[QE-users] Issue with 'Relax' Calculation Upon Introducing Br Anion - Seeking Assistance

NIKUNJ KUMAR n_kumar2 at cy.iitr.ac.in
Sun Feb 4 10:18:24 CET 2024


Dear Giuseppe,

Thank you for your insightful reply and valuable suggestions. I am trying
to simulate the ring opening of boron oxide-bounded epoxide through the
nucleophilic attack of Br- anion.

I will implement your recommendations, including trying alternative pseudo
potentials and exploring additional factors you highlighted. As a newcomer
to quantum espresso, I am eager to learn and experiment with different
approaches to enhance my understanding.

I noticed that the paper I've been following on Boron oxide used the pbesol
pseudopotential, but they focused on neutral molecules. Given your
suggestions, I plan to explore variations using different pseudo potentials
and different ecut and erho values to assess their impact on the simulation.

Once again, thank you for your support, and I look forward to further
refining my simulations with your insights.

Best regards,
Nikunj kumar
Research Scholar
Chemistry Department
IIT Roorkee


On Sat, Feb 3, 2024 at 9:43 PM Giuseppe Mattioli <
giuseppe.mattioli at ism.cnr.it> wrote:

>
> Dear Nikunj Kumar
> You are trying to attach an excess electron to a Br atom placed in the
> vacuum above a boron oxide slab in contact with an organic molecule.
> Br is not screened by some dielectric environment like water or a
> surrounding solid structure. When treated at the GGA level of theory,
> excess electrons in anions in vacuum are unbound, i.e., their energy
> is above the vacuum level; it is a theoretical problem, not a
> technical problem. I don't know your system, maybe your excess
> electron is delocalized across the oxide conduction band, maybe not.
> It is unpredictable but if you are trying to model Br(-) this is not
> the correct way. Moreover, you are using a huge and likely useless
> basis set for paw pseudopotentials, with ecutwfc=250 Ry and
> ecutrho=1000 Ry. occupations='fixed' and smearing='gaussian' are also
> incompatible. All of these issues can lead to scf instabilites. As I
> don't know what you expect to simulate, I cannot say more than this.
> HTH
> Giuseppe
>
>
> Quoting NIKUNJ KUMAR <n_kumar2 at cy.iitr.ac.in>:
>
> > Hello everyone,
> >
> > I hope this message finds you well. I am currently facing a challenge in
> a
> > 'relax' type calculation, specifically when introducing a Br anion into
> my
> > system with a total charge of -1. The issue arises as the calculation
> stops
> > after just 2 SCF iterations, accompanied by the following error message:
> >      Error in routine  rdiaghg (640):
> >       problems computing cholesky
> >
> >
> > Interestingly, the calculation was running smoothly before the
> introduction
> > of Br into the system. For context, I am utilizing the PBEsol paw type pp
> > from the pseudo dojo database, and the input file is written below for
> your
> > reference.
> >
> >
> > &CONTROL
> >     calculation   = "relax"
> >     forc_conv_thr =  1.00000e-06
> >     max_seconds   =  1.72800e+05
> >     nstep         = 500
> >     disk_io       = 'none'
> >     pseudo_dir    = "./"
> >     outdir        ="./temp"
> > /
> >
> > &SYSTEM
> >     a           =  9.43592e+00
> >     b           =  1.30441e+01
> >     c           =  4.02484e+01
> >     cosab       = -2.30389e-01
> >     degauss     =  1.00000e-02
> >     ecutrho     =  1.00000e+03
> >     ecutwfc     =  2.50000e+02
> >     ibrav       = 12
> >     nat         = 146
> >     ntyp        = 5
> >     tot_charge  =-1
> >     occupations = "fixed"
> >     smearing    = "gaussian"
> > /
> >
> > &ELECTRONS
> >     conv_thr         =  1.00000e-08
> >     electron_maxstep = 300
> >     mixing_beta      =  7.00000e-01
> >     startingpot      = "atomic"
> >     startingwfc      = "atomic+random"
> > /
> >
> > &IONS
> >     ion_dynamics = "bfgs"
> > /
> >
> >
> > K_POINTS {gamma}
> >
> > ATOMIC_SPECIES
> > B      10.81100  B.upf
> > O      15.99940  O.upf
> > C      12.01070  C.upf
> > H       1.00794  H.upf
> > Br     79.90400  Br.upf
> >
> > ATOMIC_POSITIONS {angstrom}
> > O        3.754834000      3.515156000     17.208519000
> > O        0.034436000      1.520892000     16.066045000
> > O        7.160635000      1.044462000     16.356461000
> > O        3.357263000      1.185774000     16.842398000
> > O        0.519323000      1.958041000     18.342909000
> > O        1.455747000      3.299351000     16.553832000
