[QE-users] Questions regarding parallelism and memory usage of ph.x calculations
Dear QE-users, I tried to run a ph.x calculation on 100 processors of a system with 5 unique k-points so I used the -nk 5 command to divide the calculation into 5 pools of 20 processors. After printing which representations will be calculated in this run, the output returns the following error message: ... Representation 469 1 modes -A To be done Representation 470 1 modes -A To be done Representation 471 1 modes -A To be done Compute atoms: 149, 150, 151, 152, 153, 154, 155, 156, 157, === = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = PID 16398 RUNNING AT r3c4cn08.hopper = EXIT CODE: 9 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES === Intel(R) MPI Library troubleshooting guide: https://software.intel.com/node/561764 === However, if I perform the same calculation without parallellization over the unique k-points, the calculation achieves convergence without a problem. Parallellization over the 5 unique k-points works without a problem in the corresponding pw.x calculation. Any idea what can cause this issue? Except for this, I had an additional question regarding the memory usage of a ph.x calculation. While running such calculations, the memory usage goes up until approximately 200G. I'm performing calculations on a cluster and the amount of memory I can use is limited. Are there general tricks/methods to reduce the memory usage of ph.x calculations? Thanks in advance, Laurens Siemons PhD Student, UAntwerp ___ Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso) users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Negatively charged isolated molecule
Dear QE-users, I always thought that it is not correct to calculate energies of isolated ionic species under PBC due to the introduction of a Jellium background inside the vacuum which has physically no meaning. But after reading this post I assume that I am wrong and that you can perform calculations on ionic species in a vacuum with QE? With kind regards, Laurens Siemons PhD, UAntwerp (Belgium) Van: users namens Nattino Francesco Verzonden: zaterdag 16 maart 2019 9:02 Aan: Quantum Espresso users Forum Onderwerp: Re: [QE-users] Negatively charged isolated molecule Dear Ernane, As Giuseppe already pointed out, many anionic species are actually unbound with standard density functionals. The continuum solvation model helps to achieve convergence because the dielectric embedding stabilizes the localized electronic configuration. A way to circumvent the issue and to obtain the energy of carbonate in vacuum could be the following: you calculate the energy of the system for decreasing values of the dielectric constant and you extrapolate the energy to the vacuum dielectric constant (epsilon=1). Best regards, Francesco Nattino, EPFL On Mar 15, 2019 7:30 PM, Michal Krompiec wrote: Dear Ernane, Have you thought of using a more sophisticated method (like GW) on [CO3]- to calculate its EA? This would give you the energy of [CO3]2- in vacuum. Best, Michal Krompiec University of Southampton & Merck KGaA On Fri, 15 Mar 2019 at 18:22, Ernane de Freitas Martins mailto:ernane...@gmail.com>> wrote: Dear Giuseppe, I really appreciate your answer. Thank you very much for using your time to answer my question. I'll think on your suggestion about trying hybrid functionals. The point is that I need to estimate the solvation energy for carbonate ion using the environ module, then I'll need to run a vacuum calculation using the same functional I'm already using rVV-10). Thank you again for replying. Atenciosamente, Dr. Ernane de Freitas Martins Postdoctoral researcher IF - USP São Paulo, SP - Brazil Em sex, 15 de mar de 2019 15:04, Giuseppe Mattioli mailto:giuseppe.matti...@ism.cnr.it>> escreveu: Dear Ernane Your question contains part of the answer! Carbonate ion (CO3 2-) is not stable outside water, and calculations of its properties in gas phase are likely not so meaningful, but in the case of model thermodynamics cycles (e.g. Born-Haber). The excess negative charge is unbound when not stabilized by a strongly polar solvent, and this is likely responsible for instabilities in the construction of the Kohn-Sham potential along scf iterations. Moreover, this happens on top of the strong delocalization error you experience when you use a standard GGA exchange-correlation functional, when the self-interaction of strongly localized electrons in the J[n] Coulomb potential is not cancelled by a same term in the semi local exchange potential. You may minimize this latter source of error by using a hybrid GGA-EXX functional such as B3LYP, where the non local Hartree-Fock part of the exchange functional can recover part of the delocalization error, but you are not free yet from the instability of carbonate in gas phase. HTH Giuseppe Ernane de Freitas Martins mailto:ernane...@gmail.com>> ha scritto: > Hello, > > I'm experiencing a problem to run a negatively charge molecule in quantum > espresso. The system is CO32-. > > I try both vacuum and solvated (environ) calculations. The solvated one > works fine. > > The problem is the calculation in vacuum. It never give the first ionic > step because the SCF accuracy never reaches the convence criterion. > > I tried many different solutions (increase cutoffs and box size, use assume > isolated, decreasing and changing the mixing scheme and etc) and nothing > works. > > The unique calculation that works fine for vacuum is the one with a box > size of 7.9 x 7.9 x 7.9 A. I really don't understand why it only works for > this specific box size. > > I ran several other charged systems (+1, +2 and -1 total charge) and all of > them worked fine. The problem appears for -2 total charge in vacuum. > > Would some of you kindly help me in this? > > Cheers, > > Dr. Ernane de Freitas Martins > Postdoctoral researcher > IF - USP > São Paulo, SP - Brazil GIUSEPPE MATTIOLI CNR - ISTITUTO DI STRUTTURA DELLA MATERIA Via Salaria Km 29,300 - C.P. 10 I-00015 - Monterotondo Scalo (RM) Mob (*preferred*) +39 373 7305625 Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: mailto:giuseppe.matti...@ism.cnr.it>> ___ users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users ___ users mailing list users@lists.quantum-espresso.org<mailto:users@l
Re: [QE-users] Wrong number of k-points?
