November Module of the Month: PerGauss, Periodic Boundary Conditions for gaussian bases

 

Description

The module PerGauss (Per iodic Gauss ians) consists on an implementation of periodic boundary conditions for gaussian bases for the Quantics program package.

In quantum dynamics, the choice of coordinates is crucial to obtain meaningful results. While xyz or normal mode coordinates are linear and do not need a periodical treatment, particular angles, such as dihedrals, must be included to describe accurately the (photo-)chemistry of the system under consideration. In these cases, periodicity can be taken into account, since the value of the wave function and hamiltonian repeats itself after certain intervals.

Practical application

The module is expected to provide the quantum dynamics community with a more efficient way of treating large systems whose excited state driving forces involve periodic coordinates. When used on precomputed potentials (in G-MCTDH and vMCG), the model can improve the convergence since smaller grid sizes are needed. Used on-the-fly, it reduces considerably the amount of electronic structure computations needed compared to cartesian coordinates, since conformations that seemed far in the spanned space may be closer after applying a periodic transformation.

Source code

Currently PerGauss resides within the Quantics software package available upon request through gitlab. For more information see the PerGauss documentation here.

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CLstunfti: An extendable Python toolbox to compute scattering of electrons with a given kinetic energy in liquids and amorphous solids

 

Description

CLstunfti is an extendable Python toolbox to compute scattering of electrons with a given kinetic energy in liquids and amorphous solids. It uses a continuum trajectory model with differential ionization and scattering cross sections as input to simulate the motion of the electrons through the medium.

Originally, CLstunfti was developed to simulate two experiments: A measurement of the effective attenuation length (EAL) of photoelectrons in liquid water [1] and a measurement of the photoelectron angular distribution (PAD) of photoelectrons in liquid water [2]. These simulations were performed to determine the elastic mean free path (EMFP) and the inelastic mean free path (IMFP) of liquid water [3].

Practical application

The EMFP and IMFP are two central theoretical parameters of every simulation of electron scattering in liquids, but they are not directly accessible experimentally. As CLstunfti can be used to determine the EMFP and IMFP from experimental data, and as it can be easily extended to simulate other problems of particle scattering in liquids, it was decided to make the source code publicly available. For this purpose, within the E-CAM module, the necessary steps were taken to make CLstunfti a useful toolbox for other researchers by providing a documentation, examples, and also extensive inline documentation of the source code.

Source code

CLstunfti is available at https://gitlab.com/axelschild/CLstunfti .

 

References

[1] Suzuki, Nishizawa, Kurahashi, Suzuki, Effective attenuation length of an electron in liquid water between 10 and 600 eV, Phys. Rev. E 90, 010302 (2014)

[2] Thürmer, Seidel, Faubel, Eberhardt, Hemminger, Bradforth, Winter, Photoelectron Angular Distributions from Liquid Water: Effects of Electron Scattering, Phys. Rev. Lett. 111, 173005 (2013)

[3] Schild, Peper, Perry, Rattenbacher, Wörner, Alternative approach for the determination of mean free paths of electron scattering in liquid water based on experimental data, J. Phys. Chem. Lett., 11, 1128−1134 (2020)

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6 software modules delivered in the area of Quantum Dynamics

 

In this report for Deliverable 3.5 of E-CAM [1], 6 software modules in quantum dynamics are presented.

All modules stem from the activities initiated during the State-of-the-Art Workshop held at Lyon (France) in June 2019 and the Extended Software Development Workshop in Quantum Dynamics, held at Durham University (UK) in July 2019. The modules originate from the input of E-CAM’s academic user base. They have been developed by members of the project (S. Bonella – EPFL), established collaborators (G. Worth – University College London, S. Gomez – University of Vienna, C. Sanz – University of Madrid, D. Lauvergnat – Univeristy of Paris Sud) and new contributors to the E-CAM repository (F. Agostini – University of Paris Sud, Basile Curchod – University of Durham, A. Schild – ETH Zurich, S. Hupper and T. Plé – Sorbonne University, G. Christopoulou – University College London). The presence of new contributors indicates the interest of the community in our efforts. Furthermore, the contributors to modules in WP3 continue to be at different stages of their careers (in particular, Thomas Plé and G. Christopoulou are PhD students) highlighting the training value of our activities.

Following the order of presentation, the 6 modules are named: CLstunftiPIM_QTBPerGaussDirect Dynamics DatabaseExact Factorization Analysis Code (EFAC), and GuessSOC. In this report, a short description is written for each module, followed by a link to the respective Merge-Request document on the GitLab service of E-CAM. These merge requests contain detailed information about the code development, testing and documentation of the modules. 