> > O        7.803889000      3.883560000     17.375196000
> > O        5.437775000      1.991195000     17.699831000
> > B        2.514843000      4.050588000     16.913192000
> > B        8.488318000      0.701095000     16.527892000
> > B        6.473887000      1.125469000     17.544128000
> > B        4.175154000      2.200028000     17.242716000
> > B        0.715437000      2.263118000     17.003418000
> > O        5.720922000      1.823850000     20.878023000
> > O        1.438122000      3.840152000     19.415577000
> > O        7.744065000      3.462649000     19.686233000
> > O        7.036262000      0.570535000     18.688600000
> > O        4.307513000      3.723392000     20.530664000
> > O        2.769498000      0.048093000     21.722688000
> > O        3.480766000      1.602073000     20.023812000
> > O        0.469955000      2.038326000     20.704597000
> > O        7.410831000      0.298249000     21.385070000
> > B        4.489103000      2.357617000     20.570624000
> > B        0.775613000      2.638077000     19.505559000
> > B        7.418619000      3.693276000     21.006039000
> > B        7.183884000      4.035133000     18.588513000
> > B        6.170982000      0.521811000     20.838073000
> > B        2.956880000      0.400145000     20.402662000
> > O        4.699394000     12.674672000     24.573063000
> > O        3.697946000      2.010965000     22.720733000
> > O        0.462997000      1.946967000     23.066403000
> > O        8.235206000      3.218267000     21.993446000
> > O        6.303865000      1.885557000     24.211038000
> > O        3.369105000      2.381461000     25.051568000
> > O        4.484631000      4.000335000     23.708815000
> > O        2.522918000      0.399802000     24.032915000
> > O        8.458849000      2.724160000     24.854635000
> > B        6.519079000      0.521498000     24.171811000
> > B        3.012943000      0.811264000     22.820437000
> > B        0.150363000      2.131320000     24.405538000
> > B       -0.070477000      2.439831000     21.903483000
> > B        7.173750000      2.920360000     24.501766000
> > B        3.950419000      2.759753000     23.864979000
> > O        2.753087000      7.746220000     17.208561000
> > O       -0.967323000      5.751970000     16.066081000
> > O        6.158876000      5.275511000     16.356477000
> > O        2.355519000      5.416843000     16.842391000
> > O       -0.482390000      6.189090000     18.342952000
> > O        0.454016000      7.530423000     16.553849000
> > O        6.802161000      8.114608000     17.375205000
> > O        4.436024000      6.222260000     17.699837000
> > B        1.513087000      8.281653000     16.913251000
> > B        7.486569000      4.932166000     16.527915000
> > B        5.472143000      5.356533000     17.544135000
> > B        3.173410000      6.431096000     17.242725000
> > B       -0.286307000      6.494181000     17.003439000
> > O        4.719193000      6.054910000     20.878019000
> > O        0.436375000      8.071207000     19.415579000
> > O        6.742321000      7.693691000     19.686251000
> > O        6.034527000      4.801615000     18.688628000
> > O        3.305773000      7.954452000     20.530671000
> > O        1.767778000      4.279151000     21.722684000
> > O        2.479032000      5.833133000     20.023815000
> > O       -0.531763000      6.269387000     20.704630000
> > O        6.409076000      4.529299000     21.385089000
> > B        3.487370000      6.588693000     20.570626000
> > B       -0.226116000      6.869125000     19.505577000
> > B        6.416861000      7.924320000     21.006056000
> > B        6.182148000      8.266183000     18.588552000
> > B        5.169244000      4.752884000     20.838058000
> > B        1.955162000      4.631204000     20.402686000
> > O        6.702867000      4.212530000     24.573064000
> > O        2.696219000      6.242038000     22.720750000
> > O       -0.538742000      6.178032000     23.066436000
> > O        7.233459000      7.449290000     21.993473000
> > O        5.302127000      6.116622000     24.211072000
> > O        2.367344000      6.612542000     25.051580000
> > O        3.482901000      8.231408000     23.708851000
> > O        1.521183000      4.630874000     24.032930000
> > O        7.457120000      6.955218000     24.854674000
> > B        5.517340000      4.752563000     24.171827000
> > B        2.011219000      5.042342000     22.820454000
