly. Then I would look for a set of >> parameters which are a good compromise between computational time and the >> accuracy you need. >> You might also try to modify the parameter ecutfock to gain some speed. >> For sure a hybrid functional calculation on a CNT+Fullerene system might >> be rather challenging. >> Best, >> Dario >> >> On Wed, Aug 3, 2016 at 11:16 AM, Narendranath Ghosh < >> ghosh.nare...@gmail.com> wrote: >> >>> Dear all >>> >>>After optimizing a system "CNT+Fullerene" with "PBE" >>> I am trying to calculate "scf" calculation with "PBE0" hybrid functional >>> using NC Pseudopotential. >>> >>> In output file I found "*convergence has been achieved in 15 >>> iterations" *But the job was not finished even after more than one >>> week. I could not find any mistake in my input. >>> >>> >>> Please suggest any idea. >>> >>> >>> >>> >>> >>> >>> ___ >>> 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] "scf" calculation with "PBE0" hybrid functional
Dear Narendranath, Your calculation has reached convergence if you read the message "EXX self-consistency reached". You can learn some details about the scf procedure with hybrid functionals in PW/examples/EXX_example. PBE0 and hybrid functional calculations are in general very expensive. I would suggest you run an example to see what to expect. You might also try to perform a calculation on your system with minimal computational parameters (very small cut-off, few/one k-points) just to see that your run can indeed terminate smoothly. Then I would look for a set of parameters which are a good compromise between computational time and the accuracy you need. You might also try to modify the parameter ecutfock to gain some speed. For sure a hybrid functional calculation on a CNT+Fullerene system might be rather challenging. Best, Dario On Wed, Aug 3, 2016 at 11:16 AM, Narendranath Ghosh wrote: > Dear all > >After optimizing a system "CNT+Fullerene" with "PBE" I > am trying to calculate "scf" calculation with "PBE0" hybrid functional > using NC Pseudopotential. > > In output file I found "*convergence has been achieved in 15 iterations" > *But the job was not finished even after more than one week. I could not > find any mistake in my input. > > > Please suggest any idea. > > > > > > > ___ > 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] Turbo TDDFT for a quantum dot
Dear Sunghwan, That's my guess. If you set occupations='fixed' (the default) for the ground state calculation, the turboTDDFT will not complain that your system is metallic. If your system has a 0.5 eV gap there will not be any problem. If the gap goes below 0.1 eV it migh be hard or impossible to converge the ground state calculation with occupations='fixed'. In that case the turboTDDFT cannot be used. According to me as long as the ground state energy converges with occupations='fixed' the turboTDDFT will run smoothly and give reasonable results for your nanoparticles. Once again this is my guess, you should try. Best, Dario On Sat, Jul 23, 2016 at 6:45 PM, SungHwan Choi wrote: > Dear Dario, > Thank you for a kind reply. You mean that if it is converged without > smearing option, then there is no problem on doing turboTDDF calculation. > Am I correct? > Sincerely, > Sunghwan Choi > > > > Sunghwan Choi > Ph.D candidate > Computational Quantum Molecular Science Lab > Department of Chemistry, KAIST, Republic of Korea > > 2016-07-23 16:43 GMT+09:00 dario rocca : > >> Dear Sunghwan, >> I have not used the code on systems with the characteristics you >> describe. This is my guess: As far as the ground state of your quantum dot >> converges without a smearing the turboTDDFT code can be used and will be >> stable. While the independent electron polarizability of a 0 gap system >> diverges for \omega-->0, the Hartree part in the TDDFT kernel will increase >> the value of the gap and/or will "push" the oscillator strength to higher >> energies. >> Best, >> Dario >> >> >> On Fri, Jul 22, 2016 at 6:37 PM, SungHwan Choi >> wrote: >> >>> Dear all, >>> I am checking whether turboTDDFT program is suitable for my project. My >>> project is to calculate absorption spectrum of metallic quantum dot. I have >>> two questions. >>> >>> 1) From other post, I read the fact that turboTDDFT cannot calculate a >>> metallic system. Here, how do we define metallic system? just system that >>> have no band gap? then for small metallic quantum dot can be a non-metallic >>> system since it has small band gap (0.1~0.5eV). case that fractional >>> occupation does not happen? then, we can control the occupation parameter >>> not to make fractional occupation. >>> >>> 2) A metallic quantum dot has a size-dependency for band gap. Thus, if >>> size become larger, then band gap become narrow. When turboTDDFT failed to >>> predict an absorption spectrum? and do you know a numerical trend of >>> artifact, which come from low band gap? >>> >>> By the way, does this limit come from algorithm or implementation of >>> turboTDDFT? As far as I understood there is no limit of algorithm itself. I >>> think there is some practical issues on there. Would you tell me where some >>> troubles come up? >>> >>> Sincerely >>> Sunghwan Choi >>> >>> >>> >>> Sunghwan Choi >>> Ph.D candidate >>> Computational Quantum Molecular Science Lab >>> Department of Chemistry, KAIST, Republic of Korea >>> >>> >>> ___ >>> 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] Turbo TDDFT for a quantum dot
Dear Sunghwan, I have not used the code on systems with the characteristics you describe. This is my guess: As far as the ground state of your quantum dot converges without a smearing the turboTDDFT code can be used and will be stable. While the independent electron polarizability of a 0 gap system diverges for \omega-->0, the Hartree part in the TDDFT kernel will increase the value of the gap and/or will "push" the oscillator strength to higher energies. Best, Dario On Fri, Jul 22, 2016 at 6:37 PM, SungHwan Choi wrote: > Dear all, > I am checking whether turboTDDFT program is suitable for my project. My > project is to calculate absorption spectrum of metallic quantum dot. I have > two questions. > > 1) From other post, I read the fact that turboTDDFT cannot calculate a > metallic system. Here, how do we define metallic system? just system that > have no band gap? then for small metallic quantum dot can be a non-metallic > system since it has small band gap (0.1~0.5eV). case that fractional > occupation does not happen? then, we can control the occupation parameter > not to make fractional occupation. > > 2) A metallic quantum dot has a size-dependency for band gap. Thus, if > size become larger, then band gap become narrow. When turboTDDFT failed to > predict an absorption spectrum? and do you know a numerical trend of > artifact, which come from low band gap? > > By the way, does this limit come from algorithm or implementation of > turboTDDFT? As far as I understood there is no limit of algorithm itself. I > think there is some practical issues on there. Would you tell me where some > troubles come up? > > Sincerely > Sunghwan Choi > > > > Sunghwan Choi > Ph.D candidate > Computational Quantum Molecular Science Lab > Department of Chemistry, KAIST, Republic of Korea > > > ___ > 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] absorption spectrum &dielectric constant of turboTDDFT
Hi Manu, The last release of the code does not allow for k-point sampling, that's why you get an error message. You would need to use a supercell. If you have done a gamma only calculation for your system that's probably why you get a spectrum that does not match at all experiments. Additionally, the Bethe-Salpeter equation is considered the most accurate method for bulk solids. Best, Dario On Thu, Jul 21, 2016 at 9:42 AM, Manu Hegde wrote: > Hi Dario, > Thank you very much. I have done some calculations for UV-Vis (see > attached) and it is no where matching my experimental results in case of > bcc-In2O3. Is it due to pseudopotential (I have used PBE USPP)?. Also I am > unable to BZ sampling on k-mesh and TDDFT shown me an error. > > Regards, > Manu > (University of Waterloo) > > On Wed, Jul 20, 2016 at 8:09 PM, dario rocca wrote: > >> Dear Manu, >> You can simply extract it with the command >> $ grep "S(E)" prefix.plot_chi.dat > file_for_plot >> and use your favorite program to plot it. >> Best, >> Dario >> >> On Wed, Jul 20, 2016 at 10:49 AM, Manu Hegde wrote: >> >>> Hello Dario, >>> >>> I have done the similar calculations, it went well, after running >>> turbo_spectrum.x Do you have any code to extract S(E) or I have to do it >>> manually? >>> >>> Manu >>> (University of Waterloo) >>> >>> On Tue, Jul 19, 2016 at 8:24 PM, dario rocca wrote: >>> >>>> Dear SungHwan, >>>> please refer to >>>> http://arxiv.org/pdf/1402.0486.pdf >>>> and >>>> >>>> http://urania.sissa.it/xmlui/bitstream/handle/1963/5797/turboTDDFT-CPC.pdf?sequence=1 >>>> for more details. >>>> >>>> In the output of the postprocessing chi_1_1 is the xx component