[Pw_forum] neb.x with v5.0.2
paolo paoli100
thesis.outputfiles at gmail.com
Sat Jun 1 17:18:09 CEST 2013
Dear all pw users,
I tried to do neb calculations with the new version of quantum-ESPRESSO,
v5.0.2.
I set atomic positions of the first and last image, but after running the
first iteration, the file.crd has showed atomic positions different from
the ones I choose. In the last image, a “-“ appeared before the “x”
coordinate of an oxygen.
This is my input file:
BEGIN
BEGIN_PATH_INPUT
&PATH
restart_mode = 'from_scratch'
string_method = 'neb',
nstep_path = 30,
ds = 2.D0,
opt_scheme = "broyden",
num_of_images = 12,
k_max = 0.70D0
k_min = 0.20D0
path_thr = 0.2D0,
CI_scheme = 'no-CI'
/
END_PATH_INPUT
BEGIN_ENGINE_INPUT
&CONTROL
prefix = "CO2_C_2CO_Rh_5.0.3_ds2"
pseudo_dir = '/home/hpc/pr47ma/di34xeq/QE_pseudo',
outdir='./tmp'
/
&system
ibrav = 4, celldm(1) = 10.30961687, celldm(3) = 3.016065406,
nat=16 , ntyp= 3,
ecutwfc = 25, ecutrho= 250,
occupations='smearing', smearing = 'mv', degauss = 0.001,
/
&electrons
mixing_mode='local-TF'
diago_david_ndim = 8
mixing_beta = 0.2
conv_thr = 1.0d-8
startingwfc = 'random',
electron_maxstep = 500
/
&ions
/
ATOMIC_SPECIES
Rh 1.00 Rh.pbe-nd-rrkjus.UPF
O 1.00 O.pbe-rrkjus.UPF
C 1.00 C.pbe-rrkjus.UPF
K_POINTS {automatic}
6 6 1 1 1 1
BEGIN_POSITIONS
FIRST_IMAGE
ATOMIC_POSITIONS { alat }
O -0.249691167 -0.144586201 1.590660412
O 0.075612730 0.047924934 1.794802571
C -0.087015648 -0.048326397 1.692608147
C 0.500246619 0.288820855 1.018089208
Rh 0.250000000 0.144337570 0.000000000 0 0 0
Rh 0.500000000 0.288675130 0.408248290 0 0 0
Rh 0.000000000 0.000000000 0.816496580 0 0 0
Rh 0.750000000 0.144337570 0.000000000 0 0 0
Rh 1.000000000 0.288675130 0.408248290 0 0 0
Rh 0.500000000 0.000000000 0.816496580 0 0 0
Rh 0.500000000 0.577350270 0.000000000 0 0 0
Rh 0.750000000 0.721687840 0.408248290 0 0 0
Rh 0.250000000 0.433012700 0.816496580 0 0 0
Rh 1.000000000 0.577350270 0.000000000 0 0 0
Rh 1.250000000 0.721687840 0.408248290 0 0 0
Rh 0.750000000 0.433012700 0.816496580 0 0 0
LAST_IMAGE
ATOMIC_POSITIONS { alat }
O 0.000000000 0.000000000 1.372625677
O 0.500000000 0.288675130 1.288410561
C 0.000000000 0.000000000 1.161373807
C 0.500000000 0.288675130 1.069896147
Rh 0.250000000 0.144337570 0.000000000 0 0 0
Rh 0.500000000 0.288675130 0.408248290 0 0 0
Rh 0.000000000 0.000000000 0.816496580 0 0 0
Rh 0.750000000 0.144337570 0.000000000 0 0 0
Rh 1.000000000 0.288675130 0.408248290 0 0 0
Rh 0.500000000 0.000000000 0.816496580 0 0 0
Rh 0.500000000 0.577350270 0.000000000 0 0 0
Rh 0.750000000 0.721687840 0.408248290 0 0 0
Rh 0.250000000 0.433012700 0.816496580 0 0 0
Rh 1.000000000 0.577350270 0.000000000 0 0 0
Rh 1.250000000 0.721687840 0.408248290 0 0 0
Rh 0.750000000 0.433012700 0.816496580 0 0 0
END_POSITIONS
END_ENGINE_INPUT
END
And this is my file.crd, created after the first iteration:
FIRST_IMAGE
ATOMIC_POSITIONS (alat)
O -0.2496911670 -0.1445862010 1.5906604120
O 0.0756127300 0.0479249340 1.7948025710