Thanks for the information and quick response.
Laurens
Van: users namens Giovanni Cantele
Verzonden: donderdag 31 januari 2019 10:15
Aan: Quantum Espresso users Forum
Onderwerp: Re: [QE-users] Wrong number of k-points?
The symmetry k -> -k is still present even though your system has no spatial
symmetry. As such the number of k-points is halved.
Giovanni
PS from a quick google search I found for example this document you might find
of help
https://people.sissa.it/~degironc/FIST/Slides/8%20Symmetry.pdf
On 31 Jan 2019, at 10:09, Laurens Siemons wrote:
Dear QE users,
I'm running a relax calculation and I encountered something that I do not
understand in the output file. I used a 2 2 1 1 1 0 Monkhorst-Pack grid in my
input file (which is shown below) but the output file tells me I only have 2
k-points:
116 H tau( 116) = ( 3.8845153 0.8033970 -0.3177301 )
117 H tau( 117) = ( 3.8658215 1.2769290 -0.3107519 )
118 H tau( 118) = ( 4.1682098 1.0557090 -0.6030099 )
number of k points= 2
cart. coord. in units 2pi/alat
k(1) = ( 0.000 0.083 -0.0984507), wk = 1.000
k(2) = ( 0.000 0.083 0.0984507), wk = 1.000
Dense grid: 5866317 G-vectors FFT dimensions: ( 180, 160, 480)
Smooth grid: 1484065 G-vectors FFT dimensions: ( 108, 96, 320)
I would expect at least 4 k-point right? The system possesses no symmetry.
Thanks in advance,
Laurens Siemons,
PhD, University of Antwerp
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'a101mpa1'
tprnfor = .true.
pseudo_dir =
'/data/antwerpen/204/vsc20442/pseudo/pslibrary.1.0.0/wc/PSEUDOPOTENTIALS'
outdir = '/scratch/antwerpen/204/vsc20442/TMP'
wf_collect = .true.
nstep = 100
/
ibrav = 0
A =3.77449
nat = 118
ntyp = 5
ecutwfc = 60
ecutrho = 600
spline_ps = .true.
/
electron_maxstep = 500
diagonalization = 'david'
conv_thr = 1.0d-10
mixing_beta = 0.70
/
ion_dynamics = 'bfgs'
/
ATOMIC_SPECIES
O 15.99900 O.wc-n-kjpaw_psl.1.0.0.UPF
Ti 47.86700 Ti.wc-spn-kjpaw_psl.1.0.0.UPF
H 1.0079H.wc-kjpaw_psl.1.0.0.UPF
C 12.0107 C.wc-n-kjpaw_psl.1.0.0.UPF
P 30.973761 P.wc-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {crystal}
Ti 0 0.000.026316 0 0 0
Ti 2/3 0.000.026316 0 0 0
Ti 1/3 0.000.026316 0 0 0
Ti 1/6 1/2 0.026316 0 0 0
Ti 1/2 1/2 0.026316 0 0 0
Ti 5/6 1/2 0.026316 0 0 0
Ti 0 0.9958560.266326
Ti 1/3 0.9958560.266326
Ti 2/3 0.9958560.266326
Ti 1/6 0.4958560.266326
Ti 1/2 0.4958560.266326
Ti 5/6 0.4958560.266326
Ti 0 0.9892020.145250
Ti 1/3 0.9892020.145250
...
...
...
CELL_PARAMETERS {alat}
0.000 3.000 0.000
1.000 -0.000 -2.539341738883929
8.551 0.000 0.000
K_POINTS {automatic}
2 2 1 1 1 0
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--
Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it
gcant...@gmail.com
Phone: +39 081 676910
Skype contact: giocan74
Web page: https://sites.google.com/view/giovanni-cantele
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[QE-users] Wrong number of k-points?
Dear QE users,
I'm running a relax calculation and I encountered something that I do not
understand in the output file. I used a 2 2 1 1 1 0 Monkhorst-Pack grid in my
input file (which is shown below) but the output file tells me I only have 2
k-points:
116 H tau( 116) = ( 3.8845153 0.8033970 -0.3177301 )
117 H tau( 117) = ( 3.8658215 1.2769290 -0.3107519 )
118 H tau( 118) = ( 4.1682098 1.0557090 -0.6030099 )
number of k points= 2
cart. coord. in units 2pi/alat
k(1) = ( 0.000 0.083 -0.0984507), wk = 1.000
k(2) = ( 0.000 0.083 0.0984507), wk = 1.000
Dense grid: 5866317 G-vectors FFT dimensions: ( 180, 160, 480)
Smooth grid: 1484065 G-vectors FFT dimensions: ( 108, 96, 320)
I would expect at least 4 k-point right? The system possesses no symmetry.