of the >>>> dynamical polarizability, chi_1_2 the xy component, etc. >>>> Often chi is indicated as \alpha in the papers. >>>> Specifically you would have >>>> >>>> Component energy of the perturbation real part of >>>> chi imaginary >>>> (indicated either as E or \omega) >>>> chi_1_1= 0.000E+00 0.955769346791472E+01 >>>> 0.000E+00 >>>> . >>>> >>>> As you correctly say the absorption spectrum is related to the >>>> imaginary part of the average of chi multiplied by E (the energy E is often >>>> indicated as \omega). >>>> This averaged quantity is contained in S(E). Specifically S(E) is the >>>> strength function defined as >>>> S(E)=2m/(\pi*e^2*\hbar) * E*Im[chi(E)], where chi has been averaged >>>> over the 3 spatial directions. >>>> This definition is convenient because S(E) satisfies the f-sum rule. >>>> So if you extract S(E) and plot it you will have the absorption >>>> spectrum. >>>> Let me know if it's still not clear >>>> Best, >>>> Dario >>>> >>>> >>>> >>>> >>>> On Tue, Jul 19, 2016 at 4:01 PM, SungHwan Choi < >>>> sunghwancho...@gmail.com> wrote: >>>> >>>>> hi, I am a newbie for turboTDDFT. Now, I ran a simple example. It >>>>> was assume. Now I have prefix.plot_chi.dat file. then I don't know >>>>> how to generate absorption spectrum from that file and dielectric >>>>> constant values. As far as I understood, the absorption spectrum is >>>>> related to imaginary part of average \chi value. but in the file there >>>>> are 9 >>>>> values >>>>> chi_1_1 >>>>> chi_2_1 >>>>> chi_3_1 >>>>> chi_1_2 >>>>> chi_2_2 >>>>> chi_3_2 >>>>> chi_1_3 >>>>> chi_2_3 >>>>> chi_3_3 >>>>> This is 3*3*3 tensor. how do I get an absorption spectrum and >>>>> dieletric constant values? by the way S(E) means what? >>>>> >>>>> Sincerely >>>>> Sunghwan Choi >>>>> >>>>> ___ >>>>> 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 >> > > > ___ > 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] absorption spectrum &dielectric constant of turboTDDFT
Dear Manu, You can simply extract it with the command $ grep "S(E)" prefix.plot_chi.dat > file_for_plot and use your favorite program to plot it. Best, Dario On Wed, Jul 20, 2016 at 10:49 AM, Manu Hegde wrote: > Hello Dario, > > I have done the similar calculations, it went well, after running > turbo_spectrum.x Do you have any code to extract S(E) or I have to do it > manually? > > Manu > (University of Waterloo) > > On Tue, Jul 19, 2016 at 8:24 PM, dario rocca wrote: > >> Dear SungHwan, >> please refer to >> http://arxiv.org/pdf/1402.0486.pdf >> and >> >> http://urania.sissa.it/xmlui/bitstream/handle/1963/5797/turboTDDFT-CPC.pdf?sequence=1 >> for more details. >> >> In the output of the postprocessing chi_1_1 is the xx component of the >> dynamical polarizability, chi_1_2 the xy component, etc. >> Often chi is indicated as \alpha in the papers. >> Specifically you would have >> >> Component energy of the perturbation real part of >> chi imaginary >> (indicated either as E or \omega) >> chi_1_1= 0.000E+00 0.955769346791472E+01 >> 0.000E+00 >> . >> >> As you correctly say the absorption spectrum is related to the imaginary >> part of the average of chi multiplied by E (the energy E is often >> indicated as \omega). >> This averaged quantity is contained in S(E). Specifically S(E) is the >> strength function defined as >> S(E)=2m/(\pi*e^2*\hbar) * E*Im[chi(E)], where chi has been averaged over >> the 3 spatial directions. >> This definition is convenient because S(E) satisfies the f-sum rule. >> So if you extract S(E) and plot it you will have the absorption spectrum. >> Let me know if it's still not clear >> Best, >> Dario >> >> >> >> >> On Tue, Jul 19, 2016 at 4:01 PM, SungHwan Choi >> wrote: >> >>> hi, I am a newbie for turboTDDFT. Now, I ran a simple example. It >>> was assume. Now I have prefix.plot_chi.dat file. then I don't know how >>> to generate absorption spectrum from that file and dielectric constant >>> values. As far as I understood, the absorption spectrum is related to >>> imaginary part of average \chi value. but in the file there are 9 values >>> chi_1_1 >>> chi_2_1 >>> chi_3_1 >>> chi_1_2 >>> chi_2_2 >>> chi_3_2 >>> chi_1_3 >>> chi_2_3 >>> chi_3_3 >>> This is 3*3*3 tensor. how do I get an absorption spectrum and dieletric >>> constant values? by the way S(E) means what? >>> >>> Sincerely >>> Sunghwan Choi >>> >>> ___ >>> 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] absorption spectrum &dielectric constant of turboTDDFT