C -0.0870156480 -0.0483263970 1.6926081470
C 0.5002466190 0.2888208550 1.0180892080
Rh 0.2500000000 0.1443375700 0.0000000000 0 0 0
Rh 0.5000000000 0.2886751300 0.4082482900 0 0 0
Rh 0.0000000000 0.0000000000 0.8164965800 0 0 0
Rh 0.7500000000 0.1443375700 0.0000000000 0 0 0
Rh 1.0000000000 0.2886751300 0.4082482900 0 0 0
Rh 0.5000000000 0.0000000000 0.8164965800 0 0 0
Rh 0.5000000000 0.5773502700 0.0000000000 0 0 0
Rh 0.7500000000 0.7216878400 0.4082482900 0 0 0
Rh 0.2500000000 0.4330127000 0.8164965800 0 0 0
Rh 1.0000000000 0.5773502700 0.0000000000 0 0 0
Rh 1.2500000000 0.7216878400 0.4082482900 0 0 0
Rh 0.7500000000 0.4330127000 0.8164965800 0 0 0
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS (alat)
O -0.2269919700 -0.1314420009 1.5708390725
O 0.0232843000 0.0698113155 1.7487669337
C -0.0791051345 -0.0439330882 1.6443141161
C 0.5002241991 0.2888076073 1.0227989297
Rh 0.2500000000 0.1443375700 0.0000000000
Rh 0.5000000000 0.2886751300 0.4082482900
Rh 0.0000000000 0.0000000000 0.8164965800
Rh 0.7500000000 0.1443375700 0.0000000000
Rh 1.0000000000 0.2886751300 0.4082482900
Rh 0.5000000000 0.0000000000 0.8164965800
Rh 0.5000000000 0.5773502700 0.0000000000
Rh 0.7500000000 0.7216878400 0.4082482900
Rh 0.2500000000 0.4330127000 0.8164965800
Rh 1.0000000000 0.5773502700 0.0000000000
Rh 1.2500000000 0.7216878400 0.4082482900
Rh 0.7500000000 0.4330127000 0.8164965800
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS (alat)
O -0.2042927730 -0.1182978008 1.5510177329
O -0.0290441300 0.0916976969 1.7027312965
C -0.0711946211 -0.0395397794 1.5960200852
C 0.5002017792 0.2887943595 1.0275086515
Rh 0.2500000000 0.1443375700 0.0000000000
Rh 0.5000000000 0.2886751300 0.4082482900
Rh 0.0000000000 0.0000000000 0.8164965800
Rh 0.7500000000 0.1443375700 0.0000000000
Rh 1.0000000000 0.2886751300 0.4082482900
Rh 0.5000000000 0.0000000000 0.8164965800
Rh 0.5000000000 0.5773502700 0.0000000000
Rh 0.7500000000 0.7216878400 0.4082482900
Rh 0.2500000000 0.4330127000 0.8164965800
Rh 1.0000000000 0.5773502700 0.0000000000
Rh 1.2500000000 0.7216878400 0.4082482900
Rh 0.7500000000 0.4330127000 0.8164965800
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS (alat)
O -0.1815935760 -0.1051536007 1.5311963934
O -0.0813725600 0.1135840784 1.6566956592
C -0.0632841076 -0.0351464705 1.5477260543
C 0.5001793593 0.2887811118 1.0322183732
Rh 0.2500000000 0.1443375700 0.0000000000
Rh 0.5000000000 0.2886751300 0.4082482900
Rh 0.0000000000 0.0000000000 0.8164965800
Rh 0.7500000000 0.1443375700 0.0000000000
Rh 1.0000000000 0.2886751300 0.4082482900
Rh 0.5000000000 0.0000000000 0.8164965800
Rh 0.5000000000 0.5773502700 0.0000000000
Rh 0.7500000000 0.7216878400 0.4082482900
Rh 0.2500000000 0.4330127000 0.8164965800
Rh 1.0000000000 0.5773502700 0.0000000000
Rh 1.2500000000 0.7216878400 0.4082482900
Rh 0.7500000000 0.4330127000 0.8164965800
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS (alat)
O -0.1588943790 -0.0920094006 1.5113750538
O -0.1337009900 0.1354704598 1.6106600219
