[Pw_forum] Crash with Environ-0.2
Oliviero Andreussi
oliviero.andreussi at usi.ch
Tue Jan 23 22:21:50 CET 2018
Dear Dr. Huu Chuong Nguyen,
I see from your input that you are trying to run a spin-polarised, DFT+U plus empirical dispersion plus smearing calculation coupled with the Environ plugin. Although I would assume that these different features are all compatible with Environ, I have never tried such a combination and it may be that there are some bugs in the combination that lead to the segmentation fault. Have you tried running a simplified calculation to isolate the source of error (say removing the Hubbard U, the dispersion, doing a spin-unpolarized calculation)? Moreover, you may want to simplify the Environ input as well, trying to only test one embedding effect at a time: for example you can activate only the dielectric screening by setting environ_type = 'input' and env_static_permittivity = 78.3 (assuming water is what you are looking for). Or you can try to only activate the surface tension contribution by setting env_surface_tension to an arbitrary value. This would also help in understanding where the source of the segmentation fault is. Unfortunately this seems like an expensive example to debug from scratch, if you can provide more details or a simpler case where the problem occur, I would be happy to have a look and see if we can fix the problem. Moreover, if you can send me the output of your tests I could try to see if there is any indication of a problem already from those files.
Thanks for reporting the issue!
Best regards,
Oliviero Andreussi
--
Assistant Professor
Department of Physics
University of North Texas
E-mail: oliviero.andreussi at unt.edu
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________________________________
From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of Huu Chuong Nguyën <hnguyen at ICIQ.ES>
Sent: Saturday, January 20, 2018 11:37:26 AM
To: pw_forum at pwscf.org
Subject: [Pw_forum] Crash with Environ-0.2
Hello,
I am running a relax calculation with QE 6.1 and Environ-0.2. In vacuum, the calculation finish without problem but when I change the medium to water. The calculation always suddenly stop after " add environment contribution to local potential" with an ominous segmentation fault. This bug is reproducible on all machines that we have but I cannot figure out from where it could come from. Does anyone has had a similar issue or has an idea on how to solve it?
My inputs:
c1nO1.in:
&CONTROL
calculation = 'relax' ,
restart_mode = 'from_scratch' ,
wf_collect = .true. ,
prefix = 'c1nO1' ,
verbosity = 'high' ,
etot_conv_thr = 1.0D-8 ,
forc_conv_thr = 1.0D-4 ,
tstress = .true. ,
tprnfor = .true. ,
dipfield = .true. ,
nstep = 400 ,
max_seconds = 171000 , !47h30
/
&SYSTEM
ibrav = 4,
A = 10.230375737 ,
B = 10.230375737 ,
C = 28.9421830966 ,
cosAB = -0.5 ,
cosAC = 0 ,
cosBC = 0 ,
nat = 122 ,
ntyp = 4,
ecutwfc = 40.0 , !J. Chem. Phys. 138, 194709
ecutrho = 320.0 ,!J. Chem. Phys. 138, 194709
input_dft = 'PBE' ,
occupations = 'smearing' ,
degauss = 0.02 ,
smearing = 'gaussian' ,
nspin = 2 ,
starting_magnetization(1) = 1.0,
starting_magnetization(2) = -1.0,
starting_magnetization(3) = 0.0,
lda_plus_u = .true. ,
lda_plus_u_kind = 0 , !type 1 not implemented, ignores J
Hubbard_U(1) = 4.2,
Hubbard_U(2) = 4.2,
Hubbard_J0(1) = 0.0, !Is ignored!
Hubbard_J0(2) = 0.0, !Is ignored!
