57,917 research outputs found
Anharmonic Vibrational Eigenfunctions and Infrared Spectra from Semiclassical Molecular Dynamics
We describe a new approach based on semiclassical molecular dynamics that
allows to simulate infrared absorption or emission spectra of molecular systems
with inclusion of anharmonic intensities. This is achieved from semiclassical
power spectra by computing first the vibrational eigenfunctions as a linear
combination of harmonic states, and then the oscillator strengths associated to
the vibrational transitions. We test the approach against a 1D Morse potential
and apply it to the water molecule with results in excellent agreement with
discrete variable representation quantum benchmarks. The method does not
require any grid calculations and it is directly extendable to high dimensional
systems. The usual exponential scaling of the basis set size with the
dimensionality of the system can be avoided by means of an appropriate
truncation scheme. Furthermore, the approach has the advantage to provide IR
spectra beyond the harmonic approximation without losing the possibility of an
intuitive assignment of absorption peaks in terms of normal modes of vibration
First-Principles Semiclassical Initial Value Representation Molecular Dynamics
A method for carrying out semiclassical initial value representation
calculations using first-principles molecular dynamics (FP-SC-IVR) is
presented. This method can extract the full vibrational power spectrum of
carbon dioxide from a single trajectory providing numerical results that agree
with experiment even for Fermi resonant states. The computational demands of
the method are comparable to those of classical single-trajectory calculations,
while describing uniquely quantum features such as the zero-point energy and
Fermi resonances. By propagating the nuclear degrees of freedom using
first-principles Born-Oppenheimer molecular dynamics, the stability of the
method presented is improved considerably when compared to dynamics carried out
using fitted potential energy surfaces and numerical derivatives.Comment: 5 pages, 2 figures, made stylistic and clarity change
Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the Alanine dipeptide
If constraints are imposed on a macromolecule, two inequivalent classical
models may be used: the stiff and the rigid one. This work studies the effects
of such constraints on the Conformational Equilibrium Distribution (CED) of the
model dipeptide HCO-L-Ala-NH2 without any simplifying assumption. We use ab
initio Quantum Mechanics calculations including electron correlation at the MP2
level to describe the system, and we measure the conformational dependence of
all the correcting terms to the naive CED based in the Potential Energy Surface
(PES) that appear when the constraints are considered. These terms are related
to mass-metric tensors determinants and also occur in the Fixman's compensating
potential. We show that some of the corrections are non-negligible if one is
interested in the whole Ramachandran space. On the other hand, if only the
energetically lower region, containing the principal secondary structure
elements, is assumed to be relevant, then, all correcting terms may be
neglected up to peptides of considerable length. This is the first time, as far
as we know, that the analysis of the conformational dependence of these
correcting terms is performed in a relevant biomolecule with a realistic
potential energy function.Comment: 37 pages, 4 figures, LaTeX, BibTeX, AMSTe
Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity
We present the implementation of an electronic-structure approach dedicated
to ionization dynamics of molecules interacting with x-ray free-electron laser
(XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states
are represented by linear combination of numerical atomic orbitals that are
solutions of corresponding atomic core-hole states. We demonstrate that our
scheme efficiently calculates all possible multiple-hole configurations of
molecules formed during XFEL pulses. The present method is suitable to
investigate x-ray multiphoton multiple ionization dynamics and accompanying
nuclear dynamics, providing essential information on the chemical dynamics
relevant for high-intensity x-ray imaging.Comment: 28 pages, 6 figure
By-passing the Kohn-Sham equations with machine learning
Last year, at least 30,000 scientific papers used the Kohn-Sham scheme of
density functional theory to solve electronic structure problems in a wide
variety of scientific fields, ranging from materials science to biochemistry to
astrophysics. Machine learning holds the promise of learning the kinetic energy
functional via examples, by-passing the need to solve the Kohn-Sham equations.
This should yield substantial savings in computer time, allowing either larger
systems or longer time-scales to be tackled, but attempts to machine-learn this
functional have been limited by the need to find its derivative. The present
work overcomes this difficulty by directly learning the density-potential and
energy-density maps for test systems and various molecules. Both improved
accuracy and lower computational cost with this method are demonstrated by
reproducing DFT energies for a range of molecular geometries generated during
molecular dynamics simulations. Moreover, the methodology could be applied
directly to quantum chemical calculations, allowing construction of density
functionals of quantum-chemical accuracy
WavePacket: A Matlab package for numerical quantum dynamics. III: Quantum-classical simulations and surface hopping trajectories
WavePacket is an open-source program package for numerical simulations in
quantum dynamics. Building on the previous Part I [Comp. Phys. Comm. 213,
223-234 (2017)] and Part II [Comp. Phys. Comm. 228, 229-244 (2018)] which dealt
with quantum dynamics of closed and open systems, respectively, the present
Part III adds fully classical and mixed quantum-classical propagations to
WavePacket. In those simulations classical phase-space densities are sampled by
trajectories which follow (diabatic or adiabatic) potential energy surfaces. In
the vicinity of (genuine or avoided) intersections of those surfaces
trajectories may switch between surfaces. To model these transitions, two
classes of stochastic algorithms have been implemented: (1) J. C. Tully's
fewest switches surface hopping and (2) Landau-Zener based single switch
surface hopping. The latter one offers the advantage of being based on
adiabatic energy gaps only, thus not requiring non-adiabatic coupling
information any more.
The present work describes the MATLAB version of WavePacket 6.0.2 which is
essentially an object-oriented rewrite of previous versions, allowing to
perform fully classical, quantum-classical and quantum-mechanical simulations
on an equal footing, i.e., for the same physical system described by the same
WavePacket input. The software package is hosted and further developed at the
Sourceforge platform, where also extensive Wiki-documentation as well as
numerous worked-out demonstration examples with animated graphics are
available
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