Re: [Pw_forum] Problems computing cholensky

[Paolo Giannozzi]

On Fri, Feb 23, 2018 at 7:19 PM,  wrote:

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.
>

 with pw.x or with other codes? in the former case: pw.x can run without
any significant I/O. For recent versions, it is the default.


> Eleni
>
>
> Quoting Laurens Siemons :
>
> > 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   

Re: [Pw_forum] Problems computing cholensky

[Paolo Giannozzi]

On Mon, Feb 26, 2018 at 10:26 AM, Laurens Siemons  wrote:


>  Does anybody have a suggestion why it does work on 1 node with 20 cores,
> but fails when I try to increase my nodes?
>

The final results do not depend upon the number of processors (modulo minor
numerical differences, within the convergence threshold) but intermediate
results may depend, due to a different starting point and to small
numerical differences. This may unfortunately lead some calculations that
are "on the brink" to fail. I have no evidence that this is related to a
bug or to any other easily solvable problem.

The "Cholesky" problem signals that the overlap matrix is not positive
definite (has a zero or negative eigenvalue). When it happens, it is
invariably due either to a badly wrong structure (not the case here) or to
USPP/PAW with small negative values of augmentation charges. It is a known
problem and there is no simple solution available.

Paolo

Thanks in advance,
>
> Laurens Siemons
>
>
> --
> *Van:* pw_forum-boun...@pwscf.org  namens
> Paolo Giannozzi 
> *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  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,  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 :
>
> > 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/PSEU
> DOPOTENTIALS'
> >   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  

[Pw_forum] toothed and noisy bands

[Riemann Derakhshan]

Dear all,

Hope you are doing well.

During my calculations, I've faced a strange thing. My considered system is
a 2D sheet which is placed on TiO2 surface. I've calculated a band
structure of the mentioned system and in the absence of spin-orbit
interaction everything was normal but after turning the spin-orbit
interaction on, bands above Fermi level becomes toothed and noisy while
bands in below of Fermi level are normal. At the end, I should mention that
in my calculations in the presence of spin-orbit interaction the number of
bands is about 600 ( nbnd  = 580). Would you do me a favor by providing me
with a guidance to fix this issue? it would be a great help and I'll
appreciate it.

Bests,
Riemann


-- 
Physics Department of Damghan University
Tel : +98 938 903 6759
P.O.Box:36716-41167
Damghan, Iran
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Re: [Pw_forum] calculating atoms oxidation states

[pboulet]

Hello Daniel,

Thanks for your answer. I have the value for z=0:
P =   0.049  (mod  14.7398000)  (e/Omega).bohr