C -0.0553735942 -0.0307531617 1.4994320234
C 0.5001569394 0.2887678641 1.0369280949
Rh 0.2500000000 0.1443375700 0.0000000000
Rh 0.5000000000 0.2886751300 0.4082482900
Rh 0.0000000000 0.0000000000 0.8164965800
Rh 0.7500000000 0.1443375700 0.0000000000
Rh 1.0000000000 0.2886751300 0.4082482900
Rh 0.5000000000 0.0000000000 0.8164965800
Rh 0.5000000000 0.5773502700 0.0000000000
Rh 0.7500000000 0.7216878400 0.4082482900
Rh 0.2500000000 0.4330127000 0.8164965800
Rh 1.0000000000 0.5773502700 0.0000000000
Rh 1.2500000000 0.7216878400 0.4082482900
Rh 0.7500000000 0.4330127000 0.8164965800
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS (alat)
O -0.1361951820 -0.0788652005 1.4915537143
O -0.1860294200 0.1573568413 1.5646243846
C -0.0474630807 -0.0263598529 1.4511379925
C 0.5001345195 0.2887546164 1.0416378166
Rh 0.2500000000 0.1443375700 0.0000000000
Rh 0.5000000000 0.2886751300 0.4082482900
Rh 0.0000000000 0.0000000000 0.8164965800
Rh 0.7500000000 0.1443375700 0.0000000000
Rh 1.0000000000 0.2886751300 0.4082482900
Rh 0.5000000000 0.0000000000 0.8164965800
Rh 0.5000000000 0.5773502700 0.0000000000
Rh 0.7500000000 0.7216878400 0.4082482900
Rh 0.2500000000 0.4330127000 0.8164965800
Rh 1.0000000000 0.5773502700 0.0000000000
Rh 1.2500000000 0.7216878400 0.4082482900
Rh 0.7500000000 0.4330127000 0.8164965800
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS (alat)
O -0.1134959850 -0.0657210005 1.4717323747
O -0.2383578500 0.1792432227 1.5185887474
C -0.0395525673 -0.0219665441 1.4028439615
C 0.5001120995 0.2887413686 1.0463475384
Rh 0.2500000000 0.1443375700 0.0000000000
Rh 0.5000000000 0.2886751300 0.4082482900
Rh 0.0000000000 0.0000000000 0.8164965800
Rh 0.7500000000 0.1443375700 0.0000000000
Rh 1.0000000000 0.2886751300 0.4082482900
Rh 0.5000000000 0.0000000000 0.8164965800
Rh 0.5000000000 0.5773502700 0.0000000000
Rh 0.7500000000 0.7216878400 0.4082482900
Rh 0.2500000000 0.4330127000 0.8164965800
Rh 1.0000000000 0.5773502700 0.0000000000
Rh 1.2500000000 0.7216878400 0.4082482900
Rh 0.7500000000 0.4330127000 0.8164965800
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS (alat)
O -0.0907967880 -0.0525768004 1.4519110352
O -0.2906862800 0.2011296042 1.4725531101
C -0.0316420538 -0.0175732353 1.3545499306
C 0.5000896796 0.2887281209 1.0510572601
Rh 0.2500000000 0.1443375700 0.0000000000
Rh 0.5000000000 0.2886751300 0.4082482900
Rh 0.0000000000 0.0000000000 0.8164965800
Rh 0.7500000000 0.1443375700 0.0000000000
Rh 1.0000000000 0.2886751300 0.4082482900
Rh 0.5000000000 0.0000000000 0.8164965800
Rh 0.5000000000 0.5773502700 0.0000000000
Rh 0.7500000000 0.7216878400 0.4082482900
Rh 0.2500000000 0.4330127000 0.8164965800
Rh 1.0000000000 0.5773502700 0.0000000000
Rh 1.2500000000 0.7216878400 0.4082482900
Rh 0.7500000000 0.4330127000 0.8164965800
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS (alat)
O -0.0680975910 -0.0394326003 1.4320896956
O -0.3430147100 0.2230159856 1.4265174728
C -0.0237315404 -0.0131799265 1.3062558997
C 0.5000672597 0.2887148732 1.0557669818
