[Q-e-developers] Problems converging anions in vacuum
Oliviero Andreussi
oliviero.andreussi at epfl.ch
Wed May 9 15:24:49 CEST 2012
Dear developers,
The title says it all, we have been having problems with calculations of
organic anions (isolated molecules) with pw.x. The problem arises when
the cell size is increased above a minimum value, the SCF will almost
converge, but an error will show up in the diagonalization and the SCF
will go bananas. The error is quite reproducible, it happens for several
different organic anions (but also for OH-) and it may be something
already known to the community. If this is the case, if you know any
solution it would be very helpful and I apologise for the attachments
and the rest of the mail.
We tried to play a bit with the standard parameters of pw, in particular
we tried changing diagonalization scheme (cg vs davidson), changing the
number of iterations, changing mixing scheme (thomas-fermi, broyden,
local thomas-fermi), changing mixing parameter (from a starting one of
0.4 to as low as 0.01), changing the cutoffs, adding a smearing
(gaussian, with several values of degauss), different functionals (pbe,
pw91 and lda), we also restarted from a converged density (obtained from
a calculation in a dielectric environment), but nothing worked. We have
also tried some combinations of the above variations, probably not all
of them.
Attached you find an input and an output for an acetate anion (CH3COO-,
as in figure molecule.png), the output has been obtained with a modified
version of the code that does noting but printing a cube file of the
electronic density at each SCF step. This is to show you what happens
when the SCF goes bananas: in a normal SCF step the density changes
little and in a smooth way (attachement normal.png, difference between
the density at step 24 and the density at step 25 of the SCF cycle,
surfaces plotted at an isovalue of the differential density of 0.00001
); when the SCF start failing, the difference between two successive
densities is much larger (attachement critical.png, surfaces plotted at
an isovalue of 0.00010), it resembles the combination of two pz atomic
orbitals on the oxygen atoms, and it is highly modulated (in particular
one can see regular patterns when looking along cell axis, e.g.
critical_z.png). Any insight on what is happening would be very
helpful. Note that calculations with a cell size <= 40 a.u. actually
converge for this system in a reasonable number of steps (20-30).
Best,
Oliviero Andreussi
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&CONTROL
!
calculation = 'scf'
restart_mode = 'from_scratch'
pseudo_dir = '/home/andreuss/PWSCF/pslibrary.0.1/pbe/PSEUDOPOTENTIALS'
outdir = './'
prefix = 'c64197'
tprnfor = .TRUE.
!
/
&SYSTEM
!
ecutrho = 300
ecutwfc = 30
!
ibrav = 1
celldm( 1 ) = 50
!
nat = 7
ntyp = 3
!
tot_charge = -1
!
assume_isolated = 'makov-payne'
/
&ELECTRONS
!
conv_thr = 5.D-9
diagonalization = 'cg'
mixing_beta = 0.4
electron_maxstep = 200
!
/
&IONS
!
ion_dynamics = 'bfgs'
!
/
K_POINTS (automatic)
1 1 1 0 0 0
ATOMIC_SPECIES
C 12 C.pbe-rrkjus.UPF
H 1 H.pbe-rrkjus.UPF
O 16 O.pbe-rrkjus.UPF
ATOMIC_POSITIONS (angstrom)
C -1.301514464 0.322267800 -0.013534662
H -0.992221776 -0.730771277 -0.017468400
H -0.953317139 0.822347547 -0.927803089
H -2.403944997 0.357568238 -0.004148297
C -0.798965029 0.994835251 1.231555280
O -0.624449875 2.333980957 1.186305977
O -0.565657575 0.408425490 2.283827156
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Program PWSCF v.4.99 starts on 7May2012 at 10:42:54
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.php
Parallel version (MPI), running on 4 processors
R & G space division: proc/pool = 4
Current dimensions of program PWSCF are:
Max number of different atomic species (ntypx) = 10
Max number of k-points (npk) = 40000
Max angular momentum in pseudopotentials (lmaxx) = 3
Waiting for input...
