[gpaw-users] Strange feature from time propagation TDDFT
Arto Sakko
arto.sakko at aalto.fi
Wed Jul 4 13:49:47 CEST 2012
Dear gpaw-users,
I am calculating the photoabsorption spectrum using the time
propagation TDDFT method. I find a strange feature in the 60-70 eV
regime when the system contains gold or silver atoms. The continuum part
of the spectrum always contains unphysical peaks (standing waves), but
this seems different. For example, the f-sum rule is not obeyed because
of this peak (the value of the integrated spectrum is too large by
several electrons). The low-energy part of the spectrum is ok, but I
would like to understand the origin of this peak, partly because I am
also interested in the features at the high energy range.
I attach an example script (silver dimer) for generating that peak, as
well as standard output and a figure of the resulting spectrum.
The feature appears also with smaller time steps, smaller spacings,
and larger box sizes. Is there an explanation for this feature?
With best regards,
Arto Sakko
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___ ___ ___ _ _ _
| | |_ | | | |
| | | | | . | | | |
|__ | _|___|_____| 0.10.0.9137
|___|_|
User: sakkoa1 at cn127
Date: Wed Jul 4 10:05:18 2012
Arch: x86_64
Pid: 17559
Dir: /triton/tfy/work/sakkoa1/Programs/gpaw/gpaw-web/build/lib.linux-x86_64-2.6/gpaw
ase: /cvmfs/fgi.csc.fi/apps/ase/3.6.0/ase (version 3.6.0.2515)
numpy: /usr/lib64/python2.6/site-packages/numpy (version 1.3.0)
units: Angstrom and eV
cores: 12
Memory estimate
---------------
Process memory now: 35.72 MiB
Calculator 1.80 MiB
Density 0.76 MiB
Arrays 0.27 MiB
Localized functions 0.44 MiB
Mixer 0.06 MiB
Hamiltonian 0.42 MiB
Arrays 0.18 MiB
XC 0.00 MiB
Poisson 0.21 MiB
vbar 0.03 MiB
Wavefunctions 0.62 MiB
Arrays psit_nG 0.17 MiB
Eigensolver 0.21 MiB
Projectors 0.08 MiB
Overlap op 0.17 MiB
Positions:
0 Ag 2.7350 3.0000 3.0000
1 Ag 5.2650 3.0000 3.0000
.-------------------.
/| |
/ | |
/ | |
* | |
| | |
| | Ag Ag |
| .-------------------.
| / /
| / /
|/ /
*-------------------*
Unit Cell:
Periodic X Y Z Points Spacing
--------------------------------------------------------------------
1. axis: no 8.000000 0.000000 0.000000 32 0.2500
2. axis: no 0.000000 6.000000 0.000000 24 0.2500
3. axis: no 0.000000 0.000000 6.000000 24 0.2500
Ag-setup:
name : Silver
id : aac732a7f42225a52edcbbb6e277d3cd
Z : 47
valence: 11
core : 36
charge : 0.0
file : /cvmfs/fgi.csc.fi/apps/gpaw/gpaw-setups-0.8.7929/Ag.LDA.gz
cutoffs: 1.30(comp), 2.31(filt), 2.78(core), lmax=2
valence states:
energy radius
5s(1) -4.708 1.296
5p(0) -0.844 1.296
4d(10) -7.664 1.296
*s 22.503 1.296
*p 26.368 1.296
*d 19.547 1.296
Using partial waves for Ag as LCAO basis
Using the LDA Exchange-Correlation Functional.
