EPW for 2-dimensional buckled system

[beda]

Dear all,
First of all, my apologies for posting a lengthy question (I have included all the inputs to make the problem clear).
I am trying to get electron-phonon interaction for 2-D buckled Silicene system using EPW-4.2 and qe-6.1. I followed the steps given in test-05 of MgB2 and https://github.com/QEF/q-e/tree/master/ ... Inputs/t05.
The result of test05 and other examples given in tutorial of EPW (Pb, GaN, etc.,) can be exactly reproduced in my lab computer. The problem arises when I tried for silicene. The epw.x calculation remains paused ( i mean the after the G-vector sticks info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Sum 1069 433 163 75009 19037 4655) the calculation does not proceed.

I am unable to understand whether my input is wrong or there is some mistake in executing the commands.

The steps which i followed are

mpirun -np 4 ../../../../bin/pw.x < scf.in > scf.out
mpirun -np 4 ../../../../bin/ph.x < ph.in > ph.out
python pp.py < pp.in
mpirun -np 4 ../../../../bin/pw.x < scf_epw.in > scf_epw.out
mpirun -np 4 ../../../../bin/pw.x -npool 4 < nscf_epw.in > nscf_epw.out
mpirun -np 4 ../../../src/epw.x -npool 4 < epw_iso.in > epw_iso.out


And the inputs are
************************************************************
scf.in
&control
calculation = 'scf'
restart_mode='from_scratch',
prefix='silicene',
pseudo_dir = './',
outdir='./',
/
&system
ibrav=4,nat=2,ntyp=1,
a=3.824512950,
c=10.0,
ecutwfc =30, ecutrho=300,
occupations = 'smearing'
smearing = 'mp'
degauss = 0.02
/
&electrons
conv_thr = 1.0d-10
mixing_beta = 0.7
mixing_mode = 'plain'
/

ATOMIC_SPECIES
Si 28.0855 Si.pz-vbc.UPF
ATOMIC_POSITIONS (crystal)
Si 0.333333330 0.666666660 0.491879248
Si 0.666666660 0.333333330 0.533106764


K_POINTS {automatic}
10 10 1 0 0 0
************************************************
ph.in

phonons of silicene
&inputph
prefix='silicene',
amass(1)=28.0855,
fildvscf = 'dvscf'
fildyn='silicene.dyn',
ldisp=.true.,
nq1= 5,
nq2= 5,
nq3= 1,
tr2_ph=1.0d-20,
/
********************************************************
pp.py


#
# Post-processing script QE --> EPW
# 14/07/2015 - Samuel Ponce
#

import numpy as np
import os

# Enter the number of irr. q-points
user_input = raw_input('Enter the prefix used for PH calculations (e.g. diam)\n')
prefix = str(user_input)

# Enter the number of irr. q-points
user_input = raw_input('Enter the number of irreducible q-points\n')
nqpt = user_input
try:
nqpt = int(user_input)
except ValueError:
raise Exception('The value you enter is not an integer!')

os.system('mkdir save')

for iqpt in np.arange(1,nqpt+1):
label = str(iqpt)

os.system('cp '+prefix+'.dyn'+str(iqpt)+' save/'+prefix+'.dyn_q'+label)
if (iqpt == 1):
os.system('cp _ph0/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q'+label)
os.system('cp -r _ph0/'+prefix+'.phsave save/')
else:
os.system('cp _ph0/'+prefix+'.q_'+str(iqpt)+'/'+prefix+'.dvscf1 save/'+prefix+'.dvscf_q'+label)
os.system('rm _ph0/'+prefix+'.q_'+str(iqpt)+'/*wfc*' )
***************************************************************
pp.in

silicene
5
*********************************************************************
scf_epw.in

