[QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)

Timrov Iurii iurii.timrov at epfl.ch
Wed Nov 13 19:12:13 CET 2019 

Dear Shenli and Paolo,


> I used Iurii’s input, it works well using QE 6.4.1, but would crash using QE 6.4 (not sure if this is because a compilation issue as I just used the module on the cluster)


Ok. Your system has 6 fractional translations. In QE 6.4 there is a bug in the HP code to compute U using DFPT when there are fractional translations - there is no this bug in QE 6.4.1. I am wondering if this is also a bug for DFPT+U phonon code in QE 6.4. In any case, the version QE 6.4.1 is working fine, so I think there is no point in trying to figure out what is wrong with QE 6.4 (if there is indeed an issue, as you say that you are not sure about the compilation).


> I verified each different parameters using QE 6.4.1 (add/remove nbnd, change ecutwfc/ecutrho ratio, conv_thr and add ‘’ for outdir), and found ecutwfc/ecutrho is the reason for my previous crash.


Ok, thanks for sharing this information!


> I set the occupations to be “fixed” because I want to calculate dielectric constant, it seems the ph.x program will complain if I use “smearing”, even if it converges to an insulating state

Ok. Yes, epsil=.true. with smearing will not work.

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 Shenli Zhang <shlzhang at uchicago.edu>
Sent: Wednesday, November 13, 2019 5:46:27 PM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)


Dear Iurii and Paolo,



Thank you so much for all the advice! It works for me now. And I’ve tested a bit to see which factor matters:

  1.  I used Iurii’s input, it works well using QE 6.4.1, but would crash using QE 6.4 (not sure if this is because a compilation issue as I just used the module on the cluster)
  2.  I verified each different parameters using QE 6.4.1 (add/remove nbnd, change ecutwfc/ecutrho ratio, conv_thr and add ‘’ for outdir), and found ecutwfc/ecutrho is the reason for my previous crash.
  3.  I set the occupations to be “fixed” because I want to calculate dielectric constant, it seems the ph.x program will complain if I use “smearing”, even if it converges to an insulating state.



Thank you!

Shenli

--
Shenli Zhang
Postdoc
Pritzker School of Molecular Engineering
The University of Chicago
5640 South Ellis Avenue, Chicago, IL 60637

From: users <users-bounces at lists.quantum-espresso.org> on behalf of Timrov Iurii <iurii.timrov at epfl.ch>
Reply-To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Date: Wednesday, November 13, 2019 at 4:54 AM
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)


Dear Shenli and Paolo,



I changed a bit the input for PW and PH and it did not crash for me (only at the very end, for some reason). I used QE 6.4.1, 8 cores, ifort 15.0.2 20150121.



The input and output files are here (available temporary):

https://drive.google.com/open?id=1Z4fSndJZPcK_A5PVa3hMsft8IGqXWHZB



For reference, I show here only the input files:
&control
    calculation='scf',
    restart_mode='from_scratch',
    prefix='LCO'
    pseudo_dir = '/scratch/timrov/q-e-qe-6.4.1/pseudo/',
    outdir='/scratch/timrov/q-e-qe-6.4.1/tempdir/'
 /
 &system
    ibrav = -5,
    celldm(1) = 10.1352,
    celldm(4) = 0.47876847,
    nat = 10,
    ntyp = 3,
    ecutwfc = 40.0
    ecutrho = 320.0
    occupations='fixed'
    lda_plus_u = .true.,
    lda_plus_u_kind = 0,
    U_projection_type = 'atomic',
    Hubbard_U(2) = 3.0
 /
 &electrons
    conv_thr =  1.d-14
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
La 138.9055 La.pbe-spfn-kjpaw_psl.1.0.0.UPF
Co 58.9332  Co.pbe-spn-kjpaw_psl.0.3.1.UPF
O  16       O.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {crystal}
O        0.312627155   0.750000000   0.187372845
O        0.750000000   0.187372845   0.312627155
O        0.187372845   0.312627155   0.750000000
O        0.687372845   0.250000000   0.812627155
O        0.812627155   0.687372845   0.250000000
O        0.250000000   0.812627155   0.687372845
Co       0.000000000   0.000000000   0.000000000
Co       0.500000000   0.500000000   0.500000000
La       0.250000000   0.250000000   0.250000000
La       0.750000000   0.750000000   0.750000000
K_POINTS {automatic}
 4 4 4 0 0 0


phonons of LCO at Gamma
 &inputph
  prefix = 'LCO',
  outdir='/scratch/timrov/q-e-qe-6.4.1/tempdir/',
  tr2_ph = 1.0d-14,
  epsil = .true.
  fildyn='LCO.dynG',
 /
0.000000000000000   0.000000000000000   0.000000000000000



Shenli: Could you try please to use exactly the same inputs as me with QE 6.4.1 and see what happens?



Paolo: I do not know what to say why you obtain NaN's... Do you use exactly the same input as Shenli?



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 Paolo Giannozzi <p.giannozzi at gmail.com>
Sent: Wednesday, November 13, 2019 11:13:09 AM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)

It doesn't segfaults for me but it produces NaN's. Note that:
- SCF convergence with fixed occupancies is very bad. I started from the charge density and wavefunctions obtained with smearing.
-  outdir='rhomb_U3', between ' '
Paolo

On Tue, Nov 12, 2019 at 10:52 PM Shenli Zhang <shlzhang at uchicago.edu<mailto:shlzhang at uchicago.edu>> wrote:
Dear Iurii,

Thank you so much for your reply. The output error “forrtl: severe (174): SIGSEGV, segmentation fault occurred” is not in the output file of ph.x, but is in the output file generated by the slurm system, which is a job scheduler for the cluster I use. In the ph.x output, there is no error message, but the program just stopped in the line “Calculating the dnsorth_cart matrix…”
I double checked the memory setting, it doesn’t seem to be the problem here. As I’ve increased the number of CPUs used to the point where I could actually run DFPT+U on an orthorhombic supercell of the same system.