Spin-Paired Calculation
Total Charge: 0.000000
Fermi Temperature: 0.000000
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 64*48*48 grid
Interpolation: tri-quintic (5. degree polynomial)
Poisson solver: Jacobi solver with 5 multi-grid levels
Stencil: 6*3+1=19 point O(h^6) finite-difference Laplacian
Reference Energy: -288929.166771
Total number of cores used: 12
Domain Decomposition: 3 x 2 x 2
MatrixOperator buffer_size: default value or
see value of nblock in input file
Diagonalizer layout: Serial LAPACK
Orthonormalizer layout: Serial LAPACK
Symmetries present: 1
1 k-point (Gamma)
1 k-point in the Irreducible Part of the Brillouin Zone
Linear Mixing Parameter: 0.25
Pulay Mixing with 3 Old Densities
No Damping of Long Wave Oscillations
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: 2
Number of Atomic Orbitals: 18
Number of Bands in Calculation: 18
Bands to Converge: Occupied States Only
Number of Valence Electrons: 22
log10-error: Total Iterations:
Time WFS Density Energy Fermi Poisson
iter: 1 10:05:19 +2.3 -1.509548 0 12
iter: 2 10:05:19 +0.0 -2.447504 0
iter: 3 10:05:19 -1.1 -2.527664 0
iter: 4 10:05:20 -1.3 -1.3 -2.277267 0 7
iter: 5 10:05:20 -1.0 -1.5 -2.191553 0 7
iter: 6 10:05:20 -1.7 -2.2 -2.229288 0 6
iter: 7 10:05:20 -2.0 -2.4 -2.238248 0 5
iter: 8 10:05:20 -2.6 -2.7 -2.238699 0 5
iter: 9 10:05:20 -2.6 -2.8 -2.239669 0 4
iter: 10 10:05:20 -3.8 -3.0 -2.239738 0 4
iter: 11 10:05:20 -4.0 -3.1 -2.239135 0 5
iter: 12 10:05:20 -4.8 -3.7 -2.239199 0 3
iter: 13 10:05:20 -5.1 -4.1 -2.239254 0 3
iter: 14 10:05:21 -5.6 -4.3 -2.239035 0 1
iter: 15 10:05:21 -6.0 -4.4 -2.239207 0 2
iter: 16 10:05:21 -6.6 -4.7 -2.239383 0 1
iter: 17 10:05:21 -6.4 -4.8 -2.239606 0 1
iter: 18 10:05:21 -7.3 -5.2 -2.239253 0 1
iter: 19 10:05:21 -6.7 -5.1 -2.239385 0 1
iter: 20 10:05:21 -8.2 -5.0 -2.239195 0 1
------------------------------------
Converged After 20 Iterations.
Energy Contributions Relative to Reference Atoms:(reference = -288929.166771)
-------------------------
Kinetic: +1.092416
Potential: -1.051590
External: +0.000000
XC: -2.384707
Entropy (-ST): -0.000000
Local: +0.104686
-------------------------
Free Energy: -2.239195
Zero Kelvin: -2.239195
Fermi Level: -3.82729
Band Eigenvalues Occupancy
0 -8.24284 2.00000
1 -7.69906 2.00000
2 -7.69906 2.00000
3 -7.13898 2.00000
4 -7.13757 2.00000
5 -6.92557 2.00000
6 -6.92349 2.00000
7 -6.63739 2.00000
8 -6.63739 2.00000
9 -6.47296 2.00000
10 -5.00584 2.00000
11 -2.64873 0.00000
12 0.05614 0.00000
13 0.05614 0.00000
14 0.74302 0.00000
15 2.36074 0.00000
16 2.36074 0.00000
17 7.23839 0.00000
Total Charge: -0.000000 electrons
Dipole Moment: [ 1.53926251e-13 1.00698319e-13 1.00874570e-13]
___ ___ ___ _ _ _
| | |_ | | | |
| | | | | . | | | |
|__ | _|___|_____| 0.10.0.9137
|___|_|
User: sakkoa1 at cn127
Date: Wed Jul 4 10:05:21 2012
Arch: x86_64
Pid: 17559
Dir: /triton/tfy/work/sakkoa1/Programs/gpaw/gpaw-web/build/lib.linux-x86_64-2.6/gpaw
ase: /cvmfs/fgi.csc.fi/apps/ase/3.6.0/ase (version 3.6.0.2515)
numpy: /usr/lib64/python2.6/site-packages/numpy (version 1.3.0)
units: Angstrom and eV
cores: 12
Memory estimate
---------------
Process memory now: 45.01 MiB
Calculator 2.30 MiB
Density 0.71 MiB
Arrays 0.27 MiB
Localized functions 0.44 MiB
Mixer 0.00 MiB
Hamiltonian 0.42 MiB
Arrays 0.18 MiB
XC 0.00 MiB
Poisson 0.21 MiB
vbar 0.03 MiB
Wavefunctions 1.17 MiB
Arrays psit_nG 0.33 MiB
Eigensolver 0.42 MiB
Projectors 0.08 MiB
Overlap op 0.34 MiB
.-------------------.
