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

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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

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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

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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: CLstunfti, PIM_QTB, PerGauss, Direct Dynamics Database, Exact 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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Extended software development workshop in quantum dynamics

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If you are interested in attending this event, please visit the CECAM website here.

Workshop Description

Quantum molecular dynamics simulations are pivotal to understanding and predicting the microscopic details of molecules, and strongly rely on a combined theoretical and computational effort. When considering molecular systems, the complexity of the underlying equations is such that approximations have to be devised, and the resulting theories need to be translated into algorithms and computer programs for numerical simulations. In the last decades, the joint effort of theoretical physicists and quantum chemists around the challenges of quantum dynamics made it possible to investigate the quantum dynamics of complex molecular systems, with applications ranging from energy conversion, energy storage, organic electronics, light-emitting devices, biofluorescent molecules, or photocatalysis, to name a few.
Two different strategies have been successfully applied to perform quantum molecular dynamics: wavepacket propagation or trajectories. The first family of methods includes all quantum nuclear effects, but their computational cost hampers the simulation of systems with moderate number of more than 10-12 degrees of freedom. The method coined multi-configuration time-dependent Hartree (MCTDH) constitutes one of the most successful developments in this field and is often considered as a gold standard for quantum dynamics [1]. Other strategies for wavepacket propagation try to identify procedures to optimize the “space” where the wavefunction information is computed, such that Cartesian grids can be replaced with Smolyak grids [2]. The second family of methods introduces the idea of trajectories as a way to approximate the nuclear subsystem, either classically or semiclassically, and is exemplified by methods like the trajectory surface hopping and Ehrenfest schemes [3], or the more accurate methods coupled-trajectory mixed quantum-classical (CT-MQC) [4] and quantum-classical Liouville equation (QCLE) [5].
From a computational perspective, both families of methods require extensive electronic structure calculations, as the nuclei move under the effect of the electronic subsystem, either “statically” occupying its ground state or “dynamically” switching between excited states. Solving the quantum nuclear dynamics equations also becomes in itself very expensive in the case of wavepacket propagation methods. Contrary to other, more consolidated, areas of modeling, quantum dynamics simulations do not benefit from established community packages and most of the progress occurs based on in-house codes, difficult to maintain and with limits in optimization and portability. One of the core actions of E-CAM has been to seed a change in this situation, by promoting systematic developments of software, providing a repository to host and share code, and fostering collaborations on adding functionalities and improving the performance of common software scaffolds for wavepacket (Quantics) and trajectory-based (PaPIM) packages. Collaborations on developments on other codes have also been initiated. This workshop aims at continuing and extending these activities based on input from the community.

 

References

[1] H. D. Meyer, U. Manthe, L. S. Cederbaum. Chem. Phys. Lett. 165 (1990) 73.
[2] D. Lauvergant, A. Nauts. Spectrochimica Acta Part A 119 (2014) 18.
[3] J. C. Tully. Faraday Discuss. 110 (1998) 407.
[4] S. K. Min, F. Agostini, I. Tavernelli, E. K. U. Gross. J. Phys. Chem. Lett. 8 (2017) 3048.
[5] R. Kapral. Annu. Rev. Phys. Chem. 57 (2006) 129.

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CTMQC, a module for excited-state nonadiabatic dynamics

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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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Recent developments in quantum dynamics, an E-CAM state-of-the-art workshop

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If you are interested in attending this event, please visit the CECAM website here.

Workshop Description

The proposed workshop will gather a broad community of researchers in the field of quantum dynamics, who are actively investigating the interplay of electronic and nuclear correlation in problems spanning multiple length and time scales, and who are seeking to develop and apply state-of-the-art (SOA) methodologies to systems of increasing complexity.

Continuing in the spirit of the first E-CAM SOA workshop, held in 2016 in Lausanne, a broad overview of the field of quantum dynamics will be presented. Current and emergent quantum dynamics methodologies will be critically discussed from their basic assumptions to their most recent extensions, including their pitfalls and possible improvements, in the hope that the ideas exchanged will promote exciting new developments. Participants will also be asked to address, in particular, aspects related to the software tools that implement the different methods, evaluating development schemes (community efforts, in-house coding), HPC-readiness (e.g. portability, scalability, benchmarking), and ease of use. An assessment of the “readiness for experiments and industry” will also be pursued, identifying new problems of experimental and industrial interest where quantum-dynamical effects are relevant, presenting success stories, and – crucially – evaluating critically the gap between available methods and codes and the needs of non-professional users to suggest means to reduce it.

The format of the workshop will conform to the Tentative Timetable included in this proposal. This format is based on positive feedback following the CECAM Quantum Dynamics meetings that took place in Paris (2016) and Lausanne (2017). Ample time for discussions is set aside, in agreement with CECAM and E-CAM recommendations. We will organize the topics into five sessions:

I. Theoretical Foundations of Quantum Dynamics in Molecular and Condensed Phase Systems
II. Real-time Path Integral and Quantum Master Equation Techniques
III. Trajectory-Based Quantum Molecular Dynamics: Methods and Applications
IV. Nuclear Quantum Effects, Path Integral Molecular Dynamics, and Vibrational Spectroscopy
V. Numerically Exact Methods

We will also invite chairpeople that will be asked to actively encourage exchanges and cross-fertilization in the discussion sessions. Speakers and participants will also be asked to highlight formal and algorithmic connections between different methods and to mention, or propose sets of benchmarks to assess relative performances. In this SOA workshop, we have chosen not to allot time for contributed talks. All participants are, however, expected to contribute to the discussions and will be given a chance to present their work at the poster session or, informally, as has become customary in the CECAM environment, during the long coffee breaks.