[1] “D3.5.: Quantum dynamics e-cam modules IV,” Dec. 2019. [Online]. Available: https://doi.org/10.5281/zenodo.3598325

Full report available here.

 

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CTMQC, a module for excited-state nonadiabatic dynamics

 

CTMQC is a module for excited-state nonadiabatic dynamics. It is used to simulate the coupled dynamics of electrons and nuclei (ideally in gas phase molecular systems) in response to, for instance, an initial electronic excitation.

The CTMQC module is based on the coupled-trajectory mixed quantum-classical (CT-MQC) algorithm [1,2] that has been derived starting from the evolution equations in the framework the exact factorization of the electron-nuclear wavefunction [3,4,5]. The CTMQC algorithm belongs to the family of quantum-classical methods, as the time evolution of the nuclear degrees of freedom is treated within the classical approximation, whereas electronic dynamics is treated fully quantum mechanically. Basically, the nuclei evolve as point particles, following classical trajectories, while the electrons generate the potential inducing such time evolution.

In its current implementation (used in Refs. [6,7]), the module cannot deal with arbitrary nuclear dimensions, but it is restricted to treat up to 3-dimensional problems, which gives the possibility to compare quantum-classical results easily and directly with quantum wavepacket dynamics. CTMQC has been analyzed and benchmarked against exact propagation results on typical low-dimensional model systems [1,2,6,7], and applied for the simulation of the photo-initiated ring-opening process of Oxirane [8]. For this study, CTMQC has been implemented in a developer version of the CPMD electronic structure package based on time-dependent density functional theory. Concerning electronic input properties, the CTMQC module requires a grid representation of the adiabatic potential energy surfaces and of the nonadiabatic coupling vectors, since the electronic dynamics is represented and solved in the adiabatic basis.

This feature allows the algorithm to be easily adaptable, in the current form, to any quantum chemistry electronic structure package. The number of electronic states to be included is not limited and can be specified as input.

Practical application and exploitation of the code
The purpose of the module is to familiarize the user with a new simulation technique, i.e., the CTMQC method, for treating problems where electronic excited states are populated during the molecular dynamics. Photo-activated ultrafast processes are typical situations in which an approach like CTMQC can be used to predict molecular properties, like structures, quantum yields, or quantum coherence.
 
The module is designed to apply the CTMQC procedure to one-, two-, and three-dimensional model systems where an arbitrary number of electronic states are coupled via the nuclear dynamics. Tully model systems [9] are within the class of problems that can be treated by the module, as well as a wide class of multidimensional problems involving, for instance, ultrafast radiationless relaxation of photo-excited molecules [10] through conical intersections.

 

Software documentation can be found in our E-CAM software Library here.
 

 

[1] S. K. Min, F. Agostini, E. K. U. Gross Coupled-trajectory quantum-classical approach to electronic decoherence in nonadiabatic processes Phys. Rev. Lett. 115 (2015) 073001
[2] F. Agostini, S. K. Min, A. Abedi, E. K. U. Gross Quantum-classical nonadiabatic dynamics: Coupled- vs independent-trajectory methods J. Chem. Theory Comput. 12 (2016) 2127
[3] A. Abedi, N. T. Maitra, E. K. U. Gross Exact factorization of the time-dependent electron-nuclear wave function Phys. Rev. Lett. 105 (2010) 123002
[4] A. Abedi, F. Agostini, Y. Suzuki, E. K. U. Gross Dynamical steps that bridge piecewise adiabatic shapes in the exact time-dependent potential energy surface Phys. Rev. Lett. 110 (2013) 263001
[5] F. Agostini, B. F. E. Curchod, R. Vuilleumier, I. Tavernelli, E. K. U. Gross, TDDFT and Quantum-Classical Dynamics: A Universal Tool Describing the Dynamics of Matter Springer International Publishing (2018) 1
[7] G. H. Gossel, F. Agostini, N. T. Maitra Coupled-trajectory mixed quantum-classical algorithm: A deconstruction J. Chem. Theory Comput. 14 (2018) 4513
[8] S. K. Min, F. Agostini, I. Tavernelli, E. K. U. Gross Ab initio nonadiabatic dynamics with coupled trajectories: A rigorous approach to quantum (de)coherence J. Phys. Chem. Lett. 8 (2017) 3048
[9] J. C. Tully Molecular dynamics with electronic transitions J. Chem. Phys. 93 (1990) 1061
[10] B. F. E. Curchod, F. Agostini On the dynamics through a conical intersection J. Phys. Chem. Lett. 8 (2017) 831
 