> > B       -0.851385000      6.362375000     24.405579000
> > B       -1.072217000      6.670889000     21.903521000
> > B        6.172007000      7.151421000     24.501813000
> > B        2.948682000      6.990824000     23.864988000
> > O        1.751358000     11.977290000     17.208560000
> > O       -1.969011000      9.982977000     16.066085000
> > O        5.157183000      9.506595000     16.356501000
> > O        1.353766000      9.647903000     16.842472000
> > O       -1.484108000     10.420131000     18.342941000
> > O       -0.547722000     11.761459000     16.553848000
> > O        5.800420000     12.345689000     17.375160000
> > O        3.434303000     10.453319000     17.699866000
> > B        0.511368000     12.512710000     16.913221000
> > B        6.484857000      9.163207000     16.527937000
> > B        4.470421000      9.587610000     17.544172000
> > B        2.171680000     10.662166000     17.242767000
> > B       -1.288002000     10.725220000     17.003453000
> > O        3.717455000     10.285980000     20.878022000
> > O       -0.565377000     12.302292000     19.415566000
> > O        5.740577000     11.924763000     19.686206000
> > O        5.032803000      9.032678000     18.688644000
> > O        2.304042000     12.185525000     20.530674000
> > O        0.766025000      8.510198000     21.722689000
> > O        1.477279000     10.064188000     20.023840000
> > O       -1.533488000     10.500450000     20.704628000
> > O        5.407345000      8.760358000     21.385107000
> > B        2.485638000     10.819745000     20.570636000
> > B       -1.227842000     11.100195000     19.505580000
> > B        5.415136000     12.155400000     21.006013000
> > B        5.180404000     12.497244000     18.588499000
> > B        4.167507000      8.983948000     20.838079000
> > B        0.953421000      8.862268000     20.402697000
> > O        5.701119000      8.443598000     24.573135000
> > O        1.694495000     10.473076000     22.720741000
> > O       -1.540481000     10.409130000     23.066430000
> > O        6.231728000     11.680379000     21.993433000
> > O        4.300402000     10.347699000     24.211071000
> > O        1.365633000     10.843622000     25.051563000
> > O        2.481179000     12.462473000     23.708784000
> > O        0.519432000      8.861950000     24.032934000
> > O        6.455369000     11.186313000     24.854672000
> > B        4.515612000      8.983625000     24.171867000
> > B        1.009477000      9.273392000     22.820457000
> > B       -1.853101000     10.593479000     24.405573000
> > B       -2.073947000     10.901966000     21.903504000
> > B        5.170284000     11.382499000     24.501782000
> > B        1.946953000     11.221874000     23.864965000
> > O        1.091093000      1.770835000     25.342768000
> > B        2.336349000      1.479483000     24.879956000
> > O        0.089354000      6.001874000     25.342804000
> > B        1.334608000      5.710544000     24.879962000
> > O       -0.912369000     10.232995000     25.342798000
> > B        0.332877000      9.941635000     24.879959000
> > O        1.169790100      6.398079898     26.506082736
> > C        1.709966097      6.138246887     27.857097216
> > H        2.707261284      5.674065569     27.859423989
> > H        0.950878912      5.727882556     28.541990554
> > C        1.592297489      7.517135394     27.386071061
> > H        2.536403144      7.989815029     27.065205411
> > C        0.502211237      8.436139117     27.843173529
> > H        0.277193205      9.207901622     27.080667387
> > H        0.866246418      8.935911811     28.764585931
> > H       -0.425494252      7.878719382     28.079324886
> > Br       3.392772496      8.082664561     30.255606626
> >
> > Thank you in advance for your assistance!
> > Nikunj kumar
> > Research Scholar
> > Chemistry Department
> > IIT Roorkee
>
>
>
> GIUSEPPE MATTIOLI
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> Via Salaria Km 29,300 - C.P. 10
> I-00015 - Monterotondo Scalo (RM)
> Mob (*preferred*) +39 373 7305625
> Tel + 39 06 90672342 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
>
> _______________________________________________
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> _______________________________________________
> 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
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20240204/18b8064e/attachment.html>


More information about the users mailing list