The connection to E-CAM will be highlighted through a special discussion session (VI: Software development in Quantum Dynamics) and presentation of the most recent software modules developed during the extended software development workshops, which runs in parallel to this workshop series. Experts from E-CAM and from other experiences of systematic software development in the area (e.g. MolSSI, GPU based codes, i-PI) will discuss their experience with the goal to share good practices, identify new synergies, provide all participants with an opportunity to know and contribute (if interested) to community based codes or to initiate new coordinated activities in the area.

 

References

[1] D. Schapers, B. Zhao, U. Manthe, Chemical Physics 509, 37-44, (2018).
[2] Robert Wodraszka, Tucker Carrington, J. Chem. Phys. 148, 044115, (2018).
[3] D. E. Makarov, and N. Makri, Chem. Phys. Lett. 221, 482 (1994).
[4] N. Makri, and D. E. Makarov, J. Chem. Phys. 102, 4600 (1994).
[5] L.Muhlbacher,andE.Rabani,Phys.Rev.Lett., 100,176403 (2008).
[6] G. Cohen and E. Rabani, Phys. Rev. B 84, 075150 (2011).
[7] Y. Tanimura and R. Kubo, J. Phys. Soc. Jpn. 58, 101-114 (1989); Y. Tanimura, J. Chem. Phys., 141, 044114 (2014).
[8] Abedi, A., Maitra, N. T., and Gross, E. K. U., Phys. Rev. Lett., 105, 123002 (2010).
[9] H. D. Meyer, U. Manthe, and L. S. Cederbaum, Chem. Phys. Lett. 165, 73 (1990); I. Burghardt, H.-D. Meyer, and L. S. Cederbaum, J. Chem. Phys. 111, 2927 (1999); H. Wang and M. Thoss, ibid. 119, 2003 (2003).
[10] I. Burghardt, K. Giri, and G. A. Worth, J. Chem. Phys. 129, 174104 (2008).
[11] G. A. Worth. and I. Burghardt, Chem. Phys. Lett. 368, 502 (2003).
[12] G. Albareda, H. Appel, I. Franco, A. Abedi, Angel Rubio, Phys. Rev. Lett.,113, 083003, (2014).
[13] R. Kapral and G. Ciccotti, J. Chem. Phys. 110, 8919 (1999); R. Kapral, Annu. Rev. Phys. Chem. 57, 129 (2006).
[14] S. Bonella and D. F. Coker, J. Chem. Phys. 122, 194102 (2005), P. Huo and D. F. Coker, J. Chem. Phys. 133, 184108 (2011), P. Huo and D. F. Coker, ibid. 137, 22A535 (2012).
[15] S. K. Min, F. Agostini, and E. K. U. Gross, Phys. Rev. Lett. 115, 073001 (2015).
[16] J. Beutier, D. Borgis, R. Vuilleumier, and S. Bonella, J. Chem. Phys. 141, 084102 (2014).
[17] M. Ben-Nun and T. J. Mart ́ınez, J. Chem. Phys. 108, 7244 (1998); M. Ben-Nun, J. Quenneville, and T. J. Mart ́ınez, J. Phys.Chem. A 104, 5161 (2000).
[18] Tully, J., Faraday Discussions, 110, 407-419 (1998).
[19] TE Markland, M Ceriotti – Nature Reviews Chemistry, 2018.
[20] Dammak, H.; Chalopin, Y.; Laroche, M.; Hayoun, M.; Greffet, J. J. Phys. Rev. Lett. 2009, 103, 19060.
[21] Ceriotti, M.; Bussi, G.; Parrinello, M. Phys. Rev. Lett. 2009, 103, 030603.
[22] Javier Hernández-Rojas, Florent Calvo, and Eva Gonzalez Noya, J. Chem. Theo. Comp. 2015 11 (3), 861-870.
[23] N. Ananth, J. Chem. Phys. 139, 124102 (2013); J.O. Richardson and M. Thoss ibid., 139, 031102, 2013.
[24] S. Nakajima, Prog. Theor. Phys. 20, 948 (1958).
[25] R. Zwanzig, J. Chem. Phys. 33, 1338 (1960).
[26] Q. Shi and E. Geva, J. Chem. Phys. 119, 12063 (2003).
[27] M.-L. Zhang, B. J. Ka and E. Geva, J. Chem. Phys. 125, 044106 (2006).
[28] A. Kelly and T. E. Markland, J. Chem. Phys. 139, 014104 (2013).
[29] E. Y. Wilner, H. Wang, M. Thoss, and E. Rabani, Phys. Rev. B 90, 115145 (2014)
[30] G Albareda, A Kelly, A Rubio, arXiv preprint arXiv:1805.11169 (2018).

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QQ-Interface (Quantics-QChem-Interface)

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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

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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

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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

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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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