Thanks in advance,
Laurens Siemons,
PhD, University of Antwerp
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'a101mpa1'
tprnfor = .true.
pseudo_dir =
'/data/antwerpen/204/vsc20442/pseudo/pslibrary.1.0.0/wc/PSEUDOPOTENTIALS'
outdir = '/scratch/antwerpen/204/vsc20442/TMP'
wf_collect = .true.
nstep = 100
/
ibrav = 0
A =3.77449
nat = 118
ntyp = 5
ecutwfc = 60
ecutrho = 600
spline_ps = .true.
/
electron_maxstep = 500
diagonalization = 'david'
conv_thr = 1.0d-10
mixing_beta = 0.70
/
ion_dynamics = 'bfgs'
/
ATOMIC_SPECIES
O 15.99900 O.wc-n-kjpaw_psl.1.0.0.UPF
Ti 47.86700 Ti.wc-spn-kjpaw_psl.1.0.0.UPF
H 1.0079H.wc-kjpaw_psl.1.0.0.UPF
C 12.0107 C.wc-n-kjpaw_psl.1.0.0.UPF
P 30.973761 P.wc-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {crystal}
Ti 0 0.000.026316 0 0 0
Ti 2/3 0.000.026316 0 0 0
Ti 1/3 0.000.026316 0 0 0
Ti 1/6 1/2 0.026316 0 0 0
Ti 1/2 1/2 0.026316 0 0 0
Ti 5/6 1/2 0.026316 0 0 0
Ti 0 0.9958560.266326
Ti 1/3 0.9958560.266326
Ti 2/3 0.9958560.266326
Ti 1/6 0.4958560.266326
Ti 1/2 0.4958560.266326
Ti 5/6 0.4958560.266326
Ti 0 0.9892020.145250
Ti 1/3 0.9892020.145250
...
...
...
CELL_PARAMETERS {alat}
0.000 3.000 0.000
1.000 -0.000 -2.539341738883929
8.551 0.000 0.000
K_POINTS {automatic}
2 2 1 1 1 0
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Re: [QE-users] Atomic distances are doubled after dynmat.x calculation
No thats not it. When I load the scf.out file in XCrysden the O--H bond for example measures 1.046A and 1.9766 Bohr. When I load the .axsf file in XCrysden the same distance becomes 2.0919A and 3.9532 Bohr. On 1/11/19 4:02 PM, Paolo Giannozzi wrote: ... the usual "Bohr radii vs Angstrom" problem ? On Fri, Jan 11, 2019 at 3:45 PM Laurens Siemons mailto:laurenssiem...@hotmail.be>> wrote: Dear QE-users, I'm trying to calculate vibrational frequencies of a molecule adsorbed on a surface. I first run a pw.x calculation followed by a ph.x calculation and finally a dynmat.x calculation which generates a dynmat.mold and dynmat.axsf (and some other) files. When I open the .mold file in JMol I do not see any connectivity between the atoms, no bonds are shown (the same happens when I open the .axsf file in XCrysden). I now realize that JMol does not show any connectivity since all atomic distances are doubled! When I load the phonon output file in JMol all atomic distances are the way they need to be, so this should happen when running dynmat.x or when the dynamical matrix file is generated. Can anyone explain why this is happening? My ph.in<http://ph.in> and dynmat.in<http://dynmat.in> files are as followed: freq van molecule op opp prefix = 'a101mpa4' nat_todo = 11 amass(1) = 15.99900 amass(2) = 47.86700 amass(3) = 1.0079 amass(4) = 12.0107 amass(5) = 30.973761 outdir = '/scratch/antwerpen/204/vsc20442/TMP' fildyn = 'a101mpa4.dynG' epsil = .true. / 0.0 0.0 0.0 22 73 74 75 76 77 78 79 80 81 82 fildyn = 'a101mpa4.dynG' asr = 'zero-dim' / Thanks in advance, Laurens Siemons PhD student, University of Antwerp ___ users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Atomic distances are doubled after dynmat.x calculation
Dear QE-users, I'm trying to calculate vibrational frequencies of a molecule adsorbed on a surface. I first run a pw.x calculation followed by a ph.x calculation and finally a dynmat.x calculation which generates a dynmat.mold and dynmat.axsf (and some other) files. When I open the .mold file in JMol I do not see any connectivity between the atoms, no bonds are shown (the same happens when I open the .axsf file in XCrysden). I now realize that JMol does not show any connectivity since all atomic distances are doubled! When I load the phonon output file in JMol all atomic distances are the way they need to be, so this should happen when running dynmat.x or when the dynamical matrix file is generated. Can anyone explain why this is happening? My ph.in and dynmat.in files are as followed: freq van molecule op opp prefix = 'a101mpa4' nat_todo = 11 amass(1) = 15.99900 amass(2) = 47.86700 amass(3) = 1.0079 amass(4) = 12.0107 amass(5) = 30.973761 outdir = '/scratch/antwerpen/204/vsc20442/TMP' fildyn = 'a101mpa4.dynG' epsil = .true. / 0.0 0.0 0.0 22 73 74 75 76 77 78 79 80 81 82 fildyn = 'a101mpa4.dynG' asr = 'zero-dim' / Thanks in advance, Laurens Siemons PhD student, University of Antwerp ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Error while parsing atomic position card
