Error in routine read_xml_file (4): fatal error reading xml file

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yq_zhao
Posts: 13
Joined: Sun Mar 28, 2021 1:06 pm
Affiliation: condensed state physics

Error in routine read_xml_file (4): fatal error reading xml file

Post by yq_zhao »

hey EPW user


I am still having problems calculating the superconducting gap and Tc using The Eliashberg formalism.but getting an error:



Reading supplied temperature list.

Reading xml data from directory:

./NbS2.save/
Message from routine qes_read:magnetizationType:
do_magnetization: wrong number of occurrences
Message from routine qexsd_readschema :
error reading output_obj of xsd data file

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine read_xml_file (4):
fatal error reading xml file
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

stopping ...
Any help is appreciated. the input file is :



&inputepw
prefix = 'NbS2',
amass(1) = 92.9064,
amass(2) = 32.065,
outdir = './'

ep_coupling = .true.
elph = .true.
kmaps = .false.
epbwrite = .true.
epbread = .false.

epwwrite = .true.
epwread = .false.

etf_mem = 1

nbndsub = 16,

wannierize = .true.
num_iter = 300


proj(1) = 'S:pz'

wdata(1) = 'bands_plot = .true.'
wdata(2) = 'begin kpoint_path'
wdata(3) = 'G 0.00 0.00 0.00 M 0.50 0.00 0.00'
wdata(4) = 'X 0.50 0.00 0.00 K 0.33 0.33 0.00'
wdata(5) = 'end kpoint_path'
wdata(6) = 'bands_plot_format = gnuplot'

iverbosity = 2

eps_acustic = 2.0 ! Lowest boundary for the phonon frequency
ephwrite = .true. ! Writes .ephmat files used when Eliasberg = .true.

fsthick = 0.4 ! eV
degaussw = 0.10 ! eV
nsmear = 1
delta_smear = 0.04 ! eV

degaussq = 0.5 ! meV
nqstep = 500

eliashberg = .true.

laniso = .true.
limag = .true.
lpade = .true.

conv_thr_iaxis = 1.0d-4

wscut = 1.0 ! eV Upper limit over frequency integration/summation in the Elisashberg eq

nstemp = 1 ! Nr. of temps
temps = 2.00 ! K provide list of temperetures OR (nstemp and temps = tempsmin tempsmax for even space mode)

nsiter = 500

muc = 0.16

dvscf_dir = '../Phonon/save'

nk1 = 6
nk2 = 6
nk3 = 6

nq1 = 6
nq2 = 6
nq3 = 6

mp_mesh_k = .true.
nkf1 = 20
nkf2 = 20
nkf3 = 20

nqf1 = 20
nqf2 = 20
nqf3 = 20
/

hlee
Posts: 369
Joined: Thu Aug 03, 2017 12:24 pm
Affiliation: The University of Texas at Austin

Re: Error in routine read_xml_file (4): fatal error reading xml file

Post by hlee »

Dear yq_zhao:
Reading xml data from directory:

./NbS2.save/
Message from routine qes_read:magnetizationType:
do_magnetization: wrong number of occurrences
Message from routine qexsd_readschema :
error reading output_obj of xsd data file
Your error is not directly related to EPW and related to reading the data from the previous pw.x runs.

You need to check the inputs or outputs of scf or nscf calculations.

Sincerely,

H. Lee

yq_zhao
Posts: 13
Joined: Sun Mar 28, 2021 1:06 pm
Affiliation: condensed state physics

Re: Error in routine read_xml_file (4): fatal error reading xml file

Post by yq_zhao »

dear h.lee

i have check the inputs or outputs of scf or nscf calculations. it's all done and there's no error. out is


total cpu time spent up to now is 3555.3 secs

End of self-consistent calculation

Number of k-points >= 100: set verbosity='high' to print the bands.

the Fermi energy is 0.3018 ev

! total energy = -320.14512623 Ry
estimated scf accuracy < 4.5E-16 Ry
smearing contrib. (-TS) = -0.47134806 Ry
internal energy E=F+TS = -319.67377817 Ry

