Self-consistent continuum solvation for optical absorption of complex molecular systems in solution

We introduce a new method to compute the optical absorption spectra of complex molecular systems in solution, based on the Liouville approach to time-dependent density-functional perturbation theory and the revised self-consistent continuum solvation model. The former allows one to obtain the absorption spectrum over a whole wide frequency range, using a recently proposed Lanczos-based technique, or selected excitation energies, using the Casida equation, without having to ever compute any unoccupied molecular orbitals. The latter is conceptually similar to the polarizable continuum model and offers the further advantages of allowing an easy computation of atomic forces via the Hellmann-Feynman theorem and a ready implementation in periodic-boundary conditions. The new method has been implemented using pseudopotentials and plane-wave basis sets, benchmarked against polarizable continuum model calculations on 4-aminophthalimide, alizarin, and cyanin and made available through the QUANTUM ESPRESSO distribution of open-source codes. (c) 2015 AIP Publishing LLC.

turboTDDFT 2.0 Hybrid functionals and new algorithms within time-dependent density-functional perturbation theory

We present a new release of the turboTDDFT code featuring an implementation of hybrid functionals, a recently introduced pseudo-Hermitian variant of the Liouville-Lanczos approach to time-dependent density-functional perturbation theory, and a newly developed Davidson-like algorithm to compute selected interior eigenvalues/vectors of the Liouvillian super-operator. Our implementation is thoroughly validated against benchmark calculations performed on the cyanin (C21O11H21) molecule using the Gaussian 09 and turboTDDFT 1.0 codes. Program summary Program title: turboTDDFF 2.0 Catalogue identifier: AEIX_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEDCv2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 2 No. of lines in distributed program, including test data, etc.: 5995995 No. of bytes in distributed program, including test data, etc.: 122184812 Distribution format: tar.gz Programming language: Fortran 95, MAI. Computer: Any computer architecture. Operating system: GNU/Linux, AIX, IRIX, Mac OS X, and other UNIX-like OS's. Classification: 16.2, 16.6, 7.7. External routines: turboTDDFT 2.0 is a tightly integrated component of the Quantum ESPRESSO distribution and requires the standard libraries linked by it: BIAS, LAPACK, FFTW, MPI. Does the new version supercede the previous version?: Yes Nature of problem: Calculation of the optical absorption spectra of molecular systems. Solution method: Electronic excited states are addressed by linearized time-dependent density-functional theory within the plane-wave pseudo-potential method. The dynamical polarizability can be computed in terms of the resolvent of the Liouvillian super-operator, using a pseudo-Hermitian variant of the Lanczos recursion scheme. As an alternative, individual eigenvalues of the Liouvillian can be computed via a newly introduced variant of the Davidson method. In both cases, hybrid functionals can now be used. Reasons for new version: To implement new features. Summary of revisions: New features implemented: 1. Hybrid functionals. 2. Pseudo-Hermitian Lanczos recursion algorithm. 3. All-new Davidson-like solver for the Liouvillian eigenvalue equation ("Casida equation"). Restrictions: Spin-restricted formalism. Linear-response regime. Adiabatic XC kernels only. Hybrid functionals are only accessible using norm-conserving pseudo-potentials. Unusual features: No virtual orbitals are used, nor even calculated. Within the Lanczos method a single recursion gives access to the whole optical spectrum; when computing individual excitations using the Davidson method, interior eigenvalues can be easily targeted. Additional comments: !!!!! The distribution file for this program is over 121 Mbytes and therefore is not delivered directly when download or E-mail is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: From a few minutes for small molecules on serial machines up to many hours on multiple processors for complex nanosystems with hundreds of atoms. (C) 2014 Elsevier B.V. All rights reserved.

Elsevier Science Bv2014

Characterization of the Photochemical Properties of 5-Benzyluracil via Time-Dependent Density Functional Theory

Sara Bonella, Basile Curchod, Ursula Röthlisberger, Ivano Tavernelli, Mohammadhassan Valadan

We present a detailed study of the excited state properties of 5-benzyluracil (5BU) in the gas phase and in implicit solvent using different electronic structure approaches ranging from time-dependent density functional theory in the linear response regime (LR-TDDFT) to a set of different wave-function-based methods for excited states, namely perturbed coupled cluster (CC2), algebraic diagrammatic construction method to second order (ADC(2)), and perturbed configuration interaction (CIS(D)). 5BU has been used to investigate DNA base-amino acid interactions. In particular, it served as a model of protein-DNA photoinduced cross-linking. While LR-TDDFT is computationally the most efficient first-principles approach for static and dynamic simulations of this bichromophoric system, its accuracy is difficult to assess due to the presence of excited states with charge transfer character. In this work, the performance of different exchange correlation functionals is compared against accurate benchmarks obtained either from high level wave-function-based methods or directly from experimental absorption spectra. Our investigation shows that accurate results for the excitation energies can be obtained using the hybrid meta-GGA functional M06. In view of dynamical studies of the relaxation of 5BU after photoexcitation, we also show that the PBE functional, while failing in the Franck-Condon region, provides qualitatively good results for the characterisation of a possible photocyclization path.

