[Pw_forum] Original Symmetry Operations Not Satisfied
Sai Kumar Ramadugu
sramadugu at gmail.com
Wed Dec 3 16:19:19 CET 2014
Dear Giuseppe,
The structure of the clay I have in the input file is a (110) surface of Fe
containing clay with 2:1 ration of tetrahedral sheet to octahedral sheet.
I have *tried* to center the surface at the origin of my simulation
supercell. The surface was created in Materials Studio. Xcrysden does not
orient the surface to the center of the supercell.
I have attached a picture of the structure using Discovery Studio.
If the attached structure is reasonable (I think it is!), is there any
other place in the input file that I should look into to solve this problem?
Please let me know!
Thanks again,
Sai
PS: Sorry if this is duplicate, the original message was larger than 200kB.
So shortened the size of the figure.
---
Sai Ramadugu
Post-Doctoral Scholar
University of Iowa
On Tue, Dec 2, 2014 at 5:10 PM, Giuseppe Mattioli <
giuseppe.mattioli at ism.cnr.it> wrote:
> Dear Sai
> I've opened your input file with xcrysden. I do not know the structure
> of your clay, but the structure contained in your file is *very*
> strange, and I doubt it is what you are tryng to simulate... Check the
> atom positions first of all!
> HTH
> Giuseppe
>
> Giuseppe Mattioli
> ISM-CNR
> Italy
>
> Quoting Sai Kumar Ramadugu <sramadugu at gmail.com>:
>
> > Dear All,
> >
> > I performing a relaxation of a monoclinic surface supercell of clay
> mineral.
> > The system has Fe, Si, O, H atoms and I am using Hubbard U for Fe atom
> and
> > according a previous paper (JPCC 2013, 117, 22800) I am using
> ferromagnetic
> > ordering for Fe. The supercell has 116 atoms. After the first
> optimization
> > cycle, there are NAN for forces and atomic coordinates and the job quits
> > with "some of the original symmetry operations not satisfied" message. I
> > read some of the previous threads on this but even after using
> nosym=true,
> > I cannot prevent this outcome. I am using QE v. 5.1, USPP.
> > Here is my input file:
> >
> > &CONTROL
> > pseudo_dir = '/import/u/u1/uaf/uasramadugu1/pseudo',
> > calculation = 'relax',
> > prefix = 'nga1',
> > outdir = './tmp/',
> > restart_mode = 'restart',
> > /
> > &SYSTEM
> > ibrav = 0,
> > nat = 116,
> > ntyp = 4,
> > ecutwfc = 40,
> > ecutrho = 320,
> > occupations = 'smearing',
> > smearing = 'mv',
> > degauss = 0.02,
> > nspin = 2,
> > starting_magnetization(4) = 0.5,
> > lda_plus_u = .TRUE.
> > Hubbard_U(4) = 4.0,
> > nosym = .TRUE.
> > /
> > &ELECTRONS
> > conv_thr = 1.D-7,
> > mixing_beta = 0.20D0,
> > electron_maxstep = 200,
> > /
> > &IONS
> > /
> > ATOMIC_SPECIES
> > Si 1.00 Si.pbe-n-rrkjus_psl.0.1.UPF
> > O 1.00 O.pbe-rrkjus.UPF
> > H 1.00 H.pbe-rrkjus_psl.0.1.UPF
> > Fe 1.00 Fe.pbe-nd-rrkjus.UPF
> > CELL_PARAMETERS {bohr}
> > 18.4815288646 0 0
> > -3.8055093495 39.4697757527 0
> > 0.0 0 81.1208726003
> > K_POINTS {automatic}
> > 2 1 1 1 1 1
> > ATOMIC_POSITIONS {Angstrom}
> > Si 3.244236583 -0.172014720 -1.094825338
> > Si 2.228369492 2.411697260 3.448017655
> > O 2.736303038 5.113595723 -1.094825338
> > O 2.736303038 -2.873913184 3.448017655
> > O -2.981392825 0.184537563 -0.467912953
> > O -3.997259916 2.768249543 4.074930040
> > O -2.473459279 -5.101072881 -0.467912953
> > Si -3.489326371 -2.517360901 4.074930040
> > Si -1.970779189 -5.092209359 -3.448018036
> > O -2.981392825 -2.563165356 1.094824954
> > O -2.473459279 0.138733107 -3.448018038
> > O -3.489326371 2.722445087 1.094824954
> > O 3.244236583 5.067791268 -4.074930424
> > O 3.244236583 -2.919717639 0.467912569
> > Si 3.752170129 -0.217819176 -4.074930424
> > Si 2.736303038 2.365892804 0.467912569
> > O 1.484554833 -0.225310670 -1.467338541
> > O 0.468687742 2.358401311 3.075504451
> > O 0.976621287 5.060299774 -1.467338541
> > O 0.976621287 -2.927209133 3.075504451
> > O -0.205843983 -2.106252953 -4.774528173
> > Si -1.221711074 0.477459027 -0.231685180
> > Si -2.237578166 3.061171007 4.311157813
> > O -0.713777529 3.179357491 -4.774528173
> > O -0.713777529 -4.808151417 -0.231685180
> > O -1.729644620 -2.224439436 4.311157813
> > O -0.205843983 -5.093581387 -3.075504835
> > O -1.221711074 -2.509869407 1.467338158
> > Si -0.713777529 0.192029056 -3.075504835
> > Si -1.729644620 2.775741037 1.467338158
> > O 1.484554833 4.774869803 -4.311158196
> > O 1.484554833 -3.212639104 0.231684797
> > O 0.468687742 -0.628927124 4.774527789
> > O 1.992488379 -0.510740641 -4.311158196
> > O 0.976621287 2.072971340 0.231684797
> > Si -0.039245804 4.656683320 4.774527789
> > Si 3.634300016 6.536830035 -4.592814486
