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Javier Junquera
Born-Oppenheimer dynamics
mn >> me electronic
decoupling
nuclear
Extracting information from the Potential
Energy Surface (PES)
h=δt
t0 t1 t2 tn-1 tn tn+1 tN
Notes:
ECONOMY
ACCURACY
Remark 1
The velocities are not needed to compute the trajectories, but they are useful
for estimating the kinetic energy (and the total energy).
They can be computed a posteriori using
[ can only be computed once is known]
Remark 2
Remark 3
The Verlet algorithm is properly centered: and
play symmetrical roles.
The Verlet algorithm is time reversible
Remark 4
• Amorphous systems:
• Molecular Liquids (H2O,CO2)
• Glasses (Si, SiO2)
• Displacive Phase transitions (P and T
relevant).
• Study of kinetic effects.
• Diffusion at surfaces
• Thermal stability
Nose-Hoover thermostat
• MD.TypeOfRun Verlet
NVE ensemble dynamics
• MD.TypeOfRun Nose
NVT dynamics with Nose thermostat
• MD.TypeOfRun ParrinelloRahman
NPE dynamics with P-R barostat
• MD.TypeOfRun NoseParrinelloRahman
NPT dynamics with thermostat/barostat
• MD.TypeOfRun Anneal
Anneals to specified p and T
Molecular Dynamics in SIESTA(2)
1. MD simulations (NVE)
2. Fourier transform of
Velocity-Velocity autocorrelation function.
1. Anharmonic effects: ω(T)
2. Expensive, but information available for MD
simulations.
How to run a Molecular Dynamic in Siesta: the
Verlet algorithm (NVE-microcanonical ensemble)
Computing the instantaneous temperature,
kinetic energy and total energy
How to run a Molecular Dynamic in Siesta: the
Verlet algorithm (NVE-microcanonical ensemble)
Maxwell-Boltzmann
Output of a Molecular Dynamic in Siesta:
the Verlet algorithm (NVE-microcanonical ensemble)
SystemLabel.MDE
Conserved quantity
Compare:
Total energy
with
KS energy
Compare:
Total energy
with
KS energy
Compare:
Total energy
with
KS energy
Compare:
Total energy
with
KS energy
Symmetric Distribution
at delta~0 there is non zero probability:
centrosymmetric complexes of the Zundel
(H5O2)+ type. Barrier ~ 40 meV
bulk-bulk diffusion
Symmetric Distribution
at delta~0 there is non zero probability:
centro-symmetric complexes of the Zundel
(H5O2)+ type. Barrier ~ 20 meV
Surface-bulk diffusion
at the! GaN
), where β is 1/k
1010/Aqueous
T and
interf
proton from a surface water to a bu
#
R
The pK can dRA(R)exp[−β∆F (R)] a
be derived from
" cut
(0)
∆G = −kB T ln C0a
at the GaN ? 1010/Aqueous
Ref the standard-state
0 interface
deproton
(1)
Thehere C pK
0
via
a =
denotescan−log
1.0 Mbe
10 derived
exp(−β∆G
concentration, R
(0)
from
is ),
the a
where
reaction sim
?
Ref the standard-state deprotonatio ! "
Rcut
(0)
via −log10 ∆G exp(−β∆G
(0)
= −kB T ln ),Cwhere 0
β dR is
Once H+ leave the surface, the barriers to diffuse within the bulk0liquid region
∗
To whom correspondence should be addressed:
are smaller than those to return to the surface.
! This agrees with the large
maria.fernandez-serra@stonybrook.edu
acidity obtained.
" Rcut
K. (0)
Maeda, K. Teramura, D. Lu, T. Takata, N. Saito, Y. In-
∆G = −k T ln C
here
oue, and K. C
Domen, denotes
B0Nature 01.0
440, 295 M concentra
(2006). dRA(R
K. Maeda, K. Teramura, N. Saito, N. Saito,
0 Y. Inoue, and
K. Domen, Bull. Chem. Soc. Jpn 80, 1004 (2007).
PHONONS FROM MOLECULAR DYNAMICS
Fourier Transform
Vibrational Spectrum