/| |
/ | |
/ | |
* | |
| | |
| | Ag Ag |
| .-------------------.
| / /
| / /
|/ /
*-------------------*
Unit Cell:
Periodic X Y Z Points Spacing
--------------------------------------------------------------------
1. axis: no 8.000000 0.000000 0.000000 32 0.2500
2. axis: no 0.000000 6.000000 0.000000 24 0.2500
3. axis: no 0.000000 0.000000 6.000000 24 0.2500
Ag-setup:
name : Silver
id : aac732a7f42225a52edcbbb6e277d3cd
Z : 47
valence: 11
core : 36
charge : 0.0
file : /cvmfs/fgi.csc.fi/apps/gpaw/gpaw-setups-0.8.7929/Ag.LDA.gz
cutoffs: 1.30(comp), 2.31(filt), 2.78(core), lmax=2
valence states:
energy radius
5s(1) -4.708 1.296
5p(0) -0.844 1.296
4d(10) -7.664 1.296
*s 22.503 1.296
*p 26.368 1.296
*d 19.547 1.296
Using partial waves for Ag as LCAO basis
Using the LDA Exchange-Correlation Functional.
Spin-Paired Calculation
Total Charge: 0.000000
Fermi Temperature: 0.000000
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 64*48*48 grid
Interpolation: tri-quintic (5. degree polynomial)
Poisson solver: Jacobi solver with 5 multi-grid levels
Stencil: 6*3+1=19 point O(h^6) finite-difference Laplacian
Reference Energy: -288929.166771
Total number of cores used: 12
Domain Decomposition: 3 x 2 x 2
MatrixOperator buffer_size: default value or
see value of nblock in input file
Diagonalizer layout: Serial LAPACK
Orthonormalizer layout: Serial LAPACK
Symmetries present: 1
1 k-point (Gamma)
1 k-point 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: 2
Number of Atomic Orbitals: 18
Number of Bands in Calculation: 18
Bands to Converge: Occupied States Only
Number of Valence Electrons: 22
Positions:
0 Ag 2.7350 3.0000 3.0000
1 Ag 5.2650 3.0000 3.0000
------------------------------------------
Time-propagation TDDFT
------------------------------------------
Charge epsilon: 1e-05
Solver: CSCG
Preconditioner: None
Propagator: SICN
States per processor = 18
Delta kick = (0.001, 0.0, 0.0)
Starting time: 0.00 as
Time step: 10.00 as
Simulation Total log10 Iterations:
Time time Energy Norm Propagator
iter: 0 10:05:23 0.00 -0.082278 -13.3 0
iter: 10 10:05:31 100.00 -0.082278 -13.4 73
iter: 20 10:05:40 200.00 -0.082278 -13.5 73
iter: 30 10:05:48 300.00 -0.082278 -13.5 72
iter: 40 10:05:56 400.00 -0.082278 -13.3 71
iter: 50 10:06:05 500.00 -0.082278 -13.2 73
iter: 60 10:06:13 600.00 -0.082278 -13.6 70
iter: 70 10:06:21 700.00 -0.082278 -13.2 71
iter: 80 10:06:30 800.00 -0.082278 -13.3 70
iter: 90 10:06:38 900.00 -0.082278 -13.5 72
iter: 100 10:06:46 1000.00 -0.082278 -13.2 73
iter: 110 10:06:55 1100.00 -0.082278 -13.4 72
iter: 120 10:07:03 1200.00 -0.082278 -13.3 70
iter: 130 10:07:11 1300.00 -0.082278 -13.5 71
iter: 140 10:07:20 1400.00 -0.082278 -13.5 74
iter: 150 10:07:28 1500.00 -0.082278 -13.4 71
iter: 160 10:07:37 1600.00 -0.082278 -13.5 73
iter: 170 10:07:45 1700.00 -0.082278 -13.4 72
iter: 180 10:07:54 1800.00 -0.082278 -13.6 69
iter: 190 10:08:02 1900.00 -0.082278 -13.3 70
iter: 200 10:08:11 2000.00 -0.082278 -13.3 72
iter: 210 10:08:19 2100.00 -0.082278 -13.3 70
iter: 220 10:08:27 2200.00 -0.082278 -13.4 73
iter: 230 10:08:36 2300.00 -0.082278 -13.4 73
iter: 240 10:08:44 2400.00 -0.082278 -13.4 72
iter: 250 10:08:53 2500.00 -0.082278 -13.7 72
iter: 260 10:09:01 2600.00 -0.082278 -13.3 72
iter: 270 10:09:09 2700.00 -0.082278 -13.8 70
iter: 280 10:09:18 2800.00 -0.082278 -13.5 70
iter: 290 10:09:26 2900.00 -0.082278 -13.2 74
Calculating photoabsorption spectrum from file "dm.dat"
Using kick strength = [ 0.001 0. 0. ]
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Calculated photoabsorption spectrum saved to file "spec.txt"
Memory usage: 46.41 MB
============================================================
Timing: incl. excl.
