Computer Physics Communications

The third-order elastic constants (TOECs) are fundamental to describe crystal’s nonlinear response to stress, and can be applied to explore anharmonic properties of crystals such as Grüneisen parameters, thermal expansion coefficient, and the effect of pressure on second-order elastic constants (SOECs). Here, we report an open-source python package, Elastic3rd, which is able to calculate the SOECs and TOECs using the strain–energy method for crystals with any symmetry from first-principles calculations. An algorithm to generate necessary strain modes and the corresponding coefficients for a given symmetry is proposed. These strain modes are then applied to the fully relaxed structure to generate the deformed structures. The total energies of the strained structures are calculated by a chosen first-principles code, and the SOECs and TOECs are determined by fitting the resulted strain–energy data. The present code has been validated by several case studies of C, Si and Mg, and the case of MnP4 shows the ability for low-symmetry crystals.

In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (≈20pJ/word on-die to ≈10,000 pJ/word on the network). To increase memory locality at the hardware level and reduce energy consumption related to data movement, future exascale computers tend to use many-core processors on each compute nodes that will have a reduced clock speed to allow for efficient cooling. To compensate for frequency decrease, machine vendors are making use of long SIMD instruction registers that are able to process multiple data with one arithmetic operator in one clock cycle. SIMD register length is expected to double every four years. As a consequence, Particle-In-Cell (PIC) codes will have to achieve good vectorization to fully take advantage of these upcoming architectures. In this paper, we present a new algorithm that allows for efficient and portable SIMD vectorization of current/charge deposition routines that are, along with the field gathering routines, among the most time consuming parts of the PIC algorithm. Our new algorithm uses a particular data structure that takes into account memory alignement constraints and avoids gather/scatter instructions that can significantly affect vectorization performances on current CPUs. The new algorithm was successfully implemented in the 3D skeleton PIC code PICSAR and tested on Haswell Xeon processors (AVX2-256 bits wide data registers). Results show a factor of ×2 to ×2.5 speed-up in double precision for particle shape factor of order 1–3. The new algorithm can be applied as is on future KNL (Knights Landing) architectures that will include AVX-512 instruction sets with 512 bits register lengths (8 doubles/16 singles).

Title of program: ISING Catalogue Id: ACCP_v1_0 Nature of problem We wish to study the critical temperature and critical exponents of the three-dimensional Ising model. Versions of this program held in the CPC repository in Mendeley Data ACCP_v1_0; ISING; 10.1016/0010-4655(84)90142-5 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)

Title of program: PYTHIA Catalogue Id: ACCB_v1_0 Nature of problem In high pT reactions, QCD, the candidate theory of strong interactions, can be used to calculate perturbatively the subprocesses on the parton level: the probability for two quarks or gluons reacting, their momentum distributions, etc. However, what is experimentally observed is the final state hadrons, not the partons themselves. Hence, to be able accurately to predict the outcome of an experiment, one needs to take into account the hadronization process. We present a Monte Carlo program for hi ... Versions of this program held in the CPC repository in Mendeley Data ACCB_v1_0; PYTHIA; 10.1016/0010-4655(84)90018-3 ACCB_v2_0; PYTHIA 3.4; 10.1016/0010-4655(85)90003-7 ACCB_v3_0; PYTHIA 4.8; 10.1016/0010-4655(87)90036-1 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)

Title of program: BESSCC Catalogue Id: ABBM_v1_0 Nature of problem The BESSCC subroutine calculates the modified Bessel functions Imu(z) and Kmu(z) (and derivatives) for complex argument z and a sequence of real orders mu,mu+1,...,mu+n-1 for integer N >/= 1. These functions arise in the solutions of potential problems in spherical and cylindrical coordinates. They can also be used to calculate ordinary Bessels Jmu(z), Ymu(z), spherical Bessels Jmu(z), Ymu(z), Kelvin and Airy functions. CORRECTION SUMMARY: Vol:Year:Page 159:2004:243 "000A CORRECTION 20/04/04" "Modified Bessel functions Imu(z) and Kmu(z) of real order and complex argument, to selected accuracy." I.J. Thompson Note: correction instructions are contained in source code Versions of this program held in the CPC repository in Mendeley Data ABBM_v1_0; BESSCC; 10.1016/0010-4655(87)90111-1 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)

Title of program: PSEUDO Catalogue Id: ACDZ_v1_0 Nature of problem Purely outgoing solution of the one-particle Schrodinger equation is searched in special cases. The program PSEUDO (Potential Separable Expansion for Unbound Deformed Orbits) either calculates single particle resonant or bound state energies and wave functions in an axially or spherically symmetric potential or gives the well-depths of the potential belonging to a prescribed energy value (Sturmian problem). Versions of this program held in the CPC repository in Mendeley Data ACDZ_v1_0; PSEUDO; 10.1016/0010-4655(85)90018-9 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)

