[Pw_forum] Problem with ld1.x

[elchatz]

Hello all,

I am having a hard time understanding this error in ld1.x

   
%%
  Error in routine ld1_setup (4):
  no all electron for this ps
   
%%

I am trying to create a US pseudopotential for Mo. The all-electron  
runs ok on its own with the following configuration:

  
title='Mo',
zed=42.,
rel=1,
config='[Kr] 4d5 5s1',
iswitch=1,
dft='PZ'
/

However, when I add the cards for PP generation, it fails giving the  
previous error.

I copied the configuration from pslibrary, but I have added the Mo 3d  
states in the valence.





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Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elch...@auth.gr - tel:+30 2310 998109

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Re: [Pw_forum] Problem with ld1.x

[elchatz]

Thank you,

I have tried before with atomPAW, but I have given that up. It seems  
that there is more experience shared with ld1.x in the literature so I  
thought I should give it a try.

So, to be clear, when you say all-electron list you mean this:

config='[Kr] 4d5 5s1'

?




Quoting Lorenzo Paulatto :

> it means that one of the orbitals you put in the pseudo configuration,
> was not computed in the all-electron calculation. Every label that
> appears in the list of the pseudo-orbitals must also appear in the
> all-electron list, if for some reason it cannot be computed (i.e.
> because it is not bound) you can specify negative occupation to skip it.
>
> hth
>
> p.s. Molybdenum is a really hard case, I recommend:
> 1. you use a pseudo from an online library instead, unless you have a
> really good reason (pslibrary, GBRV,..)
> 2. you start from an existing input file, i.e. from the pslibrary
> 3. you brew a big cup of coffee
> 4. you test it properly
>
> On 26/01/18 14:07, elch...@auth.gr wrote:
>> Hello all,
>>
>> I am having a hard time understanding this error in ld1.x
>>
>>
>> %%
>>Error in routine ld1_setup (4):
>>no all electron for this ps
>>
>> %%
>>
>> I am trying to create a US pseudopotential for Mo. The all-electron
>> runs ok on its own with the following configuration:
>>
>>
>>  title='Mo',
>>  zed=42.,
>>  rel=1,
>>  config='[Kr] 4d5 5s1',
>>  iswitch=1,
>>  dft='PZ'
>> /
>>
>> However, when I add the cards for PP generation, it fails giving the
>> previous error.
>>
>> I copied the configuration from pslibrary, but I have added the Mo 3d
>> states in the valence.
>>
>>
>>
>>
>>
>
> --
> Lorenzo Paulatto - Paris
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Dr. Eleni Chatzikyriakou
Computational Physics lab
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elch...@auth.gr - tel:+30 2310 998109

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Re: [Pw_forum] Problem with ld1.x

[elchatz]

Ok, now I get it. I needed to include a 5p0 state that the pslibrary  
suggests in the all-electron list.

The calculation has been completed with just one warning:

Warning: n=3, l=2 expected 0 nodes, found 1
Setting wfc to zero for this iteration
(This warning will only be printed once per wavefunction)


So, one final question: If I need to include an unoccupied 3d state in  
the pseudo-orbitals list, even though I already have the Kr 3d10, does  
that need to be mentioned explicitly in the all-electron list too?







Quoting Lorenzo Paulatto :

> it means that one of the orbitals you put in the pseudo configuration,
> was not computed in the all-electron calculation. Every label that
> appears in the list of the pseudo-orbitals must also appear in the
> all-electron list, if for some reason it cannot be computed (i.e.
> because it is not bound) you can specify negative occupation to skip it.
>
> hth
>
> p.s. Molybdenum is a really hard case, I recommend:
> 1. you use a pseudo from an online library instead, unless you have a
> really good reason (pslibrary, GBRV,..)
> 2. you start from an existing input file, i.e. from the pslibrary
> 3. you brew a big cup of coffee
> 4. you test it properly
>
> On 26/01/18 14:07, elch...@auth.gr wrote:
>> Hello all,
>>
>> I am having a hard time understanding this error in ld1.x
>>
>>
>> %%
>>Error in routine ld1_setup (4):
>>no all electron for this ps
>>
>> %%
>>
>> I am trying to create a US pseudopotential for Mo. The all-electron
>> runs ok on its own with the following configuration:
>>
>>
>>  title='Mo',
>>  zed=42.,
>>  rel=1,
>>  config='[Kr] 4d5 5s1',
>>  iswitch=1,
>>  dft='PZ'
>> /
>>
>> However, when I add the cards for PP generation, it fails giving the
>> previous error.
>>
>> I copied the configuration from pslibrary, but I have added the Mo 3d
>> states in the valence.
>>
>>
>>
>>
>>
>
> --
> Lorenzo Paulatto - Paris
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Computational Physics lab
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elch...@auth.gr - tel:+30 2310 998109

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Re: [Pw_forum] Problem with ld1.x

[elchatz]

Ok, I am closer to understanding the difference between projectors,  
unoccupied states and bound/unbound states.