============================================================
Apply approximate inverse overlap: 0.032 0.032 0.0% |
Apply time-dependent operators: 0.082 0.065 0.0% |
Apply overlap: 0.017 0.017 0.0% |
CSCG: 0.933 0.215 0.1% |
Apply time-dependent operators: 0.703 0.559 0.2% |
Apply overlap: 0.144 0.144 0.1% |
Solve TDDFT preconditioner: 0.015 0.015 0.0% |
Hamiltonian: 0.105 0.000 0.0% |
Atomic: 0.000 0.000 0.0% |
Communicate energies: 0.059 0.059 0.0% |
Hartree integrate/restrict: 0.001 0.001 0.0% |
Initialize Hamiltonian: 0.002 0.002 0.0% |
Poisson: 0.040 0.040 0.0% |
XC 3D grid: 0.003 0.003 0.0% |
vbar: 0.000 0.000 0.0% |
Propagate: 251.839 2.490 1.0% |
Apply approximate inverse overlap: 1.976 1.976 0.8% |
Apply time-dependent operators: 4.008 2.928 1.2% |
Apply overlap: 1.080 1.080 0.4% |
CSCG: 193.786 56.038 22.1% |--------|
Apply time-dependent operators: 133.216 95.453 37.6% |--------------|
Apply overlap: 37.763 37.763 14.9% |-----|
Solve TDDFT preconditioner: 4.532 4.532 1.8% ||
Density: 0.056 0.001 0.0% |
Atomic density matrices: 0.000 0.000 0.0% |
Mix: 0.024 0.024 0.0% |
Multipole moments: 0.020 0.020 0.0% |
Pseudo density: 0.011 0.011 0.0% |
Symmetrize density: 0.000 0.000 0.0% |
Hamiltonian: 2.139 0.006 0.0% |
Atomic: 0.000 0.000 0.0% |
Communicate energies: 1.789 1.789 0.7% |
Hartree integrate/restrict: 0.015 0.015 0.0% |
Poisson: 0.247 0.247 0.1% |
XC 3D grid: 0.079 0.079 0.0% |
vbar: 0.004 0.004 0.0% |
Update time-dependent operators: 47.383 0.875 0.3% |
Density: 1.132 0.012 0.0% |
Atomic density matrices: 0.006 0.006 0.0% |
Mix: 0.492 0.492 0.2% |
Multipole moments: 0.402 0.402 0.2% |
Pseudo density: 0.220 0.212 0.1% |
Symmetrize density: 0.008 0.008 0.0% |
Hamiltonian: 45.376 0.126 0.0% |
Atomic: 0.003 0.003 0.0% |
Communicate energies: 35.898 35.898 14.2% |-----|
Hartree integrate/restrict: 0.295 0.295 0.1% |
Poisson: 7.393 7.393 2.9% ||
XC 3D grid: 1.583 1.583 0.6% |
vbar: 0.079 0.079 0.0% |
Read: 0.004 0.001 0.0% |
Atomic matrices: 0.001 0.001 0.0% |
Band energies: 0.000 0.000 0.0% |
Projections: 0.000 0.000 0.0% |
Pseudo-density: 0.002 0.002 0.0% |
Pseudo-potential: 0.001 0.001 0.0% |
Pseudo-wavefunctions: 0.000 0.000 0.0% |
Redistribute: 0.000 0.000 0.0% |
Symmetrize density: 0.000 0.000 0.0% |
Update time-dependent operators: 0.016 0.016 0.0% |
Other: 0.601 0.601 0.2% |
============================================================
Total: 253.614 100.0%
============================================================
date: Wed Jul 4 10:09:35 2012
Memory usage: 46.41 MB
============================================================
Timing: incl. excl.