Dear SungHwan, please refer to http://arxiv.org/pdf/1402.0486.pdf and http://urania.sissa.it/xmlui/bitstream/handle/1963/5797/turboTDDFT-CPC.pdf?sequence=1 for more details. In the output of the postprocessing chi_1_1 is the xx component of the dynamical polarizability, chi_1_2 the xy component, etc. Often chi is indicated as \alpha in the papers. Specifically you would have Component energy of the perturbation real part of chi imaginary (indicated either as E or \omega) chi_1_1= 0.000E+00 0.955769346791472E+01 0.000E+00 . As you correctly say the absorption spectrum is related to the imaginary part of the average of chi multiplied by E (the energy E is often indicated as \omega). This averaged quantity is contained in S(E). Specifically S(E) is the strength function defined as S(E)=2m/(\pi*e^2*\hbar) * E*Im[chi(E)], where chi has been averaged over the 3 spatial directions. This definition is convenient because S(E) satisfies the f-sum rule. So if you extract S(E) and plot it you will have the absorption spectrum. Let me know if it's still not clear Best, Dario On Tue, Jul 19, 2016 at 4:01 PM, SungHwan Choi wrote: > hi, I am a newbie for turboTDDFT. Now, I ran a simple example. It was > assume. > Now I have prefix.plot_chi.dat file. then I don't know how to generate > absorption spectrum from that file and dielectric constant values. As far > as I understood, the absorption spectrum is related to imaginary part of > average \chi value. but in the file there are 9 values > chi_1_1 > chi_2_1 > chi_3_1 > chi_1_2 > chi_2_2 > chi_3_2 > chi_1_3 > chi_2_3 > chi_3_3 > This is 3*3*3 tensor. how do I get an absorption spectrum and dieletric > constant values? by the way S(E) means what? > > Sincerely > Sunghwan Choi > > ___ > 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] analysis of TDDFPT results
Dear Sergi, I would like just to add that in the examples folder of the turboTDDFT code you can find examples on how to perform the Davidson diagonalization. Best, Dario Rocca On Fri, May 20, 2016 at 11:00 AM, Timrov Iurii wrote: > Dear Dr. Sergi Vela, > > > With the current implementation of the Lanczos algorithm in the turboTDDFT > program it is not possible to perform analysis of the origin of individual > peaks in the absorption spectrum. However, such an analysis can be done > using another flavor of the turboTDDFT code, namely the turbo_davidson.x > program. More information can be found in this publication: > > > X. Ge, S. J. Binnie, D. Rocca, R. Gebauer, and S. Baroni, "turboTDDFT > 2.0—Hybrid functionals and new algorithms within time-dependent > density-functional perturbation theory", Comput. Phys. Commun. 185, 2080 > (2014). > > > With the so-called turboDavidson code (turbo_davidson.x) you can > compute the absorption spectrum (the same as with Lanczos) but as a > plus in the output file you will find the information about the origin of > the peaks (from which occupied level to which empty level there was a > transition and what is the corresponding intensity etc.). However, > if you are interested in computing the spectrum in a very > wide energy range, then turboDavidson becomes too expensive, and hence it > is recommended to use the Lanczos algorithm (at the cost described above, > i.e. no information about the origin of the peaks). > > > HTH > > > Best regards, > > Iurii > > > -- > Dr. Iurii Timrov > Postdoctoral Researcher > Swiss Federal Institute of Technology Lausanne (EPFL) > Laboratory of Theory and Simulation of Materials (THEOS) > CH-1015 Lausanne, Switzerland > +41 21 69 34 881 > http://people.epfl.ch/265334 > -- > *From:* pw_forum-boun...@pwscf.org on behalf > of Sergi Vela > *Sent:* Friday, May 20, 2016 10:30 AM > *To:* PWSCF Forum > *Subject:* [Pw_forum] analysis of TDDFPT results > > Dear QE users and developers, > > I've successfully performed a TDDFPT (Lanczos approach) calculation on a > system of my interest, and now I would like to analyze the different bands > of the resulting spectrum. I would like to ascribe them to chemical > (orbital-excitations, charge-transfer) processes such as I would do when > using standard TDDFT codes. > > I'd like to know if this is indeed possible and, if so, I'd appreciate > some information on how to do it. > > All my best, > Dr. Sergi Vela, > Laboratoire de Chimie Quantique, Universitè de Strasbourg, France > > ___ > 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] G vector used to represent wfcs