The total energy is F=E-TS. E is the sum of the following terms:
one-electron contribution = -631.20182508 Ry
hartree contribution = 319.30152387 Ry
xc contribution = -57.71365110 Ry
ewald contribution = 49.94017414 Ry

convergence has been achieved in 35 iterations

negative rho (up, down): 1.472E-05 0.000E+00

Forces acting on atoms (cartesian axes, Ry/au):

atom 1 type 1 force = -0.04711203 0.08157864 0.85420280
atom 2 type 1 force = 0.10521036 0.00913841 -0.13833855
atom 3 type 2 force = 0.00006968 0.00000702 -0.00227483
atom 4 type 2 force = -0.00001038 0.00002062 0.00244982
atom 5 type 2 force = 0.04710880 -0.08159195 -0.85691639
atom 6 type 2 force = -0.10526642 -0.00915275 0.14087716

Total force = 1.242188 Total SCF correction = 0.000000


Computing stress (Cartesian axis) and pressure


negative rho (up, down): 1.472E-05 0.000E+00
total stress (Ry/bohr**3) (kbar) P= 60.84
-0.00010851 0.00000080 -0.00023507 -15.96 0.12 -34.58
0.00000080 -0.00015862 0.00011190 0.12 -23.33 16.46
-0.00023507 0.00011190 0.00150790 -34.58 16.46 221.82


Writing output data file ./NbS2.save/

init_run : 31.31s CPU 32.69s WALL ( 1 calls)
electrons : 3376.99s CPU 3522.51s WALL ( 1 calls)
forces : 8.51s CPU 8.85s WALL ( 1 calls)
stress : 27.28s CPU 27.81s WALL ( 1 calls)

Called by init_run:
wfcinit : 29.09s CPU 30.42s WALL ( 1 calls)
potinit : 2.03s CPU 2.05s WALL ( 1 calls)
hinit0 : 0.08s CPU 0.09s WALL ( 1 calls)

Called by electrons:
c_bands : 2967.32s CPU 3093.11s WALL ( 35 calls)
sum_band : 406.29s CPU 425.90s WALL ( 35 calls)
v_of_rho : 3.88s CPU 3.95s WALL ( 36 calls)
newd : 1.41s CPU 1.44s WALL ( 36 calls)
mix_rho : 0.08s CPU 0.09s WALL ( 35 calls)
vdW_kernel : 1.95s CPU 1.96s WALL ( 1 calls)

Called by c_bands:
init_us_2 : 41.51s CPU 49.48s WALL ( 120450 calls)
cegterg : 2772.69s CPU 2871.42s WALL ( 57750 calls)

Called by *egterg:
cdiaghg : 400.01s CPU 404.66s WALL ( 241585 calls)
h_psi : 1993.25s CPU 2077.74s WALL ( 243235 calls)
s_psi : 68.35s CPU 69.55s WALL ( 243235 calls)
g_psi : 5.59s CPU 5.66s WALL ( 183835 calls)

Called by h_psi:
h_psi:calbec : 116.78s CPU 123.97s WALL ( 243235 calls)
vloc_psi : 1786.74s CPU 1860.90s WALL ( 243235 calls)
add_vuspsi : 73.23s CPU 76.02s WALL ( 243235 calls)

General routines
calbec : 153.61s CPU 163.68s WALL ( 309235 calls)
fft : 1.20s CPU 1.25s WALL ( 2435 calls)
ffts : 0.02s CPU 0.02s WALL ( 71 calls)
fftw : 1989.43s CPU 2073.34s WALL (14243148 calls)
interpolate : 0.03s CPU 0.03s WALL ( 36 calls)

Parallel routines
fft_scatt_xy : 177.32s CPU 184.51s WALL (14245654 calls)
fft_scatt_yz : 733.79s CPU 766.10s WALL (14245654 calls)

PWSCF : 57m34.03s CPU 1h 0m WALL


This run was terminated on: 21:32: 5 11Apr2021

=------------------------------------------------------------------------------=
JOB DONE.
=------------------------------------------------------------------------------=

Is it because I didn't set the magnetic parameters ?

