BornAgain: simula/ng X- ray and neutron sca7ering at grazing incidence

Transcription

1 BornAgain: simula/ng X- ray and neutron sca7ering at grazing incidence Céline Durniak, Walter Van Herck, Gennady Pospelov, Joachim Wu7ke Scien&fic Compu&ng Group at FRM- II Jülich Center for Neutron Science Emerging themes in Analysis of Grazing Incidence Small Angle Sca7ering Data 1 st and 2 nd July, Cosener s House, Abingdon

2 Outline o Mo/va/on o Architecture o Usage examples o Infrastructure for code development o Future plans BornAgain GISAS Workshop, Abingdon, 1-2 July,13 02

3 Motivation Heinz Maier- Leibnitz Zentrum (MLZ) FRM- II neutron source in Garching bei Munich Scien/fic compu/ng at FRM- II o Support of instruments with focus on simula/on and data analysis HDRI o High Data Rate Processing and Analysis Ini/a/ve From local (MLZ) and more broader needs (HDRI) o Start community project for different user experiments (neutron and x- ray grazing incidence) o More generally structured than exis/ng so^ware o IsGISAXS as reference so^ware BornAgain GISAS Workshop, Abingdon, 1-2 July,13 03

4 Starting IsGISAXS as a star/ng point: o Successful so^ware which is a de facto standard in the user community o Simula/on in DWBA o FORTRAN 90, 13k lines of code o Windows (with GUI), Linux (without GUI) o No longer ac/vely supported BornAgain GISAS Workshop, Abingdon, 1-2 July,13 04

5 Starting New so^ware pladorm or extend exis/ng? Extending IsGISAXS o code reuse From scratch C++ o developers background o object oriented approach in sample descrip/on Mul/Layer Layer 1 Interface 1 Layer 2 Interface 2 Layer 3 Nanopar/cles 1 Nanopar/cles 2 Roughness parameter Formfactor Interference func/on Formfactor Interference func/on BornAgain GISAS Workshop, Abingdon, 1-2 July,13 05

6 Strategy Reproduce func/onality of IsGISAXS o IsGISAXS examples as milestones along the way Extend it with most demanded features o Mul/layers, par/cle assemblies, polarized neutrons and magne/c domains Follow rules o Decouple physical modelling, data, GUI o Depend on open source and ac/vely maintained libraries o Produce open source code o Be pladorm independent Build user community and follow their demands BornAgain GISAS Workshop, Abingdon, 1-2 July,13 06

7 BornAgain Development started in April 2012 The name of the so^ware, BornAgain, indicates the central role of the Distorted Wave Born Approxima/on o generic frame for modeling and fiing mul/ layer samples at grazing incidence geometry Supported sample structures o Mul/layer o Interface roughness (also correlated) o Mul/ple nanopar/cles (shapes, densi/es) o Interference func/ons o Nanopar/cles assemblies Supports X- rays and non- polarized neutrons Current status beta Transi/on to produc/on release with user help BornAgain GISAS Workshop, Abingdon, 1-2 July,13 07

8 Basic software architecture Main features: o Programming language C++ o Core library consist of 25k lines of code o Python bindings with boost- python o Mac/Linux, Windows soon BornAgain Python bindings Python bindings libcore Samples and algorithms libfit Interface to minimizers BornAgain GISAS Workshop, Abingdon, 1-2 July,13 08

9 Basic software architecture External dependencies: o Well established libraries: Boost, nw3, Eigen, GSL o ROOT from High Energy Physics community for fiing BornAgain Python bindings Python bindings libcore Samples and algorithms libfit Interface to minimizers GSL Boost Eigen ROOT BornAgain GISAS Workshop, Abingdon, 1-2 July,13 08

10 Basic software architecture Working with BornAgain. o Running user C++ program User C++ program External graphics BornAgain Python bindings Python bindings libcore Samples and algorithms libfit Interface to minimizers GSL Boost Eigen ROOT BornAgain GISAS Workshop, Abingdon, 1-2 July,13 08

