Re: [Pw_forum] Simple question on vc-relax
Hi Pablo, Don't worry, it is natural in vc-relax calculations. When the lattice parameters change, number of basis function changes as well. Cheers On Mon, Jul 3, 2017 at 1:57 PM, Pablo García Risueño < garcia.risu...@gmail.com> wrote: > Dear Espresso community > > Sorry if my question is too simple. So far I have run many 'relax' > calculations with QE, but now I am running my first 'vc-relax' > calculations. In contrast to what happens with 'relax', if I copy the > ATOMIC_POSITONS (and CELL_PARAMETERS) from an output file into a new input > file and I rerun, the total forces of the new output file are not the same > as the ones of the first output files (but much worse). What is the reason > of this behaviour? Am I forgetting to copy something? > > Thank you very much for your advice, it is very valuable for me. > > Best regards. > > -- > -- > > Dr. Pablo García Risueño > > Institut für Physikalische Chemie, Universität Hamburg, Grindelallee 117, > 20146 Hamburg > > Tel. +49 040 42 83 84 82 7 > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Simple question on vc-relax
Dear Espresso community Sorry if my question is too simple. So far I have run many 'relax' calculations with QE, but now I am running my first 'vc-relax' calculations. In contrast to what happens with 'relax', if I copy the ATOMIC_POSITONS (and CELL_PARAMETERS) from an output file into a new input file and I rerun, the total forces of the new output file are not the same as the ones of the first output files (but much worse). What is the reason of this behaviour? Am I forgetting to copy something? Thank you very much for your advice, it is very valuable for me. Best regards. -- -- Dr. Pablo García Risueño Institut für Physikalische Chemie, Universität Hamburg, Grindelallee 117, 20146 Hamburg Tel. +49 040 42 83 84 82 7 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] QE 6.1 Error
Hello, I am using QE 6.1, it is doing fine with pw.x calculations, whenever i use plotting utilities like bands.x or projwfc.x i am getting following error, Image PCRoutineLineSource projwfc.x 0083872A Unknown Unknown Unknown projwfc.x 0064C8D5 Unknown Unknown Unknown projwfc.x 00645BAF Unknown Unknown Unknown projwfc.x 004BEA60 Unknown Unknown Unknown projwfc.x 004BD50E Unknown Unknown Unknown projwfc.x 004BCE0E Unknown Unknown Unknown projwfc.x 00449FBF Unknown Unknown Unknown projwfc.x 0044910C Unknown Unknown Unknown libc.so.6 7F3BA10BAD5D Unknown Unknown Unknown projwfc.x 00449009 Unknown Unknown Unknown [gb35][[27039,1],1][../../../../../../../openmpi-1.6.2/ompi/mca/btl/tcp/btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] [gb29][[27039,1],2][../../../../../../../openmpi-1.6.$ [gb29][[27039,1],4][../../../../../../../openmpi-1.6.2/ompi/mca/btl/tcp/btl_tcp_frag.c:215:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv failed: Connection reset$ Thanks, Manu (University of Waterloo) ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Neb restart
Dear QE-users,
I am doing a restart Neb calculation with QE v.5.4.
The input files are the followings:
neb_ad_config.path
neb.dat (with the restart)
the folder with the output files of each images (just three in this case
with the name neb_ad_config_i, i: 1,2,3)
*in files
and I run : $QEDIR/neb.x -nimage 1 --input_images 3
#
On the output file of the run is written:
/Atomic positions and unit cell read from directory: //
// .///neb_ad_config_i/neb_ad_config.save//
for each i Image. And read the file 'neb_ad_config.path'.
The problem is that in the folder of the last image three other folder
are created and the *path are written. Also the PW.out of image 2 it is
written :
/Cannot read rho : file not found /
It is not clear to me why it creates 3 other output folders? For image 2
reads the correct positions but it doesn't find the charge density.
Probably I am writing something wrong, I hope anyone could help me.
