[QE-users] Calculating U parameter for Ni in LiNiO2 using hp.x
Mohammad Moaddeli
mohammad.moaddeli at gmail.com
Wed Oct 21 19:28:29 CEST 2020
Dear Iurii,
I appreciate all your considerations. I could handle the HP run and the U
parameter for Ni is calculated. Based on your suggestions on pw_forum, all
atomic positions were fully relaxed with the new U parameter in order to
perform a self-consistent loop calculation and compute the U parameter
again until no meaningful difference between two consecutive computed "U"s
was observed. Since I encountered the " problems computing cholesky "
error, PARO diagonalization was used. Although hp.x went well for all q
points, there was an error in computing U. Is it related to the
diagonalization algorithm?
Order of calculations:
=---------------------------------------------------------------------------------=
pw.x -input scf.in > scf.out
hp.x -input hp1.in > hp1.out # for q point number 1
hp.x -input hp2.in > hp2.out
hp.x -input hp3.in > hp3.out
hp.x -input hp4.in > hp4.out
hp.x -input hp_sum.in > hp_sum.out
hp.x -input hp_compute_hp.in > hp_compute_hp.out
=---------------------------------------------------------------------------------=
A google drive link is provided as following:
https://drive.google.com/file/d/1SCNNOfcJGZPAM4gpgXThkTvsibv-ijNv/view?usp=sharing
With best regards,
Mohammad
ShirazU
On Tue, Oct 13, 2020 at 2:32 PM Timrov Iurii <iurii.timrov at epfl.ch> wrote:
> Dear Mohammad,
>
>
> > There are 4 q points in hp.out:
>
>
> Ok. I was looking at the old files that you shared and there were 6 q
> points. Probably you have changed something in your PW input, and now you
> have more symmetries and hence fewer q points.
>
>
> To solve the convergence problem for the q point #4 I suggest to use conv_thr_chi
> = 3.0d-5 instead of conv_thr_chi = 1.0d-5. Indeed, the residue for q#4 is
> below 3.d-5 after 25 iterations:
>
>
> atom # 1 q point # 4 iter # 25
> chi: 1 -0.0982377516 residue: 0.0000065024
> chi: 2 -0.0000089671 residue: 0.0000205352
> chi: 3 -0.0000484762 residue: 0.0000067400
> chi: 4 -0.0000000000 residue: 0.0000000000
> chi: 5 -0.0000333051 residue: 0.0000117502
> chi: 6 -0.0000089671 residue: 0.0000205352
> chi: 7 0.0032070938 residue: 0.0000015134
> chi: 8 -0.0000089671 residue: 0.0000205352
> chi: 9 -0.0000333051 residue: 0.0000117502
> chi: 10 0.0000000000 residue: 0.0000000000
> chi: 11 -0.0000484762 residue: 0.0000067400
> chi: 12 -0.0000089671 residue: 0.0000205352
> Average number of iter. to solve lin. system: 30.0
> Total CPU time : 85250.2 s
>
>
> Greetings,
>
> Iurii
>
>
> --
> Dr. Iurii TIMROV
> Postdoctoral Researcher
> STI - IMX - THEOS and NCCR - MARVEL
> Swiss Federal Institute of Technology Lausanne (EPFL)
> CH-1015 Lausanne, Switzerland
> +41 21 69 34 881
> http://people.epfl.ch/265334
> ------------------------------
> *From:* users <users-bounces at lists.quantum-espresso.org> on behalf of
> Mohammad Moaddeli <mohammad.moaddeli at gmail.com>
> *Sent:* Tuesday, October 13, 2020 11:29:57 AM
> *To:* Quantum ESPRESSO users Forum
> *Subject:* Re: [QE-users] Calculating U parameter for Ni in LiNiO2 using
> hp.x
>
> Dear Iurii,
>
> Thanks for your prompt reply.
>
> A google drive link is provided:
>
> https://drive.google.com/file/d/1-wXwPi5t4gSRBAilDT0ym5vOK8vxosif/view?usp=sharing
>
> There are 4 q points in hp.out:
> =-----------------------------------------------------------------
> .
> .
> .