Abstract The method of symmetry adaptation of wave functions with respect to any semisimple symmetry chain originating from a SU(l+1) algebra for completely symmetrical representations [N, 0, 0,...] of SU(l+1) was extended to the case of arbitrary representations [N_1 , N_2 ,...,N_(l+1)] of SU(l+1) with N_1 ≥N_2 ≥...≥N_(l+1)and N_1 + N_2 +... + N_(l+1)=N, recently. Programs covering this general case are presented in this contribution. Title of program: LIE_A0, LIE_A1, LIE_A2 Catalogue Id: ACHL_v1_0 Nature of problem 1. Calculation of orthonormal bases for irreducible unitary representations of the special unitary algebras (groups) SU(l+1) of any symmetry, and of orthonormal bases for direct products of such representations. <P> 2. Calculation of orthonormal bases of irreducible unitary representations of the Lie algebras L=SU(l'+1), SO(2l'), SO(2l'+1), Sp(2l'), l' <=l, and direct products of these algebras, considered as subalgebras of an algebra SU(l+1) or a direct product of SU(l+1)'s. The bases for the i ... Versions of this program held in the CPC repository in Mendeley Data ACHL_v1_0; LIE_A0, LIE_A1, LIE_A2; 10.1016/0010-4655(92)90200-I This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2019)

Reactive molecular dynamics (RMD) simulations are becoming popular, with the recent developments in high-performance and efficient computing architecture, for investigating fundamental physico-chemical behaviors of reacting species. Due to the complexity of hydrocarbon systems, characterization of molecules formed during RMD simulations of hydrocarbons can be very challenging for simulations involving a large number of molecules. The novel post-processing utility “MAFIA-MD” – an acronym for “Molecular Arrangement and Fringe Identification and Analysis from Molecular Dynamics” – presented in this manuscript can analyze and perform molecular characterization of a large number of RMD trajectory files (.XYZ files) simultaneously. The utility will be useful for analysis and chemical characterization of trajectories without the large bond information files. A graphical user interface (GUI) is developed for easy operation. The utility analyzes the existing cyclic structures in the domain and generates statistics of alicyclic and aromatic hydrocarbons based on the number of carbon atoms. Alongside the statistical analysis, the program also separates the constituent molecules and extracts their chemical information in terms of Simplified Molecular-Input Line-Entry System (SMILES) and Spatial Data File (.SDF)”. A methodology for calculating fringe spacing is also implemented in the code for validation of RMD simulation with High-Resolution Transmission Electron Microscopy (HRTEM) images.

Abstract Pythia version 6 represents a merger of the Pythia 5, Jetset 7 and SPythia programs, with many improvements. It can be used to generate high-energy-physics ‘events’, i.e. sets of outgoing particles produced in the interactions between two incoming particles. The objective is to provide as accurate as possible a representation of event properties in a wide range of reactions. The underlying physics is not understood well enough to give an exact description; the programs therefore contain a com... Title of program: PYTHIA V6.154 Catalogue Id: ACTU_v2_0 [ADNN] Nature of problem High-energy collisions between elementary particles normally give rise to complex final states, with large multiplicities of hadrons, leptons, neutrinos and photons. The relation between these final states and the underlying physics description is not a simple one, for two main reasons. Firstly, we do not even in principle have a complete understanding of the physics. Secondly, any analytical approach is made intractable by the large multiplicities. Versions of this program held in the CPC repository in Mendeley Data ACTU_v1_0; PYTHIA 5.7 AND JETSET 7.4; 10.1016/0010-4655(94)90132-5 ACTU_v2_0; PYTHIA V6.154; 10.1016/S0010-4655(00)00236-8 ACTU_v2_1; PYTHIA Version number: 6.420; 10.1016/j.cpc.2009.08.008 ACTU_v3_0; Pythia 8.1; 10.1016/j.cpc.2008.01.036 ACTU_v4_0; Pythia 8.2; 10.1016/j.cpc.2015.01.024 This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018)

This program has been imported from the CPC Program Library held at Queen's University Belfast (1969-2018) Abstract SuperIso Relic v3.0 is a public program for evaluation of relic density and flavour physics observables in the minimal supersymmetric extension of the Standard Model (MSSM) and next-to-minimal extension of the Standard Model (NMSSM). SuperIso Relic is an extension of the SuperIso program which adds to the flavour observables of SuperIso the computation of all possible annihilation and coannihilation processes of the LSP which are required for the relic density calculation. All amplitudes have... Title of program: SuperIso Relic v3.0 Catalogue Id: AEGD_v2_0 Nature of problem Calculation of the lightest supersymmetric particle relic density, as well as flavour physics observables, in the MSSM and NMSSM, in order to derive constraints on the supersymmetric parameter space. Versions of this program held in the CPC repository in Mendeley Data AEGD_v1_0; SuperIso Relic; 10.1016/j.cpc.2010.03.010 AEGD_v2_0; SuperIso Relic v3.0; 10.1016/j.cpc.2011.03.019