Dear Ryky, For more details about the G vector generation you can take a look in the ggen subroutine in Modules/recvec_subs.f90. Take a look also in n_plane_waves.f90 In gereral the G vectors are determined with the condition G^2 * hbar^2 / (2m_e) < E_cut(density)=4*E_cut(wfc) (without the k point; inside QE Rydberg atomic units are used) This is a sphere in reciprocal space centered in (0,0,0). Concerning each orbital corresponding to a specific k point you apply the condition (G+k)^2 * hbar^2 / (2m_e) < E_cut(wfc) In this case the G vectors are a subset of the vectors used for the density. In this case we have a sphere in reciprocal space shifted from the origin. Depending on k you can have a different set of G vectors included in the sphere and also their number could differ. In order to menage the g vectors for each k-point, you can use the arrays ngk (number of G vectors for each k-point) and igk (index of G corresponding to a given index of k+G; basically an index that allows you to identify the G vectors corresponding to a given k and order them). For example the kinetic energy corresponding to a given k-point ik is g2kin(1:ngk(ik)) = ( ( xk(1,ik) + g(1,igk(1:ngk(ik))) )**2 + & ( xk(2,ik) + g(2,igk(1:ngk(ik))) )**2 + & ( xk(3,ik) + g(3,igk(1:ngk(ik))) )**2 ) * tpiba2 where tpiba2 = (2\pi/a)^2 There is only one FFT for the wavefunctions so the grid does not depend on the k-points; however, for a given wavefunction, only the components corresponding to a G vector that satisfy (G+k)^2 * hbar^2 / (2m_e) < E_cut(wfc) are different from 0 Best, Dario On Thu, May 12, 2016 at 1:38 PM, Ryky Nelson wrote: > Hello QE users and developers, > > I'm trying to figure out how G vectors in PWscf are selected to represent > the corresponding wfcs. Could someone tell me if the following is the only > criterion used to determine G vectors? > > abs(G+k)^2 * hbar^2 / (2m_e) < E_cut > > and does the code basically start from the origin (0,0,0) and scan through > all grid coordinates (positive and negative) and check if the grid agrees > with the above criterion? Also, does the number of G vectors (for each k) > have relation to the FFT dimensions? > > Thank you! > > Ryky Nelson > Institut für Anorganische Chemie > RWTH Aachen University > > ___ > 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] Hartree-Fock in quantum espresso
Dear Stefano, The HF calculation is just a normal self-consistent HF calculation like in "quantum chemical" codes. HF is done "in the same way as a hybrid functional" because HF is a hybrid functional with 100% of exchange and 0% of other exchange-correlation contributions. In general HF will converge more slowly then PBE0 or B3LYP. I would pay attention to the fact that: -No HF pseudopotentials are available on the QE library. So you will need to test the effect of the pseudopotentials -Since there is a q-->0 limit to be evaluated I would test carefully convergence with respect to k-points (solids) or cell size (molecules). In general convergence is good but not necessarily the same as in the PBE/LDA case Best, Dario On Wed, May 11, 2016 at 12:24 AM, stefano < stefano.di-sabat...@polytechnique.edu> wrote: > Dear all, > > I am interested in the possibility of doing Hartree-Fock calculation > with quantum espresso. > I saw that HF calculations are performed basically in the same way as a > hybrid functional calculation. I wonder if the HF calculation, as > implemented in QE, are equivalent to a "standard" HF calculation (i.e. > using Green's functions or solving self-consistently the Hartree-Fock > eigenvalue equations), and if not what are the difference between the > two methods. > > Thanks in advance > > Stefano > ___ > 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] Bader Analysis for charge transfer
Dear Mahendra, I suggest you generate a gaussian cube file of the density with the QE postprocessing and then you can use this program http://theory.cm.utexas.edu/henkelman/code/bader/ You shoud use PAW to generate the ground-state density. Best, Dario Rocca On Tue, Feb 23, 2016 at 1:42 PM, Mahendra Jalkhediya < jalkhediya.mahen...@gmail.com> wrote: > Hello, > I am trying to calculate the charge transfer form adatom to the monolayer > MoS2. I tried with by taking difference between Lowdin charge, but it is > not matching with literature. So I want to calculate charge transfer by > Bader analysis. So please guide me how to perform it in Quantum Espresso. > > Regards > Mahendra Jalkhediya > M.Tech Microelectronics & VLSI > IIT Kanpur, 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] Postdoctoral position on ab initio calculations at University of Lorraine (Nancy, France)