&control
prefix = 'NbS2'
calculation = 'scf'
restart_mode = 'from_scratch'
tstress = .true.
tprnfor = .true.
outdir = './'
wfcdir = './wfcdir'
pseudo_dir = '../'
nstep = 1000 ,
! etot_conv_thr = 3.0E-9 ,
forc_conv_thr = 1.0D-5 ,
/
&system
ibrav = 4
A = 3.482607807
C = 30
nat = 6
ntyp = 2
ecutwfc=50,
ecutrho=300,
input_dft='vdw-DF',
occupations='smearing',
smearing='gaussian',
degauss=0.1,
nspin = 1,
nbnd = 40,
lda_plus_u = .false. ,
/
&electrons
electron_maxstep = 100
conv_thr = 1.0d-14
mixing_mode = 'plain'
/
&IONS
ion_dynamics='bfgs'
/
&CELL
cell_dynamics = 'bfgs' ,
press = 0.00 ,
cell_dofree=2Dxy,
/
ATOMIC_SPECIES
Nb 92.91 Nb.pbe-nsp-van.UPF
S 32.065 S.pbe-n-rrkjus_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal
Nb 0 0 9.93675
Nb 0 0 3.31225
S 1.68138 0.970743 11.5033
S 0 1.94149 1.74571
S 0 1.94149 4.87878
S 1.68138 0.970743 8.37021

K_POINTS crystal
324
0.00000000 0.00000000 0.00000000 0.00308642
0.00000000 0.05555556 0.00000000 0.00308642
0.00000000 0.11111111 0.00000000 0.00308642

hlee
Posts: 369
Joined: Thu Aug 03, 2017 12:24 pm
Affiliation: The University of Texas at Austin

Re: Error in routine read_xml_file (4): fatal error reading xml file

Post by hlee »

Dear yq_zhao:

Code: Select all

input_dft='vdw-DF',
occupations='smearing',
smearing='gaussian',
degauss=0.1,
nspin = 1,
nbnd = 40, 
lda_plus_u = .false. ,
As I already said, it seems that there is an issue with importing the data from the previous scf or nscf runs.

I would suggest you to try to remove the following unnecessary inputs in scf.in and nscf.in:
nspin = 1,
lda_plus_u = .false. ,

Sincerely,

H. Lee

sabrine
Posts: 1
Joined: Tue May 03, 2022 3:09 pm
Affiliation: LPENS

Re: Error in routine read_xml_file (4): fatal error reading xml file

Post by sabrine »

Dear
I am now doing a calculation of epsilon .x
i am new in DFT calculation , and i amusing quantum espresso , i have the same error msg .

can you please help me .


this is the program of scf and epsilon
&CONTROL
calculation = 'scf'
outdir = './out/'
prefix = 'aiida'
pseudo_dir = './pseudo/'
verbosity = 'high'
/
&SYSTEM
ibrav = 4
a= 3.78111e+00
c=5.18997e+00
nat = 3
ntyp = 2
ecutwfc = 5.0000000000d+01
occupations = 'smearing'
smearing = 'gauss'
degauss = 1.00000e-02
/
&ELECTRONS
conv_thr = 1.00000e-06
electron_maxstep = 80
mixing_beta = 4.0000000000d-01
startingpot = "atomic"
startingwfc = "atomic+random"
/
ATOMIC_SPECIES
Pt 195.084 pt_pbe_v1.4.uspp.F.UPF
Se 78.96 Se_pbe_v1.uspp.F.UPF
ATOMIC_POSITIONS {angstrom}
Pt 0.000000 0.000000 0.000000
Se -0.000002 2.183024 3.881137
Se 1.890555 1.091510 1.308833
K_POINTS {automatic}
6 6 6 0 0 0

and for epsilon


&inputpp
outdir = './out/'
prefix = 'aiida'
calculation='eps'
/
&energy_grid
smeartype='gauss'
intersmear=0.136d0
intrasmear=0.0d0
wmax=10.0d0
wmin=0.0d0
nw=500
shift=0.0d0
/

hlee
Posts: 369
Joined: Thu Aug 03, 2017 12:24 pm
Affiliation: The University of Texas at Austin

Re: Error in routine read_xml_file (4): fatal error reading xml file

Post by hlee »

Dear sabrine:
I am now doing a calculation of epsilon .x
Regarding epsilon.x, you need to ask your question on the quantum-espresso users forum (https://www.quantum-espresso.org/users-forum/).

Sincerely,

H. Lee

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