[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>
>
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