So, I have tried different options and I can't seem to make a nodeless  
PS for the 3d state:

---
  Warning: n=3, l=2 expected 0 nodes, found 1
Setting wfc to zero for this iteration
(This warning will only be printed once per wavefunction)
---

And since I see in my output the energy and special extension  
'peculiarities' of the 3d state as in Paolo Giannozzi's tutorial:


s(1S/1S) =  1.00   =   0.0352   =0.0017  r(max) =   0.0229
s(2S/2S) =  1.00   =   0.1539   =0.0279  r(max) =   0.1303
s(2P/2P) =  1.00   =   0.1340   =0.0220  r(max) =   0.1041
s(3S/3S) =  1.00   =   0.4297   =0.2116  r(max) =   0.3819
s(3P/3P) =  1.00   =   0.4312   =0.2165  r(max) =   0.3771
s(4S/4S) =  1.00   =   1.1027   =1.3794  r(max) =   0.9874
s(4P/4P) =  1.00   =   1.2284   =1.7316  r(max) =   1.0643
s(3D/3D) =  1.00   =   0.4155   =0.2077  r(max) =   0.3206
s(4D/4D) =  1.00   =   1.7989   =3.9209  r(max) =   1.3496
s(5S/5S) =  1.00   =   3.1133   =   10.9492  r(max) =   2.7178
s(5P/5P) =  1.00   =   3.8857   =   17.1277  r(max) =   3.3613

  1 0 1S 1( 2.00) -1455.6680  -727.8340-19805.3703
  2 0 2S 1( 2.00)  -206.2934  -103.1467 -2806.7649
  2 1 2P 1( 6.00)  -184.6412   -92.3206 -2512.1715
  3 0 3S 1( 2.00)   -35.6967   -17.8483  -485.6778
  3 1 3P 1( 6.00)   -28.6019   -14.3010  -389.1492
  4 0 4S 1( 2.00)-5.4732-2.7366   -74.4663
  4 1 4P 1( 6.00)-3.5649-1.7825   -48.5034
  3 2 3D 1(10.00)   -17.0205-8.5102  -231.5751
  4 2 4D 1( 4.00)-0.9536-0.4768   -12.9742
  5 0 5S 1( 1.00)-0.8298-0.4149   -11.2899
  5 1 5P 1( 0.00)-0.5082-0.2541-6.9150
-

So, I was wondering how a multiple projector configuration would look  
like in the input file. Do you have any examples?


Regards,

Eleni




Quoting Lorenzo Paulatto :

> On 26/01/18 14:54, elch...@auth.gr wrote:
>>
>> So, one final question: If I need to include an unoccupied 3d state in
>> the pseudo-orbitals list, even though I already have the Kr 3d10, does
>> that need to be mentioned explicitly in the all-electron list too?
>>
>
> No, but if you put an unoccupied 3d, when the ground state configuration
> has a 3d with 10 electrons, you're not going to get much further. If you
> want to specify an additional empty d orbital, it will have to be 4d,
> you'll have to specify it as "4d-1" in config (i.e. reserve the name 4d,
> but do not compute it) and like this is the pseudo configuration:
>
> 4D 3 2  0.00 nrg rcut rcutus
>
> Where rng is important (because there is no eigenvalue), and "3 2" means
> that this state, while called 4D, is going to be without nodes
>
> --
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Computational Physics lab
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elch...@auth.gr - tel:+30 2310 998109

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Re: [Pw_forum] Problem with ld1.x

[elchatz]

Dear Lorenzo Paulatto,

The point of putting the 3d state into the valence is so that I can  
perform electronic minimization with a core-hole.

I am using two starting configurations provided by pslibrary. One of  
them is actually the one you suggested.

