[QE-developers] Fwd: assume_isolated = '2D' SEGMENTATION FAULT

[sohier]

Dear Sara,

You are using the 2D flag properly. I'm not sure where the error comes 
from. Running your inputs on my machine, I also get an error.

But I don't get an error if running the phonon by itself (single q-point 
calculation)... Also, re-launching the ph calculation with 
recover=.true. works fine, i.e. the ph calculation is recovered and 
proceeds fine. So that could be a quick fix for you.

For a more permanent solution, I will have to look more into it. If 
someone has an idea, help would be much appreciated.

Thibault Sohier
Post-Doc
THEOS-MARVEL, EPFL
Lausanne, Switzerland



On 08/05/2018 10:57, developers-request at lists.quantum-espresso.org wrote:
> Send developers mailing list submissions to
> 	developers at lists.quantum-espresso.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> 	https://lists.quantum-espresso.org/mailman/listinfo/developers
> or, via email, send a message with subject or body 'help' to
> 	developers-request at lists.quantum-espresso.org
>
> You can reach the person managing the list at
> 	developers-owner at lists.quantum-espresso.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of developers digest..."
>
>
> Today's Topics:
>
>     1. Fwd: assume_isolated = '2D' SEGMENTATION FAULT (Paolo Giannozzi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 8 May 2018 10:57:09 +0200
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> To: General discussion list for Quantum ESPRESSO developers
> 	<developers at lists.quantum-espresso.org>
> Subject: [QE-developers] Fwd: assume_isolated = '2D' SEGMENTATION
> 	FAULT
> Message-ID:
> 	<CAPMgbCva-j3hqUoTa+3gBPCqRsspoKEE_dXoo4nf1wBAmqy68A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> ---------- Forwarded message ----------
> From: Sara Fiore <sara.fiore63 at gmail.com>
> Date: Tue, May 8, 2018 at 10:53 AM
> Subject: assume_isolated = '2D' SEGMENTATION FAULT
> To: developers-owner at lists.quantum-espresso.org
>
>
> Dear all,
>
> I am writing because I am trying to simulate an isolated monolayer of
> MoS2 using the new keyword  assume_isolated = '2D'
>
> Below my input files and in attachment the outputs.
>
> The scf calculation reaches the end
>
> ------------------------------------------------------------------
> &control
>       calculation='scf'
>       max_seconds = 1746
>       title ='MoS2'
>       restart_mode='from_scratch'
>       pseudo_dir='/home/safiore/SSSP_accuracy_pseudos'
>       outdir='/usr/scratch2/babba/Sara/MoS2/phonons_rho240_ethr-
> 10_k12_phthr-18_beta07_alpha04_SSSP_q8_2D'
>       prefix='MoS2',
>       verbosity = 'high'
>    /
>    &system
>       assume_isolated = '2D'
>       ibrav=0
>       nat=3,
>       ntyp=2,
>       ecutwfc = 35,
>       ecutrho = 240,
>
>    /
>    &electrons
>       conv_thr = 1.0d-10
>    /
>   ATOMIC_SPECIES
>    Mo  95.94    Mo_ONCV_PBE-1.0.upf
>    S   32.065   s_pbe_v1.4.uspp.F.UPF
>
> ATOMIC_POSITIONS angstrom
> Mo -0.013930471 1.826687135     3.073772837
> S  1.581961748  0.905312344     4.642141936
> S  1.581970298  0.905306278     1.505335227
>
>
> K_POINTS automatic
> 12 12 1 0 0 0
>
> CELL_PARAMETERS angstrom
>        3.1927000000      -0.0000000000       0.0000000000
>       -1.5963500000       2.7649593067       0.0000000000
>        0.0000000000       0.0000000000      23.1547020881
>
> ------------------------------------------------------------------
>
>   while the phonon calculation gives errors:
>
> ------------------------------------------------------------------
> phonons of MoS2
>   &INPUTPH
>    alpha_mix(1) =   4.0000000000d-01
>    epsil = .true.
>    fildrho = 'drho'
>    fildvscf = 'dvscf'
>    fildyn = '/usr/scratch2/babba/Sara/MoS2/phonons_rho240_ethr-
> 10_k12_phthr-18_beta07_alpha04_SSSP_q8_2D/dyn'
>    iverbosity = 1
>    ldisp = .true.
>    nq1 = 8
>    nq2 = 8
>    nq3 = 1
>    outdir='/usr/scratch2/babba/Sara/MoS2/phonons_rho240_ethr-
> 10_k12_phthr-18_beta07_alpha04_SSSP_q8_2D'
>    prefix = 'MoS2'
>    tr2_ph =   1.0000000000d-18
> /
>
> ------------------------------------------------------------------
>
> it suddenly stops after the 1st dynamical matrix (output file ph.out in
> attachment), giving the following error
>
> --------------------------------------------------------------------
>
> Program received signal SIGSEGV: Segmentation fault - invalid memory
> reference.
>
> Backtrace for this error:
> #0  0x2ae1a95cc26f in ???
> #1  0x2ae1a9613418 in ???
> #2  0x5b02c4 in init_us_2_
>          at /scratch/local/quantumespresso/PW/src/init_us_2.f90:153
> #3  0x45be8a in phq_init_
>          at /scratch/local/quantumespresso/PHonon/PH/phq_init.f90:187
> #4  0x43b3c9 in initialize_ph_
>          at
> /scratch/local/quantumespresso/PHonon/PH/initialize_ph.f90:69
> #5  0x40aa20 in do_phonon_
>          at /scratch/local/quantumespresso/PHonon/PH/do_phonon.f90:74
> #6  0x4052c5 in phonon
>          at /scratch/local/quantumespresso/PHonon/PH/phonon.f90:77
> #7  0x40517c in main
>          at /scratch/local/quantumespresso/PHonon/PH/phonon.f90:43
>
> --------------------------------------------------------------------
>
>
> The same calculation without "assume_isolated = '2D'" works well.
>
>
> Am I misunderstanding something about that keyword or does the problem
> concern something else?
>
> Thank you in advance
>
> best regards
>
>
> Sara Fiore
>
> ETH Z?rich | PhD Student | Doctorate at D-ITET
> Rechn. Modellierung Nanostrukturen
> ETZ J 66 | Gloriastrasse 35 | 8092 Z?rich | Switzerland
>         sara.fiore63 at gmail.com
>         safiore at iis.ee.ethz.ch
>         Tel: +41 44 632 23 48
>
>
>