[gpaw-users] Changes in the new PAW setups bundle of 26/10 ("gpaw-setups-0.9.9672")
Niels Theis Bendtsen
ntben at fysik.dtu.dk
Tue Nov 27 13:40:41 CET 2012
So I did my own little test with the new setups on rutile RuO2. I was unable to converge using RM-DIIS (not surprised anymore) and switching to cg works. I got RM-DIIS to converge using basis = dzp
My calculation is just a single calculitation so no structure optimization.
Using the old setups I get a total energy of -39.895 eV with 34 bands and 40 valence electrons. It took only 6 m 42s and 44 iterations
Using new setups:
cg and default parameters:
-42.983 eV, 42 bands, 56 valence electrons and 9 min 14 s and 24 iterations.
RM-DIIS and basis = 'dzp' try 1:
-42.983 eV, 102 bands, 56 valence electrons and 11 min 52 s and 28 iterations.
RM-DIIS and basis = 'dzp' try 2:
-42.983 eV, 78 bands, 56 valence electrons and 14 min 18 s and 46 iterations.
The total energies does deviate on the fourth decimal. In this small set cg is actually faster than RM-DIIS??? I saw that Ask did something with basis set that I cannot replicate here. Can it have something to do with the structure optimisation?
Script is provided below together with the output file.
#!/usr/bin/env python
#PBS -N RuO2cg
#PBS -m ae
#PBS -l nodes=1:ppn=8:xeon
#PBS -l walltime=20:00:00
from ase.parallel import paropen
from gpaw import GPAW, Mixer
#from ase.data import reference_states, atomic_numbers
from ase.utils.eos import EquationOfState
from ase.io import read, write
from ase import units
from ase.lattice.spacegroup import crystal
import numpy as np
from scipy.optimize import fmin
from ase.optimize import BFGS
import sys
import os
from gpaw import setup_paths
setup_paths.insert(0, '/home/camp/ntben/localnewsetup/gpaw-setups-0.9.9672')
element = 'RuO2dzp'
a = 4.49
c = 3.10
atoms =crystal(['Ru', 'O'], basis=[(0, 0, 0),(0.3, 0.3, 0.0)],
spacegroup=136, cellpar=[a, a, c, 90, 90, 90])
uc = atoms.get_cell()
print "Suggested k points:", np.round(30 / uc.diagonal())
kpts = [7, 7, 10]
print "Used k points:", kpts
calc = GPAW(h=0.15,
kpts=kpts,
basis='dzp',
xc='RPBE',
txt='test' + element+'.txt')
atoms.set_calculator(calc)
atoms.get_potential_energy()
Output:
___ ___ ___ _ _ _
| | |_ | | | |
| | | | | . | | | |
|__ | _|___|_____| 0.9.0.8965
|___|_|
User: ntben at a032.dcsc.fysik.dtu.dk
Date: Tue Nov 27 11:12:54 2012
Arch: x86_64
Pid: 26527
Dir: /opt/campos-gpaw/0.9.0.8965/1.el5.fys.open64.4.2.3.python2.4.without_ase.openmpi.1.3.3.acml.4.4.0.acml.4.4.0/lib64/python2.4/site-packages/gpaw
ase: /opt/campos-ase3/3.6.0.2515/1.el5.fys.python2.4/lib64/python2.4/site-packages/ase (version 3.6.0.2515)