--

  
title='Mo',
zed=42.,
rel=1,
config='[Ar] 3d10 4s2 4p6 4d5.0 5s1 5p0',
iswitch=3,
dft='PZ',
nld=3
  /
  
pseudotype=3,
file_pseudopw='Mo.spn-rrkjus_psl.UPF',
lloc=-1,  ! Specifies which l component is chosen as the local  
component of the pseudopotential
rcloc=1.4, ! Matching radius for local pseudopotential
which_augfun='PSQ',
rmatch_augfun_nc=.true.,
nlcc=.true.,
new_core_ps=.true.,
rcore=1.0,  ! Matching radius (a.u.) for the smoothing of the core charge.
tm=.true.
  /
7
4S  1  0  2.00  0.00  0.95  1.30  0.0
5S  2  0  1.00  0.00  0.95  1.30  0.0
4P  2  1  6.00  0.00  0.95  1.70  0.0
5P  3  1  0.00  0.00  0.95  1.70  0.0
3D  3  2 10.00  0.00  0.95  1.30  0.0
4D  3  2  5.00  0.00  0.95  1.70  0.0
4D  3  2 -2.00  0.30  0.95  1.70  0.0
---






Quoting Lorenzo Paulatto :

> On 30/01/18 10:52, elch...@auth.gr wrote:
>> So, I have tried different options and I can't seem to make a nodeless
>> PS for the 3d state:
>>
>> s(3D/3D) =  1.00   =   0.4155   =0.2077  r(max) =   0.3206
>
> I do not understand your question, the 3d state is very deep in energy,
> already nodeless in the all-electron calculation, very localized. It is
> pointless to put it in valence, and difficult to make it *not* nodeless.
>
> Please attach your input file, if you want a more meaningful answer.
> Also, I repeat, you should try to start from an existing input
> configuration. You can find the input at the beginning of UPF files
> generated by ld1, like this one, with semi-core in valence:
> http://www.quantum-espresso.org/wp-content/uploads/upf_files/Mo.pbe-spn-rrkjus_psl.0.2.UPF
>
>
> --
> Lorenzo Paulatto - Paris
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Computational Physics lab
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elch...@auth.gr - tel:+30 2310 998109

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Re: [Pw_forum] Problem with ld1.x

[elchatz]

Dear Giuseppe Mattioli,

It was my impression that if I put the Mo 3d state in the valence and  
then somehow remove one electron during minimization, I could relax  
the core hole too. I guess this is not possible.

I will probably take your advice on all-electron calculations.


Thank you.


Quoting Giuseppe Mattioli :

> Dear Eleni
>
>> The point of putting the 3d state into the valence is so that I can
>> perform electronic minimization with a core-hole.
>
> I don't understand this statement. In plane wave calculations you
> cannot place a core hole in a valence shell. You can embed the core
> hole within the pseudopotential instead. It is quite easy in the case
> of the K edge (1s core hole). You can find a lot of "1sstar"
> preudopotential in the online library, generated for XPS calculations.
> It is not at all straightforward in the case of a shell with l>0,
> where a proper treatment would imply a fully relativistic (i.e., with
> spin-orbit coupling) all-electron calculation.
> HTH
> Giuseppe
>
> Quoting elch...@auth.gr:
>
>> Dear Lorenzo Paulatto,
>>
>> The point of putting the 3d state into the valence is so that I can
>> perform electronic minimization with a core-hole.
>>
>> I am using two starting configurations provided by pslibrary. One of
>> them is actually the one you suggested.
>>
>> --
>>
>>   
>> title='Mo',
>> zed=42.,
>> rel=1,
>> config='[Ar] 3d10 4s2 4p6 4d5.0 5s1 5p0',
>> iswitch=3,
>> dft='PZ',
>> nld=3
>>   /
>>   
>> pseudotype=3,
>> file_pseudopw='Mo.spn-rrkjus_psl.UPF',
>> lloc=-1,  ! Specifies which l component is chosen as the local
>> component of the pseudopotential
>> rcloc=1.4, ! Matching radius for local pseudopotential
>> which_augfun='PSQ',
>> rmatch_augfun_nc=.true.,
>> nlcc=.true.,
>> new_core_ps=.true.,
>> rcore=1.0,  ! Matching radius (a.u.) for the smoothing of the
>> core charge.
>> tm=.true.
>>   /
>> 7
>> 4S  1  0  2.00  0.00  0.95  1.30  0.0
>> 5S  2  0  1.00  0.00  0.95  1.30  0.0
>> 4P  2  1  6.00  0.00  0.95  1.70  0.0
>> 5P  3  1  0.00  0.00  0.95  1.70  0.0
>> 3D  3  2 10.00  0.00  0.95  1.30  0.0
>> 4D  3  2  5.00  0.00  0.95  1.70  0.0
>> 4D  3  2 -2.00  0.30  0.95  1.70  0.0
>> ---
>>
>>
>>
>>
>>
>>
>> Quoting Lorenzo Paulatto :
>>
>>> On 30/01/18 10:52, elch...@auth.gr wrote:
 So, I have tried different options and I can't seem to make a nodeless
 PS for the 3d state:

 s(3D/3D) =  1.00   =   0.4155   =0.2077  r(max) =   0.3206
>>>
>>> I do not understand your question, the 3d state is very deep in energy,
>>> already nodeless in the all-electron calculation, very localized. It is
>>> pointless to put it in valence, and difficult to make it *not* nodeless.
>>>
>>> Please attach your input file, if you want a more meaningful answer.
>>> Also, I repeat, you should try to start from an existing input
>>> configuration. You can find the input at the beginning of UPF files
>>> generated by ld1, like this one, with semi-core in valence:
>>> http://www.quantum-espresso.org/wp-content/uploads/upf_files/Mo.pbe-spn-rrkjus_psl.0.2.UPF
>>>
>>>
>>> --
>>> Lorenzo Paulatto - Paris
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>>
>>
>>
>> --
>> Dr. Eleni Chatzikyriakou
>> Computational Physics lab
>> Aristotle University of Thessaloniki
>> elch...@auth.gr - tel:+30 2310 998109
>>
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>
>
>
> GIUSEPPE MATTIOLI
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> I-00015 - Monterotondo Scalo (RM)
> Mob (*preferred*) +39 373 7305625
> Tel + 39 06 90672342 - Fax +39 06 90672316
> E-mail: 
>
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[Pw_forum] Plotting phonon dispersion

[elchatz]

Hello all,

I am using ph.x to get the phonon frequencies and dynamical matrices  
for an epw.x calculation, however, I would like to plot my phonon  
dispersions from the ph.x calculation for far, as for example is shown  
in

http://epw.org.uk/Documentation/B-dopedDiamond

I am lost as to how I can do that. My ph.x file is as follows,


   prefix   = 'Si',
   epsil= .false.,
   fildyn   = 'diam.dyn',
   ldisp= .true.
   fildvscf = 'dvscf'
   nq1=6,
   nq2=6,
   nq3=1,
   tr2_ph   =  1.0d-12,
   recover = .true.
  /

Do I need to use q2r.x and matdyn.x to the files for plotting?


Thank you



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Dr. Eleni Chatzikyriakou
Computational Physics lab
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elch...@auth.gr - tel:+30 2310 998109

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Re: [Pw_forum] Plotting phonon dispersion

[elchatz]

Thank you Vahid Askarpour.

I have two questions:

a) Is there a problem if I don't specify amass?

b) I have already done this procedure using the following files:

ph.x:


   prefix   = 'Si',
   epsil= .false.,
   fildyn   = 'diam.dyn',
   ldisp= .true.
   fildvscf = 'dvscf'
   nq1=6,
   nq2=6,
   nq3=1,
   tr2_ph   =  1.0d-12,
   recover = .true.
  /

This run ok

q2r.in:

  
   fildyn='diam.dyn',
   flfrc='Si.rc'
  /

This run ok

matdyn.in:

  
 flfrc='Si.rc',
 flfrq='Si.freq',
 q_in_band_form=.true.
  /
  4
  gG 50
   X 50
   M 50
   gG 8

And I got the following error:

   
%%
  Error in routine find_bz_type (1):
  Wrong ibrav
   
%%

Is it possible that this is because I messed up the names of the  
files, or do I need to include explicitly the coordinates of the high  
symmetry points?


