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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SCDM_WFs

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Module SCDM_WFs implements the selected columns of the density matrix (SCDM) method [1] for building localized Wannier Functions (WFs). Wannier90 [2] is a post-processing tool for the computation of the Maximally Localised Wannier Functions (MLWFs) [3,4,5], which have been increasingly adopted by the electronic structure community for different purposes. The reasons are manifold: MLWFs provide an insightful chemical analysis of the nature of bonding, and its evolution during, say, a chemical reaction. They play for solids a role similar to localized orbitals in molecular systems. In the condensed matter community, they are used in the construction of model Hamiltonians for, e.g., correlated-electron and magnetic systems. Also, they are pivotal in first-principles tight-binding Hamiltonians, where chemically-accurate Hamiltonians are constructed directly on the Wannier basis, rather than fitted or inferred from macroscopic considerations, and many other applications, e.g. dielectric response and polarization in materials, ballistic transport, analysis of phonons, photonic crystals, cold atom lattices, and the local dielectric responses of insulators, for reference see [3]. This module is a first step towards the automation of MLWFs. In the original Wannier90 framework, automation of MLWFs is hindered by the difficult step of choosing a set of initial localized functions with the correct symmetries and centers to use as an initial guess for the optimization. As a result, high throughput calculations (HTC) and big data analysis with MLWFs have proved to be problematic to implement.

This module is part of the newly developed Wannier90 utilities within the pilot project on Electronic Structure Functionalities for Multi-Thread Workflows. The module is part of the pw2wannier interface between the popular QUANTUM ESPRESSO code link and Wannier90. It will be part of the next version of QUANTUM ESPRESSO v.6.3 and Wannier90. Moreover, it has been successfully added in a developer branch of the AiiDA workflow [6] to perform HTC on large material datasets.

Practical application and exploitation of the code

The SCDM-k method [1] removes the need for an initial guess altogether by using information contained in the single-particle density matrix. In fact, the columns of the density matrix are localized in real space and can be used as a vocabulary to build the localized WFs. The SCDM-k method can be used in isolation to generate well localized WFs. More interestingly is the possibility of coupling the SCDM-k method to Wannier90. The core idea is to use WFs generated by the SCDM-k method as an initial guess in the optimization procedure within Wannier90. This module is a big step towards the automation of WFs and simplification of the use of the Wannier90 program. The module is therefore intended for all the scientists that benefit from the use of WFs in their research. Furthermore, by making the code more accessible and easier to use, this module will certainly increase the popularity of the Wannier90 code.

 
[1] A. Damle, L. Lin, L. Ying SCDM-k: Localized orbitals for solids via selected columns of the density matrix J.Comp.Phys. 334 (2017) 1
[2] A. A. Mostofi, J. R. Yates, Y.-S. Lee, I. Souza, D. Vanderbilt, N. Marzari wannier90: A tool for obtaining maximally-localised Wannier functions Com. Phys. Comm. 178 (2008) 685
[3] N. Marzari, A. A. Mostofi, J. R. Yates, I. Souza, D. Vanderbilt Maximally localized Wannier functions: Theory and applications Rev. Mod. Phys. 84 (2012) 1419
[4] N. Marzari, D. Vanderbilt Maximally localized generalized Wannier functions for composite energy bands Phys. Rev. B 56 (1997) 12847
[5] I. Souza, N. Marzari, D. Vanderbilt Maximally localized Wannier functions for entangled energy bands Phys. Rev. B 65 (2001) 035109
[6] G. Pizzi, A. Cepellotti, R. Sabatini, N. Marzari, B. Kozinsky AiiDA: automated interactive infrastructure and database for computational science Comp. Mat. Sci. 111 (2016) 218

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E-CAM Case Study: Mesoscale models for polarisable solvents: application to oil-water interfaces

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Dr. Silvia Chiacchiera, Science and Technology Facilities Council, United Kingdom

Abstract

Water is a polar liquid and has a dielectric permittivity much higher than typical apolar liquids, such as light oils. This strong dielectric contrast at water-oil interfaces affects electrostatics and is important, for example, to include these effects to describe biomolecular processes and water-oil mixtures involving surfactants, as detergents. In this pilot project, developed in collaboration with Unilever and Manchester University, we have proposed and analysed a class of polarisable solvent models to be used in Dissipative Particle Dynamics (DPD), a coarse-grained particle-based simulation method commonly used in various industrial sectors. Related software modules for the DL_MESO package have also been developed.