Can you attach your input file please? Kind regards, Laurens Siemons PhD - University of Antwerp Op 12/11/18 om 12:14 PM schreef hamed asadi: Dear users, I'm trying to relax CoFe2O4 lattice but after executing calculation, I faced following error, does anybody know how can I solve this error? CRASH %% task # 3 from card_atomic_positions : error # 1 Error while parsing atomic position card. %% %% task # 1 from card_atomic_positions : error # 1 Error while parsing atomic position card. %% Best regards, H. Asadi KN Toosi university of technology Attachments area ___ users mailing list users@lists.quantum-espresso.org<mailto:users@lists.quantum-espresso.org> https://lists.quantum-espresso.org/mailman/listinfo/users ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] GIPAW f-sum rule
Dear users, I understand that the f-sum rule can be used in order to check the reliability of results obtained via gipaw.x. In most documents I find that "the f-sum rule should be matched as good as possible" , but this is rather vague to me. Can someone put a value on the error that is still acceptable? As an example, here is the f-sum rule from a GIPAW calculations of a methyl group adsorbed on a TiO2-surface (76 atoms in total): f-sum rule (should be -569.3617): -571.1240 0.0002 -0.3758 0.0001 -570.9898 -0.0002 -0.3808 -0.0002 -570.0995 Is this good enough or should it be better? Thanks in advance, Laurens Siemons PhD, University of Antwerp ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] Bader Charge
Dear Sudha, After you have done a scf or relax (pw.x) calculation on your structure, you can use pp.x to obtain a .cube file from the .save file. I use plot_num = 17 for this (I use PAW pseudopotentials), iflag = 3 and output_format = 6 to make the .cube file as shown here: prefix = 'adsorption101-4pa-m' outdir = '/TMP' filplot = 'adsorption101-4pa-m-bader' plot_num= 17 / nfile = 1 iflag = 3 output_format = 6 fileout = 'adsorption101-4pa-m.cube' / >From this site you can download a simple program to obtain the bader charges >out of the .cube file: http://theory.cm.utexas.edu/henkelman/code/bader/ Best of luck! Laurens Siemons Master student, University of Antwerp [http://theory.cm.utexas.edu/henkelman/code/bader/bader.gif]<http://theory.cm.utexas.edu/henkelman/code/bader/> Code: Bader Charge Analysis - University of Texas at Austin<http://theory.cm.utexas.edu/henkelman/code/bader/> theory.cm.utexas.edu Code: Bader Charge Analysis News. 09/25/17 - Version 1.03 Released Default to -vac off Introduction. Richard Bader, from McMaster University, developed an intuitive way of dividing molecules into atoms. Van: users namens Sudha Priyanka Verzonden: vrijdag 8 juni 2018 11:45 Aan: users@lists.quantum-espresso.org Onderwerp: [QE-users] Bader Charge <mailto:users@lists.quantum-espresso.org> Dear users & experts Can we perform Bader charge analysis by using QE? If so, please guide me. I need input format for the same. With warm regards Sudha Priyanka G Assistant Professor, Lady Doak College, Madurai, Tamilnadu, India. ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] 'Tot_charge = x' on surface calculations
Dear all, If I see it the right way, it is fundamentally wrong to use the 'tot_charge' argument from pw.x when performing calculations on surface slabs. Because using the 'tot_charge' argument will introduce a uniform Jellium background over the whole cel. For a surface slab with a vacuum width this means that there will be some charge background in the vacuum as well, which is illogical. Now if you try to run pw.x however on a surface slab (with vacuum), the code will not crash and will come to a result eventually. My questions: 1) If my thought is right that it is illogical to use 'tot_charge' for surfaces, why doesn't the code crash when you try to do this? 2) Is there any idea how wrong the results are that you obtain by doing calculations this way? For example on first order parameters like energy and second order parameters as chemical shifts? Kind regards, Laurens Siemons Master student University of Antwerp ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] cholesky Error
If your sure there's nothing wrong with your structure or your input parameters, then you can try to add 'nd 1' to your script when you submit it like: pw.x -nd 1 -inp name.rx.in > name.rx.out This worked for me. Laurens Siemons Van: users <users-boun...@lists.quantum-espresso.org> namens Amin Mirzai <amin.mir...@mek.lth.se> Verzonden: maandag 9 april 2018 12:49 Aan: Quantum Espresso users Forum Onderwerp: Re: [QE-users] cholesky Error Thanks for the hint, I understand this topic has already been discussed. However, after doing all possible variations I still get the same error. Anyhow, I believe there is not any explicit answer to this issue. Regards, Amin From: users <users-boun...@lists.quantum-espresso.org> on behalf of Lorenzo Paulatto <paul...@gmail.com> Sent: Monday, April 9, 2018 10:00:13 AM To: users@lists.quantum-espresso.org Subject: Re: [QE-users] cholesky Error On 09/04/18 09:57, Amin Mirzai wrote: > %% > Error in routine cdiaghg (251): >problems computing cholesky > % > This is one of the most regularly asked questions. This error typically comes from bad geometry (i.e. ions core regions overlapping), bad pseudopotentials (should not happen with anything from usual libraries) or problematic input parameters with advanced features (i.e. lda+U, exx,...) kind regards -- Lorenzo Paulatto - Paris ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