Reading input from standard input
Subspace diagonalization in iterative solution of the eigenvalue problem:
a serial algorithm will be used
Parallelization info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Min 14915 5970 1492 2742228 693699 86741
Max 14917 5971 1494 2742229 693706 86744
Sum 59665 23881 5973 10968915 2774807 346971
bravais-lattice index = 1
lattice parameter (alat) = 50.0000 a.u.
unit-cell volume = 125000.0000 (a.u.)^3
number of atoms/cell = 7
number of atomic types = 3
number of electrons = 24.00
number of Kohn-Sham states= 12
kinetic-energy cutoff = 30.0000 Ry
charge density cutoff = 300.0000 Ry
convergence threshold = 5.0E-09
mixing beta = 0.4000
number of iterations used = 8 plain mixing
Exchange-correlation = PBE ( 1 4 3 4 0)
EXX-fraction = 0.00
Environ Module
==============
Please cite
"O. Andreussi, I. Dabo and N. Marzari, J. Chem. Phys. 136, 064102 (2012);"
in publications or presentations arising from this work.
compensation onset threshold = 0.1000E+00
switching function adopted = SCCS
density limit for vacuum region = 0.5000E-02
density limit for bulk solvent = 0.1000E-03
celldm(1)= 50.000000 celldm(2)= 0.000000 celldm(3)= 0.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of alat)
a(1) = ( 1.000000 0.000000 0.000000 )
a(2) = ( 0.000000 1.000000 0.000000 )
a(3) = ( 0.000000 0.000000 1.000000 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 1.000000 0.000000 0.000000 )
b(2) = ( 0.000000 1.000000 0.000000 )
b(3) = ( 0.000000 0.000000 1.000000 )
PseudoPot. # 1 for C read from file:
/home/andreuss/PWSCF/pslibrary.0.1/pbe/PSEUDOPOTENTIALS/C.pbe-rrkjus.UPF
MD5 check sum: 95fa12f085d2e18f476bcc6e9c8e426e
Pseudo is Ultrasoft + core correction, Zval = 4.0
Generated using "atomic" code by A. Dal Corso (Quantum ESPRESSO distribution)
Using radial grid of 1073 points, 4 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 0 coefficients
PseudoPot. # 2 for H read from file:
/home/andreuss/PWSCF/pslibrary.0.1/pbe/PSEUDOPOTENTIALS/H.pbe-rrkjus.UPF
MD5 check sum: bfac04b7ccebeaf0326b5278624b3e08
Pseudo is Ultrasoft, Zval = 1.0
Generated using "atomic" code by A. Dal Corso (Quantum ESPRESSO distribution)
Using radial grid of 929 points, 2 beta functions with:
l(1) = 0
l(2) = 0
Q(r) pseudized with 0 coefficients
PseudoPot. # 3 for O read from file:
/home/andreuss/PWSCF/pslibrary.0.1/pbe/PSEUDOPOTENTIALS/O.pbe-rrkjus.UPF
MD5 check sum: a2d6ea7c9cd2620aae7e5676ca7d6432
Pseudo is Ultrasoft + core correction, Zval = 6.0
Generated using "atomic" code by A. Dal Corso (Quantum ESPRESSO distribution)
Using radial grid of 1095 points, 4 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 0 coefficients
atomic species valence mass pseudopotential
C 4.00 12.00000 C( 1.00)
H 1.00 1.00000 H( 1.00)
O 6.00 16.00000 O( 1.00)
No symmetry found
Cartesian axes
site n. atom positions (alat units)
1 C tau( 1) = ( -0.0491901 0.0121800 -0.0005115 )
2 H tau( 2) = ( -0.0375005 -0.0276192 -0.0006602 )
3 H tau( 3) = ( -0.0360302 0.0310802 -0.0350659 )
4 H tau( 4) = ( -0.0908560 0.0135141 -0.0001568 )
5 C tau( 5) = ( -0.0301965 0.0375993 0.0465460 )
6 O tau( 6) = ( -0.0236008 0.0882117 0.0448359 )
7 O tau( 7) = ( -0.0213788 0.0154362 0.0863162 )
number of k points= 1
cart. coord. in units 2pi/alat
k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 2.0000000
Dense grid: 10968915 G-vectors FFT dimensions: ( 288, 288, 288)
Smooth grid: 2774807 G-vectors FFT dimensions: ( 180, 180, 180)
Largest allocated arrays est. size (Mb) dimensions
Kohn-Sham Wavefunctions 15.88 Mb ( 86742, 12)
NL pseudopotentials 50.30 Mb ( 86742, 38)
Each V/rho on FFT grid 91.12 Mb (5971968)
Each G-vector array 20.92 Mb (2742229)
G-vector shells 0.12 Mb ( 15831)
Largest temporary arrays est. size (Mb) dimensions
Each subspace H/S matrix 0.00 Mb ( 12, 12)
Each <psi_i|beta_j> matrix 0.01 Mb ( 38, 12)
Arrays for rho mixing 729.00 Mb (5971968, 8)
Check: negative/imaginary core charge= -0.000001 0.000000
Initial potential from superposition of free atoms
Check: negative starting charge= -0.007891
starting charge 22.99989, renormalised to 24.00000
negative rho (up, down): 0.823E-02 0.000E+00
Starting wfc are 19 randomized atomic wfcs
total cpu time spent up to now is 56.0 secs
per-process dynamical memory: 1011.2 Mb
Self-consistent Calculation
iteration # 1 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 1.00E-02, avg # of iterations = 2.8
negative rho (up, down): 0.677E-02 0.000E+00
total cpu time spent up to now is 123.6 secs
total energy = -94.38436288 Ry
Harris-Foulkes estimate = -94.56736853 Ry
estimated scf accuracy < 0.39995625 Ry