I send the pw_1.in(in the other just the geometry and the respective
folder are changed) neb.dat.
Thanks in advance,
&PATH
restart_mode = 'restart'
string_method = 'neb',
nstep_path= 300,
opt_scheme= 'broyden',
num_of_images = 3,
k_max = 0.3D0,
k_min = 0.2D0,
path_thr = 0.01D0,
/
&CONTROL
prefix ='neb_ad_config',
restart_mode ='restart'
outdir ='./neb_ad_config_1/'
pseudo_dir ='/sfs/fs5/home-sh/supas331/pseudo_qe/',
tefield =.true.,
dipfield =.true.,
tprnfor =.true.,
forc_conv_thr= 1.0D-4,
/
&SYSTEM
ibrav = 0,
celldm(1) = 7.853,
nat = 73,
ntyp = 2,
ecutwfc = 30,
smearing ='mp',
degauss = 0.01,
occupations ='smearing',
edir = 3,
emaxpos= 0.70,
eamp = 0,
/
&ELECTRONS
mixing_beta=0.3,
conv_thr=1.0D-5,
startingwfc ='atomic+random',
/
&IONS
/
ATOMIC_SPECIES
Au 1.0 au_pbe_v1.uspp.F.UPF
Cl 1.0 cl_pbe_v1.4.uspp.F.UPF
CELL_PARAMETERS { alat }
2.02.0 0.0
2.0 -2.0 0.0
0.00.0 5.0
ATOMIC_POSITIONS { alat }
Au0.00 0.00 0.000 0 0
Au0.50 0.50 0.000 0 0
Au1.00 1.00 0.000 0 0
Au1.50 1.50 0.000 0 0
Au -0.50 0.50 0.000 0 0
Au0.00 1.00 0.000 0 0
Au0.50 1.50 0.000 0 0
Au1.00 2.00 0.000 0 0
Au -1.00 1.00 0.000 0 0
Au -0.50 1.50 0.000 0 0
Au0.00 2.00 0.000 0 0
Au0.50 2.50 0.000 0 0
Au -1.50 1.50 0.000 0 0
Au -1.00 2.00 0.000 0 0
Au -0.50 2.50 0.000 0 0
Au0.00 3.00 0.000 0 0
Au0.00 0.50 0.500 0 0
Au0.50 1.00 0.500 0 0
Au1.00 1.50 0.500 0 0
Au1.50 2.00 0.500 0 0
Au -0.50 1.00 0.500 0 0
Au0.00 1.50 0.500 0 0
Au0.50 2.00 0.500 0 0
Au1.00 2.50 0.500 0 0
Au -1.00 1.50 0.500 0 0
Au -0.50 2.00 0.500 0 0
Au0.00 2.50 0.500 0 0
Au0.50 3.00 0.500 0 0
Au -1.50 2.00 0.500 0 0
Au -1.00 2.50 0.500 0 0
Au -0.50 3.00 0.500 0 0
Au0.00 3.50 0.500 0 0
Au -0.002015-0.002677 1.001449
Au0.507829 0.499742 1.002336
Au0.999209 1.000542 1.004718
Au1.496940 1.504451 1.004191
Au -0.497971 0.502669 1.001441
Au0.003061 0.995531 1.004189
Au0.500808 1.499459 1.004716
Au0.992169 2.000238 1.002331
Au -1.003294 0.998323 1.005014
Au -0.498226 1.491768 0.995927
Au0.004598 1.993385 0.990745
Au0.504897 2.506412 0.31
Au -1.496721 1.501664 1.005025
Au -1.004918 1.993600 0.29
Au -0.504626 2.506631 0.990750
Au -0.001786 3.008235 0.995936
Au -0.009901 0.509581 1.495298
Au0.528046 0.973409 1.495806
Au0.971942 1.526592 1.495817
Au1.509896 1.990416 1.495287
Au -0.487690 0.983372 1.495802
Au -0.011815 1.515766 1.495225
Au0.486286 2.013284 1.503700
Au0.981082 2.508584
Re: [Pw_forum] Regarding error during adsorption of bromine in graphene
WHen using ultrasoft pseudopotentials (as you do), this error may
indicate that the atoms got much closer to each other than they should.