Regards

Eleni




Quoting Vahid Askarpour :

> Once you get all the .dyn files from the ph.x run, use the following  
> input to q2r.x to get the force constants:
>
>  
>fildyn=’Si.dyn', zasr='simple', flfrc=’Si.ifc2’
> /
>
> Then use the following input to matdyn.x:
>
> 
> asr='simple',  amass(1)= 28.0855
> flfrc=’Si.ifc2', flfrq=’Si.freq', q_in_band_form=.true.
> /
> 6  ! number of high-symmetry points
> 0.0 0.0 0.0 200
> 0.0 0.0 1.0 200
> etc.
>
> The coordinates of the high symmetry points should be in cartesian  
> coordinates. 200 points will be calculated for each segment. The  
> phonon dispersion is in the .gp output file.
>
> Cheers,
>
> Vahid
>
> Vahid Askarpour
> Department of Physics and Atmospheric Science
> Dalhousie University,
> Halifax, NS, Canada
>
>> On Feb 19, 2018, at 4:54 AM, elch...@auth.gr wrote:
>>
>> Hello all,
>>
>> I am using ph.x to get the phonon frequencies and dynamical matrices
>> for an epw.x calculation, however, I would like to plot my phonon
>> dispersions from the ph.x calculation for far, as for example is shown
>> in
>>
>> http://epw.org.uk/Documentation/B-dopedDiamond
>>
>> I am lost as to how I can do that. My ph.x file is as follows,
>>
>> 
>>   prefix   = 'Si',
>>   epsil= .false.,
>>   fildyn   = 'diam.dyn',
>>   ldisp= .true.
>>   fildvscf = 'dvscf'
>>   nq1=6,
>>   nq2=6,
>>   nq3=1,
>>   tr2_ph   =  1.0d-12,
>>   recover = .true.
>>  /
>>
>> Do I need to use q2r.x and matdyn.x to the files for plotting?
>>
>>
>> Thank you
>>
>>
>>
>> --
>> Dr. Eleni Chatzikyriakou
>> Computational Physics lab
>> Aristotle University of Thessaloniki
>> elch...@auth.gr - tel:+30 2310 998109
>>
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>
>
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elch...@auth.gr - tel:+30 2310 998109

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Re: [Pw_forum] Plotting phonon dispersion

[elchatz]

Thank you. That makes sense.

Eleni


Quoting Vahid Askarpour :

> a) If you skip amass, I think the codes use the mass in the previous runs.
>
> b) Did you use ibrav=0 in the scf run? The high-symmetry points you  
> defined are for ibrav=2. Otherwise, just specify the coordinates  
> explicitly.
>
> Cheers,
>
> Vahid
>
>> On Feb 19, 2018, at 9:29 AM, elch...@auth.gr wrote:
>>
>>
>> Thank you Vahid Askarpour.
>>
>> I have two questions:
>>
>> a) Is there a problem if I don't specify amass?
>>
>> b) I have already done this procedure using the following files:
>>
>> ph.x:
>>
>> 
>>   prefix   = 'Si',
>>   epsil= .false.,
>>   fildyn   = 'diam.dyn',
>>   ldisp= .true.
>>   fildvscf = 'dvscf'
>>   nq1=6,
>>   nq2=6,
>>   nq3=1,
>>   tr2_ph   =  1.0d-12,
>>   recover = .true.
>>  /
>>
>> This run ok
>>
>> q2r.in:
>>
>>  
>>   fildyn='diam.dyn',
>>   flfrc='Si.rc'
>>  /
>>
>> This run ok
>>
>> matdyn.in:
>>
>>  
>> flfrc='Si.rc',
>> flfrq='Si.freq',
>> q_in_band_form=.true.
>>  /
>>  4
>>  gG 50
>>   X 50
>>   M 50
>>   gG 8
>>
>> And I got the following error:
>>
>>
>> %%
>>  Error in routine find_bz_type (1):
>>  Wrong ibrav
>>
>> %%
>>
>> Is it possible that this is because I messed up the names of the
>> files, or do I need to include explicitly the coordinates of the high
>> symmetry points?
>>
>>
>> Regards
>>
>> Eleni
>>
>>
>>
>>
>> Quoting Vahid Askarpour :
>>
>>> Once you get all the .dyn files from the ph.x run, use the following
>>> input to q2r.x to get the force constants:
>>>
>>> 
>>>   fildyn=’Si.dyn', zasr='simple', flfrc=’Si.ifc2’
>>> /
>>>
>>> Then use the following input to matdyn.x:
>>>
>>> 
>>>asr='simple',  amass(1)= 28.0855
>>>flfrc=’Si.ifc2', flfrq=’Si.freq', q_in_band_form=.true.
>>> /
>>> 6  ! number of high-symmetry points
>>> 0.0 0.0 0.0 200
>>> 0.0 0.0 1.0 200
>>> etc.
>>>
>>> The coordinates of the high symmetry points should be in cartesian
>>> coordinates. 200 points will be calculated for each segment. The
>>> phonon dispersion is in the .gp output file.
>>>
>>> Cheers,
>>>
>>> Vahid
>>>
>>> Vahid Askarpour
>>> Department of Physics and Atmospheric Science
>>> Dalhousie University,
>>> Halifax, NS, Canada
>>>
 On Feb 19, 2018, at 4:54 AM, elch...@auth.gr wrote:

 Hello all,

 I am using ph.x to get the phonon frequencies and dynamical matrices
 for an epw.x calculation, however, I would like to plot my phonon
 dispersions from the ph.x calculation for far, as for example is shown
 in

 http://epw.org.uk/Documentation/B-dopedDiamond

 I am lost as to how I can do that. My ph.x file is as follows,

 
  prefix   = 'Si',
  epsil= .false.,
  fildyn   = 'diam.dyn',
  ldisp= .true.
  fildvscf = 'dvscf'
  nq1=6,
  nq2=6,
  nq3=1,
  tr2_ph   =  1.0d-12,
  recover = .true.
 /

 Do I need to use q2r.x and matdyn.x to the files for plotting?


 Thank you



 --
 Dr. Eleni Chatzikyriakou
 Computational Physics lab
 Aristotle University of Thessaloniki
 elch...@auth.gr - tel:+30 2310 998109

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>>
>>
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>> Dr. Eleni Chatzikyriakou
>> Computational Physics lab
>> Aristotle University of Thessaloniki
>> elch...@auth.gr - tel:+30 2310 998109
>>
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Re: [Pw_forum] Plotting phonon dispersion

[elchatz]

Ok, I am confused again.

I used ibrav=0 in the scf run that eventually gave me the error in matdyn.x.

I am running it again. This time I've used,

-
ibrav = 6,
celldm(1) = [..]
celldm(3) = [..]
--

in the scf. It's good to know if this is more possible to work as ph.x  
takes about 4 days.


Eleni



Quoting Lorenzo Paulatto :

> On 02/19/2018 03:14 PM, Saif Ullah wrote:
>> Dear Eleni,
>>
>> Did you use ibrav=0? If so, then you need to use q_in_band_form=.false.
>> q_in_cryst_coord=.true.
>>
> Neither of these two bits of advice is correct:
>
> 1. q_in_band_form can be used with ibrav=0 as usual, and works just as
> well as long as you specify the point coordinates
> 2. there is no specific reason to use crystal coordinates with ibrav=0,
> you can, as usual, but by no mean you "need to"
>
>
> kind regards
>
>
> --
> Lorenzo Paulatto - Paris
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[Pw_forum] LPZ functional in ld1.x

[elchatz]

Hello all,

Does anyone know what the LPZ XC functional is?


   scalar relativistic calculation

   atomic number is 42.00
   dft =LPZ   lsd =0 sic =0 latt =0  beta=0.20 tr2=1.0E-14
   Exchange-correlation  = LPZ ( 0  1  0  0 0 0)
   mesh =1229 r(mesh) = 100.71859 a.u. xmin = -7.00 dx = 0.01250
   1 Ry =  13.60569193 eV, c = 137.03599966
---

I can't find it in the functionals.f90 file or in libXC.

Regards,


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Computational Physics lab
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elch...@auth.gr - tel:+30 2310 998109

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Re: [Pw_forum] Problems computing cholensky

[elchatz]

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/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
> 

[Pw_forum] Relax keeping orthogonality

[elchatz]

Dear all,

Are there any options for relaxing the atomic positions and optimize  
the cell without changing the corners between the vectors?


Thank you

Eleni



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[QE-users] M45 edges in Xspectra

[elchatz]

Dear all,

Is it possible to use Xspectra for M45 edges? It is mentioned in the  
slides, but I don't see it in the INPUT file.



Regards




--
Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elch...@auth.gr - tel:+30 2310 998109

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Re: [QE-users] Format of filp output file in bands.x

[elchatz]

Hello all,


I have managed to make a script that takes out the results after going  
through the source code, however, I see now that for each k-point the  
occupied bands may differ and this complicates things a bit for me. Is  
there any other way to make a plot of the momentum matrix elements in  
QE??



Regards,

Eleni







Quoting elch...@auth.gr:


So, I've managed to bring the file into the format:

kx  ky  kz  20(??) 1(??) and the rest of the columns.