Re: [QE-users] PP.x page not found
Dear Mohammadreza, In the Doc directory of your QE you should find a INPUT_PP.html file which you can open with your desired browser to see the pp.x input description. Kind regards, Laurens Siemons Van: users <users-boun...@lists.quantum-espresso.org> namens Mohammadreza Hosseini <mhr.hosse...@modares.ac.ir> Verzonden: dinsdag 3 april 2018 14:10 Aan: users@lists.quantum-espresso.org Onderwerp: [QE-users] PP.x page not found Dear users I am searching for pp.x input description. google can find this but the page is written not found. Is there anybody help me to find this ? Mohammadreza Hosseini Tarbiat Modares university, Iran ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Defining a radical
Dear all, I'm not sure about the parameters you have to specify when you want to perform a (relax) calculation on a radical. For example, I want to perform a relax calculation on an ethyl radical. I don't find a lot of information about it in the manual/archives, but from the things I found I guess you have to specify 'nspin = 2' and 'tot_magnetization = 1'. Is this correct? Or do you have to specify starting magnetization as well? Do you have to specify this as well for an ethyl anion? or is it in this case enough to specify the charge like: ibrav = 0, nat = 7, ntyp = 2, ecutwfc = 60, ecutrho = 480, tot_charge = -1 Thanks in advance, Laurens Siemons ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Defining a radical
Dear all, I'm not sure about the parameters you have to specify when you want to perform a (relax) calculation on a radical. For example, I want to perform a relax calculation on an ethyl radical. I don't find a lot of information about it in the manual/archives, but from the things I found I guess you have to specify 'nspin = 2' and 'tot_magnetization = 1'. Is this correct? Or do you have to specify starting magnetization as well? Do you have to specify this as well for an ethyl anion? or is it in this case enough to specify the charge like: ibrav = 0, nat = 7, ntyp = 2, ecutwfc = 60, ecutrho = 480, tot_charge = -1 Thanks in advance, Laurens Siemons ___ users mailing list users@lists.quantum-espresso.org https://lists.quantum-espresso.org/mailman/listinfo/users
[QE-users] Wrong adsorption energy
Dear all,
I'm calculating parameters like adsorption energy, geometric parameters, NMR
chemical shifts of adsorbates on a surface. In this specific case I calculated
the adsorption energy of an ethyl anion on an anatase 001 surface of titania. I
got the following energies:
Esurface + adsorbate = -4301.05337244
Esurface = -4258.9387474
Eadsorbate = -42.37757742
So Eads = Esurface + adsorbate - (Esurface + Eadsorbate) = 0.26
Now this seems wrong. If Eads is positive, so adsorption is not favourable,
then the ethyl-anion should migrate away from the surface in the relax
calculation of a001cti. correct? I executed the three calculations with the
exact same parameters as the other ones so I don't see how this is possible. I
attached my input files of the calculations. I hope someone can guide me
through this.
Thanks in advance,
Laurens Siemons
Master student chemistry
University of Antwerp
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'a001cti'
tstress = .false.
tprnfor = .true.
pseudo_dir =
'/data/antwerpen/204/vsc20442/pseudo/pslibrary.1.0.0/wc/PSEUDOPOTENTIALS'
outdir = '/data/antwerpen/204/vsc20442'
wf_collect = .true.
verbosity='high'
nstep = 100
/
ibrav = 0
A =7.5703200
nat = 55
ntyp = 4
ecutwfc = 60
ecutrho = 600
spline_ps = .true.
tot_charge = -1
occupations = 'smearing'
smearing ='gaussian'
degauss = 0.01
/
electron_maxstep = 800
diagonalization = 'david'
conv_thr = 1.0d-8
diago_thr_init = 1e-4
mixing_mode = 'local-TF'
mixing_beta = 0.10
/
ion_dynamics = 'bfgs'
ion_positions = 'default'
/
ATOMIC_SPECIES
O 15.99900 O.wc-n-kjpaw_psl.1.0.0.UPF
Ti 47.86700 Ti.wc-spn-kjpaw_psl.1.0.0.UPF
H 1.0079 H.wc-kjpaw_psl.1.0.0.UPF
C 12.0107C.wc-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
