[Q-e-developers] NEB.x "from test_input_xml: Empty input file .. stopping"
Paolo Giannozzi
paolo.giannozzi at uniud.it
Tue Jan 6 21:46:13 CET 2015
I don't' know why you get that specific error message, but there are
several errors in your input. Once fixed, I do not see anything wrong,
at least not with the latest version
Paolo
On Tue, 2015-01-06 at 23:36 +0800, Kun Wang wrote:
> Hi, dear professor,
> Now I'm applying neb.x ( Version is QE5.0.2) to calculate the
> potential energy of the pathway given by CPMD. But when I submit the
> file, it always reminds me that "from test_input_xml: Empty input
> file .. stopping". I checked the input file many times as the tutorial
> of the website, but I cannot find any problem.
> Here I have copied the submission file:
> #!/bin/bash
>
>
> #PBS -V
> #PBS -l nodes=1:ppn=8
> #PBS -l walltime=00:10:00
> #PBS -N ALB-H2.neb
>
>
> cd $PBS_O_WORKDIR/
>
>
> . enable_arcus_mpi.sh
>
>
> mpirun $MPI_HOSTS neb.x -in ALB-H2.neb.in
>
>
> I'm not sure if there is any problem about the submission of mpirun. I
> also attached the input file (ALB-H2.neb.in) and output file
> (ALB-H2.neb.o280753 and ALB-H2.neb.e280753). I tried to use pw.x code
> to run it but it also failed. How can I submit this job.
> Is there any differences from that submitting a job of cp.x code?
> Every jobs I submitted before are successful only change the keyword
> of neb.x to cp.x in the submission file.
> Many thanks
> Best
> KUN WANG
>
> _______________________________________________
> Q-e-developers mailing list
> Q-e-developers at qe-forge.org
> http://qe-forge.org/mailman/listinfo/q-e-developers
-------------- next part --------------
BEGIN
BEGIN_PATH_INPUT
&PATH
string_method = 'neb',
ds = 4.D0,
opt_scheme = 'broyden',
num_of_images = 8,
k_max = 0.6D0,
k_min = 0.4D0,
path_thr = 0.2D0,
use_freezing = .TRUE.,
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
&CONTROL
title = ' ALB ' ,
calculation = 'relax' ,
verbosity = 'default',
restart_mode = 'from_scratch' ,
outdir = './boh' ,
pseudo_dir = './boh' ,
prefix = 'ALB-H2' ,
iprint = 1,
/
&SYSTEM
nosym = .true.,
ibrav = 8,
celldm(1) = 11.157,
celldm(2) = 0.7571,
celldm(3) = 2.4590,
nat = 40,
ntyp = 4,
ecutwfc = 40 ,
ecutrho = 400 ,
nr1b = 12,
nr2b = 12,
nr3b = 12,
input_dft = 'PBE'
/
&ELECTRONS
conv_thr = 1.0D-6,
mixing_beta = 0.3D0,
/
&IONS
pot_extrapolation = "second_order",
wfc_extrapolation = "second_order",
/
ATOMIC_SPECIES
Li 6.941 Li.pbe-n-van.UPF
H 1.00d0 H.pbe.UPF
B 10.81d0 B.pbe.UPF
N 14.00d0 N.pbe.UPF
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS { angstrom }
Li 5.179205510 3.352454035 8.312421428 0 0 0
Li -2.227190452 -3.352454035 15.571409787 0 0 0
Li -5.179205510 5.587423392 -8.312421428 0 0 0
Li 8.131231152 -1.117484678 -1.053396027 0 0 0
H 5.496457830 2.364115055 5.120255169 0 0 0
H 2.805274218 2.534637118 9.149050595 0 0 0
H -2.544437480 -2.364115055 12.379254111
H 0.146738723 -2.534637118 16.408091871 0 0 0
H -5.496457830 4.599084412 -5.120255169 0 0 0
H -2.805274218 4.769606475 -9.149050595 0 0 0
H 8.448472888 -0.129145698 2.138749065 0 0 0
H 5.757289276 -0.299665116 -1.890072819 0 0 0
H -5.496457830 -2.364115055 -5.120255169 0 0 0
H -2.805274218 -2.534637118 -9.149050595 0 0 0
H 8.448472888 2.364115055 2.138749065 0 0 0
H 5.757289276 2.534637118 -1.890072819 0 0 0
H 5.496457830 -0.129145698 5.120255169 0 0 0
H 2.805274218 -0.299665116 9.149050595 0 0 0
H -2.544437480 4.599084412 12.379254111 0 0 0
H 0.146738723 4.769606475 16.408091871 0 0 0
H 4.384603597 3.352454035 6.462259154 0 0 0
H 6.403837990 3.352454035 6.617519747 0 0 0
H 3.572708173 3.352454035 10.358696776
H -1.432588539 -3.352454035 13.721247512 0 0 0
H -3.451796473 -3.352454035 13.876561023 0 0 0
H -0.620693115 -3.352454035 17.617685135 0 0 0
H -4.384603597 5.587423392 -6.462259154 0 0 0
H -6.403837990 5.587423392 -6.617519747 0 0 0
H -3.572708173 5.587423392 -10.358696776 0 0 0
H 7.336618655 -1.117484678 0.796750372 0 0 0