 

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QQ-Interface (Quantics-QChem-Interface)

 
The QQ-Interface module connects the full quantum nonadiabatic wavefunction propagation code Quantics to the time-dependent density functional theory (TDDFT) module of the electronic structure program Q-Chem. Q-Chem provides analytic gradients, Hessians and derivative couplings at TDDFT level. With this module, it is possible to use the Q-Chem TDDFT module for excited state direct dynamics calculations. Quantics will start Q-Chem calculations whenever needed, prepare the input file from a template and will read the Q-Chem output file. The Q-Chem results are stored in the Quantics database and can be used in dynamics simulations. Due to the modular design of Quantics the TDDFT module of Q-Chem can be used for all dynamics simulations, e.g. direct dynamics variational multi-configurational Gaussian (dd-vMCG) or surface hopping simulations.

This module is part of a set of new functionalities developed for the Quantics program package during the E-CAM Extended Software Development Worksop: Quantum MD held at the University College Dublin.

Practical application and exploitation of the code

The module will be used to examine the nonadiabatic excited state dynamics of small to medium-sized molecules. The TDDFT module of Q-Chem allows treating systems that are too large for efficient multireference, such as CASSCF calculations. Until now photoinduced dynamics simulations of such molecules were only possible using trajectory-based algorithms. With Quantics a full quantum-mechanical description of the nuclear motion is possible.
 

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Scientific reports from the 2018 E-CAM workshops are now available on our website

 

The scientific reports* from the following workshops conducted in year 3 of the project E-CAM (2018):

  1. E-CAM Scoping Workshop: “Solubility prediction”, 14 – 15 May 2018, Ecole Normale Supérieure de Lyon, France,
  2. E-CAM Scoping Workshop: “Dissipative particle dynamics: Where do we stand on predictive application?”, 24 – 26 April 2018, Daresbury Laboratory, United Kingdom,
  3. E-CAM Extended Software Development Workshop 11: “Quantum Dynamics”, 18 – 29 June 2018, Maison de la Simulation, France,

are now available for download on our website at this location. Furthermore, they will also be integrated in the CECAM Report of Activities for 2018, published every year on the website www.cecam.org.

 

*© CECAM 2018, all rights reserved.

Please address any comments or questions to info@e-cam2020.eu.

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PaPIM: A code for Quantum Time Correlation Functions

 

PaPIM code is a package to study the (quantum) properties of materials, and in particular time correlation functions, via the so-called mixed quantum-classical methods. In these schemes, quantum evolution is approximated by appropriately combining a set of classical trajectories for the system. Several quantum effects, for example, the possibility to find atoms in classically forbidden regions (tunneling), are reproduced at a manageable fraction of the cost of exact solutions.

The PaPIM module is a high-performance Fortran 90/95 MPI parallelized package for calculating system’s time-dependent observables. The code represents the current optimized assembly of the following modules:

  • PIM_wd and PIM_qcfmodules (described in deliverable D3.3) for exact quantum sampling of the Wigner phase space probability distribution function and the corresponding calculation of specific quantum correlation functions, respectively;
  • ClassMC module (described in D3.1) for Monte Carlo sampling of classical Maxwell-Boltzmann distribution and calculation of corresponding correlation-functions;
  • PotMod module (described in D3.1), a library for model potentials and interfaces to external codes for potential energy calculations used by the sampling modules. This module is currently being enhanced with an interface to couple PaPIM with the CP2K package for electronic structure calculations;
  • AuxMod module (described in D3.1) which provides a tailored set of MPI commands used for code parallelisation as well as input handling subroutines.

Practical application and exploitation of the code

The code has been extensively used for the calculation of the infrared absorption spectrum of CH5+ in the gas phase. [1] This highly flexible molecule is considered a standard benchmark of approximate quantum methods, and has experimental interest, for example, in the context of green chemistry. The calculations performed with PaPIM were used to benchmark both the PIM method for time-correlation functions [2] and to realize the code performance analysis.

Through collaborations the code is also currently employed by several groups in their study of: properties of H2 molecules in clathrates (materials for capture and storage of hydrogen and CO2 in energy applications (University College Dublin); infrared characterisation of molecules, and from it understand the effect that the environment has on their chemical properties, in the atmosphere (Université Pierre et Marie Curie); hydrogen at extreme pressures in the context of geophysical applications (Ecole Normale Supérieure Paris); new potentials to efficiently characterise the chemical reactivity of small water clusters, again with possible applications on the physics of the atmosphere in reactions related to greenhouse effect (University of Bochum).