numpy: /opt/numpy/1.3.0/1.el5.fys.gfortran.4.1.2.python2.4.acml.4.0.1.acml.4.0.1/lib64/python2.4/site-packages/numpy (version 1.3.0)
units: Angstrom and eV
cores: 8
Memory estimate
---------------
Process memory now: 27.33 MiB
Calculator 333.36 MiB
Density 29.54 MiB
Arrays 3.11 MiB
Localized functions 25.71 MiB
Mixer 0.72 MiB
Hamiltonian 6.05 MiB
Arrays 2.03 MiB
XC 0.00 MiB
Poisson 2.32 MiB
vbar 1.70 MiB
Wavefunctions 297.77 MiB
Arrays psit_nG 244.04 MiB
Eigensolver 25.60 MiB
Projectors 3.57 MiB
Overlap op 24.56 MiB
Positions:
0 Ru 0.0000 0.0000 0.0000
1 Ru 2.2450 2.2450 1.5500
2 O 1.3470 1.3470 0.0000
3 O 3.1430 3.1430 0.0000
4 O 0.8980 3.5920 1.5500
5 O 3.5920 0.8980 1.5500
O
Ru
O
O
Ru
Unit Cell:
Periodic X Y Z Points Spacing
--------------------------------------------------------------------
1. axis: yes 4.490000 0.000000 0.000000 28 0.1604
2. axis: yes 0.000000 4.490000 0.000000 28 0.1604
3. axis: yes 0.000000 0.000000 3.100000 20 0.1550
Ru-setup:
name : Ruthenium
id : 76477906e28f51dc1b29884d53556fe9
Z : 44
valence: 16
core : 28
charge : 0.0
file : /home/camp/ntben/localnewsetup/gpaw-setups-0.9.9672/Ru.RPBE.gz
cutoffs: 1.23(comp), 2.16(filt), 1.30(core), lmax=2
valence states:
energy radius
4s(2) -76.255 1.281
5s(1) -4.126 1.281
4p(6) -46.371 1.286
5p(0) -0.913 1.286
4d(7) -5.146 1.254
*d 22.066 1.254
LCAO basis set for Ru:
Name: dzp
Basis set was loaded from file /home/camp/ntben/localnewsetup/gpaw-setups-0.9.9672/Ru.dzp.basis.gz
Number of radial functions: 9
Number of spherical harmonics: 25
l=0, rc=3.2969 Bohr: 4s-sz confined orbital
l=0, rc=9.6875 Bohr: 5s-sz confined orbital
l=1, rc=3.7656 Bohr: 4p-sz confined orbital
l=2, rc=6.3281 Bohr: 4d-sz confined orbital
l=0, rc=2.0781 Bohr: 4s-dz split-valence wave
l=0, rc=5.8281 Bohr: 5s-dz split-valence wave
l=1, rc=2.4219 Bohr: 4p-dz split-valence wave
l=2, rc=3.7500 Bohr: 4d-dz split-valence wave
l=2, rc=3.7656 Bohr: d-type Gaussian polarization
O-setup:
name : Oxygen
id : 08071ca1eed670e7821b24b7eb4d558c
Z : 8
valence: 6
core : 2
charge : 0.0
file : /home/camp/ntben/localnewsetup/gpaw-setups-0.9.9672/O.RPBE.gz
cutoffs: 0.67(comp), 1.17(filt), 0.83(core), lmax=2
valence states:
energy radius
2s(2) -24.041 0.688
2p(4) -8.984 0.598
*s 3.170 0.688
*p 18.228 0.598
*d 0.000 0.619
LCAO basis set for O:
Name: dzp
Basis set was loaded from file /home/camp/ntben/localnewsetup/gpaw-setups-0.9.9672/O.dzp.basis.gz
Number of radial functions: 5
Number of spherical harmonics: 13
l=0, rc=4.3438 Bohr: 2s-sz confined orbital
l=1, rc=5.3906 Bohr: 2p-sz confined orbital
l=0, rc=2.2969 Bohr: 2s-dz split-valence wave
l=1, rc=2.8906 Bohr: 2p-dz split-valence wave
l=2, rc=5.3906 Bohr: d-type Gaussian polarization
Using the RPBE Exchange-Correlation Functional.