============================================================
IO: 0.151 0.000 0.0% |
Write: 0.151 0.000 0.0% |
Atomic matrices: 0.000 0.000 0.0% |
Band energies: 0.000 0.000 0.0% |
Close: 0.001 0.001 0.0% |
Meta data: 0.133 0.133 0.1% |
Projections: 0.000 0.000 0.0% |
Pseudo-density: 0.001 0.001 0.0% |
Pseudo-potential: 0.001 0.001 0.0% |
Pseudo-wavefunctions: 0.014 0.014 0.0% |
Initialization: 1.437 1.240 0.5% |
Hamiltonian: 0.104 0.000 0.0% |
Atomic: 0.000 0.000 0.0% |
Communicate energies: 0.058 0.058 0.0% |
Hartree integrate/restrict: 0.000 0.000 0.0% |
Initialize Hamiltonian: 0.002 0.002 0.0% |
Poisson: 0.040 0.040 0.0% |
XC 3D grid: 0.003 0.003 0.0% |
vbar: 0.000 0.000 0.0% |
LCAO initialization: 0.093 0.082 0.0% |
LCAO eigensolver: 0.002 0.000 0.0% |
Atomic Hamiltonian: 0.000 0.000 0.0% |
Calculate projections: 0.000 0.000 0.0% |
Distribute overlap matrix: 0.001 0.001 0.0% |
Orbital Layouts: 0.000 0.000 0.0% |
Potential matrix: 0.000 0.000 0.0% |
LCAO to grid: 0.001 0.001 0.0% |
Set positions (LCAO WFS): 0.008 0.007 0.0% |
Basic WFS set positions: 0.000 0.000 0.0% |
Basis functions set positions: 0.000 0.000 0.0% |
TCI: Calculate S, T, P: 0.001 0.001 0.0% |
SCF-cycle: 1.625 0.011 0.0% |
Density: 0.032 0.000 0.0% |
Atomic density matrices: 0.000 0.000 0.0% |
Mix: 0.020 0.020 0.0% |
Multipole moments: 0.008 0.008 0.0% |
Pseudo density: 0.003 0.002 0.0% |
Symmetrize density: 0.000 0.000 0.0% |
Hamiltonian: 1.262 0.004 0.0% |
Atomic: 0.000 0.000 0.0% |
Communicate energies: 1.011 1.011 0.4% |
Hartree integrate/restrict: 0.008 0.008 0.0% |
Poisson: 0.193 0.193 0.1% |
XC 3D grid: 0.044 0.044 0.0% |
vbar: 0.002 0.002 0.0% |
Orthonormalize: 0.035 0.001 0.0% |
Band Layouts: 0.001 0.000 0.0% |
Inverse Cholesky: 0.001 0.001 0.0% |
calc_s_matrix: 0.021 0.021 0.0% |
projections: 0.007 0.007 0.0% |
rotate_psi: 0.005 0.005 0.0% |
RMM-DIIS: 0.244 0.092 0.0% |
Apply hamiltonian: 0.024 0.024 0.0% |
precondition: 0.121 0.121 0.0% |
projections: 0.007 0.007 0.0% |
Subspace diag: 0.042 0.001 0.0% |
Band Layouts: 0.003 0.000 0.0% |
Diagonalize: 0.002 0.002 0.0% |
Distribute results: 0.000 0.000 0.0% |
calc_h_matrix: 0.030 0.007 0.0% |
Apply hamiltonian: 0.023 0.023 0.0% |
rotate_psi: 0.009 0.009 0.0% |
Other: 253.713 253.713 98.7% |--------------------------------------|
============================================================
Total: 256.925 100.0%
============================================================
date: Wed Jul 4 10:09:35 2012
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