<div dir="ltr"><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Sara Fiore</b> <span dir="ltr"><<a href="mailto:sara.fiore63@gmail.com" target="_blank">sara.fiore63@gmail.com</a>></span><br>Date: Tue, May 8, 2018 at 10:53 AM<br>Subject: assume_isolated = '2D' SEGMENTATION FAULT<br>To: <a href="mailto:developers-owner@lists.quantum-espresso.org" target="_blank">developers-owner@lists.<wbr>quantum-espresso.org</a><br><br><br>Dear all, <br>
<br>
I am writing because I am trying to simulate an isolated monolayer of<br>
MoS2 using the new keyword assume_isolated = '2D'<br>
<br>
Below my input files and in attachment the outputs.<br>
<br>
The scf calculation reaches the end<br>
<br>
------------------------------<wbr>------------------------------<wbr>------<br>
&control<br>
calculation='scf'<br>
max_seconds = 1746 <br>
title ='MoS2'<br>
restart_mode='from_scratc<wbr>h'<br>
pseudo_dir='/home/safiore<wbr>/SSSP_accuracy_pseudos'<br>
outdir='/usr/scratch2/bab<wbr>ba/Sara/MoS2/phonons_rho240_<wbr>ethr-<br>
10_k12_phthr-18_beta07_alpha04<wbr>_SSSP_q8_2D'<br>
prefix='MoS2',<br>
verbosity = 'high'<br>
/<br>
&system<br>
assume_isolated = '2D'<br>
ibrav=0<br>
nat=3, <br>
ntyp=2, <br>
ecutwfc = 35, <br>
ecutrho = 240,<br>
<br>
/<br>
&electrons<br>
conv_thr = 1.0d-10 <wbr> <br>
/<br>
ATOMIC_SPECIES<br>
Mo 95.94 Mo_ONCV_PBE-1.0.u<wbr>pf<br>
S 32.065 s_pbe_v1.4.uspp.F<wbr>.UPF<br>
<br>
ATOMIC_POSITIONS angstrom<br>
Mo -0.013930471 1.826687135 3.073772837<br>
S 1.581961748 0.905312344 4.642141936<br>
S 1.581970298 0.905306278 1.505335227<br>
<br>
<br>
K_POINTS automatic<br>
12 12 1 0 0 0<br>
<br>
CELL_PARAMETERS angstrom<br>
3.1927000000 -0.000<wbr>0000000 0.0000000000<br>
-1.5963500000 2.764<wbr>9593067 0.0000000000<br>
0.0000000000 0.000<wbr>0000000 23.1547020881<br>
<br>
------------------------------<wbr>------------------------------<wbr>------<br>
<br>
while the phonon calculation gives errors:<br>
<br>
------------------------------<wbr>------------------------------<wbr>------<br>
phonons of MoS2<br>
&INPUTPH<br>
alpha_mix(1) = 4.0000000000d-01<br>
epsil = .true.<br>
fildrho = 'drho'<br>
fildvscf = 'dvscf'<br>
fildyn = '/usr/scratch2/babba/Sara/MoS2<wbr>/phonons_rho240_ethr-<br>
10_k12_phthr-18_beta07_alpha04<wbr>_SSSP_q8_2D/dyn'<br>
iverbosity = 1<br>
ldisp = .true.<br>
nq1 = 8<br>
nq2 = 8<br>
nq3 = 1<br>
outdir='/usr/scratch2/babba/Sa<wbr>ra/MoS2/phonons_rho240_ethr-<br>
10_k12_phthr-18_beta07_alpha04<wbr>_SSSP_q8_2D'<br>
prefix = 'MoS2'<br>
tr2_ph = 1.0000000000d-18<br>
/<br>
<br>
------------------------------<wbr>------------------------------<wbr>------<br>
<br>
it suddenly stops after the 1st dynamical matrix (output file ph.out in<br>
attachment), giving the following error<br>
<br>
------------------------------<wbr>------------------------------<wbr>--------<br>
<br>
Program received signal SIGSEGV: Segmentation fault - invalid memory<br>
reference.<br>
<br>
Backtrace for this error:<br>
#0 0x2ae1a95cc26f in ???<br>
#1 0x2ae1a9613418 in ???<br>
#2 0x5b02c4 in init_us_2_<br>
at /scratch/local/quantumespresso<wbr>/PW/src/init_us_2.f90:153<br>
#3 0x45be8a in phq_init_<br>
at /scratch/local/quantumespresso<wbr>/PHonon/PH/phq_init.f90:187<br>
#4 0x43b3c9 in initialize_ph_<br>
at<br>
/scratch/local/quantumespresso<wbr>/PHonon/PH/initialize_ph.f90:<wbr>69<br>
#5 0x40aa20 in do_phonon_<br>
at /scratch/local/quantumespresso<wbr>/PHonon/PH/do_phonon.f90:74<br>
#6 0x4052c5 in phonon<br>
at /scratch/local/quantumespresso<wbr>/PHonon/PH/phonon.f90:77<br>
#7 0x40517c in main<br>
at /scratch/local/quantumespresso<wbr>/PHonon/PH/phonon.f90:43<br>
<br>
------------------------------<wbr>------------------------------<wbr>--------<br>
<br>
<br>
The same calculation without "assume_isolated = '2D'" works well.<br>
<br>
<br>
Am I misunderstanding something about that keyword or does the problem<br>
concern something else?<br>
<br>
Thank you in advance <br>
<br>
best regards<br>
<br>
<br>
Sara Fiore<br>
<br>
ETH Zürich | PhD Student | Doctorate at D-ITET<br>
Rechn. Modellierung Nanostrukturen<br>
ETZ J 66 | Gloriastrasse 35 | 8092 Zürich | Switzerland<br>
<a href="mailto:sara.fiore63@gmail.com" target="_blank">sara.fiore63@gmail.com</a><br>
<a href="mailto:safiore@iis.ee.ethz.ch" target="_blank">safiore@iis.ee.ethz.ch</a><br>
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