&control
calculation = 'scf'
restart_mode='from_scratch',
prefix='silicene',
pseudo_dir = './',
outdir='./',
wf_collect = .true.
verbosity = 'high'
tprnfor = .true.,
tstress = .true.,
/
&system
ibrav=4,nat=2,ntyp=1,
a=3.824512950,
c=10.0,
ecutwfc =30, ecutrho=300,
occupations = 'smearing'
smearing = 'mp'
degauss = 0.02
/
&electrons
conv_thr = 1.0d-10
mixing_beta = 0.7
mixing_mode = 'plain'
/

ATOMIC_SPECIES
Si 28.0855 Si.pz-vbc.UPF
ATOMIC_POSITIONS (crystal)
Si 0.333333330 0.666666660 0.491879248
Si 0.666666660 0.333333330 0.533106764


K_POINTS {automatic}
5 5 1 0 0 0
*************************************************************************

nscf_epw.in

&control
calculation = 'nscf'
restart_mode='from_scratch',
prefix='silicene',
pseudo_dir = './',
outdir='./',
wf_collect = .false.
/
&system
ibrav=4,nat=2,ntyp=1,
a=3.824512950,
c=10.0,
ecutwfc =30, ecutrho=300,
occupations = 'smearing'
smearing = 'mp'
degauss = 0.02
/
&electrons
conv_thr = 1.0d-10
mixing_beta = 0.7
mixing_mode = 'plain'
/

ATOMIC_SPECIES
Si 28.0855 Si.pz-vbc.UPF
ATOMIC_POSITIONS (crystal)
Si 0.333333330 0.666666660 0.491879248
Si 0.666666660 0.333333330 0.533106764

K_POINTS crystal
25
0.00000000 0.00000000 0.00000000 4.000000e-02
0.00000000 0.20000000 0.00000000 4.000000e-02
0.00000000 0.40000000 0.00000000 4.000000e-02
0.00000000 0.60000000 0.00000000 4.000000e-02
0.00000000 0.80000000 0.00000000 4.000000e-02
0.20000000 0.00000000 0.00000000 4.000000e-02
0.20000000 0.20000000 0.00000000 4.000000e-02
0.20000000 0.40000000 0.00000000 4.000000e-02
0.20000000 0.60000000 0.00000000 4.000000e-02
0.20000000 0.80000000 0.00000000 4.000000e-02
0.40000000 0.00000000 0.00000000 4.000000e-02
0.40000000 0.20000000 0.00000000 4.000000e-02
0.40000000 0.40000000 0.00000000 4.000000e-02
0.40000000 0.60000000 0.00000000 4.000000e-02
0.40000000 0.80000000 0.00000000 4.000000e-02
0.60000000 0.00000000 0.00000000 4.000000e-02
0.60000000 0.20000000 0.00000000 4.000000e-02
0.60000000 0.40000000 0.00000000 4.000000e-02
0.60000000 0.60000000 0.00000000 4.000000e-02
0.60000000 0.80000000 0.00000000 4.000000e-02
0.80000000 0.00000000 0.00000000 4.000000e-02
0.80000000 0.20000000 0.00000000 4.000000e-02
0.80000000 0.40000000 0.00000000 4.000000e-02
0.80000000 0.60000000 0.00000000 4.000000e-02
0.80000000 0.80000000 0.00000000 4.000000e-02
*********************************************************************************************
epw_iso.in

--
&inputepw
prefix = 'silicene',
amass(1) = 28.0855,
outdir = './'
ep_coupling = .true.
elph = .true.
kmaps = .false.
epbwrite = .true.
epbread = .false.
epwwrite = .true.
epwread = .false.
etf_mem = .true.
nbndsub = 5,
nbndskip = 0
wannierize = .true.
num_iter = 500
! dis_froz_max= 8.8
proj(1) = 'random'
iverbosity = 0
parallel_k = .true.
parallel_q = .false.
eps_acustic = 5.0 ! Lowest boundary for the
ephwrite = .true. ! Writes .ephmat files used when wliasberg = .true.
fsthick = 0.4 ! eV
eptemp = 300 ! K
degaussw = 0.10 ! eV
degaussq = 0.5 ! meV
nqstep = 500
eliashberg = .true.
liso = .true.
limag = .true.
lpade = .true.
lacon = .true.
conv_thr_iaxis = 1.0d-2
conv_thr_racon = 1.0d-2
wscut = 0.5 ! eV Upper limit over frequency integration/summation in the Elisashberg eq
nstemp = 1
tempsmin = 25.00
tempsmax = 30.00
nsiter = 500
muc = 0.16
dvscf_dir = './save'