Spin-Paired Calculation
Total Charge: 0.000000
Fermi Temperature: 0.100000
Wave functions: Uniform real-space grid
Kinetic energy operator: 6*3+1=19 point O(h^6) finite-difference Laplacian
Eigensolver: rmm-diis
XC and Coulomb potentials evaluated on a 56*56*40 grid
Interpolation: tri-quintic (5. degree polynomial)
Poisson solver: Jacobi solver with 4 multi-grid levels
Stencil: 6*3+1=19 point O(h^6) finite-difference Laplacian
Reference Energy: -254678.132380
Total number of cores used: 8
Parallelization over k-points: 8
MatrixOperator buffer_size: default value or
see value of nblock in input file
Diagonalizer layout: Serial LAPACK
Orthonormalizer layout: Serial LAPACK
Symmetries present: 8
490 k-points (7 x 7 x 10 Monkhorst-Pack grid)
80 k-points in the Irreducible Part of the Brillouin Zone
Linear Mixing Parameter: 0.1
Pulay Mixing with 3 Old Densities
Damping of Long Wave Oscillations: 50
Convergence Criteria:
Total Energy Change: 0.0005 eV / electron
Integral of Absolute Density Change: 0.0001 electrons
Integral of Absolute Eigenstate Change: 4e-08 eV^2
Number of Atoms: 6
Number of Atomic Orbitals: 102
Number of Bands in Calculation: 102
Bands to Converge: Occupied States Only
Number of Valence Electrons: 56
log10-error: Total Iterations:
Time WFS Density Energy Fermi Poisson
iter: 1 11:13:33 +3.6 -45.656478 4 15
iter: 2 11:13:57 -0.2 -48.491408 4
iter: 3 11:14:21 -1.0 -48.580999 2
iter: 4 11:14:46 -1.1 -1.2 -44.853351 9 7
iter: 5 11:15:11 -1.0 -1.3 -42.964989 9 8
iter: 6 11:15:36 -1.3 -1.6 -43.635732 5 7
iter: 7 11:16:01 -1.5 -1.6 -43.108654 7 8
iter: 8 11:16:26 -2.2 -2.0 -43.030008 3 7
iter: 9 11:16:51 -2.7 -2.1 -42.981454 3 6
iter: 10 11:17:16 -3.3 -2.4 -42.980521 3 5
iter: 11 11:17:41 -3.3 -2.4 -42.981560 3 6
iter: 12 11:18:06 -3.5 -2.6 -42.984099 3 6
iter: 13 11:18:31 -3.8 -2.7 -42.983144 3 5
iter: 14 11:18:56 -4.1 -3.0 -42.983235 2 5
iter: 15 11:19:20 -4.8 -3.1 -42.983202 2 4
iter: 16 11:19:45 -4.0 -3.2 -42.982700 3 5
iter: 17 11:20:10 -4.8 -3.7 -42.982800 2 3
iter: 18 11:20:35 -5.6 -3.7 -42.982379 2 3
iter: 19 11:21:00 -6.0 -3.8 -42.982337 2 3
iter: 20 11:21:25 -5.7 -3.8 -42.982226 2 3
iter: 21 11:21:50 -6.5 -4.0 -42.982674 2 2
iter: 22 11:22:14 -6.5 -4.0 -42.982677 2 3
iter: 23 11:22:39 -6.0 -4.1 -42.982764 2 3
iter: 24 11:23:04 -6.8 -4.2 -42.982445 2 2
iter: 25 11:23:29 -7.3 -4.3 -42.982215 2 2
iter: 26 11:23:54 -6.8 -4.4 -42.982439 2 3
iter: 27 11:24:19 -7.0 -4.6 -42.982253 2 2
iter: 28 11:24:43 -7.8 -4.7 -42.982604 1 1
------------------------------------
Converged After 28 Iterations.
Energy Contributions Relative to Reference Atoms:(reference = -254678.132380)
-------------------------
Kinetic: +41.038599
Potential: -50.993219
External: +0.000000
XC: -33.726018
Entropy (-ST): -0.121683
Local: +0.758877
-------------------------
Free Energy: -43.043445
Zero Kelvin: -42.982604
Fermi Level: 8.06960
Total Charge: -0.000000 electrons
Dipole Moment: [-0.95402944 -0.95402944 -2.94283037]
Memory usage: 400.61 MB
============================================================
Timing: incl. excl.