Ti 0.000 0.000 1.9087670 0 0 0
Ti 3.7851600 3.7851500 1.9087670 0 0 0
Ti 3.7851600 0.000 1.9087670 0 0 0
Ti 0.000 3.7851500 1.9087670 0 0 0
Ti 1.8987801 1.9072538 6.6653189
Ti 5.6847274 5.6910109 6.6668078
Ti 5.6829787 1.9073371 6.6660252
Ti 1.8988482 5.6908822 6.6673040
Ti 7.5556487 1.8925750 4.2620477
Ti 3.7707991 5.6777250 4.2626203
Ti 3.7706326 1.8925750 4.2612651
Ti 7.5563300 5.6777250 4.2619331
Ti 1.8209799 0.0147848 8.9752324
Ti 5.6042776 3.7983526 8.9766449
Ti 5.6063519 0.0134524 8.9757859
Ti 1.8188148 3.7978378 8.9763395
O 7.5578290 0.000 3.8386641
O 3.7728582 3.7851500 3.8379196
O 3.7728658 0.000 3.8383777
O 7.5578214 3.7851500 3.8381296
O 2.0533736 1.9066709 8.6237139
O 5.8371104 5.6904280 8.6250500
O 5.8301987 1.9065346 8.6250309
O 2.0455686 5.6908670 8.6248591
O 7.5448913 1.9081774 6.2507347
O 3.7603899 5.6924947 6.2503530
O 3.7599887 1.9082834 6.2488260
O 7.5457165 5.6921388 6.2497422
O 1.8925800 0.000 1.5017606 0 0 0
O 5.6777400 3.7851500 1.5017606 0 0 0
O 5.6777400 0.000 1.5017606 0 0 0
O 1.8925800 3.7851500 1.5017606 0 0 0
O 1.7713489 0.0137931 7.0572842
O 5.5548131 3.7984964 7.0573797
O 5.5558351 0.0131875 7.0575705
O 1.7694639 3.7983299 7.0573415
O 0.000 1.8925750 2.3162697 0 0 0
O 3.7851600 5.6777250 2.3162697 0 0 0
O 3.7851600 1.8925750 2.3162697 0 0 0
O 0.000 5.6777250 2.3162697 0 0 0
O 1.8768640 1.8913335 4.6819764
O 5.6628340 5.6747953 4.6816710
O 5.6621754 1.8903645 4.6819191
O 1.8775453 5.6755599 4.6822055
O 0.1607103 0.0185624 9.5272860
O 3.9456886 3.8013277 9.5290611
O 3.9459006 0.0124531 9.5278586
O 0.1607179 3.7978681 9.5300537
C 3.3681670 3.6634367 11.7587988
H 3.9107122 2.8615381 11.2166472
H 3.2707791 3.2800956 12.8197770
H 4.0867365 4.5064364 11.8259000
C 2.1131000 4.0648547 11.0384011
H 1.4171240 3.1988251 11.0020987
H 1.5828076 4.8499215 11.6216489
K_POINTS {automatic}
3 3 1 1 1 0
CELL_PARAMETERS {alat}
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 2.5213822
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'anatase001-2x2-4'
tstress = .false
[QE-users] Wrong adsorption energy
Dear all,
I'm calculating parameters like adsorption energy, geometric parameters, NMR
chemical shifts of adsorbates on a surface. In this specific case I calculated
the adsorption energy of an ethyl anion on an anatase 001 surface of titania. I
got the following energies:
Esurface + adsorbate = -4301.05337244
Esurface = -4258.9387474
Eadsorbate = -42.37757742
So Eads = Esurface + adsorbate - (Esurface + Eadsorbate) = 0.26
Now this seems wrong. If Eads is positive, so adsorption is not favourable,
then the ethyl-anion should migrate away from the surface in the relax
calculation of a001cti. correct? I executed the three calculations with the
exact same parameters as the other ones so I don't see how this is possible. I
attached my input files of the calculations. I hope someone can guide me
through this.
Thanks in advance,
Laurens Siemons
Master student chemistry
University of Antwerp
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'a001cti'
tstress = .false.
tprnfor = .true.
pseudo_dir =
'/data/antwerpen/204/vsc20442/pseudo/pslibrary.1.0.0/wc/PSEUDOPOTENTIALS'
outdir = '/data/antwerpen/204/vsc20442'
wf_collect = .true.
verbosity='high'
nstep = 100
/
ibrav = 0
A =7.5703200
nat = 55
ntyp = 4
ecutwfc = 60
ecutrho = 600
spline_ps = .true.
tot_charge = -1
occupations = 'smearing'
smearing ='gaussian'
degauss = 0.01
/
electron_maxstep = 800
diagonalization = 'david'
conv_thr = 1.0d-8
diago_thr_init = 1e-4
mixing_mode = 'local-TF'
mixing_beta = 0.10
/
ion_dynamics = 'bfgs'
ion_positions = 'default'
/
ATOMIC_SPECIES
O 15.99900 O.wc-n-kjpaw_psl.1.0.0.UPF
Ti 47.86700 Ti.wc-spn-kjpaw_psl.1.0.0.UPF
H 1.0079 H.wc-kjpaw_psl.1.0.0.UPF
C 12.0107C.wc-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
Ti 0.000 0.000 1.9087670 0 0 0
Ti 3.7851600 3.7851500 1.9087670 0 0 0
Ti 3.7851600 0.000 1.9087670 0 0 0
Ti 0.000 3.7851500 1.9087670 0 0 0
Ti 1.8987801 1.9072538 6.6653189
Ti 5.6847274 5.6910109 6.6668078
Ti 5.6829787 1.9073371 6.6660252
Ti 1.8988482 5.6908822 6.6673040
Ti 7.5556487 1.8925750 4.2620477
Ti 3.7707991 5.6777250 4.2626203
Ti 3.7706326 1.8925750 4.2612651
Ti 7.5563300 5.6777250 4.2619331
Ti 1.8209799 0.0147848 8.9752324
Ti 5.6042776 3.7983526 8.9766449
Ti 5.6063519 0.0134524 8.9757859
Ti 1.8188148 3.7978378 8.9763395
O 7.5578290 0.000 3.8386641
O 3.7728582 3.7851500 3.8379196
O 3.7728658 0.000 3.8383777
O 7.5578214 3.7851500 3.8381296
O 2.0533736 1.9066709 8.6237139
O 5.8371104 5.6904280 8.6250500
O 5.8301987 1.9065346 8.6250309
O 2.0455686 5.6908670 8.6248591
O 7.5448913 1.9081774 6.2507347
O 3.7603899 5.6924947 6.2503530