11 Basic software architecture Working with BornAgain. o Running user Python script User Python script External graphics BornAgain Python bindings libcore Samples and algorithms Python bindings libfit Interface to minimizers Matplotlib GSL Boost Eigen (Py)ROOT BornAgain GISAS Workshop, Abingdon, 1-2 July,13 08

12 Usage examples BornAgain GISAS Workshop, Abingdon, 1-2 July,13 09

13 Usage examples Example #1: simula/on of cylindrical nano par/cles with interference func/on on top of substrate using python script BornAgain GISAS Workshop, Abingdon, 1-2 July,13 10

14 Usage example: simulation with python script BornAgain GISAS Workshop, Abingdon, 1-2 July,13 11

15 Usage example: simulation with python script ambience material substrate material BornAgain GISAS Workshop, Abingdon, 1-2 July,13 11

16 Usage example: simulation with python script air layer substrate layer BornAgain GISAS Workshop, Abingdon, 1-2 July,13 11

17 Usage example: simulation with python script Nano par/cle is defined by the refrac/ve index and form factor Addi/onal transforma/on can be defined for orienta/on and posi/on of the par/cle BornAgain GISAS Workshop, Abingdon, 1-2 July,13 11

18 Usage example: simulation with python script InterferenceFunc/on1DParaCrystal defines interference func/on of regular laice with long range order gradually destroyed BornAgain GISAS Workshop, Abingdon, 1-2 July,13 11

19 Usage example: simulation with python script InterferenceFunc/on1DParaCrystal defines interference func/on of regular laice with long range order gradually destroyed Par/cleDecora/on Holds informa/on about par/cle types, posi/ons and interference BornAgain GISAS Workshop, Abingdon, 1-2 July,13 11

20 Usage example: simulation with python script InterferenceFunc/on1DParaCrystal defines interference func/on of regular laice with long range order gradually destroyed Par/cleDecora/on Holds informa/on about par/cle types, posi/ons and interference LayerDecorator Decorates air layer with par/cle decora/on BornAgain GISAS Workshop, Abingdon, 1-2 July,13 11

21 Usage example: simulation with python script Mul/Layer owns decorated air layer and substrate layer BornAgain GISAS Workshop, Abingdon, 1-2 July,13 11

22 Usage example: simulation with python script Mul/Layer owns decorated air layer and substrate layer Simula/on Holds beam and detector parameters, accept mul/ layer as an input and perform calcula/ons BornAgain GISAS Workshop, Abingdon, 1-2 July,13 11

23 Usage example: simulation with python script OutputData Simulated intensity as a func/on of outgoing α f, φ f angles can be retrieved as NumPy array BornAgain GISAS Workshop, Abingdon, 1-2 July,13 11

24 Usage examples Example #2: fiing the data BornAgain GISAS Workshop, Abingdon, 1-2 July,13 12

25 Usage example: fitting o Every number (or group of numbers) used in sample construc/on can be used as fit parameter Mul/ Layer Layer #0 Layer #1 thickness Par/cleDecora/on thickness FormFactorCylinder radius height Library Minuit2 GSL TMVA Minimiza&on algorithms provided by ROOT Algorithm Migrad, Simplex, Fumili, Scan Fletcher- Reeves Conjugate Gradient Algorithm BFGS Conjugate Gradient Algorithm Levenberg- Marquardt Algorithm Simulated Annealing Algorithm Gene/c Algorithm Name to find corresponding parameters in sample parameter database BornAgain GISAS Workshop, Abingdon, 1-2 July,13 13

26 Usage examples Example #3: mesocrystals BornAgain GISAS Workshop, Abingdon, 1-2 July,13 14

27 Usage example: mesocrystals Grazing incidence small- angle x- ray sca7ering from a mesocrystalline system o mesocrystals have cylindrical shape and size of ~1000 nm o mesocrystal consist of an FCC laice composed of 5 nm spherical par/cles BornAgain GISAS Workshop, Abingdon, 1-2 July,13 15