============================================================
Initialization: 8.716 0.942 0.1% |
Hamiltonian: 0.852 0.011 0.0% |
Atomic: 0.338 0.001 0.0% |
XC Correction: 0.337 0.337 0.0% |
Communicate energies: 0.000 0.000 0.0% |
Hartree integrate/restrict: 0.002 0.002 0.0% |
Initialize Hamiltonian: 0.002 0.002 0.0% |
Poisson: 0.394 0.394 0.1% |
XC 3D grid: 0.104 0.104 0.0% |
vbar: 0.001 0.001 0.0% |
LCAO initialization: 6.922 0.795 0.1% |
LCAO eigensolver: 1.035 0.001 0.0% |
Atomic Hamiltonian: 0.012 0.012 0.0% |
Calculate projections: 0.010 0.010 0.0% |
Distribute overlap matrix: 0.001 0.001 0.0% |
Orbital Layouts: 0.161 0.161 0.0% |
Potential matrix: 0.656 0.656 0.1% |
Sum over cells: 0.193 0.193 0.0% |
LCAO to grid: 2.848 2.848 0.4% |
Set positions (LCAO WFS): 2.244 0.002 0.0% |
Basic WFS set positions: 0.001 0.001 0.0% |
Basis functions set positions: 0.000 0.000 0.0% |
TCI: Calculate S, T, P: 2.241 2.241 0.3% |
SCF-cycle: 700.769 0.216 0.0% |
Density: 4.911 0.000 0.0% |
Atomic density matrices: 0.153 0.153 0.0% |
Mix: 0.464 0.464 0.1% |
Multipole moments: 0.002 0.002 0.0% |
Pseudo density: 4.291 4.075 0.6% |
Symmetrize density: 0.216 0.216 0.0% |
Hamiltonian: 14.386 0.283 0.0% |
Atomic: 8.506 0.017 0.0% |
XC Correction: 8.489 8.489 1.2% |
Communicate energies: 0.000 0.000 0.0% |
Hartree integrate/restrict: 0.071 0.071 0.0% |
Poisson: 2.945 2.945 0.4% |
XC 3D grid: 2.559 2.559 0.4% |
vbar: 0.021 0.021 0.0% |
Orthonormalize: 169.089 0.017 0.0% |
Band Layouts: 0.358 0.003 0.0% |
Inverse Cholesky: 0.355 0.355 0.1% |
calc_s_matrix: 54.200 54.200 7.6% |--|
projections: 76.031 76.031 10.7% |---|
rotate_psi: 38.483 38.483 5.4% |-|
RMM-DIIS: 368.106 171.084 24.1% |---------|
Apply hamiltonian: 27.076 27.076 3.8% |-|
precondition: 95.610 95.610 13.5% |----|
projections: 74.335 74.335 10.5% |---|
Subspace diag: 144.062 0.013 0.0% |
Band Layouts: 3.706 0.007 0.0% |
Diagonalize: 3.690 3.690 0.5% |
Distribute results: 0.009 0.009 0.0% |
calc_h_matrix: 65.289 38.585 5.4% |-|
Apply hamiltonian: 26.704 26.704 3.8% |-|
rotate_psi: 75.054 75.054 10.6% |---|
Other: 0.019 0.019 0.0% |
============================================================
Total: 709.504 100.0%
============================================================
date: Tue Nov 27 11:24:43 2012
Niels Theis Bendtsen
Ph.d.-studerende
FYS-CAMD
DTU Fysik
Bygning 307
2800 Kgs. Lyngby
Direkte telefon 45253177
ntben at fysik.dtu.dk
www.fysik.dtu.dk
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