O 3.7599887 1.9082834 6.2488260
O 7.5457165 5.6921388 6.2497422
O 1.8925800 0.000 1.5017606 0 0 0
O 5.6777400 3.7851500 1.5017606 0 0 0
O 5.6777400 0.000 1.5017606 0 0 0
O 1.8925800 3.7851500 1.5017606 0 0 0
O 1.7713489 0.0137931 7.0572842
O 5.5548131 3.7984964 7.0573797
O 5.5558351 0.0131875 7.0575705
O 1.7694639 3.7983299 7.0573415
O 0.000 1.8925750 2.3162697 0 0 0
O 3.7851600 5.6777250 2.3162697 0 0 0
O 3.7851600 1.8925750 2.3162697 0 0 0
O 0.000 5.6777250 2.3162697 0 0 0
O 1.8768640 1.8913335 4.6819764
O 5.6628340 5.6747953 4.6816710
O 5.6621754 1.8903645 4.6819191
O 1.8775453 5.6755599 4.6822055
O 0.1607103 0.0185624 9.5272860
O 3.9456886 3.8013277 9.5290611
O 3.9459006 0.0124531 9.5278586
O 0.1607179 3.7978681 9.5300537
C 3.3681670 3.6634367 11.7587988
H 3.9107122 2.8615381 11.2166472
H 3.2707791 3.2800956 12.8197770
H 4.0867365 4.5064364 11.8259000
C 2.1131000 4.0648547 11.0384011
H 1.4171240 3.1988251 11.0020987
H 1.5828076 4.8499215 11.6216489
K_POINTS {automatic}
3 3 1 1 1 0
CELL_PARAMETERS {alat}
1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 2.5213822
calculation = 'relax'
restart_mode = 'from_scratch'
prefix = 'anatase001-2x2-4'
tstress = .false
Re: [Pw_forum] Problems computing cholensky
Hi,
Thanks all for the response. I tried to run Will DeBenedetti's script for his
anatase (001) slab and the calculation runs without an error (on 4 nodes and 20
cores per node). I don't understand though why his script does run and mine
does not. Does anybody has an idea about this?
I also tried to add 'ndiag=1' for some of my scripts like Mostafa Youssef
suggested, but unfortunately without succes.
Somebody at my departement suggested to try and run it on 1 node with 20 cores.
For some reason this does work. This will probably not be enough power to
complete the calculation, but I don't get the error 'problems computing
cholensky'. Does anybody have a suggestion why it does work on 1 node with 20
cores, but fails when I try to increase my nodes? (except when I try to run
Will's script)
Thanks in advance,
Laurens Siemons
Van: pw_forum-boun...@pwscf.org <pw_forum-boun...@pwscf.org> namens Paolo
Giannozzi <p.gianno...@gmail.com>
Verzonden: zondag 25 februari 2018 8:33
Aan: PWSCF Forum
Onderwerp: Re: [Pw_forum] Problems computing cholensky
You can use cell_parameters together with A or celldm(1).
On Sat, Feb 24, 2018 at 8:53 PM, Manu Hegde
<mhe...@uwaterloo.ca<mailto:mhe...@uwaterloo.ca>> wrote:
Hi,
I do not know much about your system but looking quickly into the crystal
structure there is something that might be causing problem. Looks like you have
set ibrav=0, in that case you have to use card cell_parameters. A=xx not
required. Also double check ypur system with xcrysden before starting the
calculations.
Manu
(SFU)
On Fri, Feb 23, 2018 at 10:19 AM, <elch...@auth.gr<mailto:elch...@auth.gr>>
wrote:
Hello Laurens Siemons,
Although I am not one of the experts, I had the same problem in one of
the scf runs I was doing for a GW calculation. Because of the high
number of bands and ecutwfc that I needed to use and in order to get
any results, I had to run the simulation on 100 cores. The strange
thing for me also was that the first one I tried run, but then nothing
again. After a few weeks of trying I was notified by our cluster
services that I should not use more than 60 cores as the I/O
operations that are done by QE were too high and the disk could not
cope. I gave up GW since then, but if there is a solution to this
problem, I would like to hear it too :S
Eleni
Quoting Laurens Siemons
<laurenssiem...@hotmail.be<mailto:laurenssiem...@hotmail.be>>:
> Dear all,
>
>
> I'm a master student chemistry and I'm using QE (v. 6.1) for a relax
> calculation of a rutile 101 slab with a vacuum above it.
>
> I'm getting the famous error:
>
>
>
> %%
> Error in routine cdiaghg (161):
> problems computing cholesky
>
> %%
>
> I've read almost every related topic on the forum that I could find
> and I tried a lot already to overcome this, like:
> - changing values for ecutwfc and ecutrho
> - changing mixing_beta
> - changing functionals
> - Tried to run the calcualtion with other input files (anatase 101, 001...)
> - Changed diagonalization to 'cg' (In this case it calculates some
> itterations but then crashes with the error: 'Error in routine
> c_bands (1): >> too many bands are not converged')
>
> Nothing seems to help and I'm out of options... I even tried to run
> a calculation of my predecessor (that has succeeded in the past) but
> this also failed (he used an older version of QE though...).
>
> I'm postig my input file at the end here and I really hope somebody
> can help me.