28 Usage example: mesocrystals Experimental data compared to a BornAgain simula/on o 11 parameters fit o 12 hours on six core (12 threads), 2000 itera/ons, 20 sec/itera/on beam_intensity 5.01e+12 laice_length_a 6.21 laice_length_c 6.57 nanopar/cle_radius 4.70 sigma_nanopar/cle_radius 0.37 meso_height meso_radius sigma_meso_height 1.00 sigma_meso_radius 1.61 sigma_laice_length_a 1.16 surface_filling_ra/o 0.17 roughness experimental data courtesy Elisabeth Josten et al Born BornAgain simula&on in collabora&on with Artur Glavic and Elisabeth Josten BornAgain GISAS Workshop, Abingdon, 1-2 July,13 16

29 Usage examples Example #4: working with graphical user interface BornAgain GISAS Workshop, Abingdon, 1-2 July,13 17

30 Usage example: development of graphical user interface Status prototyping o rely on Qt5 (Qt4) and ROOT libraries o BornAgainCore library used as a plugin In plans o drag and drop sample editor o interac/ve plots o access to large collec/on of minimizers o Python and C++ scrip/ng BornAgain GISAS Workshop, Abingdon, 1-2 July,13 18

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32 Development process General prac/ces o More agile development o Quality control o Good documenta/on So^ware tools o Bug/issue tracking: Redmine o Version control: Git o Nightly build server: TeamCity o Code documenta/on: Doxygen o Code browser: OpenGrok o Unit tests: Googletest BornAgain git repository number of lines of code vs &me BornAgain GISAS Workshop, Abingdon, 1-2 July,13 19

33 Development process: agile development o workflow consist of sprint cycles every 3-4 weeks during which the team create finished por/ons of product One day I want to fly away Users lasts 3-4 weeks Backlog: Sprint: Release Developers Item 124 Item 125 Learn to fly Fly away Item 124 Item 125 Item 127 Item 98 Item 101 Item 102 BornAgain GISAS Workshop, Abingdon, 1-2 July,13 20

34 Development process: agile development Workflow is managed via Redmine management tool o user request handling, bug tracking tool, issue tracking BornAgain GISAS Workshop, Abingdon, 1-2 July,13 21

35 Development process: quality assurance Unit test control o small test cases are executed a^er each compila/on to ensure code stability Func/onal tests o higher level tests produces sca7ering plots which are automa/cally analyzed o special tests compare BornAgain results with IsGISAXS results BornAgain IsGISAXS rela/ve difference rela/ve difference spectra BornAgain- IsGISAXS IsGISAXS BornAgain GISAS Workshop, Abingdon, 1-2 July,13 22

36 Conclusion and plans o BornAgain is a new so^ware for simula/ng and fiing grazing incidence small angle sca7ering (x- rays and neutrons) o Current status beta o It reproduces and enhances the func/onality of the present reference so^ware, IsGISAXS o Everyone is welcome to try it out, when their experiment requires extension of IsGISAXS Plans o Usable GUI, Windows version (October- November, 2013) o Neutron polariza/on and magne/c domains (April, 2014) h7p://apps.jcns.fz- juelich.de/doku/sc/bornagain:start BornAgain GISAS Workshop, Abingdon, 1-2 July,13 23

37 Backup BornAgain GISAS Workshop, Abingdon, 1-2 July,13 24

38 BornAgain GISAS Workshop, Abingdon, 1-2 July,13 25

39 Development process: quality assurance Nightly build system o based on TeamCity, one build configura/on Code profiling o regular tracking of memory and CPU consump/on BornAgain GISAS Workshop, Abingdon, 1-2 July,13 26

40 Development process: good documentation Code documenta/on o Doxygen generated, star/ng to write user manual Theory and conven/ons o described and stored in the repository parallel to the code development GISAS simula/on development Scien/fic Compu/ng at FRM II, PNI- HDRI Workshop, 4-5 March 13, DESY 27