This module, SodLib, provides exact wavefunction propagation using the second-order differencing (SOD) integrator scheme to solve the time-dependent Schrödinger equation as described by Leforestier et al, J. Comp Phys, 94, 59-80, 1991. Within this scheme the time interval is determined through dividing hbar by the eigenvalue of the Hamiltonian operator with the largest absolute value. This routine has been implemented and tested as an added functionality within the Quantics software package available through CCPForge.
Quantics is a package to study chemical reactions of molecules whose main developer (G. Worth, University College London) is a member of E-CAM’s WP3 – Quantum Dynamics. It incorporates a variety of quantum dynamical methods joined by the fact that the state system is usually described via wavefunctions (containing the quantum analogue of the information given by positions and velocities for classical atoms). It is increasingly used by the computational chemistry community for scientific applications. Work is on-going in E-CAM to improve its scalability (see E-CAM deliverable D7.2 ) and add new functionalities in view of applications to study materials and light harvesting complexes.
Module documentation can be found here, including a link to the source code.
Practical application and exploitation of the code
The module is currently being used in a Phd thesis and the results of this application will provide benchmarks for a model describing proton-transfer in a condensed phase system.
DL_MESO_DPD, is the Dissipative Particle Dynamics (DPD) code from the mesoscopic simulation package DL_MESO , developed by Dr. Michael Seaton at Daresbury Laboratory (UK). This open source code is available from Science and Technology Facilities Council (STFC) under both academic (free) and commercial (paid) licenses. E-CAM’s Work-package 4 (WP4), Meso and Multi-scale Modelling, makes use of the DL_MESO_DPD code. See this article on our news feed, for more information on how it is used within E-CAM.
In order to accelerate the DL_MESO_DPD code on the latest and future exascale hardware, a first version for NVidia GPUs has been developed. This is only a starting point, it does not yet cover all the possible cases and it does not yet support multiple GPUs. However, it represents an HPC milestone for the application, complementing the already present parallel versions developed for shared and distributed memory (MPI/OpenMP).
The library LibOMM solves the Kohn-Sham equation as a generalized eigenvalue problem for a fixed Hamiltonian. It implements the orbital minimization method (OMM), which works within a density matrix formalism. The basic strategy of the OMM is to find the set of Wannier functions (WFs) describing the occupied subspace by direct unconstrained minimization of an appropriately-constructed functional. The density matrix can then be calculated from the WFs. The solver is usually employed within an outer self-consistency (SCF) cycle. Therefore, the WFs resulting from one SCF iteration can be saved and then re-used as the initial guess for the next iteration.
More information on the module’s documentation can be found here, and the source code is available from the E-CAM Gitlab here. The algorithms and implementation of the library are described in https://arxiv.org/abs/1312.1549v1.
This module is an effort from the Electronic Structure Library Project (ESL), and it was initiated during an E-CAM Extended Software Development Workshop in Zaragoza in June 2016. This and other codes revolved around the broad theme of solvers, were recently reported in Deliverable D2.1.: Electronic structure E-CAM modules I, available for download and consultation here.
Practical application and exploitation of the module
libOMM is one of the libraries supported and enhanced by the Electronic Structure Infrastructure ELSI , which in turn is interfaced with the DGDFT, FHI-aims, NWChem, and SIESTA codes.
 The electronic structure infrastructure ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, molecular biochemistry, and many other fields [https://arxiv.org/abs/1705.11191v1].
The present module, gen_dipole.f90, is a generalization of the dipole.f90 post-processing utility of DL_MESO_DPD, the Dissipative Particle Dynamics (DPD) code from the DL_MESO package. It processes the trajectory (HISTORY) files to obtain the charge dipole moments of all the (neutral) molecules in the system. It produces files dipole_* containing the time evolution of relevant quantities (see module documentation for more information). In the case of a single molecular species, it also prints to the standard output the Kirkwood number and the relative electric permittivity for this species, together with an estimate for their errors (standard error).
The module can be applied to systems including molecules with a generic charge structure, as long as each molecule is neutral (otherwise the charge dipole moment would be frame-dependent).
gen_dipole.f9 is available under BSD license, and is a post-processing utilities to be used with DL_MESO in its last released version, version 2.6 (dating November 2015). They have been developed in the context of the pilot project 1 of WP 4, which concerns the derivation of a realistic polarizable model of water to be used in DPD simulations. This project involves a collaboration between computational scientists (STFC Daresbury), academia (University of Manchester), and industry (Unilever). This and other modules based on DL_MESO_DPD have recently been reported in deliverable D4.2: Meso- and multi-scale modelling E-CAM modules I, available for consultation here.
SQARE (solvers for quantum atomic radial equations) is a library of utilities intended for dealing with functions discretized on radial meshes, wave-equations with spherical symmetry and their corresponding quantum states. The utilities are segregated into three levels: radial grids and functions, ODE solvers, and states.
Module ClassMC samples the system phase space using the classical Boltzmann distribution function and calculates the time correlation functions from the sampled initial conditions. For more information check the module documentation here.
This module, based on OpenPathSampling, calculates the flux out of a state and through an interface, or the rate of the transition between two states, while running a trajectory. For more information check the module documentation here.