> The grid of q-points ( 2, 2, 2) ( 4 q-points ) :
> N xq(1) xq(2) xq(3) wq
> 1 0.000000000 0.000000000 0.000000000 0.125000000
> 2 0.000000000 0.000000000 -0.202041221 0.125000000
> 3 0.000000000 -0.577350269 0.000000000 0.375000000
> 4 0.000000000 -0.577350269 -0.202041221 0.375000000
> =-----------------------------------------------------------------
>
> Best,
>
> Mohammad
> ShirazU
>
> On Tue, Oct 13, 2020 at 12:21 PM Timrov Iurii <iurii.timrov at epfl.ch>
> wrote:
>
>> Dear Mohammad,
>>
>>
>> > Based on your recommendations, everything went well for q point #3.
>> However, q point #4 did not converge. Required converging iterations from q
>> point #1 to 3 is as following: 45 iterations for q1, 63 iterations for q2,
>> and 51 iterations for q3. q4 did not converge after 196 iterations. It took
>> 6 days. Finally I stopped hp.x because of fluctuation in "residue" for
>> "chi".
>>
>>
>> Did you use conv_thr_chi = 1.0d-5 and alpha_mix(1)= 0.05 for q#4 ? Can
>> you share your input and output files (PW and HP) via Google Drive?
>>
>>
>> > Is it possible and reasonable to run hp.x for q point #1, 2, and 3
>> separately and use sum_pertq=.true. as well as start_q=1, last_q=3, and
>> perturb_only_atom(1)=.true. to calculate the U parameter? (There are
>> totally 4 q points)
>>
>>
>> I do not understand what you want to do. But I can tell that you cannot
>> use sum_pertq=.true. if you do not have all calculations for all q
>> points done (there are 6 q points in your case, not 4):
>>
>>
>> The grid of q-points ( 2, 2, 2) ( 6 q-points ) :
>> N xq(1) xq(2) xq(3) wq
>> 1 0.000000000 0.000000000 0.000000000 0.125000000
>> 2 1.747932183 1.009169115 -0.353154352 0.125000000
>> 3 -0.000000002 -1.009169115 -0.176577175 0.250000000
>> 4 1.747932182 0.000000000 -0.529731527 0.250000000
>> 5 -0.873966092 -0.504584557 -0.353154351 0.125000000
>> 6 0.873966092 0.504584557 -0.706308703 0.125000000
>>
>> Greetings,
>>
>> Iurii
>>
>>
>> --
>> Dr. Iurii TIMROV
>> Postdoctoral Researcher
>> STI - IMX - THEOS and NCCR - MARVEL
>> Swiss Federal Institute of Technology Lausanne (EPFL)
>> CH-1015 Lausanne, Switzerland
>> +41 21 69 34 881
>> http://people.epfl.ch/265334
>> ------------------------------
>> *From:* users <users-bounces at lists.quantum-espresso.org> on behalf of
>> Mohammad Moaddeli <mohammad.moaddeli at gmail.com>
>> *Sent:* Tuesday, October 13, 2020 8:25:12 AM
>> *To:* Quantum ESPRESSO users Forum
>> *Subject:* Re: [QE-users] Calculating U parameter for Ni in LiNiO2 using
>> hp.x
>>
>> Dear Iurii,
>>
>> Based on your recommendations, everything went well for q point #3.
>> However, q point #4 did not converge. Required converging iterations from q
>> point #1 to 3 is as following: 45 iterations for q1, 63 iterations for q2,
>> and 51 iterations for q3. q4 did not converge after 196 iterations. It took
>> 6 days. Finally I stopped hp.x because of fluctuation in "residue" for
>> "chi".
>>
>> Is it possible and reasonable to run hp.x for q point #1, 2, and 3
>> separately and use sum_pertq=.true. as well as start_q=1, last_q=3, and
>> perturb_only_atom(1)=.true. to calculate the U parameter? (There are
>> totally 4 q points)
>>
>> alpha_mix is also reduced down to 0.01 as another alternative. It is
>> still running...
>>
>> Any help will be greatly appreciated
>>
>> Best,
>>
>> Mohammad
>> ShirazU
>>
>> On Fri, Sep 18, 2020 at 6:24 PM Timrov Iurii <iurii.timrov at epfl.ch>
>> wrote:
>>
>>> Dear Mohammad,
>>>
>>>
>>> Your system seems to be delicate to converge. So I found that the mixing
>>> parameter alpha_mix needs to be reduce further, down to 0.05 (which is very
>>> small). With this, you can converge the HP calculation for the third q
>>> point with the accuracy conv_thr_chi = 1.0d-5 (which is still fine).