More description of the code and its systematic tests are reported in the E-CAM deliverable D3.3.

 

[1] O. Asvany, P. K. P, B. Redlich, I. Hegemann, S. Schlemmer, D. Marx Understanding the infrared spectrum of bare CH5+ Science 309 (2005) 1219

[2] M. Monteferrante, S. Bonella, G. Ciccotti Quantum dynamical structure factor of liquid neon via a quasiclassical symmetrized method J. Chem. Phys. 138 (2013) 054118


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E-CAM Case Study: Designing control pulses for superconducting qubit systems with local control theory

Dr. Momir Mališ, École Polytechnique Fédérale de Lausanne, Switzerland

 

Abstract

A quantum logic gate is one of the key components of the quantum computer, and designing an effective quantum universal gate is one of the major goals in the development of quantum computers. We have developed a software based on local control theory to design efficient state preparation control pulses for universal quantum gates which drive full population transfer between qubit states.

Continue reading…

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PIM_wd: Module for sampling of the quantum Wigner distribution

 

The PIM_wd module implements the exact quantum Wigner probability distribution function sampling algorithm of the Phase Integration Method [1], and is the main subroutine for the quantum correlation function calculations in the PaPIM code. The module samples the thermal Wigner density using a generalised Monte Carlo scheme for sampling phase space points. The scheme combines the Penalty [2] and Kennedy [3] algorithms to sample noisy probability densities. This is necessary because the estimator of the quantum thermal density is not known analytically but must be computed via a statistical average affected by uncertainty. The sampled points are the basis for the calculation of time-independent and time-dependent system observables.

The module was developed as the main component of the PaPIM code, but also as a standalone subroutine that can be easily implemented in other methods (e.g. the whole family of so-called linearised approximations of quantum dynamics) for which phase space sampling of the exact quantum Wigner probability distribution is required. Because the Phase Integration Method samples a set of independent phase space points, independent instances of the PIM_wd module can be run in parallel in order to parallelise the phase space sampling. In the PaPIM package, the parallelisation is accomplished using MPI, which has proved to provide good scalability of the PaPIM code. The module will also be adapted for HTC capabilities.

Practical application and exploitation of the code

The code has been extensively used for the calculation of the infrared absorption spectrum of CH5+ in the gas phase. [4] This highly flexible molecule is considered a standard benchmark of approximate quantum methods, and has experimental interest, for example, in the context of green chemistry.

This module is part of the modules in deliverable D3.3 which were developed during the E-CAM ESDW7.

 

[1] M. Monteferrante, S. Bonella, G. Ciccotti Quantum dynamical structure factor of liquid neon via a quasiclassical symmetrized method J. Chem. Phys. 138 (2013) 054118

[2] D. M. Ceperley, M. Dewing The penalty method for random walks with uncertain energies J. Chem. Phys. 110 (1999) 9812

[3] A. D. Kennedy, J. Kuti Noise without Noise: A New Monte Carlo Method Phys. Rev. Lett. 54 (1985) 2473

[4] O. Asvany, P. K. P, B. Redlich, I. Hegemann, S. Schlemmer, D. Marx Understanding the infrared spectrum of bare CH5+ Science 309 (2005) 1219

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6 software modules recently delivered in the area of Quantum Dynamics

 

In this report for Deliverable 3.3 of E-CAM [1], 6 software modules in quantum dynamics are presented. Four modules stem from some of the activities performed during the Extended Software Development Workshop (ESDW) held by E-CAM at University College Dublin in July 2017 and originate from input of E-CAM’s academic user base. The other two modules were developed following discussions with our industrial partner IBM, in the framework of E-CAM’s pilot project on Quantum Computing.

Following the order of presentation, the 6 modules are named: LocConQubit, OpenQubit, PaPIM, PIM_wd, PIM_qcf, Openmpbeads. They include code for generation of controlled pulses for qubits and for calculation of quantum time correlation functions and their documentation.

In this report, a short description is written for each module, followed by a link to the respective Merge-Request on theGitLab service of E-CAM. These merge requests contain detailed information about the code development, testing and documentation of the modules. A performance analysis for PaPIM, a package merging the functionality of several modules for quantum dynamics developed in E-CAM and structured to act as a high-performance container for future modules, is also presented. This analysis was performed by the E-CAM software group, in collaboration with the POP Center of Excellence for Computing Applications.

[1] S. Bonella, M. Mališ, A. O’Cais, and L. Liang, “D3.3.: Quantum dynamics e-cam modules ii,” Mar. 2018. [Online]. Available: https://doi.org/10.5281/zenodo.1210077.

Full report available here.

 

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