Dear Users and Developers, I'd like to advertise here this postdoctoral position tightly related to Quantum Espresso. Best regards, Dario Rocca Applications are invited for a two-year ANR-funded postdoctoral position in the Quantum Modeling Group (http://crm2.univ-lorraine.fr/lab/en/research/mq/) at the University of Lorraine (Nancy, France) under the supervision of Dr. Dario Rocca and Dr. Sébastien Lebègue. The position is available from January 2016 but starting date is negotiable. The research project is based on algorithms and methodologies recently developed within the Quantum Modeling Group to compute the correlation energy within the random phase approximation and beyond. The successful candidate will apply these new ab initio methods to challenging problems in materials science and chemistry, in particular involving the stability of molecular crystal polymorphs and problems of surface catalysis. Depending on the candidate’s interest and background they will have the opportunity to participate in methodological development. Candidates should have completed a PhD in physics or chemistry and should have a background in the domain of electronic structure calculations. Experience with plane-wave codes, ab initio Green's function methods, and programming preferred. Interested candidates should send a copy of their CV (including a list of publications and references) to Dr. Dario Rocca by email: dario.ro...@univ-lorraine.fr. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] problem with phonon calculation
Dear Chaitanya As the error message says you cannot use "occupations=tetrahedra" with the phonon code since this approach is not implemented The only solution is to use a smearing instead Best regards, Dario On Sat, Sep 5, 2015 at 8:39 AM, chaitanya varma wrote: > Dear Sir, > I am trying to calculate DOS, pDOS and phonon densities etc of PbTiO3 > -(tetragonal structure) > SCF, NSCF and BANDS calculations worked out nicely with tetrahedra, > but while doing ph.x calculation i am getting the following error > > > > > %% > Error in routine phq_setup (1): > phonon + tetrahedra not implemented > > > %% > > stopping ... > > can i know where i am doing wrong. > i am attaching the scf.in and phG.in/out files > > thanks and regards > > Chaitanya Varma M > Asst Professor > GITAM University > 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
Re: [Pw_forum] Problem to restart calculus in PWscf
Dear Yenner, in order to restart a calculation has to end smoothly in the previous run and write the restart files. The prefix.wfc1 file that you see is probably created only at the moment of the restart and is, of course, empty You can find the solution to your problem here http://www.quantum-espresso.org/wp-content/uploads/Doc/pw_user_guide/node19.html Best, Dario Rocca On Wed, Aug 12, 2015 at 7:00 PM, Yenner Bentarcurt < yenner.bentarc...@ciens.ucv.ve> wrote: > Dear PWSCF users and developers > > Now I carry out simulation of polar surfaces of iron oxides, but when I > try to restart a > calculus, this fails and reports the message "error while reading from > file > ./wfcdir/prefix.wfc1". When I search for this file in the directory > ./wfcdir this is present > but shows 0 bytes. The Namelist &CONTROL for this calculus is > > &CONTROL > restart_mode = 'restart' , >calculation = 'relax' , > wf_collect = .true. , > outdir = './outdir' , > wfcdir = './wfcdir' , > pseudo_dir = '/opt/espresso-5.1.2/pseudo/' , > prefix = 'magh-slab100-3v124-111-pbeUwithcorrefield01-relax02' , > etot_conv_thr = 1.0D-5 , > forc_conv_thr = 1.0D-4 , > nstep = 500 , > tefield = .true. , > dipfield = .true. , > > > I'm using of the QE 5.1.2 version, compiled in centOS 7 on a Dell tower > server with 16 > processors and 16 Gb of memory > I hope all your help > > > Yenner > Student of PhD > Central University of Venezuela > Science Faculty, Department of Chemistry > > > ___ > 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] Dielectric constant of Monolyer MoS2 in .ph