efermi_read=.true.
fermi_energy= -0.9566 ! ev

nk1 = 5
nk2 = 5
nk3 = 1

nq1 = 5
nq2 = 5
nq3 = 1

mp_mesh_k = .true.
nkf1 = 10
nkf2 = 10
nkf3 = 1

nqf1 = 10
nqf2 = 10
nqf3 = 1
/
5 cartesian
0.000000000 0.000000000 0.000000000 1.0
0.000000000 0.230940108 0.000000000 1.0
0.000000000 0.461880215 0.000000000 1.0
0.200000000 0.346410162 0.000000000 1.0
0.200000000 0.577350269 0.000000000 1.0
***********************************************************************************************



If I run in series without mpirun the error shows up as:

**********************************************************************************************************************************************
Program EPW v.4.1.0 (svn rev. 13369) starts on 24May2017 at 16:30:17

This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Parallel version (MPI), running on 4 processors
K-points division: npool = 4
Reading data from directory:
./silicene.save
Info: using nr1, nr2, nr3 values from input
Info: using nr1, nr2, nr3 values from input
IMPORTANT: XC functional enforced from input :
Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0 0)
Any further DFT definition will be discarded
Please, verify this is what you really want
G-vector sticks info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Sum 1069 433 163 75009 19037 4655
*** Error in `/home/physics/QE/qe-6.1/EPW/src/epw.x': malloc(): memory corruption: 0x0000000003fd9ce0 ***
Program received signal SIGABRT: Process abort signal.
Backtrace for this error:
*****************************************************************************************************************************


Thank you for your kind help.

Sincerely,
Bedamani
Nagaland University, India

[sponce]

Hello,

I do not see anything obvious yet.
However, the last run you did was clearly not serial:

Code: Select all

Parallel version (MPI), running on 4 processors
K-points division: npool = 4

But it is a good idea to have more info on the issue. Try:
mpirun -np 1 ../../../../bin/pw.x < nscf_epw.in > nscf_epw.out
mpirun -np 1 ../../../src/epw.x < epw_iso.in > epw_iso.out

Let me know the error message you get.

Also if you can, try to compile with "-g" flag and then run gdb to see exactly which line is problematic.

Best,

Samuel

[beda]

Dear Sponce,
First of all thank you for your quick response and valuable suggestion. I run the epw.x calculation as per your suggestion and the calculation ends after some writing epb.files. Now the problem seems to be with memory of my computer and I will try to look into it. The output is attached here.

