This is a collection of the modules that have been created by E-CAM community within the area of Quantum Dynamics. This documentation is created using ReStructured Text and the git repository for the documentation source files can be found at https://gitlab.e-cam2020.eu/e-cam/Quantum-Dynamics-Modules which are open to contributions from E-CAM members.
In the context of E-CAM, the definition of a software module is any piece of software that could be of use to the E-CAM community and that encapsulates some additional functionality, enhanced performance or improved usability for people performing computational simulations in the domain areas of interest to us.
This definition is deliberately broader than the traditional concept of a module as defined in the semantics of most high-level programming languages and is intended to capture inter alia workflow scripts, analysis tools and test suites as well as traditional subroutines and functions. Because such E-CAM modules will form a heterogeneous collection we prefer to refer to this as an E-CAM software repository rather than a library (since the word library carries a particular meaning in the programming world). The modules do however share with the traditional computer science definition the concept of hiding the internal workings of a module behind simple and well-defined interfaces. It is probable that in many cases the modules will result from the abstraction and refactoring of useful ideas from existing codes rather than being written entirely de novo.
Perhaps more important than exactly what a module is, is how it is written and used. A final E-CAM module adheres to current best-practice programming style conventions, is well documented and comes with either regression or unit tests (and any necessary associated data). E-CAM modules should be written in such a way that they can potentially take advantage of anticipated hardware developments in the near future (and this is one of the training objectives of E-CAM).
Software development in quantum dynamics has so far been less systematic than in other fields of modelling, such as classical molecular dynamics or electronic structure. Although some packages have been developed to implement specific methods, e.g. Quantics for dynamics with MCTDH, or subroutines added to electronic structure packages, e.g. Surface Hopping and Ehrenfest in CPMD, these efforts are not the standard.
One of the goals of E-CAM’s WP3 is then to provide an environment to stimulate the transition from in-house codes, often developed and used by single groups, to the development of modular, well documented community-based software packages capable of multiple functionalities and adopting the common set of standards and benchmarks.
To foster this development, we have initiated five parallel activities:
One of primary activity of E-CAM is to engage with pilot projects with industrial partners. These projects are conceived together with the partner and typically are to facilitate or improve the scope of computational simulation within the partner. The related code development for the pilot projects are open source (where the licence of the underlying software allows this) and are described in the modules associated with the pilot projects.
Below is a list of the current pilot projects within E-CAM:
The first Quantum Dynamics ESDW was held in June-July 2016 at the Maison de la Simulation near Paris. 10 students and 6 tutors, including Dr. Ivano Tavernelli representing the industrial partner of the WP3, IBM, worked to develop software modules in the following areas:
Work was performed by teams of 2-4 students, assisted by the senior participants and by E-CAM’s Software Manager, Dr. Alan O’Cais, and the Software Developer associated to WP3, Dr. Liang Liang.
In addition to the software development activities, the Workshop enjoyed lively scientific discussions centered on presentations made by the students and the senior participants. The on-line E-CAM tools for software development, including the Git repository, and tools for the documentation (Doxygen) and performance analysis were presented by E-CAM staff members and participants were instructed on their use via tutorials. The program was further enriched by the interactions with experts on software and hardware development working at La Maison de la Simulation who gave talks on topics such as architectures and programming paradigms and the use of advanced visualization tools such as the Image wall hosted by the Maison de la Simulation.
The second Quantum Dynamics ESDW was held in July 2017 at the University College Dublin.
The SodLib module provides exact wavefunction propagation using the second-order differencing (SOD) integrator scheme to solve the time-dependent Schroedinger equation. This routine has been implemented and tested as an added functionality within the Quantics quantum dynamics package.
The ChebLib module implements the Chebyshev integration scheme for exact wavefunction propagation on the grid. This routine has been implemented and tested as an added functionality within the Quantics quantum dynamics package.
The PhysConst enables the use of physical constants and the correct isotopic masses.
PaPIM is a code for calculation of equilibrated system properties (observables). Some properties can be directly obtained from
the sampled system distribution function, while properties that depends on the exact dynamics of the system, such as the structure
factor, [Mon2] infrared spectrum [Beu] or reaction rates, can be easily obtained from corresponding correlation functions.
PaPIM code samples either the quantum (Wigner) or classical (Boltzmann) density functions and calculates the corresponding correlation
functions. The code is highly parallelized which makes it suitable for use on large HPC machines.
The code’s modular structure enables an easy update/change of any of its modules as well as that the coded functionalities
can be used independently of each other.
The code is specifically design with simplicity and readability in mind to enable any user to easily implement its own functionalities.
The code has been extensively used for the calculation of the infrared spectrum of the 
cation in gas phase,
while recently new calculations on water dimer, and protonated water dimer systems were started.
PaPIM is the current version of the code with all included functionalities.
The following modules make up the PaPIM code and can be used as stand-alone software libraries for e.g. sampling of the Wigner distribution, sampling of the classical Boltzmann distribution, or building MPI parallelized Fortran codes. Such libraries are rarely available to the community in a Fortran program format. Some of the functionalities coded within the code are specifically design for computation of infrared spectra, and serve as a template for the user to implement its own functionalities.
PIM_wd samples, via the Phase Integration Method, [Mon1] the system’s quantum Wigner density distribution function. The distribution is given in the phase-space representation and is the basis for any further calculation of system’s quantum observables.
PIM_qcf is a library of quantum correlation functions for computing system’s time-dependent properties.
ClassMC samples, via Metropolis Monte Carlo algorithm, the system’s classical Boltzmann distribution function and calculates the classical time-dependent correlation functions from the sampled phase space. Results obtained from classical sampling can be used to assess the relevance of quantum effects for a given system.
PotMod is a library of potential energy functions and interfaces for external potential energy calculation codes.
Currently available in the library are the harmonic and Morse potentials (different molecular systems can be simulated depending on parameters
provided by the user); empirical potential of the ground state of based on high level
electronic structure calculations [Jin], and interface to the ab initio CP2K code.
AuxMod is a library of subroutines which enables any user to easily construct its own Fortran input parser. It also contains a library of adapted MPI subroutines for easier programming of Fortran MPI parallel codes.
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| [Jin] | Jin, Braams, Bowman An ab Initio Based Global Potential Energy Surface Describing :math:’text{CH}_{5}^{+} rightarrow text{CH}_{3}^{+} + text{H}_{2}’ J. Phys. Chem. A 110 (2006) 1569 |
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This documentation is completely open and we welcome both internal and external contributions. If you would like to contribute to this effort then please follow the steps below to allow us to include your contribution.