You can try to check the last relaxed positions with xcrysden or, put
them back in an input file and use dist.x, to verify that nothing is
suspect.
hth
On 03/07/17 06:05, nipesh dulal wrote:
> Dear QE experts
>
> i am doing adsorption of bromine in 3*3 graphene sheet. But there comes
> an error after one scf cycle which is mentioned below,
>
>
>
> Writing output data file bromine_relax_pb.save
> NEW-OLD atomic charge density approx. for the potential
>
> negative rho (up, down): 1.894E-04 0.000E+00
>
> total cpu time spent up to now is 3015.2 secs
>
> per-process dynamical memory: 765.2 Mb
>
> Self-consistent Calculation
>
> iteration # 1 ecut=45.00 Ry beta=0.60
> Davidson diagonalization with overlap
>
>
> Error in routine cdiaghg (332):
> S matrix not positive definite
>
>
> stopping ...
>
> Here is the input file i have used
>
> &control
> calculation='relax'
> restart_mode='from_scratch'
> prefix='bromine_relax_pb'
> outdir='/home/physics/Downloads/graphene/bromine',
> pseudo_dir = '/home/physics/Downloads/graphene/pseudopotentials',
> tstress=.true.
> tprnfor=.true.
> verbosity='high'
> forc_conv_thr=1.0d-3
> etot_conv_thr=1.0d-4
> /
> &SYSTEM
> ibrav=4
> celldm(1)=13.95
> celldm(3)=2.71
> nat=20
> ntyp=2
> ecutwfc=45.0
> ecutrho=450
> occupations='smearing'
> smearing='mv'
> degauss=0.002
> vdw_corr='dft-d'
> /
> &ELECTRONS
> diagonalization='david'
> mixing_mode='plain'
> electron_maxstep = 100
> mixing_beta=0.6
> conv_thr = 1.0D-8
> /
> &IONS
> ion_dynamics='bfgs'
> /
>
> ATOMIC_SPECIES
> C 12.011 C.pbe-rrkjus.UPF
> Br 79.90 Br.pbe-n-rrkjus_psl.0.2.UPF
> ATOMIC_POSITIONS (angstrom)
> C 0.001428319 -0.002221684 0.0
> C 1.231420386 0.708643125 0.0
> C 2.46214 -0.002217662 0.0
> C 3.692093444 0.708644819 0.0
> C -1.228907612 2.128792409 0.0
> C 0.001083491 2.839646136 0.0
> C 1.231766190 2.128786536 0.0
> C 2.461756350 2.839644042 0.0
> C 4.922778865 -0.002223457 0.0
> C 6.152768802 0.708640258 0.0
> C 3.692440675 2.128788864 0.0
> C 4.922431282 2.839647087 0.0
> C -2.459244768 4.259790447 0.0
> C -1.229251320 4.970648411 0.0
> C 0.001427750 4.259792429 0.0
> C 1.231421212 4.970653053 0.0
> C 2.462102410 4.259795383 0.0
> C 3.692093014 4.970654542 0.0
> Br 2.461756350 2.558726619 3.5
> Br 2.461756350 0.278726619 3.5
>
> K_POINTS {automatic}
> 5 5 1 0 0 0
>
>
> With Best Regards
> Nipesh Dulal
> Tribhuwan University
> Kathmandu , Nepal
>
>
> ___
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>
--
Dr. Lorenzo Paulatto
IdR @ IMPMC -- CNRS & Université Paris 6
phone: +33 (0)1 442 79822 / skype: paulatz
www: http://www-int.impmc.upmc.fr/~paulatto/
mail: 23-24/423 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05
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