>
> Kind Regards,
> Laurens Siemons
>
>
> calculation = 'relax'
> restart_mode = "from_scratch",
> prefix = "testen",
> pseudo_dir =
> '/data/antwerpen/204/vsc20442/pseudo/pslibrary.1.0.0/wc/PSEUDOPOTENTIALS'
> outdir = '/data/antwerpen/204/vsc20442'
> nstep = 100
> /
>
> ibrav = 0
> A =4.59631
> nat = 36
> ntyp = 2
> ecutwfc = 60
> ecutrho = 600
> /
>
> electron_maxstep = 300
> mixing_beta = 0.10
> conv_thr = 1.0d-8
> mixing_mode = 'local-TF'
> diago_thr_init = 1e-4
> /
>
> ion_dynamics = 'bfgs'
> ion_positions = 'default'
> /
> CELL_PARAMETERS {alat}
> 1.000 0.000 0.640859733133753
> 0.000 2.000 0.000
> 0.000 0.000 3.845158398802518
> ATOMIC_SPECIES
>O 15.99900 O.wc-n-kjpaw_psl.1.0.0.UPF
> Ti 47.86700 Ti.wc-spn-kjpaw_psl.1.0.0.UPF
> ATOMIC_POSITIONS {crystal}
> Ti -0.000 -0.000 0.075 0 0 0
> Ti -0.0
[Pw_forum] Problems computing cholensky
Dear all,
I'm a master student chemistry and I'm using QE (v. 6.1) for a relax
calculation of a rutile 101 slab with a vacuum above it.
I'm getting the famous error:
%%
Error in routine cdiaghg (161):
problems computing cholesky
%%
I've read almost every related topic on the forum that I could find and I tried
a lot already to overcome this, like:
- changing values for ecutwfc and ecutrho
- changing mixing_beta
- changing functionals
- Tried to run the calcualtion with other input files (anatase 101, 001...)
- Changed diagonalization to 'cg' (In this case it calculates some itterations
but then crashes with the error: 'Error in routine c_bands (1): >> too many
bands are not converged')
Nothing seems to help and I'm out of options... I even tried to run a
calculation of my predecessor (that has succeeded in the past) but this also
failed (he used an older version of QE though...).
I'm postig my input file at the end here and I really hope somebody can help me.
Kind Regards,
Laurens Siemons
calculation = 'relax'
restart_mode = "from_scratch",
prefix = "testen",
pseudo_dir =
'/data/antwerpen/204/vsc20442/pseudo/pslibrary.1.0.0/wc/PSEUDOPOTENTIALS'
outdir = '/data/antwerpen/204/vsc20442'
nstep = 100
/
ibrav = 0
A =4.59631
nat = 36
ntyp = 2
ecutwfc = 60
ecutrho = 600
/
electron_maxstep = 300
mixing_beta = 0.10
conv_thr = 1.0d-8
mixing_mode = 'local-TF'
diago_thr_init = 1e-4
/
ion_dynamics = 'bfgs'
ion_positions = 'default'
/
CELL_PARAMETERS {alat}
1.000 0.000 0.640859733133753
0.000 2.000 0.000
0.000 0.000 3.845158398802518
ATOMIC_SPECIES
O 15.99900 O.wc-n-kjpaw_psl.1.0.0.UPF
Ti 47.86700 Ti.wc-spn-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {crystal}
Ti -0.000 -0.000 0.075 0 0 0
Ti -0.000 -0.000 0.408
Ti -0.000 0.500 0.2416667
Ti -0.000 -0.000 0.2416667
Ti -0.000 0.500 0.075 0 0 0
Ti -0.000 0.500 0.408
Ti 0.500 0.250 0.075 0 0 0
Ti 0.500 0.250 0.408
Ti 0.500 0.750 0.2416667
Ti 0.500 0.250 0.2416667
Ti 0.500 0.750 0.075 0 0 0
Ti 0.500 0.750 0.408
O 0.3043030 0.1521515 0.0242828 0 0 0
O 0.3043030 0.1521515 0.35761616667
O 0.3043030 0.6521515 0.1909495
O 0.3043030 0.1521515 0.1909495
O 0.3043030 0.6521515 0.0242828 0 0 0
O 0.3043030 0.6521515 0.35761616667
O 0.6956970 0.3478485 0.4590505
O 0.6956970 0.3478485 0.2923838
O 0.6956970 0.8478485 0.12571716667 0 0 0
O 0.6956970 0.3478485 0.12571716667 0 0 0
O 0.6956970 0.8478485 0.4590505
O 0.6956970 0.8478485 0.2923838
O 0.8043030 0.0978485 0.0242828 0 0 0
O 0.8043030 0.0978485 0.35761616667
O 0.8043030 0.5978485 0.1909495
O 0.8043030 0.0978485 0.1909495
O 0.8043030 0.5978485 0.0242828 0 0 0
O 0.8043030 0.5978485 0.35761616667
O 0.1956970 0.4021515 0.12571716667 0 0 0
O 0.1956970 0.4021515 0.4590505
O 0.1956970 0.9021515 0.2923838
O 0.1956970 0.4021515 0.2923838
O 0.1956970 0.9021515 0.12571716667 0 0 0
O 0.1956970 0.9021515 0.4590505
K_POINTS {automatic}
4 4 6 1 1 1
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