[Pw_forum] Run using a relaxed structure as initial one NOT converge in fir st few ionic steps.

Giovanni Cantele giovanni.cantele at spin.cnr.it
Tue Dec 20 11:25:20 CET 2016


So, you didn’t actually paste the relaxed positions into the new input file, but you have made a coordinate conversion!

The first thing one would say is that the conversion has some problems. What I suggest is to make an scf run by using
the ibrav variable. and full coordinate list. In this case I’m quite sure you’ll figure out that just one scf cycle with no relaxation
steps is needed to converge the structure. After you are convinced that QE is properly working, you can rerun the second
relaxation cycle just in the same way as you did but with nstep=1. In this case I think that QE will print in the output atomic coordinates
in crystal units, that will be the same as the input ones because with nstep=1 no coordinate change takes place. By comparing those crystal
coordinates with the ones you pasted into the e-mail, you can probably understand what is wrong with the conversion.

Did you try to visualise the last coordinates of the first output and the initial coordinates of the second output to see if the two structures
look the same?

Giovanni

> On 20 Dec 2016, at 11:05, quantum <quantum at mail.ncyu.edu.tw> wrote:
> 
> Dear Giovanni and Stefano:
> 
> Thank you very much for your response.  
> 
> Listed below are the details of input and output.
> 
> ----- The first input file --------------------------------------
> &control
>  title = 'Gypsum (CaSO4.2H20 Z=4)'
>  prefix = 'gyp-pbe-mt_fhi-exp1.01G-opt'
>  outdir = '/work2/u2equa02/tempdir/gyp-pbe-mt_fhi-exp1.01G-opt'
>  pseudo_dir = '/home/u2equa02/quantumhome/pseudo'
>  calculation = 'relax'
>  restart_mode = 'from_scratch'
>  disk_io = 'low'
>  verbosity = 'high'
>  wf_collect = .true.
>  tstress = .true.
>  tprnfor = .true.
>  etot_conv_thr = 1.0D-4
>  forc_conv_thr = 1.0D-3
>  max_seconds = 466560
> /
> &system
>  space_group = 15
>  uniqueb = .true.
>  origin_choice = 1
>  celldm(1) = 11.79378074341055 ! bohr
>  celldm(2) = 2.42429097900977
>  celldm(3) = 0.904502483576350
>  celldm(5) = -0.413422293216829
>  ntyp = 4
>  nat = 7
>  ecutwfc = 240
>  ecutrho = 960
>  vdw_corr = 'grimme-d2'
> /
> &electrons
>  electron_maxstep = 200
>  conv_thr = 1.0D-6
>  startingpot = 'atomic'
>  startingwfc = 'atomic+random'
>  mixing_mode = 'plain'
>  mixing_beta = 0.5
>  mixing_ndim= 8
>  diagonalization = 'david'
> /
> &ions
>  ion_dynamics = 'bfgs'
> /
> 
> ATOMIC_SPECIES
>   Ca   40.0780000000  Ca.pbe-mt_fhi.UPF
>    S   32.0650000000  S.pbe-mt_fhi.UPF
>    O   15.9994000000  O.pbe-mt_fhi.UPF
>    H    1.0079000000  H.pbe-mt_fhi.UPF
> 
> ATOMIC_POSITIONS crystal_sg
>    Ca  0.00000   0.16960   0.25000
>    S   0.00000   0.32680   0.75000
>    O   0.08400   0.27200   0.59000
>    O   0.20000   0.38200   0.91500
>    O  -0.21300   0.06300  -0.08000
>    H  -0.25800   0.08700  -0.23400
>    H  -0.24400   0.02000  -0.07700
> 
> K_POINTS automatic
>    12 12 12 0 0 0
> ----------------------------------------------
> 
> The last section of "ATOMIC_POSITIONS (crystal)" ----------------
> 
> ATOMIC_POSITIONS (crystal)
> Ca       0.831507586   0.168492414   0.250000000
> Ca       0.168492414   0.831507586   0.750000000
> S        0.670838834   0.329161166   0.750000000
> S        0.329161166   0.670838834   0.250000000
> O        0.814789681   0.361192199   0.593221086
> O        0.638807801   0.185210319   0.906778914
> O        0.185210319   0.638807801   0.406778914
> O        0.361192199   0.814789681   0.093221086
> O        0.817560716   0.587016680   0.921747159
> O        0.412983320   0.182439284   0.578252841
> O        0.182439284   0.412983320   0.078252841
> O        0.587016680   0.817560716   0.421747159
> O        0.713851138   0.844837552   0.919788047
> O        0.155162448   0.286148862   0.580211953
> O        0.286148862   0.155162448   0.080211953
> O        0.844837552   0.713851138   0.419788047
> H        0.650318830   0.820912679   0.741084444
> H        0.179087321   0.349681170   0.758915556
> H        0.349681170   0.179087321   0.258915556
> H        0.820912679   0.650318830   0.241084444
> H        0.749428151   0.753450611   0.911642228
> H        0.246549389   0.250571849   0.588357772
> H        0.250571849   0.246549389   0.088357772
> H        0.753450611   0.749428151   0.411642228
> 
> ----------------------------------------------------------------
> 
> 
> I understand, when using space_group to specify atomic positions
> a conversion between coordinates of convectional and centered cells
> is performed.  (Thanks to Andrea Dal Corso)
> 