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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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New publication is out: “Unimolecular FRET Sensors: Simple Linker Designs and Properties”

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A new publication by researchers at University College Dublin and Boston University including E-CAM funded corresponding author Dr. Donal MacKernan was published in Nano Communication Networks. The measurement of biomarkers and ligands are increasingly used to study transport, signaling, and communication in cells, and as diagnostics/prognostics of disease, or the presence of pathogens, allergens and pollutants in foods, and the environment. Accurate measurement in assays or cellular environments is important, and protein-based biosensors can be used in this context. Using simple Coarse-Grained models of unimolecular fusion protein based FRET sensors of target ligands, the authors address four main questions. Can simple CG models reproduce qualitatively experimental results? Is there an advantage in replacing flexible protein linkers with hinge-like peptides? To enhance the precision of measurement, is it  better to increase or decrease the Föster radius of fluorescent proteins? Is precision enhanced or reduced if the binding energy of the ligand and sensor domains is attractive or repulsive in the absence of the target ligand? The answers are disclosed in the paper.

The publication post-print version is open access and can be downloaded directly from the Zenodo repository here. The publisher’s version can be found at https://doi.org/10.1016/j.nancom.2018.10.003.

This work is a particular part of  E-CAM Pilot Project on Food and Pharmaceutical Proteins focused on the development of protein-based sensors and therapeutics. The software used in the publication will soon be published in the E-CAM software library. Industry partners of the Pilot Project include Kerry Group, APC and others.

Article

Title: Unimolecular FRET Sensors: Simple Linker Designs and Properties

Authors: Shourjya Sanyal, David F. Coker, Donal MacKernan

Abstract: Protein activation and deactivation is central to a variety of biological mechanisms, including cellular signaling and transport. Unimolecular fluorescent resonance energy transfer (FRET) probes are a class of fusion protein sensors that allow biologists to visualize using an optical microscope whether specific proteins are activated due to the presence nearby of small drug-like signaling molecules, ligands or analytes. Often such probes comprise a donor fluorescent protein attached to a ligand binding domain, a sensor or reporter domain attached to the acceptor fluorescent protein, with these ligand binding and sensor domains connected by a protein linker. Various choices of linker type are possible ranging from highly flexible proteins to hinge-like proteins. It is also possible to select donor and acceptor pairs according to their corresponding Föster radius, or even to mutate binding and sensor domains so as to change their binding energy in the activated or inactivated states. The focus of the present work is the exploration through simulation of the impact of such choices on sensor performance.

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PLUMED wrapper for OpenPathSampling

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PLUMED is a widely used and versatile rare-event sampling and analysis code that can be used with various Molecular Dynamics (MD) engines. It has a very intuitive and versatile syntax for the definition of Collective Variables (CVs), and a wide variety of sampling methods, which accounts for its widespread use. The present module allows PLUMED and OPS to be used together. More details on the module can be found here.

Practical application and exploitation of the code

Transition path sampling simulations and analysis rely on accurate state definitions. Such states are typically defined as volumes in a Collective Variables space. OPS already supports a number of CVs, including the ones defined in the MDTraj python library. PLUMED offers a wide variety of extra CVs, which are enabled in OPS by this module. Many of PLUMED’s dozens of CVs have a biomolecular focus, but they are also general enough for other applications. PLUMED’s popularity (over 500 citations in 4 years after the release of PLUMED2 [1]) is greatly based on the fact that it works with many MD codes. OPS is now added to that list. The PLUMED code is well-maintained and documented for both users and developers. Several tutorials and a mailing list are available to address FAQs. More information about PLUMED is available here.