> > O 3.629046564 -1.396010889 -0.049971498
> > O 2.613179472 1.187701091 4.492871495
> > O 4.136980109 1.305887574 -4.592814491
> > O 3.121113018 3.889599555 -0.049971498
> > O 3.121113018 -4.097909353 4.492871495
> > Si -2.350335714 -3.922881168 -4.492871878
> > Si -3.366202805 -1.339169188 0.049971115
> > O -4.382069896 1.244542793 4.592814107
> > O -2.858269259 1.362729276 -4.492871878
> > O -3.874136351 3.946441256 0.049971115
> > O -3.874136351 -4.041067651 4.592814107
> > O 4.179848986 3.963518711 -4.919899104
> > Si 4.179848986 -4.023990196 -0.377056111
> > Si 3.163981894 -1.440278216 4.165786881
> > O 4.687782531 -1.322091733 -4.919899104
> > O 3.671915440 1.261620248 -0.377056111
> > O 2.656048349 3.845332228 4.165786881
> > O -2.901138136 -4.985131076 -2.066993745
> > O -3.917005227 -2.401419096 2.475849247
> > O -3.409071682 0.300479368 -2.066993745
> > O -4.424938773 2.884191348 2.475849247
> > O -2.901138136 -1.294901861 -4.165787265
> > H -3.917005227 1.288810119 0.377055728
> > H -4.932872319 3.872522099 4.919898721
> > O -2.398458040 -6.525844328 -4.165787266
> > O -3.409071682 -3.996800325 0.377055728
> > O -4.424938773 -1.413088344 4.919898721
> > H 4.179848986 -0.333760981 -2.475849631
> > H 3.163981894 2.249950999 2.066993362
> > O 3.671915440 4.951849462 -2.475849631
> > O 3.671915440 -3.035659445 2.066993362
> > O 1.452047081 2.357458364 -2.743877369
> > H 0.436179989 4.941170344 1.798965624
> > H 1.959980626 -2.928152080 -2.743877369
> > O 0.944113535 -0.344440100 1.798965624
> > O -1.189203322 2.894870467 -1.798966007
> > O -1.189203322 -5.092638441 2.743876985
> > H -0.681269776 -2.390739977 -1.798966007
> > H -1.697136868 0.192972003 2.743876985
> > O -0.665406237 -1.837117046 -0.825551760
> > O -1.681273329 0.746594934 3.717291232
> > O -1.173339783 3.448493397 -0.825551760
> > O -1.173339783 -4.539015510 3.717291232
> > O 1.944117087 -3.481775011 -3.717291616
> > O 0.928249996 -0.898063030 0.825551377
> > O 1.436183541 1.803835433 -3.717291616
> > O 0.420316450 4.387547413 0.825551377
> > Fe 0.639355425 -3.993359982 -1.512766928
> > Fe -0.376511666 -1.409648002 3.030076065
> > Fe 0.131421879 1.292250462 -1.512766928
> > Fe -0.884445212 3.875962442 3.030076065
> > Fe 0.639355425 -1.325532075 -3.030076448
> > Fe -0.376511666 1.258179905 1.512766544
> > Fe 0.131421879 3.960078369 -3.030076448
> > Fe 0.131421879 -4.027430539 1.512766544
> > H -0.330486013 -1.370310935 4.983743911
> > H -0.380473528 0.085683105 4.755623060
> > H -0.658084122 5.576125416 4.713164954
> > H -0.652159651 3.742806044 4.628702666
> > H -4.427569708 3.782916231 5.904144710
> > H -3.602562722 1.472178451 5.349550961
> > H -3.633502006 -1.231158556 5.676621530
> > H -3.230548684 -3.888975775 5.484308909
> > H 2.080475062 3.564355425 5.072355961
> > H 1.955333207 0.980964115 5.362698017
> > H 2.538530040 -1.610432101 5.066873837
> > H 2.397170127 -4.136241468 5.333429287
> > H 0.205066887 2.556899870 -4.755254151
> > H 0.516960094 -2.927561392 -4.587160198
> > H 0.654975044 -1.407396893 -4.826401650
> > H -0.023070297 4.048169258 -4.788300904
> > H -1.517074941 -3.838757062 -5.221363272
> > H -1.486326426 -6.574176125 -4.796485322
> > H -2.091934330 1.505338311 -5.283120860
> > H -2.257230613 -1.219591574 -5.066793073
> > H 3.859525324 -1.289248815 -5.658147957
> > H 3.530413611 1.325355867 -5.522221885
> > H 3.397463119 4.028877693 -5.704565012
> > H 3.132772235 6.610409095 -5.580314384
> > -----
> >
> > The crash file writes the following:
> >
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > task # 0
> > from checkallsym : error # 1
> > some of the original symmetry operations not satisfied
> >
> >
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> > Any suggestions could be of great help.
> >
> > Thanks for your time in advance.
> >
> > Regards
> > Sai
> >
> > -------------
> > Sai Ramadugu
> > Post-Doctoral Scholar,
> > Department of Chemistry,
> > University of Iowa.
>
>
> --
> ********************************************************
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> ne peuvent être fondèes que sur l'utilitè commune
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> la propriètè, la sùretè et la rèsistance à l'oppression.
> ********************************************************
>
> Giuseppe Mattioli
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> v. Salaria Km 29,300 - C.P. 10
> I 00015 - Monterotondo Stazione (RM)
> Tel + 39 06 90672836 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
>
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