iteration # 2 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 1.67E-03, avg # of iterations = 5.2
negative rho (up, down): 0.903E-02 0.000E+00
total cpu time spent up to now is 201.2 secs
total energy = -94.74420127 Ry
Harris-Foulkes estimate = -94.77861381 Ry
estimated scf accuracy < 0.12863024 Ry
iteration # 3 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 5.36E-04, avg # of iterations = 3.9
negative rho (up, down): 0.210E-01 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 298.5 secs
total energy = -94.75927816 Ry
Harris-Foulkes estimate = -94.77532585 Ry
estimated scf accuracy < 0.04207723 Ry
iteration # 4 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 1.75E-04, avg # of iterations = 4.1
negative rho (up, down): 0.103E-01 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 396.1 secs
total energy = -94.76839010 Ry
Harris-Foulkes estimate = -94.77054534 Ry
estimated scf accuracy < 0.00493734 Ry
iteration # 5 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 2.06E-05, avg # of iterations = 5.8
negative rho (up, down): 0.687E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 503.0 secs
total energy = -94.77273727 Ry
Harris-Foulkes estimate = -94.77479229 Ry
estimated scf accuracy < 0.00389591 Ry
iteration # 6 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 1.62E-05, avg # of iterations = 4.1
negative rho (up, down): 0.647E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 602.0 secs
total energy = -94.77379533 Ry
Harris-Foulkes estimate = -94.77389558 Ry
estimated scf accuracy < 0.00037473 Ry
iteration # 7 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 1.56E-06, avg # of iterations = 6.4
negative rho (up, down): 0.595E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 712.4 secs
total energy = -94.77399362 Ry
Harris-Foulkes estimate = -94.77447145 Ry
estimated scf accuracy < 0.00075190 Ry
iteration # 8 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 1.56E-06, avg # of iterations = 5.4
negative rho (up, down): 0.535E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 817.7 secs
total energy = -94.77431193 Ry
Harris-Foulkes estimate = -94.77432019 Ry
estimated scf accuracy < 0.00021328 Ry
iteration # 9 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 8.89E-07, avg # of iterations = 4.2
negative rho (up, down): 0.506E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 916.1 secs
total energy = -94.77425671 Ry
Harris-Foulkes estimate = -94.77438382 Ry
estimated scf accuracy < 0.00035173 Ry
iteration # 10 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 8.89E-07, avg # of iterations = 3.2
negative rho (up, down): 0.494E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 1010.8 secs
total energy = -94.77415401 Ry
Harris-Foulkes estimate = -94.77427252 Ry
estimated scf accuracy < 0.00015650 Ry
iteration # 11 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 6.52E-07, avg # of iterations = 4.8
negative rho (up, down): 0.487E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 1111.7 secs
total energy = -94.77423748 Ry
Harris-Foulkes estimate = -94.77431636 Ry
estimated scf accuracy < 0.00016839 Ry
iteration # 12 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 6.52E-07, avg # of iterations = 3.8
negative rho (up, down): 0.484E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 1207.7 secs
total energy = -94.77427843 Ry
Harris-Foulkes estimate = -94.77429062 Ry
estimated scf accuracy < 0.00005597 Ry
iteration # 13 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 2.33E-07, avg # of iterations = 3.6
negative rho (up, down): 0.482E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 1303.7 secs
total energy = -94.77428316 Ry
Harris-Foulkes estimate = -94.77428611 Ry
estimated scf accuracy < 0.00002776 Ry
iteration # 14 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 1.16E-07, avg # of iterations = 3.3
negative rho (up, down): 0.482E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 1397.9 secs
total energy = -94.77428571 Ry
Harris-Foulkes estimate = -94.77428670 Ry
estimated scf accuracy < 0.00001407 Ry
iteration # 15 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 5.86E-08, avg # of iterations = 3.2
negative rho (up, down): 0.482E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 1492.0 secs
total energy = -94.77428455 Ry
Harris-Foulkes estimate = -94.77428654 Ry
estimated scf accuracy < 0.00001239 Ry
iteration # 16 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 5.16E-08, avg # of iterations = 3.3
negative rho (up, down): 0.483E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 1586.7 secs
total energy = -94.77428730 Ry