Dear Kanak You probably used a smearing for metals in your ground state calculation. You should set up occupations='fixed' Best, Dario Rocca On Sat, Aug 8, 2015 at 11:06 PM, Bahadır salmankurt wrote: > Dear Kanak Datta > > if the system is considered metalic, it gives a error like "no elec. > field with metals". Please do calculation in non-metalic condition. > > regards > > 2015-08-08 23:48 GMT+03:00 Kanak Datta : > >> Dear researchers >> >> Is it possible to calculate static dielectric constant of mono/bi layer >> MoS2 using .ph package in quantum espresso? I have performed self >> consistent formulation already and have been using the following code for >> .ph package found in a tutorial: >> &inputph >> tr2_ph=1.0d-14, >> prefix='MoS210', >> epsil=.true. >> outdir='D:\QuantumEspresso\Quantum ESPRESSO 64-bit 5.1.2- >> mpich2\MoS210\outdir', >> !outdir='./' >> fildyn='MoS210.dynG', >> / >> 0.0 0.0 0.0 >> >> The code however would terminate saying " no elec. field with >> metals".can anyone please help me with this? >> >> Thanks in advance. >> Sincerely yours >> Kanak Datta >> Dept. of EEE, BUET >> >> >> >> >> ___ >> 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] (no subject)
Hello, first of all is the variable Q_ESP_DIR properly set up during the run? It doesn't seem that that is the case Just give the explict path to the pseudopotential Best, Dario Rocca On Tue, Aug 4, 2015 at 4:56 PM, mohammed shambakey wrote: > Hi > > I trying to run the following command > > mpirun -np 8 pw.x < ./6x6-6+6H+F.scf.in > ./results/6x6-6+6H+F.scf.out > > but it fails due to missing file /C.pz-vbc.UPF. The file is downloaded and > accessible in "pseudo" folder, but still have the same error. > > Please help > > Attached is the "CRASH" and "6x6-6+6H+F.scf.out" files > > -- > Mohammed > > ___ > 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] Bandstructure plot with HSE
Hi Dhirendra, I suggest you perform a calculation on an uniform grid as dense as possible with some empty bands and you extract the band structure along the high symmetry directions with a script or manually (of course make sure that the uniform grid you choose contains points along the high symmetry directions of your interest). In principle, as Nicola suggested, you could write down explicitly the k-points and add some 0 weight k-points for the band structure. In practice I always got an error message. I think that the problem is that an "arbitrary" grid of k points do not contain the k+q points necessary for the exact exchange calculation; this is not a conceptual problem but simply the code does not automatically compute the missing k+q orbitals and energies. Dario Rocca On Thu, Jul 30, 2015 at 10:18 PM, DHIRENDRA VAIDYA < dhirendra22121...@gmail.com> wrote: > Hi, > > As HSE doesn't allow nscf calculations, its not possible to plot a > bandstructure along high symmetry lines. I am wondering if I can use > wannier90 post processing after HSE-scf calculations? > Can anyone please provide an expert comment? > > Thanks, > Dhirendra > > ___ > 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] K PAW pseudopontential
Dear Users, does anybody has generated a PAW PBE pseudopotential for potassium that would be willing to share? Thanks! Dario Rocca Universit? de Lorraine -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140717/b5db481e/attachment.html
[Pw_forum] PhD Position in Computational Physics/Chemistry, Nancy, France
Dear all, The CRM2 Lab of the University of Lorraine (Nancy-France) is seeking a candidate for a PhD position in the Quantum Modeling Group. The successful candidate will work with Dr. Janos Angyan and Dr. Dario Rocca on the developement and application of new methods to include van der Waals interactions within density functional theory. The PhD student activity will involve the implementation in computational physics/chemistry packages of new approaches to compute the correlation energies within time-dependent DFT. The aim of this project is to improve both the numerical scability and accuracy of currently available techniques. Applications to realistic models will include the study of the structural properties of molecular crystals and biologically-relevant systems. The candidate will have to be approved by the Doctoral School of the University of Lorraine and the PhD fellowship will be awarded only to highly qualified applicants. Interested candidates should send their CV including the name of at least one reference at: janos.angyan at univ-lorraine.fr and dario.rocca at univ-lorraine.fr For further information, please visit the site: http://www.crm2.uhp-nancy.fr/People/Angyan Best regards, Dario Rocca -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130423/38bffb15/attachment.html
[Pw_forum] Excited State Gradients in TDDFT
Dear Yukihiro
> You mean if we diagonalize the Liouvillean operator by usual method
> instead of using Lanczos chain, and get
>
> eigenvalue and eigenvectors, we can get excited-state gradient ?