vdw_corr = Grimme-D2, ! DFT-D2 dispersion correction
/
&ELECTRONS
electron_maxstep = 900,
conv_thr_init = 1e-4 ,
conv_thr = 1e-9 ,
startingpot = 'atomic' ,
startingwfc = 'random' ,
adaptive_thr = .true. ,
mixing_beta = 0.514,
diagonalization = 'david' ,
/
&IONS
ion_dynamics = 'bfgs' ,
trust_radius_min = 1.D-5 ,
/
ATOMIC_SPECIES
Fe1 55.84500 Fe.pbe-sp-van_ak.UPF
Fe2 55.84500 Fe.pbe-sp-van_ak.UPF
O 15.99990 O.pbe-van_ak.UPF
Zn 65.39000 Zn_pbe_v1.uspp.F.UPF
ATOMIC_POSITIONS angstrom
Zn -0.0097298770 2.9563834880 3.0182116970
Zn 5.1249630590 5.9033469620 14.9239945730
Zn -2.5673345130 7.3862810510 3.0182106910
Zn 7.6825620740 1.4734584610 14.9239945540
Fe1 5.1053013770 2.9595540620 2.9148486100
Fe1 2.5477093370 7.3894410440 2.9148493100
Fe2 2.5555487200 1.4784729480 8.6328442770
Fe2 -0.0020447680 5.9083579240 8.6328455510
Fe2 7.6742460480 1.4747037680 8.6386973260
Fe2 5.1166499380 5.9045905230 8.6386971800
Fe1 2.5674925870 1.4703262560 15.0273595790
Fe1 0.0098990960 5.9002114620 15.0273602790
Fe2 -0.0014802610 2.9551937710 9.3035025680
Fe2 -2.5590762610 7.3850795960 9.3035029170
Fe2 5.1172241320 2.9514287310 9.3093378120
Fe2 2.5596299030 7.3813138660 9.3093373220
Fe1 0.0071780640 -0.0081645250 6.9924511410
Fe1 -2.5504156510 4.4217197940 6.9924587430
Fe1 5.1091120980 0.0095368600 6.9984449860
Fe1 2.5515166150 4.4394221440 6.9984460930
Fe2 0.0066064420 2.9395638740 13.4514587650
Fe2 -2.5509901970 7.3694544670 13.4514578580
Fe2 5.1228937830 2.9685272210 13.4499520490
Fe2 2.5653017030 7.3984134280 13.4499534780
Fe1 0.0071059300 2.9481284620 6.3559666860
Fe1 -2.5504915050 7.3780190750 6.3559673810
Fe1 5.1057836840 2.9609859820 6.3665609480
Fe1 2.5481926450 7.3908729030 6.3665605540
Fe2 0.0042821000 -0.0105742680 13.8102225240
Fe2 -2.5533112150 4.4193112530 13.8102220900
Fe2 5.1255258970 0.0035537070 13.7981673080
Fe2 2.5679283770 4.4334394800 13.7981659840
Fe1 2.5669858700 1.4689051280 11.5756396750
Fe1 0.0093933150 5.8987909180 11.5756398940
Fe1 7.6656797000 1.4817571350 11.5862373860
Fe1 5.1080833360 5.9116454910 11.5862375160
Fe2 -0.0042614820 0.0105670880 4.1320189190
Fe2 -2.5618586840 4.4404518860 4.1320208830
Fe2 5.1048506000 -0.0035747330 4.1440081100
Fe2 2.5472582910 4.4263070990 4.1440083420
Fe1 -0.0071868200 0.0081725700 10.9497714470
Fe1 -2.5647824910 4.4380570870 10.9497682980
Fe1 5.1212500650 -0.0095184850 10.9437362090
Fe1 2.5636552240 4.4203658880 10.9437352290
Fe2 2.5499011480 1.4613400250 4.4922360730
Fe2 -0.0076898090 5.8912281540 4.4922383830
Fe2 7.6661845650 1.4903042710 4.4907724000
Fe2 5.1085860530 5.9201980080 4.4907689920
O 1.5876418620 0.0061446290 5.5311746490
O -0.9699511870 4.4360280150 5.5311770370
O 6.6878388300 0.0275069840 5.4972293360
O 4.1302431560 4.4573925660 5.4972277060
O -0.8016266570 1.3480339810 5.4927865090
O -3.3592246400 5.7779222790 5.4927871470
O 4.3070194810 1.3712917610 5.5234470860
O 1.7494276300 5.8011778800 5.5234473970
O 1.7866691600 3.0472196360 5.5138718580
O -0.7709266780 7.4771078630 5.5138730830
O 6.8873023040 3.0640978090 5.5036041720
O 4.3297073080 7.4939855400 5.5036028960
O 3.5425295780 -0.0275138930 12.4449599780