*************************************
Parallel version (MPI), running on 1 processors
Reading data from directory:
./silicene.save
Info: using nr1, nr2, nr3 values from input
Info: using nr1, nr2, nr3 values from input
IMPORTANT: XC functional enforced from input :
Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0 0)
Any further DFT definition will be discarded
Please, verify this is what you really want
G-vector sticks info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Sum 1069 433 163 75009 19037 4655
--
bravais-lattice index = 4
lattice parameter (a_0) = 7.2273 a.u.
unit-cell volume = 854.8295 (a.u.)^3
number of atoms/cell = 2
number of atomic types = 1
kinetic-energy cut-off = 30.0000 Ry
charge density cut-off = 300.0000 Ry
convergence threshold = 0.0E+00
beta = 0.0000
number of iterations used = 0
Exchange-correlation = SLA PZ NOGX NOGC ( 1 1 0 0 0 0)
celldm(1)= 7.22728 celldm(2)= 0.00000 celldm(3)= 2.61471
celldm(4)= 0.00000 celldm(5)= 0.00000 celldm(6)= 0.00000
crystal axes: (cart. coord. in units of a_0)
a(1) = ( 1.0000 0.0000 0.0000 )
a(2) = ( -0.5000 0.8660 0.0000 )
a(3) = ( 0.0000 0.0000 2.6147 )
reciprocal axes: (cart. coord. in units 2 pi/a_0)
b(1) = ( 1.0000 0.5774 -0.0000 )
b(2) = ( 0.0000 1.1547 0.0000 )
b(3) = ( 0.0000 -0.0000 0.3825 )
Atoms inside the unit cell:
Cartesian axes
site n. atom mass positions (a_0 units)
1 Si 28.0879 tau( 1) = ( 0.00000 0.57735 1.28612 )
2 Si 28.0879 tau( 2) = ( 0.50000 0.28868 1.39392 )
7 Sym.Ops. (with q -> -q+G )
G cutoff = 396.9278 ( 75009 G-vectors) FFT grid: ( 40, 40,108)
G cutoff = 158.7711 ( 19037 G-vectors) smooth grid: ( 25, 25, 25)
number of k points= 25 gaussian broad. (Ry)= 0.0200 ngauss = 1
cart. coord. in units 2pi/a_0
k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0800000
k( 2) = ( 0.0000000 0.2309401 0.0000000), wk = 0.0800000
k( 3) = ( 0.0000000 0.4618802 0.0000000), wk = 0.0800000
k( 4) = ( 0.0000000 0.6928203 0.0000000), wk = 0.0800000
k( 5) = ( 0.0000000 0.9237604 0.0000000), wk = 0.0800000
k( 6) = ( 0.2000000 0.1154701 0.0000000), wk = 0.0800000
k( 7) = ( 0.2000000 0.3464102 0.0000000), wk = 0.0800000
k( 8) = ( 0.2000000 0.5773503 0.0000000), wk = 0.0800000
k( 9) = ( 0.2000000 0.8082904 0.0000000), wk = 0.0800000
k( 10) = ( 0.2000000 1.0392305 0.0000000), wk = 0.0800000
k( 11) = ( 0.4000000 0.2309401 0.0000000), wk = 0.0800000
k( 12) = ( 0.4000000 0.4618802 0.0000000), wk = 0.0800000
k( 13) = ( 0.4000000 0.6928203 0.0000000), wk = 0.0800000
k( 14) = ( 0.4000000 0.9237604 0.0000000), wk = 0.0800000
k( 15) = ( 0.4000000 1.1547005 0.0000000), wk = 0.0800000
k( 16) = ( 0.6000000 0.3464102 0.0000000), wk = 0.0800000
k( 17) = ( 0.6000000 0.5773503 0.0000000), wk = 0.0800000
k( 18) = ( 0.6000000 0.8082904 0.0000000), wk = 0.0800000
k( 19) = ( 0.6000000 1.0392305 0.0000000), wk = 0.0800000
k( 20) = ( 0.6000000 1.2701706 0.0000000), wk = 0.0800000
k( 21) = ( 0.8000000 0.4618802 0.0000000), wk = 0.0800000
k( 22) = ( 0.8000000 0.6928203 0.0000000), wk = 0.0800000
k( 23) = ( 0.8000000 0.9237604 0.0000000), wk = 0.0800000
k( 24) = ( 0.8000000 1.1547005 0.0000000), wk = 0.0800000
k( 25) = ( 0.8000000 1.3856406 0.0000000), wk = 0.0800000
PseudoPot. # 1 for Si read from file:
./Si.pz-vbc.UPF
MD5 check sum: 6dfa03ddd5817404712e03e4d12deb78
Pseudo is Norm-conserving, Zval = 4.0
Generated by new atomic code, or converted to UPF format