>
There are not "usual methods" to get eigenvalues and eigenvectors for TDDFT
because the eigenvalue problem is non-Hermitian. I have been lately working
on this type of eigenvalue problems in order to diagonalize the Liouvillian
in the TDDFT formalism without empty states (J. Chem. Phys. 136, 034111
(2012)). This new method seems very promising but at this stage it still
needs an efficient preconditioner to become more practical.
>
> Are there already formalism to calculate the excited energy gradient
> within occupied state only method ?
>
I think that a necessary ingredient for the calculation of gradients is the
diagonalization of the Liouvillian. Once this is done I think that the
formalism used for the Casida's equations can be extended to the TDDFT
without empty states.
>
> Usual Casida's matrix, the dimension of the Matrix is \Omega_{i_j, k_q}
> where, i and j are occupied and unoccupied state (k and q are also occupied
> and unoccupied state pair),
>
> and the dimension is (2*Nc*Nv) * (2* Nc * Nv) where Nc and Nv is the
> number of the unoccupied and occupied states.
>
> But your Liouvillean matrix dimension is (2*Nv) * (2 *Nv), and it is very
> small than the usual Casida's one.
>
The dimension of the Liouvillian is actually (2*Nv*Npw)*(2*Nv*Npw). This
dimension is basically the same as that of Casida's equation when Nc is the
total number of conduction states. The advantage of the Liouvillian
approach is not exactly in the matrix dimension but I would say that some
of the advantages are:
-The matrix is big but never built explicitly and its application to a
vector involve a number of orbitals that is equal to the number of occupied
states (it scales better than Casida's equations, that involve a number of
orbitals equal to Nc)
-The convergence of the spectra with the number of empty states in never an
issue (even at high energy or when there is a strong dependence of the
spectrum at low energy on the states at higher energy)
-The use of plane-waves avoids the convergence problems with respect to the
basis set typical of the localized basis sets
Dario Rocca
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[Pw_forum] scaling of turbo_lanczos.x
2012/1/10 Eduardo Ariel Menendez Proupin > > > a) the itermax parameter to achieve an equivalent resolution of the > spectrum (is the same or must be scaled) > > The itermax depends on the cutoff but not on the number of electrons. If for example in a calculation you use a single or 8 repeated units the total number of iterations to converge is basically the same (but of course the convergence should always be tested in each case). Dario -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120114/252f2f78/attachment.htm
[Pw_forum] FFT on a small mesh
Dear Developers I would be interested in calculating the FFT with a small reciprocal space cutoff. Namely beyond the FFT for wavefunctions and density I would like to use an additional FFT on an "object" that requires a cutoff smaller than the wavefunctions (but of course the real space mesh would still be the same). All the standard FFT machinery seems very specialized to the wavefunction/density case, and I was wondering if there is an easy option or if someone has developed more general subroutines and is willing to share them. Thanks for your help Dario Rocca, UCDavis -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110921/85ec9c27/attachment.htm
[Pw_forum] k point convergence of dielectric properties
Dear Users I have an issue related to the convergence of the static dielectric matrix using the PH code. I have performed calculations on bulk silicon using different k point meshes and I have obtained the following results: k grid diagonal component of number of k points in the dielectric tensor the irreducible Brillouin zone 4*4*4 23.6683500658 6 *6*616.297485614 16 8 *8*8 14.044830694 29 10 *10*10 13.288531964 47 12*12*12 13.029602882 72 16 *16*16 12.908820645145 20 *20*20 12.894538380256 k grid+ 1 1 1 shift diagonal component of number of k points in the dielectric tensor the irreducible Brillouin zone 4*4*4 13.840844632 10 6*6*6 12.997009732 28 8*8*8 12.903849607 60 10*10*10 12.893711596 110 12*12*12 12.892685597 182 16*16*16 12.892482798 408 20*20*20 12.892537346 770 I was surprised of the improvement in the convergence due to the shift of the grid. I don't think this is related to the number of k points in the IBZ (at least not exclusively). I have observed a similar behavior in diamond. The ground state energy convergence also benefits from the shift, but the improvement is not so striking. Does someone has any hint on why the shift of the grid improves the calculation of the dielectric properties of silicon? Thanks a lot Dario Rocca, dept. of chemistry, UC Davis -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20081009/5e75ab99/attachment.htm