 

[1] G. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, G. Bussi PLUMED 2: New feathers for an old bird Comput. Phys. Commun. 185 (2014) 604

 

 

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The Curse of Dimensionality in Data-Intensive Modeling in Medicine, Biology, and Diagnostics

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With Prof. Tim Conrad (TC), Free University of Berlin, and Dr. Donal Mackernan (DM), University College Dublin.

Abstract

Until recently the idea that methods rooted in statistical physics could be used to elucidate phenomena and underlying mechanisms in biology and medicine was widely considered to be a distant dream.  Elements of that dream are beginning to be realized, aided very considerably by machine learning and advances in measurement, exemplified by the development of large-scale biomedical data analysis for next-generation diagnostics. In this E-CAM interview of Tim Conrad,  the growing importance of diagnostics in medicine and biology is discussed. One difficulty faced by such developments and shared with particle-based simulation is the “curse of dimensionality”. It is manifest in problems such as: (a) the use of a very large number of order parameters when trying to identify reaction mechanisms, nucleation pathways, metastable states, reaction rates; polymorph recognition (b) machine learning  applied to electronic structure  problems – such as neural network based potentials need very high dimensional basis sets; (c) systematic coarse-graining would ideally start with a very high dimensional space and systematically reduce the dimension.  The opportunities and challenges for scientists engaging with industry are also discussed. Tim Conrad is Professor of “Medical Bioinformatics” at the Institute of Mathematics of the Free University of Berlin and head of MedLab, one of the four laboratories of the Modal research campus. MODAL is a public-private partnership project which conducts mathematical research on data-intensive modeling, simulation, and optimization of complex processes in the fields of energy, health, mobility, and communication.  Tim Conrad is also the founder of three successful start-up companies.

In this E-CAM interview with Prof. Tim Conrad, the growing importance of diagnostics in medicine and biology is discussed, including concepts rooted in signal analysis relevant to systematic dimensional reduction, and pattern recognition, and the possibilities of their application to systematic coarse-graining. The opportunities and challenges for scientists of start-up companies are also discussed based on experience.

 

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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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Improving I/O of DL_MESO_DPD files using SIONlib

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This module implements the SIONlib library to optimize the I/O (writing/reading) of the trajectory files generated by DL_MESO_DPD, the Dissipative Particle Dynamics (DPD) code from the DL_MESO package. SIONlib is a library for writing and reading binary data to/from several thousands of processors into one or a small number of physical files. For parallel access to files, only the open and close functions are collective, while the writing and reading of files can be done asynchronously. [1] In DL_MESO_DPD’s last release (version 2.6), the MPI version of DL_MESO_DPD generates multiple trajectory files, one for each MPI task. The interface with SIONlib optimizes the data writing so that just one physical file is produced from several MPI tasks. This drastic reduction in the number of output files is a benefit for the I/O of the code, and simplifies the maintenance of the output, especially for a large number of MPI tasks.

This module is part of the newly developed utilities for the DL_MESO_DPD code within the pilot project on Polarizable Mesoscale Models.

Practical application and exploitation of the code

The implementation of this module generates a single trajectory file (history.sion) in a parallel run of DL_MESO_DPD, instead of multiple (HISTORY) ones. Accordingly, analogous modifications have to be implemented in the post-processing utilities that read the HISTORY files. As an example, the changes were implemented in a formatting utility. Besides showing how to adapt the reading, this allows a robust check of the implementation, since the output is human readable, contains the full trajectories, and can be readily compared with outputs obtained using the standard version of DL_MESO_DPD.

The next released version of DL_MESO_DPD (in development) will tackle the writing of files differently, producing a single trajectory file from the start. However, the interface proposed here provides this feature to the users of version 2.6, and represents an alternative solution for the handling of the trajectories.

It should be noted that this implementation is meant to show the feasibility of the interfacing, not to deal with all the possible cases. Thus, the module’s functionality is restricted to the relevant case in which: i) the simulation is run in parallel using MPI, ii) a single SIONlib-type physical file is produced, and iii) the post-processing is done by a single process.

While SIONlib is optimized for a large number of MPI tasks, even the reduction from several output files to just one represents a benefit, for example when it comes to the maintenance of the simulation output.

 

[1] http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html

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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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