My bands are 64, the columns are 2642. My k-points are 225.


Any clues???

Thank you.

Eleni





Quoting elch...@auth.gr:


Hello everyone,

Is there a guide on the format of the filp file in the bands.x  
calculation for me to parse it?



Regards,

Eleni


--
Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elch...@auth.gr - tel:+30 2310 998109

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--
Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elch...@auth.gr - tel:+30 2310 998109

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Computational Physics lab
Aristotle University of Thessaloniki
elch...@auth.gr - tel:+30 2310 998109

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[QE-users] Format of filp output file in bands.x

[elchatz]

Hello everyone,

Is there a guide on the format of the filp file in the bands.x  
calculation for me to parse it?



Regards,

Eleni


--
Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elch...@auth.gr - tel:+30 2310 998109

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[QE-users] 2D band surface plot

[elchatz]

Hello everyone,

Do you have an example with a grid used for 2D surface plot in  
bands.x? I am getting some really strange output.


Regards,

Eleni


--
Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elch...@auth.gr - tel:+30 2310 998109

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Re: [QE-users] Format of filp output file in bands.x

[elchatz]

So, I've managed to bring the file into the format:

kx  ky  kz  20(??) 1(??) and the rest of the columns.

My bands are 64, the columns are 2642. My k-points are 225.


Any clues???

Thank you.

Eleni





Quoting elch...@auth.gr:


Hello everyone,

Is there a guide on the format of the filp file in the bands.x  
calculation for me to parse it?



Regards,

Eleni


--
Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elch...@auth.gr - tel:+30 2310 998109

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--
Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elch...@auth.gr - tel:+30 2310 998109

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Re: [QE-users] 2D band surface plot

[elchatz]

Dear Oleksandr Motornyi,

If you mean for the energy, I am around the fermi level, but not  
exactly there.


If you mean for ky, it is the result exactly as I got it from the .dat file.

Regards,

Eleni




Quoting Oleksandr Motornyi :

What does look strange to me is scale on your plot. SCF in/out files  
would actually be more helpful here as so far we have little idea  
about your system.


Oleksandr


On 30/04/19 08:50, elch...@auth.gr wrote:


Quoting Oleksandr Motornyi :


Hello Eleni

Could you please provide an input as well as the strange outputs?  
It is hard to give any advice or example without knowing what are  
you dealing with exactly.


Regards,

Oleksandr

Oleksandr Motornyi
PhD

Laboratoire des Solides Irradies
Ecole Polytechnique (Palaiseau, France)

On 29/04/19 18:12, elch...@auth.gr wrote:

Hello everyone,

Do you have an example with a grid used for 2D surface plot in  
bands.x? I am getting some really strange output.


Regards,

Eleni




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--
Oleksandr Motornyi
PhD candidate

Laboratoire de Solides Irradies
Ecole Polytechnique (Palaiseau, France)




--
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Computational Physics lab
Aristotle University of Thessaloniki
elch...@auth.gr - tel:+30 2310 998109

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Re: [QE-users] Three-dimensional plot of a band structure

[elchatz]

Lorenzo Paulatto,


Thank you so much. Using k-points from matplotlib instead of those  
from the Wannier90 tool I was using worked perfect.


Regards,

Eleni



Quoting elch...@auth.gr:


Hello everyone,

Do you have an example with a grid used for 2D surface plot in  
bands.x? I am getting some really strange output.


Regards,

Eleni





Quoting Lorenzo Paulatto :

Any advice how to create 3D plot of a band structure in QE? It  
means, for example, axis x == kx,  y = ky and z = E ?


Dear Arena,
there are two problems here:
1. compute the bands in a list of k-points that form a 2D surface
2. plot these points

1. Can be done by hand, by generating the list of k-points with  
mathlab or similar software, or it can be done marginally easier by  
using the "tpiba_c" option in the KPOINTS card. Check the  
INPUT_PW.html manual that you can find in PW/Doc or online.
Of course, this list of k-points must be computed with pw.x as a non  
self-consistent BANDS calculation, starting from a well converged  
total energy calculation.


2. You can extract the list of points and energies using bands.x, be  
sure to use the plot_2d=.true. option to get a file suitable for the  
kind of plot you need. Then you should be able to plot it with gnuplot

  plot "file.dat" using 1:2:3 with image
or any other plotting software

hth


--
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