2017

HP - A code for the calculation of Hubbard parameters using density-functional perturbation theory

Matteo Cococcioni, Nicola Marzari, Iurii Timrov

We introduce HP, an implementation of density-functional perturbation theory, designed to compute Hubbard parameters (on-site U and inter-site V ) in the framework of DFT+U and DFT+U+V. The code does not require the use of computationally expensive supercells of the traditional linear-response approach; instead, unit cells are used with monochromatic perturbations that significantly reduce the computational cost of determining Hubbard parameters. HP is an open-source software distributed under the terms of the GPL as a component of QUANTUM ESPRESSO. As with other components, HP is optimized to run on a variety of different platforms, from laptops to massively parallel architectures, using native mathematical libraries (LAPACK and FFTW) and a hierarchy of custom parallelization layers built on top of MPI. The effectiveness of the code is showcased by computing Hubbard parameters self-consistently for the phospho-olivine LixMn1/2Fe1/2PO4 (x = 0, 1/2, 1) and by highlighting the accuracy of predictions of the geometry and Li intercalation voltages. Program summaryProgram Title: HP CPC Library link to program files: https://doi .org /10 .17632 /xsbtkpknf7 .1 Licensing provisions: GNU General Public License v 2.0 Programming language: Fortran 95 External routines: HP is a tightly integrated component of the QUANTUM ESPRESSO distribution and requires the standard libraries linked by it: BLAS, LAPACK, FFTW, MPI.Nature of problem: Calculation of Hubbard interaction parameters for DFT+U and DFT+U+V.Solution method: Hubbard parameters are expressed in terms of the inverse response matrices to localized perturbations of the atomic occupations. The response matrices are computed using densityfunctional perturbation theory to first order (linear-response theory) in the reciprocal space, that allows to reconstruct the response to a localized perturbation (obtained from calculations in an appropriately sized supercell) as the superposition of the responses to a series of monochromatic perturbations in a primitive unit cell, thus reducing significantly the computational cost. The response matrices are computed via a self-consistent solution of the static Sternheimer equation, whose implementation does not require the calculation of any virtual states. Pseudopotentials (norm-conserving, ultrasoft, projector augmented wave) are used in conjunction with plane-wave basis sets and periodic boundary conditions. Additional comments including restrictions and unusual features: Local and semi-local exchange-correlation kernels only. Noncollinear spin-polarized formalism is not supported, only collinear spin-polarized or non-spin-polarized cases can be treated. Spin-orbit coupling cannot be used. Calculation of Hund's J is not supported. Multiple Hubbard channels per atom are not supported. The Hubbard manifold can be only constructed on atomic orbitals, both orthogonalized and non-orthogonalized, while Wannier functions (as well as other localized basis sets) are not supported. The linear-response approach we adopt here typically results in Hubbard parameters that are unphysically large for closed shell states [1]. No virtual orbitals are used, nor even calculated.The distribution file of this program can be downloaded from the QUANTUM ESPRESSO website: http:// www.quantum -espresso .org/, and the development version of this program can be downloaded via Git from the GitLab website: https://gitlab .com /QEF /q-e. Interactions with end users of the HP code happen via a mailing-list forum of QUANTUM ESPRESSO: https://www.quantum -espresso .org /forum. Documentation of the HP code is tightly coupled with the code and is done via standard code comments; different subroutines that implement different equations of the DFPT formalism contain references to the two main papers [2,3] describing in detail theory behind the implementation.(c) 2022 The Author(s). Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

ELSEVIER2022

turboTDDFT 2.0 Hybrid functionals and new algorithms within time-dependent density-functional perturbation theory

Elsevier Science Bv2014

HP - A code for the calculation of Hubbard parameters using density-functional perturbation theory

Matteo Cococcioni, Nicola Marzari, Iurii Timrov

ELSEVIER2022