And thanks for the advice on the parameter settings. I reduced the ecutrho/ecutwfc here  in order to do a quick test. I tried the ultrasoft pseudopotentials, and the error still persists. And yes my system is a nonmagnetic insulator and the scf calculation converged successfully.

The reason I think this error is probably due to the unit cell shape is because I also created an orthorhombic supercell of the same system with the same parameter settings, and I could run the DFPT+U without any problem.

Regards,
Shenli

--
Shenli Zhang
Postdoc
Pritzker School of Molecular Engineering
The University of Chicago
5640 South Ellis Avenue, Chicago, IL 60637

From: users <users-bounces at lists.quantum-espresso.org<mailto:users-bounces at lists.quantum-espresso.org>> on behalf of Timrov Iurii <iurii.timrov at epfl.ch<mailto:iurii.timrov at epfl.ch>>
Reply-To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>>
Date: Tuesday, November 12, 2019 at 11:31 AM
To: "users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>" <users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>>
Subject: Re: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)


Dear Shenli Zhang,



> with an output error “forrtl: severe (174): SIGSEGV, segmentation fault occurred”



Was is printed in the output file of the PHonon calculation after the crash?



Check if you have enough RAM to run DFPT+U, because it is heavy.



Your input for a PW SCF calculation has some problem:

- ecutrho/ecutwfc = 4 - this is true for norm-conserving pseudopotentials. But you are using PAW, for which the ratio should be 8 or more. Try to use DFPT+U with ultrasoft pseudopotentials (the ratio should be also 8 or more).

- nbnd=50 - this is not needed: just remove it from the input file

- occupations='fixed' : is your system a nonmagnetic insulator? Did your PW SCF calculation converged successfully?

- conv_thr=1.0d-12 : I suggest to try conv_thr=1.0d-14 if you plan to compute phonons afterwards.



HTH



Regards,

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<mailto:users-bounces at lists.quantum-espresso.org>> on behalf of Shenli Zhang <shlzhang at uchicago.edu<mailto:shlzhang at uchicago.edu>>
Sent: Tuesday, November 12, 2019 5:57:47 PM
To: users at lists.quantum-espresso.org<mailto:users at lists.quantum-espresso.org>
Subject: [QE-users] Problem using ph.x with DFPT+U in QE 6.4.(1)

Dear all,

I’m testing phonon calculations using ph.x with DFPT+U in QE 6.4 and QE 6.4.1, however the calculation always stops at the line “Calculating the dnsorth_cart matrix…”  with an output error “forrtl: severe (174): SIGSEGV, segmentation fault occurred”
I ran my system without U successfully. And I also ran the LiCoO2 +U example successfully. The only difference I can think of between my input file and the example file is the unit cell shape, where my LaCoO3 system has a rhombohedral unit cell and the example LiCoO2 has an orthorhombic one. Could this be a problem or did I make some mistakes?

Attached are the input files for my system LCO. Thank you!

SCF calculation input:
&control
    calculation='scf'
    prefix='LaCoO3p_relax'
    outdir=rhomb_U3
    pseudo_dir = '/home/shlzhang/QE_simulation/LaCoO3/pseudo',
/
&system
    nbnd=50
    ibrav=-5, celldm(1)=10.1352, celldm(4) =0.47876847, nat=10, ntyp= 3,
    ecutwfc =90, ecutrho =360, !for PAW ecutrho=4*ecutwfc, but need test
    occupations='fixed' !energy units in Ry
    lda_plus_u=.true.  Hubbard_U(2)=3
/
&electrons
conv_thr=1.0d-12
/
&ions
/
&cell
!cell_dofree='shape'
/
ATOMIC_SPECIES
La 138.9055 La.pbe-spfn-kjpaw_psl.1.0.0.UPF
Co 58.9332 Co.pbe-spn-kjpaw_psl.0.3.1.UPF
O  16 O.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS (crystal)
O        0.312627155   0.750000000   0.187372845
O        0.750000000   0.187372845   0.312627155
O        0.187372845   0.312627155   0.750000000
O        0.687372845   0.250000000   0.812627155
O        0.812627155   0.687372845   0.250000000
O        0.250000000   0.812627155   0.687372845
Co      -0.000000000   0.000000000  -0.000000000
Co       0.500000000   0.500000000   0.500000000
La       0.250000000   0.250000000   0.250000000
La       0.750000000   0.750000000   0.750000000
K_POINTS automatic
  4 4 4 0 0 0

Phonon calculation input:

phonons of bulk LaCoO3 at Gamma
&inputph
   prefix='LaCoO3p_relax'
   outdir=rhomb_U3
   fildyn='LaCoO3.dyn'
   max_seconds=82800
   tr2_ph=1.0d-14
   verbosity='debug'
   amass(1)=138.9055
   amass(2)=58.9332
   amass(3)=16
   epsil=.true.
   trans=.true.
/
0.00000000000 0.000000000000 0.000000000000000


--
Shenli Zhang
Postdoc
Pritzker School of Molecular Engineering
The University of Chicago
5640 South Ellis Avenue, Chicago, IL 60637
_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso<http://www.max-centre.eu/quantum-espresso>)
users mailing list users at lists.quantum-espresso.org<mailto:users at 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20191113/0699a3b2/attachment.html>

More information about the users mailing list