> So, I manually reverted the conversion, following the PW code below.
> ============================================================
> espresso-5.3.0/PW/src/wyckoff.f90:
> 
>       SUBROUTINE ccord(outco,sym_n,not_eq,ibrav,unique)
> 
>       CASE (-13) !Centrato B unique MONOCLINO
>       DO k=1,not_eq
>          DO i=1,sym_n
>             tmpx=outco(1,i,k)
>             tmpy=outco(2,i,k)
> 
>             outco(1,i,k)=tmpx-tmpy
>             outco(2,i,k)=tmpy+tmpx
>          END DO
>       END DO
> ===========================================================
> 
> After manually reverting the above process, I identify the positions of the 7 inequivelent atoms, and use them for the new run.
> 
> The new input file --------------------------------------------------------
> &control
>  title = 'Gypsum (CaSO4.2H20 Z=4)'
>  prefix = 'gyp-pbe-mt_fhi-exp1.01G-opt-cont'
>  outdir = '/work2/u2equa02/tempdir/gyp-pbe-mt_fhi-exp1.01G-opt-cont'
>  pseudo_dir = '/home/u2equa02/quantumhome/pseudo'
>  calculation = 'relax'
>  restart_mode = 'from_scratch'
>  disk_io = 'low'
>  verbosity = 'high'
>  wf_collect = .true.
>  tstress = .true.
>  tprnfor = .true.
>  etot_conv_thr = 1.0D-4
>  forc_conv_thr = 1.0D-3
> /
> &system
>  space_group = 15
>  uniqueb = .true.
>  origin_choice = 1
>  celldm(1) = 11.79378074341055 ! bohr
>  celldm(2) = 2.42429097900977
>  celldm(3) = 0.904502483576350
>  celldm(5) = -0.413422293216829
>  ntyp = 4
>  nat = 7
>  ecutwfc = 240
>  ecutrho = 960
>  vdw_corr = 'grimme-d2'
> /
> &electrons
>  electron_maxstep = 200
>  conv_thr = 1.0D-6
>  startingpot = 'atomic'
>  startingwfc = 'atomic+random'
>  mixing_mode = 'plain'
>  mixing_beta = 0.5
>  mixing_ndim= 8
>  diagonalization = 'david'
> /
> &ions
>  ion_dynamics = 'bfgs'
> /
> 
> ATOMIC_SPECIES
>   Ca   40.0780000000  Ca.pbe-mt_fhi.UPF
>    S   32.0650000000  S.pbe-mt_fhi.UPF
>    O   15.9994000000  O.pbe-mt_fhi.UPF
>    H    1.0079000000  H.pbe-mt_fhi.UPF
> 
> ATOMIC_POSITIONS crystal_sg
>  Ca       0.000000000   0.168492414   0.250000000
>  S        0.000000000   0.329161166   0.750000000
>  O        0.087990940   0.273201259   0.593221086
>  O        0.202288698   0.384727982   0.921747159
>  O       -0.220655655   0.065493207  -0.080211953
>  H       -0.264384246   0.085296924  -0.258915556
>  H       -0.248560619   0.002011230  -0.088357772
> 
> 
> K_POINTS automatic
>    12 12 12 0 0 0
> 
> ------------------------------------------------------------
> 
> The new run does not converge after an ionic step.
> 
> 
> 
> Sincerely,
> Tsung-Lung Li
> 
> 
> 
> 
> 
> 
> 
> 
> -----Original message-----
> From:stefano de gironcoli <degironc at sissa.it>
> To:pw_forum at pwscf.org
> Date:Tue, 20 Dec 2016 17:34:17
> Subject:Re: [Pw_forum] Run using a relaxed structure as initial one NOT converge in fir st few ionic steps.
> 
> dear Tsung-Lung Li,
> 
> Your expectations are correct.
> If this is what you experience you probably are not doing what you think 
> you are doing but it is difficult to make any suggestion without further 
> information
> 
> stefano
> 
> 
> On 20/12/2016 10:26, quantum wrote:
>> Dear QE Friends:
>> 
>> I did a "relax" calculation with PW (version 5.3.0)
>> and obtained the relaxed atomic positions.
>> 
>> Then, I took the atomic positions
>> in the last "ATOMIC_POSITIONS (crystal)"
>> section of the output file to replace the
>> atomic positions in the original input file
>> without changing any other things except new
>> prefix and outdir.
>> 
>> The atoms in the relaxed structure should
>> all satisfy etot_conv_thr and forc_conv_thr
>> thresholds.  With this in mind, I started
>> the new run.
>> 
>> I expected the run to
>> converge after the first or two ionic steps.
>> But it did not stop, and continued running
>> for many ionic steps without convergence.
>> 
>> Is my expectation correct? or it is a problem
>> of QE?
>> 
>> Sincerely,
>> Tsung-Lung Li
>> 
>> 
>> Tsung-Lung Li, Ph. D.
>> Professor
>> Department of Applied Physics
>> National Chia-Yi University
>> 300 Hsueh-Fu Road, Chiayi 60004, Taiwan
>> Phone: 886-5-2717904.  FAX: 886-5-2717909.
>> E-mail:quantum at mail.ncyu.edu.tw
>> URL:http://web.ncyu.edu.tw/~quantum
>> 
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
> 
> 
> _______________________________________________
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> 
> 
> Tsung-Lung Li, Ph. D.
> Professor
> Department of Applied Physics
> National Chia-Yi University
> 300 Hsueh-Fu Road, Chiayi 60004, Taiwan
> Phone: 886-5-2717904.  FAX: 886-5-2717909.
> E-mail:quantum at mail.ncyu.edu.tw    
> URL:http://web.ncyu.edu.tw/~quantum
> 
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