udkm1Dsim—A simulation toolkit for 1D ultrafast dynamics in condensed matter

The udkm1Dsim  toolbox is a collection of matlab (MathWorks Inc.) classes and routines to simulate the structural dynamics and the according X-ray diffraction response in one-dimensional crystalline sample structures upon an arbitrary time-dependent external stimulus, e.g. an ultrashort laser pulse. The toolbox provides the capabilities to define arbitrary layered structures on the atomic level including a rich database of corresponding element-specific physical properties. The excitation of ultrafast dynamics is represented by an NN-temperature model which is commonly applied for ultrafast optical excitations. Structural dynamics due to thermal stress are calculated by a linear-chain model of masses and springs. The resulting X-ray diffraction response is computed by dynamical X-ray theory. The udkm1Dsim  toolbox is highly modular and allows for introducing user-defined results at any step in the simulation procedure.Program summaryProgram title: udkm1DsimCatalogue identifier: AERH_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERH_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: BSDNo. of lines in distributed program, including test data, etc.: 130221No. of bytes in distributed program, including test data, etc.: 2746036Distribution format: tar.gzProgramming language: Matlab (MathWorks Inc.).Computer: PC/Workstation.Operating system: Running Matlab installation required (tested on MS Win XP - 7, Ubuntu Linux 11.04-13.04).Has the code been vectorized or parallelized?:   Parallelization for dynamical XRD computations. Number of processors used: 1–12 for Matlab Parallel Computing Toolbox; 1−∞1−∞ for Matlab Distributed Computing ToolboxRAM: Matlab’s typical RAM requirement of 196 MB is sufficient for most simulations Classification: 7.8, 7.9, 8.External routines:Optional: Matlab Parallel Computing Toolbox, Matlab Distributed Computing Toolbox Required (included in the package): mtimesx Fast Matrix Multiply for Matlab by James Tursa, xml io tools by Jaroslaw Tuszynski, textprogressbar by Paul ProteusNature of problem:Simulate the lattice dynamics of 1D crystalline sample structures due to an ultrafast excitation including thermal transport and compute the corresponding transient X-ray diffraction pattern.Solution method:The program provides an object-oriented toolbox for building arbitrary layered 1D crystalline sample structures including a rich database of element-specific parameters. The excitation, thermal transport and lattice dynamics are simulated utilizing Matlab’s ODE solver. Alternatively, the lattice dynamics can also be calculated analytically utilizing Matlab eigenproblem solver. The dynamical X-ray diffraction is computed in a parallelized matrix formalism.Restrictions:The program is restricted to 1D sample structures and is further limited to longitudinal acoustic phonon modes and symmetrical X-ray diffraction geometries.Unusual features:The program is highly modular and allows the inclusion of user-defined inputs at any time of the simulation procedure.Running time:The running time is highly dependent on the number of unit cells in the sample structure and other simulation parameters such as time span or angular grid for X-ray diffraction computations. However, the example files are computed in approx. 1–5 min each on a 8 Core Processor with 16 GB RAM available.