H 9.355853048 -1.117484678 0.641463320 0 0 0
H 6.524702064 -1.117484678 -3.099681958 0 0 0
B 5.446133078 3.352454035 5.839999674 0 0 0
B -2.494091561 -3.352454035 13.099040951
B -5.446133078 5.587423392 -5.839999674 0 0 0
B 8.398148136 -1.117484678 1.418988685 0 0 0
N 3.406414235 3.352454035 9.340401073
N -0.454397590 -3.352454035 16.599389432 0 0 0
N -3.406414235 5.587423392 -9.340401073 0 0 0
N 6.358434585 -1.117484678 -2.081375672 0 0 0
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS { angstrom }
Li 5.179205510 3.352454035 8.312421428
Li -2.227190452 -3.352454035 15.571409787
Li -5.179205510 5.587423392 -8.312421428
Li 8.131231152 -1.117484678 -1.053396027
H 5.496457830 2.364115055 5.120255169
H 2.805274218 2.534637118 9.149050595
H -2.550406599 -2.158736088 12.217643392
H 0.146738723 -2.534637118 16.408091871
H -5.496457830 4.599084412 -5.120255169
H -2.805274218 4.769606475 -9.149050595
H 8.448472888 -0.129145698 2.138749065
H 5.757289276 -0.299665116 -1.890072819
H -5.496457830 -2.364115055 -5.120255169
H -2.805274218 -2.534637118 -9.149050595
H 8.448472888 2.364115055 2.138749065
H 5.757289276 2.534637118 -1.890072819
H 5.496457830 -0.129145698 5.120255169
H 2.805274218 -0.299665116 9.149050595
H -2.544437480 4.599084412 12.379254111
H 0.146738723 4.769606475 16.408091871
H 4.384603597 3.352454035 6.462259154
H 6.403837990 3.352454035 6.617519747
H 3.685888595 3.361741095 10.987570971
H -1.432588539 -3.352454035 13.721247512
H -3.451796473 -3.352454035 13.876561023
H -0.620693115 -3.352454035 17.617685135
H -4.384603597 5.587423392 -6.462259154
H -6.403837990 5.587423392 -6.617519747
H -3.572708173 5.587423392 -10.358696776
H 7.336618655 -1.117484678 0.796750372
H 9.355853048 -1.117484678 0.641463320
H 6.524702064 -1.117484678 -3.099681958
B 5.446133078 3.352454035 5.839999674
B -2.494038643 -3.352697457 13.096818406
B -5.446133078 5.587423392 -5.839999674
B 8.398148136 -1.117484678 1.418988685
N 3.460194515 3.351538559 9.320504010
N -0.454397590 -3.352454035 16.599389432
N -3.406414235 5.587423392 -9.340401073
N 6.358434585 -1.117484678 -2.081375672
LAST_IMAGE
ATOMIC_POSITIONS { angstrom }
Li 5.179205510 3.352454035 8.312421428
Li -2.227190452 -3.352454035 15.571409787
Li -5.179205510 5.587423392 -8.312421428
Li 8.131231152 -1.117484678 -1.053396027
H 5.496457830 2.364115055 5.120255169
H 2.805274218 2.534637118 9.149050595
H -2.583623053 -1.796043321 11.942259573
H 0.146738723 -2.534637118 16.408091871
H -5.496457830 4.599084412 -5.120255169
H -2.805274218 4.769606475 -9.149050595
H 8.448472888 -0.129145698 2.138749065
H 5.757289276 -0.299665116 -1.890072819
H -5.496457830 -2.364115055 -5.120255169
H -2.805274218 -2.534637118 -9.149050595
H 8.448472888 2.364115055 2.138749065
H 5.757289276 2.534637118 -1.890072819
H 5.496457830 -0.129145698 5.120255169
H 2.805274218 -0.299665116 9.149050595
H -2.544437480 4.599084412 12.379254111
H 0.146738723 4.769606475 16.408091871
H 4.384603597 3.352454035 6.462259154
H 6.403837990 3.352454035 6.617519747
H 3.867962597 3.405017208 11.871667333
H -1.432588539 -3.352454035 13.721247512
H -3.451796473 -3.352454035 13.876561023
H -0.620693115 -3.352454035 17.617685135
H -4.384603597 5.587423392 -6.462259154
H -6.403837990 5.587423392 -6.617519747
H -3.572708173 5.587423392 -10.358696776
H 7.336618655 -1.117484678 0.796750372
H 9.355853048 -1.117484678 0.641463320
H 6.524702064 -1.117484678 -3.099681958
B 5.446133078 3.352454035 5.839999674
B -2.494938244 -3.336255921 13.078032615
B -5.446133078 5.587423392 -5.839999674
B 8.398148136 -1.117484678 1.418988685
N 3.582212196 3.348395246 9.295632682
N -0.454397590 -3.352454035 16.599389432
N -3.406414235 5.587423392 -9.340401073
N 6.358434585 -1.117484678 -2.081375672
END_POSITIONS
K_POINTS { gamma }
# CELL_PARAMETERS { angstrom }
# 5.904030116 0.000000000 0.000000000
# 0.000000000 4.469941201 0.000000000
# 0.000000000 0.000000000 14.518010056
END_ENGINE_INPUT
END
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