O 0.9849346730 4.4023692630 12.4449598520
O 8.6427386860 -0.0061247470 12.4110699890
O 6.0851421260 4.4237615070 12.4110701570
O -1.7559514520 3.0818416160 12.4494141880
O -4.3135469120 7.5117280380 12.4494138240
O 3.3657478530 3.0585955260 12.4187662170
O 0.8081544520 7.4884809740 12.4187667800
O 0.7854904350 1.3657858200 12.4386307900
O -1.7721043000 5.7956720070 12.4386314070
O 5.8860951440 1.3826649650 12.4282866260
O 3.3284994720 5.8125502800 12.4282864440
O 4.1166614340 1.4645996620 10.1145453140
O 1.5590674520 5.8944851520 10.1145451050
O 9.2269974080 1.4803687950 10.1217680730
O 6.6694017510 5.9102550170 10.1217676140
O 1.7818482420 2.8207026990 10.1174819610
O -0.7757469790 7.2505879530 10.1174825190
O 6.9010841860 2.8305873780 10.1181246180
O 4.3434894840 7.2604730540 10.1181249160
O 1.7741966510 0.1288704280 10.1210857390
O -0.7833973170 4.5587539860 10.1210854260
O 6.8899562970 0.1330665840 10.1120475200
O 4.3323605940 4.5629516570 10.1120471380
O 0.9701331880 1.3601825970 3.2282024340
O -1.5874686030 5.7900769690 3.2282067890
O 6.0424281310 1.4307853840 3.2268102980
O 3.4848329690 5.8606717640 3.2268088460
O 3.4497130460 0.1594407470 3.2299878150
O 0.8921189880 4.5893199730 3.2299897900
O 8.4991414710 0.1178429460 3.2194029720
O 5.9415422800 4.5477245100 3.2194026110
O 3.3132459900 2.9096380620 3.2197995640
O 0.7556552770 7.3395256070 3.2198009610
O 8.3518434290 2.9122553130 3.2310509720
O 5.7942432590 7.3421413850 3.2310463280
O 1.6303686080 2.9990986700 14.7154264290
O -0.9272253740 7.4289841310 14.7154271030
O 6.7026748000 3.0696443590 14.7139669070
O 4.1450783670 7.4995301020 14.7139661290
O -0.8263228630 4.3120244250 14.7228303440
O -3.3839199740 8.7419091050 14.7228297620
O 4.2230749100 4.2704404770 14.7121629510
O 1.6654822570 8.7003239570 14.7121628730
O -0.6790130500 1.5176273280 14.7112304960
O -3.2366092980 5.9475136980 14.7112310180
O 4.3595390350 1.5202210420 14.7223422960
O 1.8019453980 5.9501066020 14.7223415410
O -1.5542259670 2.9495219770 7.8204389860
O -4.1118223300 7.3794095700 7.8204372890
O 3.5560997970 2.9653009210 7.8276209960
O 0.9985058630 7.3951864550 7.8276207880
O 0.7716877980 1.5993129060 7.8240644920
O -1.7859066240 6.0291996150 7.8240663310
O 5.8909212760 1.6091960660 7.8246984280
O 3.3333264010 6.0390821070 7.8246977240
O 0.7828089050 4.2968328780 7.8301175690
O -1.7747868400 8.7267182450 7.8301170030
O 5.8985724020 4.3010382430 7.8211076630
O 3.3409793080 8.7309223000 7.8211058410
O 2.5674925870 1.4703262560 17.0273595790
O 2.5477093370 7.3894410440 0.9148493100
K_POINTS gamma
environ.in
&ENVIRON
!
verbose = 0
environ_thr = 1.d-1
environ_type = 'water'
tolrhopol = 1.d-11
mixrhopol = 0.6
!mixtype = 'pcg'
!
/
Best regards,
Dr. Huu Chuong Nguyën (Bob)
Postdoc Researcher – Group of Prof. Núria López
Institute of Chemical Research of Catalonia (ICIQ)
The Barcelona Institute of Science and Technology
Av. Països Catalans 16 – 43007 Tarragona (Spain)
PB-11 Huu Chuong Nguyën – PERSONAL
hnguyen at iciq.es<mailto:user at iciq.es> - www.iciq.es<http://www.iciq.es/>
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