Harris-Foulkes estimate = -94.77428631 Ry
estimated scf accuracy < 0.00000638 Ry
iteration # 17 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 2.66E-08, avg # of iterations = 3.5
negative rho (up, down): 0.482E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 1682.8 secs
total energy = -94.77428550 Ry
Harris-Foulkes estimate = -94.77428844 Ry
estimated scf accuracy < 0.00000914 Ry
iteration # 18 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 2.66E-08, avg # of iterations = 3.7
negative rho (up, down): 0.480E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 1778.7 secs
total energy = -94.77428800 Ry
Harris-Foulkes estimate = -94.77428631 Ry
estimated scf accuracy < 0.00000292 Ry
iteration # 19 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 1.22E-08, avg # of iterations = 5.1
negative rho (up, down): 0.477E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 1881.1 secs
total energy = -94.77428948 Ry
Harris-Foulkes estimate = -94.77429044 Ry
estimated scf accuracy < 0.00001262 Ry
iteration # 20 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 1.22E-08, avg # of iterations = 3.4
negative rho (up, down): 0.472E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 1976.8 secs
total energy = -94.77428613 Ry
Harris-Foulkes estimate = -94.77429001 Ry
estimated scf accuracy < 0.00000951 Ry
iteration # 21 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 1.22E-08, avg # of iterations = 4.5
negative rho (up, down): 0.471E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 2077.1 secs
total energy = -94.77428765 Ry
Harris-Foulkes estimate = -94.77428793 Ry
estimated scf accuracy < 0.00000106 Ry
iteration # 22 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 4.40E-09, avg # of iterations = 4.4
negative rho (up, down): 0.470E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 2176.8 secs
total energy = -94.77428822 Ry
Harris-Foulkes estimate = -94.77428837 Ry
estimated scf accuracy < 0.00000085 Ry
iteration # 23 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 3.53E-09, avg # of iterations = 3.6
negative rho (up, down): 0.470E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 2272.5 secs
total energy = -94.77428850 Ry
Harris-Foulkes estimate = -94.77428840 Ry
estimated scf accuracy < 0.00000056 Ry
iteration # 24 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 2.34E-09, avg # of iterations = 3.6
negative rho (up, down): 0.468E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 2367.8 secs
total energy = -94.77428835 Ry
Harris-Foulkes estimate = -94.77428862 Ry
estimated scf accuracy < 0.00000074 Ry
iteration # 25 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 2.34E-09, avg # of iterations = 3.2
negative rho (up, down): 0.466E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 2461.9 secs
total energy = -94.77428832 Ry
Harris-Foulkes estimate = -94.77428840 Ry
estimated scf accuracy < 0.00000025 Ry
iteration # 26 ecut= 30.00 Ry beta=0.40
CG style diagonalization
ethr = 1.04E-09, avg # of iterations = 5.2
negative rho (up, down): 0.464E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 2566.3 secs
total energy = -94.77428870 Ry
Harris-Foulkes estimate = -94.77428869 Ry
estimated scf accuracy < 0.00000008 Ry
iteration # 27 ecut= 30.00 Ry beta=0.40
CG style diagonalization
c_bands: 1 eigenvalues not converged
ethr = 3.22E-10, avg # of iterations = 6.0
negative rho (up, down): 0.462E-02 0.000E+00
add environment contribution to local potential
total cpu time spent up to now is 2842.4 secs
total energy = -94.77428965 Ry
Harris-Foulkes estimate = -94.77428964 Ry
estimated scf accuracy < 0.00000028 Ry
iteration # 28 ecut= 30.00 Ry beta=0.40
CG style diagonalization
c_bands: 1 eigenvalues not converged
ethr = 3.22E-10, avg # of iterations = 5.3
negative rho (up, down): 0.116E+00 0.000E+00
total cpu time spent up to now is 2921.7 secs
total energy = -94.78295397 Ry
Harris-Foulkes estimate = -94.77524064 Ry
estimated scf accuracy < 1.78307693 Ry
iteration # 29 ecut= 30.00 Ry beta=0.40
CG style diagonalization
c_bands: 2 eigenvalues not converged
ethr = 3.22E-10, avg # of iterations = 8.4
negative rho (up, down): 0.190E+00 0.000E+00
total cpu time spent up to now is 3017.1 secs
total energy = -94.79984104 Ry
Harris-Foulkes estimate = -94.79242399 Ry
estimated scf accuracy < 1.82610274 Ry
iteration # 30 ecut= 30.00 Ry beta=0.40
CG style diagonalization
c_bands: 2 eigenvalues not converged
ethr = 3.22E-10, avg # of iterations = 10.2
negative rho (up, down): 0.239E+00 0.000E+00
Ctrl-C caught... cleaning up processes
[press Ctrl-C again to force abort]
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