Pascal

> Le 27 févr. 2018 à 07:09, Daniel Stoeffler 
>  a écrit :
> 
> Hello Pascal,
> 
> Don't forget the polarization quantum : the jump at z=0.5 looks like coming 
> from a quantum of polarization and can be removed (I mean by adding 1 to your 
> numbers for z > 0.5). In principle, variation of P should remain small 
> between points on your path.
> 
> Why don't you have the value for z=0 ?
> 
> Best wishes,
> 
> Daniel
> 
>  
>  
> Le 2018-02-26 22:13, pboulet a écrit :
> 
>> Dear all,
>>  
>> Does anyone have tried to used Jiang, Levchenko and Rappe’s method to 
>> calculate oxidation state of atoms?  (Phys. Rev Letters, 108, 2012, 166403.
>>  
>> In brief, the formula is N=V/e \Delta(P) x R /R^2,
>> where N, V, e, \Delta(P) and R are the oxidation state, cell volume, 
>> electron charge, change in polarisation and lattice vector, respectively. 
>> \Delta(P) x R corresponds to the dot product.
>> The idea is just to displace an atom along a path traversing the cell in a 
>> way that the atom goes from its location to that in the next cell.
>>  
>>  I have tried with the PbTiO3 example of QE for the calculation of 
>> polarization via the Berry phase. If I am right I should obtain +2 as an 
>> oxidation state. 
>>  
>> I have displaced the Pb atom (crystal position at 0. 0. 0.) along the z axis 
>> from 0 to 1. 
>>  
>> The enclosed picture depicts N versus z for z=0..1. I used the polarization 
>> P given by QE in units of (e/Omega).bohr, since it is similar to the formula 
>> above.
>> I have just divided P by z since Delta(P) and R are collinear… and I guess 
>> V/e of the formula cancels with e/Omega… I am not sure of these assumptions, 
>> however…
>>  
>> First the variation is -2 instead of +2. In addition the evolution is not 
>> smooth and the missing points on the curve are calculated to be negative. I 
>> have removed them but it is nonsense to me. 
>>  
>> Does anyone know what is wrong?
>>  
>> Thank you for your suggestions,
>>  
>> Pascal
>>  
>>  
>> 
>>  
>>  
>>  
>>  
>>  
>>  
>>  
>> 
>> Pascal Boulet
>> —
>> Professor in computational chemistry - DEPARTMENT OF CHEMISTRY
>> Director of the Madirel laboratory
>> Aix-Marseille University - Avenue Escadrille Normandie Niemen - F-13013 
>> Marseille - FRANCE
>> Tél: +33(0)4 13 55 18 10 et +33(0)4 13 55 18 19 - Fax : +33(0)4 13 55 18 50
>> Email : pascal.bou...@univ-amu.fr 
>>  
>>  
>> 
>> 
>> 
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[Pw_forum] 答复: 答复: 答复: PW input ibrav = 0

[Zhou Jianqiang]

Thank you very much for your information, and I will discuss this issue with my 
boss (Matteo Calandra) and see what to do next.


Cheers,

Sky


--
Jianqiang (Sky) ZHOU
European Theoretical Spectroscopy Facility
Institut des NanoSciences de Paris (INSP)
Sorbonne Université - Case 840 - 4 place Jussieu
Barre 2232, étage 2, pièce 11
75005 PARIS
http://etsf.polytechnique.fr/People/Sky
tel : +33 (0)1 69 33 44 85



发件人: pw_forum-boun...@pwscf.org  代表 Pietro Delugas 

发送时间: 2018年2月27日 6:21
收件人: PWSCF Forum
主题: Re: [Pw_forum] 答复: 答复: PW input ibrav = 0

It runs.  but you are still using two pseudopotentials made for different 
functionals and it is wrong.

Il 26 feb 2018 10:29 PM, Zhou Jianqiang  ha scritto:

Thank you very much! By changing the order, the code finally runs!


All the best,


Sky


--
Jianqiang (Sky) ZHOU
European Theoretical Spectroscopy Facility
Institut des NanoSciences de Paris (INSP)
Sorbonne Université - Case 840 - 4 place Jussieu
Barre 2232, étage 2, pièce 11
75005 PARIS
http://etsf.polytechnique.fr/People/Sky
tel : +33 (0)1 69 33 44 85



发件人: pw_forum-boun...@pwscf.org  代表 Pietro Delugas 

发送时间: 2018年2月26日 19:36
收件人: PWSCF Forum
主题: Re: [Pw_forum] 答复: PW input ibrav = 0


The order is different and there is Hubbard_U(1) set in both inputs. In one 
case refering to to Ti d orbitals in the other case it is refering to Se; for 
which the program should actually stop, because it is not no l is defined and 
the program sets l the index to -1.
The program is possibly writing something out of bounds and causing the check 
on dft to fail.


Il 26 feb 2018 6:24 PM, Lorenzo Paulatto  ha scritto:
It looks like you are using two pseudopotentials with different functionals, 
this is not allowed and will cause an error independently of the ibrav value. I 
don't think changing the order of the elements can make a difference, this is 
probably a PEBKAC. Take a consistent choice of pseudopotentials and you will 
not have this problem anymore.

--
Lorenzo Paulatto
Written on a virtual keyboard with real fingers

On Feb 26, 2018 17:45, "Zhou Jianqiang" 
> wrote:

Dear Paolo,


I really did not find anything else different... Here I attach the result from 
a vimdiff.