Using radial grid of 431 points, 2 beta functions with:
l(1) = 0
l(2) = 1
EPW : 0.44s CPU 0.47s WALL
EPW : 1.67s CPU 1.70s WALL
No wavefunction gauge setting applied
-------------------------------------------------------------------
Wannierization on 5 x 5 x 1 electronic grid
-------------------------------------------------------------------
Spin CASE ( default = unpolarized )
Initializing Wannier90
Initial Wannier projections
( 0.99756 0.56682 0.96592) : l = 0 mr = 1
( 0.74793 0.36739 0.48064) : l = 0 mr = 1
( 0.07375 0.00536 0.34708) : l = 0 mr = 1
( 0.34224 0.21795 0.13316) : l = 0 mr = 1
( 0.90052 0.38677 0.44548) : l = 0 mr = 1
- Number of bands is ( 8)
- Number of wannier functions is ( 5)
- All guiding functions are given
Reading data about k-point neighbours
- All neighbours are found
AMN
k points = 25 in 1 pools
1 of 25 on ionode
2 of 25 on ionode
3 of 25 on ionode
4 of 25 on ionode
5 of 25 on ionode
6 of 25 on ionode
7 of 25 on ionode
8 of 25 on ionode
9 of 25 on ionode
10 of 25 on ionode
11 of 25 on ionode
12 of 25 on ionode
13 of 25 on ionode
14 of 25 on ionode
15 of 25 on ionode
16 of 25 on ionode
17 of 25 on ionode
18 of 25 on ionode
19 of 25 on ionode
20 of 25 on ionode
21 of 25 on ionode
22 of 25 on ionode
23 of 25 on ionode
24 of 25 on ionode
25 of 25 on ionode
AMN calculated
MMN
k points = 25 in 1 pools
1 of 25 on ionode
2 of 25 on ionode
3 of 25 on ionode
4 of 25 on ionode
5 of 25 on ionode
6 of 25 on ionode
7 of 25 on ionode
8 of 25 on ionode
9 of 25 on ionode
10 of 25 on ionode
11 of 25 on ionode
12 of 25 on ionode
13 of 25 on ionode
14 of 25 on ionode
15 of 25 on ionode
16 of 25 on ionode
17 of 25 on ionode
18 of 25 on ionode
19 of 25 on ionode
20 of 25 on ionode
21 of 25 on ionode
22 of 25 on ionode
23 of 25 on ionode
24 of 25 on ionode
25 of 25 on ionode
MMN calculated
Running Wannier90
Wannier Function centers (cartesian, alat) and spreads (ang):
( 0.49498 0.01785 -1.26927) : 1.93722
( 0.24407 0.43967 -1.27865) : 1.71330
( 0.36137 -0.37260 0.23395) : 21.44755
( 0.54404 0.02337 -0.16374) : 21.92331
( 0.74319 0.42266 -0.55262) : 21.25720
-------------------------------------------------------------------
WANNIER : 32.25s CPU 32.66s WALL ( 1 calls)
-------------------------------------------------------------------
Dipole matrix elements calculated
Calculating kmap and kgmap
Progress kmap: #########################
Progress kgmap: ########################################
kmaps : 141.61s CPU 142.07s WALL ( 1 calls)
Symmetries of bravais lattice: 24
Symmetries of crystal: 6
===================================================================
irreducible q point # 1
===================================================================
Symmetries of small group of q: 6
in addition sym. q -> -q+G:
Number of q in the star = 1
List of q in the star:
1 0.000000000 0.000000000 0.000000000
Imposing acoustic sum rule on the dynamical matrix
q( 1 ) = ( 0.0000000 0.0000000 0.0000000 )
===================================================================
irreducible q point # 2
===================================================================
Symmetries of small group of q: 2
Number of q in the star = 3
List of q in the star:
1 0.000000000 0.230940108 0.000000000
2 0.200000000 -0.115470054 0.000000000
3 -0.200000000 -0.115470054 0.000000000
In addition there is the -q list:
1 -0.000000000 -0.230940108 -0.000000000
2 -0.200000000 0.115470054 -0.000000000
3 0.200000000 0.115470054 -0.000000000
q( 2 ) = ( 0.0000000 0.2309401 0.0000000 )
q( 3 ) = ( -0.0000000 -0.2309401 -0.0000000 )
q( 4 ) = ( 0.2000000 -0.1154701 0.0000000 )
q( 5 ) = ( -0.2000000 0.1154701 -0.0000000 )
q( 6 ) = ( -0.2000000 -0.1154701 0.0000000 )
q( 7 ) = ( 0.2000000 0.1154701 -0.0000000 )
===================================================================
irreducible q point # 3
===================================================================
Symmetries of small group of q: 2
Number of q in the star = 3
List of q in the star:
1 0.000000000 0.461880215 0.000000000
2 0.400000000 -0.230940107 0.000000000
3 -0.400000000 -0.230940108 0.000000000
In addition there is the -q list:
1 -0.000000000 -0.461880215 -0.000000000
2 -0.400000000 0.230940107 -0.000000000
3 0.400000000 0.230940108 -0.000000000
q( 8 ) = ( 0.0000000 0.4618802 0.0000000 )
q( 9 ) = ( -0.0000000 -0.4618802 -0.0000000 )
q( 10 ) = ( 0.4000000 -0.2309401 0.0000000 )
q( 11 ) = ( -0.4000000 0.2309401 -0.0000000 )
q( 12 ) = ( -0.4000000 -0.2309401 0.0000000 )
q( 13 ) = ( 0.4000000 0.2309401 -0.0000000 )
===================================================================
irreducible q point # 4
===================================================================
Symmetries of small group of q: 1
Number of q in the star = 6
List of q in the star:
1 0.200000000 0.346410162 0.000000000
2 -0.200000000 0.346410162 0.000000000
3 0.200000000 -0.346410162 0.000000000
4 -0.400000000 -0.000000000 0.000000000
5 0.400000000 -0.000000000 0.000000000
6 -0.200000000 -0.346410162 0.000000000
q( 14 ) = ( 0.2000000 0.3464102 0.0000000 )
q( 15 ) = ( -0.2000000 0.3464102 0.0000000 )
q( 16 ) = ( 0.2000000 -0.3464102 0.0000000 )
q( 17 ) = ( -0.4000000 -0.0000000 0.0000000 )
q( 18 ) = ( 0.4000000 -0.0000000 0.0000000 )
q( 19 ) = ( -0.2000000 -0.3464102 0.0000000 )
===================================================================
irreducible q point # 5
===================================================================
Symmetries of small group of q: 1
Number of q in the star = 6
List of q in the star:
1 0.200000000 0.577350269 0.000000000
2 -0.200000000 0.577350269 0.000000000
3 0.400000000 -0.461880215 0.000000000
4 -0.600000000 -0.115470054 0.000000000
5 0.600000000 -0.115470054 0.000000000
6 -0.400000000 -0.461880215 0.000000000
q( 20 ) = ( 0.2000000 0.5773503 0.0000000 )
q( 21 ) = ( -0.2000000 0.5773503 0.0000000 )
q( 22 ) = ( 0.4000000 -0.4618802 0.0000000 )
q( 23 ) = ( -0.6000000 -0.1154701 0.0000000 )
q( 24 ) = ( 0.6000000 -0.1154701 0.0000000 )
q( 25 ) = ( -0.4000000 -0.4618802 0.0000000 )
Writing epmatq on .epb files
The .epb files have been correctly written
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
************************************************************************
Thanking you again.

With regards,
Bedamani
Nagaland University

[sponce]

Hello,

This was also my hint. Since the .epb have been correctly written to file, you can restart from there.

Just change the input variable to

Code: Select all

  wannierize  = .false.
  epbwrite    = .false.
  epbread     = .true.

I also suggest you to use the memory optimized version with the input parameter:

Code: Select all

  etf_mem     = .false.

Let me know if it helps,

Best,

Samuel