>>>
>>>
>>> By the way, if you want to test the convergence of the HP code for a
>>> specific q point, you can use the input parameters start_q and last_q and
>>> specify for which perturbed atom you do this. In your case, you need to
>>> specify the following in the input for HP:
>>>
>>> perturb_only_atom(1) = .true.
>>> start_q = 3
>>> last_q = 3
>>> Here is the documentation:
>>> https://www.quantum-espresso.org/Doc/INPUT_HP.html
>>> Also, when using iverbosity = 4 the HP code prints a lot of information
>>> in the output. This is not really needed in this case. I would use iverbosity
>>> = 2.
>>>
>>>
>>> Greetings,
>>>
>>> Iurii
>>>
>>>
>>> --
>>> Dr. Iurii TIMROV
>>> Postdoctoral Researcher
>>> STI - IMX - THEOS and NCCR - MARVEL
>>> Swiss Federal Institute of Technology Lausanne (EPFL)
>>> CH-1015 Lausanne, Switzerland
>>> +41 21 69 34 881
>>> http://people.epfl.ch/265334
>>> ------------------------------
>>> *From:* users <users-bounces at lists.quantum-espresso.org> on behalf of
>>> Mohammad Moaddeli <mohammad.moaddeli at gmail.com>
>>> *Sent:* Friday, September 18, 2020 6:14:48 AM
>>> *To:* Quantum ESPRESSO users Forum
>>> *Subject:* Re: [QE-users] Calculating U parameter for Ni in LiNiO2
>>> using hp.x
>>>
>>> Dear Iurii,
>>>
>>> Unfortunately the q pont #3 did not converge. All input and output files
>>> are available in this link:
>>>
>>>
>>> https://drive.google.com/file/d/1zWoYq3kfBfH-6bw8s5llDm-BYFxM3ndQ/view?usp=sharing
>>>
>>> Any help will be greatly appreciated.
>>>
>>> Regards,
>>>
>>> Mohammad
>>>
>>> On Wed, Sep 16, 2020 at 1:00 PM Timrov Iurii <iurii.timrov at epfl.ch>
>>> wrote:
>>>
>>>> Dear Mohammad,
>>>>
>>>>
>>>> > By changing the threshold values you mentioned, nscf calculation
>>>> finished (no "cholesky" error)...
>>>>
>>>>
>>>> Great!
>>>>
>>>>
>>>> > ...but there is divergence in computing "chi".
>>>>
>>>>
>>>> The HP calculation for q points #1 and #2 has converged, but the
>>>> problem is for the q point #3. In the HP input, please setup
>>>>
>>>> alpha_mix(1) = 0.1
>>>>
>>>> and try again.
>>>>
>>>> Also I suggest to use the default value nmix = 4, because I have never
>>>> tried changing it to something else (you are using nmix=5) and so I do not
>>>> know what to expect.
>>>>
>>>> Also note that the parameter conv_thr_chi = 1.0d-8 is very tight, so
>>>> can try even something like conv_thr_chi = 1.0d-6 which should also be
>>>> fine (because your calculations take a lot of time with 16 cores that you
>>>> use).
>>>>
>>>>
>>>> Greetings,
>>>>
>>>> Iurii
>>>>
>>>>
>>>> --
>>>> Dr. Iurii TIMROV
>>>> Postdoctoral Researcher
>>>> STI - IMX - THEOS and NCCR - MARVEL
>>>> Swiss Federal Institute of Technology Lausanne (EPFL)
>>>> CH-1015 Lausanne, Switzerland
>>>> +41 21 69 34 881
>>>> http://people.epfl.ch/265334
>>>> ------------------------------
>>>> *From:* users <users-bounces at lists.quantum-espresso.org> on behalf of
>>>> Mohammad Moaddeli <mohammad.moaddeli at gmail.com>
>>>> *Sent:* Wednesday, September 16, 2020 7:21:53 AM
>>>> *To:* Quantum ESPRESSO users Forum
>>>> *Subject:* Re: [QE-users] Calculating U parameter for Ni in LiNiO2
>>>> using hp.x
>>>>
>>>> Dear Iurii,
>>>>
>>>> By changing the threshold values you mentioned, nscf calculation
>>>> finished (no "cholesky" error), but there is divergence in computing "chi".