Many thanks!


Sky


--
Jianqiang (Sky) ZHOU
European Theoretical Spectroscopy Facility
Institut des NanoSciences de Paris (INSP)
Sorbonne Université - Case 840 - 4 place Jussieu
Barre 2232, étage 2, pièce 11
75005 PARIS
http://etsf.polytechnique.fr/People/Sky
tel : +33 (0)1 69 33 44 85



发件人: pw_forum-boun...@pwscf.org 
> 代表 Paolo 
Giannozzi >
发送时间: 2018年2月26日 12:45
收件人: PWSCF Forum
主题: Re: [Pw_forum] PW input ibrav = 0

The error you get cannot come from  ibrav, a, c, cell_parameter. Please do a 
"diff" of the two inputs and you will find something else.

On Mon, Feb 26, 2018 at 11:48 AM, Zhou Jianqiang 
> wrote:

Dear Developers,


I have a problem when setting ibrav = 0. I did two tests and the only 
differences between the two are:

  1.
 ibrav=  4,
 celldm(1)=6.6893,
 celldm(3)=1.697,

2.
 ibrav =  0,
 A = 3.53600 ,

CELL_PARAMETERS {alat}
  0.866025403784439  -0.500   0.000
  0.000   1.000   0.000
  0.000   0.000   1.697963800904977

The first test can run, but the second run reports error message:

 Error in routine set_dft_from_name (1):
  conflicting values for icorr


Can someone tell me the reason? I am using " Program PWSCF v.6.2".

Many thanks!

Sky



--
Jianqiang (Sky) ZHOU
European Theoretical Spectroscopy Facility
Institut des NanoSciences de Paris (INSP)
Sorbonne Université - Case 840 - 4 place Jussieu
Barre 2232, étage 2, pièce 11
75005 PARIS

Re: [Pw_forum] 答复: 答复: PW input ibrav = 0

[Pietro Delugas]

It runs.  but you are still using two pseudopotentials made for different functionals and it is wrong. Il 26 feb 2018 10:29 PM, Zhou Jianqiang  ha scritto:

Thank you very much! By changing the order, the code finally runs!


All the best,


Sky





--
Jianqiang (Sky) ZHOU

European Theoretical Spectroscopy Facility
Institut des NanoSciences de Paris (INSP)

Sorbonne Université - Case 840 - 4 place Jussieu


Barre 2232, étage 2, pièce 11
75005 PARIS

http://etsf.polytechnique.fr/People/Sky
tel : +33 (0)1 69 33 44 85






发件人: pw_forum-bounces@pwscf.org  代表 Pietro Delugas 
发送时间: 2018年2月26日 19:36
收件人: PWSCF Forum
主题: Re: [Pw_forum] 答复: PW input ibrav = 0
 





The order is different and there is Hubbard_U(1) set in both inputs. In one case refering to to Ti d orbitals in the other case it is refering to Se; for which the program should actually stop, because it is not no l is defined and the program sets l the
 index to -1.
The program is possibly writing something out of bounds and causing the check on dft to fail. 


Il 26 feb 2018 6:24 PM, Lorenzo Paulatto  ha scritto:

It looks like you are using two pseudopotentials with different functionals, this is not allowed and will cause an error independently of the ibrav value. I don't think changing the order of the elements can make a difference, this is probably
 a PEBKAC. Take a consistent choice of pseudopotentials and you will not have this problem anymore. 

-- 
Lorenzo Paulatto
Written on a virtual keyboard with real fingers


On Feb 26, 2018 17:45, "Zhou Jianqiang"  wrote:



Dear Paolo,


I really did not find anything else different... Here I attach the result from a vimdiff.




Many thanks!