Rh 0.2500000000 0.1443375700 0.0000000000
Rh 0.5000000000 0.2886751300 0.4082482900
Rh 0.0000000000 0.0000000000 0.8164965800
Rh 0.7500000000 0.1443375700 0.0000000000
Rh 1.0000000000 0.2886751300 0.4082482900
Rh 0.5000000000 0.0000000000 0.8164965800
Rh 0.5000000000 0.5773502700 0.0000000000
Rh 0.7500000000 0.7216878400 0.4082482900
Rh 0.2500000000 0.4330127000 0.8164965800
Rh 1.0000000000 0.5773502700 0.0000000000
Rh 1.2500000000 0.7216878400 0.4082482900
Rh 0.7500000000 0.4330127000 0.8164965800
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS (alat)
O -0.0453983940 -0.0262884002 1.4122683561
O -0.3953431400 0.2449023671 1.3804818355
C -0.0158210269 -0.0087866176 1.2579618688
C 0.5000448398 0.2887016255 1.0604767035
Rh 0.2500000000 0.1443375700 0.0000000000
Rh 0.5000000000 0.2886751300 0.4082482900
Rh 0.0000000000 0.0000000000 0.8164965800
Rh 0.7500000000 0.1443375700 0.0000000000
Rh 1.0000000000 0.2886751300 0.4082482900
Rh 0.5000000000 0.0000000000 0.8164965800
Rh 0.5000000000 0.5773502700 0.0000000000
Rh 0.7500000000 0.7216878400 0.4082482900
Rh 0.2500000000 0.4330127000 0.8164965800
Rh 1.0000000000 0.5773502700 0.0000000000
Rh 1.2500000000 0.7216878400 0.4082482900
Rh 0.7500000000 0.4330127000 0.8164965800
INTERMEDIATE_IMAGE
ATOMIC_POSITIONS (alat)
O -0.0226991970 -0.0131442001 1.3924470165
O -0.4476715700 0.2667887485 1.3344461983
C -0.0079105135 -0.0043933088 1.2096678379
C 0.5000224199 0.2886883777 1.0651864253
Rh 0.2500000000 0.1443375700 0.0000000000
Rh 0.5000000000 0.2886751300 0.4082482900
Rh 0.0000000000 0.0000000000 0.8164965800
Rh 0.7500000000 0.1443375700 0.0000000000
Rh 1.0000000000 0.2886751300 0.4082482900
Rh 0.5000000000 0.0000000000 0.8164965800
Rh 0.5000000000 0.5773502700 0.0000000000
Rh 0.7500000000 0.7216878400 0.4082482900
Rh 0.2500000000 0.4330127000 0.8164965800
Rh 1.0000000000 0.5773502700 0.0000000000
Rh 1.2500000000 0.7216878400 0.4082482900
Rh 0.7500000000 0.4330127000 0.8164965800
LAST_IMAGE
ATOMIC_POSITIONS (alat)
O 0.0000000000 0.0000000000 1.3726256770
O -0.5000000000 0.2886751300 1.2884105610
C 0.0000000000 0.0000000000 1.1613738070
C 0.5000000000 0.2886751300 1.0698961470
Rh 0.2500000000 0.1443375700 0.0000000000
Rh 0.5000000000 0.2886751300 0.4082482900
Rh 0.0000000000 0.0000000000 0.8164965800
Rh 0.7500000000 0.1443375700 0.0000000000
Rh 1.0000000000 0.2886751300 0.4082482900
Rh 0.5000000000 0.0000000000 0.8164965800
Rh 0.5000000000 0.5773502700 0.0000000000
Rh 0.7500000000 0.7216878400 0.4082482900
Rh 0.2500000000 0.4330127000 0.8164965800
Rh 1.0000000000 0.5773502700 0.0000000000
Rh 1.2500000000 0.7216878400 0.4082482900
Rh 0.7500000000 0.4330127000 0.8164965800
I also properly ran a neb calculation with v5.0.2, but I had to add all
intermediate images (found after running 1 iteration with v5.0.1).
How can I deal with this problem?
Thanks to all,
Luca Dietz
Bachelor of Science in Chemical Engineering
Politecnico di Milano, Italy
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