>>>> Please find the link below. All input and output files are attached.
>>>>
>>>>
>>>> https://drive.google.com/file/d/1TWDQ3X_jG7HsgaVvhUiu3oVWt28g3DNz/view?usp=sharing
>>>>
>>>> Best,
>>>>
>>>> Mohammad
>>>>
>>>> ShirazU
>>>>
>>>>
>>>> On Sun, Sep 13, 2020 at 2:13 PM Timrov Iurii <iurii.timrov at epfl.ch>
>>>> wrote:
>>>>
>>>>> Dear Mohammad,
>>>>>
>>>>>
>>>>> 1.In the SCF input for the supercell you have:
>>>>>
>>>>> conv_thr = 1.0d-20
>>>>>
>>>>> This is extremely low! Try some value in-between 1.0d-10 and 1.d-15.
>>>>>
>>>>>
>>>>> 2.In the HP input for the supercell you have:
>>>>>
>>>>> ethr_nscf = 1.D-14
>>>>>
>>>>> This is also extremely low! Try the default value of 1.0d-11.
>>>>>
>>>>>
>>>>> If you still have a problem when using e.g. conv_thr=1.d-10 and
>>>>> ethr_nscf=1.d-11 then please put input and output files on Google Drive or
>>>>> Dropbox and send a link to us (do not forget to check the permissions of
>>>>> the shared folder).
>>>>>
>>>>>
>>>>> HTH
>>>>>
>>>>>
>>>>> Iurii
>>>>>
>>>>>
>>>>> --
>>>>> Dr. Iurii TIMROV
>>>>> Postdoctoral Researcher
>>>>> STI - IMX - THEOS and NCCR - MARVEL
>>>>> Swiss Federal Institute of Technology Lausanne (EPFL)
>>>>> CH-1015 Lausanne, Switzerland
>>>>> +41 21 69 34 881
>>>>> http://people.epfl.ch/265334
>>>>> ------------------------------
>>>>> *From:* users <users-bounces at lists.quantum-espresso.org> on behalf of
>>>>> Mohammad Moaddeli <mohammad.moaddeli at gmail.com>
>>>>> *Sent:* Sunday, September 13, 2020 6:12:27 AM
>>>>> *To:* Quantum ESPRESSO users Forum
>>>>> *Subject:* Re: [QE-users] Calculating U parameter for Ni in LiNiO2
>>>>> using hp.x
>>>>>
>>>>> Dear Lorenzo,
>>>>>
>>>>> Thank you for your prompt reply.
>>>>> Using qe_6.6 (in which calculating force and stress is implemented)
>>>>> the 221 supercell relaxed with the U obtained from the output of hp.x for
>>>>> the primitive cell, but the same error appeared. What do you recommend?
>>>>>
>>>>> Best,
>>>>>
>>>>> Mohammad,
>>>>>
>>>>> ShirazU
>>>>>
>>>>> On Mon, Sep 7, 2020 at 12:07 PM Lorenzo Paulatto <paulatz at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> > I am trying to calculate the U parameter for Ni in LiNiO2. The hp.x
>>>>>> > (qe_6.5) runs without any error for the primitive cell, however the
>>>>>> > "problems computing cholesky" error occurs for running a 2×2×1
>>>>>> supercell
>>>>>>
>>>>>> The most likely cause is that you did a mistake in the atomic
>>>>>> position
>>>>>> or cell size.
>>>>>>
>>>>>> kind regards
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Lorenzo Paulatto - Paris
>>>>>> _______________________________________________
>>>>>> Quantum ESPRESSO is supported by MaX (
>>>>>> www.max-centre.eu/quantum-espresso)
>>>>>> users mailing list users at lists.quantum-espresso.org
>>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>>>
>>>>> _______________________________________________
>>>>> Quantum ESPRESSO is supported by MaX (
>>>>> www.max-centre.eu/quantum-espresso)
>>>>> users mailing list users at lists.quantum-espresso.org
>>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>>
>>>> _______________________________________________
>>>> Quantum ESPRESSO is supported by MaX (
>>>> www.max-centre.eu/quantum-espresso)
>>>> users mailing list users at lists.quantum-espresso.org
>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>> _______________________________________________
>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso
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>>> users mailing list users at lists.quantum-espresso.org
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>>
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
>> users mailing list users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
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