Sky





--
Jianqiang (Sky) ZHOU

European Theoretical Spectroscopy Facility
Institut des NanoSciences de Paris (INSP)

Sorbonne Université - Case 840 - 4 place Jussieu


Barre 2232, étage 2, pièce 11
75005 PARIS

http://etsf.polytechnique.fr/People/Sky
tel : 
+33 (0)1 69 33 44 85






发件人:
pw_forum-bounces@pwscf.org  代表 Paolo Giannozzi 
发送时间: 2018年2月26日 12:45
收件人: PWSCF Forum
主题: Re: [Pw_forum] PW input ibrav = 0
 


The error you get cannot come from  ibrav, a, c, cell_parameter. Please do a "diff" of the two inputs and you will find something else.


On Mon, Feb 26, 2018 at 11:48 AM, Zhou Jianqiang  wrote:



Dear Developers,


I have a problem when setting ibrav = 0. I did two tests and the only differences between the two are:
 
 ibrav=  4,
 celldm(1)=6.6893,
 celldm(3)=1.697,


2. 
 ibrav =  0,
 A = 3.53600 ,



CELL_PARAMETERS {alat}
  0.866025403784439  -0.500   0.000
  0.000   1.000   0.000
  0.000   0.000   1.697963800904977


The first test can run, but the second run reports error message:


 Error in routine set_dft_from_name (1):
  conflicting values for icorr


Can someone tell me the reason? I am using " Program PWSCF v.6.2".

Many thanks!

Sky 







--
Jianqiang (Sky) ZHOU

European Theoretical Spectroscopy Facility
Institut des NanoSciences de Paris (INSP)

Sorbonne Université - Case 840 - 4 place Jussieu


Barre 2232, étage 2, pièce 11
75005 PARIS

http://etsf.polytechnique.fr/People/Sky
tel : 
+33 (0)1 69 33 44 85





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-- 




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












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Re: [Pw_forum] calculating atoms oxidation states

[Daniel Stoeffler]

 

Hello Pascal, 

Don't forget the polarization quantum : the jump at
z=0.5 looks like coming from a quantum of polarization and can be
removed (I mean by adding 1 to your numbers for z > 0.5). In principle,
variation of P should remain small between points on your path. 

Why
don't you have the value for z=0 ? 

Best wishes, 

Daniel 

Le
2018-02-26 22:13, pboulet a écrit : 

> Dear all, 
> 
> Does anyone have
tried to used Jiang, Levchenko and Rappe's method to calculate oxidation
state of atoms? (Phys. Rev Letters, 108, 2012, 166403. 
> 
> In brief,
the formula is N=V/e Delta(P) x R /R^2, 
> where N, V, e, Delta(P) and R
are the oxidation state, cell volume, electron charge, change in
polarisation and lattice vector, respectively. Delta(P) x R corresponds
to the dot product. 
> The idea is just to displace an atom along a path
traversing the cell in a way that the atom goes from its location to
that in the next cell. 
> 
> I have tried with the PbTiO3 example of QE
for the calculation of polarization via the Berry phase. If I am right I
should obtain +2 as an oxidation state. 
> 
> I have displaced the Pb
atom (crystal position at 0. 0. 0.) along the z axis from 0 to 1. 
> 
>
The enclosed picture depicts N versus z for z=0..1. I used the
polarization P given by QE in units of (e/Omega).bohr, since it is
similar to the formula above. 
> I have just divided P by z since
Delta(P) and R are collinear… and I guess V/e of the formula cancels
with e/Omega… I am not sure of these assumptions, however… 
> 
> First
the variation is -2 instead of +2. In addition the evolution is not
smooth and the missing points on the curve are calculated to be
negative. I have removed them but it is nonsense to me. 
> 
> Does
anyone know what is wrong? 
> 
> Thank you for your suggestions, 
> 
>
Pascal 
> 
> Pascal Boulet 
> -- 
> _Professor in computational
chemistry - DEPARTMENT OF CHEMISTRY_ 
> 
> Director of the Madirel
laboratory 
> Aix-Marseille University - Avenue Escadrille Normandie
Niemen - F-13013 Marseille - FRANCE 
> Tél: +33(0)4 13 55 18 10 et
+33(0)4 13 55 18 19 - Fax : +33(0)4 13 55 18 50 
> Email :
pascal.bou...@univ-amu.fr 
> 
>
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